compositions and methods for selective protein degradation

专利摘要:
These are compositions including a fusion polypeptide and methods for producing a fusion polypeptide that includes a COF1 / CRBN binding polypeptide, COF2 / CRBN binding polypeptide or COF3 / CRBN binding polypeptide and a heterologous polypeptide of interest .
公开号:BR112020007576A2
申请号:R112020007576-0
申请日:2018-10-18
公开日:2020-09-24
发明作者:James E. Bradner；Seth Carbonneau；Andrei Golosov；Carleton Proctor Goold；Carla Patricia Pinto Guimaraes；Marc Horst Peter Hild；Gregory Motz；Nathan Thomas Ross；Jonathan M. Solomon；Rohan Eric John Beckwith
申请人:Novartis Ag；
IPC主号:

专利说明:

[0001] [0001] This application claims priority for U.S. Patent Serial No. 62 / 574,188 filed on October 18, 2017, the contents of which are hereby incorporated by reference in their entirety. SEQUENCE LISTING
[0002] [0002] The present application contains a Sequence Listing that was submitted electronically in ASCII format and is incorporated herein by reference, in its entirety. The said copy of ASCII, created on October 17, 2018 is called N2067-7136WO SL.txt and is 2,052,554 bytes in size. BACKGROUND OF THE INVENTION
[0003] [0003] Many therapeutic proteins have been developed as important drugs to prevent or treat diseases. Side effects can occur during or after treatment, ranging from loss of drug effectiveness to severe toxicities. It is desirable to develop strategies to modulate the level of expression of proteins, for example, to modulate the levels of therapeutic proteins in order to increase efficacy and / or reduce side effects. SUMMARY OF THE INVENTION
[0004] [0004] The present description discloses, at least in part, a fusion polypeptide comprising a compound of Formula (1) (COF1) / CRBN binding polypeptide, a compound of Formula (Il) a (COF2) binding polypeptide / CRBN, or a compound of Formula (III) (COF3) -binding polypeptide / CRBN for targeting protein inactivation. In some embodiments, the fusion polypeptide includes one or more COF1 / CRBN-binding polypeptides, COF2 / CRBN or COF3 / CRBN and one or more heterologous polypeptides, for example,
[0005] [0005] Without sticking to the theory, in some modalities, the COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN provides an amino acid sequence and / or a structural motif that, in the presence of COF1 or COF2 (such as thalidomide and derivatives thereof (for example, lenalidomide, pomalidomide and thalidomide)), or in the presence of COF3 (for example, a compound shown in Table 29), results in a post-translational modification (for example , ubiquitination) of the fusion polypeptide, resulting in a modified fusion polypeptide, for example, ubiquitinated. For example, one or more amino acids, for example, lysine or methionine, in the fusion polypeptide can be ubiquitinated, in the presence of COF1, COF2 or COF3. In some embodiments, the ubiquitinated fusion polypeptide is selectively degraded. In some embodiments, post-translational modification of the fusion polypeptide increases the degradation (for example, an increase in level and / or rate of degradation) of the fusion polypeptide. In some modalities, the level and / or rate of degradation is increased by at least 1.5, 2, 3, 4, 5, 10, 20, 30, 40 or 50 times in relation to the level and / or rate degradation of a reference polypeptide, for example, the fusion polypeptide in the absence of
[0006] [0006] In one aspect, a fusion polypeptide is provided which comprises a compound of Formula (Il) (COF1) / CRBN-binding polypeptide and a heterologous polypeptide, wherein the compound of Formula (1) is: x (R41 Dr RE R '(1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, wherein: XéOousS; R' is C1-C6 alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl , carbocicil, heterocicila, arila or heteroaryl, each of which is independently and optionally substituted by one or more R $; each of R * and R º is independently hydrogen or C1-C6 alkyl; or R º and R , together with the carbon atom to which they are attached, form a carbonyl group or a thiocarbonyl group; each of R 'is independently C1-Cs alkyl, C2-C6 alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, halo, cyan, -C (O) Rô, - C (O0) ORº, -OR8, -N (Rº) (RP), -C (O) N (RNRO), -N (R) C (O) RA , -S (O) .RE, -S (O) .N (RºI (RP ) Or -N (Rº) S (O), RE, where each alkyl, alkenyl, alkynyl and het eroalkyl is independent and optionally replaced by one or more R $; each Rº is independently C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl, halo, cyano, oxo, -C (OJ) Rô, - C (O) ORE, -OR8, - N (R) (R ), -C (O) N (RNRP), -N (RO) C (O) RA, -S (O) .RE,
[0007] [0007] In some embodiments, the heterologous polypeptide is a heterologous mammal polypeptide. In some embodiments, the heterologous polypeptide is a heterologous bacterial polypeptide. In some embodiments, the heterologous polypeptide is a heterologous viral polypeptide. In some embodiments, the heterologous polypeptide comprises an amino acid sequence of, or derived from, a mammalian polypeptide, a bacterial polypeptide, a viral polypeptide, a vegetable polypeptide, a yeast polypeptide, a fungal polypeptide , an archaeobacterial polypeptide, a fish polypeptide, for example, zebrafish. In some embodiments, the heterologous polypeptide comprises a polypeptide from Table 2, for example, a cytoplasmic and / or nuclear polypeptide, or a transmembrane polypeptide as described in Table 2.
[0008] [0008] In some embodiments, the polypeptide binding to
[0009] [0009] In some embodiments, the COF1 / CRBN-binding polypeptide is attached to the C-terminus of the heterologous polypeptide. In some embodiments, the COF1 / CRBN-binding polypeptide is attached to the N-terminus of the heterologous polypeptide. In some modalities, the COF1 / CRBN-binding polypeptide is in the middle of the heterologous polypeptide.
[0010] [0010] In some embodiments, the association of the COF1 / CRBN-binding polypeptide with cerenlon (CRBN) in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COFI / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation. In some embodiments, the COF1I / CRBN-binding polypeptide does not bind CRBN in the absence of COF1. In some embodiments, the association of the fusion polypeptide with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation. In some embodiments, the fusion polypeptide does not bind CRBN in the absence of COF1. In some embodiments, the association or bond is as measured in a mammalian cell, for example, a human cell.
[0011] [0011] In some embodiments, the ubiquitination of the heterologous polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50 %, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described herein. In some embodiments, the ubiquitination of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described herein. In some embodiments, the heterologous polypeptide or the fusion polypeptide is ubiquitinated to one or more lysine or methionine residues in the presence of COF1. In some embodiments, ubiquitination is as measured in a mammalian cell, for example, a human cell.
[0012] [0012] In some embodiments, the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western analysis blot or flow cytometry analysis. In some modalities, the
[0013] [0013] In some embodiments, the fusion polypeptide is a cell surface polypeptide. In some embodiments, the rate of recycling of cell surface fusion polypeptides to an intracellular compartment in the absence of COF1 is no more than, for example, 10%, 20%, 30%, 40%, 50%, 60%, 70 %, 80%, or 90%, of recycling the fusion polypeptide from the cell surface to an intracellular compartment in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document. In some embodiments, recycling is as measured in a mammalian cell, for example, a human cell.
[0014] [0014] In some embodiments, the COF1 / CRBN-binding polypeptide is between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues in length, between and 85 amino acid residues in length, between 25 and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length , between 50 and 65 amino acid residues in length or between 55 and 65 amino acid residues in length.
[0015] [0015] In some embodiments, the COF1 / CRBN-binding polypeptide comprises a beta curve. In some embodiments, the COF1 / CRBN-binding polypeptide comprises a beta curve of IKZF1 or IKZF3 (e.g., IKZF1 or human IKZF3). In some
[0016] [0016] In some embodiments, the polypeptide binding to
[0017] [0017] In some embodiments, the COF1 / CRBN-binding polypeptide comprises an IKZF polypeptide or a structural motif thereof.
[0018] [0018] In some embodiments, the IKZF polypeptide is an IKZF1 polypeptide, an IKZF3 polypeptide, an IKZF2 polypeptide that has H141Q substitution (numbered according to SEQ ID NO: 21), or an IKZF4 polypeptide which has H188Q replacement (numbered according to SEQ ID NO: 22).
[0019] [0019] In some embodiments, the COF1 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or an IKZF structural motif (for example, IKZF1 or IKZF3) which: i) the association of the COF1-binding polypeptide / CRBN with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the binding polypeptide to COF1 / CRBN with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[0020] [0020] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0021] [0021] In some embodiments, the COF1 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues, about 15 to about 90 amino acid residues, about to about 85 amino acid residues, about 25 to about 80 amino acid residues, about 30 to about 75 amino acid residues, about 35 to about 70 amino acid residues, about 40 to about 65 amino acid residues, about 45 to about 65 amino acid residues, about 50 to about 65 amino acid residues, or about 55 to about 65 amino acid residues of IKZF1 or IKZF3.
[0022] [0022] In some embodiments, the COF1 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 of SEQ ID NO: 19) that: i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[0023] [0023] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0024] [0024] In some embodiments, the COF1 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COFI / CRBN-binding polypeptide comprises the sequence amino acids of SEQ ID NO: 5) or a sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues) (for example, a sequence that has no more than 1,2,3,4, 5, 10, 15, 20, 25 , 30, 35, or 40 amino acid substitutions of amino acid residues 136 to 180 of SEQ ID NO: 19).
[0025] [0025] In some embodiments, the COF1 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 170 of SEQ ID NO: 19) that: i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of
[0026] [0026] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0027] [0027] In some embodiments, the COF1 / CRBN-binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COFI / CRBN-binding polypeptide comprises the sequence amino acids of SEQ ID NO: 6) or a sequence that differs from amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25 or 30 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 170 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 10, 15 , 20, 25, or 30 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid substitutions of 136 amino acid residues to 170 of SEQ ID NO: 19).
[0028] [0028] In some embodiments, one, two, three or all of the following amino acid residues remain unchanged: glutamine at position 147, cysteine at position 148, glutamine at position 150, glycine at position 152, leucine at position 161 or leucine in position 162, numbered according to SEQ ID NO: 19. In some modalities, the glutamine in position 147 remains unchanged, numbered according to SEQ ID NO: 19. In some modalities, the cysteine in position 148 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, the glutamine at position 150 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, the glycine at position 152 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, leucine at position 161 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, leucine at position 162 remains unchanged, numbered according to SEQ ID NO: 19.
[0029] [0029] In some embodiments, the COF1 / CRBN-binding polypeptide comprises amino acid residues 136 to 139 of IKZF3 (numbered according to SEQ ID NO: 19) for example, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 40.
[0030] [0030] In some embodiments, the COF1 / CRBN binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19). In some modalities, the COFI / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 5. In some embodiments, the COF1I / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 77. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 5. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO:
[0031] [0031] In some embodiments, the polypeptide binding to
[0032] [0032] In some embodiments, the COF1 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 236 to 249 of SEQ ID NO: 19) that: i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterogeneous polypeptide
[0033] [0033] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0034] [0034] In some embodiments, the COF1 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COFI / CRBN-binding polypeptide comprises the sequence amino acids of SEQ ID NO: 11) or a sequence that differs from amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues (for example, a sequence that differs from amino acid residues 236 to 249 of SEQ ID NO: 19 by no more than 1,2,3,4, 5, 6 or 7 amino acid residues) ( for example, a sequence that has no more than 1, 2, 3, 4, 5, 6, or 7 amino acid substitutions of amino acid residues 236 to 249 of SEQ ID NO: 19).
[0035] [0035] In some embodiments, the COF1 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19). In some modalities, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 11.
[0036] [0036] In some embodiments, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ | D NO: 91.
[0037] [0037] In some embodiments, the COF1 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 and 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 and 236 to 249 of SEQ ID NO: 19) that: i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 it is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterogeneous polypeptide
[0038] [0038] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0039] [0039] In some embodiments, the COF1 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, a first sequence comprising the amino acid sequence of SEQ ID NO: 5) or a first sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4 , 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a first sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues); and a second sequence comprising amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, a sequence
[0040] [0040] In some embodiments, the COF1 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 and 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19). In some embodiments, the COF1I / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 1. In some modalities, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 3. In some embodiments, the COFI / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 1. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 3.
[0041] [0041] In some embodiments, the COF1 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) and a second sequence comprising the sequence of amino acids of MALEKMALEKMALE (SEQ ID NO: 91). In some embodiments, the COF1I / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 14. In some embodiments, the COF1I / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 85. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 14. In some embodiments, the COFI / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 85.
[0042] [0042] In some embodiments, the COF1 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) and a second sequence comprising the sequence of amino acids of MALEKMALEKMALE (SEQ ID NO: 91). In some embodiments, the COF1I / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 15. In some embodiments, the COF1I / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 86. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 15. In some embodiments, the COFI / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 86.
[0043] [0043] In some embodiments, the COF1 / CRBN-binding polypeptide comprises at least one lysine unless the corresponding native sequence. In some embodiments, one or more lysine residues in the corresponding native sequence are replaced by a different amino acid, for example, arginine. In some embodiments, the COF1I / CRBN-binding polypeptide comprises less than 1, 2, 3, 4 or 5 lysine residues. In some embodiments, the COF1I / CRBN-binding polypeptide does not comprise a lysine residue. In some embodiments, the COF1 / CRBN-binding polypeptide is not ubiquitinated, for example, in the presence of COF1, for example, as measured by an assay described in this document, optionally where ubiquitination is as measured in a cell of mammal, for example, a human cell.
[0044] [0044] In some embodiments, the COF1 / CRBN-binding polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 41, 42 and 43. In some
[0045] [0045] In some embodiments, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 2. In some embodiments, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ | D NO: 4. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 2. In some embodiments, the COF1 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 4.
[0046] [0046] In some embodiments, COF1 is an immunomodulatory imide drug (IMID), or a pharmaceutically acceptable salt thereof.
[0047] [0047] In some modalities, COF1 has the structure of Formula (| -a): (Ro o "om
[0048] [0048] In some modalities of Formula (Il-a), XKé O. In some modalities, M is absent. In some embodiments, Ring A is heterocyclic (for example, a nitrogen containing heterocyclic, for example 2- (2,6-dioxopiperidin-3-yl) isoindoline-1,3-dione). In some modalities, Rº is oxo or ORº (for example, -OCH; 3 or - OCH2CH; 3) and o is 0, 1, or 2. In some modalities, each one between R ºº and R it is independently hydrogen, or R2º and R2º, together with the carbon atom to which they are attached, form a carbonyl group. In some embodiments, Rº * º is heteroalkyl (for example, - CHaNHC (O) CH2), —-N (RºNKNRP) (for example, -NH2) or —N (Rº) C (O) RºA (for example, - NHC (O) CH3). In some embodiments, n is 0.
[0049] [0049] In some embodiments, COF1 is thalidomide or analogous, or a pharmaceutically acceptable salt thereof.
[0050] [0050] In some embodiments, COF1 is selected from the group consisting of lenalidomide, pomalidomide, thalidomide and 2- (4- (tert-butyl) phenyl) - N - (((2- (2,6-dioxopiperidin-3 -yl) -1-oxoisoindolin-5-yl) methyl) acetamide or a pharmaceutically acceptable salt thereof.
[0051] [0051] In some modalities, COF1 is selected from the group consisting of: COS OX o Co NH O; NH O; o and oo i UCÓ So, or a pharmaceutically acceptable salt thereof.
[0052] [0052] In some embodiments, COF1 is lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof. In some embodiments, COF1 is lenalidomide or the like, or a pharmaceutically acceptable salt thereof. In some embodiments, COF1 is lenalidomide, or a pharmaceutically acceptable salt thereof.
[0053] [0053] In some embodiments, the fusion polypeptide further comprises a degradation domain, in which the degradation domain is separated from the COF1 / CRBN-binding polypeptide and the heterologous polypeptide by a protease cleavage site heterologous.
[0054] [0054] In some embodiments, the fusion polypeptide comprises, from the N termination to the C termination: i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF1 / CRBN binding polypeptide; ii) the degradation domain, the heterologous protease cleavage site, the COF1 / CRBN binding polypeptide and the heterologous polypeptide; iii) the COF1 / CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site and the degradation domain; or iv) the heterologous polypeptide and the COF1 / CRBN binding polypeptide, the heterologous protease cleavage site and the degradation domain.
[0055] [0055] In some embodiments, the fusion polypeptide comprises, from the N termination to the C termination, the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF1 / CRBN-binding polypeptide.
[0056] [0056] In some embodiments, the degradation domain has a first state associated with a first level of expression of the fusion polypeptide and a second state associated with a second level of expression of the fusion polypeptide, in which the second level is increased, for example, at least 2 times, 3 times, 4 times, times, 10 times, 20 times or 30 times in relation to the first level in the presence of a stabilizing compound.
[0057] [0057] In some embodiments, in the absence of the stabilizing compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%, 90% or more of the polypeptide fusion is degraded, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[0058] [0058] In some embodiments, the level of expression and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0059] [0059] In some embodiments, in the presence of the stabilizing compound: i) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; or ii) the conformation of the fusion polypeptide is more permissible to cleavage at the heterologous protease cleavage site in relation to a conformation in the absence of the stabilizing compound.
[0060] [0060] In some embodiments, the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB protein (FKBP) domain or a dihydrofolate reductase (DHFR) domain.
[0061] [0061] In some embodiments, the degradation domain is an estrogen receptor (ER) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 46 or 48. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 48.
[0062] [0062] In some embodiments, the stabilizing compound is bazedoxifene or 4-hydroxy tamoxifen (4-OHT), or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain is an estrogen receptor (ER) domain and the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46 and the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof.
[0063] [0063] In some embodiments, the degradation domain is an FKB protein (FKBP) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 50. In some embodiments, the degradation domain comprises the sequence amino acids of SEQ ID NO: 50. In some embodiments, the stabilizing compound is Shield-1, or a pharmaceutically acceptable salt thereof.
[0064] [0064] In some embodiments, the degradation domain is a dihydrofolate reductase (DHFR) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO:
[0065] [0065] In some embodiments, the heterologous protease cleavage site is cleaved by an intracellular mammalian protease. In some embodiments, the heterologous protease cleavage site is cleaved by a protease selected from the group consisting of furin, POSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, protease from precision, thrombin, TEV protease and elastase 1. In some embodiments, the heterologous protease cleavage site comprises a sequence that has a cleavage motif selected from the group consisting of the RX (K / RJ) R consensus motif (X may be any amino acid; SEQ ID NO: 52), RXXX consensus motive [KRI] IR (X can be any amino acid; SEQ ID NO: 53), RRX consensus motive (SEQ ID NO: 54), consensus motive from | -EPDX (SEQ ID NO: 55), Ille-Glu / Asp-Gly-Arg (SEQ IDNO: 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-Gly-Ala -Ala-His-Tyr (SEQ ID NO: 58), LPXTG / A consensus reason (SEQ ID NO: 59), Leu-Glu-Val-Phe-Gln-Gly-Pro (SEQ ID NO: 60) ), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), ENLYFQG (SEQ ID NO: 62) and [AGSV] -X (X can be any amino acid; SEQ ID NO: 63). In some embodiments, the heterologous protease cleavage site is cleaved by furin. In some embodiments, the heterologous protease cleavage site comprises a furin cleavage site selected from the group consisting of RTKR (SEQ ID NO: 123); GSTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125); GTGAED-PRPSRKRR (SEQ ID NO: 127); LAWLEQQAVAKRRTKR (SEQ ID NO: 129); GTGAEDPRPSRKRRSLGG (SEQ ID NO: 131); GTGAED-PRPSRKRRSLG (SEQ ID NO: 133); SLNLTESHNSRKKR (SEQ ID
[0066] [0066] In one aspect, a fusion polypeptide comprising a first domain and a second domain separated by a heterologous protease cleavage site is provided herein, wherein the first domain comprises a degradation domain and the second domain comprises a compound of Formula (II), a polypeptide binding to (COF2) / CRBN and a heterologous polypeptide, for example, a bacterial or viral heterologous polypeptide, wherein the compound of Formula (II) is: x (Rh Ra R p (11)
[0067] [0067] In some embodiments, the degradation domain has a first state associated with a first level of expression of the fusion polypeptide and a second state associated with a second level of expression of the fusion polypeptide, in which the second level is increased, for example, at least 2 times, 3 times, 4 times, times, 10 times, 20 times or 30 times in relation to the first level in the presence of a stabilizing compound.
[0068] [0068] In some embodiments, in the absence of the stabilizing compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%, 90% or more of the polypeptide fusion is degraded, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[0069] [0069] In some embodiments, the level of expression and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0070] [0070] In some embodiments, in the presence of the stabilizing compound: i) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; or ii) the conformation of the fusion polypeptide is more permissible to cleavage at the heterologous protease cleavage site in relation to a conformation in the absence of the stabilizing compound.
[0071] [0071] In some embodiments, the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB protein (FKBP) domain or a dihydrofolate reductase (DHFR) domain.
[0072] [0072] In some embodiments, the degradation domain is an estrogen receptor (ER) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 46 or 48. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 48.
[0073] [0073] In some embodiments, the stabilizing compound is bazedoxifene or 4-hydroxy tamoxifen (4-OHT), or a pharmaceutical salt.
[0074] [0074] In some embodiments, the degradation domain is an FKB protein (FKBP) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 50. In some embodiments, the degradation domain comprises the sequence amino acids of SEQ ID NO: 50. In some embodiments, the stabilizing compound is Shield-1, or a pharmaceutically acceptable salt thereof.
[0075] [0075] In some embodiments, the degradation domain is a dihydrofolate reductase (DHFR) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO:
[0076] [0076] In some embodiments, the heterologous protease cleavage site is cleaved by an intracellular mammalian protease. In some embodiments, the heterologous protease cleavage site is cleaved by a protease selected from the group consisting of furin, POSK1, PCSK5, PCSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, protease from precision, thrombin, TEV protease and elastase 1. In some embodiments, the heterologous protease cleavage site comprises a sequence that has a cleavage motif selected from the group consisting of a consensus motif of RX (K / R) R (X can be any amino acid; SEQ ID NO: 52), reason for consensus of RXXX [KRIJR (X can be any amino acid; SEQ ID NO: 53), reason for consensus of RRX (SEQ ID NO: 54), reason for consensus of | -EPDX (SEQ ID NO: 55), Ile-Glu / Asp-Gly-Arg (SEQ IDNO: 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-Gly- Ala-Ala-His-Tyr (SEQ ID NO: 58), LPXTG / A consensus reason (SEQ ID NO: 59), Leu-Glu-Val-Phe-GlIn-Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), ENLYFQG (SEQ ID N O: 62) and [AGSV] -X (X can be any amino acid; SEQ ID NO: 63). In some embodiments, the heterologous protease cleavage site is cleaved by furin.
[0077] [0077] In some embodiments, the degradation domain is merged with the heterologous protease cleavage site, which is further fused to the second domain.
[0078] [0078] In some embodiments, the fusion polypeptide comprises, from the N-terminus to the C-terminus: i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF2 / CRBN-binding polypeptide; li) the degradation domain, the heterologous protease cleavage site, the COF2 / CRBN binding polypeptide and the heterologous polypeptide; iii) the COF2 / CRBN binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site and the degradation domain; or iv) the heterologous polypeptide and the COF2 / CRBN binding polypeptide, the heterologous protease cleavage site and the degradation domain.
[0079] [0079] In some embodiments, the fusion polypeptide comprises, from the N termination to the C termination, the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF2 / CRBN binding polypeptide. In some embodiments, the fusion polypeptide comprises, from the N termination to the C termination, the degradation domain, the heterologous protease cleavage site, the COF2 / CRBN-binding polypeptide and the heterologous polypeptide. In some embodiments, the fusion polypeptide comprises, from the N-termination to the termination, the COF2 / CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site, and the degradation domain. In some embodiments, the fusion polypeptide comprises, from the N-termination to the termination, the heterologous polypeptide, and the COF2 / CRBN-binding polypeptide, the heterologous protease cleavage site and the degradation domain.
[0080] [0080] In some embodiments, the association of the COF2 / CRBN-binding polypeptide with cerenlon (CRBN) in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation. In some embodiments, the COF2 / CRBN-binding polypeptide does not bind CRBN in the absence of COF2. In some embodiments, the association of the fusion polypeptide with CRBN in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation. In some embodiments, the fusion polypeptide does not bind CRBN in the absence of COF2. In some embodiments, association and / or attachment is as measured in a mammalian cell, for example, a human cell.
[0081] [0081] In some embodiments, the ubiquitination of the heterologous polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50 %, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described herein. In some embodiments, the ubiquitination of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described herein. In some embodiments, the heterologous polypeptide or the fusion polypeptide is ubiquitinated to one or more lysine or methionine residues in the presence of COF2. In some embodiments, ubiquitination is as measured in a mammalian cell, for example, a human cell.
[0082] [0082] In some embodiments, the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western analysis blot or flow cytometry analysis. In some embodiments, the degradation of the fusion polypeptide is mediated by ubiquitination in the presence of COF2. In some embodiments, degradation is as measured in a mammalian cell, for example, a human cell.
[0083] [0083] In some embodiments, the COF2 / CRBN-binding polypeptide has between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues in length, between and 85 amino acid residues in length, between 25 and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length , between 50 and 65 amino acid residues in length or between 55 and 65 amino acid residues in length.
[0084] [0084] In some embodiments, the COF2 / CRBN-binding polypeptide comprises a beta curve. In some embodiments, the COF2 / CRBN-binding polypeptide comprises a beta curve of IKZF1 or IKZF3 (e.g., IKZF1 or human IKZF3). In some embodiments, the COF2 / CRBN-binding polypeptide comprises a beta clamp format. In some embodiments, the COF2 / CRBN-binding polypeptide comprises a beta clip format of IKZF1 or IKZF3 (e.g., IKZF1 or human IKZF3). In some embodiments, the COF2 / CRBN-binding polypeptide comprises a beta strand. In some embodiments, the COF2 / CRBN-binding polypeptide comprises a beta strand of IKZF1 or IKZF3 (e.g., IKZF1 or human IKZF3). In some embodiments, the COF2 / CRBN-binding polypeptide comprises an alpha helix. In some embodiments, the COF2 / CRBN-binding polypeptide comprises an alpha helix of IKZF1 or IKZF3 (for example, IKZF1 or human IKZF3). In some embodiments, the COF2 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clip format, a second beta strand and a first alpha helix. In some embodiments, the COF2 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clip format, a second beta strand and a first IKZF1 alpha helix or IKZF3 (e.g., IKZF1 or human IKZF3). In some modalities, the COF2 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clamp format, a second beta strand, a first alpha helix and a second alpha helix . In some embodiments, the COF2 / CRBN-binding polypeptide comprises, from the N-terminus to the C-terminus,
[0085] [0085] In some embodiments, the COF2 / CRBN-binding polypeptide comprises a COF2 / CRBN-binding sequence of a naturally occurring polypeptide or a COF2 / CRBN-binding variant thereof. In some embodiments, the COF2 / CRBN-binding polypeptide comprises a COF2 / CRBN-binding sequence of a naturally occurring IKZF polypeptide or a COF2 / CRBN-binding variant thereof. In some modalities, the COF2 / CRBN binding polypeptide comprises a COF2 / CRBN binding sequence of a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4 or IKZF5, or a COF2 / CRBN binding variant thereof. In some embodiments, the COF2 / CRBN binding sequence comprises two or more discontinuous sequences of the naturally occurring polypeptide, for example, a naturally occurring IKZF polypeptide, for example, an IKZF1, IKZF2, IKZF3, IKZF4 or naturally occurring IKZF5.
[0086] [0086] In some embodiments, the COF2 / CRBN-binding polypeptide comprises an IKZF polypeptide or a structural motif thereof.
[0087] [0087] In some embodiments, the IKZF polypeptide is an IKZF1 polypeptide, an IKZF3 polypeptide, an IKZF2 polypeptide that has H141Q substitution (numbered according to SEQ ID NO: 21), or an IKZF4 polypeptide which has H188Q replacement (numbered according to SEQ ID NO: 22).
[0088] [0088] In some embodiments, the COF2 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or an IKZF structural motif (for example, IKZF1 or IKZF3) that:
[0089] [0089] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0090] [0090] In some embodiments, the COF2 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues, about 15 to about 90 amino acid residues, about to about 85 amino acid residues, about 25 to about 80 amino acid residues, about 30 to about 75 amino acid residues, about 35 to about 70 amino acid residues, about 40 to about 65 amino acid residues, about 45 to about 65 amino acid residues, about 50 to about 65 amino acid residues, or about 55 to about 65 amino acid residues of IKZF1 or IKZF3.
[0091] [0091] In some embodiments, the COF2 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 of SEQ ID NO: 19) that: i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the
[0092] [0092] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0093] [0093] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COF2 / CRBN-binding polypeptide comprises the sequence amino acids of SEQ ID NO: 5) or a sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues) (for example, a sequence that has no more than 1,2,3,4, 5, 10, 15, 20, 25 , 30, 35, or 40 amino acid substitutions of amino acid residues 136 to 180 of SEQ ID NO: 19).
[0094] [0094] In some embodiments, the COF2 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 170 of SEQ ID NO: 19) that: i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[0095] [0095] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[0096] [0096] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COF2 / CRBN-binding polypeptide comprises the sequence amino acids of SEQ ID NO: 6) or a sequence that differs from amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 170 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid substitutions of amino acid residues 136 to 170 of SEQ ID NO: 19).
[0097] [0097] In some embodiments, one, two, three or all of the following amino acid residues remain unchanged: glutamine at position 147, cysteine at position 148, glutamine at position 150, glycine at position 152, leucine at position 161 or leucine in position 162, numbered according to SEQ ID NO: 19. In some modalities, the glutamine in position 147 remains unchanged, numbered according to SEQ ID NO: 19. In some modalities, the cysteine in position 148 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, the glutamine at position 150 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, the glycine at position 152 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, leucine at position 161 remains unchanged, numbered according to SEQ ID NO: 19. In some embodiments, leucine at position 162 remains unchanged, numbered according to SEQ ID NO: 19.
[0098] [0098] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 139 of IKZF3 (numbered according to SEQ ID NO: 19) for example, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 40.
[0099] [0099] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19). In some modalities, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 5. In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 77. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 5. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO:
[00100] [00100] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19). In some modalities, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 6. In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 78. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 6. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO:
[00101] [00101] In some embodiments, the COF2 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif for amino acid residues 236 to 249 of SEQ ID NO: 19) that: i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the
[00102] [00102] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[00103] [00103] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COF2 / CRBN-binding polypeptide comprises the sequence amino acids of SEQ ID NO: 11) or a sequence that differs from amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues (for example, a sequence that differs from amino acid residues 236 to 249 of SEQ ID NO: 19 by no more than 1,2,3,4, 5, 6 or 7 amino acid residues) ( for example, a sequence that has no more than 1, 2, 3, 4, 5, 6, or 7 amino acid substitutions of amino acid residues 236 to 249 of SEQ ID NO: 19).
[00104] [00104] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19). In some modalities, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 11.
[00105] [00105] In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 91.
[00106] [00106] In some embodiments, the COF2 / CRBN-binding polypeptide comprises sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 and 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif of amino acid residues 136 to 180 and 236 to 249 of SEQ ID NO: 19) that: i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 it is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitating
[00107] [00107] In some embodiments, the association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[00108] [00108] In some embodiments, the polypeptide binding to
[00109] [00109] In some embodiments, the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 and 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19). In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 1. In some modalities, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 3. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 1. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 3.
[00110] [00110] In some embodiments, the COF2 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) and a second sequence comprising the sequence of amino acids of MALEKMALEKMALE (SEQ ID NO: 91). In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 14. In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 85. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 14. In some modalities, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 85.
[00111] [00111] In some embodiments, the COF2 / CRBN binding polypeptide comprises a first sequence comprising amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) and a second sequence comprising the sequence of amino acids of MALEKMALEKMALE (SEQ ID NO: 91). In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 15. In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 86. In some embodiments, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 15. In some modalities, the COF2 / CRBN-binding polypeptide consists of the amino acid sequence of SEQ ID NO: 86.
[00112] [00112] In some embodiments, the COF2 / CRBN-binding polypeptide comprises at least one lysine unless the corresponding native sequence. In some embodiments, one or more lysine residues in the corresponding native sequence are replaced
[00113] [00113] In some embodiments, the COF2 / CRBN-binding polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 41, 42 and 43. In some embodiments, the a-binding polypeptide COF2 / CRBN comprises the amino acid sequence of SEQ ID NO: 4. In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 41. In some embodiments, the polypeptide of COF2 / CRBN binding comprises the amino acid sequence of SEQ ID NO: 42. In some embodiments, the COF2 / CRBN binding polypeptide comprises the amino acid sequence of SEQ ID NO: 43.
[00114] [00114] In some embodiments, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO:
[00115] [00115] In some embodiments, COF2 is an immunomodulatory imide drug (IMiD), or a pharmaceutically acceptable salt thereof.
[00116] [00116] In some embodiments, COF2 has the structure of Formula (|): x (R »n Do R2a R2 (1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where : XéOousS; R 'is C1-Cs alkyl, C2-C6 alkenyl, C2-Cs alkynyl, C1-C6 heteroalkyl, carbocicyl, heterocicyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $; each of R º and R is independently hydrogen or C1-C6 alkyl, or Rºº and R , together with the carbon atom to which they are attached, form a carbonyl group or a thiocarbonyl group; each of R3 is independently C1-Cs alkyl, C2-C6 alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) Rô, - C (O0) ORE, -OR8, -N (RE) (R ), -C (O) IN (RNRP), -N (RO) C (O) RA, -S (O) .RE, -S (O) KN (RNR ) Or -N (R) IS ( O), RE, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by one or more R $, each Rº is independently C1-Cs alkyl, C2-C6 alkenyl a, C2-C6 alkynyl, C1-C6 heteroalkyl, halo, cyano, oxo, -C (OJ) Rô, - C (O) ORE, -OR8, -N (RE) (R ), -C (O) IN (RNRP), -N (RO) C (O) RA, -S (O) .RE, -S (O) .N (RNRP), -N (Rº) S (O) .RE, carbocicila, heterocicila , aryl or heteroaryl, in which each alkyl, alkenyl, alkynyl, heteroalkyl, carococyl, heterocyclic, aryl and heteroaryl is independent and optionally substituted by one or more R; each of R4, RB, Rº, RP and RF is independently hydrogen or C1-Cs alkyl; each Rô is independently C1-Cs alkyl, oxo, cyano, - ORE, -N (RºNRP), -C (OIN (RNRP), -N (RO) C (O) RA, aryl or heteroaryl, where each aryl and heteroaryl is independent and optionally substituted by one or more R $; each R 'is independently halo, oxo, cyano, -OR8, - N (RE) (R ), -C (O) N (R) (Rº ) or -N (Rº) C (O) Rº; each Rº is independently C1-Cs alkyl, cyano, -ORº, - N (RENR ), -C (O) N (RNRP) or -N (R) C (O) RA; ne 0, 1,2,3ou4; and xéO, 1ou2.
[00117] [00117] In some embodiments, COF2 has the structure of Formula (| -a): Ro o (R% OO Ç) N — M R2p Frog Frog (Ia) or a pharmaceutically acceptable salt, ester, hydrate or tautomer the same, in which: Ring A is carbocicyl, heterocicyl, aryl or heteroaryl, each of which is independent and optionally replaced by one or more R $; M is absent, C1-Cs alkyl, C2-C6 alkenyl, C2-Cs alkynyl or C1-Cs heteroalkyl, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R $; each between R º and R it is independently hydrogen or C1-C6 alkyl; or R º and R , together with the carbon atom to which they are attached, form a carbonyl group or thiocarbonyl group; R * is hydrogen, C1-Cs alkyl, C2-C6 alkenyl, C2-Cs6 al-
[00118] [00118] In some embodiments, COF2 is thalidomide or analogous, or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 is selected from the group consisting of lenalidomide, pomalidomide, thalidomide and 2- (4- (tert-butyl) phenyl) -N - ((2- (2,6-dioxopiperidin-3-yl) -1-oxoisoindolin-5-yl) methyl) acetamide or a pharmaceutically acceptable salt thereof.
[00119] [00119] In some modalities, COF2 is selected from the group consisting of: COS CS o Co NO; NH O; o and oo
[00120] [00120] In some embodiments, COF2 is lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 is lenalidomide or the like, or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 is lenalidomide, or a pharmaceutically acceptable salt thereof.
[00121] [00121] In some embodiments, COF2 comprises the structure of Formula (1): (Rn (A + RE RA (1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where: XéOousS; R ' is C1-C6 alkyl, C2-Cs alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, carbocicyl, heterocycyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $;
[00122] [00122] In some modalities, COF2 comprises the structure of Formula (I-a): (Ro o "om
[00123] [00123] In some embodiments, COF2 comprises an immunomodulatory imide drug (IMID), or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 comprises thalidomide or the like, or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 comprises lenalidomide, pomalidomide, thalidomide and 2- (4- (tert-butyl) phenyl) -N - ((2- (2,6-dioxopipeidin-3-yl) -1-oxoisoindolin- 5-yl) methyl) acetamide or a pharmaceutically acceptable salt thereof.
[00124] [00124] In some modalities, COF2 comprises a compound selected from the group consisting of:
[00125] [00125] In some embodiments, COF2 comprises lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 comprises lenalidomide or the like, or a pharmaceutically acceptable salt thereof. In some embodiments, COF2 comprises lenalidomide, or a pharmaceutically acceptable salt thereof.
[00126] [00126] In some embodiments, COF2 further comprises a linker (for example, where R * º in Formula (II) is L-Tag). In some embodiments, R * º in Formula (11) is L-Tag, L is a linker selected from a linker disclosed in International Patent Publication No. WO2017 / 024318 (for example, in Figures 28 to 31), and Tag is selected from a dTAG Bleaching Binder disclosed in International Patent Publication No. WO2017 / 024318 (for example, in Table T, pages 119 to 129). In some embodiments, COF2 comprises IMID (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) and a binder, in which IMiD (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) it is linked to the linker, for example, by means of a linker. In some embodiments, the COF2 / CRBN-binding polypeptide binds to the linker and the link between the COF2 / CRBN-binding polypeptide and IMID (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) in the absence of the ligand it is no more than 0.0001, 0.001, 0.01,
[00127] [00127] In one aspect, a fusion polypeptide is provided which comprises a compound of Formula (III) (COF3) / CRBN-binding polypeptide and a heterologous polypeptide, wherein the compound of Formula (III) is: oo PExi Rx RN (11) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where: X1 is CR3; ====== is optionally a double bond when X: is CR3 and R3a is absent; each R: is independently C1-Cs alkyl, C1-C6 haloalkyl, C1-Cs hydroxyalkyl or halo, or two R1, together with the carbon atom to which they are attached, form a 5- or 6-membered heterocyclic ring, or two R1, when in adjacent atoms, together with the atoms to which they are attached, form a Cs-C11 aryl or a 5- or 6-membered heteroaryl ring comprising 1 to 3 heteroatoms selected from O Ne S; R2 is hydrogen, C1-Cs alkyl, -C (O) C1-Cs alkyl, -C (O) (CH2) 0-3- C6-C109 aryl, -C (O0) O (CH2) 0-3-Ce -Cioaryl, Ce-C10 aryl or 5- or 6-membered heteroaryl comprising 1 to 3 selected heteroatoms
[00128] [00128] In one embodiment, the compound of Formula (Ill) is a compound of Formula (III-b): o Ws. RE No (I1I-b), or a pharmaceutically acceptable salt, hydrate, solvate, stereoisomer and tautomer thereof, where X1, R1, R2, n, q and sub-variables thereof are defined as described for the Formula (Ill)
[00129] [00129] In one embodiment, the compound of Formula (Ill) is a compound of Formula (III-d): (Rida N o 2 RÓ (111-d), or to salt, hydrate, solvate, prodrug, stereoisomer and pharmaceutically acceptable tautomer thereof, wherein R1, R2, q, and sub-variables thereof are defined as described for Formula (Ill) above.
[00130] [00130] In one embodiment, the COF3 / CRBN-binding polypeptide is fused to the heterologous polypeptide. In one embodiment, the COF3 / CRBN-binding polypeptide and the heterologous polypeptide are linked by a peptide bond. In one embodiment, the COF3 / CRBN-binding polypeptide and the heterologous polypeptide are linked by a different bond than a peptide bond. In a fashion, the heterologous polypeptide is linked directly to the COF3 / CRBN binding polypeptide. In one embodiment, the heterologous polypeptide is indirectly linked to the COF3 / CRBN binding polypeptide. In one embodiment, the COF3 / CRBN-binding polypeptide and the heterologous polypeptide are operably linked by means of a linker, for example, a glycine-serine linker, for example, a linker comprising the SEQ amino acid sequence ID NO:
[00131] [00131] In one embodiment, the association of the fusion polypeptide with CRBN in the absence of COF3 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15% , or 20% of the polypeptide association
[00132] [00132] In one embodiment, the COF3 / CRBN-binding polypeptide is between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues in length, between 20 and 85 amino acid residues in length, between 25 and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length length, between 50 and 65 amino acid residues in length or between 55 and 65 amino acid residues in length. In one embodiment, the COF3 / CRBN-binding polypeptide is 59 amino acid residues in length.
[00133] [00133] In one embodiment, the COF3 / CRBN-binding polypeptide comprises a beta curve. In one embodiment, the COF3 / CRBN-binding polypeptide comprises a beautiful clip format. In one embodiment, the COF3 / CRBN-binding polypeptide comprises a beta strand. In one embodiment, the COF3 / CRBN-binding polypeptide comprises an alpha helix. In one embodiment, the COF3 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clip format, a second beta strand and a first alpha helix. In one embodiment, the COF3 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clamp format, a second beta strand, a first alpha helix and a second alpha helix. In one embodiment, the beta clip format and the second alpha helix are separated by no more than 60, 50, 40 or amino acid residues.
[00134] [00134] In one embodiment, the COF3 / CRBN binding polypeptide comprises a COF3 / CRBN binding sequence of a naturally occurring polypeptide or a COF3 / CRBN binding variant thereof. In one embodiment, the COF3 / CRBN binding polypeptide comprises a COF3 / CRBN binding sequence of a naturally occurring IKZF polypeptide or a COF3 / CRBN binding variant thereof. In one embodiment, the COF3 / CRBN binding polypeptide comprises a COF3 / CRBN binding sequence of a naturally occurring IKZF2 or a COF3 / CRBN binding variant thereof. In a fashion, the COF3 / CRBN-binding polypeptide comprises two or more discontinuous sequences from a naturally occurring IKZF polypeptide, for example, a naturally occurring IKZF2.
[00135] [00135] In one embodiment, the COF3 / CRBN-binding polypeptide comprises amino acid residues 130 to 174 of IKZF2 (numbered according to SEQ ID NO: 21). In one embodiment, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 113. In one embodiment, the COF3 / CRBN-binding polypeptide comprises a sequence that differs from residues of amino acids 130 to 174 of IKZF2 (numbered according to SEQ ID NO: 21) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues. In one embodiment, the COF3 / CRBN-binding polypeptide comprises the sequence that differs from amino acid residues 130 to 174 of SEQ ID NO: 21 by no more than 1,2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues. In one embodiment, the COF3 / CRBN-binding polypeptide comprises a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid substitutions of amino acid residues 130 to 174 of SEQ ID NO: 21.
[00136] [00136] In one embodiment, the COF3 / CRBN-binding polypeptide comprises amino acid residues 230 to 243 of IKZF2 (numbered according to SEQ ID NO: 21). In one embodiment, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 114. In one embodiment, the COF3 / CRBN-binding polypeptide comprises a sequence that differs from residues of amino acids 230 to 243 of IKZF2 (numbered according to SEQ ID NO: 21) by no more than 1, 2, 3, 4, 5 or 10 amino acid residues. In one embodiment, the COF3 / CRBN-binding polypeptide comprises the sequence that differs from amino acid residues 230 to 243 of SEQ ID NO: 21 by no more than 1, 2, 3, 4, 5 or 10 amino acid residues . In one embodiment, the COF3 / CRBN-binding polypeptide comprises a sequence that has no more than 1, 2, 3, 4, 5 or 10 amino acid substitutions of amino acid residues
[00137] [00137] In one embodiment, histidine at position 141 remains unchanged, numbered according to SEQ ID NO: 21.
[00138] [00138] In one embodiment, the COF3 / CRBN-binding polypeptide comprises amino acid residues 130 to 174 of IKZF2 (numbered according to SEQ ID NO: 21). In one embodiment, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 113. In one embodiment, the COF3 / CRBN-binding polypeptide comprises amino acid residues 230 to 243 of IKZF2 ( numbered according to SEQ ID NO: 21). In a fashion, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 114. In one embodiment, the COF3 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 109.
[00139] [00139] In some embodiments, the fusion polypeptide further comprises a degradation domain, in which the degradation domain is separated from the COF3 / CRBN-binding polypeptide and the heterologous polypeptide by a protease cleavage site heterologous.
[00140] [00140] In some embodiments, the fusion polypeptide comprises, from the N termination to the C termination: i) the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF3 / CRBN-binding polypeptide; ii) the degradation domain, the heterologous protease cleavage site, the COF3 / CRBN-binding polypeptide and the heterologous polypeptide; ili) the COF3 / CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site and the degradation domain; or iv) the heterologous polypeptide and the polypeptide binding to
[00141] [00141] In some embodiments, the fusion polypeptide comprises, from the N termination to the C termination, the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF3 / CRBN binding polypeptide.
[00142] [00142] In some embodiments, the degradation domain has a first state associated with a first level of expression of the fusion polypeptide and a second state associated with a second level of expression of the fusion polypeptide, in which the second level is increased, for example, at least 2 times, 3 times, 4 times, times, 10 times, 20 times or 30 times in relation to the first level in the presence of a stabilizing compound.
[00143] [00143] In some embodiments, in the absence of the stabilizing compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%, 90% or more of the polypeptide fusion is degraded, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[00144] [00144] In some embodiments, the level of expression and / or degradation is as measured in a mammalian cell, for example, a human cell.
[00145] [00145] In some embodiments, in the presence of the stabilizing compound: i) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; or ii) the conformation of the fusion polypeptide is more permissible to cleavage at the heterologous protease cleavage site in relation to a conformation in the absence of the stabilizing compound.
[00146] [00146] In some embodiments, the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB protein (FKBP) domain or a dihydrofolate reductase (DHFR) domain.
[00147] [00147] In some embodiments, the degradation domain is an estrogen receptor (ER) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 46 or 48. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 48.
[00148] [00148] In some embodiments, the stabilizing compound is bazedoxifene or 4-hydroxy tamoxifen (4-OHT), or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain is an estrogen receptor (ER) domain and the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46 and the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof.
[00149] [00149] In some embodiments, the degradation domain is an FKB protein (FKBP) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 50. In some embodiments, the degradation domain comprises the sequence amino acids of SEQ ID NO: 50. In some embodiments, the stabilizing compound is Shield-1, or a pharmaceutically acceptable salt thereof.
[00150] [00150] In some embodiments, the degradation domain is a dihydrofolate reductase (DHFR) domain. In some embodiments, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO:
[00151] [00151] In some embodiments, the heterologous protease cleavage site is cleaved by a mammalian intracellular protease. In some embodiments, the heterologous protease cleavage site is cleaved by a protease selected from the group consisting of furin, POSK1, PCSK5, POSK6, PCSK7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, protease from precision, thrombin, TEV protease and elastase 1. In some embodiments, the heterologous protease cleavage site comprises a sequence that has a cleavage motif selected from the group consisting of a consensus motif of RX (K / R) R (X can be any amino acid; SEQ ID NO: 52), RXXX consensus motive [KRI] R (X can be any amino acid; SEQ ID NO: 53), RRX consensus motive (SEQ ID NO: 54), consensus motive for | -EPDX (SEQ ID NO: 55), Ile-Glu / Asp-Gly-Arg (SEQ IDNO: 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro- GIy-Ala-Ala-His-Tyr (SEQ ID NO: 58), LPXTG / A consensus reason (SEQ ID NO: 59), Leu-Glu-Val-Phe-Gln-Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), ENLYFQG (SEQ ID NO : 62) and [AGSV] -X (X can be any amino acid; SEQ ID NO: 63). In some embodiments, the heterologous protease cleavage site is cleaved by furin. In some embodiments, the heterologous protease cleavage site comprises a furin cleavage site selected from the group consisting of RTKR (SEQ ID
[00152] [00152] In certain embodiments, the heterologous polypeptide is chosen from a cytoplasmic and / or nuclear polypeptide, or a transmembrane polypeptide, for example, a heterologous polypeptide in Table 2. In some embodiments, the cytoplasmic polypeptide and / or nuclear is selected from the group consisting of a component of the apoptosis pathway (eg, Caspase 9), a component of a CRISPR / Cas system (eg, Cas9), a transcription factor (eg, MITF, c -Myc, STAT3, STATS, NF-capaB, beta-catenin, Notch, GLI or c-JUN), Tet methylcytosine dioxige-nase 2 (TET2), FKBP and Tau. In some embodiments, the transmembrane polypeptide is selected from the group consisting of CD62L, CCR1, CCR2, CCR5, CCR7, CCRIO, CXCR2, CXCR3, CXCRA, CXCR6, CTLA4, PD1, BTLA, VISTA, CD137L, CD80, CD86, TIGIT, CD3, CD8, CD19, CD22, CD20, BOCMA and a chimeric antigen receptor (CAR). In some embodiments, the heterologous polypeptide is selected from the group consisting of a chimeric antigen receptor (CAR), a component of a CRISPR / Cas system (for example, Cas9), CD8, CD19 and CD22.
[00153] [00153] In some embodiments, the heterologous polypeptide is a chimeric antigen receptor (CAR). In some embodiments, said CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a transmembrane domain and one or more intracellular signaling domains. In some modalities, the intracellular signaling domain comprises one or more primary signaling domains. In some embodiments, the intracellular signaling domain comprises one or more co-stimulating signaling domains. In some modalities, one of the one or more domains of primary signaling comprises a stimulating domain of CD3-zeta. In some modalities, one or more of the different co-stimulating signaling domains in an intracellular domain of a co-stimulating protein is selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, GITR, CD30, CDA40 , ICOS, BAFFR, HVEM, ICAM-1, lymphocyte-associated antigen-1 (LFA-1), CD2, CDS, CD7, CD287, LIGHT, NKG2C, NKG2D, SLAMF7, NKp80, NKp30, NKp44, NKp46 , CD160, B7-H3 and a linker that specifically binds to CD83. In some embodiments, the one or more of said co-stimulating signaling domains comprises the 4-1BB co-stimulating domain. In some embodiments, the one or more of said co-stimulating signaling domains comprises the CD28 co-stimulating domain. In some embodiments, the antigen-binding domain is an scFv.
[00154] [00154] In some modalities, said antigen-binding domain binds an antigen selected from the group consisting of CD19; CD123; CD22; CD30; CD171; CS-1; lectin type C molecule-1, CD33; epidermal growth factor receptor (EGFRvII!) variant Ill; ganglioside G2 (GD2); ganglioside GD3; member of TNF receptor family; B cell maturation antigen; Tn antigen ((Tn Ag) or (GalNAca-Ser / Thr)); prostate-specific membrane antigen (PSMA); Receptor 1 orphan tyrosine kinase receptor (ROR1); tyrosine kinase 3 type Fms (FLT3); tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor alpha-2 subunit; Mesothelin; Alpha Interleukin 11 receptor (IL-11Ra); prostate stem cell antigen (PSCA); Protease serine 21; vascular endothelial growth factor receptor 2 (VEGFR2); Lewis antigen (Y); CD24; Beta receptor for platelet-derived growth factor (PDGFR-beta); specific stage embryonic antigen-4 (SSEA-4); CD20; alpha folate receptor; ERBB2 receptor tyrosine protein kinase (Her2 / neu); mucin 1, associated with the cell surface (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); Prostasis; prostatic acid phosphatase (PAP); mutated stretching factor 2 (ELF2M); Ephrin B2; alpha fibroblast activation protein (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CAIX); Proteasome subunit (Prossoma, Macropaína), Type Beta, 9 (LMP2); glycoprotein 100 (gp100); oncogen polypeptide consisting of the breaking point clustering region (BCR) and Abelson murine leukemia viral oncogen homologue 1 (Abl) (bcr-abl); tyrosinase; ephrin type A receptor 2 (EphA2); Fucosyl GM1; Lewis sialyl adhesion molecule (sLe); ganglioside GM3; transglutaminase 5 (TGS5); antigen associated with high molecular weight melanoma (HMWMAA); o-acetyl-GD2 ganglioside (OAcGD 2); beta folate receptor; tumor endothelial marker 1 (TEM1 / CD248); marker 7 related to the endothelial tumor (TEM7R); claudin 6 (CLDNG6); thyroid stimulating hormone receptor (TSHR); group 5 class C receptor coupled to protein G, member D (GPRC5D); X chromosome open reading frame 61 (CXORF61); CD97; CD179a; anaplastic lymphoma kinase (ALK); polyisalic acid; placenta-specific 1 (PLAC1); Glucoceramide hexasaccharide portion of globoH (GloboH); mammary gland differentiation antigen (NY-BR-1); uroplacin 2 (UPK2); hepatitis A virus cell receptor 1 (HAVCR1); beta 3 adenoreceptor (ADRB3); panexin 3 (PANX3); receptor 20 coupled to the G protein (GPR20); lymphocyte antigen 6 complex, K 9 locus (LY6K); olfactory receptor 51E2 (OR51E2); gamma TCR alternating frame protein (TARP); Wilms' tumor protein (WT1); cancer / testis antigen 1 (NY-ESO-1); cancer / testis antigen 2 (LAGE-1a); antigen 1 associated with melanoma (MAGE-A1); gene 6 variant of ETS translocation, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); antigen family X, member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); antigen-1 from melanoma cancer testicles (MAD-CT-1); antigen-2 from melanoma cancer testicles (MAD-CT-2); Fos-related antigen 1; tumor protein p53 (p53); mutant p53; prostein; survivor; telomerase; prostate carcinoma tumor antigen-1, recognized melanoma antigen
[00155] [00155] In one aspect, a nucleic acid molecule encoding a fusion polypeptide disclosed herein is provided in this document. In another aspect, a vector comprising the nucleic acid molecule is provided herein. In some embodiments, the vector is a viral vector. In some modalities, the vector is a lentiviral vector. In another aspect, a viral particle comprising the vector is provided herein.
[00156] [00156] In another aspect, a cell, for example, a host cell, which comprises a fusion polypeptide disclosed in this document, a nucleic acid molecule disclosed in this document or a vector disclosed in the present document is provided in this document. this document. In some embodiments, said cell, for example, host cell, is a mammalian cell, for example, a human cell, for example, a human effector cell, for example, a human T cell or a human NK cell.
[00157] [00157] In some embodiments, said cell, for example, host cell, is a CAR expression cell, for example, a CAR T cell. In some embodiments, the cell, for example, a host cell, comprises a component of a CRISPR / Cas system. In some embodiments, the cell, for example, a host cell, is a human cancer cell, for example, a human tumor cell.
[00158] [00158] In some embodiments, the cell, for example, a host cell, comprises a ubiquitin ligase complex, for example, an E3 ubiquitin ligase complex, wherein the ubiquitin ligase complex comprises CRBN.
[00159] [00159] In some embodiments, the cell comprises a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF1 / CRBN-binding polypeptide and a heterologous polypeptide), wherein when the cell is put in contact with COF1, for example, an excess of COF1: i) the association of the COF1 / CRBN-binding polypeptide with CRBN is increased by at least 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the COFI / CRBN-binding polypeptide with CRBN when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN is increased at least, for example, 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the fusion polypeptide with CRBN when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times in comparison comparison with the ubiquitination of the heterologous polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times with - comparison with the ubiquitination of the fusion polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document; v) the degradation of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to degradation of the fusion polypeptide when the cell is not loaded with COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis ; or vi) the expression level of the fusion polypeptide is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the expression level of the fusion polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis of flow.
[00160] [00160] In some embodiments, the cell additionally comprises COF1, for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof.
[00161] [00161] In some embodiments, the cell comprises a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF3 / CRBN-binding polypeptide and a heterologous polypeptide), in which the cell is placed. - in contact with COF3, for example, an excess of COF3: i) the association of the COF3 / CRBN-binding polypeptide with CRBN is increased by at least 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the COF3 / CRBN-binding polypeptide with CRBN when the cell is not brought into contact with COF3, for example, as measured by an assay described in this document, for example, immunoprecipitation;
[00162] [00162] In some embodiments, the cell further comprises COF3, for example, a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof.
[00163] [00163] In some embodiments, the cell comprises a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide, a hetero polypeptide - therefore and a degradation domain), in which in the absence of a stabilization compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80% , 90% or more of the fusion polypeptide is degraded, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[00164] [00164] In some embodiments, the fusion polypeptide additionally comprises a heterologous protease cleavage site. In some embodiments, the cell further comprises a protease capable of cleaving the heterologous protease cleavage site.
[00165] [00165] In some embodiments, the cell comprises a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide, a heterogeneous polypeptide - therefore and a degradation domain), in which when the cell is placed in contact with a stabilization compound, for example, an excess of a stabilization compound: i) the degradation domain assumes a more resistant structure to degradation cellular in relation to a conformation in the absence of the stabilizing compound; ii) the conformation of the fusion polypeptide is more permissible
[00166] [00166] In some embodiments, the cell additionally comprises a stabilizing compound. In some embodiments, the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO:
[00167] [00167] In some embodiments, the cell comprises a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide, a hetero polypeptide - therefore and a degradation domain), in which when the cell is placed in contact with both a stabilizing compound, for example, an excess of a stabilizing compound, such as with COF1, COF2 or COF3, for example , an excess of COF1, COF2 or COF3: i) the association of the binding polypeptide with COF1 / CRBN, COF2 / CRBN or COF3 / CRBN with CRBN is increased by at least, for example, 10 times, 50 times, 100 times, 1,000 times or
[00168] [00168] In some embodiments, the cell additionally comprises COF1 (eg, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof), COF2 (eg, lenalidide or pomalidomide, or a pharmaceutically acceptable salt thereof) or COF3 (a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof).
[00169] [00169] In some embodiments, the heterologous polypeptide is a chimeric antigen receptor (CAR), optionally in which the CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a domain transmembrane and one or more domains of intracellular signaling.
[00170] [00170] In one aspect, a pharmaceutical composition comprising a fusion polypeptide disclosed herein or a cell disclosed herein, and a pharmaceutically acceptable carrier, excipient or stabilizer is disclosed in this document.
[00171] [00171] In one aspect, a method for making a cell disclosed in this document is disclosed in this document.
[00172] [00172] In one aspect, a method of degrading a fusion polypeptide disclosed in this document (for example, a fusion polypeptide comprising a COF1 / CRBN binding polypeptide and a heterologous polypeptide is disclosed in this document. (for example, a CAR polypeptide)), which comprises bringing the fusion polypeptide or a cell comprising said fusion polypeptide into contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) . In some embodiments, in the presence of COF1 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof), the level of expression of said fusion polypeptide is substantially decreased, for example, by at least about 1,2,3, 4,5,6,7,8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent in relation to the expression level of said polypeptide from fusion in the absence of COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof), for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis flow. In some embodiments, the fusion polypeptide or cell is brought into contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) ex vivo. In some embodiments, the fusion polypeptide or cell is placed in contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) in vivo.
[00173] [00173] In one aspect, a method of regulating the expression of a fusion polypeptide disclosed in this document (for example, a fusion polypeptide comprising a COF1 / CRBN or COF2 / CRBN binding polypeptide) is disclosed in this document. , a heterologous polypeptide (for example, a CAR polypeptide) and a degradation domain), comprising: i) bringing the fusion polypeptide or a cell comprising the fusion polypeptide into contact with a stabilization compound, optionally where, in the presence of the stabilizing compound
[00174] [00174] In some embodiments, the method additionally comprises, after step ii): li) placing the fusion polypeptide or a cell comprising the fusion polypeptide in contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) or COF2 (e.g. lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof), optionally wherein in the presence of COF1 or COF 2, the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 per center in relation to the expression level of the fusion polypeptide after step i) and before step ii), for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis flow.
[00175] [00175] In some embodiments, the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[00176] [00176] In some embodiments, the fusion polypeptide or cell is brought into contact with COF1 or COF2 (eg, lenalide or pomalidomide, or a pharmaceutically acceptable salt thereof) and / or the stabilizing compound ex alive. In some embodiments, the fusion polypeptide or cell is brought into contact with COF1 or COF 2 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) and / or the in vivo stabilizing compound.
[00177] [00177] In some embodiments, the heterologous polypeptide is a chimeric antigen (CAR) receptor. In some embodiments, said CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a transmembrane domain and one or more intracellular signaling domains.
[00178] [00178] In one aspect, a method for making a cell is disclosed herein which comprises: i) providing a cell comprising a nucleic acid molecule encoding a fusion polypeptide comprising a compound of formula 1, polypeptide of binding of (COF1 / CRBN and a chimeric antigen receptor (CAR), optionally wherein the CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a transmembrane domain and one or more domains intracellular signaling, and li) putting the cell ex vivo in contact with COF1, optionally where: in the presence of COF1, the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide in the absence of COF1, for example, as measured by a test described in this document, for example, an analysis Western blot analysis or flow cytometry analysis, wherein the compound of Formula (l) is: x (R »n Do Roa R2 (1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where:
[00179] [00179] In some embodiments, after the cell is brought into contact with COF1 ex vivo, the cell proliferation is increased by at least, for example, 1.2 times, 1.5 times, 2 times, 5 times or times in cell proliferation prior to contact with COF1. In some embodiments, COF1 is lenalidomide or pomalido-mide, or a pharmaceutically acceptable salt thereof. In some embodiments, the COF1 / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78 , 84-86, and 100 (for example, the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 3).
[00180] [00180] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided in this document, which comprises: i) contacting a cell revealed in the present document (eg example, a cell comprising a fusion polypeptide comprising a COF1 / CRBN-binding polypeptide and a heterologous polypeptide (for example, a CAR polypeptide))
[00181] [00181] In some embodiments, the method additionally comprises after step il): iii) administering to the individual an effective amount of COF1, optionally in which the administration of COF1 decreases, for example, by at least about 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the level of expression of the fusion polypeptide in relation to expression level of the fusion polypeptide after step ii) and before step iii), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the administration of COF1 is in response an occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) administration of COF1 reduces or prevents an adverse effect.
[00182] [00182] In some modalities, the method additionally comprises, after step iii): iv) discontinuing the administration of COF1, optionally in which discontinuing the administration of COF1 increases, for example,
[00183] [00183] In some modalities, the method additionally comprises, after step iv): v) repeating step iii) and / or iv), thus treating the disease.
[00184] [00184] In some embodiments, COF1 is lenalidomide or pomalide, or a pharmaceutically acceptable salt thereof, optionally in which the COFI / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-86, and 100 (for example, the COF1I / CRBN binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 3). In some embodiments, COF1 is lenalidomide, or a pharmaceutically acceptable salt thereof, optionally in which lenalidomide, or a pharmaceutically acceptable salt thereof, is administered, for example, at 2.5 mg, 5 mg, 10 mg, 15 mg, or 25 mg per day.
[00185] [00185] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided herein which comprises: i) administering to the individual an effective amount of a cell disclosed in this document (for example, a cell comprising a fusion polypeptide comprising a COFI / CRBN binding polypeptide and a heterologous polypeptide (for example, a CAR polypeptide)), optionally in which the cell is brought into contact with COF1 ex vivo, before administration, optionally where: in the presence of COF1, the expression level of the fusion polypeptide is decreased, for example, by at least about 1, 2, 3, 4, 5, 6 , 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide before the cell is brought into contact with COF1 ex vivo, optionally that after the cell is put in contact with COF1 ex vivo and before the cell once administered to the individual, the amount of COF1 in contact with the cell, for example, inside and / or surrounding the cell, is reduced, thus treating the disease.
[00186] [00186] In some embodiments, the cell is not brought into contact with COF1 ex vivo prior to administration.
[00187] [00187] In some embodiments, the method additionally comprises after step i): ii) administering to the individual an effective amount of COF1, optionally in which the administration of COF1 decreases, for example, by at least about 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step i) and before step li), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the administration of COF1 is in response to a occurrence
[00188] [00188] In some embodiments, the method additionally comprises after step ii): iii) discontinuing the administration of COF1, optionally in which discontinuing the administration of COF1 increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step ii) and before step iii) (for example, when discontinuing COF1 administration restores the expression level of the fusion polypeptide to the expression level after step i) and before step ii)), optionally where: a) the individual has had a relapse, is relapsing or is expected to have a relapse, b) discontinuation of COF1 administration is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) discontinuing COF1 administration treats or prevents a tumor relapse.
[00189] [00189] In some modalities, the method additionally comprises, after step iii): iv) repeating step ii) and / or iii), thus treating the disease.
[00190] [00190] In some embodiments, COF1 is lenalidomide or pomalide, or a pharmaceutically acceptable salt thereof, optionally in which the COFI / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-
[00191] [00191] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided in this document, comprising: i) administering an effective amount of COF1 to the individual, wherein the individual comprises a cell disclosed in the present document (for example, a cell comprising a fusion polypeptide comprising a COF1 / CRBN-binding polypeptide and a heterologous polypeptide (for example, a CAR polypeptide)), optionally wherein the administration of COF1 decreases, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the level of expression of the fusion polypeptide in relation to the level of expression of the fusion polypeptide before administration of COF1, optionally in which: a) the individual has developed, is developing, or is expected to develop an adverse reaction , b) COF1 administration is in response to an occurrence of a reaction adverse in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) administration of COF1 reduces or prevents an adverse effect.
[00192] [00192] In some embodiments, the method additionally comprises after step i): ii) discontinuing the administration of COF1, optionally in which discontinuing the administration of COF1 increases, for example,
[00193] [00193] In some modalities, the method additionally comprises after step ii): iii) repeating step i) and / or ii), thus treating the disease.
[00194] [00194] In some embodiments, COF1 is lenalidomide or pomalide, or a pharmaceutically acceptable salt thereof, optionally in which the COFI / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-86, and 100 (for example, the COF1I / CRBN binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 3). In some embodiments, COF1 is lenalidomide, or a pharmaceutically acceptable salt thereof, optionally in which lenalidomide, or a pharmaceutically acceptable salt thereof, is administered, for example, at 2.5 mg, 5 mg, 10 mg, 15 mg, or 25 mg per day.
[00195] [00195] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided herein, comprising: i) administering to the subject: (1) a stabilizing compound, and (2) an effective amount of a cell disclosed in this document (for example, a cell comprising a fusion polypeptide comprising a COF1 / CRBN binding polypeptide or COF2 / CRBN, a heterologous polypeptide (for example - eg, a CAR polypeptide) and a degradation domain), optionally where: the expression level of the fusion polypeptide in the presence of the stabilizing compound is, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times higher than the expression level of the fusion polypeptide in the absence of the stabilizing compound, thus treating the disease.
[00196] [00196] In some embodiments, the method further comprises after step i): ii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilizing compound reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression of the polypeptide of fusion after step |) and before step ii), optionally where: a) the individual responded to the treatment in step i) (for example, the individual has a complete response to the treatment in step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment in step i) is effective in the individual), and / or b) discontinuation of the administration of the
[00197] [00197] In some embodiments, the method additionally comprises after step i): iii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilizing compound reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression of the polypeptide of fusion after step |) and before step ii), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) discontinuation of the administration of the stabilizing compound is in response to an adverse reaction occurring in the individual, or in response to waiting for an adverse reaction occurring in the individual, and / or c) discontinuing the administration of the stabilizing compound reduces or prevents an adverse effect.
[00198] [00198] In some embodiments, the method additionally comprises after step i): iv) discontinue the administration of the stabilization compound and administer to the individual an effective amount of COF1 or COF 2, optionally in which step iv ) reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the polypeptide of fusion in relation to the expression of the fusion polypeptide after step i) and before step iv), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) step iv) is in response to an occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) step iv) reduces or prevents an adverse effect. In some modalities, the adverse effect is acute toxicity.
[00199] [00199] In some embodiments, the method additionally comprises, after step iv): v) discontinuing the administration of COF1 or COF2, for example, after the amount of cells expressing the surface fusion polypeptide is less than one predefined value, for example, for 1 day, 5 days, 10 days or 15 days.
[00200] [00200] In some embodiments, the method additionally comprises, after step ii), iii), iv) or v): vi) administering an effective amount of a stabilizing compound, optionally in which the administration of the stabilizing compound increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the polypeptide of fusion in relation to the expression level of the fusion polypeptide after step ii), ili), iv), or v) and before step vi), optionally in which: a) the individual has had a relapse, is relapsing or waiting - if it has a relapse, b) administration of the stabilizing compound is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) administration of the stabilizing compound treats or prevents a tumor relapse.
[00201] [00201] In some modalities, the method additionally comprises after step vi): vii) repeat step iii), iv), v), or vi), thus treating the disease.
[00202] [00202] In some embodiments, the method additionally comprises before step i): viii) putting the cell in contact with an ex vivo stabilization compound, optionally where the level of expression of the fusion polypeptide in the presence of the stabilizing compound is, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times greater than the level of expression of the fusion polypeptide in the absence of the stabilizing compound.
[00203] [00203] In some embodiments, the cell is not contacted with the ex vivo stabilizing compound prior to administration. In some embodiments, the cell is not brought into contact with any of the following: the stabilizing compound, COF1 or COF2 ex vivo prior to administration.
[00204] [00204] In some embodiments, the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof, and optionally the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[00205] [00205] In some embodiments, COF1 is lenalidomide or pomalide, or a pharmaceutically acceptable salt thereof, optionally wherein the COFI / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-86, and 100 (for example, the COF1I / CRBN binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 3).
[00206] [00206] In some modalities, COF2 is lenalidomide or pomali-
[00207] [00207] In some modalities, COF1 or COF is lenalidomide, or a pharmaceutically acceptable salt thereof, optionally where lenalidomide, or a pharmaceutically acceptable salt thereof, is administered, for example, at 2.5 mg, 5 mg, 10 mg, 15 mg, or 25 mg per day .
[00208] [00208] In one aspect, a method of degrading a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF3 / CRBN binding polypeptide and a heterologous polypeptide is disclosed) go (for example, a CAR polypeptide), which comprises placing the fusion polypeptide or a cell comprising said fusion polypeptide in contact with COF3 (for example, a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof). In one embodiment, in the presence of COF3, the level of expression of said fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the level of expression of said fusion polypeptide in the absence of COF3, for example, as measured by an assay described herein document, for example, a Western blot analysis or a flow cytometry analysis. In one embodiment, the fusion polypeptide or cell is brought into contact with COF3 ex vivo. In one embodiment, the fusion polypeptide or cell is brought into contact with COF3 in vivo.
[00209] [00209] In one aspect, a method for regulating the expression of a fusion polypeptide disclosed in this document (e.g., a fusion polypeptide comprising a COF3 / CRBN-binding polypeptide, a polypeptide, is disclosed in this document. - heterologous deo (for example, a CAR polypeptide) and a degradation domain), comprising: i) bringing the fusion polypeptide or a cell comprising the fusion polypeptide into contact with a stabilizing compound, optionally where, in the presence of the stabilizing compound: a) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; b) the conformation of the fusion polypeptide is more permissive to cleavage at the heterologous protease cleavage site compared to a conformation in the absence of the stabilizing compound; or c) the expression level of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the expression level of the fusion polypeptide in the absence of the stabilizing compound, for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis of flow.
[00210] [00210] In some embodiments, the method additionally comprises, after step i): li) placing the fusion polypeptide or a cell comprising the fusion polypeptide in contact with COF3 (for example, a compound disclosed in the Table 29, or a pharmaceutically acceptable salt thereof), optionally where in the presence of COF3, the expression level of the fusion polypeptide is substantially decreased
[00211] [00211] In some embodiments, the fusion polypeptide or cell is placed in contact with COF3 ex vivo. In some modalities, the fusion polypeptide or cell is brought into contact with COF3 in vivo. In some embodiments, the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[00212] [00212] In one aspect, a method for making a cell is disclosed herein which comprises: i) providing a cell comprising a nucleic acid molecule encoding a fusion polypeptide comprising a COF3 / CRBN binding polypeptide and a chimeric antigen receptor (CAR), optionally wherein the CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a transmembrane domain and one or more signaling domains intracellular; and ii) putting the cell ex vivo in contact with COF3, optionally where: in the presence of COF3, the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide in the absence of COF3 , for example, as measured by an assay described in this document, for example, an analysis of
[00213] [00213] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided in this document, comprising: i) contacting a cell revealed in the present document (for example) For example, a cell comprising a fusion polypeptide comprising a COF3 / CRBN-binding polypeptide and a heterologous polypeptide (for example, a CAR polypeptide) with COF3 ex vivo, optionally where: in the presence of COF3, the level expression of the fusion polypeptide is decreased, for example, by at least about 1,2, 3, 4,5, 6,7,8, 9, 10, 20, 30, 40, 50, 60, 70 , 80, 90, or 100 percent relative to the expression level of the fusion polypeptide before the cell is brought into contact with COF3 ex vivo, and ii) administering to the individual an effective amount of the cell, optionally where the method comprises further, after step i) and before step ii): reduce the amount of COF3 in contact with the cell, for example it, inside and / or surrounding the cell, thus treating the disease.
[00214] [00214] In some embodiments, the method additionally comprises after step ii): iii) administering to the individual an effective amount of COF3, optionally in which the administration of COF3 decreases, for example, by at least about 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the level of expression of the fusion polypeptide in relation to expression level of the fusion polypeptide after step ii) and before step iii), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the administration of COF3 is in response to an occurrence
[00215] [00215] In some embodiments, the method additionally comprises, after step iii): iv) discontinuing the administration of COF3, optionally in which discontinuing the administration of COF3 increases, for example, by at least about 1.5 times , 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the level of expression of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step iii) and before step iv) (for example, when discontinuing COF3 administration restores the expression level of the fusion polypeptide to the expression level after step ii) and before step ili)), optionally where : a) the individual has had a relapse, is relapsing or is expected to have a relapse, b) discontinuation of COF3 administration is in response to a tumor relapse in the individual or in response to waiting for a relapse in individual, and / or c) discontinuing COF3 administration treats or prevents a tumor relapse.
[00216] [00216] In some modalities, the method additionally comprises, after step iv): v) repeating step iii) and / or iv), thus treating the disease.
[00217] [00217] In some embodiments, COF3 is a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof. In some embodiments, the COF3 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 109 or an amino acid sequence of at least 80, 85, 90% or
[00218] [00218] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided herein, comprising: i) administering to the individual an effective amount of a cell disclosed in this document (for example, a cell comprising a fusion polypeptide comprising a COF3 / CRBN-binding polypeptide and a heterologous polypeptide (for example, a CAR polypeptide)), optionally in which the cell is brought into contact with COF3 ex vivo, before administration, optionally where: in the presence of COF3, the level of expression of the fusion polypeptide is decreased, for example, by at least about 1,2, 3, 4, 5, 6 , 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide before the cell is brought into contact with COF3 ex vivo, optionally that after the cell is put in contact with COF3 ex vivo and before the cell is when administered to the individual, the amount of COF3 in contact with the cell, for example, inside and / or surrounding the cell, is reduced, thus treating the disease.
[00219] [00219] In some embodiments, the cell is not brought into contact with COF3 ex vivo before administration.
[00220] [00220] In some embodiments, the method additionally comprises after step i): ii) administering to the individual an effective amount of COF3, optionally in which the administration of COF3 decreases, for example, by at least about 1, 2 , 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step i) and before step ii), optionally where:
[00221] [00221] In some embodiments, the method additionally comprises after step ii): iii) discontinuing the administration of COF3, optionally in which discontinuing the administration of COF3 increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step ii) and before step iii) (for example, when discontinuing COF3 administration restores the expression level of the fusion polypeptide to the expression level after step i) and before step ii)), optionally where: a) the individual has had a relapse, is relapsing or is expected to have a relapse, b) the discontinuation of COF3 administration is in response to a tumor relapse in the individual or in response to waiting for a relapse in the individual , and / or c) discontinuation of COF3 administration treats or prevents tumor relapse.
[00222] [00222] In some modalities, the method additionally comprises, after step iii): iv) repeating step ii) and / or iii), thus treating the disease.
[00223] [00223] In some embodiments, COF3 is a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof. In some embodiments, the COF3 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 109 or an amino acid sequence with at least 80, 85, 90% or 95% identity thereto.
[00224] [00224] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided herein, comprising: i) administering an effective amount of COF3 to the individual, wherein the individual comprises a cell disclosed in the present document (for example, a cell comprising a fusion polypeptide comprising a COF3 / CRBN-binding polypeptide and a heterologous polypeptide (for example, a CAR polypeptide)), optionally wherein the administration of COF3 decreases, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 7O, 80, 90, or 100 percent the level of expression of the fusion polypeptide in relation to the level of expression of the fusion polypeptide before administration of COF3, optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction , b) COF3 administration is in response to the occurrence of a reaction adverse in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) administration of COF3 reduces or prevents an adverse effect.
[00225] [00225] In some embodiments, the method additionally comprises after step i): ii) discontinuing the administration of COF3, optionally in which discontinuing the administration of COF3 increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step i) and before step ii) (for example, when discontinuing COF3 administration restores the expression level of the fusion polypeptide to the expression level before COF3 administration), optionally where: a) the individual had a relapse, is relapsed or is expected to have a relapse, b) discontinuation of COF3 administration is in response to a tumor relapse in the individual or in response to waiting for a relapse in the individual, and / or c ) discontinuation of COF3 administration treats or prevents tumor relapse.
[00226] [00226] In some modalities, the method additionally comprises after step il): ili) repeat step i) and / or ii), thus treating the disease.
[00227] [00227] In some embodiments, COF3 is a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof. In some embodiments, the COF3 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 109 or an amino acid sequence with at least 80, 85, 90% or 95% identity thereto.
[00228] [00228] In one aspect, a method of treating an individual who has a disease associated with the expression of a tumor antigen is provided herein, comprising: i) administering to the subject: (1) a stabilizing compound, and (2) an effective amount of a cell disclosed in this document (for example, a cell comprising a fusion polypeptide comprising a COF3 / CRBN binding polypeptide, a heterologous polypeptide (for example, a polypeptide)
[00229] [00229] In some embodiments, the method additionally comprises after step i): ii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilizing compound reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression of the polypeptide of fusion after step |) and before step ii), optionally where: a) the individual responded to the treatment in step i) (for example, the individual has a complete response to the treatment in step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment of step i) is effective in the individual), and / or b) discontinuation of the administration of the stabilizing compound is in response to a response of the individual to the treatment of step i) (for example, the individual has a response complete with the treatment of step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment of step i) is effective in the individual).
[00230] [00230] In some embodiments, the method additionally comprises after step i): iii) discontinue the administration of the stabilizing compound
[00231] [00231] In some embodiments, the method additionally comprises after step i): iv) discontinue the administration of the stabilizing compound and administer to the individual an effective amount of COF3, optionally in which step iv) reduces , for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, times, 40 times or 50 times the level of expression of the fusion polypeptide in relation to expression of the fusion polypeptide after step i) and before step iv), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) step iv) is in response to a occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) step iv) reduces or prevents an adverse effect. In some modalities, the adverse effect is acute toxicity.
[00232] [00232] In some embodiments, the method additionally comprises, after step iv): v) discontinuing the administration of COF3, for example, after the amount of cells expressing the surface fusion polypeptide is less than a predefined value , for example, for 1 day, 5 days, 10 days, or 15 days.
[00233] [00233] In some embodiments, the method additionally comprises, after step ii), iii), iv) or v): vi) administering an effective amount of a stabilizing compound, optionally in which administration of the stabilizing compound increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the polypeptide of fusion in relation to the expression level of the fusion polypeptide after step ii), ili), iv), or v) and before step vi), optionally in which: a) the individual has had a relapse, is relapsing or waiting - if it has a relapse, b) administration of the stabilizing compound is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) administration of the stabilizing compound treats or prevents a tumor relapse.
[00234] [00234] In some modalities, the method additionally comprises after step vi): vii) repeating step iii), iv), v), or vi), thus treating the disease.
[00235] [00235] In some modalities, the method additionally comprises before step i): viii) putting the cell in contact with an ex vivo stabilization compound, optionally in which the level of expression of the poly-
[00236] [00236] In some embodiments, the cell is not brought into contact with the ex vivo stabilizing compound prior to administration.
[00237] [00237] In some embodiments, the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof, and optionally the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[00238] [00238] In some embodiments, COF3 is a compound disclosed in Table 29, or a pharmaceutically acceptable salt thereof. In some embodiments, the COF3 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 109 or an amino acid sequence with at least 80, 85, 90% or 95% identity thereto.
[00239] [00239] In some embodiments, the heterologous polypeptide of the fusion polypeptide is a chimeric antigen (CAR) receptor, optionally in which the CAR comprises, in an N-terminal to C-terminal direction, a domain of antigen binding, a transmembrane domain and one or more domains of intracellular signaling.
[00240] [00240] In one aspect, this invention also provides a fusion polypeptide, nucleic acid molecule, vector, viral particle, cell, or pharmaceutical composition disclosed herein for use as a medicament. In one aspect, this invention also provides a fusion polypeptide, nucleic acid molecule, vector, viral particle, cell, or pharmaceutical composition disclosed in this document for use in treating an individual who has a disease associated with the expression of a tumor antigen.
[00241] [00241] In certain modalities of the methods mentioned above, the disease associated with the expression of a tumor antigen is a cancer.
[00242] [00242] In some modalities, the cancer is mesothelioma (for example, malignant pleural mesothelioma), for example, in an individual who has progressed in at least one previous standard therapy; lung cancer (for example, non-small cell lung cancer, small cell lung cancer, scalable cell lung cancer or large cell lung cancer); pancreatic cancer (for example, pancreatic ductal adenocarcinoma or metastatic pancreatic ductal adenocarcinoma (PDA), for example, in an individual who has progressed on at least one previous standard therapy); esophageal adenocarcinoma, ovarian cancer (for example, serous epithelial ovarian cancer, for example, in an individual who has progressed after at least one previous standard therapy regimen), breast cancer, colorectal cancer, bladder cancer, or any combination of them.
[00243] [00243] In some embodiments, the disease associated with the expression of a tumor antigen is hematological cancer, for example, a hematological cancer chosen from a leukemia or lymphoma.
[00244] [00244] In some modalities, cancer is chosen from: chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), multiple myeloma, acute lymphoid leukemia (ALL), Hodgkin's lymphoma, acute cell lymphoid leukemia B (BALL), acute T-cell lymphoid leukemia (TALL), small lymphocytic leukemia (SLL), prolimititic B-cell leukemia, blast plasmacytoid dendritic cell neoplasm, Burkitt's lymphoma, large diffuse B-cell lymphoma (DLBCL) , DLBCL associated with chronic inflammation, chronic myeloid leukemia, myeloproliferative neoplasms, follicular lymphoma, pediatric follicular lymphoma, capillary cell leukemia, small or large cell follicular lymphoma, malignant lymphoproliferative conditions, lymphoma of
[00245] [00245] In some modalities, cancer is chosen from MCL, CLL, ALL, Hodgkin's lymphoma, AML, or multiple myeloma.
[00246] [00246] In certain modalities of the previously mentioned methods, the cell is autologous to said individual. In certain modalities of the previously mentioned methods, the cell is allogeneic to said individual. In some embodiments, the cell is a CAR expression cell, for example, a CART cell.
[00247] [00247] In some embodiments, the individual was administered with a cell that expresses at least one fusion polypeptide disclosed herein, prior to administration of COF1, COF2 or COF3.
[00248] [00248] In one aspect, a method is revealed in this document to identify a genetic element associated with a specific biological phenotype, for example, a genetic element associated with the development and / or progression of a cancer, in which the method comprises the steps of: i) modulating the expression of a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF1I / CRBN or COF3 / CRBN binding polypeptide and a heterologous polypeptide) in cells exposing said cell COF1 or COF3, for example, lenalidomide, or a pharmaceutically acceptable salt thereof, (ii) select for cells with a phenotype of interest, for example, a phenotype associated with the development and / or progression of a cancer, and (iii) identifying said fusion polypeptide that induces said phenotype of interest, wherein the exposure of said cell to COF1 or COF3, for example, lenalidomide, or a pharmaceutically acceptable salt thereof, decreases, for example, at least about 1, 2,3,4,5,6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the level expression of said fusion polypeptide in relation to the level of expression of said fusion polypeptide before exposure to COF1 or COF3, for example, lenalidomide, or a pharmaceutically acceptable salt thereof.
[00249] [00249] In one aspect, a method is revealed in this document to identify a genetic element associated with a specific biological phenotype, for example, a genetic element associated with the development and / or progression of a cancer, in which the method comprises the steps of: i) modulating the expression of a fusion polypeptide disclosed herein (for example, a fusion polypeptide comprising a COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide, a heterologous polypeptide and a step domain
[00250] [00250] In certain embodiments of the aspects mentioned above, the heterologous polypeptide is a chimeric antigen receptor (CAR) polypeptide. In some embodiments, the CAR polypeptide comprises an amino acid sequence disclosed herein, for example, an amino acid sequence disclosed in Table 3. In some embodiments, the CAR polypeptide is an anti-CD19 CAR polypeptide and comprises an amino acid sequence disclosed in this document, for example, an amino acid sequence disclosed in any of: Table 5, Table 6, Table 7 and Table 30. In some modalities, the polypeptide CAR is an anti-CD123 CAR polypeptide and comprises an amino acid sequence revealed in the present document, for example, an amino acid sequence revealed in any of: Table 8, Table 9, Table 10, Table 11, Table 12, Table 13 and Table 14. In some embodiments, the CAR polypeptide is an anti-BCMA CAR polypeptide and comprises an amino acid sequence disclosed in the present document, for example, a sequence of amino acids reveals any of the following: Table 15, Table 16, Table 17, Table 18 and Table 31. In some embodiments, the CAR polypeptide is an anti-CD22 CAR polypeptide and comprises an amino acid sequence revealed in the present document, for example, an amino acid sequence revealed in any one of: Table 19 and Table 20. In some embodiments, the CAR polypeptide is an anti-CD20 CAR polypeptide and comprises an amino acid sequence revealed in the present document, for example, an amino acid sequence disclosed in Table 32. In some embodiments, the CAR polypeptide is an anti-EGFRVvIIl CAR polypeptide and comprises an amino acid sequence disclosed in this document, for example, a amino acid sequence disclosed in Table 33. In some embodiments, the CAR polypeptide is an anti-mesothelin CAR polypeptide and comprises an amino acid sequence disclosed herein, for example, an amino acid sequence revealed in Table 34.
[00251] [00251] In certain embodiments of the aspects mentioned above, the fusion polypeptide comprises an amino acid sequence disclosed in this document, for example, an amino acid sequence disclosed in Table 4 or Table 28.
[00252] [00252] In certain embodiments, the COF1 / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide comprises an amino acid sequence disclosed in this document, for example, an amino acid sequence disclosed in Table 1.
[00253] [00253] In certain embodiments of the aspects mentioned above, the degradation domain comprises an amino acid sequence disclosed in this document, for example, an amino acid sequence disclosed in Table 22.
[00254] [00254] In certain embodiments of the aspects mentioned above, the heterologous protease cleavage site comprises an amino acid sequence disclosed in this document, for example, an amino acid sequence disclosed in Table 23. Brief Description of the DRAWINGS
[00255] [00255] Figure 1A is a degron scheme of 136 to 180 and 236 to 249 of IKZF3 of HilID tag fused to Nanoluciferase via a 16 glycine-serine linker. Figure 1B is a graph showing the luminescence level measured from HEK293T cells reverse transfected with 50 ng of pNL1.1CMV construct that encodes NanoLuciferase linked to IKZF3 136 to 180 and 236 to 249. IKZF3 136 to 180 and 236 to 249 facilitated a reduction in luminescence in cells treated with 1 µM, 10 µM or 100 µM lenalidomide for 6 hours compared to cells treated with DMSO alone. Treatment with MG132 blocked lenalidomide-dependent degradation of NanoLuciferase.
[00256] [00256] Figure 2 is a Western blot showing that IKZF3 136 to 180 and 236 to 249 facilitated lenalidomide dependent degradation of NanoLuciferase (IC50 = 10 nM) in HEK293GT cells transfected with a pNL1.1CMV construct encoding NanoLuciferase eti - quetched with IKZF3 136 to 180 and 236 to 249. Lenalidomide-dependent degradation was not observed in HEK293GT Ceblon (CRBN) KO cells that were similarly transfected. Treatment with a proteasome inhibitor, MG132, blocked the ability of IKZF3 136 to 180 and 236 to 249 to facilitate lenalidomide-dependent degradation.
[00257] [00257] Figure 3A is a schematic showing IKZF3 136 to 180 which contains two beta sheets flanking a clamp format and an alpha helix, as well as IKZF3 236 to 249, which is provided as an additional alpha helix. Below, the scheme is a diagram of the reduced versions of the IKZF3 degron 136 to 180, eliminating the amino acids at the termination N and C (SEQ ID NOs: 3, 5 and 7 to 10, respectively, in order of appearance). Figure 3B is a Western blot showing the results of studies that test the nanoLuciferase leonalidomide-dependent degradation fused with various IKZF3-based degradation tags. The degradation tags based on IKZF3 were fused with the N-terminus of NanoLuciferase, cloned into pNL1.1CMV vectors and transfected into HEK293T cells. The transfected cells were treated with DMSO or 10 µM lenalideide for 4 hours before being analyzed by Western blot. Two exposures (one long and one short) were shown for NanoLuciferase ("Nanoluc"). IKZF3 136 to 180 and 236 to 249, IKZF3 136 to 180 and K245R 236 to 249, IKZF3 136 to 180 and K245S 236 to 249, IKZF3 136 to 180 MALEK, and IKZF3 136 to 170 MALEK facilitated lenalidomide-induced degradation, while IKZF3 140 to 170 MA-LEK, IKZF3 141 to 163 MALEK and IKZF3 145 to 155 MALEK do not measure the degradation induced by lenalidomide.
[00258] [00258] Figures 4A and 4B are Western blot graphs showing
[00259] [00259] Figure 5A is a Western blot showing melalidomide-dependent degradation of melanogenesis-associated transcription factor (MITF) marked with IKZF3 136 to 180 and 236 to 249 (left panel) as well as MITF marked with IKZF3 136 to 180 (right panel). Fusions of labeled MITF were transfected into HEK293T using pNL1.1CMV constructs. Degradation of IKZF3-labeled MITF 136 to 180 and 236 to 249 shows an IC 50 of -100 nM. This degradation depended on the proteasome activity since the degradation was blocked by treatment with MG132. IKZF3 136 to 180 also mediated lenalidomide-dependent degradation, albeit to a lesser extent than IKZF3 136 to 180 and 236 to 249. Figure 5B is a Wester blot showing the MITF-labeled lenalidomide-dependent degradation with IKZF3 136 to 180 and 236 to 249 (left panel) as well as IKZF3-labeled MITF 136 to 180 (right panel) after cells expressing these fusion proteins are treated with 10 µM lenalidomide for various periods of time. Among the tested time points, the 4-hour treatment shows a maximum amount of degradation.
[00260] [00260] Figures 6A and 6B are Western blot graphs showing
[00261] [00261] Figure 7 is a Western blot showing the degradation dependent on MITF-labeled lenalidomide with IKZF3 136 at 180 Q147H. HEK293T cells transfected with pNL1.1CMV constructs encoding MITF-labeled fusions were treated with various doses of lenalidomide for 24 hours. MITF labeled with IKZF3 136 to 180 Q147H did not show degradation in the presence of lenalido-mide.
[00262] [00262] Figure 8 is a Western blot showing degradation dependent on lenalidomide from an avian myelocyte viral oncogene homolog (MYC) labeled with IKZF3 136 to 180 and 236 to 249 with an IC50 of approximately 10 nM. HEK293T cells expressing fusions of labeled MYC using pNL1.1CMV constructs were treated with various doses of lenalidomide for 4 hours.
[00263] [00263] Figure 9A is a Western showing the dependent degradation of lenalidomide in 4 hours of single-pass membrane proteins labeled with C terminal degron, CD3zeta, CD8 / CD3zeta chimera, CD8, CD19 and CD22. Jurkat cells were infected with construct virus pnNGX LV VO002-CDx-IKZF3 136 to 180 and 236 to 249, selected with G418, and treated with UM of lenalidomide or DMSO. Staining using an anti-V5 antibody (long exposure of 1 min and short exposure of 1 second) and an anti-beta-actin antibody are shown in Figure 9A. All constructs were expressed and degraded with treatment with 10 UM of lenalinomide. The table in Figure 9A shows the molecular weight (MW) of protein, number of cytosolic amino acid residues ("cytosolic AA"), and number of cytosolic lysines for each protein. Interestingly, degradation correlates better with the total number of cytoplasmic amino acids ("AA") than with the number of cytosolic lysine residues. Figures 9B, 9C and 9D are Western blot graphs showing the lenalidomide-dependent degradation of CD19 labeled in a C-terminal fashion (Figure 9B), CD3zeta labeled in a C-terminal fashion (Figure 9C), and CD8 / CD3zeta tagged in a fashion. C-terminal (Figure 9D). Cells expressing CD19, CD3zeta or CD8 / CD3zeta labeled with IKZF3 136-180 and 236 to 249 were treated with 10 µM lenalidomide for 6 hours or several doses of lenalidomide for 24 hours. In Figure 9B, the degradation of IKZF3-labeled CD19 136 to 180 and 236 to 249 shows an IC50 of approximately 100 nM and strong degradation was detected in 6 hours. The degradation of IKZF3-labeled Cd3zeta 136 to 180 and 236 to 249 shown in Figure 9C is weaker than that of IKZF3-labeled CD19 136 to 180 and 236 to 249. The degradation of labeled Cd3zeta was evident after the cells were dry. treated with 10 CUU of lenalidomide for 24 hours. The degradation of Cd3zeta labeled with IKZF3 136 to 180 and 236 to 249 shown in Figure 9D is stronger than that of CD3zeta labeled with IKZF3 136 to 180 and 236 to 249.
[00264] [00264] Figures 10A, 10B, 10C and 10D are a series of flow cytometry histograms that compare IKZF3 labeled cell surface expression 136 to 180 and 236 to 249 in Jurkat cells that have been treated with 1 µM or 10 µM lenalidomide for 1 hour (Figure 10A), 6 hours (Figure 10B), 16 hours (Figure 10C) or 24 hours (Figure 10D). Some cells were pretreated with 10 µM of MG132 before treatment with 10 µM of lenalidomide. DMSO served as vehicle control. IKZF3 136 to 180 and 236 to 249 were fused to the C terminus of CD19. Figures 10E and 10F are bar graphs showing% CD19 positive cells (Figure 10E) or average fluorescence intensity (MFI) of CD19 positive cells (Figure 10F) across all lenalidomide doses and time points tested . There was minimal degradation in 1 hour and minor degradation in 6 hours. The degradation was much more evident at 16 and 24 hours in the treatment groups with 1 µM and UM and this degradation could be partially blocked by the proteasome inhibitor MG132. There was a reduction of approximately 50% of CD19 positive cells in 16 hours in the treatment groups with 1 µM and 10 µM (Figure 10E), and this reduction corresponds to a reduction in MFI (Figure 10F).
[00265] [00265] Figure 11 is a schematic showing an exemplary fusion protein comprising a degradation domain (degron), protease cleavage site and a second protein domain (a CAR), and the change in protein degradation of fusion in the presence of a drug, for example, stabilizing compound.
[00266] [00266] Figures 12A, 12B and 12C are diagrams showing the regulation of CAR molecules fused with FurON (Figure 12A), HilD (Figure 12B), or both FurON and HIilD (Figure 12C). As shown in Figure 12A, a CAR fused to FurON can be activated by administering a stabilizing compound (for example, a small molecule ligand that binds to and stabilizes the degradation domain, for example, bazedoxifene (BZA)) or disabled by removing the stabilizing compound. As shown in Figure 12B, a CAR fused to the HilD tag can be deactivated by administering an IMID compound (for example, lenalidomide or pomalidomide) and activated again by interrupting the administration of the IMiD compound. As shown in Figure 12C, a CAR fused with FurON and the HilID tag can be activated by administering the stabilization compound, deactivated by discontinuing the stabilization compound and administering an IMiD compound, and activated again by discontinuing the compound IMID and stabilization compound administration. The combination of the FurON switch and HilID switch adds additional layers of regulation to the expression and activity of a CAR molecule.
[00267] [00267] Figures 13A, 13B and 13C are Western blot plots showing lenalidomide-dependent degradation of CAR molecules. The JNL cells that express construct 765 (FurON CAR19) (Figure 13A), construct 766 (FurON CAR19 16GS HIilD tag V5) (Figure 13B) or construct 767 (FurON CAR19 16GS HIlD label) (Figure 13C) were incubated in the presence of 10 µM lenalidomide ("+") or DMSO ("-") for 24 hours before Western Blot analysis. All samples received 1UuM of Bazedoxifene. "A" represents cells transduced with 275 μl of viral supernatant. "B" represents cells transduced with 700 μl of viral supernatant.
[00268] [00268] Figures 14A, 14B, 14C and 14D are Western blot plots showing lenalidomide-dependent degradation of CAR molecules. The JNL cells that express construct 771 (CAR1I9 HilD tag V5) (Figure 14A), construct 769 (CAR1I9 16GS HIlD tag V5) (Figure 14B), or construct 768 (CARI9 16GS HIilD V5 label) (Figure 14C), or construct 770 (CAR1I9 16GS HILD tag NoK) were incubated in the presence of 10 µM lenalidomide ("+") or DMSO ("-") for 24 hours before Western Blot analysis. "A" represents cells transduced with 275 μl of viral supernatant. "B" represents cells transduced with 700 µl of viral supernatant.
[00269] [00269] Figures 15A and 15B are Western blot plots showing the lenalidomide-dependent degradation of CAR molecules. JNL cells expressing the 769 construct (CAR1I9 16GS HIilD tag) were incubated with 10 µM lenalidomide or DMSO for 2, 4.8, 16 or 24 hours (Figure 15A) or incubated with various doses of lenalidomide or DMSO for 24 hours (Figure 15B) before Western blot analysis. Figure 15A shows the course of treatment time with 10 µM lenalidomide. Figure 15B shows a 24 hour dose response to lenalidomide.
[00270] [00270] Figures 16A, 16B, 16C, 16D, 16E, 16F and 16G are a set of flow cytometry histograms showing surface CAR expression in the presence or absence of lenalidomide. The constructs tested include: construct 769 (CARI9 16GS - HIilD tag) (Figure 16A), construct 771 (CAR1I9 HIilD tag V5) (Figure 16B), construct 6761 (CAR1I9 16KGS HIilD tag V5) (Figure 16C), construct 768 (CAR1I9 16GS HiID tag V5) (Figure 16D), construct 770 (CAR19 16GS HIlD tag NoK) (Figure 16E), construct 773 (HilD tag CAR19 modSigPep) (Figure 16F) and construct 774 (HilD tag CAR1I9) (Figure 16G). JNL cells that express the indicated constructs were incubated with or without 10 µM lenalidomide for 24 hours and then subjected to flow cytometry analysis.
[00271] [00271] Figures 17A, 17B and 17C are a set of flow cytometry histograms showing the expression of surface-regulated CAR by lenalidomide and / or bazedoxifene (BZA). The constructs tested include: construct 765 (FurON CAR19) (Figure 17A), construct 767 (FurON CAR19 16GS HIilD tag) (Figure 17B), and construct 766 (FurON CAR19 16GS HIID tag V5) (Figure 17C). JNL cells expressing the indicated constructs were incubated in the presence or absence of lenalidomide and / or bazedoxifene (BZA) for 24 hours before flow cytometry analysis.
[00272] [00272] Figures 18A, 18B, 18C and 18D are a set of flow cytometry histograms showing the expression of surface CAR in the presence or absence of varying concentrations of linalidomide. The constructs tested include: construct 769 (label CAR19 16GS HIilD) (Figures 18A and 18C) and construct 770 (CARI9-16GS HIilD tag NoK) (Figures 18B and 18D). JNL cells that express the indicated constructs were incubated in the presence or absence of lenalidomide for 4 hours (Figures 18A and 18B) or 20 hours (Figures 18C and 18D) before flow cytometry analysis. Figures 18E and 18F are bar graphs showing the% of expression
[00273] [00273] Figures 19A and 19B are a series of bar graphs showing comparisons of response to lenalidomide between the conditions of treatment with JNL target cell line, duration of treatment with target cell line, length of treatment with lenali - dominance and number of cells. Figure 19A is a set of graphs showing the luminescence signals from a study in which the JNL cells that express the 769 construct (CAR1I9 16GS HIID tag) (9000 or 12000 cells / well) were treated with 10 µM of lenalide-mide during 4 hours or 24 hours and then incubated with Nalm6 cells, K562 cells that express CD19 ("K562 + CD19"), K562 cells or media (without cells) for 4 hours, 8 hours or 20 hours. Figure 19B is a set of graphs showing a subset of the study data described in Figure 19A: The JNL cells that express construct 769 (CAR1I9 16GS HilD tag) (9000 cells / well) were treated with 10 µM of lenalidomide for 4 hours and then incubated with Nalm6 cells, K562 cells that express CD19 ("K562 + CD19"), K562 cells or media (without cells) for hours. The y-axis in Figure 19B shows the luminance signals after the background signals (medium sample signals) are subtracted. In both Figures 19A and 19B, the two bars in each graph represent samples treated with DMSO ("DMSO") and samples treated with lenalidomide ("Lenalidomide (10 UM)"), respectively.
[00274] [00274] Figures 20A and 20B are a series of bar graphs showing comparisons of response to lenalidomide between the conditions of treatment with JNL target cell line, duration of treatment with target cells, length of treatment with lenalidomide and number of cells. Figure 20A is a set of graphs showing the luminescence signals from a study in which the JNL cells that express the 767 construct (FurON CAR19 16GS HIilD tag) (9000 or 12000 cells / well) were treated with 10 µM of lenalide-mide for 4 hours or 24 hours and then incubated with Nalm6 cells, K562 cells that express CD19 ("K562 + CD19"), K562 cells or media (without cells) for 4 hours, 8 hours or 20 hours. Figure 20B is a set of graphs showing a subset of the study data described in Figure 20A: The JNL cells that express construct 767 (FurON CAR19 16GS HIilD tag) (9000 cells / well) were treated with 10 µM lenalidomide for 4 hours and then incubated with Nalm6 cells, K562 cells that express CD19 ("K562 + CD19"), K562 cells or media (without cells) for hours. The y-axis in Figure 20B shows the luminescence signals after the background signals (media sample signals) are subtracted. In both Figures 20A and 20B, the four bars in each graph represent samples not treated with lenalidomide and bazedoxifene ("DMSO >> DMSO"), samples treated with bazedoxifene, but not with lenalidomide ("DMSO >> BZA (1 uM) "), samples treated with lenalidomide but not bazedoxifene (" Lenalidomide (10 uM) >> DMSO "), and samples treated with lenalidomide and bazedoxifene (" Lenalidomide (10 UuM) >> BZA (1 uM)) "), respectively.
[00275] [00275] Figures 21A, 21B, 21C and 21D are graphs showing a dose-response effect of lenalidomide in an NFAT luciferase reporter across three points in time. The JNL cells that express construct 765 (FurON CAR19) (Figure 21A), construct 767 (FurON CAR19 16GS HIlD label) (Figure 21B), construct 769 (CARI9 16GS HIilD tag) (Figure 21C), or construct 770 (CARI9- 16GS HIilD tag NoK) (Figure 21D) were incubated with K562 target cells ("K562") or K562 target cells that express CD19 ("K562 +
[00276] [00276] Figures 22A, 22B, 22C and 22D are graphs showing data from the study described in Figures 21A, 21B, 21C and 21D, in which JNL cells were treated with MG132 5 hours before treatment with target cells from K562 + CD19, and were treated with lenalidomide 4 hours before treatment with K562 + CD19 target cells. The cells tested include: JNL cells that express construct 765 (FurON CAR19) (Figure 22A), construct 767 (FUurON CAR19 16GS HILD label) (Figure 22B), construct 769 (CARI9-16GG HIilD label) (Figure 22C), or construct 770 (CAR1I9 16GS HIilD tag NoK) (Figure 22D). The four bars in each graph represent samples treated with bazedoxifene (BZA), MG132 and lenalidomide ("BZA, MG132, Lenalidomide"), samples treated with bazedoxifene (BZA) and lenalidomide ("BZA, Lenalidomide"), samples treated with bazedoxifene ( BZA) ("BZA") and samples treated with DMSO only ("DMSO"), respectively. The y-axis in each graph shows raw luminescence.
[00277] [00277] Figure 23 is a set of diagrams showing HilD-Tau fusion products. The ON4R Tau isoform was used, it includes the C-terminal repeat domain exon, but does not include the N-terminal exons. Lentiviral constructs were used, despite all
[00278] [00278] Figures 24A and 24B are graphs showing the design and results of a study examining the recruitment of EBN ligase CRBN fusion proteins with HilD-Tau. Figure 24A: Experiment diagram. Lenalidomide recruits E3 Cereblon ligase (CRBN) into the IKZF3 beta clamp format, resulting in ubiquitination and degradation of the associated protein. To test whether this recruitment occurred in HilD-Tau fusions, HilD-Tau- biotin ligase fusions were generated. In the presence of biotin, biotin ligase generates a reactive species of biotin that covalently binds to nearby proteins. If lenalidomide is added, CRBN must be recruited for HilD-Tau fusion, and should be in the biotinylation mediated by biotin ligase range. Figure 24B: HEK293T cells were transfected with FLAG-labeled CRBN and fusions of HilID-Tau-biotin ligase or Tau-biotin ligase. 48 hours after transfection, the cells were treated for 21 hours with 50 µl of biotin and DMSO or 1 µM of lenalidomide. The cells were subsequently washed in PBS and then lysed in ice-cold M-PER buffer and protease inhibitors. It is estimated that approximately 1 million cells are lysed, in a volume of 300 ul. Western cell lysate analysis is shown in the lower spot, probed with anti-Tau (HT7) or anti-GAPDH antibodies. Biotinylated proteins were immunoprecipitated by incubating 20% cell lysate with 50 µl of streptavidin magnetic microspheres (Dynabeads M-280) for 30 minutes at room temperature. Biotinylated proteins were eluted from microspheres by boiling and then analyzed by Western. With the FLAG signal probe in FLAG-CRBN, strong bands were observed only in immunoprecipitated material from HEK293T cells treated with lenalidomide and containing HilD tags, but not in cells treated with DMSO or cells treated with lenalidomide, but transfected with constructs Tau not containing the HIilD tag.
[00279] [00279] Figures 25A, 25B and 25C are graphs showing the reduction of toxic Tau protein by inducible recruitment of EBN ligase CRBN. HEK293T cells were transfected with HilD-Tau (P301S) -YFP fusion constructs. Tau (P301S) is a form prone to the aggregation of Tau, identified in patients with familial neurodegenerative diseases. By treating lenalidomide overnight, YFP fluorescence was reduced in a dose-dependent manner by lenalidodmide, as seen in YFP fluorescence imaging (Figure 25A). Nine fields of view per condition are shown. Figure 25B: The YFP fluorescence intensity was quantified after treatment with lenalidomide in various doses. Figure 25C: Toxicity due to overexpression of Tau prone to aggregation was observed, quantified by the number of cells and identified by fluorescence segmentation of Hoecht dye. Cell death was revoked by treatment with lenalidomide and reduced Tau levels, indicating that lenalidomide-induced degradation may reveal a cytoprotective action of targeted protein degradation of toxic proteins.
[00280] [00280] Figures 26A, 26B, 26C and 26D are graphs showing the quantification of reduction of Tau protein and reduction of specific forms of Tau in HEK293T cells by inducible recruitment of CRBN. Figure 26A: HEK293T cells were transfected with HilD-Tau fusion constructs (wild type) and treated with lenalido-mide, in varying doses, or DMSO. Upper and lower western blots are representative of experiments repeated in triplicate. The intensity of Tau bands, a polyclonal anti-Tau antibody (Dako) or an antibody against phosphorylated forms of Tau (AT8) was quantified
[00281] [00281] Figure 27 is a set of graphs showing the assessment of HilID-Tau (P301S) -YFP fusion aggregation propensity, expressed in rodent cortical neurons. Cortical rodent neurons were nucleofected with HilD-Tau (P301S) - YFP fusion and then subsequently incubated with insoluble Tau fractions isolated from an internally generated transgenic mouse. The fluorescence of live YFP was imaged using the Analyzer
[00282] [00282] Figure 28 is a set of graphs showing lenalidomide-mediated degradation of HilD-Tau (P301S) -YFP expressed in rat neurons. The rodent cortical neurons were nucleo-infected with HilD-Tau (P301S) -YFP fusion or Tau (P301S) -YFP fusion. Cotransfection with FLAG-labeled CRBN was also tested (upper lines). Starting at 9 days in vitro, neurons were treated with indicated doses of lenalidomide. The neurons were imaged alive for YFP fluorescence at indicated intervals. Lenalidomide treatment reduced YFP intensity over time compared to neurons that express HilD-Tau (P301S) -YFP treated with neurons that express DMSO or Tau (P301S) -YFP treated with lenalidomide. Degradation occurred with or without human CRBN cotransfection, indicating that the HiID-Tau fusion can be degraded by lenalidomide by rodent or human CRBN.
[00283] [00283] Figure 29 is a set of graphs showing lenalidomide-mediated degradation of HiID-Tau (P301S) -YFP expressed in rat neurons. A single cell suspension of 63 days of dissociated human neurospheres in vitro, derived from embryonic stem cells, was nucleofected with HilD - Tau (P301S) - YFP. Neurospheres contain neurons and neuronal progenitors. After 10 days in culture, the neurons were treated with lenalidomide (at a total age of 73 days in vitro). The images show YFP fluorescence after 20 hours of treatment with lenalidomide, at the indicated dose. Lenalidomide substantially reduced YFP fluorevolution intensity in a dose-dependent manner.
[00284] [00284] Figures 30A and 30B are a set of graphs showing degradation mediated by lenalidomide of CAR19-16GS-HilDtag. Figure 30A is a set of Western blot plots of Jurkat cells transduced by CAR19-HilDtag treated with a single dose of lenalidomide over time. Samples of post-compound treatment or post-wash period were tested. Figure 30B is a set of flow cytometry histograms analyzing the same samples used in Western blot analysis. An anti-CD3zeta antibody was used in Western blot analysis and the CD19-PE conjugate was used in flow cytometry analysis.
[00285] [00285] Figures 31A, 31B and 31C are a set of flow cytometry histograms that analyze the expression of CAR under different conditions. Figure 31A is a set of flow cytometry histogram showing the expression of CAR in primary T cells. The effect of lenalidomide on CAR1I9 expression in 24 hours is shown in Figure 31B. The effect of lenalidomide on the expression of CAR19-HIilD in 24 or 48 hours is shown in Figure 31C.
[00286] [00286] Figures 32A, 32B and 32C are a set of graphs showing% extermination mediated by CART cells. Figure 32A is a graph showing the percentage of extermination against CD19 negative cells. Figures 32B and 32C are graphs showing the percentage of extermination of CAR19 T cells (Figure 32B) or CAR1I9-HIilD T cells (Figure 32C) against CD19 positive cells in the presence or absence of 1um of lenalidomide.
[00287] [00287] Figures 33A and 33B are graphs showing the levels of IFN gamma and IL2 secreted, respectively, from T cells expressing CAR19 or CAR19-HIilD in the presence or absence of 1 µM lenalidomide. On the x-axis, the lenalidomide concentration is shown in UM.
[00288] [00288] Figure 34 is a graph showing that lenalidomide cancels the ability of CART19.HIilD to control tumor growth in vivo. The total flow of RO! it is represented against days after Nalm implant6.
[00289] [00289] Figure 35 is a set of flow cytometry graphs showing the loss of expression of CAR19-HIilD after treatment with lenalidomide.
[00290] [00290] Figure 36 is a graph showing the levels of tumor control in different treatment groups. The total flow of RO! is represented against days after Nalm6 implantation6. The initial injection of lenalidomide effectively canceled the expression of CART in mice treated with CART-HIID, leading to the absence of tumor control in this group. The subsequent treatment of lenalidomide (day 5 after the injection of CART) also reduced the function of CARTs, as shown by the loss of tumor control in this group of mice.
[00291] [00291] Figures 37A, 37B, 37C, 37D and 37E are graphs that analyze the expression of CAR in splenocyte CD3 + cells. Figure 37A is a graph showing the expression of CAR in CD3 + cells from splenocytes of mice treated with CART-HIiID (Group 1). Figures 37B, 37C and 37D are graphs showing the expression of CAR in CD3 + cells from splenocytes of mice treated with CART-HIID and lenalidomide (Group 2, Group 3 and Group 4, respectively). The peaks in Figures 37A to 37D represent the levels of CD3 expression for individual mice. Group 1 CART19.HilD (5x106) Group 2 CART19-HIilD (5x106) + Lena qd. Group 3 CART19-HIilD (5x106) + Lena bid. Group 4 CART19.HilD (5x106) + Lena + 5 Days. Figure 37E is a graph summarizing the data.
[00292] [00292] Figures 38A, 38B and 38C are graphs showing the impact of Compound | -112 on the expression and activity of CAR1I9-CARBtag. Figure 38A is a western blot of luciferous Jurkat NFAT cells
[00293] [00293] Figure 39 is a Western blot of HEK293T cells temporarily transfected with CARBtag-MITF-FLAG and treated with 10uUM, 1UM, 0.1UM, or 0.01UM of Compound 1-112 or lenalidomide, or DMSO, showing specific degradation to | -112 of the MITF marked with CARB.
[00294] [00294] Figures 40A and 40B are graphs analyzing the impact of lenalidomide on BCMACAR-HIilDtag expression and activity. Figure 40A is a set of histograms showing results of flow cytometry analysis of JNL cells infected with BCMACAR HILD tag treated with a dose response to lenalidomide for 24 hours, showing a dose-dependent degradation of lena-lidomide from BOCMACAR . Figure 40B is a graph showing the assay results of Jurkat NFAT luciferase cells expressing BCMA-HilDtag treated with a dose response to lenalidomide for 15 hours followed by co-treatment with KMS11 cells with a reading of luciferase activity. DETAILED DESCRIPTION
[00295] [00295] This description discloses, at least in part, a fusion polypeptide comprising a compound of Formula (! I), a (COF1) / CRBN-binding polypeptide, a compound of Formula (II), a-binding polypeptide (COF2) / CRBN, or a compound of Formula (III), (COF3) / CRBN-binding polypeptide for targeted protein inactivation. In some embodiments, the fusion polypeptide includes one or more COFI / CRBN-binding polypeptides, COF2 / CRBN or COF3 / CRBN and one or more heterologous polypeptides, for example, heterologous mammalian, bacterial or viral polypeptides, for example, one or more polypeptides of interest. The COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide can be functionally linked to the heterologous polypeptide, for example, via a linker. In some embodiments, in the presence of COF1 or COF2 (such as thalidomide and derivatives thereof (for example, lenalide, pomalidomide and thalidomide)), or in the presence of COF3 (for example, a compound disclosed in Table 29) the polypeptide of binding to COF1I / CRBN, COF2 / CRBN or COF3 / CRBN increases the degradation, for example, ubiquitination-mediated degradation, of the fusion polypeptide; and / or alters the level and / or activity of the fusion polypeptide. In some embodiments, the degradation of the fusion polypeptide is dependent on ubiquitin.
[00296] [00296] Without: stick to theory, in some modalities, the COFI / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN provides an amino acid sequence and / or a structural motif that, in the presence of COF1 or COF2 (such as thalidomide and derivatives thereof (for example, lenalidomide, pomalidomide and thalidomide)), or in the presence of COF3 (for example, a compound shown in Table 29), results in a post-translational modification (for example, ubiquitination) of the fusion polypeptide, resulting in a modified fusion polypeptide, for example, ubiquitinated. For example, one or more amino acids, for example, lysine or methionine, in the fusion polypeptide can be ubiquitinated, in the presence of COF1, COF2 or COF3. In some embodiments, the ubiquitinated fusion polypeptide is selectively degraded. In some embodiments, post-translational modification of the fusion polypeptide increases the degradation (for example, an increase in level and / or rate of degradation) of the fusion polypeptide (for example, all or part of the heterologous polypeptide). In some modalities, the increase in the level and / or rate of degradation is at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55 %, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 500%, 10 times, 100 times, 1,000 times, or more than the level and / or degradation rate of a reference protein, for example, the fusion polypeptide in the absence of COF1, COF2 or COF3, the heterologous polypeptide, a fusion of the heterologous polypeptide without the binding polypeptide COFI / CRBN, COF2 / CRBN or COF3 / CRBN, or a fusion of the heterologous polypeptide with a portion except the COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN.
[00297] [00297] Without sticking to the theory, degradation of the fusion polypeptide can include one, two or all of the following steps: (1) binding of COF1 or COF2 (eg, thalidomide and derivatives thereof (eg, lenalidoma )), or COF3 (for example, a compound shown in Table 29) to one or more subunits of a ubiquitin ligase complex (for example, a ubiquitin ligase E3 complex), for example, binding to CUL4, RBX1, DDBI and / or CRBN, also known as CRL4 (CRBN), typically a complex of DDB1- CRBN, thus forming a complex of COF1-ligase or COF2-ligase; (2) the COF1-ligase, COF2-ligase or COF3-ligase complex binds to and increases the ubiquitination of one or more amino acids, for example, lysine or methionine, in the fusion polypeptide, thus forming a polypeptide of ubiquitinated fusion, for example, a mono- or poly-ubiquitinated fusion polypeptide; and
[00298] [00298] In some embodiments, the COF1 / CRBN or COF2 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues, about 15 to about 90 amino acid residues, about 20 to about 85 amino acid residues, about 25 to about 80 amino acid residues, about 30 to about 75 amino acid residues, about 35 to about 70 amino acid residues, about 40 to about 65 amino acid residues , about 45 to about 65 amino acid residues, about 50 to about 65 amino acid residues, or about 55 to about 65 amino acid residues of IKZF1 (for example, SEQ ID NO: 20) or IKZF3 (for example , SEQ ID NO: 19).
[00299] [00299] In some embodiments, the COF3 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues, about 15 to about 90 amino acid residues, about to about 85 amino acid residues, about 25 to about 80 amino acid residues, about 30 to about 75 amino acid residues, about 35 to about 70 amino acid residues, about 40 to about 65 amino acid residues, about 45 to about 65 amino acid residues, about 50 to about 65 amino acid residues, or about 55 to about 65 amino acid residues of IKZF2 (for example, SEQ ID NO: 21).
[00300] [00300] In some embodiments, the COF1 / CRBN or COF2 / CRBN binding polypeptide comprises a beta curve (for example, a beta curve of IKZF3). In some embodiments, the COF1 / CRBN or COF2 / CRBN binding polypeptide comprises a beta curve (for example, a beta curve of IKZF3) and an alpha helix (for example, an alpha helix of IKZF3). In some modalities, the
[00301] [00301] In some embodiments, the COF3 / CRBN-binding polypeptide comprises a beta curve (for example, a beta curve of IKZF2). In some embodiments, the COF3 / CRBN-binding polypeptide comprises a beta curve (e.g., an IKZF2 beta curve) and an alpha helix (e.g., an IKZF2 alpha helix). In some embodiments, the COF3 / CRBN-binding polypeptide comprises amino acid residues 130 to 174 and / or 230 to 243 of IKZF2 (numbered according to SEQ ID NO: 21) or an amino acid sequence substantially identical to the same (for example , at least 85, 87, 90, 95, 97, 98, 99, or 100% identical). In some embodiments, the COF3 / CRBN-binding polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 109, 113 and 114, or an amino acid sequence substantially identical to the same (for example, at least 85 , 87, 90, 95, 97, 98, 99, or 100% identical to the same).
[00302] [00302] In some embodiments, the COF1 / CRBN or COF2 / CRBN binding polypeptide comprises a beta curve (for example, a beta curve of IKZF1). In some modalities, the polypeptide
[00303] [00303] In some embodiments, the heterologous polypeptide of the fusion polypeptide is susceptible to post-translational modification (for example, ubiquitination in one or more residues) and degradation in the presence of COF1 or COF 2 (for example, thalidomide and derivatives thereof, for example, lenalidomide, pomalidomide and thalidomide), or in the presence of COF3 (for example, a compound disclosed in Table 29).
[00304] [00304] —Optionally, the COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and the heterologous polypeptide can be functionally linked, for example, via a linker, for example, a glycine-serine linker (for example, SEQ ID NO: 28, 37, 38, 39 or 99). For example, fusion polypeptides can include three elements: a COF1I / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN, for example, a portion of a degrading amino acid sequence (for example, a degron), a heterologous polypeptide of interest that will be degraded, and a linker that separates the two. The heterologous polypeptide can be a cytosolic protein, a nuclear protein, a transmembrane protein (for example, including one or more transmembrane domains), or a secreted protein. For example, heterologous polypeptides of interest may include, for example, a chimeric antigen (CAR) receptor, a protein associated with CRISPR, CD8, CD19, CD22, a transcription factor (for example, STAT3, STAT5 , NF-kappaB, beta-catenin, Notch, GLI or c-JUN), for example, as described in this document.
[00305] [00305] In some embodiments, the fusion polypeptide of this invention further comprises a degradation domain. In some embodiments, the degradation domain has a first state associated with a first level of expression of the fusion polypeptide and a second state associated with a second level of expression of the fusion polypeptide, in which the second level is increased , for example, at least 2 times, 3 times, 4 times, 5 times, 10 times, 20 times or 30 times in relation to the first level in the presence of a stabilizing compound. In some embodiments, the degradation domain is separated from the COF1 / CRBN-binding polypeptide and the heterologous polypeptide by a heterologous cleavage site. In some embodiments, the degradation domain is separated from the COF2 / CRBN-binding polypeptide and the heterologous polypeptide by a heterologous cleavage site. In some embodiments, the degradation domain is separated from the COF3 / CRBN-binding polypeptide and the heterologous polypeptide by a heterologous cleavage site.
[00306] [00306] In some embodiments, the fusion polypeptide comprises a first domain and a second domain, wherein the first domain comprises a degradation domain and the second domain comprises a COF1 / CRBN, COF2 / CRBN-binding polypeptide or COF3 / CRBN and a heterologous polypeptide. In some modalities, the first domain and the second domain are separated by a heterologous cleavage site. Without sticking to the theory, the level of expression of the fusion polypeptide can be regulated by a stabilizing compound and COF1, COF2 or COF3. In some embodiments, in the absence of the stabilizing compound, the degradation domain is unable to acquire adequate conformation and is directed to degradation by intracellular degradation pathways along with the rest of the fusion polypeptide. In some embodiments, in the presence of the stabilizing compound, the degradation domain assumes an adequate conformation and is less susceptible to degradation by means of intracellular degradation. In some embodiments, in the presence of the stabilizing compound, adequate folding of the degradation domain exposes the heterologous cleavage site, resulting in the cleavage of the heterologous cleavage site and removal of the degradation domain from the rest of the fusion polypeptide. . The level of the fusion polypeptide can be further regulated by COF1, COF2, or COF3 as described above.
[00307] [00307] In some embodiments, the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB protein (FKBP) domain or a dihydrofolate reductase (DHFR) domain. In some embodiments, the degradation domain is an estrogen receptor (ER) domain, for example, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 46 or 48, for example, the degradation domain comprises the amino acid sequence of SEQ ID NO: 46. In some embodiments, the degradation domain is an estrogen receptor (ER) domain and the Stabilization post is bazedoxifene or 4-hydroxy tamoxifen (4-OHT). In some embodiments, the degradation domain is an FKB protein (FKBP), for example, the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO: 50, for example, the degradation domain comprises the amino acid sequence of SEQ ID NO:
[00308] [00308] “Consequently, polypeptides which include a heterologous polypeptide, a COF1 / CRBN binding polypeptide, COF2 / CRBN or COF3 / CRBN, and / or a degradation domain, for example, polypeptides of interest for selective protein degradation, as well as nucleic acid molecules encoding the fusion polypeptides, vectors and cells, for example, host cells, which include the aforementioned fusion polypeptides. The fusion polypeptides and related compositions disclosed herein can be used to activate or inactivate, for example, degrade, a variety of target proteins to regulate therapies, for example, secreted, cellular or trans-membrane therapies (for example, therapies with CAR), regulate gene expression (for example, by regulating the expression and / or activity of a component of the CRISPR / CAS system), target validation, as well as screening libraries. Methods for selectively regulating (e.g., degrading) said fusion polypeptides, for example, for treating an individual are further disclosed.
[00309] [00309] The compositions and methods disclosed in this document offer innovative and inventive features on the regulatory systems known in the art, including the fact that the COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide it is acting at the protein level (as opposed to MRNA) and leads to the active degradation of existing and recently produced proteins in a cell (as opposed to blocking the production of a nascent protein). In addition, the COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide can be short in length and COF1, COF2 and COF3 are typically of low molecular weights.
[00310] [00310] Without sticking to the theory, as described in Example 16,
[00311] [00311] Similarly, COF3 (for example, a compound disclosed in Table 29) does not lead to, or substantially does not lead to, degradation of a fusion polypeptide comprising a COF1 / CRBN or COF2 binding polypeptide / CRBN described in this document (for example, a fusion polypeptide that comprises a HIilD tag described herein, for example, a fusion polypeptide that comprises a HilID tag that comprises a sequence of amino acids selected from among the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-86, and 100). In some embodiments, the degradation of a fusion polypeptide comprising a COFI / CRBN or COF2 / CRBN-binding polypeptide described herein in the presence of COF3 is no more than 1, 2, 3, 4, 5, 6, 7 , 8, 9, 10, 15, or 20% of the degradation of said fusion polypeptide in the presence of COF1 or COF2 under the same conditions.
[00312] [00312] As a consequence, two target polypeptides, one marked with a COF1 / CRBN or COF2 / CRBN binding polypeptide (for example, a HilD tag described in this document), the other marked with a polypeptide of connection to COF3 / CRBN (for example, a CARB label described in this document), can be regulated independently using COF1 or COF2 and COF3. For example, a cell that expresses a protein labeled with HIilD and a protein labeled with CARB can be manipulated to express only the protein labeled with HIilD (for example, by putting the cell in contact with COF3), express only the protein labeled with CARB (for example, putting the cell in contact with COF1 or COF2), or expressing no protein (for example, putting the cell in contact with COF1 or COF2 and COF3). Definitions
[00313] [00313] Unless otherwise defined, all technical and scientific terms used in this document have the same meaning as is commonly understood by a person of ordinary skill in the technique to which the invention belongs.
[00314] [00314] As used herein, the term "compound of Formula (1) (COF1) / CRBN binding polypeptide" "refers to a polypeptide that binds to COF1, a polypeptide that binds to a complex of COF1 and CRBN, or a polypeptide that binds to CRBN in the presence of COF1. In some embodiments, the COF1 / CRBN-binding polypeptide binds to COF1 with an affinity (Kp) that is less than 10%, 104, 10, 108, 107, or 108 M, for example, as measured by a recognized method in technique, for example, Biacore. In some embodiments, the COF1 / CRBN-binding polypeptide binds to the COF1 and CRBN complex with an affinity (Kp) that is less than 10, 104, 105, 108, 107, or 108 M, for example, as measured by a method recognized in the art, for example, Biacore. In some embodiments, the COF1 / CRBN-binding polypeptide binds to CRBN in the presence of COF1 with an affinity (Kp) that is less than 10, 104, 105, 108, 107, or 10 M, for example, as measured by a method recognized in the art, for example, Biacore.
[00315] [00315] “As used herein, the term" Formula (II) compound (COF2) / CRBN-binding polypeptide "'" refers to a polypeptide that binds to COF2, a polypeptide that binds to a complex of COF2 and CRBN, or a polypeptide that binds to CRBN in the presence of COF2. In some embodiments, the COF2 / CRBN-binding polypeptide binds to COF2 with an affinity (Kp) that is less than 103, 10%, 10, 108, 107, or 10 M, for example, as measured by a method recognized in the art, for example, Biacore In some embodiments, the COF2 / CRBN-binding polypeptide binds to the COF2 and CRBN complex with an affinity (Kp) which is less than 10, 104, 105, 108, 107, or 108 M, for example, as measured by a method recognized in the art, for example, Biacore. In some embodiments, the binding polypeptide COF2 / CRBN binds to CRBN in the presence of COF2 with an affinity (Kp) that is less than 103, 104, 105, 108, 107, or 10º M, for example, as measured by a recognized method in technique, for example, Biacore. In some embodiments, the COF2 / CRBN-binding polypeptide, when present in a fusion polypeptide (for example, functionally linked to a heterologous polypeptide (for example, a fusion polypeptide as described herein) document)), may result in an increase in ubiquitination of the fusion polypeptide. In some embodiments, the COF2 / CRBN-binding polypeptide, when present in a fusion polypeptide (for example, functionally linked to a heterologous polypeptide (for example, a fusion polypeptide as described in this document)), may result in an increase in degradation of the fusion polypeptide. In some embodiments, the COF2 / CRBN-binding polypeptide, when present in a fusion polypeptide (for example, functionally linked to a heterologous polypeptide (for example, a fusion polypeptide as described in this document)), may result in an increase in inactivation of the fusion polypeptide. In some embodiments, the increase in ubiquitination, degradation and / or inactivation occurs in the presence of COF2 and one or more components of a ubiquitination ligase complex (for example, CRBN). In some modalities, the increase in ubiquitination, degradation and / or inactivation is at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 500%, 10 times, 100 times, 1,000 times, or greater than ubiquitination, degradation and / or inactivating a reference polypeptide, for example, a reference fusion polypeptide with the COF2 / CRBN binding polypeptide in the absence of COF2, or a reference polypeptide without the COF2 binding polypeptide / CRBN. In some embodiments, degradation of the fusion polypeptide containing the COF2 / CRBN-binding polypeptide is dependent on ubiquitin. For example, one or more amino acids, for example, lysine or methionine, in the fusion polypeptide with the COF2 / CRBN binding polypeptide are ubiquitinated in the presence of COF 2.
[00316] [00316] As used herein, the term "compound of Formula (III) (COF3) / CRBN-binding polypeptide" refers to a polypeptide that binds to COF3, a polypeptide that binds to a complex of COF3 and CRBN, or a polypeptide that binds to CRBN in the presence of COF3. In some embodiments, the COF3 / CRBN-binding polypeptide binds to COF3 with an affinity (Kp) that is less than 10º, 104, 10º, 108, 107, or 10º M, for example, as measured by a method recognized in technique, for example, Biacore.
[00317] [00317] As used herein, "ubiquitination" refers to the addition of a ubiquitin molecule, for example, a single ubiquitin (mono-ubiquitination) or more than one ubiquitin (for example, a chain of ubiquitin or poly-ubiquitination molecules). Ubiquitination can be performed by an enzymatic machinery including one or more of an ubiquitin activating enzyme (E1), a ubiquitin conjugating enzyme (E2), and a ubiquitin ligase (E3).
[00318] [00318] “As used herein, the term" CRBN "refers to a protein that in humans is encoded by the CRBN gene, or fragment or variant thereof (for example, a sequence of amino acids substantially identical to the same, for example, at least 85, 87, 90, 95, 97, 98, 99, or 100% identical to the same). The Swiss-Prot accession number Q96SW2 provides exemplary human CRBN amino acid sequences.
[00319] [00319] “As used herein, an" IKZF polypeptide "refers to an IKZF, or fragment or variant thereof (for example, an amino acid sequence substantially identical to it, for example, at least 85, 87 , 90, 95, 97, 98, 99, or 100% identical to the same).
[00320] [00320] As used in this document, the term "IKZF3" referred to
[00321] [00321] As used herein, the term "IKZF1" refers to a protein that in humans is encoded by the IKZF1 gene. The Swiss-Prot accession number Q13422 provides exemplary human IKZF1 amino acid sequences. An exemplary human IKZF1 amino acid sequence is provided in SEQ ID NO: 20. The term, "IKZF1 polypeptide" refers to IKZF1, or a fragment or variant thereof (for example, a substantially amino acid sequence identical to the same, for example, at least 85, 87, 90, 95, 97, 98, 99, or 100% identical to the same).
[00322] [00322] As used herein, the term "IKZF2" refers to a protein that in humans is encoded by the IKZF2 gene. The Swiss-Prot accession number Q9UKS7 provides exemplary human IKZF2 amino acid sequences. An exemplary human IKZF2 amino acid sequence is provided in SEQ ID NO: 21. The term, "IKZF2 polypeptide" refers to IKZF2, or a fragment or variant thereof (for example, a substantially amino acid sequence identical to the same, for example, at least 85, 87, 90, 95, 97, 98, 99, or 100% identical to the same).
[00323] [00323] “As used in this document, the term" IKZF4 "refers to a protein that in humans is encoded by the IKZF4 gene. The Swiss-Prot accession number Q9H2S9 provides exemplary human IKZF4 amino acid sequences. An exemplary human IKZF4 amino acid sequence is provided in SEQ ID NO: 22. The term, "IKZF4 polypeptide" refers to IKZFA4, or a fragment or variant thereof (for example, a sequence of substantially amino acids) identical to the same, for example, at least 85, 87, 90, 95, 97, 98, 99, or 100% identical to the same).
[00324] [00324] As used herein, the term "IKZF5" refers to a protein that in humans is encoded by the IKZF5 gene. The Swiss-Prot accession number Q9H5V7 provides exemplary human IKZF5 amino acid sequences. An exemplary human IKZF5 amino acid sequence is provided in SEQ ID NO: 23. The term, "IKZF5 polypeptide" refers to IKZF5, or a fragment or variant thereof (for example, a substantially amino acid sequence identical to the same, for example, at least 85, 87, 90, 95, 97, 98, 99, or 100% identical to the same).
[00325] [00325] “As used herein, a" fusion polypeptide "or" chimeric polypeptide "refers to a polypeptide that includes two or more heterologous amino acid sequences and / or protein domains in a single polypeptide continuous. In some modes, the two or more heterologous protein domains are covalently linked directly or indirectly, for example, via a linker.
[00326] [00326] “As used herein, the term" estrogen receptor (ER) "refers to a protein that in humans is encoded by the ESR1 gene. The Swiss-Prot PO3372 accession number provides exemplary human estrogen receptor (ER) amino acid sequences. An estrogen receptor (ER) domain "refers to IKZF2, or a fragment or variant thereof (for example, an amino acid sequence substantially identical to the same, for example, at least 85, 87, 90, 95, 97, 98, 99, or 100% identical.) Exemplary estrogen receptor domain (ER) amino acid sequences are provided in SEQ ID NOs: 44, 46, and 48. The nucleotide sequences of the receptor domain Exemplary estrogen (ER) are provided in SEQ ID NOs: 45, 47 and
[00327] [00327] “As used herein, an" FKB protein domain (FKBP) "refers to FKBP, or a fragment or variant thereof. An exemplary FKB protein domain (FKBP) amino acid sequence is provided in SEQ ID NO: 50.
[00328] [00328] As used herein, the term "dihydrofolate reductase (DHFR)" refers to a protein that in humans is encoded by the DHFR gene. The Swiss-Prot accession number POO0374 provides exemplary human dihydrofolate reductase (DHFR) amino acid sequences. A "dihydrofolate reductase (DHFR) domain" refers to DHFR, or a fragment or variant thereof. An exemplary dihydrofolate reductase (DHFR) domain amino acid sequence is provided in SEQ ID NO: 51.
[00329] [00329] “As used herein, the term" degradation domain "refers to a domain of a fusion polypeptide that assumes a stable conformation when expressed in the presence of a stabilizing compound. In the absence of stable conformation, when expressed in a cell of interest, a large fraction of degradation domains (and, typically, any protein to which they fuse) will be degraded by endogenous cellular machinery. Notably, a degradation domain is not a naturally occurring domain of a protein, but instead it is designed to be unstable without contact with the stabilizing compound. In this way, a degradation domain is identifiable by the following characteristics: (1) it is not naturally occurring; (2) its expression is regulated in a co-translational or post-translational way through increased or reduced degradation rates; (3) the rate of degradation is
[00330] [00330] The degradation domain is not an aggregation domain as defined in PCT Application Number PCT / US2017 / 027778.
[00331] [00331] By "stabilizing compound" or "stabilizing compound" is meant a compound that, when added to a cell that expresses a degradation domain, stabilizes the degradation domain and any protein that is fused to the same, and decreases the rate at which it is subsequently degraded. The stabilizing compounds or stabilizing compounds can be naturally occurring or synthetic.
[00332] [00332] By the term "heterologous polypeptide" is meant an amino acid sequence (for example, a protein domain) that is different from a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide (for example , by at least one amino acid) and which is not an active luciferase domain or has a luciferase sequence. In some embodiments, the heterologous polypeptide is not a reporter polypeptide, for example, a luciferase, a green fluorescent protein or a b-galactosidase. In some modalities, the power
[00333] [00333] Furthermore, "heterologous protease cleavage site" means a protease cleavage site that has a different origin from one or more protein domains to which it is fused (for example, it is not naturally merged with at least one of the reference domains).
[00334] [00334] By "protease" is meant a protein that cleaves another protein based on the presence of a cleavage site in the protein that will be cleaved.
[00335] [00335] By "intracellular protease" is meant a protease that is natively expressed within a cell of interest.
[00336] [00336] By "extracellular protease" is meant a protease that is natively expressed in an organism (for example, a mammal) and secreted or exposed to the outside of cells (for example, in the blood or skin surface).
[00337] [00337] As used herein, the term "cleavage" refers to the breaking of covalent bonds, as in the backbone of a nucleic acid molecule or the hydrolysis of peptide bonds. Cleavage can be initiated by a variety of methods, including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-strand cleavage and double-strand cleavage are possible. Double-strand cleavage can occur
[00338] [00338] Additional terms are described later in this document.
[00339] [00339] The terms "one" and "one" relate to one or more than one (that is, at least one) of the grammatical object of the article. By way of example, "an element" means an element or more than an element.
[00340] [00340] The term "about", when referring to a measurable value, such as a quantity, a time duration, and the like, is intended to cover variations of + 20% or, in some cases, + 10%, or in some cases + 5%, or in some cases + 1%, or in some cases + 0.1% of the specified value, since such variations are appropriate to carry out the disclosed methods.
[00341] [00341] The term "antibody", as used in this document, refers to a protein or polypeptide sequence derived from an immunoglobulin molecule that specifically binds to an antigen. Antibodies can be polyclonal or monoclonal, single or multiple chain, or intact immunoglobulins, and can be derived from natural or recombinant sources. Antibodies can be tetramers of immunoglobulin molecules.
[00342] [00342] The term "antibody fragment" refers to at least a portion of an antibody, which retains the ability to interact specifically with (for example, by binding, steric hindrance, stabilization / destabilization, spatial distribution) a epitope of an antigen. Examples of antibody fragments include, but are not limited to, Fab, Fab ', F (ab') ', Fv fragments, scFv antibody fragments, disulfide-linked Fvs (sdFv), an Fd fragment consisting of the VH and CH1, linear antibodies, single domain antibodies, such as sdAb (VL or VH), camelid VHH domains, multispecific antibodies formed from antibody fragments, such as a divalent fragment comprising two Fab fragments linked by a bridge disulfide in the hinge region, and an isolated CDR or other epitope-binding fragments of an antibody. An antigen-binding fragment can also be incorporated into single-domain antibodies, maxibodies, minibodies, nanobodies, intrabodies, diabodies, tribodies, tetribodies, v-NAR and bis-scFv (see, for example, Hollinger and Hudson, Nature Bio-technology 23: 1126-1136, 2005). Antigen-binding fragments can also be grafted into polypeptide-based templates such as an fibronectin type Ill (Fn3) (see U.S. Patent No. 6,703,199, which describes fibronectin polypeptide minibodies).
[00343] [00343] The term "antibody heavy chain" refers to the greater of the two types of polypeptide chains present in antibody molecules in their naturally occurring conformations, and which usually determines the class to which the antibody belongs.
[00344] [00344] The term "antibody light chain" refers to the smaller of the two types of polypeptide chains present in antibody molecules in their naturally occurring conformations. Kappa (K) and lambda (A) light chains refer to the two main isotypes of antibody light chains.
[00345] [00345] The term "antigen", "Ag" or "antigen molecule" refers to a molecule that causes an immune response. This immune response may involve the production of antibodies or the activation of specific immunologically competent cells, or both. In some embodiments, an antigen is any macromolecule, including all proteins or peptides. In other modalities, antigens are derived from recombinant or genomic DNA. Any DNA, which comprises nucleotide sequences, or a partial nucleotide sequence, which encodes a protein that produces an immune response, therefore encodes an "antigen", as the term is used herein.
[00346] [00346] An antigen need not be encoded exclusively by a full-length nucleotide sequence of a gene. In the modalities, antigens include, but are not limited to, the use of partial nucleotide sequences from more than one gene and that these nucleotide sequences are arranged in various combinations to encode polypeptides that produce the desired immune response. In one embodiment, an antigen does not need to be encoded by a "gene" at all. In one embodiment, an antigen may be generated, synthesized, or may be derived from a biological sample, or may be a macromolecule other than a polypeptide. Such a biological sample may include, but is not limited to, a tissue sample, a tumor sample, a cell or a fluid with other biological components. In the modalities, antigens include, for example, carbohydrates (for example, monosaccharides, disaccharides, oligosaccharides and polysaccharides).
[00347] [00347] The term "antigen presenting cell" or "APC" refers to an immune system cell, such as an accessory cell (for example, a B cell, a dendritic cell and the like), which exhibits a complexed foreign antigen with major histocompatibility complexes (MHCs) on its surface. T cells can recognize these complexes using their T cell receptors (TCRs). APCs process antigens and present them to T cells.
[00348] [00348] The term "Chimeric Antigen Receptor" or alternatively a "CAR" refers to a set of polypeptides, typically two in the simplest modalities, which, when in an immune effector cell, endow the cell with specificity for a target cell, typically a cancer cell, and for intracellular signal generation. In some embodiments, a CAR comprises at least one extracellular antigen-binding domain, a transmembrane domain and a cytoplasmic signaling domain (also referred to herein as "an intracellular signaling domain") that comprises a functional signaling domain derived from a stimulating molecule and / or co-stimulating molecule as defined below.
[00349] [00349] The term "cancer" refers to a disease characterized by uncontrolled growth of aberrant cells. Cancer cells can spread locally or through the bloodstream and lymphatic system to other parts of the body. Examples of various cancers are described in this document and include, but are not limited to, breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer,
[00350] [00350] "CAR molecule", depending on the context, refers to a CAR (for example, a CAR polypeptide), a nucleic acid encoding a CAR, or both.
[00351] [00351] A CAR that comprises an antigen-binding domain (for example, a scFv or TCR) that targets a specific tumor antigen X, such as those described in this document, is also called XCAR. For example, a CAR that comprises an antigen-binding domain that targets CD19 or BCMA is called CD19CAR or BCMACAR, respectively.
[00352] [00352] As used here, the term "BCMA '" relates to the B cell maturation antigen. BCMA (also known as TNFRSF17, BCM or CD269) is a member of the tumor necrosis receptor (TNFR) family. and it is predominantly expressed in terminally differentiated B cells, for example, memory B cells, and plasma cells. Its ligand is called TNF B cell activator (BAFF) and a proliferation-inducing ligand (APRIL). BCMA is involved in mediating the survival of plasma cells to maintain long-lasting humoral immunity. The BCMA gene is encoded on chromosome 16 producing a 994 nucleotide long primary mMRNA transcript (NCBI access NM 001192.2) which encodes a 184 amino acid protein (NP 001183.2). A second antisense transcript derived from the BCMA locus has been described, which may play a role in regulating BCMA expression. (Laabi Y. et al, Nucleic Acids Res., 1994, 22: 1147-1154). Variants of additional transcripts have been described with unknown importance (Smirnova AS et al. Mol Immunol., 2008, 45 (4): 1179-1183). A second isoform, also known as TVA, has been identified (Uniprot identifier Q02223-2). As used herein, "BCMA" includes proteins comprising mutations, for example, point mutations, fragments, insertions, deletions and stranded variants of complete wild-type BCMA.
[00353] [00353] As used here, the term "CD19" refers to Protein 19 from the Differentiation Cluster which is a detectable antigenic determinant in leukemia precursor cells. The human and murine amino acid and nucleic acid sequences can be found in a public database, such as GenBank, UniProt and Swiss-Prot. For example, the human CD19 amino acid sequence can be found in UniProt / Swiss-Prot Accession No. P15391 and the nucleotide sequence encoding human CD19 can be found in Accession No. NM 001178098. As used here, "CD19 "includes proteins comprising mutations, for example, point mutations, fragments, insertions, deletions, and full-length wild-type CD19 splice variants.
[00354] [00354] CD19 is expressed in most cancers of lineage B, including, for example, acute lymphoblastic leukemia, chronic lymphocytic leukemia and non-Hodgkin's lymphoma. Other cells that express CD19 are provided below in the definition of "disease associated with CD19 expression". It is also an initial marker for B cell progenitors. See, for example, Nicholson et al. Mol. Immun. 34 (16-17): 1157-1165 (1997). In one aspect, the antigen-binding portion of CART recognizes and binds to an antigen in the extracellular domain of the CD19 protein. In one aspect, the CD19 protein is expressed in a cancer cell.
[00355] [00355] “As used here, the term" CD20 "relates to an antigenic determinant that is known to be detectable in B cells. Human CD20 is also called membranes spanning 4 domains, subfamily A, member 1 (MS4A1). The human and murine amino acid and nucleic acid sequences can be found in a public database, such as GenBank, UniProt and Swiss-Prot. For example, the human CD20 amino acid sequence can be found in Accession Numbers NP 690605.1 and NP 068769.2, and the nucleotide sequence encoding transcript 1 and 3 variants of human CD20 can be found in Accession No. NM 152866.2 and NM 021950.3, respectively. In one aspect, the antigen-binding portion of the CAR recognizes and binds to an antigen in the extracellular domain of the CD20 protein. In one aspect, the CD20 protein is expressed in a cancer cell. As used herein, "CD20" includes proteins comprising mutations, for example, point mutations, fragments, insertions, deletions and splicing variants of full-length wild-type CD20.
[00356] [00356] As used here, the term "CD22" relates to an antigenic determinant which is known to be detectable in leukemia precursor cells. The human and murine amino acid and nucleic acid sequences can be found in a public database, such as GenBank, UniProt and Swiss-Prot. For example, the amino acid sequences of isoforms 1-5 of human CD22 can be found in Accession Numbers NP 001762.2, NP 001172028.1, NP
[00357] [00357] “As used here, the term" CD123 "relates to an antigenic determinant that is known to be detectable in some malignant hematological cancer cells, for example, leukemia cells. The human and murine amino acid and nucleic acid sequences can be found in a public database, such as GenBank, UniProt and Swiss-Prot. For example, the amino acid sequences of human CD123 can be found in Accession No. NP 002174.1 (isoform precursor 1); NP 001254642.1 (isoform precursor 2), and the mRNA sequences that encode them can be found in Accession numbers NM 002183.3 (variant 1); NM 001267713.1 (variant 2). In one aspect, the antigen-binding portion of the CAR recognizes and binds to an antigen in the extracellular domain of the CD123 protein. In one aspect, the CD123 protein is expressed in a cancer cell. As used herein, "CD123" includes proteins comprising mutations, for example, point mutations, fragments, insertions, deletions and splicing variants of full-length wild-type CD123.
[00358] The portion of the CAR comprising an antibody or its antibody fragment can exist in a variety of ways in which the antigen binding domain is expressed as part of a contiguous polypeptide chain including, for example, an antibody fragment of single domain (sdAb), a single chain antibody (scFv), a humanized antibody or bispecific antibody (Harlow et al., 1999, In: "Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York; Harlow et al., 1989, In: "Antibody-
[00359] [00359] The term "cognate antigen molecule" refers to any antigen described in this document. In one embodiment, it refers to an antigen recognized, for example, targeted by a CAR molecule, for example, any CAR described in this document. In another embodiment, it refers to a cancer-associated antigen described in this document. In one embodiment, the cognate antigen molecule is a recombining molecule.
[00360] [00360] The term "conservative sequence modifications" refers to amino acid modifications that do not significantly affect or alter the binding characteristics of the antibody or antibody fragment containing the amino acid sequence. Such conservative modifications include amino acid substitutions, additions and deletions. Modifications can be made to an antibody or antibody fragment of the invention by common techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis. Conservative amino acid substitutions are those in which the amino acid residue is replaced by an amino acid residue having a similar side chain. Families of amino acid residues with similar side chains have been defined in the art. These families include amino acids with basic side chains (eg lysine, arginine, histidine), acidic side chains (eg aspartic acid, glutamic acid), uncharged polar side chains (eg glycine, asparagine, glutamine, serine,
[00361] [00361] The term "co-stimulating molecule" refers to the cognate binding partner in a T cell that specifically binds to a co-stimulating ligand, thereby mediating a co-stimulating response by the T cell, such as, but not limited to, proliferation. Co-stimulatory molecules are molecules on the cell surface different from antigen receptors or their ligands that are necessary for an efficient immune response. Co-stimulating molecules include, but are not limited to, an MHC class | molecule, TNF receptor proteins, immunoglobulin-like proteins, cytokine receptors, integrins, lymphocyte activation signaling molecules (SLAM proteins), activator NK cells, BTLA, a Toll ligand receptor, OX40, CD2, CD7, CD27, CD28, CD30, CD40, CDS, ICAM-1, LFA-1 (CD11a / CD18), 4-1BB (CD137), B7- H3, CDS, ICAM-1, ICOS (CD278), GITR, BAFFR, LIGHT, HVEM (LIGHTR), KIRDS2, SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD19, CDA4, CD8alfa, CD8beta, IL2R beta IL2PR gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGAA, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7,
[00362] [00362] "Derived from", as that term is used in this document, indicates a relationship between a first and a second molecule. It generally refers to the structural similarity between the first molecule and a second molecule and is not connotated nor does it include a process or source limitation on a first molecule that is derived from a second molecule. For example, in the case of an intracellular signaling domain that is derived from a CD3zeta molecule, the intracellular signaling domain retains sufficient CD3zeta structure so that they have the required function, namely, the ability to generate a signal under the appropriate conditions. It is not connected to or includes a limitation to a particular process of producing the intracellular signaling domain, for example, does not mean that, to provide the intracellular signaling domain, one must start with a CD3zeta sequence and delete unwanted sequence, or impose mutations, to reach the intracellular signaling domain.
[00363] [00363] The term "disease associated with the expression of a tumor antigen" as described herein "includes but is not limited to a disease associated with the expression of a tumor antigen as described herein or a condition associated with cells expressing an antigen tumor as described here, including, for example, proliferative diseases such as cancer or malignancy or a precancerous condition such as myelodysplasia, myelodysplastic syndrome or pre-leukemia; or a non-cancer indication associated with cells expressing a tumor antigen as described in this document In one embodiment, a cancer associated with the expression of a tumor antigen as described in this document is a hematological cancer In one embodiment, a cancer associated with the expression of a tumor antigen as described in this document is a solid cancer Other diseases associated with the expression of a tumor antigen as described in this document include, but are not limited to, for example, atypical and / or non-classical cancers, malignancies, pre-cancer conditions or proliferative diseases associated with the expression of a tumor antigen as described in this document. Non-cancer-related indications associated with the expression of a tumor antigen as described here include, but are not limited to, for example, autoimmune disease (eg, lupus), inflammatory disorders (allergy and asthma) and transplantation. In some modalities, cells that express tumor antigen express, or at any time expressed, mRNA that encodes the tumor antigen. In one mode, the cell expressing a tumor antigen produces the tumor antigen protein (eg, wild-type or mutant), and the tumor antigen protein may be present at normal levels or reduced levels. In one embodiment, cells expressing a tumor antigen produced detectable levels of a tumor antigen protein at a time and subsequently produced substantially no detectable tumor antigen protein.
[00364] [00364] The expression "disease associated with CD19 expression" includes
[00365] [00365] Other diseases associated with CD19 expression include, but are not limited to, for example, atypical and / or non-classical cancers, malignancies, precancerous conditions or proliferative diseases associated with CD19 expression. Non-cancer indications associated with CD19 expression include, but are not limited to, for example, autoimmune disease (eg, lupus), inflammatory disorders (allergy and asthma) and transplantation. In some modalities, cells expressing CD19 express, or have expressed at some point, CD19 mMRNA. In one embodiment, cells expressing CD19 produce a CD19 protein (for example, wild-type or mutant), and the CD19 protein can be present at normal levels or at reduced levels. In one embodiment, cells expressing CD19 produced detectable levels of a CD19 protein at any given time and subsequently did not substantially produce any CD19 protein.
[00366] [00366] In some modalities, cells that express tumor antigen express, or at any time expressed, MRNA that encodes the tumor antigen. In one embodiment, the cell expressing a tumor antigen produces the protein of the tumor antigen (for example, wild-type or mutant), and the protein of the tumor antigen may be present at normal or reduced levels. In one embodiment, cells expressing a tumor antigen produced detectable levels of a tumor antigen protein at a time and subsequently produced substantially no detectable tumor antigen protein. In other modalities, the disease is a CD19-negative cancer, for example, a recurrent CD19-negative cancer. In some embodiments, the cell that expresses tumor antigen (for example, CD19) expresses, or at any time expressed, mRNA that encodes the tumor antigen. In one embodiment, cells that express tumor antigen (for example, CD19) produce the tumor antigen protein (for example, wild-type or mutant), and the tumor antigen protein may be present at normal or reduced levels . In one embodiment, cells expressing a tumor antigen (eg, CD19) produced detectable levels of a tumor antigen protein at a time and subsequently produced substantially no detectable tumor antigen protein.
[00367] [00367] The term "effector function" refers to a specialized function of a cell. The effector function of a T cell, for example, can be cytolytic activity or auxiliary activity including cytokine secretion. The term "coding" refers to the inherent property of specific nucleotide sequences in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for the synthesis of other polymers and macromolecules in bio processes - logical having a defined sequence of nucleotides (for example, rRNA, tRNA and mMRNA) or a defined sequence of amino acids and the resulting biological properties. Thus, a gene, cDNA, or RNA, encodes a protein if the transcription and translation of the correct mMRNA
[00368] [00368] The term "endogenous" refers to any material from or produced within an organism, cell, tissue or system.
[00369] [00369] The term "exogenous" refers to any material introduced from or produced outside an organism, cell, tissue or system.
[00370] [00370] The term "expression" refers to the transcription and / or translation of a particular nucleotide sequence triggered by a promoter.
[00371] [00371] The term "4-1BB" refers to a member of the TNFR superfamily with an amino acid sequence provided as the GenBank accession number AAAG62478.2, or the equivalent residues of a non-human species, for example, mouse, rodent, monkey, simian and the like; and a "4-1BB co-stimulatory domain" is defined as amino acid residues 214 to 255 of GenBank accession number AAAG62478.2, or equivalent residues of a non-human species, for example, mouse, rodent , monkey, simian and the like. In one aspect, the "4-1BB co-stimulatory domain" is the sequence provided as SEQ ID NO: 158 or the equivalent residues of a non-human species, for example, mouse, rodent, monkey, simian and the like.
[00372] [00372] The term "expression vector" refers to a vector that comprises a recombinant polynucleotide that comprises expression control sequences operably linked to a sequence.
[00373] [00373] The term "homologous" or "identity" relates to the identity of subunit sequences between two polymeric molecules, for example, between two nucleic acid molecules, such as two DNA molecules or two RNA molecules, or between two polypeptide molecules. When a subunit position in both molecules is occupied by the same monomeric subunit; for example, when a position in each of two DNA molecules is occupied by adenine, then they are homologous or identical in that position. The homology between two sequences is a direct function of the number of corresponding or homologous positions; for example, if half (for example, five positions in a polymer ten subunits in length) of the positions in two sequences are homologous, the two sequences are 50% homologous; if 90% of the positions (for example, 9 out of 10) are corresponding or homologous, the two strings are 90% homologous.
[00374] [00374] The compositions and methods of the present invention encompass polypeptides and nucleic acids that have the specified sequences or sequences substantially identical or similar to the same, for example, at least 85%, 90%, 95% identical sequences or greater than the specified sequence. In the context of an amino acid sequence, the term "substantially identical" is used in this document to refer to a first amino acid that contains
[00375] [00375] In the context of nucleotide sequences, the term "substantially identical" is used in this document to refer to a first nucleic acid sequence that contains a sufficient or minimal number of nucleotides that are identical to nucleotides aligned in one second nucleic acid sequence so that the first and second nucleotide sequences encode a polypeptide that has common functional activity or encode a common structural polypeptide domain or a common functional polypeptide activity. For example, nucleotide sequences that have at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identity with a reference sequence, for example, a sequence provided in this document.
[00376] [00376] The term "variant" refers to a polypeptide that has an amino acid sequence substantially identical to the naturally occurring sequence, or is encoded by a substantially identical sequence of nucleotides. In some modalities, the variant is a functional variant.
[00377] [00377] The term "functional variant" refers to a polypeptide that has an amino acid sequence substantially identical to the naturally occurring sequence, or is encoded by a substantially identical nucleotide sequence, and is capable of having one or more activities of the naturally occurring sequence.
[00378] [00378] The term "COFI / CRBN binding variant" of sequence X refers to a polypeptide that: (1) has an amino acid sequence substantially identical to sequence X, and (2) binds to COF1, binds to a complex of COF1 and CRBN, or binds to CRBN in the presence of COF1.
[00379] [00379] The term "COF2 / CRBN binding variant" of sequence X refers to a polypeptide that: (1) has an amino acid sequence substantially identical to sequence X, and (2) binds to COF2, binds to a complex of COF2 and CRBN, or binds to CRBN in the presence of COF2.
[00380] The term "COF3 / CRBN binding variant" of sequence X refers to a polypeptide that: (1) has an amino acid sequence substantially identical to sequence X, and (2) binds to COF3, binds to a complex of COF3 and CRBN, or binds to CRBN in the presence of COF3.
[00381] [00381] "Immuno-defective cell", as the term is used in this document, refers to a cell that is involved in an immunological response, for example, in promoting an immune response. Examples of immune effector cells include T cells, for example, alpha / beta T cells and gamma / delta T cells, B cells, natural killer cells (NK), natural killer T cells (NKT), mast cells and phagocytes derived from the lineage myeloid.
[00382] [00382] The "immuno-defective function" or "immuno-defective response", as such term is used in this document, refers to the function or response, for example, of an immuno-defective cell, which enhances or promotes an immune attack by a cell -target. For example, an immune function or effector response refers to a property of a T or NK cell that promotes the extermination or inhibition of the growth or proliferation of a target cell. In the case of a T cell, primary stimulation and co-stimulation are examples of an immune effector function or response.
[00383] [00383] The term "inhibition" or "inhibitor" includes a reduction in a certain parameter, for example, an activity, of a certain molecule, for example, CD19, CD20, CD10, CD22, CD34, CD123, FLT-3, ROR1, CD79b, Cd179b, mesothelin or CD79a. For example, the inhibition of an activity, for example, an activity of CD 20, CD10, CD19, CD22, CD34, CD123, FLT-3, ROR1, CD79b, CD179b, mesothelin or CD79a of at least 5%, 10% , 20%, 30%, 40% or more is included by that term. Thus, the inhibition does not need to be 100%. The activities for the inhibitors can be determined as described in this document or by assays known in the art.
[00384] [00384] An "intracellular signaling domain", as the term is used herein, refers to an intracellular portion of a molecule. The intracellular signaling domain can generate a signal that promotes an immune effector function of the cell containing CAR, for example, a CART cell. Examples of immune effector function, for example, in a CART cell, include cytolytic activity and helper activity, including cytokine secretion. In the modalities, the "intracellular signaling domain" is the portion of a protein that transduces the signal of the effector function and directs the cell to perform a specialized function. Although the entire intracellular signaling domain can be used, in many cases it is not necessary to use the entire chain. As much as a truncated portion of the intracellular signaling domain is used, such a truncated portion can be used instead of the intact chain as long as it transduces the signal from the effector function. Thus, the term intracellular signaling domain
[00385] [00385] In one embodiment, the intracellular signaling domain may comprise a primary intracellular signaling domain. Exemplary primary intracellular signaling domains include derivatives of the molecules responsible for primary stimulation or antigen-dependent stimulation. In one embodiment, the intracellular signaling domain can comprise a co-stimulating intracellular domain. Exemplary co-stimulatory intracellular signaling domains include those derived from molecules responsible for co-stimulatory signals or antigen-independent stimulation. For example, in the case of a CART, a primary intracellular signaling domain can comprise a cytoplasmic sequence of a T cell receptor, and a co-stimulating intracellular signaling domain can comprise a co-stimulating or co-stimulating molecule cytoplasmic sequence.
[00386] [00386] “A primary intracellular signaling domain can comprise a signaling motif that is known as the tyrosine-based activation motif of the immunoreceptor or ITAM. Examples of ITAMs containing primary cytoplasmic signal sequences include, but are not limited to, derivatives of CD3 zeta, FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, CD278 ( "ICOS"), FceRI, CD66d, CD32, DAP1IO and DAP12.
[00387] [00387] The term "isolated" means altered or removed from the natural state. For example, a nucleic acid or peptide naturally present in a living animal is not "isolated", but the same nucleic acid or peptide partially or completely separated from coexisting materials in its natural state is "isolated". An isolated nucleic acid or protein can exist in substantial form
[00388] [00388] “As used here, the term" mesothelin ”relates to the 40 kDa protein, mesothelin, which is anchored in the cell membrane by a glycosylphosphatidylinositol (GPI) bond and a 31 kD amino-terminated fragment, called megakaryocyte enhancing factor (MPF). The two fragments contain N-glycosylation sites. The term also relates to a soluble linking variant of the 40 kDa carboxyl-terminal fragment also called "MPF-soluble / related mesothelin". Preferably, the term relates to a human mesothelin from Gen-Bank accession number AAHO3512.1, and its naturally cleaved portions, for example, expressed on a cell membrane, for example, a cancer cell membrane. As used in this document, "mesothelin" includes proteins comprising mutations, for example, point mutations, fragments, insertions, deletions, and full-length wild-type mesothelin splicing variants.
[00389] [00389] Unless otherwise specified, a "nucleotide sequence that encodes an amino acid sequence" includes all nucleotide sequences that are degenerate versions of one another and that encode the same amino acid sequence. The expression nucleotide sequence that encodes a protein or an RNA can also include introns in that the nucleotide sequence that encodes the protein may contain in some versions an Intron (s).
[00390] [00390] In the context of the present invention, the following abbreviations for commonly occurring nucleic acid bases are used. "A" refers to adenosine, "C" refers to cytosine, "G" refers to guanosine, "T" refers to thymidine, and "U" refers to uridine.
[00391] [00391] The term "nucleic acid" or "polynucleotide" refers to deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), or a combination of a DNA or RNA therefrom, and polymers thereof in a single-stranded form or double tape. The term "nucleic acid" includes a gene, cDNA or an mRNA. In one embodiment, the nucleic acid molecule is synthetic (for example, chemically synthesized) or recombinant. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have binding properties similar to those of the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses its conservatively modified variants (for example, degenerate codon substitutions), alleles, orthologs, SNP and complementary sequences, as well as the sequence explicitly stated. Specifically, degenerate codon substitutions can be obtained by generating sequences in which the third position of one or more (or all) selected codons is replaced by mixed base residues and / or deoxy-inosine (Batzer et al., Nucleic Acid Res. 19: 5081 (1991); Ohtsuka et a., J. Biol. Chem. 260: 2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8: 91-98 (1994) ).
[00392] [00392] The terms "peptide", "polypeptide" and "protein" are used interchangeably and relate to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that a protein or peptide sequence can comprise. Polypeptides include any peptide or protein that comprises two or more amino acids linked to each other by peptide bonds. As used herein, the term refers to short chains, which are also commonly referred to in the art as peptides, oligopeptides and oligomers, for example, and with longer chains, which are generally referred to in the art as proteins, of which there are many types. "Polypeptides" include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, polypeptide variants, modified polypeptides, derivatives, analogs, fusion proteins, among others. A polypeptide includes a natural peptide, a recombinant peptide, or a combination of these.
[00393] [00393] The term "operably linked" or "transcription control" relates to a functional link between a regulatory sequence and a heterologous nucleic acid sequence resulting in the expression of the latter. For example, a first nucleic acid sequence is operably linked to a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For example, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operatively linked DNA sequences can be contiguous with each other and, for example, when it is necessary to unite two protein coding regions, they are in the same reading frame.
[00394] [00394] The term "parenteral" administration of an immunogenic composition includes, for example, subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.) or intrasternal, intratumoral or infusion injection techniques.
[00395] [00395] The term "promoter" refers to a DNA sequence recognized by the synthetic machinery of the cell or synthetic machinery introduced, required to initiate the specific transcription of a
[00396] [00396] The term "promoter / regulatory sequence" refers to a sequence of nucleic acids that is necessary for expression of a genetic product operably linked to the promoter / regulatory sequence. In some cases, this sequence may be the main sequence of the promoter, and in other cases, that sequence may also include an enhancer sequence and other regulatory elements that are necessary for the expression of the genetic product. The promoter / regulatory sequence can, for example, be one that expresses the gene product in a tissue-specific manner.
[00397] [00397] The term "signaling domain" refers to the functional portion of a protein that acts by transmitting information within the cell to regulate cellular activity through signaling pathways defined by the generation of second messengers or functioning as effectors by response to such messengers.
[00398] [00398] The term "scFv" refers to a fusion protein comprising at least one antibody fragment comprising a variable region of a light chain and at least one antibody fragment comprising a variable region of a heavy chain , in which the variable regions of the light and heavy chain are contiguously linked, for example, via a synthetic linker, for example, a flexible short polypeptide linker, and can be expressed as a single chain polypeptide, and where scFv retains the specificity of the intact antibody from which it is derived. Unless specified, as used here, an scFv can have the VL and VM variable regions in any order, for example, with respect to the N-terminal and C-terminal ends of the fusion polypeptide, the scFv can comprise VL-ligand-VH or can comprise VH-ligand-VL.
[00399] [00399] The portion of a CAR comprising an antibody or antibody fragment thereof may exist in a variety of ways in which the antigen binding domain is expressed as part of a contiguous polypeptide chain including, for example, a single domain antibody (sdAb) fragment, a single chain antibody (scFv) and a humanized antibody (Harlow et a /., 1999, In: "Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New lorque; Harlow et al., 1989, In: "Antibodies: A Laboratory Manual", Cold Spring Harbor, New York; Houston et al., 1988, Proc.
[00400] [00400] The term "stimulation" refers to a primary response induced by the attachment of a stimulating molecule (for example, a TCR / CD3 or CAR complex) to its cognate ligand (for example, antigen molecule), thereby mediating an event signal transduction, such as, but not limited to, signal transduction via the TOR / CD3 complex or signal transduction via the appropriate NK receptor or CAR signaling domains. Stimulation can mediate altered expression of certain molecules.
[00401] [00401] The term "stimulator molecule" relates to a molecule expressed by an immune cell (for example, T cell, NK cell, B cell) that provides the cytoplasmic signaling sequence (s) ( s) that regulates (m) the activation of the immune cell in a stimulatory pathway for at least some aspect of the immune cell signaling pathway. In one aspect, the signal is a primary signal that is initiated, for example, by binding a TCR / CD3 complex to a peptide-loaded MHC molecule, and which leads to the mediation of a T cell response, including , but not limited to, proliferation, activation, differentiation, and the like. A primary cytoplasmic signaling sequence (also referred to as a "primary signaling domain") that acts in a stimulating manner may contain a signaling motif that is known as the tyrosine-based activation motif of the immunoreceptor or ITAM. Examples of a cytoplasmic signaling sequence containing ITAM that are of particular use in the invention include, but are not limited to, derivatives of CD3 zeta, FcR common gamma (FCER1G), Fc gamma Rlla, FcR beta (Fc Épsilon Rib), CD3 gamma, CD3 delta, CD3 epsilon, CD79a, CD79b, DAP10 and DAP12. In a specific CAR of the invention, the intracellular signaling domain in any one or more CARs of the invention comprises an intracellular signaling sequence, for example,
[00402] [00402] The term "transfer vector" refers to a composition of matter that comprises an isolated nucleic acid and that can be used to deliver the isolated nucleic acid within a cell. Numerous vectors are known in the art, including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids and viruses. Thus, the term "transfer vector" includes a plasmid or an autonomously replicating virus. The term is also to be understood as additionally including non-plasmid and non-viral compounds that facilitate the transfer of nucleic acid to cells, such as, for example, a polylysine compound, liposome and the like. Examples of viral transfer vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors and the like.
[00403] [00403] The term "zeta" or alternatively "zeta chain", "CD3-zeta" or "TCR-zeta" is defined as the protein provided as the GenBank accession number BAG36664.1, or equivalent residues non-human species, for example, mouse, rodent, monkey, simian and the like, and a "zeta stimulating domain" or alternatively a "CD3-zeta stimulating domain" or a "TCR-zeta stimulating domain "is defined as the amino acid residues of the cytoplasmic domain of the zeta chain, which are sufficient to functionally transmit an initial signal necessary for the activation of T cells. In one aspect, the cytoplasmic domain of zeta comprises residues 52 to 164 of the GenBank access number BAG36664.1 or the equivalent residues of a non-human species, for example, mouse, rodent, monkey, simian and the like, which are its functional orthologists. In one aspect, the "zeta-stimulating domain" or a "CD3-zeta stimulating domain" is the sequence provided as SEQ ID NO: 163 (mutant CD3 zeta). In one aspect, the "zeta stimulating domain" or a "CD3-zeta stimulating domain" is the sequence provided as SEQ ID NO: 166 (wild-type human CD3 zeta).
[00404] [00404] The term "constitutive" promoter refers to a sequence of nucleotides that, when operatively linked to a polynucleotide that encodes or specifies a genetic product, causes the genetic product to be produced in a cell in the majority or in all the physiological conditions of the cell.
[00405] [00405] The term "inducible" promoter refers to a sequence of nucleotides that, when operatively linked to a polynucleotide that encodes or specifies a genetic product, causes the genetic product to be produced in a cell substantially only when an inducer that corresponds to the promoter is present in the cell.
[00406] [00406] The term "tissue specific" promoter refers to a sequence of nucleotides that, when operatively linked to a polynucleotide that encodes or specified by a gene, causes the genetic product to be produced in a cell substantially only if the cell is a cell of the tissue type corresponding to the promoter.
[00407] [00407] The terms "cancer-associated antigen", "tumor antigen"
[00408] [00408] The term "flexible polypeptide linker" or "linker" as used refers to a peptide linker that comprises, or consists of, amino acids such as glycine and / or serine residue used individually or in combination , to link two polypeptides, for example, a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a heterologous polypeptide, or variable heavy chain and variable light chain regions. In one embodiment, the flexible polypeptide ligand is a Gly / Ser ligand and comprises the amino acid sequence (Gly-Gly-Gly-Ser) n (SEQ ID NO: 173), where n is a positive integer equal to or greater than 1. For example, n = 1, n = 2, n = 3, n = 4, n = 5, n = 6, n = 7, n = 8, n = 9 and n = 10. In one embodiment, flexible polypeptide ligands include, but are not limited to, (Gly4 Ser) 4 (SEQ ID NO: 141) or (Gly4 Ser) 3 (SEQ ID NO: 142). In another embodiment, the ligands include multiple repetitions of (Gly2Ser), (GlySer) or (Gly3Ser) (SEQ ID NO: 143). Also included in the scope of the invention are binders described in WO2012 / 138475 (incorporated by reference).
[00409] [00409] “As used in this document," transient "refers to an expression of a non-integrated transgene over a period of hours, days or weeks, in which the period of expression is less than the period of time for gene expression whether integrated into the genome or contained within a stable plasmid replicon in the cell. In the modalities, a CAR molecule is temporarily expressed in a cell, for example, host cell, for a finite period of time or number of cell replications, for example, less than 50 days (for example, less than 40 days) , 30, 25, 20, 15, 10, 5, 4, 3, 2 or less days). In one embodiment, transient expression is performed using an RNA transcribed in vitro.
[00410] [00410] As used herein, "stable" refers to the expression of a transgene that occurs for a longer period than the transient expression. In the modalities, the transgene is integrated into the genome of a cell, for example, a host cell, or contained within a replicon of a stable plasmid in the cell. In one embodiment, a transgene is integrated into the cell's genome using a gene delivery vector vector, for example, a retroviral vector as a lentiviral vector.
[00411] [00411] As used herein, the terms "treating", "treatment" and "treating" refer to reducing or improving the progression, severity and / or duration of a proliferative disease, or improving one or more more symptoms (for example, one or more discernible symptoms) of a proliferative disease resulting from the administration of one or more therapies (for example, one or more therapeutic agents, such as a CAR of the invention). In specific modalities, the terms "treat", "treatment" and "treating" refer to the improvement of at least one measurable physical parameter of a proliferative dysfunction, such as tumor growth, not necessarily discernible by the patient. In other modalities, the terms "treat", "treatment" and "treating" refer to inhibiting the progression of a proliferative dysfunction, whether physically, for example, stabilizing a discernible symptom, physiologically by, for example, stabilizing a physical parameter or both. In other embodiments, the terms "treat", "treatment" and "that treats" refer to the reduction or stabilization of tumor size or cancer cell count. The treatment need not be 100% and, in some modalities, a reduction or delay in at least one symptom of the disease or disorder by at least 50%, 60%, 70%, 80%, 90%, 95% , or 99% is sufficient to be considered within these terms.
[00412] [00412] The term "subject" is intended to include living organisms in which an immune response can be triggered (for example,
[00413] [00413] The term "transfected" or "transformed" or "transduced" refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A "transfected" or "transformed" or "transduced" cell is one that has been transfected, transformed or transduced with exogenous nucleic acid. The cell includes the main cell in question and its descendants.
[00414] [00414] The term "specifically binds" refers to an antibody, or a ligand, that recognizes and binds to the protein of a cognate-binding partner protein present in a sample, but whose antibody or ligand does not recognizes or binds substantially to other molecules in the sample.
[00415] [00415] Banners: throughout this description, various aspects of the invention can be presented in a banner format. It should be understood that the description in interval format is merely presented for reasons of convenience and brevity and should not be interpreted as an inflexible limitation on the scope of the invention. Therefore, the description of an interval should be considered as having specifically revealed all possible subintervals, as well as individual numerical values within that interval. For example, the description of a range, such as 1 to 6, should be considered to have specifically revealed sub-ranges, such as 1 to 3, 1 to 4, 1 to 5, 2 to 4, 2 to 6, 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4.5, 53 and 6.
[00416] [00416] Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified according to the Periodic Table of Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., Inside cover, and specific functional groups are generally defined as described there. In addition, the general principles of organic chemistry, as well as specific functional chemical portions and reactivity, are described in Thomas Sorrell, Organic Chemistry, University Science Books, Sausalito, 1999; Smith and March, March's Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishing, Inc., New York, 1989; and Carruthers, Some Modern Methods of Organic Synthesis, 3rd Edition, Cambridge University Press, Cambridge, 1987.
[00417] [00417] The term "alkyl;" as used herein, refers to a monovalent saturated hydrocarbon of straight or branched chain as a linear or branched group of 1 to 12, 1a 10 0 or 1 to 6 carbon atoms, referred to herein as C1-C12 alkyl , C1-C10 alkyl and C1-Cs alkyl, respectively. Examples of alkyl groups include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, iso-butyl, sec-butyl, sec-pentyl, iso-pentyl, tert-butyl, n-pentyl, neopentyl, n-hexyl, sec-hexyl, and the like.
[00418] [00418] The terms "alkenyl" and "alkynyl" as used in this document refer to unsaturated aliphatic groups analogous in length and possible substitutions to the alkyls described above, may
[00419] [00419] The term "alkoxy" as used herein, refers to a saturated straight or branched chain hydrocarbon containing 1 to 12 carbon atoms, containing an "O" terminal in the chain, for example, -O (alkyl). Examples of alkoxy groups include, without limitation, methoxy, ethoxy, propoxy, butoxy, t-butoxy or pentoxy groups.
[00420] [00420] The term "aryl" as used herein, refers to a monocyclic, bicyclic or polycyclic ring system, in which at least one ring is aromatic. Representative aryl groups include completely aromatic ring systems, such as phenyl (eg (Cs) aryl), naphthyl (eg (C10) aryl), and anthracenyl (eg (C14) aryl), and systems of rings in which an aromatic carbon ring is fused with one or more non-aromatic carbon rings, such as indanyl, phthalimidyl, naphthymidyl or tetrahydronaphthyl, and the like.
[00421] [00421] The term "carbocyclyl" as used herein, refers to a monocyclic, or fused, spiro-fused and / or bridged or polycyclic hydrocarbon ring system containing 3 to 18 carbon atoms, where each ring is completely saturated or contains one or more units of unsaturation, but where no ring is aromatic. Representative carbocyclyl groups include cycloalkyl groups (for example, cyclopentyl, cyclobutyl, cyclopentyl, cyclohexyl and the like), and cycloalkenyl groups (for example, cyclopentenyl, cyclohexenyl, cyclopentadienyl, and the like).
[00422] [00422] The term "carbonyl", as used herein, refers to —-C = O.
[00423] [00423] The term "cyan" as used herein refers to —-CN.
[00424] [00424] The terms "halo" or "halogen" as used in this document refer to fluorinated (fluorine, -F), chlorinated (chlorine, -CI), brominated (bromine, —Br), or iodized (iodine , -!).
[00425] [00425] The term "haloalkyl" as used herein, refers to a linear or branched saturated monovalent alkyl chain in which at least one carbon atom in the chain is replaced by one or more halogen atoms. In some embodiments, a haloalkyl group may comprise, for example, 1 to 12, 1 to 10, or 1 to 6 carbon atoms, referred to herein as C1- C12 haloalkyl, C1-C10 haloalkyl and C1-C6 haloalkyl. Examples of haloalkyl groups include, but are not limited to, trifluoromethyl, difluoromethyl, pentafluoroethyl, trichloromethyl, etc.
[00426] [00426] The term "haloalkoxy" refers to a straight or branched chain hydrocarbon containing 1 to 12 carbon atoms containing an "O" terminal in the chain, where at least one carbon atom in the chain is replaced by one or more halogens. Examples of haloalkoxy groups include, but are not limited to, trifluoromethoxy, difluoro-methoxy, pentafluoroethoxy, tricyloromethoxy, etc.
[00427] [00427] The term "heteroalkyl" as used herein, refers to a straight or branched saturated monovalent alkyl chain in which at least one carbon atom in the chain is replaced by a hetero atom, such as O, S, or N, provided that upon substitution, the chain comprises at least one carbon atom. In some modalities, a hateroalkyl group may comprise, for example, 1 to 12, 1 to 10, or 1 to 6 carbon atoms, referred to in this document as C1-C12 hateroalkyl, C1-C10 hateroalkyl and C1- Heteroalkyl Cs. In certain cases, a hateroalkyl group comprises 1, 2, 3 or 4 heteroatoms independently selected in place of 1, 2, 3 or 4 individual carbon atoms in the alkyl chain. Representative heteroalkyl groups include -CH2aNHC (O) CH3, -CH2CH20CH3, -CH2CH> 2 NHCH3, -CH2CHaN (CH3) CHs, and the like.
[00428] [00428] The terms "alkylene," "alkenylene", "" alkylene, "and" heteroalkylene "as used herein refer to a divalent radical of an alkyl, alkenyl, alkynyl or heteroalkyl group, respectively. Any one of a monovalent alkyl, alkynyl, alkynyl or heteroalkyl group can be an alkylene, alkenylene, alkynylene or heteroalkylene by abstraction of a second hydrogen atom of the alkyl, alkenyl, alkynyl or heteroalkyl group.
[00429] [00429] The term "heteroaryl" as used herein refers to a monocyclic, bicyclic or polycyclic ring system in which at least one ring is aromatic and comprises a heteroatom; and where no other ring is heterocyclyl (as defined below). Representative heteroaryl groups include ring systems in which (i) each ring comprises a heteroatom and is aromatic, for example, imidazolyl, oxazolyl, thiazolyl, triazolyl, pyrrolyl, furanyl, thiophenyl, pyrazolyl, pyridinyl, pyrazinyl, pyridininyl, pyrimidinyl, pyrimidine , indolizinyl, purinyl, naphthyridinyl and pteridinyl; (ii) each ring is aromatic or carbocyclyl, at least one aromatic ring comprises a heteroatom and at least one other ring is a hydrocarbon ring or, for example, indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinol , isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, pyrido [2,3-b] -1,4-o0xazin-3 (4H) -one, thiazole- [ 4,5-c] -pyridinyl, 4,5,6,7-tetrahydrothieno [2,3-c] pyridinyl, 5,6-dihydro-4H-thieno [2,3-c] lpyrrolyl, 4,5 , 6,7,8-tetrahydroquinolinyl and 5,6,7,8-tetrahydroisoquinolinyl; and (ili) each ring is aromatic or carbocyclyl, and at least one aromatic ring shares a bridge heteroatom with another aromatic ring, for example, 4H-quinolizinyl. In certain modalities, heteroaryl is a monocyclic or bicyclic ring, in which each of the said rings contains 5 or 6 ring atoms, where 1,2, 3 or 4 of said ring atoms are an independently separate heteroatom.
[00430] [00430] The term "heterocyclyl" as used herein refers to monocyclic or fused, spiro-fused and / or bicyclic and polycyclic bridged ring systems in which at least one ring is saturated or partially unsaturated (however, not aromatic) and comprises a heteroatom. A heterocyclyl can be attached to its pendant group on any heteroatom or carbon atom which results in a stable structure and any of the atoms in the ring can be optionally substituted. Representative heterocyclics include ring systems where (i) each ring is non-aromatic and at least one ring comprises a heteroatom, for example, tetrahydro-furanyl, tetrahydrothienyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl dioxan, , dioxolanil, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl and quinuclidinyl; (ii) at least one ring is non-aromatic and comprises a heteroatom and at least one other ring is an aromatic carbon ring, for example, 1,2,3 4-tetrahydroquinolinyl; and (ili) at least one ring is non-aromatic and comprises a heteroatom and at least one other ring is aromatic and comprises a heteroatom, for example, 3,4-dihydro-1H-pyran [4,3-c ] pyridinyl, and 1,2,3,4-tetrahydro-2,6-naphthyridinyl. In certain embodiments, the heterocyclyl is a monocyclic or bicyclic ring, in which each of the said rings contains 3 to 7 ring atoms in which 1, 2, 3 or 4 of said ring atoms are an independently selected hetero atom among N, O and S.
[00431] [00431] As described herein, compounds of the invention may contain "optionally substituted" portions. In general, the term "substituted", whether or not preceded by the term "optionally", means that one or more hydrogens in the designated moiety are replaced by a suitable substituent. Unless otherwise indicated, an optionally substituted group may have a suitable substituent in each substitutable position in the group, and when more than one position in any given structure can be substituted by more than one substituent selected from among a specific group, the substituent can be the same or different in each position. Combinations of substituents provided for under this invention are preferably those that result in the formation of stable or chemically viable compounds. The term "stable", as used in the present document, refers to compounds that are not substantially altered when subjected to conditions to allow their production, detection, and, in certain modalities, their recovery, purification, and use for one or more of the purposes disclosed in this document.
[00432] [00432] The term "oxo", as used herein, refers to aro.
[00433] [00433] The term "thiocarbonyl", as used in this document, refers to C = S.
[00434] [00434] "As used herein, the term" pharmaceutically acceptable salt "refers to those salts that are, within the scope of solid medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like and are proportionate to a reasonable risk / benefit ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 119, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable non-toxic acid addition salts are salts of an amino group formed by inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or organic acids
[00435] [00435] The term "solvate" refers to forms of the compound that are associated with a solvent, usually by a solvolysis reaction. This physical association can include hydrogen bonding. Conventional solvents include water, methanol, ethanol, acetic acid, DMSO, THF, diethyl ether, and the like. The compounds of Formula (1), Formula (I-a), and / or Formula (Il) can be prepared, for example, in crystalline form, and can be solvated. Suitable solvates include pharmaceutically acceptable solvates and additionally include both stoichiometric and non-stoichiometric solvates.
[00436] [00436] The term "hydrate" refers to a compound that is associated with water. Typically, the number of water molecules contained in a hydrate of a compound is in a defined ratio to the number of compound molecules in the hydrate. Therefore, a hydrate of a compound can be represented, for example, by the general formula Rx H2O, where R is the compound and where x is a number greater than 0. A given compound can form more than one type of hydrate. , including, for example, monohydrates (x is 1), lower hydrates (x is a number greater than O and less than 1, for example, hemihydrates (R-0.5 H2O)), and polyhydrates (x is a number greater than 1, for example, dihydrates (R-2 H2O) and hexahydrates (R-6 H2O)).
[00437] [00437] It will be understood that compounds that have the same molecular formula, but differ in the nature or binding sequence of their atoms or in the arrangement of their atoms in space are called "isomers". Isomers that differ in the arrangement of their atoms in space are called "stereoisomers".
[00438] [00438] Stereoisomers that are not mirror images of each other are called "diastereomers" and those that are mirror images not overlapping each other are called "enantiomers". When a compound has an asymmetric center, for example, it is linked to four different groups, and a pair of enantiomers is possible. An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by Cahn and Prelog's R and S sequencing rules, or by the way in which the molecule rotates the polarized light plane and is designated as dextrorotatory or levorotatory (that is, as isomers (+) or (-) respectively). A chiral compound can exist either as an individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a "racemic mixture".
[00439] [00439] The term "tautomers" refers to compounds that are interchangeable forms of a particular compound structure and that vary in the displacement of hydrogen atoms and electrons. Thus, two structures can be in equilibrium through the movement of mt electrons and an atom (usually H). For example, enols and ketones are tautomers because they are quickly interconverted by treatment with acid or base. Another example of tautomerism is the acid and nitro forms of phenylnitromethane, which are also formed by treatment with acid or base.
[00440] [00440] Tautomeric forms may be relevant for obtaining the ideal chemical reactivity and biological activity of a compound of interest.
[00441] [00441] Unless otherwise stated, the structures represented in this document must also include all isomeric (for example, enantiomeric, diastereomeric, and geometric (or conformational) shapes) of the structure; for example, the configurations of R and S for each asymmetric center, double bond isomers Z and E, and conformational isomers Z and E. Therefore, unique stereochemical isomers as well as enantiomeric, diastereomeric and geometric (or conformational) mixtures of the compounds present are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention. In addition, unless otherwise stated, the structures represented in this document are also intended to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds that have the present structures that include replacing hydrogen with deuterium or tritium, or replacing a carbon with a carbon enriched with * ºC- or! ºC are within the scope of this invention. In one embodiment, the hydrogen atoms present within any of the compounds disclosed in the present document (for example, a compound of Formula (1)) are isotopically enriched in deuterium. Such compounds are useful, for example, as analytical tools, as probes in biological assays, or as therapeutic agents according to the present invention.
[00442] [00442] When a specific enantiomer is preferred, it can, in some modalities, be supplied substantially free of the corresponding enantiomer and can also be referred to as "optically enriched". "Optically enriched" as used herein means that the compound is made up of a significantly greater proportion of an enantiomer. In certain embodiments, the compound consists of at least about 90% by weight of a preferred enantiomer. In other embodiments, the compound consists of at least about 95%, 98% or 99% by weight of a preferred enantiomer. Preferred enantiomers can be isolated from racemic mixtures by any method known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts or prepared by asymmetric syntheses. See, for example, Jacques et al., Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen, et al., Tetrhedron 33: 2,725 (1977); Eliel, E.-L. Stereochemistry of Carbon Compounds (McGraw-Hill, NY, 1962); Wilen, S.H. Tables of Resolving Agents and Optical Resolutions page 268 (E.L. Eliel, Ed., Univ. Of Notre Dame Press, Notre Dame, IN 1972).
[00443] [00443] These and other exemplary substituents are described in more detail in the Detailed Description, Figures, Examples and Claims. The invention is not intended to be limited in any way by the exemplary listing of substituents. COF1I / CRBN binding polypeptide, COF2 / CRBN binding polypeptide or COF3 / CRBN binding polypeptide
[00444] [00444] Disclosed herein are, inter alia, fusion polypeptides that include a compound of Formula (1), a (COF1) -binding polypeptide / CRBN, a compound of Formula (II), a -binding polypeptide ( COF2) / CRBN, or a compound of Formula (III), (COF3) / CRBN binding polypeptide. In the modalities, in the presence of COF1 or COF (for example, thalidomide and derivatives thereof, for example, lenalidomide, pomalidomide and thalidomide)), or in the presence of COF3 (for example, a compound disclosed in Table 29) the COF1 / CRBN-binding polypeptide / COF2 / CRBN or COF3 / CRBN in the fusion polypeptide increases post-translational modification and / or degradation of the fusion polypeptide. In some embodiments, the post-translational modification may include ubiquitination (for example, mono- or poly-ubiquitination) of one or more amino acid residues, for example, one or more of lysine or methionine, in the fusion polypeptide (for example, a or all: all or part of a heterologous polypeptide and / or the COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide).
[00445] [00445] In certain embodiments, one or more lysine residues of the fusion polypeptide (for example, all or part of a heterologous polypeptide and / or the COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide) are ubiquitinated. In some embodiments, one or more methionine residues of the fusion polypeptide (for example, all or part of a heterologous polypeptide and / or the COFI1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide) are ubiquitinated. (for example, mono or poly-ubiquitinated).
[00446] [00446] Without adhering to the theory, in some modalities, the inactivation, for example, degradation, of a fusion polypeptide described in this document can include one, two, three or all of the following steps, for example, in a cell or a reaction mixture: (1) association of the fusion polypeptide comprising the COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN to one or more subunits (for example, CRBN) of a complex ubiquitin ligase (eg, a ubiquitin ligase E3 complex) in the presence of COF1 or COF 2 (eg, thalidomide and derivatives thereof (eg, lenalidomide)) or in the presence of COF3 (eg, a compound disclosed in Table 29); (2) ubiquitination of the fusion polypeptide (for example, ubiquitination in a heterologous polypeptide and / or the COFI / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN), thereby providing a ubiquitinated fusion polypeptide; and (3) degradation of the ubiquitinated fusion polypeptide.
[00447] [00447] In some embodiments, any COF1I / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide described in this document increases a post-translational modification and / or degradation of the fusion polypeptide in the presence of COF1, COF2 or COF3, for example, in relation to modification and / or degradation in the absence of COF1, COF2 or COF3. In one embodiment, the COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide increases the selective ubiquitination of the fusion polypeptide in the presence of COF1, COF2 or COF3, for example, in relation to ubiquitination in absence of COF1, COF2 or COF3.
[00448] [00448] In some embodiments, a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide is derived from an amino acid sequence and / or structural motif (for example, a domain) that binds to one or more components of a ubiquitin ligase complex (for example, the ubiquitin ligase E3 complex) in the presence of COF1, COF2 or COF3. In some embodiments, COF1 or COF2 is a class of compound thalidomide (eg, lenalidomide, pomalidomide and thalidomide), for example, as described in this document. In some embodiments, COF3 is a compound disclosed in Table 29. In some embodiments, the COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide comprises a zinc finger domain (for example, a zinc finger domain zinc fingerprint 2) or a portion thereof. In some embodiments, the COFI / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide comprises a B curve. In some embodiments, the COF1I / CRBN or COF2 / CRBN binding polypeptide comprises a B curve of a lkaros family of transcription factors, for example, IKZF1 or IKZF3, or a sequence substantially identical to the same (for example, at least 85%, 87, 90, 95, 97, 98, 99, or 100% identical to the same). In some embodiments, the COF1 / CRBN or COF2 / CRBN-binding polypeptide comprises a B-clip format of a lIkaros family of transcription factors, for example, IKZF1 or IKZF3, or a substantially identical sequence (for example, by minus 85%, 87, 90, 95, 97, 98, 99, or 100% to a clip B format of IKZF1 or IKZF3, for example, as described in Kronke, J. et al. (2014) Science 343 (6168): 301-5). In some embodiments, the COF3 / CRBN-binding polypeptide comprises an IKZF2 B curve, or a substantially identical sequence to it (for example, at least 85%, 87, 90, 95, 97, 98, 99, or 100% identical to the same). In some embodiments, the COF3 / CRBN-binding polypeptide comprises an IKZF2 clip B format, or a sequence substantially identical to the same (for example, at least 85%, 87, 90, 95, 97, 98, 99 , or 100% identical to the same).
[00449] [00449] In some embodiments, the polypeptide binding to
[00450] [00450] In some embodiments, the COF3 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues
[00451] [00451] In some embodiments, the exemplary full-length strings of IKZF1, IKZF2, IKZF3, IKZF4 and IKZF5 or a fragment thereof are provided in Table 1.
[00452] [00452] This document discloses, inter alia, degradation compounds that can, for example, increase the ubiquitination and / or degradation of fusion proteins including the degradation tag.
[00453] [00453] In some embodiments, the degradation compound comprises a member of the thalidomide class of compounds. In some embodiments, members of the class of thalidomide compounds include, but are not limited to, lenalidomide (CC-5013), pomalidomide (CC-4047 or ACTIMID), thalidomide, or salts or derivatives thereof. In some embodiments, the degradation compound may be a mixture of one, two, three, or more members of the thalidomide class of compounds. Thalidomide analogues and the immunomodulatory properties of thalidomide analogues are described in Bodera and Stankywicz, Recent Pat Endocr Metab Immune Drug Discov. September 2011; 5 (3): 192-6, which is incorporated in this document as a reference in its entirety. The structural complex of thalidomide and ubiquitin E3 analogs is described in Gandhi et al., Br J Haema-tol. March 2014; 164 (6): 811-21, which is incorporated in this document as a reference in its entirety. Modulation of ubiquitin ligase E3 by thalidomide analogs is described in Fischer et al., Nature. August 20147; 512 (7512): 49-53, which is incorporated in this document as a reference in its entirety.
[00454] [00454] In some embodiments, the degradation compound comprises a compound of Formula (!): X (R »
[00455] [00455] In some modalities, XKé O.
[00456] [00456] In some embodiments, R 'is C1-Cs alkyl, C2-Cs alkynyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, carbocyclyl, heterocyclyl, aryl or heteroaryl, each of which is independently and optionally substituted by 1 to 12 Rº (for example, 1 Rº, 2Rº, 3 Ri, 4 Rº, 5Rº, 6Rº, 7 Rº, BR, 9Rº1, 10 Rº, 11 Rº or 12 Rº). In some modalities, R 'is heterocyclyl. In some embodiments, R 'is a 6-membered heterocyclic or a 5-membered heterocyclic. In some embodiments, R 'is a 6-membered heterocyclyl or 5-membered heterocyclyl, each of which is independently and optionally substituted by 1 to 6 Rº (for example, 1 Rº, 2R% º, 3 R% 1, 4 Rº, 5Rº or 6 Rº). In some embodiments, R 'is a nitrogen-containing heterocyclyl. In some embodiments, R 'is piperidinyl (for example, piperidine-2,6-dionyl).
[00457] [00457] In some modalities, each Rº and Rº it is independently hydrogen. In some modalities, R º and R2 º together with the carbon to which they are attached form a carbon group.
[00458] [00458] In some embodiments, each Rº is independently C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-Cs heteroalkyl, halo, cyano, -C (O) Rô, -C (O0) ORE , -OR8, -N (RO) (R ), -C (O) N (RURP), - N (R) C (O) RA, -S (O) .RE, -S (O) .N (RNRP), or -N (RIS (O)., RE, where each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by 1 to 12 R $ (for example, 1 R6, 2 Rº, 3 Rô, 4 Rº, 5 Rº, 6 Rô, 7 Rº, 8 Rº, 9 R $ 6, 10 R $, 11 Rº or 12 R $). In some modalities, Rº is heteroalkyl C1-Cs, -N (Rº) ( RP) or -N (Rº) C (O) RA In some embodiments, Rº is C1-Cs heteroalkyl (for example,
[00459] [00459] In some embodiments, each R is independently C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-Cs heteroalkyl, halo, cyano, oxo, C (O) R, -C (O0) ORE, OR, -N (RºI (RP), -C (O) N (Rº) (R2), - N (RO) C (O) RA, S (O) .RE, -S (O) N ( RNHRP), -N (ROIS (O) .RE, carbocyclyl, heterocyclyl, aryl, or heteroaryl, where each alkyl, alkenyl, alkynyl, heteroalkyl, carbocyclyl, heterocyclyl, aryl and heteroaryl is independent and optionally substituted by 1 to 12 R '(e.g., 1 R', 2R /, 3 R /, 4R7, 5R ', 6R', 7R /, 8R '/, 9R /, 10R /, 11Rº or 12R).
[00460] [00460] In some embodiments, each Rº is independently C1-C6 alkyl, oxo, cyano, -OR8, -N (Rº) (R ), -C (O) N (RNRº), -N (Rº) C ( O) RA, aryl or heteroaryl, in which each aryl and heteroaryl is independent
[00462] [00462] In one embodiment, X is O. In one embodiment, R 'is heterocyclyl (for example, piperidinyl-2,6-dionyl). In some modalities, R º and R together with the carbon to which they are attached they form a carbonyl group. In one mode, n is 1. In one mode, R is -N (Rº) (RP) (for example, -NH2). In one embodiment, the degradation compound comprises pomalidomide, for example, 4-amino-2- (2,6-dioxopiperidin-3-yl) isoindoline-1,3-dione, or a pharmaceutically acceptable salt thereof. . In one embodiment, the degradation compound is pomalidomide, for example, according to the following formula: o
[00463] [00463] In one embodiment, X is O. In one embodiment, R 'is heterocyclyl (for example, piperidinyl-2,6-dionyl)). In one embodiment, R º and R together with the carbon to which they are attached they form a carbonyl group. In one embodiment, n is 0. In a modality, the degradation compound comprises thalidomide, for example 2- (2,6-dioxopiperidin-3-yl) isoindoline-1,3-dione, or a pharmaceutically acceptable salt of the same. In one embodiment, the degradation product is thalidomide, for example, according to the following formula: o o "Cox Fº o.
[00464] [00464] In one embodiment, X is O. In one embodiment, R 'is heterocyclyl (for example, piperidine-2,6-dionyl) .. In one embodiment, each R and R º is independently hydrogen. In one embodiment, n is 1. In one embodiment, Rº is C1-Cs heteroalkyl (for example, CHaNHC (O) CH,> - phenyl-t-butyl). In one mode, R is hetero C1-Cs
[00465] [00465] In some embodiments, the degradation compound is a compound of Formula (I-a): (Ro o "om
[00466] [00466] In some modalities, XKé O.
[00467] [00467] M is absent, M is C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl or C1-Cs heteroalkyl, where each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by 1a6Rº (by example, 1 Rà, 2Rº, 3 Rº, 4Rº, 5Rº or 6Rº). In some modalities, M is absent.
[00468] [00468] In some embodiments, Ring A is carbocyclyl, heterocyclyl, aryl or heteroaryl, each of which is independent and optionally substituted by 1 to 6 Rº (for example, 1 Rº, 2 Ri, 3 R4, 4 Rº, Rº or 6 Rº *). In some embodiments, Ring A is heterocyclyl. In some embodiments, Ring A is heterocyclyl, for example, a 6-membered heterocyclyl or a 5-membered heterocyclyl. In some modalities, Ring A is a heterocyclyl containing nitrogen. In some embodiments, Ring A is piperidinyl (for example, piperidine-2,6-dionyl).
[00469] [00469] In some embodiments, M is absent and Ring A is heterocyclyl (for example, piperidinyl, for example, piperidine-2,6-dionyl).
[00470] [00470] In some modalities, each Rºº and R it is independently hydrogen. In some embodiments, R º and R º together with the carbon to which they are attached form a carbonyl group.
[00471] [00471] In some embodiments, R * º is hydrogen, C1-Cs alkyl, C2-C6 alkenyl, C2-C alkynyl, C1-Cs6 heteroalkyl, halo, cyan, - C (O) R, -C (0) ORE , -OR8, -N (RºNRP), -C (O) N (RNRP), -N (RO) C (O) RA, -S (O) .RE, -S (O) .N (RENRP), or -N (R9) S (O) .RE, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by 1 to 12 R $ (for example, 1 Rº, 2 Rº, 3 R $, 4 R $, 5Rô, 6 Rº, 7 Rº, 8 Rº, 9 Rº, 10 Rô, 11 Rô or 12 R $). In some embodiments, R * º is hydrogen, -N (Rº) (RP) or -N (Rº) C (O) RA. In some modalities, R * º is hydrogen. In some embodiments, R º is -N (Rº) (R ) (For example, -NH2). In some embodiments, R * º is -N (Rº) C (O) Rº (for example, NHC (O) CH; 3).
[00472] [00472] In some modalities, each Rº is independently
[00473] [00473] In some embodiments, each Rº is independently C1-Cs alkyl, C2-Cs alkenyl, C2-Cs6 alkynyl, C1-Cs heteroalkyl, halo, cyano, oxo, C (O) Rô, -C (O0) ORE, OR, -N (RºI (RP), -C (O) N (Rº) (R2), - N (RO) C (O) RA, S (O) .RE, -S (O) N ( RNHRP), -N (ROIS (O) .RE, carbocyclyl, heterocyclyl, aryl, or heteroaryl, where each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl and heteroaryl is independently and optionally substituted by 1 to 12 Rº (e.g. 1 Rº /, 2Rº, 3 R ', 4Rº, 5R', 6R /, 7R ', 8R /, 9R /, 10R /, 11 R' or 12R).
[00474] [00474] In some embodiments, each Rº is independently C1-Ce6 alkyl, oxo, cyano, -OR8, -N (Rº) (R ), -C (O) N (RENR ), -N (Rº) C (O) RS, aryl or heteroaryl, where each aryl and heteroaryl is independent and optionally replaced by 1 to 6 Rº (for example, 1 Rô, 2 Rô, 3 R8, 4 R &, 5R8 or 6 R $).
[00475] [00475] In some modalities, n is O or 1. In some modalities, n is 0. In some modalities, n is 1.
[00476] [00476] In some embodiments, the degradation compound is a compound of Formula (Ill): o PROEXxi R. RE (1), or a pharmaceutically acceptable salt, ester, hydrate or tautomer thereof, where:
[00477] [00477] In some embodiments, the degradation compound of Formula (III) is a compound of Formula (III-a): o Px: R RP (Ill-a), or a pharmaceutically acceptable salt, ester, hydrate or tautomer of even, where: X1 is CR3; ===== - it is optionally a double bond when X: is CR3 and Ra is absent; each R: is independently C1-Cs alkyl, C1-C6 haloalkyl, C1-Cs hydroxyalkyl or halo, or R2 is hydrogen, C1-Cs alkyl, Ce-C10 aryl, heteroaryl with or 6 members comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cs carbocyclyl or 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, where the alkyl is optionally substituted by one or more Rs; and aryl, heteroaryl, carbocyclyl and heterocycloalkyl are optionally substituted by one or more Rs; R3 is hydrogen or R; 3 is absent when ====== is a double bond; each Ra is independently selected from - C (O) ORs, -C (O) NReR6, -NREC (O) R6, C6-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 4 heteroatoms selected from O , N, and S, C3-Cg carbocicyl, and 5 to 7 membered heterocyclic ring comprising 1 to 3 heteroatoms selected from O, N, eS, in which aryl, heteroaryl, carbocicyl and heterocicyl are optional. finally replaced by one or more Rr;
[00478] [00478] In one embodiment, the compound of Formula (Ill) is a compound of Formula (Ill-b): o o Ws.
[00479] [00479] In one embodiment, the compound of Formula (Ill) is a compound of Formula (Ill-c): oo to OUT: í RA (Ill-c), or to salt, hydrate, solvate, pro-
[00480] [00480] In one embodiment, the compound of Formula (Ill) is a compound of Formula (II-d): (R1) to N o 2 O RÓ (Ill-d), or a salt, hydrate, solvate, prodrug, stereoisomer and pharmaceutically acceptable tautomer thereof, wherein R1, R2, q and subvariables thereof are defined as described for Formula (III).
[00481] [00481] In one embodiment, the compound of Formula (Ill) is a compound of Formula (Ill-e): o o (Ria no O
[00482] [00482] In some Formula (Ill) modalities, Xr is CHené1. In another modality, X, it is CH, right 1, egé O.
[00483] [00483] In some modalities of Formula (III), XKr is CH, right l, and q is O or 1. In another modality, X; is CH, right 1, g9 is 0 or 1, and D is C1- Cs alkyl. In another embodiment, X: is CH, right 1, gq is 0 or 1, Ri is C1-Cs alkyl, and R2 is C1-Cs alkyl optionally substituted by one to three Ra. In another embodiment, X, is CH, right 1, gq is 0 or 1, R: 1 is C1-Cs alkyl, and R2 is C1-C6 alkyl substituted by one to three Ra.
[00484] [00484] In another modality, X; is CH, right 1, gender 0, and R2 is C1-Cs alkyl optionally substituted by one to three Ra. In another way,
[00485] [00485] In some modalities of the above formulas, X is CH, right 1, 9 is O or 1, R1 is C1-Cs alkyl, R2 is C1-Cs alkyl optionally substituted by one to three Ru, and each R, is independently selected from -C (O) ORs, Ce6-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cg carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, in which aryl, heteroaryl, carbocyclyl and heterocyclyl are optionally substituted by one to three Rr.
[00486] [00486] In some modalities of Formula (III), X1 is CH, right 1, q is 0 or 1, R1 is C1-Cs alkyl, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from -C (O) ORs, Ce6-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cs carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, carbo-cyclyl and heterocyclyl groups are optionally substituted by one to three Rx.
[00487] [00487] In some modalities of Formula (III), X1 is CH, right 1, q is 0 or 1, R: 1 is C1-Cs alkyl, R2 is C1-Cs6 alkyl optionally substituted by one to three Ru, and each Ra is independently selected from Ce-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cs carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 selected heteroatoms among O, Ne S, in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R7.
[00488] [00488] In some modalities of Formula (III), X1 is CH, right 1, q is O or 1, R1 is C1-Cs alkyl, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from Cs-C1o aryl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, Ne S, (C3-Csg) cycloalkyl and heterocycloalkyl with 5 to 7 members comprising 1 to 3 heteroatoms sele - cited from O, Ne S, in which the aryl, heteroaryl, cycloalkyl and heterocycloalkyl groups are optionally substituted by one to three R7.
[00489] [00489] In some modalities of Formula (III), X1 is CH, right 1, q is 0, and R2 is Cs6-C10 aryl, C3-Cg carbocyclyl or heterocyclic with 5 to 7 members comprising 1 to 3 hetero atoms selected from O, Nes, where aryl, carbocyclyl and heterocyclyl are optionally substituted by one to three Rs. In yet another embodiment, X, is CH, n is 1, g9É is O, and Ro is C6-C10 aryl, Ca-Cg carbocyclyl or 5- to 7-membered heterocycly comprising 1 to 3 heteroatoms selected from O, NeS.
[00490] [00490] In some modalities of Formula (III), X1 is CH, right 1, q is 0, and R2 is Cs-C10 aryl optionally substituted by one to three R5. In another modality, X: is CH, right 1.9 is O, and Ro is a 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Nes optionally substituted by one to three Rs. In yet another modality, X; is CH, right 1, gq is 0, and R2 is C3-Cs carbocyclyl optionally substituted by one to three Rs. In another modality, X; is CH, n is 1.9 is O, and R2 is 5- to 7-membered heterocyclic comprising 1 to 3 heteroatoms selected from O, Ne S, optionally substituted by one to three Rs.
[00491] [00491] In some modalities of Formula (III), X1 is CH, right 1, q is O or 1, R1 is C1-Cs alkyl, and R2 is Ce6-C10 aryl, C3-Cg carbocyclyl or heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, where aryl, carbocyclyl and heterocyclyl are optionally substituted by one to three Rs. In yet another modality, X; is CH, right 1.9 is 0 or 1, R: is C1-Cs alkyl, and Ro is Cs-C10o aryl, C3-Cg carbocyclyl or 5- to 7-membered heterocyclic comprising 1 to 3 heteroatoms selected from O, Ne S.
[00492] [00492] In some modalities of Formula (III), X1 is CH, right 1, q is 0 or 1, R1 is C1-Cs alkyl, and R2 is C6-C10 aryl optionally substituted by one to three R5. In another modality, X: is CH, right 1.9 is 0, and Ra is a 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S optionally substituted by one to three Rs. In yet another embodiment, X, is CH, right 1.9 is 0 or 1, Rr is C1-Cs6 alkyl, and R2 is C3-Cg carbocyclyl optionally substituted by one to three Rs. In another modality, X is CH, right 1.9 is 0 or 1, D C1-Cs alkyl, and R2 is a 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, N and S, optionally substituted by a to three Rs.
[00493] [00493] In some modalities of Formula (III), X1 is CH, right 1, q is 0, and R2 is C1-Cs alkyl optionally substituted by one to three Ra. In another modality, X; is CH, 1.9 is 0, and R2 is C1-Cs alkyl substituted by one to three Ra.
[00494] [00494] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs6 alkyl optionally substituted by one to three Ra, and each R. is independently selected from -C (O) JORs, Ce-C1o aryl, 5 or 6 membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cg carbocyclyl and 5 to 7 membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R's.
[00495] [00495] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from -C (O) ORs, Ce-C109 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 selected heteroatoms
[00496] [00496] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl optionally substituted by one to three Ru, and each R «is independently selected from halo, -OH, Ces-C1o aryl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cs carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R's.
[00497] [00497] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from halo, OH, C6 -Ca1o aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cs carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S , in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R ;.
[00498] [00498] In some modalities of the formulas above, X, is CH, right 1, N1 is 1, g9 is O, R2 is C1-Cs6 alkyl optionally substituted by one to three Ra, and each Ra is independently selected from halo, -OH, Ce6-C1o aryl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cs carbocyclyl and heterocyclic with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, carbo-cyclyl and heterocyclyl groups are optionally substituted by one to three Rx.
[00499] [00499] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9géoO, D C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from halo, -OH, Cs6-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cg carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Nes, where the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R; 7.
[00500] [00500] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl optionally substituted by one to three R1, and each R, is independently selected from Ce-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cs carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Nes, in which groups aryl, heteroaryl, carbocyclyl and heterocyclyl are optionally substituted by one to three R's.
[00501] [00501] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from Ceg-C10 aryl, heteroaryl with 5 or 6 members comprising 1 to 3 hetero atoms selected from O, NeSsS, C3-Cg carbocyclyl and heterocyclic with 5 to 7 members comprising 1 to 3 hetero atoms selected from O, Ne S, in which the aryl groups, heteroaryl, carbocyclyl and heterocyclyl are optionally substituted by one to three R's.
[00502] [00502] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl optionally substituted by one to three Ra, and each R, is independently selected from halo, -OH, phenyl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cg carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, NeS, in which the aryl groups , heteroaryl, carbocyclyl and heterocyclyl are optionally substituted by one to three R ;.
[00503] [00503] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from halo, -OH, phenyl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cg carbocyclyl and 5- to 7-membered heterocyclic comprising 1 to 3 heteroatoms selected from O, Ne S, where the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R ;.
[00504] [00504] In some modalities of Formula (III), X1 is CH, right 1, n1é1, genoO, R is C1-Cs alkyl optionally substituted by one to three Ra, and each R, is independently selected from halo, -OH, phenyl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cg carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R's.
[00505] [00505] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9géO, D C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from halo, -OH, phenyl, heteroaryl with 5 or 6 members comprising 1 to 3 hetero atoms selected from O, Ne S, C3-Cs carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 hetero atoms selected from O, Ne S, in which the groups phenyl, heteroaryl, carbocyclyl and heterocyclic are optionally substituted by one to three R7.
[00506] [00506] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl optionally substituted by one to three Ra, and each Ra is independently selected from phenyl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cg carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne
[00507] [00507] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from phenyl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, NeS, C3-Cg carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, in which the phenyl, heteroaryl, carbocyclic groups and heterocyclyl are optionally substituted by one to three R7.
[00508] [00508] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9gé0O, R is C1-Cs alkyl optionally substituted by one to three Ra, and each Ra is independently selected from phenyl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cg carbocyclyl and 5 to 7 members comprising 1 to 3 heteroatoms selected from O, NeS, in which the phenyl, heteroaryl, carbocyclic groups and heterocyclyl are optionally substituted by one to three R7.
[00509] [00509] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9géoO, D C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from phenyl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, NeS, C3-Cg carbocyclyl and 5- to 7-membered heterocyclics comprising 1 to 3 heteroatoms selected from O, Ne S, in which the phenyl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally replaced by one to three R .;
[00510] [00510] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs6 alkyl optionally substituted by one to three Ra, and each Ra. is independently selected from 5 or 6-membered phenyl and heteroaryl comprising 1 to 3 selected heteroatoms
[00511] [00511] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from phenyl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, NeS, C3-Cg carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, where the phenyl and heteroaryl groups are optionally replaced by one to three R7.
[00512] [00512] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9gé0O, R is C1-Cs alkyl optionally substituted by one to three Ra, and each Ra is independently selected from phenyl and heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, Ne S, in which the phenyl and heteroaryl groups are optionally substituted by one to three R ;.
[00513] [00513] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9é0O, D C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from phenyl and heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cg carbocyclyl and 5 to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, where the phenyl and heteroaryl groups are optionally substituted by one to three Rr.
[00514] [00514] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl optionally substituted by one to three Ra, and each Ra is phenyl optionally substituted by one to three R7.
[00515] [00515] In some modalities of Formula (III), X1 is CH, right 1, q is O, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is phenyl optionally substituted by one to three R ;.
[00516] [00516] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9géOO, D C1-Cs alkyl optionally substituted by one to three Ra, and each Ra is phenyl optionally substituted by one to three R ;.
[00517] [00517] In some modalities of Formula (III), X1 is CH, right 1, n1é1,9é0, D C1-Cs alkyl substituted by one to three Ra, and each Ra is phenyl optionally substituted by one to three Rz7.
[00518] [00518] In some modalities of Formula (Ill), X1 is CHené . In another modality, X; is CH, right 2, and gender O. In yet another modality, X; is CH, right 2, and gq is O or 1. In another embodiment, X, is CH, n is 2,960 or 1, eR; is C1-Cs alkyl.
[00519] [00519] In some modalities of Formula (III), X1 is CH, right 2, q is 0 or 1, R1 is C1-Cs alkyl, and R2 is C1-Cs alkyl optionally substituted by one to three Ra. In another embodiment, X: is CH, right 2, gender O or 1, R1 is C1-Cs alkyl, and R2 is C1-Cs alkyl substituted by one to three Ra.
[00520] [00520] In some modalities of Formula (III), X1 is CH, right 2, q is 0, and R2 is C1-Cs alkyl optionally substituted by one to three Ra. In another modality X: it is CH, right 2, gender 0, and R2 is C1-Cs alkyl substituted by one to three Ra.
[00521] [00521] In some modalities of Formula (III), X1 is CH, right 2, q is 0 or 1, R1 is C1-Cs alkyl, R2 is C1-Cs6 alkyl optionally substituted by one to three Ra, and each Ra is independently selected from -C (O0) ORs, Ce6-C10 aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Ne S, C3-Cs carbocyclyl and 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R; 7.
[00522] [00522] In some modalities of Formula (III), X1 is CH, right 2, q is O or 1, R1 is C1-Cs alkyl, R2 is C1-Cs alkyl substituted by one to three Ru, and each Ra is independently selected from -C (O) ORs,
[00523] [00523] In some modalities of Formula (III), X1 is CH, right 2, q is 0 or 1, R: 1 is C1-Cs alkyl, R2 is C1-Cs6 alkyl optionally substituted by one to three Ra, and each Ra is independently selected from Cs-C1o aryl, heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, N and S, C3-Cs carbocyclyl and heterocyclyl with 5 to 7 members comprising 1 to 3 selected heteroatoms among O, Ne S, in which the aryl, heteroaryl, carbocyclyl and heterocyclyl groups are optionally substituted by one to three R7.
[00524] [00524] In some modalities of Formula (III), X1 is CH, right 2, q is O or 1, R: is C1-Cs alkyl, R2 is C1-Cs alkyl substituted by one to three Ra, and each Ra is independently selected from Cs-C1o aryl, 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S, (C3-Cg) cycloalkyl and heterocycloalkyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, in which the aryl, heteroaryl, cycloalkyl and heterocycloalkyl groups are optionally substituted by one to three R7.
[00525] [00525] In some modalities of Formula (III), X 'is CH, right 2, q is 0, and R2 is Cs6-C10o aryl, C3-Cg carbocyclyl or heterocyclic with 5 to 7 members comprising 1 to 3 selected heteroatoms among O, NesS, where aryl, carbocyclyl and heterocyclic are optionally substituted by one to three Rs. In yet another embodiment, X, is CH, n is 2.9 is O, and R2 is C6-C10 aryl, Ca-Cg carbocyclyl or 5- to 7-membered heterocycly comprising 1 to 3 heteroatoms selected within
[00526] [00526] In some modalities of Formula (III), X1 is CH, right 2, q is O, and Ro is Cs-C10o aryl optionally substituted by one to three Rs. In another modality, X is CH, right 2, q is O, and Ro is a 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, Nes optionally substituted by one to three Rs. In yet another modality, X; is CH, n is 2, gq is 0, and R2 is C3-Cg carbocyclyl optionally substituted by one to three Rs. In another modality, X, is CH, right 2,9 is É 0, and R2 is a 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, N and S, optionally substituted by one to three Rs.
[00527] [00527] In some modalities of Formula (III), X1 is CH, right 2, q is 0 or 1, R1 is C1-Cs alkyl, and R2 is C6-C10 aryl, C3-Cg carbocyclyl or heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S, where aryl, carbocyclyl and heterocyclyl are optionally substituted by one to three Rs. In yet another modality, X; is CH, n is 2, q is 0 or 1, R: is C1-Cs alkyl, and Ro is Cs-C1o aryl, C3-Cg carbocyclyl or heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O) Ne S.
[00528] [00528] In some modalities of Formula (III), X1 is CH, right 2, q is 0 or 1, R1 is C1-Cs alkyl, and R2 is C6-C10 aryl optionally substituted by one to three R5. In another modality, X is CH, 2.9 is 0, and R2 is a 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N and S optionally substituted by one to three Rs. In yet another embodiment, X, is CH, right 2, gq is 0 or 1, R is C1-Cs6 alkyl, and R2 is C3-Cs8 carbocyclyl optionally substituted by one to three R5. In another modality, X, is CH, right 2.9 is 0 or 1, R is C1-Cs alkyl, and R2 is heterocyclyl with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, N and S, optionally substituted by one to three Rs.
[00529] [00529] In some Formula (III) modalities,
[00530] [00530] In some modalities of Formula (III),
[00531] [00531] In some modalities of Formula (Ill), (Ri). MINUTES:% E CS is AO! Ro | R $: “KO RO E Ur, a
[00532] [00532] A degradation compound can comprise one or more chiral centers or present itself as one or more stereoisomers. In some embodiments, the degradation compound comprises a single chiral center and is a mixture of stereoisomers, for example, a stereoisomer R and a stereoisomer S. In some embodiments, the mixture comprises a ratio between stereoisomers R and stereoisomers S, for for example, a ratio of about 1: 1 between stereoisomers R and stereoisomers S (ie, a racemic mixture). In some embodiments, the mixture comprises a ratio between stereoisomers R and stereoisomers S of about 51:49, about 52: 48, about 53:47, about 54:46, about 55:45, about 60:40, about 65:35, about 70:30, about 75:25, about 80:20, about 85:15, about 90:10, about 95: 5, or about 99 :1. In some embodiments, the mixture comprises a ratio between S stereoisomers and R stereoisomers of about 51:49, about 52: 48, about 53:47, about 54:46, about 55:45, about 60:40, about 65:35, about 70:30, about 75:25, about 80:20, about 85:15, about 90:10, about 95: 5, or about 99 :1. In some embodiments, the degradation compound is a single
[00533] [00533] In some embodiments, the degradation compound (for example, a compound of Formulas (1), (Ia), (III), (Ill-a), (Ill-b), (Ill-c), ( Ill-d), or (Ill-e)) is not attached to a linker or linker. In some embodiments, the degradation compound (for example, a compound of Formula (1), (Ia), (III), (Ill-a), (Ill-b), (Ill-c), (I11 -d), or (Ill-e)) does not comprise another portion, for example, a binder, a bleaching agent, or a dimerization capable portion.
[00534] [00534] In one embodiment, the degradation compound is a compound of Formula (1) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (l-a) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (Ill) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (Ill-a) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (Ill-b) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (Ill-c) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (Ill-d) or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound is a compound of Formula (Ill-e) or a pharmaceutically acceptable salt thereof.
[00535] [00535] Exemplary degradation compounds of the description (for example, a compound of Formula (III), (Ill-a), (Ill-b), (Ill-c), (Ill-d), or (Ill- e) or a pharmaceutically acceptable salt thereof include those in Table 29.
[00536] [00536] In another aspect, the degradation compound is a compound of Formula (Il):
[00537] [00537] In some modalities, X is O.
[00538] [00538] In some embodiments, R 'is C1-Cs alkyl, C2-C6 alkynyl, C2-Cs alkynyl, C1-Cs heteroalkyl, carbocyclyl, heterocyclyl, aryl or heteroaryl, each of which is independently and optionally substituted by 1 to 12 Rº (for example, 1 R4, 2Rº, 3R4, 4 Ri, 5Rº, 6R% º, 7 Ri, 8 Ri, 9Rº1, 10Rº, 11 Rº or 12 Rº). In some modalities, R 'is C1-Cs alkyl or heterocyclyl. In some embodiments, R 'is C1-Cs alkyl (for example, methyl or ethyl) replaced by Rº. In some modalities, R is C1-Cs alkyl (for example, methyl or ethyl) replaced by 1 to 6 Rº. In some embodiments, R * is heterocyclyl. In some embodiments, R 'is a 6-membered heterocyclic or 5-membered heterocyclic. In some embodiments, R 'is a 6-membered heterocyclyl or a 5-membered heterocyclyl optionally substituted by 1 to 6 Rº (for example, 1 Rº, 2Rº, 3 R $, 4 Rº, 5Rº or 6 Rº). In some embodiments, R 'is a nitrogen-containing heterocyclyl. In some embodiments, R 'is piperidinyl (for example, piperidine-2,6-dionyl).
[00539] [00539] In some modalities, each Rº and Rº is independently hydrogen. In some modalities, Rºº and R º together with the carbon to which they are attached they form a carbon group.
[00540] [00540] In some embodiments, each R'º is independently C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-Cs heteroalkyl, halo, cyano, -C (O) Rô, -C (O0 ) ORE, -OR8, -N (RO) (R ), -C (O) N (RNHRP), - N (RC) C (O) RA, -S (O) .RFE, -S (O) .N (RºHRP) or -N (Rº) S (O) .RE or L-Tag, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by 1 to 12 R'º (for example, 1 R11, 2 RR ", 3 RU, 4R, 5R, 6R !, 7 R1, 8 RU, 9 RU, 10 RR, 11 RU or 12 R '!). In some embodiments, R'º is C1-Cs heteroalkyl , - N (RºNRP) or -N (Rº) C (OJRA. In some embodiments, R'º is C1-Ce heteroalkyl (for example, CHANHC (O) CH> 2), -N (RºI (Rº ) ( for example, NH2), or -N (Rº) C (O) Rº (for example, NHC (O) CH;).
[00541] [00541] In some embodiments, each Rº is independently C1-Cs alkyl, C2-C alkenyl, C2-Cs alkynyl, C1-Cs heteroalkyl, ha-
[00542] [00542] In some embodiments, each R'º is independently C1-Cs alkyl, halo, oxo, cyano, -OR8, -N (RºN (R ), -C (O) N (RºKNRL), - N (Rº ) C (O) RS, aryl or heteroaryl, where each aryl and heteroaryl is independent and optionally substituted by 1 to 6 Rº (for example, 1 Rº, 2R8, 3 Rô, 4Rº, 5Rº or 6 Rº).
[00543] [00543] In some embodiments, each L is independently C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-Cs heteroalkyl, - C (O) JR ”, -C (O) JORP ', -ORP, -N (ROI (R!), -C (OIN (RI) (R), - N (R) C (O) RY !, -S (O) .REI, -S (O) .N (RE ( RP), or -N (Rº) S (O) .RE, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by 1 to 12 R ' (For example, 1 R , 2R " , 3 R ' , 4R , 5R , 6R , 7 Rº, 8 RV, 9R , 10 Rº, 11 Rº Or 12 R2).
[00544] [00544] In some modalities, each one among Rºº, R81, RO, Rº 'and RE is independently hydrogen, C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-C6 heteroalkyl, carbocyclyl, heterocyclyl, aryl or heteroaryl, where each alkyl, alkenyl, alkynyl, heteroalkyl, carbocyclyl, heterocyclyl , aryl and heteroaryl is independent and optionally substituted by 1 to 12 R (for example, 1 Rº , 2R , 3 R ' , 4 R , 5R , 6 RP, 7 Rº , 8 RP, 9 RP, 10 Rº, 11 Rº or 12 R2).
[00545] [00545] In one embodiment, X is O. In one embodiment, R 'is heterocyclic (for example, piperidine-2,6-dionyl).). In one mode,
[00546] [00546] In one embodiment, X is O. In one embodiment, R 'is heterocyclyl (for example, piperidinyl-2,6-dionyl). In some modalities, R º and R together with the carbon to which they are attached they form a carbonyl group. In a modality, n is 1. In a modality, R * º is -N (Rº) (RP) (for example, -NH2). In one embodiment, the degradation compound comprises pomalidomide, for example, 4-amino-2- (2,6-dioxopiperidin-3-yl) isoindoline-1,3-dione, or a pharmaceutically acceptable salt thereof. . In one embodiment, the degradation compound is pomalidomide, for example, according to the following formula: o
[00547] [00547] In one embodiment, X is O. In one embodiment, R 'is heterocyclyl (for example, piperidinyl-2,6-dionyl)). In one mode, R ºº and R together with the carbon to which they are attached they form a carbonyl group. In one embodiment, n is 0. In a modality, the degradation compound comprises thalidomide, for example 2- (2,6-dioxopiperidin-3-yl) isoindoline-1,3-dione, or a pharmaceutically acceptable salt of the same. In one modality, the pro-
[00548] [00548] In one embodiment, X is O. In one embodiment, R 'is heterocyclyl (for example, piperidine-2,6-dionyl) .. In one embodiment, each R º and R it is independently hydrogen. In one embodiment, n is 1. In one embodiment, R'º is C1-C65 heteroalkyl (for example, CHaNHC (O) CH> 2-phenyl-t-butyl). In one embodiment, the degradation compound comprises 2- (4- (tert-butyl) phenyl) -N - ((2- (2,6-dioxopiperidin-3-yl) -1-oxoisoindolin-5-yl) methyl) acetamide, or a pharmaceutically acceptable salt thereof. In one embodiment, the degradation compound has the structure as shown in the following formula: o O
[00549] [00549] In some embodiments, the degradation compound (for example, a compound of Formula (1I)) is not attached to a linker or linker. In some embodiments, the degradation compound (for example, a compound of Formula (1I)) does not comprise another portion, for example, a binder, a bleaching agent, or a portion capable of dimerization. In some modalities, R'º is not an L-Tag.
[00550] [00550] In some embodiments, the degradation compound (for example, a compound of Formula (1I)) is not linked to a linker or linking group (for example, at least one R * º is L-Tag). In some embodiments, the degradation compound (for example, a compound of Formula (1II)) comprises another portion, for example, a binder, a bleaching agent, or a portion capable of dimerization.
[00551] [00551] In some modalities, R'º is L-Tag, and Tag is a targeting portion that is capable of binding or is linked to a target protein. A Tag can comprise a small molecule compound or an amino acid sequence (for example, a peptide or polypeptide). In some embodiments, the Tag is a kinase inhibitor, a protein inhibitor containing BET bromodomain, a cytosolic signaling protein FKBP12 linker, an HDAC inhibitor, a lysine methyltransferase inhibitor, an angiogenesis inhibitor, an immunosuppressive compound, or an aryl hydrocarbon receptor (AHR) inhibitor.
[00552] [00552] In certain modalities, the Label is a SERM (selective estrogen receptor modulator) or SERD (selective estrogen receptor degradator). Non-limiting examples of SERMs and SERDs are provided in Patent Publication No. WO 2014/191726, WO2013 / 090921, WO2014 / 203129, WO2014 / 205136, WO2014 / 205138, and WO 2014/203132; US patent publications No. US2013 / 0178445 and US 2015/0005286; and US Patent No. * 9,078,871,
[00553] [00553] Additional tags include, for example, any portion that binds to an endogenous protein (binds to a target protein). Exemplary labels include Hsp90 inhibitors, kinase inhibitors, HDM 2 and MDM2 inhibitors, compounds that target proteins containing human BET bromodomain, HDAC inhibitors, human lysine methyl transferase inhibitors, angiogenesis inhibitors, receptor compounds nuclear hormone, immunosuppressive compounds
[00554] [00554] In one embodiment, the Tag is a bleaching ligand from Ubc9 SUMO E 2 ligase 5F6D, for example, as described in Hewitt, W.M ,, et. al. (2016) Angew.Chem.! Int.Ed.Engl.55: 5703-5707
[00555] [00555] In one embodiment, the Tag is a Tank1 bleaching binder, for example, as described in Kirby, C.A. et al, (2012) Acta Crystallogr. Sect.F 68: 115-118; and Shultz, M.D., et al. (2013) J.Med.Chem.56: 7049-7059.
[00556] [00556] In one embodiment, the Tag is an SH2 domain of | pp60 Src bleaching agent, for example, as described in Gudrun Lange, et al., (2003) J. Med. Chem. 46, 5184-5195.
[00557] [00557] In one embodiment, the Tag is a bleaching ligand from the Sec7 domain, for example, as described in Huta, B.P., et al., (2016) Chemmedchem 11: 277.
[00558] [00558] In one embodiment, the Tag is a bleaching binder from Saposina-B, for example, as described in |. Nemcovicova and D. M. Zajonc Acta Cryst. (2014). D70, 851-862.
[00559] [00559] In one embodiment, the Tag is a S100-A7 2OWS protein bleaching binder, for example, as described in Leon, R., Murray, et al., (2009) Biochemistry 48: 10591-10600.
[00560] [00560] In one embodiment, the Tag is a phospholipase A2 bleaching binder, for example, as described in Schevitz, R.W ,, et al., (1995) Nat. Struct. Biol. 2, 458-465.
[00561] [00561] In one embodiment, the Tag is a PHIP bleaching binder, for example, as described in Krojer, T .; et al. Chem. Sci.2016, 7, 2322-2330.
[00562] [00562] In one embodiment, the Tag is a PDZ bleaching binder, for example, as described in Mangesh Joshi, et al. Angew. Chem. Int. Ed. (2006) 45, 3790-3795.
[00563] [00563] In one embodiment, the Tag is a bleaching ligand of PARP15, for example, as described in Karlberg, T., et al., (2015) J.Biol. Chem.290: 7336-7344.
[00564] [00564] In one embodiment, the Tag is a bleaching binder of PARP14, for example, as described in Andersson, C.D ,, et al., (2012) J.Med.Chem. 55: 7706-7718 .; Wahlberg, E., et al. (2012) Nat.Biotechnol. 30: 283-288; Andersson, C.D., et al. (2012) J. Med. Chem.55: 7706-7718.
[00565] [00565] In one embodiment, the Tag is a MTH1 bleaching binder, for example, as described in Helge Gad, et. al. Nature, (2014) 508, 215-221.
[00566] [00566] In one embodiment, the Tag is a targeting linker for mPGES, for example, as described in Luz, J.G., et al., (2015) J.Med.Chem.58: 4727-4737.
[00567] [00567] In one embodiment, the Tag is a FLAP-5-lipoxygenase activating protein targeting ligand, for example, as described in Ferguson, A.D., et al. (2007) Science 317: 510-512.
[00568] [00568] In one embodiment, the Tag is an FA Binding Protein bleaching binder, for example, as described in Kuhn, B .; et al. J. Med. Chem. (2016) 59, 4087-4102.
[00569] [00569] In one embodiment, the Tag is a BCL2 bleaching binder, for example, as described in Souers, A.J., et al. (2013) Nat Med 19: 202-208.
[00570] [00570] In one embodiment, the Tag is any small molecule or protein that can bind to a target protein and is acted upon or degraded by a ubiquitin ligase to be a target protein. In some embodiments, the Label is a dTAG Bleaching Binder disclosed in International Patent Publication No. WO2017 / 024318 (for example, Table T, pages 119 to 129).
[00571] [00571] When R * º is Label L, the Label is capable of binding to or is bound to a target protein. Exemplary target proteins include FK506-binding protein-12 (FKBP12), protein containing bromodomain 4 (BRD4), CREB-binding protein (CREBBP), or transcriptional activator BRG1 (SMARCA4). In some modalities, the target protein comprises a hormone receptor, for example, estrogen receptor protein, androgen receptor protein, retinoid x receptor protein (RXR), or dihydrofolate reductase (DHFR ), including bacterial DHFR. In some embodiments, the target protein comprises an amino acid sequence derived from a bacterial dehalogenase. In other embodiments, the target protein comprises amino acid sequences derived from 7,8-dihydro-8-oxoguanine triphosphatase, AFAD, Arachidonate activating protein 5-lipoxygenase, ASH1L, ATAD 2, protein containing baculoviral IAP repeat 2, BAZIA, BAZIB, BAZ2A, BAZ2B, Bcl-2, Bel-xL, BRD1, BRD2, BRD3, BRD4, BRD5, BRD6, BRD7, BRD8, BRDS9, BRD10, BRDT, BRPF1, BRPF3, BRWD3, CD209, CECR2, CREBBP, E3 ligase XIAP, EP300, FALZ, adipocyte fatty acid binding protein 4 (FABP4), GCN5L2, GTPase k-RAS, HDACS6, hematopoietic prostaglandin D synthase, KIAA1I240, lactoilglutatione liase, LOC933 MLL, PA2GA, PB1, PCAF, peptide-prolyl cis-trans isomerase interacting with NIMA 1, PHIP, poly-ADP-ribose polymerase 14, poly-ADP-ribose polymerase 15, PRKCBP1, prosaposine, prostaglandin AND synthase , delta subunit of cyclic phosphodiesterase cGMP 3 ',' 5 sensitive to the retinal stem, S100-A7, SMARCA2, SMARCAA, SP100, SP110, SP140, Src, Sumo UBC9 conjugate enzyme, supox dismutase acid, TAF1, TAF1L, tankerase 1, tankerase 2, TIF1a, TRIM28, TRIM33, TRIM66, WDR9, ZMYND11 or MLLA4. In other embodiments, the target protein comprises an amino acid sequence derived from MDM2. In some embodiments, the target protein is a dTAG disclosed in International Patent Publication No. WO 2017/024318 (for example, pages 112 to 114).
[00572] [00572] In one embodiment, the target protein is derived from BRD2, BRD3, BRD4 or BRDT. In one embodiment, the target protein is a modified or mutant BRD2, BRD3, BRD4 or BRDT protein. In certain embodiments, one or more BRD 2 mutations includes a tryptophan (W) mutation at amino acid position 97, a Valine (V) mutation at amino acid position 103, a Leucine (L) mutation at amino acid position 110, a mutation of W at amino acid position 370, a mutation of V at amino acid position 376, or a mutation of L at amino acid position 381.
[00573] [00573] In one embodiment, the target protein is derived from the cytosolic signaling protein FKBP12. In certain embodiments, the target protein is a modified or mutated FKBP12 cytosolic signaling protein. In certain embodiments, the modified or mutated FKBP12 cytosolic signaling protein contains one or more mutations that create an enlarged binding cavity for FKBP12 ligands. In certain embodiments, the one or more mutations include a mutation from phenylalanine (F) at the amino acid position 36 to valine (V) (F36V) (referred to interchangeably as FKBP12 * or FKBP *).
[00574] [00574] In some embodiments, the degradation compound is a compound disclosed in US patent No. 7,973,057; US Patent No.
[00575] [00575] Fusion polypeptides including a COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN and a heterologous polypeptide of interest are provided herein. In some embodiments, the COF1 / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide and the heterologous polypeptide are separated by a linker (for example, a glycine-serine linker). In some embodiments, the fusion polypeptide described herein comprises three elements: a COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN (for example, a portion of a degron amino acid sequence as described herein), a heterologous polypeptide, and a linker that separates the COFI / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN and the heterologous polypeptide. In other embodiments, the fusion polypeptide described in this document comprises two elements: a COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN (for example, a portion of a degron amino acid sequence, for example example, as described in this document) directly linked to a heterologous polypeptide. These elements can be arranged so that the COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide (for example, a portion of a degron amino acid sequence, for example, as described in this document) is located at the N-terminus of the heterologous polypeptide of interest, at the C-terminus of the heterologous polypeptide of interest, or in the middle of the heterologous polypeptide of interest. In one embodiment, the heterologous polypeptide is a cytosolic and / or nuclear protein and the COFI / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide is located N-terminal to the heterologous polypeptide. In one embodiment, the heterologous polypeptide is a transmembrane protein and the COFI / CRBN-binding polypeptide, COF2 / CRBN or
[00576] [00576] In some embodiments, the fusion polypeptide additionally comprises a degradation domain. In some modalities, the degradation domain is separated from the COF1I / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN and the heterologous polypeptide by a heterologous protease cleavage site.
[00577] [00577] The fusion polypeptides disclosed in the present document can include any heterologous polypeptide of interest. In some embodiments, the heterologous polypeptide may be a transmembrane protein (for example, a transmembrane receptor). In certain embodiments, the heterologous polypeptide of interest may, for example, be an ion-bound receptor, an enzyme-bound receptor (for example, tyrosine kinase receptor, a receptor associated with tyrosine kinase, a tyrosine phosphatase similar to re - ceptor, a serine / threonine kinase receptor; a guanylyl cyclase receptor, and a receptor associated with histidine kinase), or a receptor coupled to protein G. In some embodiments, the trans-membrane protein is a chimeric antigen receptor, for example, as described in this document.
[00578] [00578] In another embodiment, the heterologous polypeptide is a secreted protein (for example, a small secreted protein). In some embodiments, the heterologous polypeptide can be, for example, an antibody, a nanocorp, or a protein-binding molecule in the manufacture of cells. In some embodiments, the heterologous polypeptide may be a therapeutic or clinical protein (for example, insulin, growth hormone, erythropoietin, or a therapeutic antibody). In certain embodiments, the protein may be toxic to a cell for manufacture (for example, bacterial toxins and proteases).
[00579] [00579] Table 2 includes a list of exemplary heterologous polypeptides for use in the fusion polypeptides disclosed herein. Heterologous polypeptides of additional interest include Chimeric Antigen T Cell Receptors as described in the section below. Table 2. Heterologous Polypeptides of Cytoplasmic Interest or | Secreted Transmembranes
[00580] [00580] In one aspect, the CAR of the description linked to a COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN and / or a degradation domain comprises a target-specific binding element, another way, called an antigen-binding domain. In one embodiment, the portion of the CAR comprising the antigen-binding domain comprises an antigen-binding domain that aims, for example, to specifically bind to an antigen, for example, an antigen described herein, for example. example, CD19. In one embodiment, the antigen-binding domain aims, for example, to specifically bind to human CD19.
[00581] [00581] In some embodiments, the heterologous polypeptide linked to a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and / or a degradation domain comprises a chimeric antigen (CAR) receptor. In some embodiments, the CAR comprises an antigen-binding domain (for example, an antibody or antibody fragment, a TCR, or a TCR fragment) that binds to a tumor antigen, a transmembrane domain and a intracellular signaling (for example, an intracellular signaling domain comprising a co-stimulatory domain) and / or a primary signaling domain. The constructs of CAR nucleic acid, encoded proteins, containing vectors, host cells, pharmaceutical compositions, and methods of administration and treatment related to the present description are disclosed in detail in International Patent Application Publication No. WO2015142675, which is incorporated into this document as a reference in its entirety.
[00582] [00582] In some embodiments, the heterologous polypeptide is a chimeric antigen (CAR) receptor, wherein the CAR comprises an antigen-binding domain (e.g., antibody or antibody fragment, TCR or TCR fragment) that binds a tumor support antigen (for example, a tumor support antigen as described in this document), a transmembrane domain (for example, a transmembrane domain described in this document), and an intracellular signaling domain (for example example, an intracellular signaling domain described in this document) (for example, an intracellular signaling domain comprising a co-stimulating domain (for example, a co-stimulating domain described in this document) and / or a primary signaling domain (for example example, a primary signaling domain described in this document.) In some embodiments, the antigen supporting a tumor is an antigen present in a stromal cell or cell myeloid-derived suppressor (MDSC). In other aspects, the invention features polypeptides encoded by such nucleic acids and host cells containing such nucleic acids and / or polypeptides.
[00583] [00583] In some embodiments, a CAR molecule comprises at least one intracellular signaling domain selected from a CD137 signaling domain (4-1BB), a CD28 signaling domain, a CD27 signaling domain, a ICOS signaling domain, a CD3zeta signal domain, or any combination thereof. In some embodiments, a CAR molecule comprising at least one intracellular signaling domain is selected from one or more co-stimulating molecule (s) selected from CD137 (4-1BB), CD28, CD27 or ICOS.
[00584] [00584] In some embodiments, a plurality of immune-effector cells, for example, the population of depleted T regulatory cells, includes a nucleic acid encoding a CAR that comprises a target-specific binding domain element, called another as an antigen-binding domain. The choice of linker depends on the type and number of ligands that define the surface of a target cell. For example, the antigen-binding domain can be chosen to recognize a ligand that acts as a cell surface marker in target cells associated with a particular disease state. Thus, examples of cell surface markers that can act as ligands for the antigen-binding domain in a CAR of the invention include those associated with viral, bacterial and parasitic infections, autoimmune disease and cancer cells.
[00585] [00585] —Sequences of non-limiting examples of various components that may be part of a CAR molecule (for example, a CAR TA or a CAR BCA) described in this document, are listed in Table 3, where "aa" means amino acids, and "na" means nucleic acids that encode the corresponding peptide.
[00586] [00586] In one aspect, exemplary CAR constructs comprise an optional leader sequence (for example, a leader sequence described here), an extracellular antigen binding domain (for example, an antigen binding domain described here), an hinge (for example, a hinge region described herein), a transmembrane domain (for example, a transmembrane domain described herein) and an intracellular stimulator domain (for example, an intracellular stimulator domain described here) In one aspect, a CAR construct example comprises an optional leader sequence (for example, a leader sequence described here), an extracellular antigen binding domain (for example, an antigen binding domain described here), a hinge (for example, a region hinge described herein), a transmembrane domain (for example, a transmembrane domain described herein), an intracellular co-stimulating signaling domain (for example, a self domain co-stimulator signaling described here) and / or a primary intracellular signaling domain (for example, a primary signaling domain described herein).
[00587] [00587] In one aspect, the CARs (e.g., CD19 CARs) of the invention comprise at least one intracellular signaling domain selected from the group of a CD137 signaling domain (4-1BB), a CD28 signaling domain , a CD27 signaling domain, an ICOS signaling domain, a CD3zeta signal domain, and any combination of these. In one aspect, CARs comprise at least one intracellular signaling domain that comes from one or more co-stimulating molecule (s) selected from CD137 (4-1BB), CD28, CD27 or ICOS. CAR Antigen Binding Domain
[00588] [00588] In one aspect, the CAR of the description linked to a COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN and / or a degradation domain comprises a target-specific binding element, another way, called an antigen-binding domain. In one embodiment, the portion of the CAR comprising the antigen-binding domain comprises an antigen-binding domain that aims, for example, to specifically bind to an antigen, for example, an antigen described herein, for example. example, CD19. In one embodiment, the antigen-binding domain aims, for example, to specifically bind to human CD19.
[00589] [00589] In some embodiments, a plurality of immune-effector cells, for example, the population of depleted T regulatory cells, includes a nucleic acid encoding a CAR that comprises a target-specific binding domain element, called another. as an antigen-binding domain. The choice of linker depends on the type and number of ligands that define the surface of a target cell. For example, the antigen-binding domain can be chosen to recognize a ligand that acts as a cell surface marker in target cells associated with a particular disease state. Thus, examples of cell surface markers that can act as ligands for the antigen-binding domain in a CAR of the invention include those associated with viral, bacterial and parasitic infections, autoimmune disease and cancer cells.
[00590] [00590] In one aspect, the portion of the CAR that comprises the antigen binding domain comprises an antigen binding domain that targets a tumor antigen, for example, a tumor antigen described here. In some modalities, the antigen-binding domain is chosen from: CD19; CD123; CD22; CD30; CD171; CS-1; lectin type C molecule-1, CD33; epidermal growth factor receptor (EGFRvIll) variant Ill; ganglioside G2 (GD2); ganglioside GD3; member of TNF receptor family; B cell maturation antigen (BCMA); Tn antigen ((Tn Ag) or (Gal-NAca-Ser / Thr)); prostate-specific membrane antigen (PSMA); Orphan receptor 1 tyrosine kinase receptor (ROR1); tyrosine kinase 3 type Fms (FLT3); tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor alpha-2 subunit; Mesothelin; Alpha Interleukin 11 receptor (IL-11Ra); prostate stem cell antigen (PSCA); Protease serine 21; vascular endothelial growth factor receptor 2 (VEGFR2); Lewis antigen (Y); CD24; Platelet-derived growth factor beta receptor (PDGFR-beta); embryonic antigen-4 of specific stage (SSEA-4); CD20; alpha folate receptor; ERBB2 receptor tyrosine protein kinase (Her2 / neu); mucin 1, associated with the cell surface (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); Prostasis; prostatic acid phosphatase (PAP); mutated stretching factor 2 (ELF2M); Ephrin B2; alpha fibroblast activation protein (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CAIX); proteasome subunit (prosome, macropaine), Type Beta, 9 (LMP2); glycoprotein 100 (gp100); oncogen fusion protein consisting of the breaking point (BCR) cluster region and Abelson murine leukemia viral (Abl) homolog 1 (bcr-abl); tyrosinase; ephrin type A receptor 2 (EphA2); Fucosyl GM1; Lewis sialyl adhesion molecule (sLe); ganglioside GM3; transgalutaminase 5 (TGS5); antigen associated with high molecular weight melanoma (HMWMAA); o-acetyl-GD2 ganglioside (OAcGD2); beta folate receptor; tumor endothelial marker 1 (TEM1 / CD248); marker 7 related to the endothelial tumor (TEM7R); claudin 6 (CLDN6); thyroid stimulating hormone receptor (TSHR); group 5 class C receptor coupled to protein G, member D (GPRC5D); X chromosome open reading frame 61 (CXORF61); CD97; CD179a; anaplastic lymphoma kinase (ALK); polyisalic acid; specific for tablet 1 (PLAC1); portion of glycoceramide hexasaccharide of globose (GloboH); mammary gland differentiating antigen (NY-BR-1); uroplacin 2 (UPK2); hepatitis A virus cell receptor 1 (HAVCR1); beta 3 adenoreceptor (ADRB3); panexin 3 (PANX3); receptor 20 coupled to protein G (GPR20); lymphocyte antigen 6 complex, K 9 locus (LY6K); olfactory receptor 51E2 (OR51E2); gamma TOR alternating frame protein (TARP); Wilms' tumor protein (WT1); cancer / testis antigen 1 (NY-ESO-1); cancer / testis antigen 2 (LAGE-1a); antigen 1 associated with melanoma (MAGE-A1); gene 6 variant of ETS translocation, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); antigen family X, member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); antigen-1 from melanoma cancer testicles (MAD-CT-1); antigen-2 from melanoma cancer testicles (MAD-CT-2); Fos-related antigen 1; tumor protein p53 (p53); mutant p53; prostein; survivor; telomerase; prostate carcinoma tumor antigen-1, melanoma antigen recognized by T 1 cells; mutant rat sarcoma (Ras); human telomerase reverse transcriptase (hTERT); sarcoma translocation rupture points; apoptosis melanoma inhibitor (ML-IAP); ERG (transmembrane protease ETS fusion gene, serine 2 (TMPRSS2)); N-actyl glucosaminyl transferase V (NA17); pax-3 paired box protein (PAX3); anhydrogen receptor; cyclin B1; homologous derived from viral oncogen neuroblastoma of avian v-myc myelocytomatosis (MYCN); member C of Ras homologous family (RhoC); tyrosinase-related protein 2 (TRP-2); cytochrome P450 1B1 (CYP1B1); type CCCTC binding factor (zinc finger protein), squamous cell carcinoma antigen recognized by T 3 cells (SART3); pax-5 paired box protein (PAX5); proacrosin sp32 binding protein (OY-TES1); lymphocyte-specific protein tyrosine kinase (LCK); kinase A anchor protein 4 (AKAP-4); synovial sarcoma, X 2 rupture point (SSX2); Receiver for advanced glycation end products (RAGE-1); ubiquitous renal 1 (RU1); ubiquitous renal 2 (RU2); legumaine; human papilloma virus E6 (HPV E6); human papilloma virus E7 (HPV E7); intestinal carboxyl esterase; mutated 70-2 heat shock protein (mut hsp70-2); CD79a; CD79b; CD72; leukocyte-associated immunoglobulin type 1 receptor (LAIR1); IgA receptor Fc fragment (FCAR or CD89); member 2 of sub-family A of leukocyte immunoglobulin-like receptor (LILRA2); member of the CD300 molecule family (CD300LF); member A of family 12 of type C lectin domain (CLEC12A); bone marrow stromal cell antigen 2 (BST2); mucin hormone receptor 2 type containing EGF-type module (EMR2); lymphocyte antigen 75 (LY75); glypican-3 (GPC3); Fc 5 receptor type (FOCRLB5); and lambda immunoglobulin-like polypeptide 1 (IGLL1).
[00591] [00591] In one embodiment, the antigen-binding domain binds to CD19. In another embodiment, the antigen-binding domain binds to CD123. In another modality, the antigen-binding domain binds to BCMA. In another embodiment, the antigen-binding domain binds to CD20.
[00592] [00592] The antigen binding domain can be any domain that binds to the antigen including, but not limited to, a monoclonal antibody, a polyclonal antibody, a recombinant antibody, a human antibody, a humanized antibody and a fragment functionality, including, but not limited to, a single domain antibody such as a heavy chain variable domain (VH), a light chain variable domain (VL) and a variable domain (VHH) of a nanocorp derived from camelid, and an alternative framework known in the art for functioning as the antigen binding domain, such as a recombinant fibronectin domain, a T cell receptor (TOR) or a fragment thereof, for example, TCR of single chain and the like. In some cases, it is beneficial that the antigen-binding domain is derived from the same species in which the CAR will ultimately be used. For example, for use in humans, it may be beneficial that the CAR antigen-binding domain comprises human or humanized residues for the antigen-binding domain of an antibody or antibody fragment.
[00593] [00593] The antigen-binding domain can be any domain that binds to the antigen including, but not limited to, a monoclonal antibody, a polyclonal antibody, a recombinant antibody, a human antibody, a humanized antibody , and a functional fragment thereof, including, but not limited to, a single domain antibody such as a heavy chain variable domain (VH), a light chain variable domain (VL) and a variable domain (VHH) of nanocorp derived from camelid, and an alternative skeleton that is known in the art to act as a binding antigen domain, such as a recombinant fibronectin domain, and the like. In some cases, it is beneficial that the antigen-binding domain is derived from the same species in which the CAR will ultimately be used. For example, for use in humans, it may be beneficial that the CAR antigen-binding domain comprises human or humanized residues for the antigen-binding domain of an antibody or antibody fragment. Thus, in one aspect, the antigen-binding domain comprises an antibody or a human antibody fragment.
[00594] [00594] In one embodiment, the antigen-binding domain comprises
[00595] [00595] In modalities, the antigen-binding domain is an antigen-binding domain described in documents No. WO2015 / 142675, US-2015-0283178-A1, US-2016-0046724-A1, US2014 / 0322212A1, US2016 / 0068601A1 , US2016 / 0051651A1, US2016 / 0096892A1, US2014 / 0322275A1 or WOZ2015 / 090230, incorporated herein by reference.
[00596] [00596] Examples of target antigens that can be targeted using CAR expressing cells include, but are not limited to, CD19, CD123, EGFRvIIl, CD33, mesothelin, BCMA and GFR AL-PHA-A, among others, as described, for example, in documents No. WO2014 / 153270, WO 2014/130635, WO2016 / 028896, WO 2014/130657, WO2016 / 014576, WO 2015/090230, WO2016 / 014565, WO 2016/014535 and WO2016 / 025880, each one of which is incorporated in this document as a reference in its entirety. Multispecific CAR
[00597] [00597] In some embodiments, the CAR molecule is a multispecific CAR molecule, for example, bispecific, which has a first binding specificity for a first antigen, for example, a B cell epitope, and a second specificity of binding to an identical or different antigen, for example, a B cell epitope. In some embodiments, the bispecific CAR molecule has a first binding specificity for CD19 (for example, the bispecific CAR molecule comprises a Anti-CD19 CAR revealed in Tables 5, 6, 7 and 30) and a second binding specificity for CD22 (for example, the bispecific CAR molecule comprises an anti-CD22 CAR revealed in Tables 19 and 20). In some embodiments, the bispecific CAR molecule has a first binding specificity for CD19 (for example, the bispecific CAR molecule comprises an anti-CD19 CAR disclosed in Tables 5, 6, 7 and 30) and a second specificity of binding for CD 20 (for example, the bispecific CAR molecule comprises an anti-CD20 CAR disclosed in Table 32).
[00598] [00598] In one embodiment, the first and second binding specificities are an antibody molecule, for example, an antibody-binding domain (for example, an scFv). Within each antibody molecule (e.g., scFv) of a bispecific CAR molecule, VH can be upstream or downstream of VL.
[00599] [00599] In some embodiments, the antibody or antibody fragment (for example, scFv) upstream is arranged with its VH (VH1) upstream of its VL (VL1) and the antibody or antibody fragment (for example , scFv) downstream is arranged with its VL (VL2) upstream of its VH (VH2), so that the global bispecific CAR molecule has the VH1-VL1-VL2-VH2 orientation of an N-
[00600] [00600] In some embodiments, the antibody or antibody fragment (for example, scFv) upstream is arranged with its VL (VL1) upstream of its VH (VH1) and the antibody or antibody fragment (for example , scFv) downstream is arranged with its VH (VH2) upstream of its VL (VL2), so that the global bispecific CAR molecule has the VL1-VH1-VH2-VL2 arrangement, of an N orientation - terminal for C-terminal.
[00601] [00601] In some embodiments, the antibody or antibody fragment (for example, scFv) upstream is arranged with its VL (VL1) upstream of its VH (VH1) and the antibody or antibody fragment (for example , scFv) downstream is arranged with its VL (VL2) upstream of its VH (VH2), so that the global bispecific CAR molecule has the VL1-VH1-VL2-VH2 arrangement, of an N orientation - terminal for C-terminal.
[00602] [00602] In some embodiments, the antibody or antibody fragment (for example, scFv) upstream is arranged with its VH (VH1) upstream of its VL (VL1) and the antibody or antibody fragment (for example , scFv) downstream is arranged with its VH (VH2) upstream of its VL (VL2), so that the global bispecific CAR molecule has the VH1-VL1-VH2-VL2 arrangement, of an N orientation - terminal for C-terminal.
[00603] [00603] In any of the above configurations, optionally, a ligand is disposed between the two antibodies or antibody fragments (for example, scFvs), for example, between VL, and VL>, if the construct is arranged as VH1-VL1-VL2-VH2; between VH1 and VH; z, if the construct is arranged as VL1-VH1-VH2-VL2; between VH, and VL>, if the construct is arranged as VL1-VH1-VL2-VH> 2; or between VL: and VH2 if the construct is arranged as VH1-VL1-VH2-VL2. In general, the linker between the two scFvs will be long enough to avoid faulty pairing between the domains of the two scFvs. The linker can be a linker as described in this document. In some embodiments, the ligand is a (Gly4-Ser) n ligand, where n is 1, 2, 3,4, 5 or 6. In some embodiments, the ligand is (Gly14-Ser) n, where n = 1 (SEQ ID NO: 168), for example, the linker has the amino acid sequence Gly4-Ser (SEQ ID NO: 168). In some embodiments, the linker is (Gly1-Ser) n, where n = 3 (SEQ ID NO: 142). In some modalities, the linker is (Gly4-Ser) n, where n = 4 (SEQ ID NO: 141). In some embodiments, the linker comprises, for example, consists of, the amino acid sequence: LAEAAAK (SEQ ID NO: 822).
[00604] [00604] In any of the above configurations, optionally, a ligand is disposed between the VL and VH of the first scFv. Optionally, a ligand is placed between the VL and VH of the second scFv. In constructs that have multiple ligands, any two or more of the ligands can be the same or different. Consequently, in some embodiments, a bispecific CAR comprises VLs, VHs, and optionally one or more ligands in an arrangement as described herein.
[00605] [00605] In some embodiments, each antibody molecule, for example, each antigen-binding domain (for example, each scFv) comprises a linker between the VH and VL regions. In some modalities, the ligand between the VH and VL regions is a (Gly1-Ser) n ligand, where n is 1, 2, 3, 4, 5 or 6. In some modalities, the ligand is (Gly4 -Ber) n, where n = 1 (SEQ ID NO: 168), for example, the linker has the amino acid sequence Glya-Ser (SEQ ID NO: 168). In some embodiments, the linker is (Glya-Ser) n, where n = 3 (SEQ ID NO: 142). In some embodiments, the linker is (Gly4-Ser) n, where n = 4 (SEQ ID NO: 141). In some embodiments, the VH and VL regions are connected without a ligand.
[00606] [00606] Additional exemplary multispecific CAR molecules are revealed on pages 26 to 39 of document No. WO2018 /
[00607] [00607] In other embodiments, cells expressing CAR may specifically bind to CD19, for example, they may include a CAR molecule or an antigen-binding domain (for example, a humanized antigen-binding domain) according to with Table 3 of WO2014 / 153270, incorporated herein by reference.
[00608] [00608] In modalities, the CAR molecule comprises an antigen-binding domain that specifically binds to CD19 (CAR CD19). In one embodiment, the antigen-binding domain targets human CD19. In one embodiment, the CAR antigen-binding domain has an identical or similar binding specificity to the FMC63 scFv fragment described in Nicholson et al. Mol. Immun. 34 (16-17): 1157-1165 (1997). In one embodiment, the CAR antigen-binding domain includes the scFv fragment described in Nicholson et al. Mol. Immun. 34 (16-17): 1157-1165 (1997). A CD19 antibody molecule can be, for example, an antibody molecule (for example, a humanized anti-CD19 antibody molecule) described in WO2014 / 153270, which is incorporated herein by reference in its entirety. WO2014 / 153270 also describes methods of assessing the linkage and effectiveness of various CAR constructs.
[00609] [00609] In one aspect, the parental murine scFv sequence is the CAR19 construct provided in PCT Publication WO2012 / 079000 (incorporated herein by reference). In one embodiment, the anti-CD19 binding domain is an scFv described in WO2012 / 079000.
[00610] [00610] In one embodiment, the CAR molecule comprises the fusion polypeptide sequence provided as SEQ ID NO: 12 in PCT publication WO2012 / 079000, and provided in the present document in Table 5, which provides an scFv fragment of murine origin that specifically binds to human Cd19. The humanization of this mouse scFv may be desired for the clinical setting, where specific mouse residues can induce a human-anti-mouse antigen (HAMA) response in patients receiving CART19 treatment, for example, treatment with T cells transduced with the CAR19 construct.
[00611] [00611] In one embodiment, CAR CD19 comprises an amino acid sequence provided as SEQ ID NO: 12 in PCT publication WO2012 / 079000. In one embodiment, the sequence is aminoá- acids (MALPVTALLLPLALLLHAARP) diqgmtaqttssI | saslgdrvtiscrasqdiskylnwyqgq kpdgtvklliyhtsrlhsgvpsrfsgsgsgtdysltisnlegediatyfegggntlpytfagatkleitagg gsggggsggggsevklgesgpalvapsqgslsvtctvsgvs pdygvswirgpprkglewlgviw gsettyynsalksritiilkkinsksqvflkmnslgtddtaiyycakhyyyggsyamdywgggtsvtv sstttpaprpptpaptiasqplIslrpeacrpaaggavhtraldfacdiyiwaplagtegvllislvitlye krgrkkllyifkgpfmrpvattgeedgescripeeeeggcelrvkfsrsadapaykKkqgggnaglyneln Igrreeydvldkrrgrdpemggkprrknpgeglynelgkdkmaeayseigmkgerrrakghdg! yaglstatkdtydalhmgalppr (SEQ ID NO: 181), or a sequence substantially homologous to it. The optional signaling peptide sequence is shown in capital letters and parentheses.
[00612] [00612] In one embodiment, the amino acid sequence is DiqgmtgttssIsaslgdrvtiscrasqdiskylnwyggkpdgtvklliyhtsrlhsgvpsrfsgsgsgt dysltisnlegediatyfcgggntipytfgggtkleitagggsaggagsgagggsevkigesgpalvap saslsvtctvsgvs | pdygvswirgpprkglewlgviwasettyynsalksritikdnsksqvflkm nslgtddtaiyycakhyyyggsyamdywgqggtsvtvsstttpaprpptpaptiasqplIslrpeacr paaggavhtrgldfacdiyiwaplagtcgvlllslvitlyckrgrkkllyifkgpfmrpvgttaeedgesc paeglynelgkdkmaeayseigmkgerrrgkghdglygaglstatkdtydalhmgalppr rípeeeeggcelrvkfsrsadapaykqggqgnalynelnigrreeydvidkrrgrdpemggkprrkn (SEQ ID NO: 182) or a sequence substantially homologous thereto.
[00613] [00613] In one embodiment, CAR CD19 has the designation USAN TISAGENLECLEUCEL-T. In modalities, CTLO19 is done by a modification of T cell genes mediated by stable insertion via transduction with a lentiviral vector (LV) deficient in self-inactivating replication containing the CTLO19 transgene under the control of the EF-1 alpha promoter. CTLO19 can be a mixture of transgene positive and negative T cells that are administered to the individual based on the percentage of transgene positive T cells.
[00614] [00614] In other embodiments, CAR CD19 comprises an antigen binding domain (for example, a humanized antigen binding domain) according to Table 3 of WO2014 / 153270, incorporated herein by reference.
[00615] [00615] Humanization of murine CD19 antibody can be desired for the clinical setting, where mouse-specific residues can induce a human-anti-mouse antigen (HAMA) response in patients who have received CART19 treatment, that is, treatment with T cells transduced with the CAR19 construct. The production, characterization and efficacy of humanized CD19 CAR sequences are described in International Application WO2014 / 153270 which is incorporated herein by reference in its entirety, including Examples 1 to 5 (p. 115-159).
[00616] [00616] In some modalities, CAR CD19 constructs are described in PCT publication No. WO 2012/079000, incorporated into this document as a reference, and the amino acid sequence of murine constructs CAR CD189 and scFv is shown in the Table 5 below, or a sequence substantially identical to any of the sequences mentioned above (for example, at least 85%, 90%, 95% or more identical to any of the sequences described herein).
[00617] [00617] The CAR CD19 constructs containing humanized anti-CD19 scFv domains are described in PCT publication No. WO 2014/153270, incorporated by reference in this document.
[00618] [00618] The sequences of murine and humanized CDR sequences from the anti-CD19 scFv domains are shown in Table 6 for the heavy chain variable domains and in Table 7 for the light chain variable domains. In some embodiments, the HCDR1 of a humanized CD19 binding domain is GVSLPDYGVS (SEQ ID NO: 230).
[00619] [00619] “Any known CD19 CAR, for example, the CD19 antigen binding domain of any known CD19 CAR, in the art can be used according to the present description. For example, LG-740; CAR CD189 described in US Patent No. 8,399,645; US Patent 7,446,190; Xu et al, Leuk Lymphoma. 2013 54 (2): 255 to 260 (2012); Cruz et al., Blood 122 (17): 2,965 to 2,973 (2013); Brentjens et al., Blood, 118 (18): 4,817 to 4,828 (2011); Kochenderfer et al., Blood 116 (20): 4,099 to 4,102 (2010); Kochenderfer et al, Blood 122 (25): 4,129 to 4,139 (2013); and 16 ! Annu Meet Am Soc Gen Cell Ther (ASGCT) (May 15-18, Salt Lake City) 2013, Abst 10.
[00620] [00620] Exemplary CD19 CARs include CD19 CARs described in this document, for example, in one or more tables described in this document, or an anti-CD19 CAR described in Xu et al. Blood 123.24 (2014): 3750-9; Kochenderfer et al. Blood
[00621] [00621] In other embodiments, cells expressing CAR may specifically bind to CD123, for example, may include a CAR molecule (for example, any one from CAR1I to CAR8) or an antigen binding domain according to Tables 1-2 of WO 2014/130635, incorporated herein by reference. The amino acid and nucleotide sequences encoding the CAR CD123 molecules and antigen-binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia)) as specified in document No. 2014/130635, are provided in Tables 8 to 14. The identical and substantially identical amino and nucleotide sequences to the aforementioned nucleotide sequences provided in Tables 8 to 14 are specifically incorporated in this specification.
[00622] [00622] The CDRs for CD123 binding domain provided in Tables 8 to 14 are in accordance with a combination of the Kabat and Chothia numbering scheme.
[00623] [00623] In embodiments, a CAR molecule described here comprises a scFv that specifically binds to CD123, and does not contain a leader sequence, for example, the amino acid sequence SEQ ID NO: 64. Table 14 below provides sequences for amino acids and nucleotides for CD123 scFv sequences that do not contain a leader sequence SEQ ID NO: 64.
[00624] [00624] In other embodiments, cells expressing CAR can specifically bind to CD123, for example, they can include a CAR molecule (for example, any one of CAR123-1 or CAR123-4 and hzCAR123-1 to hzCAR123- 32) or an antigen binding domain according to Tables 2, 6 and 9 of document No. WO2016 / 028896, incorporated by reference in this document. The amino acid and nucleotide sequences encoding the CAR CD123 molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia), as specified in document No. WO2016 / 028896, are hereby incorporated by reference in their entirety for reference.
[00625] [00625] In other embodiments, cells expressing CAR may specifically bind to EGFRvIIII, for example, may include a CAR molecule or an antigen binding domain according to Table 2 or SEQ ID NO: 11 of document No. WO 2014/130657, incorporated by reference in this document. Exemplary amino acid and nucleotide sequences encoding the CAR EGFRvIll molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia) , are provided in document No. WO 2014/130657. Exemplary anti-EGFRvI11 CAR sequences can comprise a CDR, a variable region, a scFv, or a full-length CAR sequence from a sequence disclosed in Table 33 (or a sequence at least about 85%, 90%, 95 %, 99% or more identical to the same, and / or having one, two, three or more substitutions, insertions, deletions or modifications). Table 33. EGFRvIII CAR sequences. Name jsEgIDNo: PR | ES RN
[00626] [00626] In other embodiments, cells expressing CAR may specifically bind to CD33, for example, they may include a CAR molecule (for example, any one from CAR33-1 to CAR-33-9) or a domain of antigen binding according to Table 2 or 9 of WO 2016/014576, incorporated herein by reference. The exemplary amino acid and nucleotide sequences encoding the CAR CD33 molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia), are provided in document No. WO2016 / 014576. Mesothelin CAR
[00627] [00627] In some embodiments, cells expressing CAR can specifically bind to mesothelin, for example, they can include a CAR molecule or an antigen-binding domain according to Tables 2-3 of WO 2015/090230, incorporated here by reference. The exemplary amino acid and nucleotide sequences encoding mesothelin CAR molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs from according to Kabat or Chothia), are provided in document No. WO 2015/090230. Exemplary anti-mesothelin CAR sequences may comprise a CDR, a variable region, a scFv, or a full-length CAR sequence from a sequence disclosed in Table 34 (or a sequence at least about 85%, 90% , 95%, 99% or more identical, and / or having one, two, three or more substitutions, insertions, deletions or modifications). Table 34. Mesothelin CAR sequences. The amino acid sequences of human scFvs and CARs that bind to mesothelin (the bold underline is the leader sequence). In the case of scFvs, the remaining amino acids are the heavy chain variable region and the light chain variable region, with each of the HC CDRs (HC CDR1, HC CDR2, HC CDR3) and LC CDRs ( LC CDR1, LC CDR-2, LC CDR3) underlined. In the case of CARs, the additional remaining amino acids are the remaining amino acids in the CARs.
[00628] [00628] In other embodiments, cells expressing CAR can specifically bind to BCMA, for example, can include a CAR molecule or an antigen-binding domain according to Table 1 or 16 or SEQ ID NO: 271 or SEQ ID NO: 273 of document No. WO2016 / 014565, incorporated by reference in this document. The amino acid and nucleotide sequences encoding the CAR BCMA molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia ), as specified in document No. WO2016 / 014565, are provided in Tables 15 to 18 in this document.
[00629] [00629] Additional exemplary BMA targeting sequences that can be used in anti-BCMA CAR constructs are disclosed in WO 2017/021450, WO 2017/011804, WO 2017/025038, WO 2016/090327, WO 2016 / 130598, WO 2016/210293, WO 2016/090320, WO 2016/014789, WO 2016/094304,
[00630] [00630] In modalities, additional exemplary CAR BCMA constructs are generated using the VT and VL sequences of PCT Publication WO2012 / 0163805 (whose content is thus incorporated by reference in their entirety). The exemplary CAR BCMA constructs and their corresponding DNA sequences are shown in Table 17. CAR CD22
[00631] [00631] In other embodiments, cells expressing CAR may specifically bind to humanized CD22, for example, they may include a CAR molecule or an antigen-binding domain (eg, a humanized antigen-binding domain ) according to document No. WO2016 / 164731, incorporated in this document as a reference.
[00632] [00632] In embodiments, the CAR molecule comprises an antigen-binding domain that specifically binds to CD22 (CAR CD22). In one embodiment, the antigen-binding domain targets human CD22. In one embodiment, the antigen-binding domain includes a single-stranded Fv sequence as described in this document.
[00633] [00633] Human CD22 CAR sequences are provided below
[00634] [00634] Human CD22 CAR scFv sequence (VH- (G4S) 3-VL) EVOALAQASGPGLVKPSQTLSLTCAISGDSMLSNSDTWNWIRQSPSRG LEWLGRTYHRSTWYDDYASSVRGRVSINVDTSKNQYSLQLNAVTPE DTGVYYCARVRLADGNSWSDAFDVWGQGTMVTVSSGGGGSGGG GSGGGGSQSALTQAQPASASGSPGQSVTISCTGTSSDVGGYNYVSWY
[00635] [00635] Human CD22 CAR heavy chain variable region EVAQLAQASGPGLVKPSQTLSLTCAISGDSMLSNSDTWNWIRQSPSRG
[00636] [00636] Human CD22 CAR light chain variable region QSALTQAPASASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKA
[00637] [00637] In some embodiments, the antigen binding domain comprises an HC CDR1, an HC CDR2 and an HC CDR3 of any amino acid sequences of the heavy chain binding domain listed in Table 19. In the embodiments, the domain antigen binding agent further comprises an LC CDR1, an LC CDR2 and an LC CDR3. In embodiments, the antigen-binding domain comprises an LC CDR1, an LC CDR2 and an LC CDR3 of the amino acid sequences listed in Table 20.
[00638] [00638] In some embodiments, the antigen binding domain comprises one, two, or all of the LC CDR1, LC CDR2 and LC CDR3 of any light chain binding domain amino acid sequences listed in Table 20, and one, two or all of HC CDR1, HC CDR2 and HC CDR3 of any heavy chain binding domain amino acid sequences listed in Table 19.
[00639] [00639] In some modalities, CDRs are defined according to the Kabat numbering scheme, the Chothia numbering scheme or a combination of them.
[00640] [00640] Additional anti-CD20 scFv sequences are provided below:
[00641] [00641] Human CD22 CAR scFvy sequence (VH- (G4S) -VL) EVOLQOQASGPGLVKPSQTLSLTCAISGDSMLSNSDTWNWIRQSPSRG LEWLGRTYHRSTWYDDYASSVRGRVSINVDTSKNQYSLQLNAVTPE DTGVYYCARVRLAODGNSWSDAFDVWGQGTMVTVSSGGGGSQSAL TQPASASGSPGOQSVTISCTGTSSDVGGYNYVSWYQQHPGKAPKLMI
[00642] [00642] Human CD22 CAR scFv sequence (VL- (G4S) 3-VH) QSALTQPASASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKA PKLMIYDVSNRPSGVSNRFSGSKSGNTASLTISGLQOAEDEADYYCSS YTSSSTLYVFGTGTQLTVLGGGGSGCSGGESGGGGSEVALAQASGPGL VKPSQTLSLTCAISGDSMLSNSDTWNWIRQOSPSRGLEWLGRTYHRS
[00643] [00643] Human CD22 CAR scFvy sequence (VL- (G4S) -VH) QSALTAPASASGSPGQSVTISCTGTSSDVGGYNYVSWYQQHPGKA PKLMIYDVSNRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSS YTSSSTLYVFGTGTQLTVLGGGGSEVALAQASGPGLVKPSQTLSLTC AISGDSMLSNSDTWNWIRQSPSRGLEWLGRTYHRSTWYDDYASSV
[00644] [00644] The order in which the VL and VH domains appear in scFv can be varied (that is, VL-VH or VH-VL orientation), and in which any one, two, three or four copies of the "G4S" (SEQ ID NO: 168), where each subunit comprises the sequence GGGGS (SEQ | D NO: 168) (for example, (G4S); (SEQ ID NO: 142) or (G4S) (SEQ ID NO: 141) ), you can connect the variable domains to create the entire scFv domain. Alternatively, the CAR construct can include, for example, a linker that includes the sequence GSTSGSGKPGSGEGSTKG (SEQ ID NO: 821). Alternatively, the CAR construct can include, for example, a linker that includes the sequence LAEAAAK (SEQ ID NO: 822). In one embodiment, the CAR construct does not include an | iegant between the VL and VH domains.
[00645] [00645] These clones contained an alteration of Q / K residues in the signal domain of the co-stimulatory domain derived from the CD3zeta chain.
[00646] [00646] In some embodiments, the CAR molecule described in this document is a bispecific CAR molecule. In one embodiment, the bispecific CAR molecule comprises a first binding specificity for CD19, for example, a binding specificity from VL1-VH1 to CD19, and a second specificity of | i-
[00647] [00647] In one embodiment, the bispecific CAR molecule comprises a first binding specificity for CD22, for example, a binding specificity of VL2-VH2 or VH2-VL1 for CD22, and a second binding specificity for CD19, for example example, a binding specificity from VL1-VH1 to CD19. In one embodiment, the first and second binding specificities are in a contiguous polypeptide chain, for example, a single chain. In some embodiments, the first and second binding specificities optionally comprise a binder as described in this document.
[00648] [00648] In some modalities, the ligand is a ligand (Glys-Ser) n, where n is 1, 2, 3, 4, 5 or 6. In some modalities, the ligand is (Gly4-Ser) n , where n = 1 (SEQ ID NO: 168), for example, the linker has the amino acid sequence Gly4-Ser (SEQ ID NO: 168). In some embodiments, the linker is (Gly4-Ser) n, where n = 3 (SEQ ID NO: 142). In some embodiments, the linker is (Glya-Ser) n, where n = 4 (SEQ ID NO: 141). In some embodiments, the linker comprises, for example, consists of, the amino acid sequence: LA-EAAAK (SEQ ID NO: 822). CAR CD20
[00649] [00649] In some modalities, the cell that expresses CAR
[00650] [00650] In other embodiments, cells expressing CAR may specifically bind to CLL-1, for example, they may include a CAR molecule or an antigen binding domain according to Table 2 of WO 2016/014535, incorporated herein by reference. Exemplary amino acid and nucleotide sequences encoding the CAR CLL-1 molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia), are provided in document No. WO2016 / 014535. GFR ALPHA-4
[00651] [00651] In other embodiments, cells expressing CAR may specifically bind to GFR ALPHA-4, for example, may include a CAR molecule or an antigen binding domain according to Table 2 of WO 2016/025880 , incorporated here by reference. The amino acid and nucleotide sequences encoding the CAR GFR ALPHA-4 molecules and antigen binding domains (for example, including one, two or three VH CDRs; and one, two or three VL CDRs according to Kabat or Chothia ), are specified in WO2016 / 025880.
[00652] [00652] In one embodiment, the antigen-binding domain of any of the molecules described herein (for example, any of CD19, CD123, EGFRvIll, CD33, mesothelin, BCMA and GFR ALPHA-4) comprises one, two or three (for example, the three) heavy chain CDRs, HC CDR1, HC CDR2 and HC CDR3, from an antibody listed above, and / or one, two or three (for example, all three) light chain CDRs, LC CDR1, LC CDR2 and LC CDR3, from an antigen binding domain listed above. In one embodiment, the antigen binding domain comprises a heavy chain variable region and / or the light chain variable region of an antibody listed or described above.
[00653] [00653] In one aspect, the antitumor antigen-binding domain is a fragment, for example, a single-chain variable fragment (scFv). In one aspect, the cancer-associated antigen antigen binding domain as described herein is an Fv, a Fab, a (Fab ') 2 or a bifunctional hybrid antibody (for example,
[00654] [00654] In some cases, scFvs can be prepared according to a method known in the art (see, for example, Bird et al., (1988) Science 242: 423-426 and Huston et al., (1988) Proc. Natl. Acad. Sci. USA 85: 5879-5883). ScFv molecules can be produced by ligating together VH and VL regions using flexible polypeptide ligands. The scFv molecules comprise a linker (e.g., a Ser-Gly linker) with an optimized length and / or composition of amino acids. The length of the ligand can greatly affect how the variable regions of an scFv fold and interact. In fact, if a short polypeptide linker (for example, between 5-10 amino acids) is used, intrachain folding is prevented. Intrachain folding is also required to join the two variable regions together to form a functional epitope binding site. For examples of the orientation and size of ligands see, for example, Hollinger et al. 1993 Proc Natl Acad. Sci. U.S.A. 90: 6444-6448, U.S. Patent Application Publication No. 2005/0100543, 2005/0175606, 2007/0014794 and PCT Publication No. WO2006 / 020258 and WO 2007/024715, incorporated herein by reference.
[00655] [00655] In another aspect, the antigen binding domain is a T cell receptor ("'TCR") or a fragment thereof, for example, a single chain TCR (scTCR). Methods for producing such TCRs are known in the art. See, for example, Willemsen RA et al, Gene Therapy 7: 1,369 to 1,377 (2000); Zhang T et al, Cancer Gene Ther 11: 487 to 496 (2004); Aggen et al, Gene Ther. 19 (4): 365 to 374 (2012) (references are incorporated in this document in their entirety). For example, scTCR can be engineered to contain the Va and VB genes of a T cell clone linked by a ligand (for example, a flexible peptide). This approach is very useful for a cancer-associated target in which it is intracellular, however, a fragment of such an antigen (peptide) is presented on the surface of cancer cells by MHC. Antigen-binding domains and additional exemplary CARs
[00656] [00656] In one embodiment, an antigen-binding domain against GD2 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Mujoo et al., Cancer Res. 47 (4): 1098-1104 (1987); Cheung et al., Cancer Res 45 (6): 2642-2649 (1985), Cheung et al., J Clin Oncol 5 (9): 1430-1440 (1987), Cheung et al., J Clin Oncol 16 (9 ): 3053-3060 (1998), Handgretinger et al., Cancer Immunol Immunother 35 (3): 199-204 (1992). In some embodiments, an antigen-binding domain against GD2 is an antigen-binding portion of an antibody selected from mAb 14.18, 14G2a, ch14.18, hu14.18, 3F8, hu3F8, 3G6, 8B6, 60C3, 10B8 , ME36.1 and 8H9, see, for example, WO2012033885, WO2013040371, WO2013192294, WO2013061273, WO2013123061, WO2013074916 and WO201385552. In some embodiments, an antigen-binding domain against GD 2 is an antigen-binding portion of an antibody described in Publication No. US: 20100150910 or PCT Publication No. WO
[00657] [00657] In one embodiment, an antigen-binding domain against the Tn antigen, the sTn antigen, a Tn-O-glycopeptide antigen or an sTn-O-glycopeptide antigen is an antigen-binding moiety, for example, CDRs, of an antibody described, for example, in US 2014/0178365, US8,440,798, EP 2083868 A2, Brooks et al., PNAS 107 (22): 10056-10061 (2010), and Stone et al, Oncolmmunology 1 ( 6): 863-873 (2012).
[00658] [00658] In one embodiment, an antigen-binding domain against PSMA is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Parker et al., Protein Expr Purif 89 (2): 136-145 (2013), US 20110268656 (J591 ScFv); Frigeário et al, European J Cancer 49 (9): 2223-2232 (2013) (scFvD2B); WO 2006125481 (mAbs 3 / A12, 3 / E7 and 3 / F11) and fragments of single chain antibodies (scFv A5 and D7).
[00659] [00659] In one embodiment, an antigen-binding domain against CD97 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in US6,846,911; de Groot et al., J Inmunol. 183 (6): 4127-4134 (2009); or an R&D antibody: MAB3734.
[00660] [00660] In one embodiment, an antigen-binding domain against TAG72 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Hombach et al, Gastroenterology 113 (4): 1163-1170 (1997); and Abcam ab691.
[00661] [00661] In one embodiment, an antigen-binding domain against CD44v6 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Casucci et a /., Blood 122 (20): 3461 -3472 (2013).
[00662] [00662] In one embodiment, an antigen-binding domain against CEA is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Chmielewski et a / l., Gastroenterology 143 (4 ): 1095-1107 (2012).
[00663] [00663] In one embodiment, an antigen-binding domain against EPCAM is an antigen-binding portion, for example, CDRS, of an antibody selected from MT110, Bispecific Ab for EpcAM-CD3 (very, for example, clinicaltrials.gov / ct2 / show / NCT 00635596); Edrecolomab; 3622W94; ING-1; and adecatumumab (MT201).
[00664] [00664] In one embodiment, an antigen-binding domain against KIT is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in US7915391, US2012 0288506, and various antibodies from commercial catalogs.
[00665] [00665] In one embodiment, an antigen-binding domain against IL-13Ra2 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in WO2008 / 146911, WO2004087758, various antibodies from commercial catalogs and WO2004087758.
[00666] [00666] In one embodiment, an antigen-binding domain against CD171 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Hong et al, J Immunother 37 (2): 93- 104 (2014).
[00667] [00667] In one embodiment, an antigen-binding domain against PSCA is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Morgenroth et al., Prostate 67 (10): 1121- 1131 (2007) (scFv 7F5); Nejatollahi et al., J of Oncology 2013 (2013), article ID 839831 (scFv C5-ll); and US Pat Publication No. 20090311181.
[00668] [00668] In one embodiment, an antigen-binding domain against MAD-CT-2 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in PMID: 2450952; US7635753.
[00669] [00669] In one embodiment, an antigen-binding domain against the alpha folate receptor is an antigen-binding portion, for example, CDRs, of the IMGN853 antibody or an antibody described in US20120009181; US4851332, LK26: US5952484.
[00670] [00670] In one embodiment, an antigen-binding domain against ERBB2 (Her2 / neu) is an antigen-binding portion, for example, CDRs, of the trastuzumab or pertuzumab antibody.
[00671] [00671] In one embodiment, an antigen-binding domain against MUC1 is an antigen-binding portion, for example, CDRs, of the SAR566658 antibody.
[00672] [00672] In one embodiment, the antigen-binding domain against EGFR is an antigen-binding portion, for example, CDRs, of the cetuximab antibody, panitumumab, zalutumumab, nimotuzumab or matuzumab.
[00673] [00673] In one embodiment, an antigen-binding domain against NCAM is an antigen-binding portion, for example, CDRs, of the clone 2-2B antibody: MAB5324 (EMD Millipore).
[00674] [00674] In one embodiment, an antigen-binding domain against CAIX is an antigen-binding portion, for example, CDRs, of clone antibody 303123 (R&D Systems).
[00675] [00675] In one embodiment, an antigen-binding domain against the Fos 1-related antigen is an antigen-binding portion, for example, CDRs, of antibody 12F9 (Novus Biologicals).
[00676] [00676] In one embodiment, an antigen-binding domain against SSEA-4 is an antigen-binding portion, for example, CDRs, of the MC813 antibody (Cell Signaling) or other commercially available antibodies.
[00677] [00677] In one embodiment, an antigen-binding domain against PDGFR-beta is an antigen-binding portion, for example, CDRs, of an Abcam ab32570 antibody.
[00678] [00678] In one embodiment, an antigen-binding domain against ALK is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Mino-Kenudson et al., Clin Cancer Res 16 (5 ): 1561-1571 (2010).
[00679] [00679] In one embodiment, an antigen-binding domain against polysialic acid is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Nagae et al., J Biol Chem 288 (47) : 33784-33796 (2013).
[00680] [00680] In one embodiment, an antigen-binding domain against PLAC1 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Ghods et a / l., Bio-technol Appl Biochem 2013 doi: 10.1002 / bab.1177.
[00681] [00681] In one embodiment, an antigen-binding domain against GloboH is an antigen-binding portion of the VK9 antibody; or an antibody described, for example, in Kudryashov V et al, Glyco-conj J. 15 (3): 243-9 (1998), Lou et al., Proc Natl Acad Sci USA 111 (7): 2482-2487 ( 2014); MBr1: Bremer E-G et al. J Biol Chem 259: 14,773 a
[00682] [00682] In one embodiment, an antigen-binding domain against NY-BR-1 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Jager et al., Appl Immunohistochem Mol Morphol 15 (1): 77-83 (2007).
[00683] [00683] In one embodiment, an antigen-binding domain against sperm protein 17 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Song et al., Target Oncol 14 of August 2013 (PMID: 23943313); Song et al., Med Oncol 29 (4): 2,923 to 2,931 (2012).
[00684] [00684] In one embodiment, an antigen-binding domain against TRP-2 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Wang et al, J Exp Med. 184 (6 ): 2207-16 (1996).
[00685] [00685] In one embodiment, an antigen-binding domain against CYP1B1 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in Maecker et al, Blood 102 (9): 3287-3294 (2003).
[00686] [00686] In one embodiment, an antigen-binding domain against RAGE-1 is an antigen-binding moiety, for example,
[00687] [00687] In one embodiment, an antigen-binding domain against human telomerase reverse transcriptase is an antigen-binding portion, for example, CDRs, of the antibody cat: LS-B95-100 (Lifespan Biosciences)
[00688] [00688] In one embodiment, an antigen-binding domain against intestinal carboxyl esterase is an antigen-binding moiety, for example, CDRs, of antibody 4F12: cat no: LS-B6190-50 (LIfespan Biosciences ).
[00689] [00689] In one embodiment, an antigen-binding domain against mut hsp70-2 is an antigen-binding moiety, for example, CDRs, of the Lifespan Biosciences antibody: monoclonal: cat no: LS-C133261-100 (Lifespan Biosciences).
[00690] [00690] In one embodiment, an antigen-binding domain against MAD-CT-2 is an antigen-binding portion, for example, CDRs, of an antibody described, for example, in PMID: 2450952; US7635753.
[00691] [00691] In one embodiment, the antigen binding domain comprises one, two, three (for example, the three) heavy chain CDRs, HC CDR1, HC CDR2 and HC CDR3, from an antibody listed above, and / or one , two or three (for example, all three) light chain CDRs, LC CDR1, LC CDR2 and LC CDR3, of an antibody listed above. In one embodiment, the antigen binding domain comprises a heavy chain variable region and / or a light chain variable region of an antibody listed above.
[00692] [00692] In some modalities, the antigen-binding domain of a CAR directs a tumor antigen that is an antigen expressed in a myeloid tumor (both a surface antigen and presented by MHC), and a cell that comprises such a CAR recognizes a myeloid tumor antigen.
[00693] [00693] In one embodiment, the myeloid tumor antigen is an antigen that is preferentially or specifically expressed on the surface of a myeloid tumor cell.
[00694] [00694] In one embodiment, the antigen-binding domain of a CAR can be chosen so that a myeloid tumor population is targeted. Alternatively, when it is desired to target more than one type of myeloid tumor, an antigen-binding domain that targets a myeloid tumor antigen that is expressed by more than one, for example, all, of the myeloid tumors to be targeted dos can be selected.
[00695] [00695] A CAR can target the following additional tumor antigens: CD123, CD34, FIt3, CD33 and CLL-1. In modalities, the tumor antigen is selected from CD123, CD33 and CLL-1. In some modalities, the tumor antigen is CD123. In some modalities, the tumor antigen is CD33. In some modalities, the tumor antigen is CD34. In some modalities, the tumor antigen is FIt3. In modalities, the tumor antigen is CLL-1. In modalities, the antigen-binding domain targets the human antigen.
[00696] [00696] In one aspect, the antigen-binding domain of a CAR binds to CD123, for example, human CD123. Any known CD123 binding domain can be used in the invention. In one embodiment, an antigen-binding domain against CD123 is an antigen-binding portion, for example, CDRs or VH and VL, of an antibody, antigen-binding fragment or CAR described, for example, in PCT publication WO2014 / 130635, incorporated by reference in this document. In one embodiment, an antigen-binding domain against CD123 is an antigen-binding portion, for example, CDRs or VH and VL, of an antibody, antigen-binding fragment or CAR described, for example, in the publication. PCT classification WOZ2016 / 028896, incorporated by reference in this document. In one embodiment, an antigen-binding domain against CD123 is an antigen-binding portion, for example, CDRs, of an antibody, antigen-binding fragment or CAR described, for example, in PCT publication WO1997 / 024373, WO2008 / 127735 (for example, a CD123 binding domain of 26292, 32701, 37716 or 32703), WO2014 / 138805 (for example, a CD123 binding domain of CSL362) WO 2014/138819, WO 2013/173820 , WO2014 / 144622, WO2001 / 66139, WO2010 / 126066 (for example, the CD123 binding domain of any of Old4, Old5, Old1i7, Old19, New102 or Old6), WO 2014/14462 2, WO2016 / 028896 or US2009 / 0252742, incorporated by reference in this document. In embodiments, the antigen binding domain is or is derived from a murine anti-human CD123 binding domain. In embodiments, the antigen-binding domain is a humanized antibody or antibody fragment, for example, scFv domain. In one embodiment, the antigen-binding domain is a human antibody or antibody fragment that binds to human CD123. In embodiments, the antigen binding domain is an scFv domain that includes a light chain variable region (VL) and a heavy chain variable region (VH). VL and VH can be linked by a linker described here, for example, comprising the sequence GCGGGSGGGGSGCGGGGS (SEQ ID NO: 142), and can be in any orientation, for example, VL-linker-VH or VH-linker-VL.
[00697] [00697] In some embodiments, the antigen-binding domain of a CAR targets a B-cell antigen. In one embodiment, the B-cell antigen is an antigen that is preferentially or specifically expressed on the surface of the B-cell. The antigen can be expressed on the surface of any of the following types of B cells: progenitor B cells (eg, pre-B cells or pro-B cells), early pro-B cells, late pro-B cells, large, pre-B cells
[00698] [00698] The present description provides CARs that can target the following antigens: CD19; CD123; CD22; CD30; CD171; CS-1; type C lectin type 1 molecule, CD33; epidermal growth factor receptor (EGFRvIII) variant Ill; ganglioside G2 (GD2); ganglioside GD3; member of TNF receptor family; B cell maturation antigen; Tn antigen ((Tn Ag) or (GalNAca-Ser / Thr)); prostate-specific membrane antigen (PSMA); Orphan receptor 1 tyrosine kinase receptor (ROR1); tyrosine kinase 3 type Fms (FLT3); tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor alpha-2 subunit; Mesothelin; Alpha Interleukin 11 receptor (IL-11Ra); prostate stem cell antigen (PSCA); Protease serine 21; vascular endothelial growth factor receptor 2 (VEGFR2); Lewis antigen (Y); CD24; Platelet-derived growth factor beta receptor (PDGFR-beta); specific stage embryonic antigen-4 (SSEAH44); CD20; alpha folate receptor; ERBB2 receptor tyrosine protein kinase (Her2 / neu); mucin 1, associated with the cell surface (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); Prostasis; prostatic acid phosphatase (PAP); mutated stretching factor 2 (ELF2M); Ephrin B2; alpha fibroblast activation protein (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CAIX); proteasome subunit (prosome, macropaine), Type Beta, 9 (LMP2); glycoprotein
[00699] [00699] In another modality, the antigen targeted by the CAR is chosen from CD19, BCMA, CD20, CD22, FcRn5, FeRn2, CS-1 and CD138. In one embodiment, the antigen targeted by the CAR is CD19. In one embodiment, the antigen targeted by the CAR is CD20. In one way, the antigen targeted by the CAR is CD22. In one embodiment, the antigen targeted by the CAR is BCMA. In one embodiment, the antigen targeted by the CAR is FcRn5. In one embodiment, the antigen targeted by the CAR is FcRn2. In one embodiment, the antigen targeted by the CAR is CS-1. In one embodiment, the antigen targeted by the CAR is CD138.
[00700] [00700] In one embodiment, the antigen-binding domain of a CAR, for example, the CAR expressed by a cell of the invention (for example, a cell that also expresses a CAR), can be chosen in order to target a population of preferential B cells. For example, in a mode where it is desired to target regulatory B cells, an antigen-binding domain is selected that targets an antigen that is expressed on regulatory B cells and not on other B cell populations, for example, plasma B cells and memory B cells. Cell surface markers expressed on regulatory B cells include: CD19, CD24, CD25, CD38 or CD86 or markers described in He et al., 2014, J Immunology Research, Article ID 215471. When it is desired to target more than one type of B cells, an antigen-binding domain that targets an antigen that is expressed by all the B cells to be targeted can be selected. Transmembrane domain of CAR
[00701] [00701] In relation to the transmembrane domain, in several modalities, a CAR can be designed to comprise a transmembrane domain that is linked to the extracellular domain of the CAR. A transmembrane domain can include one or more additional amino acids adjacent to the transmembrane region, for example, one or more amino acids associated with the extracellular region of the protein from which the transmembrane was derived (for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 to 15 amino acids from the extracellular region) and / or one or more additional amino acids associated with the intracellular region of the protein from which the transmembrane protein is derived (for example, 1, 2, 3, 4 , 5,6,7,8,
[00702] [00702] The transmembrane domain can be derived from a natural or recombinant source. When the source is natural, the domain can be derived from any membrane-bound or trans-membrane protein. In one aspect, the transmembrane domain is capable of signaling the intracellular domain (s) whenever the CAR has linked to a target. A transmembrane domain of particular use in this invention may include at least the transmembrane region (s), for example, of the alpha, beta or zeta chain of the T cell receptor, CD28, CD27, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD1I5A4. In some embodiments, a transmembrane domain may include at least the transmembrane region (s), for example, from KIR2DS2, OX40, CD2, CD27, LFA-1 (CD11a, CD18), ICOS (CD278), 4-1BB (CD137), GITR, CD40, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD160, CD19, IL2R beta, IL2R gamma, IL7R qa, ITGA1, VLA1, CD49a, VLA1, CD49a ITGAA4, IA4, CD49D, ITGAS6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1,
[00703] [00703] In some cases, the transmembrane domain can be | attached to the extracellular region of the CAR, for example, the antigen binding domain of the CAR, through a hinge region, for example, a hinge region of a human protein. For example, in one embodiment, the hinge can be a human Ig (immunoglobulin) hinge, for example, an I9G4 hinge or a CD8a hinge. In one embodiment, the hinge or spacer comprises (for example, consists of) the amino acid sequence of SEQ ID NO: 147. In one aspect, the transmembrane domain comprises (for example, consists of) a transmembrane domain of SEQ ID NO: 155.
[00704] [00704] In one aspect, the hinge or spacer comprises an IgG4 hinge. For example, in one embodiment, the hinge or spacer comprises a hinge of the amino acid sequence ESKYGPPCPPCPAPEFLGGPSVFLFPPKPKDTLMISRTPEVTCVVVD VSQEDPEVQFNWYVDGVEVHNAKTKPREEQFNSTYRVVSVLTVLHQ DWLNGKEYKCKVSNKGLPSSIEKTISKAKGQPREPQVYTLPPSQEEM TKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFF
[00705] [00705] GAGAGCAAGTACGGCCCTCCCTGCCCCCCTTGCCCTG SAMSCGAGTTCETGGGCGGACCCAGCGTGTTCCTGTTCCCCCCC AAGCCCAAGGACACCCTGATGATCAGCCGGACCCCCGAGGTGAC CTSGTGTGGTGGTGGACGTGTCCCAGGAGGACCCCGAGGTCCAGT TCAACTGGTACGTGGACGGCGTGGAGGTGCACAACGCCAAGACC AAGCCCCGGGAGGAGCAGTTCAATAGCACCTACCGGGTGGTGTC CGTGCTGACCGTGCTGCACCAGGACTGGCTGAACGGCAAGGAAT ACAAGTGTAAGGTGTCCAACAAGGGCCTGCCCAGCAGCATCGAG AAAACCATCAGCAAGGCCAAGGGCCAGCCTCGGGAGCCCCAGGT GTACACCCTGCCCCCTAGCCAAGAGGAGATGACCAAGAACCAGG TGTCCCTGACCTGCCTGGTGAAGGGCTTCTACCCCAGCGACATC GCCGTEGGAGTGGGAGAGCAACGGCCAGCCCGAGAACAACTACAA GACCACCCCCCCTGTGCTGGACAGCGACGGCAGCTTCTTCCTGT ACAGCCGGCTGACCGTGGACAAGAGCCGGTGGCAGGAGGGCAA
[00706] [00706] In one aspect, the hinge or spacer comprises an IgD hinge. For example, in one embodiment, the hinge or spacer comprises a hinge of the amino acid sequence RWPESPKAQASSVPTAQPQAEGSLAKATTAPATTRNTGRGGEEKKK EKEKEEQEERETKTPECPSHTQPLGVYLLTPAVQDLWLRDKATFTCF VVGSDLKDAHLTWEVAGKVPTGGVEEGLLERHSNGSQSQHSRLTLP RSLWNAGTSVTCTLNHPSLPPQRLMALREPAAQAPVKLSLNLLASSD PPEAASWLLCEVSGFSPPNILLMWLEDOQREVNTSGFAPARPPPQPG
[00707] [00707] In one aspect, the transmembrane domain may be a combination, in which case it will comprise predominantly hydrophobic residues, such as leucine and valine. In one aspect, a phenylalanine, tryptophan and valine triplet can be found at each end of a recombinant transmembrane domain.
[00708] [00708] Optionally, a short oligo- or polypeptide linker, between 2 and 10 amino acids in length, can form the link between the transmembrane domain and the cytoplasmic region of the CAR. A glycine-serine doublet provides a particularly suitable binder. For example, in one aspect, the linker comprises the amino acid sequence of GGGGSGGGGS (SEQ ID NO: 153). In some
[00709] [00709] In one aspect, the hinge or spacer comprises a KIR2DS 2 hinge. Cytoplasmic domain
[00710] [00710] The CAR cytoplasmic domain or region includes an intracellular signaling domain. An intracellular signaling domain is, in general, responsible for the activation of at least one of the normal effector functions of the immune cell in which the CAR was introduced.
[00711] [00711] Examples of intracellular signaling domains for use in a CAR described in this document include the cytoplasmic T cell receptor (TCR) sequences and co-receptors that act together to initiate signal transduction after coupling the T cell receptor. antigen, as well as any derivative or variant of these sequences and any recombinant sequence that has the same functional capacity.
[00712] [00712] It is known that signals generated through the TCR alone are insufficient for complete activation of the T cell and that a secondary and / or co-stimulator signal is also required. Thus, it can be said that T cell activation is mediated by two distinct classes of cytoplasmic signaling sequences: those that initiate primary antigen-dependent activation through TCR (primary intracellular signaling domains) and those that act in an intrinsic way. - dependent on antigens to provide a secondary or co-stimulatory signal (secondary cytoplasmic domain, for example, a co-stimulatory domain).
[00713] [00713] A primary signaling domain regulates the primary activation of the TCR complex in a stimulatory or inhibitory manner. Primary intracellular signaling domains that act in a stimulating manner may contain signaling motifs that are known as immunoreceptor tyrosine-based activation motifs or ITAMs.
[00714] [00714] Examples of primary intracellular signaling domains containing ITAMs that have particular use in the invention include those of zeta TCR, FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, CD278 (also known as "ICOS"), FceRI, DAP10, DAP12, and CD66d. In one embodiment, a CAR of the invention comprises an intracellular signaling domain, for example, a primary CD3-zeta signaling domain, for example, a CD3-zeta sequence described herein.
[00715] [00715] In one embodiment, a primary signaling domain comprises a modified ITAM domain, for example, a mutated ITAM domain that has altered activity (for example, increased or decreased) compared to the ITAM domain native. In one embodiment, a primary signaling domain comprises a primary intracellular signaling domain containing modified ITAM, for example, a primary intracellular signaling domain containing optimized and / or truncated ITAM. In one embodiment, a primary signaling domain comprises one, two, three, four or more ITAM motifs. Co-Stimulating Signaling Domain
[00716] [00716] The intracellular signaling domain of the CAR can comprise the CD3-zeta signaling domain alone or can be combined with any other desired intracellular signaling domain (or domains) useful in the context of a CAR of the invention. For example, the CAR intracellular signaling domain may comprise a portion of the CD3 zeta chain and a co-stimulating signal domain. The co-stimulatory signaling domain refers to a portion of the CAR that comprises the intracellular domain of a co-stimulating molecule. In one embodiment, the intracellular domain is designed to comprise the CD3-zeta signaling domain and the CD28 signaling domain. In one aspect, the intracellular domain is designed to understand the CD3-zeta signaling domain and the ICOS signaling domain.
[00717] [00717] The co-stimulating molecule can be a molecule of the cell surface that is not an antigen receptor or its ligands that is necessary for an efficient lymphocyte response to an antigen. Examples of such molecules include CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, antigen associated with lymphocyte-1 (LFA-1), CD2, CD7, LIGHT function , NKG2C, B7-H3 and a linker that specifically binds to CD83 and the like. For example, co-stimulation with CD27 has been shown to enhance the expansion, effector function and survival of human CART cells in vitro and increase the persistence and antitumor activity of human T cells in vivo (Song et al. Blood. 2012 119 (3): 696-706). Additional examples of such co-stimulating molecules include CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), NKp30, NKp44, NKp46, CD160, CD19, CDA4, CD8alfa, CD8beta, IL2R beta, IL2R beta, IL2R beta, IL2R beta gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGAA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1 , CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE / RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile) ,, CEACAM1, CRTAM, Ly9 (CD229), CD160 ( BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3)) BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP- 76, NKG2D, NKG2C and PAG / Cbp.
[00718] [00718] The intracellular signal sequences within the cytoplasmic portion of the CAR can be linked together at random
[00719] [00719] In one aspect, the intracellular signaling domain is designed to comprise two or more, for example, 2, 3, 4, 5 or more, co-stimulating signaling domains. In one embodiment, the two or more, for example 2, 3, 4, 5 or more co-stimulatory signaling domains are separated by a linker molecule, for example, a linker molecule described herein. In one embodiment, the intracellular signaling domain comprises two co-stimulating signaling domains. In some embodiments, the binding molecule is a glycine residue. In some embodiments, the binder is an alanine residue.
[00720] [00720] In one aspect, the intracellular signaling domain is designed to understand the CD3 zeta signaling domain and the CD28 signaling domain. In one aspect, the intracellular signaling domain is designed to understand the CD3 zeta signaling domain and the 4-1BB signaling domain. In one aspect, the 4-1BB signaling domain is a signaling domain of SEQ ID NO: 158. In one aspect, the CD3-zeta signaling domain is a signaling domain of SEQ ID NO: 163.
[00721] [00721] In one aspect, the intracellular signaling domain is designed to understand the CD3 zeta signaling domain and the CD27 signaling domain. In one aspect, the CD27 signaling domain comprises an amino acid sequence of
[00722] [00722] In one aspect, the CAR expressing cell described in this document may further comprise a second CAR, for example, a second CAR that includes a different antigen binding domain, for example, for the same target or a different target - close (for example, a target other than a cancer-associated antigen described in this document or a different cancer-associated antigen described in this document, for example, CD19, CD33, CLL-1, CD34, FLT3 or beta folate receptor ). In a fashion, the second CAR includes an antigen-binding domain for a target expressed in the same type of cancer cell as the cancer-associated antigen. In one embodiment, the CAR-expressing cell comprises a first CAR that targets a first antigen and includes an intracellular signaling domain that has a co-stimulating signaling domain, but not a primary signaling domain, and a second CAR that targets a different second antigen and includes an intracellular signaling domain that has a primary signaling domain, but not a co-stimulating signaling domain. Without sticking to the theory, the placement of a co-stimulating signaling domain, for example, 4-1BB, CD28, ICOS, CD27 or OX-40, in the first CAR, and the primary signaling domain, for example, CD3 zeta, in according to CAR it can limit the activity of CAR to cells in which both targets are expressed. In one embodiment, the cell expressing CAR comprises a first CAR for an antigen
[00723] [00723] In another aspect, the description presents a population of cells that express CAR, for example, CART cells. In some modalities, the population of cells that expresses CAR comprises a mixture of cells that expresses different CARs. For example, in one embodiment, the population of CART cells may include a first cell expressing a CAR having an antigen-binding domain for a cancer-associated antigen described here, and a second cell expressing a CAR having a binding domain to different antigens, for example, an antigen-binding domain for a different cancer-associated antigen described here, for example, an antigen-binding domain for a cancer-associated antigen described here that differs from the antigen associated with cancer linked by the CAR antigen-binding domain expressed by the first cell. As another example, the population of cells expressing CAR may include a first cell that expresses
[00724] [00724] In another aspect, the present description presents a population of cells in which at least one cell in the population expresses a CAR that has an antigen-binding domain for a cancer-associated antigen described in this document and a second cell that expresses another agent, for example, an agent that enhances the activity of a cell that expresses CAR. For example, in one embodiment, the agent can be an agent that inhibits an inhibitory molecule. Inhibitory molecules, for example, PD-1, may, in some modalities, decrease the ability of a cell expressing CAR to mount an effective immune response. Examples of inhibitory molecules include PD-1, PD-L1, CTLAA4, TIM3, CEACAM (CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4, CD80 , CD86, B7-H3 (CD276), B7-H4 (VTCN1), HVEM (TNFRSF14 or CD270), KIR, A2aR, MHC class |, MHC class Il, GAL9, adenosine and TGF (for example, TGF beta) . In one embodiment, the agent that inhibits an inhibitory molecule comprises a first polypeptide, for example, an inhibitor molecule, associated with a second polypeptide that provides a positive signal to the cell, for example, an intracellular signaling domain described in this document. In one embodiment, the agent comprises a first polypeptide, for example, from an inhibitory molecule, such as PD-1, PD-L1, CTLA4, TIM3, CEACAM (CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG3, VISTA, BTLA, TIGIT, LAIRI1, CD160, 2B4 and TGF beta, or a fragment of either, and a second polypeptide that is an intracellular signaling domain described in this document (for example, that comprises a co-stimulatory domain (for example, 41BB, CD27, OX40 or CD28, for example, as described in this document) and / or a primary signaling domain (for example, a CD3 zeta signaling domain described in In one embodiment, the agent comprises a first PD-1 polypeptide or fragment thereof, and a second polypeptide from an intracellular signaling domain described here (for example, a described CD28 signaling domain here and / or a zeta CD3 signaling domain described here).
[00725] [00725] In some embodiments, the heterologous polypeptide of interest linked to a COFI / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN and / or a degradation domain is a regulatory protein. Regulatory polypeptides and coding sequences for regulatory polypeptides useful in genetic control circuits, cells, and methods for identifying, selecting or producing a cell or cell line capable of producing high yields of a product, for example, are provided in this document. recombinant or therapeutic polypeptide. In general, regulatory polypeptides regulate the expression of the product, for example, a recombinant or therapeutic polypeptide. In some embodiments, the regulatory polypeptide is a gene-editing polypeptide. In some modalities, the regulatory polypeptide coding sequence is under the transcriptional control of a control element that activates the transcription of the regulatory polypeptide coding sequence depending on
[00726] [00726] It is contemplated that the present description is not specific for a specific regulatory polypeptide. Exemplary regulatory polypeptides include, but are not limited to: Cas9 molecules, TALE molecules and zinc finger molecules. In some modalities, the regulatory polypeptide is a Cas-related protein known in the art. In some embodiments, the regulatory polypeptide is a protein from a CRISPR / Cas system type |, Il or Ill (for example, as described in KS Makarova et al., Nat. Rev. Microbiol. 9, 467 (2011 ); KS Makarova, NV Grishin, SA Shabalina, Y. |. Wolf, EV Koonin, Biol. Direct 1, 7 (2006); or KS Makarova, L. Aravev, Y. 1. Wolf, EV Koonin, Biol Direct 6, 38 (2011)).
[00727] [00727] In some embodiments, the regulatory polypeptide is a Cas9 molecule. Regulatory polypeptides that are Cas9 molecules require one or more (for example, one, two, three, four or more) suitable gRNAs to inhibit the expression of a recombinant or therapeutic polypeptide.
[00728] [00728] In some embodiments, the regulatory polypeptide is a TALE molecule.
[00729] [00729] In some embodiments, the regulatory polypeptide is a zinc finger molecule.
[00730] [00730] In some embodiments, the regulatory polypeptide is an endogenous regulator of the first control element, for example, the first promoter element. In one embodiment, the endogenous gene encoding the regulatory polypeptide is inactive, for example, it has been inactivated or mutated to produce a loss of function. Cas9 Molecules and Other CRISPR / CAS System Components
[00731] [00731] In some embodiments, the heterologous polypeptide of interest linked to a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and / or a degradation domain is a Cas9 molecule, a Cas12 molecule, a molecule Cas13, or another component of the CRISPR / CAS system (for example, a ribonucleoprotein (RNP) molecule). For gene therapies that use the CRISPR / CAS system, an important consideration is to limit the side effects caused by the off-target activity of a Cas molecule (for example, a Cas9 molecule). The fusion of a degron, for example, a COF1I / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN described in this document, for example, the HilD tag or CARB label described in this document, with a component of the CRISPR / CAS system (for example, a Cas9 molecule or an RNP molecule) helps to generate gene therapy in which the activity of the CRISPR / CAS system can be regulated by a step compound
[00732] [00732] The Cas9 molecules that will be used in the genetic control circuits, cells and methods of the present description can comprise polypeptides that originate in a variety of species. In addition, one or more domains of a Cas9 molecule in one species can be combined with one or more domains of a Cas9 molecule in another species, for example, in a fusion protein. Species comprising additional Cas9 polypeptides include: Acidovorax avenae, Actinobacillus pleuropneumoniae, Actinobacillus succinogenes, Actinobacillus suis, Actinomyces sp., Cycliphilus denitrificans, Aminomonas paucivorans, Bacillus cereus, Bacillus cereus, Bacillus Systisi, Bacillus Syltisis Bradyrhizobium sp., Brevibacillus laterosporus, Campylobacter coli, Campylobacter jejuni, Campylobacter lari, Candidatus Puniceispirillum, Clostridium cellulolyticum, Clostridium perfringens, accolens Corynebacterium, Corynebacterium diphtheria, Corynebacterium matruchotii, Dinoroseobacter shibae, Eubacterium dolichum, gamma proteobacte- RIUM, Gluconacetobacter diazotrophicus, Haemophilus parainfluenzae , Haemophilus sputorum, Helicobacter canadensis, Helicobacter cinaedi, Helicobacter mustelae, Ilyobacter polytropus, Kingella kingae, Lacto-bacillus crispatus, Listeria ivanovii, Listeria monocytogenes, Listeriace-ae bacterium, Methylocystis sp., Methylylystis sp. osinus trichosporium, Mobiluncus mulieris, Neisseria bacilliformis, Neisseria cinerea, Neisseria flavescens, Neisseria lactamica, Neisseria meningitidis, Neisseria sp., Neisseria wadsworthii, Nitrosomonas sp., Parvibaculum lavamentivo, richard, pasteur Rhodopseudomonas palustris, Rhodovulum sp., Si monsiella muelleri, Sphingomonas sp., Sporolactobacillus vineae, Staphylococcus lugdunensis, Streptococcus sp., Subdoligranulum sp., Tis-
[00733] [00733] The Cas12 molecules (eg, Cas12a, Cas12b and Cas12c) have been disclosed, for example, in Chen et al., Science. April 2018 27; 360 (6387): 436-439 and Shmakov et al., Nat Rev Microbiol. March 2017; 15 (3): 169-182, incorporated in this document as a reference in its entirety. CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind to DNA and generate targeted double-stranded DNA breaks. Like CRISPR-Cas9, Cas12 is also a useful tool in genome editing. Additional Cas molecules that are useful for editing genes include, but are not limited to, Cas13, for example, Cas13a, Cas13b, and Cas13c, as disclosed, for example, in document No. WO2017219027 and Shmakov et al., Nat Rev Microbiol . March 2017; 15 (3): 169-182, incorporated in this document as a reference in its entirety. In some embodiments, the heterologous polypeptide of interest is Cas12. In some embodiments, the heterologous polypeptide of interest is Cas13. Cas9 Structure and Activity
[00734] [00734] Crystal structures are available for naturally occurring Cas9 polypeptides (Jinek et al., Science, 343 (6176): 1247997, 2014) and for S. pyogenes Cas9 with a guide RNA (for example, a synthetic fusion de cr »RNA and tracrRNA) (Nishimasu et al., Cell, 156: 935-949, 2014; and Anders et al., Nature, 2014, doi: 10.1038 / natural13579).
[00735] [00735] In one embodiment, a Cas9 molecule or Cas9 polypeptide comprises one or more of the following domains: a domain similar to RuvC and a domain similar to HNH. In a fashion, a Cas9 molecule or Cas9 polypeptide is a dCas9 molecule or dCas9 polypeptide and the dCas9 molecule or dCas9 polypeptide comprises a domain similar to RuvC, for example, a domain similar to RuvC that is devoid of nu-
[00736] [00736] In one embodiment, the Cas9 molecule or Cas9 polypeptide can include more than one RuvC-like domain (for example, one, two, three or more RuvC-like domains). In one embodiment, a domain similar to RuvC comprises one or more mutations that alter its activity, so that the RuvC domain does not cleave DNA or has reduced DNA cleavage activity. In one embodiment, a RuvC-like domain is at least 5, 6, 7, 8 amino acids in length, but no more than 20, 19, 18, 17, 16 or 15 amino acids in length. In one embodiment, the Cas9 molecule or Cas9 polypeptide comprises an N-terminal RuvC-like domain of about 10 to 20 amino acids, for example, about 15 amino acids in length.
[00737] [00737] In one embodiment, the Cas9 molecule or Cas9 polypeptide can include more than one HNH-like domain (for example, one, two, three or more HNH-like domains). In one embodiment, an HNH-like domain comprises one or more mutations that alter its activity, so that the HNH-like domain does not cleave DNA or has reduced DNA cleavage activity. In one embodiment, an HNH-like domain is at least 15, 20, 25 amino acids in length, but no more than 40, 35 or 30 amino acids in length, for example, 20 to 35 amino acids in length, for example, 25 to 30 long amino acids.
[00738] [00738] In some embodiments, Cas9 molecules or Cas9 polypeptides have the ability to interact with a gRNA molecule and in conjunction with the gRNA molecule for a major target domain, but are unable to cleave the target nucleic acid , or unable to cleave at efficient rates. Cas9 molecules that have no cleavage activity, or have no substantial cleavage activity are referred to herein as dCas9 molecules or dCas9 polypeptides. For example, a dCas9 molecule or dCas9 polypeptide may be devoid of cleavage activity or have substantially less, for example, less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule or Cas9 polypeptide, as measured by assays known in the art or assays described herein. Targeting and PAMs
[00739] [00739] A Cas9 molecule or Cas9 polypeptide is a polypeptide that can interact with a guide RNA (gRNA) molecule and, in conjunction with the gRNA molecule, is located at a site that comprises a target domain and a PAM sequence.
[00740] [00740] In one embodiment, the ability of a Cas9 molecule or Cas9 polypeptide to interact with a target nucleic acid is dependent on the PAM sequence. A PAM sequence is a sequence in the target nucleic acid. Cas9 molecules of different bacterial species can recognize different sequence motifs (for example, PAM sequences). Cas9 molecules can be manipulated to alter the PAM specificity of the Cas9 molecule. Examples of naturally occurring Cas9 molecules are described in Chylinski et al., RNA BioLOGY 2013; 10: 5, 727-737. Changes to the Cas9 Structure
[00741] [00741] In some embodiments, one or more mutations may be present, for example, in: one or more domains similar to RuvC, for example, a domain similar to RuvC in N-terminal; a domain similar to HNH; a region outside the RuvC-like domains and the HNH-like domain of the Cas9 molecule or Cas9 polypeptide. In some modalities, a mutation (or mutations) is (or are) present (s) in a domain similar to RuvC,
[00742] [00742] In one embodiment, a Cas9 molecule or Cas9 polypeptide, for example, a dCas9 molecule or dCas9 polypeptide, comprises an amino acid sequence: having 60%, 65%, 70%, 75%, 80%, 85%, 90 %, 95%, 96%, 97%, 98% or 99% homology with; which differs by no more than, 2, 5, 10, 15, 20, 30 or 40% of the amino acid residues compared to; which differs by at least 1, 2, 5, 10 or 20 amino acids, but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or that it is identical to any sequence of Cas9 molecules described herein, or a sequence of naturally occurring Cas9 molecules, for example, a Cas9 molecule of a species listed herein or described in Chylinski et a /. , RNA Bio-LoGY 2013 10: 5, 727-737; Hou et al., PNAS Initial Edition 2013, 1-6 ;. In one embodiment, the Cas9 molecule or Cas9 polypeptide comprises one or more of the following activities: a helical activity; or the ability, along with a gRNA molecule, to locate itself in a target nucleic acid. In one embodiment, the Cas9 molecule or Cas9 polypeptide does not comprise a nickase activity or a double-stranded cleavage activity (for example, an endonuclease and / or exonuclease activity).
[00743] [00743] Exemplary mutations that can be made in the RuvC domain or HNH domain with reference to the sequence of S. pyo-genes include: D10A, E762A, H840A, N854A, N863A and / or D986A.
[00744] [00744] The exemplary Cas9 polypeptide sequences and Cas9 domains can be found in Tables 50 to 54 of document No. WO2015 / 157070. DCas9 polypeptides
[00745] [00745] In one embodiment, the heterologous polypeptide of interest linked to a COFI / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and / or a degradation domain is a dCas9 molecule, for example, a dCas9 polypeptide which comprises one or more differences in a RuvC domain and / or an HNH domain compared to a Cas9 reference molecule, and the dCas9 molecule or dCas9 polypeptide does not cleave a nucleic acid, or cleaves significantly less efficiently than the type wild, for example, compared to wild type in a cleavage assay, for example, as described in this document, cuts with less than 50, 25, 10 or 1% of a Cas9 reference molecule, as measured by a test described in this document.
[00746] [00746] The mutation of the main mutation residues in both DNA cleavage domains of the Cas9 protein (for example, mutations of D10A and H840A) results in the generation of a catalytically active Cas9 molecule (dCas9 which is also known as Cas9 dead). An enzymatically inactive Cas9, for example, dCas9, complexes with a gRNA and is located in the DNA sequence specified by the gRNA targeting domain; however, it does not cleave the target DNA. An enzymatically inactive Cas9 molecule (eg, dCas9) can block transcription when recruited to initial regions in the coding sequence. Additional repression can be accomplished by merging a transcriptional repression domain (eg KRAB, SID or ERD) with enzymatically inactive Cas9, eg dCas9, and recruiting it into the target sequence, for example, within 1000bp of 3 'sequence of the initial codon or within 500 bp of a control element, for example, promoter element, for example, 5' of the initial codon of a gene. Targeting of DNase hypersensitive sites | (DHSs) of the promoter (for example, making gRNAs complementary to DHSs) can be an additional strategy for genetic repression, for example, inhibition of a recombinant or therapeutic polypeptide coding sequence, as these regions are more likely to be accessible to the Enzymatically inactive Cas9, for example, dCas9, and also host sites for endogenous transcription factors. Without adhering to theory, it is contemplated in this document that blocking the binding site of an endogenous transcription factor or RNA polymerase could assist in the down-regulation of gene expression, for example, expression of a coding sequence of recombinant or therapeutic polypeptide. In one embodiment, one or more enzymatically inactive Cas9 molecules, for example, dCas9 molecules, can be used to block the binding of one or more endogenous transcription factors. In another embodiment, an enzymatically inactive Cas9 molecule, for example, dCas9, can be fused with an effector domain, for example, a repression domain, an activation domain, a methylation enzyme, etc. The fusion of the enzymatically inactive Cas9 molecule, for example, dCas9, with an effector domain allows the recruitment of the effector to any DNA site specified by the gRNA. Changing the chromatin status can result in reduced expression of the target gene. One or more enzymatically inactive Cas9 molecules, for example, dCas9, fused with one or more chromatin-modifying proteins can be used to alter the chromatin status.
[00747] [00747] In one embodiment, a gRNA molecule can be targeted to a control element (eg, promoter element), for example, the control element functionally linked to a recombinant polypeptide coding sequence or therapeutic. In one embodiment, a gRNA molecule can be targeted to a sequence that encodes a recombinant or therapeutic polypeptide. TALE molecules
[00748] [00748] In some embodiments, the heterologous polypeptide of interest linked to a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and / or a degradation domain, is an effector molecule similar to a transcription activator ( TALE) or TALE polypeptide. A TALE molecule or polypeptide, as the term is used herein, refers to a molecule or polypeptide that comprises multiple TALE DNA-binding repeat domains (TALE DBDs) that can host or locate at nucleic acid position specified by the TALE DBDs. The TALE molecule and the TALE polypeptide, as used in this document, refer to naturally occurring TALE molecules and to manipulated, altered or modified TALE molecules or TALE polypeptides that differ, for example, in at least an amino acid residue, from a reference sequence, for example, the most similar naturally occurring TALE molecule known in the art.
[00749] [00749] The DBD of TALE, as the term is used in this document, refers to an amino acid motif 33 to 35, including two hypervariable residues (ie, a variable repeat residue, RVD) in positions 12 and 13 of the subject. The RVD of a TALE DNA binding domain (DBD) specifies the basic pair or basic pairs of DNA with which the TALE DBD has binding affinity. When TALE DBDs are combined into arrays within a TALE molecule or TALE polypeptide, the order of TALE DBDs (and their RVD) determines the DNA sequence with which a molecule
[00750] [00750] The variable repeat residue (RVD), as the term is used in this document, refers to the two hypervariable amino acid residues at positions 12 and 13 of a DBD of TALE. RVD determines the affinity of basic pairs of DNA from a TALE DBD. All possible combinations of RVDs and their respective basic pair affinities are known in the art. See, for example, Cong L., et al. Nat Commun. 2012 Jul 24; (3): 968; Juillerat A., et al. Sci Rep. 2015 Jan 30; 5 (): 8150; Miller J. C. et al. Nat Methods 12, 465471 (2015); Streubel J., et al. Nat Biotechnol 30, 593-595 (2012); and Yang J. et al. Cell Res 24, 628-631 (2014), incorporated in this document as a reference in its entirety. All possible RVDs are contemplated for use with the repressing polypeptides, for example, TALE molecules, described in this document.
[00751] [00751] The DBD matrix of TALE, as the term is used in this document, refers to the identities and order of DBDs of TALE, for example, the RVDs of each DBD of TALE, within a hand - TALE molecule or TALE polypeptide. The TALE DBD matrix determines the sequence specific binding affinity of a TALE molecule or TALE polypeptide.
[00752] [00752] In some embodiments, the repressor polypeptide is a TALE molecule or TALE polypeptide. The DBDs of TALE and TALE polypeptide of any species of Xanthomonas can be used in genetic control circuits, cells, and methods to identify, select or produce a cell or cell line capable of producing high yields of a product, for example example, a recombinant or therapeutic polypeptide, described herein. And bad-
[00753] [00753] In some embodiments, a manipulated TALE molecule or TALE polypeptide comprises an amino acid sequence: having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with; which differs by no more than, 2, 5, 10, 15, 20, 30 or 40% of the amino acid residues compared to; which differs by at least 1, 2, 5, 10 or 20 amino acids, but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or that is identical to any sequence of TALE molecules described in this document, or a sequence of naturally occurring TALE molecules, for example, a TALE molecule of a species listed in this document or described in a publication mentioned. in this document.
[00754] [00754] In some embodiments, a TALE molecule is located in the target DNA sequence specified by that TALE DBD matrix of TALE molecules. In some embodiments, the TA-LE molecule can block transcription when recruited to initial regions in a coding sequence, for example, the coding sequence for a recombinant or therapeutic polypeptide. In some embodiments, a TALE molecule can block transcription when recruited to a control element, for example, a promoter element, functionally linked to a recombinant or therapeutic polypeptide coding sequence. In some modalities
[00755] [00755] In some embodiments, a TALE molecule comprises two or more (for example 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 , 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42 , 43, 44, 45, 46, 47, 48, 49, 50, or more) TALE DBDs.
[00756] [00756] In some embodiments, the TALE DBD matrix of a repressor polypeptide, for example, TALE molecule, specifies a target DNA sequence. In some embodiments, the target sequence specified by the TALE DBD matrix is comprised within a control element, for example, promoter element, functionally linked to a recombinant or therapeutic polypeptide coding sequence. In some embodiments, the target sequence specified by the TALE DBD matrix is comprised of a recombinant or therapeutic polypeptide coding sequence.
[00757] [00757] Exemplary naturally occurring and manipulated polypeptide sequences and methods for the design and testing of TALE polypeptides for use with genetic control circuits, cells, and methods for identifying, selecting or marking a cell or cell line capable of producing high yields of a product, for example, a recombinant or therapeutic polypeptide, described in this document, can be found in the art, for example, in Zhang F, et al. Nat Biotechnol. 2011; 29: 149—153; Geissler R, et al. PLoS One. 2011; 6: 219509; Garg A, et al. Nucleic Acids Res. 2012; Bultmann S, et al. Nucleic Acids Res. 2012; 40: 5368-5377; Cermak T, et al. Efficient design and assembly of custom TALEN and others
[00758] [00758] In some embodiments, the heterologous polypeptide of interest linked to a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and / or a degradation domain is a zinc finger molecule. A zinc finger molecule, as the term is used herein, refers to a molecule or polypeptide that comprises multiple zinc finger domains (ZFDs). A zinc finger molecule has an affinity for a specific DNA sequence determined by the identity and order of the ZFDs that the zinc finger molecule comprises.
[00759] [00759] - A zinc finger domain (ZFD), as the term is used in this document, refers to any one of a family of polypeptides that binds DNA in a specific sequence and requires that a zinc ion ligand to bind to DNA. Many families of ZFDs have been studied and characterized (see, for example, Krishna, SS., Et al. Nucl. Acids Res. (2003) 31 (2): 532-550). The description includes zinc finger molecules that can comprise ZFDs of any type or origin known to those skilled in the art. Without limiting itself to any specific type of ZFD, the description includes zinc finger molecules that comprise ZFDs of Cys2His2, which are the most prevalent and well-studied ZFDs in the art. The Cys2His2 ZFDs comprise two beta strips that form an antiparallel beta sheet and an alpha helix. The alpha-helix positions -1, 1,2,3, 5 and 6 are known to specify specific DNA sequence binding by interacting with basic DNA pairs. In one embodiment, a Cys2His2 ZFD may have specific binding affinity with a target sequence of 3 basic pairs. In one embodiment, a Cys2His2 ZFD can specifically interact with an additional base pair adjacent to the target sequence in a context specific manner, that is, dependent on the presence or identity of adjacent ZFDs within a zinc finger molecule.
[00760] [00760] A zinc finger domain matrix, or ZFD matrix, as the term is used in this document, refers to the identities and order of ZFDs, within a zinc finger molecule or zinc finger polypeptide . The ZFD matrix determines the sequence-specific binding affinity of a zinc finger molecule or zinc finger polypeptide.
[00761] [00761] In some embodiments, the repressor polypeptide is a zinc finger molecule or zinc finger polypeptide. ZFDs and zinc finger polypeptides of any species (for example, a mammalian species, for example, humans) can be used in genetic control circuits, cells, and methods to identify, select or produce a cell or cell line able to produce high yields of a product, for example, a recombinant or therapeutic polypeptide, described in the present document. In some embodiments, the repressor polypeptide is a zinc finger molecule or zinc finger polypeptide. In some embodiments, the repressor polypeptide is a manipulated zinc finger molecule or zinc finger polypeptide, that is, a zinc finger molecule or zinc finger polypeptide that differs by one or more amino acids from a zinc finger molecule or naturally occurring zinc finger polypeptide or other zinc finger molecule or manipulated zinc finger polypeptide known in the art.
[00762] [00762] In some embodiments, a manipulated zinc finger molecule or zinc finger polypeptide comprises a sequence
[00763] [00763] In some embodiments, a zinc finger molecule is located in the target DNA sequence specified by that ZFD matrix of zinc finger molecules. In some embodiments, the zinc finger molecule may block transcription when recruited to initial regions in a coding sequence, for example, the coding sequence for a recombinant or therapeutic polypeptide. In some embodiments, a zinc finger molecule can block transcription when recruited to a control element, for example, a promoter element, functionally linked to a recombinant or therapeutic polypeptide coding sequence. In some embodiments, additional repression can be achieved by fusing a transcriptional repression domain (for example, KRAB, SID or ERD) with the zinc finger molecule, allowing recruitment of the effector to any specific DNA site. specified by the ZFD matrix.
[00764] [00764] In some embodiments, a zinc finger molecule comprises two or more (for example 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
[00765] [00765] In some embodiments, the ZFD matrix of a repressor polypeptide, for example, a zinc finger molecule, specifies a target DNA sequence. In some embodiments, the target sequence specified by the ZFD matrix is comprised within a control element, for example, a promoter element, functionally linked to a recombinant or therapeutic polypeptide coding sequence. In some embodiments, the target sequence specified by the ZFD matrix is comprised of a recombinant or therapeutic polypeptide coding sequence.
[00766] [00766] Exemplary naturally occurring and manipulated polypeptide sequences and methods for the design and testing of zinc finger polypeptides for use with genetic control circuits, cells, and methods for identifying, selecting or marking a cell or cell line capable of producing high yields of a product, for example, a recombinant or therapeutic polypeptide, described in this document, can be found in the art, for example, in Wolfe SA, et al. Annu Rev Biophys Biomol Struct. 2000; 29: 183—212; Pabo CO, et al. Annu Rev Biochem. 2001; 70: 313—340; Greisman HA, Pabo CO. Science. 1997; 275: 657-661; Isalan M, et al, Proc Natl Acad Sci U S. A. 1997; 94: 5617—5621; Wolfe SA, et al. J Mol Biol. 1999; 285: 1917—1934, hereby incorporated by reference in their entirety for reference.
[00767] [00767] Design methods of ZFD and ZFD arrays for binding to specific target DNA sequences can be found in the art, for example, in Maeder ML, et al. Mol Cell. 2008; 31: 294-
[00768] [00768] In some embodiments, the fusion polypeptide of this invention further comprises a degradation domain. In some modalities, the degradation domain has a first state and a second state, for example, stabilization / destabilization states, or folding / unfolding states. The first state is associated with, causes, or mediates, the expression of the fusion polypeptide at a first rate or level, and the second state is associated with, causes, or mediates, the expression of the fusion polypeptide at a second rate or level. In some embodiments, the second state has a level or rate that is, for example, 2, 3, 4, 5.6, 7, 8, 9, 10, 20, or 30 times higher than the rate or level of the first state. - of. In some embodiments, the second state is associated with, maintained by, or caused by, the presence of a stabilizing compound. In some embodiments, the presence of the stabilizing compound may be associated with, causing, or mediating the transformation from a first folding state to a second folding state, for example, from the unveiled state to a more adequately folded state, for example example, a first state susceptible to degradation to a second state less susceptible to degradation than the first state; or from a first folding state that has a first level of degradation to a second folding state that has a lower second level of degradation, for example, in a cell of interest.
[00769] [00769] In one embodiment, the addition of a stabilizing compound to a plurality of cells, for example, host cells or cells comprising fusion polypeptides described in the preceding
[00770] [00770] In one embodiment, the degradation domain is separated from the rest of the fusion polypeptide by a heterologous protease cleavage site.
[00771] [00771] Without adhering to theory, in some modalities, the degradation domain is unstable and / or unable to bend in a stable formation in the absence of a stabilizing compound. This abnormally folded / unfolded degradation domain can be degraded via intracellular degradation along with the rest of the fusion polypeptide. In the presence of the stabilizing compound, the degradation domain assumes an adequate conformation and is less susceptible to intracellular degradation pathways. Thus, the level of expression of the fusion polypeptide can be regulated by the presence or absence of the stabilizing compound.
[00772] [00772] In some embodiments, adequate folding of the degradation domain exposes the heterogeneous protease cleavage site
[00773] [00773] Methods of generating degradation domains that are selectively stable in the presence of a stabilizing compound are well known in the art and discussed further below. Several of these stabilizing domain-compound pairs have been generated so far and are shown in the present invention. These include FKBP-based degradation domains (for example, using a "Shield" stabilizing compound) as described in: A Rapid, Reversible, and Tunable Method to Regulate Protein Function in Living Cells Using Synthetic Small Molecules. " Banaszynski, LA; Chen, L.-C .; Maynard-Smith, LA; Ooi, À. GL; Wandless, TJ Cell, 2006, 126, 995-1004; DHFR-based domains (for example, using trimethoprim as a stabilizing compound) as described in general chemical method A to regulate protein stability in the mammal's central nervous system. lwamoto, M .; Bjôrklund, T .; Lundberg, C .; Kirik, D .; Wandless, TJ Chemistry & Biology, 2010, 17, 981-988; and domains based on alpha estrogen receptor (for example, where 4O0HT is used as a stabilizing compound) as described in Destabilizing domains derived from the human estrogen receptor Y Miyazaki, H Imoto, Lc Chen, TJ Wandless J. Am. Chem. Soc. 2012, 134, 3942-3945. these references are incorporated by reference in their entirety.
[00774] [00774] The present description covers degradation domains derived from naturally occurring protein. Preferably, the fusion polypeptides of the invention include a degradation domain for which there is no ligand expressed natively in the cell compartments of interest. For example, if the fusion polypeptide is designed for expression in T cells, it is preferable to select a degradation domain for which there is no naturally occurring ligand present in T cells. Thus, the degradation domain, when expressed in cell of interest, it will only be stabilized in the presence of a compound added exogenously. In particular, this property can be manipulated by manipulating the degradation domain to no longer bind to a natively expressed ligand (in such a case the degradation domain will only be stable in the presence of a synthetic compound) or by expressing the degradation domain in a compartment in which the natively expressed ligand does not occur (for example, the degradation domain can be derived from a species other than the species in which the fusion polypeptide will be expressed).
[00775] [00775] Degradation domain-stabilization compound pairs can be derived from any naturally occurring or synthetically developed protein. Stabilizing compounds can be any naturally occurring or synthetic compounds. In certain modalities, the stabilizing compounds will be prescription drugs or over-the-counter drugs. Examples of proteins that can be engineered to have the properties of a degradation domain are shown in Table 21 below together with a corresponding stabilizing compound.
[00776] [00776] In some embodiments, the degradation domain is derived from a protein mentioned in Table 21.
[00777] [00777] In some modalities, the degradation domain is derived from an estrogen receptor (ER). In some embodiments, the degradation domain comprises an amino acid sequence selected from SEQ ID NO: 46 or a sequence that has at least 90%, 95%, 97%, 98%, or 99% identity with it, or SEQ ID NO: 48 or a sequence that is at least 90%, 95%,
[00778] [00778] In some embodiments, the degradation domain is derived from an FKB protein (FKBP). In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 50 or a sequence that has at least 90%, 95%, 97%, 98%, or 99% sequence identity therewith. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 50. When the degradation domain is derived from an FKBP, the stabilizing compound can be Shield-1.
[00779] [00779] In some embodiments, the degradation domain is derived from dihydrofolate reductase (DHFR). In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 51 or a sequence that has at least 90%, 95%, 97%, 98%, or 99% sequence identity therewith. In some embodiments, the degradation domain comprises the amino acid sequence of SEQ ID NO: 51. When the degradation domain is derived from a DHFR, the stabilizing compound can be Trimethoprim.
[00780] [00780] In some embodiments, the degradation domain is derived from an FKB protein, estrogen receptor, or DHFR.
[00781] [00781] Degradation domains can be manipulated from known proteins (for example, those proteins shown in Table 21) by any of a variety of routine methods known in the art. In general, such methods employ, first, to create a library of interest including proteins derived, for example, from naturally occurring protein. Second, cells or populations of cells that express proteins from individual library constructs will be selected based on whether the expression of the derived protein is dependent on the presence of the desired stabilizing compound. The derivation and selection process can be repeated as many cycles as necessary to identify a suitable candidate.
[00782] [00782] For example, a library can be created using rational protein design based on different sample structures and supposed affinities of the protein domain with the selected compound. Alternatively, a library can be generated by random mutagenesis of the target protein. In each case, for example, Jurkat cells can be transduced with a lentiviral library generated from the constructs. Jurkat cells can then undergo a FACS classification round to eliminate cells that constitutively express the protein of interest. In the next stage, the classified cells are incubated with the compound of choice for 24 h and the positive cells are classified by FACS. These are expanded through single cell cloning. Thereafter, the individual transduced clones will be evaluated for the ability to induce expression of the protein of interest in a compound-dependent manner.
[00783] [00783] In some embodiments, the invention fusion polypeptide comprises a degradation domain, a COF1 / CRBN-binding polypeptide, COF2 / CRBN or COF3 / CRBN, and a polypeptide
[00784] [00784] In some embodiments, the invention fusion polypeptide comprises a first domain and a second domain separated by a heterologous cleavage site, where the first domain comprises a degradation domain and the second domain comprises a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a heterologous polypeptide.
[00785] [00785] The cleavage site can be an autocleavage site and / or a protease cleavage site. The cleavage site can be designed to be cleaved by any site-specific protease that is expressed in a cell of interest (either through recombinant or endogenous expression) at levels suitable for cleaving the degradation domain. In important aspects of the invention, the protease cleavage site is chosen to correspond to a protease natively (or due to cell engineering) that will be present in a cell compartment relative to the expression of the protein of interest. The intracellular traffic of the protease should overlap or partially overlap with the intracellular traffic of the protein of interest that contains the degradation domain employed. For example, if the protein of interest is located on the cell surface, the enzyme to cleave it can be added exogenously to the cell.
[00786] [00786] If the protein of interest resides in the endosomal / lysosomal system, a protease cleavage site for an enzyme residing in those compartments can be used. Such protease / consensus motifs include, for example, Furin: RXXX consensus motif [KRIR (X can be any amino acid; SEQ ID NO: 52) PCSK1: RXXX consensus motif [KRIR (X can be any amino acid; SEQ ID NO: 52) PCSK5: RXXX consensus motive [KRIR (X can be any amino acid; SEQ ID NO: 52) PCSK6: RXXX consensus motive [KRIR (X can be any amino acid; SEQ ID NO: 52) PCSKT7 : RXXX consensus reason [KRIR (X can be any amino acid; SEQ ID NO: 53) Cathepsin B: RRX (SEQ ID NO: 54) Granzyme B: | -EPDX (SEQ ID NO: 55) X factor: Ile- Glu / Asp-Gly-Arg (SEQ IDNO: 56) Enterokinase: Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57) Genenase: Pro-Gly-Ala-Ala-His-Tyr (SEQ ID NO: 58) ) Sortase: LPXTG / A (SEQ ID NO: 59) PreScission Protease: Leu-Glu-Val-Phe-Gln-Gly-Pro (SEQ ID NO: 60) Thrombin: Leu-Val-Pro-Arg-Gly-Ser ( SEQ ID NO: 61) Protease TEV: ENLYFQG (SEQ ID NO: 62) Elastase 1: [AGSV] -X (X can be any amino acid; SEQ ID NO: 63)
[00787] [00787] In some embodiments, the fusion polypeptide described herein includes a furin cleavage site. In some embodiments, the fusion polypeptides described herein include any of the mentioned furin cleavage sites.
[00788] [00788] In some embodiments, the fusion polypeptides described herein include a furin cleavage site selected from RTKR (SEQ ID NO: 123) or a sequence that is at least 90%, 95%, 97%, 98% or 99% identity with the same; GTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125) or a string that has at least 90%, 95%, 97%, 98% or 99% identity with it; GTGAEDPRPSRKRR (SEQ ID NO: 127) or a string that has at least 90%, 95%, 97%, 98%, or 99% identity with it; LOWLEQQVAKRRTKR (SEQ ID NO: 129) or a sequence that has at least 90%, 95%, 97%, 98%, or 99% identity with it; GTGAEDPRPSRKRRSLGG (SEQ ID NO: 131) or a sequence that has at least 90%, 95%, 97%, 98%, or 99% identity with it; GTGAEDPRPSRKRRSLG (SEQ ID NO: 133) or a string that has at least 90%, 95%, 97%, 98%, or 99% identity with it; SLNLTESHNSRKKR (SEQ ID NO: 135) or a sequence that has at least 90%, 95%, 97%, 98%, or 99% identity with it; or CKINGYPKRGRKRR (SEQ ID NO: 137) or a sequence that has at least 90%, 95%, 97%, 98%, or 99% identity to it.
[00789] [00789] In some embodiments, the fusion polypeptides described herein include a furin cleavage site selected from RTKR (SEQ ID NO: 123); GTGAEDPRPSRKRRS-LGDVG (SEQ ID NO: 125); GTGAEDPRPSRKRR (SEQ ID NO: 127); LQWLEQQVAKRRTKR (SEQ ID NO: 129); GTGAEDPRPSRKRRS-LGG (SEQ ID NO: 131); GTGAEDPRPSRKRRSLG (SEQ ID NO: 133); SLNLTESHNSRKKR (SEQ ID NO: 135); or CKINGYPKRGRKRR (SEQ ID NO: 137).
[00790] [00790] In some embodiments, the fusion polypeptides described herein include a furin cleavage site selected from GTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125) or a sequence that is at least 90%, 95%, 97%, 98%, or 99% identity with the same, or GTGAEDPRPSRKRR (SEQ ID NO: 127) or a sequence that has at least 90%, 95%, 97%, 98%, or 99% identity with the same.
[00791] [00791] In some embodiments, the fusion polypeptides described in this document include a furin cleavage site selected from GTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125) or GTGAEDPRPSRKRR (SEQ ID NO: 127).
[00792] [00792] In some embodiments, the fusion polypeptides described herein include the furin cleavage site of GTGAEDPRPSRKRRSLGDVG (SEQ ID NO: 125).
[00793] [00793] In certain embodiments, the fusion polypeptides of the invention additionally include a signal peptide. Signaling peptides are useful if the protein is to follow the secretory pathway. In some embodiments, the signaling peptide will be engineered to be present at the N termination of the fusion polypeptide itself. Exemplary signaling peptides are shown below: CD8: MALPVTALLLPLALLLHAARP (SEQ ID NO: 64) GMCSFR: MLLLVTSLLLCELPHPAFLLIP (SEQ ID NO: 65) I1L2: MYRMQLLSCIALSLALVTNS (SEQ ID NO: 66) ) NPC2: MRFLAATFLLLALSTAAQA (SEQ ID NO: 68) LAMB1: MGLLQLLAFSFLALCRARVRA (SEQ ID NO: 69) P3IP1: MLLAWVQAFLVSNMLLAEAYG (SEQ ID NO: 70) DMKN: MKFQGPLACLLLALFVGA: IDK: ) PCSK9: MGETVSSRRSWWPLPLLLLLLLLLGPAGARAQEDED (SEQ ID NO: 73)
[00794] [00794] KDEL (SEQ ID NO: 74) or KKXX (X can be any amino acid; SEQ ID NO: 75) and derivatives at the C terminus of interest can be manipulated if the protein of interest is a protein. resident in ER. These sequences must be inserted together with the signal peptide.
[00795] [00795] The proteins of interest can be manipulated to include glycosylation patterns for internalization through the mannose-6-phosphate receptor and targeting for the endosomal / lysosomal system. These must be included in the protein of interest, if that is a protein residing in that compartment. The consensus for N-glycosylation is Asn-X-Ser / Thr, where X is any amino acid except proline (Pro), serine (Ser) and threonine (Thr) (SEQ ID NO: 76).
[00796] [00796] In the modalities in which it is desired to have proteins of interest targeted in the peroxisome, the fusion polypeptide can be manipulated to include a C-terminal peroxisomal targeting signal (for example, PTS1: -SKL). Nucleic Acid and Vectors Encoding Fusion Polypeptides
[00797] [00797] In another aspect, the invention belongs to a nucleic acid that encodes any of the fusion polypeptides described herein, or a vector that comprises such a nucleic acid. In one embodiment, the vector is chosen from a DNA vector, an RNA vector, a plasmid, a lentiviral vector, an adenoviral vector or a retroviral vector. In one embodiment, the vector is a vector of lytic viruses.
[00798] [00798] The present description also provides vectors in which a DNA of the present description is inserted. Vectors derived from retroviruses, such as lentivirus, are suitable tools for achieving long-term gene transfer, since they allow long-term stable integration of a transgene and its propagation in daughter cells. Lentiviral vectors have the additional advantage over vectors derived from oncorretroviruses, such as murine leukemia virus, that they can transduce non-proliferative cells, such as hepatocytes. They also have the additional advantage of having low immunogenicity. A retroviral vector can also be, for example, a gamma-retroviral vector. A gamma-retroviral vector can include, for example, a promoter, a packaging signal (y), a primer binding site (PBS), one or more (for example, two) long terminal repeats (LTR) and a transgene of interest , for example, a gene encoding a CAR. A gamma-retroviral vector may not have viral viral genes like gag, pol and env. Exemplary gamma-retroviral vectors include Murine Leukemia Virus
[00799] [00799] In another embodiment, the vector comprising the nucleic acid encoding the desired fusion polypeptide of the invention is an adenoviral vector (A5 / 35). In another embodiment, the expression of nucleic acids encoding chimeric molecules can be achieved using transposons such as sleeping beauty, using gene editing tools such as CRISPR (eg CAS9), or using zinc finger nucleases. See, for example, June et al. 2009 Nature Reviews Immunology 9.10: 704-716, which is incorporated by reference in this document.
[00800] [00800] The nucleic acid can be cloned in some types of vectors. For example, the nucleic acid can be cloned into a vector including, but not limited to, a plasmid, a phagemid, a phage derivative, an animal virus and a cosmid. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors. Nucleic acid constructs that encode Fusion Polypeptides, for example, a CAR comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide
[00801] [00801] The present description provides nucleic acid molecules that encode one or more fusion polypeptides disclosed in this document.
[00802] [00802] In one embodiment, the fusion polypeptide comprises a CAR construct that targets a tumor antigen and / or a B cell antigen described in this document. In one aspect, the nucleic acid molecule is provided as a messenger RNA transcript. In one aspect, the nucleic acid molecule is provided as a DNA construct.
[00803] [00803] Consequently, in one aspect, the invention relates to a nucleic acid molecule encoding a fusion polypeptide comprising a COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a heterologous polypeptide. In some embodiments, the heterologous polypeptide is a chimeric antigen (CAR) receptor, where the CAR comprises an antigen binding domain that binds to a tumor antigen described in the present document or a B cell antigen described herein. document, a transmembrane domain (for example, a transmembrane domain described in this document), and an intracellular signaling domain (for example, an intracellular signaling domain described here) comprising a stimulator domain, for example, a co-stimulating signaling domain (for example, a co-stimulating signaling domain described in this document) and / or a primary signaling domain (for example, a primary signaling domain described in this document, for example, a chain described in this document). In one embodiment, the transmembrane domain is the transmembrane domain of a protein selected from the group consisting of the alpha, beta or zeta chain of the T cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137 and CD154. In some embodiments, a transmembrane domain may include at least the transmembrane region (s), for example, from KIRDS2, OX40, CD2, CD27, LFA-1 (CD11a, CD18), ICOS (CD278), 4-1BB (CD137), GITR, CD40, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD160, CD19, IL2R beta, IL2R gamma, IL7R to, ITGA1, VLA1, CD49a, ITGAA, IAA4,
[00804] [00804] In one embodiment, the transmembrane domain comprises the sequence of SEQ ID NO: 155 (or a sequence with 95 to 99% identity thereof). In one embodiment, the antigen-binding domain is connected to the transmembrane domain by a hinge region, for example, a hinge region described here. In one embodiment, the hinge region comprises SEQ ID NO: 147, or SEQ ID NO: 149, or SEQ ID NO: 151, or SEQ ID NO: 153 (or a sequence with 95 to 99% identity with the same ). In one embodiment, the isolated nucleic acid molecule further comprises a sequence encoding a co-stimulating domain. In one embodiment, the co-stimulatory domain is a functional signaling domain of a protein selected from the group consisting of OX40, CD27, CD28, CDS, ICAM-1, LFA-1 (CD11a / CD18), ICOS (CD278); and 4-1BB (CD137). Additional examples of such co-stimulating molecules include CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), NKp44, NKp30, NKp46, CD160, CD19, CD4, CD8alfa, CD8beta, IL2R beta , IL2PR gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGAA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c , ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, NKG2D, NKG2C, TNFR2, TRANCE / RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 ( CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6
[00805] [00805] In another aspect, the invention relates to an isolated nucleic acid molecule encoding a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR construct comprising a leader sequence of SEQ ID NO: 64, a scFv domain as described herein, a hinge region of SEQ ID NO: 147, or SEQ ID NO: 149, or SEQ ID NO: 151 or SEQ ID NO: 153 (or a sequence with 95 to 99% identity to it), a transmembrane domain having a sequence of SEQ ID NO: 155 (or a sequence with 95 to 99% identity to it), a co-stimulatory domain of 4-1BB having a sequence of SEQ ID NO: 158, a co-stimulatory domain of CD27 having a sequence of SEQ ID NO: 161 (or a sequence with 95 to 99% identity to it), an ICOS co-stimulatory domain having the sequence of SEQ ID NO : 176 (or a sequence with 95 to 99% identity to it) or a co-stimulatory domain of CD28 te n the sequence of SEQ ID NO: 180 and a CD3 stimulator domain zeta having the sequence of SEQ ID NO: 163, or SEQ ID NO: 166 (or a sequence with 95 to 99% identity to it).
[00806] [00806] The nucleic acid sequences encoding the desired molecules can be obtained using recombinant methods known in the art, such as, for example, by screening libraries of cells expressing the gene, by derivating the gene from a vein. tor that is known to include the same, or by isolation directly from cells and tissues containing it, using common techniques. Alternatively, the gene of interest can be produced synthetically, instead of being cloned.
[00807] [00807] The present description also provides vectors in which a nucleic acid of the present description is inserted. Vectors derived from retroviruses, such as lentivirus, are suitable tools to achieve long-term genetic transfer since they allow a stable long-term integration of a transgene and its propagation in daughter cells. Lentiviral vectors have the additional advantage over vectors derived from oncorretroviruses, such as murine leukemia virus, that they can transduce non-proliferating cells, such as hepatocytes. They also have the added advantage of low immunogenicity.
[00808] [00808] In summary, the expression of recombinant nucleic acids encoding a fusion polypeptide of this invention is typically accomplished by functionally binding a nucleic acid encoding the fusion polypeptide to a promoter, and incorporating the construct into a expression vector. The vectors may be suitable for replication and integration in eukaryotes. Typical cloning vectors contain transcription and translation terminators, initiation sequences and promoters useful for regulating expression of the desired nucleic acid sequence.
[00809] [00809] The expression constructs of the present description can also be used for immunization with nucleic acids and gene therapy, using common gene transfer protocols. Genetic transfer methods are known in the art. See, for example, U.S. Patent Nos. 5.3.99.346, 5,580,859, 5,589,466, incorporated by reference here in their entirety. In another embodiment, the invention provides a gene therapy vector.
[00810] [00810] The nucleic acid can be cloned in some types of vectors. For example, the nucleic acid can be cloned into a vector including, but not limited to, a plasmid, a phagemid, a phage derivative, an animal virus and a cosmid. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors.
[00811] [00811] In addition, the expression vector can be supplied to a cell in the form of a viral vector. Viral vector technology is well known in the art and is described, for example, in Sambrook et al., 2012, MOLECULAR CLONING: A LABORATORY MANUAL, volumes 1 to 4, Cold Spring Harbor Press, NY) and in other virology manuals and molecular biology. Viruses useful as vectors include, but are not limited to, retroviruses, adenoviruses, adenoassociated viruses, herpes viruses and lentivirus. In general, a suitable vector contains a functional origin of replication in at least one organism, a promoter sequence, convenient restriction endonuclease sites and one or more selectable markers, (for example, WO 01/96584; WO 01 / 29058; and U.S. Pat. No. 6,326,193).
[00812] [00812] Some viral based systems have been developed for gene transfer in mammalian cells. For example, retroviruses provide a convenient platform for gene transfer systems. A selected gene can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and administered to the individual's cells in vivo or ex vivo. Some retro-
[00813] [00813] Additional promoter elements, for example, enhancers, regulate the frequency of initiation of transcription. These are typically located in the region 30 to 110 bp upstream of the start site, although it has been shown that some promoters also contain functional elements downstream of the start site. The spacing between the promoter elements is often flexible, so that the promoter function is preserved when the elements are inverted or displaced in relation to each other. In the thymidine kinase (tk) promoter, the spacing between the promoter elements can be increased to 50 bp before activity begins to decline. Depending on the promoter, it appears that individual elements can act cooperatively or independently to activate transcription. Exemplary promoters include promoters of the CMV IE gene, EF-1a, ubiquitin C or phosphoglycerocinase (PGK).
[00814] [00814] In some embodiments, the promoter is a tissue-specific promoter. In some embodiments, the promoter is activated at a specific stage of development. In some embodiments, the promoter is an inducible promoter. In some embodiments, the promoter is a tetracycline-inducible promoter. In some modalities, the promoter is a metallothionein promoter. In some ways, the promoter is an HSV TK promoter.
[00815] [00815] An example of a promoter that is capable of expressing a fusion polypeptide, for example, as described in the present document, which comprises a domain that includes a nucleic acid molecule encoding CAR in a mammalian T cell is the EF1a promoter. The native EF1a promoter drives expression of the
[00816] [00816] Another example of a promoter is the immediate cytomegalovirus (CMV) initial promoter sequence. This promoter sequence is a strong constitutive promoter sequence with the ability to trigger high levels of expression of any polynucleotide sequence operatively to it. However, other sequences of constitutive promoters can also be used, including, but not limited to, the simian virus 40 initial promoter (SV40), mouse mammary tumor virus (MMTV), long term repeat promoter (LTR) ) of the human immunodeficiency virus (HIV), promoter of MoMuLV, a promoter of the avian leukemia virus, an immediate initial promoter of the Epstein-Barr virus, a promoter of the Rous sarcoma virus, as well as promoters of human genes such as such as, but not limited to, the actin promoter, the myosin promoter, the elongation factor-1 promoter, the hemoglobin promoter and the creatine kinase promoter. In addition, the invention should not be limited to the use of constitutive promoters. Inducible promoters are also contemplated as part of the invention. The use of an inducible promoter provides a molecular switch with the ability to turn on the expression of the polynucleotide sequence that is optionally turned on when that expression is desired or to turn off the expression when the expression is not desired. Examples of inducible promoters include, but are not limited to, a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter and a tetracycline promoter.
[00817] [00817] Another example of a promoter is the phosphoglycerate kinase (PGK) promoter. In embodiments, a truncated PGK promoter (for example, a PGK promoter with one or more, for example, 1, 2, 5, 10, 100, 200, 300, or 400 nucleotide deletions when compared to the sequence promoter of wild type PGK). The nucleotide sequences of exemplary PGK promoters are provided below. PGKTS Promoter ACCCCTCTCTCCAGCCACTAAGCCAGTTGCTCCCTCGGCTGACGG CTGCACGCGAGGCCTCCGAACGTCTTACGCCTTGTGGCGCGCCC GTCCTTGTCCCGGGTEGTGATGGCGGGGTESETGGGGCGGAGGGCGÇ TGGCGGGGAAGGGCCEGGCGACGAGAGCCGCGCGGGACGACTC GTCGGCGATAACCGGTGTCGGGTAGCGCCAGCCGCGCGACGGT AACGAGGGACCGCGACAGGCAGACGCTCCCATGATCACTCTGCA
[00818] [00818] A vector can also include, for example, a signal sequence to facilitate secretion, a polyadenylation signal and transcription terminator (for example, from the Growth Hormone gene
[00819] [00819] To evaluate the expression of a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR polypeptide or portions thereof, the expression vector to be introduced into a cell also it may contain a selectable marker gene or a reporter gene or both to facilitate the identification and selection of expression cells from the population of cells to be transfected or infected by viral vectors. In other respects, the selectable marker can be contained in a separate portion of DNA and be used in a cotransfection procedure. Selectable markers and reporter genes can be flanked with appropriate regulatory sequences to allow expression in host cells. Useful selectable markers include, for example, antibiotic resistance genes, such as neo and the like.
[00820] [00820] Reporter genes are used to identify potentially transfected cells and to assess the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, for example, enzymatic activity. The expression of the reporter gene is evaluated at an appropriate time after the DNA has been introduced into the recipient cells. Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase or the green fluorescent protein gene (eg, Ui-Tei et al., 2000 FEBS Letters 479: 79 to 82) . Suitable expression systems are well known and can be prepared using known or commercially obtained techniques. In general, the construct with the minimum 5 'flanking region exhibiting the highest level of expression of the reporter gene is identified as the promoter. Such promoter regions can be linked to a reporter gene and used to evaluate agents for the ability to modulate promoter-driven transcription.
[00821] [00821] In some embodiments, the vector comprising a nucleic acid sequence encoding a fusion polypeptide described herein, for example, a fusion polypeptide comprising a CAR molecule described in the present document, can further comprising a second nucleic acid sequence encoding a polypeptide, for example, an agent that enhances the activity of the fusion polypeptide, for example, as described herein, which comprises a domain that includes the CAR molecule. In some embodiments, a single nucleic acid molecule, or vector comprising said nucleic acid molecule, encodes multiple fusion polypeptides, for example, as described herein, each comprising domains that include a CAR, described in this document. In some embodiments, the nucleic acid encoding a first fusion polypeptide is under separate regulatory control (for example, by a promoter described herein) from the nucleic acid encoding a second fusion polypeptide (for example, by a promoter described in this document). In other embodiments, the two or more nucleic acid sequences are encoded by a single nucleic molecule in the same frame and as a single polypeptide chain. In this regard, the two or more fusion polypeptides, for example, as described herein, each comprising a domain that includes a CAR may, for example, be separated by one or more peptide cleavage sites (for example, an autocleavage site or a substrate for an intracellular protease). Examples of peptide cleavage sites include the following, in which GSG residues are optional: T2A (GSG) AND GRGSLLTCGDVEENPGP (SEQ ID NO: 828) P2A (GSG) ATNFSLLKQAGDVEENPGP (SEQID NO: 829) E2A: (GSG) QCTNYALLKLAGDVESNP6GP (SEQ ID NO: 830) F2A (GSG) VK QTLNFDLLKLAGDVESNP6GP (SEQID NO: 831)
[00822] [00822] In some embodiments, the present description provides, for example, a nucleic acid molecule comprising a first nucleic acid sequence that encodes a first molecule and a second nucleic acid sequence that encodes a second molecule. In some embodiments, the first molecule is a first fusion polypeptide comprising a first COF1 / CRBN, COF2 / CRBN or COF3 / CRBN-binding polypeptide and a first heterologous polypeptide (for example, a first CAR molecule) and / or the second molecule is a second fusion polypeptide comprising a second COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a second heterologous polypeptide (for example, a second CAR molecule). In some modes, the first and second nucleic acid sequences are arranged in a single nucleic acid molecule. In some embodiments, the first and second nucleic acid sequences are arranged in separate nucleic acid molecules. In some embodiments, the first CAR molecule binds to CD19 (for example, the first CAR molecule is an anti-CD19 CAR revealed in
[00823] [00823] Methods of introducing and expressing genes in a cell are known in the art. In the context of an expression vector, the vector can be readily introduced into a host cell, for example, mammalian, bacterial, yeast or insect cell by any method of the technique. For example, the expression vector can be transferred to a host cell by physical, chemical or biological means.
[00824] [00824] Physical methods for introducing a polynucleotide into a host cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation and the like. Methods for producing cells that comprise exogenous vectors and / or nucleic acids are well known in the art. See, for example, Sambrook et a /., 2012, MOLECULAR CLOINING: A LABORATORY MANUAL, volumes 1-4, Cold Spring Harbor Press, NY). A preferred method for introducing a polynucleotide into a host cell is transfection with calcium phosphate or electroporation.
[00825] [00825] “Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian, for example, human cells. Other viral vectors can be derived from lentiviruses, poxviruses, herpes simplex viruses |, adenoviruses and adeno-associated viruses and the like. See, for example, U.S. Patent Nos. 5,350,674 and 5,585,362.
[00826] [00826] Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as complexes of macromolecules, nanocapsules, microspheres, spherules and lipid-based systems including oil-in-water emulsions, mycelia, mixed mycelia and liposomes. An exemplary colloidal system for use as a vehicle for in vitro and in vivo administration is a liposome (for example, an artificial membrane vesicle). Other methods of targeted delivery of nucleic acids common in the art are available, such as administration of polynucleotides with targeted nanoparticles or another suitable delivery system at the sub-micron scale.
[00827] [00827] If a non-viral delivery system is used, an exemplary delivery vehicle is a liposome. The use of lipid formulations is contemplated for the introduction of nucleic acids in a host cell (in vitro, ex vivo or in vivo). In another aspect, the nucleic acid can be associated with a lipid. The nucleic acid associated with a lipid can be encapsulated in the aqueous interior of a liposome, interspersed in the lipid bilayer of a liposome, linked to a liposome via a binding molecule that is associated with the liposome and the oligonucleotide, enclosed in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a mycelium or otherwise associated with a lipid. Compositions associated with lipids, lipids / DNA or lipids / expression vectors are not limited to any particular structure in solution. For example, they can be present in a bilayer structure, such as mycelia or with a "collapsed" structure. also
[00828] [00828] Lipids suitable for use can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine ("DMPC") can be obtained from Sigma, St. Louis, MO; dicetyl phosphate "DCP") can be obtained from K & K Laboratories (Plainview, NI); cholesterol ("Choi") can be obtained from Calbiochem-Behring; dimyristyl-phosphatidylglycerol ("DMPG") and other lipids can be obtained from Avanti Polar Lipids, Inc. (Birmingham, AL.). Stock solutions of lipids in chloroform or chloroform / methanol can be stored at about -20 ºC. Chloroform is used as the only solvent since it is more readily evaporated than methanol. "Liposome" is a generic term that encompasses a variety of uni- and multilayer lipid vehicles formed by the generation of closed bilayer or lipid aggregates. Liposomes can be characterized as having vesicular structures with a phospholipid bilayer membrane and an internal aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-alignment before the formation of closed structures and contain water and dissolved solutions between the lipid bilayers (Ghosh et a /., 1991 Glyco-biology 5: 505 to 510). However, compositions that have different structures in solution compared to the normal vesicular structure also
[00829] [00829] “Regardless of the method used to introduce exogenous nucleic acids into a host cell or otherwise expose a cell to the inhibitor of the present description, to confirm the presence of the recombinant DNA sequence in the host cell, a variety of tests can be performed. Such assays include, for example, "molecular biology" assays well known to those skilled in the art, such as Southern and Northern blot, RT-PCR and PCR; "biochemical" assays, such as detecting the presence or absence of a particular peptide, for example, by immunological means (ELISAs and Western blots) or by assays described here to identify agents that fall within the scope of the invention.
[00830] [00830] The present description further provides a vector comprising a fusion polypeptide, for example, as described herein, comprising a domain that includes a nucleic acid molecule encoding CAR. In one embodiment, the vector comprises a nucleic acid molecule encoding CAR, for example, as described here. In one embodiment, the vector comprises two nucleic acid molecules that encode CAR. In one aspect, the one or more CAR vectors (for example, the vector that comprises a first nucleic acid molecule that encodes CAR and the vector that comprises a second nucleic acid molecule that encodes CAR, or the vector that comprises a first and a second nucleic acids encoding CAR) can be directly transduced into a cell, for example, a T cell or an NK cell. In one aspect, the vector is a cloning or expression vector, for example, a vector including, but not limited to, one or more plasmids (for example, expression plasmids, cloning vectors, minicircles, minivectors, double minute chromosomes ), retroviral and lentiviral vector constructs. In one aspect, the vector is able to express the CAR construct in mammalian immune effector cells (for example, T cells, NK cells).
[00831] [00831] In one embodiment, when the stable expression of one or more fusion polypeptides (for example, one or two), for example, as described in this document, each comprising a domain that includes a CAR, is desired, a vector that comprises one or more (for example, one or two) molecules of nucleic acids that encode CAR is transduced into an immuno-protective cell. For example, immune expression cells with stable expression of two fusion polypeptides, for example, as described herein, each comprising a domain that includes a CAR, can be generated using lentiviral vectors. Cells that exhibit stable expression of two fusion polypeptides, for example, as described herein, each comprising a domain that includes a CAR, express the CARs for at least 1 weeks, 2 weeks, 3 weeks, 4 weeks , 5 weeks, 6 weeks, 7 weeks, 8 weeks, 3 months, 6 months, 9 months or 12 months after transduction.
[00832] [00832] In one embodiment, when the temporary expression of one or more fusion polypeptides (for example, one or two), for example, as described in this document, comprising a domain that includes a CAR, one or more is desired (for example, one or two) nucleic acid molecules encoding fusion polypeptides are transfected into an immuno-protective cell. The one or more (for example, one or two) fusion polypeptides, for example, as described in this document, which comprise a domain that includes nucleic acid molecules that encode
[00833] [00833] Methods of producing an in vitro transcribed RNA encoding a fusion polypeptide, for example, as described herein, are disclosed in this document, comprising a domain that includes a CAR. The present description also includes a fusion polypeptide, for example, as described herein, which comprises a domain that includes an RNA construct that encodes CAR that can be directly transfected in a cell. A method for generating mMRNA for use in transfection may involve in vitro transcription (IVT) of a model with specially designed primers, followed by addition of polyA, to produce a construct containing untranslated 3 'and 5' sequences (" RTU "), a 5" cap "and / or Internal Ribosome Entry Site (IRES), the nucleic acid to be expressed and a polyA tail, typically 50-5000 bases in length (SEQ ID NO: 174 ). The RNA produced in this way can efficiently transfect different types of cells. In one aspect, the model includes sequences for the CAR.
[00834] [00834] In one aspect, a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR, of the present description is encoded by a messenger RNA (mMRNA). In one aspect, the MRNA encoding a CAR described here is introduced into a T cell or an NK cell.
[00835] [00835] In one embodiment, the RNA transcribed in vitro encoding a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR can be introduced into a cell as a form of temporary transfection . RNA is produced by in vitro transcription using a model generated by polymerase chain reaction (PCR). DNA of interest from any source can be directly converted by PCR into a model for in vitro MRNA synthesis using appropriate primers and RNA polymerase. The source of the DNA can be, for example, genomic DNA, plasmid DNA, phage DNA, cDNA, synthetic DNA sequence or any other appropriate source of DNA. The desired model for in vitro transcription is a fusion polypeptide, for example, as described herein, which comprises a domain that includes a CAR described herein. For example, the model for the CAR RNA comprises an extracellular region comprising a single-stranded variable domain of an antibody to an antigen described here; a hinge region (for example, a hinge region described here), a trans-membrane domain (for example, a transmembrane domain described here such as a CD8a transmembrane domain); and a cytoplasmic region that includes an intracellular signaling domain, for example, an intracellular signaling domain described here, for example, comprising the CD3-zeta signaling domain and the 4-1BB signaling domain.
[00836] [00836] In one embodiment, the DNA to be used for PCR contains an open reading frame. DNA can come from a naturally occurring DNA sequence in an organism's genome. In one mode, the nucleic acid may include some or all of the 5 'and / or 3' untranslated regions (RTUs). The nucleic acid can include exons and introns. In one embodiment, the DNA to be used for PCR is a sequence
[00837] [00837] PCR is used to generate a template for in vitro transcription of mMRNA that is used for transfection. Methods for performing PCR are well known in the art. Primers for use in PCR are designed to have regions that are substantially complementary to regions of the DNA to be used as a template for PCR. "Substantially complementary", as used in this document, refers to nucleotide sequences in which most or all of the bases of the primer are complementary, or one or more bases are not complementary or mismatched. Substantially complementary sequences have the ability to anneal or hybridize to the desired DNA target under annealing conditions used for PCR. Primers can be designed to be substantially complementary to any portion of the DNA model. For example, primers can be designed to amplify the portion of a nucleic acid that is normally transcribed into cells (the open reading frame), including 5 'and 3' RTUs. Primers can also be designed to amplify a portion of a nucleic acid that encodes a domain of particular interest. In one embodiment, the initiators are designed to amplify the coding region of a
[00838] [00838] “Any DNA polymerase useful for POR can be used in the methods disclosed in this document. Reagents and polymerase are commercially available from some sources.
[00839] [00839] Chemical structures with the capacity to promote the stability and / or efficiency of translation can also be used. The RNA preferably has 5 'and 3' RTUs. In one embodiment, the 5 'UTR is between one and 3000 nucleotides in length. The length of the 5 'and 3' RTU sequences to be added to the coding region can be altered by different methods, including, but not limited to, designing primers for PCR that ring different regions of the RTUs. Using this approach, the person of ordinary skill in the art can modify the lengths of the 5 'and 3' RTU required to obtain optimal translation efficiency after transfection of the transcribed RNA.
[00840] [00840] As5'e3 RTUs can be the 5 'and 3' naturally occurring endogenous RTUs for the nucleic acid of interest. Alternatively
[00841] [00841] In one embodiment, the 5 'UTR may contain the Kozak sequence of the endogenous nucleic acid. Alternatively, when a 5 'RTU that is not endogenous to the nucleic acid of interest is being added by PCR as described above, a Kozak consensus sequence can be redesigned by adding the 5' RTU sequence. Kozak sequences can increase the translation efficiency of some RNA transcripts, but they do not appear to be required for all RNAs to allow efficient translation. The Kozak sequence requirement for many mMRNAs is known in the art. In other embodiments, the 5 'UTR can be the SUTR of an RNA virus whose RNA genome is stable in cells. In other embodiments, several nucleotide analogs can be used in the 3 'or 5' UTR to prevent mRNA degradation by exonucleases.
[00842] [00842] To allow the synthesis of RNA from a DNA model without the need for gene cloning, a transcription promoter must be added to the DNA model upstream of the sequence to be transcribed. When a sequence that acts as a promoter for an RNA polymerase is added to the 5 'end of the forward primer, the RNA polymerase promoter becomes incorporated into the PCR product upstream of the open reading frame that must be transcribed. In a preferred embodiment, the promoter is a T7 polymerase promoter, as described here elsewhere. Other useful promoters include, but are not limited to, T3 and SP6 RNA polymerase promoters. Consensus nucleotide sequences for T7, T3 and SP6 promoters are known in the art.
[00843] [00843] In a preferred embodiment, the MRNA has a cap at the 5 'end and a 3' poly (A) tail that determine the binding of ribosomes, initiation of translation and stability of the MRNA in the cell. In a circular DNA model, for example, plasmid DNA, RNA polymerase gives rise to a long concatameric product that is not suitable for expression in eukaryotic cells. Transcription of linearized plasmid DNA at the end of the 3 'UTR gives rise to normal sized mMRNA which is not effective in eukaryotic transfection even if it is polyadenylated after transcription.
[00844] [00844] In a linear DNA model, T7 phage RNA polymerase can extend the 3 'end of the transcript beyond the last base of the model (Schenborn and Mierendorf, Nuc Acids Res., 13: 6.223 to
[00845] [00845] The conventional method of integrating polyA / T extensions into a DNA model is molecular cloning. However, a polyA / T sequence integrated in plasmid DNA can cause plasmid instability, which is why plasmid DNA models obtained from bacterial cells are often highly contaminated with deletions and other aberrations. This makes cloning procedures not only laborious and time consuming, but often unreliable. That is why a method that allows the construction of DNA models with 3 'polyA / T extension without cloning is highly desirable.
[00846] [00846] The polyA / T segment of the transcriptional DNA model can be produced during PCR using a reverse primer containing a polyT tail, such as 100T tail (SEQ ID NO: 832) (size can be 50 to 5,000 T (SEQ ID NO: 833)), or after PCR by any other method, including, but not limited to, DNA binding or in vitro combination. Poly (A) tails also provide stability to RNAs and reduce their degradation. Generally, the length of a poly (A) tail is positively correlated with the stability of the transcribed RNA. In one embodiment, the poly (A) tail has between 100 and 5000 adenosines (SEQ ID NO: 834).
[00847] [00847] Poly (A) tails of RNAs can be further extended after in vitro transcription with the use of a poly (A) polymerase, such as E. coli polyA polymerase (E-PAP). In one embodiment, increasing the length of a poly (A) tail from 100 nucleotides to between 300 and 400 nucleotides (SEQ ID NO: 835) results in an increase of about twice the efficiency of RNA translation. In addition, the attachment of different chemical groups to the 3 'end may increase the stability of the mMRNA. Such a bond may contain modified / artificial nucleotides, aptamers and other compounds. For example, ATP analogs can be incorporated into the po-Ili (A) tail using poly (A) polymerase. ATP analogs can further increase the stability of RNA.
[00848] [00848] Caps 5 'also provide stability to RNA molecules. In a preferred embodiment, RNAs produced by the methods disclosed here include a 5 'cap. Chapter 5 'is provided using techniques known in the art and described in this document (Cougot, et al., Trends in Biochem. Sci., 29: 436 to 444 (2001); Stepinski, et al, RNA , 7: 1,468 to 1,495 (2001); Elango, et al., Biochim. Biophys. Res. Commun., 330: 958 to 966 (2005)).
[00849] [00849] The RNAs produced by the methods disclosed in this document can also contain an internal ribosome entry site sequence (IRES). The IRES sequence can be any viral, comosomal or artificially planned sequence that initiates binding of the ribosome independent of cap to mRNA and facilitates the initiation of translation. Any solutes suitable for electroporation of cells can be included, which may contain factors that facilitate cell permeability and viability, such as sugars, peptides, lipids, proteins, antioxidants and surfactants.
[00850] [00850] RNA can be introduced into target cells using any of a few different methods, for example, commercially available methods that include, but are not limited to, electroporation (Amaxa Nucleofector-ll (Amaxa Biosystems, Cologne, Germany) ), (ECM 830 (BTX) (Harvard Instruments, Boston, Mass.) Or the Gene Puler | l (BioRad, Denver, Colo.), Multiporator (Eppendort, Hamburg Germany), cationic liposome-mediated transfection using lipofection, polymer encapsulation, peptide-mediated transfection, or biological particle delivery systems such as "gene weapons" (see, for example, Nishikawa, et al. Hum Gene Ther., 12 (8): 861 to 870 ( 2001.) Non-viral methods of administration
[00851] [00851] In some respects, non-viral methods can be used to deliver a nucleic acid that encodes a chimeric molecule or fusion polypeptide described herein into a cell or tissue or an individual.
[00852] [00852] In some modalities, the non-viral method includes the use of a transposon (also called a transposition element). In some modalities, a transposon is a piece of DNA that can be inserted into a location in a genome, for example, a piece of DNA that has the capacity to self-replicate and insert its copy into a genome, or a piece of DNA which can be removed by splicing a longer nucleic acid and inserted elsewhere in a genome. For example, a transposon comprises a DNA sequence consisting of inverted repeats flanking genes for transposition.
[00853] [00853] In some embodiments, cells, for example, T or NK cells, are generated that express a chimeric molecule or fusion polypeptide, for example, as described in this document using a combination of gene insertion using the SBTS and genetic editing using a nuclease (for example, Zinc-depleted nucleases (ZFNs), Transcription Activator-Type Effector Nucleases (TALENs), the CRISPR / Cas system or addressing endonucleases remanipulated by manipulated meganuclease) .
[00854] [00854] In some modalities, the use of a non-viral method of administration allows reprogramming of cells, for example, T or NK cells, and direct infusion of cells into an individual. The advantages of non-viral vectors include, but are not limited to, ease and relatively low cost of producing sufficient quantities required to satisfy a patient population, stability during storage and absence of immunogenicity. Cells
[00855] [00855] “Cells are also provided in this document, for example, immuno-effector cells (for example, a cell population, for example, a population of immuno-effector cells) comprising a nucleic acid molecule, a polypeptide molecule of fusion or a vector, for example, as described in this document. In some embodiments, the cells provided comprise a fusion polypeptide, for example, as described herein, which comprise a domain that includes a CAR, a nucleic acid molecule encoding a fusion polypeptide that comprises a domain that includes a CAR, or a vector that comprises the same.
[00856] [00856] In certain aspects, immuno-effector cells, for example, T cells or NK cells can be obtained from a unit of blood collected from an individual using any techniques known to the person skilled in the art, such as separation with Ficoll "". In a preferred aspect, an individual's circulating blood cells are obtained by apheresis. The apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells and platelets. In one aspect, cells collected by apheresis can be washed to remove the plasma fraction and, optionally, to place the cells in a buffer or medium appropriate for subsequent processing steps. In one embodiment, the cells are washed with phosphate buffered saline (PBS). In an alternative way, the washing solution is devoid of calcium and may be devoid of magnesium or may be devoid of many, if not all, bivalent cations.
[00857] [00857] Initial activation steps in the absence of calcium can lead to amplified activation. As will be readily appreciated by those skilled in the art, a washing step can be performed by methods known to those skilled in the art, such as by using a semi-automated "continuous flow" centrifuge (for example, the Cobe 2991 cell processor, Baxter CytoMate or Haemonetics Cell Saver 5) according to the manufacturer's instructions. After washing, cells can be resuspended in a variety of biocompatible buffers, such as, for example, PBS without Ca, without Mg, PlasmaLyte A, or another saline solution with or without buffer. Alternatively, the undesirable components of the apheresis sample can be removed and the cells can be directly resuspended in culture medium.
[00858] [00858] It is recognized that the application methods can employ culture medium conditions comprising 5% or less, for example, 2%, of human AB serum, and employ known culture medium conditions and compositions, for example, those described in Smith et al., "Ex vivo expansion of human T cells for adoptive immu- notherapy using the novel Xeno-free CTS Immune Cell Serum Re-cement" Clinical & Translational Immunology (2015) 4, e31; doi: 10.1038 / cti.2014.31.
[00859] [00859] In one aspect, T cells are isolated from peripheral blood lymphocytes by lysis of erythrocytes and depletion of monocytes, for example, by centrifugation through a PERCOLLTM gradient or by countercurrent centrifugal elutriation.
[00860] [00860] The methods described in this document may include, for example, selecting a specific subpopulation of immune effector cells, for example, T cells, which are a population depleted of regulatory T cells, CD25 + depleted cells, using, for example, a negative selection technique, for example, described in this document. Preferably, the population of regulatory T-depleted cells contains less than 30%, 25%, 20%, 15%, 10%, 5%, 4%, 3%, 2%, 1% of CD25 + cells.
[00861] [00861] In one embodiment, regulatory T cells, for example, CD25 + T cells, are removed from the population using an anti-CD25 antibody, or its fragment, or a CD25 binding ligand, IL-2. In one embodiment, the anti-CD25 antibody, or a fragment thereof, or CD25 binding ligand is conjugated to a substrate, for example, a sphere, or is otherwise coated on a substrate, for example, a sphere . In one embodiment, the anti-CD25 antibody, or fragment thereof, is conjugated to a substrate as described herein.
[00862] [00862] In one embodiment, regulatory T cells, for example, CD25 + T cells, are removed from the population using MiltenyiTM CD25 depletion reagent. In one embodiment, the ratio of cells to CD25 depletion reagent is 1e7 cells for 20 ul, or 1e7 cells for 15 ul, or 1e7 cells for 10 ul, or 1e7 cells for 5 ul, or 1e7 cells for 2.5 ul or 1 and 7 cells for 1.25 µl. In one embodiment, for example, for depletion of regulated T cells, for example, CD25 +, more than 500 million cells / ml are used. In an additional aspect, a cell concentration of 600, 700, 800 or 900 million cells / ml is used.
[00863] [00863] In one embodiment, the population of immune effector cells to be depleted includes about 6 x 10 th CD25 + T cells. In other respects, the population of immune effector cells to be depleted includes about 1 x 10º to 1x 1010 CD25 + T cells and any integer value between them. In one embodiment, the resulting population depleted of regulatory T cells has 2 x 10º regulatory T cells, for example, CD25 + cells, or less (for example, 1 x 10º, 5x 108, 1 x 108, 5x 107, 1 x 107 or less CD25 + cells).
[00864] [00864] In one embodiment, regulatory T cells, for example, CD25 + cells, are removed from the population using the CIiniMAC system with a set of depletion tubing, such as, for example, 162-01 tubing . In one embodiment, the CIliniMAC system is operated in a depletion scenario such as, for example, DEPLE-TION2.1.
[00865] [00865] Without wishing to be limited by a particular theory, decrease the level of negative immune cell regulators (eg, decrease the number of unwanted immune cells, eg TREG cells) in an individual before apheresis or during manufacture of a fusion polypeptide, for example, as described in this document, comprising a domain that includes a cell product expressing CAR, can reduce the risk of relapse in an individual. For example, methods for depleting TREG cells are known
[00866] [00866] In some embodiments, manufacturing methods comprise reducing the number (e.g., depletion) of TREG cells prior to making the fusion polypeptide, for example, as described in this document, which comprises a domain that includes a cell that expresses CAR. For example, manufacturing methods include placing the sample, for example, the apheresis sample, in contact with an anti-GITR antibody and / or an anti-CD25 antibody (or fragment thereof or a CD25 binding ligand ), for example, to deplete TREG cells prior to making the CAR expressing cell product (eg, T cell, NK cell).
[00867] [00867] In one embodiment, an individual is pre-treated with one or more therapies that reduce TREG cells before collecting cells for fusion polypeptide, for example, as described in this document, comprising a domain that includes a product of cells expressing CAR, thus reducing the individual's risk of relapse to fusion polypeptide, for example, as described in this document, comprising a domain that includes treatment with cells expressing a CAR. In one embodiment, methods of decreasing TREG cells include, but are not limited to, administering one or more of the cyclophosphamide to the individual, anti-GITR antibody, CD25 depletion or a combination thereof. Administration of one or more of cyclophosphamide, anti-GITR antibody, CD25 depletion or a combination thereof can occur before, during or after an infusion of the CAR expressing cell product.
[00868] [00868] In one embodiment, a subject is pre-treated with cyclophosphamide before collecting cells to manufacture the cell product.
[00869] [00869] In one embodiment, the population of cells to be removed does not consist of regulatory T cells or tumor cells, but of cells that negatively affect the expansion and / or function of CART cells in any other way, for example, cells that express CD14, CD11b, CD33, CD15 or other markers expressed by potentially immunosuppressive cells. In a modality, it is contemplated that such cells are removed concurrently with regulatory T cells and / or tumor cells, or after depletion, or in another order.
[00870] [00870] The methods described here may include more than one selection step, for example, more than one depletion step. The enrichment of a population of T cells by negative selection can be achieved, for example, with a combination of antibodies directed to surface markers unique to the negatively selected cells. One method consists of screening and / or selecting cells via negative magnetic immunoadhesion or flow cytometry using a cocktail of monoclonal antibodies directed at cell surface markers present in the negatively selected cells. For example, for enrichment for CD4 + cells by negative selection, a cocktail of monoclonal antibodies can include antibodies to CD14, CD20, CD11b, CD16, HLA-DR and CD8.
[00871] [00871] The methods described here may additionally include removing cells from the population that express a tumor antigen, for example, a tumor antigen that does not comprise CD25, for example, CD19, CD30, CD38, CD123, CD20, CD14 or CD11b, for so providing a population depleted of regulatory T's, for example, depleted of CD25 +, and cells depleted of tumor antigens that are suitable for expression of a fusion polypeptide, for example, as described in this document, comprising a domain which includes a CAR, for example, a CAR described here. In one embodiment, cells that express tumor antigens are removed simultaneously with regulatory T cells, for example, CD25 +. For example, an anti-CD25 antibody, or its fragment, and an anti-tumor antigen antibody, or its fragment, can be attached to the same substrate, for example, a spherical, which can be used to remove cells or a anti-CD25 antibody, or its fragment, or anti-tumor antigen antibody, or its fragment, can be attached to separate spherules, a mixture from which it can be used to remove cells. In other modalities, the removal of regulatory T cells, for example, CD25 + cells, and the removal of cells that express tumor antigen, is sequential and can occur, for example, in any order.
[00872] [00872] Methods are also provided which include removing cells from the population expressing a checkpoint inhibitor, for example, a checkpoint inhibitor described here, for example, one or more of PD1 + cells, LAG3 + cells and TIM3 + cells, to thereby provide a population depleted of regulatory T cells, for example, depleted of CD25 +, and depleted of cells with a checkpoint inhibitor, for example, depleted of PD1 +, LAG3 + and / or TIM3 +. Exemplary checkpoint inhibitors include B7-H1, B7-1, CD160, P1H, 2B4, PD1, TIM3, CEACAM (e.g. CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG3, TIGIT, CTLA -H4, BTLA and LAIR1I. In one mode, cells expressing checkpoint inhibitor are removed simultaneously with regulatory T cells, for example, CD25 +. For example, an anti-CD25 antibody or fragment thereof, and an anti-checkpoint inhibitor antibody or fragment thereof, can be attached to the same microsphere that can be used to remove cells, or an anti-CD25 antibody or its fragment, and the anti-checkpoint inhibitor antibody or its fragment, can be attached to separate microspheres, a mixture of which can be used to remove cells. In other embodiments, the removal of regulatory T cells, for example, CD25 + cells, and the removal of cells expressing checkpoint inhibitors are sequential, and can occur, for example, in any order.
[00873] [00873] The methods described in this document may include a positive selection step. For example, T cells can be isolated by incubation with microspheres conjugated to anti-CD3 / anti-CD28 (eg 3x28), such as T CD3 / CD28 DYNABEADSO M-450, for a period of time sufficient for positive selection of the desired T cells. In one embodiment, the time period is about 30 minutes. In an additional modality, the time period varies from minutes to 36 hours or more and all integers between them. In an additional embodiment, the time period is at least 1, 2, 3, 4, 5 or 6 hours. In yet another modality, the time period is 10 to 24 hours, for example, 24 hours. Longer incubation times can be used to isolate T cells in any situation where there are few T cells compared to other cell types, such as in the isolation of tumor infiltrating lymphocytes (TIL) from tumor tissue or immunocompromised individuals. In addition, the use of longer incubation times can increase the efficiency of capturing CD8 + T cells. So, simply
[00874] [00874] In one embodiment, a population of T cells expressing one or more of IFN-γ, TNFα, IL-17A, IL-2, II-3, IL-4, GM-CSF, 11-10 can be selected , 11-13, granzyme B and perforin, or other appropriate molecules, for example, other cytokines. Methods for screening cell expression can be determined, for example, by the methods described in PCT Publication No .: WO 2013/126712.
[00875] [00875] For isolation of a population of cells by positive or negative selection, the concentration of cells and surface (for example, particles such as spherules) may vary. In certain aspects, it may be desirable to significantly decrease the volume at which spheres and cells are mixed together (for example, to increase the concentration of cells), to ensure maximum contact of cells and spheres. For example, in one aspect, a concentration of 10 billion cells / ml, 9 billion / ml, 8 billion / ml, 7 billion / ml, 6 billion / ml or 5 billion / ml is used. In one aspect, a concentration of 1 billion cells / ml is used. Still in one aspect, a cell concentration of 75, 80, 85, 90, 95 or 100 million cells / ml is used. In additional aspects, concentrations of 125 or 150 million cells / ml can be used.
[00876] [00876] The use of high concentrations can result in yields
[00877] [00877] In a related aspect, it may be desirable to use smaller concentrations of cells. By significantly diluting the T-cell and surface mixture (for example, particles such as spherules), interactions between the particles and cells are minimized. This process selects cells that express high amounts of desired antigens to be bound to the particles. For example, CDA4 + T cells express higher levels of CD28 and are more efficiently captured than CD8 + T cells in diluted concentrations. In one aspect, the cell concentration used is 5 x 106 / ml. In other aspects, the concentration used can be from about 1 x 10º / ml to 1 x 106 / ml, and any integer value between them.
[00878] [00878] In other respects, cells can be incubated on a rotator for varying lengths of time, at varying speeds, at a temperature of 2 to 10ºC or at room temperature.
[00879] [00879] T cells for stimulation can also be frozen after a washing step. Without wishing to be restricted by theory, the subsequent freezing and thawing step provides a more uniform product by removing granulocytes and, to some extent, monocytes from the cell population. After the washing step, which removes plasma and platelets, cells can be suspended
[00880] [00880] In certain respects, cryopreserved cells are thawed and washed as described in this document and allowed to stand for one hour at room temperature before activation using the methods of the present invention.
[00881] [00881] “It is also contemplated, in the context of the invention, the collection of blood samples or apheresis product from an individual in a period of time before the expanded cells may be necessary as described in this document. In this way, the source of the cells to be expanded can be collected at any time needed, and desired cells, such as T cells, can be isolated and frozen for later use in therapy with immune effector cells for any diseases or conditions that benefit from the therapy. with immune effector cells, such as those described in this document. In one respect, a blood sample or apheresis is taken from a generally healthy individual. In some respects, a blood sample or apheresis is taken from a generally healthy individual who is at risk of developing a disease, but who has not yet developed a disease, and the cells of interest are isolated and frozen for later use. In some ways, T cells can be expanded, frozen, and used at a later time. In certain respects, samples are collected from a patient shortly after the diagnosis of a particular disease as described in this document, but before any treatments. In an additional aspect, the cells are isolated from a blood sample or an apheresis from an individual prior to any relevant treatment modalities, including, but not limited to treatment with agents such as natalizumab, efalizumab, antiviral agents , chemotherapy, radiation, immunosuppressive agents, such as cyclosporine, azathioprine, methotrexate, mycophenolate, and FK506, antibodies or other immunoablating agents such as CAM-PATH, anti-CD3 antibodies, cytoxane, fludarabine, cyclosporine, FK506, rapamycin, mycophenolic acid, steroids, FR901228 and irradiation.
[00882] [00882] In a further aspect of the present invention, T cells are obtained from a patient directly after treatment that leaves the individual with functional T cells. In this regard, it was observed that, after certain treatments for cancer, in particular treatments with drugs that damage the immune system, shortly after treatment and during the period in which patients are normally recovering from treatment, the quality of T cells obtained can be optimal or improved in terms of their ex vivo expansion capacity. Likewise, after ex vivo manipulation using the methods described in this document, these cells may be in a preferential state for enhanced in vivo grafting and expansion. Thus, it is contemplated, in the context of the present description, to collect blood cells, including T cells, dendritic cells, or other cells of the hematopoietic lineage, during this recovery phase. In addition,
[00883] [00883] In one embodiment, the immuno-effector cells that express a fusion polypeptide, for example, as described in this document, comprising a domain that includes a CAR molecule, for example, a CAR molecule described herein document, are obtained from a subject who received a low immunity-enhancing dose from an MTOR inhibitor. In a fashion, the population of immuno-effector cells, for example, T cells, to be manipulated to express a CAR, is collected after sufficient time or after sufficient low dose of immune intensification of an MTOR inhibitor, so that the level of PD1 negative immune effector cells, for example, T cells, or the ratio of PD1 negative immune effector cells, for example, PD1 positive T cells / immune effector cells, for example, T cells, in the individual or collected from the individual was, at least temporarily, increased.
[00884] [00884] In other embodiments, the population of immune effector cells, for example, T cells, which has been or will be engineered to express a fusion protein, for example, as described in this document, comprising a domain that includes a CAR , can be treated ex vivo by contact with an amount of an MTOR inhibitor that increases the number of immune effector cells negative for PD1, for example, T cells, or increases the ratio of immune negative effector cells to PD1, for example, cells
[00885] [00885] In one embodiment, the T cell population is deficient in diaglycerol kinase (DGK). DGK-deficient cells include cells that do not express RNA or DGK protein, or have reduced or inhibited DGK activity. DGK deficient cells can be generated by genetic approaches, for example, administration of RNA interference agents, for example, siRNA, shRNA, miRNA, to reduce or prevent the expression of DGK. Alternatively, DGK-deficient cells can be generated by treatment with DGK inhibitors described in this document.
[00886] [00886] In one embodiment, a population of T cells is deficient in lkaros. Ilkaros-deficient cells include cells that do not express RNA or lkaros protein, or have reduced or inhibited lkaros activity, Ikaros-deficient cells can be generated by genetic approaches, for example, administration of RNA interfering agents, for example, siRNA, shRNA, miRNA, to reduce or prevent expression of lkaros. Alternatively, cells deficient in lkaros can be generated by treatment with lkaros inhibitors, for example, lenalidomide.
[00887] [00887] In modalities, a population of T cells is deficient in DGK and deficient in Ikaros, for example, does not express DGK or lkaros, or has reduced or inhibited DGK and Ikaros activity. Such DGK and Ilkaros deficient cells can be generated by any of the methods described in this document.
[00888] [00888] In one embodiment, NK cells are obtained from the individual. In another embodiment, NK cells are an NK cell line, for example, NK-92 cell line (Conkwest). Additional Express Agents
[00889] [00889] In another embodiment, a fusion polypeptide, for example, as described in this document, comprising a domain that includes an immuno-protective cell that expresses CAR described in this document can additionally express another agent, for example, an agent that increases the activity of a CAR expression cell. For example, in one embodiment, the agent can be an agent that inhibits an inhibitory molecule. Examples of inhibitory molecules include PD-1, PD-L1, CTLA-4, TIM-3, CEA-CAM (e.g., CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4 and TGFR beta, as described in this document. In one embodiment, the agent that inhibits an inhibitory molecule comprises a first polypeptide, for example, an inhibitor molecule, associated with a second polypeptide that provides a positive signal for the cell, for example, an intracellular signaling domain described here. In one embodiment, the agent comprises a first polypeptide, for example, from an inhibitory molecule such as PD-1, PD-L1, CTLAH4, TIM-3, CEACAM (for example, CEACAM-1, CEACAM-3 and / or CEACAM -5), LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4 or TGFR beta, or a fragment of any of these, and a second polypeptide which is an intracellular signaling domain described here (for example, comprising a co-stimulatory domain (for example, 41BB, CD27 or CD28, for example, as described here) and / or a primary signaling domain (for example, a CD3 zeta signal domain described here)). In one embodiment, the agent comprises a first PD-1 polypeptide or fragment thereof, and a second polypeptide from an intracellular signaling domain described here (for example, a signaling domain of CD28, CD27, OX40 or 4-1BB described in this document and / or a CD3 zeta signaling domain described in this document).
[00890] [00890] In one embodiment, the fusion polypeptide, for example, as described in this document, comprising a domain
[00891] [00891] Without sticking to the theory, the placement of a co-stimulating signaling domain, for example, 4-1BB, CD28, CD27 or OX-40, in the first CAR, and in the primary signaling domain, for example, CD3 zeta, in the second CAR can limit the CAR activity to cells where both targets are expressed. In one embodiment, the CAR expressing immune cell comprises a first CAR that includes an antigen-binding domain that targets, for example, a target described above, a transmembrane domain and a co-stimulating domain, and a second CAR that targets an antigen other than the antigen targeted by the CAR (for example, an antigen expressed on the same type of cancer cells as the first target) and includes an antigen-binding domain, a transmembrane domain and a primary signaling domain. In another embodiment, the CAR expressing immune cell comprises a first CAR that includes an antigen-binding domain that targets, for example, a target described above, a transmembrane domain and a primary signaling domain, and a second CAR that targets a antigen different from the antigen targeted by the first CAR (for example, an antigen expressed in the same type of cancer cells as the first target) and includes an antigen-binding domain for the antigen, a transmembrane domain and a co-stimulating signaling domain.
[00892] [00892] In one embodiment, the CAR-expressing immune cell comprises a CAR described in this document, for example, a CAR for a target described above, and an inhibitory CAR. In one embodiment, the CAR inhibitor comprises an antigen-binding domain that binds an antigen found in normal cells, but not cancer cells, for example, normal cells that also express the target. In one embodiment, the inhibitory CAR comprises the antigen-binding domain, a transmembrane domain and an intracellular domain of an inhibitory molecule. For example, the intracellular domain of the inhibiting CAR may be an intracellular domain of PD1, PD-L1, CTLA-4, TIM-3, CEACAM (e.g., CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG -3, VISTA, BTLA, TIGIT, LAIRI1, CD160, 2B4 or TGFR beta.
[00893] [00893] In one embodiment, an immunosuppressive cell (for example, T cell, NK cell) comprises a first CAR that comprises an antigen-binding domain that binds to a tumor antigen as described in this document , and a second CAR comprising an extracellular PD1 domain or a fragment thereof.
[00894] [00894] In one embodiment, the cell further comprises an inhibitory molecule as described above.
[00895] [00895] In one embodiment, the second CAR in the cell is an inhibitory CAR, in which the inhibiting CAR comprises an antigen-binding domain, a transmembrane domain and an intracellular domain of an inhibitory molecule. The inhibitory molecule can be chosen from one or more of: PD1, PD-L1, CTLA-4, TIM-3, LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4, TGFR beta, CEACAM -1, CEACAM-3 and CEACAM-5. In one embodiment, the second CAR molecule comprises the extracellular domain of PD1 or a fragment thereof.
[00896] [00896] In the embodiments, the second CAR molecule in the cell further comprises an intracellular signaling domain comprising a primary signaling domain and / or an intracellular signaling domain.
[00897] [00897] In other embodiments, the intracellular signaling domain in the cell comprises a primary signaling domain comprising the CD3 zeta functional domain and a co-stimulating signaling domain comprising the 4-1BB functional domain.
[00898] [00898] In certain embodiments, the antigen-binding domain of the first CAR molecule comprises an scFv and the antigen-binding domain of the second CAR molecule does not comprise an scFv. For example, the antigen-binding domain of the first CAR molecule comprises an scFv and the antigen-binding domain of the second CAR molecule comprises a scelv domain of camelid. Split CAR
[00899] [00899] In some embodiments, the cell that expresses CAR uses a split CAR. The split CAR approach is described in more detail in publications WO2014 / 055442 and WO2014 / 055657, incorporated by reference in this document. In summary, a split CAR system comprises a cell that expresses a first CAR that has a first antigen-binding domain and a co-stimulatory domain (for example, 41BB), and the cell also expresses a second CAR that has a second domain of antigen binding and an intracellular signaling domain (eg CD3 zeta). When the cell encounters the first antigen, the co-timer domain is activated, and the cell proliferates. When the cell encounters the second antigen, the intracellular signaling domain is activated and cell death activity begins. Thus, the cell that expresses CAR is fully activated only in the presence of both antigens. Multiple CAR expression
[00900] [00900] In one aspect, the fusion polypeptide, for example, as described herein, comprising a domain that includes a CAR expression cell described herein can additionally comprise a second fusion polypeptide, for example. example, as described in this document comprising a domain that includes a CAR, for example, a second CAR that includes a different antigen-binding domain, for example, the same target or a different target (for example, a different target cancer-associated antigen described in this document or a different cancer-associated antigen described in this document). In one embodiment, the second CAR includes an antigen-binding domain for a target expressed on the same type of cancer cell as the cancer-associated antigen. In one mode, the CAR expressing cell comprises a first CAR that targets a first antigen and includes an intracellular signaling domain that has a co-stimulating signaling domain, but not a primary signaling domain, and a second CAR that targets a different second antigen and includes an intracellular signaling domain that has a primary signaling domain, but not a co-stimulating signaling domain. Without sticking to the theory, the placement of a co-stimulating signaling domain, for example, 4-1BB, CD28, CD27 or OX-40, in the first CAR, and the domain
[00901] [00901] In some embodiments, the claimed invention comprises a first and a second CAR, wherein the antigen-binding domain of one of said first CAR and said second CAR does not comprise a light variable domain and a heavy domain variable. In some embodiments, the antigen-binding domain of one of said first CAR and said second CAR is scFv, and the other is not scFv. In some embodiments, the antigen-binding domain of one of said first CAR and said second CAR comprises a simple VH domain, for example, a simple camelid, shark or lamprey VH domain, or a simple VH domain derived from a human or mouse sequence. In some embodiments, the antigen-binding domain of one of said first CAR and said second CAR comprises a nanobody. In some embodiments, the antigen-binding domain of one of said first CAR and said second CAR comprises a camelid VHH domain. Allogeneic cells
[00902] [00902] In embodiments described in this document, the immune effector cell can be an allogeneic immune effector cell, for example, T cell or NK cell. For example, the cell may be an allogeneic T cell, for example, an allogeneic T cell devoid of expression of a functional T cell receptor (TCR) and / or human leukocyte antigen (HLA), for example, HLA class | and / or HLA class | or beta 2 microglobulin (B2M).
[00903] [00903] “A T cell lacking a functional TCR can be manipulated, for example, so that it does not express any functional TCR on its surface, manipulated in a way that does not express one or more subunits that comprise a functional TCR, for example, TRAC, TRBC1, TRBC2, CD3E, CD3G or CD3D or manipulated in such a way that it produces very little functional TCR on its surface. Alternatively, the T cell can express a substantially compromised TCR, for example, by expression of mutated or truncated forms of one or more of the TCR subunits. The term "substantially weakened TCR" means that this TOR will not induce an adverse immune reaction in a host.
[00904] [00904] A T cell described here can be manipulated, for example, so that it does not express a functional HLA on its surface. For example, a T cell described in this document can be genetically modified so that the expression HLA on the cell surface, for example, HLA class | and / or HLA class | l, or HLA expression subunit or regulator, for example, B2M,
[00905] [00905] A T cell described here can be manipulated, for example, so that it does not express a functional B2M on its surface. For example, a T cell described here can be manipulated so that B2M cell surface expression is under-regulated.
[00906] [00906] In some embodiments, the T cell may be devoid of a functional TCR and a functional HLA, for example, HLA class | and / or HLA class | l.
[00907] [00907] Modified T cells devoid of expression of a functional TCR and / or HLA can be obtained by any suitable means, including knocking out or silencing one or more subunits of the TCR or HLA. For example, the T cell may include silencing TOR and / or HLA using siRNA, shRNA, short palindromic repeats grouped regularly (CRISPR), effector transcription activator nuclease (TALEN), or endonuclease zinc fingers ( ZFN).
[00908] [00908] In some embodiments, the allogeneic cell may be a cell that does not express or express itself at low levels an inhibitory molecule, for example, by any method described in this document. For example, the cell may be a cell that does not express or express at low levels an inhibitory molecule, for example, which may decrease the ability of a cell expressing CAR to mount an immune effector response. Examples of inhibitory molecules include PD1, PD-L1, CTLA4, TIM3, CEACAM (eg, CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4 and TGFR beta. The inhibition of an inhibitory molecule, for example, by inhibition at the level of DNA, RNA or protein, can optimize the performance of a cell that expresses CAR. In embodiments, an inhibitory nucleic acid, for example, an inhibitory nucleic acid, for example, a dsRNA, for example, a siRNA or shRNA, short palindromic repetitions clustered regularly (CRISPR), effector nuclease of the activator type of transcription (TALEN), or a zinc finger endonuclease (ZFN), for example, as described here. sSiRNA and shRNA
[00909] [00909] In some embodiments, TCR expression and / or HLA or B2M expression can be inhibited using siRNA or shRNA targeting a nucleic acid encoding a TCR and / or HLA in a T cell. CRISPR
[00910] [00910] "CRISPR" or "CRISPR for TCR and / or HLA" or "CRISPR for inhibiting TOR and / or HLA", as used herein, refers to a set of short palindromic repetitions grouped at regular intervals, or a system that comprises such a set of repetitions. "Cas", as used herein, refers to a protein associated with CRISPR. A "CRISPR / Cas" system refers to a system derived from CRISPR and Cas that can be used to silence or mutate a TCR and / or HLA or B2M gene.
[00911] [00911] Artificial CRISPR / Cas systems that inhibit TCR and / or HLA can be generated using technology known in the art, for example, that described in US Publication No. 20140068797, and Cong (2013) Science 339: 819-823, incorporated in this document as a reference in its entirety. Other artificial CRISPR / Cas systems, which are known in the art, that inhibit TCR and / or HLA can also be generated, for example, that described in Tsai (2014) Nature Biotechnol., 32: 6 569-576, US Patent No. : 8,871,445; 8,865,406;
[00912] [00912] "TALEN" or "TALEN for HLA and / or TCR" or "TALEN for inhibiting HLA and / or TCR" refers to an effector transcription-activating nuclease, an artificial nuclease that can be used to edit the HLA or B2M and / or TCR gene.
[00913] [00913] TALENs are produced artificially by fusing a TAL effector DNA binding domain to a DNA cleavage domain. Transcription activator-like effects (TALEs) can be modified to bind to any desired DNA sequence, including a portion of the HLA or TCR gene. With the combination of a modified TALE with a DNA cleavage domain, a restriction enzyme can be produced that is specific to any desired DNA sequence, including an HLA or TCR sequence. These can then be introduced into a cell, where they can be used for genomic editing, as described in Boch (2011) Nature Biotech. 29: 135-6; Boch et al. (2009) Science 326: 1509-112; and Moscow et al. (2009) Science 326: 3501, incorporated in this document as a reference in its entirety.
[00914] [00914] TALENs specific for HLA or TCR sequences can be constructed using any method known in the art, including various schemes using modular components, as described in Zhang et al. (2011) Nature Biotech. 29. 149-53; and Geibler et al. (2011) PLoS ONE 6: e19509, incorporated in this document as a reference in its entirety. Nuclease zinc fingers to inhibit HLA and / or TCR
[00915] [00915] "ZFN" or "Zinc Finger Nuclease" or "ZFN for HLA and / or TOR" or "ZFN for inhibiting HLA and / or TCR" refers to a zinc finger nuclease, a nuclease that can be used to edit the HLA and / or TCR or B2M gene.
[00916] [00916] ZFNs specific for HLA and / or TCR sequences can be constructed using any method known in the art, as described in Provasi (2011) Nature Med. 18: 807- 815; Torikai (2013) Blood 122: 1341-1349; Cathomen et al. (2008) Mol. Ther. 16: 1200-7; Guo et al. (2010) J. Mol. Biol. 400: 96; Patent Publication No. U.S. 2011/0158957; and U.S. Patent Publication No. 2012/0060230, incorporated herein by reference in its entirety. Telomerase expression
[00917] [00917] Without, if you stick to any particular theory, in some modalities, a therapeutic T cell has short-term persistence in a patient, due to shortened telomeres in the T cell; consequently, transfection with a telomerase gene can extend T cell telomeres and improve T cell persistence in the patient. See, Carl June, "Adoptive T cell therapy for cancer in the clinic", Journal of Clinical Investigation, 117: 1466-1476 (2007), incorporated in this document as a reference in its entirety. Thus, in one embodiment, an immune effector cell, for example, a T cell, ectopically expresses a telomerase subunit, for example, the catalytic telomerase subunit, for example, TERT, for example, hTERT. In some respects, this description provides a method of producing a cell expressing CAR, comprising contacting a cell with a nucleic acid encoding a telomerase subunit, for example, the catalytic telomerase subunit, for example TERT , for example, hTERT. The cell can be brought into contact with the nucleic acid before, simultaneously or after being brought into contact with a construct encoding a CAR. Expansion and Activation
[00918] [00918] Immuno-effector cells such as T cells can be activated and expanded generally using methods as described,
[00919] [00919] Generally, a population of immune effector cells, for example, cells depleted of regulatory T cells, can be expanded by contact with a surface having bound an agent that stimulates a signal associated with the CD3 / TCR complex and a ligand that stimulates a co-stimulating molecule on the surface of T cells. In particular, populations of T cells can be stimulated as described here, such as by contact with an anti-CD3 antibody, or its antigen-binding fragment, or an anti-CD2 antibody immobilizes - on a surface, or by contact with a protein kinase C activator (eg, briostatin) in conjunction with a calcium ionophore. For the co-stimulation of an accessory molecule on the surface of T cells, a ligand is used that binds to the accessory molecule. For example, a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under appropriate conditions to stimulate the proliferation of T cells. To stimulate the proliferation of CD4 + T cells or CD8 + T cells, an anti-CD3 antibody and an anti-CD28 antibody can be used. Examples of an anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besançon, France) that can be used, as well as other methods commonly known in the art (Berg et a /., Transplant Proc. 30 (8):
[00920] [00920] In certain aspects, the primary stimulatory signal and the co-stimulatory signal for the T cell can be provided by different protocols
[00921] [00921] In one aspect, the two agents are immobilized in microspheres, in the same microsphere, that is, "cis", or in separate microspheres, that is, "trans". By way of example, the agent that provides the primary activation signal is an anti-CD3 antibody or an antigen-binding fragment thereof and the agent that provides the co-stimulating signal is an anti-CD28 antibody or its fragment binding to antigens; and the two agents are co-immobilized in the same microsphere in equivalent molecular amounts. In one aspect, a 1: 1 ratio of each antibody bound to the microspheres is used for CD4 + T cell expansion and T cell growth. In certain aspects of the present invention, an anti-CD3: CD28 antibody ratio is used. connected to the microspheres in order to observe an
[00922] [00922] “Particle to cell ratios from 1: 500 to 500: 1 and any integer values between these can be used to stimulate T cells or other target cells. As those of ordinary skill in the art can readily understand, the ratio of particles to cells may depend on the size of the particles relative to the target cell. For example, small microspheres can bind only a few cells, while larger microspheres can bind many. In certain aspects, the ratio between cells and particles is in the range from 1: 100 to 100: 1 and any integer values between them and, in additional aspects, the ratio between 1: 9 to 9: 1 and any integer values between them can also be used to stimulate T cells.
[00923] [00923] In additional aspects, the cells, such as T cells, are combined with microspheres coated with agents, the microspheres and the cells are subsequently separated, and then the cells are cultured. In an alternative aspect, prior to culture, microspheres coated with agents and cells are not separated, but are cultivated together. In a further aspect, microspheres and cells are first concentrated by applying a force, such as a magnetic force, resulting in increased binding of cell surface markers, thereby inducing stimulation of cells.
[00924] [00924] By way of example, cell surface proteins can be linked by allowing paramagnetic microspheres to which anti-CD3 and anti-CD28 (3x28 microspheres) are attached to make contact with T cells. the cells (eg, 10th to 10th T cells) and microspheres (eg, CD3 / CD28 DYNABEADSO M-450 paramagnetic T microspheres at a 1: 1 ratio) are combined in a buffer, for example, PBS (without divalent cations, such as calcium and magnesium). Again, those skilled in the art can readily understand that any cell concentration can be used. For example, the target cell can be very rare in the sample and comprise only 0.01% of the sample or the entire sample (i.e., 100%) can comprise the target cell of interest. Consequently, any number of cells are within the context of the present invention. In certain aspects, it may be desirable to significantly decrease the volume at which particles and cells are mixed together (i.e., to increase the concentration of cells), to ensure maximum contact of cells and particles. For example, in one aspect, a concentration of about 10 billion cells / ml, 9 billion / ml, 8 billion / ml, 7 billion / ml, 6 billion / ml, 5 billion / ml or 2 billion is used / ml. In one respect, more than 100 million
[00925] [00925] In one embodiment, cells transduced with a nucleic acid encoding a fusion polypeptide, for example, as described in this document, comprising a domain that includes CAR, for example, a CAR described in this document, are expanded, for example, by a method described in this document. In one embodiment, the cells are expanded in culture for a period of several hours (for example, about 2, 3, 4, 5,6,7,8,9, 10, 15, 18, 21 hours) at about 14 days (e.g. 1, 2, 3.4, 5.6, 7, 8, 9, 10, 11, 12, 13, or 14 days). In one embodiment, the cells are expanded over a period of 4 to 9 days. In one embodiment, the cells are expanded over a period of 8 days or less, for example, 7, 6 or 5 days. In one embodiment, the cells are expanded in culture for 5 days, and the resulting cells are more potent than the same cells expanded in culture for 9 days under the same culture conditions. The power can be defined
[00926] [00926] Several stimulation cycles may also be desired, so that the T cell culture time can be 60 days or more. Suitable conditions for T cell culture include an appropriate medium (for example, Minimum Essential Medium or RPMI 1640 or X-vivo 15 medium (Lonza)) that may contain factors necessary for proliferation and viability, including serum (for example, serum - such as bovine or human), interleukin-2 (IL-2), insulin, IFN-y, IL-4, IL-7, GM-CSF, 11-10, 11-12, IL-15, TGFB and TNF -a or any other cell growth additives known to the skilled person. Other additives for cell growth include, but are not limited to, surfactant, plasmanate and reducing agents such as N-acetyl-cysteine and 2-mercaptoethanol. Media may include RPMI 1640, AIM-V, DMEM, MEM, a-MEM, F-12, X-Vivo 15 and X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate and vitamins, without serum or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones and / or an amount of cytokine (or cytokines) sufficient for the growth and expansion of T cells. Antibiotics, for example, penicillin and streptomycin, are included only in experimental cultures, not in cell cultures to be infused in a subject. The target cells are maintained under conditions necessary to support growth, for example, an appropriate temperature (for example, 37 ºC) and atmosphere (for example, air plus 5% CO ”).
[00927] [00927] In one embodiment, cells are expanded in an appropriate medium (for example, medium described here) that includes one or more interleukins that results in at least a 200-fold increase (for example, 200 times, 250 times , 300 times, 350 times) the number of cells over a 14-day expansion period, for example, measured by a method described here such as flow cytometry. In one embodiment, cells are expanded in the presence of IL-15 and / or IL-7 (for example, IL-15 and IL-7).
[00928] [00928] In embodiments, methods described in this document, for example, fusion polypeptide, for example, as described in this document, comprising a domain that includes methods of making CAR expression cells, comprise removing cells Regulatory T, for example, CD25 + T cells, from a population of cells, for example, using an anti-CD25 antibody, or fragment thereof, or a CD25 binding ligand, IL-2. Methods for removing regulatory T cells, for example, CD25 + T cells, from a cell population are described in this document. In embodiments, the methods, for example, manufacturing methods, further comprise contacting a cell population (for example, a cell population in which regulatory T cells, such as CD25 + T cells, have been depleted; or a cell population - them that were previously contacted with an anti-CD25 antibody, its fragment, or CD25 binding ligand) with IL-15 and / or IL-7. For example, the cell population (for example, which has been previously contacted with an anti-CD25 antibody, its fragment, or CD25 binding ligand) is expanded in the presence of IL-15 and / or IL-7.
[00929] [00929] In some embodiments, a fusion polypeptide, for example, as described herein, comprising a domain that includes a CAR expression cell described herein is contacted with a composition comprising an interleukin-15 (IL-15 polypeptide) ), an interleukin-15 alpha receptor polypeptide (IL-15Ra), or a combination of an IL-15 polypeptide and an IL-15Ra polypeptide, for example, hetlL-15, during cell preparation expressing CAR, for example, ex vivo. In the embodiments, a CAR expressing cell described herein is contacted with a composition comprising an IL- polypeptide during the preparation of the CAR expressing cell, for example, ex vivo. In embodiments, the CAR expressing cell described here is contacted with a composition comprising a combination of an IL-15 polypeptide and an IL-15 Ra polypeptide during the manufacture of the CAR expressing cell, for example, ex vivo . In modalities, the cell expressing CAR described here is contacted with a composition comprising hetLL-15 during the manufacture of the cell expressing CAR, for example, ex vivo.
[00930] [00930] In one embodiment, the fusion polypeptide, for example, as described in this document, comprising a domain that includes a cell expressing CAR described in the present document is contacted with a composition comprising hetlL-15 during ex vivo expansion. In one embodiment, the cell expressing CAR described in this document is contacted with a composition that comprises an IL-15 polypeptide during ex vivo expansion. In one embodiment, the CAR expressing cell described herein is contacted with a composition comprising an I | L-15 polypeptide and an IL-15Ra polypeptide during ex vivo expansion. In one embodiment, contact results in the survival and proliferation of a subpopulation of lymphocytes, for example, CD8 + T cells.
[00931] [00931] T cells that have been exposed to varying stimulation times may exhibit different characteristics. For example, typical blood products or peripheral blood mononuclear cells undergoing apheresis have a population of adjuvant T cells (TH, CD4 +) that is greater than the population of cytotoxic or suppressive T cells (TC, CD8 +). The ex vivo expansion of T cells by stimulating the CD3 and CD28 receptors produces a population of T cells that, before about 8 to 9 days, predominantly consists of TH cells, whereas after about 8 to 9 days , the T cell population comprises an increasing population of TC cells. Consequently, depending on the purpose of the treatment, infusing an individual with a population of T cells that predominantly comprises TH cells can be advantageous. Similarly, if a subset of antigen-specific TC cells has been isolated, it may be beneficial to expand this subset to a greater degree.
[00932] [00932] Furthermore, in addition to the CD4 and CD8 markers, other phenotypic markers vary significantly but, to a large extent, in a reproducible way during the cell expansion process. Thus, such a reproducible character allows you to customize a product of activated T cells for specific purposes.
[00933] [00933] Since a fusion polypeptide, for example, as described in this document, comprising a domain that includes a CAR, described in this document is constructed, several assays can be used to evaluate the activity of the molecule , such as, but without limitation, the ability to expand T cells after stimulation by antigens, sustain the expansion of T cells in the absence of restimulation and anticancer activities in appropriate in vitro models and animals. Assays to assess the effects of a CAR of the present description are described in more detail below.
[00934] [00934] In Western blot analyzes of fusion polypeptide, for example, as described in this document, comprising a domain that includes a CAR, expression in primary T cells can be used to detect the presence of monomers and dimers. See, for example, Milone et a /., Molecular Therapy 17 (8): 1453 a
[00935] [00935] The in vitro fusion polypeptide expansion ”, for example, as described in this document, comprising a domain that includes a CAR, for example, CAR”, T cells after antigen stimulation can be measured by flow cytometry . For example, a mix of CD4 * and CD8 * T cells is stimulated with aCD3 / aCD28 aAPCs followed by transduction with lentiviral vectors that express GFP under the control of the promoters to be analyzed. Exemplary promoters include CMV IE gene promoters, EF-1a, ubiquitin C or phosphoglycerokinase (PGK). GFP fluorescence is assessed on day 6 of culture in the CD4 * and / or CD8 * T cell subsets by flow cytometry. See, for example, Milone et al., Molecular Therapy 17 (8): 1,453 to 1,464 (2009). Alternatively, a mixture of CD4 * and CD8 * T cells is stimulated with magnetic microspheres coated with aCD3 / aCD28 on day 0 and transduced with CAR on day 1 using a bicistronic lentiviral vector that expresses CAR together with eGFP with the use of 2A ribosomal omission sequence. Cultures are stimulated again with a cancer-associated antigen as described here * K562 cells (K562 expressing a cancer-associated antigen as described here), wild-type K562 cells (wild-type K562) or K562 cells expressing hCD32 and 4 -1BBL in the presence of anti-CD3 and anti-CD28 antibody (K562-BBL-3/28) after washing. Exogenous IL-2 is added to the cultures on alternate days at 100 IU / ml. GFP * T cells are listed by flow cytometry using microsphere based counting. See, for example, Milone et al., Molecular Therapy 17 (8): 1453 a
[00936] [00936] The sustained fusion polypeptide *, for example, as described in this document, comprising a domain that includes a CAR, for example, CAR *, the expansion of T cells in the absence of restimulation can also be measured . See, for example, Milone et al /., Molecular Therapy 17 (8): 1,453 to 1,464 (2009). In short, the average volume of T cells (fl) is measured on day 8 of the culture using a Coulter Multisizer Ill particle counter, a Nexcelom Cellometer Vision or Millipore Scepter, after stimulation with aCD3 / aCD28 coated magnetic beads. on day O and transduction with the CAR indicated on day 1.
[00937] [00937] “Animal models can also be used to measure a CART activity. For example, a xenograft model using CAR * T cells specific for an
[00938] [00938] The dose-dependent fusion polypeptide, for example, as described in this document, comprising a domain
[00939] [00939] The evaluation of cell proliferation and cytokine production was previously described, for example, in Milone et al /., Molecular Therapy 17 (8): 1,453 to 1,464 (2009). In summary, the evaluation of CAR-mediated proliferation is performed on microtiter plates mixing T cells washed with K562 cells that express a cancer-associated antigen described here (K19) or CD32 and CD137 (KT32-BBL) for a final T: K562 ratio of 2: 1. K562 cells are irradiated with gamma radiation before use. Anti-CD3 (clone OKT3) and anti-CD28 (clone 9.3) monoclonal antibodies are added to cultures with KT32-BBL cells to serve as a positive control to stimulate T cell proliferation since these signals support long-term CD8 * T cells ex vivo. T cells are enumerated in cultures using CountBright 'Y' fluorescent microspheres (Invitrogen, Carlsbad, CA) and flow cytometry, as described by the manufacturer. CAR * T cells are identified by GFP expression using T cells that are manipulated with lentiviral vectors that express CAR linked to eGFP-2A. For T CAR + cells that do not express GFP, T CAR + cells are detected with recombinant biotinylated protein from a cancer-associated antigen described here and a secondary avidin-PE conjugate. The expression of CD4 + and CD8 * in T cells is also simultaneously detected with specific monoclonal antibodies (BD Biosciences). Cytokine measurements are performed on supernatants collected 24 hours after further stimulation using the human TH1 / TH2 cytokine spherical array kit (BD Biosciences, San Diego, CA) according to the manufacturer's instructions. Fluorescence is assessed using a FACScalibur flow cytometer and the data is analyzed according to the manufacturer's instructions.
[00940] [00940] Cytotoxicity can be assessed by a standard 51 Cr release assay. See, for example, Milone et al., Molecular The- rapy 17 (8): 1,453 to 1,464 (2009). In summary, the target cells (K562 lines and primary pro-B ALL cells) are loaded with 51Cr (such as NaCrO4, New England Nuclear, Boston, MA) at 37 ° C for 2 hours with frequent agitation, washed twice in complete RPMI and placed on microtiter plates. Effector T cells are mixed with target cells in the wells in complete RPMI in varying effector cell: target cell (E: T) ratios. Additional wells containing the medium only (spontaneous release, SR) or a 1% solution of triton-X 100 detergent (total release, TR) are also prepared. After 4 hours of incubation at 37 ºC, the supernatant from each well is collected. The released 51Cr is then measured using a gamma particle counter (Packard Instrument Co., Waltham, MA). Each condition is performed at least in triplicate, and the percentage of lysis is calculated using the formula:% of Lysis = (ER-SR) / (TR— SR), where ER represents the average 51Cr released for each experimental condition .
[00941] [00941] “Imaging technologies can be used to assess the specific traffic and proliferation of CARs in models of animals with tumor. Such assays have been described, for example, in Barrett et al., Human Gene Therapy 22: 1575-1586 (2011). In short,
[00942] [00942] Other assays, including those described in the Examples section in this document as well as those that are known in the art, can also be used to evaluate the CARs described in this document.
[00943] [00943] In another aspect, the invention belongs to a method of producing a cell (for example, an immuno-protective cell or population of it) which comprises introducing (for example, translating) into a cell, for example, a T cell or NK cell described herein, a vector comprising a nucleic acid encoding a fusion polypeptide, for example, as described herein, which comprises a domain that includes a CAR, for example, a CAR described herein document; or a nucleic acid that encodes a CAR molecule, for example, a CAR described herein.
[00944] [00944] The cell in the methods is an immunosuppressive cell (for example, a T cell or an N cell, or a combination thereof). In some embodiments, the cell in the methods is deficient in diaglycerol kinase (DGK) and / or lkaros.
[00945] [00945] In some embodiments, the introduction of the CAR encoding nucleic acid molecule comprises transducing a vector encoding the nucleic acid molecule encoding a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR, or transfecting the nucleic acid molecule that encodes a CAR, wherein the nucleic acid molecule is an RNA transcribed in vitro.
[00946] [00946] In some embodiments, the method additionally comprises: providing a population of immuno-effector cells, for example, (for example, T cells or NK cells); and removing regulatory T cells from the population, thereby providing a depleted population of regulatory T cells; wherein steps a) and b) are performed prior to the introduction of the nucleic acid encoding the fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR, in the population.
[00947] [00947] In the method modalities, regulatory T cells comprise CD25 + T cells that are removed from the cell population using an anti-CD25 antibody, or fragment thereof. The anti-CD25 antibody, or fragment thereof, can be conjugated to a substrate, for example, a microsphere.
[00948] [00948] In other modalities, the population depleted of regulatory T cells provided from step (b) contains less than 30%, 25%, 20%, 15%, 10%, 5%, 4%, 3%, 2 %, 1% of CD25 + cells.
[00949] [00949] In still other modalities, the method additionally comprises removing cells from the population that expresses a tumor antigen that does not comprise CD25 to provide a population depleted of regulatory T cells and depleted of tumor antigen before the introduction of the acid nucleic encoding a fusion polypeptide, for example, as described herein, which comprises a domain that includes a CAR, in the population. The tumor antigen can be selected from among CD19, CD30, CD38, CD123, CD20, CD14 or CD11b, or a combination thereof.
[00950] [00950] In other embodiments, the method further comprises removing cells from the population expressing a checkpoint inhibitor to provide a population depleted of regulatory T cells and depleted of inhibitory molecule prior to the introduction of the nucleic acid encoding a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR, in the population. The exemplary checkpoint inhibitor can be chosen from PD-1, LAG-3, TIM3, B7-H1, CD160, P1H, 2B4, CEACAM (eg CEACAM-1, CEA-CAM-3 and / or CEACAM-5), TIGIT, CTLA-4, BTLA and LAIR1.
[00951] [00951] Additional modalities disclosed in the present document cover a population of immuno-effector cells. The population of immune cells provided can be selected based on the expression of one or more CD3, CD28, CD4, CD8, CD45RA and / or CD45RO. In certain modalities, the population of immuno-effector cells supplied is CD3 + and / or CD28 +.
[00952] [00952] In certain embodiments of the method, the method further comprises expanding the cell population after the nucleic acid molecule encoding a fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR, have been introduced.
[00953] [00953] In the modalities, the cell population is expanded over a period of 8 days or less.
[00954] [00954] In certain embodiments, the cell population is expanded in culture for 5 days, and the resulting cells are more potent than the same cells expanded in culture for 9 days under the same culture conditions.
[00955] [00955] In other embodiments, the cell population expanded in culture for 5 days exhibits an increase of at least once, twice, three or four times in duplication of cells by stimulation with antigens compared to the same cells expanded in culture for 9 days under the same culture conditions.
[00956] [00956] In yet other embodiments, the cell population is expanded in culture for 5 days, and the resulting cells exhibit higher levels of pro-inflammatory IFN-y and / or GM-CSF, compared to the same cells expanded in culture for 9 days under the same culture conditions.
[00957] [00957] In other modalities, the cell population is expanded by culturing the cells in the presence of an agent that stimulates a signal associated with a CD3 / TCR complex and / or a ligand that stimulates a co-stimulating molecule on the cell surface. The agent can be a microsphere conjugated to anti-CD3 antibody, or a fragment thereof, and / or anti-CD28 antibody, or a fragment thereof.
[00958] [00958] In other embodiments, the cell population is expanded in a suitable medium that includes one or more interleukins that result in at least an increase of 200 times, 250 times, 300 times or 350 times the number of cells over a expansion period of 14 days, as measured by flow cytometry.
[00959] [00959] In other modalities, the cell population is expanded in the presence of IL-15 and / or IL-7.
[00960] [00960] In certain modalities, the method additionally includes: cryopreserving the cell population after the appropriate expansion period.
[00961] [00961] In yet other embodiments, the production method discussed in this document further comprises bringing the population of immuno-effector cells into contact with a nucleic acid encoding a telomerase subunit, for example, hTERT. The nucleic acid encoding the telomerase subunit can be DNA.
[00962] [00962] The present description provides a method for generating a population of cells with genetically modified RNA, for example, the cells described in this document, for example, immuno-effector cells (for example, T cells or NK cells), temporarily expressing Exogenous RNA. The method comprises introducing an in vitro transcribed RNA or synthetic RNA into a cell, wherein the RNA comprises a nucleic acid encoding a fusion polypeptide, for example, as described in this document, comprising a domain that includes a CAR molecule described in this document.
[00963] [00963] In another aspect, the invention pertains to a method for providing anti-tumor immunity in an individual comprising administering to the individual an effective amount of a cell comprising a fusion polypeptide, for example, as described herein, which comprises a domain that includes a CAR molecule, for example, a cell that expresses a CAR molecule described herein. In one embodiment, the cell is a T cell or autologous NK cell. In one embodiment, the cell is an allogeneic T cell or NK cell. In one embodiment, the individual is a human being.
[00964] [00964] In one aspect, the invention includes a cell population
[00965] [00965] In another aspect, the present description provides a population of fusion polypeptides, for example, as described in this document, which comprises a domain that includes cells that express CAR, for example, immune-expressing cells that express CAR (for example, T cells or NK cells). In some embodiments, the population of cells that expresses CAR comprises a mixture of cells that expresses different CARs. For example, in one embodiment, the population of immune-expressing cells expressing CAR (for example, T cells or NK cells) can include a first cell expressing a CAR that has an antigen-binding domain that binds to a first tumor antigen as described in this document, and a second cell expressing a CAR that has a different antigen-binding domain that binds to a second tumor antigen as described in this document. As another example, the population of cells expressing CARs may include a first cell expressing a CAR that includes an antigen binding domain that binds to a tumor antigen as described herein, and a second cell expressing a CAR which includes an antigen-binding domain for a target other than a tumor antigen as described here. In one embodiment, the population of cells expressing CAR includes, for example, a first cell expressing a CAR that includes a primary intracellular signaling domain, and a second cell expressing a CAR that includes a secondary signaling domain, for example. example, a co-stimulating signaling domain.
[00966] [00966] In another aspect, the present description provides a population of cells in which at least one cell in the population expresses a fusion polypeptide, for example, as described herein, comprising a domain that includes a CAR having a binding domain to antigens that bind to a tumor antigen as described in this document, and a second cell expressing another agent, for example, an agent that intensifies the activity of a cell expressing CAR. For example, in one embodiment, the agent can be an agent that inhibits an inhibitory molecule. Examples of inhibitory molecules include PD-1, PD-L1, CTLA-4, TIM-3, CEACAM (for example, CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4 and TGFR beta. In one embodiment, the agent that inhibits an inhibitory molecule, for example, is a molecule described here, for example, an agent that comprises a first polypeptide, for example, an inhibitor molecule, associated with a second polypeptide that provides a positive signal to the cell, for example, an intracellular signaling domain described here. In one embodiment, the agent comprises a first polypeptide, for example, an inhibitory molecule such as PD-1, LAG-3, CTLA-4, CD160, BTLA (for example, (for example, CEACAM-1, CEACAM- 3 and / or CEACAM-S5), 2B4 and TIGIT, or a fragment
[00967] [00967] In one embodiment, the nucleic acid molecule that co-complicates a fusion polypeptide, for example, as described herein, comprising a domain that includes a CAR of the present description, for example, as described herein , is expressed as an mMRNA molecule. In one mode, cells expressing the genetically modified CAR of the present invention, for example, immune-defective cells (for example, T cells, NK cells), can be generated by transfection or electroporation of an RNA molecule that encodes the desired CARs (for example, without a vector sequence) in the cell. In one mode, a CAR of the present description is translated from the RNA molecule once it is incorporated and expressed on the surface of the recombinant cell.
[00968] [00968] “A method to generate MRNA for use in transfection involves in vitro transcription (IVT) of a model with specially designed primers, followed by the addition of polyA, to produce a construct containing 3 'and 5' sequences not translated ("RTU") (for example, a 3 'and / or 5' RTU described here), a 5 "cap" (for example, a "5" cap described here) and / or Internal Site of Entrance to Ribos-
[00969] [00969] In one embodiment, the fusion polypeptide, for example, as described in this document, which comprises a domain that includes a CAR is introduced into immune effector cells (for example, T cells, NK cells), for example , using in vitro transcription, and the individual (e.g., human) receives an initial administration of fusion polypeptide, for example as described in this document, which comprises a domain that includes a CAR, immune-cells (for example, T cells, NK cells) CAR of the invention, and one or more subsequent administrations of the fusion polypeptide, for example, as described herein, comprising a domain that includes a CAR, immune cells (for example, cells T, NK) CAR cells of the invention, in which one or more subsequent administrations are administered in less than 15 days, for example, 14, 13, 12, 11, 10, 9, 8, 7, 6.5, 4, 3 or 2 days after the previous administration. In one embodiment, more than one administration of the immune effector cells (e.g., T cells, NK cells) CAR of the invention are administered to the subject (e.g., human) per week, e.g., 2, 3 or 4 administrations of the cells immune effectors (e.g., T cells, NK cells) CAR of the invention are administered weekly. In one embodiment, the subject (for example, human subject) receives more than one administration of immune effector cells (for example, T cells, NK cells) CAR per week (for example, 2, 3, or 4 administrations per week). - mana) (also referred to here as cycle), followed by a week without administrations of immune effector cells (eg, T cells, NK cells) CAR, and then one or more additional administrations of immune effector cells (eg, T cells , NK cells) CAR (e.g., more than one administration of immune effector cells (e.g., T cells, NK cells) CAR per week) are administered to the subject. In another embodiment, the subject (for example, human subject) receives more than one cycle of immune effector cells (for example, T cells, NK cells) CAR, and the time between each cycle is less than 10, 9 , 8, 7, 6, 5, 4 or 3 days. In one embodiment, immune effector cells (eg, T cells, NK cells) CAR are administered every other day for 3 administrations per week. In one embodiment, the immune effector cells (for example, T cells, NK cells) CAR of the invention are administered for at least two, three, four, five, six, seven, eight or more weeks.
[00970] [00970] In one aspect, cells expressing CAR are generated using lentiviral viral vectors, such as lentivirus. Cells, for example, CARTs, generated in this way will exhibit stable CAR expression.
[00971] [00971] In one aspect, cells expressing CAR, for example, CARTs, are generated using a viral vector such as a gamma-retroviral vector, for example, a gamma-retroviral vector described here. CARTs generated using these vectors can have stable CAR expression.
[00972] [00972] In one aspect, CARTs transiently express CAR vectors for 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 days after transduction. The transient expression of CARs can be performed by administering RNA CAR vectors. In one aspect, RNA CAR is transduced into the T cell by electroporation.
[00973] [00973] A potential issue that may arise in patients being treated using immune effector cells (eg, T cells, NK cells) transiently expressing CAR (particularly with CARTs containing murine scFv) is anaphylaxis after multiple treatments.
[00974] [00974] Without being restricted by this theory, it is believed that such anaphylactic response may be caused by the fact that a patient develops a humoral anti-CAR response, that is, anti-CAR antibodies having an anti-IgE isotype. Antibody-producing cells in a patient are believed to undergo a class change from the IgG isotype (which does not cause anaphylaxis) to the IgE isotype when there is a pause of ten to fourteen days of exposure to the antigen. If a patient is at high risk of generating an anti-CAR antibody response during therapy with transient CAR (such as those generated by RNA transductions), pauses in the CART infusion should not last more than ten to fourteen days. Pharmaceutical Composition
[00975] [00975] The pharmaceutical compositions of the present description may comprise any fusion polypeptide, nucleic acid encoding such a fusion polypeptide, or cells comprising the fusion polypeptide, as described herein, and one or more vehicles, pharmaceutically or physiologically acceptable diluents or excipients. Such compositions may comprise buffers, such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates, such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents, such as EDTA or glutathione; adjuvants (for example, aluminum hydroxide); and con-
[00976] [00976] The pharmaceutical compositions of the present description can be administered in a manner appropriate to the disease to be treated (or prevented). The amount and frequency of administration will be determined by factors such as the patient's condition and the type and severity of the patient's illness, although appropriate dosages can be determined by clinical trials.
[00977] [00977] In one aspect, the invention includes a pharmaceutical composition formulated for use in the method as described herein, the composition comprising a modified T cell comprising a nucleic acid encoding a suicide gene and a nucleic acid encoding a chimeric antigen receptor comprising an anti-B cell binding domain, a trans-membrane domain, a co-stimulatory domain and an intracellular signaling domain.
[00978] [00978] In another aspect, the invention includes a pharmaceutical composition formulated for use in the method as described in the present document, the composition comprising a modified T cell comprising a nucleic acid encoding a dimerization domain and a chimeric antigen receptor (CAR) comprising an anti-B cell binding domain, a transmembrane domain, a co-stimulatory domain and an intracellular signaling domain
[00979] [00979] In one embodiment, the pharmaceutical composition is substantially devoid, for example, there are no detectable levels of a contaminant, for example, selected from the group consisting of endotoxin, mycoplasma, replication competent lentivitus (RCL), p24, nucleic acid of VSV-G, HIV gag, residual anti-CD3 / anti-CD28 coated beads, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture medium components, packaging cell components or vector plasmids , a bacterium and a fungus. In one way, the bacterium is at least one selected from the group consisting of Alcaligenes faecalis, Candida albicans, Escherichia coli, Haemophilus influenza, Neisseria meningitidis, Pseudomonas aeruginasa, Staphylococcus aureus, Streptococcus pneumoniae and Strepto- pneumoniae and Strepto- group A cogenus pyogenes.
[00980] [00980] When "an immunologically effective amount", "an effective antitumor amount", "an effective tumor-inhibiting amount" or "therapeutic amount" is indicated, the precise amount of the compositions of the present description to be administered can be be determined by a physician considering individual differences in age, weight, size of the tumor, extent of infection or metastasis, and condition of the patient (subject). It can generally be determined that a pharmaceutical composition comprising the immune effector cells (for example, T cells, NK cells) described in the present document can be administered at a dosage of 10 to 10 cells / kg body weight, in some cases 10 to 10 cells / kg of body weight, including all integer values within these ranges. T cell compositions can also be administered multiple times at these dosages. The cells can be administered using infusion techniques that are commonly known in immunotherapy (see, for example, Rosenberg et al., New Eng. J. of Med. 319: 1676, 1988).
[00981] [00981] In certain aspects, it may be desired to administer immune effector cells (eg, T cells, NK cells) to a subject and then subsequently collect blood again (or perform an apheresis), activate immune effector cells (eg, cer - T cells, NK cells) of that according to the present invention and
[00982] [00982] The administration of the compositions in question can be carried out in any convenient way, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein can be administered to a patient transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullarily, intramuscularly, by intravenous (i.v.) or intraperitoneal injection. In one aspect, the cell compositions of the present description are administered to a patient by intradermal or subcutaneous injection. In one aspect, the cellular compositions of the present description are administered by IV injection. Compositions of immune effector cells (for example, T cells, NK cells) can be injected directly into a tumor, lymph node or site of infection.
[00983] [00983] In a particular exemplary aspect, subjects can undergo leukapheresis, in which leukocytes are collected, enriched or depleted ex vivo to select and / or isolate the cells of interest, for example, T cells. T can be expanded by methods known in the art and treated so that one or more CAR constructs of the invention can be introduced, thereby creating a CAR T cell of the invention. The needy subjects can subsequently be subjected to
[00984] [00984] The dosage of the above treatments to be administered to a patient will vary with the precise nature of the condition being treated and the recipient of the treatment. Scaling of dosages for human administration can be performed according to practices accepted in the art.
[00985] [00985] “Also provided herein are methods of selectively regulating (for example, degrading) a fusion polypeptide (for example, a fusion polypeptide comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a heterologous polypeptide, for example, a CAR polypeptide). Such methods may include placing a cell comprising any of the fusion polypeptides described herein or a nucleic acid encoding that fusion polypeptide in contact with COF1, COF2 or COF3. In some embodiments, the COFI / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide increases post-translational modification and / or degradation of the fusion polypeptide in the presence of COF1, COF2 or COF3, for example, in relation to modification and / or degradation in the absence of COF1, COF2 or COF3. In one embodiment, the COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide increases the selective ubiquitination of the fusion polypeptide in the presence of COF1, COF2 or COF3, for example, in relation to ubiquitination in the absence COF1, COF2 or
[00986] [00986] “As used herein," selectively degrade "a target fusion polypeptide or polypeptide, or the like, refers to an increase in degradation (for example, an increased level and / or rate of degradation , for example, at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75% , 80%, 85%, 90%, 95%, 100%, 200%, 500%, 10 times, 100 times,
[00987] [00987] Also provided herein are methods of selectively regulating (e.g., degrading) a fusion polypeptide comprising a COF1I / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide, a heterologous polypeptide and a domain of degradation. Such methods comprise one or more of the following steps: i) placing the fusion polypeptide or a cell comprising the fusion polypeptide in contact with a stabilizing compound, optionally in which in the presence of the stabilizing compound , the expression level of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times in comparison with the level of expression of the fusion polypeptide in the absence of the stabilizing compound, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis; and li) placing the fusion polypeptide or a cell comprised
[00988] [00988] In another aspect, the present description provides methods that comprise administering a fusion polypeptide of the invention as a therapy. Typically, such administration will be in the form of cells (e.g., autologous or allogeneic host cells) that express the fusion polypeptide of the invention to the individual. Consequently, through the administration of COF1, COF2 or COF3 (both in vivo and ex vivo), the expression of the therapeutic product (for example, the heterologous protein) can be regulated. Consequently, through the administration of COF1, COF2 or COF3 (both in vivo and ex vivo), the expression of the therapeutic product (for example, the heterologous protein) can be regulated. Accordingly, the expression of synthetic therapeutic proteins or known trans-membrane receptors (for example, a fusion polypeptide, for example, as described in this document, for example, comprising a domain that includes a CAR molecule described in this document) can be regulated. In one embodiment, the individual has a disorder described in this document, for example, the individual has cancer, for example, the individual has a cancer that expresses the target antigen described in this document. In one embodiment, the subject is a human.
[00989] [00989] Methods of treatment are provided in this document.
[00990] [00990] In another aspect, the invention features a method of treating an individual who has a disease associated with the expression of a tumor antigen (for example, an antigen described in this document), which comprises administering to the individual a effective amount of a cell, for example, an immuno-effector cell (for example, a population of immuno-effector cells) comprising a fusion polypeptide comprising a CAR molecule, wherein the CAR molecule comprises an antigen binding domain , a transmembrane domain, and an intracellular domain, said intracellular domain comprises a co-stimulatory domain and / or a primary signaling domain, wherein said antigen-binding domain binds to the disease-associated tumor antigen, for example, an antigen tumor as described in this document.
[00991] [00991] In a related aspect, the invention presents a method of treating an individual who has a disease associated with the expression of a tumor antigen. The method comprises administering to the individual an effective amount of a cell, for example, an immune-defective cell (for example, a population of immune-defective cells), which comprises a fusion polypeptide comprising a CAR molecule in combination with an agent that increases the effectiveness of the immune cell, in which: the agent that increases the effectiveness of the immune cell is chosen from one or more of: (i) a protein phosphatase inhibitor; (ii) a kinase inhibitor; (iii) a cytokine; (iv) an inhibitor of an immune inhibitory molecule; or (v) an agent that decreases the level or activity of a Tree cell.
[00992] [00992] In another aspect, the invention features a composition that comprises an immuno-defective cell (for example, a population of immuno-defective cells) that comprises a fusion polypeptide that comprises a CAR molecule (for example, a fusion polypeptide which comprises a CAR molecule as described in this document) for use in treating an individual with a disease associated with the expression of a tumor antigen, for example, a disorder as described herein.
[00993] [00993] In certain modalities of any of the aforementioned methods or uses, the disease associated with a tumor antigen, for example, a tumor antigen described in this document, is selected from a proliferative disease, such as cancer or malignancy , or a precancerous condition, such as myelodysplasia, a myelodysplastic syndrome or a pre-leukemia, or is an indication unrelated to cancer associated with the expression of a tumor antigen described in this document. In one mode,
[00994] [00994] In one embodiment, hematological cancer is leukemia. In one embodiment, cancer is selected from the group that consists of one or more acute leukemias, including, but not limited to, acute B-cell lymphoid leukemia ("BALL"), acute cell-lymphoid leukemia T ("TALL"), acute lymphoid leukemia (ALL); one or more chronic leukemias including, but not limited to, chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL); haematological cancers or additional haematological disorders including, but not limited to, pro-lymphocytic B-cell leukemia, blast plasmacytoid dendritic cell neoplasm, Burkitt's lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, hair cell leukemia, small-cell or large-cell follicular lymphoma, malignant lymphoproliferative disorders, MALT lymphoma, mantle cell lymphoma, marginal zone lymphoma, multiple myeloma, myelodysplasia and myelodysplastic syndrome, non-Hodgkin's lymphoma, Hodgkin's lymphoma, plasmablastic lymphoma, of plasmacytoid dendritic cells, Waldenstrom's macroglobulinemia, and "pre-leukemia", which is a diverse set of hematological disorders linked by the ineffective production (or dysplasia) of myeloid blood cells and disease associated with the expression of a tumor antigen described in document including, but not limited to, atypical and / or non-classical cancers, malignancies, precancerous conditions or proliferative diseases that express a tumor antigen as described in this document; and any combination thereof. In another embodiment, the disease associated with a tumor antigen described herein is a solid tumor.
[00995] [00995] In certain embodiments, the methods or uses are carried out in combination with an agent that increases the effectiveness of the immune cell, for example, an agent as described in this document.
[00996] [00996] In any of the aforementioned methods or uses, the disease associated with the expression of the tumor antigen is selected from the group consisting of a proliferative disease, a precancerous condition, a cancer and an indication unrelated to cancer associated with expression of the tumor antigen.
[00997] [00997] Cancer can be a hematological cancer, for example, cancer chosen from one or more of chronic lymphocytic leukemia (CLL), acute leukemia, acute lymphoid leukemia (ALL), acute B-cell lymphoid leukemia (B-ALL), acute T-cell lymphoid leukemia (T-ALL), chronic myelogenous leukemia (CML), pro-lymphocytic B-cell leukemia, plasmacytoid dendritic blast cell neoplasm, Burkitt's lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, hair cell leukemia, small cell or large cell follicular lymphoma, malignant lymphoproliferative disorders, MALT lymphoma, mantle cell lymphoma, marginal zone lymphoma, multiple myeloma, myelodysplasia and myelodysplastic syndrome, non-Hodgkin's lymphoma, Hodgkin's lymphoma plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, Waldenstrom's macroglobulinemia or pre-leukemia.
[00998] [00998] Cancer can also be chosen from colon cancer, rectal cancer, renal cell carcinoma, liver cancer, non-small cell lung cancer, small intestine cancer, esophageal cancer, melanoma , bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, malignant cutaneous or intraocular melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, testicular cancer, uterine cancer, Fallopian tube carcinoma, endometrial carcinoma, cervical carcinoma, carcinoma of the vagina, vulvar carcinoma, Hodgkin's disease, non-Hodgkin's lymphoma, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, canon - adrenal gland cancer, soft tissue sarcoma, cancer of the urethra, cancer of the penis, solid tumors of childhood, cancer of the bladder, cancer of the kidney or ureter, carcinoma of the renal pelvis, neoplasm of the central nervous system (CNS), primary lymphoma of SN C, tumor angiogenesis, spinal axis tumor, brain stem glioma, pituitary adenoma, Kaposi's sarcoma, epidermoid cancer, scaly cell cancer, T-cell lymphoma, cancers induced by the environment, combinations of these cancers and metastatic lesions of said cancers.
[00999] [00999] In certain modalities of the methods or uses described in this document, the cell is administered in combination with an agent that increases the cell's effectiveness, for example, one or more of a protein phosphatase inhibitor, a kinase inhibitor , a cytokine, an inhibitor of an immune inhibitory molecule; or an agent that decreases the level or activity of a Tree cell. In certain modalities of the methods or uses described in this document, the protein phosphatase inhibitor is an inhibitor of SHP-1 and / or an inhibitor of SHP-2.
[001000] [001000] In other modalities of the methods or uses described in this document, the kinase inhibitor is chosen from one or more of a CDKA inhibitor, a CDK4 / 6 inhibitor (for example, palbocyclib), a BTK inhibitor (for example, ibrutinib or RN-486), an MTOR inhibitor (for example, rapamycin or everolimus (RADOO01)), an MNK inhibitor or a dual P13K / mMTOR inhibitor. In a modality, the BTK inhibitor does not reduce or inhibit interleukin-2-inducible kinase (ITK) kinase activity.
[001001] [001001] In other modalities of the methods or uses described in this document, the agent that inhibits the immune inhibitory molecule comprises an antibody or antibody fragment, an inhibitory nucleic acid, short palindromic repetitions, regularly spaced together (CRISPR), a effector nuclease similar to the transcription activator (TALEN), or a zinc finger endonuclease (ZFN) that inhibits the expression of the inhibitory molecule.
[001002] [001002] In other modalities of the methods or uses described in this document, the agent that decreases the level or activity of TREG cells is chosen from among cyclophosphamide, anti-GITR activity, CD25 depletion, or a combination thereof.
[001003] [001003] In certain modalities of the methods or uses described in this document, the immune inhibitory molecule is selected from the group consisting of PD1, PD-L1, CTLA-4, TIM-3, LAG-3, VISTA, BTLA, TIGIT, LAIR1I, CD160, 2B4, TGFR beta, CEACAM-1, CEACAM-3 and CEACAM-5.
[001004] [001004] In other embodiments, the agent that inhibits the inhibitory molecule comprises a first polypeptide that comprises an inhibitory molecule or a fragment thereof and a second polypeptide that provides a positive signal to the cell, and in which the first and the second polypeptides are expressed in CAR containing immune cells, where (i) the first polypeptide comprises PD1, PD-L1, CTLA-4, TIM-3, LAG3, VISTA, BTLA, TIGIT, LAIR1I, CD160, 2B4, TGFR beta , CEACAM-1, CEACAM-3, and CEACAM-5 or a fragment thereof; and / or (ii) the second polypeptide comprises an intracellular signaling domain comprising a primary signaling domain and / or a co-stimulating signaling domain. In one mode, the primary signaling domain comprises a functional CD3 zeta domain; and / or the co-stimulatory signaling domain comprises a functional domain of a protein selected within
[001005] [001005] In other embodiments, the immuno-defective cell that comprises the fusion polypeptide and a second, for example, any of the combination therapies disclosed in this document (for example, the agent that increases the effectiveness of immune cell) is administered substantially simultaneously or sequentially.
[001006] [001006] In other embodiments, the immune cell comprising the fusion polypeptide is administered in combination with a molecule that targets GITR and / or modulates GITR function. In certain modalities, the molecule that targets GITR and / or modulates GITR function is administered before the cell or cell population that expresses CAR, or before apheresis.
[001007] [001007] In one embodiment, lymphocyte infusion, for example, allogeneic lymphocyte infusion, is used in the treatment of cancer, wherein the lymphocyte infusion comprises at least one CAR expression cell of the present invention. In one embodiment, the infusion of autologous lymphocytes is used to treat cancer, in which the infusion of autologous lymphocytes comprises at least one CAR expression cell described in this document.
[001008] [001008] In one embodiment, the cell is a T cell and the T cell is deficient in diaglycerol kinase (DGK). In one embodiment, the cell is a T cell and the T cell is deficient in Ikaros. In a modality, the cell is a cell and the T cell is deficient in DGK and lkaros.
[001009] [001009] In one embodiment, the method includes administering a cell that expresses the fusion polypeptide that comprises a CAR molecule, as described in this document, in combination with an agent that increases the activity of a cell that expresses
[001010] [001010] In other embodiments, cells expressing a fusion polypeptide comprising a CAR molecule are administered in combination with an agent that mitigates one or more side effects associated with the administration of a cell that expresses a CAR molecule. Side effects associated with the cell expressing CAR can be selected from cytokine release syndrome (CRS) or hemophagocytic lymphohistiocytosis (HLH).
[001011] [001011] In the modalities of any of the aforementioned methods or uses, the cells that express the CAR molecule are administered in combination with an agent that treats the disease associated with the expression of the tumor antigen, for example, any of the second or third therapies disclosed in this document.
[001012] [001012] Additional exemplary combinations include one or more of the following.
[001013] [001013] In another embodiment, the cell expressing the CAR molecule, for example, as described in this document, can be administered in combination with another agent, for example, a kinase inhibitor and / or verification described in this document. In one embodiment, a cell expressing the CAR molecule can additionally express another agent, for example, an agent that enhances the activity of a cell expressing CAR.
[001014] [001014] For example, in one embodiment, the agent that increases the activity of a cell expressing CAR may be an agent that inhibits an inhibitory molecule (for example, an immune inhibitory molecule). Examples of inhibitory molecules include PD1, PD-L1, CTLA-4, TIM-3, CEACAM (e.g. CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG-3, VISTA, BTLA, TIGIT, LAIRI, CD160, 2B4 and TGFR beta.
[001015] [001015] In one embodiment, the agent that inhibits the inhibitory molecule is an inhibitory nucleic acid is a dsRNA, a siRNA or a shR-NA. In the embodiments, the inhibitory nucleic acid is linked to the nucleic acid that encodes a component of the CAR molecule. For example, the inhibitory molecule can be expressed in the cell by expressing CAR.
[001016] [001016] In another embodiment, the agent that inhibits an inhibitory molecule is a molecule described here, for example, an agent that comprises a first polypeptide, for example, an inhibitor molecule, associated with a second polypeptide that provides a cell positive signal, for example, an intracellular signaling domain described here. In one embodiment, the agent comprises a first polypeptide, for example, from an inhibitory molecule such as PD-1, PD-L1, CTLA-4, TIM-3, CEACAM (for example, CEACAM-1, CEA-CAM-3 and / or CEACAM-5), LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160,
[001017] [001017] In one embodiment, the cell of the present invention, for example, T cell or NK cell, is administered to an individual who has received a previous stem cell transplant, for example, autologous stem cell transplant .
[001018] [001018] In one embodiment, the cell of the present invention, for example, T cell or NK cell, is administered to an individual who has received a dose of previous melphalan.
[001019] [001019] In one embodiment, the cell expressing a fusion polypeptide comprising a CAR molecule, for example, a CAR molecule described herein, is administered in combination with an agent that increases the effectiveness of a cell that expresses a CAR molecule, for example, an agent described in this document.
[001020] [001020] In one embodiment, cells expressing a fusion polypeptide comprising a CAR molecule, for example, a CAR molecule described herein, are administered in combination with a low immunity-enhancing dose of an MTOR inhibitor.
[001021] [001021] In one embodiment, this approach can be used to optimize the performance of CAR cells described in the present document in the subject. Without adhering to the theory, it is believed that, in one modality, the performance of endogenous unmodified immune effector cells, for example, T cells or NK cells, is improved. Without sticking to theory, it is believed that, in one modality, the performance of a cell that expresses target antigen CAR is enhanced. In other embodiments, cells, for example, T cells or NK cells, which have been or will be engineered to express a CAR, can be treated ex vivo by contact with an amount of an MTOR inhibitor that increases the number of negative immune effector cells. for PD1, for example, T cells or increases the ratio of PD1-negative immune cells, for example, T-cells / PD1-positive immune cells, for example, T-cells.
[001022] [001022] In one embodiment, administration of a low dose of immune enhancement of an MTOR inhibitor, for example, an allosteric inhibitor, for example, RADOO01, or a catalytic inhibitor, is initiated before administration of an cell expressing CAR described in this document, for example, T cells or NK cells. In one embodiment, CAR cells are administered after sufficient time, or sufficient dosage, of an MTOR inhibitor, so that the level of PD1-negative immune cells, for example, T cells, or the effector cell ratio PD1-negative immune, for example, T-cells / PD1-positive immune cells, for example, T-cells, were, at least temporarily, increased.
[001023] [001023] In one embodiment, the cell, for example, T cell or NK cell, to be manipulated to express a CAR, is collected after sufficient time or after sufficient dosage of low dose of immune boosting, dose of an MTOR inhibitor, so that the level of PD1-negative immune cells, for example, T cells, or the ratio of PD1-negative immune cells, for example, PD1-positive T cells / immune cells, for example, T cells in the individual or collected from the individual were, at least temporarily, increased.
[001024] [001024] In one embodiment, the cell expressing a CAR molecule, for example, a CAR molecule described in this document, is administered in combination with an agent that mitigates one or more side effects associated with the administration of a cell that expresses a CAR molecule, for example, an agent described in this document.
[001025] [001025] In one embodiment, the cell expressing a fusion polypeptide comprising a CAR molecule, for example, a CAR molecule described herein, is administered in combination with an agent that treats the disease associated with an antigen associated with cancer as described in this document, for example, an agent described in this document.
[001026] [001026] In one embodiment, a cell that expresses two or more fusion polypeptides comprising CAR molecules, for example, as described in this document, is administered to an individual who needs it to treat cancer. In a
[001027] [001027] In one embodiment, the cell expressing a fusion polypeptide comprising a CAR molecule, for example, a CAR molecule described herein, is administered in a dose and / or dosing program described in this document. to.
[001028] [001028] In one embodiment, the fusion polypeptide comprising a CAR molecule is introduced into immune immuno-effector cells (for example, T cells, NK cells), for example, using in vitro transcription, and the individual (eg, human) receives an initial administration of cells comprising a fusion polypeptide comprising a CAR molecule, in which one or more subsequent administrations are administered in less than 15 days, for example, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3 or 2 days after the previous administration. In one embodiment, more than one administration of cells comprising a fusion polypeptide comprising a CAR molecule is administered to the individual (eg, human) per week, eg 2, 3 or 4 administrations of cells that comprise a fusion polypeptide that comprises a CAR molecule are administered weekly. In one embodiment, the subject (eg, human subject) receives more than one administration of cells that comprise a fusion polypeptide that comprises one CAR molecule per week (for example, 2, 3 or 4 administrations per week) (also called in this document cycle), followed by a week without administration of cells comprising a fusion polypeptide that comprises a CAR molecule, and then one or more additional administrations of cells that comprise a fusion polypeptide that comprises a CAR molecule (for example, more than one administration of the cells comprising one CAR molecule per week) are administered to the individual. In another embodiment, the individual (for example, human individual) receives more than one cycle of cells comprising a fusion polypeptide comprising a CAR molecule, and the time between each cycle is less than 10, 9, 8, 7.6, 5, 4 or 3 days. In one embodiment, cells comprising a fusion polypeptide comprising a CAR molecule are administered every other day for 3 administrations per week. In one embodiment, cells that comprise a fusion polypeptide that comprises a CAR molecule are administered for at least two, three, four, five, six, seven, eight or more weeks.
[001029] [001029] In one embodiment, cells expressing a fusion polypeptide comprising a CAR molecule, for example, a CAR molecule described in this document, are administered as a first-line treatment for the disease, for example, cancer , for example, the cancer described in this document. In another embodiment, cells expressing a fusion polypeptide comprising a CAR molecule, for example, a CAR molecule described herein are administered as a second, third, fourth line treatment for the disease, for example, cancer, for example, the cancer described in this document.
[001030] [001030] In one embodiment, a population of cells described in this document is administered.
[001031] [001031] In another aspect, the invention relates to a cell that expresses a fusion polypeptide that comprises a CAR molecule described herein for use as a medication in combination with a kinase inhibitor and / or a checkpoint inhibitor as described in this document. In another aspect, the invention relates to a kinase inhibitor and / or a checkpoint inhibitor described herein for use as a medicament in combination with a cell that expresses a CAR molecule described herein.
[001032] [001032] In another aspect, the invention relates to a cell expressing a fusion polypeptide that comprises a CAR molecule described herein for use in combination with a cytokine, for example, IL-7, IL- 15 and / or IL-21 as described herein, in the treatment of a disease that expresses a tumor antigen targeted by CAR. In another aspect, the invention relates to a cytokine described in this document for use in combination with a cell that expresses a fusion polypeptide that comprises a CAR molecule described in this document, in the treatment of a disease that expresses a tumor antigen targeted by the CAR.
[001033] [001033] In another aspect, the invention relates to a cell expressing a fusion polypeptide comprising a CAR molecule described herein for use in combination with a kinase inhibitor and / or a point inhibitor verification as described in this document, in the treatment of a disease that expresses a tumor antigen targeted by the CAR. In another aspect, the invention relates to a kinase inhibitor and / or a checkpoint inhibitor described herein for use in combination with a cell that expresses a fusion polypeptide that comprises a CAR molecule. described in this document, in the treatment of a disease that expresses a tumor antigen targeted by the CAR.
[001034] [001034] In another aspect, the present description provides a method which comprises administering a fusion polypeptide which comprises
[001035] [001035] In one embodiment of the methods or uses described in this document, the fusion polypeptide comprising the CAR molecule is administered in combination with another agent. In one embodiment, the agent can be a kinase inhibitor, for example, a CDK4 / 6 inhibitor, a BTK inhibitor, MTOR inhibitor, MNK inhibitor, or a dual PISK / MTOR inhibitor, and combinations thereof. In one embodiment, the kinase inhibitor is a CDKA inhibitor, for example, a CDKA4 inhibitor described herein, for example, a CD4 / 6 inhibitor, such as, for example, 6-Acetyl-8-cyclopentyl hydrochloride 5-methyl-2- (5-piperazin-1-yl-pyridin-2-ylamino) -8H-pyrido [2,3-dlpyrimidin-7-one (also referred to as palbocyclib or PDO332991). In one embodiment, the kinase inhibitor is a BTK inhibitor, for example, a BTK inhibitor described herein, such as, for example, ibrutinib. In one embodiment, the kinase inhibitor is an mMTOR inhibitor, for example, an MTOR inhibitor described herein, such as, for example, rapamycin, a rapamycin analogue, OSI-027. The mTOR inhibitor can be, for example, an MTORC1 inhibitor and / or an MTORCβ2 inhibitor, for example, an MTORC1 inhibitor and / or MTORCβ2 inhibitor described herein. In one embodiment, the kinase inhibitor is an MNK inhibitor, for example, an MNK inhibitor described herein, such as, for example, 4-amino-5- (4-fluoroanilino) -pyrazole
[001036] [001036] In an embodiment of the methods or uses described in this document, the kinase inhibitor is a CDK4 inhibitor selected from aloisine A; flavopyridol or HMR-1275, 2- (2-chlorophenyl) -5,7-dihydroxy-8 - [(3S, 4R) -3-hydroxy-1-methyl-4-piperidinyl] -4-chromenone; cryosinib (PF-02341066; 2- (2-Chlorophenyl) -5,7-dihydroxy-8 - [(2R, 3S) -2- (hydroxymethyl) -1-methyl-3-pyrrolidinyl] - hydrochloride 4H-1-benzopyran-4-o0na (P276 -00); 1-methyl-5 - [[2- [5- (trifluoro-methyl) - 1H-imidazo | -2-i1] -4-pyridinyl] oxy] lN- [4- (trifluoromethyl) phenyl] | -1 H-benzimidazole-2-amine (RAF265); indisulam (E7070); roscovitine (CYC202); palbocyclib (PDO332991); dinaciclib (SCH727965); N- [5- [ [(5-tert-butyloxazol-2-yl)] methyl] thiazol-2-yl] piperidine-4-carboxamide (BMS 387032); 4 - [[9-chloro-7- (2,6-difluorophenyl) - acid 5H-pyrimido [5.4-0] [2] benzazepin-2-ylJamino] -benzoic (MLN8054); 5- [3- (4,6-difluoro-1H-benzimidazole | -2-yl) -1H-indazole -5-yl] -N-ethyl-4-methyl-3-pyridinamethanamine (AG-024322); 4- (2,6-dichlorobenzoylamino) -1H-pyrazol-3-carboxylic acid N- (piperidin-4- il) amide (AT7519); 4- [2-methyl1 - (- 1-methylethyl) -1 H-imidazol-5-yl] -N- [4- (methylsulfonyl) phenyl] - 2-pyrimidinamine (AZD5438); and XL281 (BMS908662).
[001037] [001037] In an embodiment of the methods or uses described in this document, the kinase inhibitor is a CDKA4 inhibitor, for example, palbocyclib (PD0332991), and palbocyclib is administered at a dose of about 50 mg, 60 mg, 70 mg, 75 mg, 80 mg, 90 mg, 100 mg, 105 mg, 110 mg, 115 mg, 120 mg, 125 mg, 130 mg, 135 mg (for example, 75 mg, 100 mg or 125 mg) daily for a period of time, for example, daily for 14-21 days of a 28-day cycle, or daily for 7-12 days of a 21-day cycle. In one embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more cycles of palbocyclib are administered.
[001038] [001038] In one embodiment of the methods or uses described in this document, the kinase inhibitor is a BTK inhibitor selected from ibrutinib (PClI-32765); GDC-0834; RN-486; CGI-560; CGI-1764; HM-71224; CC-292; ONO-4059; CNX-774; and LEM-A13. In one embodiment, the BTK inhibitor does not reduce or inhibit interleukin-2-inducible kinase kinase activity (ITK), and is selected from GDC-0834; RN-486; CGI-560; CGI-1764; HM-71224; CC-292; ONO-4059; CNX-774; and LFEM-A13.
[001039] [001039] In one embodiment of the methods or uses described in this document, the kinase inhibitor is a BTK inhibitor, for example, ibrutinib (PClI-32765), and ibrutinib is administered at a dose of about 250 mg , 300 mg, 350 mg, 400 mg, 420 mg, 440 mg, 460 mg, 480 mg, 500 mg, 520 mg, 540 mg, 560 mg, 580 mg, 600 mg (e.g. 250 mg, 420 mg or 560 mg) daily for a period of time, for example, daily for a 21-day cycle, or daily for a 28-day cycle. In one embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more cycles of ibrinib are administered.
[001040] [001040] In one embodiment of the methods or uses described in this document, the kinase inhibitor is a BTK inhibitor that does not inhibit ITK kinase activity, for example, RN-486, and RN-486 is administered at a dose from about 100 mg, 110 mg, 120 mg, 130 mg, 140 mg, 150 mg, 160 mg, 170 mg, 180 mg, 190 mg, 200 mg, 210 mg, 220 mg, 230 mg, 240 mg, 250 mg (eg 150 mg, 200 mg or 250 mg) daily for a period of time, for example, daily for a 28-day cycle. In one embodiment, 1, 2,3,4,5,6,7, or more RN-486 cycles are administered.
[001041] [001041] In one embodiment of the methods or uses described in this document, the kinase inhibitor is an MTOR inhibitor selected from temsirolimus; ridaforolimo (1R, 2R, 4S8) -4 - [(2R) -2 [(1R, 9S,
[001042] [001042] In one embodiment of the methods or uses described in this document, the kinase inhibitor is an mMTOR inhibitor, for example, rapamycin, and rapamycin is administered at a dose of about 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg (for example, 6 mg) daily for a period of time, for example, daily for a 21-day cycle or daily for a 28-day cycle. In one embodiment, 1,2,3,4, 5, 6, 7, 8, 9, 10, 11, 12 or more rapamycin cycles are administered. In one embodiment, the kinase inhibitor is an MTOR inhibitor, for example, eve-rolimus, and everolimus is administered at a dose of about 2 mg, 2.5 mg, 3 mg, 4 mg, 5 mg , 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, 11 mg, 12 mg, 13 mg, 14 mg, 15 mg (for example, 10 mg) daily for a period of time, for example, daily per cycle 28 days. In one embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more cycles of everolimus are administered.
[001043] [001043] In an embodiment of the methods or uses described in this document, the kinase inhibitor is an MNK inhibitor selected from CGPO052088; 4-amino-3- (p-fluorophenylamino) -pyrazolo [3,4-0] pyrimidine (CGP57380); cercosporamide; ETC-1780445-2; and 4-amino-5-
[001044] [001044] In one embodiment of the methods or uses described in this document, the kinase inhibitor is a dual phosphatidylinositol 3-kinase (PI3SK) and MTOR inhibitor selected from 2-Amino-8- [trans-4- (2-hydroxyethoxy) ) cyclohexyl] -6- (6G-methoxy-3-pyridinyl) -4-methyl-pyrido [2,3-d] pyrimidin-7 (8H) -one (PF-04691502); N- [4 - [[4- (Dimethylamino) -1- piperidinyl] | carbonyl] phenyl] -N '- [4- (4,6-di-4-morpholinyl-1,3,5-triazin-2- il) phenyl] urea (PF-05212384, PKI-587); 2-Methyl-2- (4- [3-methyl-2-0x0-8- (quinolin-3-11) -2,3-dihydro-1H-imidazo [4,5-c] quinolin-1- il] phenylXpropanonitrile (BEZ -235); apitolisib (GDC-0980, RG7422); 2,4-Difluoro-N- (2- (methyloxy) -5- [4- (4-pyridazinyl) -6-quinolinyl] -3 -pyridinyl> benzenesulfonamide (GSK2126458); - 8- (6-methoxypyridin-3-yl) -3-methyl-1- (4- (piperazin-1-yl) -3- (trifluoromethyl) phenyl) -1H-imidazo [ 4,5-c] quinolin-2 (3H) -one, maleic acid (NVP-BGT226); 3- [4- (4-Morpholinylpyride [3 ', 2': 4,5] hole [3,2-d ] pyrimidin-2-yl] phenol (PI-103); 5- (9-isopropyl-8-methyl-2-morpholino-9H-purin-6-yl) pyrimidin-2-amine (VS-5584, SB2343) and N- [2 - [(3,5-Dimethoxyphenyl) amino] quinoxalin-3-iI] -4 - [(4-methyl-3-methoxyphenyl) carbonylJaminophenylsulfonamide (XL765).
[001045] [001045] In one embodiment of the methods or uses described herein, a cell comprising a fusion polypeptide described herein is administered to a subject in combination with a protein tyrosine phosphatase inhibitor, for example, an inhibitor of tyrosine phosphatase protein described in the present document. In one embodiment, the protein tyrosine phosphatase inhibitor is an SHP-1 inhibitor, for example, an SHP-1 inhibitor described herein, such as, for example, sodium stibogluconate. In a fashion, the protein tyrosine phosphatase inhibitor is an SHP-2 inhibitor.
[001046] [001046] In one embodiment of the methods or uses described herein, a cell comprising a fusion polypeptide described herein is administered in combination with another agent, and the agent is a cytokine. The cytokine can be, for example, IL-7, I1L-15, I1L-21, or a combination thereof. In another embodiment, a cell comprising a fusion polypeptide described herein is administered in combination with a checkpoint inhibitor, for example, a checkpoint inhibitor described herein. For example, in one embodiment, the checkpoint inhibitor inhibits an inhibitory molecule selected from PD-1, PD-L1, CTLA-4, TIM-3, CEACAM (for example, CEACAM-1, CEACAM-3 and / or CEACAM-5), LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4 and TGFR beta.
[001047] [001047] In one aspect, the fusion polypeptide described in this document can be used to eradicate a normal cell that expresses a tumor antigen as described here, thereby applicable for use as cell conditioning therapy prior to cell transplantation. In one aspect, the normal cell that expresses a tumor antigen as described here is a normal stem cell and the transplantation of cells is a transplantation of stem cells. Checkpoint Inhibitors
[001048] [001048] In other embodiments of the methods or uses described herein, a cell comprising a fusion polypeptide described herein is administered in combination with another agent, and the agent is an inhibitor of a checkpoint inhibitor, for example. example, a PD-1 inhibitor, PD-L1 inhibitor, TIM-3 inhibitor, a LAG-3 inhibitor. Exemplary inhibitors are disclosed in more detail in the present document below. PD-1 inhibitors
[001049] [001049] In certain embodiments, the checkpoint inhibitor is a PD-1 inhibitor. In some embodiments, the PD-1 inhibitor is chosen from PDROO01 (Novartis), Nivolumab (Brisol-Myers Squibb), Pembrolizumab (Merck & Co), Pidilizumab (Cure-
[001050] [001050] In one embodiment, the PD-1 inhibitor is an anti-PD-1 antibody molecule. In one embodiment, the PD-1 inhibitor is an anti-PD-1 antibody molecule as described in US 2015/0210769, published on July 30, 2015, entitled "Antibody Molecules to PD- 1 and Uses Thereof,", incorporated by reference in its entirety. The antibody molecules described in this document can be produced by vectors, host cells and methods described in document No. US 2015/0210769, incorporated by reference in their entirety. Other Exemplary PD-1 Inhibitors
[001051] [001051] In one embodiment, the anti-PD-1 antibody molecule is Nivolumab (Bristol-Myers Squibb), also known as MDX-1106, MDX-1106-04, ONO-4538, BMS-936558 or OPDIVOGO. Nivolumab (clone 5C4) and other anti-PD-1 antibodies are revealed in US
[001052] [001052] In one embodiment, the anti-PD-1 antibody molecule is Pembrolizumab (Merck & Co), also known as Lambrolizumab, MK-3475, MK03475, SCH-900475 or KEYTRUDAGO. Pembroli- zumab and other anti-PD-1 antibodies are disclosed in Hamid, O. et al. (2013) New England Journal of Medicine 369 (2): 13444, U.S. No.
[001053] [001053] In one embodiment, the anti-PD-1 antibody molecule is Pidilizumab (CureTech), also known as CT-011. Pidilizumab and other anti-PD-1 antibodies are disclosed in Rosenblatt, J. et al. (2011) J Immunotherapy 34 (5): 409-18, U.S. No. 7,695,715, 0 ° US.
[001054] [001054] In one embodiment, the anti-PD-1 antibody molecule is MEDIO680 (Medimmune), also known as AMP-514. ME-DIO0680 and other anti-PD-1 antibodies are disclosed in US 9,205,148 and WO 2012/145493, incorporated by reference in their entirety. In one embodiment, the anti-PD-1 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the DNA sequence. heavy chain or light chain of ME-DIO0680.
[001055] [001055] In one embodiment, the anti-PD-1 antibody molecule is REGN2810 (Regeneron). In one embodiment, the anti-PD-1 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the chain sequence heavy or light chain of REGN2810.
[001056] [001056] In one embodiment, the anti-PD-1 antibody molecule is PF-06801591 (Pfizer). In one embodiment, the anti-PD-1 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or light chain of PF-06801591.
[001057] [001057] In one embodiment, the anti-PD-1 antibody molecule is BGB-A317 or BGB-108 (Beigene). In one embodiment, the anti-PD-1 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain or chain sequence lightweight BGB-A317 or BGB-108.
[001058] [001058] In one embodiment, the anti-PD-1 antibody molecule is INCSHR1210 (Incyte), also known as INCSHRO01210 or SHR-1210. In one embodiment, the anti-PD-1 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or light chain of INCSHR1210.
[001059] [001059] In one embodiment, the anti-PD-1 antibody molecule is TSR-042 (Tesaro), also known as ANBO11. In one fashion, the anti-PD-1 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or TSR-042 light chain.
[001060] [001060] Other anti-PD-1 antibodies include those described, for example, in WO 2015/112800, WO 2016/092419, WO 2015/085847, WO 2014/179664, WO 2014/194302, WO 2014/209804, WO 2015 / 200119, US 8,735,553, US 7,488,802, US 8,927,697, US 8,993,731 and US 9,102,727, incorporated by reference in their entirety.
[001061] [001061] In one embodiment, the anti-PD-1 antibody is an antibody that competes for binding and / or binds to the same epitope on PD-1 as one of the anti-PD-1 antibodies described herein.
[001062] [001062] In one embodiment, the PD-1 inhibitor is a peptide that inhibits the PD-1 signaling pathway, for example, as described in US
[001063] [001063] In certain embodiments, the checkpoint inhibitor is a PD-L1 inhibitor. In some modalities, the PD-L1 inhibitor is chosen from FAZO53 (Novartis), Atezolizumab (Genentech / Roche), Avelumab (Merck Serono and Pfizer), Durvalumabe (MedlImmune / AstraZeneca) or BMS-936559 (Bristol- Myers Squibb). Exemplary PD-L1 inhibitors
[001064] [001064] In one embodiment, the PD-L1 inhibitor is an anti-PD-L1 antibody molecule. In one embodiment, the PD-L1 inhibitor is an anti-PD-L1 antibody molecule as disclosed in document No. US 2016/0108123, published on April 21, 2016, entitled "Antibody Molecules to PD-L1 and Uses Thereof ", incorporated by reference in its entirety. The antibody molecules described in this document can be produced by vectors, host cells and methods described in document No. US 2016/0108123, incorporated by reference in their entirety. Other Exemplary PD-L1 Inhibitors
[001065] [001065] In one embodiment, the anti-PD-L1 antibody molecule is Atezolizumab (Genentech / Roche), also known as MPDL 3280A, RG7446, ROS541267, YW243.55.870 or TECENTRIQTY. Atezolizumab and other anti-PD-L1 antibodies are disclosed in document No. US 8,217,149, incorporated as a reference in its entirety.
[001066] [001066] In one embodiment, the anti-PD-L1 antibody molecule is Avelumab (Merck Serono and Pfizer), also known as MSB 0010718C. Avelumab and other anti-PD-L1 antibodies are disclosed in document No. WO 2013/079174, incorporated by reference in its entirety.
[001067] [001067] In one embodiment, the anti-PD-L1 antibody molecule is Durvalumabe (MedlImmune / AstraZeneca), also known as MEDI4736. Durvalumab and other anti-PD-L1 antibodies are disclosed in US No. 8,779,108, which is incorporated by reference in its entirety.
[001068] [001068] In one embodiment, the anti-PD-L1 antibody molecule is BMS-936559 (Bristol-Myers Squibb), also known as MDX-1105 or 12A4. BMS-936559 and other anti-PD-L1 antibodies are disclosed in US 7,943,743 and WO 2015/081158, incorporated by reference in their entirety.
[001069] [001069] The additionally known anti-PD-L1 antibodies include those described, for example, in WO 2015/181342, WO 2014/100079, WO 2016/000619, WO 2014/022758, WO 2014/055897, WO 2015 / 061668, WO 2013/079174, WO 2012/145493, WO 2015/112805, WO 2015/109124, WO 2015/195163, US 8,168,179, US 8,552,154, US 8,460,927 and US 9,175,082, incorporated into reference title in its entirety.
[001070] [001070] In one embodiment, the anti-PD-L1 antibody is an antibody that competes for binding and / or binds to the same epitope on PD-L1 as one of the anti-PD-L1 antibodies described in this document. LAG-3 inhibitors
[001071] [001071] In certain embodiments, the checkpoint inhibitor is a LAG-3 inhibitor. In some modalities, the LAG-3 inhibitor is selected from LAG525 (Novartis), BMS-986016 (Bristol-Myers Squibb) or TSR-033 (Tesaro). Exemplary LAG-3 Inhibitors
[001072] [001072] In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule. In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule as disclosed in document No. US 2015/0259420, published on Thursday, September 17, 2015, entitled "Antibody Molecules to LAG -3 and Uses Thereof ", incorporated by reference in its entirety. The antibody molecules described in this document can be produced by vectors, host cells and methods described in document No. US 2015/0259420, incorporated by reference in their entirety. Other Exemplary LAG-3 Inhibitors
[001073] [001073] In one embodiment, the anti-LAG-3 antibody molecule is BMS-986016 (Bristol-Myers Squibb), also known as BMS
[001074] [001074] In one embodiment, the anti-LAG-3 antibody molecule is TSR-033 (Tesaro). In one embodiment, the anti-LAG-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or TSR-033 light chain.
[001075] [001075] In one embodiment, the anti-LAG-3 antibody molecule is IMP731 or GSK2831781 (GSK and Prima BioMed). IMP731 and other anti-LAG-3 antibodies are disclosed in documents No. WO 2008/132601 and US 9,244,059, incorporated by reference in their entirety. In one embodiment, the anti-LAG-3 antibody molecule comprises one or more of the CDR sequences (or collectively all the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or IMP731 light chain. In one embodiment, the anti-LAG-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or GSK2831781 light chain.
[001076] [001076] In one embodiment, the anti-LAG-3 antibody molecule is IMP761 (Prima BioMed). In one embodiment, the anti-LAG-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or IMP761 light chain.
[001077] [001077] Other known anti-LAG-3 antibodies include those described, for example, in documents No. WO 2008/132601, WO 2010/019570, WO 2014/140180, WO 2015/116539, WO 2015/200119, WO 2016/028672 , US 9,244,059, US 9,505,839, incorporated by reference in their entirety.
[001078] [001078] In one embodiment, the anti-LAG-3 antibody is an antibody that competes for binding and / or binds to the same epitope on LAG-3 as one of the anti-LAG-3 antibodies described in this document.
[001079] [001079] In one embodiment, the anti-LAG-3 inhibitor is a soluble LAG-3 protein, for example, IMP321 (Prima BioMed), for example, as disclosed in document No. WO 2009/044273, incorporated by way of reference in its entirety. TIM-3 inhibitors
[001080] [001080] In certain embodiments, the checkpoint inhibitor is a TIM-3 inhibitor. In some embodiments, the TIM-3 inhibitor is MGB453 (Novartis) or TSR-022 (Tesaro). Exemplary TIM-3 inhibitors
[001081] [001081] In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule. In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule as revealed in document No. US 2015/0218274, published on August 6, 2015, entitled "Antibody Molecules to TIM-3 and Uses Thereof ", incorporated by reference in its entirety.
[001082] [001082] The antibody molecules described in this document
[001083] [001083] In one embodiment, the anti-TIM-3 antibody molecule is TSR-022 (AnaptysBio / Tesaro). In one embodiment, the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain sequence or TSR-022 light chain. In one embodiment, the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or APES137 or APE5S121 light chain. APE5S137, APES121 and other anti-TIM-3 antibodies are disclosed in document No. WO 2016/161270, incorporated by reference in its entirety.
[001084] [001084] In one embodiment, the anti-TIM-3 antibody molecule is the F38-2E2 antibody clone. In one embodiment, the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or light chain of F38-2E2.
[001085] [001085] Other known anti-TIM-3 antibodies include those described, for example, in documents No. WO 2016/111947, WO 2016/071448, WO 2016/144803, US 8,552,156, US 8,841,418 and US
[001086] [001086] In one embodiment, the anti-TIM-3 antibody is an antibody that competes for binding and / or binds to the same epitope on TIM-3 as one of the anti-TIM-3 antibodies described in this document.
[001087] [001087] In certain embodiments, the fusion polypeptide is administered in combination with a GITR agonist. In some embodiments, the GITR agonist is GWN323 (NVS), BMS-986156, MK-4166 or MK-1248 (Merck), TRX518 (Leap Therapeutics), IN-CAGN1876 (Incyte / Agenus), AMG 228 (Amgen) or INBRX-110 (Inhi- brx). Exemplary GITR Agonists
[001088] [001088] In one embodiment, the GITR agonist is an anti-GITR antibody molecule. In one embodiment, the GITR agonist is an anti-GITR antibody molecule as described in document No. WO 2016/057846, published on April 14, 2016, entitled "Compositions and Methods of Use for Augmented Immune Response and Cancer Therapy", incorporated as a reference in its entirety.
[001089] [001089] The antibody molecules described in this document can be produced by vectors, host cells and methods described in document No. WO 2016/057846, incorporated by reference in their entirety. Other Exemplary GITR Agonists
[001090] [001090] In one embodiment, the anti-GITR antibody molecule is BMS-986156 (Bristol-Myers Squibb), also known as BMS 986156 or BMS986156. BMS-986156 and other anti-GITR antibodies are disclosed, for example, in U.S. No. 9,228,016 and WO 2016/196792, which are incorporated by reference in their entirety. In one embodiment, the anti-GITR antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or BMS- light chain
[001091] [001091] In one embodiment, the anti-GITR antibody molecule is MK-4166 or MK-1248 (Merck). MK-4166, MK-1248 and other anti-GITR antibodies are disclosed, for example, in U.S. No. documents
[001092] [001092] In one embodiment, the anti-GITR antibody molecule is TRX518 (Leap Therapeutics). TRX518 and other anti-GITR antibodies are disclosed, for example, in documents No. US 7,812,135, US
[001093] [001093] In one embodiment, the anti-GITR antibody molecule is INCAGN1876 (Incyte / Agenus). INCAGN1876 and other anti-GITR antibodies are disclosed, for example, in documents No. US 2015/0368349 and WO 2015/184099, incorporated by reference in their entirety. In one embodiment, the anti-GITR antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the heavy chain sequence or INCAGN1876 light chain.
[001094] [001094] In one embodiment, the anti-GITR antibody molecule is
[001095] [001095] In one embodiment, the anti-GITR antibody molecule is INBRX-110 (Inhibrx). INBRX-110 and other anti-GITR antibodies are disclosed, for example, in documents No. US 2017/0022284 and WO 2017/015623, incorporated by reference in their entirety. In one embodiment, the GITR agonist comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence or the INBRX-110 heavy chain or light chain sequence .
[001096] [001096] In one embodiment, the GITR agonist (for example, a fusion polypeptide) is MEDI 1873 (MedImmune), also known as MEDI1873. MEDI 1873 and other GITR agonists are revealed, for example, in documents No. US 2017/0073386, WO 2017/025610 and Ross et al. Cancer Res 2016; 76 (14 Suppl): Abstract nr 561, incorporated by reference in its entirety. In one embodiment, the GITR agonist comprises one or more of an IgG Fc domain, a functional multimerization domain, and a receptor binding domain of a MEDI glucocorticoid-induced TNF receptor ligand (GITRL) 1873.
[001097] [001097] Other known GITR agonists (for example, anti-GITR antibodies) include those described, for example, in document No. WO 2016/054638, incorporated by reference in its entirety.
[001098] [001098] In one embodiment, the anti-GITR antibody is an antibody that competes for binding and / or binds to the same epitope in GITR as one of the anti-GITR antibodies described herein.
[001099] [001099] In one embodiment, the GITR agonist is a peptide that activates the GITR signaling pathway. In one embodiment, the GITR agonist is an immunoadhesin binding fragment (for example, an immunoadhesin binding fragment comprising a GITR or extracellular GITRL binding portion) fused to a constant region (for example, an Fc region immunoglobulin sequence). IL15 / IL-15Ra complexes
[001100] [001100] In certain embodiments, the fusion polypeptide is administered in combination with an IL-15 / IL-15Ra complex. In some embodiments, the IL-15 / IL-15Ra complex is chosen from NIZ985 (Novartis), ATL-803 (Altor) or CYP0150 (Cytune). Exemplary IL-15 / IL-15Ra complexes
[001101] [001101] In one embodiment, the IL-15 / IL-15Ra complex comprises human IL-15 complexed with a soluble form of human IL-15Ra. The complex can comprise IL-15 covalently or non-covalently linked to a soluble form of IL-15Ra. In a particular embodiment, human IL-15 is non-covalently linked to a soluble form of IL-15Ra. In a specific embodiment, the human 11-15 of the composition comprises a sequence of amino acids as described in document No. WO 2014/066527, incorporated by reference in its entirety. The molecules described in this document can be produced by vectors, host cells and methods described in document No. WO 2007/084342, incorporated by reference in its entirety. Other exemplary IL-15 / IL-15Ra complexes
[001102] [001102] In one embodiment, the IL-15 / IL-15Ra complex is ALT-803, an IL-15 / IL-15Ra Fc polypeptide (soluble IL-15N72D complex: IL-15RaSu / Fc). ALT-803 is disclosed in document No. WO 2008 / 14379A4, incorporated by reference in its entirety.
[001103] [001103] In one embodiment, the IL-15 / IL-15Ra complex comprises IL-15 fused to the IL-15Ra sushi domain (CYP0150, Cytan). The IL-15Ra sushi domain refers to a domain that begins at the first cysteine residue after the IL-15Ra signal peptide and ends at the fourth cysteine residue after said signal peptide. The IL-15 complex fused to the IL-15Ra sushi domain is revealed in documents No. WO 2007/04606 and WO 2012/175222, which are incorporated by reference in their entirety. Screening Methods
[001104] [001104] The present invention includes methods for identifying a genetic element associated with a specific biological phenotype, for example, a genetic element associated with the development and / or progression of a disorder, for example, cancer. The method includes the steps of: (i) modulating the expression of a fusion polypeptide in a cell, for example, a host cell, exposing said cell to COF1, COF2 or COF3, (ii) selecting the cells with a phenotype of interest, for example, a phenotype associated with the development and / or progression of a disorder, for example, cancer, and (iii) identifying the fusion polypeptide that induces the phenotype of interest, in which the cell's exposure to COF1, COF2 or COF3 decreases, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 per percent, the expression of said fusion polypeptide in relation to the level of expression of said fusion polypeptide before exposure to COF1, COF2 or COF3. Methods of treating an individual
[001105] [001105] In some respects, the description provides a method of treating a patient, which comprises administering a fusion polypeptide (for example, which comprises a binding polypeptide
[001106] [001106] In some respects, the description provides a method of treating a patient, which comprises receiving the fusion polypeptide (for example, comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a polypeptide heterologous of interest) or cells expressing the fusion polypeptide (for example, cells expressing CAR) which was produced as described herein, and further comprising administering the fusion polypeptide or cells expressing the polypeptide fusion (eg, cells expressing CAR) to the patient, optionally in combination with one or more other therapies. In some respects, the description provides a method for treating a patient that comprises producing the fusion polypeptide or cells that express the fusion polypeptide (for example, cells that express CAR) as described in this document and that further comprises administering the fusion polypeptide or cells that express the fusion polypeptide (e.g., cells that express CAR) to the patient, optionally in combination with one or more other therapies. The other therapy can be, for example, cancer therapy, such as chemotherapy.
[001107] [001107] The methods described herein may further include formulating the fusion polypeptide (for example, comprising a COF1 / CRBN, COF2 / CRBN or COF3 / CRBN binding polypeptide and a heterologous polypeptide of interest) or cells that express the fusion polypeptide (for example, cells that express CAR) in a pharmaceutical composition. The pharmaceutical compositions can comprise a fusion polypeptide or cells that express the fusion polypeptide (for example, cells that express CAR), for example, a plurality of fusion polypeptides or cells that express the fusion polypeptide (for example, CAR expressing cells), as described in this document, in combination with one or more pharmaceutically or physiologically acceptable vehicles, diluents or excipients. Such compositions may comprise buffers, such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates, such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids, such as glycine; antioxidants; chelating agents, such as EDTA or glutathione; adjuvants (for example, aluminum hydroxide); and preservatives. The compositions can be formulated, for example, for intravenous administration.
[001108] [001108] In one embodiment, the pharmaceutical composition is substantially devoid, for example, there are no detectable levels of a contaminant, for example, selected from the group consisting of endotoxin, mycoplasma, replication competent lentivirus (RCL), p24, nucleic acid of VSV-G, HIV gag, residual anti-CD3 / anti-CD28 coated beads, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture medium components, packaging cell components or vector plasmids , a bacterium and a fungus. In one way, the bacterium is at least one selected from the group consisting of Alcaligenes faecalis, Candida albicans, Escherichia coli, Haemophilus influenza, Neisseria meningitidis, Pseudomonas aeruginasa, Staphylococcus aureus, Streptococcus pneumoniae and Strepto- pneumoniae and Strepto- group A cogenus pyogenes.
[001109] [001109] When "an immunologically effective amount", "an anti-cancer effective amount", "a cancer-inhibiting effective amount", or "therapeutic amount" is indicated, the precise amount of the compositions to be administered can be determined by a physician considering individual differences in age, weight, tumor size, extent of infection or metastasis and condition of the patient (individual). It can generally be determined that a pharmaceutical composition comprising the immune effector cells (for example, T cells, NK cells) described herein can be administered at a dosage of 10 to 10 cells / kg body weight, in some cases 10 to 10 cells / kg of body weight, including all integer values within these ranges. T cell compositions can also be administered multiple times at these doses. The cells can be administered using infusion techniques that are commonly known in immunotherapy (see, for example, Rosenberg et al., New Eng. J. of Med. 319: 1676, 1988).
[001110] [001110] In some embodiments, a dose of CAR cells (e.g., CD19 CAR cells) comprises about 1 x 105, 1.1 x 108, 2 x 1086, 3.6 x 106, 5 x 108, 1 x 107, 1.8 x 107, 2x 107, 5x 107, 1x 108, 2 x 10º or 5 x 108 cells / kg. In some embodiments, a dose of CAR cells (e.g., CD19 CAR cells) comprises at least about 1 x 106, 1.1 x 106, 2 x 106, 3.6 x 106, 5 x 1086, 1 x 107, 1.8 x 107, 2x 107, 5x 107, 1 x 108, 2 x 10º or 5 x 10º cell
[001111] [001111] In modalities, cells expressing CAR (for example, cells expressing CAR CD19) are administered in several domains
[001112] [001112] In modalities, the method comprises administering a dose of 2 to 5x10º cells expressing viable CAR / kg, in which the individual has a body mass less than 50 kg; or administer a dose of 1.0 to 2.5 x10º cells expressing viable CAR, in which the individual has a body mass of at least 50 kg.
[001113] [001113] In modalities, a single dose is administered to the subject, for example, pediatric subject.
[001114] [001114] In modalities, doses are administered on sequential days, for example, the first dose is administered on day 1, the second dose is administered on day 2 and the optional third dose (if administered) is administered on day 3.
[001115] [001115] In modalities, a fourth, fifth or sixth dose, or more doses, is administered.
[001116] [001116] In modalities, the first dose comprises about 10% of the total dose, the second dose comprises about 30% of the total dose, the third dose comprises about 60% of the total dose, in which the percentages previously mentioned make up a sum of 100%. In embodiments, the first dose comprises about 9 to 11%, 8 to 12%, 7 to 13% or 5 to 15% of the total dose. In modalities, the second dose comprises about 29 to 31%, 28 to 32%, 27 to 33%, 26 to 34%, 25 to 35%, 24 to 36%, 23 to 37%, 22 to 38%, 21 39%, or 20 to 40% of the total dose. In embodiments, the third dose comprises about 55 to 65%, 50 to 70%, 45 to 75% or 40 to 80% of the total dose. In modalities, the total dose refers to the total number of cells expressing viable CAR administered over 1 week, 2 weeks, 3 weeks or 4 weeks. In some modalities where two doses are administered, the total dose refers to the sum of the number of cells expressing viable CAR administered to the subject in the first and second doses. In some modalities where three doses are administered, the total dose refers to the sum of the number of cells expressing viable CAR administered to the subject in the first, second and third doses.
[001117] [001117] In modalities, the dose is measured according to the number of cells expressing viable CAR here. CAR expression can be measured, for example, by flow cytometry using an antibody molecule that binds to the CAR molecule and a detectable marker. Viability can be measured, for example, by Cellometer.
[001118] [001118] In modalities, cells expressing viable CAR are administered in ascending doses. In modalities, the second dose is greater than the first dose, for example, greater by 10%, 20%, 30% or 50%. In modalities, the second dose is twice, three times, four times or five times the size of the first dose. In modalities, the third dose is greater than the second dose, for example, greater by 10%, 20%, 30% or 50%. In modalities, the third dose is twice, three times, four times or five times the size of the second dose.
[001119] [001119] In certain modalities, the method includes one, two, three, four, five, six, seven or all of a) -h) of the following: a) the number of viable cells expressing CAR administered in the first dose is not more than 1/3 of the number of viable cells expressing CAR administered in the second dose; b) the number of viable cells expressing CAR administered
[001120] [001120] In modalities, the total dose is about 5 x 10º of viable cells expressing CAR. In modalities, the total dose is about 5 x 107 - 5x 108 viable cells expressing CAR. In modalities, the first dose is about 5 x 107 (for example, + 10%, 20% or 30%) of viable cells expressing CAR, the second dose is about 1.5 x 10º (for example, + 10% , 20% or 30%) of viable cells expressing
[001121] [001121] In modalities, the subject is evaluated after receiving a dose, for example, after receiving the first dose, the second dose and / or the third dose.
[001122] [001122] In modalities, the subject receives a CRS treatment, for example, tocilizumab, a corticosteroid, etanercept or siltuximab. In embodiments, the CRS treatment is administered before or after the first dose of cells comprising the CAR molecule. In modalities, CRS treatment is administered before or after the second dose of cells comprising the CAR molecule. In modalities, the CRS treatment is administered before or after the third dose of cells comprising the CAR molecule. In embodiments, the CRS treatment is administered between the first and second doses of cells comprising the CAR molecule, and / or between the second and third doses of cells comprising the CAR molecule.
[001123] [001123] The administration of the compositions in question can be performed in any convenient way. The compositions described in this document can be administered to a patient transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullarily, intramuscularly, by intravenous (i.v.) or intraperitoneal injection, for example, by intradermal or subcutaneous injection. Compositions of immune effector cells (eg, T cells, NK cells) can be injected directly into a tumor, lymph node or site of infection.
[001124] [001124] In one embodiment, cells expressing a CAR described in this document are administered to an individual in combination with a molecule that decreases the population of Tree cells. Methods that decrease the number of (for example, deplete) Treg cells are known in the art and include, for example,
[001125] [001125] In one embodiment, cells expressing a CAR described here are administered to a subject in combination with a molecule targeting GITR and / or modulating GITR functions, such as a GITR agent and / or an antibody to GITR that depletes regulatory T cells (Trees). In the embodiments, cells that express a CAR described in this document are administered to an individual in combination with cyclophosphamide. In one embodiment, GITR-binding molecules and / or molecules modulating GITR functions (eg, GITR agonist and / or antibodies to GITR that deplete Treg) are administered prior to administration of the cell expressing CAR. For example, in a modality, the GITR agonist can be administered before cell apheresis. In modalities, cyclophosphamide is administered to the subject before administration (for example, infusion or reinfusion) of the cell expressing CAR or before apheresis of the cells. In embodiments, cyclophosphamide and an anti-GITR antibody are administered to the subject prior to administration (e.g., infusion or reinfusion) of the cell expressing CAR or before apheresis of the cells. In a modality, the subject has cancer (for example, a solid cancer or a hematological cancer such as ALL or CLL). In one modality, the individual has CLL. In modalities, the individual has ALL. In modalities, the subject has a solid cancer, for example, a solid cancer described here. Examples of GITR agonists include, for example, GITR fusion polypeptides and anti-GITR antibodies (for example, anti-
[001126] [001126] In one embodiment, a cell expressing CAR described in this document is administered to a subject in combination with a GITR agonist, for example, a GITR agonist described in this document. In one embodiment, the GITR agonist is administered before the cell that expresses CAR. For example, in one embodiment, the GITR agonist can be administered prior to cell apheresis. In one mode, the individual has CLL. EXAMPLES
[001127] [001127] The invention is further described in detail with reference to the following experimental examples. These examples are provided for illustrative purposes only and are not intended to be limiting unless otherwise specified. Thus, the invention should in no way be considered to be | limited to the following examples, instead it should be considered to cover any and all variations that become evident as a result of the teachings provided in this document.
[001128] [001128] In this example, an IKZF3-based degradation tag was tested for its ability to facilitate lenalidomide-dependent degradation of a target protein. The IKZF3-based degradation label includes amino acid residues 136 to 180 and 236 to 249 of human IKZF3 and comprises the amino acid sequence of SEQ ID NO: 3. This label is referred to herein as "IKZF3 136 to 180 and 236 to 249 "or the" HilD tag ". IKZF3 136 to 180 and 236 to 249 were fused to the N-terminus of NanoLuciferase via a 16GS GGGGSGGGGTGGGGSG linker (SEQ ID NO: 28) (Figure 1A). A pNL1.1CMV vector encoding the NanoLuciferase labeled with IKZF3 136 to 180 and 236 to 249 was reverse-transfected into HEK293T cells using a total of O ng, 5 ng, 50 ng or 250 ng of DNA (DNA values here they were based on a transfection of 254! into 384 wells which was then scaled up to a 6-well plate).
[001129] [001129] The transfected cells received a 1 hour pretreatment with 128 ng / ml cyclohexamide, 12.8 ng / ml cyclohexamide, or 10 µM MG132 prior to treatment with 0 µM, 1 µM, or 100 µM ONE of lenalidomide for 2, 4 or 6 hours. DMSO was included as a vehicle control. Luminescence was measured by reading each 384-well plate in a ViewLuxO with exposures of 1 second and seconds. The data was imported into Spotfire & and the visualizations were made by performing an NC3 normalization according to the following formulas: 100 * ([Luminescence] / [DMSO]).
[001130] [001130] The degradation tag including amino acid residues 136 to 180 and 236 to 249 of IKZF3 can facilitate lenalidomide-dependent degradation of a target protein (Figure 1B). The step
[001131] [001131] Lenalidomide-dependent degradation facilitated by IKZF3 136 to 180 and 236 to 249 of NanoLuciferase was evaluated by Western blot. The pNL1.1CMV vector encoding the IKZF3 labeled NanoLuciferase 136 to 180 and 236 to 249 described above was transfected into 293GT cells and 293GT cereblon (CRBN) cells. The transfected cells were then treated with 100 µM, ONE, 1 µM, 0.1 µM, 0.01 µM, or 0.001 µM lenalidomide, or DMSO for one hour at 37 ° C. The pretreatment samples were treated with 10 µM of MG132 for one hour at 37ºC before treatment with 100 UM of lenalidomide. The samples were pelleted, lysed, tested on a protein gel, transferred to a membrane, probed with antibody and developed with film.
[001132] [001132] The data further show that IKZF3 136 to 180 and 236 to 249 could facilitate lenalidomide-dependent degradation of the target protein with increased concentrations of lenalidomide (IC50 = -10 nM) (Figure 2). Lenalidomide-dependent degradation of NanoLuciferase was not observed in transfected KO 293GT CRBN cells or cells pre-treated with MG132 (Figure 2). Es-
[001133] [001133] To determine whether a shorter IKZF3-based degradation tag could facilitate the leonalidomide-dependent degradation of a target protein, the following IKZF3-based tags were designed: "IKZF3 136 to 180," which included residues of amino acids 136 to 180 of IKZF3 (a tag comprising the amino acid sequence of SEQ ID NO: 5); "IKZF3 145 to 170," which included amino acid residues 145 to 170 of IKZF3 (a tag comprising the amino acid sequence of SEQ ID NO: 9); and "IKZF3 140 to 169," which included amino acid residues 140 to 169 of IKZF3 (a tag comprising the amino acid sequence of SEQ ID NO: 24).
[001134] [001134] Additionally, the degradation tags based on IKZF3 were modified using the following strategies: (1) delete the N-terminal and / or C-terminal amino acid residues; (2) replace amino acid residues 236 to 249, which correspond to an IKZF3 alpha helix, with the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91); and / or (3) mutate the lysine residue at amino acid position 245 in the IKZF3 alpha helix to arginine or serine (i.e., incorporating a K245R or K245S mutation, numbered according to SEQ ID NO: 19).
[001135] [001135] These degradation tags based on IKZF3 have been fused with the N-terminus of NanoLuciferase and cloned into the vector pNL1.1CMV, which has a CMV promoter. 5 ng (for all labels that do not include residues 236 to 249 of SEQ ID NO: 19) or 50 ng (for all labels that include residues 236 to 249 of SEQ ID NO: 19) from each construct were transfected into cells HEK293T. The transfected cells were treated with 100 µM, 10 µM, 1 µM, 0.1 µM, 0.01 µM, or 0.001 µM lenalidomide, or DMSO control for 2 to 4 hours at 37 ° C. Pre-treatment samples were treated with 10 µM of MG132 for one hour at 37 ° C before treatment with 100 µL of lenalidomide. Protein degradation was measured using western blot as described in Example 2.
[001136] [001136] The results of two studies are described below.
[001137] [001137] In a first study, IKZF3 136 to 180 and 236 to 249 (a tag comprising the amino acid sequence of SEQ ID NO: 3) facilitated lenalidomide-dependent degradation of NanoLuciferase (Figure 3B). Mutation of the lysine residue at position 245 (numbered according to SEQ ID NO: 19) to arginine (a label that comprises the amino acid sequence of SEQ ID NO: 84) or serine (a label that comprises the sequence amino acids of SEQ ID NO: 100) did not have a significant impact on the ability of the tag to mediate degradation (Figure 3B). Similarly, IKZF3 136 to 180 MALEK (a tag comprising the amino acid sequence of SEQ ID NO: 85) and IKZF3 136-170 MALEK (a tag comprising the amino acid sequence of SEQ ID NO: 86), where residues 236 to 249 (numbered according to SEQ ID NO: 19) were replaced by a MALEKMALEKMALE helix (SEQ ID NO: 91), also maintained the ability to facilitate lenalidomide-dependent degradation (Figure 3B). In contrast, IKZF3 140 to 170 MALEK (a tag comprising the amino acid sequence of SEQ ID NO: 87), IKZF3 141 to 163 MALEK (a tag comprising the amino acid sequence of SEQ ID NO: 88), and IKZF3 145 155 MALEK (a label comprising the following
[001138] [001138] In a second study, cells expressing IKZF3 136 to 180 labeled Nano-Luciferase or NanoLuciferase labeled with IKZF3 136 to 170 MALEK were treated with various doses of lenalidomide for 2 hours and analyzed using Western blot as described above . Both labels were able to measure lenalidomide-dependent degradation (Figures 4A and 4B). The level of degradation increased as the concentrations of lena- lidomide increased (Figures 4A and 4B). In addition, cells expressing IKZF3-labeled NanoLuciferase 136 to 180 were treated with 10 µM lenalidomide to increase the lengths of time before Western Blot analysis. The degradation was initially evident in 1 hour and was almost complete in 4 hours (Figure 4C). Example 4: Evaluation of degradation tags based on IKZF3 coupled with transcription factors
[001139] [001139] IKZF3-based degradation tags have been assessed for their ability to facilitate the degradation of melanogenesis-associated transcription factor (MITF) or homologous viral avian myelocytomatosis (MYC) homolog by Western blot. In addition to the degradation tags based on IKZF3, MITF and MYC have also been fused with a FLAG tag to facilitate their detection using an anti-FLAG antibody.
[001140] [001140] In a first study, MITF marked with IKZF3 136 to 180 and 236 to 249 or MITF marked with IKZF3 136 to 180 were examined as to their sensitivity to oil-dependent degradation
[001141] [001141] In a second study, IKZF3 136 to 180 and 236 to 249 lysine-free (a variant of IKZF3 136 to 180 and 236 to 249 in which each lysine residue on the label was mutated to arginine) (a which comprises the amino acid sequence of SEQ ID NO: 4) were tested for their ability to mediate lenalidomide-dependent degradation. Without sticking to the theory, if lenalidomide-dependent degradation is mainly mediated through the ubiquitination of the target protein (MITF in this example) instead of the IKZF-based label itself, the replacement of all lysine residues on the arginine label it may not have a significant impact on the level of degradation. As shown in Figures 6A, 6B, 6C and 6D, the replacement of all lysine residues on the degradation label of IKZF3 136 to 180 and 236 to 249 did not have a significant impact on the ability of that label to mediate lenalidomide-dependent degradation of MITF, suggesting that degradation of labeled MITF occurred mainly through ubiquitination of
[001142] [001142] In a third study, IKZF3 136 to 180 Q147H (a variant of IKZF3 136 to 180 in which the glutamine residue at position 147, numbered based on SEQ ID NO: 19, was replaced by histidine) (SEQ ID NO: 27) has been tested. Glutamine at position 147 has been shown to be essential for IMBN-induced CRBN binding and degradation of IKZF1 or IKZF3 (Krôónke et al, Science. January 2014, 343 (6168): 301-5, incorporated herein by reference - reference). As expected, Q147H substitution blocked the ability of IKZF3 136 to 180 to mediate LITL-dependent degradation of MITF (Figure 7).
[001143] [001143] In a fourth study, IKZF3 136 to 180 and 236 to 249 were examined for their ability to mediate degradation dependent on lenalidomide from another transcription factor of homologous viral oncogene of avian myelocytomatosis (MYC). HEK293T cells transfected with a fusion molecule, in which IKZF3 136 to 180 and 236 to 249 were fused with the N-terminus of MYC, were treated with varying concentrations of lenalidomide for 4 hours. Levels of tagged MYC, which was also fused with a FLAG tag, were evaluated by Western blot using an anti-FLAG antibody. As shown in Figure 8, IKZF3 136 to 180 and 236 to 249 also mediated lenalidomide-dependent degradation of labeled MYC. The level of degradation correlated with the concentration of lenalidomide (Figure 8). Example 5: Evaluation of IKZF3-based degradation tags linked to transmembrane proteins by Western blot
[001144] [001144] The ability of IKZF3-based degradation tags to facilitate lenalidomide-dependent degradation of the single-pass membrane of cell surface proteins
[001145] [001145] As shown in Figures 9A, 9B, 9C and 9D, all the constructs tested were sensitive to lena lidomide-dependent degradation, although the level of sensitivity varied between the constructs. Above all, there appears to be a correlation between the level of lenalidomide-dependent degradation and the number of cytosolic amino acids in the target protein (Figure 9A), as the target proteins with more amino acids in the cytosine | have been degraded to a higher level.
[001146] [001146] In general, these data suggest that degradation tags based on IKZF3 may be able to mediate the degradation of CD proteins (and single-pass membrane proteins in general) in the presence of lenalidomide. Example 6: Evaluation of degradation tags based on IKZF3 joined to transmembrane proteins by flow cytometry
[001147] [001147] The dose-responsive effect of lenalidomide treatment on target proteins fused with IKZF3-based degradation tags was assessed by flow cytometry. In particular, flow cytometry analysis was performed to determine whether there was a difference between the total amount of degraded target protein and the total amount of target protein expressed on the cell surface.
[001148] [001148] Jurkat cells expressing IKZF3-labeled CD19 136 to 180 and 236 to 249 were analyzed by flow cytometry O, 1, 6, 16 and 24 hours after treatment with 1 µM or 10 µM lenalide. CD19 was stained with anti-human CD19 antibody (BD Pharmingen 555413).
[001149] [001149] 90% of transduced Jurkat cells expressed CD19 on the surface, with no CD19 expression detectable in parental Jurkat cells (Figure 10E). A reduction in mean fluorescence intensity (MFl) and percentage of CD19 expression was observed after cells were treated with lenalidomide for 16 hours or 24 hours, which can be blocked by treatment with MG132 (Figures 10C, 10D, 10E and 10F) . This differs from what was observed in the western blot analysis described in Example 5, which shows a greater reduction in CD19 levels after a treatment with 10 µM lenalidomide for 6 hours.
[001150] [001150] These data show that a degradation tag based on IKZF3 can be used to selectively degrade single-pass transmembrane proteins. Example 7: Evaluation of chimeric antigen receptors (CARs) fused with the HilD and / or FurON tag by Western blot
[001151] [001151] In this example, the CAR19 chimeric anti-CD19 antigen receptor has been modified with the HilID tag and / or a furin degron (FurON). FurON can serve as a switch when fused to a CAR molecule. FurON comprises two components: (1) a degron or degradation domain, which is a mutated protein domain unable to acquire adequate conformation in the absence of a small molecule ligand (eg, bazedoxifene), and (2) a furin cleavage site (Figure 11). Without sticking to theory, in
[001152] [001152] The polynucleotide sequences encoding HIilD-labeled CAR19 were cloned to form the LING expression vector DINGX-LV vOO2. gBlocks were ordered from IDT. Table 24 provides information on these gBlocks. Construct 765 comprises, from the N termination to the C termination, a signal peptide, FurOn, and CAR19. Construct 766 comprises, from the N termination to the C termination, a signaling peptide, FurON, CAR19, a 16GS linker, the HilD tag and a V5. Construct 767 comprises, from the N termination to the C termination, a signaling peptide, FurON, CAR19, a 16GS linker and the HilD tag. Construct 768 comprises, from the N termination to the C termination, a signal peptide, CAR19, a 16GS linker, the HilD tag, and a V5. Construct 769 comprises, from the N termination to the C termination, a signaling peptide, CAR1I9, a 16GS linker and the HilD tag. Construct 770 comprises, from the N termination to the C termination, a signal peptide, CAR19, a 16GS linker and the lysine-free HilD tag. On the lysine-free HilD tag (shown as "HilD tag NoK" in Table 24), each lysine residue on the tag was replaced with arginine. Construct 771 comprises, from the N termination to the C termination, a signal peptide, CAR19, the HilD tag and a V5. Construct 6761 comprises, from the N termination to the C termination, a signal peptide, CAR1I9, a 16KGS, the HilD tag and a V5. Construct 773 comprises, from the N termination to the C termination, a modified signaling peptide, the HilD tag, a furin cleavage site and CAR1I9. Construct 774 comprises, from the N termination to the C termination, a signaling peptide, the HilD tag, a furin cleavage site, and CAR1I9. In short, gBlocks were digested, purified using the Qiagen MinElute PCR Purification Kit (cat% 28004), and ligated into the DNGX-LV lentiviral expression vector. vO02. The resulting clones were confirmed by sequencing. Table 24. Components of gBlocks Construct f gBlocks SEQ ID NO of amino acid sequence (signal peptide included)
[001153] [001153] Viruses were prepared from maxi preps and used to transduce JNL cells. 275 ul viral supernatant or 700 ul viral supernatant were used for transduction. JNL cells are Jurkat cells engineered with a luciferase gene under the control of the NFAT promoter. The transduced JNL cells were examined
[001154] [001154] In short, the cells were diluted to 0.5x10º in 3 ml in total in 6-well plates. Each cell line was plated in two wells (one for DMSO, one for treatment with 10 UM of lenalidomide). Bazedoxifene was added at a final concentration of 1 µM to each well that contained a cell line that expresses a fusion comprising FurON. For all cell lines, 10 µM of final lenalidomide or DMSO was added. The cells were incubated at 37ºC and 5% CO », overnight.
[001155] [001155] 24 hours after compounding, the cells were pelleted, washed with PBS, and lysed with 50 μl of RIPA buffer (Boston Bioproducts BP-115D) containing protease inhibitors (Roche 04693124001). The lysates were centrifuged, the supernatant transferred to new tubes and the protein quantities read by Lowry Assay (BioRad 5000111). Each sample was normalized to ug of total protein in a volume of 20 µl with 4X sample buffer (Thermo Scientific NPOO0O7) and 10X reducing agent (Thermo Scientific NPOOOS9). The samples were subjected to Western blot analysis using a mouse anti-V5 antibody (Thermo Scientific MAS5-15253) in dilution 1: 1000, a mouse anti-actin antibody (Sigma Aldrich A5441) in dilution 1: 10000 and / or a mouse anti-CD3z antibody (BD 551034) in dilution 1: 1000.
[001156] [001156] As expected, lenalidomide had no impact on FurON-CAR19 without the HilD tag (Figure 13A). In the presence of the HilD tag, treatment with 10 µM lenalidomide degraded almost completely FurON-CAR19 regardless of the presence of the V5 tag (Figures 13B and 13C). Treatment with 10 µM of lena-lidomide degraded almost all CAR19-HIilD constructs, regardless of the presence of the 16GS ligand or the label.
[001157] [001157] Next, the degradation kinetics of CAR1I9 as well as the effective doses of lenalidomide for reducing expression of CAR19 were examined by Western blot. The JNL cells that express construct 769 (label CAR1I9 16GS HIilD) were diluted to 0.5x10º in 3 ml in total in 6-well plates. Each cell line was plated in multiple wells for treatment with lenalidomide / time points. Once the wells were plated, the samples were treated with various doses (10 CU, 1 CU, 0.1 CU, 0.01 CU or 0.001 CU) of lenalidomide or DMSO for different durations. The cells were collected and subjected to Western blot as described above using a mouse anti-actin antibody (Sigma Aldrich A5441) in dilution 1: 10000 or a mouse anti-CD3 zeta antibody (BD 551034) in dilution 1: 1000.
[001158] [001158] 10 UM of lenalidomide degraded the CAR19-16GS-HIilD tag fusion protein in a time-dependent manner (Figure 15A). The degradation was evident in 4 hours and seemed to reach the maximum degradation in 8 hours (Figure 15A). The level of degradation was stable for 8 to 24 hours, with no evident recovery of protein expression (Figure 15A).
[001159] [001159] As shown in Figure 15B, lenalidomide has degraded the CAR19-16GS-HIilD tag fusion protein in concentrations as low as 100 nM. CAR19 degradation was evident with each compound dose greater than 100 nM (Figure 15B), indicating that there was no compound hook effect. The titration of protein degradation observed in concentrations of inferred lenalidomide
[001160] [001160] Next, the surface expression of CAR1I9 in stably transduced JNL cells was examined by flow cytometry. On Day 1, the transduced JNL cells were plated with or without lenalidomide in 10 µM for 24 hours. The cells that express the FurON-CAR19 constructs were cultured with and without linalidomide in the presence or absence of bazedoxifene. On Day 2, cells were collected, stained using biotinylated L protein (Genscript, MOOO97) followed by PE-conjugated streptavidin (Jackson Lab, 016-110-084), and subjected to flow cytometry analysis using the Fortessa instrument .
[001161] [001161] For molecules where the HIilD tag was fused to the C terminus of CAR19 (constructs 769, 771, 6761, 768 and 770), the transduced cells showed CAR expression in more than 60% of the cells (Figures 16A, 16B, 16C, 16D and 16E). No CAR expression was detected in parental JNL cells (Figures 16A, 16B, 16C, 16D and 16E). Treatment with 10 µM lenalidomide for 24 hours significantly reduced the expression of CAR on the surface (Figures 16A, 16B, 16C, 16D and 16E). Notably, the lysine-free HilD tag also mediated the lenalidomide-dependent reduction of CAR expression on the surface (Figure 16E).
[001162] [001162] For molecules where the HIilD tag was fused to a furin cleavage site and then, with the N termination of CAR1I9 (constructs 773 and 774), the transduced cells showed CAR expression (Figures 16F and 16G) . Incubation with 10 µM lenalidomide for 24 hours did not impact the expression of CAR on the surface (Figures 16F and 16G).
[001163] [001163] In addition, the FurON-CAR19 constructs with or without the HilD tag were examined for their expression on the surface under the regulation of bazedoxifene and / or lenalidomide. As shown in Figures 17A, 17B and 17C, CAR expression on the surface was only detected in the presence of bazedoxifene and the lenalidomide-dependent reduction in CAR levels on the surface was only observed when CAR19 was fused with the HilD tag. .
[001164] [001164] Table 25 provides a summary of the flow cytometry data shown in Figures 16A, 16B, 16C, 16D, 16E, 16F, 16G, 17A, 17B and 17C. Table 25. Summary of HE HeCAR flow cytometry data jbazedoxifenolenalidomidation in delpressure
[001165] [001165] Next, the expression of CAR on the surface in the presence of a lenalidomide dose titration was examined by flow cytometry. In short, JNL cells transduced stably with construct 769 (label CAR1I9 16GS HIilD) or construct 770 (CAR1I9 16GS HILD tag NoK) were incubated with 8 different concentrations of lenalidomide (starting at 2 µM during a 4-treatment) hours or 1 µM during a 20-hour treatment) to determine the dose response effect. The cells were then analyzed by flow cytometry as described above using biotinylated L protein (Genscript, MOO0O097) followed by PE-conjugated streptavidin (Jackson Lab, 016-110-084).
[001166] [001166] The results of the 4-hour treatment groups are shown in Figures 18A and 18B and Table 26. The results of the 20-hour treatment groups are shown in Figures 18C, 18D, 18E and 18F and Table 27. After a lenalidomide treatment for 4 hours, a reduction in MFI was detected with a slight reduction in% CAR expression (% of cells expressing CAR) (Table 26). After a 20-hour treatment, lenalidomide most prominently reduced the% CAR expression and MFI in a dose-dependent manner (Table 27, Figures 18E and 18F). There was no significant difference between the results of construct 769 (label CARI9 16GS - HIilD) and the results of construct 770 (CAR1I9 16GS HIilD tag NoK), suggesting that ubiquitination can occur mainly through lysine residues in the target protein, instead of the HIilD tag itself. Table 26. Effect of lenalidomide after 4 hours of treatment E vB Er pe in Ron (UM) of CAR MF! AR MF! pe e Rs sr ER ps e) pes ez ess pe mp POE Em ss)
[001167] [001167] In this example, several studies were conducted to determine whether CAR1I9 and FurON-CAR19 were functional when labeled with HIilD and whether lenalidomide-induced degradation was sufficient to negate CAR19 function in Jurkat cells.
[001168] [001168] This study used the JNL cell line described above, which is a Jurkat cell line modified with a NFAT luciferase reporter. Coculture of J19L cells expressing CAR19 activates NFA signaling, leading to luciferase expression.
[001169] [001169] In a first study, JNL cells expressing the 767 construct (FurON CAR19 16GS HIilD tag) or 769 construct (CAR1I9 16GS HIilD tag) were plated. JNL cells expressing the 767 construct (FurON CAR1I9 16GS - HIilD tag) were incubated with 1 µM bazedoxifene. All JNL cells were treated with 10 µM lenalidomide for 4 hours or 24 hours. The JNL cells treated with lenalidomide were incubated with Nalm6 cells, K562 cells or K562 cells expressing CD19 for 4 hours, 8 hours or 20 hours. The samples were treated with
[001170] [001170] As expected, luminescence signals were only observed when the JNL cells expressing the 769 construct (CAR1I9 16GS HIilD tag) were co-cultured with CD19 + target cells (Nalm6 cells and K562 cells expressing CD19) (Figure 19A). Lenalidomide treatment reduced the luminescence signal to background levels in each case with the exception of 4 hour lenalidomide / 4 hour target cell treatments (Figure 19A). One possible explanation is that the JNL cells that express the 769 construct (CARI9 label 16GS HILD) had to be treated with lenalidomide for more than 8 hours to reduce the luminance signal in that NFAT luciferase reporter assay. After subtracting the background signals (medium sample signals), treatment with lenalimide reduced the luminescence signal by -95% in JNL cells that express CAR co-cultured with K562 Cd19 expression cells and by -88% in cells CAR expression JNL co-cultured with Nalm6 cells. These data suggest that the HilD tag is sufficient to significantly reduce the function of CAR1I9 in the presence of lenalidomide.
[001171] [001171] Similarly, the luminescence signals were only observed when the JNL cells expressing the 767 construct (FurON CAR19 16GS HIlD tag) were co-cultured with CD19 + cells (Nalm6 cells and K562 cells expressing CD19) in the presence of bazedoxifene (Figure 20A). Treatment with lenalidomide reduced the luminescence signal to background levels in samples co-treated with bazedoxifene (Figure 20A). After subtracting the background signals (medium sample signals), lenalidomide treatment reduced the luminescence signal by -90% in JNL cells that express
[001172] [001172] A second study was conducted to determine the sensitivity of HIilD-labeled CAR1I9 or FurON-CAR19 to lenalidomide-dependent degradation. JNL cells expressing construct 765 (FurON CAR19), construct 767 (FurON CAR1I9 16GS —HIiID tag), construct 769 (CARI9 16GS HIlD tag), or construct 770 (CAR19 16GS HIilD tag NoK) were plated. JNL cells expressing construct 765 (FurON CAR19) or construct 767 (FurON CAR19 16GS HIilD tag) were incubated with 1 µM bazedoxifene. There were three treatment groups: "pre-target cells for 20 hours" (a total of 44 hours of lenalidomide treatment), "pre-target cells for 4 hours" (a total of 28 hours of lenalidomide treatment) ), and "post-target cells for 16h" (a total of 8 hours of lenalidomide treatment). For the group "pre-target cells for hours", MG132 (final concentration of 10 µM) was added to the transduced JNL cells three hours after the addition of bazedoxifene, lenalidomide was added 1 hour after the addition of MG132 and the cells - K562 cells or CD19 expression K562 cells were added 20 hours after the addition of lenalidomide. For the group "pre-target cells for 4 hours", MG132 (final concentration of 10 µM) was added to JNL cells transduced 19 hours after the addition of bazedoxifene, lenalidomide was added 1 hour after the addition of MG132 and K562 cells or CD19 expression K562 cells were added 20 hours after the addition of lenalidomide. For the group "group of post-target cells for 16 hours", K562 cells or K562 target cells expressing CD19 were added to JNL cells transduced 24 hours after the addition of bazadoxifene, MG132 (final concentration of UM) was added 15 hours after the addition of the target cells, and linalidomide was added 1 hour after the addition of MG132. For the target cell co-culture, K562 cells or K562 cells expressing Cd19 were added to each well containing JNL cells and cultured in an ultra-high-throughput GNF System sorting system in an incubator with 5% CO »at 37ºC. 24 hours after adding K562 cells or CD19 expression K562 cells, the samples were treated with Brightglo (Promega E2620) following the manufacturer's protocol and the luminescence was read on a Perkin Elmer Viewlux with an exposure 5 seconds.
[001173] [001173] As specified, the transduced JNL cells responded only to K562 cells expressing CD19, but not to K562 cells (Figures 21A, 21B, 21C and 21D). Without the HIilD tag, lenalidomide treatment had no impact on the reporter's response (Figure 21A). In the presence of bazedoxifene, the JNL cells that express the 767 construct (FurON CAR19 16GS HILD tag) showed reporter activation after coculture with K562 CD19 expression cells and this reporter activation was inhibited by lenalide in a dose-dependent manner (Figure 21B). IC50s range from -5 µM to 0.1 µM. The IC50s of lenalidomide reduced potency over time, with the highest IC50 in the 8-hour treatment ("16h with post-target cells" in Figure 21B) and the lowest IC50 in the 44-hour treatment ("20h with pre-target cells "in Figure 21B). Higher doses of lenalidomide reduced the luminescence signal by 100% in the 44-hour treatment group ("20h with pre-target cells" in Figure 21B) and in the 28-hour treatment group ("4h with cells b-pre-target "in Figure 21B), and 90% in the 8-hour treatment group (" 16h with post-target cells "in Figure 21B). Lenalidomide also
[001174] [001174] The treatment with 10 UM of 28 hours lenalidomide caused a reduction in the expression of CAR19 in all cell lines that express a HIilD-labeled CAR molecule and this reduction can be partially rescued by the proteasome inhibitor MG132 (data not shown). JNL cells that express different constructs could not be directly compared since they had different levels of CAR expression, resulting in different levels of responses to CD19 + cells. Instead, comparisons were made between treatments in the same cell lines (Figures 22A, 22B, 22C and 22D). For constructs that comprise FurON, treatment with bazedoxifene was necessary to activate the NFAT-luciferase reporter in the presence of cells
[001175] [001175] The constructs were generated by gene block synthesis (IDT) and the introduction into plasmids internally through the Gibson assembly. Table 28 lists the sequences of the constructs used in this example.
[001176] [001176] HEK293T cells cultured in 6-well tissue culture plates were transfected with 3 micrograms of FLAG-labeled CRBN and 2.1 micrograms of Tau fusion construct indicated using 6 μl of lipofectamine 2000, in one final volume of 200 ul of Optimem medium. 48 hours after transfection, the cells were treated with 50 µl of biotin (diluted with 100 mM of stock prepared in DMSO) and DMSO (1 to 10,000) or 1 micromolar of lenalidomide. The cells were incubated for 21 hours, then lysed after washing in ice PBS with 300 µl of cold M-PER buffer (Thermo Fisher% 78501) containing 1X Halt protease inhibitors (Thermo Fisher 41861281). The cell lysate was eliminated and the protein quantified by the BCA reaction, and the protein concentration normalized in M-PER buffer. 20% cell lysate (60 µl) was diluted 4 times in an IP lysis buffer (15 mM Tris pH7.5, 120 MM NaCl, 25 mM KCl, 2 mM EGTA, 2 mM EDTA, 0, 5% Triton X-100, 1X Halt protease inhibitor) and incubated with 50 µl Streptavidin M-280 magnetic Dynabeads (Thermo Fisher Cat IS 11205D) for 30 minutes at room temperature. The microspheres were subsequently washed three times with IP lysis buffer, then, finally, dissolved in 20 µl of M-PER buffer containing protease inhibitors. The LDS 4X NuPage buffer was added to a final concentration of 1X in that immunoprecipitated material and the cell lysates were similarly diluted. The 10X NuPage reducing buffer was then added to a concentration of 1X, and the samples were heated to 95ºC for 5 minutes. The cell lysate or immunoprecipitated material was tested on a 10% Bis-Tris Criterion XT gel (BioRad 3450111), stained (TurboBlot), and incubated with primary antibodies as indicated. Secondary goat antibodies LiCor RDye 800CW (H925-32211) or 680 RD
[001177] [001177] One day before transfection, HEK 293T wild type cells or HEK293T CRBN knockout (KO) were inoculated into 22.5K cells per well in 96-well plates. The cells were transfected with 0.02 microgram of HilID-Tau fusion construct (P301S). One day after transfection, the wells were treated with varying concentrations of lenalidomide. After overnight treatment, the cells were fixed in a final solution of 4% PFA and 4% sucrose for 15 minutes. The fixed cells were washed with PBS. The cells were then incubated with 1: 5000 Hoechst and 1: 10,000 Cellmask HCS for fifteen minutes, then washed, imaged.
[001178] [001178] The plates were imaged in the Incell Analyzer 6000 using a 20X objective capture and DAPI, FITC and Cy5 channels. The image data were quantified using a cellprofiler, in which the cell nucleus was segmented by means of Hoechst staining and then the cell body identified by the expansion of the nuclear object to the edges of the segmented cell, identified by Cell mask staining. This cellular object was then used to measure the intensity of FITC, corresponding to HiID-Tau (P301S) -YFP. Transfection of HEK293T and quantification of HilD-Tau degradation by Western analysis
[001179] [001179] The day before transfection, HEK293T cells were plated at a density of 150,000 per well in a 24-well plate. The cells were transfected with 0.175 micrograms of HilD-Tau fusion construct (wild type). Four hours or 24 hours after transfection, the wells were treated with a response to Lenalidomide dosing. The cells were incubated overnight. The cells were then washed with PBS ice and lysed in 85 µl of N-PER buffer (Thermo Fisher% 87792) supplemented with protease inhibitors and Halt phosphatase. The plates were incubated on ice with occasional shaking for 15 minutes. The lysate was then cleaned by centrifugation at 15000g, 4ºC for 15 minutes. The LDS buffer and the reducing agent were added to the clean lysate, and then samples were heated to 95ºC for 8 minutes. The samples were tested on a 10% bis-tris gel at 150V for 70 minutes. The spots were transferred using the Biorad turboblot (Mixed molecular weight configuration). The spots were probed with DAKO Tau (total tau) (Dako tXAO024), actin (Cell signal technologies ft3700S), and AT8 (phospho-Tau) (Thermo Fisher tMN1020). The spots were developed with Supersinal west femto chemiluminescent substrate (Thermo Fisher% 34095).
[001180] [001180] Western band quantification was in accordance with Molecular Psychiatry (2017) 22, 417-429.
[001181] [001181] Rat cortexes were isolated from 18.5 day old embryonic rats. Single cell suspensions were prepared by dilution for 15 minutes at 37ºC in papain (Brainbits & PAP) diluted in 3 ml of Hibernate E (-Ca) solution (Brainbits XHECA); then supplemented with DNAse (up to a concentration of 0.5 mg / ml); shredded; incubated for 10 minutes at 37ºC; crushed; and, finally, filtered through a 40 µm cell filter. Approximately 8 million cells were nucleofected using P3 solution (Lonza nucleofection kit% & V4XP-1024) with 2 micrograms of plasmids indicated. The CU-133 program on the 4D nucleofector was used. The cells were then diluted in a neurobasal medium (Life Technologies 421103) containing 1% serum, and plated at a density of
[001182] [001182] The medium was changed by 50% every 7 days. On day 9, the compounds were added to the medium in final indicated concentrations. YFP signal imaging was carried out at specified intervals using the InCell 6000 (General Electric) system, coupled to a Liconic Instruments IC incubator (Cat 391180700) / plate hotel using a Thermo Scientific Orbitor RS robot. Nucleofection of human neurons
[001183] [001183] Human pluripotent stem cells (hPSCs) were maintained in E8 medium (Stem Cell Technologies) in tissue culture plates coated with vitronectin. The confluent hPSC monolayers were converted neurally by changing the medium to Ph | (see middle recipes). Seven days after induction, cells were dissociated for single cell suspension with Accutase, inoculated into 1.5 million cells per milliliter in spinner flasks with Ph I! / Ill medium supplemented with 2 micromolar and 10 ng / ml Thiazovivine of FGF 2 (final) and incubated at 37ºC in a micro-agitation plate at 40 rpm for 4 days. The medium was then changed to Ph II / IIl and the neurospheres were cultured for 17 days at 60 rpm, changing 50% of the medium twice a week. On day 28, the medium was changed to Ph IV and the cultures were maintained for another 21 days with 50% exchange of medium twice a week. As of day 49, the cultures were switched to the Ph V medium for maintenance and dissociated with the papain kit (Worthington Sciences) for neuronal plating on plates coated with laminin, fibronectin and matrigel. The single cell suspension was nucleofected (10 million cells per reaction), 2 micrograms of construct. 80,000 cells were plated per well of 96-well plates. The neurons were incubated in Phase 5 + blasticidine medium. The medium was changed (50%) twice a week.
[001184] [001184] Medium of Phase |: Base: Advanced DMEM / F12; Glutamax (1X) (Life Technologies tH35050); Pen / Strep (1x) (Life Technologies 15140); N-acetyl-cysteine (500 micromolar); Heparin (2 micrograms / ml); SB431542 (10 micromolar); LODN193189 (100 nM); XAV939 (2 micromolar); N2 supplement (0.5% v / v).
[001185] [001185] Phase II / Ill Medium: Base: Advanced DMEM / F12; Glutamax (1X); Pen / Strep (1X); N-acetyl-cysteine (500 micromolar); Heparin (2 micrograms / ml); N2 supplement (0.5% v / v); B27 supplement (1% v / v) (Life Technologies% 17504); FGF2 (10 ng / ml, first 4 days; 2.5 ng / ml, remainder of Phase II / I111); LON193189 (100 nM); CHIR99021 (20 NM); Retinoic acid (5 nM).
[001186] [001186] Phase V Medium: Base: Advanced DMEM / F12; GlutaMax (1x); Pen / Strep (1x); Heparin (2 micrograms / ml); N2 supplement (0.5% v / v); B27 supplement (1% v / v); Forskolin (10 micromolar); Calcium chloride (600 micromolar); BDNF (5 ng / ml); GDNF (5 ng / ml). Generation of insoluble fractions of Tau
[001187] [001187] The insoluble fractionation in sarcosil was carried out in 58/4 transgenic mice (tg / ta) at 6 months of age, an internal tau transgenic mouse model that overexpresses the human tau-length is4 form with the P301S mutation. In short, the brain tissue isolated from mice was homogenized in 9: 1 (v / w) buffer with a high salt content (10mM Tris-HCL, pH 7.4, 0.8Nacl, EDTA IMM and 2mM of dithiothreitol) with protease and phosphatase inhibitor and 0.1% sarcosil. The homogenate was centrifuged at 10,000g for 10 minutes at 4ºC, and the supernatant was collected. The pellet was re-extracted twice using the same buffer conditions, and all supernatants were pooled. Additional sarcosil was added to the supernatant to achieve a final concentration of 1% sarcosil. After 1 hour of nutrition at room temperature, the sample was centrifuged at 280,000 g for 1 hour at 4ºC. Finally, the resulting pellet was resuspended in PBS (300 µl / g of tissue) and briefly sonicated (20% power for 10, 10-second cycles) using a portable probe (QSonica). This final fraction was stored at -80ºC until use and was called the tau fraction insoluble in sarcosil. Results
[001188] [001188] HilD-Tau fusions, including aggregation-prone Tau mutations, were generated to create tools to monitor the degradation of toxic and aggregate-prone forms of Tau protein (Figure 23).
[001189] [001189] In a first experiment, it was tested whether the fusion of the HilD tag with Tau could induce the recruitment of E3 Ceblblon ligase (CRBN) through treatment with the immunomodulatory drug lenalidomide. A fusion of HilD-Tau-biotin ligase was generated (Figure 24A). Biotin ligase, upon exposure to biotin, generates a species of reactive biotin that binds covalently to nearby proteins within a radius of tens of nanometers. Upon treatment with Lenalidomide, but not under control conditions, HilD-Tau-biotin ligase caused robust biotinylation of a CRBN construct labeled with FLAG cotransfected with HIilD-Tau- biotin ligase constructs in HEK293T cells (Figure 24B). This confirms that the HIID tag can recruit CRBN for Tau by forming a ternary lenalidomide complex.
[001190] [001190] Next, it was examined whether Tau could be degraded by recruiting CRBN into heterologous cells. HEK293T cells were transfected with a toxic form prone to aggregation of Tau, ON4R Tau P301S, fused with a HilD N-terminal tag reporter and a C-terminal YFP tag (fluorescent yellow protein). The expression of this construct leads to toxicity over time in cells. Treatment with lenalidomide reduced YFP expression (Figures 25A and 25B) and improved the viability of HEK cells (Figure 25C). This indicates that HilID-Tau fusion can be used to reveal the cytoprotective action of degradation of toxic Tau proteins, as found in neurodegenerative diseases.
[001191] [001191] In addition, it was tested whether Tau lacking a YFP tag could be degraded in HEK293T cells. Lenalidomide treatment reduced Tau levels, as quantified by Western analysis versus Actin loading control (Figure 26A). Above all, reducing the amount of Tau expression by decreasing the amount of transfected DNA increased the degradation efficiency, particularly in a phosphorylated form of Tau (Figure 26A, lower panels). This suggests that the system can be used to exploit the ability of the E3 ligase and the proteasome system to degrade different levels of the Tau protein and, in addition, that system can be used to exploit the selective vulnerability of specific forms of a toxic protein to inducible degradation. The increased reduction in phosphorylated Tau suggests that a specific subtype of Tau is more susceptible to degradation or that a fragment of Tau containing that epitope is more significantly degraded than other isoforms of Tau.
[001192] [001192] In a series of control experiments to verify whether the degradation of Tau was mediated by recruiting free E3
[001193] [001193] Next, it was explored whether Tau could be degraded in neurons, which are the cell type relevant to the disease of Tau-mediated neurodegenerative diseases, and whether this degradation process, by ubiquitinating Tau, would produce any aggregate Tau as a by-product. First, it was established that the HiID-Tau (P301S) -YFP fusions were competent for aggregation, treating nucleofected neurons with this construct with an insoluble fraction of the rodent brain, isolated from a mutant transgenic mouse overexpression Tau. The aggregation of HilD-Tau (P301S) -YFP was clearly visible, as shown by intense and punctual YFP fluorescence in the cell body and neuron dendrites (Figure 27).
[001194] [001194] In addition, HilD-Tau (P301S) -YFP degradation sensitivity was tested in primary cortical neurons of rats prepared from embryonic tissue, as well as neurons and neuronal progenitors transfected from neurospheres derived from human embryonic stem cells (Figures 28 and 29). In primary neurons, HiID-Tau (P301S) -YFP was tested for degradation induced by lenalidomide, individually and when cotransfected with the human Cereblon with FLAG. Although so-called immunomodulatory drugs, such as thalidomide and lenalidomide, exhibit different effects in rodents and humans, such as teratogenicity, in this system lenalidomide induced the degradation of HilD-Tau- YFP, even when not co-transfected with human CRBN (Figure
[001195] [001195] As the HilD-Tau system can be induced to aggregate, it is anticipated that it can be used to assess situations in which the aggregated Tau is or is not able to be ubiquitinated and degraded by the teasome. Example 11: Evaluation of CAR19-HilD in Jurket cells
[001196] [001196] This study examines the kinetics of lenalidomide on CAR19-HilD in Jurkat cells and whether the expression of CAR19 could return after lenalidomide was washed out of the cells. Methods
[001197] [001197] Cell treatment: Jurkat cells transduced by CAR19-16GS-HIilD tag were diluted and inoculated in two flasks. Once the cells are plated, one vial was treated with DMSO and the other with 10uM lenalidomide during a course of collection time. 3 ml of cells from each flask were collected for flow cytometry and western blot 1, 2, 4, 6, 8, 12 and 24 hours after treatment with the compound. The cells in the lenalideide-treated flask were divided into two flasks at one point in time for 24 hours. One was labeled "washed" and the other as "treatment". Lenalidomide was removed by washing the "washed" cells by centrifugation at 300g and resuspended in fresh medium three times, and the other half was divided with the residual lenalidomide present in the medium before (treatment with 10 CU of lenalidomide was performed only once). The cells were collected 1, 2, 4, 6 hours after washing and 36, 48, 60 and 72 hours after treatment with compound.
[001198] [001198] Western blot: The cells were pelleted, washed with PBS, and the pellets were lysed with 50 µl of RIPA buffer (Boston Bio-products BP-115D) with protease inhibitors (Roche 04693124001). The lysates were centrifuged, the supernatant transferred to new tubes and the protein quantities read by Lowry Assay (BioRad 5000111). Each sample was normalized to 30 µg of total protein in a volume of 20 µl with 4X sample buffer (Thermo Scientific NPOO0O7) and 10X reducing agent (Thermo Scientific NPOOO9). The samples were tested on a 4 to 12% Bis-Tris acrylamide gel (Thermo Scientific WG1402BOX). The gels were tested in duplicate, one to be probed against actin and the other against V5 or CD3Z. The gels were transferred to nitrocellulose membranes and the membranes were incubated overnight in 3% milk in TBS-0.1% Tween-20 with one of the following antibodies: anti-mouse actin (Sigma Aldrich AS441) with dilution 1: 10,000 and anti-mouse CD3z (BD 551034) with 1: 1000 dilution. The stains were washed the next day in TBS-0.1% Tween-20, placed in 3% milk in TBS-0.1% Tween-20 with secondary anti-mouse sheep HRP antibody 1: 10000 (GE Healthcare NA931) at room temperature
[001199] [001199] Flow cytometry: The cells were collected in a bottom plate and washed using 1X PBS. The washed cells were stained with 100yu! of Biotinylated Protein L (Genscript MOO0097) diluted in 1: 1000X to 1ug / ml. The primary antibody was incubated at 4'C for 45 minutes. After incubation, the cells were washed using PBS. The cells were incubated at 4'C with PE-conjugated streptavidin (Jackson Lab 016-110-084) in dilution 1: 300X for 30 minutes. The cells were washed twice with PBS and suspended in 100yu! of fixation buffer (2% Paraformaldehyde in PBS) for 10 minutes at room temperature. The fixed cells were washed with PBS and suspended in 150 µl PBS. These cells were then acquired using the BD LSRF Fortessa cell analyzer. Dead cells were excluded based on size using the FSC and SSC graph. Live cells were analyzed for PE CAR expression. FACS results were identified using the uncolored parental JNL cell line and 10,000 events were recorded for each sample. Results
[001200] [001200] As shown using Western blot in Figure 30A, 10uUM of lenalidomide degraded CAR19-HIilD in a time-dependent manner and after lenalidomide was washed away, the CAR19-HIilD expression was recovered. This observation was confirmed using flow cytometry analysis. Lenalidomide continued to degrade CAR19-HIilD over time and washout of lenalidomide increased the expression of the CAR19-HIilD surface (Figure 30B). Example 12: Evaluation of CAR19-HilD in primary T cells
[001201] [001201] This study analyzes the effect of response to the dose of lenali-
[001202] [001202] First, CAR surface expression in CAR19-HILD CART cells with or without lenalidomide treatment for 24 and 48 h was examined. Second, the impact of lenalideide on the extermination of CAR T and the production of cytokines in the presence of cells that express CD19 was analyzed. Methods
[001203] [001203] Viral pELPS vector production: LentiX-293T cells (Clonetech 632180) were cultured in DMEM with 10% FBS at 37 'C and 5% CO>. The cells were inoculated into five 15 cm tissue culture plates (BD Biosciences 356451) in 14x1006 cells per plate in 25 ml of DMEM, 10% FBS and incubated overnight. The next day, 15pg of the pELPs vector was combined with a mixture of lentiviral packaging (18ug of pRSV.REV, 181ug of pMDLg / p.RRE, and 7pug of pvSV-G), 90ul of Lipofectamine 2000 (Invitrogen 11668-019) and 3ml of OptiMEM (Invitrogen 11058021) per 15cm plate and added to the cultured cells. The next day, the medium was removed and replaced with 15 ml of fresh medium. The cells were incubated for 30 hours and then the virus was collected, centrifuged at 500g for 10 minutes and filtered through a 0.45UM cellulose acetate filter (Corning 430314). The viral supernatant was concentrated using the Lenti-X concentrator (Clonetech 611232) at 4ºC overnight, pelleted at 1500g for 45 minutes at 4'C, followed by aspiration of supernatant and resuspension in DMEM, 10% of FBS in 1/100 of the initial volume. The virus was aliquoted and stored at -80 ° C.
[001204] [001204] SUPT1 titer: 100uI of SUPT1 cells were cultured in 2E5 cells / ml in a 96-well flat bottom plate. 50 µl of diluted virus was added to the cells. The plate was incubated at 37ºC in CO, overnight. 100ul of RPMI medium was added
[001205] [001205] 10 days of CART expansion: CART cells were generated starting with the apheresis product of healthy donors whose naive T cells were obtained by negative selection for T cells, CD3 lymphocytes. T cells were cultured at 0.5x10º T cells in 1 ml of medium per well of a 24-well plate. These cells were activated by adding CD3 / CD28 microspheres (Dynabeads & Human T-Expander CD3 / CD28) in a 1: 3 ratio (T cell to microsphere) in T cell medium.
[001206] [001206] After 24 hours, T cells were left untransduced (UTD) or transduced in a multiplicity of infection (MOI) from 4 to CART19 or CART19-HIilD. T cell growth was monitored by measuring cell counts per ml, and T cells were diluted in fresh medium every two days. On day 7, 1 million cells were transferred to a 24-well plate to evaluate the effect of lenalidomide, in three different concentrations 1UuM, 0.1UM, and 0.01UM, for 24 h or 48 h. The percentage of cells transduced (cells that express the specific CD19 CAR on the cell surface) was determined by flow cytometry analysis on a FACS Fortessa (BD). FACS coloring:
[001207] [001207] The cells were collected and washed with PBS. The cells were then incubated with 100yu! Biotinylated Protein L at 4'C for 45 minutes. The cells were then washed using PBS and incubated at 4'C with Streptavidin conjugated to PE in dilution 1: 300X and BV421 CD3 antibody in dilution 1: 200, for 30 minutes. The cells were then washed twice with PBS and suspended in 100yu! of fixation buffer with 2% Paraformaldehyde for 10 minutes at room temperature. The fixed cells were washed with PBS and suspended in 150yu! of PBS. The cells were then acquired in a Fortessa instrument and the results analyzed using the Flow Jo software.
[001208] [001208] Frozen CART cells were thawed in T cell medium and co-cultured with CD19 negative (K562 cells) or CD19 positive (Nalm6 cells) target cells, both expressing luciferase. Both the number of CART cells and the total number of T cells were normalized through samples; the latter was obtained by adding UTD cells. A CART cell titration was performed maintaining the target cell number constant in
[001209] [001209] As shown in Figure 31A, the transduction efficiency of CAR1I9 and CAR19-HIilD was comparable. The expansion in times of primary T cells transduced with CAR19 or CAR19-HilD was also comparable. Lenalidomide treatment did not affect the expression of CAR19 (Figure 31B). In contrast, cells that express CAR19-HilD showed a dose-dependent reduction in CAR expression under treatment with lenalidomide (Figure 31C). Hi m-
[001210] [001210] Low background extermination against CD19 negative cells was observed through samples, regardless of the addition of lenalidomide (Figure 32A). The ability of CART1I9 and CART19-HIilD to exterminate CD19 positive cells in the absence of lenalidomide was comparable (Figures 32B and 32C). Upon the addition of lenalidomide, the CART19-HilD extermination curve shifted slightly (Figure 32C).
[001211] [001211] CART19 and CART19 HIilD secreted comparable levels of IFN gamma (Figure 33A) and IL2 (Figure 33B) in response to CD19 positive cells in the absence of lenalidomide. In the presence of lenalide, the levels of IFN gamma and IL2 secreted by CART1I9 HilD cells decreased (Figures 33A and 33B). CART19's ability to secrete cytokines was immune to the addition of lenalidomide (Figures 33A and 33B).
[001212] [001212] In short, this study demonstrates that the addition of the HIilD tag to the CAR19 structure does not affect the expansion capacity of these CARTs in culture. Lenalidomide leads to the reduction of CAR surface expression in T cells that express CAR19-HIilD, in a dose-dependent manner.
[001213] [001213] The activity of CART19 HIilD is comparable with CART19, in the absence of lenalidomide. Cytokine extermination and secretion by CART19.HIilD cells are specific to target cells.
[001214] [001214] In the extermination assay performed here, lenalidomide slightly impairs the ability of CART19-HIilD to exterminate target cells. Under the experimental condition used in this document, the target cells started to die as soon as the CARTs were co-added. The slight change in cell death in Figure 32C is probably due to the fact that the cell death kinetics is
[001215] [001215] Lenalidomide interferes with the ability of CART19.HilD, but not CART19, to secrete cytokines. Example 13: Evaluation of CAR19-HIiID in vivo
[001216] [001216] This study examines the in vivo activity of T cells expressing CAR19-HIilD and its regulation by lenalidomide. Methods Xenograft mouse model
[001217] [001217] Female NOD.Cg-Prkdc * Ҽ [/ 2rg" WSzJ (NSG) mice aged 6 to 8 weeks were purchased from Jackson Laboratories. Animal studies were carried out under protocols approved by the Institutional Animal Care and Use Committee on NIBR. NSG mice were inoculated with 1.0 x 10 6 Nalm-6 luciferized intravenously. A few days later, CAR-T cells were infused intravenously into tumor-bearing mice; unless otherwise specified, lenalidomide was administered orally at the same time.The tumor load was measured by IVIS and quantified as radiance in the region of interest (ROI), which was usually the area of a mouse. Mice were sacrificed by losing more than 20% of the body weight or development of hind limb paralysis Graft vs. host disease was defined in animals indicated as hair loss, behavioral changes and a clear reduction in health not attributable to the sign of Nalm-6 luciferase. Analysis of splenocyte CAR expression
[001218] [001218] The spleens were collected from the mice used in the in vivo efficacy study described above at the end of the study. The harvested spleen was homogenized in a single cell suspension (spleens or cells derived from the spleen were not grouped). The cells were washed with RPMI medium and frozen in 1 ml of freezing medium.
[001219] [001219] Below is the group of mice from which the spleen was collected. Each group had three mice: Group 1 - CART19.HilD (5x10º) Group 2 - CART19-HIilD (5x108) + Lena qd Group 3 - CART19-HIilD (5x108) + Lena bid Group 4 - CART19.HilD (5x108) + Lena +5 Days Results
[001220] [001220] Lenalidomide had little effect on Nalm6 growth in vivo (data not shown).
[001221] [001221] To determine the therapeutic efficacy of CART19.HilD in vivo, tumor-bearing mice were treated with 5.0x106, 2.5x10º or 1.0x10º of CART19.HilD. While 5.0x10º of CART19.HilD produced comparable rates of tumor regression to 2.5x10º of CART19, 2.5x10º of CART19.HilD managed to partially control tumor growth (Figure 34). 1.0x10º of CART19.HilD did not show efficacy (Figure 34). In addition to dose-dependent activities, which were maintained for> 40 days, treatment with lenalidomide at 30 mg / kg bid can completely negate the ability of CART19.HIilD to control tumor growth in vivo (Figure 34). These results contrast with the results obtained in vitro, in the tumor cytolysis assay shown in Figure 32C. The loss of CART cells in peripheral blood after treatment with lenalidomide was also confirmed by flow cytometry (Figure 35).
[001222] [001222] Control of adoptive transfer T cell function in vivo is important to prevent or overcome potential toxicities associated with CART therapy. Thus, it was further investigated whether the activity of CART19.HilD could be canceled after CART19.HilD controlled the tumor. A temporal study of the dose of lena- lidomide was performed on the NSG model with a Nalm6 tumor. Mice treated with lenalidomide immediately after transfer of CART19.HilD lost the ability to control tumor growth in vivo (Figure 36). The mice treated with lenalidomide on day 5 after the adoptive transfer of CART19HIID cells showed tumor recurrence a few days after the administration of lenalidomide (Figure 36). CART19.HIilD activity was comparable with CART189 in the absence of lenalidomide (Figure 36).
[001223] [001223] The expression of CAR in CD3 + cells derived from mouse spleens was analyzed. CAR expression in CD3 cells derived from mice treated with T cells expressing CAR19 or CAR19-HIilD was comparable (Figure 37E). All mice treated with CAR19-HIilD and lenalidomide showed significantly reduced CAR expression in CD3 positive cells derived from the spleen (Figures 37B to 37E). Example 14: CARB label design
[001224] [001224] CARBtag is based on a clamp-shaped sequence derived from IKZF2 that can be used as a degron tag along with Compound | -112 revealed in Table 29.
[001225] [001225] IMID compounds, such as lenalidomide, can induce the degradation of IKZF1 and 3, but not of IKZF2. Compound 1-112 has been identified to specifically degrade IKZF2, but not IKZF1 or IKZF3. Since HilDtag is based on the IKZF1 / IKZF3 clamp format, it can only be degraded by IMiDs. This study explores whether a clamp format based on IKZF2 (CARB label) can be degraded with Compound | -112. Methods
[001226] [001226] Project: The initial sequence of CARBtag comes from IKZF2 CDS (NM 016260). The N part of the label belongs to H130-S174, and the C-terminal belongs to A230-D243. The complete amino acid sequence is: HKRSHTGERPFHCNQCGASFTQAQKGNLLRHIKLH- SGEKPFKCPFCSAGQVMSHHVPPMED (SEQ ID NO: 109)
[001227] [001227] The region underlined above is the C-terminal portion. Like HilDtag, CARBtag is attached to a protein of interest with a 16GS linker (GGGGSGSGGGTGGGGSG (SEQ ID NO: 28)). The 16GS-CARBtag DNA was designed with restriction enzyme sites on each side and was synthesized as a gBlock by Integrated DNA technologies. The DNA sequence is shown below:
[001228] [001228] Cloning: The gBlocks were digested with restriction enzymes as an expression vector with a CMV promoter that directs MITF (NM 000248) with a FLAG tag or CD19 (NM 001770) with a V5 tag, generating these final constructs : CD19-16GS-HilD-V5 (a construct described in Example 5), and CARBtag-16GS-MITF-FLAG.
[001229] [001229] The CTL119-16GS-CARBtag gBlocks were also digested with restriction enzymes, however they were cloned into a Lentiviral mammalian expression vector containing an EF1a promoter. Example 15: Response to the dose of Compound | -112 CARB label, Western blot, flow cytometry and functional JNL assay CAR1I9
[001230] [001230] This study aims to determine the efficacy of the CARB tag in the degradation of CAR19 by measuring Compound | 1-112. Methods
[001231] [001231] Viral production of vector pNGX LV VOO02: HEK293T cells (ATCC CRL-3216) were cultured in DMEM with 10% FBS at 37'C and CO at 5%. The cells were inoculated into 6-well plates coated with collagen in 0.75x106 cells / well in 2ml DMEM, 10% FBS and incubated overnight. On the next day, the DNGX LV VOO02 vector (0.221g) and lentiviral packing mix DNA (0.28pg) (Cellecta CPC-K2A) were mixed with 1.5ul TransIT transfection reagent (Mirus MIR2700) in 55.14] of OptiMEM (Invitrogen 11058021) and added to the cultured cells, which were incubated overnight. On the next day, the medium was removed from the cells and 1 ml of fresh medium was added. The cells were incubated for 72 hours. The viral supernatant was collected from cells and filtered through a 0.45pyM cellulose acetate filter (Corning 430516) and divided into aliquots and stored at -80 ° C.
[001232] [001232] Viral titer: An eight-fold dilution of the virus was performed starting at 1: 3 times using RPMI and 10% FCS. 100u4I of SUPT1 cells were cultured in 2E5 cells / ml in a 96-well flat bottom plate. 50yuI! of diluted virus were added to the duplicate cells. The plate was incubated at 37ºC in CO, overnight. 1004! RPMI medium was added to each well and the plate was returned to the incubator. On Day 4 of transduction, cells were collected and stained for Protein L and the expression of CAR was analyzed using Flow Jo.
[001233] [001233] Cell treatment: Jurkat cells containing an NFAT luciferase reporter were infected with CAR1I9 or CAR19-CARBtag in a multiplicity of infection (MOI) of 4. The cells were expanded for one week before use. The cells were diluted by 0.5x10% 6 in 3 ml in total in 6-well plates. Once the cells were plated, the samples were immediately treated with 10uM, 1UuM, 0.1UM, 0.01UM and 0.001UM of Compound | -112 and DMSO. All cells were collected 24 hours after the initial treatment with the compound for analysis by western blotting and flow cytometry.
[001234] [001234] Western Blot: The cells were pelleted, washed with PBS, and the pellets were lysed with 50 µl of RIPA buffer (Boston Bioproducts “BP-115D) with protease inhibitors (Roche 04693124001). The lysates were centrifuged, the supernatant transferred to new tubes and the protein quantities read by Lowry Assay (BioRad 5000111). Each sample was normalized to 30 µg of total protein in a volume of 20 µl with 4X sample buffer (Thermo Scientific NPOOO07) and 10X reducing agent (Thermo Scientific NPOOOS9). The samples were tested on a 4 to 12% Bis-Tris acrylamide gel (Thermo Scientific WG1402BOX). The gels were tested in duplicate, one for actin and the other for V5 or CD3Z. The gels were transferred to nitrocellulose membranes and the membranes were incubated overnight in 3% milk in TBS-0.1%
[001235] [001235] Flow cytometry: The cells were collected in a bottom plate and washed using 1X PBS. The washed cells were stained with 100 µl of Biotinylated Protein L (Genscript MOO0097) diluted 1: 1000X to 1 µg / ml. The primary antibody was incubated at 4'C for 45 minutes. After incubation, the cells were washed using PBS. The cells were incubated at 4'C with PE-conjugated streptavidin (Jackson Lab 016-110-084) in dilution 1: 300X for 30 minutes. The cells were washed twice with PBS and suspended in 100yu! of fixation buffer (2% Paraformaldehyde in PBS) for 10 minutes at room temperature. The fixed cells were washed with PBS and suspended in 150 µl of PBS. These cells were then acquired using the BD LSRF Fortessa cell analyzer. Dead cells were excluded based on size using the FSC and SSC graph. Live cells were analyzed for PE CAR expression. The results of flow cytometry were identified using the uncolored parental JNL cell line and 10,000 events were recorded for each sample.
[001236] [001236] Functional CAR Assay for NFAT luciferase (JNL) in Jurkat: The CAR1I9-CARB label cells were diluted to 0.5x10º6 in 20ml of RPMI 1640 medium (Thermo Fisher Scientific 11875-085) 10% FBS 1X pen / strep. 20u! (0.5xX106 cells) from this cell line were plated in 384-well plates with a solid white background (Greiner789163-G). Compound 1-112 was added to the 384-well plate in an 8-point 2-log dilution with 10uUM of maximum final concentration using the LaBcyte ECHO acoustic distributor. The plates were incubated for 15 hours at 37 ° C, 5% CO ». K562 and Nalm6 cells were resuspended in 0.5x10º6 cells / ml. Half of the cells treated with Compound 1-112 of 8 points received 20yu! of K562 cells and the other half received 20ul of Nalm6 cells. The cells were stored at 37'C, incubator with 5% CO, for eight hours. The samples were then treated with 40yu! L (1: 1) Bright Glo (Promega E2620) and the luminescence was read using Perkin Elmer's Viewlux with a 20 second exposure. Results
[001237] [001237] CARI9-CARBtag protein levels show a dose-dependent reduction after 24 hours of treatment with Compound 1-112 (Figure 38A). Similarly, treatment with Compound 1-112 also reduced CAR surface expression in JNL CAR1I9-CARBtag cells (Figure 38B). As shown in the functional JNL CAR assay described above, CAR1I9-CARBtag cells respond only to CD19 + Nalm6 cells and this response is reduced in a dose-dependent manner with increasing amounts of treatment with the compound (Figure 38C). Example 16: Use of CARB-tagq and HilDtag as an orthogonal system for protein breakdown
[001238] [001238] This study aims to determine whether CARB-labeled proteins can be degraded by treatment with Compound 1-112. It is also examined when a protein labeled with HIilD and a protein labeled with CARB are coexpressed, whether the expression of each protein can be regulated independently with treatment with lenalidomide (for protein labeled with HilD) or with the compound treatment | -112 (for CARB-labeled protein).
[001239] [001239] Expression and treatment of cellular genes: HEK293T cells (ATCC CRL-3216) were cultured in DMEM with 10% FBS and pen / strep at 37'C and CO to 5%. The cells were transfected with CARBtag-16GS-MITF-FLAG or CARBtag-16GS-MITF-FLAG and CD19-16GS-HilD-V5 using FuGene HD (Promega E2311) using a FuGene HD to DNA ratio of 3: 1. The transfected cells were incubated for 24 hours, followed by treatment with lenalideide or Compound | -112 in a 4-point log dilution starting at the final 10 µM. The cells were treated with the indicated compound for 24 hours and then were prepared for western blotting.
[001240] [001240] Western blot: 24 hours after treatment with the compound, the cells were pelleted, washed with PBS, and the pellets were lysed with 50 µl of RIPA buffer (Boston Bioproducts BP-115D) with protease inhibitors ( Roche 04693124001). The lysates were centrifuged, the supernatant transferred to new tubes and the protein quantities read by Lowry Assay (BioRad 5000111). Each sample was normalized to 30ug of total protein in a volume of ul with 4X sample buffer (Thermo Scientific NPOOO7) and 10X reducing agent (Thermo Scientific NPOOO9). The samples were tested on a 4 to 12% Bis-Tris acrylamide gel (Thermo Scientific WG1402BOX). The gels were tested in triplicate (one for each antibody). The gels were transferred to nitrocellulose membranes and the membranes were incubated overnight in 3% milk in TBS-0.1% Tween-20 with one of the following three antibodies: anti-mouse V5 (Thermo Scientific MA5-15253 ) with 1: 1000 dilution; mouse anti-actin (Sigma Aldrich A5441) with dilution 1: 10,000; and anti-mouse M2 FLAG (BD 551034) with 1: 1000 dilution. The spots were washed the next day in TBS-0.1% Tween-20, placed in 3% milk in TBS-0.1% Tween-20 with anti-
[001241] [001241] MITF marked with CARB was effectively degraded by Compound | -112, but not by lenalidomide (Figure 39). In contrast, CD19-HilDtag expression remained constant under different doses of Compound | -112 treatment (data not shown). Example 17: Characterization of HilD tag fusion construct with BCMA CAR
[001242] [001242] This study aims to determine whether the HilD tag can be used to degrade other CARs, for example, a BCMA CAR. The BCMA CAR-16GS ligand-HilD tag sequence is shown below. The HilD tag has a single underline. The 16GS ligand has a double underline. The signaling peptide is shown in italics. MALPVTALLLPLALLLHAARPEVQLVESGGGLVQPGGSLRLSCAVSG FALSNHGMSWVRRAPGKGLEWVSGIVYSGSTYYAASVKGRFTISRD NSRNTLYLQMNSLRPEDTAIY YCSAHGGESDVWGQGTTVTVSSASG GGGSGGRASGGGGSDIQLTASPSSLSASVGDRVTITCRASQSISSYL NWYQQKPGKAPKLLIYAASSLASGVPSRFSGSGSGTDFTLTISSLQP EDFATYYCQQASYSTPYTFGQGTKVEIKTTTPAPRPPTPAPTIASQPLS LRPEACRPAAGGAVHTRGLDFACDIYIWAPLAGTCGVLLLSLVITLYC KRGRKKLLYIFKAPFMRPVQTTQEEDGCSCRFPEEEEGGCELRVKF SRSADAPAYQQGQANQLYNELNLGRREEYDVLDKRRGRDPEMGGKP RRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLS TATKDTYDALHMQALPPRGGGGSGGGGTEGGGSEGMHKRSHTGER
[001243] [001243] Viral production of pELPS vector: LentiXx-293T cells
[001244] [001244] Viral titer: An eight-fold dilution of the virus was performed starting at 1: 3 times using RPMI and 10% FCS. 100ul of SUPT1 cells were cultured in 2E5 cells / ml in a 96-well flat bottom plate. 50 µl of diluted virus was added to the cells in duplicate. The plate was incubated at 37ºC in CO> overnight. 1004! RPMI medium was added to each well and the plate was returned to the incubator. On Day 4 of transduction, cells were collected, stained for CAR expression and analyzed using Flow Jo.
[001245] [001245] Cell treatment: Jurkat cells containing an NFAT luciferase reporter were infected with BCMACAR-HIiLDtag in a multiplicity of infection (MOI) of 4. The cells were expanded
[001246] [001246] Flow cytometry: The cells were collected in a lower plate and washed using 1X PBS. The washed cells were stained with Alexa flour 647 anti-BCMACAR conjugated antibody (Bio-Legend t94581) and diluted 1: 300X. The primary antibody was incubated at 4'C for 45 minutes. After incubation, the cells were washed twice with PBS and suspended in 100ul of Fixation buffer with 2% Paraformaldehyde for 10 minutes at room temperature. The fixed cells were washed with PBS and suspended in 1504! of PBS. These cells were then acquired using the Fortessa instrument. Dead cells were excluded based on size using the FSC and SSC graph. Live cells were analyzed for their expression of APC CAR. The results of flow cytometry were identified using the uncolored parental JNL cell line and 10,000 events were recorded for each sample.
[001247] [001247] Functional CAR Assay for NFAT luciferase (JNL) in Jurkat: The BCMACAR HIID tag cell line was diluted to 0.5x10º6 in 20ml of RPMI 1640 medium (Thermo Fisher Scientific 11875-085) 10% FBS 1X pen / strep. 20u! (0.5xX106 cells) from this cell line were plated in 384-well plates with a solid white background (Greiner789163-G). Lenalidomide was added to the 384-well plate in an 8-point Y4-log dilution with 10UM of maximum final concentration using the LaBcyte ECHO acoustic distributor. The plates were incubated for 15 hours at 37'C, 5%
[001248] [001248] As shown in Figure 40A, treatment with lena- lidomide leads to a dose-dependent reduction in BCMACAR HIID label surface expression. Jurkat NFAT luciferase cells that express the BCMACAR HILD tag respond to BCM expression KMS11 cells, as evidenced by an increase in luciferase activity, which can be inhibited in a dose-dependent manner with increasing amounts of lenalide-mide treatment (Figure 40B). Example 18: Synthesis of exemplary compounds
[001249] [001249] The compounds of the present description can be prepared in various ways well known to those skilled in the technique of organic synthesis. As an example, the compounds of the present description can be synthesized using the methods described below, in combination with synthetic methods known in the art of synthetic organic chemistry, or variations thereof as found by those skilled in the art. Preferred methods include, but are not limited to, the methods described below.
[001250] [001250] The compounds of the present description can be synthesized following the steps described in Scheme | which comprise different assembly sequences of intermediates A-1, A-2, A-3, AH, A-5, A-5a, A-6a, A-6b and A-7. The starting materials are commercially available or produced by procedures known in the reported literature or as illustrated. Scheme 1 is intended to provide general guidance in conjunction with the preparation of a selection of the compounds of the invention. The person skilled in the art could understand that the steps shown in the Scheme can be modified or optimized using general knowledge of organic chemistry to prepare various compounds of the invention.
[001251] [001251] The general way of preparing the Compounds of Formula (Ill), where === is a double bond and R3 is absent and where ==== - is a single bond and R; 3 is hydrogen using intermediates A-1, A-2, A-3, A-4, A-5, A-5a, A-6a, A-6b and A-7 are described in the Scheme
[001252] [001252] Hydrogenation of A-5 in the presence of an appropriate catalyst (for example, Pd / C or PtO> z) in a solvent (for example, DMF) and under a hydrogen gas atmosphere provides A-Sa. Deprotection of A-5a using a strong acid such as trifluoroacetic acid (TFA) or hydrochloric acid (HCI) in a solvent (for example, tetrahydrofuran (THF), 1,2, -dichloroethane, dioxane or dichloromethane (DCM)) optionally at elevated temperature it supplies A-6b. The reducing amination of A-6b with aldehyde or ketone A-7 provides a compound of Formula (Ill) in which - === --- is a single bond and R3 is hydrogen. Alternatively, compounds of Formula (Ill) in which ==== - = is a single bond and R3 is hydrogen can be obtained by alkylating A-6b with an A-7 alkyl halide in the presence of a base ( for example, NEt3, Cs2CO ;, etc.), in a solvent (for example, DCM, DMF, etc.) and optionally at elevated temperature.
[001253] [001253] A mixture of enantiomers, diastereomers and cis / trans isomers resulting from the process described above can be prepared in its unique components by the chiral salt technique, chromatography using normal phase, reverse phase or chiral column, depending on the nature of the separation.
[001254] [001254] Any racemates resulting from compounds of the present description or from intermediates can be solved in the optical antipodes through known methods, for example, by separating the diastereomeric salts thereof, obtained with an optically acid or base active, and release of the optically active acidic or basic compound. In particular, a basic fraction can thus be employed for the resolution of the compounds of the present description in their optical antipodes, for example, by fractional crystallization of a salt formed with an optically active acid, for example, tartaric acid, dibenzoyl tartaric acid , diacetyl tartaric acid, di-O, O'-p-toluyl tartaric acid, mandelic acid, malic acid or camphor-sulfonic acid. The racemic compounds of the present description or racemic intermediates can also be resolved by chiral chromatography, for example, high pressure liquid chromatography (HPLC) with the use of a chiral adsorbent.
[001255] [001255] Any mixtures resulting from stereoisomers can be separated based on the physical-chemical differences of the constituents, in the pure or substantially pure optical or geometric isomers, diastereoisomers, racemates, for example, by chromatography and / or fractional crystallization.
[001256] [001256] It should be understood that, in the description and formula shown above, the various groups X1, R1, R2, Rx, n and y and other variables are as described above, except where otherwise indicated. In addition, for synthetic purposes, the compounds of Scheme 1 are only representative with radicals chosen to illustrate the general synthetic methodology of the compounds of Formula (Ill), as defined herein. Analytical Methods, Materials and Instrumentation
[001257] [001257] Unless otherwise noted, reagents and solutions
[001258] [001258] Mass spectra (ESI-MS) were collected using a Waters System (Acquity UPLC and a Micromass ZQ mass spectrometer) or Agilent-1260 Infinity (6120 Quadrupole); all reported masses are m / z of protonated parent ions unless otherwise reported. The sample was dissolved in a suitable solvent such as MeCN, DMSO or MeOH and was injected directly into the column with the use of an automated sample manipulator. The analysis is performed in the Waters Acquity UPLC system (Column: Waters Acquity UPLC BEH C18 1.7 um, 2.1 x 30 mm; Flow rate: 1 ml / min; 55 ° C (column temperature); Solvent A: acid formic 0.05% in water, Solvent B: formic acid 0.04% in MeOH; gradient 95% Solvent A from 0 to 0.10 min; 95% Solvent A to 20% Solvent A from 0, 10 to 0.50 min; 20% Solvent A to 5% Solvent A from 0.50 to 0.60 min; 5% retention of Solvent A from 0.6 min to 0.8 min; 5% Solvent A to 95% Solvent A from 0.80 to 0.90 min, and 95% retention of Solvent A from 0.90 to 1.15 min Abbreviations used in the following examples and other parts of this document are:
[001259] [001259] To a stirred solution of methyl 4-bromo-2- (bromomethyl) benzoate (A-1, 15 g, 48.7 mmol) in DMF (150 ml) were added 3-aminopiperidine-2,6-dione -HCI (A-2, 6.9 g, 53.6 mmol) and K2CO; 3 (20.2 g, 146.1 mmol). The resulting mixture was heated to 70 ºC for 16 h, after such time, the reaction mixture was cooled to room temperature and then concentrated until dry. Water was then added and the mixture stirred at room temperature for 30 min. The resulting solid was filtered and washed with ether and ethyl acetate and dried under vacuum filtration to produce A-10 (10.6 g, 32.9 mmol, 67% yield). MS [M + H] * = 323.0. * 'H NMR (400 MHz, DMSO-ds) 5 10.99 (s, 1H), 7.91-7.88 (m, 1H), 7.72 (dd, J = 8.1, 1.6 Hz, 1H), 7.67 (d, J = 8.0 Hz, 1H), 5.11 (dd, JU = 13.3, 5.1 Hz, 1H), 4.47 (d, J = 17 , 7 Hz, 1H), 4.34 (d, J = 17.7 Hz, 1H), 2.98-2.83 (m, 1H), 2.65-2.55 (m, 1H), 2 , 45-2.29 (m, 1H), 2.01 (dtd, J = 12.7, 5.3, 2.3 Hz, 1H). Step 2. tert-Butyl 4- (2- (2,6-dioxopiperidin-3-yl) -1-oxoisoindolin-5-yl) -3,6-dihydro-pyridine-1 (2H) -carboxylate (A -12)
[001260] [001260] A solution of A-10 (1.8 g, 5.6 mmol) in DMF (10 ml) in a sealed tube was purged with argon for 5 min before the addition of pinacol ester of 3,6-di acid -hydro-2H-pyridine-1-tert-butoxycarbonyl-4-boronic acid (A-11, 2.2 g, 7.2 mmol), K3POa (1.42 g, 6.7 mmol) and Pd (dppf) CI2 : DCM (227 mg, 0.28 mmol). The reaction mixture was again purged with argon for 5 min and then heated to 90 ºC for 16 h. After that time, the reaction mixture was cooled to room temperature and then concentrated under reduced pressure. Water was added to the residue, which was then extracted with EtOAc. The organic layer was washed with brine, dried over Na> SO:;, filtered and then concentrated under reduced pressure. The crude product was purified by chromatography on silica gel, eluting with 70 to 80% EtOAc in hexanes, to provide A-12 as a solid (1.0 g, 2.4 mmol, 42% yield). MS [M + H] * = 426.3. Step 3. 4- (2- (2,6-Dioxopiperidin-3-yl) -1-oxoisoindolin-5-yl) piperidine-1-tert-butyl carboxylate (A-13)
[001261] [001261] To a stirred solution of A-12 (1.0 g, 2.35 mmol) in DMF (20 ml), 10% Pd / C (150 mg) was added, and the mixture was stirred under an atmosphere of hydrogen (balloon) at rt for 6 h. The reaction mixture was then filtered through a bed of Celiteº filter aid. The filtrate was concentrated under reduced pressure yielding A-12 as a solid (0.85 g, 1.97 mmol, 84% yield). MS [M-tBu] * = 372.3. '"H NMR (400 MHz, CDCIs) 5 8.40 (s, 1H), 7.81 (d, J = 7.9 Hz, 1H), 7.32 (d, J = 8.0 Hz, 1H ), 7.29 (s, 1H), 5.22 (dd, J = 13.3, 5.1 Hz, 1H), 4.46 (d, J = 16 Hz, 1H), 4.31 (d, J = 16.1 Hz, 1H), 4.27 (d J = 16.2 Hz, 2H), 2.97-2.67 (m, 5H), 2.41-2.26 (m , 1H), 2.23-2.13 (m, 1H), 1.83 (d, J = 12.6 Hz, 2H), 1.71-1.55 (m, 2H), 1.48 ( s, 9H) Step 4. 3- (1-ox0-5- (piperidin-4-yl) isoindolin-2-yl) piperidine-2,6-dione hydrochloride (1-155):
[001262] [001262] To a stirred solution of A-12 (0.85 g, 2.0 mmol) in dioxane (10 ml), 4 N HCI in dioxane (5.0 ml) was added. The reaction mixture was then stirred at room temperature for 2 h. The reaction mass was concentrated under reduced pressure to provide the HCl salt of the desired compound | -155 as a solid (0.65 g, 1.8 mmol, 90% yield, hydrochloride salt). MS [M + H] * = 328.3. *H
[001263] [001263] A stirred solution of A-10 (150 mg, 0.46 mmol) in DMF (5 ml) in a sealed tube was purged with argon for 5 min before adding 2,2,6,6- tetramethyl-4- (4,4,5,5-tetramethyl-1,3,2-dioxabo-rolan-2-yl) piperidine (A-14, 185 mg, 0.69 mmol), Cs2CO; 3 (300 mg , 0.92 mmol) and Pd (dppf) CIl2: DCM (19 mg, 0.02 mmol), and the resulting mixture was again purged with argon for 5 min. The reaction mixture was then heated to 90 ºC for 5 h, after such time, the reaction mixture was cooled to room temperature, water was added and the mixture was extracted with EtOAc. The organic layer was washed with brine, dried over Na2SO2, filtered, and then concentrated under reduced pressure. The crude material was purified by chromatography on silica gel (eluting with 15% MeOH / DCM) to produce A-15 as a solid (35 mg, 0.092 mmol, 20% yield). MS [M + H] * = 382.3. Step 2. 3- (1-0x0-5- (2,2,6,6-tetramethylpiperidin-4-yl) isoindolin-2-yl) piperidine-2,6-dione (1-171)
[001264] [001264] To a stirred solution of 3- (1-0x0-5- (2,2,6,6-tetramethyl-
[001265] [001265] The following compounds were prepared according to the general protocol presented in Scheme 1 and the examples provided above:
[001266] [001266] To a stirred solution of 3-hydroxy-8-azabicyclo [3,2,1] octane-8-carboxylate (A-16, 570 mg, 2.51 mmol), EtadN (0.52 ml, 3.8 mmol) and DMAP (61 mg, 0.50 mmol) in DCM (5 ml) TsCI (574 mg, 3.01 mmol) was added and the resulting mixture was stirred overnight at room temperature. The reaction mixture was then quenched with NaHCO; aqueous saturated and extracted with DCM (3x). The combined organic phases were dried with Na2SO2, filtered and concentrated, and the raw material was purified by chromatography on silica gel eluting with 0% to 40% EtOAc in heptane to produce A-17 (91 mg, 0, 22 mmol, 9% yield) as a solid. 1H NMR (400 MHz, Chloroform-d) 5 7.79 (d, J = 8.3 Hz, 2H), 7.36 (d, J = 8.5 Hz, 2H), 4.83 (t, J = 5.0 Hz, 1H), 4.16 (s, 2H), 2.47 (s, 3H), 2.12-2.02 (m, 4H), 2.00-1.90 (m, 2H), 1.84 (d, J = 15.3 Hz, 2H), 1.45 (s, 9H). Step 2. tert-Butyl 3- (2- (2,6-dioxopiperidin-3-yl) -1-oxoisoindolin-5-yl) -8-azabicyclo [3.2, TJoctan-8-carboxylate (A-20 )
[001267] [001267] To a stirred suspension of A-18 (56 mg, 0.15 mmol), 56b (69 mg, 0.18 mmol), NIBre (DME) (4.7 mg, 0.015 mmol), 4.4 ' -di-tert-butyl-2,2'-dipyridyl (4.1 mg, 0.015 mmol), KI (25 mg, 0.45 mmol), and manganese powder (17 mg, 0.30 mmol) in DMA ( 0.7 ml) under a nitrogen atmosphere 4-ethylpyridine (0.017 ml, 0.415 mmol) was added and the resulting mixture was stirred vigorously at 80 ºC for 4 hours. The reaction mixture was then diluted with MeCN and filtered through a Celiteº filter aid filter and eluting with MeCN. The filtrate was concentrated to dry by azeotropy with heptane. The crude material was purified by chromatography on silica gel eluting with 0% to 5% MeOH in DCM to provide A-20 (38.4 mg, 0.085 mmol, 56% yield) as a solid. MS [M + H] * = 454.5. 'H NMR (400 MHz, Chloroform-d) 5 8.58 (s, 1H), 7.80 (dd, J = 7.9, 0.6 Hz, 1H), 7.32 (dd, J = 7 , 9, 1.4 Hz, 1H), 7.29 (s, 1H), 5.23 (dd, JU = 13.3, 5.1 Hz, 1H), 4.46 (d, J = 16, 0 Hz, 1H), 4.39-4.24 (m, 3H), 3.20 (tt, J = 11.8, 5.2 Hz, 1H), 2.94-2.74 (m, 2H ), 2.34 (gd, J = 12.8, 5.6 Hz, 1H), 2.23-2.13 (m, 1H), 2.09-2.02 (m, 2H), 1, 90 (t, J = 12.9 Hz, 2H), 1.80 (q, J = 8.0, 6.6, 6.2 Hz, 2H), 1.76-1.69 (m, 2H) , 1.51 (s, 9H). Step 3. 3- (5- (8-azabicyclo [3,2,1] octan-3-yl) -1-oxoisoin-dolin-2-yl) piperidine-2,6-dione hydrochloride (1-188)
[001268] [001268] To a stirred solution of A-20 (38 mg, 0.084 mmol) in THF (1 ml) was added 4 M HCl in dioxane (0.7 ml, 2.8 mmol) and the resulting mixture was stirred for 3 hours at 60 ºC. The formation of a white precipitate was observed. The reaction mixture was then diluted with Et2O and filtered. The precipitate was washed with Et2O and then dried to provide the hydrochloride salt of 1-188 (31.9 mg, 0.082 mmol, 98%) as a solid. MS [M + H] * = 354.3. * H NMR (400 MHz, DMSO-ds) 5 10.98 (s, 1H), 9.18 (s, 1H), 7.69 (dd, J = 7.8, 2.3 Hz, 1H), 7.56 (s, 1H), 7.50 (d, J = 7.9 Hz, 1H), 5.10 (ddd, J = 13.2, 5.2, 2.1 Hz, 1H), 4 , 45 (d, J = 18.1 Hz, 1H), 4.30 (dd, J = 17.3, 2.2 Hz, 1H), 4.03 (s, 2H), 3.26-3, 21 (m, 1H), 2.92 (tt, J] = 14.0, 5.2 Hz, 1H), 2.67-2.54 (m, 1H), 2.45-2.31 (m , 1H), 2.17 (t J = 13.1 Hz, 2H), 2.09-1.92 (m, 5H), 1.89-1.73 (m, 2H).
[001269] [001269] To a stirred solution of 1-188 (20 mg, 0.051 mmol) and benzaldehyde (0.016 ml, 0.154 mmol) in DMF (1 ml) was added sodium triacetoxyborohydride (33 mg, 0.15 mmol) in one portion and the resulting mixture was stirred vigorously at room temperature overnight. A drop of HCOOH was then added and the reaction mixture was concentrated under reduced pressure. The raw material was purified by reverse phase HPLC (eluting with MeCN / H2O0 with 0.1% formic acid) and the lyophilized product to produce the 1-265 format salt (15.0 mg, 0.031 mmol, 60% yield) as a solid. MS [M + H] * = 444.3. * H NMR (400 MHz, DMSO-ds) 5 10.98 (s, 1H), 8.25 (s, 1H), 7.64 (d, J = 7.9 Hz, 1H), 7.52 ( s, 1H), 7.42 (d, J = 8.1 Hz, 3H), 7.35-7.31 (m, 2H), 7.24 (t, J = 7.3 Hz, 1H), 5.10 (dd, JU = 13.0, 5.0 Hz, 1H), 4.42 (d, J = 17.2 Hz, 1H), 4.29 (d, J = 17.1 Hz, 1H ), 3.61 (s, 2H), 3.25 (s, 2H), 3.13-3.01 (m, 1H), 2.91 (ddd, J = 17.9, 13.2, 5 , 3 Hz, 1H), 2.59 (d, J = 17.0 Hz, 1H), 2.46-2.31 (m, 1H), 2.14-1.94 (m, 3H), 1 , 85 (t, / J = 12.4 Hz, 2H), 1.76 (d, J = 7.8 Hz, 2H), 1.63 (d, J = 12.7 Hz, 2H).
[001270] [001270] Compound | -260 was synthesized according to the route described in Example 18-3 (MS [M + H] * = 404.2). Example 18-4: Diastereomers of 3- (5- (1-benzylazepan-4-yl) -1- oxoisoindolin-2-yl) piperidine-2,6-dione (1-190) and (1-273) <L bo fas: FP O SA, dm & d Sem Em O eee SOTO
[001271] [001271] To a stirred solution of A-10 (3.0 g, 9.28 mmol) in DMF (20 ml) in a sealed tube, bis (pinacolate) diboro (A-21, 2.6 g, 10.2 mmol), KOAc (2.379, 27.9 mmol) and PdCl2 (dppf) 2 (0.22 g, 0.28 mmol). The reaction mixture was purged with argon for min, sealed and then heated to 100 ºC for 16 h. Water was added to the reaction mixture and stirred at room temperature for 15 min. The solid was precipitated, filtered and dried in vacuo to produce A-22a as a solid (2.3 g, 6.2 mmol, 66% yield). MS [M + H] * = 371.0. Step 2: tert 5- (2- (2,6-dioxopiperidin-3-yl) -1-oxoisoindolin-S-yl) -2,3,4,7-tetrahydro-1H-azepine-1-carboxylate -butyl (A-23) -5 - (((trifluoromethyl) sulfonyl) oxy) -2,3,4,7-tetrahydro-1H-azepine-1-carboxylate A-22b was prepared as reported in PCT Order Publication No. 2007/111904.
[001272] [001272] To a stirred solution of A-22a (1.0 g, 2.70 mmol) in DMF (10.0 ml) in a sealed tube, 5 - (((trifluoromethyl) sulfonyl) oxide) was added) -2,3,4,7-tert-butyl tetrahydro-1H-azepine-1-carboxylate (A-22b, 1.19 g, 3.24 mmol), Pd (PPh3) 4 (0.16 9 , 0.43 mmol) and Na2CO; (0.85 g, 8.10 mmol). The mixture was purged with argon for 5 min and then sealed and heated to 100 ºC for 3 h. After that time, the reaction was cooled, and water added before extraction with EtOAc. The organic layer was dried with Na2SO2, filtered, concentrated under reduced pressure and purified by silica gel chromatography (eluting with 60 to 70% EtOAc / hexanes) to provide A-23 as a solid (350 mg, 0.796 mmol, 29% yield). MS [M + H] * = 440.0. Step 3. tert-Butyl 4- (2- (2,6-Dioxopiperidin-3-yl) -1-oxoisoindolin-5-yl) azepane-1-carboxylate (A-24).
[001273] [001273] To a stirred solution of A-23 (0.35 g, 0.80 mmol) in
[001274] [001274] Chiral separation of A-24 (350 mg) was performed using a 5.0 uy Kinetex column (150 mm X 21 mm), with eluent consisting of the mobile phase A = 0.05% TFA in water; mobile phase B = acetonitrile and a flow rate of 20 ml / min at 25 ºC with 20 to 70% mobile phase B: mobile phase A over 20 min. Under these conditions, two compounds were isolated A-24 (peak 1) Ta = 11.64 min and A-24 (peak 2) Ta = 17.41 min). The fractions corresponding to peak 1 and peak 2 were collected and concentrated under reduced pressure, then neutralized with saturated aqueous NaHCO solution; before extraction with DCM. The organic layers were combined, dried with Na2SO4 ;, filtered and concentrated to dry providing peak 1 (50 mg) and peak 2 (45 mg) as white solids. MS [M + H] * = 442.0. Step 4b: 3- (5- (azepan-4-yl) -1-oxoisoindolin-2-yl) piperidine-2,6-dione (I-166 & 1-167)
[001275] [001275] To a stirred solution of A-24 (peak 1) (50 mg, 0.113 mmol) in dioxane (2.0 ml) at 0 ° C, 4 M HCl in dioxane (0.5 ml) was added. The reaction was then allowed to stir and warm to room temperature over 2 h. The reaction mixture was then concentrated under reduced pressure to provide diastereomer A (40 mg, 0.106 mmol, 94%, hydrochloride salt). MS [M + H] * = 342.3. * H NMR (CD3OD, 300 MHz): 5 7.74 (d, J = 8.1 Hz, 1H), 7.49 (1H, s), 7.43 (d, J
[001276] [001276] To a stirred solution of A-24 (peak 2) (40 mg, 0.091 mmol) in dioxane (2.0 ml) at 0 ° C, 4 M HCl in dioxane (0.5 ml) was added. The reaction was then allowed to stir and warm to rt over 2 h. The reaction mixture was then concentrated under reduced pressure to provide diastereomer B (30 mg, 0.079 mmol, 87% yield, hydrochloride salt). MS [M + H] * = 342.4. * H NMR (CD3OD, 300 MHz): 5 7.74 (d, J = 7.5 Hz, 1H), 7.49 (s, 1H), 7.42 (d, J = 7.8 Hz, 1H ), 5.15 (dd, J = 13.5, 5.1 Hz, 1H), 4.47-4.45 (d, 2H), 3.74-3.71 (m, 1H), 3, 67-3.62 (m, 3H), 3.58-3.55 (m, 1H), 3.43-3.38 (m, 2H), 3.02 (m, 1H), 2.90- 2.78 (m, 2H), 2.51-2.48 (m, 1H), 2.17-2.08 (m, 5H), 2.09-1.87 (m, 1H). Step 5. Diastereomers of 3- (5- (1-benzylazepan-4-yl) -1-oxoisoindolin-2-yl) piperidine-2,6-dione (1-190 and 1-273)
[001277] [001277] Compound | -190 was prepared from 1-166 (80 mg, 0.21 mmol) and benzaldehyde (27 mg, 0.25 mmol) by means of reducing amination. After complete consumption of the starting materials, the crude reaction mixture was concentrated under reduced pressure, and saturated aqueous NaHCO; 3 was added. The resulting mixture was extracted with DCM, and the organic layer was dried with Na2SO4, filtered and concentrated to dryness. The resulting solid was washed with ether (5 ml) and EI! OAc (0.1 ml) providing 1 | 1-190 as a solid (55 mg, 0.13 mmol, 60% yield). Absolute stereochemistry is not known and has been arbitrarily attributed. MS [M + H] * = 439.1. * H NMR (CD3OD, 600 MHz): 5 7.69 (d, J = 5.2 Hz, 1H), 7.44 (s, 1H), 7.39-7.36 (m, 3H), 7 , 32- 7.30 (m, 2H), 7.26-7.24 (m, 1H), 5.12 (dd, J = 8.8, 3.2 Hz, 1H), 4.47 (d , J = 11.6 Hz, 1H), 4.41 (d, J = 11.2 Hz, 1H), 3.71 (2H, s), 2.98-2.97 (m,
[001278] [001278] Compound 1-273 was prepared from 1-167 (80 mg, 0.21 mmol) and benzaldehyde (27 mg, 0.25 mmol) in a similar manner as described above for 1-190. 1-273 was isolated as a solid (55 mg, 0.13 mmol, 60% yield). Absolute stereochemistry is not known and has been arbitrarily attributed. MS [M + H] * = 439.1. * H NMR (DMSO-des, 400 MHz): 5 11.0 (1H, s), 7.62 (d, J = 5.2 Hz, 1H), 7.46 (s, 1H), 7.38 -7.32 (m, 5H), 7.24-7.23 (m, 1H), 5.09 (dd, J = 8.8, 3.6 Hz, 1H), 4.31 (d, J = 11.6 Hz, 1H), 4.28 (d, J = 11.6 Hz, 1H), 3.65 (d, J = 9.1 Hz, 1H), 3.63 (d, J = 9 , 2 Hz, 1H), 2.96-2.88 (m, 2H), 2.76-2.69 (m, 1H), 2.67-2.62 (m, 3H), 2.61 2.50 (m, 2H), 2.46-2.36 (m, 3H), 1.99 (m, 2H), 1.82 (m, 2H). Example 18-5: 3- (5- (1-benzyl-2-0x0-1,2-dihydropyridin-4-yl) -1-0x0-isoindolin-2-yl) piperidine-2,6-dione ( 1-192) o Br o A Bn o SeNg, A-22a A-25 1-192
[001279] [001279] To a stirred suspension of A-22a (500 mg, 1.35 mmol), A-25 (428 mg, 1.62 mmol) and KCO3 in DMF (5 ml) was added PdCl2 (dppf) - DCM ( 55 mg, 0.07 mmol) and the resulting mixture was sparged with argon for 10 min and then stirred at 130 ° C for 90 min. After complete consumption of the starting material, the reaction mixture was abruptly cooled with ice water and extracted with EtOAc (3 x 50 ml). The combined organic extracts were washed with brine, dried with Na2SO. and concentrated under reduced pressure. The crude material was purified by chromatography on silica gel eluting with 5% MeOH in DCM to provide | -192 as a solid (20 mg, 0.46 mmol, 35% yield). MS [M + H] * = 427.8. * H NMR (400 MHz, DMSO-ds): 5 10.98 (s, 1H), 7.94 (s, 1H), 7.90 (d, J = 7.6 Hz,
[001280] [001280] The following compounds were synthesized according to the protocol described in Example 18-5: | -184: MS [M + H] "= 356.1. 1-186: MS [M + H] * = 342, 1. 1-192: MS [M + H] * = 427.8 Example 18-6: 3- (1-0x0-5- (1,2,3,4-tetrahydroquinolin-4-yl) isoindo - lin-2-yl) piperidine-2,6-dione (1-196) o and DD. FT) "á O a a -” o O Step 1: 3- (1-0x0-5-vinylisoindolin-2-yl) piperidine-2,6-dione (A-26)
[001281] [001281] To a solution of A-10 (1.5 g, 4.66 mmol) and tributyl (vinyl) stannane (2.04 ml, 6.95 mmol) in dioxane (15 ml) was added PdCl2 ( PPh3) 2 (162 mg, 0.23 mmol) and the resulting mixture was purged with argon for 10 min and then stirred at 110 ° C for 1 h in the microwave. After complete consumption of the starting material, the reaction mixture was quenched with water and extracted with EtOAc (2 x 50 ml). The combined organic extracts were washed with brine, dried with Na2SO, and concentrated under reduced pressure. The obtained crude material was purified by chromatography on silica gel eluting with 90% EtOAc in hexane. The pure fractions were collected and evaporated under reduced pressure to provide A-26 as a solid (500 mg, 1.85 mmol, 40% yield). MS [M + H] * = 271.2. Step 2: 3- (1-0x0-5- (1,2,3,4-tetrahydroquinolin-4-yl) isoindolin-2-yl) pipe-ridina-2,6-dione (1-196)
[001282] [001282] To a solution of A-26 (200 g, 0.74 mmol) and (azidome-
[001283] [001283] Compound | -197 was synthesized in the same manner as described above in Example 18-6. 1-197: MS [M + H] * = 466.2. EQUIVALENTS
[001284] [001284] The disclosures of each and all patents, patent applications and publications cited in this document are thus incorporated into this document as a reference in its entirety. Although this invention was revealed with reference to specific aspects, it is evident that other aspects and variations of this invention can be conceived by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be interpreted to include all of these aspects and equivalent variations.

权利要求:
Claims (353)
[1]
1. Fusion polypeptide, characterized by the fact that it comprises a compound of Formula (1) (COF1 / CRBN-binding polypeptide (cereblon) and a heterologous polypeptide, for example, a heterologous mammalian bacterial or viral polypeptide, compound of Formula (I) is: (Rn Ç
DO RERo (O) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where: XéOousS; R 'is C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-Cs6 heteroalkyl, carbocicyl, heterocycyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $; each of R º and Rº º is independently hydrogen or C1-C6 alkyl; or R º and R , together with the carbon atom to which they are attached, form a carbonyl group or a thiocarbonyl group; each of R3 is independently C1-Cs alkyl, C2-C6 alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) Rô, - C (O0) ORº, -OR8, -N ( Rº) (RP), -C (O) N (RNRO), -N (R) C (O) RA, -S (O) .RE, -S (O) .N (Rº NR ) Or -N (Rº) S (O)., RF, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R $; each Rº is independently C1-Cçs alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-Cs heteroalkyl, halo, cyano, oxo, -C (O) Rô, - C (O0) ORº, -OR8, - N (Rº) (RP), -C (O) N (RNRO), -N (R) C (O) RA, -S (O) .RE, -S (O) .N (RºI (RP), -N (Rº) S (O) .RF, carbocicil, heterocicila, arila or heteroaryl, where each alkyl, alkenyl, alkynyl, heteroalkyl, car-
bocicilla, heterocicila, arila e heteroarila is independent and optionally substituted by one or more R '; each of R4, R8, Rº, Rº , and RE is independently hydrogen or C1-Cs alkyl; each Rº is independently C1-Cs alkyl, oxo, cyano, - OR, -N (RºN (RP), -C (OIN (RNRP), -N (Rº) C (O) RA, aryl or heteroaryl, where each aryl and heteroaryl is independent and optionally substituted by one or more R ; each R 'is independently halo, oxo, cyano, -OR , - N (RºN (RP), -C (O) IN (R NRP) or -N (R) C (O) Rº; each Rº is independently C1-Cçs alkyl, cyano, -OR3, - N (REN (RP), -C (O) N (RºNR ) or -N (Rº) C (O) RA; né0o0 1,2 3or4; and xé0O, 1, ou2.
[2]
2. Fusion polypeptide according to claim 1, characterized in that the COF1 / CRBN-binding polypeptide is fused to the heterologous polypeptide.
[3]
Fusion polypeptide according to claim 1 or 2, characterized in that the COF1 / CRBN-binding polypeptide and the heterologous polypeptide are linked by a peptide bond.
[4]
Fusion polypeptide according to claim 1 or 2, characterized in that the COF1 / CRBN-binding polypeptide and the heterologous polypeptide are linked by a different bond than a peptide bond.
[5]
A fusion polypeptide according to any one of claims 1 to 4, characterized in that the heterologous polypeptide is linked directly to the COF1 / CRBN binding polypeptide.
[6]
Fusion polypeptide according to any one of claims 1 to 4, characterized in that the heterogeneous polypeptide
rologer is indirectly linked to the COF1 / CRBN binding polypeptide.
[7]
Fusion polypeptide according to any one of claims 1 to 6, characterized in that the COF1 / CRBN-binding polypeptide and the heterologous polypeptide are operably linked by means of a linker, for example, a linker glycine-serine, for example, a linker comprising the amino acid sequence of SEQ ID NO: 28.
[8]
Fusion polypeptide according to any one of claims 1 to 7, characterized in that the COFI / CRBN-binding polypeptide is linked to the C-terminus or N-terminus of the heterologous polypeptide.
[9]
Fusion polypeptide according to any one of claims 1 to 8, characterized by the fact that the association of the COF1 / CRBN-binding polypeptide with cereblon (CRBN) in the absence of COF1 is no more than, for example , 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation.
[10]
Fusion polypeptide according to any one of claims 1 to 9, characterized in that the COF1 / CRBN binding polypeptide does not bind CRBN in the absence of COF1.
[11]
11. Fusion polypeptide according to any one of claims 1 to 10, characterized by the fact that the association of the fusion polypeptide with CRBN in the absence of COF1 is not more than, for example, 0.01%, 0.1 %, 1%, 5%, 10%, 15%, or 20%, of the CRBN fusion polypeptide association in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation.
[12]
Fusion polypeptide according to any one of claims 1 to 11, characterized in that the fusion polypeptide does not bind CRBN in the absence of COF1.
[13]
13. Fusion polypeptide according to any one of claims 1 to 12, characterized by the fact that the ubiquitination of the heterologous polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1% , 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by a test described in this document.
[14]
14. Fusion polypeptide according to any one of claims 1 to 13, characterized in that the ubiquitination of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1 %, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by a test described in this document.
[15]
Fusion polypeptide according to claim 13 or 14, characterized in that the heterologous polypeptide or fusion polypeptide is ubiquitinated in one or more lysine or methionine residues in the presence of COF1.
[16]
16. Fusion polypeptide according to any one of claims 1 to 15, characterized by the fact that the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1 %, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[17]
17. Fusion polypeptide according to claim
16, characterized by the fact that the degradation of the fusion polypeptide is mediated by ubiquitination in the presence of COF1.
[18]
18. Fusion polypeptide according to any one of claims 9 to 17, characterized by the fact that association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[19]
19. Fusion polypeptide according to any one of claims 1 to 18, characterized in that the COF1 / CRBN-binding polypeptide is between 10 and 95 amino acid residues in length, between 15 and 90 residues amino acid in length, between 20 and 85 amino acid residues in length, between and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length, between 50 and 65 amino acid residues in length or between 55 and 65 amino acid residues in length.
[20]
20. Fusion polypeptide according to any one of claims 1 to 19, characterized in that the COF1 / CRBN-binding polypeptide comprises a beta curve.
[21]
21. The fusion polypeptide according to any one of claims 1 to 20, characterized in that the COF1 / CRBN-binding polypeptide comprises a beautiful clip format.
[22]
22. The fusion polypeptide according to any one of claims 1 to 21, characterized in that the COF1 / CRBN-binding polypeptide comprises a beta strand.
[23]
23. The fusion polypeptide according to any one of claims 1 to 22, characterized in that the COF1 / CRBN-binding polypeptide comprises an alpha helix.
[24]
24. The fusion polypeptide according to any one of claims 1 to 23, characterized in that the COF1I / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strip, a shape beta clamp, a second beta tape and a first alpha helix.
[25]
25. The fusion polypeptide according to any one of claims 1 to 24, characterized in that the COFI / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a format beta clamp, a second beta tape, a first alpha helix and a second alpha helix.
[26]
26. The fusion polypeptide according to claim 25, characterized by the fact that the beta clamp format and the second alpha helix are separated by no more than 60, 50, 40 or 30 amino acid residues.
[27]
27. The fusion polypeptide according to any one of claims 1 to 26, characterized in that the COF1 / CRBN-binding polypeptide comprises a COF1 / CRBN-binding sequence of a naturally occurring polypeptide or a variant of COF1 / CRBN binding thereof, for example, a naturally occurring IKZF polypeptide or a COF1 / CRBN binding variant thereof, for example, a naturally occurring IKZF1, IKZF2, IKZF3, IKZFA4, IKZF5 a COF1 / CRBN binding variant thereof.
[28]
28. The fusion polypeptide according to claim 27, characterized in that the COF1 / CRBN binding sequence comprises two or more discontinuous sequences of the naturally occurring polypeptide, for example, a naturally occurring IKZF polypeptide , for example, a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4 or IKZF5.
[29]
29. The fusion polypeptide according to any one of claims 1 to 28, characterized by the fact that the polypeptide
COF1I / CRBN binding deo comprises an IKZF polypeptide or a structural motif thereof.
[30]
30. The fusion polypeptide according to claim 29, characterized in that the IKZF polypeptide is an IKZF1 polypeptide, an IKZF3 polypeptide, an IKZF2 polypeptide that has H141Q substitution (numbered according to SEQ ID NO: 21), or an IKZF4 polypeptide that has H188Q substitution (numbered according to SEQ ID NO: 22).
[31]
31. The fusion polypeptide according to any one of claims 1 to 30, characterized in that the COF1I / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of IKZF (for example, example, IKZF1 or IKZF3) that: i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; ili) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[32]
32. Fusion polypeptide according to claim 31, characterized by the fact that association, ubiquitination and / or degradation is like the measure in a mammalian cell, for example, a human cell.
[33]
33. The fusion polypeptide according to any one of claims 1 to 32, characterized in that the COF1 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues, about 15 to about 90 amino acid residues, about 20 to about 85 amino acid residues, about to about 80 amino acid residues, about 30 to about 75 amino acid residues, about 35 to about 70 amino acid residues noacid, about 40 to about 65 amino acid residues, about 45 to about 65 amino acid residues, about 50 to about 65 amino acid residues, or about 55 to about 65 amino acid residues of IKZF1 or IKZF3.
[34]
34. The fusion polypeptide according to any one of claims 1 to 33, characterized in that the COF1 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - from 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural pattern of amino acid residues 136 to 180 of SEQ ID NO: 19) that:
i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20 %, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document;
iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[35]
35. Fusion polypeptide according to claim 34, characterized by the fact that association, ubiquitination and / or degradation is as measured in a mammalian cell, for example, a human cell.
[36]
36. The fusion polypeptide according to any one of claims 1 to 35, characterized in that the COF1 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO : 19) (for example, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 5) or a sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO : 19) by no more than 1, 2, 3, 4, 5, 10,15, 20, 25, 30, 35, or 40 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid substitutions of amino acid residues 136 to 180 of SEQ ID NO: 19).
[37]
37. Fusion polypeptide according to any one of claims 1 to 33, characterized by the fact that the polypeptide
COF1 / CRBN binding video comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sequence of sufficient amino acids and / or a structural motif of amino acid residues 136 to 170 of SEQ ID NO: 19) that:
i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20 %, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document;
iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document.
to; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[38]
38. Fusion polypeptide according to claim 37, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[39]
39. Fusion polypeptide according to any one of claims 1 to 33, 37 or 38, characterized in that the COF1 / CRBN binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to to SEQ ID NO: 19) (for example, the COFI / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 6) or a sequence that differs from amino acid residues 136 to 170 of IKZF3 ( numbered according to SEQ ID NO: 19) by no more than 1,2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 170 of SEQ ID NO: 19 for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid substitutions of amino acid residues 136 to 170 of SEQ ID NO: 19).
[40]
40. Fusion polypeptide according to any of claims 36 to 39, characterized in that one, two, three or all of the following amino acid residues remain unchanged: glutamine at position 147, cysteine at position 148, glutamine in position 150, glycine in position 152, leucine in position 161 or leucine in position 162, numbered according to SEQ ID NO: 19.
[41]
41. The fusion polypeptide according to claim 40, characterized by the fact that the glutamine in position 147 remains unchanged, numbered according to SEQ ID NO: 19.
[42]
42. The fusion polypeptide according to claim 40, characterized by the fact that cysteine at position 148 remains unchanged, numbered according to SEQ ID NO: 19.
[43]
43. The fusion polypeptide according to claim 40, characterized by the fact that glycine at position 152 remains unchanged, numbered according to SEQ ID NO: 19.
[44]
44, Fusion polypeptide according to any one of claims 1 to 43, characterized in that the COFI / CRBN-binding polypeptide comprises amino acid residues 136 to 139 of IKZF3 (numbered according to SEQ ID NO : 19) for example, the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 40.
[45]
45. Fusion polypeptide according to any one of claims 1 to 44, characterized in that the COF1 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO : 19) for example, the COFI / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 5 or 77.
[46]
46. Fusion polypeptide according to any one of claims 1 to 44, characterized in that the COFI / CRBN-binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO : 19), for example, the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 6 or 78.
[47]
47. The fusion polypeptide according to any one of claims 1 to 46, characterized in that the COF1I / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - from 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural pattern of amino acid residues 236 to 249 of SEQ ID NO: 19) that:
i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20 %, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document;
iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[48]
48. Fusion polypeptide according to claim 47, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[49]
49. The fusion polypeptide according to any one of claims 1 to 48, characterized in that the COF1 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO : 19) (for example, the COFI / CRBN binding polypeptide comprises the amino acid sequence of SEQ ID NO: 11) or a sequence that differs from amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO : 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues (for example, a sequence that differs from amino acid residues 236 to 249 of SEQ ID NO: 19 by no more than 1 , 2, 3, 4, 5, 6, or 7 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 6, or 7 amino acid substitutions for amino acid residues 236 to 249 of SEQ ID NO: 19).
[50]
50. Fusion polypeptide according to any one of claims 1 to 49, characterized in that the COF1 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO : 19) for example, the COFI / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 11.
[51]
51. The fusion polypeptide according to any one of claims 1 to 49, characterized in that the COF1 / CRBN-binding polypeptide comprises the amino acid sequence of MALEKMALEKMALE (SEQ | D NO: 91).
[52]
52. The fusion polypeptide according to any one of claims 1 to 51, characterized in that the COF1 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - from 136 to 180 and 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural pattern of amino acid residues 136 to 180 and 236 to 249 of SEQ ID NO: 19) that: i) the association of the COF1 / CRBN-binding polypeptide with CRBN in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10 %, 15%, or 20%, of the association of the COF1 / CRBN-binding polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, by example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of the association of the fusion polypeptide with CRBN in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterogeneous polypeptide
rologer in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF1 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF1 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF1, for example, an excess of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[53]
53. The fusion polypeptide according to claim 52, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[54]
54. The fusion polypeptide according to any one of claims 1 to 53, characterized in that the COFI / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered from according to SEQ ID NO: 19) (for example, a first sequence comprising the amino acid sequence of SEQ ID NO: 5) or a first sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to to SEQ ID NO: 19) for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a first sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues); and a second sequence comprising amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, a second sequence comprising the amino acid sequence of SEQ ID NO: 11) or a second sequence that differs from amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1,2,3,4,5,6, or 7 amino acid residues (for example, a second sequence that differs from amino acid residues 236 to 249 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 6 or 7 amino acid residues).
[55]
55. The fusion polypeptide according to any one of claims 1 to 54, characterized in that the COFI / CRBN-binding polypeptide comprises amino acid residues 136 to 180 and 236 to 249 of IKZF3 (numbered according to to SEQ ID NO: 19), for example, the COF1I / CRBN binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 1 or 3.
[56]
56. The fusion polypeptide according to any one of claims 1 to 55, characterized in that the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 1 or 3.
[57]
57. The fusion polypeptide according to any one of claims 1 to 56, characterized in that the COF1 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered from according to SEQ ID NO: 19) and a second sequence comprising the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91), for example, the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO : 14 or 85.
[58]
58. The fusion polypeptide according to any one of claims 1 to 56, characterized in that the COF1I / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 170 of IKZF3 (numbered from according to SEQ ID NO: 19) and a second sequence comprising the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91), for example, the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO : 15 or 86.
[59]
59. The fusion polypeptide according to any one of claims 1 to 58, characterized in that the COFI / CRBN-binding polypeptide comprises at least one lysine unless the corresponding native sequence.
[60]
60. The fusion polypeptide according to claim 59, characterized in that one or more lysine residues in the corresponding native sequence are replaced by a different amino acid, for example, arginine.
[61]
61. The fusion polypeptide according to claim 59 or 60, characterized in that the COF1 / CRBN-binding polypeptide comprises less than 1, 2, 3, 4 or 5 lysine residues.
[62]
62. The fusion polypeptide according to claim 61, characterized in that the COF1 / CRBN-binding polypeptide does not comprise a lysine residue.
[63]
63. The fusion polypeptide according to any one of claims 1 to 62, characterized in that the COFI / CRBN binding polypeptide is not ubiquitinated, for example, in the presence of COF1, for example, as measured by an assay described in this document, optionally wherein ubiquitination is as measured in a mammalian cell, for example, a human cell
manna.
[64]
64. Fusion polypeptide according to any one of claims 1 to 63, characterized in that the COF1 / CRBN-binding polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 41.42e43.
[65]
65. The fusion polypeptide according to any one of claims 1 to 63, characterized in that the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 2 or 4.
[66]
66. The fusion polypeptide according to any one of claims 1 to 65, characterized by the fact that COF1 is an immunomodulatory imide drug (IMID) or a pharmaceutically acceptable salt thereof.
[67]
67. Fusion polypeptide according to any one of claims 1 to 65, characterized by the fact that COF1 has the structure of Formula (l-a): (Ro o "oe
NM R2º Ra Frog (Ia) or a pharmaceutically acceptable salt, ester, hydrate or tautomer thereof, in which: ring A is carbocicyl, heterocyclic, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $; M is absent, or is C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl or C1-Cs heteroalkyl, where each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R $;
each between R º and R it is independently hydrogen or C1-Cs alkyl; or R º and R , together with the carbon atom to which they are attached to form a carbonyl group or thiocarbonyl group;
R * º is hydrogen, C1-Cs alkyl, C2-C6 alkenyl, C2-Cs alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) Rô, -C (0) ORE, -OR, - N (RºNRP), -C (O) N (RNHRP), -N (RO) C (O) RA, -S (O) .RF, -S (O) N (Rº (RP) or -N (Rº ) S (O) .RE, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R $;
each of Rº is independently C1-Cs alkyl, C2-Cs6 alkenyl, C2-Ce6 alkynyl, C1-Ces heteroalkyl, halo, cyano, -C (O) RS, - C (O0) ORE, -OR8, -N ( Rº) (RP), -C (O) N (RNHRPO), -N (RO) C (O) RA, -S (O) .RE, -S (O) .N (RNRP) or -N (R ) IS (O), RE, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R $;
each Rº is independently C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-Cs heteroalkyl, halo, cyano, oxo, -C (OJ) R5, - C (O0) ORE, -OR8, - N (Rº) (R ), -C (O) IN (RONR ), -N (RIC (OJRA, -S (O), RE, -S (O) .N (RºI (RP), -N (Rº) S (O) .RF, carbocicil, heterocicila, arila or heteroaryl, in which each alkyl, alkenyl, alkynyl, carbocicyl, heterocyclic, aryl and heteroaryl is independent and optionally substituted by one or more R ';
each of Rô, R8, Rº, R , and RF is independently hydrogen or C1-Cs alkyl;
each R $ is independently C1-Cs alkyl, oxo, cyano, - OR, -N (RºHRP), -C (O) N (RNHRP ), -N (RC (OJRA, aryl or heteroaryl, where each aryl and heteroaryl is independent and optionally substituted by one or more R ;
each R 'is independently halo, oxo, cyano, -ORº, - N (Rº) (RP), -C (O) IN (Rº NRP) or -N (R) C (O) RA;
each Rº is independently C1-Cs alkyl, cyano, -ORº, -
N (RºN (RP), -C (O) IN (R NRP) or -N (R) C (O) Rº; right oO, 1.20u3; 0é0 1,2,3,40u5; and xéO, 1ou2.
[68]
68. The fusion polypeptide according to claim 67, characterized by the fact that Xé O.
[69]
69. Fusion polypeptide according to claim 67 or 68, characterized by the fact that M is absent.
[70]
70. The fusion polypeptide according to any one of claims 67 to 69, characterized by the fact that ring A is heterocyclic (for example, a nitrogen-containing heterocyclic, for example 2- (2,6-dioxopiperidin-3- il) isoindoline-1,3-dione).
[71]
71. The fusion polypeptide according to any one of claims 67 to 70, characterized by the fact that Rº is oxo or OR (for example, -OCH3 or -OCH2CH3) and o is 0, 1, or 2.
[72]
72. The fusion polypeptide according to any one of claims 67 to 71, characterized by the fact that each of R º and R * Is independently hydrogen, or R º and R º>, together with the atom of carbon to which they are attached, form a carbon group.
[73]
73. The fusion polypeptide according to any one of claims 67 to 72, characterized by the fact that R * º is heteroalkyl (for example, = CHANHC (O) CH> 2), -N (Rº) (R ) (for example, - NH2) or —-N (Rº) C (O) Rº (for example, -NHC (O) CH3).
[74]
74. The fusion polypeptide according to any one of claims 67 to 73, characterized by the fact that ne O.
[75]
75. Fusion polypeptide according to any of the claims | to 74, characterized by the fact that COF1 is thalidomide or analog, or a pharmaceutically acceptable salt thereof.
[76]
76. Fusion polypeptide according to any one of claims 1 to 74, characterized by the fact that COF1 is selected from the group consisting of lenalidomide, pomalido-mide, thalidomide and 2- (4- (tert-butyl) phenyl) -N - ((2- (2,6-dioxopiperidin-3-yl) -1- oxoisoindolin-5-yl) methyl) acetamide or a pharmaceutically acceptable salt thereof.
[77]
77. Fusion polypeptide according to any one of claims 1 to 74, characterized by the fact that COF1 is selected from the group consisting of: CÁ CÁRIE CÁ eos to non-O 2 NO; eT ”or a pharmaceutically acceptable salt thereof.
[78]
78. The fusion polypeptide according to any one of claims 1 to 74, characterized by the fact that COF1 is lenalidide or pomalidomide or a pharmaceutically acceptable salt thereof.
[79]
79. The fusion polypeptide according to any one of claims 1 to 74, characterized by the fact that COF1 is lenalidomide or the like, or a pharmaceutically acceptable salt thereof.
[80]
80. The fusion polypeptide according to any one of claims 1 to 79, characterized in that the fusion polypeptide further comprises a degradation domain, wherein the degradation domain is separated from the COF1 / binding polypeptide CRBN and the heterologous polypeptide by a heterologous protease cleavage site.
[81]
81. The fusion polypeptide according to claim 80, characterized in that the fusion polypeptide comprises, from the N termination to the C termination: i) the degradation domain, the heterologous protease cleavage site, the polypeptide heterologous and the COF1 / CRBN binding polypeptide; ii) the degradation domain, the heterologous protease cleavage site, the COF1 / CRBN binding polypeptide and the heterologous polypeptide; iii) the COF1 / CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site and the degradation domain; or iv) the heterologous polypeptide and the COF1 / CRBN binding polypeptide, the heterologous protease cleavage site and the degradation domain.
[82]
82. The fusion polypeptide according to claim 80, characterized in that the fusion polypeptide comprises, from the N termination to the C termination, the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF1 / CRBN binding polypeptide.
[83]
83. Fusion polypeptide comprising a first domain and a second domain separated by a heterologous protease cleavage site, where the first domain comprises a degradation domain and the second domain comprises a compound of Formula (II), (cereblon) (COF2) / CRBN-binding polypeptide and a heterologous polypeptide, for example, a heterologous mammalian bacterial or viral polypeptide, characterized by the fact that the compound of Formula (II) is: x (Rh Oo R2a R2 (11) or a pharmaceutically acceptable salt, ester, hydrate, tautomer or prodrug thereof, wherein: XéOousS;
R 'is C1-Cs alkyl, C2-Cs6 alkenyl, C2-Cs6 alkynyl, C1-Ce6 heteroalkyl, carbocicyl, heterocyclyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $;
each between R º and R it is independently hydrogen or C1-Cs alkyl; or R º and R º, together with the carbon atom to which they are attached to form carbonyl group or thiocarbonyl group;
each of R * º is independently C1-Cs alkyl, C2-Cs6 alkenyl, C2-Cs6 alkynyl, C1-Cs heteroalkyl, halo, cyano, -C (O) RS, - C (0) ORE, -OR8, - N (RºI (R ), -C (OIN (RONR), -N (RIC (OJRA, -S (O), RE, -S (O) .N (Rº) (RP) or -N (Rº)) S (O) .RF or L-Tag, where each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R * ';
each Rº is independently C1-Cs alkyl, C2-Ce6 alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl, halo, cyano, oxo, -C (O) R, - C (0) ORE, -ORE, - N (RºNRP), -C (OIN (RNR ), -N (RIC (O) RA, -S (O) .RE, -S (O) .N (RºNRP), -N (RO) IS (O ) .RE, carbocicil, heterocicila, arila or heteroaryl, in which each alkyl, alkenyl, alkynyl, heteroalkyl, carococyl, heterocyclic, aryl and heteroaryl is independent and optionally substituted by one or more R ';
each of Rô, R8, Rº, RP, and RF is independently hydrogen or C1-Cs alkyl;
each R '* is independently C1-Cs alkyl, halo, oxo, cyano, -OR8, -N (Rº) (RP), -C (O) N (RNRO ), -N (ROC (O) RA , aryl or heteroaryl, where each aryl and heteroaryl is independent and optionally replaced by one or more Rº;
each R 'is independently halo, oxo, cyano, -OR', - N (REIRP), -C (O) N (RENRP) or -N (R) C (O) R ';
each Rº is independently C1-Cs alkyl, halo, cyano, - ORE, -N (Rº) (R ), -C (O) N (RENR ) or -N (R) C (O) RA;
each L is independently C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-C6 heteroalkyl, -C (O) RY, -C (O0) ORP !, -ORP !, - N (RINRP!), -C (OIN (REINR!), -N (REIC (O) RY !, -S (O) .REI, -S (O) .N (RE NR) or -N (Rº1) S (O), RFI , in which each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R ' ; each Tag is a chemical targeting portion capable of binding to a target protein; each of Rº !, RE, Rº , RPº and RE Is independently hydrogen, C1-Cs alkyl, C2-Cs6 alkenyl, C2-Cs alkynyl, C1-C6s heteroalkyl, carbocicyl, heterocicyl, aryl or heteroaryl, in which each alkyl, alkenyl, alkynyl, heteroalkyl, carbocicyl, heterocycyl, aryl and heteroaryl is independently and optionally substituted by one or more R ' ; each R' 'is independently C1-Cs alkyl, halo, cyano, carbocicyl or heterocyclic; ; and xé0O, 1or2.
[84]
84. The fusion polypeptide according to any one of claims 80 to 83, characterized in that the degradation domain has a first state associated with a first expression level of the fusion polypeptide and a second state associated with a second level of expression of the fusion polypeptide, in which the second level is increased, for example, by at least 2 times, 3 times, 4 times, 5 times, 10 times, 20 times or 30 times in relation to the first level in the presence of a stabilizing compound.
[85]
85. The fusion polypeptide according to claim 84, characterized in that in the absence of the stabilizing compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%,
90% or more of the fusion polypeptide is degraded, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[86]
86. The fusion polypeptide according to claim 84 or 85, characterized in that the level of expression and / or degradation is as measured in a mammalian cell, for example, a human cell.
[87]
87. The fusion polypeptide according to any one of claims 84 to 86, characterized by the fact that, in the presence of the stabilizing compound: i) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; or ii) the conformation of the fusion polypeptide is more permissible to cleavage at the heterologous protease cleavage site in relation to a conformation in the absence of the stabilizing compound.
[88]
88. Fusion polypeptide according to any one of claims 80 to 87, characterized in that the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB ( FKBP), or a dihydrofolate reductase (DHFR) domain.
[89]
89. The fusion polypeptide according to claim 88, characterized by the fact that the degradation domain is an estrogen receptor (ER) domain.
[90]
90. Fusion polypeptide according to claim 89, characterized in that the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO : 46 or 48.
[91]
91. Fusion polypeptide according to claim
90, characterized by the fact that the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[92]
92. The fusion polypeptide according to any one of claims 89 to 91, characterized in that the stabilizing compound is bazedoxifene or 4-hydroxy tamoxifen (4-OHT), or a pharmaceutically acceptable salt thereof.
[93]
93. The fusion polypeptide according to claim 88, characterized by the fact that the degradation domain is an FKB protein (FKBP) domain.
[94]
94. The fusion polypeptide according to claim 93, characterized in that the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO : 50.
[95]
95. The fusion polypeptide according to claim 93 or 94, characterized in that the stabilizing compound is Shield-1, or a pharmaceutically acceptable salt thereof.
[96]
96. The fusion polypeptide according to claim 88, characterized by the fact that the degradation domain is a dihydrofolate reductase (DHFR) domain.
[97]
97. The fusion polypeptide according to claim 96, characterized in that the degradation domain comprises an amino acid sequence that is at least 90, 95, 97, 98, 99 or 100% identical to SEQ ID NO : 51.
[98]
98. The fusion polypeptide according to claim 96 or 97, characterized in that the stabilizing compound is trimethoprim, or a pharmaceutically acceptable salt thereof.
[99]
99. The fusion polypeptide according to any one of claims 80 to 98, characterized in that the heterologous protease cleavage site is cleaved by a mammalian intracellular protease.
[100]
100. Fusion polypeptide according to claim 99, characterized in that the heterologous protease cleavage site is cleaved by a protease selected from the group consisting of furin, POSK1, PCSK5, PCSK6, PCSK7 , cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease and elastase 1.
[101]
101. Fusion polypeptide according to claim 99 or 100, characterized by the fact that the heterologous protease cleavage site comprises a sequence that has a cleavage motif selected from the group consisting of consensus motif of RX (K / R) R (X can be any amino acid; SEQ ID NO: 52), consensus reason RXXX [KRI] R (X can be any amino acid; SEQ ID NO: 53), consensus reason RRX (SEQ ID NO: 54), reason for consensus of | -EPDX (SEQ ID NO: 55), Ile-Glu / Asp-Gly-Arg (SEQ ID NO: 56), Asp-Asp-Asp-Asp- Lys (SEQ ID NO: 57), Pro-Gly-Ala-Ala-His-Tyr (SEQ ID NO: 58), LPXTG / A consensus motive (SEQ ID NO: 59), Leu-Glu-Val-Phe -GIn-Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), ENLYFQG (SEQ ID NO: 62) and [AGSV] -X (X can be any amino acid; SEQ ID NO: 63).
[102]
102. The fusion polypeptide according to claim 99, characterized in that the heterologous protease cleavage site is cleaved by furin.
[103]
103. The fusion polypeptide according to claim 102, characterized in that the heterologous protease cleavage site comprises a furin cleavage site selected from the group consisting of RTKR (SEQ ID NO: 123); GTGAED- PRPSRKRRSLGDVG (SEQ ID NO: 125); GTGAEDPRPSRKRR (SEQ ID NO: 127); LAWLEQQVAKRRTKR (SEQ ID NO: 129); GTGAED- PRPSRKRRSLGG (SEQ ID NO: 131)) GTGAEDPRPSRKRRSLG
(SEQ ID NO: 133)) SLNLTESHNSRKKR (SEQ ID NO: 135); CKINGYPKRGRKRR (SEQ ID NO: 137); and SARNRQKR (SEQ ID NO: 34).
[104]
104. The fusion polypeptide according to claim 102, characterized in that the heterologous protease cleavage site comprises the furin cleavage site of GTGAED-PRPSRKRRSLGDVG (SEQ ID NO: 125).
[105]
105. The fusion polypeptide according to any of claims 80 to 98, characterized in that the heterologous protease cleavage site is cleaved by a mammalian extracellular protease.
[106]
106. Fusion polypeptide according to claim 105, characterized by the fact that the mammalian extracellular protease is selected from the group consisting of Factor XA, Enteroquinase, genenase, sortase, precision protease, thrombin, TEV protease and elastase 1.
[107]
107. The fusion polypeptide according to claim 106, characterized in that the heterologous protease cleavage site comprises an amino acid sequence selected from the group consisting of Ile-Glu / Asp-Gly-Arg (SEQ ID NO : 56), Asp-Asp-Asp-Asp-Lys (SEQ ID NO: 57), Pro-GlIy-Ala-Ala-His-Tyr (SEQ ID NO: 58), LPXTG / A consensus motive (SEQ ID NO: 59), Leu- Glu-Val-Phe-Gln-Gly-Pro (SEQ ID NO: 60), Leu-Val-Pro-Arg-Gly-Ser (SEQ ID NO: 61), ENLYFQG (SEQ ID NO : 62) and [AGSV] -X (X can be any amino acid; SEQ ID NO: 63).
[108]
108. The fusion polypeptide according to any one of claims 83 to 107, characterized in that the degradation domain is fused to the heterologous protease cleavage site, which is additionally fused to the second domain.
[109]
109. The fusion polypeptide according to any one of claims 83 to 108, characterized by the fact that it comprises, from the N termination to the C termination: i) the degradation domain, the heterologous protease cleavage site, the polypeptide heterologous and the COF2 / CRBN binding polypeptide; ii) the degradation domain, the heterologous protease cleavage site, the COF2 / CRBN binding polypeptide and the heterologous polypeptide; iii) the COF2 / CRBN binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site and the degradation domain; or iv) the heterologous polypeptide and the COF2 / CRBN binding polypeptide, the heterologous protease cleavage site and the degradation domain.
[110]
110. Fusion polypeptide according to any one of claims 83 to 108, characterized in that it comprises, from the N termination to the C termination, the degradation domain, the heterologous protease cleavage site, the heterologous polypeptide and the COF2 / CRBN binding polypeptide.
[111]
111. Fusion polypeptide according to any of claims 83 to 110, characterized by the fact that the association of the COF2 / CRBN-binding polypeptide with cereblon (CRBN) in the absence of COF2 is, for example, only , 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an COF2 process, for example, as measured by an assay described in this document, for example, immunoprecipitation.
[112]
112. The fusion polypeptide according to any one of claims 83 to 111, characterized in that the COF2 / CRBN binding polypeptide does not bind CRBN in the absence of
COF 2.
[113]
113. Fusion polypeptide according to any one of claims 83 to 112, characterized by the fact that the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0 , 1%, 1%, 5%, 10%, 15%, or 20%, of the fusion polypeptide association with CRBN in the presence of COF 2, for example, an excess of COF2, for example, as measured by a assay described in this document, for example, immunoprecipitation.
[114]
114. The fusion polypeptide according to any one of claims 83 to 113, characterized in that the fusion polypeptide does not bind CRBN in the absence of COF 2.
[115]
115. Fusion polypeptide according to any one of claims 83 to 114, characterized by the fact that the ubiquitization of the heterologous polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1% , 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by a test described in this document.
[116]
116. Fusion polypeptide according to any one of claims 83 to 115, characterized in that the ubiquitization of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1 %, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF 2, for example, an excess of COF2, for example , as measured by a test described in this document.
[117]
117. The fusion polypeptide according to claim 115 or 116, characterized in that the heterologous polypeptide or fusion polypeptide is ubiquitinated to one or more lysine or methionine residues in the presence of COF 2.
[118]
118. Fusion polypeptide according to any of claims 83 to 117, characterized in that the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1 %, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the degradation of the fusion polypeptide in the presence of COF 2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[119]
119. Fusion polypeptide according to claim 118, characterized in that the degradation of the fusion polypeptide is mediated by ubiquitination in the presence of COF 2.
[120]
120. Fusion polypeptide according to any one of claims 111 to 119, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[121]
121. Fusion polypeptide according to any one of claims 83 to 120, characterized in that the COF2 / CRBN-binding polypeptide is between 10 and 95 amino acid residues in length, between 15 and 90 residues of amino acid in length, between 20 and 85 amino acid residues in length, between and 80 amino acid residues in length, between 30 and 75 amino acid residues in length, between 35 and 70 amino acid residues in length, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length, between 50 and 65 amino acid residues in length or between 55 and 65 amino acid residues in length.
[122]
122. The fusion polypeptide according to any of claims 83 to 121, characterized in that the COF2 / CRBN binding polypeptide comprises a beta curve.
[123]
123. The fusion polypeptide according to any one of claims 83 to 122, characterized in that the COF2 / CRBN-binding polypeptide comprises a beta clip format.
[124]
124. The fusion polypeptide according to any one of claims 83 to 123, characterized in that the COF2 / CRBN binding polypeptide comprises a beta strand.
[125]
125. The fusion polypeptide according to any one of claims 83 to 124, characterized in that the COF2 / CRBN-binding polypeptide comprises an alpha helix.
[126]
126. Fusion polypeptide according to any one of claims 83 to 125, characterized in that the COF2 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta ribbon, a format beta clamp, a second beta tape and a first alpha helix.
[127]
127. Fusion polypeptide according to any one of claims 83 to 126, characterized in that the COF2 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta ribbon, a format beta clamp, a second beta tape, a first alpha helix and a second alpha helix.
[128]
128. Fusion polypeptide according to claim 127, characterized by the fact that the beta clip format and the second alpha helix are separated by no more than 60, 50, 40 or 30 amino acid residues.
[129]
129. The fusion polypeptide according to any one of claims 83 to 128, characterized in that the COF2 / CRBN binding polypeptide comprises a COF2 / CRBN binding sequence of a naturally occurring polypeptide or a COF2 / CRBN binding variant thereof, for example, a naturally occurring IKZF polypeptide or a COF2 / CRBN binding variant thereof, for example, an occurring IKZF1, IKZF2, IKZF3, IKZF4 or IKZF5 natural or a COF2 / CRBN binding variant thereof.
[130]
130. The fusion polypeptide according to claim 129, characterized in that the COF2 / CRBN binding sequence comprises two or more discontinuous sequences of the naturally occurring polypeptide, for example, a naturally occurring IKZF polypeptide, for example example, a naturally occurring IKZF1, IKZF2, IKZF3, IKZF4 or IKZF5.
[131]
131. The fusion polypeptide according to any one of claims 83 to 130, characterized in that the COF2 / CRBN-binding polypeptide comprises an IKZF polypeptide or a structural motif thereof.
[132]
132. The fusion polypeptide according to claim 131, characterized in that the IKZF polypeptide is an IKZF1 polypeptide, an IKZF3 polypeptide, an IKZF2 polypeptide that has H141Q substitution (numbered according to SEQ ID NO: 21), or an IKZF4 polypeptide that has H188Q substitution (numbered according to SEQ ID NO: 22).
[133]
133. Fusion polypeptide according to any one of claims 83 to 132, characterized in that the COF2 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of IKZF (for example, example, IKZF1 or IKZF3) that: i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation;
ii) the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[134]
134. Fusion polypeptide according to claim 133, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[135]
135. The fusion polypeptide according to any of claims 83 to 134, characterized in that the COF2 / CRBN-binding polypeptide comprises about 10 to about 95 amino acid residues, about 15 to about 90 amino acid residues, about 20 to about 85 amino acid residues, about 25 to about 80 amino acid residues, about 30 to about 75 amino acid residues, about 35 to about 70 amino acid residues, about from 40 to about 65 amino acid residues, about 45 to about 65 amino acid residues, about 50 to about 65 amino acid residues, or about 55 to about 65 amino acid residues of IKZF1 or IKZF3.
[136]
136. The fusion polypeptide according to any one of claims 83 to 135, characterized in that the COF2 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - acid 136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif for amino acid residues 136 to 180 of SEQ ID NO: 19) which : i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document.
to, for example, immunoprecipitation; ili) the ubiquitination of the heterologous polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[137]
137. Fusion polypeptide according to claim 136, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[138]
138. Fusion polypeptide according to any of claims 83 to 137, characterized in that the COF2 / CRBN binding polypeptide comprises amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO : 19) (for example, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 5) or a sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to SEQ ID NO : 19) by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid substitutions of amino acid residues 136 to 180 of SEQ ID NO: 19).
[139]
139. The fusion polypeptide according to any one of claims 83 to 137, characterized in that the COF2 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - acid 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif for amino acid residues 136 to 170 of SEQ ID NO: 19) which : i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[140]
140. The fusion polypeptide according to claim 139, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[141]
141. Fusion polypeptide according to any one of claims 83 to 137, 139 or 140, characterized in that the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 6) or a sequence that differs from amino acid residues 136 to 170 of IKZF3 (numbered from according to SEQ ID NO: 19) by no more than 1.2,
3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues (for example, a sequence that differs from amino acid residues 136 to 170 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, or 30 substitutions amino acid residues 136 to 170 of SEQ ID NO: 19).
[142]
142. Fusion polypeptide according to any one of claims 138 to 141, characterized in that one, two, three or all of the following amino acid residues remain unchanged: glutamine at position 147, cysteine at position 148, glutamine in position 150, glycine in position 152, leucine in position 161 or leucine in position 162, numbered according to SEQ ID NO: 19.
[143]
143. Fusion polypeptide according to claim 142, characterized by the fact that the glutamine in position 147 remains unchanged, numbered according to SEQ ID NO: 19.
[144]
144. Fusion polypeptide according to claim 142, characterized by the fact that cysteine at position 148 remains unchanged, numbered according to SEQ ID NO: 19.
[145]
145. Fusion polypeptide according to claim 142, characterized in that glycine at position 152 remains unchanged, numbered according to SEQ ID NO: 19.
[146]
146. The fusion polypeptide according to any one of claims 83 to 145, characterized in that the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 139 of IKZF3 (numbered according to SEQ ID NO : 19) for example, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 40.
[147]
147. Fusion polypeptide according to any one of claims 83 to 146, characterized in that the COF2 / CRBN-binding polypeptide comprises amino acid residues
136 to 180 of IKZF3 (numbered according to SEQ ID NO: 19), for example, the COF2 / CRBN binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 5 or 77.
[148]
148. Fusion polypeptide according to any one of claims 83 to 146, characterized in that the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 170 of IKZF3 (numbered according to SEQ ID NO : 19), for example, the COF2 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 6 or 78.
[149]
149. The fusion polypeptide according to any one of claims 83 to 148, characterized in that the COF2 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - acid 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural motif for amino acid residues 236 to 249 of SEQ ID NO: 19) which : i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; ii) the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation;
ili) the ubiquitination of the heterologous polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[150]
150. The fusion polypeptide according to claim 149, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[151]
151. Fusion polypeptide according to any one of claims 83 to 150, characterized in that the COF2 / CRBN binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO : 19) (for example, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 11) or a sequence that differs from amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO : 19) by no more than 1, 2, 3, 4, 5, 6, or 7 amino acid residues (for example, a sequence that differs from amino acid residues 236 to 249 of SEQ ID NO: 19 by no more than 1 , 2, 3, 4, 5, 6, or 7 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 6, or 7 amino acid substitutions for amino acid residues 236 to 249 of SEQ ID NO: 19).
[152]
152. Fusion polypeptide according to any one of claims 83 to 151, characterized in that the COF2 / CRBN-binding polypeptide comprises amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO : 19) for example, the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 11.
[153]
153. The fusion polypeptide according to any one of claims 83 to 152, characterized in that the COF2 / CRBN-binding polypeptide comprises the amino acid sequence of MALEKMALEKMALE (SEQ ID NO: 91).
[154]
154. The fusion polypeptide according to any of claims 83 to 153, characterized in that the COF2 / CRBN-binding polypeptide comprises a sequence of sufficient amino acids and / or a structural motif of amino acid residues - acid 136 to 180 and 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, sufficient amino acid sequence and / or a structural pattern of amino acid residues 136 to 180 and 236 to 249 of SEQ ID NO: 19) that: i) the association of the COF2 / CRBN-binding polypeptide with CRBN in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 5%, 10 %, 15%, or 20%, of the association of the COF2 / CRBN-binding polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, by example, immunoprecipitation
dog; ii) the association of the fusion polypeptide with CRBN in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 5%, 10%, 15%, or 20% of association of the fusion polypeptide with CRBN in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation; iii) the ubiquitination of the heterologous polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the heterologous polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; iv) the ubiquitination of the fusion polypeptide in the absence of COF2 is, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60% , or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document; or v) the degradation of the fusion polypeptide in the absence of COF2 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60 %, or 70% of the degradation of the fusion polypeptide in the presence of COF2, for example, an excess of COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[155]
155. Fusion polypeptide according to claim 154, characterized by the fact that association, ubiquitination and / or degradation are as measured in a mammalian cell, for example, a human cell.
[156]
156. Fusion polypeptide according to any one of claims 83 to 155, characterized in that the COF2 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered from according to SEQ ID NO: 19) (for example, a first sequence comprising the amino acid sequence of SEQ ID NO: 5) or a first sequence that differs from amino acid residues 136 to 180 of IKZF3 (numbered according to to SEQ ID NO: 19) for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a first sequence that differs from amino acid residues 136 to 180 of SEQ ID NO: 19 for no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues); and a second sequence comprising amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) (for example, a second sequence comprising the amino acid sequence of SEQ ID NO: 11) or a second sequence that differs from amino acid residues 236 to 249 of IKZF3 (numbered according to SEQ ID NO: 19) by no more than 1,2,3,4,5,6, or 7 amino acid residues (for example, a second sequence that differs from amino acid residues 236 to 249 of SEQ ID NO: 19 by no more than 1, 2, 3, 4, 5, 6 or 7 amino acid residues).
[157]
157. The fusion polypeptide according to any one of claims 83 to 156, characterized in that the COF2 / CRBN-binding polypeptide comprises amino acid residues 136 to 180 and 236 to 249 of IKZF3 (numbered according to to SEQ ID NO: 19), for example, the COF2 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 1 or 3.
[158]
158. The fusion polypeptide according to any one of claims 83 to 157, characterized by the fact that the polypeptide
COF2 / CRBN binding peptide comprises or consists of the amino acid sequence of SEQ ID NO: 1 or 3.
[159]
159. Fusion polypeptide according to any one of claims 83 to 158, characterized in that the COF2 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 180 of IKZF3 (numbered from according to SEQ ID NO: 19) and a second sequence comprising the MALEKMALEKMALE amino acid sequence (SEQ ID NO: 91), for example, the COF2 / CRBN binding polypeptide comprises or consists of the SEQ amino acid sequence ID NO: 14 or 85.
[160]
160. The fusion polypeptide according to any one of claims 83 to 159, characterized in that the COF2 / CRBN-binding polypeptide comprises a first sequence comprising amino acid residues 136 to 170 of IKZF3 (numbered from according to SEQ ID NO: 19) and a second sequence comprising the MALEKMALEKMALE amino acid sequence (SEQ ID NO: 91), for example, the COF2 / CRBN binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 15 or 86.
[161]
161. The fusion polypeptide according to any one of claims 83 to 160, characterized in that the COF2 / CRBN-binding polypeptide comprises at least one lysine unless the corresponding native sequence.
[162]
162. The fusion polypeptide according to claim 161, characterized by the fact that one or more lysine residues in the corresponding native sequence are replaced by a different amino acid, for example, arginine.
[163]
163. The fusion polypeptide according to claim 161 or 162, characterized in that the polypeptide binding to
COF2 / CRBN comprises less than 1, 2, 3, 4 or 5 lysine residues.
[164]
164. The fusion polypeptide according to claim 163, characterized in that the COF2 / CRBN-binding polypeptide does not comprise a lysine residue.
[165]
165. Fusion polypeptide according to any one of claims 83 to 164, characterized in that the COF2 / CRBN-binding polypeptide is not ubiquitinated, for example, in the presence of COF2, for example, as measured by an assay described in this document, optionally wherein ubiquitination is as measured in a mammalian cell, for example, a human cell.
[166]
166. Fusion polypeptide according to any one of claims 83 to 165, characterized in that the COF2 / CRBN-binding polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 41.42e043.
[167]
167. The fusion polypeptide according to any one of claims 83 to 165, characterized in that the COF2 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 2 or 4.
[168]
168. The fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 is an immunomodulatory imide drug (IMID) or a pharmaceutically acceptable salt thereof.
[169]
169. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 has the structure of Formula (1): x (R4
R2a R º (1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where:
XéOousS;
R 'is C1-Cs alkyl, C2-C6 alkenyl, C2-Cs alkynyl, C1-Ce6 heteroalkyl, carbocicyl, heterocycyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $;
each between R º and R it is independently hydrogen or C1-Cs alkyl; or R2º and R2º, together with the carbon atom to which they are attached, form a carbonyl group or a thiocarbonyl group;
each of Rº is independently C1-Cs alkyl, C2-Cs6 alkenyl, C2-Ce6 alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) R, - C (O0) ORE, -ORE, -N ( RºNRP), -C (OIN (RNRP ), -N (RIC (O) RA, -S (O) .RE, -S (O) .N (RºIR ) Or -N (Rº) S (O) ., RF, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R $;
each R * is independently C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-Cs heteroalkyl, halo, cyano, oxo, -C (O) R, - C (O0) ORE, -OR8, -N ( Rº) (RP), -C (O) N (RURP), -N (ROC (O) RA, -S (O), RE, -S (O) N (RNRP), -N (Rº) S ( O) .RE, carbocicyl, heterocyclic, aryl or heteroaryl, where each alkyl, alkenyl, alkynyl, heteroalkyl, carococyl, heterocyclic, aryl and heteroaryl is independent and optionally substituted by one or more R ”;
each of R4, R8, Rº, RP, and RE is independently hydrogen or C1-Cs alkyl;
each Rº is independently C1-Cçs alkyl, oxo, cyano, - OR, -N (RºNRP), -C (O) N (RNHRP ), -N (RC (OJRA, aryl or heteroaryl, where each aryl and heteroaryl it is independent and optionally substituted by one or more R ;
each R 'is independently halo, oxo, cyano, -OR , - N (RºN (RP), -C (O) IN (R NRP) or -N (R) C (O) RA;
each Rô is independently C1-Cs alkyl, cyano, -ORº, - N (RENR ), -C (OIN (R NR ) or -N (R) C (O) RA; right 0, 1,2,3 or 4 ; and xéO, 1or2.
[170]
170. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 has the structure of Formula (| -a): (Ro Oo "o
NM R2o Re RE (Ia) or a pharmaceutically acceptable salt, ester, hydrate or tautomer thereof, in which: ring A is carbocicyl, heterocicyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more Rº ; M is absent, or is C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl or C1-Cs heteroalkyl, where each alkyl, alkenyl, alkynyl and heteroalkyl is independent and optionally substituted by one or more R *; each between R º and R " it is independently hydrogen or C1-C6 alkyl; or R º and R , together with the carbon atom to which they are attached to form a carbonyl group or thiocarbonyl group; R * º is hydrogen, C1-Cs alkyl, C2-C6 alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) RA, -C (O0) ORº, -OR , - N (RENHRP), -C (OIN (RNRL), -N (R) C (O) RA, -S (O) .RF, -S (O) .N (Rº) (RP) or -N ( Rº) S (O) .RE, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by one or more R $; each of R3 is independently C1-Cs alkyl, C2-C6 alkenyl, C2 -Cs alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) R5, -
C (O0) ORE, -OR8, -N (RºN (R ), -C (OIN (RNR ), -N (RIC (OJRA, -S (O), RE, -S (O) N (RNRP ) or -N (Rº) IS (O)., RE, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by one or more R $; each Rº is independently C1-Cs alkyl, C2-Cs6 alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl, halo, cyano, oxo, -C (O) R, - C (O0) ORE, -ORE, -N (RºNRP), -C (OIN (RNRP ), -N (RIC (O) RA, -S (O) .RE, -S (O) .N (RNHRP), -N (RO) S (O) .RE, carbocicyl, heterocicyl, aryl or he- teroaryl, in which each alkyl, alkenyl, alkynyl, carbocicyl, heterocyclic, aryl and heteroaryl is independently and optionally substituted by one or more R '; each of Rô, R8, Rº, Rº , and RE is independently hydrogen or C1-Cs alkyl; each R $ is independently C1-Cs alkyl, oxo, cyano, - OR, -N (RºN (RP), -C (OIN (RNRP), -N (R) C (O) RA, aryl or heteroaryl, where each aryl and heteroaryl is independently and optionally substituted by one or more R '; each R' is independently halo, oxo, cyano, -ORº, - N (Rº) (Rº ), -C (O) N (RºI (Rº) or -N (Rº) C (O) RA; each R $ is independently C1-Cçs alkyl, cyano, -ORº, - N (RºN (RP), -C (O) IN (R NRP) or -N (R) C (O) RA; né0o 1.20u3; 0 is 0 1,2,3,40u5; and x is O, 1 or 2.
[171]
171. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 is thalidomide or analog, or a pharmaceutically acceptable salt thereof.
[172]
172. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 is selected from the group consisting of lenalidomide, pomalido-mide, thalidomide and 2- (4- (tert-butyl) phenyl) -N - ((2- (2,6-dioxopiperidin-3-yl) -1- oxoisoindolin-5-yl) methyl) acetamide, or a pharmaceutically acceptable salt thereof.
[173]
173. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 is selected from the group consisting of: PR NH oo LX "o N o KA NA and LOS So fr Go ot o | or a pharmaceutically acceptable salt thereof.
[174]
174. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 is lenalidomide or pomalidomide or a pharmaceutically acceptable salt thereof.
[175]
175. The fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 is lenalidomide or the like, or a pharmaceutically acceptable salt thereof.
[176]
176. Fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 comprises the structure of Formula (1): x (Rn
ADO RER () or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where: XéOousS; R 'is C1-Cs6 alkyl, C2-C6 alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, carbocicyl, heterocyclyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more
R$; each between R º and R " it is independently hydrogen or C1-Cs alkyl; or R º and R , together with the carbon atom to which they are attached, form a carbonyl group or a thiocarbonyl group; each of Rº is independently C1-Cs alkyl, C2-Cs6 alkenyl, C2-Ce6 alkynyl, C1-C6s heteroalkyl, halo, cyano, -C (O) R, - C (O0) ORE, -ORE, -N ( RºNRP), -C (OIN (RNRP ), -N (RIC (O) RA, -S (O) .RE, -S (O) .N (RNRP ) Or -N (Rº) IS (O) ., RE, in which each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by one or more R $; each Rº is independently C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl, halo, cyano, oxo, -C (O) R, - C (O) ORE, -ORE, -N (Rº) (R ), -C (O) IN (RONR ), -N (RIC (OJRA, -S (O), RE, -S (O) .N (RNRP), -N (Rº) S (O) .RFE, carbocicyl, heterocyclic, aryl or heteroaryl, where each alkyl, alkenyl , alkynyl, heteroalkyl, carocicyl, heterocycyl, aryl and heteroaryl is independently and optionally substituted by one or more R ”; each of Rô, Rô, Rº, R , and Rº is independently hydrogen or C1-Cs alkyl each Rº is independently C1-Cs alkyl, oxo, cyano, - OR, -N (RºNRP), -C (OIN (RENRO), -N (ROIC (O) RA, aryl or hetero aryl, in which each aryl and heteroaryl is independent and optionally substituted by one or more R ; each R 'is independently halo, oxo, cyano, -ORº, - N (REN (RP), -C (O) N (RCNR ) or -N (Rº) C (O) RA; each R $ is independently C1 -Cs alkyl, cyano, -ORº, - N (REIRP), -C (O) N (RENRP) or -N (R) C (O) RA; né0o, 1,2,3ou4; and xé O, 1ou2.
[177]
177. The fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 comprises the structure of Formula (I-a): (Ro Oo "o
NM R2p Rº RE (Ia) or a pharmaceutically acceptable salt, ester, hydrate or tautomer thereof, in which: ring A is carbocicyl, heterocicyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $; M is absent, or is C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl or C1-Cs heteroalkyl, where each alkyl, alkenyl, alkynyl and heteroalkyl is optionally substituted by one or more Rº; each between R2º and Rº º is independently hydrogen or C1-C6 alkyl; or R º and R º , together with the carbon atom to which they are attached to form a carbonyl group or thiocarbonyl group; R * º is hydrogen, C1-Cs alkyl, C2-C6 alkenyl, C2-Ce alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) Rô, -C (O0) ORº, -OR , - N (RºNHRP), -C (OIN (RNRO), -N (R) C (O) RA, -S (O) .RF, -S (O) .N (Rº) (RP) or -N ( Rº) S (O)., RF, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by one or more R $; each of Rº is independently C1-Cs alkyl, C2-C6 alkenyl, C2-Cs6 alkynyl, C1-C6 heteroalkyl, halo, cyano, -C (O) Rô, - C (O0) ORE, -OR8, -N (REI (R ), -C (O) N (RENRPL), -N (R) C (OJ) RA, -S (O), RE, -S (O) .N (RºNRºP ) Or -N (R) S (O) .RF, where each alkyl, alkenyl, alkynyl and heteroalkyl is independently and optionally substituted by one or more R $; each Rº is independently C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-C6 heteroalkyl, halo, cyano, oxo, -C ( O) R , -
C (O0) ORE, -OR8, -N (Rº (RP), -C (O) IN (RURP), -N (ROIC (O) RA, -S (O), RE, -S (O) N (RNRP), -N (Rº) S (O) .RE, carbocicyl, heterocyclic, aryl or heteroaryl, where each alkyl, alkenyl, alkynyl, carbocicyl, heterocyclic, aryl and heteroaryl is independently and optionally substituted by one or more R; each of Rô, R8, Rº, R , and RF is independently hydrogen or C1-Cs alkyl; each Rº is independently C1-Cs alkyl, oxo, cyano, - OR, -N (RºNHRP), -C (OIN (RHRP), -N (RC (O) RA, aryl or heteroaryl, where each aryl and heteroaryl is independently and optionally substituted by one or more R '; each R' is independently halo, oxo, cyan, -OR , - N (RºN (RP), -C (O) IN (Rº NRP) or -N (Rº) C (O) Rº; each Rº is independently C1-Cs alkyl, cyan, -OR, - N (Rº) (RºP), -C (O) N (RºI (Rº) or -N (Rº) C (O) RA; né0o 1,2o0u3; oé0, 1,23,40u5; and xé0O, 1ou2.
[178]
178. Fusion polypeptide according to any of claims 83 to 167, characterized in that COF2 comprises an immunomodulatory imide drug (IMID) or a pharmaceutically acceptable salt thereof.
[179]
179. Fusion polypeptide according to any one of claims 83 to 167, characterized in that the COF2 comprises thalidomide or the like, or a pharmaceutically acceptable salt thereof.
[180]
180. Fusion polypeptide according to any of claims 83 to 167, characterized in that COF2 comprises lenalidomide, pomalidomide, thalidomide and 2- (4- (tert-butyl) phenyl) -N - ((2- (2,6-dioxopiperidin-3-yl) -1-0xoisoindolin-5-
il)] Mmethyl) acetamide, or a pharmaceutically acceptable salt thereof.
[181]
181. Fusion polypeptide according to any one of claims 83 to 167, characterized in that COF2 comprises a compound selected from the group consisting of: NH, SE AND O; or a pharmaceutically acceptable salt thereof.
[182]
182. The fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 comprises lenalidomide or pomalidomide or a pharmaceutically acceptable salt thereof.
[183]
183. The fusion polypeptide according to any one of claims 83 to 167, characterized by the fact that COF2 comprises lenalidomide or the like, or a pharmaceutically acceptable salt thereof.
[184]
184. The fusion polypeptide according to any one of claims 176 to 183, characterized by the fact that COF2 further comprises a linker (for example, where R * º in Formula (11) is L-Tag).
[185]
185. Fusion polypeptide according to any one of claims 176 to 184, characterized by the fact that R'º in Formula (11) is L-Tag, L is a linker selected from a linker disclosed in the Patent Publication International No. WO2017 / 024318 (for example, Figures 28 to 31), and Tag is selected from a dTAG Targeting Binder disclosed in International Patent Publication No. WO2017 / 024318 (for example, Table T, pages 119 to 129 ).
[186]
186. Fusion polypeptide according to any one of claims 83 to 184, characterized in that the COF2 comprises IMID (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) and a linker, wherein IMID (eg lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) is attached to the linker, for example, by means of a linker.
[187]
187. The fusion polypeptide according to any one of claims 184 to 186, characterized in that the COF2 / CRBN-binding polypeptide binds to the linker and in which the connection between the COF2-binding polypeptide / CRBN and IMID (eg lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) in the absence of the linker is not more than 0.0001, 0.001, 0.01, 0.1, 1 or 10% the binding between the COF2 / CRBN-binding polypeptide and the linker, for example, the COF2 / CRBN-binding polypeptide does not bind to IMiD (for example, lenalidomide or pomalide, or a pharmaceutically acceptable salt thereof), optionally wherein the COF2 / CRBN-binding polypeptide is selected from a dTAG disclosed in International Patent Publication No. WO2017 / 024318 (for example, pages 36 to 65).
[188]
188. Fusion polypeptide according to any one of claims 1 to 187, characterized in that the heterologous polypeptide is chosen from a cytoplasmic and / or nuclear polypeptide, or a transmembrane polypeptide, for example, a polypeptide heterologous in Table 2.
[189]
189. Fusion polypeptide according to claim 188, characterized by the fact that the cytoplasmic and / or nuclear polypeptide is selected from the group consisting of a component of the apoptosis pathway (for example, Caspase 9), a component of a CRISPR / Cas system (eg Cas9), a transcription factor (eg MITF, c-Myc, STAT3, STAT5, NF-capaB, beta-catenin, Notch, GLI or c-JUN) , Tet methylcytosine dioxigenase 2
(TET2), FKBP and Tau.
[190]
190. Fusion polypeptide according to claim 188, characterized by the fact that the transmembrane polypeptide is selected from the group consisting of CD62L, CCR1, CCR 2, CCR5, CCR7, CCRIO, CXCR2, CXCR3, CXCR4, CXCR6 , CTLAA, PD1, BTLA, VISTA, CD137L, CD80, CD86, TIGIT, CD3, CD8, CD19, CD22, CD20, BCMA and a chimeric antigen receptor (CAR).
[191]
191. Fusion polypeptide according to claim 188, characterized by the fact that the heterologous polypeptide is selected from the group consisting of a chemical antigen receptor (CAR), a component of a CRISPR / Cas system (e.g., Cas9), CD8, CD19, and CD22.
[192]
192. The fusion polypeptide according to claim 191, characterized by the fact that the heterologous polypeptide is a chimeric antigen (CAR) receptor.
[193]
193. Fusion polypeptide according to claim 192, characterized in that said CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a transmembrane domain and one or more domains of intracellular signaling.
[194]
194. The fusion polypeptide according to claim 193, characterized in that said intracellular signaling domain comprises one or more primary signaling domains.
[195]
195. Fusion polypeptide according to claim 193 or 194, characterized in that said intracellular signaling domain comprises one or more co-stimulating signaling domains.
[196]
196. A fusion polypeptide according to claim 194, characterized by the fact that one of said one or more primary signaling domains comprises a stimulating domain of CD3-
zeta.
[197]
197. Fusion polypeptide according to claim 195, characterized in that one or more of said co-stimulating signaling domains in an intracellular domain of a co-stimulating protein selected from the group consisting of CD27, CD28, 4- 1BB (CD137), OX40, GITR, CD30, CDA40, ICOS, BAFFR, HVEM, ICAM-1, antigen-1 associated with lymphocyte function (LFA-1), CD2, CDS, CD7, CD287, LIGHT, NKG2C, NKG2D , SLAMF7, NKp80, NKp30, NKp44, NKp46, CD160, B7-H3 and a linker that specifically binds to CD83.
[198]
198. Fusion polypeptide according to claim 197, characterized in that said one or more of said co-stimulating signaling domains comprises the 4-1BB co-stimulating domain.
[199]
199. The fusion polypeptide according to claim 197 or 198, characterized in that said one or more of said co-stimulating signal domains comprises the co-stimulating domain of CD28.
[200]
200. Fusion polypeptide according to any one of claims 193 to 199, characterized in that said antigen binding domain is an scFv.
[201]
201. Fusion polypeptide according to any one of claims 193 to 200, characterized in that said antigen binding domain binds an antigen selected from the group consisting of CD19; CD123; CD22; CD30; CD171; CS-1; lectin type C molecule-1, CD33; epidermal growth factor receptor (EGFRvII!) variant Ill; ganglioside G2 (GD2); ganglioside GD3; member of TNF receptor family; B cell maturation antigen; Tn antigen ((Tn Ag) or (GalNAca-Ser / Thr)); prostate-specific membrane antigen (PSMA); Receptor 1 orphan tyrosine kinase receptor (ROR1); tyrosine kinase 3 type Fms (FLT3); tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor alpha-2 subunit; Mesothelin; Alpha Interleukin 11 receptor (IL-11Ra); prostate stem cell antigen (PSCA); Protease serine 21; vascular endothelial growth factor receptor 2 (VEGFR2); Lewis antigen (Y); CD24; Platelet-derived growth factor beta receptor (PDGFR-beta); specific stage embryonic antigen-4 (SSEA-4); CD20; alpha folate receptor; ERBB2 receptor tyrosine protein kinase (Her2 / neu); mucin 1, associated with the cell surface (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); Prostasis; prostatic acid phosphatase (PAP); mutated stretching factor 2 (ELF2M); Ephrin B2; alpha fibroblast activation protein (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CAIX); proteasome subunit (prosome, macropaine), Type Beta, 9 (LMP2); glycoprotein 100 (gp100); oncogen polypeptide consisting of the breaking point clustering region (BCR) and Abelson murine leukemia viral oncogen homologue 1 (Abl) (bcr-abl); tyrosinase; ephrin type A receptor 2 (EphA2); Fucosyl GM1; Lewis sialyl adhesion molecule (sLe); ganglioside GM3; transglutaminase 5 (TGSS5); antigen associated with high molecular weight melanoma (HMWMAA); o-acetyl-GD2 ganglioside (OAcGD2); beta folate receptor; tumor endothelial marker 1 (TEM1 / CD248); marker 7 related to the endothelial tumor (TEM7R); claudin 6 (CLDN6); thyroid stimulating hormone receptor (TSHR); group 5 class C receptor coupled to protein G, member D (GPRC5D); X chromosome open reading frame 61 (CXORF61); CD97; CD179a; lymphoma kinase
plastic (ALK); polyisalic acid; placenta-specific 1 (PLAC1); Glucoceramide hexassaccharide portion of globoH (GloboH); mammary gland differentiation antigen (NY-BR-1); uroplacin 2 (UPK2); hepatitis A virus cell receptor 1 (HAVCR1); adenor-beta 3 receptor (ADRB3); panexin 3 (PANX3); receptor 20 coupled to the G protein (GPR20); lymphocyte antigen 6 complex, locus K 9 (LY6K); olfactory receptor 51E2 (OR51E2); gamma TOR alternating frame protein (TARP); Wilms' tumor protein (WT1); cancer / testis antigen 1 (NY-ESO-1); cancer / testicle antigen 2 (LAGE-1a); antigen 1 associated with melanoma (MAGE-A1); gene 6 variant of ETS translocation, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); antigen family X, member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); antigen-1 from melanoma cancer testicles (MAD-CT-1); antigen-2 from melanoma cancer testicles (MAD-CT-2); Fos-related antigen 1; tumor protein p53 (p53); mutant p53; prostein; survivor; telomerase; prostate carcinoma tumor antigen-1, melanoma antigen recognized by T 1 cells; mutant rat (Ras) sarcoma; human telomerase reverse transcriptase (hTERT); sarcoma translocation rupture points; apoptosis melanoma inhibitor (ML-IAP); ERG (transmembrane protease ETS fusion gene, serine 2 (TMPRSS2)); N-acetyl glucosaminyl transferase V (NA1I7); pax-3 paired box protein (PAX3); androgen receptor; cyclin B1; homologous derived from viral oncogen neuroblastoma of avian v-myc myelocytomatosis (MYCN); member C of the Ras family (RhoC); tyrosinase-related protein 2 (TRP-2); cytochrome P450 1B1 (CYP1B1); type CCCTC binding factor (zinc finger protein), squamous cell carcinoma antigen known by T 3 cells (SART3); paired box protein
Pax-5 (PAXS5); proacrosin sp32 binding protein (OY-TES1); lymphocyte-specific protein tyrosine kinase (LCK); kinase A anchor protein 4 (AKAP-4); synovial sarcoma, X 2 rupture point (SSX2); Receiver for advanced glycation endoproducts (RA-GE-1); ubiquitous renal 1 (RU1); ubiquitous renal 2 (RU2); legumaine; human papilloma virus E6 (HPV E6); human papilloma virus E7 (HPV E7); intestinal carboxyl esterase; mutated 70-2 heat shock protein (mut hsp70-2); CD79a; CD79b; CD72; leukocyte-associated immunoglobulin type 1 receptor (LAIR1); IgA receptor Fc fragment (FCAR or CD89); member 2 of subfamily A of leukocyte immunoglobulin-like receptor (LILRA2); member of the CD300 molecule-like family (CD300LF); A member of family 12 of type C lectin domain (CLEC12A); bone marrow stromal cell antigen 2 (BST2); mucin hormone receptor 2 type containing EGF type module (EMR2); lymphocyte antigen 75 (LY75); glyptone-3 (GPC3); Fc 5 receptor type (FCRL5); and lambda immunoglobulin-like polypeptide 1 (IGLL1).
[202]
202. Fusion polypeptide according to any one of claims 193 to 200, characterized in that said antigen is chosen from CD19, CD22, BCMA, CD20, CD123, EGFRVvIIl, or mesothelin.
[203]
203. Fusion polypeptide according to any one of claims 193 to 200, characterized by the fact that said antigen is CD19.
[204]
204. Fusion polypeptide according to any one of claims 193 to 200, characterized in that said antigen is CD22.
[205]
205. Fusion polypeptide according to any one of claims 193 to 200, characterized by the fact that said antigen is BCMA.
[206]
206. Fusion polypeptide according to any one of claims 193 to 200, characterized by the fact that said antigen is CD20.
[207]
207. Fusion polypeptide according to any one of claims 193 to 200, characterized in that said antigen is CD123.
[208]
208. Fusion polypeptide according to any one of claims 193 to 200, characterized by the fact that said antigen is EGFRvIII.
[209]
209. Nucleic acid molecule characterized by the fact that it encodes the fusion polypeptide according to any one of claims 1a 208.
[210]
210. Vector characterized by the fact that it comprises the nucleic acid molecule, as defined in claim 209.
[211]
211. Vector, according to claim 210, characterized by the fact that said vector is a viral vector.
[212]
212. Vector, according to claim 210, characterized by the fact that said vector is a lentiviral vector.
[213]
213. Vector particle characterized by the fact that it comprises the vector, according to any one of claims 210 to 212.
[214]
214. A cell, for example, a host cell characterized by the fact that it comprises the fusion polypeptide according to any one of claims 1a 208, the nucleic acid molecule as defined in claim 209 or the vector, as defined in any of claims 210 to 212.
[215]
215. Cell according to claim 214, characterized by the fact that said cell, for example, host cell, is a mammalian cell, for example, a human cell, for example, a human effector cell , for example, a human T cell or a human NK cell.
[216]
216. A cell according to claim 214 or 215, characterized by the fact that said cell, for example, host cell, is a CAR expression cell, for example, a CAR T cell.
[217]
217. Cell, according to claim 214 or 215, characterized by the fact that said cell, for example, host cell, comprises a component of a CRISPR / Cas system.
[218]
218. Cell according to any of claims 214 to 217, characterized by the fact that said cell, for example, host cell, is a human cancer cell, for example, a human tumor cell.
[219]
219. Cell according to any one of claims 214 to 218, characterized in that said cell, for example, host cell, comprises a ubiquitin ligase complex, for example, an E3 ubiquitin ligase complex, characterized by the fact that the ubiquitin ligase complex comprises CRBN.
[220]
220. Cell according to any one of claims 214 to 219, characterized in that the cell comprises the fusion polypeptide as defined in any of the claims | 208 or the cell comprises a nucleic acid molecule encoding the fusion polypeptide as defined in any one of claims 1 to 208, wherein, when the cell is brought into contact with COF1, for example, an excess of COF1: i ) the association of the COF1 / CRBN binding polypeptide with CRBN is increased by at least, for example, 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the COFI / CRBN binding polypeptide with CRBN when the cell is not put in contact with COF1, for example,
as measured by an assay described in this document, for example, immunoprecipitation;
ii) the association of the fusion polypeptide with CRBN is increased at least, for example, 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the fusion polypeptide with CRBN when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
iii) the ubiquitination of the heterologous polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times in comparison comparison with the ubiquitination of the heterologous polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document;
iv) the ubiquitination of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times with - comparison with the ubiquitination of the fusion polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document;
v) the degradation of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the degradation of the fusion polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis ; or vi) the expression level of the fusion polypeptide is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the expression level of the fusion polypeptide when the cell is not brought into contact with COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis of flow.
[221]
221. Cell according to claims 214 to 220, characterized by the fact that said cell still comprises COF1, for example, lenalidomide or pomalidomide or a pharmaceutically acceptable salt thereof.
[222]
222. Cell according to any one of claims 214 to 219, characterized in that the cell comprises the fusion polypeptide as defined in any one of claims 80 to 82, 84 to 107, or 188 to 208 or the cell comprises a nucleic acid molecule encoding the fusion polypeptide according to any one of claims 80 to 82, 84 to 107, or 188 to 208, wherein, in the absence of a stabilizing compound, the polypeptide of fusion is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%, 90% or more of the fusion polypeptide is degraded, for example, as measured by an assay described in this document , for example, a Western blot analysis or a flow cytometry analysis.
[223]
223. Cell according to any one of claims 214 to 219, characterized in that the cell comprises the fusion polypeptide according to any one of claims 83 to 208 or the cell comprises an acid molecule nucleic encoding the fusion polypeptide according to any one of claims 83 188 to 208, wherein, in the absence of a stabilizing compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%, 90% or more of the fusion polypeptide is degraded, for example, as measured by an assay described in this document, for example, a Western analysis blot or cytology analysis
flow methodology.
[224]
224. A cell according to claim 222 or 223, characterized by the fact that it further comprises a protease capable of cleaving said heterologous protease cleavage site.
[225]
225. Cell according to any one of claims 222 to 224, characterized by the fact that it is placed in contact with a stabilizing compound, for example, an excess of a stabilizing compound: i) the degradation domain assumes a conformation more resistant to cell degradation in relation to a conformation in the absence of the stabilizing compound; ii) the conformation of the fusion polypeptide is more permissible to cleavage at the heterologous protease cleavage site in relation to a conformation in the absence of the stabilizing compound; or iii) the expression level of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the expression level of the fusion polypeptide when the cell is not brought into contact with the stabilizing compound, for example, as measured by an assay described in this document, for example, an analysis of Western blot or flow cytometry analysis.
[226]
226. Cell according to any one of claims 222 to 225, characterized by the fact that it further comprises a stabilizing compound.
[227]
227. Cell according to any one of claims 222 to 226, characterized by the fact that the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof, and optionally in which the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[228]
228. Cell according to any of claims 222 or 224 to 227, characterized by the fact that when the cell is brought into contact with either a stabilizing compound, for example, an excess of a stabilization, as with COF1, for example, an excess of COF1:
i) the association of the COF1 / CRBN binding polypeptide with CRBN is increased by at least 10 times, for example, 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the COFI / CRBN binding polypeptide with CRBN when the cell is only brought into contact with the stabilizing compound, but not with COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
ii) the association of the fusion polypeptide with CRBN is increased at least, for example, 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the fusion polypeptide with CRBN when the cell is only placed in contact with the stabilizing compound, but not with COF1, for example, as measured by an assay described in this document, for example, immunoprecipitation;
iii) the ubiquitination of the heterologous polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times in comparison comparison with the ubiquitination of the heterologous polypeptide when the cell is only placed in contact with the stabilizing compound, but not with COF1, for example, as measured by an assay described in this document;
iv) the ubiquitination of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times with -
comparison with the ubiquitination of the fusion polypeptide when the cell is only brought into contact with the stabilizing compound, but not with COF1, for example, as measured by an assay described in this document; v) the degradation of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the degradation of the fusion polypeptide when the cell is only brought into contact with the stabilizing compound, but not with COF1, for example, as measured by an assay described in this document, for example, a Western analysis blot or flow cytometry analysis; or vi) the expression level of the fusion polypeptide is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the expression level of the fusion polypeptide when the cell is only brought into contact with the stabilizing compound, but not with COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or flow cytometry analysis.
[229]
229. Cell according to any one of claims 222 or 224 to 228, characterized in that it further comprises COF1, for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof.
[230]
230. Cell according to any one of claims 223 to 229, characterized by the fact that when the cell is brought into contact with both a stabilizing compound, for example, an excess of a stabilizing compound, regarding COF2, for example, an excess of COF2: i) the association of the COF2 / CRBN-binding polypeptide with CRBN is increased by at least 10 times, 50 times, 100 times, 1,000 times or 10,000 times in comparison with the association of the COF2 / CRBN-binding polypeptide with CRBN when the cell is only brought into contact with the stabilizing compound, but not with COF2, for example, as measured by an assay described in this document, for example, immunoprecipitation. dog;
ii) the association of the fusion polypeptide with CRBN is increased at least, for example, 10 times, 50 times, 100 times, 1,000 times or 10,000 times compared to the association of the fusion polypeptide with CRBN when the cell is only placed in contact with the stabilizing compound, but not with COF 2, for example, as measured by an assay described in this document, for example, immunoprecipitation;
iii) the ubiquitination of the heterologous polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times in comparison comparison with the ubiquitination of the heterologous polypeptide when the cell is only placed in contact with the stabilizing compound, but not with COF2, for example, as measured by an assay described in this document;
iv) the ubiquitination of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times with - comparison with the ubiquitination of the fusion polypeptide when the cell is only brought into contact with the stabilizing compound, but not with COF2, for example, as measured by an assay described in this document;
v) the degradation of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times in comparison
interaction with the degradation of the fusion polypeptide when the cell is only brought into contact with the stabilizing compound, but not with COF 2, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis; or vi) the expression level of the fusion polypeptide is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the expression level of the fusion polypeptide when the cell is only brought into contact with the stabilizing compound, but not with COF2, for example, as measured by an assay described in this document, for example, a Western blot analysis or flow cytometry analysis.
[231]
231. Cell according to any one of claims 223 to 230, characterized by the fact that it further comprises COF 2, for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof.
[232]
232. Cell according to any of claims 214 to 231, characterized by the fact that the heterologous polypeptide is a chimeric antigen (CAR) receptor, optionally in which the CAR comprises, in an N- direction terminal to C-terminal, an antigen binding domain, a transmembrane domain and one or more intracellular signaling domains.
[233]
233. Pharmaceutical composition characterized by the fact that it comprises the fusion polypeptide, as defined in any one of claims 1 to 208 or the cell, as defined in any one of claims 214 to 232, and a carrier, excipient or pharmaceutically stabilizer acceptable.
[234]
234. Method for producing the cell according to any one of claims 214 to 232, characterized in that said method comprises providing a cell, for example, a cell.
immuno-protective cell, with the nucleic acid molecule, as defined in claim 209, the vector, as defined in any one of claims 210 to 212, or the viral particle, as defined in claim 213.
[235]
235. Method for degrading a fusion polypeptide characterized by the fact that it comprises placing the fusion polypeptide according to any one of claims 1 to 79 or 188 to 208 or a cell characterized by the fact that it comprises said polypeptide fusion peptide in contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof), optionally where, in the presence of COF1 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof) , the expression level of said fusion polypeptide is substantially decreased, for example, by at least about 1, 2,3, 4,5, 6,7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of said fusion polypeptide in the absence of COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof), for example , as measured by a test described in this document, for example, an analysis and Western blot or flow cytometry analysis.
[236]
236. Method according to claim 235, characterized in that the fusion polypeptide or cell is brought into contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) ex vivo.
[237]
237. Method according to claim 235, characterized in that the fusion polypeptide or cell is brought into contact with COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof) in vivo.
[238]
238. Method for regulating the expression of a fusion polypeptide characterized by the fact that it comprises:
i) placing the fusion polypeptide according to any one of claims 80 to 208 or a cell comprising said fusion polypeptide with a stabilizing compound, optionally in which, in the presence of the stabilizing compound: a) the domain degradation assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; b) the conformation of the fusion polypeptide is more permissive to cleavage at the heterologous protease cleavage site compared to a conformation in the absence of the stabilizing compound; or c) the expression level of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the expression level of the fusion polypeptide in the absence of the stabilizing compound, for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis of flow.
[239]
239. Method according to claim 238, characterized in that it further comprises, after step ii): ii) placing the fusion polypeptide according to any one of claims 83 to 208 or a cell comprising the said fusion polypeptide, in contact with COF1 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof), optionally where in the presence of COF1 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt of the same ), the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1,2,3,4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 per cent in relation to the expression level of the fusion polypeptide after step i) and before step ii), for example, as measured by an assay described in this document, by example, a Western blot analysis or a flow cytometry analysis.
[240]
240. Method according to claim 238 or 239, characterized in that the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof, and optionally wherein the degradation domain comprises the amino acid sequence SEQ ID NO: 46.
[241]
241. Method according to any one of claims 238 to 240, characterized in that the fusion polypeptide or cell is brought into contact with COF1 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof) and / or the ex vivo stabilizing compound.
[242]
242. Method according to any of claims 238 to 240, characterized by the fact that the fusion polypeptide or cell is brought into contact with COF1 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt and / or the in vivo stabilizing compound.
[243]
243. Method for regulating the expression of a fusion polypeptide characterized by the fact that it comprises: i) placing the fusion polypeptide according to any one of claims 83 to 208 or a cell comprising said fusion polypeptide, in contact with a stabilizing compound, optionally in which, in the presence of the stabilizing compound: a) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; b) the conformation of the fusion polypeptide is more permissive to cleavage at the heterologous protease cleavage site compared to a conformation in the absence of the stabilizing compound; or c) the level of expression of the fusion polypeptide is increased
at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the expression level of the polypeptide melting in the absence of the stabilizing compound, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[244]
244. Method according to claim 243, characterized in that it further comprises, after step i): ii) placing the fusion polypeptide according to any one of claims 83 to 208 or a cell comprising the said fusion polypeptide, in contact with COF2 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof), optionally where in the presence of COF2 (for example, lenalidomide or pomalidomide, or a pharmaceutically acceptable salt of the same ), the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1,2,3,4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 per cent in relation to the expression level of the fusion polypeptide after step i) and before step ii), for example, as measured by an assay described in this document, by example, a Western blot analysis or a flow cytometry analysis.
[245]
245. Method according to claim 243 or 244, characterized in that the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof, and optionally wherein the degradation domain comprises the amino acid sequence SEQ ID NO: 46.
[246]
246. Method according to any one of claims 243 to 245, characterized in that the fusion polypeptide or cell is brought into contact with COF2 (for example, lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt thereof) and / or the ex vivo stabilizing compound.
[247]
247. Method according to any one of claims 243 to 245, characterized in that the fusion polypeptide or cell is brought into contact with COF2 (eg lenalido-mide or pomalidomide, or a pharmaceutically acceptable salt and / or the in vivo stabilizing compound.
[248]
248. Method according to any one of claims 234 to 247, characterized by the fact that the heterologous polypeptide is a chimeric antigen (CAR) receptor, optionally in which the CAR comprises, in a direction of N- terminal to C-terminal, an antigen binding domain, a transmembrane domain and one or more intracellular signaling domains.
[249]
249. Method for producing a cell characterized by the fact that it comprises: i) providing a cell comprising a nucleic acid molecule encoding a fusion polypeptide comprising a compound of formula 1, (COF1 / CRBN binding polypeptide and a receptor for chimeric antigen (CAR), optionally wherein the CAR comprises, in an N-terminal to C-terminal direction, an antigen binding domain, a transmembrane domain and one or more intracellular signaling domains; and li) placing the cell ex vivo in contact with COF1, optionally where: in the presence of COF1, the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide in the absence of COF1, for example, as measured by an assay described in this document, for example, a Western blot analysis or an analysis and flow cytometry, in which the
the formula (l) is: x (Rº)
R2a R2 '(1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, wherein: XéOousS; R 'is C1-Cs alkyl, C2-Cs alkenyl, C2-C6 alkynyl, C1-Cs6 heteroalkyl, carbocicyl, heterocycyl, aryl or heteroaryl, each of which is independent and optionally substituted by one or more R $; each between R º and R " it is independently hydrogen or C1-C6 alkyl; or R º and R2º , together with the carbon atom to which they are attached, form a carbonyl group or a thiocarbonyl group; each of R is independently C1-Cs alkyl, C2-C6 alamenyl Ca-Ca alovinyl O0 hatarnaltyl halo, siana, -ONIDIDA teroaryl, in which each alkyl, alkenyl, alkynyl, heteroalkyl, carococyl, heterocyclic, aryl and heteroaryl is independent and optionally replaced by one or more R; each of R4, R8, Rº, RP, and RE is independently hydrogen or C1-Cs alkyl; each Rô is independently C1-Cç alkyl, oxo, cyan, -
OR, -N (RºNHRP), -C (OIN (RHRP), -N (R) C (O) RA, aryl or heteroaryl, where each aryl and heteroaryl is independently and optionally substituted by one or more R each R 'is independently halo, oxo, cyano, -OR , - N (RºNRP), -C (O) N (RNRP) or -N (R) C (O) R'; each Rº is independently C1- Alkyl, cyano, -OR , - N (REN (RP), -C (O) N (RºNR ) Or -N (Rº) C (O) RA; né0o0 1,2 3ou4; and xé O, 1ou2 .
[250]
250. Method according to claim 249, characterized by the fact that after the cell is brought into contact with COF1 ex vivo, the cell proliferation is increased by at least, for example, 1.2 times, 1, 5 times, 2 times, 5 times or 10 times in relation to cell proliferation before contact with COF1.
[251]
251. The method of claim 250, characterized by the fact that COF1 is lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof.
[252]
252. Method according to claim 249 or 250, characterized in that the COF1 / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6 , 11-15, 40, 41-43, 77, 78, 84-86, and 100 (for example, the COF1 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 3).
[253]
253. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) placing a cell comprising the fusion polypeptide, according to any one of claims 1 to 208 in contact with COF1 ex vivo, optionally where:
in the presence of COF1, the level of expression of the fusion polypeptide is decreased, for example, by at least about 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide before the cell is brought into contact with COF1 ex vivo, and ii) administering to the individual an effective amount of the cell , optionally in which the method further comprises, after step i) and before step ii): reduce the amount of COF1 in contact with the cell, for example, inside and / or surrounding the cell, thus treating the disease.
[254]
254. Method according to claim 253, characterized by the fact that it further comprises, after step ii): iii) administering to the individual an effective amount of COF1, optionally in which the administration of COF1 decreases, for example, at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step ii) and before step iii), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b ) the administration of COF1 is in response to an occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) administration of COF1 reduces or prevents an ad effect - verse.
[255]
255. Method according to claim 254, characterized by the fact that it further comprises, after step iii): iv) discontinuing the administration of COF1, optionally in which discontinuing the administration of COF1 increases, for example,
at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the level of expression of the fusion polypeptide in relation to expression level of the fusion polypeptide after step iii) and before step iv) (for example, where discontinuing COF1 administration restores the expression level of the fusion polypeptide to the expression level after step ii) and before from step iii)), optionally where: a) the individual has had a relapse, is relapsed or is expected to have a relapse, b) discontinuation of COF1 administration is in response to a tumor relapse in the individual , or in response to waiting for a relapse in the individual, and / or c) discontinuation of COF1 administration treats or prevents a tumor relapse.
[256]
256. Method, according to claim 255, characterized by the fact that it also comprises, after step iv): v) repeating step iii) and / or iv), thus treating the disease.
[257]
257. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) administering to the individual an effective amount of a cell comprising the fusion polypeptide according to any one of claims 1 to 208, optionally in which the cell is brought into contact with COF1 ex vivo prior to administration, optionally in which: in the presence of COF1, the level of expression of the fusion polypeptide is decreased, for example , by at least about 1,2, 3,4, 5, 6,7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent in relation to the level expression of the fusion polypeptide before the cell is brought into contact with COF1 ex vivo, optionally in which after the cell is brought into contact with COF1 ex vivo and before the cell is administered to the individual, the amount of COF1 in contact with the cell, for example, inside and / or surrounding the cell, is reduced, thus treating the disease. The.
[258]
258. Method according to claim 257, characterized by the fact that the cell is not brought into contact with COF1 ex vivo prior to administration.
[259]
259. Method according to claim 257 or 258, characterized by the fact that it further comprises, after step): ii) administering to the individual an effective amount of COF1, optionally in which the administration of COF1 decreases, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 7O, 80, 90, or 100 percent the expression level of the polypeptide of fusion in relation to the expression level of the fusion polypeptide after step i) and before step ii), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) administration COF1 is in response to the occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction in the individual, and / or c) administration of COF1 reduces or prevents an adverse effect.
[260]
260. Method according to claim 259, characterized by the fact that it further comprises, after step ii): iii) discontinuing the administration of COF1, optionally in which discontinuing the administration of COF1 increases, for example, by at least minus about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step ii) and before step iii) (for example, where discontinuing COF1 administration restores the expression level of the fusion polypeptide to the expression level after step i) and before step li)), optionally where: a) the individual has had a relapse, is relapsing or is expected to have a relapse, b) discontinuation of COF1 administration is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) discontinuing COF1 administration treats or prevents a tumor relapse.
[261]
261. Method, according to claim 260, characterized by the fact that it also comprises, after step iii): iv) repeating step ii) and / or iii), thus treating the disease.
[262]
262. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) administering an effective amount of COF1 to the individual, in which the individual comprises a cell comprising the polypeptide; fusion peptide according to any one of claims 1 to 208, optionally wherein the administration of COF1 decreases, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide relative to the expression level of the fusion polypeptide before COF1 administration, optionally where : a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the administration of COF1 is in response to an occurrence
of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) administration of COF1 reduces or prevents an adverse effect.
[263]
263. Method according to claim 262, characterized by the fact that it further comprises, after step i): ii) discontinuing the administration of COF1, optionally in which discontinuing the administration of COF1 increases, for example, by at least minus about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step |) and before step ii) (for example, where discontinuing the administration of COF1 restores the level of expression of the fusion polypeptide to the level of expression before administration of COF1), optionally where: a) the individual has had a relapse, is relapsed or is expected to have a relapse, b) discontinuation of COF1 administration is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) discontinuation of COF1 administration treats or prevents a r tumor elapse.
[264]
264. Method, according to claim 263, characterized by the fact that it also comprises, after step ii): iii) repeating step i) and / or ii), thus treating the disease.
[265]
265. The method of any one of claims 253 to 264, wherein COF1 is lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof, optionally wherein the COF1 / CRBN-binding polypeptide comprises or consists of a sequence number of amino acids selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-86, and 100 (for example, the COFI / CRBN comprises or consists of the amino acid sequence of SEQ ID NO: 3).
[266]
266. Method according to any one of claims 259 to 265, characterized in that COF1 is lenalidomide, or a pharmaceutically acceptable salt thereof, optionally in which lenalidomide, or a pharmaceutically acceptable salt thereof, is admissible administered, for example, at 2.5 mg, 5 mg, 10 mg, 15 mg, or 25 mg per day.
[267]
267. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) administering to the subject: (1) a stabilizing compound, and (2) an effective amount of a cell comprising the fusion polypeptide according to any one of claims 80 to 208 or an effective amount of a cell comprising the fusion polypeptide according to any one of claims 83 to 208, optionally in that: the expression level of the fusion polypeptide in the presence of the stabilizing compound is, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times - zes, 40 times or 50 times greater than the level of expression of the fusion polypeptide in the absence of the stabilizing compound, thus treating the disease.
[268]
268. Method according to claim 267, characterized by the fact that it further comprises, after step i): ii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilization reduces, for example, at least about 1.5 times
zes, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression of the fusion polypeptide after step |) and before step ii), optionally where: a) the individual responded to the treatment in step i) (for example, the individual has a complete response to the treatment in step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment in step i) is effective in the individual), and / or b) discontinuation of the administration of the stabilizing compound is in response to an individual's response to the treatment in the step i) (for example, the individual has a complete response to the treatment in step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment in step i) is effective in the individual ).
[269]
269. Method according to claim 267, characterized by the fact that it further comprises, after step i): iii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilization reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the polypeptide of fusion in relation to the expression of the fusion polypeptide after step |) and before step ii), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the discontinuation of administration of the stabilizing compound is in response to the occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) discontinuation of the administration of the stabilizing compound reduces or prevents an adverse effect.
[270]
270. Method according to claim 267, characterized by the fact that it further comprises, after step i): iv) discontinuing the administration of the stabilizing compound and administering to the individual an effective amount of COF1 or COF2, optionally where step iv) reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression of the fusion polypeptide after step i) and before step iv), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b ) step iv) is in response to the occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) step iv) reduces or prevents an adverse effect.
[271]
271. Method according to claim 270, characterized by the fact that the adverse effect is an acute toxicity.
[272]
272. Method according to claim 270 or 271, characterized by the fact that it further comprises, after step iv): v) discontinuing the administration of COF1 or COF2, for example, after the amount of cells expressing the polypeptide of melting on the surface is less than a predefined value, for example, for 1 day, 5 days, 10 days or 15 days.
[273]
273. Method according to any one of claims 268 to 272, characterized in that it further comprises after step ii), li), iv), or v): vi) administering an effective amount of a compound of stabilization, optionally in which the administration of the stabilizing compound increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step ii), ili), iv), or v) and before step vi), optionally where: the individual has had a relapse, is relapsed or is expected to have a relapse, b) administration of the stabilizing compound is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) administration of the stabilizing compound treats or prevents tumor relapse.
[274]
274. Method, according to claim 273, characterized by the fact that it further comprises, after step vi): vii) repeating step iii), iv), v) or vi), thus treating the disease .
[275]
275. Method according to any one of claims 267 to 274, characterized by the fact that it also comprises, before step |): viii) putting the cell in contact with an ex vivo stabilization compound, optionally where the level of expression of the fusion polypeptide in the presence of the stabilizing compound is, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times , 30 times, 40 times or 50 times higher than the expression level of the fusion polypeptide in the absence of the stabilization compound.
[276]
276. Method according to any one of claims 267 to 274, characterized by the fact that the cell is not brought into contact with the ex vivo stabilizing compound prior to administration.
[277]
277. Method according to claim 276, characterized by the fact that the cell is not brought into contact with any one of: the stabilizing compound, COF1, or COF2 ex vivo before administration.
[278]
278. Method according to any one of claims 267 to 277, characterized in that the stabilizing compound is bazedoxifene, or a pharmaceutically acceptable salt thereof, and optionally in which the degradation domain comprises the amino acid sequence of SEQ ID NO: 46.
[279]
279. Method according to any one of claims 270 to 278, characterized in that COF1 is lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof, optionally in which the COFI / CRBN-binding polypeptide buys - endorse or consist of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84- 86, and 100 (for example, the polypeptide binding to COF1I / CRBN comprises or consists of the amino acid sequence of SEQ ID NO: 3).
[280]
280. Method according to any of claims 270 to 278, characterized in that COF2 is lenalidomide or pomalidomide, or a pharmaceutically acceptable salt thereof, optionally in which the COF2 / CRBN-binding polypeptide comprises or consists of an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-6, 11-15, 40, 41-43, 77, 78, 84-86, and 100 (for example, the binding polypeptide COF1 / CRBN comprises or consists of the amino acid sequence of SEQ ID NO: 3).
[281]
281. Method according to any of claims 270 to 280, characterized by the fact that COF1 or COF is lena-lidomide, or a pharmaceutically acceptable salt thereof, optionally in which lenalidomide, or a pharmaceutically acceptable salt
it is administered at, for example, 2.5 mg, 5 mg, 10 mg, mg or 25 mg per day.
[282]
282. The method of any one of claims 253 to 281, wherein the heterologous polypeptide of the fusion polypeptide is a chimeric antigen (CAR) receptor, optionally wherein the CAR comprises, in an N-terminal direction. for C-terminal, an antigen binding domain, a transmembrane domain and one or more intracellular signaling domains.
[283]
283. Fusion polypeptide, nucleic acid molecule, vector, viral particle, cell or pharmaceutical composition according to any one of claims 1 to 233, characterized in that it is for use as a medicament.
[284]
284. Fusion polypeptide, nucleic acid molecule, vector, viral particle, cell or pharmaceutical composition according to any one of claims 1 to 233, characterized in that it is for use in the treatment of an individual who has a disease associated with the expression of a tumor antigen, for example, for use in the method, as defined in any one of claims 253 to 282.
[285]
285. Method or composition for use according to any one of claims 253 to 284, characterized by the fact that the disease associated with the expression of an antigen tumor is a cancer.
[286]
286. Method or composition for use, according to claim 285, characterized by the fact that the cancer is mesothelioma (eg malignant pleural mesothelioma), for example, in an individual who has progressed on at least one therapy previous pattern; lung cancer (eg, non-small cell lung cancer, small cell lung cancer, squamous cell lung cancer or large cell lung cancer); pancreatic cancer (for example, pancreatic ductal adenocarcinoma or metastatic pancreatic ductal adenocarcinoma (PDA), for example, in an individual who has progressed on at least one previous standard therapy); esophageal adenocarcinoma, ovarian cancer (for example, serous epithelial ovarian cancer, for example, in an individual who has progressed after at least a previous standard therapy regimen), breast cancer, colorectal cancer, cancer bladder or any combination thereof.
[287]
287. Method or composition for use according to any one of claims 253 to 284, characterized by the fact that the disease associated with the expression of a tumor antigen is a hematological cancer, for example, a chosen hematological cancer from a leukemia or lymphoma.
[288]
288. Method or composition for using, according to claim 287, characterized by the fact that cancer is chosen from: chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), multiple myeloma, leukemia acute lymphoid (ALL), Hodgkin's lymphoma, acute B-cell lymphoid leukemia (BALL), acute T-cell lymphoid leukemia (TALL), small lymphocytic leukemia (SLL), B-cell prolinfocytic leukemia, plasma dendritic cell neoplasm - blast cytoid, Burkitt's lymphoma, diffuse large B-cell lymphoma (DLBCL), DLBCL associated with chronic inflammation, chronic myeloid leukemia, myeloproliferative neoplasms, follicular lymphoma, pediatric follicular lymphoma, capillary cell leukemia, small cell follicular lymphoma or large cell, malignant lymphoproliferative conditions, MALT lymphoma (extranodal marginal lymphoma of lymphoid tissue associated with mucosa), marginal zone lymphoma, myelodysplasia, myelodysplastic syndrome, lin non-Hodgkin's form, plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, Waldenstrom macroglobulinemia, splenic marginal zone lymphoma, splenic lymphoma / leukemia, small splenic red pulp B cell lymphoma, capillary cell leukemia variant, lymphoplasmacytic lymphoma
a, heavy chain disease, plasma cell myeloma, solitary bone plasmacytoma, extra-osseous plasmacytoma, nodal marginal zone lymphoma, pediatric nodal marginal zone lymphoma, primary primary cutaneous follicle lymphoma, lymphoid granulomatosis, cell lymphoma Large primary mediastinal (thymic) B, large intravascular B-cell lymphoma, large ALK + B-cell lymphoma, large B-cell lymphoma arising in HHVB8-associated multi-centric Castleman disease, primary effusion lymphoma, cell lymphoma B, acute myeloid leukemia (AML), or non-classifiable lymphoma.
[289]
289. Method or composition for use according to claim 287, characterized by the fact that the cancer is chosen from MCL, CLL, ALL, Hodgkin's lymphoma, AML or multiple myeloma.
[290]
290. Method or composition for use, according to any one of claims 253 to 289, characterized by the fact that said cell is autologous to said individual.
[291]
291. Method or composition for use, according to any one of claims 253 to 289, characterized by the fact that said cell is allogeneic to said infinite.
[292]
292. Method or composition for use according to any one of claims 253 to 291, characterized in that said cell is a CAR expression cell, for example, a CAR T cell.
[293]
293. Method or composition for use according to any one of claims 253 to 292, characterized in that the individual was administered with a cell that expresses at least one fusion polypeptide, as defined in any of the claims. 1 to 208 before administration of COF1 or COF 2.
[294]
294. Method to identify a genetic element associated with a specific biological phenotype, for example, a genetic element associated with the development and / or progression of cancer,
characterized by the fact that the method comprises the steps of: i) modulating the expression of the fusion polypeptide according to any one of claims 1 to 208 in cells by exposing said cell to COF1, for example, lenalidomide, or a pharmaceutically acceptable salt thereof, (ii) select for cells with a phenotype of interest, for example, a phenotype associated with the development and / or progression of a cancer, and (iii) identify said fusion polypeptide that induces said phenotype of interest, in which the exposure of said cell to COF1, for example, lenalidomide, or a pharmaceutically acceptable salt thereof, decreases, for example, by at least about 1, 2, 3, 4, 5, 6 , 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of said fusion polypeptide in relation to the expression level of said fusion polypeptide before exposure to COF1, for example, lena-lidomide, or a pharmaceutically acceptable salt thereof.
[295]
295. Method to identify a genetic element associated with a specific biological phenotype, for example, a genetic element associated with the development and / or progression of a cancer, characterized by the fact that the method comprises the steps of: i) modulating the expression of the fusion polypeptide according to any one of claims 80 to 82, 84 to 208 or the expression of the fusion polypeptide, as defined in any one of claims 83 to 208, in cells through exposure of said cell to a stabilizing compound, for example, bazedoxifene, or a pharmaceutically acceptable salt thereof, and then to COF1 or COF2, for example lenalidomide, or a pharmaceutically acceptable salt thereof, (ii) select for cells with a phenotype of interest,
for example, a phenotype associated with the development and / or progression of cancer, and (iii) identifying said fusion polypeptide that induces said phenotype of interest, in which the exposure of said cell to the stabilizing compound, for example, bazedoxifene, or a pharmaceutically acceptable salt thereof, increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 ve - times, 40 times or 50 times the level of expression of the fusion polypeptide in relation to the level of expression of the fusion polypeptide before exposure to the stabilizing compound, for example, bazedoxifene, or a pharmaceutically acceptable salt thereof , and wherein the exposure of said cell to COF1 or COF 2, for example, lenalidomide, or a pharmaceutically acceptable salt thereof, decreases, for example, by at least about 1, 2, 3, 4, 5 , 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of said polypeptide of f use in relation to the expression level of said fusion polypeptide after exposure to the stabilizing compound and before exposure to COF1 or COF2, for example, lenalidomide, or a pharmaceutically acceptable salt thereof.
[296]
296. Fusion polypeptide comprising a compound of Formula (Ill) (COF3) / CRBN (cereblon) -binding polypeptide and a heterologous polypeptide, for example, a heterologous mammalian bacterial or viral polypeptide, characterized by the fact that the compound Formula (Ill) is: Oo O
NH (Ra CRS ROX Rx Ra (1) or a pharmaceutically acceptable salt, ester, hydrate, solvate or tautomer thereof, where:
X1: is CR3;
== ---- is optionally a double bond when X: is CR3 and Ra is absent;
each R, is independently C1-Cs alkyl, C1-Ce haloalkyl, C1-Cs hydroxyalkyl or halo, or two R1, together with the carbon atom to which they are attached, form a 5- or 6-membered heterocyclic ring, or two R1, when in adjacent atoms, together with the atoms to which they are attached, form a Cs-C10 aryl or a 5- or 6-membered heteroaryl ring comprising 1 to 3 heteroatoms selected from O, Ne S;
R2 is hydrogen, C1-Cs alkyl, -C (O) CC «alkyl, - C (O) (CH2) 0-3- Ce-C10 aryl, -C (0) O (CH2) 0-3-Ce- C1oaryl, C6-C10o aryl or 5- or 6-membered heteroaryl comprising 1 to 3 heteroatoms selected from O, N, and S, C3-Cg carbocicyl, or 5 or 7 heterocyclyl comprising 1 to 3 heteroatoms selected from O, N, and S, where the alkyl is optionally substituted by one or more Ra '; and aryl, heteroaryl, carbocicyl and heterocicyl are optionally substituted by one or more Rs, or
R1 and R2, when in adjacent atoms, together with the atoms to which they are attached, form a 5- or 6-membered heterocyclic ring;
R3 is hydrogen or R; 3 is absent when ------ is a double bond;
each R, is independently selected from - C (O) ORs, -C (O) INRR6, -NReC (O) R6, halo, -OH, -NH> 2, cyano, Cs-C1o aryl, heteroaryl with 5 or 6 members comprising 1 to 4 heteroatoms selected from O, N, and S, C3-Cg carbocicyl, and 5 to 7 membered heterocyclic ring comprising 1 to 3 heteroatoms selected from O, N and S, wherein the aryl, heteroaryl, carbocyclyl and heterocyclic are optionally substituted by one or more R ;;
each Rs is independently selected from C1-Cs alkyl, C2-Cs alkenyl, C2-Cs alkynyl, C1-C6 alkoxy, C1-Cs haloalkyl, C1-C6 haloalkoxy, C1-Ce hydroxyalkyl, halo, -OH, -NH >, cyano, C3-C7 carbocicyl, heterocyclic with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, N, and S, Cs-Cio aryl and heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, Ne S or each R5 is independently selected from C1- Cs alkyl, C2-Cs alkenyl, C2-Cs6 alkynyl, C1-C6 alkoxy, C1-C6 haloalkyl, C1-Cs haloalkoxy, C1-Cs hydroxyalkyl, halo, -OH, -NH>, cyano, Ca-C7 carbocicyl, 5- to 7-membered heterocyclic comprising 1 to 3 heteroatoms selected from O, N, and S, Cs-C10 aryl and heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, N and S or two Rs, when in adjacent atoms, together with the atoms to which they are attached, form a Cs-C; carbocyclyl or 5- to 7-membered heterocycly comprising 1 to 3 heteroatoms selected from O, N and S optionally substituted by one or more R1o;
Re and Reg are each independently hydrogen, C 1- C alkyl or Ce-C 10 aryl;
each R; is independently selected from C1-Cs alkyl, C2-Cs alkenyl, C2-Ce alkynyl, C1-Ce6 alkoxy, C1-Cs haloalkyl, C1- Cs haloalkoxy, -C (O) Rs, - (CH2)) - 30C (0) ORs, -C (O) NRgR9, -NRgC (O) JRs, - NRgC (O0) ORs, -S (O), NRgRsg, -S (O) pR12, (C1-Ce) hydroxyalkyl, halo, -OH, -O (CH2) 1.3CN, -NH> 2, cyano, -O (CH2) x.3- C6-C1o aryl, adamantyl, - O (CH> 2) o-3-heteroaryl with 5 or 6 members comprising 1 to 3 heteroatoms selected from O, N and S, Cs6-C1o aryl, heteroaryl with 5 to 7 monocyclic or bicyclic members comprising 1 to 3 he-
teroatoms selected from O, Ne S, C3-C; carbocicyl, and 5- to 7-membered heterocyclic comprising 1 to 3 heteroatoms selected from O, Ne S, where the alkyl is optionally substituted by one or more R11, and the aryl, heteroaryl and heterocyclic are optionally substituted by one or more substituents, each independently selected from halogen, C1-Cs alkyl, C1- Cs haloalkyl, and C1-Cs6 alkoxy, or two R7, together with the carbon atom to which they are attached, form a = (O), or two R7, when in adjacent atoms, together with the atoms to which they are attached, form a Cs-C11 aryl or a 5- or 6-membered heteroaryl comprising 1 to 3 hetero atoms selected from O, Ne S, optionally substituted by one or more Ri10, or two R7, together with the atoms to which they are attached, form a Cs5-C; carbocicyl or a 5- to 7-membered heterocyclyl comprising 1 to 3 heteroatoms selected from O, Nes, optionally substituted by one or more Ri10;
Rg and Ra are each independently hydrogen or C1-Cs alkyl;
each R1o is independently selected from C1-Cs alkyl, C1-Cs alkoxy, C1-C6 haloalkyl, C1-C6 haloalkoxy C1-Cs hydroxyalkyl, halo, -OH, -NH> and cyano, or two R1o, together with the carbon atom to which they are attached, they form a = (O);
each R1; is independently selected from cyano, C1-Cs alkoxy, Ce6-C10 aryl and heterocyclic with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, N and S, where each aryl and heterocyclic is optionally substituted by one or more substituents, each independently selected from C1-Cs alkyl, C1-Cs6 alkoxy, C1-C6 haloalkyl, C1-C6 haloalkoxy, C1- Cs hydroxyalkyl, halo, -OH, -NH> and cyano ; Ri12 is C1-C6 alkyl, C1-C6 haloalkyl, Ce-C10 aryl or heterocyclic with 5 to 7 members comprising 1 to 3 heteroatoms selected from O, Ne S; Rx is hydrogen or deuterium; foot0, 1 or 2; ne0O, 1or2; yélou2emqauent + ys3i; and qéO, 1,2,3, ou4.
[297]
297. The fusion polypeptide according to claim 296, characterized by the fact that the compound of Formula (Ill) is a compound of Formula (III-b): o o (Ria SO So W.
RE (II-b), or a pharmaceutically acceptable salt, hydrate, solvate, prodrug, stereoisomer and tautomer thereof, where X1, R1, R2, n, q and sub-variables thereof are defined as described for the Formula (III) in claim 296.
[298]
298. Fusion polypeptide according to claim 296 or 297, characterized in that the compound of Formula (III) is a compound of Formula (I11 | -d): o or re DOT
It is RÉ (111-d), or to salt, hydrate, solvate, prodrug, stereoisomer and pharmaceutically acceptable tautomer thereof, where R1, R2, q, and sub-variables thereof are defined as described for Formula (Ill ) in claim 296.
[299]
299. Fusion polypeptide according to any one of claims 296 to 298, characterized in that: (i) the COF3 / CRBN-binding polypeptide is fused to the heterologous polypeptide, (ii) the COF3 / CRBN and the heterologous polypeptide are linked by a peptide bond, (iii) the COF3 / CRBN-binding polypeptide and heterologous polypeptide are linked by a different bond than a peptide bond, (iv) the heterologous polypeptide is directly linked to the COF3 / CRBN-binding polypeptide, (v) the heterologous polypeptide is indirectly linked to the COF3 / CRBN-binding polypeptide, (vi) the COF3 / CRBN-binding polypeptide and the polypeptide - heterologous deo are operably linked by means of a linker, for example, a glycine-serine linker, for example, a linker comprising the amino acid sequence of SEQ ID NO: 28, or (vii) the COF3-binding polypeptide / CRBN is linked to the C or N termination of the he polypeptide therapist.
[300]
300. Fusion polypeptide according to any one of claims 296 to 299, characterized by the fact that: (i) the association of the fusion polypeptide with CRBN in the absence of COF3 is no more than, for example, 0.01% , 0.1%, 1%, 5%, 10%, 15%, or 20% of the fusion polypeptide association with CRBN in the presence of COF3, for example, an excess of COF3, for example, as measured by an assay described in this document, for example, immunoprecipitation, optionally in which the fusion polypeptide does not bind CRBN in the absence of COF3; (ii) the ubiquitination of the fusion polypeptide in the absence of
COF3 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70%, of the ubiquitination of the fusion polypeptide in the presence of COF3, for example, an excess of COF3, for example, as measured by an assay described in this document, optionally in which the fusion polypeptide is ubiquitinated in one or more lysine or methionine residues in the presence of COF3 ; or (iii) the degradation of the fusion polypeptide in the absence of COF3 is no more than, for example, 0.01%, 0.1%, 1%, 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the fusion polypeptide degradation in the presence of COF3, for example, an excess of COF3, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometric analysis, optionally in which the degradation of the fusion polypeptide is mediated by ubiquitination in the presence of COF3; optionally where association, ubiquitination and / or degradation is like the measure in a mammalian cell, for example, a human cell.
[301]
301. Fusion polypeptide according to any one of claims 296 to 300, characterized in that the COF3 / CRBN-binding polypeptide is between 10 and 95 amino acid residues in length, between 15 and 90 amino acid residues long, between 20 and 85 amino acid residues long, between 25 and 80 amino acid residues long, between 30 and 75 amino acid residues long, between 35 and 70 amino acid residues long, between 40 and 65 amino acid residues in length, between 45 and 65 amino acid residues in length, between 50 and 65 amino acid residues in length or between 55 and 65 amino acid residues in length.
[302]
302. Fusion polypeptide according to any one of claims 296, 297, 298, 299, 300 or 301, characterized in that the COF3 / CRBN-binding polypeptide comprises a beta curve, a beta clamp format, a beta strand or an alpha helix, optionally wherein the COF3 / CRBN binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clamp format, a second beta strand and a first alpha helix, optionally in whereas the COF3 / CRBN-binding polypeptide comprises, from the N termination to the C termination, a first beta strand, a beta clip format, a second beta strand, a first alpha helix and a second alpha helix, optionally where the beta clip format and the second alpha helix are separated by no more than 60, 50, 40 or 30 amino acid residues.
[303]
303. Fusion polypeptide according to any one of claims 296 to 302, characterized in that the COF3 / CRBN-binding polypeptide comprises a COF3 / CRBN-binding sequence of a naturally occurring polypeptide or a variant of COF3 / CRBN binding thereof, for example, a naturally occurring IKZF polypeptide or a COF3 / CRBN binding variant thereof, for example, a naturally occurring IKZF2, or a COF3 / binding variant CRBN thereof, optionally wherein the COF3 / CRBN binding polypeptide comprises two or more discontinuous sequences of a naturally occurring IKZF polypeptide, for example, a naturally occurring IKZF2.
[304]
304. Fusion polypeptide according to any one of claims 296 to 303, characterized in that the COF3 / CRBN-binding polypeptide comprises amino acid residues 130 to 174 of IKZF2 (numbered according to SEQ ID NO: 21) (for example, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 113) or a sequence that differs from amino acid residues 130 to 174 of IKZF2 (number according to SEQ ID NO: 21) for no more than 1,2,3,4,5,
10, 15, 20, 25, 30, 35, or 40 amino acid residues (for example, a sequence that differs from amino acid residues 130 to 174 of SEQ ID NO: 21 by no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30 , 35, or 40 amino acid substitutions of amino acid residues 130 to 174 of SEQ ID NO: 21).
[305]
305. Fusion polypeptide according to any of claims 296 to 304, characterized in that the COF3 / CRBN-binding polypeptide comprises amino acid residues 230 to 243 of IKZF2 (numbered according to SEQ ID NO: 21) (for example, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID NO: 114) or a sequence that differs from amino acid residues 230 to 243 of IKZF2 (number according to SEQ ID NO: 21) for no more than 1,2,3,4,5 or 10 amino acid residues (for example, a sequence that differs from amino acid residues 230 to 243 of SEQ ID NO: 21 by not more than 1, 2, 3, 4, 5 or 10 amino acid residues) (for example, a sequence that has no more than 1, 2, 3, 4, 5 or 10 amino acid substitutions of amino acid residues 230 to 243 of SEQ ID NO: 21).
[306]
306. Fusion polypeptide according to claim 304 or 305, characterized by the fact that histidine at position 141 remains unchanged, numbered according to SEQ ID NO: 21.
[307]
307. Fusion polypeptide according to any one of claims 296 to 306, characterized in that: (i) the COF3 / CRBN-binding polypeptide comprises amino acid residues 130 to 174 of IKZF2 (numbered according to to SEQ ID NO: 21) for example, the COF3 / CRBN-binding polypeptide comprises the amino acid sequence of SEQ ID
NO: 113; and / or (ii) the COF3 / CRBN-binding polypeptide comprises amino acid residues 230 to 243 of IKZF2 (numbered according to SEQ ID NO: 21) for example, the COF3 / CRBN-binding polypeptide comprises the sequence of amino acids of SEQ ID NO: 114.
[308]
308. Fusion polypeptide according to any one of claims 296 to 307, characterized in that the COF3 / CRBN-binding polypeptide comprises or consists of the amino acid sequence of SEQ ID NO: 109.
[309]
309. Fusion polypeptide according to any one of claims 296 to 308, characterized in that the heterologous polypeptide is chosen from a cytoplasmic and / or nuclear polypeptide, or a transmembrane polypeptide, for example example, a heterologous polypeptide in Table 2.
[310]
310. Fusion polypeptide according to claim 309, characterized by the fact that the cytoplasmic and / or nuclear polypeptide is selected from the group consisting of a component of the apoptosis pathway (for example, Caspase 9), a component of a CRISPR / Cas system (for example, Cas9), a transcription factor (for example, MITF, c-Myc, STAT3, STAT5, NF-kapaB, beta-catenin, Notch, GLI or c-JUN) , Tet methylcytosine dioxigenase 2 (TET2), FKBP and Tau.
[311]
311. Fusion polypeptide according to claim 309, characterized in that the transmembrane polypeptide is selected from the group consisting of CD62L, CCR1, CCR2, CCR5, CCR7, CCRIO, CXCR2, CXCR3, CXCR4, CXCR6, CTLAA , PD1, BTLA, VISTA, CD137L, CD80, CD86, TIGIT, CD3, CD8, CD19, CD22, CD20, BCMA and a chimeric antigen receptor (CAR).
[312]
312. Fusion polypeptide according to claim
309, characterized by the fact that the heterologous polypeptide is selected from the group consisting of a chimeric antigen receptor (CAR), a component of a CRISPR / Cas system (for example, Cas9), CD8, CD19 and CD22, optionally characterized by the fact that the heterologous polypeptide is a chimeric antigen (CAR) receptor.
[313]
313. Fusion polypeptide according to claim 312, characterized in that the CAR comprises an antigen binding domain, a transmembrane domain and an intracellular signaling domain (for example, a primary signaling domain or a co-stimulating signaling domain), optionally wherein the primary signaling domain comprises a CD3-zeta stimulating domain and / or the co-stimulating signaling domain comprises an intracellular domain of a co-stimulating protein selected from the group consisting of CD27, CD28 , 4-1BB (CD137), OX40, GITR, CD30, CD40, ICOS, BAFFR, HVEM, ICAM-1, antigen-1 associated with lymphocyte function (LFA-1), CD2, CDS, CD7, CD287, LIGHT, NKG2C, NKG2D, SLAMF7, NKp80, NKp30, NKp44, NKp46, CD160, B7-H3 and a linker that specifically binds with CDB83.
[314]
314. Fusion polypeptide according to claim 312, characterized in that the antigen binding domain binds an antigen selected from the group consisting of CD19; CD123; CD22; CD30; CD171; CS-1; lectin type C molecule-1, CD33; epidermal growth factor receptor (EGFRvII!) variant Ill; ganglioside G2 (GD2); ganglioside GD3; member of TNF receptor family; B cell maturation antigen; Tn antigen ((Tn Ag) or (GalNAca-Ser / Thr)); prostate-specific membrane antigen (PSMA); Orphan receptor 1 tyrosine kinase receptor (ROR1); tyrosine kinase 3 type Fms (FLT3); tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor alpha-2 subunit; Mesothelin; Alpha Interleukin 11 receptor (IL-11Ra); prostate stem cell antigen (PSCA); Protease serine 21; vascular endothelial growth factor receptor 2 (VEGFR2); Lebris antigen (Y); CD24; Beta receptor for platelet-derived growth factor (PDGFR-beta); specific stage embryonic antigen-4 (SSEA-4); CD20; alpha folate receptor; ERBB2 receptor tyrosine protein kinase (Her2 / neu); mucin 1, associated with the cell surface (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); Prostasis; prostatic acid phosphatase (PAP); mutated stretching factor 2 (ELF2M); Ephrin B2; alpha fibroblast activation protein (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CAIX); proteasome subunit (prosome, macropaine), Type Beta, 9 (LMP2); glycoprotein 100 (gp100); oncogen polypeptide consisting of the breaking point clustering region (BCR) and Abelson murine leukemia viral oncogen homologue 1 (Abl) (bcr-abl); tyrosinase; ephrin type A receptor 2 (EphA2); Fucosyl GM1; Lewis sialyl adhesion molecule (sLe); ganglioside GM3; transglutaminase 5 (TGS5); antigen associated with high molecular weight melanoma (HMWMAA); o-acetyl-GD2 ganglioside (OAcGD2); beta folate receptor; tumor endothelial marker 1 (TEM1 / CD248); marker 7 related to the endothelial tumor (TEM7R); claudin 6 (CLDN6); thyroid stimulating hormone receptor (TSHR); group 5 class C receptor coupled to protein G, member D (GPRC5D); X chromosome open reading frame 61 (CXORF61); CD97; CD179a; anaplastic lymphoma kinase (ALK); polyisalic acid; placenta-specific 1 (PLAC1); portion of hexassaca-
Glucoceramide Glide H (GloboH); mammary gland differentiating antigen (NY-BR-1); uroplacin 2 (UPK2); hepatitis A virus cell receptor 1 (HAVCR1); beta 3 adenoreceptor (ADRB3); panexin 3 (PANX3); receptor 20 coupled to the G protein (GPR20); lymphocyte antigen 6 complex, K 9 locus (LY6K); olfactory receptor 51E2 (OR51E2); gamma TOR alternating frame protein (TARP); Wilms' tumor protein (WT1); cancer / testis antigen 1 (NY-ESO-1); cancer / testis antigen 2 (LAGE-1a); antigen 1 associated with melanoma (MAGE-A1); gene 6 variant of ETS translocation, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); antigen family X, member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); antigen-1 from melanoma cancer testicles (MAD-CT-1); antigen-2 from melanoma cancer testicles (MAD-CT-2); Fos-related antigen 1; tumor protein p53 (p53); mutant p53; prostein; survivor; telomerase; prostate carcinoma tumor antigen-1, melanoma antigen recognized by T 1 cells; mutant rat (Ras) sarcoma; human telomerase reverse transcriptase (hTERT); sarcoma translocation rupture points; apoptosis melanoma inhibitor (ML-IAP); ERG (transmembrane protease ETS fusion gene, serine 2 (TMPRSS 2)); N-actyl glucosaminyl transferase V (NA17); pax-3 paired box protein (PAX3); androgen receptor; cyclin B1; homologous derived from viral oncogen neuroblastoma of avian v-myc myelocytomatosis (MYCN); member C of Ras homologous family (RhoC); tyrosinase-related protein 2 (TRP-2); cytochrome P450 1B1 (CYP1B1); type CCCTOC binding factor (zinc finger protein), squamous cell carcinoma antigen recognized by T 3 cells (SART3); Pax-5 paired box protein (PAXS5); proacrosin sp32 binding protein (OY-TES1); lymphocyte-specific protein tyrosine kinase (LCK); kinase A anchor protein 4 (AKAP-4); synovial sarcoma, X 2 rupture point (SSX2); Receiver for advanced glycation endoproducts (RAGE-1); ubiquitous renal 1 (RU1); ubiquitous renal 2 (RU2); legumaine; human papilloma virus E6 (HPV E6); human papilloma virus E7 (HPV E7); intestinal carboxyl esterase; mutated 70-2 heat shock protein (mut hsp70-2); CD79a; CD79b; CD72; leukocyte-associated immunoglobulin-type 1 receptor (LAIR1); IgA receptor Fc fragment (FCAR or CD89); member 2 of subfamily A of leukocyte immunoglobulin-like receptor (LILRA2); f member of the CD300 molecule family (CD300LF); A member of family 12 of type C lectin domain (CLEC12A); bone marrow stromal cell antigen 2 (BST2); mucin hormone receptor 2 type containing EGF-type module (EMR2); lymphocyte antigen 75 (LY75); glypican-3 (GPC3); Fc 5 receptor type (FCRL5); and lambda immunoglobulin-like polypeptide 1 (IGLL1), optionally wherein the antigen binding domain binds an antigen chosen from CD19, CD22, BCMA, CD20, CD123, EGFRvII! or mesothelin.
[315]
315. The fusion polypeptide according to any one of claims 296 to 314, characterized in that the fusion polypeptide further comprises a degradation domain, wherein the degradation domain is separated from the COF3 / binding polypeptide CRBN and the heterologous polypeptide by a heterologous protease cleavage site.
[316]
316. The fusion polypeptide according to claim 315, characterized in that the fusion polypeptide comprises, from the N termination to the C termination: i) the degradation domain, the heterologous protease cleavage site, the polypeptide heterologous and the COF3 / CRBN binding polypeptide;
ii) the degradation domain, the heterologous protease cleavage site, the COF3 / CRBN-binding polypeptide and the heterologous polypeptide; iii) the COF3 / CRBN-binding polypeptide, the heterologous polypeptide, the heterologous protease cleavage site and the degradation domain; or iv) the heterologous polypeptide and the COF3 / CRBN binding polypeptide, the heterologous protease cleavage site and the degradation domain.
[317]
317. Fusion polypeptide according to claim 315 or 316, characterized in that the degradation domain has a first state associated with a first expression level of the fusion polypeptide and a second state associated with a second level expression of the fusion polypeptide, in which the second level is increased, for example, by at least 2 times, 3 times, 4 times, 5 times, 10 times, 20 times or 30 times in relation to the first level in the presence of a stabilizing compound, optionally where: in the absence of the stabilizing compound, the fusion polypeptide is degraded by a cell degradation path, for example, at least 50%, 60%, 70%, 80%, 90% or more of the fusion polypeptide is degraded, for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis; or in the presence of the stabilizing compound: i) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; or ii) the conformation of the fusion polypeptide is more permissible to cleavage at the heterologous protease cleavage site in relation to a conformation in the absence of the stabilizing compound.
[318]
318. Fusion polypeptide according to any one of claims 315 to 317, characterized in that the degradation domain is chosen from an estrogen receptor (ER) domain, an FKB ( FKBP), or a dihydrofolate reductase (DHFR) domain.
[319]
319. The fusion polypeptide according to any one of claims 315 to 318, characterized in that the heterologous protease cleavage site is cleaved by a mammalian intracellular protease selected from the group consisting of furin, PCSK1, POCSK5, PCSK6, PCSKT7, cathepsin B, Granzyme B, Factor XA, Enterokinase, genenase, sortase, precision protease, thrombin, TEV protease and elastase 1.
[320]
320. Fusion polypeptide according to any one of claims 315 to 318, characterized in that the heterologous protease cleavage site is cleaved by a mammalian extracellular protease selected from the group consisting of Factor XA, Enterokinase , genenase, sortase, precision protease, thrombin, TEV protease and elastase 1.
[321]
321. Nucleic acid molecule characterized by the fact that it encodes the fusion polypeptide, as defined in any one of claims 296 to 320.
[322]
322. Vector characterized by the fact that it comprises the nucleic acid molecule, as defined in claim 321, optionally in which the vector is a viral vector, for example, a lead vector, a retroviral vector or an adenoviral vector.
[323]
323. A cell, for example, a host cell, characterized by the fact that it comprises the fusion polypeptide according to any one of claims 296 to 320, the nucleic acid molecule, as defined in claim 321, or the vector, how to define
in claim 322, optionally wherein the cell is a T cell, an NK cell or a tumor cell.
[324]
324. Pharmaceutical composition characterized by the fact that it comprises the fusion polypeptide, as defined in any of claims 296 to 320 or the cell, as defined in claim 323, and a pharmaceutically acceptable carrier, excipient or stabilizer.
[325]
325. Method for producing the cell, according to claim 323, characterized in that said method comprises providing a cell, for example, an immunosuppressive cell, with the nucleic acid molecule, as defined in claim 321, or the vector, as defined in claim 322.
[326]
326. Method for degrading a fusion polypeptide characterized in that it comprises placing the fusion polypeptide according to any one of claims 296 to 320 or a cell comprising said fusion polypeptide in contact with COF3, optionally wherein , in the presence of COF3, the level of expression of said fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20 , 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the level of expression of said fusion polypeptide in the absence of COF3, for example, as measured by an assay described in this document. for example, a Western blot analysis or a flow cytometry analysis, optionally in which: the fusion polypeptide or the cell is contacted with COF3 ex vivo, or the fusion polypeptide or the cell is placed in contact with COF3 in vivo.
[327]
327. Method for regulating the expression of a fusion polypeptide characterized by the fact that it comprises:
i) placing the fusion polypeptide according to any one of claims 315 to 320 or a cell comprising said fusion polypeptide in contact with a stabilizing compound, optionally wherein, in the presence of the stabilizing compound : a) the degradation domain assumes a conformation more resistant to cell degradation compared to a conformation in the absence of the stabilizing compound; b) the conformation of the fusion polypeptide is more permissive to cleavage at the heterologous protease cleavage site compared to a conformation in the absence of the stabilizing compound; or c) the expression level of the fusion polypeptide is increased by at least, for example, 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times compared to the expression level of the fusion polypeptide in the absence of the stabilizing compound, for example, as measured by an assay described in this document, for example, a Western blot analysis or a cytometry analysis of flow, optionally in which the fusion polypeptide or cell is brought into contact with the stabilizing compound ex vivo or in vivo.
[328]
328. Method according to claim 327, characterized in that it further comprises, after step i): ii) placing the fusion polypeptide according to any one of claims 315 to 320 or a cell comprising the said fusion polypeptide, in contact with COF3, optionally wherein in the presence of COF3, the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide after step i) and before step ii), for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis, optionally in which the fusion polypeptide or cell is contacted with COF3 ex vivo or in vivo .
[329]
329. Method for producing a cell characterized by the fact that it comprises: i) providing a cell, for example, an immuno-effector cell, with a nucleic acid molecule encoding the fusion polypeptide according to any one of claims 296 at 320; and ii) putting the cell ex vivo in contact with COF3, optionally where: in the presence of COF3, the expression level of the fusion polypeptide is substantially decreased, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide in the absence of COF3 , for example, as measured by an assay described in this document, for example, a Western blot analysis or a flow cytometry analysis.
[330]
330. Method of treating an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) placing a cell comprising the fusion polypeptide, according to any one of claims 296 to 314, in contact with COF3 ex vivo, optionally characterized by the fact that: in the presence of COF3, the expression level of the fusion polypeptide is decreased, for example, by at least about 1,2, 3,4, 5, 6.7, 8.9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent relative to the expression level of the fusion polypeptide before the cell is brought into contact with COF3 ex vivo, and ii) administering to the individual an effective amount of the cell, optionally in which the method further comprises, after step i) and before step ii): reducing the amount of COF3 in contact with the cell, for example , inside and / or surrounding the cell, thus treating the disease.
[331]
331. Method according to claim 330, characterized by the fact that it further comprises, after step ii): iii) administering to the individual an effective amount of COF3, optionally in which the administration of COF3 decreases, for example, at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step ii) and before step iii), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b ) the administration of COF3 is in response to an occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) the administration of COF3 reduces or prevents an ad effect - verse.
[332]
332. Method according to claim 331, characterized by the fact that it further comprises, after step iii): iv) discontinuing the administration of COF3, optionally in which discontinuing the administration of COF3 increases, for example, by at least minus about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step iii) and before step iv) (for example, where discontinuing COF3 administration restores the expression level of the fusion polypeptide to the expression level after step ii) and before step iii)), optionally where: a) the individual has had a relapse, is relapsed or is expected to have a relapse, b) discontinuation of COF3 administration is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) discontinuing COF3 administration treats the u prevents a tumor relapse.
[333]
333. Method, according to claim 332, characterized by the fact that it also comprises, after step iv): v) repeating step iii) and / or iv), thus treating the disease.
[334]
334. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) administering to the individual an effective amount of a cell comprising the fusion polypeptide according to any one of claims 296 to 314, optionally in which the cell is contacted with COF3 ex vivo prior to administration, optionally in which: in the presence of COF3, the expression level of the fusion polypeptide is decreased, for example , by at least about 1,2, 3,4, 5,6,7,8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent in relation to the level expression of the fusion polypeptide before the cell is brought into contact with COF3 ex vivo, optionally in which after the cell is brought into contact with COF3 ex vivo and before the cell is administered to the individual, the amount of COF3 in contact with the cell, for example, inside and / or surrounding the cell, is reduced, thus treating the disease. The.
[335]
335. Method according to claim 334, characterized by the fact that the cell is not brought into contact with COF3 ex vivo prior to administration.
[336]
336. Method according to claim 334 or 335, characterized by the fact that it further comprises, after step i): ii) administering to the individual an effective amount of COF3, optionally in which the administration of COF3 decreases, for example, at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step i) and before step li), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) a administration of COF3 is in response to the occurrence of an adverse reaction in the individual, or in response to the expectation of an adverse reaction occurring in the individual, and / or c) administration of COF3 reduces or prevents an adverse effect .
[337]
337. Method according to claim 336, characterized by the fact that it further comprises, after step ii): iii) discontinuing the administration of COF3, optionally in which discontinuing the administration of COF3 increases, for example, by at least minus about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step ii) and before step iii) (for example, when discontinuing COF3 administration restores the expression level of the fusion polypeptide to the expression level after step i) and before step li)), optionally where: a) the individual has had a relapse, is relapsed or is expected to have a relapse, b) discontinuation of COF3 administration is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) discontinuing COF3 administration treats or prevents a tumor relapse.
[338]
338. Method, according to claim 337, characterized by the fact that it also comprises, after step iii): iv) repeating step ii) and / or iii), thus treating the disease.
[339]
339. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) administering an effective amount of COF3 to the individual, in which the individual comprises a cell comprising the polypeptide; fusion peptide according to any one of claims 296 to 314, optionally wherein the administration of COF3 decreases, for example, by at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent the expression level of the fusion polypeptide relative to the expression level of the fusion polypeptide before COF3 administration, optionally where : a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the administration of COF3 is in response to an occurrence of an adverse reaction in the individual, or in response to the expectation of an occurrence of an adverse reaction in the individual, and / or c) administration of COF3 reduces or prevents an done in reverse.
[340]
340. Method according to claim 339, characterized by the fact that it further comprises, after step i): ii) discontinuing the administration of COF3, optionally in which discontinuing the administration of COF3 increases, for example, by at least minus about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times, the expression level of the fusion polypeptide in relation to the level of expression of the fusion polypeptide after step |) and before step ii) (for example, where discontinuing the administration of COF3 restores the expression level of the fusion polypeptide to the level of expression prior to COF3 administration), optionally where: a) the individual has had a relapse, is relapsed or is expected to have a relapse, b) discontinuation of COF3 administration is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) discontinuation of COF3 administration treats or prevents a r tumor elapse.
[341]
341. Method, according to claim 340, characterized by the fact that it also comprises, after step ii): iii) repeating step i) and / or ii), thus treating the disease.
[342]
342. Method of treatment of an individual having a disease associated with the expression of a tumor antigen, characterized by the fact that it comprises: i) administering to the subject: (1) a stabilizing compound, and (2) an effective amount of a cell comprising the fusion polypeptide according to any one of claims 315 to 320 or an effective amount of a cell comprising
giving the fusion polypeptide according to any one of claims 315 to 320, optionally wherein: the level of expression of the fusion polypeptide in the presence of the stabilizing compound is, for example, at least about 1.5 times , 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times higher than the expression level of the fusion polypeptide in the absence of the stabilizing compound, treating, thus, the disease.
[343]
343. Method according to claim 342, characterized by the fact that it further comprises, after step i): ii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilization reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the polypeptide of fusion in relation to the expression of the fusion polypeptide after step |) and before step ii), optionally where: a) the individual responded to the treatment in step i) (for example, the individual has a complete response to treatment from step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment from step i) is effective on the individual), and / or b) discontinuing the administration of the stabilization is in response to an individual's response to the treatment in step i) (for example , the individual has a complete response to the treatment in step i), the individual shows a shrinkage in the tumor mass, the individual shows a reduction in the tumor cells, or the treatment in step i) is effective in the individual).
[344]
344. Method, according to claim 342, characterized by the fact that it further comprises, after step i):
iii) discontinuing the administration of the stabilizing compound, optionally in which discontinuing the administration of the stabilizing compound reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression of the fusion polypeptide after step i) and before step ii), optionally where: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) the discontinuation of the administration of the stabilizing compound is in response to an occurrence of an adverse reaction in the individual, or in response to waiting for an occurrence of an adverse reaction in the individual, and / or c) discontinuation of the administration of the stabilizing compound reduces or prevents an adverse effect.
[345]
345. Method according to claim 342, characterized by the fact that it further comprises, after step i): iv) discontinuing the administration of the stabilizing compound and administering to the individual an effective amount of COF3, op- where step iv) reduces, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, times, 40 times or 50 times the level of expression of the fusion polypeptide in relation to the expression of the fusion polypeptide after step i) and before step iv), optionally in which: a) the individual has developed, is developing or is expected to develop an adverse reaction, b) step iv) is in response to an adverse reaction occurring in the individual, or in response to waiting for an adverse reaction occurring in the individual, and / or c) step iv) reduces or prevents an adverse effect,
optionally where the adverse effect is acute toxicity.
[346]
346. Method according to claim 345, characterized by the fact that it further comprises, after step iv): v) discontinuing the administration of COF3, for example, after the number of cells expressing the fusion polypeptide in area is less than a predefined value, for example, for 1 day, 5 days, 10 days or 15 days.
[347]
347. Method according to any one of claims 343 to 346, characterized in that it further comprises after step ii), ili), iv), or v): vi) administering an effective amount of a compound of stabilization, optionally in which the administration of the stabilizing compound increases, for example, by at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times the expression level of the fusion polypeptide in relation to the expression level of the fusion polypeptide after step li), li), iv), or v) and before step vi), optionally where: a) the individual has had a relapse, is relapsed or is expected to have a relapse, b) administration of the stabilizing compound is in response to a tumor relapse in the individual, or in response to waiting for a relapse in the individual, and / or c) administration of the stabilizing compound treats or prevents tumor relapse.
[348]
348. Method, according to claim 347, characterized by the fact that it also comprises, after step vi): vii) repeating step iii), iv), v) or vi), thus treating the disease .
[349]
349. Method according to any one of the claims
342 to 348, characterized by the fact that it also comprises, before step i): viii) putting the cell in contact with an ex vivo stabilization compound, optionally in which the expression level of the polypeptide of melting in the presence of the stabilizing compound is, for example, at least about 1.5 times, 2 times, 3 times, 4 times, 5 times, 10 times, 20 times, 30 times, 40 times or 50 times greater than expression level of the fusion polypeptide in the absence of the stabilizing compound.
[350]
350. Method according to any one of claims 342 to 348, characterized by the fact that the cell is not brought into contact with the ex vivo stabilizing compound prior to administration.
[351]
351. Method according to any of claims 330 to 350, characterized by the fact that the disease associated with the expression of an antigenic tumor is a cancer.
[352]
352. Method according to claim 351, characterized by the fact that the cancer is mesothelioma (eg, malignant pleural mesothelioma), for example, in an individual who has progressed on at least one previous standard therapy; lung cancer (for example, non-small cell lung cancer, small cell lung cancer, squamous cell lung cancer or large cell lung cancer); pancreatic cancer (for example, pancreatic ductal adenocarcinoma or metastatic pancreatic ductal adenocarcinoma (PDA), for example, in an individual who has progressed on at least one previous standard therapy); esophageal adenocarcinoma, ovarian cancer (eg, serous epithelial ovarian cancer, for example, in an individual who has progressed after at least one previous standard therapy regimen), breast cancer, colorectal cancer, bladder cancer or any combination thereof.
[353]
353. Method according to claim 351, characterized by the fact that cancer is a hematological cancer chosen from: chronic lymphocytic leukemia (CLL), mantle cell lymphoma (MCL), multiple myeloma, lymphoid leukemia acute (ALL), Hodgkin's lymphoma, acute B-cell lymphoid leukemia (BALL), acute T-cell lymphoid leukemia (TALL), small lymphocytic leukemia (SLL), B-cell prolymphocytic leukemia, plasma- dendritic cell neoplasm blast cytoid, Burkitt's lymphoma, diffuse large B-cell lymphoma (DLBCL), DLBCL associated with chronic inflammation, chronic myeloid leukemia, myeloproliferative neoplasms, follicular lymphoma, pediatric follicular lymphoma, capillary cell leukemia, small cell follicular lymphoma large cell, malignant lymphoproliferative conditions, MALT lymphoma (extranodal marginal lymphoma of lymphoid tissue associated with mucosa), marginal zone lymphoma, myelodysplasia, myelodysplastic syndrome, lin non-Hodgkin's form, plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, Waldenstrom macroglobulinemia, splenic marginal zone lymphoma, splenic lymphoma / leukemia, small splenic red pulp B cell lymphoma, capillary cell leukemia variant, lymphoplasmacytic lymphoma, a heavy chain disease, plasma cell myeloma, solitary bone plasmacytoma, extra-osseous plasmacytoma, nodal marginal zone lymphoma, pediatric nodal marginal zone lymphoma, primary cutaneous follicle lymphoma, lymphoid granulomatosis, primary mediastinal (thymic) large B-cell lymphoma, intravascular large B-cell lymphoma, ALK + large B-cell lymphoma, large B-cell lymphoma arising in HHVB8-associated multi-centric Castleman disease, primary effusion lymphoma, B cell, acute myeloid leukemia (AML), or non-classifiable lymphoma.

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法律状态:
2021-11-23| B350| Update of information on the portal [chapter 15.35 patent gazette]|

优先权:

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申请号 | 申请日 | 专利标题

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US201762574188P| true| 2017-10-18|2017-10-18|

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US62/574,188|2017-10-18|

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PCT/US2018/056472|WO2019079569A1|2017-10-18|2018-10-18|Compositions and methods for selective protein degradation|

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