BICYCLIC PEPTIDE LINKERS SPECIFIC TO MT1-MMP, DRUG CONJUGATE, PROCESS FOR PREPARATION OF A DRUG CONJ

专利摘要:
The present invention relates to polypeptides that are covalently linked to molecular scaffolds, such that two or more peptide loops are subtended between points of attachment to the scaffold. in particular, the invention describes peptides which are high affinity membrane metalloprotease type 1 (mt1-mmp) ligands. the invention also describes drug conjugates comprising these peptides, conjugated to one or more effector and/or functional groups that have utility in imaging and targeted cancer therapy.
公开号:BR112017008575B1
申请号:R112017008575-5
申请日:2015-10-29
公开日:2021-07-13
发明作者:Daniel Paul Teufel；Catherine Lucy Stace；Silvia PAVAN；Edward Walker；Leonardo Baldassarre
申请人:Bicyclerd Limited；
IPC主号:

专利说明:

FIELD OF THE INVENTION
[001] The present invention relates to polypeptides that are covalently linked to molecular scaffolds (scaffolds), such that two or more peptide bonds are subtended between points of attachment with the scaffold (scaffold). In particular, the invention describes peptides that are high affinity membrane metalloprotease type 1 (MT1-MMP) ligands. The invention also describes drug conjugates comprising these peptides, conjugated to one or more effector groups and/or functional groups that have utility in imaging and targeted cancer therapy. BACKGROUND OF THE INVENTION
[002] Cyclic peptides are able to bind with high affinity and target specificity to target protein and, therefore, it is an attractive molecule class for the development of therapeutic agents. In fact, several cyclic peptides are already successfully used in clinical practice, such as the antibacterial peptide vancomycin, the immunosuppressive drug cyclosporine, or the anticancer drug octreotide (Driggers et al., (2008), Nat. Rev. Drug Discov. 7 (7), 608 24). Good binding properties result from a relatively large interaction surface formed between the peptide and the target, as well as the reduced conformational flexibility of the cyclic structures. Typically, macrocycles bind to the surfaces of several hundred square angstroms, for example the cyclic peptide CXCR4 antagonist CVX15 (400 Â2, Wu et al (2007), Science 330, 1066 71), a cyclic peptide with the Arg-Gly-Asp motif that binds to αVb3 integrin (355 A2) (Xiong et al (2002), Science 296 (5565), 151-5) or the cyclic peptide inhibitor upain-1 that binds to plasminogen activator of the urokinase type (603 A2; Zhao et al (2007), J. Struct. Biol. 160 (1), 1-10).
[003] Due to their cyclic configuration, peptide macrocycles are less flexible than linear peptides, leading to less entropy loss upon binding to targets and resulting in a higher binding affinity. The reduced flexibility also leads to blocking of target-specific conformations, increasing binding specificity compared to linear peptides. This effect was exemplified by a potent and selective inhibitor of matrix metalloproteinase 8, (MMP-8), which lost its selectivity over other MMPs when its ring was opened (Cherney et al. (1998), J. Med. Chem. 41 ( 11), 1749-51). The favorable binding properties obtained through macrocyclization are even more pronounced in multicyclic peptides that have more than one peptide ring, for example in vancomycin, nisin and actinomycin.
[004] Different research groups present polypeptides previously bound with cysteine residues with a synthetic molecular structure (Kemp and McNamara (1985), J. Org. Chem., Timmerman and others (2005), ChemBioChem). Meloen and co collaborators had used tris(bromomethyl)benzene and related molecules for rapid and quantitative cyclization of multiple peptide loops into synthetic scaffolds for structural mimicry of protein surfaces (Timmerman et al., (2005), ChemBioChem). Methods for generating drug candidate compounds where the compounds are generated by linking cysteine-containing polypeptides to a molecular framework, e.g., tris(bromomethyl)benzene are described in WO 2004/077062 and WO 2006/078161.
[005] Combinatorial approaches based on phage display are developed to generate and select large libraries of bicyclic peptides for targets of interest (Heinis et al. (2009), Nat. Chem. Biol. 5(7), 502-7 and WO2009/ 098450). Briefly, combinatorial libraries of linear peptides containing three cysteine residues and two random six amino acid regions (Cys-(Xaa)6-Cys-(Xaa)6-Cys) were displayed on phage and cyclized via covalent linkage of the cysteine side chains with a small molecule (tris-(bromomethyl)benzene). SUMMARY OF THE INVENTION
According to a first aspect of the invention there is provided a peptide linker specific to MT1-MMP comprising a polypeptide comprising at least three cysteine residues, separated by at least two loop sequences, and a molecular framework which forms covalent bonds with the cysteine residues of the polypeptide such that at least two polypeptide loops are formed in the molecular framework, wherein the peptide linker comprises an amino acid sequence of formula (I):
or a modified derivative, or pharmaceutically acceptable salt thereof, wherein: Ci, Cii and Ciii represent first, second and third cysteine residues, respectively; X represents any amino acid residue; U represents an uncharged, polar amino acid residue selected from N, C, Q, M, S and T; and O represents a non-polar aliphatic amino acid residue selected from G, A, I, L, P and V.
[007] According to a further aspect of the invention, there is provided a drug conjugate comprising a peptide linker as defined in this report, conjugated to one or more effector groups and/or functional groups, such as a cytotoxic agent, in particular , DM1 and MMAE.
[008] According to a further aspect of the invention there is provided a conjugate comprising a peptide linker as defined in this report conjugated to one or more effector groups and/or functional groups, such as a chelating group carrying radionuclide, in particular, ENDOWMENT
[009] According to a further aspect of the invention there is provided a pharmaceutical combination comprising a peptide linker or a drug conjugate as defined in this report in combination with one or more pharmaceutically acceptable excipients.
[0010] According to a further aspect of the invention, there is provided a peptide ligand as defined in this report for use in the prevention, suppression or treatment of cancer, in particular solid tumors such as non-small cell lung carcinomas. CONCISE DESCRIPTION OF THE FIGURES
[0011] Figure 1: Stability of mouse plasma from 17-69-07-N219. Several ions were monitored as indicated in the legend, as well as two transitions in MRM mode. There is an excellent correlation between the ions. The half-life of the peptide in mouse plasma at 37°C is 6 hours.
[0012] Figure 2: PK profile of Bicyclic Peptide 17-69-07-N004 in mice. 2 (two) animals per time point.
[0013] Figure 3: Mouse (A) and Human Plasma Stability (B) of two stabilized molecules 17-69-07 (with 4-bromophenylalanine in position 9: 17-69-07-N244, without 4-bromophenylalanine in position 9 : 17-69-07-N231) compared to the unstabilized 17-69-07-N219. Several MRM transitions for a given analyte were monitored, which correlated well with each other. For the purpose of this chart, only one transition is displayed.
[0014] Figure 4: Biodistribution of 177Lu 17-69-07-N144 in HT-1080 xenograft mice.
[0015] Figure 5: Biodistribution of 177Lu 17-69-07-N246 in HT-1080 xenograft mice.
Figure 6: Biodistribution of 177Lu 17-69-07-N248 in HT-1080 xenograft mice.
[0017] Figure 7: (A): Mean tumor volume versus time graph for BT17BDC-1 and 9. Doses were administered on days 0, 2, 4, 7, 9 and 11. (B): body weight during treatment , which is indicative of drug-associated toxicology and general animal health.
Figure 8: List of sequence outputs derived from affinity maturations using libraries with 2-loop residues 17-69. The sequence logo plot on the right shows the overall preference of residues at residues 1, 2, 3, 4, and 5 of loop1.
[0019] Figure 9: Top: Plot of mean tumor volume versus time for BT17BDC-17 in EBC-1 xenograft mice. Doses were administered on days 0, 2, 4, 7, 9, 11, and 14. Bottom: Body weight during treatment, which is indicative of drug-associated toxicology and general animal health.
[0020] Figure 10: Top: Plot of mean tumor volume versus time for BT17BDC-18 in EBC-1 xenograft mice. Doses were administered on days 0, 2, 4, 7, 9, 11, and 14. Bottom: Body weight during treatment, which is indicative of drug-associated toxicology and general animal health.
[0021] Figure 11: Top: Plot of mean tumor volume versus time for BT17BDC-19 in EBC-1 xenograft mice. Doses were administered on days 0, 2, 4, 7, 9, 11, and 14. Bottom: Body weight during treatment, which is indicative of drug-associated toxicology and general animal health.
[0022] Figure 12: Top: Plot of mean tumor volume versus time for BT17BDC-20 in EBC-1 xenograft mice. Doses were administered on days 0, 2, 4, 7, 9, 11, and 14. Bottom: Body weight during treatment, which is indicative of drug-associated toxicology and general animal health.
Figure 13: Plot of the area under curve (AUC) of tumor volume over time associated with a particular BDC versus the corresponding dose group. Curve fits are performed using all available data points normalized to tumor volume at zero time using standard IC 50 equations. DETAILED DESCRIPTION OF THE INVENTION
[0024] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art, such as in the art of peptide chemistry, cell culture and phage display, nucleic acid chemistry and biochemistry. Standard techniques are used for methods of molecular biology, genetics, and biochemistry (see Sambrook et al., Molecular Cloning: A Laboratory Manual, 3rd Ed., 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; Ausubel et al. , Short Protocols in Molecular Biology (1999) 4th Ed., John Wiley & Sons, Inc.), which are incorporated herein by reference. Nomenclature numbering
[0025] When referring to the positions of amino acid residues in compounds of formula (I), cysteine residues (Ci, Cii and Ciii) are omitted from the numbering when these are invariant, hence the numbering of amino acid residues in the compound of formula (I) is referred to as below:

For the purpose of this description, all bicyclic peptides are assumed to be cyclized with TBMB (1,3,5-tris(bromomethyl)benzene), yielding a trisubstituted 1,3,5-trismethylbenzene structure. Cycling with TBMB occurs in Ci, Cii and Ciii. Bicyclic Peptide Core Sequence
[0027] Each bicyclic peptide described in this report has been assigned a unique core sequence number, which is defined as the amino acid sequence between the first N-terminal cysteine (Ci) and the last C-terminal cysteine (Ciii). In the example of identifier 17-69 07, the core sequence is CiYNEFGCiiEDFYDICiii (SEQ ID NO: 2), and is referred to as "17-69-07" or "(17-69-07)". Peptide Code
[0028] Certain bicyclic peptides described in this report have also been assigned a unique identifier using a peptide code, such as 17-69-07-N241, where N241 denotes a particular derivative of the bicyclic core sequence 17-69-07. Derivatives other than 17-69-07 have different N numbers, that is, N001, N002 and Nxxx. Molecular Format
[0029] Extensions of N or C termini for the bicyclic core sequence are added on the left or right side of the core sequence, separated by a hyphen. For example, an N-terminal βAla-Sar10-Ala tail could be denoted as: βAla-Sar10-A-(17-69-07) and has the total sequence of βAla-Sar10-A-CYNEFGCEDFYDIC (SEQ ID NO: 3 ). Modifications
[0030] Unnatural amino acid substitutions within the bicyclic core sequence are indicated after the description of molecular format. For example, if tyrosine 1 at 17-69-07 is replaced with D-alanine, the description is (17-69-07) D-Ala1, and the complete sequence would be described as C(D-Ala1)NEFGCEDFYDIC (SEQ ID NO: 4).
[0031] If an N-terminus or C-terminus tail is linked with a bicyclic peptide that also contains modifications to the core sequence, then using 17-69-07 N241 as an example, the description of molecular format is: βAla -Sar10-A-(17-69-07) DAla1 1NAI4 DAla5 tBuGly11.
The complete amino acid sequence of 17-69-07-N241 is therefore: βAla-Sar10-AC(D-Ala)NE(1NaI)(D-Ala)CEDFYD(tBuGly)C (SEQ ID NO: 5 ). Peptide Binders
[0033] A peptide linker as referred to in this report refers to a peptide covalently linked to a molecular framework. Typically, such peptides comprise two or more reactive groups (ie, cysteine residues), which are capable of forming covalent bonds with the scaffold, and a sequence subtended between these reactive groups which is referred to as the loop sequence, since forms a loop when the peptide is attached to the scaffold. In the present case, the peptides comprise at least three cysteine residues (referred to in this report as Ci, Cii, and Ciii) and form at least two loops on the scaffold.
[0034] It will be appreciated by one skilled in the art that the X in positions 1, 3, 4, 10 and 11 of formula (I) can represent any amino acid following the results of the alanine scan (see Table 5) and of selection outputs (Figure 8), which allows for well-tolerated substitutions in these positions.
[0035] In one embodiment, the X at position 1 of formula (I) is selected from any of the following amino acids: Y, M, F or V. In one embodiment, the X at position 1 of formula (I) is selected from Y, M or F. In a still further modality, the X in position 1 of formula (I) is selected from Y or M. In a still further modality, the X in position 1 of formula (I) is selected of Y.
[0036] In one embodiment, the U/O at position 2 of formula (I) is selected from a U, such as an N. In an alternative embodiment, the U/O at position 2 of formula (I) is selected from an O group such as G.
[0037] In one embodiment, the X at position 3 of formula (I) is selected from U or Z, wherein U represents an uncharged polar amino acid residue selected from N, C, Q, M, S and T and Z represents a negatively charged polar amino acid residue selected from D or E. In an additional embodiment, the U at position 3 of formula (I) is selected from Q. In an alternative embodiment, the Z at position 3 of formula (I) is selected from E.
[0038] In one embodiment, the X at position 4 of formula (I) is selected from J, where J represents a non-polar aromatic amino acid residue selected from F, W and Y. In a further embodiment, the J at position 4 of formula (I) is selected from F. In an alternative embodiment, the J at position 4 of formula (I) is selected from Y. In alternative embodiment, the J at position 4 of formula (I) is selected from W.
[0039] In one embodiment, the X at position 10 of formula (I) is selected from Z, where Z represents a polar, negatively charged amino acid residue selected from D or E. In one embodiment, the Z at position 10 of formula (I) is selected from D.
[0040] In one embodiment, the X at position 11 of formula (I) is selected from O, where O represents a non-polar aliphatic amino acid residue selected from G, A, I, L, P, and V. In one embodiment. , the O at position 11 of formula (I) is selected from I.
[0041] In one embodiment, the compound of formula (I) is a compound of formula (Ia):
where U, O, J and Z are as defined above.
[0042] In one embodiment, the compound of formula (I) is a compound of formula (Ib):

[0043] In one embodiment, the compound of formula (I) is a compound of formula (Ic):

[0044] In one embodiment, the compound of formula (I) is a compound of formula (Id):

[0045] In one embodiment, the compound of formula (I) is a compound of formula (Ie):

[0046] In a still further embodiment, the peptide of formula (1) comprises a sequence selected from:


Peptides of this modality have been identified to be potent candidates after affinity maturation against the hemopexin domain of MT1-MMP (see, Example 1 and Tables 1 and 8).
[0048] In a still further embodiment, the peptide of formula (1) comprises a sequence selected from:

Peptides of this modality have been identified to be the highest affinity candidates after affinity maturation against the hemopexin domain of MT1-MMP, synthesis of the core bicyclic sequences, and quantitative measurement of affinities using competition experiments (see, Example 1 and Tables 1-3).
[0050] In a still further embodiment, the peptide of formula (I) comprises a sequence selected from -Ci-Y-N-E-F-G-Cii-E-D-F-Y-D-I-Ciii-(17-69-07) (SEQ ID NO: 2). The peptide of this modality has been identified to be the most potent, and stable member of the peptide linker family in formula (I) (see, Examples 1 to 4).
[0051] In one embodiment, certain peptide ligands of the invention are fully cross-reactive with murine, dog, cynomolgus and human MT1 -MMP. In a further embodiment, the specifically exemplified peptide ligands of the invention are fully cross-reactive with murine, dog, cynomolgus and human MT1 -MMP. For example, data are presented in this report which demonstrate that both the unstabilized and the stabilized derivatives of 17-69-07 (ie 17-69-07-N219 and 17-69-07-N241) are fully cross reaction (see Table 13).
[0052] In a still further embodiment, the peptide ligand of the invention is selective for MT1 -MMP, but does not cross-react with MMP-1, MMP-2, MMP-15 and MMP-16. Data are presented in this report, which demonstrate that the core sequence 17-69 07, and the stabilized variant 17-69-07-N258, are uniquely selective to MT1 -MMP (see Table 14). Advantages of Peptide Ligands
[0053] Certain bicyclic peptides of the present invention have several advantageous properties, which allow them to be considered as drug-like molecules suitable for injection, inhalation, nasal, ocular, oral or topical administration. Such advantageous properties include: - Cross-species reactivity. This is a typical requirement for preclinical pharmacodynamic and pharmacokinetic evaluation; - Stability of protease. Bicyclic peptide ligands should ideally demonstrate stability to plasma proteases, epithelial ("membrane-anchored") proteases, gastric and intestinal proteases, lung surface proteases, intracellular proteases, and the like. Protease stability must be maintained between different species such that a candidate bicyclic conductor can be developed in animal models as well as reliably administered to humans; - desirable solubility profile. This is a function of the ratio of charged and hydrophilic versus hydrophobic residues and intra/intermolecular H-bonds, which is important for formulation and absorption purposes; and - an optimal plasma half-life in circulation. Depending on the clinical indication and treatment regimen, it may be necessary to develop a short-exposure bicyclic peptide in an acute disease control setting, or to develop a bicyclic peptide with marked retention in circulation, and is therefore ideal for status control. of chronic disease. Other factors leading to the desirable plasma half-life are sustained exposure requirements for maximum therapeutic efficiency versus follow-up toxicology due to sustained exposure to the agent. pharmaceutically acceptable salts
[0054] It will be appreciated which salt forms are within the scope of this invention, and references to compounds of formula (I) include the salt forms of these compounds.
[0055] The salts of the present invention can be synthesized from the parent compound that contains a basic or acidic moiety by conventional chemical methods, such as methods described in Pharmaceutical Salts: Properties, Selection, and Use (Pharmaceutical Salts: Properties , Selection and Use), P. Heinrich Stahl (Editor), Camille G. Wermuth (Editor), ISBN: 3-90639-026-8, Hardcover, 388 pages, August 2002. Generally, these salts can be prepared by means of of reacting the free acid or base forms of these compounds with the appropriate base or acid in water or an organic solvent, or a mixture of the two.
[0056] Acid addition salts (mono- or di-salts) can be formed with a wide variety of acids, both inorganic and organic. Examples of acid addition salts include salts mono- or diformed with an acid selected from the group consisting of acetic, 2,2-dichloroacetic, adipic, alginic, ascorbic (eg, L-ascorbic), L-aspartic, benzenesulfonic, acid. benzoic, 4-acetamidobenzoic, butanoic, (+) camphoric, camphorsulfonic, (+)-(1S) -camphor-10-sulfonic, capric, caproic, caprylic, cinnamic, citric, cyclamic, dodecylsulfuric, ethane-1,2-disulfonic , ethanesulfonic, 2-hydroxyethanesulfonic, formic, fumaric, galactaric, gentisic, glycoeptonic, D-glyconic, glucuronic (eg D-glucuronic), glutamic (eg L-glutamic), a-oxoglutaric, glycolic, hippuric acids, hydroic acids (eg, hydrobromic, hydrochloric, hydriodic), isethionic, lactic (eg, (+)-L-lactic, (±)-DL-lactic), lactobionic, maleic, malic, (-)-L-malic , malonic, (±)-DL-mandelic acid, methanesulfonic, naphthalene-2-sulfonic, naphthalene-1,5-disulfonic, 1-hydroxy-2-naphthoic, ni cotinic, nitric, oleic, orotic, oxalic, palmitic, pamoic, phosphoric, propionic, pyruvic, L-pyroglutamic, salicylic, 4-amino-salicylic, sebacic, stearic, succinic, sulfuric, tannic, (+)-L-tartaric, thiocyanic, p-toluenesulfonic, undecylenic and valeric acids, as well as acylated amino acids and cation exchange resins.
[0057] A particular group of salts consists of salts formed from acetic, hydrochloric, hydroiodic, phosphoric, nitric, sulfuric, citric, lactic, succinic, maleic, malic, isethionic, fumaric, benzenesulfonic, toluenesulfonic, sulfuric, methanesulfonic acid mesylate), ethanesulfonic, naphthalenesulfonic, valeric, propanoic, butanoic, malonic, glucuronic and lactobionic. One particular salt is the hydrochloride salt. Another particular salt is the acetate salt.
[0058] If the compound is anionic, or has a functional group that can be anionic (for example, -COOH can be -COO-), then a salt can be formed with an organic or inorganic base, generating a suitable cation . Examples of suitable inorganic cations include, but are not limited to, alkali metal ions such as Li+, Na+ and K+, alkaline earth metal cations such as Ca2+ and Mg2+, and other cations such as Al3+ or Zn+. Examples of suitable organic cations include, but are not limited to, ammonium ion (ie, NH4+) and substituted ammonium ions (eg, NH3R+, NH2R2+, NHR3+, NR4+). Examples of some suitable substituted ammonium ions are those derived from: methylamine, ethylamine, diethylamine, propylamine, dicyclohexylamine, triethylamine, butylamine, ethylenediamine, ethanolamine, diethanolamine, piperazine, benzylamine, phenylbenzylamine, choline, meglumine, and tromethamine, as well as , amino acids such as lysine and arginine. An example of a common quaternary ammonium ion is N(CH3)4+.
[0059] When the compounds of formula (I) contain an amine function, they can form quaternary ammonium salts, for example, by reacting with an alkylating agent according to methods well known to those skilled in the art. Such quaternary ammonium compounds are within the scope of formula (I). Modified Derivatives
[0060] It will be appreciated that modified derivatives of the peptide linkers as defined in this report are within the scope of the present invention. Examples of such suitable modified derivatives include one or more modifications selected from: N-terminus and/or C-terminus modifications; replacing one or more amino acid residues with one or more unnatural amino acid residues (such as replacing one or more polar amino acid residues with one or more isosteric or isoelectronic amino acids; replacing one or more non-polar amino acid residues with other unnatural isosteric or isoelectronic amino acids); adding a spacer group; replacing one or more oxidation-sensitive amino acid residues with one or more oxidation-resistant amino acid residues; replacing one or more amino acid residues with an alanine; replacing one or more L-amino acid residues with one or more D-amino acid residues; N-alkylation of one or more amide bonds in the bicyclic peptide linker; replacing one or more peptide bonds with a substituted bond; modification of peptide backbone length; replacing the hydrogen and alpha carbon of one or more amino acid residues with another chemical group; modification of amino acids such as cysteine, lysine, glutamate/aspartate and tyrosine with suitable amine, thiol, carboxylic acid and phenol reactive reagents in order to functionalize these amino acids, and introduction or substitution of amino acids that introduce orthogonal reactivities that are suitable for functionalization, for example, azide or alkine group carrying amino acids that allow functionalization with moieties carrying alkine or azide, respectively.
[0061] In one embodiment, the modified derivative comprises a modification in position 1 and/or 9 of the amino acid. Data are presented in this report which show that these positions, especially where tyrosine is present, are more susceptible to proteolytic degradation.
[0062] In one embodiment, the modified derivative comprises an N-terminus and/or C-terminus modification. In a further embodiment, wherein the modified derivative comprises an N-terminus modification using appropriate amino reactive chemistry, and/or modification of C-terminus using suitable carboxy-reactive chemistry. In a further embodiment, the N-terminus or C-terminus modification comprises adding an effector group, including, but not limited to, a cytotoxic agent, a radiochelator or a chromophore.
In a further embodiment, the modified derivative comprises an N-terminal modification. In a further embodiment, the N-terminal modification comprises an N-terminal acetyl group, such as 17-69-07-N004 described in this report. In this embodiment, the N-terminal cysteine group (the group referred to herein as Ci) is capped with acetic anhydride or other appropriate reagents during peptide synthesis that leads to a molecule that is N-terminally acetylated. potential recognition point for aminopeptidases and avoids the degradation potential of the bicyclic peptide.
[0064] In an alternative embodiment, the N-terminus modification comprises the addition of a molecular spacer group that facilitates the conjugation of effector groups and potency retention of the bicyclic peptide to its target, such as an Ala group, G-Sar10-A or bullet-Sar10A. Data are presented in this report which show that addition of these groups to the bicyclic peptide 17-69-07 does not alter potency for the target protein (Tables 11-12).
[0065] In one embodiment, the modified derivative comprises a C-terminus modification. In a further embodiment, the C-terminal modification comprises an amide group. In this embodiment, the C-terminal cysteine group (the group referred to herein as Ciii) is synthesized as an amide during peptide synthesis leading to a molecule that is terminally amidated to C. This embodiment provides the advantage of removing a recognition point potential for carboxypeptidase and reduces the proteolytic degradation potential of the bicyclic peptide.
[0066] In one embodiment, the modified derivative comprises replacing one or more amino acid residues with one or more unnatural amino acid residues. In this embodiment, unnatural amino acids can be selected having isosteric/isoelectronic side chains that are recognized by degradative proteases or have any adverse effect on target potency.
[0067] Alternatively, unnatural amino acids can be used having limited amino acid side chains such that proteolytic hydrolysis of the close peptide bond is conformationally and sterically impeded. In particular, these concern proline analogues, bulky side chains, Cα-disubstituted derivatives (eg, aminoisobutyric acid, Aib), and cyclo amino acids, a simple derivative which is aminocyclopropylcarboxylic acid.
[0068] In one embodiment, the unnatural amino acid residue is substituted at position 4. Data are presented in this report which show that several unnatural amino acid residues are well tolerated at that position (see Table 8). In a further embodiment, unnatural amino acid residues, such as those present at position 4, are selected from: 1-naphthylalanine; 2- naphthylalanine; cyclohexylglycine, phenylglycine; tert-butylglycine; 3,4-dichlorophenylalanine; cyclohexylalanine; and homophenylalanine.
[0069] In a still further embodiment, unnatural amino acid residues, such as those present at position 4, are selected from: 1-naphthylalanine; 2-naphthylalanine; and 3,4-dichlorophenylalanine. Data are presented in this report which show that these substitutions enhanced affinity compared to the unmodified wild-type sequence (see Table 8).
[0070] In a still further embodiment, unnatural amino acid residues, such as those present at position 4, are selected from: 1-naphthylalanine. Data are presented in this report which show that this substitution provided the greatest level of affinity enhancement (greater than 7-fold) compared to wild type (see Table 8).
In one embodiment, the unnatural amino acid residue is introduced at position 9 and/or 11. Data are presented in this report which show that various unnatural amino acid residues are well tolerated at these positions (see, Table 9) .
[0072] In a further embodiment, unnatural amino acid residues, such as those present at positions 9, are selected from: 4-bromophenylalanine, pentafluorophenylalanine.
[0073] In a further embodiment, unnatural amino acid residues, such as those present at positions 11, are selected from: tert-butylglycine.
[0074] In a still further embodiment, unnatural amino acid residues such as those present at position 9 are selected from: 4-bromophenylalanine. Data are presented in this report which show alteration of the Tyr 9 proteolytic recognition point (see Table 9).
[0075] In a still further embodiment, unnatural amino acid residues, such as those present at position 11, are selected from: tert-butylglycine. Data are presented in this report which show enhancement of activity and strongly protect the vicinal amino acid structure from proteolytic hydrolysis through steric obstruction (see Table 9).
[0076] In one embodiment, the modified derivative comprises a plurality of the aforementioned modifications, such as 2, 3, 4 or 5 or more modifications. In a further embodiment, the modified derivative comprises 2, 3, 4 or 5, or more of the following modifications, such as all 5 of the following modifications: D-alanine at position 1 and 5, a 1-naphthylalanine at position 4, 4- bromophenylalanine at position 9 and a tert-butylglycine at position 11. Data are presented here which show that these are multiple substitutions (17-69-07-N252; 17-69-07-N244 and 17-69-07-N255) are tolerated for potency that is greater than wild-type (see Tables 10-12). In a still further embodiment, the modified derivative comprises the following modifications: D-alanine at position 1 and 5, a 1-naphthylalanine at position 4 and a tert-butylglycine at position 11. Data are presented in this report which show that this multiple substitution (17-69-07-N239) is tolerated for potency that is greater than wild-type (see Table 11).
[0077] In one embodiment, the modified derivative comprises the addition of a spacer group. In a further embodiment, the modified derivative comprises the addition of a spacer group to the N-terminal cysteine (Ci) and/or the C-terminal cysteine (Ciii).
[0078] In one embodiment, the modified derivative comprises replacing one or more oxidation-sensitive amino acid residues with one or more oxidation-resistant amino acid residues. In a further embodiment, the modified derivative comprises replacing a tryptophan residue with a naphthylalanine or alanine residue. This embodiment provides the advantage of improving the pharmaceutical stability profile of the resulting bicyclic peptide linker.
[0079] In one embodiment, the modified derivative comprises replacing one or more charged amino acid residues with one or more hydrophobic amino acid residues. In an alternative embodiment, the modified derivative comprises replacing one or more hydrophobic amino acid residues with one or more charged amino acid residues. The correct balance of charged versus hydrophobic amino acid residues is an important feature of bicyclic peptide ligands. For example, hydrophobic amino acid residues influence the degree of plasma protein binding and thus the concentration of the free fraction available in the plasma, while charged amino acid residues (in particular arginine) can influence the peptide's interaction with phospholipid membranes on cell surfaces. The two, in combination, can influence half-life, volume of distribution, and peptide drug exposure, and can be tailored according to clinical endpoint. Furthermore, the correct combination and number of charged versus hydrophobic amino acid residues can reduce irritation at the injection site (if the peptide drug was administered subcutaneously).
[0080] In one embodiment, the modified derivative comprises replacing one or more L-amino acid residues with one or more D-amino acid residues. This modality is believed to increase proteolytic stability through steric hindrance and by a propensity of D-amino acids to stabilize β-return conformations (Tugyi et al (2005) PNAS, 102(2), 413-418).
[0081] In a further embodiment, the amino acid residue at position 1 is replaced by a D-amino acid, such as D-alanine. Data are presented in this report which demonstrate potency retention without consequent degradation (see Table 6).
[0082] In a further embodiment, the amino acid residue at position 5 is replaced by a D-amino acid, such as D-alanine or D-arginine. Data are presented in this report which demonstrate potency retention without consequent degradation (see Table 7).
[0083] In one embodiment, the modified derivative comprises removal of any amino acid residue and substitution with alanines. This modality provides the advantage of removing potential site(s) of proteolytic attack.
[0084] It should be noted that each of the aforementioned modifications serves to deliberately improve the potency or stability of the peptide. Additional potency improvements based on modifications can be obtained through the following mechanisms: - Incorporation of hydrophobic moieties that exploit the hydrophobic effect and lead to reduced off rates, such that higher affinities are achieved; - Incorporation of charged groups that exploit long-range ionic interactions, leading to faster rates and higher affinities (see, for example, Schreiber et al., Rapid, electrostatically assisted association of proteins (1996), Nature Struct. Biol. 3, 427 -31); and - Incorporation of additional restriction to the peptide, by, for example, restricting amino acid side chains correctly, such that loss in entropy is minimal under target-bond, restricting the torsional angles of the main chain, such that loss in entropy is minimal under target binding and introduction of additional cyclizations into the molecule, for similar reasons. (For reviews see Gentilucci et al., Curr. Pharmaceutical Design (2010), 16, 3185-203, and Nestor et al., Curr. Medicinal Chem. (2009), 16, 4399-418). Isotopic variations
[0085] The present invention includes all compounds marked by pharmaceutically acceptable (radio)isotopes of the invention, i.e. compounds of formula (I), in which one or more atoms are replaced by atoms having the same atomic number, but one atomic mass or mass number different from the atomic mass or mass number usually found in nature, and compounds of formula (I), in which chelating groups of metals are attached (called "effectors") that are capable of holding (radio)isotopes of interest, and compounds of formula (I), wherein certain functional groups are covalently substituted with relevant (radio)isotopes or isotopically-labelled functional groups.
[0086] Examples of isotopes suitable for inclusion in the compounds of the invention comprise isotopes of hydrogen such as 2H (D) and 3H (T), carbon such as 11C, 13C and 14C, chlorine such as 36Cl, fluorine such as 18F, iodine such as 123I, 125l and 131l, nitrogen such as 13N and 15N, oxygen such as 15O, 17O and 18O, phosphorus such as 32P, sulfur such as 35S, copper such as 64Cu, gallium, such as 67Ga or 68Ga, yttrium such as 90Y and lutetium such as 177Lu, and bismuth such as 213Bi.
[0087] Certain isotopically-labelled compounds of formula (I), for example those that incorporate a radioactive isotope are useful in tissue distribution studies on drugs and/or substrate, and clinically assess the presence and/or absence of MT1-MMP target in diseased tissues such as tumors and elsewhere. The compounds of formula (I) can additionally exhibit valuable diagnostic properties whereby the compounds can be used to detect or identify the formation of a complex between a labeled compound and other molecules, peptides, proteins, enzymes or receptors. The detection or identification methods can use compounds that are labeled with labeling agents, such as radioisotopes, enzymes, fluorescent substances, luminous substances (e.g. luminol, luminol derivatives, luciferin, aquorin and luciferase), etc. Radioactive isotopes tritium, i.e., 3H(T), and carbon-14, i.e., 14C, are particularly useful for this purpose, in view of their ease of incorporation and ready means of detection.
[0088] Substitution with heavier isotopes such as deuterium, i.e., 2H(D), may provide certain therapeutic advantages resulting from greater metabolic stability, eg, increased in vivo half-life or reduced dosage requirements and therefore may be preferred in some circumstances.
[0089] Substitution with positron emitting isotopes such as 11C, 18F, 15O and 13N may be useful in Positron Emission Topography (TEP) studies, Positron Emission Topography (PET) to examine target occupancy.
[0090] Incorporation of isotopes into metal chelating effector groups such as 64Cu, 67Ga, 68Ga, and 177Lu can be useful for visualization of tumor-specific antigens employing PET or SPECT imaging. In particular, such biodistribution data are presented in this report in Example 3.
[0091] Incorporation of isotopes into metallic chelating effector groups, such as, but not limited to, 90Y, 177Lu, and 213Bi, may present the option of targeted radiotherapy, through which compounds that support metallic chelator of formula (I) carry the therapeutic radionuclide towards the target protein and site of action.
Isotopically labeled compounds of formula (I) can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described in the accompanying Examples, using an appropriate isotopically labeled reagent in place of the unlabeled reagent previously employed. Linking Activity
[0093] Specificity, in the context of this report, refers to the ability of a ligand to bind or otherwise interact with its cognate target to the exclusion of entities that are similar to the target. For example, specificity can refer to the ability of a ligand to inhibit the interaction of a human enzyme, but not a homologous enzyme from a different species. Using the approach described here, specificity can be modulated, this is increased or decreased, so as to make the binders more or less capable of interacting with homologues or paralogs of the intended target. Specificity is not intended to be synonymous with activity, affinity or avidity, and the potency of action of a ligand on its target (such as, for example, binding affinity or level of inhibition) is not necessarily related to its specificity.
[0094] Binding activity as used in this report refers to the quantitative measurements of binding taken from binding assays, for example, as described in this report. Therefore, binding activity refers to the amount of peptide ligand that binds to a given target concentration.
[0095] Multispecificity is the ability to bind to two or more targets. Typically, binding peptides are capable of binding to a single target, such as an epitope in the case of an antibody, due to their conformational properties. However, peptides can be developed which can bind to two or more targets; specific dual antibodies, for example, as known in the prior art as noted above. In the present invention, peptide linkers may be capable of binding to two or more targets and are therefore multispecific. Appropriately, these bind to two targets, and are specific doubles. The binding can be independent, meaning that the binding sites for the targets on the peptide are not structurally impeded by the binding of one or the other of the targets. In this case, both targets can be linked independently. More generally, it is expected that the binding of one target will at least partially prevent the binding of the other.
[0096] There is a fundamental difference between a specific dual ligand and a ligand with specificity that spans two related targets. In the first case, the ligand is specific to both targets individually, and interacts with each in a specific way. For example, a first loop in which the ligand can bind to a first target, and a second loop to a second target. In the second case, the ligand is not specific because it makes no distinction between the two targets, for example, interacting with an epitope of the targets that is common to both.
[0097] In the context of the present invention, it is possible that a ligand that exhibits activity in relation to, for example, a target and an ortholog, may be a bispecific ligand. However, in one modality, the ligand is not bispecific but has a less precise specificity such that it binds both the target and one or more orthologs. In general, a ligand that was not selected against both a target and its ortholog is less likely to be bispecific, due to the absence of selective pressure towards bispecificity. The length of the bicyclic peptide loop can be decisive in providing an adapted binding surface in such a way that good cross-reactivity of target and ortholog can be obtained, while maintaining high selectivity towards the less related homolog.
[0098] If the ligands are truly bispecific, in one modality, at least one of the target specificities of the ligands will be common among the selected ligands, and the level of this specificity can be modulated by the methods described in this report. Second or additional specifics need not be shared, and need not be the subject of the procedures presented in this report.
[0099] A target is a molecule or part thereof to which peptide ligands bind or otherwise interact. Although bonding is seen as a prerequisite for activity of most types, and can itself be an activity, other activities are considered. Thus, the present invention does not require the measurement of binding directly or indirectly.
[00100] The molecular scaffold is any molecule that is able to bind the peptide at various points to transmit one or more structural characteristics to the peptide. Preferably, the molecular framework comprises at least three attachment points for the peptide, referred to as scaffold reactive groups. These groups are able to react with cysteine residues (Ci, Cii and Ciii) in the peptide to form a covalent bond. These not merely form a disulfide bond, which undergo reductive cleavage and concomitant disintegration of the molecule, but form stable, covalent thioether bonds. Preferred structures for molecular frameworks are described below. Molecular frameworks
Molecular scaffolds are described in, for example, WO 2009/098450 and references cited herein, particularly WO 2004/077062 and WO 2006/078161.
[00102] As noted in the preceding documents, the molecular framework can be a small molecule, such as a small organic molecule.
[00103] In one embodiment, the molecular framework can be, or can be based on, natural monomers such as nucleosides, sugars or oidesteroids. For example, the molecular structure can comprise a short polymer of such entities, such as a dimer or a trimer.
[00104] In one embodiment, the molecular framework is a compound of known toxicity, for example, low toxicity. Examples of suitable compounds include cholesterols, nucleotides, steroids, or existing drugs such as tamazepam.
[00105] In one embodiment, the molecular framework can be a macromolecule. In one embodiment, the molecular structure is a macromolecule composed of amino acids, nucleotides, or carbohydrates.
[00106] In one embodiment, the molecular framework comprises reactive groups that are capable of reacting with functional (functional) group(s) of the polypeptide to form covalent bonds.
[00107] The molecular framework can comprise chemical groups that form the bond with a peptide, such as amines, thiols, alcohols, ketones, aldehydes, nitriles, carboxylic acids, esters, alkenes, alkynes, azides, anhydrides, succinimides, maleimides, halides of alkyl and acyl halides.
[00108] In one embodiment, the molecular framework may comprise or may consist of tris(bromomethyl)benzene, especially 1,3,5-tris(bromomethyl)benzene ("TBMB"), or a derivative thereof.
[00109] In one embodiment, the molecular framework is 2,4,6-tris(bromomethyl)mesitylene. This molecule is similar to 1,3,5-tris(bromomethyl)benzene, but contains three additional methyl groups attached to the benzene ring. This has the advantage that additional methyl groups can form additional contacts with the polypeptide and therefore add additional structural restriction.
[00110] The molecular framework of the invention contains chemical groups that allow functional groups of the polypeptide of the encoded library of the invention to form covalent bonds with the molecular framework. These chemical groups are selected from a wide range of functionalities, including, amines, thiols, alcohols, ketones, aldehydes, nitriles, carboxylic acids, esters, alkenes, alkynes, anhydrides, succinimides, maleimides, azides, alkyl halides and halides of acyl.
[00111] Reactive scaffold groups that can be used in the molecular scaffold to react with thiol groups of cysteines are alkyl halides (or also called haloalkanes or haloalkanes).
[00112] Examples include bromomethylbenzene (the scaffold reactive group exemplified by TBMB) or iodoacetamide. Other scaffold reactive groups that are used to selectively couple compounds with cysteines into proteins are maleimides. Examples of maleimides that can be used as molecular scaffolds in the invention include: tris-(2-maleimidoethyl)amine, tris-(2-maleimidoethyl)benzene, tris-(maleimido)benzene. Selenocysteine is also a natural amino acid that has a similar reactivity to cysteine and can be used for the same reactions. Thus, whenever cysteine is mentioned, it is typically acceptable to substitute selenocysteine, unless the context suggests otherwise. Effector and functional groups
According to a further aspect of the invention, there is provided a drug conjugate comprising a peptide linker as defined in this report, conjugated to one or more effector and/or functional groups.
[00114] Effector and/or functional groups can be linked, for example, to the N and/or C termini of the polypeptide, to an amino acid in the polypeptide, or to the molecular framework.
[00115] Suitable effector groups include antibodies and parts or fragments thereof. For example, an effector group may include an antibody light chain constant region (CL), a CH1 antibody heavy chain domain, a CH2 antibody heavy chain domain, a CH3 antibody heavy chain domain, or any combination of them, in addition to one or more domains of the constant region. An effector group may also comprise a hinge region of an antibody (such region normally being found between the CH1 and CH2 domains of an IgG molecule).
[00116] In a further embodiment of this aspect of the invention, an effector group according to the present invention is an Fc region of an IgG molecule. Advantageously, a peptide linker effector group according to the present invention comprises or consists of a peptide linker Fc fusion having a tβ half-life of one day or more, two days or more, three days or more, four days or more , five days or more, six days or more, or seven days or more. More advantageously, the peptide linker according to the present invention comprises or consists of a peptide linker Fc fusion having a tβ half-life of one day or more.
[00117] Functional groups include, in general, linking groups, drugs, reactive groups for linking other entities, functional groups that help uptake of macrocyclic peptides into cells, and the like.
[00118] The ability of peptides to penetrate cells will allow peptides against intracellular targets to be effective. Targets that can be accessed by peptides with the ability to penetrate cells include transcription factors, intracellular signaling molecules such as tyrosine kinases and molecules involved in the apoptotic pathway. Functional groups that allow cell penetration include peptides or chemical groups that have been added to the peptide or molecular scaffold. Peptides, such as those derived from: such as VP22, HIV-Tat, a Drosophila homeobox protein (Antennapedia), for example, as described in Chen and Harrison, Biochemical Society Transactions (2007), Volume 35, part 4, p. 821; Gupta and others; in Advanced Drug Discovery Reviews (2004) Volume 57, 9637. Examples of short peptides that have been shown to be efficient in translocation across plasma membranes include the Drosophila protein 16 amino acid penetratin peptide (Antennapedia) (Derossi et al. (1994) J. Biol. Chem. Volume 269, p.10444), the 18-amino acid 'amphipathic model peptide' (Oehlke et al. (1998) Biochim. Biophys. Acts volume 1414, p.127) and arginine-rich regions of the TAT protein of HIV. Non-peptide approaches include the use of small molecule mimics or SMOCs that can be easily attached to biomolecules (Okuyama et al (2007) Nature Methods Volume 4, p.153). Other chemical strategies for adding guanidinium groups to molecules also enhance cell penetration (Elson-Scwab et al (2007) J. Biol. Chem. Volume 282, p. 13585). Small molecular weight molecules such as steroids can be added to the molecular framework to enhance cell uptake.
[00119] A class of functional groups that can be linked with peptide linkers includes antibodies and binding fragments thereof, such as Fab, Fv or single domain fragments. In particular, antibodies that bind to proteins capable of increasing the half-life of the peptide ligand in vivo can be used.
[00120] RGD peptides that bind to integrins that are present in many cells can also be incorporated.
[00121] In one embodiment, a peptide ligand effector group according to the invention has a half-life tβ selected from the group consisting of: 12 hours or more, 24 hours or more, 2 days or more, 3 days or more , 4 days or more, 5 days or more, 6 days or more, 7 days or more, 8 days or more, 9 days or more, 10 days or more, 11 days or more, 12 days or more, 13 days or more , 14 days or more, 15 days or more, or 20 days or more. Advantageously, a linker effector group of peptide or composition according to the invention will have a half life tβ in the range of 12 to 60 hours. In an additional modality, it will have a tβ half-life of one day or more. In an additional modality, it will be in the range of 12 to 26 hours.
[00122] In a particular embodiment of the invention, the functional group is selected from a metallic chelator, which is suitable for the complexation of metallic radioisotopes of medicinal relevance. Such effectors, when complexed with these radioisotopes, may present useful agents for cancer therapy. Suitable examples include DOTA, NOTA, EDTA, DTPA, HEHA, SarAr and others (Targeted Radionuclide Therapy, Tod Speer, Wolters/Kluver Lippincott Williams & Wilkins, 2011).
Possible effector groups also include enzymes, for example such as carboxypeptidase G2 for use in enzyme/prodrug therapy, where the peptide linker replaces antibodies in ADEPT.
[00124] In a particular embodiment of the invention, the functional group is selected from a drug, such as a cytotoxic agent for cancer therapy. Suitable examples include: alkylating agents such as cisplatin and carboplatin as well as oxaliplatin, mechloroethamine, cyclophosphamide, chlorambucil, ifosfamide; antimetabolites, including, purine analogues; azathioprine and mercaptopurine or pyrimidine analogues; plant alkaloids and terpenoids, including vinca alkaloids such as Vincristine, Vinblastine, Vinorelbine and Vindesine; Podophyllotoxin and its etoposide and teniposide derivatives; Taxanes, including paclitaxel, originally known as Taxol; topoisomerase inhibitors including camptothecins: irinotecan and topotecan, and type II inhibitors including ansacrine, etoposide, etoposide phosphate and teniposide. Additional agents may include antitumor antibiotics which include the immunosuppressive dactinomycin (which is used in kidney transplants), doxorubicin, epirubicin, bleomycin, calicheamicins, and others.
[00125] In a particular further embodiment of the invention, the cytotoxic agent is selected from maytansinoids (such as DM1) or monomethyl auristatins (such as MMAE).
[00126] DM1 is a cytotoxic agent that is a thiol-containing derivative of maytansine and has the following structure:

[00127] Auristatin monomethyl E (MMAE) is a synthetic antineoplastic agent and has the following structure:

[00128] Data are presented in this report in Examples 4 and 5 that demonstrate the effects of peptide linkers conjugated with DM1 or MMAE containing toxins.
[00129] In one embodiment, the cytotoxic agent is linked with the bicyclic peptide via a cleavage bond, such as a disulfide bond or a protease sensitive bond. In a further embodiment, the groups adjacent to the disulfide bond are modified to control the impediment of the disulfide bond, and hence the rate of cleavage and concomitant release of cytotoxic agent.
[00130] Published work has established the potential for modifying the susceptibility of the disulfide bond to reduction by introducing steric hindrance on both sides of the disulfide bond (Kellogg et al. (2011) Bioconjugate Chemistry, 22, 717). A greater degree of steric hindrance reduces the rate of reduction through intracellular glutathione and also extracellular (systemic) reducing agents, thereby reducing the ease with which the toxin is released, both inside and outside the cell. Thus, optimal selection in circulating disulfide stability (which minimizes undesirable side effects of the toxin) versus efficient release into the intracellular environment (which maximizes the therapeutic effect) can be achieved through careful selection of the degree of impairment on both sides of the disulfide bond.
[00131] Impediment on either side of the disulfide bond is modulated by introducing one or more methyl groups into the targeting entity (here, the bicyclic peptide) or toxin side of the molecular construct.
[00132] Thus, in one embodiment, the cytotoxic agent is a maytansinoid selected from a compound of formula (II):
where n represents an integer selected from 1 to 10; and R1 and R2 independently represent hydrogen, C1-6 alkyl or a carbocyclyl or heterocyclyl group.
[00133] The term C1-6alkyl as used in this report refers to a straight or branched saturated hydrocarbon group containing from 1 to 6 carbon atoms, respectively. Examples of such groups include methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl or hexyl and the like.
[00134] The term "heterocyclyl" and "carbocyclyl" as used in this report shall, unless the context otherwise indicates, include both aromatic and non-aromatic ring systems. Thus, for example, the term "heterocyclyl group" and "carbocyclyl group" include within their scope aromatic, non-aromatic, unsaturated, partially saturated and fully saturated carbocyclyl or heterocyclyl ring systems. In general, unless the context indicates otherwise, such groups may be monocyclic or bicyclic (including, fused and bridged bicyclic groups) and may contain, for example, from 3 to 12 ring members, more usually of 5 to 10 members in the ring.
[00135] In one embodiment of the compound of formula (II), R1 and R2 independently represent hydrogen or methyl.
[00136] In one embodiment of the compound of formula (II), n represents 1 and R1 and R2 both represent hydrogen (ie, the maytansine derivative DM1).
[00137] In an alternative embodiment of the compound of formula (II), n represents 2, R1 represents hydrogen and R2 represents a methyl group (ie, the maytansine derivative DM3).
[00138] In one embodiment of the compound of formula (II), n represents 2 and R1 and R2 both represent methyl groups (ie, the maytansine derivative DM4).
[00139] It will be evaluated that the cytotoxic agent of formula (II) can form a disulfide bond, and in a conjugated structure with a bicyclic peptide of formula (I), the disulfide connectivity between the thiol-toxin peptide (II) and thiol-bicyclo(III) is introduced via several possible synthetic schemes, two being described in Scheme II or Scheme III.
[00140] In one embodiment, the bicyclic peptide component of the conjugate has the structure shown in formula (III):
wherein m represents an integer selected from 0 to 10, and R3 and R4 independently represent hydrogen, C1-6 alkyl or a carbocyclyl or heterocyclyl group.
[00141] In one embodiment of the compound of formula (III), R3 and R4 independently represent hydrogen or methyl.
Compounds of formula (III), wherein R3 and R4 are both hydrogen are considered unhindered and compounds of formula (III) wherein one or all of R3 and R4 represent, methyl are considered hindered.
[00143] It will be evaluated that the bicyclic peptide of formula (III) can form a disulfide bond, and in a conjugated structure with a cytotoxic agent of formula (II), the disulfide connectivity between the thiol-toxin peptide (II) and thiol-bicyclo(III) is introduced via several possible synthetic schemes, one being described in Scheme II.
[00144] In one embodiment, the cytotoxic agent is linked to the bicyclic peptide through a linker defined in formula (IV):
wherein R 1 , R 2 , R 3 and R 4 represent hydrogen, C 1-6 alkyl or a carbocyclyl or heterocyclyl group; Toxin refers to any suitable cytotoxic agent defined in this report; Bicycle represents any suitable bicyclic peptide defined in this report; n represents an integer selected from 1 to 10; em represents an integer selected from 0 to 10;
[00145] In one embodiment, R1, R2, R3 and R4 represent hydrogen or methyl.
[00146] When R1, R2, R3 and R4 are each hydrogen, the disulfide bond is less hindered and more susceptible to reduction. When R1, R2, R3 and R4 are each methyl, the disulfide bond is more hindered and less susceptible to reduction. Partial hydrogen and methyl substitutions produce a gradual increase in resistance to reduction and concomitant cleavage and toxin release.
[00147] In one embodiment, the toxin of compound (IV) is a maytansine and the conjugate comprises a compound of formula (V):
wherein R 1 , R 2 , R 3 and R 4 represent hydrogen, C 1-6 alkyl or a carbocyclyl or heterocyclyl group; Bicycle represents any suitable bicyclic peptide as defined in this report; n represents an integer selected from 1 to 10; em represents an integer selected from 0 to 10.
[00148] In a further embodiment of the compound of formula (V), n represents 1 and R1, R2, R3 and R4 each represents hydrogen, that is, a compound of formula (V)a:

[00149] The BDC of formula (V)a is known as BT17BDC-17. The unhindered disulfide in BDC BT17BDC-17 is the equivalent of BT17BDC-9, whereby the difference resides in the bicyclic peptide portion: BT17BDC-9 employs the unstabilized sequence (17-69-07-N219), whereas BT17BDC -17 employs the stabilized bicyclic peptide counterpart (17-69-07-N241) which is amide linked to the toxin disulfide construct. This unhindered maytansine derivative with n = 1 is called DM1.
[00150] In a further embodiment of the compound of formula (V), n represents 1, R1 represents methyl and R2, R3 and R4 each represent hydrogen, that is, a compound of formula (V)b:
(V)b
[00151] The BDC of formula (V)be known as BT17BDC-18 and contains a single hindering methyl group on the side of the bicyclic peptide, and in the context of antibody drug conjugate produces a 7-fold reduction in its sensitivity to a reducing agent such as dithiothreitol (compared to unhindered disulfide) (Kellogg et al. (2011) Bioconjugate Chemistry, 22, 717). Reduced sensitivity to reduction correlates with a lower rate of toxin release. This unhindered maytansine derivative with n = 1 is called DM1. BT17BDC-18 employs the stabilized bicyclic peptide counterpart (17-69-07-N241) which is amide linked with the toxin disulfide construct.
[00152] In a further embodiment of the compound of formula (V), n represents 2, R1 and R2 both represent hydrogen and R3 and R4 both represent methyl, that is, a compound of formula (V)c: (V)c

[00153] The BDC of formula (V)cé known as BT17BDC-19 and contains two hindering methyl groups on the maytansine side, and in the context of antibody drug conjugate produces a 14-fold reduction in its sensitivity to a reducing agent , such as dithiothreitol. Reduced sensitivity to reduction correlates with a lower rate of toxin release. This hindered maytansine derivative with n = 2 is called DM4. BT17BDC-19 employs the stabilized bicyclic peptide counterpart (17-69-07-N241) which is amide linked with the toxin disulfide construct.
[00154] In a further embodiment of the compound of formula (V), n represents 2, R1 and R3 both represent methyl and R2 and R4 both represent hydrogen, that is, a compound of formula (V)d:

[00155] The BDC of formula (V) is known as BT17BDC-20 and contains a hindering methyl group on the maytansine side, and a hindering methyl group on the bicyclic peptide side, and in the context of antibody drug conjugate it produces a 170-fold reduction in its sensitivity to a reducing agent such as dithiothreitol. Reduced sensitivity to reduction correlates with a lower rate of toxin release. This hindered maytansine derivative with n = 2 is called DM3. BT17BDC-20 employs the stabilized bicyclic peptide counterpart (17-69-07-N241) which is amide linked with the toxin disulfide construct.
[00156] Indeed, in the context of antibody drug conjugates, the balance of efficacy versus tolerability in the animal model showed that its maximum is associated with some level of impairment, ie, that of DM4 (Kellogg et al. (2011) Bioconjugate Chemistry, 22, 717) which is present as such also in BT17BDC-19.
[00157] In one embodiment, the conjugate is selected from BT17BDC-9, BT17BDC-17 (Compound of formula (V)a), BT17BDC-18 (Compound of formula (V)b), BT17BDC-19 (Compound of formula ( V)c) and BT17BDC-20 (Compound of formula Vd). Data are presented in Example 5 and Tables 16 and 17, which demonstrate the beneficial properties of BT17BDC-9, BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20.
[00158] In an additional modality, the conjugate is selected from BT17BDC-9, BT17BDC-17 (Compound of formula (V)a), BT17BDC-18 (Compound of formula (V)b) and BT17BDC-19 (Compound of formula (You). Data are presented in Example 5 and in Tables 16 and 17, which demonstrate that these conjugates were found to be suitable molecules for use in targeted cancer therapy.
[00159] In an additional modality, the conjugate is selected from BT17BDC-17 (Compound of formula (V)a), BT17BDC-18 (Compound of formula (V)b) and BT17BDC-19 (Compound of formula (V)c ). Data are presented in Example 5 and in Tables 16 and 17, which demonstrate that these conjugates are considered suitable molecules for use in targeted cancer therapy and are well tolerated at effective doses. Synthesis
[00160] The peptides of the present invention can be produced synthetically by conventional techniques followed by reaction with a molecular framework in vitro. When this is done, standard chemistry can be used. This allows for rapid large-scale preparation of soluble material for further downstream experiments or validation. Such methods could be carried out using conventional chemistry such as that described in Timmerman et al (supra).
Thus, the invention also relates to the production of selected polypeptides or conjugates as described in this report, wherein the production comprises additional optional steps as explained below. In one embodiment, these steps are performed on the final polypeptide/conjugate product produced through chemical synthesis.
Optionally, amino acid residues in the polypeptide of interest may be substituted when making a conjugate or complex.
[00163] Peptides can also be extended, to incorporate, for example, another loop and thus introduce multiple specificities.
[00164] To extend the peptide, it can simply be chemically extended at the N-terminus or C-terminus or in loops using orthogonally protected lysines (and analogues) using standard solid-phase or solution-phase chemistry. Standard (bio) conjugation techniques can be used to introduce an activated or activatable N-terminus or C-terminus. Alternatively, additions can be made by fragment condensation or native chemical bonding, for example, as described in (Dawson et al. 1994. Synthesis of Proteins by Native Chemical Ligation), Science, 266: 776-779), or by enzymes, for example, using subtiligase as described in (Chang et al. Proc. Natl. Acad. Sci. USA, December 20, 1994; 91(26):12544-8 or in Hikari et al. , Bioorganic & Medicinal Chemistry Letters Volume 18, Issue 22, November 15, 2008, pages 6000-6.003).
[00165] Alternatively, the peptides can be extended or modified by further conjugation via disulfide bonds. This has the added benefit of allowing the first and second peptides to dissociate from each other once inside the cell's reducing environment. In that case, the molecular framework (eg TBMB) can be added during the chemical synthesis of the first peptide so as to react with the three cysteine groups; an additional cysteine or thiol can then be attached to the N or C terminus of the first peptide such that that cysteine or thiol just reacts with a free cysteine or thiol of the second peptide, forming a disulfide-linked peptide-bicyclic peptide conjugate.
[00166] Similar techniques apply equally for the synthesis/coupling of two bicyclic and bispecific macrocycles, potentially creating a tetraspecific molecule.
[00167] Furthermore, addition of other functional groups or effector groups can be carried out in the same way, using appropriate chemistry, coupling at the N-terminus or C-terminus, or via side chains. In one embodiment, the coupling is conducted in such a way that it does not block the activity of each identity.
According to a further aspect of the invention there is provided a process for preparing a drug conjugate as defined in this report which comprises the synthetic route which is described in any one of Schemes I, II or III. Pharmaceutical Compositions
According to a further aspect of the invention, there is provided a pharmaceutical composition comprising a peptide linker or a drug conjugate as defined in this report in combination with one or more pharmaceutically acceptable excipients.
[00170] Generally, the present peptide ligands will be used in purified form together with excipients or pharmacologically appropriate vehicles. Typically, such excipients or vehicles include aqueous or alcoholic/aqueous solutions, emulsions or suspensions, including saline and/or buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride and Ringer's lactate. Suitable physiologically acceptable adjuvants, if necessary, to keep a polypeptide complex in suspension, can be chosen from thickeners such as carboxymethylcellulose, polyvinylpyrrolidone, gelatin and alginates.
Intravenous vehicles include fluid and nutrient replenishers and electrolyte replenishers such as those based on Ringer's dextrose. Preservatives and other additives, such as antimicrobials, antioxidants, chelating agents and inert gases, may also be present (Mack (1982) Remington's Pharmaceutical Sciences, 16th Edition).
The peptide linkers of the present invention can be used as separately administered compositions or in conjunction with other agents. These can include antibodies, antibody fragments and various immunotherapeutic drugs such as cyclosporine, methotrexate, adriamycin or cisplatin and immunotoxins. Pharmaceutical compositions may include "cocktails" of various cytotoxic or other agents, together with the protein binders of the present invention, or even combinations of selected polypeptides according to the present invention having different specificities, such as selected polypeptides using different target ligands , whether or not are gathered before administration.
[00173] The route of administration of pharmaceutical compositions according to the invention can be any of those commonly known to those skilled in the art. For therapy, including, without limitation, immunotherapy, the peptide ligands of the invention can be administered to any patient in accordance with standard techniques. Administration can be by any suitable mode, including parenterally, intravenously, intramuscularly, intraperitoneally, transdermally, pulmonary, or also, appropriately, by direct infusion with a catheter. The dosage and frequency of administration will depend on the age, sex and condition of the patient, concurrent administration of other drugs, contraindications and other parameters that must be taken into account by the clinician.
[00174] The peptide binders of this invention can be lyophilized for storage and reconstituted in a suitable vehicle before use. This technique has been shown to be effective and lyophilization and reconstitution techniques known in the prior art can be employed. It will be appreciated by those skilled in the art that lyophilization and reconstitution can lead to varying degrees of activity loss and that levels can be adjusted upwards to compensate.
The compositions containing the present peptide binders or a cocktail thereof can be administered for prophylactic and/or therapeutic treatments. In certain therapeutic applications, an amount adequate to effect at least partial inhibition, suppression, modulation, killing, or some other measurable parameter, of a selected cell population is defined as a "therapeutically effective dose". Amounts needed to achieve this dosage will depend on the severity of the disease and the general state of the patient's own immune system, but generally range from 0.005 to 5.0 mg of selected peptide ligand per kilogram of body weight, with doses from 0.05 to 2 ,0 mg/kg/dose, being more commonly used. For prophylactic applications, compositions containing the present peptide binders or cocktails thereof may also be administered in similar or slightly lower dosages.
[00176] A composition containing a peptide ligand according to the present invention can be used in prophylactic and therapeutic conditions to aid in the alteration, inactivation, death or removal of a population of selected target cells in a mammal. Furthermore, the peptide ligands described in this report can be used extracorporeally or in vitro selectively to kill, deplete or otherwise effectively remove a target cell population from a heterogeneous collection of cells. Blood from a mammal can be combined extracorporeally with selected peptide ligands, whereby unwanted cells are killed or otherwise removed from the blood to return to the mammal, in accordance with conventional techniques. Therapeutic uses
[00177] The bicyclic peptides of the invention have specific utility as high-affinity membrane metalloprotease-type ligands (MT1-MMP, also known as MMP14). MT1-MMP is a transmembrane metalloprotease that plays an important role in extracellular matrix remodeling, directly through degradation of several of its components and indirectly through pro-MPM-2 activation. MT1-MMP is crucial for tumor angiogenesis (Sounni et al (2002) FASEB J. 16(6), 555 564) and is overexpressed in a variety of solid tumors, hence the bicyclic MT1-MMP binding peptides of this invention have particular utility in targeted treatment of cancer, in particular solid tumors such as non-small cell lung carcinomas. In one embodiment, the bicyclic peptide of the invention is specific to human MT1-MMP. In a further embodiment, the bicyclic peptide of the invention is specific to mouse MT1-MMP. In a still further embodiment, the bicyclic peptide of the invention is specific to human and mouse MT1-MMP. In a still further embodiment, the bicyclic peptide of the invention is specific to human, mouse and dog MT1-MMP.
Polypeptide binders selected in accordance with the method of the present invention may be employed in in vivo therapeutic and prophylactic applications, in vitro and in vivo diagnostic applications, in vitro assay and reagent applications, and the like. Ligands that exhibit selected levels of specificity are useful in applications involving testing in non-human animals, where cross-reactivity is desirable, or in diagnostic applications, where cross-reactivity with homologs or paralogs needs to be carefully controlled. In some applications, such as vaccine applications, the ability to induce an immune response to predetermined ranges of antigens can be exploited to tailor a vaccine to specific diseases and pathogens.
Substantially pure peptide linkers of at least 90 to 95% homogeneity are preferred for administration to a mammal, and 98 to 99% or more homogeneity are more preferred for pharmaceutical uses, especially when the mammal is a human. Once purified, partially or to homogeneity as desired, selected polypeptides can be used diagnostically or therapeutically (including, extracorporeally) or in the development and performance of assay procedures, immunofluorescent stains and the like (Lefkovite and Pernis, (1979 and 1981) Methods Immunologicals, Volumes I and II, Academic Press, NI).
The effector groups and conjugates of the peptide ligands of the present invention will typically find use in the prevention, suppression or treatment of cancer, in particular solid tumors such as non-small cell lung carcinomas.
[00181] Thereby, according to a further aspect of the invention, there is provided effector groups and peptide ligand drug conjugates as defined in this report for use in the prevention, suppression or treatment of cancer, in particular, solid tumors such as carcinomas non-small cell lungs.
[00182] According to a further aspect of the invention there is provided a method of preventing, suppressing or treating cancer, in particular solid tumors such as non-small cell lung carcinomas which comprises administering to a patient in need thereof, a effector group and peptide ligand drug conjugate as defined in this report.
[00183] Examples of cancers (and their benign counterparts) that can be treated (or inhibited) include, but are not limited to, tumors of epithelial origin (adenomas and carcinomas of various types, including, adenocarcinomas, squamous cell carcinomas, transitional cell carcinomas and other carcinomas) such as carcinomas of the bladder and urinary tract, breast, gastrointestinal tract (including, the esophagus, stomach (gastric), small intestine, colon, rectum and anus), liver (hepatocellular carcinoma) , gallbladder and biliary system, exocrine pancreas, kidney, lung (eg adenocarcinomas, small cell lung carcinomas, non-small cell lung carcinomas, bronchioalveolar carcinomas and mesotheliomas), head and neck (eg, tongue, cavity cancers buccal, larynx, pharynx, nasopharynx, tonsils, salivary glands, nasal cavity and paranasal sinuses), ovary, fallopian tubes, peritoneum, vagina, vulva, penis, cervix, myometrium rio, endometrium, thyroid (eg, follicular thyroid carcinoma), adrenal, prostate, skin, and adnexal (eg, melanoma, basal cell carcinoma, squamous cell carcinoma, keratoacanthoma, dysplastic nevus); haematological malignancies (ie, leukemias, lymphomas) and premalignant haematological disorders and borderline malignant disorders, including, haematological malignancies and related lymphoid lineage conditions (eg, acute lymphocytic leukemia [ALL], chronic lymphocytic leukemia [CLL], B cell lymphomas such as diffuse large B cell lymphoma [LCBDG], follicular lymphoma, Burkitt's lymphoma, mantle cell lymphoma, T cell lymphomas and leukemias, natural killer cell lymphomas [NK], Hodgkin's lymphomas, leukemia of hairy cells, monoclonal gammopathy of uncertain significance, plasmacytoma, multiple myeloma, and post-transplant lymphoproliferative disorders), and hematologic malignancies and related myeloid lineage conditions (eg, acute myelogenous leukemia [ALL], chronic myelogenous leukemia [CLL], myelomonocyticleukemia chronic [DLBCL], hypereosinophilia syndrome, myeloproliferative disorders such as polycythemia vera, thrombocytosis essential emia and primary myelofibrosis, myeloproliferative syndrome, myelodysplastic syndrome, and promyelocyticleukemia); tumors of mesenchymal origin, e.g., soft tissue, bone or cartilage sarcomas such as osteosarcoma, fibrosarcomas, chondrosarcomas, rhabdomyosarcomas, leiomyosarcoma, liposarcoma, angiosarcoma, Kaposi's sarcoma, Ewing's sarcoma, sinonasal sarcoma, sarcoma, sarcoma, sarcoma , benign and malignant histiocytomas, and bulging dermatofibrosarcoma; central or peripheral nervous system tumors (for example, astrocytomas, gliomas and glioblastomas, meningiomas, ependymomas, pineal tumors and schwannomas); endocrine tumors (for example, pituitary tumors, adrenal tumors, pancreatic islet cell tumors, parathyroid tumors, carcinoid tumors, and medullary carcinoma of the thyroid); ocular and adnexal tumors (for example, retinoblastoma); germ cell and trophoblastic tumors (eg, teratomas, seminomas, dysgerminomas, hydatiform moles, and choriocarcinomas); and pediatric and embryonic tumors (e.g., medulloblastoma, neuroblastoma, Wilms' tumor, and primitive neuroectodermal tumors); or syndromes, congenital or otherwise, which make the patient susceptible to malignancy (eg, xeroderma pigmentosa).
[00184] References in this report to the term "prevention" involve administration of the protective composition prior to disease induction. "Suppression" refers to administration of the composition after an inducing event, but before the clinical aspect of the disease. "Treatment" involves administering the protective composition after disease symptoms manifest.
[00185] Animal model systems that can be used to track the effectiveness of peptide ligands in protecting against or treating disease are available. The use of animal model systems is facilitated by the present invention, which allows for the development of polypeptide linkers, which can cross-react with human and animal targets, to enable the use of animal models.
[00186] The invention is further described below with reference to the following examples. Examples Materials and methods Phage Selections
[00187] 6x6 bicyclic phage libraries were generated as described in Heinis et al (2009), Nat. Chem. Biol. 5(7), 502-507, WO 2009/098450, WO 2013/050615 and WO 2013/050616. Phage display selections were performed using this 6x6 phage library against the hemopexin domain of biotinylated human MT1-MMP. Protein Expression
[00188] Repeats such as hemopexin of MT1-MMP (also known as the hemopexin domain of MT1-MMP), residues Cys319-Gly511 of the human gene, were transiently expressed in HEK293 cells as soluble protein secreted with His6 tail N-terminally using the expression vector pEXPR-IBA42 (IBA). After expression, the protein was purified by nickel-NTA affinity chromatography, followed by gel filtration, and purity was verified by SDS-PAGE. Batch-to-batch variability was also monitored using fluorescence thermal shift experiments in the presence/absence of a hemopexin domain-binding cycle. Peptide Synthesis
[00189] Peptide synthesis was based on Fmoc chemistry, using a Symphony peptide synthesizer manufactured by Peptide Instruments and a Syro II synthesizer by MultiSynTech. Standard Fmoc amino acids were used (Sigma, Merck), with the following side chain protecting groups: Arg(Pbf); Asn(Trt); Asp(OtBu); Cys(Trt); Glu(OtBu); Gln(Trt); His(Trt); Lys(Boc); Ser(tBu); Thr(tBu); Trp(Boc); and Tyr(tBu) (Sigma). The coupling reagent was HCTU (Pepceuticals), diisopropylethylamine (DIPEA, Sigma) was used as a base, and deprotection was achieved with 20% piperidine in DMF (AGTC). Syntheses were performed using 0.37 mmol/g amide AM resin Fmoc-Rink (AGTC), Fmoc amino acids were used in a four-fold excess, and base was in a four-fold excess of amino acids. Amino acids were dissolved at 0.2M in DMSO, 0.4M HCTU in DMF and 1.6M DIPEA in N-methylpyrrolidone (Alfa Aesar). Conditions were such that coupling reactions contained between 20 to 50% DMSO in DMF, which reduced aggregation and deletions during solid phase synthesis and enhanced yields. Coupling times were generally 30 minutes, and deprotection times 2 x 5 minutes. Fmoc-N-methylglycine (Fmoc-Sar-OH, Merck) was coupled for 1 hour, and deprotection and coupling times for the next residue were 20 minutes and 1 hour, respectively. After synthesis, the resin was washed with dichloromethane, and dried. Cleavage of side chain and scaffold protecting groups was performed using 10 mL of 95:2.5: 2.5:2.5 v/v/v/p TFA/H2O/iPr3SiH/dithiothreitol for 3 hours. After cleavage, spent resin was removed by filtration, and the filtrate was added to 35 ml of diethyl ether which was cooled to -80°C. Peptide pellet was centrifuged, the etheric supernatant discarded, and the peptide pellet washed with cold ether twice more. The peptides were then resolubilized in 5-10 ml of acetonitrile-water and lyophilized. A small sample was removed for crude product purity analysis by mass spectrometry (MALDI-TOF, Voyager DE from Applied Biosystems). After lyophilization, peptide powders were taken up in 10 mL of 6 M guanidinium hydrochloride in H2O, supplemented with 0.5 mL of 1 M dithiothreitol, and loaded onto a C8 Luna preparative HPLC column (Phenomenex). Solvents (H2O, acetonitrile) were acidified with 0.1% heptafluorobutyric acid. The gradient ranged from 30-70% acetonitrile in 15 minutes, at a flow rate of 15-20 mL/minute, using a Gilson preparative HPLC system. Fractions containing pure linear peptide material (as identified by MALDI) were combined, and modified with 1,3,5-tris(bromomethyl)benzene (TBMB, Sigma). For this, linear peptide was diluted with H2O to ~35 mL, ~500 μL of 100 mM TBMB in acetonitrile was added, and the reaction was started with 5 mL of 1 M NH4HCO3 in H2O. The reaction was allowed to proceed for ~30 -60 minutes at room temperature, and once lyophilized the reaction was complete (assessed by MALDI). After lyophilization, the modified peptide was purified as above, while replacing the Luna C8 with a Gemini C18 column (Phenomenex), and changing the acid to 0.1% trifluoroacetic acid. Pure fractions containing the correct modified TMB material were pooled, lyophilized and kept at -20°C for storage.
[00190] All amino acids, unless otherwise noted, were used in the L configurations.
[00191] DOTA was coupled with the peptide chain during solid phase peptide synthesis using the protected precursor DOTA(tBu)3 (TCI, CAS 137076-54-1).
[00192] Unnatural amino acids were incorporated into the peptide sequence using the general methods described above.
[00193] The list of unnatural amino acid precursors employed in this report is summarized in the Table below:


[00194] Peptides used for pharmacokinetic studies were lyophilized from 0.1% TFA in water to produce the TFA salts or free acids of the compounds. Synthesis of BCDs Using 17-69-07-N219 as a Bicyclic Peptide Precursor
[00195] Two bicyclic drug conjugates (BDC) were synthesized, using 17-69-07-N219 as a precursor peptide. Activated vcMMAE or disulfide-DM1 constructs (dissolved in DMSO) were directly conjugated in excess of 1.4 x with 17-69-07-N219 under aqueous conditions (sodium phosphate 100, pH 8) (see Schemes I and II ). Concentrations were at 9 mg/ml peptide or higher. The reaction was followed by LC/MS and assessed to be complete after 3.5 hours. This was followed by standard reverse phase purification using a C18 semi-preparative column. Fractions with purity greater than 95% were isolated and lyophilized. Materials did not contain measurable amounts of free toxin. For in vitro and in vivo studies, lyophilized powders were taken as stock materials of concentrated DMSO (100 mg/mL), and diluted in the appropriate buffer for further use. Synthesis of Bicyclic Drug Conjugates (BDCs) Using 17-69-07-N241 as a Bicyclic Peptide Precursor
[00196] For synthesis of BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20, the following N-hydroxysuccinimide esters (NHS esters) of maytansinoids disulfide were used:
wherein R 1 , R 2 , R 3 , R 4 , men are as described above for compounds of formula (V)a, (V)b, (V)c, (V)d for BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20, respectively.
[00197] BT17BDC-18 was further synthesized via an alternative pathway as described below and in Scheme III. Here, 17-69-07-N277 was synthesized by reacting 17-69-07-N241 with SPP (N-succinimidyl (4-(2-pyridyldithio)pentanoate) in DMSO. Concentrations of 17-69-07-N241 were 10 mM or greater, with a 1.3-fold excess of SPP, and a 20-fold excess of diisopropylethylamine, at room temperature. The reaction was assessed to be complete after 1 hour as determined by LC/MS. Purification was carried out by reversed phase as described above. Appropriate fractions were lyophilized.
[00198] 17-69-07-N277 was disulfide exchanged with 1.15 equivalents of DM1 (as the free thiol) under semi-aqueous conditions (50% dimethylacetamide and 100 mM sodium acetate 50%, pH 5, 0, supplemented with 2 mM EDTA) for 21 hours at room temperature under a blanket of nitrogen gas. Concentrations of 17-69-07-N277 in the reaction were at 10 mM or greater. This was followed by standard reverse phase purification using a C18 semipreparative column. Fractions with purity greater than 95% were isolated and lyophilized. Materials did not contain measurable amounts of free toxin. For in vitro and in vivo studies, freeze-drying powders were either solubilized in aqueous formulation as described above or taken directly into the appropriate buffer. Determination of dissociation rate constant of Bicyclic Ligands for MT1-MMP Direct Binding Fluorescence Polarization
[00199] Direct-binding or anisotropy Fluorescence Polarization Assays are performed by titration of a constant concentration of fluorescent label (here, the bicyclic fluorescence peptide that should be studied) with its binding partner (here, the domain hemopexin from MT1-MMP). As the concentration of binding partner increases during titration, the polarization signal changes in proportion to the fraction of bound and unbound material. This allows determination of dissociation rates (Kd) quantitatively. Assay data can be fitted using standard ligand binding equations.
[00200] Typically, label concentrations are ideally well below the Kd of the label: titrant pair, and concentrations chosen are generally ~1 nM or less. The concentration of titrant (binding partner) ranged from 0.1 nM to typically 5 µM. The range is chosen such that the maximum change in fluorescent polarization can be observed. The buffers used are phosphate buffer saline solution, in the presence of 0.01% Tween. Experiments were run in black 384-well low binding/low volume plates (Corning 3820), and the fluorescence polarization signal was measured using a BMG Pherastar FS plate reader.
[00201] Fluorescent markers referred to in the text are bicyclic peptides that have been fluoresced using 5,6-carboxyfluorescein. Fluorescence can be performed on the N-terminal amino group of the peptide which is separated from the bicyclic core sequence by a sarcosine spacer (usually, Sar5). This can be done during solid phase synthesis of Fmoc or post-synthetically (after cyclization with TBMB and purification) if the N-terminal amino group is unique to the peptide. Fluorescence can also be performed at the C-terminus, usually on a lysine introduced as the first C-terminus residue, which is then separated from the bicyclic core sequence by a sarcosine spacer (usually, Sar6). Thus, N-terminus tags can have a molecular format described as Fluo-Gly-Sar5-A (BicycleCoreSequence), and (BicycleCoreSequence)-A-Sar6-K(Fluo) for a fluorescence construct terminally in C. Fluorescent tags used. in the Examples are A-(17-69)-A-Sar6-K(Fluo), A-(17-69-07)-A-Sar6-K(Fluo), and A-(17-69-12)- A-Sar6-K(Fluo). Due to the acidic nature of the 17-69 fluorescent peptides, these were typically prepared as concentrated DMSO stock materials, from which dilutions were made in 100 mM Tris buffer, pH 8. Competition Assays Using Fluorescence Polarization (Anisotropy)
Due to their high affinities for the hemopexin domain of MT1-MMP (PEX), the fluorescence derivatives 17-69 07 and 17-69-12 (denoted as 17-69-07-N040 and 17-69-12 -N005, respectively) can be used for competition experiments (using FP for detection). Here, a pre-formed complex of PEX with the fluorescent PEX binding tag is titrated with free bicyclic peptide, not labeled with fluorescein. Since all 17-69 based peptides are expected to bind to the same site, the titrant will displace the fluorescent PEX tag. Dissociation from the complex can be measured quantitatively, and the Kd of the competitor (titrator) for the target protein determined. The advantage of the competition method is that the affinities of bicyclic peptides not labeled with fluorescein can be accurately and quickly determined.
Marker concentrations are generally at or below Kd (here, 1 nM), and the binding protein (here, hemopexin from MT1-MMP) is under a 15-fold excess, such that >90% of the marker They are connected. Subsequently, the non-fluorescent competing bicyclic peptide (generally only the bicyclic core sequence) is titrated such that it displaces the fluorescent label from the target protein. Marker shift is measured and associated with a drop in fluorescence polarization. The drop in fluorescence polarization is proportional to the fraction of target protein bound with the non-fluorescent titrant, and thus is a measure of the affinity of the titrant to the target protein.
[00204] The raw data are fitted to the analytical solution of the cubic equation that describes the balances between fluorescent label, titrant, and binding protein. The adjustment requires the fluorescent label affinity value for the target protein, which can be determined separately through direct binding FP experiments (see, previous section). Curve fitting was performed using SigmaPlot 12.0 and an adapted version of the equation described by Zhi-Xin Wang (FEBS Letters 360 (1995) 111-114) was used. Plasma stability profile Method no. 1:
[00205] A rapid assay of the plasma stability profile was developed that employed mass spectrometric detection (MALDI-TOF, Voyager DE, Applied Biosystems) of the source mass, as well as protease-induced fragments of plasma from it. By evaluating the nature of the fragments, preferred cleavage sites can be determined. Here, a 1 - 1.5 mM peptide stock material (in DMSO) was directly diluted in mouse/rat/human plasma (serum labs, using citrate as an anticoagulant), providing a final concentration of 50 μM peptide, and incubated for up to 48 hours at 37°C. 5 μL samples were taken at appropriate time points and frozen at -80°C. For analysis, samples were thawed, mixed with 25 μL of acetonitrile:methanol:water 3:3:1 and centrifuged in 13K for 5 minutes. 5 μL of the peptide-containing supernatant was aspirated and mixed with 30 mM ammonium bicarbonate in a 1:1 mixture of acetonitrile:H2O. 1 μL of this mixture was then blotted onto the MALDI plate, dried, and Matrix(alpha-cyanocinnamic acid, Sigma, prepared as a saturated solution in 1:1 acetonitrile:water containing 0.1% trifluoroacetic acid) was placed layered over the sample (1 μL), dried and analyzed using the MALDI TOF. It should be noted that this is a qualitative assay that serves to detect comparative changes in plasma stability between different bicyclic peptide sequences, and serves as an excellent tool for determining preferred cleavage sites. Method no. two
[00206] To obtain plasma stability of bicyclic peptides quantitatively, peptide stock solutions (200 μM in DMSO) were mixed with plasma (human or mouse), such that final concentrations were 10 μM. 40 μL samples were taken periodically for up to 8 hours and frozen at -80°C. Prior to LC-MS analysis, samples were thawed, and mixed with 3 volumes (here, 120 µL) of 1:1 acetonitrile/MeOH/water. The milky suspensions were centrifuged for 30 minutes at 13,000 rpm, and the peptide-containing supernatants were quantified for double/triple loaded species and EM/MS fragments thereof, using a Waters Xevo TQ-D instrument, while using a standard curve extracted from the plasma of the same peptides as a reference. The plasma degradation half-life was used to assess the comparative stability of the molecules. Pharmacokinetics of 17-69-07 in mice, identification of metabolites Pharmacokinetics of 17-69-07-N004
[00207] Mouse pharmacokinetics were acquired using bicyclic peptide 17-69-04-N004, which was dosed with a group of 12 male CD1 mice as a single intravenous dose, doses of 5.925 mg/kg as a 5 mL/bolus kg of a 1.19 mg/ml solution. Formulated solutions were prepared from 100 µL of a 23.7 mg/mL DMSO stock material, which was diluted with 1.9 mL of phosphate buffered saline prior to dosing, resulting in a vehicle consisting of DMSO at 5% in PBS at pH 7.4. Blood samples were taken from two animals per time point, via cardiac puncture under terminal anesthesia, at 0.08, 0.5, 1, 2 and 4 hours post-dose, and transferred to EDTA tubes for plasma generation . Plasma samples were frozen at -20oC.
[00208] For analysis, samples were quickly thawed and 50 μL aliquots were treated with 3 volumes of extraction solvent (2:9:9 mixture of 10 mM ammonium bicarbonate, pH 8, acetonitrile and methanol, containing an internal standard analytical). Precipitated proteins were removed by centrifugation and the supernatant was analyzed by CL-MS/MS. Quantification of samples was by reference to a calibration line prepared in control mouse plasma. Pharmacokinetic parameters were determined by non-compartmental analysis using Summit Research Services PK Solutions 2.0 software package. Definition of terms: Cmax : Maximum measured concentration; Tmax: Time at which maximum concentration was measured; AUC 0-t: Area under the 0 minute plasma drug concentration/time curve for last quantifiable data point; and AUC 0-«: Area under the extrapolated 0 minute plasma drug concentration/time curve beyond the endpoint data point based on terminal half-life. Identification of Bicyclic Peptide Metabolites in Mouse Plasma
[00209] Three plasma samples were available to be used (0.5, 1 and 2 hours) for in vivo mouse metabolite potential analysis of 17-69-07-N004. Analysis was performed by means of HPLC-EM and HPLC-EM/EM with an LTQ Orbitrap XL Mass Spectrometer. The approach to observing peptide metabolites in the bloodstream was to calculate the exact mass (10 ppm window) of assumed metabolites (addition of 1 or 2 water (+18, +36) for loop1 and/or loop2 cleavage, respectively; per hence, loss of single amino acids or loss of stretched amino acids from loop1 and/or loop2). Second, a manual search was performed comparing total ion chromatograms with mouse blank plasma. Efficacy of BT17BDC-1 and BT17BDC-9 in HT-1080 Graft Mouse
Balb/c nude mice bearing subcutaneous HT-1080 xenograft tumors were treated with BDCs or vehicle (PBS). BDCs were dosed 3 times weekly for 2 weeks, dosing started when tumors measured approximately 150-200 mm3. The mice were monitored, and measurements of tumor volume and body weight recorded 3 times a week. Example 1: Identification of high-affinity bicyclic peptides using hemopexin domain of MT1-MMP
[00211] Employing previously established methods for generating bicyclic peptide phage libraries, selections were performed against the hemopexin domain of human MT1-MMP. After three cycles of selections from a simple library employing successively reduced concentrations of target, sequencing was performed at the outputs. Bicyclic 17-69 peptide (CKNRGFGCEDFYDIC) (SEQ ID NO: 16) was identified as one of the most abundant sequence outputs, and qualitative binding to the target was verified by Alphascreen.
[00212] Three small phage libraries were generated providing complete sequence coverage of each of the 3 portions of the 17-69 sequence. These three libraries were subjected to two rounds of selections against hemopexin protein. Interestingly, the most promising sequencing output products were 5 x 6 bicyclic peptides, while the starting libraries were of the 6 x 6 format. It is likely that the shorter loop length was selected due to a higher affinity of the bicyclic peptide with the target protein. Shorter loop lengths result from incorrectly synthesized primers that are incorporated during the construction of phage libraries.
The main sequencing output product was the peptide 17-69-07, which has the sequence CYNEFGCEDFYDIC (SEQ ID NO: 2).
[00214] Based on the observation that a 5x6 format seemed more useful, and that distinction between the 5x6 linkers was needed, two more libraries were generated by testing deliberate truncations of the first loop that generated bicyclic peptides 17-69-02, 17-69 -03, 17-69-04 and 17-69-12. These are contained in the sequences described in Figure 8.
The trend of certain residues was visible, although the binding assay was not able to distinguish between the best binders when they reached the assay limit.
The most frequently occurring sequences were assayed for hemopexin binding using alpha selection, where all signals were elevated compared to the original sequence of 17-69 (see Table 1): Where: Table 1: Assay of hemopexin binding using the bicyclic peptides of the invention

[00217] As all affinity mature clones based on 17-69 produced signals that were close to the assay limit, the graph shown in Table 1 does not allow unambiguous identification of the best clones. Some of the peptides were therefore synthesized as the fluorescently labeled derivatives (17-69, 17-69-07 and 17 69-12), and used for direct-binding fluorescent polarization (FP) experiments. Here, fluorescein is separated by a linker (usually, Sar6) from the bicyclic sequence, either N or C terminus to the core sequence (Table 2). Table 2: Results of Direct-Link Fluorescent Polarization (PF) Experiments

[00218] The fluorescently labeled derivatives of 17-69-07 and 1769-12 (denoted as 17-69-07-N040 and 17-69-12-N005) showed strong binding with dissociation rates of 0.52 and 3.1 nM, respectively. These are notably improved over the original unmatured 17-69 sequence (17-69-N004). It appears that sequences containing the 5x6 format induce high affinities within the context of the affinity maturation library.
[00219] Due to their high affinities for the hemopexin domain of MT1-MMP (PEX), the fluorescently labeled derivatives 17-69-07 and 17-69-12 (designated as 17-69-07-N040 and 17-69 -12-N005, respectively) were used for subsequent competition experiments (using PF for detection). Here, a pre-formed PEX complex with the fluorescent PEX binding tag is titrated with free bicyclic peptide, not labeled with fluorescein. Since all 17-69 based peptides (containing the conserved second loop motif CEDFYDIC; SEQ ID NO: 17) are expected to bind to the same site, the titrant will displace the fluorescent PEX tag. Dissociation from the complex can be measured quantitatively, and the Kd of the competitor (titrator) determined. The advantage of the competition method is that the affinities of non-fluorescence-labelled bicyclic peptides can be determined accurately and quickly.
In this context, it is important to verify that the core sequences 17-69-07 and 17-69-12 are solely responsible for high affinity to PEX. Peptides were thus synthesized as N- and C-terminal alanine variants, thereby strictly mimicking the sequence expressed on the phage particle, but lacking the Sar5/6 molecular spacer that was used with the fluorescently labeled constructs.
[00221] Affinities as determined by competition experiments were almost identical to those obtained with the fluorescently labeled derivatives, unequivocally demonstrating that the bicyclic core sequences are responsible for high affinity binding to PEX (Table 3). Furthermore, the fluorescently labeled constructs show that C-terminus bonds of molecular spacers and effector groups (here, as, -A-Sar6-K(Fluorescein)) are tolerated. Table 3: Results of direct-bound Fluorescent Polarization (FP) Experiments
Example 2: Proteolytic Stabilization of 17 69-07 Core Sequence Plasma Stability of Mouse 17-69-07
[00222] For therapeutic applications in humans, and for preclinical evaluation in animal species, it is pertinent that a major bicyclic peptide is sufficiently stable in the circulation after intravenous administration. Adequate stability is needed so that sufficient levels of bicyclic peptide can bind to its target and exert its biological function.
[00223] Preclinical models often employ species such as mouse, rat, rabbit and cynomolgus monkey. In the first example, the bicyclic peptide 17-69-07-N219 was evaluated for stability in the presence of mouse plasma using methods described above (Method no. 2). The bicyclic core sequence retains the original natural proteinogenic amino acids from the 17-69-07 sequence, and additionally contains an N-terminal molecular spacer which is used for conjugation of effector groups (sequence: G-Sar10-ACYNEFGCEDFYDIC; SEQ ID NO : 20). The affinity of 17-69-07-N219 for PEX was retained despite the presence of the molecular spacer (Kd = 0.82 nM).
[00224] This compound exhibited modest stability in mouse plasma ex vivo, with a half-life of 6 hours (see Figure 1). Identification of ex/in vivo proteolytic cleavage sites on 17-69 07
[00225] In an effort to understand the chemical nature of the degradation of 17-69-07-N219 in mouse plasma, samples were analyzed using MALDI-TOF for any potential degradation products. Mass spectra indicated a possible loss of tyrosine, which implies loop opening (hydrolysis) and removal of Tyr1 in loop1 and/or Tyr9 in loop2.
[00226] A pharmacokinetic study (PF) was conducted in mice using the minimum bicyclic peptide 17-69-07-N004 (Ac-CYNEFGCEDFYDIC (SEQ ID NO: 2), which constitutes the minimum core bicyclic peptide of 17-69 -07) in order to establish clearance and clearance rates from in vivo circulation. Resulting blood samples were further analyzed, and to analyze plasma samples for any potential proteolytic degradation products of 17-69-07-N004.
[00227] The HR profile is indicated in Figure 2: Table 4: Pharmacokinetic Parameters of 17-69-07-N004

NC: not calculated due to limited data
[00228] Table 4 shows that the peptide has an elimination half-life of 14 minutes, and is clarified at 20.7 ml/minute/kg. The clearance rate is greater than the glomerular filtration rate observed in mice (summarized in Qi et al., American Journal of Physiology - Renal Physiology (2004) Vol. 286 No. 3; F590-F596), indicating that the peptide is clarified by additional means, for example, plasma-guided proteolysis and endothelial proteases.
[00229] To address whether in vivo proteolysis contributes significantly to clearance, plasma samples taken at t = 0.5, 1 and 2 hours were subjected to targeted analysis to bicyclic fragments using CL-MS/MS techniques.
[00230] Multiple proteolytic metabolites can be identified, and fragments with the strongest signals are listed below in descending order: Ac-CiYNEFGCiiEDFYDICiii (SEQ ID NO:2): YNE excision in loop1; YNEF excision in loop1 (SEQ ID NO: 21); Excision of YNEFG (SEQ ID NO: 22) in loop1 (the entire cycle is removed); Y excision in loop1 and/or 2; YD excision in loop2; FYD excision in loop2; YDI excision in loop2; and Excision of EDFYDI (SEQ ID NO: 23) in loop2 (the entire cycle is removed).
[00231] The three major metabolites were present at the mid-level signal, while the remaining fragments were only detectable in trace amounts.
[00232] Taken together, both ex vivo and in vivo metabolites appear to center on initial cleavage at or near Tyr 1/9, followed by successive removal of debris in close proximity. This ultimately leads to the removal of one or both ties in their entirety. Proteolytic stability and potency enhancement of the 17-69-07 sequence
Approaches for stabilizing peptide sequences from proteolytic degradation are numerous (for reviews, see Gentilucci et al., Curr. Pharmaceutical Design, (2010), 16, 3185-203, and Nestor et al., Curr. Medicinal Chem. (2009). ) 16, 4399-418), and WO 2009/098450, WO 2013/050615 and WO 2013/050616). Briefly, they comprise amino acid substitution that provides a recognition point for the protease(s), amino acid backbone alteration at the cleavage site, (i.e., N-methylation, pseudopeptide bonds, etc.), steric obstruction of close bonds (ie, substituted β amino acids), and inclusion of D-enantiomeric amino acids. Some of these modifications (ie, N-methylation, D-amino acids) can protect/cover a proteolytic cleavage site from hydrolysis, even if they are located up to two residues away from the cleavage site. While it is relatively straightforward/advanced to protect a sequence from proteolytic attack, it is much more challenging to incorporate stabilization changes that do not dramatically alter the potency (and specificity) for the target protein.
[00234] From the 17-69-07 ex/in vivo proteolytic degradation data shown in the previous section, it is evident that Tyr1/9 and nearby residues are potential sites for bicyclic peptide stabilization. A quantitative means to assess successful stabilization of the peptide is by increasing its half-life in mouse and human plasma.
[00235] In the first example, eleven derivatives of 17-69-07 were generated, in which each position was replaced by an alanine (called "alanine scan"). This type of information warns about the energetic contribution and role of certain residues, and potentially removes proteolytic recognition points. Table 5: Alanine Scan Results

[00236] 17-69-07-N004 is the wild-type unmodified peptide containing an N-capped terminus (acetylation, terminally in N, termed "Ac"). Some of the Ala substitutions are well tolerated, especially at positions 1, 3, 4, 10 and 11 in the sequence. As the side chains of these residues are not required for high affinity binding to the target, compounds of formula (I) at these particular sequence positions are broadly defined.
[00237] This makes substitution at residue 1 (Tyr1) a very attractive possibility, as it can remove one of the proteolytic recognition points. The replacement of Gly5 with Ala5 is of interest when the chemical change is minor (addition of methyl group), yet it produces a dramatic reduction in potency. It is possible that Gly5 adopts unusual phi/psi angles outside the general Ramachandron plot, and these angles could potentially be induced by D-amino acids. The added benefit would be stabilization of peptide bonds adjacent to this site.
[00238] For this reason, a partial scan of D-alanine was performed to assess whether these are tolerated in relation to maintenance of potency: inclusion of D-amino acids in the sequence is highly desirable, due to its proteolytically stabilizing effect. Table 6: Effect of substitution residues on the first loop with D-Alanines

[00239] D-Ala1 in place of Tyr1 binds at 10 times lower affinity than wild type. However, it is of interest when the Tyr1 proteolytic recognition point is removed and replaced by a stabilizing amino acid, without inducing a large loss in potency.
Remarkably, substitution of Gly5 with D-Ala5 is well tolerated, when affinity compared to wild type remains unchanged.
[00241] In this context, D-Arg5 is also tolerated (and likely therefore all D-amino acids except D-Pro, see Table 6), which may be of interest if the physicochemical properties need to change during further development of the molecule (Table 7). Table 7: Effect of replacement residues at position 5

[00242] Next, due to the phage selection output products, indicating a certain preference for hydrophobic and aromatic amino acids at position 4 of the sequence, a series of derivatives was synthesized incorporating selection of aromatic amino acids, including natural tyrosine and tryptophan ( Table 8). Table 8: Effect of replacement residues at position 4

[00243] 1Nal: 1-naphthylalanine; 2NAI: 2-naphthylalanine; Chg: cyclohexylglycine; Phg: phenylglycine; tBuGly: tert-butylglycine; 3,4-DCPhe4: 3,4-dichlorophenylalanine; Cha: cyclohexylalanine; and HPhe: homophenylalanine.
[00244] Several substitutions at position 4 enhance affinity compared to wild-type, these include tyrosine, tripophan, 1 and 2-naphthylalanine (1/2 Nal) and 3,4-dichlorophenylalanine (3,4-DCPhe). The most potent substitution is 1-naphthylalanine, which enhances the affinity 7-fold.
Certain residues in loop2 of 17-69-07 were examined for the purpose of enhancing stability of the molecule. These include residue 9, which contains the potential recognition point of Tyr9. Residue 11 is also attractive, as it is permissive to substitution (Table 5) and vicinal to the recognition point of Tyr9. Table 9: Summary of tolerated amino acid substitutions

[00246] Of interest is 4-bromophenylalanine (4BrPhe), which alters the proteolytic recognition point of Tyr9, and tert-butylglycine (tBuGly), which slightly enhances affinity and importantly and strongly protects the vicinal backbone of amino acids from proteolytic hydrolysis through steric obstruction. Multi-site replacements for global proteolytic protection from 17-69-07
[00247] The previous section described multiple positions in the 17-69-07 sequence that allow inclusion of proteolytically stabilization and/or affinity enhancing amino acids.
[00248] In an effort to combine these modifications into a single molecule, a molecule was synthesized that incorporated a substitution Tyr1^D-Ala1, Phe4^1-Naphthylalanine 4, Gly5^D-Ala5, Tyr9^ 4BrPhe9 and Ile11^tBuGly11 . Remarkably, all modifications are tolerated together, and potency is greater than that of the wild-type molecule (Tables 10 and 11). Table 10: Results of a specific multiple substitution

[00249] In anticipation of attaching effector groups to such a bicyclic peptide during further development of the molecule, versions were generated with an N-terminal sarcosine molecular spacer (consecutive Sar 10, denoted as Sar10) started with an N-terminal glycine and terminated with a C-terminus alanine. For the purpose of this experiment, the N-terminus glycine (Gly) was capped with an acetyl group in order to remove the positive charge. Table 11: Comparative data after addition of G-Sar10-A

The data indicate that both molecular spacer (attached to the N-terminus as indicated) and amino acid substitutions in the bicyclic core sequence are well tolerated when potencies are retained or improved.
[00251] Table 12 shows the non-acetylated, non-stabilized derivatives of the molecules shown in Table 11. Their stabilities were quantitatively evaluated in mouse and human plasma in order to demonstrate an improvement compared to the non-stabilized 17-69-07-N219 ( Figure 1). Table 12: Selected plasma stability evaluation molecules, associated potencies

[00252] Figure 3A shows the mouse plasma stability of the penta and tetrasubstituted molecules 17-69-07-N244 and 17-69-07-N231, respectively, compared to the original unstabilized wild-type molecule 17-69-07 -N219. The half-life of the peptide in mouse plasma at 37°C is » 20 hours, compared to 6 hours for the unenhanced wild-type molecule.
[00253] Figure 3B shows the human plasma stability of the penta and tetrasubstituted molecules 17-69-07-N244 and 17-69-07-N231, respectively, compared to the original unstabilized wild-type molecule 17-69-07 -N219. The half-life of the peptide in mouse plasma at 37°C is » 20 hours, compared to 6 hours for the unenhanced wild-type molecule.
In summary, targeted substitutions at up to 5 positions in the 17-69-07 bicyclic core sequence (Tyr1 >D-Ala1, Phe4>1 Naphthylalanine4, Gly5 >D-Ala5, Tyr9 >4BrPhe9 and Ile11>tBuGly11) generated molecules superiors with enhanced potency and significant improvement in plasma stability. Selectivity of a stabilized 17-69-07 derivative (17-69-07-N241)
The stabilized molecular spacer containing derivative 17-69-07-N241 was tested by FP competition for affinity to the hemopexin domain of MT1-MMP derived from other species. The data are summarized in Table 13: Table 13: Cross-reactivity species of 17-69-07 and derivatives

[00256] Both unstabilized and stabilized derivatives of 17-69-07 are fully cross-reactive.
The N-terminally fluorescently labeled derivative of 17-69-07-N241 (named 17-69-07-N258, of the sequence: fluorescein (bAla)-Sar10-A-(17-69-07) D- Ala1 1Nal4 D-Ala5 tBuGly11) was tested against related human metalloproteinase. The data demonstrate that the core sequence 17-69-07, and this stabilized variant, are uniquely selective to MT1-MMP (Table 14). Table 14: Selectivity of 17-69-07 and derivatives for related metalloproteinase
Example 3: In vivo analysis of proteolytically stabilized 17-69-07 variants conjugated to a chelator
[00258] Peptides linked to metal chelators have multiple applications in diagnosis and therapy. Certain imaging or therapeutic radioisotopes can be "carried" to the chelator while the peptide transports these isotopes to the target. In this way, tumor-specific antigens can be visualized using, for example, PET and SPECT scanners. For targeted radiotherapy, therapeutic radionuclides (such as 90Y and 177Lu) are loaded onto the chelating peptide and selectively transported to the tumor through binding to the tumor associated antigen. These exert their antitumor activity by the high energy radiation they emit. Synthesis of Bicyclic Peptides 17-69-07 Chelating Linked
[00259] Five derivatives were synthesized in which the metallic chelator DOTA (1,4,7,10-tetrazacyclododecane-1,4,7,10-tetraacetic acid) was linked with the N-terminus alanine of the bicyclic peptide 17-69- 07. Table 15: Molecules and Structure Summary

[00260] 17-69-07-N144 is the wild type sequence of 17-69-07 in which DOTA is directly linked with an N-terminus alanine that functions as an amino acid spacer. This molecule retains full potency for MT1-MMP. To demonstrate that potency is retained when loaded with a therapeutic/imaging radionuclide, the chelator was loaded with natural (cold) Lutetium as a safe replacement. Power was withheld. The fully stabilized variant, 17-69-07-N248, also retained potency in the context of the DOTA conjugate.
[00261] A control molecule, 17-69-07-N246, which is the total D-amino acid equivalent of 17-69-07-N144, was prepared. This molecule is completely resistant to proteolytic degradation when amide bonds adjacent to D-amino acids are protected from proteases, and it lacks any activity towards MT1-MMP. Importantly, this peptide retains the same exact sequence and chemical composition. Biodistribution of 17-69-07-N144 loaded with 177Lu in mice bearing HT1080 xenograft
HT-1080 cells (which are known to abundantly express MT1-MMP) were inoculated subcutaneously into the right trunk of 6 week old male BALB/c nu/nu mice. Tumors were allowed to grow for approximately 1 week.
[00263] 150 pmoles of peptide 17-69-07-N144 were loaded with 1 MBq of the Y emitter and β 177Lu using standard complexation techniques. Per tumor-bearing mouse, 150 pmoles of the loaded 17-69-07-N144 were then injected (the equivalent of 17 µg/kg). 3 (three) animals were euthanized per time point, various organs and tumors excised and weighed, and followed by determination of gamma radiation count per gram of tumor/organ tissue. The resulting graph provides a quantitative indication of the location of the peptide in the mouse in vivo. In particular, selective tumor accumulation of HT1080 indicates binding to MT1-MMP in vivo.
[00264] Figure 4 summarizes the distribution data. Notably, the bicyclic peptide is tumor-specific and appears to persist for up to 24 hours, despite an estimated circulating half-life of 14 minutes. This likely indicates uptake into tumor cells. Significant localization is visible in the kidneys, and this is likely due to transiently binding peptide-binding amino acid transporters to the kidneys. All other organs do not show significant absorption of the molecule. Of note, the mouse hemopexin domain shares complete homology with the human counterpart, indicating that if mouse PEX was expressed elsewhere, the corresponding signals would be observed.
[00265] To assess whether tumor uptake in the xenograft model is selective and due to PEX binding, an additional study was performed using the peptide 17-69-07-N246, which is the D-amino acid counterpart of 17-69 -07-N144 (Figure 5).
[00266] Comparing the biodistribution pattern to that obtained with the active bicyclic peptide 17-69-07-N144, it is evident that the non-MT1-MMP binding bicyclic peptide 17-69-07-N246 did not target the tumor, which confirms that the tumor signal from 17-69-07-N144 is driven by in vivo binding targeted to MT1-MMP.
[00267] Finally, to evaluate the proteolytic stabilization effect of the 17-69-07 sequence on biodistribution, bicyclic peptide 17-69-07-N248 (DOTA-A-(17-69-07) D-Ala1 1Nal4 D- Ala5 4BrPhe9 tBuGly11) was used in an identical biodistribution study (Figure 6).
Surprisingly, the enhanced proteolytic stability of the peptide leads to an overall doubling of tumor uptake at any given time point compared to 17-69-07-N144, exemplifying the superior properties of the molecule compared to the 17-69 sequence -07 original not stabilized.
[00269] It is anticipated that this effect may result in an advantageous therapeutic index, both for radionuclide-targeted therapy using the conjugates described in this example and in the context of toxin-conjugated bicyclic peptides (Example 4). Example 4: Conjugation of Unstabilized Bicyclic Peptides with Cytotoxic Agents
[00270] For targeted cancer therapy, highly potent cytotoxic drugs are linked through a cleavage ligand to a targeting entity (here, a bicyclic peptide), which binds to proteins expressed on the surface of tumor-associated cells. The overexpressed tumor-associated cell surface target protein is selected for its ability to internalize into the cell. After binding of the cytotoxic agent-conjugated targeting entity to the tumor-associated cell surface protein, the complete molecular complex internalizes itself within the cell. After transitioning from the systemic circulation to the distinct intracellular environment, the cytotoxic drug is cleaved from the targeting entity through intracellular conditions, and the cleaved drug then exerts its antitumor activity through induction of targeted cell death through cell cycle arrest, followed by apoptosis.
[00271] Bicyclic peptide 17-69-07-N219 (see, Examples 2 and 3) is composed of the wild-type bicyclic core sequence linked at the N-terminus side with a molecular spacer Gly-Sar10-Ala (G-Sar10- A-(17-69-07), wherein the description of full-length sequence is G-Sar10-A-CYNEFGCEDFYDIC; SEQ ID NO: 20). This derivative of (17 69-07) retains full potency (Table 12) for MT1-MMP under a Kd of 0.8 nM. The single free amino group on the N-terminal side of the molecular spacer is ideally placed for conjugation with effector groups, such as highly potent cytotoxic substances. The long intramolecular distance transmitted by the Sar10 ligand between the conjugation site in the N-terminus glycine (Gly) and the bicyclic core sequence is employed in order to ensure full retention of target binding potency following conjugation with molecular size effector groups significant. Shorter molecular spacers can be arbitrarily selected as long as the potency of the bicyclic core sequence for the target protein is maintained.
[00272] To generate a proof of concept data with a drug bicyclic peptide conjugate (called BDC) targeting MT1-MMP, two conjugates of 17-69-07-N219 were prepared, which employed DM1 toxins inhibiting polymerization of microtubules (a maytansine, also known as N2'-deacetyl-N2'-(3-mercapto-1-oxopropyl)-maytansine) or MMAE (Monomethylauristatin E, also known as (S)-N-((3R,4S,5S) )-1-((S)-2-((1R,2R)-3-(((1S,2R)-1-hydroxy-1-phenylpropan-2-yl)amino)-1-methoxy-2-methyl -3-oxo-propyl)pyrrolidin-1-yl)-3-methoxy-5-methyl-1-oxoeptan-4-yl)-N,3-dimethyl-2-((S)-3-methyl-2- (methylamino)butanamido)butanamide).
[00273] The MMAE conjugate is called BT17BDC-1 and is separated from the precursor 17-69-07-N219 by a valine-citrulline (Val-Cit) linker, including the para-aminobenzyl-carbonyl (PABC) self-immolation group . The Val-Cit ligand is selectively cleaved (hydrolyzed) by the cathepsin B rich environment found in intracellular lysosomes, and after hydrolysis, immolation of PABC to release MMAE as the active toxic species. The Val-Cit-PABC ligand is stable in circulation, and thus, it releases the toxin only after cell internalization.
[00274] The structure of the conjugate, and the synthetic scheme for the preparation of BT17BDC-1, are shown in Scheme I: Scheme I Structure of BT17BDC-1
Reaction Scheme:
Synthetic strategy for preparation of BDC17BDC-1: The fully purified TMB cyclized bicyclic precursor 17-69-07-N219 is reacted with the succinimide ester of glutaryl-valine-citrulline-p-aminobenzylcarbonyl-MMAE (commonly abbreviated as vc-MMAE or Val-Cit-PABC-MMAE), producing the BDC17BDC-1 conjugate.
[00275] The DM1 conjugate of 17-69-07-N219 is called BT17BDC-9 and is separated from the precursor 17-69-07-N219 through a disulfide bond, which can be cleaved by the reducing environment found in the intracellular medium . The reduction is believed to occur through intracellular glutathione, which is present at concentrations of ~10 mM within the cell. In contrast, the concentration of glutathione and free reducing agents in the bloodstream is much lower (<10 μM); in this way, the toxin is predominantly released into the intracellular environment, where its cell death activity can unfold.
[00276] The structure of the conjugate, and the synthetic scheme for preparation of BT17BDC-9 are shown in Scheme II: Scheme II Structure of BT17BDC-9
Reaction Scheme:
Synthetic strategy for preparation of BDC17BDC-9: The fully purified TMB cyclized bicyclic precursor 17-69-07-N219 containing the N-terminus free amine is reacted with the DM1 disulfide succinimide ester (structure as shown), producing the conjugate BDC17BDC-9.
[00277] The release of toxins in BDC17BDC-1 and BDC17BDC-9 is therefore mechanistically distinct, that is, the former by means of intracellular proteolytic conditions, and the latter by reducing intracellular conditions.
[00278] The two BDCs were employed in in vitro cytotoxicity studies and showed low nanomolar/picomolar potency in cell cultures such as HT1080 (data not shown).
[00279] In an in vivo mouse xenograft model (housing HT1080 tumors), both BDCs caused significant reduction in tumor volume after 9 days post-injection compared to vehicle control. The dosing regimen is shown in Figure 7 (arrows). Tumors were completely cleared by 14 days for both BDCs, as assessed by palpation (Figure 7). Notably, animal weights for both BDC17BDC-1 and BDC17BDC-9 were largely stable, indicating a therapeutic window that may be sufficient for therapeutic purposes. Example 5: Conjugation of proteolytically stabilized Bicyclic Peptides with cytotoxic agents
The bicyclic core sequence 17-69-07 containing the modifications of D-alanine at position 1,1-naphthylalanine at position 4, D-alanine at position 5, and α-tert-butylglycine at position 11, with or lacking 4-bromophenylalanine at position 9, had enhanced proteolytic stability in ex vivo and in vivo plasma (Examples 2, 3).
[00281] In the context of bicyclic drug conjugates, it is likely that a more stable bicyclic core sequence may lead to greater tumor exposure due to reduced systemic clearance and greater stability in the proteolytically aggressive tumor microenvironment. Both can result in increased MT1-MMP-induced BDC uptake within the cell, leading to an increase in therapeutic efficacy.
[00282] The stabilized bicyclic peptide 17-69-07-N241 was designed with a similar overall molecular arrangement to the unstabilized 17-69-07-N219 (described in Examples 3 and 4). It has the following sequence: (B-Ala)-Sar10-AC(D-Ala)NE(1Nal)(D-Ala)CEDFYD(tBuGly)C(SEQ ID NO: 5) which is cyclized with TBMB as before.
[00283] The N-terminus beta-alanine was selected, instead of the glycine previously employed as in 17-69-07-N219, in order to minimize formation of the diketopiperazine side product during coupling with N-hydroxysuccinimide (NHS) esters (Purdie et al. (1973), J. Chem. Soc., Perkin Trans. 2, 1845), specifically in this example with NHS esters of cytotoxic agents (Scheme I, II).
[00284] The sarcosine decamer spacer is retained as in 17-69-07-N219 so as to ensure total retention of binding of the bicyclic peptide to the hemopexin domain of MT1-MMP.
[00285] The maytansine toxin class was selected for conjugation with 17-69-07-N241 based on efficacy and tolerability in the mouse xenograft model described in Example 4, and the disulfide cleavable linker was reselected.
[00286] Four BDCs were prepared (previously referred to as BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20), whereby both toxin and 17-69-07-N241 were invariant, while susceptibility to the disulfide bond for reduction/cleavage was altered by modulating the degree of hindrance adjacent to the sulfur atoms.
[00287] The synthetic route for the conjugates is as described in Scheme II, where 17-69-07-N219 is replaced with 17-69-07-N241.
[00288] Regarding BT17BDC-18, an additional route for synthesis involved generation of a bicyclic precursor pyridyl disulfide (named 17-69-07-N277), which is reacted with DM1 to form the total conjugate. The synthetic route is described in Scheme III. Scheme III Structure of BT17BDC-18
Reaction Scheme
Synthetic strategy for preparation of BDC17BDC-18: The fully purified TMB cyclized bicyclic precursor 17-69-07-N241 containing the N-terminus free amine is reacted with the SPP 4-(2-pyridyldithio)pentanoate (N-succinimidyl) ), yielding intermediate 17-69-07-N277. This is then reacted with DM1 as the free thiol, producing the desired conjugate BT17BDC-18. In vitro characterization of BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20
[00289] The four BDCs were evaluated for various in vitro parameters such as potency retention for the hemopexin domain of human MT1-MMP, stability in mouse ex vivo, murine and human plasma, and stability for reducing agents such as dithiothreitol .
[00290] The data are summarized in Table 16 below: Table 16: In vitro properties of BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20
where n/a: not applicable, and where: n = number of repeats a: determined by fluorescence polarization competition experiments using 17-69-07-N040 as a marker b: determined using quantitative CL-MS. Incubation time up to 24 hours in plasma containing 4 μM BDC. c: de Kellogg et al. (2011) Bioconjugate Chemistry, 22, 717. Note that these values refer to drug antibody conjugates containing the disulfide ligand described in the text. d: determined by quantitative CL-MS. Note that these values refer to bicyclic drug conjugates containing the disulfide linker described in the text. Methods were adapted from Kellogg et al. (2011) Bioconjugate Chemistry, 22, 717. e: Use of 17-69-07-N004 as marker in PF competition. f: Use of 17-69-07-N040 as a scorer in the PF competition.
[00291] All molecular constructs retain their affinity to the target hemopexin. (second column).
[00292] The data indicate that plasma stability is governed by the nature of the disulfide bond (as modulated by susceptibility to reduction), and not by the nature of the bicyclic peptide, since all BDCs contain the same bicyclic peptide (17-69-07 - N241) which is stable in the plasma of the three species tested.
[00293] In addition, BT17BDC-18, BT17BDC-19 and BT17BDC-20 show stabilities in human plasma suitable for therapeutic use, since early renal filtration induced clearance of peptides of this molecular size in man has an estimated half-life of 2 to 4 hours, which is several times faster than the degradation half-life of BDCs in human plasma (>14 hours of BT17BDC-18/19/20, see Table 16). Thus, it is expected that the volume of BDC clears via the kidney, with only a fraction that is degraded in the circulation, making these BDCs potentially suitable for therapeutic purposes. In vivo efficacy of BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20
[00294] All BDCs containing the stabilized bicyclic core sequence were tested for their efficacy in in vivo mouse xenograft models using the EBC-1 squamous cell lung carcinoma lineage.
[00295] BT17BDC-17, BT17BDC-18 and BT17BDC-19 were effective and clarified tumors within 9 days (Figures 9, 10 and 11). BT17BDC-17 showed good efficacy but some weight reduction at high doses. BT17BDC-20 was, while tolerated on a constant weight basis, not effective and only caused a marginal reduction in tumor sizes (Figure 12).
The area under curve (AUC) of tumor volume over time and BDC was taken and plotted against the corresponding dose group (Figure 13). From this, the effective dose required to achieve 50% reduction in tumor AUC (ED50) can be determined, which is summarized in Table 17. Table 17: Effective dose to achieve 50% reduction in tumor AUC for BT17BDC -9, BT17BDC-17, BT17BDC-18, BT17BDC-19 and BT17BDC-20
aED50 ± 95% confidence limit bunits in mg/kg in mice carrying EBC-1 tumors
[00297] Thus, BT17BDC-9, BT17BDC-17, BT17BDC-18 and BT17BDC-19 are suitable molecules for use in targeted cancer therapy based on efficacy, and BT17BDC-17, BT17BDC-18 and BT17BDC-19 are as well tolerated in effective doses.

权利要求:
Claims (43)
[0001]
1. MT1-MMP-specific peptide ligand, characterized in that it comprises a polypeptide comprising at least three cysteine residues, separated by at least two loop sequences, and a molecular framework that forms covalent bonds with the cysteine residues of the polypeptide, such that at least two polypeptide loops are formed in the molecular framework, wherein the peptide linker comprises an amino acid sequence of formula (I):
[0002]
2. Peptide ligand according to claim 1, characterized in that X1 is selected from any of the following amino acids: Y, M, F or V, such as Y, M or F, in particular Y or M , more particularly, Y.
[0003]
3. Peptide ligand according to claim 1 or claim 2, characterized in that U/O2 is selected from U, such as an N, or O, such as a G.
[0004]
4. Peptide linker according to any one of claims 1 to 3, characterized in that X3 is selected from U or Z, where U represents an uncharged polar amino acid residue selected from N, C, Q, M , S and T, and Z, represents a negatively charged polar amino acid residue selected from D or E, in particular, the U at position 3 is selected from Q or the Z at position 3 is selected from E.
[0005]
5. Peptide ligand according to any one of claims 1 to 4, characterized in that X4 is selected from J, where J represents a non-polar aromatic amino acid residue selected from F, W and Y.
[0006]
6. Peptide ligand according to any one of claims 1 to 5, characterized in that X10 is selected from Z, where Z represents a negatively charged polar amino acid residue selected from D or E, such as D.
[0007]
7. Peptide ligand according to any one of claims 1 to 6, characterized in that X11 is selected from O, where O represents a non-polar aliphatic amino acid residue selected from G, A, I, L, P and V, such as I.
[0008]
8. Peptide ligand according to any one of claims 1 to 7, characterized in that the compound of formula (I) is a compound of formula (Ia):
[0009]
9. Peptide ligand according to any one of claims 1 to 8, characterized in that the peptide of formula (I) comprises a sequence selected from
[0010]
10. Peptide ligand according to any one of claims 1 to 9, characterized in that it includes one or more modifications selected from: N-terminus and/or C-terminus modifications; replacing one or more amino acid residues with one or more unnatural amino acid residues (such as replacing one or more polar amino acid residues with one or more isosteric or isoelectronic amino acids; replacing one or more hydrophobic amino acid residues with another isosteric or unnatural isoelectronic amino acids); adding a spacer group; replacing one or more L-amino acid residues with one or more D-amino acid residues; N-alkylation of one or more amide bonds in the bicyclic peptide linker; replacing one or more peptide bonds with a substituted bond; modification of the length of the peptide backbone; replacing the hydrogen at the alpha carbon of one or more amino acid residues with another chemical group; and post-synthetic biorthogonal modification of amino acids such as cysteine, lysine, glutamate and tyrosine with suitable amine, thiol, carboxylic acid and phenol reactive reagents.
[0011]
11. Peptide ligand according to claim 10, characterized in that it comprises N-terminus modification using suitable amino-reactive chemistry, and/or C-terminus modification using suitable carboxy-reactive chemistry.
[0012]
12. Peptide ligand according to claim 10 or 11, characterized in that the N-terminus modification comprises the addition of a molecular spacer group that facilitates the conjugation of effector groups and retention of potency of the bicyclic peptide to its target , such as an Ala group, G-Sar10-A or bAla-Sar10-A group.
[0013]
13. Peptide ligand according to any one of claims 10 to 12, characterized in that the N-terminus and/or C-terminus modification comprises the addition of a cytotoxic agent.
[0014]
14. Peptide ligand according to any one of claims 10 to 13, characterized in that it comprises a modification in amino acid position 1 and/or 9.
[0015]
15. Peptide ligand according to any one of claims 10 to 14, characterized in that it comprises replacement of one or more amino acid residues with one or more unnatural amino acid residues.
[0016]
16. Peptide linker according to claim 15, characterized in that the unnatural amino acid residue is substituted at position 4 and is selected from: 1-naphthylalanine; 2- naphthylalanine; 3,4-dichlorophenylalanine; and homophenylalanine such as 1-naphthylalanine; 2-naphthylalanine; and 3,4-dichlorophenylalanine, in particular 1-naphthylalanine.
[0017]
17. Peptide linker according to claim 15 or claim 16, characterized in that the unnatural amino acid residue is substituted at position 9 and/or 11, and is selected from: 4-bromophenylalanine or pentafluor-phenylalanine for position 9 and/or tert-butylglycine for position 11.
[0018]
18. Peptide ligand according to claim 17, characterized in that the unnatural amino acid residues, such as those present in position 9, is selected from: 4-bromophenylalanine.
[0019]
19. Peptide ligand according to claim 17, characterized in that the unnatural amino acid residues, such as those present in position 11, is selected from: tert-butylglycine.
[0020]
20. Peptide ligand according to claim 15, characterized in that it comprises a plurality of modifications, such as 2, 3, 4 or 5, or more of the following modifications, in particular all of the following 5 modifications: D - alanine in position 1 and/or 5, a 1-naphthylalanine in position 4, a 4-bromophenylalanine in position 9 and a tert-butylglycine in position 11.
[0021]
21. Peptide linker according to claim 10, characterized in that the amino acid residue at position 1 is replaced by a D-amino acid, such as D-alanine.
[0022]
22. Peptide linker according to claim 10, characterized in that the amino acid residue at position 5 is replaced by a D-amino acid, such as D-alanine or D-arginine.
[0023]
23. Peptide ligand according to any one of claims 1 to 22, characterized in that the pharmaceutically acceptable salt is selected from the free acid or the sodium, potassium, calcium and ammonium salt.
[0024]
24. Peptide ligand according to any one of claims 1 to 23, characterized in that it is a high affinity ligand of the hemopexin domain of human, mouse and dog MT1-MMP.
[0025]
25. Peptide ligand according to any one of claims 1 to 24, characterized in that it is selective to MT1-MMP, but does not cross-react with MMP-1, MMP-2, MMP-15 and MMP-16.
[0026]
26. Drug conjugate, characterized in that it comprises a peptide ligand, as defined in any one of claims 1 to 25, which is conjugated with one or more effector and/or functional groups.
[0027]
27. Drug conjugate according to claim 26, characterized in that the effector and/or functional groups comprise a cytotoxic agent or a metallic chelator.
[0028]
28. Drug conjugate according to claim 27, characterized in that the cytotoxic agent is linked to the bicyclic peptide through a cleavable bond, such as a disulfide bond or a protease-sensitive bond.
[0029]
29. Drug conjugate according to claim 27 or claim 28, characterized in that the cytotoxic agent is selected from DM1 which has the following structure:
[0030]
30. Drug conjugate according to any one of claims 26 to 29, characterized in that it is a compound that has the following structure:
[0031]
31. Drug conjugate according to any one of claims 26 to 29, characterized in that it is a compound that has the following structure:
[0032]
32. Drug conjugate according to claim 27 or claim 28, characterized in that the cytotoxic agent is a maytansinoid and selected from a compound of formula (II):
[0033]
33. Drug conjugate according to claim 32, characterized in that: n represents 1 and R1 and R2 both represent hydrogen (that is, the maytansine derivative DM1); or n represents 2, R1 represents hydrogen and R2 represents a methyl group (i.e. the maytansine derivative DM3); or n represents 2 and R1 and R2 both represent methyl groups (i.e. the maytansine derivative DM4).
[0034]
34. Drug conjugate according to any one of claims 26 to 33, characterized in that the bicyclic peptide component of the conjugate has the structure shown in formula (III):
[0035]
35. Drug conjugate according to any one of claims 27 to 34, characterized in that the cytotoxic agent is linked to the bicyclic peptide by a ligand defined in formula (IV):
[0036]
36. Drug conjugate according to claim 35, characterized in that the toxin of compound (IV) is a maytansine and the conjugate comprises a compound of formula (V):
[0037]
37. Drug conjugate according to claim 36, characterized in that: n represents 1 and R1, R2, R3 and R4 each represents hydrogen, that is, a compound of formula (V)a:
[0038]
38. Drug conjugate according to claim 26 or claim 27, characterized in that it is selected from BT17BDC-9:
[0039]
39. Process for preparing a drug conjugate as defined in claim 38, characterized in that it comprises the synthetic route described in Scheme III Reaction scheme
[0040]
40. Pharmaceutical composition, characterized in that it comprises the peptide ligand according to any one of claims 1 to 25, or the drug conjugate according to any one of claims 26 to 38, in combination with one or more pharmaceutical excipients acceptable.
[0041]
41. Drug conjugate according to any one of claims 26 to 38, characterized in that it is for use in the prevention, suppression or treatment of cancer, in particular solid tumors such as non-small cell lung carcinomas.
[0042]
42. Peptide ligand according to claim 1, characterized in that it is: (β-Ala)-Sar10-AC(D-Ala)NE(1Nal)(D-Ala)CEDFYD(tBuGly)C (SEQ ID NO: 5), or a pharmaceutically acceptable salt thereof.
[0043]
43. Peptide ligand according to any one of claims 1 to 25, characterized in that the molecular framework is TBMB (1,3,5-tris(bromomethyl) benzene).

类似技术:

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同族专利:

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公开号 | 公开日

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AU2015340300A1|2017-05-11|

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PT3215518T|2021-05-25|

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RU2708459C2|2019-12-09|

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CN107148425B|2021-08-03|

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LT3215518T|2021-06-10|

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SG11201702845QA|2017-05-30|

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CA2965754A1|2016-05-06|

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US20200171161A1|2020-06-04|

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DK3215518T3|2021-05-25|

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ES2870449T3|2021-10-27|

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RS61853B1|2021-06-30|

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CN107148425A|2017-09-08|

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US10792368B1|2020-10-06|

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JP6882978B2|2021-06-02|

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RU2017118326A3|2019-04-26|

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PL3215518T3|2021-08-23|

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KR20170073611A|2017-06-28|

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JP2018502825A|2018-02-01|

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HRP20210809T1|2021-07-23|

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RU2019138346A|2019-12-13|

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US20200289657A1|2020-09-17|

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RU2017118326A|2018-11-29|

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EP3215518B1|2021-02-24|

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US20180280525A1|2018-10-04|

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JP2021130672A|2021-09-09|

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HUE054526T2|2021-09-28|

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HRP20210809T8|2021-09-17|

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AU2015340300B2|2019-12-05|

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EP3882258A1|2021-09-22|

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WO2016067035A1|2016-05-06|

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US20220023432A1|2022-01-27|

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EP3215518A1|2017-09-13|

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US11103591B2|2021-08-31|

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US10532106B2|2020-01-14|

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SI3215518T1|2021-08-31|

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HK1243438A1|2018-07-13|

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BR112017008575A2|2017-12-26|

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法律状态:
2018-03-27| B15K| Others concerning applications: alteration of classification|Ipc: C07K 7/08 (2006.01), A61K 47/00 (2006.01) |

---

2018-06-19| B25D| Requested change of name of applicant approved|Owner name: BICYCLERD LIMITED (GB) |

---

2018-07-03| B25G| Requested change of headquarter approved|Owner name: BICYCLERD LIMITED (GB) |

---

2019-01-22| B65X| Notification of requirement for priority examination of patent application|

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2019-02-12| B65Y| Grant of priority examination of the patent application (request complies with dec. 132/06 of 20061117)|

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2019-04-09| B07D| Technical examination (opinion) related to article 229 of industrial property law [chapter 7.4 patent gazette]|

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2019-08-20| B07E| Notification of approval relating to section 229 industrial property law [chapter 7.5 patent gazette]|Free format text: NOTIFICACAO DE ANUENCIA RELACIONADA COM O ART 229 DA LPI |

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2020-12-08| B06A| Patent application procedure suspended [chapter 6.1 patent gazette]|

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2021-06-01| B09A| Decision: intention to grant [chapter 9.1 patent gazette]|

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2021-07-13| B16A| Patent or certificate of addition of invention granted [chapter 16.1 patent gazette]|Free format text: PRAZO DE VALIDADE: 20 (VINTE) ANOS CONTADOS A PARTIR DE 29/10/2015, OBSERVADAS AS CONDICOES LEGAIS. |

优先权:

---

申请号 | 申请日 | 专利标题

---

GB1419237.1|2014-10-29|

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GBGB1419237.1A|GB201419237D0|2014-10-29|2014-10-29|Novel polypeptides|

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---