shp2 inhibitory compositions and methods for the treatment of cancer

专利摘要:
  The present invention relates to compositions and methods of treating or preventing diseases or disorders with SHP2 inhibitors, alone, and in combination other therapeutic agents such as RAS inhibitors (for example, MEK inhibitors); methods of stabilizing treatment plans appropriate for individuals based on the expression of one or more biomarkers indicative of SHP2 sensitivity inhibitor; and methods for determining sensitivity to an SHP2 inhibitor based on an SHP2 phosphorylation state.
公开号:BR112020004246A2
申请号:R112020004246-3
申请日:2018-09-06
公开日:2020-09-01
发明作者:Robert J. Nichols；Mark A. Goldsmith；Christopher Schulze；Jacqueline Smith；David E. Wildes；Stephen Kelsey；Mallika Singh
申请人:Revolution Medicines, Inc.；
IPC主号:

专利说明:

[001] [001] This application claims the benefit of North American Provisional Application No. 62 / 555,400, deposited on September 7, 2017; North American Provisional Application No. 62 / 558,255, filed on September 13, 2017; North American Provisional Application No. 62 / 653,831, filed on April 6, 2018; and North American Provisional Order No. 62 / 681,001, filed on June 5, 2018, the content of which is incorporated herein by reference in its entirety. FIELD OF THE INVENTION
[002] [002] The present invention relates to compositions and methods for the treatment of diseases or disorders (e.g., cancer) with SHP2 protein tyrosine phosphatase inhibitors, alone and in combination with other therapeutic agents such as an inhibitor of the pathway RAS (for example, a MEK inhibitor). Specifically, this invention relates to methods of treating diseases or disorders (such as cancer) in certain subsets of patients who are determined to be candidates for treatment with an SHP2 inhibitor. BACKGROUND OF THE INVENTION
[003] [003] Cancer remains one of the most deadly threats to human health. In the United States, cancer affects almost 1.3 million new patients each year, and is the second leading cause of death after heart disease, representing approximately 1 in 4 deaths (US20170204187). Many cancers are caused by constitutive or aberrant activation of receptor tyrosine kinases (RTKs) and / or modulators of the RAS pathway.
[004] [004] RTKs are transmembrane proteins that have an extracellular ligand binding domain, a transmembrane domain
[005] [005] The receptor tyrosine kinase class is thus named because when activated by dimerization, the RTKs intracellular domain acquires tyrosine kinase activity which can, in turn, activate a variety of signal transduction pathways.
[006] [006] FIG. 1 shows a schematic drawing of an RTK path. RTK is dimerized after binding to the ligand, which triggers auto-phosphorylation of the receptor and initiation of signal transduction downstream. Specifically, RTK phosphorylation recruits the attachment of the GRB2 adapter through its SH2 domain, and GRB2 then recruits (through its SH3 domain) downstream signaling molecules such as the GAB1 adapter protein and the GEF SOS1 protein ( McDonald et al., FEBS J. 2012 Jun 279 (2): 2156-2173).
[007] [007] RAS oscillates between "off" GDP and "on" GTP status, facilitated by interaction between a GEF protein (eg SOS1), which carries RAS with GTP, and a GAP protein (eg
[008] [008] Activation of RAS results in induction of RAF serine / threonine kinase. RAF phosphorylates MEK / 2 which in turn phosphorylates and activates ERK1 / 2 leading to signaling downstream, for example, through transcription, as well as inhibiting RTK feedback, thereby turning off signal transduction. RAF also activates MAP3 kinases which activates MKK4 / 7, MKKK3 / 6 and MEK5, which activates JNK1 / 2, p38 and ERK5, consecutively. MAP3Ks are also activated by inflammatory cytokines, oxidative stress and UV radiation. PI3K is activated by RTK autophosphorylation and results in the activation of Akt, which also induces mTOR within the mTORC1 complex. Akt is also regulated by the mTORC2 complex. The activation of PLCγ leads to the mobilization of Ca + 2 and the activation of PKC. These events play an essential role in cell proliferation, differentiation, survival and migration.
[009] [009] Overexpression or mutation of signaling molecules via the RTKs and / or RAS pathway has been shown to result in uncontrolled cell growth. The aberrant activity of such kinases has been linked to proliferation, survival, invasion and metastasis of malignant tissue. For example, mutations that affect components of the RTKs and / or RAS Ras pathway (KRAS, NRAS, HRAS), B-Raf, NF1, PI3K and AKT are common in promoting the malignancy of different types of cancers and different tissue origins.
[0010] [0010] Consequently, RTKs and signal transducers of the downstream RAS pathway represent attractive therapeutic targets.
[0011] [0011] However, therapeutic inhibition of the RAS pathway, although often initially effective, can finally prove to be ineffective, since it can lead to overactivation of RAS signaling through various mechanisms including, for example, reactivation of via the relief of negative feedback mechanisms that naturally operate on these pathways. For example, in several cancers, MEK inhibition results in increased ErbB signaling due to its MEK / ERK-mediated feedback inhibition of RTK activation. As a result, cells that were initially sensitive to such inhibitors may become resistant. Thus, there is a need for methods of effective inhibition of RAS signaling without inducing the activation of resistance mechanisms.
[0012] [0012] SHP2 is a non-receptor tyrosine phosphatase protein encoded by the PTPN11 gene that contributes to multiple cell functions including cell cycle proliferation, differentiation, maintenance and migration. SHP2 is involved in signaling through protein kinase activated by protein kinase activated by RAS-mitogen (MAPK), JAK-STAT and / or the phosphoinositol 3-kinase-AKT pathways.
[0013] [0013] SHP2 has two N-terminal Src homology 2 domains (N-SH2 and C-SH2), a catalytic domain (PTP), and a C-terminal tail. The two SH2 domains control the subcellular location and functional regulation of SHP2. The molecule exists in a self-inhibited, inactivated conformation, stabilized by a bonding network involving residues from both the N-SH2 and PTP domains. Stimulation, for example, cytokines or growth factors acting through RTKs leads to exposure of the catalytic site resulting in enzymatic activation of SHP2.
[0014] [0014] Mutations in the PTPN11 gene and subsequently in SHP2 have been identified in several human development disorders, such as Noonan Syndrome and Leopard Syndrome, as well as human cancers, such as juvenile myelomonocytic leukemias, neuroblastoma, melanoma, acute myeloid leukemia and breast, lung and colon cancers. Some of these mutations destabilize the con-
[0015] [0015] SHP2, therefore, represents a highly attractive target for the development of new therapies for the treatment of various diseases including cancer. It has been previously described that either the knockout of SHP2 expression using RNAi technology or inhibition of SHP2 by an allosteric small molecule inhibitor interferes with the signaling of various RTKs involved in boosting cancer cell growth. However, this work also concluded that such methods would be ineffective in blocking growth signaling in cells in which growth is driven by mutations in proteins that act downstream of RTKs, such as those containing protein activation mutations. Ras or Raf (Chen, Ying-Nan P. 148 Nature Vol. 535 7, 7 July 2016 on page 151). SUMMARY OF THE INVENTION
[0016] [0016] The present invention relates to the treatment or prevention of a disease or disorder (e.g., cancer) with an SHP2 inhibitor alone or in combination with another suitable therapeutic agent. Specifically, in some modalities, the present invention refers to the unexpected discovery that, contrary to the teachings of the prior art, certain subsets of cancer cells carrying mutations of the oncogenic RAS pathway are sensitive to SHP2 inhibition and can be effectively treated with SHP2 inhibitors. In some embodiments, the present invention relates to the discovery that certain subsets of cancer cells carrying RAS mutations (for example, KRASG12C and / or certain other KRAS mutations) are sensitive to SHP2 inhibition. In some embodiments, the present invention relates to the discovery that certain subsets of cancer cells carrying NF1LOF mutations are sensitive to SHP2 inhibition.
[0017] [0017] Consequently, in several embodiments, the present invention provides a method for the treatment of cells (eg cancer cells) containing mutations in the RAS pathway, which make the mutated protein dependent on upstream signaling through SHP2, with an SHP2 inhibitor.
[0018] [0018] In some embodiments, the present invention refers to the unexpected discovery that even though SHP2 activation naturally promotes MAPK signaling, which in turn can promote inhibition of RTK signaling feedback and via RAS, the inhibition of SHP2 does not result in subsequent overactivation of RTK signaling or via RAS by alleviating this inhibition of the feedback. This is particularly surprising due to the fact that SHP2 is downstream of RTKs in the RAS pathway, and SHP2 inhibition blocks the transmission of RTK signals; thus, the expected result of SHP2 inhibition was overactivation of RTKs due to the feedback disinhibition. Thus, the present invention demonstrates that unlike MAPK inhibitors, which can induce resistance by relieving feedback inhibition, SHP2 inhibitors do not, and they are able to mitigate hyperactivation of RAS in response to treatment with MEK inhibitor that can contribute to resistance to the MEK inhibitory drug.
[0019] [0019] In some embodiments, the present invention relates to the discovery that inhibition of SHP2 is an effective method to prevent and delay the emergence of tumor resistance to various therapies against cancer and to resensitize a tumor that is resistant to a MAPK inhibitor to that inhibitor.
[0020] [0020] In some embodiments, the findings described here provide a method for treating cells (for example, cancer cells) with an SHP2 inhibitor, in which the cells have been made dependent on SHP2 through a therapeutic intervention.
[0021] [0021] In some embodiments, the present invention refers to the surprising discovery that contrary to the teachings of the prior art, phosphorylation of SHP2 in Y580 occurs later, and is dependent on the previous phosphorylation in Y542, and allosteric inhibition of activity SHP2 occurs by stabilizing the closed state of the enzyme, thereby preventing the phosphorylation of Y580, but not Y542.
[0022] [0022] In some embodiments, the present invention provides a method of determining whether an SHP2 inhibitor involved its target (i.e., SHP2), the method comprising determining whether Y542, but not Y580 on SHP2 is phosphorylated in response to factor stimulation growth.
[0023] [0023] Accordingly, the present invention relates to compositions and methods for the treatment or prevention of diseases or disorders (e.g., cancer) with SHP2 protein tyrosine phosphatase inhibitors. The present invention also relates to methods of stabilizing treatment plans appropriate for individuals based on the expression of one or more biomarkers in an individual's tissue sample, where the biomarker is indicative of the sensitivity of the SHP2 inhibitor. . The present invention also relates to methods of determining sensitivity to an SHP2 inhibitor based on an SHP2 phosphorylation state.
[0024] [0024] In some embodiments, the present invention provides a method of treating an individual with a disease or disorder comprising a cell containing a mutation encoding the KRASG12C variant, comprising providing the individual with an SHP2 inhibitor. In some embodiments, the disease or condition is a tumor. In some modalities, the tumor is selected from an NSCLC, a colon cancer, an esophageal cancer, a rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and a pancreatic cancer. In some embodiments, the method also comprises providing the individual with an RAS pathway inhibitor. In some modalities, the RAS pathway inhibitor is a MAPK inhibitor. In some modalities, the RAS pathway inhibitor is an MEK inhibitor or ERK inhibitor. In some embodiments, the RAS pathway inhibitor is selected from one or more of Trametinib, Binimetinib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853 and GSK1120212. In some embodiments, the inhibitor of the RAS pathway is Abemaciclibe or Ulixertinib or Ulixertinib. In some embodiments, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof.
[0025] [0025] In some embodiments, the present invention provides a method of treating an individual with a disease or disorder comprising a cell with a mutation encoding a variant of loss of function of NF1 (NF1LOF), comprising providing the individual an SHP2 inhibitor. In some embodiments, the disease or condition is a tumor.
[0026] [0026] In some embodiments, the present invention provides a method of treating an individual with a disease or disorder associated with a mutation of the RAS pathway in an individual cell that makes the cell at least partially dependent on flow signaling via SHP2, comprising providing the individual with an SHP2 inhibitor. In some embodiments, the mutation of the RAS pathway is a mutation in an RAS, RAF, NF1, MEK, ERK, or SOS, including any specific isoforms or herotype. In some embodiments, the mutation of the RAS pathway is a mutation in an RAS, RAF, NF1, or SOS, including any specific isoforms or herotype. In some embodiments, the RAS mutation is a RAS mutation selected from a KRAS mutation, an NRAS mutation, an HRAS mutation, and a BRAF Class III mutation. In some embodiments, the KRAS mutation is selected from a KRASG12A mutation, a KRASG12C mutation, a KRASG12D mutation, a KRASG12F mutation, a KRASG12I mutation, a KRASG12L mutation, a KRASG12R mutation, a KRASG12S mutation , a KRASG12V mutation, and a KRASG12Y mutation. In some particular modalities the KRAS mutation is KRASG12C. In some particular embodiments the KRAS mutation is KRASG12A. In some modalities, the Class III BRAF mutation is selected from one or more of the following amino acid substitutions in human BRAF: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D; G596R and A762E. In some embodiments, the MEK mutation is a MEK1 or MEK2 mutation. In some embodiments, the MEK1 mutation is an RAF-dependent MEK1 mutation (ie, a "Class I" MEK1 mutation). In some embodiments, the MEK1 mutation is a RAF-regulated MEK1 mutation (ie, a "Class II" MEK1 mutation). In some embodiments, the Class I MEK1 mutation is selected from D67N; P124L; P124S; and L177V.
[0027] [0027] In some embodiments, the present invention provides a method of treating an individual with a disease associated with a loss of NF1 mutation function, comprising providing the individual with an SHP2 inhibitor. In some embodiments, the disease or condition is a tumor. In some modalities, the tumor is selected from an NSCLC, a colon cancer, an esophageal cancer, a rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and a pancreatic cancer. In some modalities, the disease is a tumor that has cells with a loss of NF1 mutation function. In some embodiments, the tumor is an NSCLC or melanoma tumor. In some modalities, the disease is selected from neurofibromatosis type I, neurofibromatosis type II, schwannomatosis, and Watson syndrome. In some modalities, the method also comprises providing the individual with an inhibitor of the RAS pathway. In some embodiments, the method also comprises providing the individual with an RAS pathway inhibitor. In some embodiments, the RAS pathway inhibitor is a MAPK inhibitor. In some embodiments, the RAS pathway inhibitor is a MEK inhibitor or ERK inhibitor. In some embodiments, the RAS pathway inhibitor is selected from one or more of Trametinib, Binimetinib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853 and GSK1120212. In some
[0028] [0028] In some embodiments, the present invention provides a method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual's cell is classified as a KRAS mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as a KRASG12C mutant, a KRASG12D mutant, a KRASG12S mutant, or a KRASG12V mutant. In some modalities, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound from Table 1,
[0029] [0029] In some embodiments, the present invention provides a method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as an NF1LOF mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as an NF1LOF mutant. In some embodiments, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) a SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof. In some modalities, the tumor is selected from an NSCLC, a colon cancer, an esophageal cancer, a rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and a pancreatic cancer.
[0030] [0030] In some embodiments, the present invention provides a method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as a BRAF Class 3 mutant; and (b) administrators
[0031] [0031] In some embodiments, the present invention provides a method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as a MEK1 Class 1 mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class 1 mutant. In some modalities, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY , Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof. In some modalities, the tumor is selected from an NSCLC, a colon cancer, an esophageal cancer, a rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and a pancreatic cancer. In some embodiments, the Class I MEK1 mutation is selected from D67N; P124L; P124S; and L177V.
[0032] [0032] In some embodiments, the present invention provides a method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as a Class 2 MEK1 mutant ; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as a Class 2 MEK1 mutant. In some embodiments, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof. In some modalities, the tumor is selected from an NSCLC, colon cancer, esophageal cancer, rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and pancreatic cancer. In some modalities, the MEK mutation of
[0033] [0033] In some embodiments, the present invention provides a method for the treatment or prevention of drug resistance in an individual receiving administration of an inhibitor of the RAS pathway, comprising administering to the individual an inhibitor of SHP2. In some modalities, the individual comprises a tumor containing cells with an NF1LOF mutation. In some embodiments, the individual comprises a tumor containing a KRASG12C mutation, a KRASG12D mutation, a KRASG12A mutation, a KRASG12S mutation, or a KRASG12V mutation. In some embodiments, the RAS pathway inhibitor is a MEK inhibitor. In some embodiments, the MEK inhibitor is selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581); Binimetinib; Vemurafenib; Pimasertibe; TAK733; RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766; AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212. In some modalities, the RAS pathway inhibitor is an ERK inhibitor. In some instances, the ERK inhibitor is selected from any ERK inhibitor known in the art. In some modalities, the ERK inhibitor is selected from LY3214996 and BVD523; in some embodiments, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) a SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound from Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof.
[0034] [0034] In some embodiments, the method also comprises providing the individual with an inhibitor of the RAS pathway. In some embodiments, the present invention provides a combination therapy that comprises administering to an individual in need thereof an inhibitor of the RAS pathway and an inhibitor of SHP2. In some modalities, the RAS pathway inhibitor is a MEK inhibitor. In some modalities, the MEK inhibitor is selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581); Binimetinib; Vemurafenib; Pimasertibe; TAK733; RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766; AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212. In some modalities, the inhibitor of the RAS pathway is Abemaciclibe or Ulixertinib or Ulixertinib. In some embodiments, the RAS pathway inhibitor is the KRASG12C specific ARS-853 inhibitor. In some embodiments, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof.
[0035] [0035] In some embodiments, the present invention provides a pharmaceutical composition comprising an inhibitor of the RAS pathway, an SHP2 inhibitor, and one or more pharmaceutically acceptable carrier, excipient, diluent, and / or surfactant. In some modalities, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof. In some embodiments, the RAS pathway inhibitor is selected from one or more of Trametinib (GSK1120212) Se- lumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212. In some embodiments, the inhibitor of the RAS pathway is Abemaciclibe or Ulixertinib or Ulixertinib.
[0036] [0036] In some embodiments, the present invention provides a method of inhibiting the growth or proliferation of a cell containing a mutation of the RAS pathway, wherein the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor. The SHP2 inhibitor can be any SHP2 inhibitor known in the art or described herein. In some modalities, the SHP2 inhibitor is selected from (i) Compound A; (ii) Composed
[0037] [0037] In some embodiments, the method also comprises contacting the cell with an inhibitor of the RAS pathway. In some modalities, the RAS pathway inhibitor is a MAPK inhibitor. In some modalities, the RAS pathway inhibitor is an SOS inhibitor. In some modalities, the SOS inhibitor is administered to a cell comprising higher than normal SOS levels or SOS activity. In some embodiments, the RAS pathway inhibitor is a MEK inhibitor or ERK inhibitor. In some embodiments, the RAS pathway inhibitor is selected from one or more of Trametinib, Binimetinib, Selumetinbe, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / AR-RY-704); RO5126766; ARS-853; LY3214996; BVD523; and GSK1120212. In some embodiments, the inhibitor of the RAS pathway is Abemaciclibe or Ulixertinib. .
[0038] [0038] In some embodiments, the present invention provides a method of inhibiting the accumulation of RAS-GTP in a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor. The SHP2 inhibitor can be any SHP2 inhibitor known in the art or described herein. In some modalities, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY , Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) a SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination of them.
[0039] [0039] In some embodiments, the present invention provides a method of inhibiting the growth of a tumor cell, comprising contacting the tumor cell with a combination therapy comprising a MEK inhibitor and an SHP2 inhibitor. Such contact may be, for example, in vivo, in an individual (for example, a mammal, preferably a human). Furthermore, such a method may, for example, in a non-limiting embodiment, comprise contacting the tumor cell with a combination therapy comprising an SHP2 inhibitor and a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212. In some embodiments, the inhibitor of the RAS pathway is Abemaciclibe or Ulixertinib. In some non-limiting modalities, the tumor cell can be contacted with a combination therapy that comprises
[0040] [0040] In various embodiments, contact of a tumor cell with combination therapy comprising the MEK inhibitor and the SHP2 inhibitor results in an inhibition of tumor growth that is more than merely additive with respect to the amount of inhibition - tion of tumor growth obtainable by contacting the tumor cell with each of the respective MEK and SHP2 inhibitors separately.
[0041] [0041] In some embodiments, the present invention provides a method of treating an individual with a tumor, comprising providing the individual with an SHP2 inhibitor and an inhibitor of the RAS pathway. In some modalities, the disease or condition is a tumor. In some embodiments, the tumor is selected from an NSCLC, colon cancer, esophageal cancer, rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and pancreatic cancer. In some modalities, the disease is a tumor that has cells with a loss of NF1 mutation function. In some modalities, the tumor is an NSCLC or melanoma tumor. In some modalities, the disease is selected from type I neurofibromatosis, type II neurofibromatosis, schwannomatosis, and Watson syndrome. In some embodiments, the method also comprises providing the individual with an RAS pathway inhibitor. In some embodiments, the RAS pathway inhibitor is a MAPK inhibitor. In some embodiments, the RAS pathway inhibitor is a MEK inhibitor or ERK inhibitor. In some modalities, the RAS pathway inhibitor is selected from one or more of Trametinib, Binimetinib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853 and GSK1120212. In some embodiments, the inhibitor of the RAS pathway is Abemaciclibe or Ulixertinib. In some embodiments, the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination of them.
[0042] [0042] In some embodiments, the present invention provides a method of treating an individual with a tumor, which comprises contacting the tumor with a combination therapy comprising an MEK inhibitor and an SHP2 inhibitor. Such contact can be, for example, in vivo, in an individual (for example, a mammal, preferably a human). In this way, the person skilled in the art will understand that the contact can be through management
[0043] [0043] In various embodiments, the method of treating an individual carrying a tumor, comprising contacting the tumor cell with combination therapy comprising the MEK inhibitor and the SHP2 inhibitor results in synergistic inhibition of tumor growth . "Synergistic inhibition of tumor growth" means inhibition of tumor growth which is more than merely additive with respect to the amount of tumor growth inhibition obtained by contacting the tumor cell with each of the respective inhibitors separately .
[0044] [0044] In some embodiments, treatment of a tumor-bearing individual with a combination therapy comprising an SHP2 inhibitor and a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212, results in synergistic inhibition of tumor growth.
[0045] [0045] In some embodiments, treatment of a tumor-bearing individual with a combination therapy comprising (a) a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212; and (b) an SHP2 inhibitor selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) an SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155,; (vii) a SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described here; (x) a compound of Table 2, described here; and (xi) a combination thereof, results in synergistic inhibition of tumor growth. BRIEF DESCRIPTION OF THE FIGURES
[0046] [0046] Figure 1 shows a schematic drawing representing the receptor tyrosine kinase (RTK) signaling pathway. FIG. 1A shows the RTK ligand binding signaling for ERK activation and subsequent inhibition of RTK activity feedback. FIG. 1B shows that SHP2 modulates the RAS-GTP load by an unknown mechanism, which we postulate to involve the preparation of GEF SOS1 protein.
[0047] [0047] Figure 2 shows the inhibitory potency (IC50 values) of allosteric inhibitor of SHP2 Compound B (Compound B) on cell viability (when measured using CTG) in a panel of mutant cell lines KRASG12C and H441 (KRASG12V ) grown in 3D culture.
[0048] [0048] Figure 3 shows that Compound B (Compound B) (allosteric SHP2 inhibitor) and ARS-853 (covalent selective KRASG12C inhibitor) caused concentration-dependent inhibition of cellular p-ERK1 / 2 levels in NSCLC KRASG12C cell lines. FIG. 3A shows inhibition of pERK1 / 2 levels in H358 cells. FIG. 3B shows the inhibition of pERK1 / 2 levels in H1792 cells. FIG. 3C shows inhibition of pERK1 / 2 levels in CALU-1 cells.
[0049] [0049] Figure 4 shows that the allosteric SHP2 inhibitor Compound A (Compound A) inhibits RAS activation and produces an inhibition dependent on the concentration of cell p-ERK1 / 2 levels and cell growth (culture 3D) in H358 KRASG12C cells in vitro. FIG. 4A shows a Western blot demonstrating that Compound A (Compound A) reduces RAS-GTP. FIG. 4B shows Compound A (Compound A) inhibits levels of p-ERK1 / 2. FIG. 4C shows Compound A (Compound A) inhibits the growth of H358 KRASG12C cell.
[0050] [0050] Figure 5 shows that the allosteric SHP2 inhibitor Compound A (Compound A) inhibits RAS activation and produces an inhibition dependent on the concentration of cellular p-ERK1 / 2 levels and cell growth in cells H1838 NF1LOF in vitro. FIG. 5A shows Com-
[0051] [0051] Figure 6 shows dose-dependent inhibition of tumor cell growth in the NSCLC H358 xenograft model in female SCID CB.17 mice after oral administration of Compound A (Compound A).
[0052] [0052] Figure 7 shows dose-dependent inhibition of tumor cell growth in the NSCLC H358 xenograft model in female athymic nude mice after oral administration of the allosteric inhibitor SHP2 Compound B (Compound B) (** p <0.01 ANOVA with multiple comparisons)
[0053] [0053] Figure 8 shows dose-dependent inhibition of tumor cell growth in the pancreatic cancer MiaPaca-2 xenograft model in nude female athymic mice after oral administration of the allosteric inhibitor SHP2 Compound B (Compound B) (* p <0.05, ** p <0.01 ANOVA with multiple comparisons).
[0054] [0054] Figure 9 shows that inhibition of MEK by selumetinib caused overactivation of p-RTK based on feedback in cell line MDA-MB-231 (KRASG13D) while Compound A (Compound A) did not.
[0055] [0055] Figure 10 shows that the inhibition of MEK by trametinib in NCI-H1838 (NF1LOF) caused the accumulation of RAS-GTP based on the feedback and Compound A (Compound A) suppressed this effect.
[0056] [0056] Figure 11 shows that the allosteric SHP2 inhibitor Compound B (Compound B) suppressed the accumulation of RAS-GTP that results from the inhibition of MEK by trametinib in H358 (KRASG12C) and A549 cells (KRASG12S). FIG. 11A shows the effect on 6-hour and 24-hour MEK inhibition RAS-GTP accumulation in H358 cells (KRASG12C) with and without SHP2 inhibition by Compound B. FIG. 11B shows the effect on MEK inhibition RAS-GTP accumulation of 6 hours and 24 hours in H358 cells (KRASG12C) with and without the specific KRASG12C inhibitor ARS-853. FIG. 11C shows the effect on 6-hour and 24-hour MEK inhibition RAS-GTP accumulation in A549 cells (KRASG12S) with and without SHP2 inhibition by Compound B. FIG. 11D shows the effect on the accumulation of RAS-GTP of MEK inhibition of 6 hours and 24 hours in A549 cells (KRASG12S) with and without the specific inhibitor of KRASG12C specific inhibitor ARS-853.
[0057] [0057] Figure 12 shows phosphorylation of Tyr-542 and Tyr-580 measured in response to both EGF and PDGF in various cell lines. FIG. 12A shows Tyr phosphorylation in mouse embryonic fibroblasts (MEFs). FIG. 12B shows phosphorylation of Tyr in H358 cells. FIG. 12C shows phosphorylation of Tyr in HEK 293 cells (C). "Comp. B" means Compound B.
[0058] [0058] Figure 13 shows that the inhibition of SHP2 suppresses the growth and signaling of RAS / MAPK in cancer cell lines with BRAF Class III mutations. FIG. 13A shows the effect of Compound B (Compound B) on the proliferation of BRAF Class I (A375, BRAFV600E) cell lines and Class II (NCI-H1755 BRAFG469A) in 3D culture. FIG. 13B shows the effect of Compound B (Compound B) on RAS-GTP levels in Class I A375 and Class II NCI-H1755 cells cultured in 2D culture. FIG. 13C shows the effect of Compound B (Compound B) on p-ERK levels in Class I A375 and Class II NCI-H1755 cells cultured in 2D culture. FIG. 13D shows the effect of Compound B (Compound B) on the proliferation of two BRAF Class III mutant cell lines (Cal-12T, BRAFG466V / +; NCI-H1666, BRAFG466V / +) cells in 3D culture. FIG. 13E shows the effect of Compound B (Compound B) on RAS-GTP levels in Class III Cal-12T cells. FIG. 13F shows the effect of Compound B (Compound B) on p-ERK levels in Class III Cal-12T and NCI-H1666 cells.
[0059] [0059] Figure 14 shows that the effects of SHP2 inhibition on RAS activation continues in SOS1. FIG. 14A shows correlation analysis of the cellular effects of genetic knockout of signaling molecules in the RTK / RAS pathway in DRIVE Project. PTPN11 knockout (SHP2) is more closely correlated with SOS1 (correlation coefficient 0.51) and GRB2 (correlation coefficient 0.4) suggesting that all of these are members of a RAS core regulatory module. FIG. 14B shows the effect of Compound B (Compound B) on cellular p-ERK in HEK293 expressing SOS-WT (wild type) or SOS-F, a mutant SOS-1 that targets SOS protein constitutively in the plasma membrane. FIG. 14C shows SOS-F expression in HEK293 cells leads to EGF-independent signaling.
[0060] [0060] Figure 15 shows caspase 3/7 activity in NCI-H358 cells cultured on ULA plates as spheroids. Spheroid cultures were treated with Compound B (Compound B) or staurosporine, as a positive control, and tested for 3/7 caspase activity after 22 h.
[0061] [0061] Figure 16 shows inhibition of synergistic tumor cell growth through combined in vitro treatment of human non-small cell lung cancer cells CALU-1 and NCI-H358 with varying concentrations of Compound B (Compound B) in combination with trametinib. FIG. 16A shows a percentage of normalized inhibition in relation to vehicle control in H358 NSCLC tumor cells cultured in spheroids (3D culture), and treated for five days with increasing amounts of Compound B (Compound B) and Trametinib. FIG. 16B shows an adjustment of the Loewe Model of Additivity in the normalized growth inhibition data in FIG. 16A. FIG. 16C shows a percentage of normalized inhibition in relation to vehicle control in CALU-1 NSCLC tumor cells cultured in spheroids (3D culture), and treated for five days with increasing amounts of Compound B (Compound B) and Trametinib. FIG. 16D shows an adjustment of the Loewe Model of Additivity in the normalized growth inhibition data in FIG. 16C. For each of FIGS 16B and 16D, numbers in a positive range (mapped in blue) are indicative of synergy.
[0062] [0062] Figure 17 shows the in vivo efficacy for tumor growth inhibition of repeated dosages of Compound B (Compound B) daily at 10 and 30 mg / kg PO (tumor growth inhibition, TGI = 54, 79% respectively) alone, and in combination with trametinib at 1 mg / kg (TGI = 79%) in the human non-small cell lung cancer model NCI-H358.
[0063] [0063] Figure 18 shows the effect of Compound B (Compound B) alone and in combination with trametinib on body weight in nude mice carrying an NCI-H358 tumor. Note that an animal in the Compound B (Compound B) group 30mg / kg + trametinib (dark green) lost> 20% of body weight on day 30 and was removed from the study.
[0064] [0064] Figure 19 shows that the inhibition of SHP2 suppresses the growth and signaling of RAS / MAPK in cancer cell lines driven by NF1LOF mutation. FIG. 19A and FIG. 19B show the effect of Compound B on the proliferation of cells with loss of NF1 function in 3D culture. One day after sowing the cells were treated with Compound B and cell viability measured on Day 7 using CTG. FIG. 19B lists the geometric mean IC50 values for inhibition of proliferation by Compound B and mutational status of NF1 in the cancer cell lines evaluated. FIG. 19C and FIG. 19D shows that NCI-H1838 and MeWo NF1 LOF cells were cultured in 2D culture and incubated with increasing concentrations of Compound B for one hour. Cell lysates were prepared and levels of RAS-
[0065] [0065] Figure 20 shows that the inhibition of SHP2 suppresses the growth and signaling of RAS / MAPK in cancer cell lines driven by NF1LOF mutation. FIGS 20A and 20B show the effect of Compound B (Comp. B) on the proliferation of cells with loss of NF1 function in 3D culture. One day after sowing the cells were treated with Compound B and cell viability measured on Day 7 using CTG. FIG. 20B lists the geometric mean IC50 values for inhibition of proliferation by Compound B and mutational state of NF1 in the evaluated cancer cell lines. FIGS 20C and 20D show that NCI-H1838 and MeWo NF1 LOF cells were cultured in 2D culture and incubated with increasing concentrations of Compound B for one hour. Cell lysates were prepared and RAS-GTP (b) and pERK (c) levels determined. Levels of RAS-GTP in NCI-H1838 and MeWo cells were inhibited in a concentration-dependent manner by Compound B. The geometric mean IC50 values for reduction in pERK was 29 nM in NCI-H1838 cells, and 24 nM in MeWo cells (data representative of ≥ 3 independent observations, each performed in duplicate; figures show means +/- SD for pERK and mean +/- SEM for RAS-GTP).
[0066] [0066] Figure 21 shows the efficacy of repeated daily dosage of SHP2 inhibitor of Compound C ("Comp. C") at 10 mg / kg PO with or without co-administration of a RAS inhibitor in the H358 KRasG12C cancer model human non-small cell lung.
[0067] [0067] Figure 22 shows the efficacy of repeated daily dosing of Compound C SHP2 inhibitor ("Comp. C") at 30 mg / kg PO with or without co-administration of Abemaciclib (CDK inhibitor) at 50 mg / kg in the model of MIA-Pa-Ca-2 xenograft of human pancreatic carcinoma. FIG. 22A shows the efficacy of Compound C and Abemaciclibe, alone or in combination, and FIG.22B shows percentage changes in body weight in these mice. DETAILED DESCRIPTION OF THE INVENTION
[0068] [0068] The details of the invention are provided in the attached description below. Although methods and materials similar or equivalent to those described here can be used in the practice or testing of the present invention, methods and materials are now described. Other features, objects, and advantages of the invention will be apparent from the description and the claims. In the specification and the appended claims, singular forms also include the plural unless the context clearly says otherwise. Unless otherwise defined, all technical and scientific terms used here have the same meaning as commonly understood by those versed in the technique to which this invention belongs. All patents and publications cited in this specification are incorporated herein by reference in their entirety.
[0069] [0069] The practice of the present invention will be employed, unless otherwise indicated, conventional techniques of cell culture, molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are within the art. Such techniques are fully explained in the literature, such as, Molecular Cloning: A Laboratory Manual, third edition (Sambrook et al., 2001) Cold Spring Harbor Press; Oligonucleotide Synthesis (P. Herdewijn, ed., 2004); Animal Cell Culture (R. I. Freshney), ed., 1987); Methods in Enzymology (Academic Press, Inc.); Handbook of Experimental Immunology (D. M. Weir & C. C. Blackwell, eds.); Gene Transfers Vectors for Mammalian Cells (J. M. Miller & M. P. Calos, eds., 1987); Current Protocols in Molecular Biology (F. M. Ausubel et al., Eds., 1987); PCR: The Polymerase Chain Reaction, (Mullis et al., Eds., 1994); Current Protocols in Immunology (J. E. Coligan et al., Eds., 1991); Short Protocols in Molecular Biology (Wiley and Sons, 1999); Manual of Clinical Laboratory Immunology (B. Detrick, N. R. Rose, and J. D. Folds eds., 2006); Immunochemical Protocols (J. Pound, ed., 2003); Lab Manual in Biochemistry: Immunology and Biotechnology (A. Nigam and A. Ayyagari, eds. 2007); Immunology Methods Manual: The Comprehensive Sourcebook of Techniques (Ivan Lefkovits, ed., 1996); Using Antibodies: A Laboratory Manual (E. Harlow and D. Lane, eds., 1988); and others. Definitions
[0070] [0070] Unless otherwise defined, all technical and scientific terms used here have the same meaning as commonly understood by those versed in the technique to which the invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, preferred methods and materials are described.
[0071] [0071] The articles "one, one (a)" and "one, one (an)" are used in this invention to refer to one or more than one (for example, at least one) of the grammatical object of the article. For example, "an element" means an element or more than an element.
[0072] [0072] The term "and / or" is used in the invention to mean either "and" or "or" unless otherwise indicated.
[0073] [0073] Throughout this specification, unless the context requires otherwise, the words "understand," "understand," and "comprising" will be understood to imply the inclusion of an established step, element or group of steps or elements, but not the exclusion of any other step or element or group of steps or elements. By "consisting of" is meant to include, and is not limited to, what follows the phrase "consisting of." Thus, the phrase "consisting of" indicates that the elements listed are required or mandatory, and that no other elements may be present. By "consisting essentially of" means including any elements listed after the sentence, and limited to other elements that do not interfere with or contribute to the activity or action specified in the invention for the elements listed. Thus, the phrase "consisting essentially of" indicates that the elements listed are required or mandatory, but that other elements are optional and may or may not be present depending on whether or not the listed elements' activity or action is materially affected.
[0074] [0074] The term "for example" is used here to mean "for example," and will be understood to imply the inclusion of an established step or element or group of steps or elements, but not the exclusion of any other step or element or group of steps or elements.
[0075] [0075] By "optional" or "optionally," it is understood that the event or circumstance described subsequently may or may not occur, and that the description includes instances where the event or circumstances occur and instances in which occur. For example, "optionally substituted aryl" encompasses both "aryl" and "substituted aryl" as defined here. It should be understood by one of ordinary skill in the art, regarding any group containing one or more substituents, that such groups are not intended to introduce any substitution or patterns of substitution that are sterically impracticable, synthetically unfeasible, and / or inherently unstable.
[0076] [0076] The term "administer", "administering", or "administration", as used in this description, refers to directly administering a described compound or pharmaceutically acceptable salt of the described compound or composition to an individual, or administering a deri - prodrug or compound analog or pharmaceutically acceptable salt of the compound or composition to the individual, which can form an equivalent amount of active compound within the individual's body.
[0077] [0077] The term "carrier", as used in this description, encompasses excipients, and diluents and means a material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in transportation or carrying a pharmaceutical agent from an organ, or body part, to another organ, or an individual body part.
[0078] [0078] The terms "Compound A" and "Comp. A" are used interchangeably here to refer to an SHP2 inhibiting compound that has the following structure:
[0079] [0079] The terms "Compound B" and "Comp. B" are used interchangeably here to refer to an SHP2 inhibiting compound that has the following structure:
[0080] [0080] The term "Compound C" and "Comp. C" are used interchangeably here to refer to an allosteric SHP2 inhibitor compound of similar structure to Compounds A and B. Compound C is described in PCT / US2017 / 041577 (WO 2018/013597), incorporated herein by reference in its entirety.
[0081] [0081] The term SHP099 refers to an SHP2 inhibitor that has the following structure:
[0082] [0082] The terms "Class III BRAF mutation"; "Class 3 BRAF mutation"; "BRAF Class 3 mutation"; "Class III BRAF mutation"; "BRAFClass 3 mutation" and "BRAFClass III mutation" are used interchangeably here to refer to a BRAF mutation of dead or lesser kinase activity (when compared to wild type BRAF) including, but not limited to, any the BRAF Class 3 mutations disclosed in Yao, Z. et al., Nature, 2017 Aug 10; 548 (7666): 234-238 or Nieto, P. et al., Nature. 2017 Aug 10; 548 (7666): 239-243, each of which are incorporated here by reference in their entirety. Class 3 BRAF mutations include, without limitation, the following amino acid substitutions in human BRAF: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D; G596R and A762E.
[0083] [0083] The terms "Class I MEK1 mutation" or "Class 1 MEK1 mutation" are used here to refer to a MEK1 mutation that causes MEK1 kinase to be dependent on and hyperactivated by phosphorylation of S218 and S222 by RAF . In some embodiments, Class I MEK1 mutations include, but are not limited to, any of the Class I MEK1 mutations disclosed in Gao Y., et al., CancerDiscov. 2018 May; 8 (5): 648-661, incorporated herein by reference in its entirety. For example, in some embodiments, the term "Class I MEK1 mutation" includes, without limitation, the following amino acid substitutions in human MEK1: D67N; P124L; P124S; and L177V.
[0084] [0084] The terms "Class II MEK1 mutation" and "Class 2 MEK1 mutation" are used here to refer to a MEK1 mutation that causes MEK1 kinase to have some level of RAF activity, baseline, but also to be activated by RAF. In some modalities, MEK1 Class II mutations include, but are not limited to any of the MEK1 Class II mutations described in Gao Y., et al., Cancer Discov. 2018 May; 8 (5): 648-661, incorporated herein by reference in its entirety. For example, in some modalities, the term "MEK1 Class II mutation" includes, without limitation, the following amino acid substitutions in human MEK1: ΔE51-
[0085] [0085] The term "combination therapy" refers to a method of treatment comprising administration to an individual of at least two therapeutic agents, optionally as one or more pharmaceutical compositions. For example, a combination therapy may comprise administration of a single pharmaceutical composition comprising at least two therapeutic agents and one or more pharmaceutically acceptable carriers, excipients, diluents, and / or surfactants. A combination therapy may comprise administration of two or more pharmaceutical compositions, each composition comprising one or more therapeutic agents and one or more pharmaceutically acceptable carriers, excipients, diluents, and / or surfactants. In several embodiments, at least one of the therapeutic agents is an SHP2 inhibitor. The two agents can optionally be administered simultaneously (as a single or as separate compositions) or sequentially (as separate compositions). Therapeutic agents can be administered in an effective amount. The therapeutic agent can be administered in a therapeutically effective amount. In some modalities, the effective amount of one or more of the therapeutic agents may be less when used in combination therapy than the therapeutic amount of the same therapeutic agent when used as a monotherapy, for example, due to a additive or synergistic effect of combining two or more therapies.
[0086] [0086] Reference to "determinant," in relation to the methods disclosed here to "determine" whether an individual who has a disease or disorder (for example, a tumor) will be responsive to SHP2 inhibition and in relation to "determine" whether a sample (for example, a tumor) is classified as a certain subtype (for example, an NF1LOF or KRASG12C subtype), comprises both determining empirically (for example, by means of an experimental method known in the art or described here) and mere reference to a record comprising adequate information for such determination.
[0087] [0087] The term "disorder" is used in this description to mean, and is used interchangeably with, the terms disease, condition, or illness, unless otherwise indicated.
[0088] [0088] An "effective amount" when used in connection with a compound is an amount effective for treating or preventing a disease or disorder in an individual as described herein.
[0089] [0089] The term "inhibitor" means a compound that prevents a biomolecule, (for example, a protein, nucleic acid) from completing or initiating a reaction. An inhibitor can inhibit a reaction by competitive, non-competitive (uncompetitive), or non-competitive (non-competitive) means. Exemplary inhibitors include, but are not limited to, nucleic acids, DNA, RNA, shRNA, siRNA, proteins, protein mimetics, peptides, peptidomimetics, antibodies, small molecules, chemicals, analogs that mimic the binding site of an enzyme, receptor, or other protein, for example, that is involved in signal transduction, therapeutic agents, pharmaceutical compositions, drugs, and combinations of these. In some embodiments, the inhibitor may be nucleic acid molecules including, but not limited to, siRNA that reduces the amount of functional protein in a cell. Accordingly, compounds said to be "capable of inhibiting" a particular protein, for example, SHP2, comprise any such inhibitor.
[0090] [0090] The term "monotherapy" refers to a method of treatment comprising administration to an individual of a single therapeutic agent, optionally as a pharmaceutical composition. For example, a monotherapy may comprise administration of a pharmaceutical composition comprising a therapeutic agent and one or more pharmaceutically acceptable carrier, excipient, diluent, and / or surfactant. The therapeutic agent can be administered in an effective amount. The therapeutic agent can be administered in a therapeutically effective amount.
[0091] [0091] The term "mutation" as used here indicates any modification of a nucleic acid and / or polypeptide that results in an altered nucleic acid or polypeptide. The term "mutation" can include, for example, point mutations, deletions or insertions of single or multiple residues in a polynucleotide, which includes changes arising within a region encoding a gene's protein as well as changes in regions outside of a protein-encoding sequence, such as, but not limited to, regulatory or promoter sequences, as well as chromosomal amplifications and / or breaks or translocations.
[0092] [0092] The terms "loss of NF1 function" and "NF1LOF" are used interchangeably here to refer to any mutation that makes NF1 enzyme catalytically inactive or that results in little or no production of NF1 transcription or protein . More than 2600 different NF1 mutations are known to be inherited, and more than 80% of all constitutional NF1 mutations are inactive (ie, NF1LOF mutations) (Philpott et al., Human Genomics (2017) 11: 13, incorporated herein by reference in its entirety).
[0093] [0093] A "patient" or "individual" is a mammal, for example, a human, mouse, rat, guinea pig, dog, cat, horse, cow, pig, or non-human primate, such as a monkey, chimpanzee, ba - buíno or rhesus.
[0094] [0094] The term "prevent" or "prevention" with respect to an individual refers to preventing a disease or disorder from afflicting the individual. Prevention includes prophylactic treatment. For example, prevention may include administering to the individual a compound disclosed here before an individual is afflicted by a disease and administration will prevent the individual from being afflicted by the disease.
[0095] [0095] The term "providing an individual" with a therapeutic agent, for example, an SHP2 inhibitor, includes administration of such an agent.
[0096] [0096] The terms "via RAS" and "via RAS / MAPK" are used alternately here to refer to a signal transduction cascade downstream of various cell surface growth factor receptors in which RAS activation ( and its various isoforms and aleotypes) is a central event that drives a variety of cellular effector events that determine cell proliferation, activation, differentiation, mobilization, and other functional properties. SHP2 transmits positive signals from growth factor receptors to the RAS activation / deactivation cycle, which is modulated by guanine nucleotide exchange factors (GEFs, such as SOS1) that carry GTP into the RAS to produce GTP-bound RAS functionally active, as well as GTP accelerating proteins (GAPs, such as NF1) that facilitate termination of signals by converting GTP to GDP. GTP-linked RAS produced by this cycle transmits positive signals essential for a series of serine / threonine kinases including RAF and MAP kinases, from which additional signals emanate for various cellular effector functions.
[0097] [0097] The terms "mutation of the RAS pathway" and "mutation of the activation of the RAS / MAPK pathway" are used interchangeably here to refer to a mutation in a gene encoding a protein directly involved in the signaling pathway processes RAS / MAPK and / or regulation (or positively or negatively) this signaling pathway that makes the pathway active, in which such a mutation can increase, change or decrease the activity level of that protein. Such proteins include but are not limited to Ras, Raf, NF1, SOS, and specific isoforms or aleotypes thereof
[0098] [0098] The term "RTK-driven tumor" refers to a tumor comprising a cell with one or more oncogenic mutations of an RTK, or a protein that is part of the RTK signaling complex, which causes high levels of RTK signaling . Such cells can be considered "addicted" to RTK, and inhibition of RTK signaling leads to the simultaneous suppression of downstream pathways, often resulting in cell growth, arrest and death. Tumors triggered by RTK include, but are not limited to, non-small cell lung cancers (NSCLCs) with mutations in EGFR or ALK.
[0099] [0099] The term "SHP2" means "Src Homologia-2 phosphatase" and is also known as SH-PTP2, SH-PTP3, Syp, PTP1D, PTP2C, SAP-2 or PTPN11.
[00100] [00100] The terms "SHP2 inhibitor" and "SHP2 inhibitor" are used interchangeably.
[00101] [00101] The term "SOS" (e.g., an "SOS mutation") refers to SOS genes, which are known in the art to include RAS guanine nucleotide exchange factor proteins that are activated by receptor tyrosine kinases to promote RAS GTP loading and signaling. The term SOS includes all SOS counterparts that promote the exchange of Ras-bound GPD by GTP. In particular modalities, SOS refers specifically to "son of sinless homolog 1" ("SOS1").
[00102] [00102] Reference to a "subtype" of a cell, (for example, an NF1LOF subtype, a KRASG12C subtype, a KRASG12S subtype, a KRASG12D subtype, a KRASG12V subtype) means that the cell contains a gene mutation encoding a change in protein of the indicated type. For example, a cell classified as a "NF1LOF subtype" contains a mutation that results in loss of
[00103] [00103] A "therapeutic agent" is any substance, for example, a compound or composition, capable of treating a disease or disorder. In some embodiments, therapeutic agents that are useful in conjunction with the present invention include without limitation SHP2 inhibitors, ALK inhibitors, MEK inhibitors, RTK inhibitors (TKIs), and cancer chemotherapeutics. Many of such inhibitors are known in the art and are disclosed here.
[00104] [00104] The terms "therapeutically effective amount", "therapeutic dose", "prophylactically effective amount", or "diagnostically effective amount" is the amount of the drug, for example, an SHP2 inhibitor, necessary for obtain the desired biological response after administration.
[00105] [00105] The term "treatment" or "treating" in relation to an individual, refers to improving at least one symptom, pathology or marker of the individual's disease or disorder, directly or enhancing the effect of another treatment. Treatment includes curing, ameliorating, or at least partially ameliorating the disorder, and may also include minimal changes or improvements in one or more measurable disease markers
[00106] [00106] The present invention relates to, inter alia, compositions, methods, and kits for treating or preventing a disease or disorder (e.g., cancer) with an SHP2 inhibitor alone or in combination with another therapeutic agent appropriate.
[00107] [00107] SHP2 is an important signaling molecule for a variety of receptor tyrosine kinases (RTKs), including platelet-derived growth factor (PDGFR) receptors, fibroblast growth factor (FGFR), and epidermal growth factor (EGFR). SHP2 is also an important signaling molecule that regulates the activation of the mitogen-activated protein kinase (MAP) pathway that can lead to cell transformation, a prerequisite for the development of cancer. For example, SHP2 is involved in signaling via the Rasmogen-activated protein kinase, the JAK-STAT and / or phosphoinositol 3-kinase-AKT pathways. SHP2 mediates the activation of Erkl and Erk2 (Erkl / 2, Erk) MAP kinases by receptor tyrosine kinases such as ErbBl, ErbB2 and c-Met by modulating RAS activation.
[00108] [00108] SHP2 has two N-terminal Src homology 2 domains (N-SH2 and C-SH2), a catalytic domain (PTP), and a C-terminal tail. The two SH2 domains control the subcellular location and functional regulation of SHP2. The molecule exists in an inactive conformation, inhibiting its own activity through a bonding network involving residues from both the N-SH2 and PTP domains. In response
[00109] [00109] SHP2 activation mutations have been associated with developmental pathologies such as Noonan Syndrome and Leopard Syndrome and can also be found in multiple types of cancer, including most RTK-driven tumors, leukemia, lung cancer and breast, gastric carcinoma, anaplastic large cell lymphoma, glioblastoma and neuroblastoma.1
[00110] [00110] Furthermore, SHP2 plays a role in the transduction of signals that originate from immune checkpoint molecules, including, but not limited to, programmed cell death protein 1 (PD-1) and lymphocyte-associated protein 4 Cytotoxic T (CTLA-4). In this context, inhibition of SHP2 function can promote the activation of immune cells expressing checkpoint molecules, including anti-cancer immune responses.
[00111] [00111] It has been previously described that either the knockout of SHP2 expression using RNAi technology or SHP2 inhibition by an allosteric small molecule inhibitor interferes with the signaling of various RTKs involved in boosting cancer cell growth. However, this work also concluded that such methods would be ineffective in blocking growth signaling in cells in which growth is driven by mutations in proteins that act downstream from RTKs, such as those containing activation mutations. in Ras or Raf proteins (Chen, Ying-Nan P. 148 Nature Vol 535 7 July 2016 on page 151).
[00112] [00112] Consequently, in some embodiments, the present invention relates to the unexpected discovery that, contrary to the teachings of the prior art, certain subsets of cells carrying mutations of the oncogenic RAS pathway (for example, KRASG12C mutations) they are sensitive to SHP2 inhibition and can be effectively treated with SHIP2 inhibitors (see, for example, Example 1). For example, the present invention demonstrates that certain subsets of cancer cells carrying particular KRAS mutations (eg, KRASG12C mutations) or NF1LOF mutations are sensitive to SHP2 inhibition and that SHP2 inhibition is an effective means for prevent and delay the emergence of tumor resistance to various therapeutic agents including cancer therapies (for example, MAPK inhibitors) and an effective means of sensitizing a tumor that is resistant to cancer therapy (for example, a MAPK inhibitor) to that inhibitor, particularly in the context of mutations in the RAS pathway. Similarly, the present invention demonstrates that certain subsets of cancer cells carrying particular BRAF mutations (eg, Class 3 BRAF mutations) or MEK mutations (eg, Class 1 MEK1 mutations) are sensitive inhibition of SHP2 and that inhibition of SHP2 is an effective means of preventing and delaying the emergence of tumor resistance to various therapeutic agents including cancer therapies (e.g. MAPK inhibitors, MEK inhibitors, Erk inhibitors, etc. .) and an effective means to resensitize a tumor that is resistant to cancer therapy (for example, a MAPK inhibitor) to that inhibitor, particularly in the context of mutations in the RAS pathway.
[00113] [00113] The observation that an SHP2 inhibitor can inhibit some, but not all, KRAS mutant cells may be a function of the nucleotide cyclization aspects of a particular KRAS mutation and its corresponding dependence on inputs signaling to maintain high levels of the active GTP-linked state. In fact Patricelli and co-workers demonstrated that KRASG12C is not a constitutively and fully active protein, but the nucleotide state of KRASG12C is in a dynamic flow state that can be modulated by upstream signaling factors (Patricelli et al., Cancer Discov 2016 Mar; 6 (3): 316-29, incorporated here by reference in its entirety). Similarly, in cells that have lost the function of the GTPase activating protein (GAP), for example, NF1LOF experiences a change to the GTP-linked state, the RAS active, which directs signaling to RAS effectors and growth dependence . In these cells, the wild type RAS undergoes nucleotide cyclization which, as for KRASG12C, makes it sensitive to input signaling inputs to maintain a highly active state. In the present invention, the sensitivity of KRASG12C and NF1LOF strains to an SHP2 allosteric inhibitor reflects the modulation of these upstream factors, and therefore the mutant / wild-type RAS nucleotide state, by the inhibitor.
[00114] [00114] Thus, the present invention provides at least in part, compositions, methods, and kits for the identification, evaluation and / or treatment of a disease or condition (for example, a cancer or tumor such as, for example, a cancer or tumor associated with the oncogene) responsive to a treatment that includes an SHP2 inhibitor alone or in combination with another cancer therapeutic agent (for example, an inhibitor of a MAP kinase pathway).
[00115] [00115] In some embodiments, the present invention provides a method for stratifying the patient based on the presence or absence of a mutation in the RAS pathway or based on the particular subtype of such mutation. As used herein, "patient stratification" means to classify one or more patients as having a disease or disorder
[00116] [00116] In some embodiments, the present invention provides a method for stratifying the individual comprising (a) determining whether a cell in the individual comprises a mutation of the RAS pathway selected from the group consisting of KRASG12A; KRASG12C; KRASG12D; KRASG12S; KRASG12V; an NF1LOF mutation; a BRAF Class 3 mutation; a MEK1 Class 1 mutation; a MEK1 Class 2 mutation; and an SOS mutation / amplification; (b) administering the SHP2 inhibitor to the individual; (c) optionally, administering to the individual an additional therapeutic agent (for example, an anti-cancer therapeutic agent).
[00117] [00117] In some embodiments, the present invention provides a method for stratifying the individual comprising (a) determining whether a cell in the individual comprises a mutation of the RAS pathway selected from the group consisting of KRASG12A; KRASG12C; KRASG12D; KRASG12S; KRASG12V; an NF1LOF mutation; a BRAF Class 3 mutation; and an SOS mutation / amplification; (b) administer to the individual the SHP2 inhibitor; (c) optionally, administering to the individual an additional therapeutic agent (for example, an anti-cancer therapeutic agent).
[00118] [00118] Any disease or condition associated with a mutation of the RAS pathway can be identified, evaluated, and / or treated in accordance with the present invention. In particular modalities, the mutation of the pathway
[00119] [00119] In various embodiments, methods for treating such diseases or disorders involve administering to an individual an effective amount of an SHP2 inhibitor or a composition (e.g., a pharmaceutical composition) comprising an SHP2 inhibitor. Any compound or substance capable of inhibiting SHP2 can be used in application with the present invention to inhibit SHP2. Non-limiting examples of such SHP2 inhibitors are known in the art and are described here.
[00120] [00120] One aspect of the invention relates to the compounds of Formula I:, and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, wherein: A is a cycloalkyl, heterocycloalkyl, aryl or heteroaryl, monocyclic or polycyclic, from 5 to 12 members; Y1 is –S– or a direct link; Y2 is –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra) -, –N (Ra ) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, - N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C (O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, or –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the pyrazine ring and the link on the right side of the Y2 portion is linked to R3; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, –NO2 , –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or –CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –R5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; R2 is independently –ORb, –CN, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, aryl, heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O; where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; and in which the heterocyclyl or heteroaryl is not linked by means of a nitrogen atom; Ra is independently, at each occurrence –H, –D, –OH, –C3-C8 cycloalkyl, or –C1-C6 alkyl, where each alkyl or cycloalkyl is optionally substituted by one or more –NH2, where 2 Ra, together with the carbon atom to which they are attached, can combine to form a 3- to 8-membered cycloalkyl; Rb is independently, in each occurrence -H, -D, -C1-
[00121] [00121] Another aspect of the description concerns the compounds of Formula II:, and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, wherein: A is a cycloalkyl, heterocycloalkyl, aryl, or monocyclic or polycyclic heteroaryl of 5 to 12 members; Y2 is –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra) -, –N (Ra ) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C (O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, or –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the pyrazine ring and the link on the right side of the Y2 portion is linked to R3; R1 is independently, at each occurrence, –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, - NO2, –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O ) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or –CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more –OH , halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O ) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; R2 is independently –ORb, –CN, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, aryl, heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O; where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; and wherein the heterocyclyl or heteroaryl is not linked via a nitrogen atom; Ra is independently, at each occurrence, –H, –D, –OH, –C3-C8 cycloalkyl, or –C1-C6 alkyl, where each alkyl or cycloalkyl is optionally substituted by one or more –NH2, where 2 Ra , together with the carbon atom to which they are attached, can combine to form a 3- to 8-membered cycloalkyl; Rb is independently, in each occurrence, –H, –D, –C1- C6 alkyl, –C3-C8 cycloalkyl, –C2-C6 alkenyl, or heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S , P, and O; where each alkyl, cycloalkyl, alkenyl, or heterocycle is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle , aryl or heteroaryl; R3 is independently –C1-C6 alkyl or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein each alkyl or heterocycle is optionally substituted by one or more –C1-C6 alkyl, –OH, or –NH2; or R3 can combine with Ra to form a 3 to 12 membered monocyclic or polycyclic heterocycle or a 5 to 12 membered spiroheterocycle, where each heterocycle or spiroheterocycle is optionally substituted by one or more –C1 -C6 alkyl, -OH, or -NH2; R4 is independently –H, –D, or –C1-C6 alkyl, where each alkyl is optionally substituted by one or more –OH, –NH2, halogen, or oxo; or Ra and R4, together with the atom or atoms to which they are attached, can combine to form a monocyclic or polycyclic C3-C12 cycloalkyl or a 3- to 12-membered monocyclic or polycyclic heterocycle, wherein the cycloalkyl or heterocycle it is optionally replaced by oxo; R5 and R6 are independently, at each occurrence, –H, –D, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, a heterocycle monocyclic or polycyclic from 3 to 12 members, –OR7, –SR7, halogen, –NR7R8, –NO2, or –CN; R7 and R8 are independently, at each occurrence, –H, –D, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, or a 3- to 12-membered monocyclic or polycyclic heterocycle, where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, or heterocycle is optionally substituted by one or more –OH, –SH, –NH2, –NO2, or –CN; m is independently, in each occurrence 1, 2, 3, 4, 5 or 6; and n is independently, in each occurrence 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
[00122] [00122] Another aspect of the description concerns compounds of
[00123] [00123] One aspect of the invention relates to compounds of Formula I-V1:, and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, or isomers thereof, wherein:
[00124] [00124] One aspect of the invention relates to compounds of Formula I-V2:, and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, and isomers thereof, wherein: A is cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, where cycloalkyl, heterocycloalkyl, aryl, and heteroaryl are monocyclic from 5 to 12 members or polycyclic from 5 to 12 members; Y1 is –S–, a direct link, –NH–, –S (O) 2–, –S (O) 2 – NH–, –C (= CH2) -, –CH–, or –S (O) -; Y2 is –NRa–, where the link on the left side of Y2, as shown, is linked to the pyrazine ring and the link on the right side of the Y2 portion, as shown, is linked to R3; R3 is combined with Ra to form a 3 to 12 membered polycyclic heterocycle or a 5 to 12 membered spiroheterocycle, where each heterocycle or spiroheterocycle is optionally substituted by one or more –C1-C6 alkyl , halogen, –OH, –ORb, –NH2, –NHRb, heteroaryl, heterocyclyl, - (CH2) nNH2, - (CH2) nOH, –COORb,
[00125] [00125] One aspect of the invention concerns the compounds of Formula IW:, and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, and isomers thereof, wherein: A is cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, in which cycloalkyl, heterocycloalkyl, aryl, and heteroaryl are monocyclic from 5 to 12 members or polycyclic from 5 to 12 members; Y1 is –S–, a direct link, –NH–, –S (O) 2–, –S (O) 2 – NH–, –C (= CH2) -, –CH–, or –S (O) -; Y2 is –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra) -, –N (Ra ) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C (O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, or –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the pyrazine ring and the link on the right side of the Y2 portion, as shown, is linked to R3; R1 is independently, at each occurrence, –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, –OR6, halogen, –NO2, –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, - S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, –CO2R5, –C (O) NR5R6, –NR5C (O) R6, polycyclic or monocyclic heterocyclyl, spiro -heterocyclyl, heteroaryl, or oxo, where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, spiroheterocyclyl, or heteroaryl is optionally substituted by one or more –OH, halogen, –NO2, oxo, = O, - CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, - S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; R2 is independently –ORb, –CN, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, halogen, –C (O) ORb, –C3-C8 cycloalkyl, aryl, heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O; where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, - NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S ( O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; and wherein the heterocyclyl or heteroaryl is not linked via a nitrogen atom; Ra is independently, at each occurrence, –H, –D, –OH, –C3-C8 cycloalkyl, –C1-C6 alkyl, 3 to 12 membered heterocyclyl, or - (CH2) n-aryl, where each alkyl or cycloalkyl is optionally substituted by one or more –NH2, or where 2 Ra, together with the carbon atom to which they are both attached, can combine to form a 3- to 8-membered cycloalkyl; Rb is independently, at each occurrence, –H, –D, –OH, –C1-C6 alkyl, –C3-C8 cycloalkyl, –C2-C6 alkenyl, - (CH2) n-aryl, heterocyclyl containing 1 to 5 selected hetero atoms the group consisting of N, S, P, and O, or heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O; where each alkyl, cycloalkyl, alkenyl, heterocycle, heteroaryl, or - (CH2) n-aryl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) NR5R6, –NR5C (O) R6, heterocycle, aryl, heteroaryl, - (CH2) nOH, –C1-C6 alkyl, –CF3, –CHF2, or –CH2F ; R3 is independently –H, –C1-C6 alkyl, a 3- to 12-membered monocyclic or polycyclic heterocycle, a 5- to 12-membered spiroheterocycle, C3-C8 cycloalkyl, or - (CH2) n-Rb, where each alkyl, spiro-heterocycle, heterocycle, or cycloalkyl is optionally substituted by one or more –C1-C6 alkyl, –OH, –NH2, –ORb, –NHRb, - (CH2) nOH, heterocyclyl, or spiro-heterocyclyl; or R3 can combine with Ra to form a 3 to 12 membered monocyclic or polycyclic heterocycle or a 5 to 12 membered spiroheterocycle, where each heterocycle or spiroheterocycle is optionally substituted by one or more –C1 -C6 alkyl, halogen, –OH, –ORb, –NH2, –NHRb, heteroaryl, heterocyclyl, - (CH2) nNH2, - (CH2) nOH, –COORb, –CONHRb, –CONH (CH2) nCOORb, –NHCOORb, –CF3, –CHF2, –CH2F, or = O; R4 is independently –H, –D, –C1-C6 alkyl, –C1-C6 haloalkyl, –C1-C6 hydroxyalkyl –CF2OH, –CHFOH –NH-NHR5, –NH- OR5, –O-NR5R6, –NHR5 , –OR5, –NHC (O) R5, –NHC (O) NHR5, –NHS (O) 2R5, –NHS (O) 2NHR5, –S (O) 2OH, –C (O) OR5, –NH (CH2 ) nOH, –C (O) NH (CH2) nOH, –C (O) NH (CH2) nRb, –C (O) Rb, –NH2, –OH, –CN, –C (O) NR5R6, –S (O) 2NR5R6, C3-C8 cycloalkyl, aryl, heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O, or heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, and O, where each alkyl, cycloalkyl, or heterocyclyl is optionally substituted by one or more –OH, –NH2, –ORb, halogen, or oxo; in which each aryl or heteroaryl is
[00126] [00126] One aspect of the invention relates to compounds of Formula I-X:, and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, or isomers thereof, wherein:
[00127] [00127] One aspect of the invention relates to compounds of Formula I-Y:,
[00128] [00128] One aspect of the invention relates to the compounds of Formula IZ:, and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, wherein: A is a cycloalkyl, heterocycloalkyl, aryl or heteroaryl, monocyclic or polycyclic, from 5 to 12 members; Y1 is –S–, a direct link, –NH-, –S (O) 2–, –S (O) 2-NH–, –C (= CH2) -, –CH–, or –S (O) -; Y2 is -NRa-, - (CRa2) m-, -C (Ra) 2NH-, - (CRa2) mO-, –C (O) N (Ra) -, -N (Ra) C (O) -, -S (O) 2N (Ra) -, -N (Ra) S (O) 2-, -N (Ra) C (O) N (Ra) -, -N (Ra) C (S) N (Ra) ) -, -OC (O) N (Ra) -, -N (Ra) C (O) O-, -C (O) N (Ra) O-, -N (Ra) C (S) -, or -C (S) N (Ra) -; wherein the bond on the left side of Y2, as shown, is bonded to the pyrazine ring and the bond on the right side of the Y2 portion, as shown, is bonded to R3; R1 is independently, at each occurrence -H, -D, -C1- C6 alkyl, -C2-C6 alkenyl, -C4-C8 cycloalkenyl, -C2-C6 alkynyl, -C3- C8 cycloalkyl, -OH, halogen, -NO2 , -CN, -NR5R6, -SR5, -S (O) 2NR5R6, -S (O) 2R5, -NR5S (O) 2NR5R6, -NR5S (O) 2R6, -S (O) NR5R6, -S (O) R5, -NR5S (O) NR5R6, -NR5S (O) R6, -C (O) R5, or -CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more - OH, halogen, -NO2, oxo, -CN, −R5, -OR5, -NR5R6, −SR5, -S (O) 2NR5R6, -S (O) 2R5, -NR5S (O) 2NR5R6, -NR5S (O) 2R6, -S (O) NR5R6, -S (O) R5, -NR5S (O) NR5R6, -NR5S (O) R6, heterocycle, aryl or heteroaryl; R2 is independently -ORb, -NH2, -CN, -C1-C6 alkyl, -
[00129] [00129] One aspect of the invention relates to the compounds of Formula IV: and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, where: A is selected from the group consisting of cycloalkyl , heterocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic of 5 to 12 members; Y1 is –S– or a direct link; Y2 is selected from the group consisting of: –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra ) -, –N (Ra) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C ( O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, and –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the pyridine ring and the link on the right side of Portion Y2 is linked to R3; R1 is independently, at each occurrence, –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, - NO2, –CN, –NR5R6, –SR5,
[00130] [00130] Another aspect of the invention concerns the compounds of Formula V: and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, in which: A is selected from the group consisting of cycloalkyl, he - terocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic from 5 to 12 members; Y2 is selected from the group consisting of: –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra ) -, –N (Ra) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C ( O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, and –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the pyridine ring and the link on the right side of Portion Y2 is linked to R3; R1 is independently, at each occurrence, –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, - NO2, –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O ) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or –CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more –OH , halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O ) 2R6, –S (O) NR5R6, –S (O) R5,
[00131] [00131] Another aspect of the invention relates to compounds of Formula VI:
[00132] [00132] One aspect of the invention relates to the compounds of Formula IV-Y: or a pharmaceutically acceptable salt, prodrug, solvate, hydrate, tautomer thereof, wherein: A is selected from the group consisting of cycloalkyl, he - terocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic, with 5 to 12 members; Y1 is –S– or a direct link; Y2 is selected from the group consisting of: –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra ) -, –N (Ra) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C ( O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, and –OC (O) O–; wherein the bond on the left side of Y2, as shown, is bonded to the pyridine ring and the bond on the right side of the Y2 portion, as depicted, is bonded R3; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, –NO2 , –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or –CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; R2 is independently –ORb, –CN, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, aryl, heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, or O, heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, or O; where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted by one or more -
[00133] [00133] One aspect of the invention relates to the compounds of Formula IV-Z: or a pharmaceutically acceptable salt, prodrug, solvate, hydrate, tautomer thereof, wherein: A is selected from the group consisting of cycloalkyl, he - terocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic, with 5 to 12 members; Y1 is –S–, a direct link, –NH-, –S (O) 2-, –S (O) 2-NH-, –C (= CH2) -, - CH-, or -S (O) -; Y2 is selected from the group consisting of: –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH–, - (CRa2) mO–, –C (O) N (Ra ) -, –N (Ra) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C ( O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, and –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the pyridine ring and the link on the right side of the Y2 portion, as shown, is linked to R3; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, –NO2 , –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or
[00134] [00134] One aspect of the invention relates to the compounds of Formula VII: and pharmaceutically acceptable salts, prodrugs, solvates, hydrates, tautomers, or isomers thereof, wherein: Q is H or; A is selected from the group consisting of cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic, with 5 to 12 members; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl,
[00135] [00135] Another aspect of the invention relates to the compounds of Formula VIII: and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, in which: A is selected from the group consisting of cycloalkyl, he - terocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic, with 5 to 12 members; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, –NO2 , –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6,
[00136] [00136] Another aspect of the invention concerns the compounds of Formula IX: and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, in which: A is selected from the group consisting of cycloalkyl, he - terocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic, with 5 to 12 members; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, –NO2 , –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or –CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; X1 is N or C; X2 is N or CH; B, including the atoms at the points of attachment, is a 5 to 12 membered monocyclic or polycyclic heterocycle or a 5 to 12 membered monocyclic or polycyclic heteroaryl; R2 is independently H, –ORb, –NR5R6, –CN, –C1-C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, -NH2, halogen, -C (O) ORa, –C3-C8 cycloalkyl, aryl, heterocyclyl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, or O, or heteroaryl containing 1 to 5 heteroatoms selected from the group consisting of N, S, P, or O; where each alkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkyl, heterocyclyl, aryl, or heteroaryl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, - NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S ( O) NR5R6, –NR5S (O) R6, heterocycle, aryl or heteroaryl; and in which the heterocyclyl or heteroaryl is not linked by means of a nitrogen atom; Y2 is selected from the group consisting of: –NRa–, - (CRa2) m–, –C (O) -, –C (Ra) 2NH -, - (CRa2) mO–, –C (O) N (Ra ) -, –N (Ra) C (O) -, –S (O) 2N (Ra) -, –N (Ra) S (O) 2–, –N (Ra) C (O) N (Ra) -, –N (Ra) C (S) N (Ra) -, –C (O) O–, –OC (O) -, –OC (O) N (Ra) -, –N (Ra) C ( O) O–, –C (O) N (Ra) O–, –N (Ra) C (S) -, –C (S) N (Ra) -, and –OC (O) O–; wherein the link on the left side of Y2, as shown, is linked to the ring and the link on the right side of the Y2 portion, as shown, is linked to R3;
[00137] [00137] Another aspect of the invention concerns the compounds of Formula X: and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, in which: A is selected from the group consisting of cycloalkyl, he - terocycloalkyl, aryl, or heteroaryl, monocyclic or polycyclic, with 5 to 12 members; R1 is independently, in each occurrence –H, –D, –C1- C6 alkyl, –C2-C6 alkenyl, –C4-C8 cycloalkenyl, –C2-C6 alkynyl, –C3-C8 cycloalkyl, –OH, halogen, –NO2 , –CN, –NR5R6, –SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5, –NR5S (O) NR5R6, –NR5S (O) R6, –C (O) R5, or –CO2R5, where each alkyl, alkenyl, cycloalkenyl, alkynyl, or cycloalkyl is optionally substituted by one or more –OH, halogen, –NO2, oxo, –CN, −R5, –OR5, –NR5R6, −SR5, –S (O) 2NR5R6, –S (O) 2R5, –NR5S (O) 2NR5R6, –NR5S (O) 2R6, –S (O) NR5R6, –S (O) R5,
[00138] [00138] Another aspect of the present invention relates to compounds, and pharmaceutically acceptable salts, solvates, hydrates, tautomers, or isomers thereof, in Table 1. Table 1 Comp. # Structure Comp. # Structure 1 2 s
[00139] [00139] Another aspect of the present invention relates to compounds, and salts, prodrugs, solvates, hydrates, tautomers, or pharmaceutically acceptable isomers thereof, in Table 2. Table 2 Structure Structure
[00140] [00140] The term "aryl" refers to groups of cyclic, aromatic hydrocarbons that have 1 to 2 aromatic rings, including monocyclic or bicyclic groups such as phenyl, biphenyl or naphthyl.
[00141] [00141] Unless otherwise specifically defined, "heteroaryl" means a monovalent or multivalent monocyclic aromatic radical or a polycyclic aromatic radical of 5 to 24 ring atoms, containing one or more ring heteroatoms selected from N, S , P, and O, the remaining ring atoms being C. Heteroaryl as defined herein also means a bicyclic heteroaromatic group in which the heteroatom is selected from N, S, P, and O. The aromatic radical is optionally substituted independently with one or more substitutes described here. Examples include, but are not limited to, furyl, thienyl, pyrrolyl, pyridyl, pyrazolyl, pyrimidinyl, imidazolyl, isoxazolyl, oxazolyl, oxadiazolyl, pyrazinyl, indolyl, thiophen-2-yl, quinolyl, benzopyranyl, isothiazolyl, thiaziazole, , benzo [d] imidazolyl, tieeno [3,2-b] thiophene, triazolyl, triazinyl, imidazo [1,2-b] pyrazolyl, furo [2,3-c] pyridinyl, imidazo [1,2-a ] pyridinyl, indazolyl, 1-methyl-1H-indazolyl, pyrrolo [2,3-c] pyridinyl, pyrrolo [3,2-c] pyridinyl, pyrazolo [3,4-c] pyridinyl, tie-no [3 , 2-c] pyridinyl, thieno [2,3-c] pyridinyl, thieno [2,3-b] pyridinyl, benzothiazolyl, indolyl, indolinyl, indolinonyl, dihydrobenzothiophenyl, dihydro-benzofuranyl, benzofuran, chromanyl , thiocromanyl, tetrahydroquinolinyl, dihydrobenzothiazine, dihydrobenzoxanil, quinolinyl, isoquinolinyl, 1,6-naphthyridinyl, benzo [de] isoquinolinyl, pyrido [4,3-b] [1,6] naphthyridinyl, thieno [2,3-b] pyrazinyl, quinazolinyl, tetrazole [1,5-a] pyridinyl, [1,2,4] triaz olo [4,3-a] pyridinyl, isoindolyl, isoindolin-1-one, indo-lin-2-one, pyrrolo [2,3-b] pyridinyl, pyrrolo [3,4-b] pyridinyl, pyrrole [3, 2-b]
[00142] [00142] "Alkyl" refers to a straight or branched chain saturated hydrocarbon. C1-C6alkyl groups contain 1 to 6 carbon atoms. Examples of a C1-C6alkyl group include, but are not limited to, methyl, ethyl, propyl, butyl, pentyl, isopropyl, isobutyl, sec-butyl and tert-butyl, isopentyl and neopentyl.
[00143] [00143] The term "alkenyl" means an aliphatic hydrocarbon group containing a carbon-carbon double bond and which can be linear or branched having about 2 to about 6 carbon atoms in the chain. Certain alkenyl groups have 2 to about 4 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl, or propyl are attached to a linear alkenyl chain. Exemplary alkenyl groups include ethylene, propylene, n-butenyl, and i-butenyl. A C2-C6 alkenyl group is an alkylene group containing between 2 and 6 carbon atoms.
[00144] [00144] The term "alkynyl" means an aliphatic hydrocarbon group containing a carbon-carbon triple bond and which can be linear or branched having about 2 to about 6 carbon atoms in the chain. Certain alkynyl groups have 2 to about 4 carbon atoms in the chain. Branched means that one or more lower alkyl groups such as methyl, ethyl, or propyl are attached to a linear alkynyl chain. Exemplary alkynyl groups include ethynyl, propynyl, n-butynyl, 2-butynyl, 3-methylbutynyl, and n-pentynyl. A C2-C6alkynyl group is an alkynyl group containing between 2 and 6 carbon atoms.
[00145] [00145] The term "cycloalkyl" means monocyclic or polycyclic saturated carbon rings containing 3 to 18 carbon atoms. Examples of cycloalkyl groups include, without limitation, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptanyl, cyclooctanyl, norboranyl, norborenyl, bicyclo [2.2.2] octanyl, or bicyclo [2.2.2] octenyl. C3-C8cycloalkyl is a cycloalkyl group containing between 3 and 8 carbon atoms. A cycloalkyl group can be fused (for example, dialine) or bridged (for example, norbornane).
[00146] [00146] The term "cycloalkenyl" means monocyclic, non-aromatic unsaturated carbon rings containing 4 to 18 carbon atoms. Examples of cycloalkenyl groups include, without limitation, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl, and norborenyl. A C4-C8cycloalkenyl is a cycloalkenyl group containing between 4 and 8 carbon atoms.
[00147] [00147] In some embodiments, the terms "heterocyclyl" or "heterocycloalkyl" or "heterocycle" refer to rings of 3 to 24 monocyclic or polycyclic members containing carbon and heteroatoms selected from oxygen, phosphorus, nitrogen, and sulfur and in which there are no delocalized π electrons (aromaticity) shared between the ring carbon or hetero atoms. Heterocyclyl rings include, but are not limited to, oxetanil, azetidinyl, tetrahydrofuranyl, pyrrolidinyl,
[00148] [00148] In some embodiments "heterocyclyl" or "heterocycloalkyl" or "heterocycle" is a mono or bicyclic ring, saturated, partially saturated or unsaturated, containing 3 to 24 atoms of which at least one atom is selected from nitrogen , sulfur or oxygen, which may, unless otherwise specified, be carbon or nitrogen bonded, where a –CH2– group may optionally be replaced by a –C (O) - or a ring sulfur atom may be optionally oxidized to form the S-oxides. "Heterocyclyl" may be a mono or bicyclic, saturated, partially saturated or unsaturated ring containing 5 or 6 atoms of which at least one atom is selected from nitrogen, sulfur or oxygen, which may, unless otherwise specified, be carbon or nitrogen bond, where a group -CH2– can optionally be replaced by a - C (O) - or a ring sulfur atom can be optionally oxidized to form S-oxide (s). Non-limiting examples and suitable values for the term "heterocyclyl" are thiazolidinyl, pyrrolidinyl, pyrrolinyl, 2-pyrrolidonyl, 2,5-dioxopyrrolidinyl, 2-benzoxazolinonyl, 1,1-dioxotetrahydrothienyl, thienyl, 2,4-dioxoimidazolidinyl, 2-oxo-1,3,4- (4-triazolinyl), 2-oxazolidinonyl, 5,6-dihydrouracilyl, 1,3-benzodioxolyl, 1,2,4-oxadiazolyl, 2-azabicyclo [2.2.1] heptyl, 4-thiazolidonyl, morpholino, 2-oxotetrahydrofuranyl, tetrahydrofuranyl, 2,3-dihydrobenzofuranyl, benzothienyl, tetrahydropyranyl, piperidyl, 1-oxo-1,3-dihydroisoindolyl, piperazinyl, thomorpholine, 1,1-dioxothiomorfolino, tetrahydropyranyl, 1,3-dioxolanyl, homopiperazinyl, thienyl, isoxazolyl, imidazolyl, pyrrolyl,
[00149] [00149] As used herein, the term "halo" or "halogen" means a group of fluorine, chlorine, bromine, or iodine.
[00150] [00150] The term "carbonyl" refers to a functional group comprising a carbon atom doubly linked to an oxygen atom. It can be abbreviated in this document as "oxo," as C (O), or as C = O.
[00151] [00151] "Spirocycle" or "spirocyclic" means carbogenic bicyclic ring systems with both rings connected by means of a single atom. The ring can be different in size and nature, or identical in size and nature. Examples include spiropentane, spirohexane, spiroheptane, spirooctane, spirononane, or spirochondane. One or both rings on a spirocycle can be fused to another carbocyclic, heterocyclic, aromatic, or heteroaromatic ring. One or more carbon atoms in the spirocycle can be replaced by a hetero atom (for example, O, N, S, or P). A C5-C12 spirocycle is a spirocycle containing between 5 and 12 carbon atoms. In some embodiments, a C5-C12 spirocycle is a spirocycle containing 5 to 12 carbon atoms. One or more carbon atoms can be replaced by a hetero atom.
[00152] [00152] The term "spirocyclic heterocycle," "spiro-heterocyclic," or "spiro-heterocycle" is understood to mean a spirocycle in which at least one of the rings is a heterocycle (for example, at least one of the rings is furanyl, morpholinyl, or piperadinyl). A spirocyclic heterocycle can contain between 5 and 12 atoms, at least one of which is a heteroatom selected from N, O, S and P. In some embodiments, a spirocyclic heterocycle can contain at least 5 to 12 atoms one of which is a heteroatom selected from N,
[00153] [00153] The term "tautomers" refers to a set of compounds that have the same number and type of atoms, but differ in bonding connectivity and are in equilibrium with one another. A "tautomer" is a unique member of this set of compounds. Typically a single tautomer is represented, but it is understood that this unique structure is intended to represent all possible tautomers that may exist. Examples include enoketone tautomerism. When a ketone is represented it must be understood that both the enol and ketone forms are part of the disclosure.
[00154] [00154] The SHP2 inhibitor can be administered alone as a monotherapy or in combination with one or more other therapeutic agent (for example, an inhibitor of a MAP kinase pathway or an anti-cancer therapeutic agent) as a combination therapy. The SHP2 inhibitor can be administered as a pharmaceutical composition. The SHP2 inhibitor can be administered before, after, and / or concurrently with one or more other therapeutic agents (for example, an inhibitor of a MAP kinase pathway or an anti-cancer therapeutic agent). If administered simultaneously with one or more other therapeutic agents, such administration can be simultaneous (for example, in a single composition) or it can be through two or more separate compositions, optionally through the same or different modes of administration ( for example, local, systemic, oral, intravenous, etc.).
[00155] [00155] The SHP2 inhibitor can be administered in combination with one or more MEK inhibitors as a combination therapy. The SHP2 inhibitor can be administered as a pharmaceutical composition in combination with one or more MEK inhibitors as a combination therapy. The SHP2 inhibitor can be administered before, after, and / or concurrently with one or more MEK inhibitors.
[00156] [00156] In some modalities, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor. The tumor may contain an activation mutation of the RAS pathway. In several modalities, the mutation of activation of the RAS pathway confers cell depen- dence in SHP2 (for example, for GTP reload in RAS).
[00157] [00157] In certain embodiments, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor comprising a cell that contains an NF1LOF mutation. NF1 is a GAP protein that modulates RAS activation by facilitating GTP hydrolysis of active RAS-GTP, thereby inactivating RAS. RAS oscillates between "off" on GDP and "on" on GTP. Loss of function of NF1 mutations reduces hydrolysis of GTP by RAS, and changes the balance regarding activated RAS, thus resulting in cancerous growth / proliferation and possibly oncogene dependence. NF1 mutations occur frequently on NSCLC (eg, 8.3% by Cancer Genome Atlas Research Network "Comprehensive molecular profiling of lung adenocarcinoma." Nature 511, 533-550 (2014)), and more than 80% of all mutations of constitutional NF1 are NF1LOF (Philpott, 2017), there are still no targeted therapies available to treat tumors of the NF1LOF subtype. As shown in this document, inhibition of SHP2 in NF1LOF cells resulted in dose-dependent suppression of p-ERK signaling and proliferation (Example 1, FIGS. 6A and 6B).
[00158] [00158] In certain embodiments, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor comprising a cell that contains a mutation in a RAS gene. In certain embodiments, the RAS gene mutation makes the RAS pathway dependent on the signaling flow through SHP2. The RAS pathway mutation can be a KRAS, NRAS, or HRAS mutation. Oncogenic RAS mutations, such as KRAS mutations, alter the RAS balance to the "bound" state linked to GTP, directing signaling to RAS effectors and oncogene dependence. As in the present document used, "oncogene dependence" refers to the phenomenon by which a tumor cell exhibits apparent dependence on a single oncogenic pathway or protein for sustained proliferation and / or survival, despite its myriad genetic changes. Treatment of KRAS cell line panels identified certain mutations as biomarkers of growth sensitivity of SHP2 inhibition (Example 1, Table 3). In certain embodiments, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor comprising a cell that contains a KRASG12C mutation. In certain embodiments, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor comprising a cell that contains a KRASG12A mutation; one from KRASG12D, one from KRASG12S, or one from KRASG12V.
[00159] [00159] In certain embodiments, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor comprising a cell containing a RAF gene mutation. Mutation of the RAF gene can make an RAS pathway dependent on the signaling flow through SHP2. In certain embodiments, the mutation is a BRAF Class III mutation. In some modalities, the BRAF Class III mutation can be selected from the group consisting of: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D;
[00160] [00160] In certain embodiments, the SHP2 inhibitor is administered to the individual as a monotherapy for the treatment of a tumor comprising a cell containing a MEK gene mutation. The MEK gene mutation can make the RAS pathway dependent on the signaling flow through SHP2. In certain embodiments, the MEK gene mutation is a MEK1 Class I mutation. In some modalities, the MEK1 Class I mutation can be selected from the group consisting of D67N; P124L; P124S; and L177V. In certain embodiments, the MEK gene mutation is a MEK1 Class II mutation. In some modalities, the MEK1 Class II mutation can be selected from the group consisting of ΔE51-Q58; ΔF53-Q58; E203K; L177M; C121S; F53L; K57E; Q56P; and K57N.
[00161] [00161] In certain embodiments, the SHP2 inhibitor is administered to the individual in combination with one or more other therapeutic agent (for example, an inhibitor of a MAP kinase pathway) as a combination therapy for the treatment of a tumor comprising a cell containing a mutation of the RAS pathway that makes the mutated protein dependent on the signaling flow through SHP2. The mutation can comprise one or more of an NF1LOF mutation; a RAS / RAF mutation; a KRAS mutation; a KRAS mutation selected from a KRASG12A mutation; a KRASG12C mutation; a KRASG12D mutation; a KRASG12S mutation; a KRASG12V mutation; a Class III BRAF mutation; a selected BRAF mutation of D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D; G596R and A762E; a Class I MEK1 mutation; a MEK1 mutation selected from D67N; P124L; P124S; and L177V; a Class II MEK1 mutation; and a MEK1 mutation selected from ΔE51-Q58; ΔF53-Q58; E203K; L177M; C121S; F53L; K57E; Q56P; and K57N.
[00162] [00162] In some particular embodiments, the present invention provides a method for treating a disease or disorder, for example a cancer, with a combination therapy comprising an SHP2 inhibitor known in the art or described in the present document in combination with a MAP kinase (MAPK) inhibitor (or "MAPK inhibitor") known in the art or described herein. The MAPK inhibitor can be a MEK inhibitor. MAPK inhibitors for use in the methods described herein may include, but are not limited to, one or more MAPK inhibitors described in Cancers (Basel). 2015 Sep; 7 (3): 1758–1784, incorporated in this document by reference in its entirety. For example, the MAPK inhibitor can be selected from one or more
[00163] [00163] In some embodiments, the present invention provides a method for treating a disease or disorder, for example a cancer, with a combination therapy comprising an SHP2 inhibitor known in the art or described herein in combination with a inhibitor of a RAS protein (or "RAS inhibitor") known in the art or described herein. The RAS inhibitor can inhibit KRAS, NRAS, or HRAS. The RAS inhibitor can inhibit a specific KRAS, NRAS, or HRAS mutation. The RAS inhibitor may be a specific KRASG12C inhibitor. For example, the RAS inhibitor may be ARS-853 (Patricelli et al., 2016), which selectively binds to the KRASG12C cysteine residue in the GDP-linked state.
[00164] [00164] The present invention also demonstrates the unexpected discovery that inhibition of SHP2 does not result in signaling via RAS of activation triggered by feedback (FIG. 9), although inhibition of SHP2 does not result in decreased ERK phosphorylation (FIG. 5B) and therefore, it can be expected to induce such activation by feedback in the same way as inhibition of MEK does not (FIG. 10). In addition, inhibition of SHP2 neutralized inhibitor of MEK-induced RAS activation (FIG. 11). Thus, unlike MAPK inhibitors, which can induce resistance, SHP2 inhibitors do not cause hyperactivation of RAS, and they are able to attenuate hyperactivation of RAS in response to the MEK treatment inhibitor that can contribute to resistance of MEK-inhibiting drug.
[00165] [00165] Consequently, in some embodiments, the present invention provides a method for preventing or delaying the emergence of resistance in a cell (eg, a tumor cell) to a therapeutic agent (eg, an anticancer agent) targeting a transducer of signal from the RAS pathway, the method comprising administering the therapeutic agent in combination with an SHP2 inhibitor. The SHP2 inhibitor can be administered before, after, or simultaneously with the therapeutic agent. In particular embodiments, the therapeutic agent is a MAPK inhibitor (for example, MEK inhibitor). MEK inhibitors induce RAS feedback activation, which, as shown in this document, can be blocked with an SHP2 inhibitor. Administration can be in vivo, for example, to an individual (such as a mammal, preferably a human). Thus, the method for preventing or delaying the emergence of resistance in a cell (for example, a tumor cell) to a therapeutic agent (for example, an anticancer agent) targeting a signal transducer of the RAS pathway, may comprise administration an SHP2 inhibitor and a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemuraphenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and
[00166] [00166] In some embodiments, the present invention provides a method for resensitizing a tumor that is resistant to a therapeutic agent by targeting a signal transducer of the RAS pathway, the method comprising administering an SHP2 inhibitor. In particular embodiments, the therapeutic agent is a MAPK inhibitor (for example, MEK inhibitor or an ERK inhibitor). Suitable MAPK inhibitors are known in the art, are described in the present document, and include, without limitation: MEK inhibitors, one or more MAPK inhibitors described in Cancers (Basel). 2015 Sep; 7 (3): 1758– 1784, incorporated in the present document by reference in its entirety, one or more from Trametinib, Binimetinibe, Selumetinibe, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766 (Roche, described in PLoS One. 2014 Nov 25; 9 (11), incorporated in this document by reference in its entirety); and GSK1120212 (or "JTP-74057", described in Clin Cancer Res. 2011 Mar 1; 17 (5): 989-1000, incorporated in this document by reference in its entirety.
[00167] [00167] In some embodiments, the present invention provides a method for treating cells (e.g., cancer cells) with an SHP2 inhibitor, wherein the cells have been processed dependent on SHP2 for treatment with a therapeutic agent (for example, example, a MAPK inhibitor). The therapeutic agent can be a MAPK inhibitor selected from a MEK inhibitor and an ERK inhibitor. The therapeutic agent can induce overactivation of the RAS pathway by relieving a negative feedback mechanism of the national RAS pathway
[00168] [00168] The present invention also provides methods for determining whether an individual has a tumor that will be responsive to SHP2 inhibitor. The method may comprise determining whether the tumor is classified as an NF1LOF subtype and administering to the individual an SHP2 inhibitor if the tumor is classified as an NF1LOF subtype. In some modalities, determination can comprise empirical determination, for example, through experimentation. Such methods for determining a subtype of a tumor are known in the art and may include genotyping, measuring NF1 protein levels, determining the size of NF1 (for example, by any suitable method such as Western blot, spectrometry, mass measurement, size exclusion chromatography), or measurement by a functional assay such as a RAS-GTP accumulation assay.
[00169] [00169] In one embodiment, the present invention provides a method for determining whether an individual who has cancer will be responsible for SHP2 inhibition, the method comprising determining whether the cancer is classified as a KRASG12C subtype and administration to the individual a SHP2 inhibitor if the biological sample is classified as a KRASG12C subtype. Methods for determining KRAS subtypes are known in the art and are suitable for use in accordance with the present invention including, but not limited to, direct sequencing, next generation sequencing, and use of a high-throughput diagnostic assay. sensitivity (with CE-IVD mark), for example, as described in Domagala, et al., Pol J Pathol 3: 145-164 (2012), incorporated in this document by reference in its entirety, including TheraScreen PCR; AmoyDx; PNAClamp; Real-Quality; EntroGen; LightMix; StripAssay; Hybcell plexA; Devyser; Surprise; Cobas; and TheraScreen Pyro.
[00170] [00170] In one embodiment, the present invention provides a method for determining whether an individual who has cancer will be responsible for SHP2 inhibition, the method comprising determining whether the cancer is classified as a KRASG12D subtype and administration to the individual of a SHP2 inhibitor if the biological sample is classified as a KRASG12D subtype.
[00171] [00171] In one embodiment, the present invention provides a method for determining whether an individual who has cancer will be responsive to SHP2 inhibition, the method comprising determining whether the cancer is classified as a KRASG12S subtype and administration to the individual a SHP2 inhibitor if the biological sample is classified as a KRASG12S subtype.
[00172] [00172] In one embodiment, the present invention provides a method for determining whether an individual who has cancer will be responsible for SHP2 inhibition, the method comprising determining whether the cancer is classified as a KRASG12V subtype and administration to the individual of an SHP2 inhibitor if the biological sample is classified as a KRASG12V subtype.
[00173] [00173] In one embodiment, the present invention provides methods of determining whether a treatment comprising an inhibitor of
[00174] [00174] As someone skilled in the art will appreciate, in various ways, all the therapeutic agents described in this document, that is, the specific TKI inhibitors, MEK inhibitors, ALK inhibitors, SHP2 inhibitors, EGFR inhibitors, etc., can be used in any one or more of the modalities described in this document that generally call for such an inhibitor. Thus, for example, a modality comprising treatment with, for example, a "SHP2 inhibitor," generally, or a "TKI inhibitor," generally, may comprise treatment with any one or more SHP2 inhibitor or TKI inhibitor, respectively, which is described in this document (unless the context requires otherwise).
[00175] [00175] Administration of the disclosed compositions and compounds (for example, SHP2 inhibitors and / or other therapeutic agents) can be accompanied by any means of administration for therapeutic agents. These modes include systemic or local administration such as oral, nasal, parenteral, transdermal, subcutaneous, vaginal, buccal, rectal or topical administration modes.
[00176] [00176] Depending on the intended mode of administration, the disclosed compounds or pharmaceutical compounds may be in solid, semi-solid, or liquid dosage form, such as, for example, injectables, tablets, suppositories, pills, release capsule over time, elixirs, tinctures, emulsions, syrups, powders, liquids, suspensions, or the like, sometimes in unit dosages and consistent with conventional pharmaceutical practices. Likewise, they can also be administered intravenously (both in bolus and infusion), intraperitoneally, subcutaneously or intramuscularly, and all forms of use are well known to those skilled in pharmaceutical techniques. Pharmaceutical compositions suitable for the release of an SHP2 inhibitor (alone or, for example, in combination with another therapeutic agent according to the present invention) and methods for its preparation will be readily apparent to those skilled in the art. Such compositions and methods for their preparation can be found, for example, at Remington’s
[00177] [00177] Illustrative pharmaceutical compositions are tablets and gelatin capsules comprising an SHP2 inhibitor alone or in combination with another therapeutic agent according to the invention and a pharmaceutically acceptable carrier, such as a) a diluent, for example, purified water, triglyceride oils, such as hydrogenated or partially hydrogenated vegetable oil, or mixtures thereof, corn oil, olive oil, sunflower oil, safflower oil, fish oils, such as EPA or DHA, or their esters or triglycerides - oils or mixtures thereof, omega-3 fatty acids or derivatives thereof, lactose, dextrose, sucrose, mannitol, sorbitol, cellulose, sodium, saccharin, glucose and / or glycine; b) a lubricant, for example, silica, talc, stearic acid, its magnesium or calcium salts, sodium oil, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and / or polyethylene glycol; for pills too; c) a binder, for example, magnesium aluminum silicate, starch paste, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose, magnesium carbonate, natural sugars such as glucose or beta-lactose, corn sweeteners, natural and synthetic gums such as acacia, tragacanth or sodium alginate, waxes and / or polyvinylpyrrolidone, if desired; d) a disintegrant, for example, starches, agar, methyl cellulose, bentonite, xanthan gum, algic acid or its sodium salts, or effervescent mixtures; e) absorbent, color, flavor and sweetener; f) an emulsifier or dispersing agent, such as Tween 80, Labrasol, HPMC, DOSS, caproil 909, labrafac, labrafil, peceol, transcutol, capmul MCM, capmul PG-12, captex 355, gelucire, vitamin E TGPS or other emulsifier appropriate; and / or g) an agent that enhances the absorption of the compound such as cyclodextrin, hydroxypropyl-cyclodextrin, PEG400, PEG200.
[00178] [00178] Liquid compositions, particularly injectable, can, for example, be prepared by dissolving, dispersing, etc. For example, an SHP2 inhibitor (alone or in combination with another therapeutic agent according to the invention) is dissolved in or mixed as a pharmaceutically acceptable solvent such as, for example, water, saline, aqueous dextrose, glycerol, ethanol , and the like, to thereby form an injectable isotonic solution or suspension. Proteins such as albumin, chylomicron particles, or whey proteins can be used to solubilize the SHP2 inhibitor (alone or in combination with another therapeutic agent according to the invention).
[00179] [00179] The SHP2 inhibitor can also be formulated as a suppository, alone or in combination with another therapeutic agent according to the invention, which can be prepared from suspensions or fatty emulsions; using polyalkylene glycols such as propylene glycol, as the carrier.
[00180] [00180] The SHP2 inhibitor can also be administered in the form of liposome delivery systems, such as small unilamellar vesicles, large unilamellar vesicles and multi-lamellar vesicles, either alone or in combination with another therapeutic agent according to the invention. Liposomes can be formed from a variety of phospholipids, containing cholesterol, stearylamine or phosphatidylcholines. In some embodiments, a film of lipid components is hydrated with an aqueous drug solution into a lipid layer form encapsulating the drug, as described, for example, in U.S. Patent No. 5,262,564, the contents of which are incorporated into this document by reference.
[00181] [00181] SHP2 inhibitors can also be released by the use of monoclonal antibodies as individual carriers to which the disclosed compounds are coupled SHP2 inhibitors can also be coupled to soluble polymers as targetable drug carriers. Such polymers can include polyvinylpyrrolidone, pyran copolymer, polyhydroxypropylmethacrylamide-phenol, polyhydroxyethylpapanamide phenol, or polyethyleneoxidepolylysine substituted by palmotoyl residues. In addition, an SHP2 inhibitor can be coupled to a class of biodegradable polymers useful in obtaining controlled release of a drug, for example, polylactic acid, polyiepsilon caprolactone, polyhydroxy butyric acid, polyiorthesters, polyacetals, polyhydro-pyranes, poly-polyacrylates and block copolymers of cross-linked or amphipathic hydrogels. In one embodiment, disclosed compounds are not covalently bound to a polymer, for example, a polycarboxylic acid polymer, or a polyacrylate.
[00182] [00182] Parental injectable administration is generally used for subcutaneous, intramuscular or intravenous injections and infusions. Injectables can be prepared in conventional forms, or as liquid solutions or suspensions or solid forms suitable for dissolving in liquid before injection.
[00183] [00183] Another aspect of the invention relates to a pharmaceutical composition comprising an SHP2 inhibitor (alone or in combination with another therapeutic agent according to the present invention) and a pharmaceutically acceptable carrier. The pharmaceutically acceptable carrier may also include an excipient, thinner, or surfactant.
[00184] [00184] Accordingly, the present invention provides compositions (for example, pharmaceutical compositions) comprising one or more SHP2 inhibitors for use in a method described herein, for example, a SHP2 monotherapy. Such compositions can comprise an SHP2 inhibitor and, for example, one or more carriers, excipients, diluents, and / or surfactants.
[00185] [00185] The present invention provides compositions (for example, pharmaceutical compositions) comprising one or more SHP2 inhibitors and one or more additional therapeutic agents for use in a method described herein, for example, a SHP2 combination therapy. Such compositions may comprise an SHP2 inhibitor, an additional therapeutic agent (for example, a TKI pathway inhibitor, a MAPK pathway, an EGFR inhibitor, an ALK inhibitor, a MEK inhibitor) and, for example , one or more carriers, excipients, thinners, and / or surfactants.
[00186] [00186] The present invention provides compositions (for example, pharmaceutical compositions) comprising one or more SHP2 inhibitors and one or more MEK inhibitors for use in a method described herein, for example, a SHP2 drug therapy combination. Such compositions may comprise an SHP2 inhibitor, a MEK inhibitor and, for example, one or more carriers, excipients, diluents, and / or surfactants. Such compositions can essentially consist of an SHP2 inhibitor, a MEK inhibitor and, for example, one or more carriers, excipients, diluents, and / or surfactants. Such compositions can consist of an SHP2 inhibitor, a MEK inhibitor and, for example, one or more carriers, excipients, diluents, and / or surfactants. For example, a non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) an SHP2 inhibitor; (b) a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212; and (c) one or more carriers, excipients, diluents, and / or surfactants. Another example
[00187] [00187] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) Compound B; (b) a MEK inhibitor selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimatertib, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212; and (c) one or more carriers, excipients, diluents, and / or surfactants. Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) Trametinib; (b) an SHP2 inhibitor selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) an SHP2 inhibitor of any compound of Formula I, Formula II, Formula
[00188] [00188] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) Compound B; (b) Trametinib (GSK1120212); and (c) one or more carriers, excipients, diluents, and / or surfactants.
[00189] [00189] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) Compound A; (b) Trametinib (GSK1120212); and (c) one or more carriers, excipients, diluents, and / or surfactants.
[00190] [00190] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) Compound C; (b) Trametinib (GSK1120212); and (c) one or more carriers, excipients, diluents, and / or surfactants.
[00191] [00191] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) a compound selected from the compounds in Table 1; (b) Trametinib (GSK1120212); and (c) one or more carriers, excipients, thinners, and / or surfactants.
[00192] [00192] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) a compound selected from the compounds in Table 2; (b) Trametinib (GSK1120212); and (c) one or more carriers, excipients, thinners, and / or surfactants.
[00193] [00193] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) SHP099; (b) Trametinib (GSK1120212); and (c) one or more carriers, excipients, diluents, and / or surfactants.
[00194] [00194] Another non-limiting example of a composition of the present invention may comprise, consist essentially of, or consist of (a) Trametinib (GSK1120212); (b) an SHP2 inhibitor of Compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula I-X, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X and (c) one or more carriers, excipients, diluents, and / or surfactants.
[00195] [00195] Compositions can be prepared according to conventional mixing, granulation or coating methods, respectively, and the present pharmaceutical compositions can contain from about 0.1% to about 99%, from about 5% about 90%, or about 1% to about 20% of the described compound by weight or volume.
[00196] [00196] The dosage regimen using the disclosed compound is selected according to a variety of factors including the type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the patient's renal or liver function; and the particular disclosed compound employed. A doctor or veterinarian skilled in the art can readily determine and prescribe the effective amount of the drug needed to prevent, contain or halt the progress of the condition.
[00197] [00197] Effective dosage amounts of an SHP2 inhibitor, when used for the indicated effects, range from about 0.5 mg to about 5000 mg as needed to treat the condition. Compositions for in vivo or in vitro use may contain about 0.5, 5, 20, 50, 75, 100, 150, 250, 500, 750, 1000, 1250, 2500, 3500, or 5000 mg of the disclosed compound , or, in a range from one quantity to another quantity in the dose list. In one embodiment, the compositions are in the form of a tablet that can be marked.
[00198] [00198] Effective dosage amounts of an ALK inhibitor, when used for the indicated effects, range from about 0.5 mg to about 5000 mg as needed to treat the condition. Compositions for in vivo or in vitro use may contain about 0.5, 5, 20, 50, 75, 100, 150, 250, 500, 750, 1000, 1250, 2500, 3500, or 5000 mg of the disclosed compound , or, in a range from one quantity to another quantity in the dose list. In one embodiment, the compositions are in the form of a tablet that can be marked.
[00199] [00199] Effective dosage amounts of an EGFR inhibitor, when used for the indicated purposes, range from about 0.5 mg to about 5000 mg as needed to treat the condition. Compositions for in vivo or in vitro use may contain about 0.5, 5, 20, 50, 75, 100, 150, 250, 500, 750, 1000, 1250, 2500, 3500, or 5000 mg of the disclosed compound , or, in a range from one quantity to another quantity in the dose list. In one embodiment, the compositions are in the form of a tablet that can be marked.
[00200] [00200] Effective dosage amounts of a MEK inhibitor, when used for the indicated purposes, range from about 0.05 mg to about 5000 mg as needed to treat the condition. Compositions for in vivo or in vitro use may contain about 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 5, 20, 50, 75, 100, 150, 250, 500, 750, 1000, 1250, 2500, 3500, or 5000 mg of the compound disclosed
[00201] [00201] The present invention also provides kits for treating a disease or disorder with an SHP2 inhibitor, one or more carriers, excipients, diluents, and / or surfactants, and a means of determining whether a sample from an individual (e.g. , a tumor sample) is likely to be sensitive for the treatment of SHP2. In some embodiments, the methods for determining comprise a method for determining whether the sample comprises an NF1LOF mutation, a KRASG12C mutation, a KRASG12D mutation, a KRASG12S mutation, and / or a KRASG12V mutation. Such methods include, but are not limited to direct sequencing, and the use of a high sensitivity diagnostic assay (CE-IVD marked), for example, as described in Domagala, et al., Pol J Pathol 3: 145-164 ( 2012), incorporated in this document by reference in its entirety, including TheraScreen PCR; AmoyDx; PNAClamp; RealQuality; EntroGen; LightMix; StripAssay; Hybcell plexA; Devyser; Surveyor; Cobas; and TheraScreen Pyro.
[00202] [00202] All US patents, US Patent Publication Application, US patent application, PCT patent application, PCT patent application publication, international patents, international patent publications and Non-patent publications referred to in this specification or listed on any Order Data Sheet are incorporated into this document by reference in its entirety. From the foregoing, it will be appreciated that, although specific modalities of the invention have been described in this document for purposes of illustration, various modifications can be made without departing from the spirit and scope of the invention.
[00203] [00203] Some modalities of this invention are Modality I, as follows:
[00204] [00204] Mode I-1. A method for the treatment of an individual with a disease or disorder comprising a cell containing a mutation encoding a KRASG12C variant, comprising providing the individual with an SHP2 inhibitor.
[00205] [00205] Mode I-1a. An SHP2 inhibitor for use in a method of treating a disease or disorder comprising a cell containing a mutation encoding the KRASG12C variant.
[00206] [00206] Mode I-1b. Use of an SHP2 inhibitor for the manufacture of a drug for the treatment of a disease or disorder comprising a cell containing a mutation encoding a variant of KRASG12C.
[00207] [00207] Mode I-2. A method for the treatment of an individual with a disease or disorder comprising a cell with a mutation encoding a loss of function of the NF1 variant (NF1LOF), comprising providing the individual with an SHP2 inhibitor.
[00208] [00208] Mode I-2a. An SHP2 inhibitor for use in a method of treating a disease or disorder comprising a cell with a mutation encoding a loss of NF1 variant function (NF1LOF).
[00209] [00209] Mode I-2b. Use of an SHP2 inhibitor for the manufacture of a drug for the treatment of a disease or disorder comprising a cell with a mutation encoding a loss of function of the NF1 variant (NF1LOF).
[00210] [00210] Mode I-3. A method for treating an individual with a disease or disorder associated with a mutation of the RAS pathway in an individual's cell that makes the cell at least partially dependent on the signaling flow through SHP2, comprising providing the individual an SHP2 inhibitor.
[00211] [00211] Mode I-3a. An inhibitor of SHP2 for use in a method of treating a disease or disorder associated with a mutation of the RAS pathway in a cell that makes the cell at least partially dependent on the signaling flow through SHP2.
[00212] [00212] Mode I-3b. Use of an SHP2 inhibitor for the manufacture of a drug for the treatment of a disease or disorder associated with a mutation of the RAS pathway in a cell that makes the cell at least partly dependent on the signaling flow through SHP2.
[00213] [00213] Mode I-4. The Method I-3 method, in which the mutation of the RAS pathway is a RAS mutation selected from a KRAS mutation, an NRAS mutation, an SOS mutation, a BRAF Class III mutation, a mutation of MEK1 Class I, a mutation of MEK1 Class II, and a mutation of NF1.
[00214] [00214] Mode I-5. Mode I-4 method, in which the KRAS mutation is selected from a KRASG12A mutation, a KRASG12C mutation, a KRASG12D mutation, a KRASG12F mutation, a KRASG12I mutation, a KRASG12L mutation , a KRASG12R mutation, a KRASG12S mutation, a KRASG12V mutation, and a KRASG12Y mutation.
[00215] [00215] Mode I-6. The I-4 Mode method, where the KRAS mutation is KRASG12C.
[00216] [00216] Mode I-7. The I-4 Mode method, in which the KRAS mutation is KRASG12A.
[00217] [00217] Mode I-8. The Mode I-4 method, in which the Class III mutation of BRAF is selected from one or more of the following amino acid substitutions in human BRAF: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I;
[00218] [00218] Mode I-9. The I-4 method, in which the NF1 mutation is a loss of function mutation.
[00219] [00219] Mode I-10. The Mode I-4 method, in which the MEK1 Class I mutation is selected from one or more of the following amino acid substitutions in human MEK1: D67N; P124L; P124S; and L177V.
[00220] [00220] Mode I-11. The Mode I-4 method, in which the MEK1 Class II mutation is selected from one or more of the following amino acid substitutions in human MEK1: ΔE51-Q58; ΔF53-Q58; E203K; L177M; C121S; F53L; K57E; Q56P; and K57N.
[00221] [00221] Mode I-12. The method of any of Modalities I-1 to I-11, also comprising providing the individual with an inhibitor of the RAS pathway.
[00222] [00222] Mode I-13. Method I-12, in which the RAS pathway inhibitor is a MAPK inhibitor.
[00223] [00223] Mode I-14. Method I-13, where the RAS pathway inhibitor is a MEK inhibitor or ERK inhibitor.
[00224] [00224] Mode I-15. The I-12 Mode method, in which the RAS pathway inhibitor is selected from one or more of Trametinib, Biminiminib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853; LY3214996; BVD523; GSK1120212; Ulixertinib, and Abemaciclibe.
[00225] [00225] Mode I-16. The method of any of Modalities I-1 to I-15, in which the disease or condition is a tumor.
[00226] [00226] Mode I-17. The I-16 Mode method, in which the tumor is selected from an NSCLC, colon cancer, esophageal cancer, rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and pancreatic cancer.
[00227] [00227] Mode I-18. A method of treating an individual with a disease associated with a loss of NF1 mutation function, comprising providing the individual with an SHP2 inhibitor.
[00228] [00228] Mode I-18a. An SHP2 inhibitor for use in a method of treating a disease associated with a loss of NF1 mutation function.
[00229] [00229] Mode I-18b. Use of an SHP2 inhibitor for the manufacture of a drug for the treatment of a disease associated with a loss of NF1 mutation function.
[00230] [00230] Mode I-19. The Mode I-18 method, in which the disease is a tumor that has cells with a loss of NF1 mutation function.
[00231] [00231] Mode I-20. Method I-19, in which the tumor is an NSCLC or melanoma tumor.
[00232] [00232] Mode I-21. The Mode I-18 method, in which the disease is selected from neurofibromatosis type I, neurofibromatosis type II, schwannomatosis, and Watson syndrome.
[00233] [00233] Mode I-22. The method of any of Modes I-18 to I-21, also comprising providing the individual with an inhibitor of the RAS pathway.
[00234] [00234] Mode I-23. The I-22 Mode method, in which the RAS pathway inhibitor is selected from one or more of Trametinib, Biimetinib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853; LY3214996; BVD523;
[00235] [00235] Mode I-24. A method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from an individual's cell is classified as a KRAS mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as a KRASG12C mutant, a KRASG12D mutant, a KRASG12S mutant, or a KRASG12V mutant.
[00236] [00236] Mode I-24a. An SHP2 inhibitor for use in a method of treating a tumor-bearing individual, wherein the tumor comprises a KRASG12C mutation, a KRASG12D mutation, a KRASG12S mutation, or a KRASG12V mutation.
[00237] [00237] Mode I-24b. A method of selecting an individual with a tumor for treatment: wherein the method comprises determining in vitro whether a cell obtained from the individual's biological sample is classified as a KRAS mutant; and wherein the individual is selected for treatment if the biological sample is classified as a KRASG12C mutant, a KRASG12D mutant, a KRASG12S mutant, or a KRASG12V mutant.
[00238] [00238] I-24c mode. An SHP2 inhibitor for use in a method for treating a tumor, wherein the method comprises: (a) determining whether a biological sample obtained from the individual's cell is classified as a KRAS mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a KRASG12C mutant, a KRASG12D mutant, a KRASG12S mutant, or a mutant of
[00239] [00239] Mode I-25. A method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as an NF1LOF mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as an NF1LOF mutant.
[00240] [00240] Mode I-25a. An SHP2 inhibitor for use in a method of treating a tumor-bearing individual, wherein the tumor comprises an NF1LOF mutation.
[00241] [00241] Mode I-25b. A method of selecting an individual with a tumor for treatment: wherein the method comprises determining in vitro whether a cell obtained from the individual's biological sample is classified as an NF1LOF mutant; and where the individual is selected for treatment if the biological sample is classified as an NF1LOF mutant.
[00242] [00242] Mode I-25c. An SHP2 inhibitor for use in a method for treating a tumor, wherein the method comprises: (a) determining whether a biological sample obtained from an individual's cell is classified as an NF1LOF mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as an NF1LOF mutant.
[00243] [00243] Mode I-26. A method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as a BRAF Class 3 mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a BRAF Class mutant
[00244] [00244] Mode I-26a. An SHP2 inhibitor for use in a method of treating an individual with a tumor, wherein the tumor comprises a BRAF Class 3 mutation.
[00245] [00245] Mode I-26b. A method of selecting an individual with a tumor for treatment: wherein the method comprises determining in vitro whether a cell obtained from the individual's biological sample is classified as a BRAF Class 3 mutant; and where the individual is selected for treatment if the biological sample is classified as a BRAF Class mutant
[00246] [00246] Mode I-26c. An SHP2 inhibitor for use in a method for treating a tumor, wherein the method comprises: (a) determining whether a biological sample obtained from an individual's cell is classified as a BRAF Class 3 mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a BRAF Class mutant
[00247] [00247] Mode I-27. A method for treating an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as a MEK1 Class I mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class I mutant.
[00248] [00248] Mode I-27a. An SHP2 inhibitor for use in a method of treating a tumor-bearing individual, wherein the tumor comprises a MEK1 Class I mutation.
[00249] [00249] Mode I-27b. A method of selecting an individual with a tumor for treatment: wherein the method comprises determining in vitro whether a cell obtained from the individual's biological sample is classified as a MEK1 Class I mutant; and where the individual is selected for treatment if the biological sample is classified as a MEK1 Class I mutant.
[00250] [00250] Mode I-27c. An SHP2 inhibitor for use in a method for treating a tumor, wherein the method comprises: (a) determining whether a biological sample obtained from the individual's cell is classified as a MEK1 Class I mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class I mutant.
[00251] [00251] Mode I-28. A method for the treatment of an individual with a tumor comprising: (a) determining whether a biological sample obtained from the individual is classified as a MEK1 Class II mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class II mutant.
[00252] [00252] Mode I-28a. An SHP2 inhibitor for use in a method of treating a tumor-bearing individual, wherein the tumor comprises a MEK1 Class II mutation.
[00253] [00253] Mode I-28b. A method of selecting an individual with a tumor for treatment: wherein the method comprises determining in vitro whether a cell obtained from the individual's biological sample is classified as a MEK1 Class II mutant; and where the individual is selected for treatment if the biological sample is classified as a MEK1 Class II mutant.
[00254] [00254] Mode I-28c. An SHP2 inhibitor for use in a method for treating a tumor, wherein the method comprises: (a) determining whether a biological sample obtained from an individual's cell is classified as a MEK1 Class II mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class II mutant.
[00255] [00255] Mode I-29. A method for the treatment or prevention of drug resistance in an individual receiving the administration of an inhibitor of the RAS pathway, comprising administering to the individual an SHP2 inhibitor.
[00256] [00256] Mode I-29a. An SHP2 inhibitor for use in a method for the treatment or prevention of drug resistance in an individual receiving administration of an inhibitor of the RAS pathway.
[00257] [00257] Mode I-29b. Use of an SHP2 inhibitor for the manufacture of a drug for the treatment or prevention of drug resistance in an individual receiving the administration of an inhibitor of the RAS pathway.
[00258] [00258] Mode I-30. Method I-29, in which the individual comprises a tumor containing cells with an NF1LOF mutation.
[00259] [00259] Mode I-31. Method I-29 or I-30, wherein the individual comprises a tumor containing a KRASG12C mutation, KRASG12D mutation, KRASG12A mutation, KRASG12S mutation, or KRASG12V mutation.
[00260] [00260] Mode I-32. The method of any of Modalities I-29 to I-31, wherein the RAS pathway inhibitor is a MEK inhibitor.
[00261] [00261] Mode I-33. The I-32 Mode method, in which the MEK inhibitor is selected from one or more of Trametinib
[00262] [00262] Mode I-34. The method of any of Modalities I-29 to I-31, wherein the inhibitor of the RAS pathway is an ERK inhibitor.
[00263] [00263] Mode I-35. Mode I-34 method, wherein the ERK inhibitor is selected from any ERK inhibitor known in the art; LY3214996; Ulixertinib; and BVD523.
[00264] [00264] Mode I-36. The method of any of the preceding modalities, in which the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Form mule X; (vi) TNO155; (vii) an SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described herein; (x) a compound of Table 2, described herein; and (xi) a combination thereof.
[00265] [00265] Mode I-37. Combination therapy comprising an inhibitor of the RAS pathway and an inhibitor of SHP2.
[00266] [00266] Mode I-38. Mode I-37 combination therapy, in which the RAS pathway inhibitor is a MEK inhibitor.
[00267] [00267] Mode I-39. Mode I- combination therapy
[00268] [00268] Mode I-40. Mode I-37 combination therapy, where the RAS pathway inhibitor is the KRASG12C specific ARS-853 inhibitor.
[00269] [00269] Mode I-41. Combination therapy of any of Modalities I-37 to I-40, wherein the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described in this document; (x) a compound of Table 2, described herein; and (xi) a combination thereof.
[00270] [00270] Mode I-42. Combination therapy of any of Modalities I-37 to I-41, for use in the treatment of a tumor.
[00271] [00271] Mode I-43. Combination therapy of Modality I-42, in which the tumor is selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myeloplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer;
[00272] [00272] Mode I-44. A pharmaceutical composition comprising an inhibitor of the RAS pathway, an inhibitor of SHP2, and one or more pharmaceutically acceptable carrier, excipient, diluent, and / or surfactant.
[00273] [00273] Mode I-45. The pharmaceutical composition of Modality I-44, wherein the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated in this document
[00274] [00274] Mode I-46. The pharmaceutical composition of Modality I-44 or I-45, wherein the RAS pathway inhibitor is selected from one or more of Trametinib (GSK1120212) Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); GSK1120212, Ulxertinib; and Abemaciclibe.
[00275] [00275] Mode I-47. The pharmaceutical composition of any of Modalities I-44 to I-46, for use in the treatment of a tumor.
[00276] [00276] Mode I-48. The pharmaceutical composition of Modality I-47, in which the tumor is selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelo-monocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; cancer of the central nervous system (eg primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; urinary tract cancer; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aerodigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; meningeal cancer; vulvar cancer and melanoma.
[00277] [00277] Mode I-49. The method of any one of Modalities from I-16, I-18, I-19, I-24 to I-28, and I-30 to I-36, in which the tumor is selected from system tumors hematopoietic and lymphoid; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; cancer of the central nervous system (eg, primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; cancer of the urinary tract; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aerodigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; meningeal cancer; vulvar cancer and melanoma.
[00278] [00278] Mode I-50. A method of inhibiting the growth or proliferation of a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent
[00279] [00279] Mode I-50a. An SHP2 inhibitor for use in a method of inhibiting the growth or proliferation of a cell containing a mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2.
[00280] [00280] Mode I-50b. Use of an SHP2 inhibitor for the manufacture of a drug to inhibit the growth or proliferation of a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the flow signaling through SHP2.
[00281] [00281] Mode I-51. A method of inhibiting the accumulation of RAS-GTP in a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor.
[00282] [00282] Mode I-51a. An SHP2 inhibitor for use in a method of inhibiting the accumulation of RAS-GTP in a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the signal flow through - through SHP2.
[00283] [00283] Mode I-51b. Use of an SHP2 inhibitor for the manufacture of a drug to inhibit the accumulation of RAS-GTP in a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the flow signaling through SHP2.
[00284] [00284] Mode I-52. A method for killing a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor.
[00285] [00285] Mode I-52a. An SHP2 inhibitor for use in a method of killing a cell by contacting the RAS pathway mutation, in which the RAS pathway mutation makes the cell at least partially dependent on the signal flow through SHP2.
[00286] [00286] Mode I-52b. Use of an SHP2 inhibitor for the manufacture of a drug to kill a cell by contacting the mutation of the RAS pathway, in which the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2.
[00287] [00287] Mode I-53. The method of any of Modalities I-50 to I-52, wherein the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in the international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated herein by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described herein; (x) a composite of Table 2, described in this document; and (xi) a combination thereof.
[00288] [00288] Mode I-54. The method of any of Modalities I-50 to I-53, in which the RAS mutation is selected from a KRAS mutation, an NRAS mutation, an HRAS mutation, an SOS mutation, a BRAF mutation Class III, and a loss of NF1 mutation function.
[00289] [00289] Mode I-55. The I-54 Mode method, wherein the KRAS mutation is selected from a KRASG12A mutation, a KRASG12C mutation, a KRASG12D mutation, a KRASG12F mutation, a KRASG12I mutation, a KRASG12L mutation, a mutation of KRASG12R, a KRASG12S mutation, a KRASG12V mutation, and a KRASG12Y mutation.
[00290] [00290] Mode I-56. The I-54 Mode method, where the KRAS mutation is KRASG12C.
[00291] [00291] Mode I-57. Method I-54, where the KRAS mutation is KRASG12A.
[00292] [00292] Mode I-58. The I-54 Mode method, in which the BRAF Class 3 mutation is selected from one or more of the following amino acid substitutions in human BRAF: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D; G596R and A762E.
[00293] [00293] Mode I-59. The method of any of Modalities I-50 to I-58, also comprising contacting the cell with an RAS pathway inhibitor.
[00294] [00294] I-60 modality. Method I-59, in which the RAS pathway inhibitor is a MAPK inhibitor.
[00295] [00295] Mode I-61. The I-60 Mode method, in which the RAS pathway inhibitor is an MEK inhibitor or ERK inhibitor.
[00296] [00296] Mode I-62. The I-61 Mode method, in which the RAS pathway inhibitor is selected from one or more of Trametinib, Biminiminib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853; LY3214996; BVD523; GSK1120212; Ulixertinib; and Abemaciclibe.
[00297] [00297] Mode I-63. The method of any of Modalities from I-1 to I-36, I-49 to I-62 also comprises contacting the cell with an SOS inhibitor.
[00298] [00298] I-64 mode. The I-63 Mode method, in which the SOS inhibitor is administered to a cell comprising higher than normal SOS levels or SOS activity.
[00299] [00299] Mode I-65. Mode I-16 method, in which the tumor is from an NSCLC tumor.
[00300] [00300] I-66 modality. The Mode I-16 method, in which the tumor is a colon cancer tumor.
[00301] [00301] Mode I-67. The I-16 method, in which the tumor is an esophageal cancer tumor.
[00302] [00302] I-68 modality. Mode I-16 method, in which the tumor is a rectal cancer tumor.
[00303] [00303] Mode I-69. The I-16 method, in which the tumor is a JMML tumor.
[00304] [00304] I-70 modality. The I-16 method, in which the tumor is a breast cancer tumor.
[00305] [00305] Mode I-71. The I-16 method, in which the tumor is a melanoma tumor.
[00306] [00306] Mode I-72. Mode I-16 method, in which the tumor is a Scwannoma tumor.
[00307] [00307] Mode I-73. Method I-16, where the tumor is a pancreatic cancer tumor.
[00308] [00308] Mode I-74. The method of any of the preceding modalities, in which the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV,
[00309] [00309] Mode I-75. A method of inhibiting the growth of a tumor cell, comprising contacting the tumor cell with a combination therapy comprising a MEK inhibitor and an SHP2 inhibitor.
[00310] [00310] Mode I-75a. Combination therapy comprising a MEK inhibitor and an SHP2 inhibitor for use in a method of inhibiting the growth of a tumor cell.
[00311] [00311] Mode I-75b. Use of a combination therapy comprising a MEK inhibitor and an SHP2 inhibitor for the manufacture of a drug for inhibiting the growth of a tumor cell.
[00312] [00312] Mode I-76. The I-75 Mode method, in which the MEK inhibitor is selected from one or more of Trametinib (GSK1120212), Selumetinib (AZD6244), Cobimetinib (GDC-0973 / XL581), Binimetinibe, Vemurafenibe, Pimasertibe, TAK733, RO4987655 ( CH4987655), CI-1040; PD-0325901, CH5126766, MAP855, Refametinib (RDEA 119 / BAY 86-9766), RO5126766, AZD8330 (ARRY-424704 / ARRY-704), and GSK1120212.
[00313] [00313] Mode I-77. Method I-75 or I-76, where the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula
[00314] [00314] Mode I-78. The method of any of Modalities I-75 to I-77, wherein the MEK inhibitor is Trametinib (GSK1120212).
[00315] [00315] Mode I-79. The method of any of Modalities I-75 to I-78, wherein the SHP2 inhibitor is Compound B.
[00316] [00316] I-80 mode. Method I-75, where the MEK inhibitor is Trametinib (GSK1120212) and the SHP2 inhibitor is Compound B.
[00317] [00317] Mode I-81. The method of any of Modalities from I-75 to I-80, wherein the tumor cell is a cell of a tumor selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (including
[00318] [00318] Mode I-82. The method of any of Modalities I-75 to I-80, wherein the tumor is an NSCLC tumor.
[00319] [00319] Mode I-83. The method of any of Modalities I-75 to I-82, in which contact occurs in vivo in an individual.
[00320] [00320] Mode I-84. Method I-83, in which the individual is a human.
[00321] [00321] Mode I-85. The method of any of Modalities I-75 to I-84, in which the contact of a tumor cell with the combination therapy comprising the MEK inhibitor and the SHP2 inhibitor results in an inhibition of the growth of the tumor that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of the respective MEK and SHP2 inhibitors separately.
[00322] [00322] Mode I-86. The method of any of Modalities I-75 to I-85, in which the MEK inhibitor and the SHP2 inhibitor do not contact the tumor cell simultaneously.
[00323] [00323] Mode I-87. The method of any of Modalities I-75 to I-85, wherein the MEK inhibitor and the SHP2 inhibitor contact the tumor cell simultaneously.
[00324] [00324] Mode I-88. The method of any of the Modalities
[00325] [00325] Mode I-89. Method I-88, wherein the administration of the MEK inhibitor precedes the administration of the SHP2 inhibitor.
[00326] [00326] Mode I-90. Method I-88, wherein the administration of the SHP2 inhibitor precedes the administration of the MEK inhibitor.
[00327] [00327] Mode I-91. Method I-88, wherein the administration of the SHP2 inhibitor and the administration of the MEK inhibitor occurs simultaneously.
[00328] [00328] Mode I-92. Mode I-91 method, in which the SHP2 inhibitor and the MEK inhibitor are administered as a single pharmaceutical composition.
[00329] [00329] Mode I-93. The Mode I-91 method, in which the SHP2 inhibitor and the MEK inhibitor are administered as separate pharmaceutical compositions.
[00330] [00330] Mode I-94. The method of any of Modalities I-75 to I-93, wherein the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[00331] [00331] Mode I-95. A method of inhibiting the growth of a tumor cell, comprising contacting the tumor cell with a combination therapy comprising trametinib (GSK1120212) and Compound B.
[00332] [00332] Mode I-95a. Combination therapy comprising trametinib (GSK1120212) and Compound B for use in a method of inhibiting the growth of a tumor cell.
[00333] [00333] Mode I-95b. Use of a combination therapy comprising trametinib (GSK1120212) and Compound B for the manufacture of a drug to inhibit the growth of a cell
[00334] [00334] Mode I-96. Method I-95, in which the tumor cell is from an NSCLC tumor.
[00335] [00335] Mode I-97. Method I-95 or I-96, in which contact occurs in vivo in an individual.
[00336] [00336] Mode I-98. The I-97 Mode method, in which the individual is a human.
[00337] [00337] Mode I-99. The method of any of Modalities I-95 to I-98, in which the contact of a tumor cell with the combination therapy comprising trametinib (GSK1120212) and Compound B results in an inhibition of the growth of the tumor that it is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound B separately.
[00338] [00338] I-100 mode. The method of any of Modes I-95 to I-99, in which the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[00339] [00339] Mode I-101. A method of treating a subject with a tumor, comprising contacting a tumor cell in the tumor in the subject with a combination therapy comprising an MEK inhibitor and an SHP2 inhibitor.
[00340] [00340] Mode I-101a. Combination therapy comprising a MEK inhibitor and an SHP2 inhibitor for use in a treatment method for an individual with a tumor.
[00341] [00341] Mode I-101b. Use of a combination therapy comprising an MEK inhibitor and an SHP2 inhibitor for the manufacture of medication for the treatment of an individual with a tumor.
[00342] [00342] Mode I-102. Mode I-101 method, in which the MEK inhibitor is selected from one or more of Trametinib
[00343] [00343] Mode I-103. Method I-101 or I-102, where the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) an SHP2 inhibitor described in international PCT application PCT / US2017 / 041577 (WO2018013597), incorporated in this document by reference in its entirety; (viii) Compound C; (ix) a compound of Table 1, described herein; (x) a composite of Table 2, described in this document; and (xi) a combination of them.
[00344] [00344] Mode I-104. Method I-101, where the MEK inhibitor is Trametinib (GSK1120212).
[00345] [00345] Mode I-105. The method of any of Modalities I-101 to I-104, wherein the SHP2 inhibitor is Compound B.
[00346] [00346] Mode I-106. Method I-101, where the MEK inhibitor is Trametinib (GSK1120212) and the SHP2 inhibitor is Compound B.
[00347] [00347] Mode I-107. The method of any of Modalities I-101 to I-106, in which the tumor cell is a cell of a tumor selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia;
[00348] [00348] Mode I-108. The method of any of Modalities I-101 to I-107, wherein the tumor cell is from an NSCLC tumor.
[00349] [00349] Mode I-109. The method of any of Modalities I-101 to I-108, in which contact occurs in vivo in an individual.
[00350] [00350] Mode I-110. The I-109 Mode method, in which the individual is a human.
[00351] [00351] Mode I-111. The method of any of Modalities I-101 to I-110, wherein contact of a tumor cell with combination therapy comprising the MEK inhibitor and the SHP2 inhibitor results in an inhibition of tumor growth that it is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of the respective MEK and SHP2 inhibitors separately.
[00352] [00352] I-112 mode. The method of any of Modalities I-101 to I-111, in which the MEK inhibitor and the SHP2 inhibitor do not contact the tumor cell simultaneously.
[00353] [00353] Mode I-113. The method of any of Modalities I-101 to I-111, wherein the MEK inhibitor and the SHP2 inhibitor contact the tumor cell simultaneously.
[00354] [00354] Mode I-114. The method of any of Modalities I-111 to I-113, in which contact is through administration of the MEK inhibitor and the SHP2 inhibitor to the individual.
[00355] [00355] Mode I-115. Method I-114, wherein the administration of the MEK inhibitor precedes the administration of the SHP2 inhibitor.
[00356] [00356] Mode I-116. Method I-114, wherein the administration of the SHP2 inhibitor precedes the administration of the MEK inhibitor.
[00357] [00357] Mode I-117. Method I-114, wherein the administration of the SHP2 inhibitor and the administration of the MEK inhibitor occurs simultaneously.
[00358] [00358] Mode I-118. Method I-117, in which the SHP2 inhibitor and the MEK inhibitor are administered as a single pharmaceutical composition.
[00359] [00359] Mode I-119. Mode I-117 method, in which the SHP2 inhibitor and the MEK inhibitor are administered as separate pharmaceutical compositions.
[00360] [00360] Mode I-120. The method of any of Modalities I-101 to I-119, in which the treatment inhibits the growth of the tumor cell.
[00361] [00361] Mode I-121. The Mode I-120 method, in which the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[00362] [00362] I-122 modality. A method of treating an individual with a tumor, comprising contacting a tumor tumor cell in the individual with a combination therapy comprising trametinib (GSK1120212) and Compound B.
[00363] [00363] Mode I-122a. Combination therapy comprising trametinib (GSK1120212) and Compound B for use in a method of treating an individual with a tumor.
[00364] [00364] Mode I-122b. Use of a combination therapy comprising trametinib (GSK1120212) and Compound B for the manufacture of a drug for the treatment of an individual with a tumor.
[00365] [00365] Mode I-123. Method I-122, in which the tumor cell is from an NSCLC tumor.
[00366] [00366] Mode I-124. Method I-122 or I-123, in which contact occurs in vivo in an individual.
[00367] [00367] Mode I-125. Method I-124, in which the individual is a human.
[00368] [00368] Mode I-126. The method of any of Modalities I-122 to I-125, in which contact of a tumor cell with combination therapy comprising trametinib (GSK1120212) and Compound B results in an inhibition of tumor growth that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound B separately.
[00369] [00369] Mode I-127. The method of any of Modalities I-122 to I-126, wherein the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[00370] [00370] I-128 mode. The method of any of the Modali-
[00371] [00371] Mode I-129. Combination therapy of any of Modalities I-37 to I-43, wherein the SHP2 inhibitor is Compound C.
[00372] [00372] Mode I-130. The pharmaceutical composition of any of Modalities I-44 to I-48, wherein the SHP2 inhibitor is Compound C.
[00373] [00373] Mode I-131. A method of inhibiting the growth of a tumor cell, comprising contacting the tumor cell with a combination therapy comprising trametinib (GSK1120212) and Compound C.
[00374] [00374] Mode I-131a. Combination therapy comprising trametinib (GSK1120212) and Compound C for use in a method of inhibiting the growth of a tumor cell.
[00375] [00375] Mode I-131b. Use of a combination therapy comprising trametinib (GSK1120212) and Compound C for the manufacture of a drug for inhibiting the growth of a tumor cell.
[00376] [00376] Mode I-132. Method I-131, in which the tumor cell is from an NSCLC tumor.
[00377] [00377] Mode I-133. Method I-131 or I-132, in which contact occurs in vivo in an individual.
[00378] [00378] Mode I-134. Method I-133, in which the individual is a human.
[00379] [00379] Mode I-135. The method of any of Modalities I-131 to I-134, wherein contact of a tumor cell with combination therapy comprising trametinib (GSK1120212) and Compound C results in an inhibition of tumor growth that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound C separately.
[00380] [00380] Mode I-136. The method of any of Modalities I-131 to I-135, wherein the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[00381] [00381] Mode I-137. A method of treating a subject with a tumor, comprising contacting a tumor tumor cell in the subject with a combination therapy comprising trametinib (GSK1120212) and Compound C.
[00382] [00382] Mode I-137a. Combination therapy comprising trametinib (GSK1120212) and Compound C for use in a treatment method for an individual with a tumor.
[00383] [00383] Mode I-137b. Use of a combination therapy comprising trametinib (GSK1120212) and Compound C for the manufacture of a drug for the treatment of an individual with a tumor.
[00384] [00384] Mode I-138. Method I-137, in which the tumor cell is from an NSCLC tumor.
[00385] [00385] Mode I-139. Method I-137 or I-138, in which contact occurs in vivo in an individual.
[00386] [00386] Mode I-140. Method I-139, in which the individual is a human.
[00387] [00387] Mode I-141. The method of any of Modalities I-137 to I-140, wherein contact of a tumor cell with combination therapy comprising trametinib (GSK1120212) and Compound C results in an inhibition of tumor growth that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound C separately.
[00388] [00388] Mode I-142. The method of any of Modali-
[00389] [00389] Mode I-143. The method of any of Modalities I-1 to I-36 and I-49, comprising administering an effective amount of the SHP2 inhibitor.
[00390] [00390] Mode I-144. The method of any of Modalities I-50 to I-128 and I-131 to I-142, comprising contacting the cell with an effective amount of the SHP2 inhibitor.
[00391] [00391] Mode I-145. Combination therapy of any of Modes I-37 to I-43, I-75a, I-95a, I-101a, I-122a, I-129, I-131a, and I-137a, comprising an effective amount of the SHP2 inhibitor.
[00392] [00392] Mode I-146. The pharmaceutical composition of any of Modalities I-44 to I-48 and I-130, comprising an effective amount of the SHP2 inhibitor.
[00393] [00393] Mode I-147. The SHP2 inhibitor for use in a method according to any of Modalities I-1a, I-2a, I-3a, I-18a, I-24a, I-24c, I-25a, I-25c, I-26a, I-26c, I-27a, I-27c, I-28a, I-28c, I-29a, I-50a, I-51a, and I-52a, where the SHP2 inhibitor is used in an effective amount.
[00394] [00394] Mode I-148. The use of a SHP2 inhibitor according to any of Modalities I-1b, I-2b, I-3b, I-18b, I-29b, I-50b, I-51b, I-52b, I-, in that the SHP2 inhibitor is used in an effective amount.
[00395] [00395] Mode I-149. The method of any of Modalities I-1 to I-36 and I-49, comprising administering a therapeutically effective amount of the SHP2 inhibitor.
[00396] [00396] Mode I-150. The method of any of Modalities I-50 to I-128 and I-131 to I-142, comprising contacting the cell with a therapeutically effective amount of the SHP2 inhibitor.
[00397] [00397] Mode I-151. Combination therapy of any of Modalities I-37 to I-43, I-75a, I-95a, I-101a, I-122a, I-129, I-131a, and I-137a, comprising a therapeutically amount efficacy of the SHP2 inhibitor.
[00398] [00398] Mode I-152. The pharmaceutical composition of any of Modes I-44 to I-48 and I-130, comprising a therapeutically effective amount of the SHP2 inhibitor.
[00399] [00399] Mode I-153. The SHP2 inhibitor for use in a method according to any of Modalities I-1a, I-2a, I-3a, I-18a, I-24a, I-24c, I-25a, I-25c, I-26a, I-26c, I-27a, I-27c, I-28a, I-28c, I-29a, I-50a, I-51a, and I-52a, where the SHP2 inhibitor is used in a therapeutically effective amount.
[00400] [00400] Mode I-154. The use of a SHP2 inhibitor according to any of Modalities I-1b, I-2b, I-3b, I-18b, I-29b, I-50b, I-51b, I-52b, I-, in that the SHP2 inhibitor is used in a therapeutically effective amount. EXAMPLES
[00401] [00401] The invention is also illustrated by the following examples and synthesis examples, which should not be construed as limiting this invention in scope or spirit to the specific procedures in this document described. It should be understood that the examples are provided to illustrate certain modalities and that no limitations on the scope of the invention are thus intended. It should also be understood that the resource can be used for various other modalities, modifications, and equivalents of them that can be suggested to those skilled in the art, without departing from the spirit of the present invention and / or the scope of the claims attached. Example 1. Effect of SHP2s allosteric inhibitor on cancer cells containing RAS mutations and dependent on GTP reload on KRAS Objective:
[00402] [00402] The effect of SHP2s allosteric inhibitor, Compound A or Compound B on activation of the RAS pathway and tumor cell growth in vitro, and in vivo, was evaluated in cancer cell lines with mutations of the RAS pathway , including distinct mutations in KRAS, NF1, and BRAF that confer cell dependence on GTP reload over RAS. Methods:
[00403] [00403] To assess cell viability in 3D culture, cells in the logarithmic growth phase were seeded in growth medium containing 0.65% methyl cellulose at an ideal seeding density. The cells were incubated overnight before treatment with different concentrations of the test article. The cells were cultured for an additional seven days and cell viability assessed using the CellTiterGlo ™ reagent (CTG), according to the manufacturer's instructions. In some cases, the cells were cultured in 3D culture as spheroids. In synthesis, 2500 cells / well were seeded in 96 wells of ultra-low round base fixation (Corning) in growth medium supplemented with 10% fetal bovine serum and 1% penicillin / streptomycin, and allowed to form spheroids for 72 hours. hours at 37C in 5% CO2. The spheroid formation was confirmed visually, and the spheroids were treated in duplicate with 3-fold serial dilutions of Compound B in complete growth medium (final concentration of DMSO = 0.1%). After exposure to the drug for five days, cell viability in spheroids was determined using the CellTiter-Glo assay kit. H1838 cells were seeded at 5 x 103 cells per well of a 12 well plate. After one day in culture, the cells were treated with the test article, which was then replenished every three days.
[00404] [00404] To determine the potency of test articles to inhibit phosphorylation of kinases 1 and 2 related to extracellular signal (ERK1 / 2) to Thr202 / Tyr204 (p-ERK), respective cell lines were cultured under standard conditions 2D culture. The cells were seeded at ~ 20 x 103 cells per well and after incubation overnight they were washed with serum-free medium. The cells were then incubated for one hour with increasing concentrations of the test article in serum-free medium containing 0.2% BSA before the end of the assay and evaluation of pERK levels in cell lysates by the AlphaLisa SureFire Ultra kit conducted according to the manufacturer's instructions.
[00405] [00405] To determine the effects of small molecules on activated RAS-GTPase levels, cell lines of interest were grown under standard 2D culture conditions. The cells were seeded and after incubation overnight incubated at 37 ° C with vehicle (DMSO) or test articles. After an appropriate incubation period, the cells were washed and cell lysis buffer added to prepare a cell lysate. The levels of Ras-GTP in the lysates were determined using affinity purification of a Raf-RBD complex (Ras-binding Raf domain) / GTP-Ras. In one method, the Pierce Active Ras Pulldown and Detection Kit was used. In synthesis, clarified lysates (500 µg of total protein, quantified by BCA) were mixed with the glutathione resin, which was preincubated with GST-Raf-RBD. The mixture was vortexed and incubated at 4 ° C for 1 hour with gentle rocking. The resin was washed three times with lysis buffer and bound Ras-GTP eluted by the addition of 2X reduction sample buffer. The eluted proteins were separated by SDS-PAGE using a 4 to 15% Tris-glycine gel (BioRad). The proteins were transferred to a nitrocellulose membrane for Western blotting using an anti-Ras antibody (Thermofisher, 1: 200) and a secondary anti-mouse antibody Liquor IRDye-800 (1: 20,000). The Odyssey CLx liquor was used for visualization.
[00406] [00406] The effects of a SHP2 inhibitor on tumor cell growth in vivo were evaluated in the NSCLC H358 KRasG12C xenograft model using CB.17 SCID (8 to 12 weeks of age) or Balb / c (6 to 8 weeks old) females. The mice were implanted with H358 tumor cells in 50% Matrigel (1x107 and 5x106 for SCID and Balb / c mice, respectively) subcutaneously in the flank. As soon as the tumors reached an average size of ~ 200 mm3, the mice were randomized to treatment groups and the administration of test article or vehicle (50 mM acetate buffer, pH 4.6 containing 10% captisol, unless otherwise indicated) started. Body weight and tumor volume (using calipers) were measured twice a week until the end of the study. Compound A or Compound B were administered by oral gavage daily. The positive control, paclibutel (30 mg / kg iv) in 5% ethanol, 5% cremophor EL, in 5% dextrose in deionized water was administered once every five days. Trametinib (1 mg / kg PO in 0.5% Methylcellulose + 0.5% Tween 80) was administered by oral gavage daily. The end of the study was defined as an average tumor volume of 2000 mm3 in the control group or 22 days, whichever comes first. The average tumor volume data are reported for all animals that remained in the study.
[00407] [00407] Similar methods were used to assess the efficacy of test articles in the pancreatic MiaPaca-2 xenograft model KRasG12C. Balb / c nude mice (6 to 8 weeks old) were implanted
[00408] [00408] By a small panel of KRAS mutant cell lines, the presence of a KRASG12C mutation enriched the sensitivity to 3D growth inhibition (defined as a CTG IC50 <10 µM) by an SHP2 inhibitor (Compound A) (Table 3; Ref # 1 Crown Bio Project # E3105-U1609). Table 3. Inhibitory potency (IC50 values) of allosteric inhibitor of SHP2 Compound A on cell viability (when measured using CTG) of a panel of KRAS mutant cell lines cultured in 3D culture.
[00409] [00409] Consistent with and extending these observations, Compound B was a potent growth inhibitor (CTG IC50 ranges from 0.4 to 7.87 µM) in the 9/10 KRASG12C strains, 2/2 KRASG12A strains, li
[00410] [00410] Such protein involved in the RAS pathway that can confer sensitivity to SHP2 signaling due to its absence or reduced function is NF1. NF1 is a RAS-GAP protein that facilitates the hydrolysis of RAS-GTP in its inactive RAS-GTP form, thereby inactivating RAS. NF1 is a tumor suppressor, and loss of function mutations in this gene result in accumulation of RAS-GTP and signaling downstream leading to cell growth in various human cancers (Nissan, Krauthammer, Redig). Therefore, we tested whether SHP2 inhibition can effectively prevent signaling of the RAS pathway and cell culture in NF1LOF models.
[00411] [00411] Similar to the observations in the KRASG12C strain, Compound A also inhibited Ras-GTP and potentially inhibited p-ERK and cell culture (crystal violet stain) in HSC38 NSCLC NF1LOF cells in vitro (Figure 5). In addition, consistent with this, proliferation of 3/4 NF1LOF cell lines exhibited sensitivity to Compound B (FIG. 19A-B). NF1LOF cell lines were prepared and treated with experimental or control agents as described above in this Example and the levels of RAS-GTP and pERK were measured as previously described above. Treatment of NCI-H1838 (lung, NF1N184fs) and MeWo (melanoma, NF1Q1336 *) cell lines with Compound B led to under-regulation of RAS-GTP levels and suppression of pERK (FIG. 19C-D), demonstrating that the inhibition of SHP2 can attenuate the accumulation of RAS-GTP, and consequent activation of the RAS / MAPK pathway that results in loss of NF1. Collectively, these data indicate that NF1 loss is a second class of downstream oncogenic mutation that can be targeted by inhibiting RAS-GTP load by inhibiting SHP2. No SHP2 inhibiting effect was observed in YUHEF (NF1Q853 * / FS-indel), melanoma cell line (FIG. 19A-B). The genomic landscape of this strain reflects that of clinical metanoma populations in which NF1LOF mutations often co-occur in cancers that contain co-occurring mutations in genes in the RAS / MAPK pathway, some of which may confer resistance to SHP2 inhibition. {Krauthammer, 2015 # 2476; Nissan, 2014 # 2426}. Specifically, YUHEF carries three mutations SOS1 and RAF1P261L, a mutation of the MAPK pathway activating Noonan Syndrome previously described {Kobayashi, 2010 # 2532; Krauthammer, 2015 # 2476}.
[00412] [00412] Together, these results suggest that an SHP2 inhibitor can attenuate RAS-MAPK signaling in cell lines
[00413] [00413] The effect of a SHP2 inhibitor on KRASG12C tumor cell growth in vivo was evaluated in the NSCLC H358 xenograft and pancreatic MiaPaca-2 models. Oral administration of Compound A or Compound B, respectively, produced a dose-dependent decrease in tumor volume in vivo in the H358 xenograft model (Figures 6 and 7). At a dose of 30 mg / kg PO qd of Compound A, the reduction in tumor volume was of an order of magnitude similar to that of the comparator paclitaxel, a well-known non-targeted chemotherapeutic agent. Similarly, the SHP2 inhibitor Compound B produced a dose-dependent decrease in tumor volume in both the H358 KRASG12C and MiaPaca-2 KRASG12C xenograft models (Figures 7 and 8). At a dose of 30 mg / kg PO qd of Compound B the reduction in tumor volume was of an order of magnitude similar to that of the MEK inhibitor trametinbe (1 m / kg PO) in model H358 but it was greater than trametinib (1 m / kg PO) in the MiaPaca-2 model.
[00414] [00414] Similarly, Compound A was also a potent inhibitor of p-ERK (Figure 5B) and cell culture (crystal violet stain) (Figure 5C) in NSCLC NF1LOF H1838 cells in vitro.
[00415] [00415] Another protein that is involved in signaling via the RAS pathway in serine / threonine kinase BRAF, and BRAF mutations are commonly present in human cancer, and such mutations are oncogenic because of their hyperactivation resulting from pERK signaling. Three classes of oncogenic BRAF mutations were reported. Class I mutations occur in V600 and result in monomers
[00416] [00416] We analyzed a representative panel of cell lines carrying oncogenic BRAF mutations in these three classes for sensitivity to SHP2 inhibition.
[00417] [00417] First, we confirm that BRAF Class I mutations were refractory to SHP2 inhibition. Consistent with the mechanical structure, we observed that Compound B did not suppress the proliferation and levels of RAS-GTP and pERK in A375 cells (FIG. 13A-C). Similar results were observed in a cell line carrying a BRAF Class II mutation, NCI-H1755 (lung, BRAFG469A), which displays the formation and signaling of RAS-dependent homodimer (Yao 2015) (FIG. 13A -Ç). Notably, Compound B did not inhibit RAS-GTP levels in these cell lines. Mutant oncoproteins of BRAF Class I and Class II work downstream of RAS but direct ERK-dependent, strong negative feedback, leading to suppression of RAS-GTP upstream of RAS. Our data suggest that this suppression is either insensitive to SHP2 inhibition, for example, if suppression occurs through indirect SOS1 inhibition (Corbalan-Garcia, 1996; Kamioka, 2011), or strong enough that low levels remaining RAS-GTP cannot be reliably quantified with our assay.
[00418] [00418] However, in three cell lines bearing BRAF Class III mutations, NCI-H1666 (BRAFG466V / +), NCI-H508 (BRAFG596R / +), and Cal-12T (BRAFG466V / +), treatment with Com - rank B led to the consistent suppression of both levels of pERK (FIG. 13F and RAS-GTP levels (FIG. 13E), and proliferation (FIG. 13D). These results are consistent with recent reports that mutations in BRAF Class III are genuine cancer controllers that remain sensitive to upstream signaling modulation and RAS-GTP levels (Yao, 2017). Therefore, BRAF Class III mutations are a third category of downstream oncogenic mutation that can be targeted through SHP2-mediated RAS-GTP load blocking upstream.
[00419] [00419] To more fully define the cellular effects of Compound B, we examine the biomarkers of the cell cycle and apopt. Caspase 3/7 Assay Activated on Spheroids. NCI-H358 cells (Lung, KRASG12C) were developed in spheroids by sowing 5,000 cells / well in 96-well round base ultra-low fixation plates (Corning) in RPMI medium (Gibco) supplemented with fetal bovine serum 10% and 1% penicillin / streptomycin. Immediately after sowing, the cells were centrifuged at 1000 RPM for 5 minutes, and incubated at 37 ° C in 5% CO2 for five days to allow spheroid formation. Spheroid formation was confirmed visually. Spheroids were treated in triplicate with Compound B, staurosporine (Sigma), or DMSO (Sigme) (0.1% final), diluted in RPMI medium supplemented with 10% fetal bovine serum and 1% penicillin / streptomycin , and incubated at 37 ° C in 5% CO2 for 20 hours. Caspase 3/7 activity when measured using the Caspase-Glo 3/7 Assay System (Pro-mega), following the manufacturer's instructions. After adding the reagent
[00420] [00420] In NCI-H358 cells (Lung, KRASG12C), treatment of spheroid cultures with Compound B led to robust activation of caspase 3/7, indicating a pro-apoptotic effect (FIG. 15).
[00421] [00421] To extend our studies on additional clinically relevant in vivo models, we evaluated the response to SHP2 inhibition mediated by Compound B in xenograft (PDX) models derived from the patient. Two PDX models of BRAF mutant NSCLC, LUN023 and LUN037 mutants of BRAF, were tested. LUN023 is a carrier of the BRAFD594N Class 3 mutation previously described {Yao, 2017 # 2432}, while LUN037 is a carrier of BRAFN581D, a known class 3 residue and established RASopathy replacement {Niihori, 2006 # 2538}. As predicted for this class of semi-autonomous RAS / MAPK signaling controller, we observed dose-dependent tumor growth inhibition after oral dose of Compound B in both models (FIGS. 20A and 20B). In addition, we tested Compound B in two additional NSCLC PDX models and KRASG12C mutations confirmed as genotypic biomarkers of sensitivity to SHP2 inhibition in these PDXs, validating our cell line and in vitro based on in vivo findings ( 20C-20D). Summary:
[00422] [00422] The observation that an SHP2 inhibitor can inhibit some, but not all, KRAS mutant cells is likely to be a function of the nucleotide cyclization aspects of a particular KRAS mutation and its corresponding dependence on signaling inputs maintain high levels of the active GTP-linked state. In fact, Patricelli and co-workers demonstrated that KRASG12C is not a constitutively and fully active protein, but the nucleotide state of KRASG12C is in a state of dynamic flow that can be modulated by upstream signaling factors (Patricelli et al., 2016 ). Similarly, in cells that have lost the function of the GTPase-activating protein (GAP), for example, NF1LOF, there is a change in the state linked to active GTP, RAS that directs signaling to RAS effectors and growth addiction. cement. In these cells, the wild type RAS undergoes nucleotide cyclization which, as for KRASG12C, makes it sensitive to signaling inputs upstream to maintain a highly active state. In addition, cells that have acquired a Class 3 mutation in BRAF direct high pERK signaling in a way that remains dependent on RAS-GTP, and therefore on upstream signaling factors. The sensitivity of KRASG12C; NF1LOF; and BRAF Class 3 cell lines to an allosteric inhibitor SHP2 reflects the modulation of these factors upstream, and therefore the nucleotide status of RAS mutant / wild type, by the inhibitor. Example 2. Effect of SHP2s allosteric inhibitor on the treatment or prevention of tumor resistance to inhibitors of the MAPK pathway.
[00423] [00423] Objective: The effect of an allosteric inhibitor of SHP2s, Compound A or Compound B, on the activation of the feed-back-oriented RAS pathway that results from MEK inhibition was evaluated in several cancer cell lines comprising different mutations in KRAS and other mutations that modulate the nucleotide cyclization of RAS, such as NF1LOF.
[00424] [00424] To determine the effects of test articles on the levels of phosphorylated RTKs, MDA-MB231 cells were seeded in 6-well plates and incubated overnight in full growth medium. The cells were treated for 24 hours with selumetinib (5 µM) or Compound A (1 and 5 µM) or left untreated (DMSO control). Lysates were generated using the lysis buffer provided with the kit (Phospho-RTK Array; R&D systems) with the inclusion of a protease inhibitor cocktail. To control the protein concentration, the total protein levels were squantified using the BCA reagent kit. Phospho-RTK levels were determined according to the manufacturer's instructions.
[00425] [00425] To determine the effects of small molecules on activated RAS-GTPase levels, cell lines of interest were grown under standard 2D culture conditions. The cells were seeded and after incubation overnight incubated at 37 ° C with vehicle (DMSO) or test articles. After an appropriate incubation period, the cells were washed and cell lysis buffer added to prepare a cell lysate. The levels of Ras-GTP in the lysates were determined using affinity purification of a Raf-RBD complex (Ras-binding Raf domain) / GTP-Ras. In one method, the Pierce Active Ras Pulldown and Detection Kit was used. In synthesis, clarified lysates (500 µg of total protein, quantified by BCA) were mixed with the glutathione resin that was preincubated with GST-Raf-RBD. The mixture was vortexed and incubated at 4 ° C for 1 hour with gentle rocking. The resin was washed three times with lysis buffer and bound Ras-GTP eluted by the addition of 2X reduction sample buffer. The eluted proteins were separated by SDS-PAGE using a 4 to 15% Tris-glycine gel (BioRad). The proteins were transferred to a nitrocellulose membrane for Western blotting using an anti-Ras antibody (Thermofisher, 1: 200) and a secondary anti-mouse antibody Liquor IRDye-800 (1: 20,000). The Odyssey CLx liquor was used for visualization. Results:
[00426] [00426] The observation that an SHP2 inhibitor can prevent RTKs feedback reactivation, as interpreted by its phosphorylation state (FIG. 9), demonstrates that SHP2 inhibition upstream of RAS does not hinder homeostatic regulation of the RAS pathway / MAPK in the same way as MEK inhibition downstream of RAS. Consistent with this principle, the addition of a SHP2 inhibitor with a MEK inhibitor suppressed the accumulation of RAS-GTP based on the feedback that is triggered by treatment with the MEK inhibitor (FIGS 10-11). As the accumulation of RAS-GTP is hypothesized to prepare cancer cells to develop resistance to targeted therapies (ie, MEK inhibitors), these data support the concept that an SHP2 inhibitor can be implanted in cancer patients for treat or prevent tumor resistance to inhibitors of the RAS / MAPK pathway. Example 3 Effect of SHP2 inhibitor (Compound B) on SHP2 phosphorylation
[00427] [00427] Objective: To determine whether inhibition of SHP2 with an allosteric inhibitor prevents tyrosine phosphorylation of the C-terminal tail (Tyr-542 and Tyr-580) of SHP2. Base:
[00428] [00428] The tyrosine phosphorylation of the C-terminal tail (Tyr-542 and Tyr-580) of SHP2 has been proposed to have both regulatory and functional consequences. Initial work has proposed that SHP2 acts as a structure protein to bind PDGFRβ to Ras by interactions with Grb2-SOS (Bennett, 1994) by tyrosine phosphorylation after stimulation of the growth factor. However, it remains controversial whether Grb2 binds pY542 or pY580 in a cellular context, and whether this interaction is the main functional consequence of Y542 / 580 phosphorylation. Lu et. al (2001) used phosphotyrosine mimics at these sites to show that phosphorylation increases the activity of SHP2 PTPase, presumably through intramolecular interactions with the SH2 domains. This suggests that phosphorylation of these residues can contribute significantly to enzyme activity rather than structures. Subsequent work identified a growth factor specificity for tyrosine phosphorylation in murine fibroblasts (PDGF, FGF, but not EGF) and also concluded that Y580 phosphorylation occurs after, and is dependent on, Y542 phosphorylation (Araki et al., 2003). This observation leads the authors to hypothesize that in a "closed state" Y580 is inaccessible to phosphorylation until a conformational change evoked by phosphorylation of Y542 occurs. They also proposed that p-Y542 is the main site of Grb2 binding in fibroblasts. A comprehensive study using FRET has corroborated that p- Y542 / 580 interacts with the SHP2 SH2 domains, and that the phosphorylation of Y580 is dependent on the phosphorylation of Y542 (Sun et al, 2013). This study identified Y580 as the most likely binding site for Grb2 in MEFs. Based on these observations, SHP2 pY542 was used as a biomarker to identify RTK-based resistance to BRAF inhibitors (Prahallad, 2015), since phosphorylation of this residue occurs in response to RTK signaling. Methods:
[00429] [00429] Cells (MEFs, HEK 293E, H358) were seeded in 6-well plates at a density of 750,000 cells / well in medium with low serum content (0.1% FBS) and allowed to develop for in the evening. The cells were incubated with DMSO (0.05%), or Compound B (5 µM) for 1 hour. The cells were stimulated with 50 ng / ml of EGF or PDGF for 5 minutes, washed with cold PBS, and 150 µL of lysis buffer (Thermo # 1862301) with Phosphatase / Interrupting Protease inhibitor (Thermo # 78440) were added das. The cells were scraped, transferred to a cold Eppendorf tube and vortexed for 10 seconds. The lysates were centrifuged at 4 ° C for 15 minutes at 13,000 rpm and transferred to a new tube. The concentration of lysate protein was assessed using the BCA assay. The lysates (30 µg / strip) were centrifuged on a 4 to 15% Tris glycine gel and transferred to a nitrocellulose membrane using iBlot2. Western blots were performed using Cell Signaling Technologies' phospho-SHP2 antibodies; pY542 (# 3751) and pY580 (# 3703) were both used at a 1: 1000 dilution in 5% BSA in TBS. The membranes were incubated with primary antibody overnight with gentle shaking at 4 ° C. Beta actin antibody (Cell Signaling Technologies # 8457, 1: 2000) was used as a charge control. The secondary antibody (IRDye 800 CW anti-rabbit liquor) was used in a 1: 20000 dilution in 5% BSA in TBS for 1 hour of stirring at room temperature. The spots were visualized using the Odyssey Clx Imager Liquor. Results
[00430] [00430] These experiments show an increase in phosphorylation of Tyr-542 and Tyr-580 in response to growth factors. In accordance with the literature, this phosphorylation is stimulated by PDGF in MEFs, but not EGF. In contrast, in HEK293 and H358 cells, where MAPK signaling is predominantly stimulated by EGF (data not shown), we observed phosphorylation with EGF, however not PDGF. These results suggest that the specificities of the SHP2 phosphorylation growth factor Y542 / Y580 is dependent on the cell line. Treatment of these cells with Compound B, an allosteric inhibitor that stabilizes the closed SHP2 conformation,
[00431] [00431] Objective: Demonstrate the inhibition of SHP2 activity with Compounds A, B, and C.
[00432] [00432] Without wishing to be bound by theory, SHP is allosterically activated by binding bis-tyrosyl phosphorylated peptides to its Src Homology 2 (SH2) domains. The last activation step leads to the release of the SHP2 autoinhibitory interface, which in turn makes SHP2 protein tyrosine phosphatase (PTP) active and available for substrate recognition and reaction catalysis. The catalytic activity of SHP2 was monitored using the DiFMUP substitute substrate in a ready fluorescence assay format.
[00433] [00433] Phosphatase reactions were carried out at room temperature on a 96-well black polystyrene plate, flat base, non-binding surface (Corning, Cat # 3650) using a final reaction volume of 100 µL and the following conditions of assay buffer: 50 mM HEPES, pH 7.2, 100 mM NaCl, 0.5 mM EDTA, 0.05% fr P-20, 1 mM DTT.
[00434] [00434] Inhibition of SHP2 by Compound A, Compound B, and Compound C was monitored using an assay in which 0.2 nM SHP2 was incubated with 0.5 µM Activation Peptide 1 (sequence: H2N-LN (pY) IDLDLV (dPEG8) LST (pY) ASINFQK-amide) or Activation Peptide 2 (sequence: H2N-LN (pY) AQLWHA (dPEG8) LTI (pY) ATIRRF-amide). After 30 to 60 minutes of incubation at 25 ° C, the replacement substrate DiFMUP (Invitrogen, Cat # D6567) was added to the reaction and the activity was determined by a kinetic reading using a microplate reader (Envision, Perkin- Elmer or Spectramax M5, Molecular Devices). The excitation and emission wavelengths were 340 nm and 450 nm, respectively. The initial rates were determined from a linear fit of the data, and the inhibitor dose-response curves were analyzed using the normalized IC50 regression curve adjustment with normalization based on the control.
[00435] [00435] Using the aforementioned protocol, the inhibition of SHP2 by Compound A, Compound B, and Compound C is shown in Table
[00436] [00436] In light of our findings that multiple classes of RAS / MAPK pathway oncoproteins that remain dependent on the RAS-GTP load can be targeted through SHP2 inhibition, we asked whether SHP2-dependent RAS-GTP modulation was due to the interruption of core RAS regulatory processes. Methods: SOS-WT and SOS-F Expression Constructions
[00437] [00437] Constructions SOS-WT and SOS-F marked by HA N- terminally were synthesized (Tuna) and subcloned into the vector pcD- NA5 / FRT / TO (ThermoFisher) using the following primers: SOS1-HA-For 5'-ACAGGTAAGCTTATGTACCCATACGATGTTCCAGATAT TAC-3 ', SOS1-HA-REV 5'-AGACTAGCGGCCGCTCAGGAAGAATGGG CATTCTCCAA-3', and SOS-F-HA-REV 5'- GATCGAGCGGCCGCTCAG- GAGAGCACACACTTGCAG-3 '. Plasmids SOS-WT and SOS-F were cotransfected with the pOG44 expression vector Flp-recombinase (ThermoFisher) in the HEK cell line Flp-In T-Rex 293 according to the manufacturer's protocol. Transfected cells were selected in drug medium (200 µg / mL hygromycin B, 15 µg / mL blastidicine) and expression of SOS constructs was verified by Western blot (SOS-1: Cell Signaling Technologies # 5890; HA: Sigma 11867423001).
[00438] [00438] 30,000 HEK-293 cells per well were seeded in 96-well plates in biotin-free RPMI (Hyclone) supplemented with 0.1% fetal bovine serum, 0.02% bovine serum albumin and 1% penicillin / streptomycin. Expression of SOS1 constructs was induced by the addition of 0.1 µg / ml doxycycline (Sigma) over 24 hours. The cells were treated with 3-fold serial dilutions of Compound B diluted in biotin-free medium supplemented with 0.02% bovine serum albumin and 1% penicillin / streptomycin (0.1% DMSO final concentration ) for one hour. For the final 5 minutes of drug treatment, the cells were stimulated with 50 ng / mL of EGF (Sigma), lysed and subjected to ERK1 / 2 phosphorylation analysis as described above. Results
[00439] [00439] First, we extracted data from the recently published Project DRIVE (McDonald, 2017), in which thousands of genes have been systematically depleted by hundreds of cell lines to study genetic dependencies of molecularly defined cancer cell lines. One way to identify functional modules for high-throughput genetic knockout experiments is to examine the phenotypic correlation of all possible gene pairs across the data set, as knockout of members of a common functional module tends to produce similar patterns of answer in many independent experiments. Adopting a hypothesis-based method, we collected data from 23 genes involved in signaling the RTK or RAS pathway and calculated a correlation matrix (FIG. 14A). Two functional modules were easily evident - the retransmission of the MAPK signal downstream of activated RAS and the RTK / convergent node module upstream of activated RAS. Of particular interest, the knockouts most closely correlated with PTPN11 (SHP2) are the GEF SOS1 protein (cc = 0.51) and the GRB2 adapter protein, which binds RTKs to the RAS SOS1-mediated GTP load (cc = 0.40 ). In fact, SOS1 and GRB2 are the gene knockouts most closely related to PTPN11 across all 7,837 genes in the Project DRIVE data set (data not shown). This analysis implies that SHP2 is an essential member of a core RAS regulatory module containing SOS1 and GRB2. Therefore, we hypothesize that Compound B sub-regulates RAS-GTP by breaking the SHP2 / SOS1 / GRB2 module that is required for RAS GTP loading.
[00440] [00440] To test this hypothesis, we first ask whether a constitutively active dominant mutant form of SOS1 can render cells insensitive to suppression mediated by pERK signaling Compound B. Indeed, in HEK293 cells, inducible expression of SOS-F, a SOS1 mutant with its C-terminus fused to the HRAS farnesylation motif that directs the protein constitutively to the plasma membrane (Aronheim, 1994), rendered the pERK signaling insensitive to stimulation of EGF and SHP2 inhibition (FIG. 14B, FIG. 14C). These data show that the suppressive effects of SHP2 inhibition can be overcome by activating constitutive SOS1 and that SOS1, therefore, works downstream of (or in parallel with) PTPN11 / SHP2. A possible explanation for these findings is that the inhibition of SHP2 may interfere with the location and activation of the plasma membrane of SOS1. summary
[00441] [00441] We discovered a new allosteric SHP2 inhibitor, Compound B, and used it and other SHP2 inhibitors for research on molecular markers of SHP2 dependence in tumors bearing mutations in the RAS. The identification of KRASG12C, NF1LOF and BRAFClass III mutations, which confer sensitivity to SHP2 inhibition in tumor cells, establishes SHP2 inhibition as a new and promising therapeutic strategy against tumors carrying these oncogenic controllers, for which current treatments are largely ineffective in the clinic.
[00442] [00442] In NSCLC, these semi-autonomous controller mutations are observed frequently: mutations of KRASG12C, NF1LOF and BRAFClass III collectively represent about 3% of all cases in the USA annually. Importantly, patients whose cancers carry these mutations are dramatically neglected, since no targeted therapy has been recommended for these molecular subtypes. The data presented in this document increases the exciting possibility that an SHP2 inhibitor can make these mutations clinically actionable and improve the outlook for patients.
[00443] [00443] Our data show that SHP2 is not only a convergent signaling node downstream of several RTKs, but is an essential regulator of the oncogenic RAS activation. Importantly, many tumors remain subject to SHP2 inhibition, even when the oncogenic "controller" mutation is apparently downstream of SHP2 in the canonical pathway. The association of SHP2 with SOS1 and GRB2 provides a mechanistic context for the precise role of SHP2 in the regulation of RAS-GTP levels and presents clear hypotheses about the impact of allosteric inhibitors on this functional module.
[00444] [00444] The preserved dependence of mutations of KRASG12C, NF1LOF and BRAFClass III on upstream signals mediated by SHP2 suggests that certain mutant forms of oncogenic controllers of the RAS pathway amplify, instead of bypassing, the homeostatic mechanisms that regulate the RAS- GTP and the exit of the road. This contrasts with a common assumption that RAS oncogenes are blocked in the GTP-linked state constitutively to target signaling and cancer and is consistent with a structure in which certain oncogenic mutations are semi-autonomous controllers, and not fully autonomous cancers. More broadly, our study highlights the power of developing selective and potent pharmacological probes to discover hidden features of RAS oncogenic signaling and unforeseen therapeutic opportunities. Example 6 Effect of SHP2 allosteric inhibitor (Compound B) on tumor cell growth in vitro alone and in combination with MEK inhibitor trametinib
[00445] [00445] Objective: To evaluate the efficacy of the allosteric inhibitor SHP2, Compound B alone and in combination with trametinib, in vitro, in tumor cells of human non-small cell lung cancer cells CALU-1 and NCI-H358. Methods:
[00446] [00446] The cells were cultured in 3D culture as spheroids. In synthesis, 2500 cells / well were seeded in 96-well ultra-low round-bottom binding plates (Corning) in growth media supplemented with 10% fetal bovine serum and 1% penicillin / streptomycin, and allowed to form spheroids for 72 hours at 37C in 5% CO2. Spheroid formation was confirmed visually, and spheroids were treated in duplicate with 3-fold serial dilutions of Compound B in complete development media (final DMSO concentration = 0.1%). After exposure to the drug for five days, cell viability in spheroids was determined using the CellTiter-Glo assay kit (Promega) Results:
[00447] [00447] As shown in Figures 16A and 16C, dose-dependent inhibition of CALU-1 NSCLC and H358 NSCLC of tumor cell growth was obtained by treatment with each of SHP2 and MEK inhibitors. In addition, SHP2 inhibition in combination with
[00448] [00448] Objective: To evaluate the efficacy of the allosteric inhibitor SHP2 Compound B alone and in combination with trametinib, after oral administration, in the NCI-H358 xenograft model of human non-small cell lung cancer in nude mice. Methods:
[00449] [00449] The effects of a SHP2 inhibitor on tumor cell growth in vivo were evaluated in the NSCLC H358 xenograft model using female athymic nude mice (6 to 8 weeks old). The mice were implanted with H358 tumor cells in 50% Matrigel (1x107 cells / animal) subcutaneously on the flank. Once the tumors reached an average size of ~ 200 mm3, the mice were randomized to treatment groups and administration of test article or vehicle (50 mM acetate buffer, pH 4.6 containing 10% captisol, unless otherwise indicated) started. Trametinib was formulated in a 0.5% Methylcellulose + 0.5% Tween 80 solution. Body weight and tumor volume (using calipers) were measured every two days until the end of the study. The compounds were administered by oral tube according to the schedule established in Table 5: Table 5: Scheme of repeated dosage evaluation
[00450] [00450] The end of the study is also shown in Table 5. The average tumor volume data is reported for all animals that remained in the study. Results:
[00451] [00451] Figure 17 shows the effectiveness of repeated daily dosage of Compound B in PO of 10 and 30 mg / kg (inhibition of tumor growth, TGI = 54, 79% respectively), and trametinib at 1 mg / kg ( TGI = 79%) in the NCI-H358 model of human non-small cell lung cancer. Compound B at both doses and trametinib as a single agent caused significant inhibition of tumor growth when compared to vehicle control. Note that the efficacy observed in treatment of 10 and 30 mg / kg with Compound B produced previous data reported in Example 1 in the NCI-H358 xenograft model (FIG. 7).
[00452] [00452] The combination of trametinib at 1 mg / kg and Compound B at 10 mg / kg resulted in an average tumor regression of 36%, and the same dose of trametinib in combination with 30 mg / kg of Compound B resulted in a mean tumor regression of 71%, ** p = 0.001, *** p <0.0001, respectively, assessed by a usual one-way ANOVA of tumor volumes along with multiple comparisons using a Tukey test post-hoc in Graphpad Prism software. Three out of ten animals that received Compound B at 30mg / kg and trametinib at 1mg / kg achieved a complete tumor regression that persisted on day 30.
[00453] [00453] Figure 18: All regimens were well tolerated during the duration of the study when evaluated by body weight, with the exception of one animal in the combination of 30 mg / kg of Compound B with 1 mg / kg of trametinib, which lost> 20% of body weight on the last day of dosing and was sacrificed for human reasons. Conclusion:
[00454] [00454] Compound B exhibits dose-dependent, statistically significant and biologically significant efficacy in the NCI-H358 non-small cell lung cancer xenograft after oral administration at 10 mg / kg daily and 30 mg / kg daily. Trametinib also showed efficacy in this model at 1 mg / kg, a dose level previously expected to be clinically relevant. Importantly, both doses of Compound B in combination with this dose of trametinib were tolerated and caused significant tumor regressions, some of which were complete regressions. Example 8 Effect of SHP2 allosteric inhibitor (Compound C) on tumor cell growth in vivo alone and in combination with MEK inhibitor trametinib
[00455] [00455] Objective: To evaluate the efficacy of the allosteric inhibitor SHP2, Compound C alone and in combination with Trametinib (MEK inhibitor), Cobimetinib (MEK inhibitor), Ulixertinib (ERK inhibitor), and Abemaciclib (CDK4 / 6 inhibitor) after oral administration, in an NCI-H358 xenograft model of human non-small cell lung cancer (Trametinib, Cobimetinib, Ulixertinib) or in a MIA-Pa-Ca-2 xenograft model of human pancreatic carcinoma (Abemaciclib ) in nude mice. Methods:
[00456] [00456] The effects on tumor cell growth in vivo of another SHP2 inhibitor (Compound C) as a monotherapy or as a combination therapy with several inhibitors of the RAS pathway were evaluated in the NSCLC H358 KRasG12C and MIA-xenograft models Pa-Ca-2 as described above in Example 1, except that the test article and vehicle formulation were (2% HPMC E-50, 0.5% Tween 80 in 50 mM sodium citrate buffer, pH 4.0 ) +/- the inhibitor compound (s). As before, body weight and tumor volume (using calipers) were measured twice a week until the end of the study. The test compounds or vehicle control were administered by oral probe daily. The end of the study was defined as an average tumor volume of 2000 mm3 in the control group or 22 days after dosing, whichever comes first. The average tumor volume data is reported for all animals that remained in the study. Results:
[00457] [00457] Figure 21 shows the effectiveness of repeated daily dosing of Compound C ("Comp. C") in 10 mg / kg PO with or without co-administration of a RAS inhibitor in the H358 KRasG12C lung cancer model human non-small cell. FIGS. 21A and 21B show studies of Compound C and Trametinib; FIGS. 21C and 21D show studies of Compound C and Cobimetinib; and FIGS. 21E and 21F show studies of Compound C and Ulixertinib. Each of Compound C (FIGS. 21A, 21C, and 21E), Trametinib (FIG. 21A), Cobimetinib (FIG.21C) and Ulixerinib (FIG. 21E) caused significant inhibition of tumor growth as a single agent when compared vehicle control. It is noted that the efficacy observed in 10 mg / kg treatment with Compound C reproduced data from previous NCI-H358 xenograft model reported in Example 1 with Compound A and Compound B (FIG 7) and reported data in Example 7 with Compound B (FIG. 17).
[00458] [00458] The combination of Trametinib at 1 mg / kg and Compound C at 10 mg / kg resulted in a significant increase in tumor regression (*** p <0.0005), assessed by a usual one-way ANOVA of tumor volumes along with multiple comparisons using a post-hoc Tukey test in Graphpad Prism software (FIG. 21A).
[00459] Similarly, each of the combinations of Cobimetinib at 2.5 mg / kg with Compound C at 10 mg / kg (FIG. 21C) and Ulixertinib at 100 mg / kg with Compound C at 10 mg / kg (FIG. 21E ) resulted in a significant increase in tumor regression (*** p <0.0005), assessed by a usual one-way ANOVA of tumor volumes along with multiple comparisons using a post-hoc Tukey test in Graphpad Prism software.
[00460] [00460] Figure 22 shows the efficacy of repeated daily dosage of Compound C at 30 mg / kg of PO with or without coadministration of Abemaciclib at 50 mg / kg in the MIA-Pa-Ca-2 xenograft model of human pancreatic carcinoma. Each of Compound C and Abemacyclib caused significant tumor growth inhibition as a single agent when compared to vehicle control (FIG. 22A). In addition, the combination of Abemaciclib at 50 mg / kg and Compound C at 30 mg / kg resulted in a significant increase in tumor regression (*** p <0.0005), assessed by a usual one-way ANOVA of tumor volumes along with multiple comparisons using a Tukey post-hoc test in Graphpad Prism software (FIG. 22A).
[00461] [00461] All regimens were well tolerated for the duration of the study when assessed by body weight (FIGS. 21B, 21D, 21F, and 22B). Conclusion:
[00462] [00462] Like Compounds A and B, Compound C exhibits statistically significant, biologically significant and dose-dependent efficacy in NCI-H358 non-small cell lung cancer and in the MIA-Pa-Ca-2 xenograft models after oral administration at 10 mg / kg daily and 30 mg / kg daily. Trametinib also showed efficacy in this model at 1 mg / kg, a dose level previously predicted to be clinically relevant, as well as Cobimetinbe, Ulixertinib, and Abemaciclib at clinically relevant doses of 2.5, 100, and 50 mg / kg, respectively.
[00463] [00463] Importantly, in all cases, doses of the SHP2 inhibitor of Compound C in combination with the dose of the other inhibitors of the RAS pathway were tolerated and caused significant tumor regressions, some of which were complete regressions. Equivalents
[00464] [00464] Although the present invention has been described in conjunction with the specific modalities set out above, many alternatives, modifications and other variations thereof will be evident to those skilled in the art. All of these alternatives, modifications and variations must be within the spirit and scope of the present invention. All United States patents, United States patent application publications, United States patent application, foreign patents, foreign patent application and non-patent publications related to this specification and / or listed on the sheet order data are incorporated in this document by reference in their entirety. Aspects of modalities can be modified, if necessary, to employ concepts from the various patents, applications and publications to provide yet other modalities. These and other changes can be made to the modalities in the light of the detailed description above. In general, in the following claims, the terms used should not be interpreted to limit claims to the specific modalities described in the specification and in the claims, but should be interpreted to include all possible modalities, together with the full scope of equivalents to which such claims are entitled.
Consequently, the claims are not limited by the invention.

权利要求:
Claims (147)
[1]
1. Method for the treatment of an individual with a disease or disorder, characterized by the fact that it comprises a cell containing a mutation encoding a variant of KRASG12C, comprising providing the individual with an SHP2 inhibitor.
[2]
2. Method for the treatment of an individual with a disease or disorder, characterized by the fact that it comprises a cell with a mutation encoding a loss of function of the NF1 variant (NF1LOF), comprising providing the individual with an SHP2 inhibitor.
[3]
3. Method for the treatment of an individual with a disease or disorder associated with a mutation of the RAS pathway in an individual cell that makes the cell at least partially dependent on the signaling flow through SHP2, characterized by the fact that it comprises providing the individual an SHP2 inhibitor.
[4]
4. Method according to claim 3, characterized by the fact that the RAS mutation is a RAS mutation selected from a KRAS mutation, an NRAS mutation, an SOS mutation, a Class III mutation of BRAF, a MEK1 Class I mutation, a MEK1 Class II mutation, and an NF1 mutation.
[5]
5. Method according to claim 4, characterized in that the KRAS mutation is selected from a KRASG12A mutation, a KRASG12C mutation, a KRASG12D mutation, a KRASG12F mutation, a KRASG12I mutation, a mutation of KRASG12L, a KRASG12R mutation, a KRASG12S mutation, a KRASG12V mutation, and a KRASG12Y mutation.
[6]
6. Method according to claim 4, characterized by the fact that the KRAS mutation is KRASG12C.
[7]
7. Method according to claim 4, characterized by the fact that the KRAS mutation is KRASG12A.
[8]
8. Method according to claim 4, characterized in that the BRAF Class III mutation is selected from one or more of the following amino acid substitutions in human BRAF: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D; G596R and A762E.
[9]
9. Method according to claim 4, characterized by the fact that the NF1 mutation is a loss of function mutation.
[10]
10. Method according to claim 4, characterized in that the MEK1 Class I mutation is selected from one or more of the following amino acid substitutions in human MEK1: D67N; P124L; P124S; and L177V.
[11]
11. Method according to claim 4, characterized in that the MEK1 Class II mutation is selected from one or more of the following amino acid substitutions in human MEK1: ΔE51-Q58; ΔF53-Q58; E203K; L177M; C121S; F53L; K57E; Q56P; and K57N.
[12]
12, Method according to any one of claims 1 to 11, characterized in that it also comprises providing the individual with an inhibitor of the RAS pathway.
[13]
13. Method according to claim 12, characterized by the fact that the inhibitor of the RAS pathway is a MAPK inhibitor.
[14]
14. Method according to claim 13, characterized by the fact that the RAS pathway inhibitor is a MEK inhibitor or ERK inhibitor.
[15]
15. Method according to claim 12, characterized by the fact that the RAS inhibitor is selected from one or more of Trametinib, Binimetinibe, Selumetinibe, Cobimetinibe, LErafAON
(NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853; LY3214996; BVD523; GSK1120212; Ulixertinib, and Abemaciclibe.
[16]
16. Method according to any of claims 1 to 15, characterized by the fact that the disease or condition is a tumor.
[17]
17. Method according to claim 16, characterized by the fact that the tumor is selected from an NSCLC, colon cancer, esophageal cancer, rectal cancer, JMML, breast cancer, melanoma, Scwannoma, and a pancreatic cancer.
[18]
18. Method of treatment of an individual with a disease associated with a loss of NF1 mutation function, characterized by the fact of understanding to provide the individual with an SHP2 inhibitor.
[19]
19. Method according to claim 18, characterized by the fact that the disease is a tumor that has cells with a loss of NF1 mutation function.
[20]
20. Method according to claim 19, characterized by the fact that the tumor is an NSCLC or melanoma tumor.
[21]
21. Method according to claim 18, characterized by the fact that the disease is selected from neurofibromatosis type I, neurofibromatosis type II, schwanomatosis, and Watson syndrome.
[22]
22. Method according to any one of claims 18 to 21, characterized in that it also comprises providing the individual with an inhibitor of the RAS pathway.
[23]
23. Method according to claim 22, characterized by the fact that the RAS pathway inhibitor is selected from one or more of Trametinib, Binimetinibe, Selumetinibe, Cobimetinibe, LErafAON
(NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853; LY3214996; BVD523; GSK1120212; Ulixertinib, and Abemaciclibe.
[24]
24. Method for the treatment of an individual with a tumor, characterized by the fact that it comprises: (a) determining whether a biological sample obtained from the individual's cell is classified as a KRAS mutant; and (b) administering to the individual a SHP2 inhibitor if the biological sample is classified as a KRASG12C mutant, a KRASG12D mutant, a KRASG12S mutant, or a KRASG12V mutant.
[25]
25. Method for the treatment of an individual with a tumor characterized by the fact that it comprises: (a) determining whether a biological sample obtained from the individual is classified as an NF1LOF mutant; and (b) administering to the individual an SHP2 inhibitor if the biological sample is classified as an NF1LOF mutant.
[26]
26. Method for the treatment of an individual with a tumor, characterized by the fact that it comprises: (a) determining whether a biological sample obtained from the individual is classified as a BRAF Class 3 mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a BRAF Class mutant
3.
[27]
27. Method for the treatment of an individual with a tumor, characterized by the fact that it comprises: (a) determining whether a biological sample obtained from the individual is classified as a MEK1 Class I mutant; and
(b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class I mutant.
[28]
28. Method for the treatment of an individual with a tumor, characterized by the fact that it comprises: (a) determining whether a biological sample obtained from the individual is classified as a MEK1 Class II mutant; and (b) administer to the individual an SHP2 inhibitor if the biological sample is classified as a MEK1 Class II mutant.
[29]
29. Method for the treatment or prevention of drug resistance in an individual receiving the administration of an inhibitor of the RAS pathway, characterized by the fact of understanding to administer to the individual an inhibitor of SHP2.
[30]
30. Method according to claim 29, characterized by the fact that the individual comprises a tumor containing cells with an NF1LOF mutation.
[31]
31. The method of claim 29 or 30, characterized in that the subject comprises a tumor containing a KRASG12C mutation, a KRASG12D mutation, a KRASG12A mutation, a KRASG12S mutation, or a KRASG12V mutation .
[32]
32. Method according to any one of claims 29 to 31, characterized in that the inhibitor of the RAS pathway is a MEK inhibitor.
[33]
33. Method according to claim 32, characterized by the fact that the MEK inhibitor is selected from one or more of Trametinib (GSK1120212), Selumetinib (AZD6244), Cobimetinib (GDC-0973 / XL581), Binimetinibe, Vemurafenibe , Pimasertibe, TAK733, RO4987655 (CH4987655), Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901, Refameti-
nibe (RDEA 119 / BAY 86-9766), RO5126766, AZD8330 (ARRY- 424704 / ARRY-704), CH5126766, MAP855, and GSK1120212.
[34]
34. Method according to any of claims 29 to 31, characterized in that the inhibitor of the RAS pathway is an ERK inhibitor.
[35]
35. Method according to claim 34, characterized by the fact that the ERK inhibitor is selected from any ERK inhibitor known in the art; LY3214996; Ulixertinib; and BVD523.
[36]
36. Method according to any one of the preceding claims, characterized in that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a compound of Table 2, described in this document; and (x) a combination of them.
[37]
37. Combination therapy, characterized by the fact that it comprises an inhibitor of the RAS pathway and an inhibitor of SHP2.
[38]
38. Combination therapy according to claim 37, characterized in that the RAS pathway inhibitor is a MEK inhibitor.
[39]
39. Combination therapy according to claim 38, characterized in that the MEK inhibitor is selected from one or more of Trametinib (GSK1120212), Selumetinib (AZD6244), Cobimetinib (GDC-0973 / XL581), Binimetinibe, Vemurafenibe , Pima-sertibe, TAK733, RO4987655 (CH4987655), CI-1040; PD-0325901,
Refametinib (RDEA 119 / BAY 86-9766), RO5126766, AZD8330 (AR-RY-424704 / ARRY-704), CH5126766, MAP855, and GSK1120212.
[40]
40. Combination therapy according to claim 37, characterized in that the RAS pathway inhibitor is the KRASG12C specific ARS-853 inhibitor.
[41]
41. Combination therapy according to any one of claims 37 to 40, characterized in that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a compound of Table 2, described in this document; and (x) a combination of them.
[42]
42. Combination therapy according to any of claims 37 to 41, characterized in that it is intended for use in the treatment of a tumor.
[43]
43. Combination therapy according to claim 42, characterized by the fact that the tumor is selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rabdomios-
sarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; cancer of the central nervous system (for example; primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; urinary tract cancer; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aigigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; meningeal cancer; vulvar cancer and melanoma.
[44]
44. Pharmaceutical composition characterized by the fact that it comprises an inhibitor of the RAS pathway, an inhibitor of SHP2, and one or more of a pharmaceutically acceptable carrier, excipient, diluent, and / or surfactant.
[45]
45. Pharmaceutical composition according to claim 44, characterized by the fact that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a compound of Table 2, described herein; and (x) a combination thereof.
[46]
46. Pharmaceutical composition according to claim 44 or 45, characterized by the fact that the RAS pathway inhibitor is selected from one or more of Trametinib (GSK1120212) Selumetinbe (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemu-
rafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); GSK1120212, Ulixertinib; and Abemaciclibe.
[47]
47. Pharmaceutical composition according to any one of claims 44 to 46, characterized in that it is intended for use in the treatment of a tumor.
[48]
48. Pharmaceutical composition according to claim 47, characterized by the fact that the tumor is selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblasts; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; cancer of the central nervous system (eg primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; urinary tract cancer; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aerodigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; cancer of the meninges; vulvar cancer and melanoma.
[49]
49. Method according to any one of claims 16, 18, 19, 24 to 28, and 30 to 36, characterized by the fact that the tumor is selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadeno-carcinoma; paraganglioma; phaeochromocyte; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; cancer of the central nervous system (eg primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; urinary tract cancer; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aerodigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; meningeal cancer; vulvar cancer and melanoma.
[50]
50. Method of inhibiting the growth or proliferation of a cell by contacting the mutation of the RAS pathway, characterized by the fact that the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor.
[51]
51. Method of inhibiting the accumulation of RAS-GTP in a cell by contacting the mutation of the RAS pathway, characterized by the fact that the mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor.
[52]
52. Method for killing a cell by contacting the mutation of the RAS pathway, characterized by the fact that mutation of the RAS pathway makes the cell at least partially dependent on the signaling flow through SHP2, the method comprising contacting the cell with an SHP2 inhibitor.
[53]
53. Method according to any of claims 50 to 52, characterized in that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155, (vii) Compound C; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a compound of Table 2, described herein; and (x) a combination thereof.
[54]
54. Method according to any one of claims 50 to 53, characterized in that the RAS mutation is selected from a KRAS mutation, an NRAS mutation, an HRAS mutation, an SOS mutation, an Class III BRAF mutation, and a loss of NF1 mutation function.
[55]
55. Method according to claim 54, characterized in that the KRAS mutation is selected from a KRASG12A mutation, a KRASG12C mutation, a KRASG12D mutation, a KRASG12F mutation, a KRASG12I mutation , a KRASG12L mutation, a KRASG12R mutation, a KRASG12S mutation, a KRASG12V mutation, and a KRASG12Y mutation.
[56]
56. The method of claim 54, characterized
due to the fact that the KRAS mutation is KRASG12C.
[57]
57. Method according to claim 54, characterized by the fact that the KRAS mutation is KRASG12A.
[58]
58. Method according to claim 54, characterized in that the BRAF Class 3 mutation is selected from one or more of the following amino acid substitutions in human BRAF: D287H; P367R; V459L; G466V; G466E; G466A; S467L; G469E; N581S; N581I; D594N; D594G; D594A; D594H; F595L; G596D; G596R and A762E.
[59]
59. Method according to any one of claims 50 to 58, characterized in that it also comprises contacting the cell with an inhibitor of the RAS pathway.
[60]
60. The method of claim 59, characterized in that the inhibitor of the RAS pathway is a MAPK inhibitor.
[61]
61. Method according to claim 60, characterized by the fact that the inhibitor of the RAS pathway is a MEK inhibitor or ERK inhibitor.
[62]
62. Method according to claim 61, characterized by the fact that the RAS pathway inhibitor is selected from one or more of Trametinib, Binimetinib, Selumetinib, Cobimetinib, LErafAON (NeoPharm), ISIS 5132; Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655); CI-1040; PD-0325901; CH5126766; MAP855; AZD6244; Refametinib (RDEA 119 / BAY 86-9766); GDC-0973 / XL581; AZD8330 (ARRY-424704 / ARRY-704); RO5126766; ARS-853; LY3214996; BVD523; GSK1120212; Ulixertinib; and Abemaciclibe.
[63]
63. Method according to any one of claims 1 to 36, 49 to 62, characterized in that it also comprises contacting the cell with an SOS inhibitor.
[64]
64. The method of claim 63, characterized in that the SOS inhibitor is administered to a cell comprising higher than normal SOS levels or SOS activity.
[65]
65. Method according to claim 16, characterized by the fact that the tumor is an NSCLC tumor.
[66]
66. Method according to claim 16, characterized by the fact that the tumor is a colon cancer tumor.
[67]
67. Method according to claim 16, characterized by the fact that the tumor is an esophageal cancer tumor.
[68]
68. Method according to claim 16, characterized by the fact that the tumor is a rectal cancer tumor.
[69]
69. Method according to claim 16, characterized by the fact that the tumor is a JMML tumor.
[70]
70. Method according to claim 16, characterized by the fact that the tumor is a breast cancer tumor.
[71]
71. Method according to claim 16, characterized by the fact that the tumor is a melanoma tumor.
[72]
72. Method according to claim 16, characterized by the fact that the tumor is a Scwannoma tumor.
[73]
73. Method according to claim 16, characterized by the fact that the tumor is a pancreatic cancer tumor.
[74]
74. Method according to any one of the preceding claims, characterized in that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ , Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a component
rank of Table 2, described in this document; and (x) a combination of them.
[75]
75. Method of inhibiting the growth of a tumor cell, characterized in that it comprises contacting the tumor cell with a combination therapy comprising an MEK inhibitor and an SHP2 inhibitor.
[76]
76. Method according to claim 75, characterized in that the MEK inhibitor is selected from one or more of Trametinib (GSK1120212), Selumetinib (AZD6244), Cobimetinib (GDC-0973 / XL581), Binimetinibe, Vemurafenibe , Pimasertibe, TAK733, RO4987655 (CH4987655), CI-1040; PD-0325901, CH5126766, MAP855, Refametinib (RDEA 119 / BAY 86-9766), RO5126766, AZD8330 (ARRY-424704 / ARRY-704), and GSK1120212.
[77]
77. Method according to claim 75 or 76, characterized in that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Formula X; (vi) TNO155; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a compound of Table 2, described in this document; and (x) a combination thereof. The method according to any of claims 75-77, wherein the MEK inhibitor is Trametinib (GSK1120212).
[78]
78. Method according to any one of claims 75 to 77, characterized in that the SHP2 inhibitor is Compound B.
[79]
79. The method of claim 75, characterized
due to the fact that the MEK inhibitor is Trametinib (GSK1120212) and the SHP2 inhibitor is Compound B.
[80]
80. Method according to any one of claims 75 to 79, characterized in that the tumor cell is a cell of a tumor selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomonocytic leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystade-carcinoma; paraganglioma; phaeochrome-cytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; central nervous system cancer (eg primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; urinary tract cancer; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aerodigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; meningeal cancer; vulvar cancer and melanoma.
[81]
81. Method according to any one of claims 75 to 80, characterized in that the tumor is an NSCLC tumor.
[82]
82. Method according to any of claims 75 to 81, characterized by the fact that contact occurs in vivo in an individual.
[83]
83. Method according to claim 82, characterized by the fact that the individual is a human.
[84]
84. Method according to any of claims 75 to 83, characterized in that the contact of a tumor cell with combination therapy comprising the MEK inhibitor and the SHP2 inhibitor results in an inhibition of the growth of the tumor that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of the respective MEK and SHP2 inhibitor separately.
[85]
85. Method according to any one of claims 75 to 84, characterized in that the MEK inhibitor and the SHP2 inhibitor do not contact the tumor cell simultaneously.
[86]
86. Method according to any one of claims 75 to 85, characterized in that the MEK inhibitor and the SHP2 inhibitor contact the tumor cell simultaneously.
[87]
87. Method according to any of claims 85 to 86, characterized by the fact that the contact is through administration of the MEK inhibitor and the SHP2 inhibitor to the individual.
[88]
88. Method according to claim 87, characterized in that the administration of the MEK inhibitor precedes the administration of the SHP2 inhibitor.
[89]
89. Method according to claim 88, characterized in that the administration of the SHP2 inhibitor precedes the administration of the MEK inhibitor.
[90]
90. Method according to claim 88, characterized in that the administration of the SHP2 inhibitor and the administration of the MEK inhibitor occurs simultaneously.
[91]
91. Method according to claim 90, characterized by the fact that the SHP2 inhibitor and the MEK inhibitor are admissible
administered as a single pharmaceutical composition.
[92]
92. Method according to claim 91, characterized in that the SHP2 inhibitor and the MEK inhibitor are administered as separate pharmaceutical compositions.
[93]
93. Method according to any one of claims 75 to 92, characterized in that the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[94]
94. Method of inhibiting the growth of a tumor cell, characterized in that it comprises contacting the tumor cell with a combination therapy comprising trametinib (GSK1120212) and Compound B.
[95]
95. The method of claim 94, characterized in that the tumor cell is from an NSCLC tumor.
[96]
96. Method according to claim 94 or 95, characterized by the fact that contact occurs in vivo in an individual.
[97]
97. Method according to claim 96, characterized by the fact that the individual is a human.
[98]
98. Method according to any of claims 94 to 97, characterized in that the contact of a tumor cell with the combination therapy comprising trametinib (GSK1120212) and Compound B results in an inhibition of the growth of the tumor that it is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound B separately.
[99]
99. Method according to any one of claims 95 to 99, characterized in that the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[100]
100. Method of treating an individual with a tumor, characterized by the fact that it comprises contacting a tumor cell in the tumor in the individual with a combination therapy comprising an MEK inhibitor and an SHP2 inhibitor.
[101]
101. Method according to claim 100, characterized by the fact that the MEK inhibitor is selected from one or more of Trametinib (GSK1120212); Selumetinib (AZD6244); Cobimetinib (GDC-0973 / XL581), Binimetinib, Vemurafenib, Pimasertibe, TAK733, RO4987655 (CH4987655), CI-1040; PD-0325901; CH5126766; MAP855; Refametinib (RDEA 119 / BAY 86-9766); RO5126766, AZD8330 (ARRY-424704 / ARRY-704); and GSK1120212.
[102]
102. Method according to claim 100 or 101, characterized by the fact that the SHP2 inhibitor is selected from (i) Compound A; (ii) Compound B; (iii) SHP099; (iv) NSC-87877; (v) a SHP2 inhibiting compound of any of Formula I, Formula II, Formula III, Formula I-V1, Formula I-V2, Formula IW, Formula IX, Formula IY, Formula IZ, Formula IV, Formula V, Formula VI, Formula IV-X, Formula IV-Y, Formula IV-Z, Formula VII, Formula VIII, Formula IX, and Form mule X; (vi) TNO155; (vii) Compound C, (viii) a compound of Table 1, described herein; (ix) a compound of Table 2, described herein; and (x) a combination thereof.
[103]
103. Method according to claim 101, characterized by the fact that the MEK inhibitor is Trametinib (GSK1120212).
[104]
104. Method according to any of claims 100 to 103, characterized in that the SHP2 inhibitor is Compound B.
[105]
105. Method according to claim 101, characterized by the fact that the MEK inhibitor is Trametinib (GSK1120212) and the SHP2 inhibitor is Compound B.
[106]
106. Method according to any one of claims 100 to 105, characterized in that the tumor cell is a cell of a tumor selected from tumors of the hematopoietic and lymphoid system; a myeloproliferative syndrome; a myelodysplastic syndrome; leukemia; acute myeloid leukemia; juvenile myelomococcal leukemia; esophageal cancer; breast cancer; lung cancer; colon cancer; gastric cancer; neuroblastoma; bladder cancer; prostate cancer; glioblastoma; urothelial carcinoma; uterine carcinoma; adenoid and ovarian serous cystadenocarcinoma; paraganglioma; phaeochromocytoma; pancreatic cancer; adrenocortical carcinoma; stomach adenocarcinomas; sarcoma; rhabdomyosarcoma; lymphoma; head and neck cancer; skin cancer; peritoneum cancer; intestinal cancer (small and large intestine); thyroid cancer; endometrial cancer; biliary tract cancer; soft tissue cancer; ovarian cancer; cancer of the central nervous system (eg primary CNS lymphoma); stomach cancer; pituitary cancer; cancer of the genital tract; urinary tract cancer; salivary gland cancer; cervical cancer; liver cancer; eye cancer; adrenal gland cancer; autonomic ganglion cancer; cancer of the upper aerodigestive tract; bone cancer; testicular cancer; pleural cancer; kidney cancer; penis cancer; parathyroid cancer; meningeal cancer; vulvar cancer and melanoma.
[107]
107. Method according to any one of claims 100 to 106, characterized in that the tumor cell is from an NSCLC tumor.
[108]
108. Method according to any of claims 100 to 107, characterized by the fact that contact occurs in vivo in an individual.
[109]
109. Method according to claim 108, characterized by the fact that the individual is a human.
[110]
110. Method according to any of claims 100 to 109, characterized in that the contact of a tumor cell with the combination therapy comprising the MEK inhibitor and the SHP2 inhibitor results in an inhibition of the tumor growth which is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of the respective MEK and SHP2 inhibitor separately.
[111]
111. Method according to any one of claims 100 to 110, characterized in that the MEK inhibitor and the SHP2 inhibitor do not contact the tumor cell simultaneously.
[112]
112. Method according to any one of claims 101 to 111, characterized in that the MEK inhibitor and the SHP2 inhibitor contact the tumor cell simultaneously.
[113]
113. Method according to any one of claims 110 to 112, characterized by the fact that the contact is through the administration of the MEK inhibitor and the SHP2 inhibitor to the individual.
[114]
114. Method according to claim 113, characterized in that the administration of the MEK inhibitor precedes the administration of the SHP2 inhibitor.
[115]
115. Method according to claim 114, characterized in that the administration of the SHP2 inhibitor precedes the administration of the MEK inhibitor.
[116]
116. Method according to claim 114, characterized in that the administration of the SHP2 inhibitor and the administration of the MEK inhibitor occur simultaneously.
[117]
117. Method according to claim 116, characterized in that the SHP2 inhibitor and the MEK inhibitor are administered as a single pharmaceutical composition.
[118]
118. Method according to claim 117, characterized in that the SHP2 inhibitor and the MEK inhibitor are administered as separate pharmaceutical compositions.
[119]
119. Method according to any one of claims 100 to 118, characterized in that the treatment inhibits the growth of the tumor cell.
[120]
120. Method according to claim 119, characterized in that the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[121]
121. Method of treatment of an individual with a tumor, characterized by the fact that it comprises contacting a tumor cell of the tumor in the individual with a combination therapy comprising trametinib (GSK1120212) and Compound B.
[122]
122. Method according to claim 121, characterized in that the tumor cell is from an NSCLC tumor.
[123]
123. Method according to claim 121 or 122, characterized by the fact that contact occurs in vivo in an individual.
[124]
124. Method according to claim 123, characterized by the fact that the individual is a human.
[125]
125. Method according to any of claims 120 to 124, characterized in that the contact of a tumor cell with the combination therapy comprising trametinib (GSK1120212) and Compound B results in an inhibition of the growth of the tumor that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound B separately.
[126]
126. Method according to any one of claims 120 to 125, characterized by the fact that the growth of the tumor cell is inhibited enough to cause partial or complete re-
tumor progression.
[127]
127. The method of any one of claims 1-36, 49-78, 80-94, 101-104, 107-121, wherein the SHP2 inhibitor is Compound C.
[128]
128. Combination therapy according to any of claims 37 to 43, characterized by the fact that the SHP2 inhibitor is Compound C.
[129]
129. Pharmaceutical composition according to any of claims 44 to 48, characterized in that the SHP2 inhibitor is Compound C.
[130]
130. Method of inhibiting the growth of a tumor cell, characterized by the fact that it comprises contacting the tumor cell with a combination therapy comprising trametinib (GSK1120212) and Compound C.
[131]
131. Method according to claim 130, characterized in that the tumor cell is from an NSCLC tumor.
[132]
132. Method according to claim 130 or 131, characterized by the fact that contact occurs in vivo in an individual.
[133]
133. Method according to claim 132, characterized by the fact that the individual is a human.
[134]
134. Method according to any of claims 130 to 133, characterized in that the contact of a tumor cell with the combination therapy comprising trametinib (GSK1120212) and Compound C results in an inhibition of the growth of the tumor that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound C separately.
[135]
135. Method according to any of claims 130 to 134, characterized by the fact that cell growth
tumor mass is inhibited enough to cause partial or complete regression of the tumor.
[136]
136. Method of treatment of an individual with a tumor, characterized by the fact of understanding to contact a tumor cell of the tumor in the individual with a combination therapy comprising trametinib (GSK1120212) and Compound C.
[137]
137. Method according to claim 136, characterized in that the tumor cell is from an NSCLC tumor.
[138]
138. Method according to claim 135 or 136, characterized by the fact that contact occurs in vivo in an individual.
[139]
139. Method according to claim 138, characterized by the fact that the individual is a human.
[140]
140. Method according to any of claims 136 to 139, characterized in that the contact of a tumor cell with the combination therapy comprising trametinib (GSK1120212) and Compound C results in an inhibition of the growth of the tumor that is more than merely additive with respect to the amount of tumor growth inhibition obtainable by contacting the tumor cell with each of trametinib (GSK1120212) and Compound C separately.
[141]
141. Method according to any of claims 136 to 141, characterized in that the growth of the tumor cell is inhibited enough to cause partial or complete regression of the tumor.
[142]
142. Method according to any one of claims 1 to 36 and 49, characterized in that it comprises the administration of a therapeutically effective amount of the SHP2 inhibitor.
[143]
143. Method according to any one of claims 50 to 128 and 131 to 142, characterized in that it comprises contacting the cell with a therapeutically effective amount of the SHP2 inhibitor.
[144]
144. Combination therapy according to any of claims 37 to 43 and 129, characterized in that it comprises a therapeutically effective amount of the SHP2 inhibitor.
[145]
145. Pharmaceutical composition according to any one of claims 44 to 48 and 130, characterized in that it comprises a therapeutically effective amount of the SHP2 inhibitor.
[146]
146. Method according to any of claims 50 to 74, characterized by the fact that the contact is in vivo in an individual.
[147]
147. Method according to claim 146, characterized by the fact that the individual is a human.

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WO2019051084A1|2019-03-14|

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TW201918260A|2019-05-16|

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

优先权:

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US201762555400P| true| 2017-09-07|2017-09-07|

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