EP4637774A1 - Cancer treatments using mta-cooperative prmt5 inhibitors - Google Patents

Cancer treatments using mta-cooperative prmt5 inhibitors

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Publication number
EP4637774A1
EP4637774A1 EP23848200.4A EP23848200A EP4637774A1 EP 4637774 A1 EP4637774 A1 EP 4637774A1 EP 23848200 A EP23848200 A EP 23848200A EP 4637774 A1 EP4637774 A1 EP 4637774A1
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EP
European Patent Office
Prior art keywords
inhibitor
cancer
mtap
prmt5
compound
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
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EP23848200.4A
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German (de)
French (fr)
Inventor
Brian BELMONTES
Paul E. Hughes
Katherine SLEMMONS
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Amgen Inc
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Amgen Inc
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Publication of EP4637774A1 publication Critical patent/EP4637774A1/en
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    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/535Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
    • A61K31/53751,4-Oxazines, e.g. morpholine
    • A61K31/53771,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445Non condensed piperidines, e.g. piperocaine
    • A61K31/4523Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
    • A61K31/454Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/50Pyridazines; Hydrogenated pyridazines
    • A61K31/502Pyridazines; Hydrogenated pyridazines ortho- or peri-condensed with carbocyclic ring systems, e.g. cinnoline, phthalazine
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/50Pyridazines; Hydrogenated pyridazines
    • A61K31/5025Pyridazines; Hydrogenated pyridazines ortho- or peri-condensed with heterocyclic ring systems
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/506Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00Medicinal preparations containing organic active ingredients
    • A61K31/33Heterocyclic compounds
    • A61K31/395Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/55Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having seven-membered rings, e.g. azelastine, pentylenetetrazole
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2300/00Mixtures or combinations of active ingredients, wherein at least one active ingredient is fully defined in groups A61K31/00 - A61K41/00

Definitions

  • Epigenetic regulation of gene expression is an important biological determinant of protein production and cellular differentiation and plays a significant pathogenic role in a number of human diseases.
  • Epigenetic regulation involves heritable modification of genetic material without changing its nucleotide sequence.
  • epigenetic regulation is mediated by selective and reversible modification (e.g., methylation) of DNA and proteins (e.g., histones) that control the conformational transition between transcriptionally active and inactive states of chromatin.
  • methyltransferases e.g., PRMT5
  • PRMT5 plays a role in diseases such as proliferative disorders, metabolic disorders, and blood disorders.
  • the homozygous deletion of tumor suppressor genes is a key driver of cancer, frequently resulting in the collateral loss of passenger genes located in close genomic proximity to the tumor suppressor. Deletion of these passenger genes can create therapeutically tractable vulnerabilities that are specific to tumor cells.
  • Homozygous deletion of the chromosome 9p21 locus which harbors the well-known tumor suppressor CDKN2A (cyclin dependent kinase inhibitor 2A)
  • CDKN2A cyclin dependent kinase inhibitor 2A
  • MTAP methylthioadenosine phosphorylase
  • Deletion of MTAP results in accumulation of its substrate, methylthioadenosine (MTA).
  • MTA shares close structural similarity to S-adenosylmethionine (SAM), the substrate methyl donor for the type II methyltransferase PRMT5. Elevated MTA levels, driven by loss of MTAP, selectively compete with SAM for binding to PRMT5, placing the methyltransferase in a hypomorphic state, vulnerable to further PRMT5 inhibition.
  • SAM S-adenosylmethionine
  • Multiple genome scale shRNA drop out screens performed in large tumor cell line panels have identified a strong correlation between MTAP loss and cell line dependency on PRMT5, further highlighting the strength of this metabolic vulnerability.
  • PRMT5 is a known cell essential gene and conditional PRMT5 knockout and siRNA knockdown studies suggest that significant liabilities could be associated with inhibiting PRMT5 in normal tissues (e.g.
  • the disclosure provides methods of treating cancer in a patient in need thereof comprising administering to the patient (a) a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in Formula (I) or having a structure pharmaceutically acceptable salt thereof; wherein
  • X 1 is NH, N(Ci-C 6 alkyl), O, or S;
  • X 2 is N(Ci-C 6 alkyl), O, or S;
  • Y 2 is H, Ci-C 6 alkyl, or Ci-Ce haloalkyl; each of Z 1 and Z 2 is independently H, F, or Ci-Ce alkyl; and each of Z 3 , Z 4 , Z 5 , and Z 6 is independently H, Ci-Cealkyl, or chloride; and
  • a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, or a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
  • a PARP inhibitor selected from a PARP inhibitor, a KRAS inhibitor, or a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
  • KIF18A Kinase-like protein 18A
  • Figure 1 is a graph showing that the combination of Compound G and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU99 NSCLC xenografts.
  • Figure 2 is a graph showing that the combination of Compound B and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU99 NSCLC xenografts.
  • Figure 3 is a graph showing that the combination of Compound B and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU5268 NSCLC patient-derived xenografts.
  • Figure 4 is a graph showing that the combination of Compound B and sotorasib resulted in decreased pancreatic cancer (MIAPACA2) cell viability.
  • FIG. 5 is a graph showing that the combination of Compound B and sotorasib significantly reduced pancreatic cancer (MIAPACA2) cell counts.
  • Figure 6A-6C show that the combination of Compound G and sotorasib significantly inhibited tumor growth in MTAP-null, KRAS G12C mutant NSCLC and PDAC xenografts.
  • Figure 6A Mice were implanted with LU99 (NSCLC CDX) tumors
  • Figure 6B LU5268 (NSCLC PDX) tumors.
  • Figure 6C MiaPaCa2 (PDAC CDX) tumors.
  • STATS P values were determined by Linear Mixed-Effects Model with a Tukey's All-Groups comparison: Combination versus either single agent; ****p ⁇ 0.0001.
  • the disclosure provides methods of treating cancer in a patient in need thereof comprising administering to the patient
  • a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in Formula (I) or having a structure pharmaceutically acceptable salt thereof;
  • X 1 is NH, N(Ci-C 6 alkyl), O, or S;
  • X 2 is N(Ci-C 6 alkyl), O, or S;
  • Y 2 is H, Ci-C 6 alkyl, or Ci-Ce haloalkyl; each of Z 1 and Z 2 is independently H, F, or Ci-Ce alkyl; and each of Z 3 , Z 4 , Z 5 , and Z 6 is independently H, Ci-Cealkyl, or chloride; and
  • the PRMT5 inhibitor has a structure of Formula (S)-l, or a pharmaceutically acceptable salt thereof:
  • X 1 is 0.
  • Z 1 and Z 2 are each H.
  • X 2 is 0.
  • each of Z 3 , Z 4 , Z 5 , and Z 6 is H.
  • Y 2 is Ci-Cehaloalkyl.
  • Y 2 is CF3.
  • the PRMT5 inhibitor is a compound having a structure of:
  • the PRMT5 inhibitor is a compound having a structure of Compound A: salt thereof.
  • the PRMT5 inhibitor is compound having a structure of Compound G: salt thereof.
  • the methods further comprise administering a standard of care therapy to the patient as a combination therapy.
  • a standard of care therapy refers to the administration of two or more therapeutic agents (e.g., a PRMT5 inhibitor as described herein and a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, Kinase-like protein 18A (KIF18A) inhibitor or a kinase inhibitor) to treat cancer.
  • a PRMT5 inhibitor as described herein
  • KIF18A Kinase-like protein 18A
  • such administration encompasses co-administration in multiple, or in separate containers (e.g., tablets, capsules, powders, and liquids) for each active ingredient. Powders and/or liquids may be reconstituted or diluted to a desired dose prior to administration.
  • administration also encompasses use of each type of therapeutic agent in a sequential manner, either at approximately the same time or at different times.
  • the second therapeutic agent is a PARP inhibitor.
  • Contemplated PARP inhibitors include, but are not limited to, olaparib, niraparib, rucaparib and talazoparib.
  • the PARP inhibitor is olaparib.
  • Olaparib is indicated as monotherapy in patients with deleterious or suspected deleterious germline BRCA mutated (as detected by an FDA-approved test) advanced ovarian cancer who have been treated with three or more prior lines of chemotherapy.
  • the recommended dose of olaparib for this indication is 400 mg (eight 50 mg capsules) taken twice daily, for a total daily dose of 800 mg.
  • the methods described herein comprise administering 400 mg twice daily to the patient.
  • the second therapeutic agent is a KRAS inhibitor.
  • Contemplated KRAS inhibitors include, but are not limited to, sotorasib (Amgen), adagrasib (MRTX849, Mirati Therapeutics), JDQ443 (Novartis Pharmaceuticals), GDC-6036 (Genentech), D-1553 (InventisBio), LY3537982 (Eli Lilly and Company), Bl 1823911 (Boehringer Ingelheim), JAB-21822 (Jacobio Pharmaceuticals), MK-1084 (Merck), YL-15293 (Shanghai YingLi Pharmaceutical Co.), RMC-6291 (Revolution Medicines), HBI-2438 (HUYABIO International), D3S-001 (D3 Bio (Wuxi) Co.), APG-1842 (Ascentage Pharma), VRTX126 (VRise Therapeutics), AZD4625 (AstraZeneca), ASP2453 (Astellas Pharma), ERAS-34
  • the KRAS inhibitor is sotorasib.
  • Sotorasib is a small molecule that irreversibly inhibits the KRAS G12C mutant protein. Sotorasib is also referred to as AMG 510 or 6-fluoro-7-(2-fluoro-6-hydroxyphenyl)-(1M)-1-[4-methyl-2-(propan-2-yl)pyridin-3-yl]-4- [(2S)-2-methyl-4-(prop-2-enoyl)piperazin-1 -yl]pyrido[2,3-d]pyrimidin-2(1 H)-one and has the following structure:
  • Dosage information can be found in LUMAKRAS® US Prescribing Information, Amgen Inc., Thousand Oaks, California, 91320 (revision 11/2022), which is herein incorporated by reference in its entirety.
  • the methods disclosed herein comprise administering 960 mg sotorasib once daily to the patient.
  • the methods disclosed herein comprise administering 240 mg sotorasib once daily to the patient.
  • the second therapeutic agent is a KIF18A inhibitor.
  • KIF18A inhibitor means any compound useful for modulating KIF18A protein alone or in a bound complex with microtubules (MT) for treating KIF18A-mediated conditions and/or diseases, e.g., cancer.
  • the KIF18A inhibitor is N-(2-(4,4-difluoropiperidin-1-yl)-6-methylpyrimidin-4-yl)-4-((2-hydroxyethyl)sulfonamido)-2-(6- azaspiro[2.5]octan-6-yl)benzamide and has the following structure:
  • the second therapeutic agent is a kinase inhibitor.
  • Contemplated kinase inhibitors include, but are not limited to, pablociclib, trametinib. bosutinib, crizotinib, dasatinib, erlotinib, osimertinib, gefitinib, lapatinib, pazopanib, ruxolitinib, sunitinib, and vemurafenib.
  • the kinase inhibitor is pablociclib.
  • the kinase inhibitor is trametinib.
  • a “therapeutically effective amount” of a PRMT5 inhibitor means an amount effective to treat or to prevent development of, or to alleviate the existing symptoms of, the patient being treated. Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. Generally, a “therapeutically effective dose” refers to that amount of a PRMT5 inhibitor described herein that results in achieving the desired effect.
  • a therapeutically effective amount of a PRMT5 inhibitor described herein decreases MTAP activity by at least 5%, compared to control, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, or at least 90%.
  • a PRMT5 inhibitor described herein is administered to a patient in need thereof orally and once a day.
  • a "patient” or “subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult.
  • a pediatric subject e.g., infant, child, adolescent
  • adult subject e.g., young adult, middle-aged adult or senior adult.
  • human human
  • patient and “subject” are used interchangeably herein.
  • the methods comprise administering a PRMT5 inhibitor described herein in an amount ranging from 40 mg to 2000 mg.
  • the PRMT5 inhibitor is administered in a divided daily dose, such as two, three, four, five, or six times a day.
  • the methods comprises administering 40 mg, 120 mg, 240 mg, 480 mg, 960 mg, 1600 mg, or 2000 mg of the PRMT5 inhibitor to the patient once daily.
  • the cancer is a MTAP -deleted cancer.
  • a MTAP-deleted (or "MTAP-null”) cancer refers to a cancer that lacks expression of the enzyme methylthioadenosine phosphorylase (MTAP).
  • the MTAP gene located at chromosomal locus 9p21 is frequently co-deleted with the CDKN2A and CDKN2B genes.
  • Selective MTAP deficiency refers to deficiency without co-deletion of the CDKN2 genes, due either to selective deletion of the MTAP locus or to methylation of the MTAP promoter.
  • MTAP-null cancers include MTAP-deficiency in at least 1% of disease cells. Terms "MTAP-null” and “MTAP-deleted” are used interchangeably herein.
  • the cancer is an MTAP-deficient and/or MTA-accumulating cancer.
  • An "MTAP- deficiency-related” or “MTAP-deficiency” or “MTAP deficient” disease for example, a proliferating disease, e.g., a cancer) or a disease (for example, a proliferating disease, e.g., a cancer)"associated with MTAP deficiency” or a disease (for example, a proliferating disease, e.g., a cancer) "characterized by MTAP deficiency” and the like refer to an ailment (for example, a proliferating disease, e.g., a cancer) wherein a significant number of cells are MTAP-deficient.
  • one or more disease cells can have a significantly reduced post-translational modification, production, expression, level, stability and/or activity of MTAP.
  • MTAP -deficiency-related diseases include, but are not limited to, cancers, including but not limited to: glioblastoma, malignant peripheral nerve sheath tumors (MPNST), esophageal cancer (e.g., esophageal squamous cell carcinoma or esophageal adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), mesothelioma, melanoma, non-small cell lung cancer (NSCLC; e.g., lung squamous or lung adenocarcinoma), astrocytoma, undifferentiated pleiomorphic sar
  • some disease cells e.g., cancer cells
  • some disease cells may be MTA-accumulating while others are not.
  • the present disclosure encompasses methods of treatment involving diseases of these tissues, or any other tissues, wherein the proliferation of MTAP-deficient and/or MTA- accumulating cells can be inhibited by administration of a PRMT5 inhibitor.
  • Some cancer cells which are MTAP-deficient are also deficient in CDKN2A; the post- translational modification, production, expression, level, stability and/or activity of the CDKN2A gene or its product are decreased in these cells.
  • MTAP and CDKN2A are in close proximity on chromosome 9p21; MTAP is located approximately 100 kb telomeric to CDKN2A. Many cancer cell types harbor CDKN2A/MTAP loss (loss of both genes). Thus, in some embodiments, a MTAP-deficient cell is also deficient in CDKN2A.
  • the patient has a cancer further comprising a KRAS G12C mutation.
  • KRAS G12C mutations occur with the alteration frequencies shown in the table below (Gerami et al., Cancer Discov. 2012, 2(5), 401; Gao et al., Science Signaling 2013, 6(269), pH ).
  • the table shows that 11.6% of patients with non-small cell lung cancer have a cancer, wherein one or more cells express KRAS G12C protein.
  • the cancer is cancer such as acute myeloid leukemia, cancer in adolescents, adrenocortical carcinoma childhood, AIDS-related cancers (e.g. Lymphoma and Kaposi's Sarcoma), anal cancer, appendix cancer, astrocytomas, atypical teratoid, basal cell carcinoma, bile duct cancer, bladder cancer, bone cancer, brain stem glioma, brain tumor, breast cancer, triple negative breast cancer, bronchial tumors, Burkitt lymphoma, carcinoid tumor, atypical teratoid, embryonal tumors, germ cell tumor, primary lymphoma, cervical cancer, childhood cancers, chordoma, cardiac tumors, chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), chronic myleoproliferative disorders, colon cancer, colorectal cancer, craniopharyngioma, cutaneous T-cell lymphoma, extra
  • the cancer is glioblastoma, malignant peripheral nerve sheath tumors (MPNST), esophageal cancer (e.g., esophageal squamous cell carcinoma or esophageal adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), mesothelioma, melanoma, non-small cell lung cancer (NSCLC; e.g., lung squamous or lung adenocarcinoma), astrocytoma, undifferentiated pleiomorphic sarcoma, diffuse large B-cell lymphoma (DLBCL), leukemia, head and neck cancer, stomach adenocarcinoma, myxofibrosarcoma, cholangiosarcoma, cancer of the brain, stomach, kidney, breast, endometrium, urinary
  • the MTAP-null cancer is lung cancer, biliary tract cancer, head and neck squamous cell carcinoma, pancreatic adenocarcinoma, gallbladder cancer, or mesothelioma.
  • the cancer is a solid tumor. In some embodiments, the tumor is malignant.
  • Exemplary MTAP-null solid tumors include, but are not limited to, MTAP-null brain cancer (including, but not limited to, MTAP-null glioma, MTAP-null oligodendroglioma, MTAP-null glioblastoma multiforme, MTAP- null astrocytoma, MTAP-null medulloblastoma, MTAP-null ependymoma, and MTAP-null meningioma), MTAP- null head and neck cancer (including, but not limited to, MTAP-null salivary gland (parotid) tumors, MTAP-null head and neck squamous cell carcinoma, and MTAP-null thyroid cancer), MTAP-null breast cancer (including, but not limited to, invasive ductal breast cancer, mixed mucinous breast cancer and lobular carcinoma),
  • the MTAP-null cancer is a hematologic tumor.
  • hematologic tumors include, but are not limited to, MTAP-null leukemia (including, but not limited to, MTAP-null acute lymphocytic leukemia, MTAP-null acute myeloid leukemia), MTAP-null lymphoma (including, but not limited to, MTAP-null mantle cell lymphoma, MTAP-null follicular lymphoma, MTAP-null diffuse large B cell lymphoma, and MTAP-null mycosis fungoides).
  • MTAP-null leukemia including, but not limited to, MTAP-null acute lymphocytic leukemia, MTAP-null acute myeloid leukemia
  • MTAP-null lymphoma including, but not limited to, MTAP-null mantle cell lymphoma,
  • compositions containing a PRMT5 inhibitor described herein can be manufactured in a conventional manner, e.g., by conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. Proper formulation is dependent upon the route of administration chosen. [0040] Monitoring Efficacy of T reatment
  • the efficacy of a given treatment for cancer can be determined by the skilled clinician. However, a treatment is considered "effective treatment," as the term is used herein, if any one or all of the signs or symptoms of e.g., a tumor are altered in a beneficial manner or other clinically accepted symptoms are improved, or even ameliorated, e.g., by at least 10% following treatment with an agent as described herein. Efficacy can also be measured by a failure of an individual to worsen as assessed by hospitalization or need for medical interventions (i.e., progression of the disease is halted). Methods of measuring these indicators are known to those of skill in the art and/or described herein.
  • the combination therapy described herein exhibits a combination benefit.
  • the term "combination benefit” refers to an observed efficacy with a combination therapy that is higher than treatment with either individual therapy alone.
  • the combination therapy described herein exhibits a combination benefit compared to PRMT5 monotherapy.
  • the combination therapy described herein exhibits a combination benefit compared to monotherapy with a second therapeutic described herein.
  • a method of treating cancer in a patient in need thereof comprising administering to the patient (a) a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in ⁇ Formula 1 > or having a structure pharmaceutically acceptable salt thereof; wherein
  • X 1 is NH, N(Ci-C 6 alkyl), O, or S;
  • X 2 is N(Ci-C 6 alkyl), O, or S;
  • Y 2 is H, Ci-C 6 alkyl, or Ci-Ce haloalkyl; each of Z 1 and Z 2 is independently H, F, or Ci-Ce alkyl; and each of Z 3 , Z 4 , Z 5 , and Z 6 is independently H, Ci-Cealkyl, or chloride; and (b) a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
  • a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
  • KRAS inhibitor is sotorasib, adagrasib, JNJ- 74699157, LY3537982, Bl 1823911, Bl 1701963, GDC-6036, tetrahydroquinazoline, JAB-2122, ARS-3248, AZD4625, or MRTX1133.
  • Table 1 Representative Compound B and olaparib concentrations and corresponding combination Fa and Cl scores in SUM149PT cells.
  • Table 2 Representative Compound B and olaparib concentrations and corresponding combination Fa and Cl scores in HCC1395 cells.
  • Table 3 Representative Compound G and olaparib concentrations and corresponding combination Fa and Cl scores in HCC1395 cells.
  • Pancreatic cancer cell lines (MIAPACA2T2) were treated with the combination of PRMT5 inhibitor (i.e., Compound B or Compound G) and sotorasib for 6 days.
  • PRMT5 inhibitor e.g., Compound B or Compound G
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 4 Representative Compound B and sotorasib concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
  • Table 5 Representative Compound G and sotorasib concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
  • Bladder cancer cell lines (UM-UC-3) were treated with the combination of PRMT5 inhibitor (i ,e. , Compound B) and sotorasib for 6 days.
  • PRMT5 inhibitor e.g., Compound B
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay.
  • Lung cancer cell lines were treated with the combination of PRMT5 inhibitor (i.e., Compound B or Compound G) and sotorasib for 6 days.
  • PRMT5 inhibitor i.e., Compound B or Compound G
  • the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 7 Representative Compound B and sotorasib concentrations and corresponding combination Fa and Cl scores in LU99 cells.
  • Table 8 Representative Compound G and sotorasib concentrations and corresponding combination Fa and Cl scores in LU99 cells.
  • Pancreatic cancer cell lines (PSN1 and MIAPACA2T2) were treated with the combination of PRMT5 inhibitor (i.e., Compound B or Compound G) and KIF18A for 6 days.
  • PRMT5 inhibitor e.g., Compound B or Compound G
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 9 Representative Compound B and KIF18A concentrations and corresponding combination Fa and Cl scores in PSN1 cells.
  • Table 10 Representative Compound G and KIF18A concentrations and corresponding combination Fa and Cl scores in PSN1 cells.
  • Table 11 Representative Compound B and KI F18A concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
  • Lung cancer cell lines were treated with the combination of PRMT5 inhibitor (e.g., Compound B) and KIF18A for 6 days.
  • PRMT5 inhibitor i.e., Compound B
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 13 Representative Compound B and KIF18A concentrations and corresponding combination Fa and Cl scores in LU99 cells.
  • Lung cancer cell lines were treated with the combination of PRMT5 inhibitor (e.g., Compound B and Compound G) and KRAS G12X inhibitor for 6 days.
  • PRMT5 inhibitor e.g., Compound B or Compound G
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the Cel ITiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 14 Representative Compound B and KRAS G12X inhibitor concentrations and corresponding combination Fa and Cl scores in A549 cells.
  • Table 15 Representative Compound G and KRAS G12X inhibitor concentrations and corresponding combination Fa and Cl scores in A549 cells.
  • Lung cancer cell lines H292 and A549 were treated with the combination of PRMT5 inhibitor (e.g., Compound B and Compound G) and palbociclib for 6 days.
  • PRMT5 inhibitor e.g., Compound B or Compound G
  • PRMT5 inhibitor was performed at a 1 .9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the Cel ITiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 16 Representative Compound B and palbociclib concentrations and corresponding combination Fa and Cl scores in H292 cells. [0079] Table 17. Representative Compound G and palbociclib concentrations and corresponding combination Fa and Cl scores in H292 cells.
  • Table 18 Representative Compound B and palbociclib concentrations and corresponding combination Fa and Cl scores in A549 cells.
  • Table 19 Representative Compound G and palbociclib concentrations and corresponding combination Fa and Cl scores in A549 cells.
  • Lung cancer cell lines were treated with the combination of PRMT5 inhibitor (e.g., Compound B and Compound G) and trametinib for 6 days.
  • PRMT5 inhibitor e.g., Compound B or Compound G
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 20 Representative Compound G and trametinib concentrations and corresponding combination Fa and Cl scores in A549 cells.
  • Table 21 Representative Compound G and trametinib concentrations and corresponding combination Fa and Cl scores in A549 cells.
  • Pancreatic cancer cell lines (MIAPACA2T2) were treated with the combination of PRMT5 inhibitor (i.e., Compound B and Compound G) and trametinib for 6 days.
  • PRMT5 inhibitor e.g., Compound B or Compound G
  • PRMT5 inhibitor was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the Cel ITiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 23 Representative Compound G and trametinib concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
  • Example 11 Combination of PRMT5 inhibitor and sotorasib inhibited tumor growth in LU99 NSCLC Xenografts
  • Example 14 Combination of PRMT5 inhibitor and sotorasib inhibited cell viability in a pancreatic cancer cell line
  • Pancreatic cancer cell line (MIAPACA2) was treated with the combination of PRMT5 inhibitor (e.g., Compound B) and sotorasib for 6 days.
  • PRMT5 inhibitor e.g., Compound B
  • the combination partner was performed at 2- fold dilution series to create an 6 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay after 6 days.
  • the combination of Compound B and sotorasib resulted in reduced MIAPACA2 cell viability.
  • nuclear counts were performed on the IncuCyte live cell imager over 8 days.
  • MIAPACA2 cells were treated with DMSO, 150nM Compound B, 50nM sotorasib, or combination (150nM Compound B + 50nM sotorasib). Results are shown in Figure 5.
  • Pancreatic cancer cell line (MIAPACA2) was treated with the combination of PRMT5 inhibitor (i.e., PRMT5 inhibitor).
  • PRMT5 inhibitor i.e., Compound B
  • the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 24 Representative Compound B and sotorasib concentrations and corresponding Cl scores in MIAPACA2 cells.
  • a MTAP-null NSCLC cancer cell line (H1650) was treated with the combination of Compound G and osimertinib for 6 days.
  • Compound G was performed at a 1 .9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the Cel ITi ter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 25. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9;
  • Table 25 Representative Compound G and osimertinib concentrations and corresponding combination Fa and Cl scores in H1650 cells.
  • a MTAP-null NSCLC cancer cell line (H1650) was treated with the combination of Compound G and erlotinib for 6 days.
  • Compound G was performed at a 1 .9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls.
  • Cell viability was measured by the Cel ITi ter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
  • Table 26 Representative Compound G and erlotinib concentrations and corresponding combination Fa and Cl scores in H1650 cells.

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Abstract

Described herein are methods of treating cancer in a patient comprising administering a PRMT5 inhibitor and a PARP inhibitor, KRAS inhibitor, or kinase-like protein 18A (KIF18A) inhibitor, or kinase inhibitor to the patient.

Description

CANCER TREATMENTS USING MTA-COOPERATIVE PRMT5 INHIBITORS
BACKGROUND
[0001] Epigenetic regulation of gene expression is an important biological determinant of protein production and cellular differentiation and plays a significant pathogenic role in a number of human diseases. Epigenetic regulation involves heritable modification of genetic material without changing its nucleotide sequence. Typically, epigenetic regulation is mediated by selective and reversible modification (e.g., methylation) of DNA and proteins (e.g., histones) that control the conformational transition between transcriptionally active and inactive states of chromatin. These covalent modifications can be controlled by enzymes such as methyltransferases (e.g., PRMT5), many of which are associated with specific genetic alterations that can cause human disease. PRMT5 plays a role in diseases such as proliferative disorders, metabolic disorders, and blood disorders.
[0002] The homozygous deletion of tumor suppressor genes is a key driver of cancer, frequently resulting in the collateral loss of passenger genes located in close genomic proximity to the tumor suppressor. Deletion of these passenger genes can create therapeutically tractable vulnerabilities that are specific to tumor cells. Homozygous deletion of the chromosome 9p21 locus, which harbors the well-known tumor suppressor CDKN2A (cyclin dependent kinase inhibitor 2A), occurs in 15% of all tumors and frequently includes the passenger gene MTAP (methylthioadenosine phosphorylase), a key enzyme in the methionine and adenine salvage pathways. Deletion of MTAP results in accumulation of its substrate, methylthioadenosine (MTA). MTA shares close structural similarity to S-adenosylmethionine (SAM), the substrate methyl donor for the type II methyltransferase PRMT5. Elevated MTA levels, driven by loss of MTAP, selectively compete with SAM for binding to PRMT5, placing the methyltransferase in a hypomorphic state, vulnerable to further PRMT5 inhibition. Multiple genome scale shRNA drop out screens performed in large tumor cell line panels have identified a strong correlation between MTAP loss and cell line dependency on PRMT5, further highlighting the strength of this metabolic vulnerability. However, PRMT5 is a known cell essential gene and conditional PRMT5 knockout and siRNA knockdown studies suggest that significant liabilities could be associated with inhibiting PRMT5 in normal tissues (e.g. pan-cytopenia, infertility, skeletal muscle loss, cardiac hypertrophy, others). Therefore, novel strategies are required to exploit this metabolic vulnerability and preferentially target PRMT5 in MTAP null tumors while sparing PRMT5 in normal tissues (MTAP WT). Targeting PRMT5 with an MTA-cooperative small molecule inhibitor could preferentially target the MTA bound state of PRMT5, enriched in MTAP null tumor cells, while providing an improved therapeutic index over normal cells where MTAP is intact and MTA levels are low.
SUMMARY
[0003] The disclosure provides methods of treating cancer in a patient in need thereof comprising administering to the patient (a) a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in Formula (I) or having a structure pharmaceutically acceptable salt thereof; wherein
X1 is NH, N(Ci-C6alkyl), O, or S;
X2 is N(Ci-C6alkyl), O, or S;
Y2 is H, Ci-C6 alkyl, or Ci-Ce haloalkyl; each of Z1 and Z2 is independently H, F, or Ci-Ce alkyl; and each of Z3, Z4, Z5, and Z6 is independently H, Ci-Cealkyl, or chloride; and
(b) a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, or a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
BRIEF DESCRIPTION OF THE FIGURES
[0004] Figure 1 is a graph showing that the combination of Compound G and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU99 NSCLC xenografts.
[0005] Figure 2 is a graph showing that the combination of Compound B and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU99 NSCLC xenografts.
[0006] Figure 3 is a graph showing that the combination of Compound B and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU5268 NSCLC patient-derived xenografts.
[0007] Figure 4 is a graph showing that the combination of Compound B and sotorasib resulted in decreased pancreatic cancer (MIAPACA2) cell viability.
[0008] Figure 5 is a graph showing that the combination of Compound B and sotorasib significantly reduced pancreatic cancer (MIAPACA2) cell counts. [0009] Figure 6A-6C show that the combination of Compound G and sotorasib significantly inhibited tumor growth in MTAP-null, KRAS G12C mutant NSCLC and PDAC xenografts. Figure 6A: Mice were implanted with LU99 (NSCLC CDX) tumors, Figure 6B: LU5268 (NSCLC PDX) tumors. Figure 6C: MiaPaCa2 (PDAC CDX) tumors. Vehicle, Compound G, and sotorasib were dosed as indicated. Data represent mean ± SD, n = 10 for each group. STATS: P values were determined by Linear Mixed-Effects Model with a Tukey's All-Groups comparison: Combination versus either single agent; ****p < 0.0001.
DETAILED DESCRIPTION
[0010] The disclosure provides methods of treating cancer in a patient in need thereof comprising administering to the patient
(a) a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in Formula (I) or having a structure pharmaceutically acceptable salt thereof;
X1 is NH, N(Ci-C6alkyl), O, or S;
X2 is N(Ci-C6alkyl), O, or S;
Y2 is H, Ci-C6 alkyl, or Ci-Ce haloalkyl; each of Z1 and Z2 is independently H, F, or Ci-Ce alkyl; and each of Z3, Z4, Z5, and Z6 is independently H, Ci-Cealkyl, or chloride; and
(b) a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor. [0011] In some embodiments, the PRMT5 inhibitor has a structure of Formula (S)-l, or a pharmaceutically acceptable salt thereof:
[0012] In some embodiments, X1 is 0. In some embodiments, Z1 and Z2 are each H. In some embodiments, X2 is 0. In some embodiments, each of Z3, Z4, Z5, and Z6 is H. In some embodiments, Y2 is Ci-Cehaloalkyl. In some embodiments, Y2 is CF3.
[0013] In some cases, the PRMT5 inhibitor is a compound having a structure of:
Compound B: salt thereof.
[0014] In some embodiments, the PRMT5 inhibitor is a compound having a structure of Compound A: salt thereof.
[0015] In some embodiments, the PRMT5 inhibitor is compound having a structure of Compound G: salt thereof.
[0016] Pharmaceutically acceptable salts of the compounds described herein include those derived from suitable inorganic and organic acids and bases. [0017] Combination therapy
[0018] In some embodiments, the methods further comprise administering a standard of care therapy to the patient as a combination therapy. The term "combination therapy" as used herein refers to the administration of two or more therapeutic agents (e.g., a PRMT5 inhibitor as described herein and a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, Kinase-like protein 18A (KIF18A) inhibitor or a kinase inhibitor) to treat cancer. Such administration encompasses co-administration of these therapeutic agents in a substantially simultaneous manner, such as in a single capsule having a fixed ratio of active ingredients. Alternatively, such administration encompasses co-administration in multiple, or in separate containers (e.g., tablets, capsules, powders, and liquids) for each active ingredient. Powders and/or liquids may be reconstituted or diluted to a desired dose prior to administration. In addition, such administration also encompasses use of each type of therapeutic agent in a sequential manner, either at approximately the same time or at different times.
[0019] In some embodiments, the second therapeutic agent is a PARP inhibitor. Contemplated PARP inhibitors include, but are not limited to, olaparib, niraparib, rucaparib and talazoparib. In some cases, the PARP inhibitor is olaparib. Olaparib is indicated as monotherapy in patients with deleterious or suspected deleterious germline BRCA mutated (as detected by an FDA-approved test) advanced ovarian cancer who have been treated with three or more prior lines of chemotherapy. The recommended dose of olaparib for this indication is 400 mg (eight 50 mg capsules) taken twice daily, for a total daily dose of 800 mg. In some embodiments, the methods described herein comprise administering 400 mg twice daily to the patient.
[0020] In some embodiments, the second therapeutic agent is a KRAS inhibitor. Contemplated KRAS inhibitors include, but are not limited to, sotorasib (Amgen), adagrasib (MRTX849, Mirati Therapeutics), JDQ443 (Novartis Pharmaceuticals), GDC-6036 (Genentech), D-1553 (InventisBio), LY3537982 (Eli Lilly and Company), Bl 1823911 (Boehringer Ingelheim), JAB-21822 (Jacobio Pharmaceuticals), MK-1084 (Merck), YL-15293 (Shanghai YingLi Pharmaceutical Co.), RMC-6291 (Revolution Medicines), HBI-2438 (HUYABIO International), D3S-001 (D3 Bio (Wuxi) Co.), APG-1842 (Ascentage Pharma), VRTX126 (VRise Therapeutics), AZD4625 (AstraZeneca), ASP2453 (Astellas Pharma), ERAS-3490 (Erasca), JN J-74699157 (ARS-3248, Janssen Research & Development), and Bl 1701963 (Boehringer Ingelheim). In some cases, the KRAS inhibitor is sotorasib. Sotorasib is a small molecule that irreversibly inhibits the KRASG12C mutant protein. Sotorasib is also referred to as AMG 510 or 6-fluoro-7-(2-fluoro-6-hydroxyphenyl)-(1M)-1-[4-methyl-2-(propan-2-yl)pyridin-3-yl]-4- [(2S)-2-methyl-4-(prop-2-enoyl)piperazin-1 -yl]pyrido[2,3-d]pyrimidin-2(1 H)-one and has the following structure:
[0021] Dosage information can be found in LUMAKRAS® US Prescribing Information, Amgen Inc., Thousand Oaks, California, 91320 (revision 11/2022), which is herein incorporated by reference in its entirety. In some embodiments, the methods disclosed herein comprise administering 960 mg sotorasib once daily to the patient. In some embodiments, the methods disclosed herein comprise administering 240 mg sotorasib once daily to the patient.
[0022] In some embodiments, the second therapeutic agent is a KIF18A inhibitor. The term "KIF18A inhibitor” means any compound useful for modulating KIF18A protein alone or in a bound complex with microtubules (MT) for treating KIF18A-mediated conditions and/or diseases, e.g., cancer. In some embodiments, the KIF18A inhibitor is N-(2-(4,4-difluoropiperidin-1-yl)-6-methylpyrimidin-4-yl)-4-((2-hydroxyethyl)sulfonamido)-2-(6- azaspiro[2.5]octan-6-yl)benzamide and has the following structure:
[0023] In some embodiments, the second therapeutic agent is a kinase inhibitor. Contemplated kinase inhibitors include, but are not limited to, pablociclib, trametinib. bosutinib, crizotinib, dasatinib, erlotinib, osimertinib, gefitinib, lapatinib, pazopanib, ruxolitinib, sunitinib, and vemurafenib. In some embodiments, the kinase inhibitor is pablociclib. In some embodiments, the kinase inhibitor is trametinib.
[0024] Dosage Regimens
[0025] A "therapeutically effective amount” of a PRMT5 inhibitor means an amount effective to treat or to prevent development of, or to alleviate the existing symptoms of, the patient being treated. Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. Generally, a "therapeutically effective dose” refers to that amount of a PRMT5 inhibitor described herein that results in achieving the desired effect. For example, a therapeutically effective amount of a PRMT5 inhibitor described herein decreases MTAP activity by at least 5%, compared to control, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, or at least 90%.
[0026] In specific embodiments, a PRMT5 inhibitor described herein is administered to a patient in need thereof orally and once a day. A "patient” or "subject” to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g., infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult. The terms "human,” "patient,” and "subject” are used interchangeably herein.
[0027] In some embodiments, the methods comprise administering a PRMT5 inhibitor described herein in an amount ranging from 40 mg to 2000 mg. In some cases, the PRMT5 inhibitor is administered in a divided daily dose, such as two, three, four, five, or six times a day. In some embodiments, the methods comprises administering 40 mg, 120 mg, 240 mg, 480 mg, 960 mg, 1600 mg, or 2000 mg of the PRMT5 inhibitor to the patient once daily.
[0028] Cancer
[0029] In some embodiments, the cancer is a MTAP -deleted cancer. A MTAP-deleted (or "MTAP-null”) cancer refers to a cancer that lacks expression of the enzyme methylthioadenosine phosphorylase (MTAP). The MTAP gene, located at chromosomal locus 9p21 is frequently co-deleted with the CDKN2A and CDKN2B genes. Selective MTAP deficiency, refers to deficiency without co-deletion of the CDKN2 genes, due either to selective deletion of the MTAP locus or to methylation of the MTAP promoter. MTAP-null cancers include MTAP-deficiency in at least 1% of disease cells. Terms "MTAP-null” and "MTAP-deleted” are used interchangeably herein.
[0030] In some embodiments, the cancer is an MTAP-deficient and/or MTA-accumulating cancer. An "MTAP- deficiency-related” or "MTAP-deficiency” or "MTAP deficient” disease (for example, a proliferating disease, e.g., a cancer) or a disease (for example, a proliferating disease, e.g., a cancer)"associated with MTAP deficiency” or a disease (for example, a proliferating disease, e.g., a cancer) "characterized by MTAP deficiency” and the like refer to an ailment (for example, a proliferating disease, e.g., a cancer) wherein a significant number of cells are MTAP-deficient. For example, in a MTAP -deficiency-related disease, one or more disease cells can have a significantly reduced post-translational modification, production, expression, level, stability and/or activity of MTAP. Examples of MTAP -deficiency-related diseases include, but are not limited to, cancers, including but not limited to: glioblastoma, malignant peripheral nerve sheath tumors (MPNST), esophageal cancer (e.g., esophageal squamous cell carcinoma or esophageal adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), mesothelioma, melanoma, non-small cell lung cancer (NSCLC; e.g., lung squamous or lung adenocarcinoma), astrocytoma, undifferentiated pleiomorphic sarcoma, diffuse large B-cell lymphoma (DLBCL), leukemia, head and neck cancer, stomach adenocarcinoma, myxofibrosarcoma, cholangiosarcoma, cancer of the brain, stomach, kidney, breast, endometrium, urinary tract, liver, soft tissue, pleura and large intestine or sarcoma. In a patient afflicted with a MTAP -deficiency-related disease, it is possible that some disease cells (e.g., cancer cells) can be MTAP-deficient while others are not. Similarly, some disease cells may be MTA-accumulating while others are not. Thus, the present disclosure encompasses methods of treatment involving diseases of these tissues, or any other tissues, wherein the proliferation of MTAP-deficient and/or MTA- accumulating cells can be inhibited by administration of a PRMT5 inhibitor. Some cancer cells which are MTAP-deficient are also deficient in CDKN2A; the post- translational modification, production, expression, level, stability and/or activity of the CDKN2A gene or its product are decreased in these cells. The genes for MTAP and CDKN2A are in close proximity on chromosome 9p21; MTAP is located approximately 100 kb telomeric to CDKN2A. Many cancer cell types harbor CDKN2A/MTAP loss (loss of both genes). Thus, in some embodiments, a MTAP-deficient cell is also deficient in CDKN2A.
[0031] In some embodiments, the patient has a cancer further comprising a KRAS G12C mutation. KRAS G12C mutations occur with the alteration frequencies shown in the table below (Gerami et al., Cancer Discov. 2012, 2(5), 401; Gao et al., Science Signaling 2013, 6(269), pH ). For example, the table shows that 11.6% of patients with non-small cell lung cancer have a cancer, wherein one or more cells express KRASG12C protein.
TABLE A [0032] In some embodiments, the cancer is cancer such as acute myeloid leukemia, cancer in adolescents, adrenocortical carcinoma childhood, AIDS-related cancers (e.g. Lymphoma and Kaposi's Sarcoma), anal cancer, appendix cancer, astrocytomas, atypical teratoid, basal cell carcinoma, bile duct cancer, bladder cancer, bone cancer, brain stem glioma, brain tumor, breast cancer, triple negative breast cancer, bronchial tumors, Burkitt lymphoma, carcinoid tumor, atypical teratoid, embryonal tumors, germ cell tumor, primary lymphoma, cervical cancer, childhood cancers, chordoma, cardiac tumors, chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), chronic myleoproliferative disorders, colon cancer, colorectal cancer, craniopharyngioma, cutaneous T-cell lymphoma, extrahepatic ductal carcinoma in situ (DCIS), embryonal tumors, CNS cancer, endometrial cancer, ependymoma, esophageal cancer, esthesioneuroblastoma, ewing sarcoma, extracranial germ cell tumor, extragonadal germ cell tumor, eye cancer, fibrous histiocytoma of bone, gall bladder cancer, gastric cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumors (GIST), germ cell tumor, gestational trophoblastic tumor, hairy cell leukemia, head and neck cancer, heart cancer, liver cancer, Hodgkin lymphoma, hypopharyngeal cancer, intraocular melanoma, islet cell tumors, pancreatic neuroendocrine tumors, kidney cancer, laryngeal cancer, lip and oral cavity cancer, liver cancer, lobular carcinoma in situ (LCIS), lung cancer, lymphoma, metastatic squamous neck cancer with occult primary, midline tract carcinoma, mouth cancer, multiple endocrine neoplasia syndromes, multiple myeloma/plasma cell neoplasm, mycosis fungoides, myelodysplastic syndromes, myelodysplastic/myeloproliferative neoplasms, multiple myeloma, merkel cell carcinoma, malignant mesothelioma, malignant fibrous histiocytoma of bone and osteosarcoma, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, non-hodgkin lymphoma, non-small cell lung cancer (NSCLC), oral cancer, lip and oral cavity cancer, oropharyngeal cancer, ovarian cancer, high-grade serous ovarian cancer, pancreatic cancer, papillomatosis, paraganglioma, paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pleuropulmonary blastoma, primary central nervous system (CNS) lymphoma, prostate cancer, rectal cancer, transitional cell cancer, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, skin cancer, stomach (gastric) cancer, small cell lung cancer, small intestine cancer, soft tissue sarcoma, T-Cell lymphoma, testicular cancer, throat cancer, thymoma and thymic carcinoma, thyroid cancer, transitional cell cancer of the renal pelvis and ureter, trophoblastic tumor, unusual cancers of childhood, urethral cancer, uterine sarcoma, vaginal cancer, vulvar cancer, or viral-induced cancer. In some cases, the cancer is pancreatic cancer; esophageal cancer; melanoma; lung cancer; mixed mullerian cancer; ovarian cancer; or gallbladder cancer.
[0033] In some embodiments, the cancer is glioblastoma, malignant peripheral nerve sheath tumors (MPNST), esophageal cancer (e.g., esophageal squamous cell carcinoma or esophageal adenocarcinoma), bladder cancer (e.g., bladder urothelial carcinoma), pancreatic cancer (e.g., pancreatic adenocarcinoma), mesothelioma, melanoma, non-small cell lung cancer (NSCLC; e.g., lung squamous or lung adenocarcinoma), astrocytoma, undifferentiated pleiomorphic sarcoma, diffuse large B-cell lymphoma (DLBCL), leukemia, head and neck cancer, stomach adenocarcinoma, myxofibrosarcoma, cholangiosarcoma, cancer of the brain, stomach, kidney, breast, endometrium, urinary tract, liver, soft tissue, pleura and large intestine or sarcoma. [0034] In some embodiments, the MTAP-null cancer is lung cancer, biliary tract cancer, head and neck squamous cell carcinoma, pancreatic adenocarcinoma, gallbladder cancer, or mesothelioma.
[0035] In some embodiments, the cancer is a solid tumor. In some embodiments, the tumor is malignant.
[0036] Exemplary MTAP-null solid tumors include, but are not limited to, MTAP-null brain cancer (including, but not limited to, MTAP-null glioma, MTAP-null oligodendroglioma, MTAP-null glioblastoma multiforme, MTAP- null astrocytoma, MTAP-null medulloblastoma, MTAP-null ependymoma, and MTAP-null meningioma), MTAP- null head and neck cancer (including, but not limited to, MTAP-null salivary gland (parotid) tumors, MTAP-null head and neck squamous cell carcinoma, and MTAP-null thyroid cancer), MTAP-null breast cancer (including, but not limited to, invasive ductal breast cancer, mixed mucinous breast cancer and lobular carcinoma), MTAP- null mesothelioma, MTAP-null gastrointestinal tract cancer (including but not limited to, MTAP-null esophageal cancer (including, but not limited to, adenocarcinoma and squamous cell carcinoma), MTAP-null gastroesophageal junction cancer, MTAP-null stomach cancer (including, but not limited to, adenocarcinoma and signet ring cell carcinoma), MTAP-null small bowel cancer, MTAP-null colon cancer, MTAP-null rectal cancer and MTAP-null gastrointestinal stromal tumor), MTAP-null neuroendocrine tumor, MTAP-null hepatobiliary cancer (including, but not limited to, MTAP-null biliary tract cancer (including cholangiocarcinoma, gallbladder cancer and ampullary cancer) and MTAP-null hepatocellular carcinoma), MTAP-null pancreatic cancer (including pancreatic adenocarcinoma), MTAP-null kidney cancer (including, but not limited to, MTAP-null renal cell carcinoma), MTAP-null adrenocortical carcinoma, MTAP-null bladder cancer (including, but not limited to, MTAP- null urothelial carcinoma), MTAP-null adrenocortical carcinoma, MTAP-null endometrial cancer, MTAP-null uterine cancer, MTAP-null testicular cancer, MTAP-null germ cell tumor, or MTAP-null prostate cancer, MTAP- null sarcoma or MTAP-null bone cancer (including, but not limited to, MTAP-null osteosarcoma, MTAP-null chondrosarcoma, MTAP-null soft tissue sarcoma, MTAP-null Ewing sarcoma, MTAP-null liposarcoma, MTAP-null leiomyosarcoma, and MTAP-null myxofibrosarcoma), MTAP-null cutaneous tumors (MTAP-null cutaneous squamous cell carcinoma and MTAP-null melanoma), MTAP-null nerve sheath tumor and MTAP-null cancer of unknown primary (CUP).
[0037] In some embodiments, the MTAP-null cancer is a hematologic tumor. Exemplary hematologic tumors include, but are not limited to, MTAP-null leukemia (including, but not limited to, MTAP-null acute lymphocytic leukemia, MTAP-null acute myeloid leukemia), MTAP-null lymphoma (including, but not limited to, MTAP-null mantle cell lymphoma, MTAP-null follicular lymphoma, MTAP-null diffuse large B cell lymphoma, and MTAP-null mycosis fungoides).
[0038] Pharmaceutical formulations and routes of administration
[0039] Pharmaceutical compositions containing a PRMT5 inhibitor described herein can be manufactured in a conventional manner, e.g., by conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. Proper formulation is dependent upon the route of administration chosen. [0040] Monitoring Efficacy of T reatment
[0041] The efficacy of a given treatment for cancer can be determined by the skilled clinician. However, a treatment is considered "effective treatment," as the term is used herein, if any one or all of the signs or symptoms of e.g., a tumor are altered in a beneficial manner or other clinically accepted symptoms are improved, or even ameliorated, e.g., by at least 10% following treatment with an agent as described herein. Efficacy can also be measured by a failure of an individual to worsen as assessed by hospitalization or need for medical interventions (i.e., progression of the disease is halted). Methods of measuring these indicators are known to those of skill in the art and/or described herein.
[0042] In some embodiments, the combination therapy described herein exhibits a combination benefit. The term "combination benefit” refers to an observed efficacy with a combination therapy that is higher than treatment with either individual therapy alone. In some embodiments, the combination therapy described herein exhibits a combination benefit compared to PRMT5 monotherapy. In some embodiments, the combination therapy described herein exhibits a combination benefit compared to monotherapy with a second therapeutic described herein.
[0043] The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. These and other changes can be made to the disclosure in light of the detailed description.
[0044] Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.
[0045] All patents and other publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents. [0046] Embodiments:
1 . A method of treating cancer in a patient in need thereof comprising administering to the patient (a) a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in <Formula 1 > or having a structure pharmaceutically acceptable salt thereof; wherein
X1 is NH, N(Ci-C6alkyl), O, or S;
X2 is N(Ci-C6alkyl), O, or S;
Y2 is H, Ci-C6 alkyl, or Ci-Ce haloalkyl; each of Z1 and Z2 is independently H, F, or Ci-Ce alkyl; and each of Z3, Z4, Z5, and Z6 is independently H, Ci-Cealkyl, or chloride; and (b) a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
2. The method of embodiment 1 , wherein the PRMT5 inhibitor has a structure of Formula (S)-l , or a pharmaceutically acceptable salt thereof:
The method of embodiment 1 or embodiment 2, wherein X1 is 0.
The method of any one of embodiments 1 -3, wherein Z1 and Z2 are each H. 5. The method of any one of embodiments 1 -4, wherein X2 is 0.
6. The method of any one of embodiments 1 -5, wherein each of Z3, Z4, Z5, and Z6 is H.
7. The method of any one of embodiments 1 -6, wherein Y2 is Ci-Cehaloalkyl .
8. The method of embodiments 7, wherein Y2 is CF3.
9. The method of any one of embodiments 1 -8, wherein the second therapeutic agent is a PARP inhibitor.
10. The method of embodiment 9, wherein the PARP inhibitor is olaparib, niraparib, rucaparib or talazoparib.
11. The method of any one of embodiments 1-10, wherein the PARP inhibitor is olaparib.
12. The method of any one of embodiments 1-11, comprising administering to the patient
(a) 40-2000 mg of PRMT5 inhibitor; and (b) 300 mg olaparib twice daily.
13. The method of any one of embodiments 1-8, wherein the second therapeutic is a KRAS inhibitor.
14. The method of embodiment 13, wherein the KRAS inhibitor is sotorasib, adagrasib, JNJ- 74699157, LY3537982, Bl 1823911, Bl 1701963, GDC-6036, tetrahydroquinazoline, JAB-2122, ARS-3248, AZD4625, or MRTX1133.
15. The method of any one of embodiments 1-8, 13 and 14, wherein the KRAS inhibitor is sotorasib.
16. The method of embodiment 15, comprising administering to the subject (a) 40-2000 mg of PRMT5 inhibitor; and (b) 960 mg sotorasib once daily.
17. The method of embodiment 15, comprising administering to the subject (a) 40-2000 mg of PRMT5 inhibitor; and (b) 240 mg sotorasib once daily.
18. The method of any one of embodiments 1-8, wherein the second therapeutic agent is kinase- like protein 18A inhibitor.
19. The method of any one of embodiments 1-8, wherein the second therapeutic agent is a kinase inhibitor.
20 The method of embodiment 19, wherein the kinase inhibitor is palbociclib or trametinib.
21 . The method of embodiment 20, wherein the kinase inhibitor is palbociclib.
22. The method of embodiment 21 , comprising administering to the subject (a) 40-2000 mg of PRMT5 inhibitor; and (b) 125 mg palbociclib once daily.
23. The method of embodiment 20, wherein the kinase inhibitor is trametinib. 24. The method of embodiment 23, comprising administering to the subject (a) 40-2000 mg of PRMT5 inhibitor; and (b) 2 mg trametinib once daily.
25. The method of any one of embodiments 1 -24, wherein the PRMT5 inhibitor is a compound having a structure o r salt thereof.
25. The method of any one of embodiments 1 -24, wherein the PRMT5 inhibitor is a compound having a structure salt thereof.
26. The method of any one of embodiments 1 -24, wherein the PRMT5 inhibitor is a compound having a structure of Compound A:
27. The method of any one of embodiments 1 -26, wherein the PRMT5 inhibitor and PARP inhibitor are administered concurrently.
28. The method of embodiment 11 , wherein the PRMT5 inhibitor and olaparib are administered concurrently.
29. The method of any one of embodiments 1 -26, wherein the PRMT5 inhibitor and PARP inhibitor are administered sequentially.
30. The method of embodiment 11 , wherein the PRMT5 inhibitor and the olaparib are administered sequentially.
31 . The method of any one of embodiments 1 -26, wherein the PRMT5 inhibitor and KRAS inhibitor are administered concurrently. 32. The method of embodiment 15, wherein the PRMT5 inhibitor and sotorasib are administered concurrently.
33. The method of any one of embodiments 1 -26, wherein the PRMT5 inhibitor and KRAS inhibitor are administered concurrently.
34. The method of embodiment 15, wherein the PRMT5 inhibitor and sotorasib are administered sequentially.
35. The method of embodiment 18, wherein the PRMT5 inhibitor and KIF18A inhibitor are administered concurrently.
36. The method of embodiment 18, wherein the PRMT5 inhibitor and KIF18A inhibitor are administered sequentially.
37. The method of any one of embodiments 1-26, wherein the PRMT5 inhibitor and kinase inhibitor are administered sequentially.
38. The method of embodiment 21, wherein the PRMT5 inhibitor and palbociclib are administered sequentially.
39. The method of embodiment 23, wherein the PRMT5 inhibitor and trametinib are administered sequentially.
40. The method of any one of embodiments 1-26, wherein the PRMT5 inhibitor and kinase inhibitor are administered concurrently.
41 . The method of embodiment 21 , wherein the PRMT5 inhibitor and palbociclib are administered concurrently.
42. The method of embodiment 23, wherein the PRMT5 inhibitor and trametinib are administered concurrently.
EXAMPLES
Example 1 - Combination of PRMT5 inhibitor and Olaparib in Breast Cancer Cell Line
[0047] Breast cancer cell lines (SUM149PT and HCC1395) were treated with the combination of PRMT5 inhibitor (i.e., Compound B and Compound G) and olaparib for 6 days. PRMT5 inhibitor (e.g., Compound B and Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation: [0048] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 1-3 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0049] Table 1. Representative Compound B and olaparib concentrations and corresponding combination Fa and Cl scores in SUM149PT cells.
[0050] Table 2. Representative Compound B and olaparib concentrations and corresponding combination Fa and Cl scores in HCC1395 cells. [0051] Table 3. Representative Compound G and olaparib concentrations and corresponding combination Fa and Cl scores in HCC1395 cells.
Example 2 - Combination of PRMT5 inhibitor and Sotorasib in Pancreatic Cancer Cell Line
[0052] Pancreatic cancer cell lines (MIAPACA2T2) were treated with the combination of PRMT5 inhibitor (i.e., Compound B or Compound G) and sotorasib for 6 days. PRMT5 inhibitor (e.g., Compound B or Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0053] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 4 and 5 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0054] Table 4. Representative Compound B and sotorasib concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
[0055] Table 5. Representative Compound G and sotorasib concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
Example 3 - Combination of PRMT5 inhibitor and Sotorasib in Bladder Cancer Cell Line
[0056] Bladder cancer cell lines (UM-UC-3) were treated with the combination of PRMT5 inhibitor (i ,e. , Compound B) and sotorasib for 6 days. PRMT5 inhibitor (e.g., Compound B) was performed at a 1.9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay.
Raw luminescent values were converted to fraction affected (Fa) with the following equation: [0057] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Table 6 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0058] Table 6. Representative Compound B and sotorasib concentrations and corresponding combination - 3Fa and Cl scores in UM-UC-3 cells.
Example 4 - Combination of PRMT5 inhibitor and Sotorasib in Lung Cancer Cell Line
[0059] Lung cancer cell lines (LU99) were treated with the combination of PRMT5 inhibitor (i.e., Compound B or Compound G) and sotorasib for 6 days. PRMT5 inhibitor (i.e., Compound B or Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0060] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 7 and 8 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0061] Table 7. Representative Compound B and sotorasib concentrations and corresponding combination Fa and Cl scores in LU99 cells.
[0062] Table 8. Representative Compound G and sotorasib concentrations and corresponding combination Fa and Cl scores in LU99 cells.
Example 5 - Combination of PRMT5 inhibitor and Kinase-like Protein 18A (KIF18A) in Pancreatic Cancer Cell Line
[0063] Pancreatic cancer cell lines (PSN1 and MIAPACA2T2) were treated with the combination of PRMT5 inhibitor (i.e., Compound B or Compound G) and KIF18A for 6 days. PRMT5 inhibitor (e.g., Compound B or Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0064] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 9-12 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0065] Table 9. Representative Compound B and KIF18A concentrations and corresponding combination Fa and Cl scores in PSN1 cells.
[0066] Table 10. Representative Compound G and KIF18A concentrations and corresponding combination Fa and Cl scores in PSN1 cells.
[0067] Table 11. Representative Compound B and KI F18A concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
[0068] Table 12. Representative Compound G and KIF18A concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
Example 6 - Combination of PRMT5 inhibitor and Kinase-like Protein 18A (KIF18A) in Lung Cancer Cell Line
[0069] Lung cancer cell lines (LU99) were treated with the combination of PRMT5 inhibitor (e.g., Compound B) and KIF18A for 6 days. PRMT5 inhibitor (i.e., Compound B) was performed at a 1.9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0070] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 13-15 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0071] Table 13. Representative Compound B and KIF18A concentrations and corresponding combination Fa and Cl scores in LU99 cells.
Example 7 - Combination of PRMT5 inhibitor and KRAS G12X inhibitor in Lung Cancer Cell Line
[0072] Lung cancer cell lines (A549) were treated with the combination of PRMT5 inhibitor (e.g., Compound B and Compound G) and KRAS G12X inhibitor for 6 days. PRMT5 inhibitor (e.g., Compound B or Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the Cel ITiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0073] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 13-15 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0074] Table 14. Representative Compound B and KRAS G12X inhibitor concentrations and corresponding combination Fa and Cl scores in A549 cells.
[0075] Table 15. Representative Compound G and KRAS G12X inhibitor concentrations and corresponding combination Fa and Cl scores in A549 cells.
Example 8 - Combination of PRMT5 inhibitor and Palbociclib in Lung Cancer Cell Line
[0076] Lung cancer cell lines (H292 and A549) were treated with the combination of PRMT5 inhibitor (e.g., Compound B and Compound G) and palbociclib for 6 days. PRMT5 inhibitor (e.g.., Compound B or Compound G) was performed at a 1 .9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the Cel ITiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0077] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 16-19 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0078] Table 16. Representative Compound B and palbociclib concentrations and corresponding combination Fa and Cl scores in H292 cells. [0079] Table 17. Representative Compound G and palbociclib concentrations and corresponding combination Fa and Cl scores in H292 cells.
[0080] Table 18. Representative Compound B and palbociclib concentrations and corresponding combination Fa and Cl scores in A549 cells.
[0081] Table 19. Representative Compound G and palbociclib concentrations and corresponding combination Fa and Cl scores in A549 cells.
Example 9 - Combination of PRMT5 inhibitor and Trametinib in Lung Cancer Cell Line
[0082] Lung cancer cell lines (A549) were treated with the combination of PRMT5 inhibitor (e.g., Compound B and Compound G) and trametinib for 6 days. PRMT5 inhibitor (e.g., Compound B or Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0083] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 20-21 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0084] Table 20. Representative Compound G and trametinib concentrations and corresponding combination Fa and Cl scores in A549 cells.
[0085] Table 21. Representative Compound G and trametinib concentrations and corresponding combination Fa and Cl scores in A549 cells.
Example 10 - Combination of PRMT5 inhibitor and Trametinib in Pancreatic Cancer Cell Line
[0086] Pancreatic cancer cell lines (MIAPACA2T2) were treated with the combination of PRMT5 inhibitor (i.e., Compound B and Compound G) and trametinib for 6 days. PRMT5 inhibitor (e.g., Compound B or Compound G) was performed at a 1.9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the Cel ITiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0087] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 22-23 below. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9; Nearly Additive: 0.9-1.1.
[0088] Table 22. Representative Compound B and trametinib concentrations and corresponding combination
Fa and Cl scores in MIAPACA2T2 cells.
[0089] Table 23. Representative Compound G and trametinib concentrations and corresponding combination Fa and Cl scores in MIAPACA2T2 cells.
Example 11 - Combination of PRMT5 inhibitor and sotorasib inhibited tumor growth in LU99 NSCLC Xenografts [0090] 10 Female NOD/SCID mice were implanted with LU99 NSCLC tumor xenografts. Mean tumor volumes for each grouping were between 100-200 mm3. Mice were allocated to the 2 different study groups by tumor volume and dosing was initiated with Vehicle or Compound G (100 mg/kg) orally once daily in combination with sotorasib (100 mg/kg). Plotted data represents the TGI (tumor growth inhibition), n = 10 for each group. Results show that the combination of Compound G and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU99 NSCLC xenografts (see Figure 1).
Example 12- Combination of PRMT5 inhibitor and sotorasib inhibited tumor growth in LU99 NSCLC Xenografts
[0091] 10 Female NOD/SCID mice were implanted with LU99 NSCLC tumor xenografts. Mean tumor volumes for each grouping were between 100-200 mm3. Mice were allocated to the 2 different study groups by tumor volume and dosing was initiated with Vehicle or Compound B (100 mg/kg) orally once daily in combination with sotorasib (100 mg/kg). Plotted data represents the TGI (tumor growth inhibition), n = 10 for each group. Results show that the combination of Compound B and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU99 NSCLC xenografts (see Figure 2).
Example 13- Combination of PRMT5 inhibitor and sotorasib inhibited tumor growth in LU5268 NSCLC Xenografts
[0092] 10 Female NOD/SCID mice were implanted with LU5268 NSCLC tumor xenografts. Mean tumor volumes for each grouping were between 100-200 mm3. Mice were allocated to the 2 different study groups by tumor volume and dosing was initiated with Vehicle or Compound B (100 mg/kg) orally once daily in combination with sotorasib (100 mg/kg). Plotted data represents the TGI (tumor growth inhibition), n = 10 for each group. Results show that the combination of Compound B and sotorasib resulted in significant anti-tumor activity versus either single agent alone in LU5268 NSCLC xenografts (see Figure 3).
Example 14 - Combination of PRMT5 inhibitor and sotorasib inhibited cell viability in a pancreatic cancer cell line
[0093] Pancreatic cancer cell line (MIAPACA2) was treated with the combination of PRMT5 inhibitor (e.g., Compound B) and sotorasib for 6 days. PRMT5 inhibitor (e.g., Compound B) was performed at a 3-fold dilution series and the combination partner was performed at 2- fold dilution series to create an 6 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay after 6 days. As shown in Figure 4, the combination of Compound B and sotorasib resulted in reduced MIAPACA2 cell viability. To assess cell growth after combination treatment, nuclear counts were performed on the IncuCyte live cell imager over 8 days. MIAPACA2 cells were treated with DMSO, 150nM Compound B, 50nM sotorasib, or combination (150nM Compound B + 50nM sotorasib). Results are shown in Figure 5.
Example 15 - Combination of PRMT5 inhibitor and Sotorasib in a Pancreatic cancer cell Line
[0094] Pancreatic cancer cell line (MIAPACA2) was treated with the combination of PRMT5 inhibitor (i.e.,
Compound B) and sotorasib for 6 days. PRMT5 inhibitor (i.e., Compound B) was performed at a 1.9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the CellTiter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0095] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Table 24 below. *CI Values (Calcusyn): Cl<1 indicates synergy. C=1 indicates additivity. C>1 indicates antagonism.
[0096] Table 24. Representative Compound B and sotorasib concentrations and corresponding Cl scores in MIAPACA2 cells.
Example 16- Combination of PRMT5 inhibitor and sotorasib inhibited tumor growth in KRAS G12C mutant NSCLC and PDAC xenografts
[0097] 10 Female NOD/SCID mice were implanted with LU99 NSCLC, LU5268 NSCLC or MisPaCa2 PDAC tumor xenografts. Mean tumor volumes for each grouping were between 100-200 mm3. Mice were allocated to the four different study groups by tumor volume and dosing was initiated with Vehicle, Compound G (100 mg/kg), sotorasib (100 mg/kg) orally once daily or a combination of Compound G (100 mg/kg) with sotorasib (100 mg/kg). Plotted data represents the TGI (tumor growth inhibition), n = 10 for each group. Results show that the combination of Compound G and sotorasib significantly inhibits tumor growth in MTAP-null, KRAS G12C mutant NSCLC and PDAC xenografts (see Figures 6A-6C).
Example 17 - Combination of PRMT5 inhibitor and osimeritinib in Lung Cancer Cell Line
[0098] A MTAP-null NSCLC cancer cell line (H1650) was treated with the combination of Compound G and osimertinib for 6 days. Compound G was performed at a 1 .9-fold dilution series and the combination partner was performed at 1.2 to 1.7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the Cel ITi ter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation: [0099] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 25. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9;
Nearly Additive: 0.9-1.1.
[0100] Table 25. Representative Compound G and osimertinib concentrations and corresponding combination Fa and Cl scores in H1650 cells.
Example 18 - Combination of PRMT5 inhibitor and erlotinib in Lung Cancer Cell Line
[0101] A MTAP-null NSCLC cancer cell line (H1650) was treated with the combination of Compound G and erlotinib for 6 days. Compound G was performed at a 1 .9-fold dilution series and the combination partner was performed at 1 .2 to 1 .7 fold dilution series to create an 8 x 10 dose matrix including DMSO-only controls. Cell viability was measured by the Cel ITi ter-Glo Luminescence assay. Raw luminescent values were converted to fraction affected (Fa) with the following equation:
[0102] Synergy analysis was performed using the CalcuSyn software to determine Cl scores based on the drug concentrations used and corresponding Fa values. Results are shown in Tables 25. *CI Values (Calcusyn): Strong Synergism: 0.1 -0.3; Synergism: 0.3-0.7; Moderate Synergism: 0.7-0.85; Slight Synergism: 0.85-0.9;
Nearly Additive: 0.9-1.1.
[0103] Table 26. Representative Compound G and erlotinib concentrations and corresponding combination Fa and Cl scores in H1650 cells.

Claims

What is claimed is:
1 . A method of treating cancer in a patient in need thereof comprising administering to the patient
(a) a PRMT5 inhibitor in an amount ranging from 40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in <Formula l> or having a structure pharmaceutically acceptable salt thereof; wherein
X1 is NH, N(Ci-C6alkyl), 0, or S;
X2 is N(Ci-C6alkyl), O, or S;
Y2 is H, Ci-C6 alkyl, or Ci-Ce haloalkyl; each of Z1 and Z2 is independently H, F, or Ci-Ce alkyl; and each of Z3, Z4, Z5, and Z6 is independently H, Ci-Cealkyl, or chloride; and
(b) a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor.
2. The method of claim 1 , wherein the PRMT5 inhibitor has a structure of Formula (S)-l , or a pharmaceutically acceptable salt thereof:
3. The method of claim 1 or claim 2, wherein X1 is O.
4. The method of any one of claims 1-3, wherein Z1 and Z2 are each H.
5. The method of any one of claims 1-4, wherein X2 is 0.
6. The method of any one of claims 1-5, wherein each of Z3, Z4, Z5, and Z6 is H.
7. The method of any one of claims 1-6, wherein Y2 is Ci-Cehaloalkyl.
8. The method of claim 7, wherein Y2 is CF3.
9. The method of any one of claims 1 -8, wherein the second therapeutic agent is a PARP inhibitor.
10. The method of claim 9, wherein the PARP inhibitor is olaparib, niraparib, rucaparib or talazoparib.
11. The method of any one of claims 1-10, wherein the PARP inhibitor is olaparib.
12. The method of any one of claims 1-11, comprising administering to the patient
(a) 40-2000 mg of PRMT5 inhibitor; and
(b) 300 mg olaparib twice daily.
13. The method of any one of claims 1-8, wherein the second therapeutic is a KRAS inhibitor.
14. The method of claim 13, wherein the KRAS inhibitor is sotorasib, adagrasib, JN J-74699157, LY3537982, Bl 1823911, Bl 1701963, GDC-6036, JAB-2122, ARS-3248, AZD4625, or MRTX1133.
15. The method of any one of claims 1-8, 13 and 14, wherein the KRAS inhibitor is sotorasib.
16. The method of claim 15, comprising administering to the subject
(a) 40-2000 mg of PRMT5 inhibitor; and
(b) 960 mg sotorasib once daily.
17. The method of claim 15, comprising administering to the subject
(a) 40-2000 mg of PRMT5 inhibitor; and
(b) 240 mg sotorasib once daily.
18. The method of any one of claims 1-8, wherein the second therapeutic agent is kinase-like protein 18A inhibitor.
19. The method of claim 18, wherein the kinase-like protein 18A inhibitor is KIF18A.
20. The method of any one of claims 1 -8, wherein the second therapeutic agent is a kinase inhibitor.
21. The method of claim 20, wherein the kinase inhibitor is palbociclib or trametinib.
22. The method of claim 21, wherein the kinase inhibitor is palbociclib.
23. The method of claim 22, comprising administering to the subject
(a) 40-2000 mg of PRMT5 inhibitor; and
(b) 125 mg palbociclib once daily.
24. The method of claim 21, wherein the kinase inhibitor is trametinib.
25. The method of claim 24, comprising administering to the subject
(a) 40-2000 mg of PRMT5 inhibitor; and
(b) 2 mg trametinib once daily.
25. The method of any one of claims 1-25, wherein the PRMT5 inhibitor is a compound having a structure salt thereof.
26. The method of any one of claims 1-25, wherein the PRMT5 inhibitor is a compound having a structure salt thereof.
27. The method of any one of claims 1-25, wherein the PRMT5 inhibitor is a compound having a structure of Compound A: salt thereof.
28. The method of any one of claims 1-27, wherein the cancer is a MTAP-null cancer.
29. The method of any one of claims 1-27, wherein the cancer is an MTAP-deficient cancer, MTA- accumulating cancer, or a combination thereof.
30. The method of any one of claims 1 -29 wherein the cancer is a solid tumor.
31 . The method of claim 30, wherein the tumor is malignant.
32. The method of any one of claims 1-31, wherein the cancer is lung cancer.
33. The method of any one of claims 1-31, wherein the cancer is pancreatic cancer.
34. The method of claim 33, wherein the MTAP-null cancer is lung cancer.
35. The method of claim 34, wherein the lung cancer is non-squamous cell lung cancer (NSCLC).
36. The method of claim 28, wherein the MTAP-null cancer is biliary tract cancer.
37. The method of claim 28, wherein the MTAP-null cancer is head and neck squamous cell carcinoma.
38. The method of claim 28, wherein the MTAP-null cancer is pancreatic adenocarcinoma.
39. The method of claim 28, wherein the MTAP-null cancer is gallbladder cancer.
40. The method of claim 28, wherein the MTAP-null cancer is mesothelioma.
41 . The method of claim 28, wherein the cancer is not a primary brain tumor or lymphoma.
42. Use of a therapeutically effective amount of (a) a PRMT5 inhibitor in an amount ranging from
40 mg to 2000 mg, wherein the PRMT5 inhibitor comprises a compound set forth in <Formula l> or having a
X1 is NH, N(Ci-C6alkyl), O, or S;
X2 is N(Ci-C6alkyl), O, or S;
Y2 is H, Ci-C6 alkyl, or Ci-Ce haloalkyl; each of Z1 and Z2 is independently H, F, or Ci-Ce alkyl; and each of Z3, Z4, Z5, and Z6 is independently H, Ci-Cealkyl, or chloride; and
(b) a second therapeutic agent selected from a PARP inhibitor, a KRAS inhibitor, a Kinase-like protein 18A (KIF18A) inhibitor, or a kinase inhibitor to treat cancer.
EP23848200.4A 2022-12-21 2023-12-20 Cancer treatments using mta-cooperative prmt5 inhibitors Pending EP4637774A1 (en)

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