EZH2 INHIBITION THERAPY FOR TREATING CANCER WITH BRCA1-RELATED PROTEIN (BAP1) mutations

Abstract

Provided herein are (R)-7-chloro-2-((1r, 4R)-4-(3-methoxyazetidin-1-yl) cyclohexyl)-2, 4-dimethyl-N-((6-methyl-4-(methylthio)-2-oxo-1, 2-dihydropyridin-3-yl) methyl) benzo [d] [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 4] triazolo [1, 2, 3] dioxol-5-carboxamide or a pharmaceutically acceptable salt thereof, or a pharmaceutically acceptable salt thereof.

Description

Related Applications

[0001] This application claims priority to U.S. Provisional Application No. 63 / 413,647, filed on October 6, 2022, the entire contents of which are incorporated by reference in their entirety. Background Art

[0002] Mutations in the BRCA1-associated protein (BAP1) gene are associated with a significantly increased risk of developing cancers, including melanoma, mesothelioma, and renal cell carcinoma. See, e.g., Cancer Genetics, (2021), vol. 256-257, 31-35; Cancer Discov (2020) 10(8):1103-112. Loss of BAP1 in mice results in elevated H3K27me3 levels, increased EZH2 expression, and enhanced inhibition of PRC2 targets. See, e.g., Nat Med (2015) 21(11):1344-1349. In addition, cancers with BAP1 mutations, such as mesothelioma, have recently been shown to display resistance to traditional platinum-based chemotherapy. See, e.g., Clin Cancer Res (2021) 27(8):2277-2291. To date, progress in treating cancers with BAP1 mutations has been limited. Therefore, new approaches to treat cancers harboring one or more BAP1 mutations are needed. Summary of the invention

[0003] It has now been discovered that mesothelioma with a BAP1 mutation can be treated with the EZH2 inhibitor (R)-7-chloro-2-((1r,4R)-4-(3-methoxyazetidin-1-yl)cyclohexyl)-2,4-dimethyl-N-((6-methyl-4-(methylthio)-2-oxo-1,2-dihydropyridin-3-yl)methyl)benzo[d][1,3]dioxole-5-carboxamide, referred to herein as Compound 1. See, e.g., the clinical data in Table 1. Thus, in one aspect, provided herein are methods of using Compound 1 to treat cancer, such as mesothelioma, having at least one BAP1 mutation. Also provided are uses of Compound 1 for the manufacture of a medicament for treating the cancer. In another aspect, provided is Compound 1 for use in the treatment of cancer, such as mesothelioma, wherein, for example, such cancer has at least one BAP1 mutation. BRIEF DESCRIPTION OF THE DRAWINGS

[0004] Figure 1 Shown is the duration of treatment with Compound 1 in subjects with malignant mesothelioma having a BAP1 loss mutation.

[0005] Figure 2Tumor growth inhibition (TGI) by treatment with Compound 1 in a BAP1 -altered patient-derived mesothelioma xenograft (PDX) model is shown.

[0006] Figure 3A Shown are mean ± SEM absolute tumor volumes over time for vehicle control and treatment groups of the mesothelioma PDX model PXF 537. Control vehicle: 10 ml / kg / day phosphate buffered saline, po. Treatment with Compound 1: 75 mg / kg / day, po.

[0007] Figure 3B Mean ± SEM absolute tumor volumes over time for vehicle control and treatment groups of the mesothelioma PDX model PXF 541 are shown. Control vehicle: 10 ml / kg / day phosphate buffered saline, po. Treatment with Compound 1: 75 mg / kg / day, po.

[0008] Figure 3C Mean ± SEM absolute tumor volumes over time for vehicle control and treatment groups of the mesothelioma PDX model PXF 680 are shown. Control vehicle: 10 ml / kg / day phosphate buffered saline, po. Treatment with Compound 1: 75 mg / kg / day, po.

[0009] Figure 3D Shown are mean ± SEM absolute tumor volumes over time for vehicle control and treatment groups of the mesothelioma PDX model PXF 1118. Control vehicle: 10 ml / kg / day phosphate buffered saline, po. Treatment with Compound 1: 75 mg / kg / day, po.

[0010] Figure 3E Mean ± SEM absolute tumor volumes over time for vehicle control and treatment groups of the mesothelioma PDX model PXF 2328 are shown. Control vehicle: 10 ml / kg / day phosphate buffered saline, oral. Treatment with Compound 1: 75 mg / kg / day, oral.

[0011] Figure 3F Mean ± SEM absolute tumor volumes over time for vehicle control and treatment groups of the mesothelioma PDX model PXF 2443 are shown. Control vehicle: 10 ml / kg / day phosphate buffered saline, oral. Treatment with Compound 1: 75 mg / kg / day, oral. DETAILED DESCRIPTION

[0012] In a first embodiment, methods of treating cancer in a subject are provided, the methods comprising administering to the subject an effective amount of Compound 1 or a pharmaceutically acceptable salt thereof, wherein the cancer has at least one BAP1 mutation. Also provided as part of the first embodiment is the use of an effective amount of Compound 1 or a pharmaceutically acceptable salt thereof for the manufacture of a medicament for treating a cancer having at least one BAP1 mutation. Also provided as part of the first embodiment is the use of an effective amount of Compound 1 or a pharmaceutically acceptable salt thereof for treating a cancer having at least one BAP1 mutation. Also provided as part of the first embodiment is a pharmaceutical composition comprising an effective amount of Compound 1 or a pharmaceutically acceptable salt thereof for treating a cancer having at least one BAP1 mutation.

[0013] Compound 1 and (R)-7-chloro-2-((1r,4R)-4-(3-methoxyazetidin-1-yl)cyclohexyl)-2,4-dimethyl-N-((6-methyl-4-(methylthio)-2-oxo-1,2-dihydropyridin-3-yl)methyl)benzo[d][1,3]dioxole-5-carboxamide are used interchangeably and each refers to a compound having the following chemical structure.

[0014] In one aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is selected from the group consisting of melanoma, mesothelioma, renal cell carcinoma, thymic carcinoma, salivary gland carcinoma, and bile duct carcinoma. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is mesothelioma. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is malignant mesothelioma. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is malignant mesothelioma of the pleura or peritoneum. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is refractory or recurrent malignant mesothelioma. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is refractory or recurrent malignant mesothelioma of the pleura or peritoneum. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is melanoma. In another aspect, as part of a second embodiment, the cancer treated by the methods of the present invention is uveal melanoma.

[0015] In a third embodiment, at least one BAP1 mutation of the methods of the invention (e.g., as in the first or second embodiment) is a loss of function (LOF) mutation. Alternatively, as part of the third embodiment, at least one BAP1 mutation of the methods of the invention (e.g., as in the first or second embodiment) results in loss of BAP1 expression. In a third embodiment, at least one BAP1 mutation of the methods of the invention (e.g., as in the first or second embodiment) is characterized as a frameshift, missense, nonsense, insertion, deletion, splice acceptor variant, or stop gain mutation. In one aspect, at least one BAP1 mutation is a p.G194R mutation or a p.L49Qfs*18 mutation. In one aspect, at least one BAP1 mutation is in the catalytic domain of BAP1.

[0016] As used herein, a BAP1 LOF mutation refers to a mutation that reduces or eliminates the function of the BAP1 protein. LOF may be due to nonsense-mediated loss of activity or loss of expression due to protein truncation (missing key residues or domains).

[0017] "Relapsed" mesothelioma or a subject characterized by relapse means a subject with cancer that had responded to a given cancer treatment (e.g., treatment with a platinum therapy such as cisplatin) but is no longer responding. "Refractory" mesothelioma or a subject characterized by refractory means a subject with cancer that has not responded or has shown worsening of the disease when undergoing a given treatment (e.g., when treated with a platinum therapy such as cisplatin).

[0018] The terms "treatment", "treat" and "treating" refer to reversing, alleviating, delaying the onset of one or more symptoms of cancer or diseases described herein, or inhibiting their progression. In some embodiments, treatment (i.e., therapeutic treatment) may be administered after one or more signs or symptoms of cancer have developed or have been observed. In other embodiments, treatment may be administered in the absence of signs or symptoms of cancer. For example, treatment (i.e., preventive treatment) may be administered to susceptible subjects before the onset of symptoms (e.g., based on a history of symptoms and / or based on exposure to pathogens). In further embodiments, treatment includes delaying the onset of at least one symptom of cancer for a period of time. Treatment may also be continued after symptoms subside, for example, to delay or prevent recurrence (i.e., maintenance therapy).

[0019] The terms "subject" and "patient" are used interchangeably and refer to mammals in need of treatment, such as companion animals (e.g., dogs, cats, etc.), farm animals (e.g., cows, pigs, horses, sheep, goats, etc.), and laboratory animals (e.g., rats, mice, guinea pigs, etc.). Typically, the subject is a human in need of treatment.

[0020] The term "effective amount" or "therapeutically effective amount" refers to the amount of compound 1 or a pharmaceutically acceptable salt thereof that will elicit a biological or medical response in a subject, such as a dose of 0.01-100 mg / kg body weight / day. In one aspect, as part of the fourth embodiment, the effective amount of compound 1 in the method of the present invention (e.g., as in any one of the first to third embodiments) ranges from about 10 mg / kg body weight / day to about 150 mg / kg body weight / day. In another aspect, as part of the fourth embodiment, the effective amount of compound 1 in the method of the present invention (e.g., as in any one of the first to third embodiments) ranges from about 50 mg to about 375 mg per day. In another aspect, as part of the fourth embodiment, the effective amount of compound 1 in the method of the present invention (e.g., as in any one of the first to third embodiments) ranges from about 200 mg to about 400 mg per day. In one aspect, as part of the fourth embodiment, the effective amount of compound 1 in the method of the present invention (e.g., as in any one of the first to third embodiments) ranges from about 200 mg to about 300 mg per day. In another aspect, as part of a fourth embodiment, the effective amount of compound 1 in the methods of the present invention (e.g., as in any one of the first to third embodiments) is about 250 mg per day. In another aspect, as part of a fourth embodiment, the effective amount of compound 1 in the methods of the present invention (e.g., as in any one of the first to third embodiments) ranges from about 325 mg to about 400 mg per day. In another aspect, as part of a fourth embodiment, the effective amount of compound 1 in the methods of the present invention (e.g., as in any one of the first to third embodiments) ranges from about 325 mg to about 375 mg per day. In another aspect, as part of a fourth embodiment, the effective amount of compound 1 in the methods of the present invention (e.g., as in any one of the first to third embodiments) is about 350 mg per day. In another aspect, as part of a fourth embodiment, the effective amount of compound 1 in the methods of the present invention (e.g., as in any one of the first to third embodiments) is about 375 mg per day. In one aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the method of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 10 mg / kg body weight / day to about 150 mg / kg body weight / day. In another aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the method of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 50 mg to about 375 mg per day. In another aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the method of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 200 mg to about 400 mg per day.In another aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the methods of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 200 mg to about 300 mg per day. In another aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the methods of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 250 mg per day. In another aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the methods of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 325 mg to about 400 mg per day. In another aspect, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of compound 1 in the methods of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of compound 1 in the range of about 325 mg to about 375 mg per day. On the other hand, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of Compound 1 in the method of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of about 350 mg of Compound 1 per day. On the other hand, as part of the fourth embodiment, the effective amount of the pharmaceutically acceptable salt of Compound 1 in the method of the present invention (e.g., in any one of the first to third embodiments) is equivalent to an amount of about 375 mg of Compound 1 per day.

[0021] The method of administration herein can be oral, parenteral, by inhalation spray, topical, rectal, nasal, buccal, vaginal or by implanted drug reservoir. The term "parenteral" as used herein includes subcutaneous, intravenous, intramuscular, intraarticular, intrasynovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques. The sterile injectable form of compound 1 described herein can be an aqueous or oily suspension. These suspensions can be formulated using suitable dispersants or wetting agents and suspending agents according to techniques known in the art. On the one hand, as part of the fifth embodiment, compound 1 in the method of the present invention (e.g., in any one of the first to fourth embodiments) is orally administered.

[0022] Compound 1 can exist in the form of a pharmaceutically acceptable salt. For use in medicine, a pharmaceutically acceptable salt refers to a non-toxic "pharmaceutically acceptable salt". Pharmaceutically acceptable salt forms include pharmaceutically acceptable acidic / anionic or basic / cationic salts (if possible).

[0023] Compound 1 or a pharmaceutically acceptable salt thereof can be formulated as part of a pharmaceutical composition comprising Compound 1 or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier. Pharmaceutically acceptable carriers (e.g., carriers, adjuvants or vehicles) that can be used in the compositions described herein include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins (e.g., human serum albumin), buffer substances (e.g., phosphates), glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes (e.g., protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts), colloidal silicon dioxide, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethyl cellulose, polyacrylates, waxes, polyethylene-polyoxypropylene block polymers, polyethylene glycol, and lanolin.

[0024] The term "pharmaceutically acceptable carrier" refers to a non-toxic carrier, adjuvant or vehicle that does not adversely affect the pharmacological activity of the compound formulated therewith, and is also safe for human use. Pharmaceutically acceptable carriers, adjuvants or vehicles that can be used for the compositions of the present disclosure include, but are not limited to, ion exchangers, aluminum oxide, aluminum stearate, magnesium stearate, lecithin, serum proteins (e.g., human serum albumin), buffer substances (e.g., phosphates), glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes (e.g., protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts), colloidal silicon dioxide, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based materials (e.g., microcrystalline cellulose, hydroxypropyl methylcellulose, lactose monohydrate, sodium lauryl sulfate and cross-linked sodium carboxymethylcellulose), polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene block polymers, polyethylene glycol and lanolin.

[0025] On the one hand, as part of the sixth embodiment, the compound 1 in the disclosed method (e.g., in any one of the first to fifth embodiments) exists in a crystalline form. The crystalline form of compound 1 is disclosed in WO 2021 / 016414 and is incorporated herein by reference. On the other hand, as part of the sixth embodiment, the compound 1 in the disclosed method (e.g., in any one of the first to fifth embodiments) is a crystalline form 1, characterized in that at least three X-ray powder diffraction peaks at 2θ angles selected from the following: 10.0°, 13.3°, 14.9°, 20.2°, 20.8°, 22.2° and 22.5°. On the other hand, as part of the sixth embodiment, the compound 1 in the disclosed method (e.g., in any one of the first to fifth embodiments) is a crystalline form 1, characterized in that at least four X-ray powder diffraction peaks at 2θ angles selected from the following: 10.0°, 13.3°, 14.9°, 20.2°, 20.8°, 22.2° and 22.5°. On the other hand, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of Compound 1 is in crystalline Form 1, characterized by at least five X-ray powder diffraction peaks at 2θ angles selected from the following: 10.0°, 13.3°, 14.9°, 20.2°, 20.8°, 22.2°, and 22.5°. On the other hand, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of Compound 1 is in crystalline Form 1, characterized by at least six X-ray powder diffraction peaks at 2θ angles selected from the following: 10.0°, 13.3°, 14.9°, 20.2°, 20.8°, 22.2°, and 22.5°. On the other hand, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of compound 1 is in crystalline form 1, characterized by an X-ray powder diffraction peak at 2θ angle selected from the following: 10.0°, 13.3°, 14.9°, 20.2°, 20.8°, 22.2°, and 22.5°. On the other hand, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of compound 1 is in crystalline form 1, characterized by an X-ray powder diffraction peak at 2θ angle selected from the following: 10.0°, 10.2°, 12.3°, 12.7°, 13.3°, 14.9°, 15.3°, 20.2°, 20.8°, 21.3°, 22.2°, 22.5°, and 23.8°.In another aspect, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of compound 1 is in crystalline form 1, characterized by an X-ray powder diffraction peak at 2θ angle selected from the following: 10.0°, 10.2°, 11.0°, 11.4°, 11.8°, 12.3°, 12.7°, 13.3°, 14.9°, 15.3°, 16.1°, 17.4°, 20.2°, 20.8°, 21.3°, 22.2°, 22.5°, and 23.8°. In another aspect, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of compound 1 is in crystalline form 1, characterized by an X-ray powder diffraction peak at 2θ angle selected from the following: 14.9°, 20.2°, and 20.8°. In another aspect, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of Compound 1 is in crystalline Form 1, characterized by an x-ray powder diffraction peak at 2θ angles selected from the group consisting of: 10.0°, 14.9°, 20.2°, and 20.8°. In another aspect, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of Compound 1 is in crystalline Form 1, characterized by an x-ray powder diffraction peak at 2θ angles selected from the group consisting of: 10.0°, 14.9°, 20.2°, 20.8°, and 22.2°. In another aspect, as part of a sixth embodiment, the disclosed method (e.g., in any one of the first to fifth embodiments) of Compound 1 is in crystalline Form 1, characterized by an x-ray powder diffraction peak at 2θ angles selected from the group consisting of: 10.0°, 13.3°, 14.9°, 20.2°, 20.8°, and 22.2°.

[0026] In one aspect, as part of the seventh embodiment, the compound 1 or a pharmaceutically acceptable salt thereof in the disclosed method (e.g., in any one of the first to fifth embodiments) is present as a solid dispersion comprising amorphous (R)-N-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide or a pharmaceutically acceptable salt thereof; and a pharmaceutically acceptable polymer. In some aspects, the pharmaceutically acceptable polymer is selected from polyvinylpyrrolidone (PVP), polyvinylpyrrolidone / vinyl acetate copolymer (PVP-VA), hydroxypropyl methylcellulose (HPMC), hydroxypropyl methylcellulose phthalate (HPMC-P) and hydroxypropyl methylcellulose acetate succinate (HPMC-AS), preferably HPMC or HPMC-AS, more preferably M grade HPMC-AS. In some aspects, the weight ratio of the pharmaceutically acceptable polymer to (R)-N-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide ranges from 10:90 wt% to 90:10 wt%, 15:85 wt% to 85:15 wt%, 20:80 wt% to 80:20 wt%, 25:75 wt% to 75:25 wt%, 30:70wt% to 70:30wt%, 35:65wt% to 65:35wt%, 40:60wt% to 60:40wt%, or 45:55wt% to 55:45wt%, preferably 25:75wt% to 75:25wt%, 30:70wt% to 70:30wt%, 40:60wt% to 60:40wt%, or 45:55wt% to 55:45wt%, more preferably 20wt% to 40wt%, or 25wt% to 35wt%, or 50%. Other aspects of the solid dispersion are described in WO 2018 / 136596.

[0027] In one aspect, as part of the eighth embodiment, Compound 1 or a pharmaceutically acceptable salt thereof in the disclosed method (e.g., in any one of the first to seventh embodiments) is administered for a period of at least about 4 days, at least about 6 days, at least about 8 days, at least about 12 days, at least about 18 days, at least about 30 days, at least about 60 days, at least about 6 months, or at least about 1 year. Examples

[0028] Preparation of compound 1

[0029] (R)-7-Chloro-2-((1r,4R)-4-(3-methoxyazetidin-1-yl)cyclohexyl)-2,4-dimethyl-N-((6-methyl-4-(methylthio)-2-oxo-1,2-dihydropyridin-3-yl)methyl)benzo[d][1,3]dioxole-5-carboxamide was prepared according to the procedures described in PCT / US2019 / 027932 and PCT / US2020 / 043163, each of which is incorporated herein by reference. Example 1

[0030] As part of a human Phase 2 clinical study, subjects with pleural or peritoneal BAP1-loss mesothelioma were administered 350 mg / day of Compound 1 for up to approximately 7.5 months ( Figure 1 ). Compound 1 was administered orally as a single agent (monotherapy). The cancer in each subject was known to have a BAP1 mutation, as determined by next-generation sequencing (NGS) or local immunohistochemistry (IHC) testing prior to treatment. The responses of efficacy-evaluable patients by cancer cohort at the intermediate cutoff date are shown in Table 1. A complete response was characterized by the disappearance of all lesions, a partial response was characterized by a reduction of at least 30% in the sum of the longest diameters (LD) of target lesions, with the baseline LD sum as reference; stable disease was characterized by neither sufficient shrinkage to meet the criteria for a partial response nor sufficient increase to meet the criteria for progressive disease, with the minimum diameter sum as reference; and progressive disease was characterized by an increase of at least 20% in the LD sum of target lesions, with the minimum LD sum recorded since the start of treatment or the appearance of one or more new lesions as reference. Table 1 Category, n (%) (N＝9) Complete remission 0 Partial remission 2(22.2) Stable disease 4(44.4) Progressive disease 3(33.3) Example 2

[0031] The ability of compound 1 to selectively inhibit the viability of mesothelioma cancer cells was evaluated in a panel of cell lines after treatment with compound 1 for 7, 14, and 21 days. 2. Luminescent cell viability assay to determine cell viability.

[0032] Cell culture conditions. MSTO-211H, H2052, H2452, H28, H226 cell lines were obtained from ATCC (Manassas, VA) and grown in the medium recommended by the supplier. For long-term assays, cells were plated in 96-well plates containing compound 1. Cell lines were treated with a dose titration of compound 1, starting with a maximum concentration of 2 μM.

[0033] Cellular Assays - Assessment of cell viability. Cell viability was assessed using a Perkin Elmer EnVision Alpha Reader (Model 2104, Waltham, MA) using the CellTiter- Relative cell number was assessed using the 2.0 Luminescent Cell Viability Assay (Promega, catalog number G9243). 50 μL of CellTiter- 2.0 reagent was added to each well containing 100 μL of cell suspension and incubated for 30 min at room temperature with low-speed shaking. GraphPad Prism was used for curve fitting and GI50 determination.

[0034] Phenotypic responses to Compound 1 in mesothelioma cell lines. In the panel of mesothelioma cell lines, most mesothelioma cell lines showed little to no viability effect from treatment with Compound 1 after 7 days of treatment. However, extended treatment for 14 and 21 days significantly increased the sensitivity of the cell lines. The observed GI50s are summarized in Table 2. At 21 days, 2 / 3 of the models with BAP1 mutation or loss were sensitive to Compound 1 treatment, while 2 / 2 of the models with intact BAP1 remained unresponsive in this setting (Table 2). In summary, Compound 1 potently affected cell viability of mutant BAP1 mesothelioma cells in long-term growth assays, with responses enriched in the BAP1 mutant model. These data suggest the applicability of Compound 1 in the treatment of BAP1 mutant mesothelioma tumors. Table 2: GI50 values ​​of mesothelioma cells treated with compound 1 for 7 days, 14 days and 21 days Example 3

[0035] Compound 1 was evaluated in 6 patient-derived pleural mesothelioma xenograft (PDX) models with BAP1 alterations (Table 3) implanted subcutaneously into immunodeficient mice (NSG mice in the case of tumor model PXF 2328 and NMRI nu / nu mice for all other tumor models). Each experiment had two groups of typically five mice each, with tumor volumes ranging from 53.9 to 198.9 mm at entry. 3 The first group was a vehicle control group, while the second group was treated with Compound 1, administered orally (po) once a day (QD) at a dose level of 75 mg / kg. The duration of the experiment ranged between 30 and 65 days. Table 3. BAP1 alteration characteristics of the PDX models used Model BAP1 alterations Zygotic PXF_537 Missense_variant Homozygous PXF_541 Frameshift_variant Heterozygous PXF_680 splice_receptor_variant Heterozygous PXF_1118 Frameshift_variant Homozygous PXF_2328 Termination obtained, splice region_variant Homozygous PXF_2443 Frameshift_variant Heterozygous

[0036] The anti-tumor efficacy of all groups was evaluated using the vehicle control group as a reference. Tumor growth inhibition was determined by comparing tumor growth in the test group with that in the vehicle control group and was expressed as the maximum tumor growth inhibition (TGI) value in percentage. The statistical significance of the difference between the test group and the control group was evaluated using a nonparametric U test. A relative TGI greater than 50% was observed in 4 of the 6 PDX models ( Figure 2 ).

[0037] Compared with the vehicle control group, compound 1 inhibited the growth of pleural mesothelioma models PXF 541 and PXF 680 with TGI values ​​> 100% and statistically significant reductions in tumor volume (non-parametric U test). Compared with the control group, compound 1 inhibited the growth of PXF 537 to almost stagnation and statistically significantly reduced tumor volume. In addition, compound 1 slowed the growth of PXF 1118 and PXF 2443, but there was no statistically significant reduction in tumor volume, while the compound was inactive against PXF 2328 implanted in NSG mice ( Figure 3A -F).

[0038] In summary, in most pleural mesothelioma PDX models, compound 1 inhibited, reduced and slowed tumor growth. These findings translated well to the clinical setting, where the majority (>60%) of patients showed (partial) responses and stable disease at the intermediate cutoff date (Table 1).

[0039] The contents of all references cited in this application (including literature references, issued patents, published patent applications, and co-pending patent applications) are expressly incorporated herein by reference in their entirety. Unless otherwise defined, all technical and scientific terms used herein are given the meanings commonly recognized by those of ordinary skill in the art.

Claims

1. A method of treating malignant mesothelioma in a subject, the method comprising administering to the subject an effective amount of a compound having the formula: or a pharmaceutically acceptable salt thereof, wherein the malignant mesothelioma has at least one BAP1 mutation.

2. The method of claim 1, wherein the at least one BAP1 mutation is a loss-of-function (LOF) mutation.

3. The method of claim 1 or 2, wherein the at least one BAP1 mutation results in loss of BAP1 expression.

4. The method according to any one of claims 1 to 3, wherein the malignant mesothelioma is pleural or peritoneal malignant mesothelioma.

5. The method according to any one of claims 1 to 4, wherein the malignant mesothelioma is pleural malignant mesothelioma.

6. The method of any one of claims 1 to 4, wherein the malignant mesothelioma is peritoneal malignant mesothelioma.

7. The method of any one of claims 1 to 6, wherein the malignant mesothelioma is characterized as relapsed or refractory.

8. The method of any one of claims 1 to 7, wherein the malignant mesothelioma is characterized by recurrence.

9. The method of any one of claims 1 to 7, wherein the malignant mesothelioma is characterized as being refractory.

10. The method of any one of claims 1 to 9, wherein about 200 to 400 mg / day of the compound is administered to the subject.

11. The method of claim 10, wherein about 350 mg / day of the compound is administered to the subject.

Images