Pyridothienopyrimidine derivatives as ALC1 inhibitors for use in treatment of homologous recombination deficient (HRD) cancers

Abstract

The present invention relates to 7-(4-bromophenyl)-2-oxo-9-(trifluoromethyl)-1, 2-dihydro-4-hydroxypyrido [3 ', 2': 4, 5] thieno [3, 2-d] pyrimidine or a pharmaceutically acceptable salt, hydrate or solvate thereof, or a hydrate or solvate of a salt thereof, for use in the treatment of advanced or metastatic cancers having a mutation in a homologous recombinant gene, and pharmaceutical compositions comprising the same.

Description

[0001] This invention relates to 7-(4-bromophenyl)-2-oxo-9-(trifluoromethyl)-1,2-dihydro-4-hydroxypyridino[3',2':4,5]thieno[3,2-d]pyrimidine or a pharmaceutically acceptable salt, hydrate or solvate thereof, or a salt thereof, and pharmaceutical compositions comprising the thereof for use in the treatment of advanced or metastatic cancers with mutations in homologous recombinant genes. Background Technology

[0002] Cancer treatment has historically revolved around inhibiting cell division. Because cancer is characterized by rapid and uncontrolled cell division, inhibiting cell division is an effective mechanism for treating patients. However, classic chemotherapy drugs are highly toxic due to their nonspecificity, and this toxicity has limited the dosage and efficacy of cancer therapies for decades.

[0003] Cancer can develop through multiple pathways, but one of the most difficult-to-treat genetic backgrounds stems from the absence of tumor suppressor genes such as BRCA1 and BRCA2. Synthetic lethal strategies have proven effective in treating these types of cancer, particularly those that have lost tumor suppressor genes involved in DNA damage repair (DDR). PARP family enzymes (which bind directly to DNA damage sites and recruit other DNA damage repair proteins) have become successful targets for small molecule inhibitors and have achieved significant clinical success. These inhibitors reduce PARP activity and trap the enzyme on DNA, thereby blocking the repair process. In the absence of BRCA1 / 2, this trapped PARP leads to DNA replication arrest, single-strand and double-strand breaks, cell cycle arrest, and ultimately cell death. Despite their clinical application, the development of resistance and severe hematologic toxicity has hampered the success of PARP inhibitors (like olaparib, niraparib, veliparib, and tapazanib), thus limiting their dosage. One strategy to expand the reach of PARP inhibitors is to combine them with other therapeutic agents. PARP inhibitors can enhance the efficacy of chemotherapy and radiotherapy because these treatments induce DNA damage in cancer cells that cannot be repaired by PARP inhibitors, thereby increasing efficacy and overcoming resistance that cancer cells may develop against PARP inhibitors. In addition to combination with approved chemotherapeutic agents, important studies have shown a high synergistic effect between ALC1 activity interference and PARP inhibition (Blessing et al., 2020; Hewitt et al., 2021; Juhász et al., 2020). Therefore, alternative treatment strategies involve targeting ALC1 (CHD1L), a chromatin remodeling enzyme, with small molecule inhibitors. This approach specifically disrupts the DNA damage process in BRCA-deficient cancers, leveraging the synthetic lethality between HRD pathway mutations and ALC1 inhibition. Notably, small molecule inhibitors targeting the helicase ALC1 for the treatment of proliferative diseases have been described in WO2022 / 117782 A1. The promising compounds disclosed in this patent application include 7-(4-bromophenyl)-2-oxo-9-(trifluoromethyl)-1,2-dihydro-4-hydroxypyridino[3',2':4,5]thieno[3,2-d]pyrimidine. Synthetic protocols for preparing these compounds are also disclosed in the document. This ALC1 inhibition approach allows for the treatment of cases where ALC1 is amplified as an oncogene, overcomes PARP inhibitor resistance mechanisms, and provides an alternative strategy for managing germline or acquired BRCA1 / BRCA2 deficiencies, including tumors characterized by "BRCAness" or other alterations to the DNA repair network.

[0004] To date, the demonstrated in vivo efficacy of ALC1 inhibitors has been limited to a very small number of compounds and a limited number of cancer types. Single-agent efficacy of specific ALC1 inhibitors has previously been reported in both in vitro and in vivo settings in ALC1-overexpressing colorectal cancer (CRC) (Abbott et al., 2020; Clune et al., 2024; Prigaro et al., 2022, WO 2021 / 195279 A2); in vitro in triple-negative breast cancer (TNBC) (WO 2022 / 117782A1); and in vitro in bone cancer, breast cancer, colorectal cancer, liver cancer, pancreatic cancer, and prostate cancer (WO 2023 / 213833A1). However, no in vivo evidence of ALC1 inhibitor activity has been shown in breast cancer, pancreatic cancer, or prostate cancer, and no in vitro evidence of ALC1 inhibitor activity in ovarian cancer has been published. Therefore, whether the proposed in vivo efficacy can actually be achieved remains to be seen.

[0005] Very few ALC1i are described in this field, such as those described by Abbott et al. in 2020 (Abbott et al., 2020). This document discloses inhibitors of CHD1L and their in vitro antitumor activity. Two of the most active ALC1i (i.e., "Compound 1" and "Compound 3") have the following chemical structures:

[0006]

[0007] Compound 1 Compound 3

[0008] Other ALC1 inhibitors that selectively kill TNBC cells in vitro are disclosed in WO 2022 / 117782 A1, and their important representatives have the following chemical structures:

[0009]

[0010] Surprisingly, certain ALC1 inhibitors, such as those used in this invention, have been found to provide excellent in vivo efficacy, making them particularly suitable for treating patients with advanced or metastatic solid tumors that have mutations in homologous recombinant genes. Specifically, although they exhibit poor properties in nucleosome remodeling assays as described in WO 2022 / 117782 A1, they surprisingly demonstrate superior in vivo efficacy, particularly in treating cancers with at least one mutation in a homologous recombinant gene. Summary of the Invention

[0011] In one embodiment, the present invention relates to 7-(4-bromophenyl)-2-oxo-9-(trifluoromethyl)-1,2-dihydro-4-hydroxypyridino[3',2':4,5]thieno[3,2-d]pyrimidine, namely compounds of formula (I), also referred herein as ALC1i-1:

[0012]

[0013] (I)

[0014] The compound, or a pharmaceutically acceptable salt thereof, its hydrate, or a hydrate of its salt, is used for the treatment of advanced or metastatic cancers (particularly solid tumors) with at least one mutation in a homologous recombinant gene.

[0015] In another embodiment, the present invention relates to a pharmaceutical composition comprising a compound of formula (I) or a pharmaceutically acceptable salt, hydrate or solvate thereof, or a hydrate or solvate thereof, and optionally a pharmaceutically suitable carrier, the pharmaceutical composition being used for the treatment of advanced or metastatic cancer having at least one mutation in a homologous recombinant gene. Attached Figure Description

[0016] Figure 1 EC50 of ALC1i-1 in various cancer cell lines 50 The two tables indicate the efficacy of ALC1i-1 as monotherapy in various cancer cell lines EC in 96-hour and 11-day cell proliferation assays with SRB-based readings as described in WO 2022 / 117782 A1. 50 .

[0017] Figure 2 ALC1i-1 treatment of the TNBC cell line SUM149PT CDX. Tumor growth curves of xenografts (CDX) derived from the triple-negative breast cancer (TNBC) cell line SUM149PT in nude mice under different doses of ALC1i-1 by NMRI.

[0018] Figure 3 ALC1i-1 treatment of prostate cancer cell line DU145 CDX. Tumor growth curves of xenografts (CDX) derived from prostate cancer cell line DU145 in nude mice under different doses of ALC1i-1 by NMRI.

[0019] Figure 4ALC1i-1 treatment of mouse PDAC cell line 60590 CDX in immune-active mice. Tumor growth curves of xenografts (CDX) derived from mouse pancreatic ductal adenocarcinoma (PDAC) cell line 60590 in NMRI mice at different doses of ALC1i-1.

[0020] Figure 5 ALC1i-1 treatment of ovarian cancer cell line OVCAR3. Cell survival curves of ovarian cancer cell line OVCAR3 after treatment with different concentrations of ALC1i-1 in a 96-hour cell proliferation assay with SRB-based readings as described in WO 2022 / 117782 A1.

[0021] Figure 6 Treatment of various cancer cell lines with compounds 1 and 3. Cell survival curves of SUM149PT, DU145, and PSN1 cells after treatment with different concentrations of compounds 1 and 3 in a 96-hour cell proliferation assay with SRB-based readings as described in WO 2022 / 117782 A1.

[0022] Figure 7 96-hour ALC1i-1 treatment of various cancer cell lines. Representative cell survival curves of SUM149PT, DU145, and PSN1 cells after treatment with different concentrations of ALC1i-1 in a 96-hour cell proliferation assay with SRB-based readings as described in WO 2022 / 117782 A1.

[0023] Figure 8 11-day treatment of SUM149PT cells. Cell survival curves of SUM149PT cells with SRB-based readings in an 11-day cell proliferation assay as described in WO 2022 / 117782 A1, compared with ALC1i-74, ALC1i-132 and ALC1i-194.

[0024] Figure 9 ALC1i-194 treatment of the TNBC cell line SUM149PT CDX. Tumor growth curves of the TNBC cell line SUM149PT CDX in NMRI nude mice treated with ALC1i-194.

[0025] Figure 10 Compared with ALC1i-74, ALC1i-132 and ALC1i-194, ALC1i-1 exhibits inhibition of ALC1 nucleosome sliding.

[0026] Figure 11List of HR genes. The following is a list of genes involved in the DNA damage response (DDR) cited in the literature (Human DNA Repair Genes, date unknown): Wood RD, Mitchell M and Lindahl T Mutation Research, 2005; Science, 2001; reference book DNA Repair and Mutagenesis, 2nd edition, 2006; and Nature Reviews Cancer, 2011 (modified by R. Wood and M. Lowery on Wednesday, June 10, 2020).

[0027] Figure 12 List of genes associated with the homologous recombination repair pathway (HR). Genes from Toh and Ngeow, 2021; Kim et al., 2021; Yamamoto and Hirasawa, 2021, and a summary of HRD signature genes from Peng et al., 2014. Detailed Implementation

[0028] Before describing the invention in detail below, it should be understood that the invention is not limited to the specific methods, schemes, and reagents described herein, as these can be modified. It should also be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the scope of the invention, which will be defined only by the appended claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.

[0029] Numerous references are cited throughout this specification. Every reference cited herein, whether above or below (including all patents, patent applications, scientific publications, manufacturer's specifications, instructions, etc.), is incorporated herein by reference in its entirety. Nothing herein should be construed as an admission that the invention is not entitled to any prior disclosure due to prior invention. Some documents cited herein are characterized as "incorporated by reference." In the event of a conflict between the definitions or teachings of such incorporated references and those listed in this specification, the text of this specification shall prevail.

[0030] The elements of the invention will be described below. These elements are listed using specific embodiments; however, it should be understood that these specific embodiments can be combined in any manner and in any number to produce other embodiments. The differentiated descriptions of embodiments and preferred embodiments should not be construed as limiting the invention to only the explicitly described embodiments. This specification should be understood to support and cover embodiments combining the explicitly described embodiments with any number of disclosed and / or preferred elements. Furthermore, unless the context otherwise indicates, any arrangement and combination of the elements described herein should be considered.

[0031] definition

[0032] To carry out this invention, unless otherwise instructed, conventional methods of chemical, biochemical, and recombinant DNA techniques as explained in the literature in the art shall be employed (see, for example, Molecular Cloning: A Laboratory Manual, 2nd edition, edited by J. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold Spring Harbor 1989).

[0033] The following provides definitions for some terms that are frequently used in this specification. These terms will have their respective defined and preferred meanings in the remainder of this specification in each instance of their use.

[0034] Unless the context clearly specifies otherwise, as used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural indicators.

[0035] "Pharmaceutical acceptable" means approved by a federal or state regulatory agency or listed in the United States Pharmacopeia (United States Pharmacopeia-33 / National Formulary-28 Reissue, published by United States Pharmacopeia Convention, Inc., Rockville, Maryland, April 2010) or other recognized pharmacopoeias for use in animals, and more particularly in humans.

[0036] The term "pharmaceutically acceptable salt" refers to a salt of the compounds of the present invention. Suitable pharmaceutically acceptable salts of the compounds of the present invention include acid addition salts, which can be formed, for example, by mixing a solution of the compounds described herein or their derivatives with a solution of a pharmaceutically acceptable acid (such as hydrochloric acid, sulfuric acid, fumaric acid, maleic acid, succinic acid, acetic acid, benzoic acid, citric acid, tartaric acid, carbonic acid, or phosphoric acid). Furthermore, in cases where the compounds of the present invention have an acidic moiety, suitable pharmaceutically acceptable salts may include alkali metal salts (e.g., sodium or potassium salts); alkaline earth metal salts (e.g., calcium or magnesium salts); and salts formed with suitable organic ligands (e.g., ammonium, quaternary ammonium, and amine cations formed using counter anions (such as halides, hydroxides, carboxylates, sulfates, phosphates, nitrates, alkyl sulfonates, and aryl sulfonates)).Illustrative examples of pharmaceutically acceptable salts include, but are not limited to: acetates, adipic acid salts, alginates, ascorbic acid salts, aspartate salts, benzenesulfonates, benzoates, bicarbonates, bisulfates, tartrates, borates, bromides, butyrates, calcium edetate, camphorates, camphorsulfonates, camsylates, carbonates, chlorides, citrates, clavulanates, cyclopentanepropionate, digluconate, dihydrochlorides, dodecyl sulfates, edetate, ethanedisulfonate, etopoate, ethanesulfonate, ethanesulfonate, formate, fumarate, gluceptate, glucoheptonate, gluconate, glutamate, glycerophosphates, glycolylarsanilates, hemisulfates, heptahydrates, hexanoates, hexylresorcinol salts, hydrabamine, hydrobromide, and salts. Salts, hydroiodates, 2-hydroxyethanesulfonate, hydroxynaphthylcarboxylate, iodides, isothiosulfates, lactates, lacturonates, laurates, lauryl sulfates, malates, maleates, malonates, mandelates, methanesulfonates, methanesulfonates, methyl sulfates, mucilages, 2-naphthalenesulfonate, naphthalenesulfonate, nicotinate, nitrates, N-methylglucosamine ammonium salts, oleates, oxalates, dihydroxynaphthylcarboxylate (p Amoate (embonate), palmitate, pantothenate, pectinate, persulfate, 3-phenylpropionate, phosphate / bisphosphate, picrate, neopentanoate, polygalacturonate, propionate, salicylate, stearate, sulfate, hypoacetate, succinate, tannic acid salt, tartrate, teoclate, toluenesulfonate, triethyliodide, undecanoate, valerate, etc. (see, for example, Berge, SM et al., "Pharmaceutical Salts", Journal of Pharmaceutical Science, 1977, 66, 1-19). Preferred salts are sodium salts of compounds of formula (I).

[0037] The neutral form of the compound can be regenerated by contacting the salt with a base or acid and separating the parent compound in a conventional manner. The parent form of the compound differs from the various salt forms in some physical properties (such as solubility in polar solvents), but in other respects, for the purposes of this invention, the salt and the parent form of the compound are equivalent.

[0038] In addition to salt forms, the present invention also provides compounds in prodrug form. The prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide compounds of formula (I). Prodrugs are active or inactive compounds that, upon administration to a patient, are chemically modified into the compounds of the present invention through physiological processes in vivo, such as hydrolysis, metabolism, etc. Furthermore, prodrugs can be converted into the compounds of the present invention in an in vitro environment by chemical or biochemical methods. For example, when placed in a transdermal patch reservoir containing suitable enzymes, prodrugs can be slowly converted into the compounds of the present invention. The suitability and techniques involved in the preparation and use of prodrugs are well known to those skilled in the art. For a general discussion of prodrugs involving esters, see Svensson LA and Tunek A. (1988) Drug Metabolism Reviews 19(2): 165-194 and Bundgaard H. “Design of Prodrugs”, Elsevier Science Ltd. (1985). Examples of masked carboxylate anions include various esters such as alkyl (e.g., methyl, ethyl), cycloalkyl (e.g., cyclohexyl), aralkyl (e.g., benzyl, p-methoxybenzyl), and alkylcarbonyloxyalkyl (e.g., neopentyloxymethyl). Amines have been masked as arylcarbonyloxymethyl-substituted derivatives, which are cleaved in vivo by esterases, releasing the free drug and formaldehyde (Bundgaard H. et al. (1989) J. Med. Chem. 32(12): 2503-2507). In addition, drugs containing acidic NH groups (e.g., imidazole, imide, indole, etc.) have been masked with N-acyloxymethyl (Bundgaard H. “Design of Prodrugs”, Elsevier Science Ltd. (1985)). Hydroxyl groups have been masked as esters and ethers. EP 0 039 051 A2 discloses the prodrug of Mannich base hydroxamic acid, its preparation, and its use.

[0039] The compounds of the present invention may also contain atomic isotopes in non-natural proportions at one or more sites among the atoms constituting such compounds. For example, radioactive isotopes (such as tritium) can be used. 3 H), Iodine-125 ( 125 I) or carbon-14 ( 14 C) Radiolabeling of the compounds. All isotopic variants of the compounds of the present invention, whether or not radioactive, are intended to be covered within the scope of the present invention.

[0040] As used herein, "patient" means any mammal or bird that may benefit from treatment with the compounds described herein. Preferably, "patient" is selected from laboratory animals, livestock, or primates (including chimpanzees and humans). Particularly preferably, "patient" is a human.

[0041] As used herein, “treat,” “treating,” or “treatment” for a disease or disorder means to accomplish one or more of the following: (a) reducing the severity of the disorder; (b) limiting or preventing the development of symptoms characteristic of one or more disorders being treated; (c) suppressing the worsening of symptoms characteristic of one or more disorders being treated; (d) limiting or preventing the recurrence of said one or more disorders in a patient who previously had one or more disorders; and (e) limiting or preventing the recurrence of symptoms in a patient who previously had symptoms of one or more disorders.

[0042] The "pharmaceutical composition" according to the invention can exist in the form of a composition in which different active ingredients and diluents and / or carriers are mixed with each other; or it can be in the form of a combination formulation in which the active ingredients exist in some or completely different forms. An example of such a combination or combination formulation is a kit.

[0043] "Effective dose" is the amount of a therapeutic agent sufficient to achieve the intended purpose. The effective dose of a given therapeutic agent will vary depending on factors such as the nature of the agent, the route of administration, the size and species of the animal to be treated, and the purpose of administration. The effective dose in each individual case can be determined empirically by a person skilled in the art using methods recognized in the field.

[0044] As used herein, the term "carrier" refers to a diluent, adjuvant, excipient, or medium that is administered with a therapeutic agent. Such drug carriers can be sterile liquids, such as saline solutions in water, and oils, including petroleum, animal, plant, or synthetic oils, such as peanut oil, soybean oil, mineral oil, sesame oil, etc. Saline solutions are preferred carriers when the drug composition is administered intravenously. Saline solutions, as well as aqueous dextran and glycerol solutions, can also be used as liquid carriers, particularly for injectable solutions. Suitable drug excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glyceryl monostearate, talc, sodium chloride, skim milk, glycerol, propylene glycol, water, ethanol, etc. If desired, the composition may also contain small amounts of wetting agents or emulsifiers, or pH buffers. These compositions can be in the form of solutions, suspensions, emulsions, tablets, pills, capsules, powders, sustained-release formulations, etc. The composition can be formulated as a suppository using conventional binders and carriers (such as triglycerides). The compounds of the present invention can be formulated in a neutral or salt form. Pharmaceutically acceptable salts include salts formed with free amino groups, such as those derived from hydrochloric acid, phosphoric acid, acetic acid, oxalic acid, tartaric acid, etc.; and salts formed with free carboxyl groups, such as those derived from sodium hydroxide, potassium hydroxide, ammonium hydroxide, calcium hydroxide, ferric hydroxide, isopropylamine, triethylamine, 2-ethylaminoethanol, histidine, procaine, etc. Sodium salts are preferred. Examples of suitable pharmaceutical carriers are described in EW Martin's "Remington's Pharmaceutical Sciences". Such compositions will contain a therapeutically effective amount of the compound (preferably in a purified form) and a suitable carrier to provide a form suitable for appropriate administration to the patient. The formulation should be appropriate for the administration method.

[0045] As used herein, the term “cancer” (preferably a tumor (also called a vegetation), particularly a solid tumor) refers to cells capable of autonomous growth. Examples of such cells include cells exhibiting an abnormal state or condition characterized by rapid proliferative cell growth. This term implies including cancerous growth, such as tumors; cells, tissues, or organs undergoing carcinogenic processes, metastatic tissues, and malignant transformations, regardless of histopathological type or stage of invasion. It also includes malignant tumors of various organ systems, such as the respiratory, cardiovascular, renal, reproductive, hematopoietic, nervous, hepatic, gastrointestinal, and endocrine systems; and adenocarcinomas, including malignant tumors such as most colon cancers, renal cell carcinomas, prostate and / or testicular tumors, non-small cell lung cancer, and small bowel cancer. “Naturally occurring” cancer includes any cancer not experimentally induced by implanting cancer cells into a subject, and includes, for example, spontaneously occurring cancer, cancer resulting from patient exposure to one or more carcinogens, cancer resulting from the insertion of a transgenic oncogene or the knockout of a tumor suppressor gene, and cancer resulting from infection (e.g., viral infection). The term "cancer" is generally accepted in the art and refers to a malignant tumor of epithelial or endocrine tissue. The term also includes carcinosarcoma, which comprises a malignant tumor composed of cancerous and sarcomatous tissue. "Adenocarcinoma" refers to cancer originating from glandular tissue or in which tumor cells form identifiable glandular structures. The term "sarcoma" is generally accepted in the art and refers to a malignant tumor of mesenchymal origin. The term "hematopoietic neoplasia" includes diseases involving proliferating / necrotrophic cells of hematopoietic origin. Hematopoietic neoplasia may originate from myeloid, lymphoid, or erythroid lineages or their precursor cells.

[0046] In some embodiments of the invention, the cancer is breast cancer, ovarian cancer, prostate cancer, pancreatic cancer, gastric cancer, gastroesophageal cancer, non-small cell lung cancer, colorectal cancer, hepatocellular carcinoma, uterine cancer, bone cancer (preferably osteosarcoma), bladder cancer, endometrial cancer, brain cancer (especially astrocytoma or glioma), cervical cancer, kidney cancer (especially RCC), thyroid cancer, fallopian tube cancer, peritoneal cancer, acute myeloid leukemia, or uveal melanoma. In some embodiments, the cancer is basaloid carcinoma, basaloid breast cancer, triple-negative breast cancer, high-grade cancer, or high-grade serous ovarian cancer. In one embodiment of various aspects of the invention, the cancer is ovarian cancer, breast cancer, prostate cancer, pancreatic cancer, fallopian tube cancer, colorectal cancer, hepatocellular carcinoma, or bone cancer (preferably osteosarcoma). In a particularly preferred embodiment, the cancer is selected from ovarian cancer, fallopian tube cancer, primary peritoneal cancer, breast cancer, castration-resistant prostate cancer, and pancreatic ductal adenocarcinoma, especially metastatic ovarian cancer, metastatic fallopian tube cancer, metastatic primary peritoneal cancer, metastatic breast cancer, metastatic castration-resistant prostate cancer, and metastatic pancreatic ductal adenocarcinoma.

[0047] According to the present invention, the cancer to be treated has at least one mutation in a homologous recombination (HR) gene, i.e., the cancer is an HR-deficient cancer. An HR-deficient cancer refers to a cancer in which at least one HR gene in one or more cells has an abnormal level or activity. These abnormal levels or activities interfere with normal HR gene function and may cause defects in HR-mediated DNA repair or reduce the stability of replication forks. In a preferred embodiment, the cancer to be treated is BRCA1-deficient and / or BRCA2-deficient. A BRCA1-deficient or BRCA2-deficient cancer refers to a cancer in which one or more cells have abnormal BRCA1 levels or activity or abnormal BRCA2 levels or activity. These abnormal levels or activities interfere with the normal function of BRCA1 or BRCA2 and may cause defects in HR-mediated DNA repair or reduce the stability of replication forks. Preferably, the proliferative disease is selected from BRCA-1 and / or BRCA-2-deficient cancers (preferably tumors), and / or the proliferative disease is selected from hepatocellular carcinoma, breast cancer, ovarian cancer, fallopian tube cancer, prostate cancer, colorectal cancer, gastric cancer, gastroesophageal cancer, non-small cell lung cancer, or pancreatic cancer.

[0048] Particularly preferred examples of cancers that can be treated according to various aspects of the present invention are ovarian cancer, fallopian tube cancer, primary peritoneal cancer, breast cancer, prostate cancer, and pancreatic cancer. Preferably, the cancer is metastatic, particularly stage IV cancer.

[0049] Preferably, the cancer to be treated according to various aspects of the invention has relapsed or progressed, preferably after first-line chemotherapy. Therefore, preferably, the compounds according to the invention are used as second- or third-line therapy, more preferably, as second- or third-line therapy for treating HR-deficient cancers.

[0050] According to the present invention, the cancer to be treated is preferably in stage III (locally advanced) or stage IV (metastatic).

[0051] Furthermore, according to the present invention, cancers to be treated according to various aspects of the present invention have a potential deficiency in DNA damage repair (such as HR repair), i.e., HR-deficient cancers (HRD cancers), particularly HR-deficient ovarian cancer, HR-deficient fallopian tube cancer, HR-deficient primary peritoneal cancer, HR-deficient breast cancer, HR-deficient (castration-resistant) prostate cancer, or HR-deficient pancreatic cancer, such as pancreatic ductal adenocarcinoma (mPDAC). In a particularly preferred embodiment, these cancers are metastatic. In one embodiment, cancer cells are in, as... Figure 11 and / or Figure 12The DNA repair genes listed herein (specifically ARID1A, ATM, ATRX, BAP1, BLM, BRCA1, BRCA2, BARD1, BRIP1, CHEK1, CHEK2, FANCA / C / D2 / E / F / G / L, MRE11A, NBN, PALB2, RAD50, RAD51C, RAD51D, RAD51, RAD51B, and / or WRN) have mutations / deletions / insertions. BRCA1 / 2 is the most preferred.

[0052] In one implementation, the cancer to be treated or the cancer patient to be treated is selected based on the presence of tumor markers. In a clinical setting, cancer / patient selection will include, but is not limited to, qualified tumor biomarkers, i.e., harmful mutations, including ARID1A, ATM, ATRX, BAP1, BLM, BRCA1, BRCA2, BARD1, BRIP1, CHEK1, CHEK2, FANCA / C / D2 / E / F / G / L, MRE11A, NBN, PALB2, RAD50, RAD51C, RAD51D, RAD51, RAD51B and / or WRN, which are preferred, with BRCA1 / 2 being the most preferred, and / or such... Figure 11 and / or Figure 12 Other gene variants in the HR pathway listed in [the original text].

[0053] Preferably, the patient to be treated according to various aspects of the invention is a cancer patient, preferably suffering from the cancers described above, such as breast cancer, ovarian cancer, prostate cancer, pancreatic cancer, gastric cancer, gastroesophageal cancer, non-small cell lung cancer, colorectal cancer, hepatocellular carcinoma, uterine cancer, bone cancer (preferably osteosarcoma), fallopian tube cancer, peritoneal cancer, acute myeloid leukemia, or uveal melanoma, more preferably ovarian cancer, fallopian tube cancer, primary peritoneal cancer, breast cancer, prostate cancer, and pancreatic cancer, and optionally in cases such as Figure 11 The cancer patient has a mutation / deletion / insertion in one or more of the HR genes listed in 12 (preferably BRCA1 / 2). In a particularly preferred embodiment, the cancer patient has HR-deficient cancer as defined above, particularly BRCA-1 and / or BRCA-2 deficient.

[0054] In a preferred embodiment, ALC1i is used as a monotherapy, i.e., not in combination with another anticancer agent.

[0055] In a preferred embodiment, as defined above, ACL1i is administered orally in a pharmaceutical composition as defined above, preferably as a tablet or capsule.

[0056] In one embodiment, the invention also relates to a method for treating patients with advanced or metastatic cancer having at least one mutation in a homologous recombinant gene as defined above, the method comprising administering a compound of formula (I) as defined above. Preferred embodiments of the treatment method (particularly the treatment of the cancer to be treated and the treatment method for the patient) are as described above.

[0057] Experimental results

[0058] The inventors tested known ALC1 inhibitors (i.e., compounds 1 and 3 as shown above) against breast cancer, pancreatic cancer, and prostate cancer cell lines SUM149PT, DU145, and PSN1 in vitro at a 96-hour cell killing assay. Compound 3 failed to elicit a 50% response in any of the tested cell lines, and compound 1 had a minimum EC50 of 20.3 µM in PSN1 cells. 50 ,like Figure 6 As shown in the image.

[0059] Furthermore, the inventors tested several ALC1 inhibitors disclosed in WO 2022 / 117782 A1, particularly the most promising compounds disclosed, such as ALC1i-74, ALC1i-132, and ALC1i-194, which were superior in the nucleosome sliding inhibition assay described in WO 2022 / 117782A1. A comparison of ALC1i-1 with ALC1i-74, ALC1i-132, and ALC1i-194 of the same compound class in various assays is shown in [reference needed]. ALC1i-1 is the least potent inhibitor of ALC1 sliding, with an IC50 of [value missing]. 50 The potency was 94.9 µM, compared to 51.4 µM, 4.0 µM, and 9.0 µM for ALC1i-74, ALC1i-132, and ALC1i-194, respectively. All compounds were brought to a further screening assay, which determined their potency and selectivity in a range of cell lines in both 96-hour and 11-day cell SRB assays, as described in WO 2022 / 117782A1. However, the most promising compounds, ALC1i-74, ALC1i-132, and ALC1i-194, showed some unsatisfactory in vivo results in treatment with breast, pancreatic, prostate, and ovarian cancer cells. Notably, the compound used according to the invention (i.e., ALC1i-1) unexpectedly demonstrated superior single-agent in vitro and in vivo efficacy in breast, pancreatic, and prostate cancers, and superior single-agent in vitro efficacy in ovarian cancer. ALC1i-1 showed potency of less than 10 µM against several cancer cell lines (see [link to relevant documentation]). Figure 1 and Figure 7 ).

[0060] Surprisingly, when comparing the potency of ALC1 inhibitors in an 11-day cell killing assay ( Figure 8 As shown in the figure, the inventors discovered a non-linear relationship between nucleosome sliding inhibition and cytotoxic efficacy. In an 11-day cytotoxicity assay of SUM149PT cells, ALC1i-1 (EC1) showed a significant increase in cytotoxicity. 50 = 140 nM) in TNBC SUM149PT cells compared to ALC1i-74 (EC) 50 = 9.6µM) or ALC1i-132 (EC 50 = 1.1 µM) was significantly more effective, but still significantly less effective than ALC1i-194 (EC). 50 = 320 pM) effective.

[0061] ALC1i-1 and ALC1i-194, as two of the most potent compounds in cell killing assays, were tested in vivo against xenografted SUM149PT cells. Given the nearly 1000-fold potency advantage of ALC1i-194 over ALC1i-1, the inventors surprisingly found that in in vivo assays using SUM149PT CDX, ALC1i-1 (TGI = 85.7%)... Figure 2 ) compared to ALC1i-194 (TGI = 29.0%) Figure 9 Significantly more effective. For example... Figure 9 As shown, even at concentrations of ALC1i-194 more than 10 times higher, the total growth inhibition (TGI) was poor.

[0062] After validating the remarkable efficacy of ALC1i-1 in breast cancer in vivo, further validation of ALC1i-1 was conducted in prostate cancer and pancreatic cancer using DU145 cells and 60590 cells respectively, with the aid of CDX models in mice. Figure 3 and Figure 4 Both studies demonstrated the strong in vivo efficacy of ALC1i-1. The effect of ALC1i-1 was also validated in vitro using the ovarian cancer cell line OVCAR3 against ovarian cancer. In a 96-hour cell killing assay, the EC50 of ALC1i-1 was significantly higher than that of ovarian cancer cells. 50 1.8µM ( Figure 5 The 96-hour assay was the lowest in any cell line from any tumor type for any test.

[0063] The data above confirms that although ALC1i-1 is not the most effective inhibitor of ALC1 nucleosome slippage or cell growth in in vitro TNBC cells, it has surprising properties that make it particularly suitable for treating patients with advanced or metastatic cancers (especially solid tumors) with mutations in homologous recombination genes.

[0064] Experimental methods

[0065] As disclosed in WO 2022 / 117782 A1, two cell proliferation assays were performed for 96 hours and 11 days.

[0066] The cell lines used

[0067]

[0068] MDA-MB-231 cells were used as the BRCA wild-type cell line. These cells were established from aneuploid human females. The cells were extracted from the mammary gland (breast) at the transfer site as pleural effusion. (MDA-MB-231 (ATCC® HTB-26™) Homo sapiens epithelial mammary gland). It is available from multiple sources, including ATCC® HTB-26™.

[0069] SUM149PT cells were used as the BRCA-negative cell line. This cell line is a triple-negative breast cancer (TNBC) cell line derived from a primary human invasive ductal carcinoma metastatic nodule in a 40-year-old woman. It contains a hemizygous BRCA1 mutation (p.Pro724Leufs*12) and is available from multiple sources, including bioIVT.

[0070] PSN1 cells were used. This human cell line was derived from pancreatic adenocarcinoma tissue. It exhibited amplification of c-myc and activated Kras, and loss of one of the two p53 alleles. This cell line can be obtained from multiple sources, including MERCK (94060601).

[0071] BxPC3 cells were used. These cells were extracted from pancreatic tissue of a 61-year-old woman with adenocarcinoma. The established cell line did not express CFTR (cystic fibrosis transmembrane transport regulator), but it did express mucin, pancreatic cancer-specific antigen, and CEA (carcinoembryonic antigen). These cells were available from multiple sources, including MERCK (93120816).

[0072] 22Rv1 cells were used. The cell line was derived from a xenograft that had been continuously propagated in mice following castration-induced regression and relapse of an androgen-dependent parental CWR22 xenograft. The cells were derived from prostate cancer and were epithelial cells. They expressed PSA (prostate-specific antigen) and had a damaging mutation in BRCA2. The cell line was available from multiple sources (Accegen (ABC-TC0004)).

[0073] Mouse cell line 60590 was derived from Ptf1awt / Cre; Kraswt / LSL-G12D; p53fl / fl (CKP) mice, which serve as an aggressive PDAC model. CKP mice have a C57BL / 6 background. This cell line was established by Dr. Marija Trajkovic-Arsic in the laboratory of Prof. Jens T Siveke.

[0074] DU145 cells were used. These cells were isolated from the brain of a 69-year-old male with prostate cancer, and the established cell line exhibited an epithelial morphology. It was hypotriploid and contained mutations in BRCA1, BRCA2, RAD50, WRN, and TP53. This cell line could be ATCC HTB-81. ™ get.

[0075] T47D cells were used. The cell line was established from a 54-year-old human woman with invasive ductal carcinoma of the breast. The cells were extracted from the breast (mammary gland) as pleural effusion. They can be obtained from multiple sources (including ATCC HTB-133). ™ )get.

[0076] MDA-MB-436 cells were used. This cell line was derived from a 43-year-old woman with breast adenocarcinoma, extracted from the breast at the metastatic site as pleural effusion. The cells are pleomorphic, possessing multinucleated components. They are available from multiple sources, including Accegen (catalog number ABC-TC0655).

[0077] SKBR3 (also known as SK-BR-3) is a human breast cancer cell line isolated in 1970 by Memorial Sloan–Kettering Cancer Center. It is used in therapeutic research, particularly in HER2-targeting contexts. SKBR3 cells are derived from pleural effusion caused by adenocarcinoma in a 43-year-old Caucasian woman. This cell line overexpresses the HER2 gene product, which is involved in several breast cancer proliferation pathways.

[0078] OVCAR3 cells were isolated from a 60-year-old patient with cisplatin-refractory ovarian adenocarcinoma. OVCAR3 cells are one of the most commonly used ovarian cancer cell lines for research purposes, especially for studying drug resistance. They can be obtained from multiple sources, including ATCC.

[0079] Capan-1 is a pancreatic ductal adenocarcinoma cell line isolated from a 40-year-old patient in 1974. Despite the presence of a BRCA2 frameshift mutation, Capan-1 cells are resistant to 5-fluorouracil. They also contain a K-Ras G12V mutation and an inactive mutant p53.

[0080] LnCAP cells are androgen-sensitive metastatic prostate adenocarcinomas isolated from a 50-year-old patient in 1977. LnCAP cells have mutations in multiple DDR genes, including ATM, ARID1A, FANCA, and CHK2.

[0081] Nucleosome sliding inhibition

[0082] Run the nucleosome sliding determination as previously described in WO 2023 / 213833 A1.

[0083] In vivo cell-derived xenograft (CDX) experiments

[0084] The tumor's length l (longest side) and width w (shortest side) are measured using calipers, and the tumor volume V is calculated using the following formula: .

[0085] Tumor growth inhibition was calculated by comparing the ratio of tumor growth in the control group to that in the treatment group using the following formula: .

[0086] SUM149PT CDX

[0087] To test ALC1i as a monotherapy in TNBC in vivo, 5 x 10 6 SUM149PT cells were injected into the flank of nude mice undergoing NMRI with 50% matrix gel and 50% PBS. For randomization, the tumor size reached an average of 150 mm. 3 With 250mm 3 During this period, treatment was initiated with ALC1i-1, ALC1i-194, and the carrier. Treatment was administered daily as an oral suspension. Both ALC1i-1 and ALC1i-194 were formulated in SyrSpend and administered at 5 ml / kg or 10 ml / kg, respectively.

[0088] DU145 CDX

[0089] To test ALC1i as a monotherapy in an in vivo prostate cancer model, 5 x 10 5 DU145 cells were injected into the lateral ventral region of nude mice undergoing NMRI with 50% matrix gel and 50% PBS. For randomization, the tumor size reached an average of 200 mm. 3 Treatment with ALC1i-1 and the carrier was initiated. It was administered daily as an oral suspension. ALC1i-1 was formulated in SyrSpend and administered at 10 ml / kg.

[0090] 60590 CDX

[0091] To test ALC1i as a monotherapy in an syngeneic mouse model, 1 x 10 6 60,590 cells were injected into the flank of NMRI mice using 50% matrix gel and 50% PBS. For randomization, the tumor size reached approximately 250 mm. 3 (In the high-dose trial) treatment was initiated with ALC1i-1 and the carrier. Treatment was administered daily as an oral suspension. ALC1i-1 was formulated in SyrSpend and administered at 10 ml / kg.

[0092] References

[0093] First-in-Class Inhibitors of Oncogenic CHD1L WithPreclinical Activity Against Colorectal Cancer. Mol. Cancer Ther., 19(8),1598–1612. https: / / doi.org / 10.1158 / 1535-7163.MCT-20-0106.First-in-Class

[0094] Blessing, C., Mandemaker, IK, Gonzalez-Leal, C., Preisser, J., Schomburg, A., & Ladurner, AG (2020). The Oncogenic Helicase ALC1Regulates PARP Inhibitor Potency by Trapping PARP2 at DNA Breaks. MolecularCell, 80(5), 862-875.e6. https: / / doi.org / 10.1016 / j.molcel.2020.10.009

[0095] Clune , S. , Awolade , P. , Zhou , Q. , Esquer , H. , Matter , B. , Kearns , JT , Kellett , T. , Akintayo , DC , Kompella , UB , & LaBarbera , DV (2024). 1–23. https: / / doi.org / 10.1016 / j.biopha.2023.116037

[0096] Hewitt , G. , Borel , V. , Segura-Bayona , S. , Takaki , T. , Ruis , P. , Bellelli , R. , Lehmann , LC , Sommerova , L. , Vancevska , A. , Tomas-Loba , A. , Zhu , K. , Cooper , C. , Fugger , K. , Patel , H. , Goldstone , R. , Schneider-Luftman , D. , Herbert , E. , Stamp , G. , Brough , R. , ... Boulton , SJ (2021). DefectiveALC1 nucleosome remodeling confers PARPi sensitization and syntheticlethality with HRD. Molecular Cell, 81(4), 767-783.e11. https: / / doi.org / 10.1016 / j.molcel.2020.12.006

[0097] Juhász , S. , Smith , R. , Schauer , T. , Spekhardt , D. , Mamar , H. ,Zentout , S. , Chapuis , C. , Huet , S. , & Timinszky , G. (2020). The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment. ScienceAdvances, 6(51), 1–15. https: / / doi.org / 10.1126 / SCIADV.ABB8626

[0098] Kim, KB, Soroceanu, L, De Semir, D, Millis, SZ, Ross, JS,Vosoughi, E, Dar, AA, Nosrati, M, Campisi, J, Ice, RJ, Chen, MM, Chetal, K, Bhattacharjee, A, Moretto, J, Leong, SPL, Singer, MI, Parrett, BM, Minor, DR, McAllister, SD, . . . . . . . . . Kashani-Sabet, M. (2021). Prevalence of Homologous Recombination Pathway Gene Mutations inMelanoma: Rationale for a New Targeted Therapeutic Approach. Journal ofInvestigative Dermatology, 141(8), 2028-2036.e2. https: / / doi.org / 10.1016 / j.jid.2021.01.024

[0099] Peng, G., Lin, C. C. J., Mo, W., Dai, H., Park, Y.-Y., Kim, S., Peng,Y., Mo, Q., Siwko, S., Hu, R., Lee, J., Hennessy, B. T., Hanash, S. M.,Mills, G. B., & Lin, S. Y. (2014). Genome-wide transcriptome profiling ofhomologous recombination DNA repair. Nature Communications, 5(1). https: / / doi.org / 10.1038 / ncomms4361

[0100] Prigaro, B. J., Esquer, H., Zhou, Q., Pike, L. A., Awolade, P., Lai,X. H., Abraham, A. D., Abbott, J. M., Matter, B., Kompella, U. B.,Messersmith, W. A., Gustafson, D. L., & LaBarbera, D. V. (2022). Design,Synthesis, and Biological Evaluation of the First Inhibitors of OncogenicCHD1L. Journal of Medicinal Chemistry, 65(5), 3943–3961. https: / / doi.org / 10.1021 / acs.jmedchem.1c01778

[0101] Toh, M., & Ngeow, J. (2021). Homologous Recombination Deficiency:Cancer Predispositions and Treatment Implications. Oncologist, 26(9), e1526–e1537. https: / / doi.org / 10.1002 / onco.13829

[0102] Yamamoto, H., & Hirasawa, A. (2021). Homologous RecombinationDeficiencies and Hereditary Tumors. International Journal of MolecularSciences, 23(1), 348. https: / / doi.org / 10.3390 / ijms23010348

[0103] Human DNA repair genes. (n.d.). https: / / www.mdanderson.org / documents / Labs / Wood-Laboratory / human-dna-repair-genes.html

Claims

1. A compound of formula (I) (I) Or a pharmaceutically acceptable salt, hydrate or solvate thereof, or a hydrate or solvate thereof, for use in the treatment of advanced or metastatic cancer having at least one mutation in a homologous recombinant gene.

2. The compound of formula (I) for the purpose according to claim 1, wherein the cancer is selected from ovarian cancer, fallopian tube cancer, primary peritoneal cancer, breast cancer, castration-resistant prostate cancer, and pancreatic ductal adenocarcinoma.

3. The compound of formula (I) for the purpose according to claim 1, wherein the cancer is selected from metastatic ovarian cancer, metastatic fallopian tube cancer, metastatic primary peritoneal cancer, metastatic breast cancer, metastatic castration-resistant prostate cancer, and metastatic pancreatic ductal adenocarcinoma.

4. A compound of formula (I) for the use according to any one of the preceding claims, wherein the compound is intended to be used as a single therapy.

5. A compound of formula (I) for the use according to any one of the preceding claims, wherein the at least one mutation in the homologous recombinant gene is a mutation, deletion, or insertion selected from one or more DNA repair genes: ARID1A, ATM, ATRX, BAP1, BLM, BRCA1, BRCA2, BARD1, BRIP1, CHEK1, CHEK2, FANCA / C / D2 / E / F / G / L, MRE11A, NBN, PALB2, RAD50, RAD51C, RAD51D, RAD51, RAD51B, and / or WRN.

6. A compound of formula (I) for the use according to any one of the preceding claims, wherein the at least one mutation in the homologous recombinant gene is a mutation, deletion, or insertion in BRCA1 and / or BRCA2.

7. A pharmaceutical composition comprising a compound of formula (I) or a pharmaceutically acceptable salt, hydrate or solvate thereof, or a hydrate or solvate thereof, and optionally a pharmaceutically suitable carrier, the pharmaceutical composition being used for the treatment of advanced or metastatic cancer having at least one mutation in a homologous recombinant gene.

8. The pharmaceutical composition for the stated use according to claim 7, wherein the cancer is selected from ovarian cancer, fallopian tube cancer, primary peritoneal cancer, breast cancer, castration-resistant prostate cancer, and pancreatic ductal adenocarcinoma.

9. The pharmaceutical composition for the use according to claim 7, wherein the cancer is selected from metastatic ovarian cancer, metastatic fallopian tube cancer, metastatic primary peritoneal cancer, metastatic breast cancer, metastatic castration-resistant prostate cancer, and metastatic pancreatic ductal adenocarcinoma.

10. The pharmaceutical composition for the said use according to any one of claims 7 to 9, wherein the compound is used as a monotherapy.

11. The pharmaceutical composition for the said use according to any one of claims 7 to 10, wherein the at least one mutation in the homologous recombinant gene is a mutation, deletion, or insertion selected from one or more DNA repair genes: ARID1A, ATM, ATRX, BAP1, BLM, BRCA1, BRCA2, BARD1, BRIP1, CHEK1, CHEK2, FANCA / C / D2 / E / F / G / L, MRE11A, NBN, PALB2, RAD50, RAD51C, RAD51D, RAD51, RAD51B, and / or WRN.

12. The pharmaceutical composition for the said use according to any one of claims 7 to 11, wherein the at least one mutation in the homologous recombinant gene is a mutation, deletion, or insertion in BRCA1 and / or BRCA2.

Images