Methods of using ATR inhibitors

Abstract

Disclosed is a method of treating a cancer in a subject using an ATR inhibitor, wherein the cancer has been previously identified as a cancer having a loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B. Also disclosed is a method of inducing cell death of an abnormal cancer cell having a loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B by contacting the cell with an effective amount of an ATR inhibitor.

Description

Field of the Invention

[0001] The present invention relates to the use of ataxia-telangiectasia and RAD-3-associated protein (ATR) kinase inhibitors to treat cancers with loss-of-function mutations in the following: stromal antigen 2 (STAG2), SET domain-containing 2 (SETD2), cyclin-dependent kinase 12 (CDK12), ATR interacting protein (ATRIP), reversal 3-like (REV3L), RAD17, chromosome transmission fidelity factor 8 (CHTF8), active and cell division cycle 20-related 1 (FZR1), RAD51B, RAD51C, RAD51D, BRCA2 chaperone and localization protein (PALB2), ribonuclease H2 subunit A (RNASEH2A) or ribonuclease H2 subunit B (RNASEH2B). Background Art

[0002] DNA damage is constantly occurring in cells due to environmental damage, including ultraviolet radiation, X-rays, and endogenous stress factors such as reactive oxygen and base hydrolysis. Cancer cells are prone to higher rates of DNA damage, which are essentially induced by higher rates of DNA replication in these cells. Several DNA damage response (DDR) pathways have developed in a highly coordinated manner, helping to repair DNA damage and acting as cell checkpoints to prevent cell replication with damaged DNA, thereby allowing repair function before the damaged DNA is passed to daughter cells. Each of the identified DNA repair pathways can sense and repair different but overlapping types of DNA damage.

[0003] One major DDR protein that serves as a key cell cycle checkpoint is the ataxia telangiectasia mutated and rad3-related (ATR) kinase, which is related to the phosphoinositide 3-kinase-related protein kinase (PIKK) family. ATR is activated by single-strand (ss) DNA damage caused by stalled replication forks or during nucleotide excision repair, but also by double-strand breaks following DNA end resection during homologous recombination. ATR is recruited to sites of DNA damage by binding to the RPA protein that wraps ssDNA together with an auxiliary factor called ATR interacting protein (ATRIP). The ATR / ATRIP complex is then activated by recruiting additional factors in the 9-1-1 complex (RAD 9, RAD 1, and HUS1), which subsequently recruits the TOPBP1 protein and represents a key step in activating the downstream phosphorylation cascade, leading to cell cycle arrest. The main target of the ATR kinase is CHK1, which, when phosphorylated, targets the cdc25 protein and Wee1, thereby inhibiting cyclin-dependent kinase activity and causing cell cycle arrest in S or G2 / M phases.

[0004] ATR has been identified as an important cancer target because it is essential for cell division. Mice deficient in ATR die in the embryonic stage, however, adult mice with conditional ATR knockout survive and have effects on rapidly proliferating tissues and stem cell populations. Therefore, cancer cells with high levels of replication stress or susceptible to DNA damaging agents such as radiotherapy or chemotherapeutic agents due to oncogenic mutations, dysfunctional G1 / S checkpoint control (e.g., p53 loss of function), defects in other DNA repair pathways (e.g., ATM) are more dependent on ATR for DNA repair and survival.

[0005] It was unexpectedly discovered that cancer cells with specific genetic mutations have increased sensitivity to ATR inhibitors, and that patients with such mutations have an increased likelihood of obtaining a beneficial response when treated with ATR inhibitors at doses that provide a therapeutic window. Summary of the invention

[0006] In general, the present invention provides a method of inhibiting ATR in a cell having a loss-of-function mutation in STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B. The method may include the step of contacting the cell with a compound disclosed herein.

[0007] In one aspect, the present invention provides a method for treating cancer in a subject, comprising administering to the subject in need thereof a therapeutically effective amount of an ATR inhibitor, wherein the cancer has been previously identified as a cancer having a loss of function (e.g., a biallelic loss-of-function mutation) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B.

[0008] In another aspect, the present invention provides a method of treating cancer in a subject, the method comprising administering to the subject in need thereof a therapeutically effective amount of an ATR inhibitor, wherein the cancer has a loss of function (e.g., a biallelic loss of function mutation) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B. In another aspect, the present invention provides a method of treating cancer in a subject, the method comprising the following steps:

[0009] (i) identifying the cancer as having loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B; and

[0010] (ii) administering to said subject in need thereof a therapeutically effective amount of an ATR inhibitor.

[0011] In another aspect, the present invention provides a method for inducing cell death of abnormal cancer cells having loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B, the method comprising contacting the cells with an effective amount of an ATR inhibitor sufficient to induce cell death of the abnormal cancer cells.

[0012] On the other hand, the present invention also provides an ATR inhibitor for use in a method for treating cancer in a subject, the method comprising administering a therapeutically effective amount of an ATR inhibitor to the subject in need thereof, wherein the cancer has been previously identified as a cancer having loss of function (e.g., biallelic loss of function) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B.

[0013] On the other hand, the present invention also provides an ATR inhibitor for use in a method for treating cancer in a subject, the method comprising administering a therapeutically effective amount of the ATR inhibitor to the subject in need thereof, wherein the cancer has a loss of function (e.g., biallelic loss of function) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B.

[0014] On the other hand, the present invention also provides an ATR inhibitor for use in a method for treating cancer in a subject, the method comprising the following steps: (i) identifying the cancer as having loss of function (e.g., biallelic loss of function) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B; and (ii) administering a therapeutically effective amount of the ATR inhibitor to the subject in need thereof.

[0015] On the other hand, the present invention also provides an ATR inhibitor for use in a method for inducing cell death of abnormal cancer cells having loss of function (e.g., biallelic loss of function) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B, the method comprising contacting the cells with an effective amount of the ATR inhibitor sufficient to induce cell death of the abnormal cancer cells.

[0016] In some embodiments of any of the above aspects, the loss of function is a loss of function of STAG2. In some embodiments, the loss of function is a loss of function of SETD2. In some embodiments, the loss of function is a loss of function of CDK12. In some embodiments, the loss of function is a loss of function of ATRIP. In some embodiments, the loss of function is a loss of function of REV3L. In some embodiments, the loss of function is a loss of function of RAD17. In some embodiments, the loss of function is a loss of function of CHTF8. In some embodiments, the loss of function is a loss of function of FZR1. In some embodiments, the loss of function is a loss of function of RAD51B. In some embodiments, the loss of function is a loss of function of RAD51C. In some embodiments, the loss of function is a loss of function of RAD51D. In some embodiments, the loss of function is a loss of function of PALB2. In some embodiments, the loss of function is a loss of function of RNASEH2A. In some embodiments, the loss of function is a loss of function of RNASEH2B.

[0017] In some embodiments, the method further comprises, prior to the administering step or the contacting step, identifying the cancer as having a biallelic STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B loss-of-function mutation.

[0018] In some embodiments, the identifying step comprises the following steps:

[0019] determining an integer total copy number and / or two integer allele-specific copy numbers of a locus segment within a STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B gene region in or in a cancer cell from the subject from read counts of a plurality of SNVs including homozygous and heterozygous SNVs obtained by sequencing a sample including the cancer cell (e.g., obtained from next generation sequencing) and from a reference read count,

[0020] wherein the cancer is identified as having biallelic loss-of-function mutations in STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B,

[0021] if at least one of the integer total copy number and the integer allele-specific copy number is 0, provided that the remaining STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B alleles, if present, include an inactivating mutation, or

[0022] If none of the integer allele-specific copy numbers is 0 and a STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B allele is present, then each of the alleles independently has an inactivating mutation.

[0023] In some embodiments, the determining step comprises the following steps:

[0024] Determining a total copy number log ratio, an allele copy number log odds ratio, and a target coverage value for the SNV from the read counts and the reference read counts;

[0025] segmenting the total copy number log ratio and the allele copy number log odds ratio;

[0026] estimating the sample purity and sample ploidy of the cancer cells from the total copy number log ratio and the target coverage value; and

[0027] From the target coverage value, the sample purity, the sample ploidy, the total copy number log ratio and the allele copy number log odds ratio, an integer total copy number of a segment comprising multiple SNVs within the STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B gene region in the cancer cells and two integer allele-specific copy numbers of the segment are generated.

[0028] In some embodiments, the method further comprises the step of adjusting the position offset ratio.

[0029] In some embodiments, a plurality of SNVs include SNVs that are always covered (e.g., each of the SNVs that are always covered has an average coverage of at least 200x reads across a normal sample group). In some embodiments, each of the SNVs that are always covered has an average coverage of at least 300x reads across a normal sample group. In some embodiments, a plurality of SNVs include frequent SNVs, which have an allele frequency of 33% to 66% in humans. In some embodiments, a plurality of SNVs include SNVs that are close to the frequent SNVs (e.g., located within 300 connected nucleobases downstream of the frequent SNVs). In some embodiments, a plurality of SNVs include SNVs, each of which has a 5'-flanking sequence of at least 20 connected nucleobases containing 25-75% GC content, wherein the 5'-flanking sequence is unique and does not include other SNVs. In some embodiments, a plurality of SNVs include at least 20 heterozygous SNVs. In some embodiments, the reference read counts are from a group of normal samples. In some embodiments, multiple SNVs include scaffold SNVs (e.g., scaffold SNVs can be used to limit the solution space of integer total copy number and integer allele-specific copy number). In some embodiments, the gene region includes flanking regions of up to 10 kilobases each. In some embodiments, the gene region includes flanking regions of up to 5 kilobases each. In some embodiments, the gene region includes flanking regions of up to 2 kilobases each. In some embodiments, the gene region is an exon region. In some embodiments, the gene region is a total transcriptome region. In some embodiments, the gene region is a genomic region. In some embodiments, biallelic STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutations include at least one somatic mutation. In some embodiments, the biallelic STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutations include at least one germline mutation. In some embodiments, the biallelic STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutations include one somatic loss-of-function mutation and one germline loss-of-function mutation.

[0030] In some embodiments, the ATR inhibitor is a compound of formula (I):

[0031]

[0032] or a pharmaceutically acceptable salt thereof,

[0033] in

[0034] is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y , carbonyl or C(R Y )2; where each R Y is independently H or optionally substituted C 1-6 alkyl;

[0035] R 1 is optionally substituted C 1-6 Alkyl or H;

[0036] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, -N(R 5 )2.-OR 5 、-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or -QR 5B ;

[0037] R 3 is optionally substituted C 1-9 heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0038] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0039] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A ; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0040] Each R 5A is independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 Aryl;

[0041] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or optionally substituted alkoxy;

[0042] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0043] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0044] X is hydrogen or halogen.

[0045] In some embodiments, the ATR inhibitor is a compound of formula (II):

[0046]

[0047] or a pharmaceutically acceptable salt thereof,

[0048] in

[0049] Each Y is independently N or CR 4 ;

[0050] R 1 is optionally substituted C 1-6 Alkyl or H;

[0051] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, -N(R 5 )2.-OR 5 、-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or -QR 5B ;

[0052] R 3 is optionally substituted C 1-9 heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0053] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0054] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A ; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0055] Each R 5A is independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 Aryl;

[0056] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or optionally substituted alkoxy;

[0057] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0058] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0059] X is hydrogen or halogen.

[0060] In some embodiments, the ATR inhibitor is selected from the group consisting of compounds 43, 57, 62, 87, 93, 94, 95, 99, 100, 106, 107, 108, 109, 111, 112, 113, 114, 115, 116, 118, 119, 120, 121, 122, 123, 135, 147, 148, and pharmaceutically acceptable salts thereof.

[0061] In some embodiments, the ATR inhibitor is compound 43 or a pharmaceutically acceptable salt thereof. In some embodiments, the ATR inhibitor is compound 121 or a pharmaceutically acceptable salt thereof. In some embodiments, the ATR inhibitor is compound 122 or a pharmaceutically acceptable salt thereof.

[0062] In some embodiments, the route of administration is oral administration.

[0063] In some embodiments, the method does not include the step of administering or contacting a PARP inhibitor. In some embodiments, the PARP inhibitor is selected from the group consisting of talazoparib, niraparib, rucaparib, olaparib, AZD5305, veliparib, iniparib, 2X-121, CEP-9722, AZD9574, pamiparib, and pharmaceutically acceptable salts thereof. In some embodiments, the ATR inhibitor is administered as a monotherapy.

[0064] In some embodiments, the cancer is renal cell carcinoma, mature B-cell neoplasm, endometrial cancer, ovarian cancer, fallopian tube cancer, primary peritoneal cancer, colorectal cancer, skin cancer, small intestine cancer, non-small cell lung cancer, melanoma, bladder cancer, pancreatic cancer, head and neck cancer, mesothelioma, glioma, prostate cancer, breast cancer, or esophageal and gastric cancer.

[0065] In some embodiments, the loss of function is loss of function of STAG2.In some embodiments, the cancer is renal cell carcinoma, endometrial cancer, acute myeloid leukemia, bladder cancer, uterine cancer, or gastric cancer.

[0066] In some embodiments, the loss of function is a loss of function of SETD2. In some embodiments, the cancer is mesothelioma, renal clear cell carcinoma, renal papillary cell carcinoma, lung adenocarcinoma, bile duct carcinoma, uveal melanoma, bladder urothelial carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, breast invasive carcinoma, lung squamous cell carcinoma, esophageal cancer, head and neck squamous cell carcinoma, or ovarian serous cystadenocarcinoma.

[0067] In some embodiments, the loss of function is a loss of function of CDK12. In some embodiments, the cancer is prostate adenocarcinoma, ovarian serous cystadenocarcinoma, uterine corpus endometrial carcinoma, skin melanoma, lung adenocarcinoma, or breast invasive carcinoma.

[0068] In some embodiments, the loss of function is loss of function of ATRIP.In some embodiments, the cancer is uveal melanoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, gastric adenocarcinoma, head and neck squamous cell carcinoma, or renal clear cell carcinoma.

[0069] In some embodiments, the loss of function is loss of function of REV3L. In some embodiments, the cancer is uterine corpus endometrial carcinoma, gastric adenocarcinoma, prostate adenocarcinoma, lung squamous cell carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, skin melanoma, or lung adenocarcinoma.

[0070] In some embodiments, the loss of function is a loss of function of RAD 17. In some embodiments, the cancer is gastric adenocarcinoma, prostate adenocarcinoma, or invasive breast carcinoma.

[0071] In some embodiments, the loss of function is loss of function of CHTF8. In some embodiments, the cancer is prostate adenocarcinoma.

[0072] In some embodiments, the loss of function is loss of function of FZR1.In some embodiments, the cancer is head and neck squamous cell carcinoma, skin melanoma, or renal papillary cell carcinoma.

[0073] In some embodiments, the loss of function is loss of function of RAD51 B. In some embodiments, the cancer is uterine corpus endometrial carcinoma, renal papillary cell carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, skin melanoma, or invasive breast carcinoma.

[0074] In some embodiments, the loss of function is loss of function of RAD51 C. In some embodiments, the cancer is cutaneous melanoma, uterine corpus endometrial carcinoma, ovarian serous cystadenocarcinoma, or invasive breast carcinoma.

[0075] In some embodiments, the loss of function is loss of function of RAD51 D. In some embodiments, the cancer is ovarian serous cystadenocarcinoma, gastric adenocarcinoma, or skin melanoma.

[0076] In some embodiments, the loss of function is loss of function of PALB2. In some embodiments, the cancer is prostate adenocarcinoma, lung adenocarcinoma, hepatocellular carcinoma, invasive breast carcinoma, uterine corpus endometrial carcinoma, lung squamous cell carcinoma, ovarian serous cystadenocarcinoma, or gastric adenocarcinoma.

[0077] In some embodiments, the loss of function is loss of function of RNASEH2A. In some embodiments, the loss of function is loss of function of RNASEH2B. In some embodiments, the cancer is sarcoma, bladder urothelial carcinoma, chronic lymphocytic leukemia.

[0078] definition

[0079] As used herein, the term "abnormal" refers to different from normal. When used to describe the activity of an enzyme, abnormal refers to an activity that is higher or lower than the average of a normal control or a normal disease-free control sample. Abnormal activity can refer to the amount of activity that causes a disease, wherein restoring the abnormal activity to a normal or disease-free amount (e.g., by administering a compound described herein or using a method described herein) causes a reduction in the disease or one or more disease symptoms. Abnormal activity can be measured by measuring the modification of the substrate of the enzyme in question; a difference in activity change greater than or equal to 2 times can be considered abnormal. Abnormal activity can also refer to an increased reliance on a specific signal transduction pathway due to a defect in a separate complementary pathway.

[0080] As used herein, the term "acyl" refers to the group -C(=0)-R, wherein R is alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl or heterocyclyl. Acyl groups may be optionally substituted as described herein for each corresponding R group.

[0081] As used herein, the term "adenocarcinoma" refers to a malignant tumor arising from glandular cells that line an organ in an organism. Non-limiting examples of adenocarcinomas include non-small cell lung cancer, prostate cancer, pancreatic cancer, esophageal cancer, and colorectal cancer.

[0082] As used herein, the term "alkanoyl" refers to a hydrogen or alkyl group attached to the parent molecular group through a carbonyl group, and is exemplified by formyl (i.e., formaldehyde), acetyl, propionyl, butyryl, and isobutyryl. Unsubstituted alkanoyl contains 1 to 7 carbons. Alkanoyl can be unsubstituted or substituted as described herein for alkyl (e.g., optionally substituted C 1-7 A terminal "-acyl" may be added to another group as defined herein, such as aryl, cycloalkyl, and heterocyclyl, to define "aroyl," "cycloalkanoyl," and "(heterocyclyl)acyl." These groups represent a carbonyl group substituted with an aryl, cycloalkyl, or heterocyclyl group, respectively. Each of "aroyl," "cycloalkanoyl," and "(heterocyclyl)acyl" may be optionally substituted as defined for "aryl," "cycloalkyl," or "heterocyclyl," respectively.

[0083] As used herein, the term "alkenyl" refers to a non-cyclic monovalent straight or branched hydrocarbon group containing one, two or three carbon-carbon double bonds. Non-limiting examples of alkenyl include vinyl, prop-1-enyl, prop-2-enyl, 1-methylvinyl, but-1-enyl, but-2-enyl, but-3-enyl, 1-methylprop-1-enyl, 2-methylprop-1-enyl and 1-methylprop-2-enyl. Alkenyl can be optionally substituted as defined herein for alkyl.

[0084] As used herein, the term "alkoxy" refers to a chemical substituent of the formula -OR, wherein R is C unless otherwise specified. 1-6Alkyl. In some embodiments, the alkyl group may be further substituted as defined herein. The term "alkoxy" may be combined with other terms defined herein, such as aryl, cycloalkyl, or heterocyclyl, to define "arylalkoxy", "cycloalkylalkoxy", and "(heterocyclyl)alkoxy" groups. These groups represent alkoxy groups substituted with aryl, cycloalkyl, or heterocyclyl, respectively. Each of "arylalkoxy", "cycloalkylalkoxy", and "(heterocyclyl)alkoxy" may be optionally substituted as defined herein for each individual moiety.

[0085] As used herein, the term "alkoxyalkyl" refers to a chemical substituent of the formula -L-O-R, wherein L is C 1-6 Alkylene, and R is C 1-6 Optionally substituted alkoxyalkyl is optionally substituted alkoxyalkyl as described herein for alkyl.

[0086] As used herein, the term "alkyl" refers to a non-cyclic straight or branched saturated hydrocarbon radical having 1 to 12 carbons when unsubstituted, unless otherwise specified. In certain preferred embodiments, the unsubstituted alkyl radical has 1 to 6 carbons. Alkyl groups are exemplified by methyl; ethyl; n-propyl and isopropyl; n-butyl, sec-butyl, isobutyl and tert-butyl; neopentyl, etc., and may be optionally substituted with one, two, three, or, in the case of an alkyl radical having two or more carbons, four or more substituents independently selected from the group consisting of amino; aryl; aryloxy; azido; cycloalkyl; cycloalkyloxy; cycloalkenyl; cycloalkynyl; halo; heterocyclyl; (heterocyclyl)oxy; heteroaryl; hydroxyl; nitro; thiol; silyl; cyano; alkylsulfonyl; alkylsulfinyl; alkylthio; =0; =S; -S02R, wherein R is amino or cycloalkyl; =NR', wherein R' is H, alkyl, aryl or heterocyclyl. Each of the substituents may itself be unsubstituted or substituted where valence permits, with an unsubstituted substituent as defined herein for each corresponding group.

[0087] As used herein, the term "alkylene" refers to a divalent alkyl group. Optionally substituted alkylene is an alkylene group optionally substituted as described herein for alkyl.

[0088] As used herein, the term "alkylamino" refers to a group having the formula -N(R N1 )2 or -NHR N1 A group in which R N1 is an alkyl group as defined herein. The alkyl portion of the alkylamino group may be optionally substituted as defined for an alkyl group. Each optional substituent on a substituted alkylamino group may itself be unsubstituted or substituted, where valence permits, with an unsubstituted substituent as defined herein for each corresponding group.

[0089] As used herein, the term "alkylthio" denotes a group of formula -S-(alkyl). Alkylthio may be optionally substituted as defined for alkyl.

[0090] As used herein, the term "alkylsulfinyl" denotes a group of formula -S(0)-(alkyl). Alkylsulfinyl may be optionally substituted as defined for alkyl.

[0091] As used herein, the term "alkylsulfonyl" denotes a group of formula -S(O)2-(alkyl). Alkylsulfonyl may be optionally substituted as defined for alkyl.

[0092] As used herein, the term "alkynyl" refers to a monovalent straight or branched chain hydrocarbon radical having two to six carbon atoms containing at least one carbon-carbon triple bond, and is exemplified by ethynyl, 1-propynyl, etc. Alkynyl groups may be unsubstituted or substituted as defined for alkyl groups (e.g., optionally substituted alkynyl groups).

[0093] As used herein, the term "amino" refers to -N(R N1 )2, wherein if the amino group is unsubstituted, the two R N1 are H; or, if the amino group is substituted, each R N1 are independently H, -OH, -NO2, -N(R N2 2. -SO2OR N2 、-SO2R N2 、-SOR N2 、-COOR N2 , N-protecting group, alkyl, alkenyl, alkynyl, alkoxy, aryl, arylalkyl, aryloxy, cycloalkyl, cycloalkenyl, heteroalkyl or heterocyclyl, provided that at least one R N1 is not H, and each R N2 Each of the substituents may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each corresponding group. In some embodiments, the amino group is an unsubstituted amino group (i.e., -NH2) or a substituted amino group (e.g., NHR N1 ), where R N1 Independently -OH, SO2OR N2 、-SO2R N2 、-SOR N2 、-COOR N2 , optionally substituted alkyl or optionally substituted aryl, and each R N2 In some embodiments, the amino group is -NHR. N1 , where RN1 is an optionally substituted alkyl group.

[0094] As used herein, the term "aryl" refers to a monocyclic, bicyclic or polycyclic carbocyclic ring system having one or two aromatic rings. The aryl group may include 6 to 10 carbon atoms. All atoms in the unsubstituted carbocyclic aryl group are carbon atoms. Non-limiting examples of carbocyclic aryl groups include phenyl, naphthyl, 1,2-dihydronaphthyl, 1,2,3,4-tetrahydronaphthyl, fluorenyl, dihydroindenyl, indenyl, etc. The aryl group may be unsubstituted or substituted with one, two, three, four or five substituents independently selected from the group consisting of: alkyl; alkenyl; alkynyl; alkoxy; alkylsulfinyl; alkylthio; alkylsulfonyl; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkyloxy; cycloalkenyl; cycloalkynyl; halo; heteroalkyl; heterocyclic; (heterocyclic)oxy; hydroxyl; nitro; thiol; silyl; and cyano. Each of the substituents may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each respective group.

[0095] As used herein, the term "arylalkyl" refers to an alkyl group substituted with an aryl group. As described herein, the aryl and alkyl moieties may be optionally substituted as individual groups as described herein.

[0096] As used herein, the term "arylene" refers to a divalent aromatic radical. Optionally substituted arylene is an alkylene radical optionally substituted as described herein for aryl.

[0097] As used herein, the term "aryloxy" refers to a chemical substituent of the formula -OR, wherein unless otherwise specified, R is an aryl group. In an optionally substituted aryloxy group, the aryl group is optionally substituted as described herein for an aryl group.

[0098] As used herein, the term "ATM" refers to ATM serine / threonine kinase.

[0099] As used herein, the term "ATR inhibitor" means a compound that, upon contact with the enzyme ATR kinase, reduces ATR kinase activity, whether in vitro, in cell culture or in animals, such that the measured ATR kinase IC 50 For certain ATR inhibitors, the ATR kinase IC 50 It may be 100 nM or less (e.g., 10 nM or less, or 1 nM or less) and may be as low as 100 pM or 10 pM. Preferably, the ATR kinase IC 50 0.1 nM to 1 μM (eg, 0.1 nM to 750 nM, 0.1 nM to 500 nM, or 0.1 nM to 250 nM).

[0100] As used herein, the term "ATR kinase" refers to ataxia-telangiectasia and RAD-3 related protein kinase.

[0101] As used herein, the term "azido" refers to a -N3 group.

[0102] As used herein, the term "BRCA2" means the breast cancer type 2 susceptibility gene or protein.

[0103] As used herein, the term "cancer" refers to all types of cancers, neoplasms or malignancies found in mammals (e.g., humans), including leukemias, carcinomas and sarcomas. Non-limiting examples of cancers that can be treated with the compounds or methods provided herein include prostate cancer, thyroid cancer, endocrine system cancer, brain cancer, breast cancer, cervical cancer, colon cancer, head and neck cancer, liver cancer, kidney cancer, lung cancer, non-small cell lung cancer, melanoma, mesothelioma, ovarian cancer, sarcoma, gastric cancer, uterine cancer, medulloblastoma, ampullary cancer, colorectal cancer and pancreatic cancer. Other non-limiting examples may include Hodgkin's disease, Non-Hodgkin's lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, essential thrombocythemia, essential macroglobulinemia, primary brain tumor, cancer, malignant pancreatic insulinoma, malignant carcinoid, bladder cancer, precancerous skin lesions, testicular cancer, lymphoma, thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenocortical carcinoma, pancreatic endocrine or exocrine tumors, medullary thyroid cancer, medullary thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid carcinoma, hepatocellular carcinoma, and prostate cancer.

[0104] As used herein, the term "carbocyclyl" refers to an optionally substituted C3-16 monocyclic, bicyclic or tricyclic structure in which the carbon atoms form a ring that may be aromatic or non-aromatic. Carbocyclic structures include cycloalkyl, cycloalkenyl, cycloalkynyl and certain aryl groups.

[0105] As used herein, the term "carbonyl" refers to a -C(0)- group.

[0106] As used herein, the term "carcinoma" refers to a malignant new growth composed of epithelial cells that tends to infiltrate surrounding tissues and give rise to metastases. Non-limiting examples of carcinomas that can be treated with the compounds or methods provided herein include, for example, medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinar carcinoma, adenoid carcinoma, adenoid cystic carcinoma, adenoid cystic carcinoma, adenomatous carcinoma, adrenal cortical carcinoma, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, basaloid carcinoma, basosquamous cell carcinoma, bronchioloalveolar carcinoma, bronchiolar carcinoma, bronchial carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, choriocarcinoma, colloid carcinoma, comedo carcinoma, uterine corpus carcinoma, cribriform carcinoma, armor carcinoma, cutaneous carcinoma, cylindrical carcinoma, cylindrical cell carcinoma, ductal carcinoma, dural carcinoma, embryonal carcinoma, cerebriform carcinoma, epidermoid carcinoma, adenoid epithelial carcinoma, exophytic carcinoma, ulcerative carcinoma, fibrocarcinoma, gelatinous carcinoma, gelatinous carcinoma, fibrocar ... carcinoma), colloid carcinoma, giant cell carcinoma, giant cell carcinoma, adenocarcinoma, granulosa cell carcinoma, hair matrix carcinoma, hematogenous carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, hyalinoid carcinoma, adrenal carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's carcinoma, Kulchitzky-cell carcinoma, large cell carcinoma, lenticular carcinoma, lenticular carcinoma, lipomatous carcinoma, lymphoepithelial carcinoma, medullary carcinoma, melanoma, soft carcinoma, mucinous carcinoma, carcinoma muciparum, mucinous cell carcinoma, mucoepidermoid carcinoma, mucous carcinoma, mucous carcinoma, myxomatous carcinoma, nasopharyngeal carcinoma, oat cell carcinoma, ossifying carcinoma, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, acanthoma cell carcinoma, erosive carcinoma, renal cell carcinoma, reserve cell carcinoma, sarcomatous carcinoma, schneiderian carcinoma, scirrhous carcinoma, scrotal carcinoma, signet ring cell carcinoma, carcinoma simplex, small cell carcinoma, potato carcinoma, spheroid cell carcinoma, spindle cell carcinoma, medullary carcinoma (carcinoma spongiosum), squamous cell carcinoma, squamous cell carcinoma, chordal carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes, transitional cell carcinoma, mass carcinoma, nodular carcinoma, verrucous carcinoma and villous carcinoma.

[0107] As used herein, the term "cyano" refers to a -CN group.

[0108] As used herein, unless otherwise indicated, the term "cycloalkenyl" refers to a non-aromatic carbocyclic group having at least one double bond and three to ten carbon atoms in the ring (e.g., C 3-10 Cycloalkenyl). Non-limiting examples of cycloalkenyl include cycloprop-1-enyl, cycloprop-2-enyl, cyclobut-1-enyl, cyclobut-1-enyl, cyclobut-2-enyl, cyclopent-1-enyl, cyclopent-2-enyl, cyclopent-3-enyl, norbornene-1-yl, norbornene-2-yl, norbornene-5-yl, and norbornene-7-yl. Cycloalkenyl may be unsubstituted or substituted as described for cycloalkyl (e.g., optionally substituted cycloalkenyl).

[0109] As used herein, the term "cycloalkenylalkyl" refers to an alkyl group substituted with a cycloalkenyl group, the alkyl group and the cycloalkenyl group being each as defined herein. The cycloalkenyl and alkyl portions may be substituted as individual groups defined herein.

[0110] As used herein, the term "cycloalkoxy" refers to a chemical substituent of the formula -OR, wherein R is a cycloalkyl group unless otherwise specified. In some embodiments, the cycloalkyl group may be further substituted as defined herein.

[0111] Unless otherwise indicated, as used herein, the term "cycloalkyl" refers to a cyclic alkyl group having three to ten carbon atoms (e.g., C 3-C10Cycloalkyl). Cycloalkyl can be monocyclic or bicyclic. Bicyclic cycloalkyl can be a bicyclic [pq0] alkyl type, wherein each of p and q is independently 1, 2, 3, 4, 5, 6 or 7, provided that the sum of p and q is 2, 3, 4, 5, 6, 7 or 8. Alternatively, bicyclic cycloalkyl can include a bridged cycloalkyl structure, such as a bicyclic [pqr] alkyl, wherein r is 1, 2 or 3, and each of p and q is independently 1, 2, 3, 4, 5 or 6, provided that the sum of p, q and r is 3, 4, 5, 6, 7 or 8. Cycloalkyl can be a spirocyclic group, such as a spiro [pq] alkyl, wherein each of p and q is independently 2, 3, 4, 5, 6 or 7, provided that the sum of p and q is 4, 5, 6, 7, 8 or 9. Non-limiting examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, 1-bicyclo[2.2.1.]heptyl, 2-bicyclo[2.2.1.]heptyl, 5-bicyclo[2.2.1.]heptyl, 7-bicyclo[2.2.1.]heptyl, and decahydronaphthyl. The cycloalkyl group may be unsubstituted or substituted (e.g., optionally substituted cycloalkyl) with one, two, three, four, or five substituents independently selected from the group consisting of: alkyl; alkenyl; alkynyl; alkoxy; alkylsulfinyl; alkylthio; alkylsulfonyl; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; cycloalkenyl; cycloalkynyl; halo; heteroalkyl; heterocyclyl; (heterocyclyl)oxy; heteroaryl; hydroxy; nitro; thiol; silyl; cyano; =0; =S; -S02R, wherein R is amino or cycloalkyl; =NR′, wherein R′ is H, alkyl, aryl, or heterocyclyl; or -CON(R A )2, where each R A are independently H or alkyl, or two R A Together with the atoms to which it is attached, it is combined to form a heterocyclyl. Each of the substituents may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each respective group.

[0112] As used herein, the term "cycloalkylalkyl" refers to an alkyl group substituted with a cycloalkyl group, alkyl and cycloalkyl being each as defined herein. The cycloalkyl and alkyl moieties may be optionally substituted as the individual groups described herein.

[0113] As used herein, the term "cycloalkylene" refers to a divalent cycloalkyl group. Optionally substituted cycloalkylene is an optionally substituted cycloalkylene group as described herein for cycloalkyl.

[0114] Unless otherwise indicated, as used herein, the term "cycloalkynyl" refers to a monovalent carbocyclic group having one or two carbon-carbon triple bonds and eight to twelve carbons. The cycloalkynyl may include a trans-ring bond or bridge. Non-limiting examples of cycloalkynyl include cyclooctynyl, cyclononynyl, cyclodecynyl and cyclodecadiynyl. The cycloalkynyl may be unsubstituted or substituted (e.g., optionally substituted cycloalkynyl) as described for cycloalkyl.

[0115] "Disease" or "disorder" refers to a state of being or health in a patient or subject that can be treated with the compounds or methods provided herein.

[0116] As used herein, the term "halogen" refers to a halogen selected from bromine, chlorine, iodine and fluorine.

[0117] As used herein, the term "heteroalkyl" refers to an alkyl, alkenyl, or alkynyl group that is mixed with one or two heteroatoms once; twice, each time independently mixed with one or two heteroatoms; three times, each time independently mixed with one or two heteroatoms; or four times, each time independently mixed with one or two heteroatoms. Each heteroatom is independently O, N, or S. In some embodiments, the heteroatom is O or N. None of the heteroalkyl groups includes two connected oxygen or sulfur atoms. The heteroalkyl group may be unsubstituted or substituted (e.g., an optionally substituted heteroalkyl group). When the heteroalkyl group is substituted and a substituent is bonded to a heteroatom, the substituent is selected according to the nature and valence of the heteroatom. Therefore, if valence permits, the substituent bonded to the heteroatom is selected from the group consisting of: =O, -N(R N2 2. -SO2OR N3 、-SO2R N2 、-SOR N3 、-COOR N3 , N-protecting group, alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, cycloalkynyl, heterocyclic group or cyano group, wherein each R N2 are independently H, alkyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl or heterocyclyl, and each R N3 alkyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl or heterocyclic radical independently. Each of these substituents may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each corresponding group. When heteroalkyl is substituted and the substituent is bonded to carbon, the substituent is selected from those described for the alkyl, provided that the substituent on the carbon atom bonded to the heteroatom is not Cl, Br or I. It should be understood that the carbon atom is located at the end of the heteroalkyl.

[0118] As used herein, the term "heteroarylalkyl" refers to an alkyl group substituted with a heteroaryl group, wherein the alkyl and heteroaryl groups are each as defined herein. The heteroaryl and alkyl portions may be optionally substituted as the individual groups described herein.

[0119] As used herein, the term "heteroarylene" refers to a divalent heteroaryl group. An optionally substituted heteroarylene is an optionally substituted heteroarylene as described herein for a heteroaryl group.

[0120] As used herein, the term "heteroaryloxy" refers to the structure -OR, wherein R is heteroaryl. Heteroaryloxy may be optionally substituted as defined for heterocyclyl.

[0121] As used herein, unless otherwise indicated, the term "heterocyclyl" refers to a monocyclic, bicyclic, tricyclic or tetracyclic ring system with a fused, bridged and / or spirocyclic 3-, 4-, 5-, 6-, 7- or 8-membered ring, containing one, two, three or four heteroatoms independently selected from the group consisting of nitrogen, oxygen and sulfur. In some embodiments, unless otherwise indicated, "heterocyclyl" is a monocyclic, bicyclic, tricyclic or tetracyclic ring system with a fused or bridged 5-, 6-, 7- or 8-membered ring, containing one, two, three or four heteroatoms independently selected from the group consisting of nitrogen, oxygen and sulfur. Heterocyclyl can be aromatic or non-aromatic. Non-aromatic 5-membered heterocyclyl has zero or one double bond, non-aromatic 6- and 7-membered heterocyclyl has zero to two double bonds, and non-aromatic 8-membered heterocyclyl has zero to two double bonds and / or zero or one carbon-carbon triple bond. Unless otherwise indicated, heterocyclic radicals include 1 to 16 carbon atoms. Certain heterocyclic radicals may include up to 9 carbon atoms. Non-aromatic heterocyclic radicals include pyrrolinyl, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, homopiperidinyl, piperazinyl, pyridazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiomorpholinyl, thiazolidinyl, isothiazolidinyl, thiazolidinyl, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl, dihydrothienyl, dihydroindole, tetrahydroquinolinyl, tetrahydroisoquinolinyl, pyranyl, dihydropyranyl, dithiazolyl, etc. If the heterocyclic ring system has at least one aromatic resonance structure or at least one aromatic tautomer, such structures are aromatic heterocyclic radicals (i.e., heteroaryl). Non-limiting examples of heteroaryl groups include benzimidazolyl, benzofuranyl, benzothiazolyl, benzothiophenyl, benzoxazolyl, furanyl, imidazolyl, indolyl, isoindazolyl, isoquinolyl, isothiazolyl, isothiazolyl, isoxazolyl, oxadiazolyl, oxazolyl, purinyl, pyrrolyl, pyridinyl, pyrazinyl, pyrimidinyl, quinazolinyl, quinolinyl, thiadiazolyl (e.g., 1,3,4-thiadiazole), thiazolyl, thienyl, triazolyl, tetrazolyl, etc. The term "heterocyclyl" also refers to heterocyclic compounds having a bridged polycyclic structure in which one or more carbon and / or heteroatoms bridge two non-adjacent members of a single ring, such as quinuclidine, tropane, or diazabicyclo[2.2.2]octane. The term "heterocyclic group" includes bicyclic, tricyclic and tetracyclic groups in which any of the above heterocyclic rings is fused with one, two or three carbon rings, such as an aromatic ring, a cyclohexane ring, a cyclohexene ring, a cyclopentane ring, a cyclopentene ring or another monocyclic heterocyclic ring. Examples of fused heterocyclic groups include 1,2,3,5,8,8a-hexahydroindolizine; 2,3-dihydrobenzofuran; 2,3-dihydroindole; and 2,3-dihydrobenzothiophene.The heterocyclyl group may be unsubstituted or substituted with one, two, three, four, five or six substituents independently selected from the group consisting of: alkyl; alkenyl; alkynyl; alkoxy; alkylsulfinyl; alkylthio; alkylsulfonyl; amino; aryl; aryloxy; azido; cycloalkyl; cycloalkoxy; cycloalkenyl; cycloalkynyl; halo; heteroalkyl; heterocyclyl; (heterocyclyl)oxy; hydroxy; nitro; thiol; silyl; cyano; =0; =S; =NR', where R' is H, alkyl, aryl or heterocyclyl. Each of the substituents may itself be unsubstituted or substituted with an unsubstituted substituent as defined herein for each respective group.

[0122] As used herein, the term "heterocyclylalkyl" refers to an alkyl group substituted with a heterocyclyl, with the alkyl and heterocyclyl groups each being as defined herein. The heterocyclyl and alkyl portions may be optionally substituted as the individual groups described herein.

[0123] As used herein, the term "heterocyclylene" refers to a divalent heterocyclyl group. Optionally substituted heterocyclylene is an optionally substituted heterocyclylene group as described herein for heterocyclyl.

[0124] As used herein, the term "(heterocyclyl)oxy" refers to a chemical structure of the formula -OR, wherein R is heterocyclyl, unless otherwise specified. The (heterocyclyl)oxy group may be optionally substituted in the manner described for heterocyclyl.

[0125] The terms "hydroxyl" and "hydroxy" are used interchangeably herein to refer to an -OH group.

[0126] As used herein, the term "isotopic enrichment" refers to an isotopic content of an isotope of a pharmaceutically active agent at a predetermined position within a molecule that is at least 100 times higher than the natural abundance of the isotope. For example, a composition isotopically enriched with deuterium includes an active agent having a deuterium abundance at least 100 times higher than the natural abundance of deuterium at at least one hydrogen atom position. Preferably, the isotopic enrichment of deuterium is at least 1000 times higher than the natural abundance of deuterium. More preferably, the isotopic enrichment of deuterium is at least 4000 times higher (e.g., at least 4750 times higher, e.g., up to 5000 times higher) than the natural abundance of deuterium.

[0127] As used herein, the term "leukemia" refers broadly to progressive malignant diseases of the blood-forming organs and is generally characterized by abnormal proliferation and development of white blood cells and their precursors in the blood and bone marrow. The clinical classification of leukemia is usually based on (1) the duration and characteristics of the disease - acute or chronic; (2) the type of cells involved: myeloid (myeloid), lymphoid (lymphoid-derived), or monocytic; and (3) the increase or absence of the number of abnormal cells in the leukemic or leukopenic (meta-leukemic) blood. Exemplary leukemias that can be treated with the compounds or methods provided herein include, for example, acute non-lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia, acute promyelocytic leukemia, adult T-cell leukemia, leukopenia leukemia, leukocytic leukemia, basophilic leukemia, blast cell leukemia, bovine leukemia, chronic myelogenous leukemia, leukemia cutis, embryonic leukemia, eosinophilic leukemia, Gross' leukemia, hairy cell leukemia, hemoblastic leukemia, hemoblastic leukemia, histiocytic leukemia , stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphoid leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenic leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myeloid leukemia, myelomonocytic leukemia, Naegelileukemia, plasma cell leukemia, multiple myeloma, plasma cell leukemia, promyelocytic leukemia, Rieder cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia and undifferentiated cell leukemia.

[0128] As used herein, the term "lymphoma" refers to a cancer caused by cells of immune origin. Non-limiting examples of T-cell and B-cell lymphomas include non-Hodgkin's lymphoma and Hodgkin's disease, diffuse large B-cell lymphoma, follicular lymphoma, mucosa-associated lymphoid tissue (MALT) lymphoma, small cell lymphocytic lymphoma-chronic lymphocytic leukemia, mantle cell lymphoma, mediastinal (thymic) large B-cell lymphoma, lymphoplasmacytic lymphoma-Waldenstrom macroglobulinemia, peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL) / follicular T-cell lymphoma (FTCL), anaplastic large cell lymphoma (ALCL), enteropathy-associated T-cell lymphoma (EATL), adult T-cell leukemia / lymphoma (ATLL) or extranodal NK / T-cell lymphoma (nasal type).

[0129] As used herein, the term "melanoma" refers to a tumor caused by the melanocyte system of the skin and other organs. Melanomas that can be treated with the compounds or methods provided herein include, for example, acral lentigo melanoma, amelanotic melanoma, benign juvenile melanoma, Claudeman's melanoma, S91 melanoma, Harding-Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungual melanoma, and superficial spreading melanoma.

[0130] As used herein, the term "nitro" refers to a -NO2 group.

[0131] As used herein, the term "oxo" refers to a divalent oxygen atom (eg, the structure of an oxo group can be shown as =0).

[0132] As used herein, the term "PARP inhibitor" means a compound that, upon exposure to PARP, reduces PARP activity, whether in vitro, in cell culture, or in animals, such that the measured PARP IC 50 For some PARP inhibitors, the PARP IC 50 It may be 100 nM or less (e.g., 10 nM or less, or 1 nM or less) and may be as low as 100 pM or 10 pM. Preferably, PARP IC 50 The amount of the active ingredient is 0.1 nM to 1 μM (eg, 0.5 nM to 750 nM, 1 nM to 500 nM, or 1 nM to 250 nM).

[0133] As used herein, the term "PARP" refers to poly ADP-ribose polymerase (PARP).

[0134] As used herein, the term "Ph" means a phenyl group.

[0135] As used herein, the term "pharmaceutical composition" means a composition containing a compound described herein, formulated together with a pharmaceutically acceptable excipient, and approved by a governmental regulatory agency for manufacture or sale as part of a therapeutic regimen for treating a disease in a mammal. The pharmaceutical composition can be formulated, for example, in unit dosage form (e.g., tablets, capsules, caplets, gel capsules, or syrups) for oral administration; for topical administration (e.g., in the form of a cream, gel, lotion, or ointment); for intravenous administration (e.g., in a non-particulate embolism and suitable for intravenous use.

[0136] The terms "pharmaceutically acceptable excipient" or "pharmaceutically acceptable carrier" as used interchangeably herein refer to any ingredient other than the compounds described herein and having non-toxic and non-inflammatory properties in patients (e.g., a vehicle capable of suspending or dissolving the active compound). Excipients may include, for example, anti-adherents, antioxidants, binders, coatings, compression aids, disintegrants, dyes (colorants), softeners, emulsifiers, fillers (diluents), film formers or coatings, flavoring agents, fragrances, glidants (flow enhancers), lubricants, preservatives, printing inks, adsorbents, suspending or dispersing agents, sweeteners, and water of hydration. Exemplary excipients include, but are not limited to, butylated hydroxytoluene (BHT), calcium carbonate, calcium phosphate (dibasic), calcium stearate, cross-linked carboxymethylcellulose, cross-linked polyvinyl pyrrolidone, citric acid, cross-linked povidone, cysteine, ethylcellulose, gelatin, hydroxypropyl cellulose, hydroxypropyl methylcellulose, lactose, magnesium stearate, maltitol, mannitol, methionine, methylcellulose, methylparaben, microcrystalline cellulose, polyethylene glycol, polyvinyl pyrrolidone, povidone, pregelatinized starch, propylparaben, retinyl palmitate, shellac, silicon dioxide, sodium carboxymethylcellulose, sodium citrate, sodium starch glycolate, sorbitol, starch (corn), stearic acid, stearic acid, sucrose, talc, titanium dioxide, vitamin A, vitamin E, vitamin C, and xylitol.

[0137] As used herein, the term "pharmaceutically acceptable salt" means those salts which are suitable for use in contact with the tissues of humans and animals without excessive toxicity, irritation, allergic response, etc., and which are commensurate with a reasonable benefit / risk ratio, within the scope of sound medical judgment. Pharmaceutically acceptable salts are well known in the art. For example, pharmaceutically acceptable salts are described in: Berge et al., J. Pharmaceutical Sciences 66: 1-19, 1977 and Pharmaceutical Salts: Properties, Selection, and Use, (P. H. Stahl and C. G. Wermuth, eds.), Wiley-VCH, 2008. Salts can be prepared in situ during the final isolation and purification of the compounds described herein, or separately by reacting a free base group with a suitable organic acid. Representative acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptonate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrobromide, hydrochloride, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, dodecylsulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, toluenesulfonate, undecanoate, valerate, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like, as well as nontoxic ammonium, quaternary ammonium, and amine cations including, but not limited to, ammonium, tetramethylammonium, tetraethylammonium, methylamine, dimethylamine, trimethylamine, triethylamine, ethylamine, and the like.

[0138] As used herein, the term "protecting group" means a group intended to protect a hydroxyl, amino or carbonyl group from participating in one or more undesirable reactions during a chemical synthesis. As used herein, the term "O-protecting group" means a group intended to protect a hydroxyl or carbonyl group from participating in one or more undesirable reactions during a chemical synthesis. As used herein, the term "N-protecting group" means a group intended to protect a nitrogen-containing group (e.g., amino, amide, heterocyclic NH or hydrazine) from participating in one or more undesirable reactions during a chemical synthesis. Commonly used O-protecting groups and N-protecting groups are disclosed in Greene, "Protective Groups in Organic Synthesis", 3rd edition (John Wiley & Sons, New York, 1999), which is incorporated herein by reference. Exemplary O-protecting groups and N-protecting groups include alkanoyl, aroyl, or carbamoyl groups, such as formyl, acetyl, propionyl, pivaloyl, tert-butylacetyl, 2-chloroacetyl, 2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthaloyl, o-nitrophenoxyacetyl, α-chlorobutyryl, benzoyl, 4-chlorobenzoyl, 4-bromobenzoyl, tert-butyldimethylsilyl, triisopropylsilyloxymethyl, 4,4′-dimethoxytrityl, isobutyryl, phenoxyacetyl, 4-isopropylphenoxyacetyl, dimethylformamidinyl, and 4-nitrobenzoyl.

[0139] Exemplary O-protecting groups for protecting carbonyl-containing groups include, but are not limited to, acetals, acylaldehydes, 1,3-dithiane, 1,3-dioxane, 1,3-dioxolane, and 1,3-dithiolane.

[0140] Other O-protecting groups include, but are not limited to, substituted alkyl, aryl, and aryl-alkyl ethers (e.g., trityl; methylthiomethyl; methoxymethyl; benzyloxymethyl; silyloxymethyl; 2,2,2-trichloroethoxymethyl; tetrahydropyranyl; tetrahydrofuranyl; ethoxyethyl; 1-[2-(trimethylsilyl)ethoxy]ethyl; 2-trimethylsilylethyl; tert-butyl ether; p-chlorophenyl, p-methoxyphenyl, p-nitrophenyl, benzyl, p-methoxybenzyl, and nitrobenzyl); silyl ethers (e.g., , trimethylsilyl; triethylsilyl; triisopropylsilyl; dimethylisopropylsilyl; tert-butyldimethylsilyl; tert-butyldiphenylsilyl; tribenzylsilyl; triphenylsilyl; and diphenylmethylsilyl); carbonates (e.g., methyl, methoxymethyl, 9-fluorenylmethyl; ethyl; 2,2,2-trichloroethyl; 2-(trimethylsilyl)ethyl; vinyl, allyl, nitrophenyl; benzyl; methoxybenzyl; 3,4-dimethoxybenzyl; and nitrobenzyl).

[0141] Other N-protecting groups include, but are not limited to, chiral auxiliary agents such as protected or unprotected D, L or D, L-amino acids, such as alanine, leucine, phenylalanine, etc.; sulfonyl-containing groups, such as benzenesulfonyl and p-toluenesulfonyl, etc.; carbamate-forming groups, such as benzyloxycarbonyl, p-chlorobenzyloxycarbonyl, p-methoxybenzyloxycarbonyl, p-nitrobenzyloxycarbonyl, 2-nitrobenzyloxycarbonyl, p-bromobenzyloxycarbonyl, 3,4-dimethoxybenzyloxycarbonyl, 3,5-dimethoxybenzyloxycarbonyl, 2,4-dimethoxybenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, 2-nitro-4,5-dimethoxybenzyloxycarbonyl, 3,4,5-trimethoxybenzyloxycarbonyl, 1-(p-biphenyl)-1-methylethoxycarbonyl

[0063] Examples of the present invention include tert-butyloxycarbonyl, α,α-dimethyl-3,5-dimethoxybenzyloxycarbonyl, diphenylmethyloxycarbonyl, tert-butyloxycarbonyl (BOC), diisopropylmethoxycarbonyl, isopropyloxycarbonyl, ethoxycarbonyl, methoxycarbonyl, allyloxycarbonyl, 2,2,2,-trichloroethoxycarbonyl, phenoxycarbonyl, 4-nitrophenoxycarbonyl, fluorenyl-9-methoxycarbonyl, cyclopentyloxycarbonyl, adamantyloxycarbonyl, cyclohexyloxycarbonyl and phenylthiocarbonyl; aryl-alkyl groups such as benzyl, p-methoxybenzyl, 2,4-dimethoxybenzyl, triphenylmethyl, benzyloxymethyl and the like; silylalkyl acetals such as [2-(trimethylsilyl)ethoxy]methyl; and silyl groups such as trimethylsilyl and the like. Suitable N-protecting groups are formyl, acetyl, benzoyl, pivaloyl, tert-butylacetyl, alanyl, phenylsulfonyl, benzyl, dimethoxybenzyl, [2-(trimethylsilyl)ethoxy]methyl (SEM), tetrahydropyranyl (THP), tert-butoxycarbonyl (Boc) and benzyloxycarbonyl (Cbz).

[0142] As used herein, the term "RNAse H2A" refers to ribonuclease H2 subunit A.

[0143] As used herein, the term "RNAse H2B" refers to ribonuclease H2 subunit B.

[0144] The term "sarcoma" generally refers to a tumor composed of material resembling embryonic connective tissue and usually consisting of tightly packed cells embedded in a fibrous or homogeneous material. Non-limiting examples of sarcomas that can be treated with the compounds or methods provided herein include, for example, chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abernethy's sarcoma, liposarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, green sarcoma, choriocarcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, B-cell immunoblastic sarcoma, T-cell immunoblastic sarcoma, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, sarcoma), angiosarcoma, leukemic sarcoma, malignant mesenchymal sarcoma, parosteal sarcoma, reticular cell sarcoma, Rous sarcoma, plasmacystic sarcoma, synovial sarcoma, and telangiectatic sarcoma.

[0145] As used herein, the term "scaffold SNV" refers to frequent well-covered single nucleotide variants outside the target gene region and distributed throughout the chromosome carrying the target gene region.

[0146] As used herein, the term "STAG2" refers to stromal antigen 2.

[0147] The term "tautomer" refers to structural isomers that are easily interconvertible, usually by relocation of protons. Tautomers are different chemical species that can be identified by different spectral features but cannot usually be separated individually. Non-limiting examples of tautomers include keto-enols, enamines-imines, amides-imidic acids, nitroso-oximes, enones-alkynols, and amino acid-ammonium carboxylates.

[0148] As used herein, the term "subject" refers to a human or non-human animal (e.g., a mammal) suffering from or at risk of a disease or disorder as determined by a qualified professional (e.g., a physician or nurse practitioner) performing laboratory tests on a sample from the subject, whether known or unknown in the art. Preferably, the subject is a human. Non-limiting examples of diseases and disorders include diseases with symptoms of cellular hyperproliferation, such as cancer.

[0149] As used herein, the term "total copy number log ratio" refers to the signal ratio of cancer cells to control cells. Deviations of the total copy number log ratio for a given region from a mean of 0 indicate that the signal intensity is higher (if greater than 0) or lower (if less than 0) than the expected signal intensity for two chromosome copies. The total copy number log ratio, also known as LogR, can be calculated using the Illumina The software makes the estimate.

[0150] As used herein, "treatment" refers to the medical management of a subject for the purpose of improving, reversing, stabilizing, preventing or curing a disease or condition. The term includes active treatment (treatment aimed at improving a disease or condition); etiological treatment (treatment for the cause of the disease or condition); palliative treatment (treatment aimed at alleviating the symptoms of a disease or condition); preventive treatment (treatment aimed at minimizing or partially or completely inhibiting the development of a disease or condition); and supportive care (treatment to supplement another therapy). The disease or condition may be cancer. Non-limiting examples of cancer include, for example, renal cell carcinoma, mature B-cell neoplasms, endometrial cancer, ovarian cancer, colorectal cancer, skin cancer (non-melanoma), small intestine cancer, non-small cell lung cancer, melanoma, bladder cancer, pancreatic cancer, head and neck cancer, mesothelioma, glioma, prostate cancer, breast cancer, and esophageal and gastric cancer. BRIEF DESCRIPTION OF THE DRAWINGS

[0151] Figure 1A :Inhibition of STAG2-K0 cell proliferation by compound 121. The STAG2 gene was knocked out in RPE1-hTERT-ΔTP53 cells using CRISPR-Cas9 (clones 1 and 2). The cells were then seeded in a 96-well plate format and treated with a specified concentration of compound 121 for a period of 7 days. The treatment was updated every 4 days. The confluence was then measured using a microscope and normalized to the untreated condition.

[0152] Figure 1B :Compound 121 preferentially induces cell death of STAG2-K0 cells. RPE1-hTERT-ΔTP53-STAG2 K0 cells were seeded in a 6-well plate format and treated with a specified dose of compound 121 for 10 days. Cells were then fixed and stained using a crystal violet-methanol solution. Colonies were counted and the percentage of survival was determined by normalizing the number of colonies after treatment to the number of colonies under untreated conditions.

[0153] Figure 2:Compound 121 preferentially induces cell death in bladder cancer cells lacking STAG2. The STAG2 gene was knocked out in T24 cells using CRISPR-Cas9 (clones 1 and 2). Cells were seeded in a 6-well plate format and treated with a specified dose of compound 121 for 9 days. Cells were then fixed and stained using a crystal violet-methanol solution. Colonies were counted, and the percentage of survival was determined by normalizing the number of colonies after treatment to the number of colonies under untreated conditions.

[0154] Figure 3A : Representative dose response curves of MCF10A cells treated with compound 121 after transfection with non-targeting siRNA (siCTRL) or siRNA targeting SETD2 (siSETD2). Cell viability was determined by CellTiter Glo (CTG) assay. Data (open symbols) were fitted with a 4-parameter dose response model (solid line). Attenuation of ATM (siATM; ATM is a known determinant of compound 121 sensitivity) was used as a positive control.

[0155] Figure 3B : Compound 121IC from CTG cell viability assay in MCF10A and RPE1 TP53- / - cell lines transfected with the indicated siRNAs 50 Data are from ≥2 independent experiments (circles) and are mean values ​​(bars) ± SD (error bars).

[0156] Figure 3C : HeLa cells are insensitive to compound 121 after SETD2 knockdown. Note that in this cell line, the positive control (siATM) is also insensitive to compound 121. Data are from 3 independent experiments (circles) and are mean (bars) ± SD (error bars).

[0157] Figure 4A : Representative immunoblots showing SETD2 expression in whole cell extracts from six SETD2 wild-type (WT) renal and colorectal cancer cell lines and loss of SETD2 in three SETD2 mutant (LOF) cell lines. Vinculin was used as a loading control.

[0158] Figure 4B : Compound 121 IC from CellTiterGlo viability assay of SETD2 WT and LOF cell lines treated with compound 121 for 4-8 population doublings 50 Circles represent the average IC from ≥3 independent experiments. 50 Values. Bars are means of each cohort (WT or LOF); error bars, ±SD.

[0159] Figure 5A: Dose response curves of isogenic CDK12 wild-type (+ / +) and knockout (- / -) RPE1 TP53- / - cells treated with compound 121. Cell viability was measured by CellTiter Glo assay. Open symbols represent mean ± SD from three independent experiments. Solid lines show nonlinear least squares fit to a four-parameter dose-response model. IC 50 There is about a 2-fold change.

[0160] Figure 5B : Dose response curves of isogenic CDK12 wild-type (+ / +) and knockout (- / -) DLD1 cells treated with compound 121. Cell viability was measured by CellTiter Glα assay. Open symbols represent mean ± SD from three independent experiments. Solid lines show nonlinear least squares fit to a four-parameter dose-response model. IC 50 That's about a 3-fold change.

[0161] Fig. 6A : Dose response curves of isogenic RNASEH2B wild-type (+ / +) and knockout (- / -) RPE1TP53- / - cells treated with compound 121. Cell viability was measured by CellTiter Glo assay. The hollow symbols represent the mean ± SD from three independent experiments. The solid line shows the nonlinear least squares fit to the four-parameter dose-response model. Fig. 6A Immunoblots showing RNASEH2B protein status in whole-cell extracts of the indicated cell lines are also shown. α-Actin was used as a loading control. IC 50 That's about a 4-fold change.

[0162] Figure 6B : Dose response curves of isogenic RNASEH2B wild-type (+ / +) and knockout (- / -) 5637 cells treated with compound 121. Cell viability was measured by CellTiter Glo assay. Open symbols represent mean ± SD from three independent experiments. Solid lines show nonlinear least squares fits to a four-parameter dose-response model. Figure 6B Immunoblots showing RNASEH2B protein status in whole-cell extracts of the indicated cell lines are also shown. α-Actin was used as a loading control. IC 50 That's about a 4-fold change.

[0163] Fig. 7A: Growth of subcutaneously transplanted 5637RNASEH2B+ / + bladder cancer cell line tumors in immunodeficient mice. Mice were treated with vehicle or the indicated doses of Compound 121 by oral gavage once daily on a 2-day / 4-day dosing schedule per week. Data are presented as mean ± SEM. N = 8 mice / group.

[0164] Figure 7B : Growth of subcutaneously transplanted 5637RNASEH2B- / - bladder cancer cell line tumors in immunodeficient mice. Mice were treated with vehicle or the indicated dose of compound 121 by oral gavage once daily on a 2-day / 4-day dosing schedule per week. Data are presented as mean ± SEM. N = 8 mice / group.

[0165] Fig. 8A : Growth of subcutaneously implanted triple-negative breast cancer (TNBC) PDX tumors with RNASEH2B IHC loss in immunodeficient mice. Mice were treated with vehicle or the specified dose of compound 121 by oral gavage once a day on a 3-day / 4-day dosing schedule per week. Data are presented as mean ± SEM. N = 9 mice / group.

[0166] Figure 8B : Using RNase H2-specific antibodies, from Fig. 8A Immunohistochemistry (IHC) staining of PDX models (upper panel) and control RNase H2-proficient PDX (lower panel).

[0167] Fig. 9A : Compound 121 dose response curves of RPE1 Cas9TP53- / - cells transduced with control sgRNA (sgAAVS1) or two sgRNAs targeting RAD51B. Cell viability was determined by CellTiter Glo assay. The open symbols show the mean viability ± SD from three independent experiments. The solid line represents the nonlinear least squares fit to the four-parameter dose response model.

[0168] Fig. 9B : Compound 121 dose response curves of RPE1 Cas9TP53- / - cells transduced with control sgRNA (sgAAVS1) or two sgRNAs targeting RAD51C. Cell viability was determined by CellTiter Glo assay. Open symbols show mean viability ± SD from three independent experiments. Solid lines represent nonlinear least squares fits to a four-parameter dose-response model.

[0169] Fig. 9C: Compound 121 dose response curves of RPE1 Cas9TP53- / - cells transduced with a control sgRNA (sgAAVS1) or two sgRNAs targeting RAD51D. Cell viability was determined by the CellTiter G1α assay. The open symbols show the mean viability ± SD from three independent experiments. The solid line represents the nonlinear least squares fit to the four-parameter dose-response model.

[0170] Fig. 10A :When using non-targeting siRNA (siCTRL), positive control siRNA targeting ATM (siATM) or targeting indicator STEP 2 Compound 121IC from the CellTiter Glα cell viability assay in MCF10A cells transfected with siRNA of the gene 50 Fold change of values. Circles represent values ​​from ≥2 independent experiments and are presented as mean (bars) ± SD (error bars). Data are normalized to siCTRL. Values ​​greater than 1 indicate increased sensitivity compared to siCTRL.

[0171] Fig. 10B :When using non-targeting siRNA (siCTRL), positive control siRNA targeting ATM (siATM) or targeting indicator STEP 2 Compound 121IC from the CellTiter Glo cell viability assay in RPE1 TP53- / - cells transfected with siRNA targeting the gene 50 Fold change of values. Circles represent values ​​from ≥2 independent experiments and are presented as mean (bars) ± SD (error bars). Data are normalized to siCTRL. Values ​​greater than 1 indicate increased sensitivity compared to siCTRL.

[0172] Fig. 10C :When using non-targeting siRNA (siCTRL), positive control siRNA targeting ATM (siATM) or targeting indicator STEP 2 Compound 121IC from the CellTiter Glα cell viability assay in HeLa cells transfected with siRNA targeting the gene 50 Fold change of values. Circles represent values ​​from ≥2 independent experiments and are presented as mean (bars) ± SD (error bars). Data are normalized to siCTRL. Values ​​greater than 1 indicate increased sensitivity compared to siCTRL.

[0173] Fig.11A: Dose response curves of isogenic ARID1A wild-type (WT) and knockout (ARID1A- / -) HCT116 cells treated with AZD-6738. Cell growth (confluence) was measured by IncuCyte automated microscopy. Data (circles) were fitted with a four-parameter dose-response model (solid line).

[0174] Fig. 11B : Dose response curves of isogenic ARID1A wild-type (WT) and knockout (ARID1A- / -) MCF1A cells treated with AZD-6738. Cell growth (confluence) was measured by IncuCyte automated microscopy. Data (circles) were fit to a four-parameter dose-response model (solid line).

[0175] Fig. 11C : Dose response curves of isogenic ARID1A wild-type (WT) and knockout (ARID1A- / -) BEAS2B cells treated with AZD-6738. Cell growth (confluence) was measured by IncuCyte automated microscopy. Data (circles) were fitted with a four-parameter dose-response model (solid line).

[0176] Fig.12 EC values ​​of ATRi AZD-6738 from the IncuCyte growth assay in a panel of cancer cell lines either wild-type for ARID1A (WT) or carrying deleterious ARID1A alterations (LOF) 50 Data (circles) are from two independent experiments and are means (bars) ± SD (error bars). DETAILED DESCRIPTION

[0177] In general, the present invention relates to the use of ATR inhibitors or pharmaceutically acceptable salts thereof for treating cancer or for inducing cell death of cancer cells. Cancers included herein can be, for example, cancers with loss of function (e.g., biallelic loss of function) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B.

[0178] Advantageously, cancers with loss of function (e.g., biallelic loss of function) of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B are particularly sensitive to ATR inhibitor therapy (e.g., ATR inhibitor monotherapy). For example, cancers with loss of function of CDK12, RNASEH2A or RNASEH2B can be treated with ATR inhibitor therapy, e.g., as ATR inhibitor monotherapy.

[0179] STAG2 is a gene encoding SA-2 protein, which is a key member of the adhesion protein complex. The complex forms a ring structure that maintains two DNA chromosomes together. This physical proximity of DNA molecules is essential for different processes such as DNA replication, DNA repair and chromosome separation during mitosis. Some cancer patients show that the STAG2 gene is changed, which may lead to the genetic instability observed in tumors. Due to this higher level of genetic instability, STAG2-deficient tumors are likely to rely on DDR signals for survival.

[0180] SETD2 is a gene that encodes a histone methyltransferase that specifically methylates lysine 36 of histone H3. The function of the SETD2 protein is important for many cellular processes, including transcription, DNA replication, and DNA repair. Some tumors carry deleterious alterations in the SETD2 gene, which may increase the level of replication stress and genomic instability in these tumors.

[0181] The CDK12 gene encodes a cyclin-dependent kinase required for DNA transcription. Deleterious alterations of CDK12 found in certain cancers lead to reduced expression of genes involved in DNA repair and DNA replication, resulting in a reduced ability of these tumors to repair damaged DNA and recover from replication stress.

[0182] The ATRIP and RAD17 genes encode proteins required for the normal function of the ATR pathway. When these genes are altered in tumors, levels of replication stress may increase.

[0183] The REV3L gene encodes the catalytic subunit of DNA polymerase ζ, a protein complex required for DNA repair by translesion synthesis. Deleterious alterations of REV3L in cancer are predicted to reduce the ability of tumors to repair DNA damage and recover from replication stress.

[0184] The CHTF8 gene encodes a subunit of the alternative replication factor C (RFC) complex, which is composed of DSCC1, CHTF8, and CHTF18. This protein complex is required for proper DNA replication, sister chromatid cohesion, and DNA repair. Some tumors carry deleterious alterations in CHTF8 that may lead to defects in DNA repair and replication.

[0185] FZR1 (also known as CDH1) is a gene that encodes a regulatory subunit of the anaphase-promoting complex (APC / C). This protein complex is essential for normal cell division. Deleterious alterations in the FZR1 gene are predicted to impair the ability of tumor cells to recover from replication stress and increase genomic instability.

[0186] RAD51B, RAD51C, RAD51D and PALB2 are genes that encode proteins required for DNA repair by homologous recombination (HR). Together, the protein products of these genes support the correct loading of the RAD51 recombinase on DNA by the BRCA2 protein and are therefore essential for completing HR DNA repair. Harmful alterations in RAD51B, RAD51C, RAD51D or PALB2 can be found in certain cancers, leading to HR defects and consequently increased genomic instability.

[0187] The RNASEH2A and RNASEH2B genes encode subunits of the ribonuclease H2 (RNase H2) complex, which is responsible for removing ribonucleotides (also known as 'genomic ribonucleotides') that are erroneously incorporated into DNA by DNA polymerases during DNA replication and DNA repair. Some tumors harbor deleterious alterations in the RNASEH2A or RNASEH2B genes, resulting in aberrant processing of genomic ribonucleotides and elevated levels of replication stress and genomic instability.

[0188] Due to underlying DNA repair defects and genomic instability, cancers with mutations in STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A, or RNASEH2B may respond to treatment with ATR inhibitors at doses that allow establishment of a therapeutic window on healthy, proliferating cells.

[0189] ATR inhibitors

[0190] An ATR inhibitor can be an inhibitor that, upon contact with the enzyme ATR kinase, reduces ATR kinase activity, whether in vitro, in cell culture, or in animals, such that the measured ATR kinase IC 50For certain ATR inhibitors, the ATR kinase IC 50 It may be 100 nM or less (e.g., 10 nM or less, or 1 nM or less) and may be as low as 100 pM or 10 pM. Preferably, the ATR kinase IC 50 0.1 nM to 1 μM (eg, 0.1 nM to 750 nM, 0.1 nM to 500 nM, or 0.1 nM to 250 nM).

[0191] Non-limiting examples of ATR inhibitors include, for example:

[0192]

[0193] and pharmaceutically acceptable salts thereof.

[0194] Non-limiting examples of ATR inhibitors include, for example, those shown in International Application Publication Nos. WO2020087170, WO2018218197, WO202020259601, WO2019036641, WO2020049017, WO2019154365, WO2020103897, WO2021233376, WO2022028598, WO2022012484, WO2022002245, WO2022002243, each of which is incorporated herein by reference; U.S. Patent Nos. 11,028,076, 10,745,420, 10,301,324, 10,196,405, 9,663,535, 9,549,932, 8,552,004 and 8,841,308, each of which is incorporated herein by reference; and U.S. Patent Application Publication Nos. 2019 / 0055240 and 2019 / 0300547, which are incorporated herein by reference.

[0195] In one embodiment, the ATR inhibitor is a compound of formula (I):

[0196]

[0197] or a pharmaceutically acceptable salt thereof,

[0198] in

[0199] is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y , carbonyl or C(R Y)2; where each R Y is independently H or optionally substituted C 1-6 alkyl;

[0200] R 1 is optionally substituted C 1-6 Alkyl or H;

[0201] R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, -N(R 5 )2.-OR 5 、-CON(R 6 )x、-SO2N(R 6 2. -SO2R 5A or -QR 5B ;

[0202] R 3 is optionally substituted C 1-9 heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0203] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0204] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A ; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0205] Each R 5A is independently optionally substituted C 1-6Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 Aryl;

[0206] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or optionally substituted alkoxy;

[0207] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0208] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0209] X is hydrogen or halogen.

[0210] The ATR inhibitor may be, for example, a compound of formula (II):

[0211]

[0212] or a pharmaceutically acceptable salt thereof,

[0213] in

[0214] Each Y is independently N or CR 4 ;

[0215] R 1 is optionally substituted C 1-6 Alkyl or H;

[0216] R 2 is optionally substituted C2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, -N(R 5 )2.-OR 5 、-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or -QR 5B ;

[0217] R 3 is optionally substituted C 1-9 heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl;

[0218] Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl;

[0219] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A ; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0220] Each R 5A is independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 Aryl;

[0221] R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9Heteroaryl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or optionally substituted alkoxy;

[0222] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0223] Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and

[0224] X is hydrogen or halogen.

[0225] In some embodiments, in the compound of Formula (II), (I) or (Ib):

[0226] Each Y is independently N or CR 4 ;

[0227] R 1 is H or optionally substituted C 1-6 alkyl;

[0228] R 2 is optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 )2 or -SO2R 5A ;

[0229] R 3 is optionally substituted C 1-9 heteroaryl;

[0230] Each R 4 is independently H or optionally substituted C 1-6 alkyl;

[0231] Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A , where each R 5A is independently optionally substituted C 1-6 Alkyl or optionally substituted C 3-8 Cycloalkyl; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group;

[0232] Each R 5A is independently optionally substituted C 1-6 Alkyl or optionally substituted C 3-8 cycloalkyl; and

[0233] Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group.

[0234] Methods for making compounds of formula (I) are described, for example, in International Application No. PCT / US2019 / 051539 (incorporated herein by reference).

[0235] The ATR inhibitor may be, for example, a compound of formula (Ia):

[0236]

[0237] or a pharmaceutically acceptable salt thereof, wherein Y, R 1 , R 2 , R 3 and R 4As described for formula (I).

[0238] The ATR inhibitor may be, for example, a compound of formula (Ib):

[0239]

[0240] or a pharmaceutically acceptable salt thereof, wherein Y, R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0241] The ATR inhibitor may be, for example, a compound of formula (IA):

[0242]

[0243] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0244] The ATR inhibitor may be, for example, a compound of formula (IA-a):

[0245]

[0246] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0247] The ATR inhibitor may be, for example, a compound of formula (IB):

[0248]

[0249] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0250] The ATR inhibitor may be, for example, a compound of formula (IB-a):

[0251]

[0252] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0253] The ATR inhibitor may be, for example, a compound of formula (IC):

[0254]

[0255] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0256] The ATR inhibitor may be, for example, a compound of formula (IC-a):

[0257]

[0258] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0259] The ATR inhibitor may be, for example, a compound of formula (ID):

[0260]

[0261] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0262] The ATR inhibitor may be, for example, a compound of formula (ID-a):

[0263]

[0264] or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 and R 4 As described for formula (I).

[0265] Preferably, R 1 It is methyl.

[0266] In some embodiments, R 2 It may be, for example, optionally substituted C 3-8 For example, R 2 It may be a group of formula (A):

[0267]

[0268] in

[0269] n is 0, 1, 2 or 3; and

[0270] R 7 is hydrogen, alkylsulfonyl, cyano, -CON(R A )2.-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A R is independently H or alkyl; or two R are combined together with the atoms to which they are attached to form C 2-9 Heterocyclic group.

[0271] In some embodiments, R 2 It may be, for example, optionally substituted C 1-6 Alkyl (e.g., optionally substituted tert-C 3-6 For example, R 2 It may be a group of formula (B):

[0272]

[0273] Where R 7 is hydrogen, alkylsulfonyl, cyano, -CON(R A )2.-SON(R A ) 2. optionally substituted C 1-9 heteroaryl, hydroxyl or alkoxy, wherein each R A are independently H or alkyl; or two R A Together with the atoms to which they are attached, they form C 2-9 Heterocyclic group.

[0274] In some embodiments, R 2 It may be, for example, an optionally substituted non-aromatic C 2-9 Heterocyclic group.

[0275] In some embodiments, R 2 It can be, for example:

[0276]

[0277]

[0278] -I, -SO2Me, -SO2Ph, -0CH2CF3,

[0279]

[0280]

[0281] In some embodiments, R 3 It may be, for example, an optionally substituted monocyclic C 1-9 For example, R 3 It may be a group of formula (C):

[0282]

[0284] Wherein A is an optionally substituted monocyclic C 1-9 Heteroaromatic ring.

[0285] In some embodiments, A may be, for example, a group of formula (C1):

[0286]

[0287] Where R 8 is hydrogen, halogen or optionally substituted C 1-6 alkyl.

[0288] In some embodiments, R 3 For example

[0289]

[0290] In some embodiments, R 3 For example

[0291]

[0292] In some embodiments, R 4 It may be, for example, hydrogen.

[0293] The ATR inhibitor may be exemplified by the compounds listed in Table 1 below or pharmaceutically acceptable salts thereof.

[0294] Table 1

[0295]

[0296]

[0297]

[0298]

[0299]

[0300]

[0301]

[0302]

[0303]

[0304]

[0305]

[0306] The ATR inhibitor may be isotopically enriched (eg, deuterium enriched).

[0307] Isomers and their combinations

[0308] The present invention includes (where possible) individual diastereomers, enantiomers, epimers and atropisomers of the compounds disclosed herein, as well as mixtures of diastereomers and / or enantiomers thereof, including racemic mixtures. Although the specific stereochemistry disclosed herein is preferred, other stereoisomers, including diastereomers, enantiomers, epimers, atropisomers and mixtures of these isomers may also be used to treat disease. Inactive or less active diastereomers and enantiomers may be used, for example, in scientific studies related to receptors and activation mechanisms.

[0309] It is understood that certain molecules may exist in multiple tautomeric forms. The present invention includes all tautomers, even though only one tautomer may be indicated in an example.

[0310] The present invention also includes pharmaceutically acceptable salts of the compounds, and pharmaceutical compositions comprising the compounds and pharmaceutically acceptable carriers. These compounds are particularly useful, for example, in certain types of cancer, and can be used to slow the progression of cancer once it has developed in a patient.

[0311] The compounds disclosed herein can be used in pharmaceutical compositions comprising (a) the compound or a pharmaceutically acceptable salt thereof, and (b) a pharmaceutically acceptable carrier. These compounds can be used in pharmaceutical compositions comprising one or more other active pharmaceutical ingredients. The compounds can also be used in pharmaceutical compositions in which the compounds disclosed herein or a pharmaceutically acceptable salt thereof is the sole active ingredient.

[0312] Optical isomers-diastereomers-geometric isomers-tautomers

[0313] The compounds disclosed herein may contain, for example, one or more stereogenic centers and may exist as racemates, racemic mixtures, single enantiomers, individual diastereomers, and mixtures of diastereomers and / or enantiomers. The present invention includes all such isomeric forms of the compounds disclosed herein. It is intended that all possible stereoisomers (e.g., enantiomers and / or diastereomers) in mixtures and as pure or partially purified compounds are included within the scope of the present invention (i.e., all possible combinations of stereogenic centers as pure compounds or in mixtures).

[0314] Some of the compounds described herein may contain a bond that is rotationally hindered, such that two individual rotamers or atropisomers may be separated and found to have different biological activities, which may be advantageous. It is intended that all possible atropisomers are included within the scope of the present invention.

[0315] Some of the compounds described herein may contain olefinic double bonds, and unless specified otherwise, are intended to include both E and Z geometric isomers.

[0316] Some of the compounds described herein may exist with different points of hydrogen attachment, known as tautomers. An example is a ketone and its enol form, known as keto-enol tautomers. The present invention encompasses individual tautomers and mixtures thereof.

[0317] Compounds disclosed herein having one or more asymmetric centers can be separated into diastereomers, enantiomers, etc. by methods well known in the art.

[0318] Alternatively, enantiomers and other compounds with chiral centers can be synthesized by stereospecific synthesis using optically pure starting materials and / or reagents of known configuration.

[0319] Metabolites – Prodrugs

[0320] The present invention includes metabolites with therapeutic activity, wherein the metabolites themselves fall within the scope of the claims. The present invention also includes prodrugs, which are compounds that are converted to the desired compound when or after administration to a patient. In some cases, the chemical structure claimed in the present application may itself be a prodrug.

[0321] Isotopically enriched derivatives

[0322] The present invention includes molecules that have been isotopically enriched at one or more positions within the molecule. Thus, deuterium-enriched compounds fall within the scope of the claims.

[0323] Method for preparing ATR inhibitors

[0324] ATR inhibitors can be prepared using reactions and techniques known in the art. For example, certain ATR inhibitors can be prepared using techniques and methods such as those disclosed in International Application Nos. PCT / US2019 / 051539 and PCT / US2018 / 034729, each of which is incorporated herein by reference; U.S. Patent Nos. 9,663,535, 9,549,932, 8,552,004 and 8,841,308, each of which is incorporated herein by reference; and U.S. Patent Application Publication No. 2019 / 0055240, which is incorporated herein by reference.

[0325] How to use

[0326] ATR inhibitors can be used to treat diseases or disorders with symptoms of cell hyperproliferation. For example, the invention described herein can be applied to treat various tumor diseases with sensitizing gene mutations, such as tumors with any harmful (loss of function) changes in STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B. Mutations in this gene are common in the following tumor types: renal cell carcinoma, mature B cell neoplasms, endometrial cancer, ovarian cancer, acute myeloid leukemia, colorectal cancer, skin cancer (non-melanoma), small intestine cancer, non-small cell lung cancer, melanoma, bladder cancer, pancreatic cancer, head and neck cancer, mesothelioma, glioma, prostate cancer, uterine cancer, breast cancer, gastric cancer and esophageal gastric cancer. Therefore, the method of the present invention is preferably used to treat these cancers.

[0327] In some embodiments, the loss of function is ATRIP and the cancer is uveal melanoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, gastric adenocarcinoma, head and neck squamous cell carcinoma, or renal clear cell carcinoma.

[0328] In some embodiments, the loss of function is RNASEH2A or RNASEH2B and the cancer is sarcoma, bladder urothelial carcinoma, chronic lymphocytic leukemia

[0329] In some embodiments, the loss of function is CHTF8 and the cancer is prostate adenocarcinoma.

[0330] In some embodiments, the loss of function is FZR1 and the cancer is head and neck squamous cell carcinoma, skin melanoma, or renal papillary cell carcinoma.

[0331] In some embodiments, the loss of function is RAD17 and the cancer is gastric adenocarcinoma, prostate adenocarcinoma, or invasive breast carcinoma.

[0332] In some embodiments, the loss of function is RAD51B and the cancer is uterine corpus endometrial carcinoma, renal papillary cell carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, skin melanoma, or invasive breast carcinoma.

[0333] In some embodiments, the loss of function is RAD51C and the cancer is cutaneous melanoma, uterine corpus endometrial carcinoma, ovarian serous cystadenocarcinoma, or invasive breast carcinoma.

[0334] In some embodiments, the loss of function is RAD51D and the cancer is ovarian serous cystadenocarcinoma, gastric adenocarcinoma, or cutaneous melanoma.

[0335] In some embodiments, the loss of function is REV3L and the cancer is uterine corpus endometrial carcinoma, gastric adenocarcinoma, prostate adenocarcinoma, lung squamous cell carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, skin melanoma, or lung adenocarcinoma.

[0336] In some embodiments, the loss of function is SETD2 and the cancer is mesothelioma, renal clear cell carcinoma, renal papillary cell carcinoma, lung adenocarcinoma, bile duct carcinoma, uveal melanoma, bladder urothelial carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, invasive breast carcinoma, lung squamous cell carcinoma, esophageal cancer, head and neck squamous cell carcinoma, or ovarian serous cystadenocarcinoma.

[0337] In some embodiments, the loss of function is CDK12 and the cancer is prostate adenocarcinoma, ovarian serous cystadenocarcinoma, uterine corpus endometrial carcinoma, skin melanoma, lung adenocarcinoma, or invasive breast carcinoma.

[0338] In some embodiments, the loss of function is PALB2 and the cancer is prostate adenocarcinoma, lung adenocarcinoma, hepatocellular carcinoma, invasive breast carcinoma, uterine corpus endometrial carcinoma, lung squamous cell carcinoma, ovarian serous cystadenocarcinoma, or gastric adenocarcinoma.

[0339] The therapeutic methods of the present invention include the step of administering a therapeutically effective amount of an ATR inhibitor to a subject in need thereof.

[0340] The disease or disorder treated using the methods of the invention may have symptoms of cell hyperproliferation. For example, the disease or disorder may be cancer. The cancer may be, for example, a carcinoma, sarcoma, adenocarcinoma, lymphoma, leukemia, or melanoma. The cancer may be, for example, a solid tumor.

[0341] Non-limiting examples of cancer include prostate cancer, breast cancer, ovarian cancer, multiple myeloma, brain cancer, glioma, lung cancer, salivary gland cancer, gastric cancer, thymic epithelial cancer, thyroid cancer, leukemia, melanoma, lymphoma, stomach cancer, pancreatic cancer, kidney cancer, bladder cancer, uterine cancer, colon cancer, and liver cancer.

[0342] Preferably, the method of the invention is used to treat renal cell carcinoma, mature B-cell neoplasms, endometrial cancer, ovarian cancer, fallopian tube cancer, primary peritoneal cancer, colorectal cancer, skin cancer (non-melanoma), small intestine cancer, non-small cell lung cancer, melanoma, bladder cancer, pancreatic cancer, head and neck cancer, mesothelioma, glioma, prostate cancer, breast cancer, or esophageal and gastric cancer.

[0343] Non-limiting examples of carcinomas include medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinar carcinoma, adenoid carcinoma, adenoid cystic carcinoma, adenoid cystic carcinoma, adenomatous carcinoma, adrenal cortical carcinoma, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, basaloid carcinoma, basosquamous cell carcinoma, bronchioloalveolar carcinoma, bronchiolar carcinoma, bronchial carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, choriocarcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, armor carcinoma, cutaneous carcinoma, cylindrical carcinoma, cylindrical cell carcinoma, ductal carcinoma, dural carcinoma, embryonal carcinoma, cerebriform carcinoma, epidermoid carcinoma, adenoid epithelial carcinoma, exophytic carcinoma, ulcerative carcinoma, fibrocarcinoma, gelatinous carcinoma, carcinoma), colloid carcinoma, giant cell carcinoma, giant cell carcinoma, adenocarcinoma, granulosa cell carcinoma, hair matrix carcinoma, hematogenous carcinoma, hepatocellular carcinoma, Hoechst cell carcinoma, vitrine carcinoma, adrenal carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Klebsiella pneumoniae carcinoma, Kuhl cell carcinoma, large cell carcinoma, lenticular carcinoma, lenticular carcinoma, lipomatous carcinoma, lymphoepithelial carcinoma, medullary carcinoma, melanoma, soft carcinoma, mucinous carcinoma, carcinomamuciparum, mucous cell carcinoma, mucoepidermoid carcinoma, mucous carcinoma, mucous carcinoma, myxomatous carcinoma, nasopharyngeal carcinoma, oat cell carcinoma, ossifying carcinoma, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, acanthoma cell carcinoma, erosive carcinoma, renal cell carcinoma, reserve cell carcinoma, sarcoma carcinoma, Snyder's carcinoma, scirrhous carcinoma, scrotal carcinoma, signet ring cell carcinoma, carcinoma simplex, small cell carcinoma, potato carcinoma, spheroid cell carcinoma, spindle cell carcinoma, medullary carcinoma (carcinoma spongiosum), squamous cell carcinoma, squamous cell carcinoma, chordal carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes, transitional cell carcinoma, mass carcinoma, nodular carcinoma, verrucous carcinoma, and villous carcinoma.

[0344] Non-limiting examples of sarcomas include chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abernethy sarcoma, liposarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chlorosarcoma, choriocarcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, B-cell immunoblastic sarcoma, T-cell immunoblastic sarcoma, Janssen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukemic sarcoma, malignant mesenchymal sarcoma, parosteal sarcoma, reticular cell sarcoma, Law's sarcoma, plasmacystic sarcoma, synovial sarcoma, and telangiectatic sarcoma.

[0345] Non-limiting examples of leukemias include acute non-lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia, acute promyelocytic leukemia, adult T-cell leukemia, leukopenia leukemia, leukocytic leukemia, basophilic leukemia, blast cell leukemia, bovine leukemia, chronic myelogenous leukemia, leukemia cutis, embryonic leukemia, eosinophilic leukemia, Gross leukemia, hairy cell leukemia, hemoblastic leukemia, hemoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukemia Cytopenic leukemia, lymphoid leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenic leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myeloid leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Negley's leukemia, plasma cell leukemia, multiple myeloma, plasma cell leukemia, promyelocytic leukemia, Reed cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia and undifferentiated cell leukemia.

[0346] Non-limiting examples of melanoma include acral lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Claudemann's melanoma, S91 melanoma, Habari's melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungual melanoma, and superficial spreading melanoma.

[0347] Pharmaceutical composition

[0348] The compounds used in the methods described herein are preferably formulated into pharmaceutical compositions that are administered to humans in a biocompatible form suitable for in vivo administration. Pharmaceutical compositions typically include a compound as described herein and a pharmaceutically acceptable excipient. Certain pharmaceutical compositions may include one or more additional pharmaceutically active agents as described herein.

[0349] The compounds described herein may also be in the form of free bases, in the form of salts, zwitterions, solvates, or used as prodrugs or their pharmaceutical compositions. All forms are within the scope of the present invention. As will be appreciated by those skilled in the art, the compounds, their salts, zwitterions, solvates, prodrugs or pharmaceutical compositions may be administered to patients in various forms, depending on the selected route of administration. The compounds used in the methods described herein may be administered, for example, orally, parenterally, buccally, sublingually, nasally, rectally, by patch, pump or transdermally, and the pharmaceutical compositions are formulated accordingly. Parenteral administration includes intravenous, intraperitoneal, subcutaneous, intramuscular, transepithelial, nasal, intrapulmonary, intrathecal, rectal and topical administration modes. Parenteral administration may be performed by continuous infusion over a selected time period.

[0350] For human use, the compounds of the invention may be administered alone or in admixture with a pharmaceutical carrier selected according to the intended route of administration and standard pharmaceutical practice. Thus, the pharmaceutical compositions used according to the invention may be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and adjuvants that facilitate processing of the compounds of the invention into pharmaceutically acceptable preparations.

[0351] The present invention also includes pharmaceutical compositions that may contain one or more pharmaceutically acceptable carriers. In preparing the pharmaceutical compositions of the present invention, the active ingredient is typically mixed with an excipient, diluted with an excipient, or encapsulated in a carrier, in the form of, for example, a capsule, sachet, paper, or other container. When an excipient is used as a diluent, it may be a solid, semisolid, or liquid material (e.g., normal saline), acting as a vehicle, carrier, or medium for the active ingredient. Thus, the composition may be in the form of tablets, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, and soft and hard gelatin capsules. As is known in the art, the type of diluent may vary depending on the intended route of administration. The resulting composition may include additional agents, such as preservatives.

[0352] The excipient or carrier is selected according to the mode and route of administration. Suitable pharmaceutical carriers and pharmaceutically necessary substances for pharmaceutical preparations are described in Remington: The Science and Practice of Pharmacy, 21st edition, Gennarα ed., Lippincott Williams & Wilkins (2005), a well-known reference text in the art, and in USP / NF (United States Pharmacopoeia and National Formulary). Examples of suitable excipients are lactose, dextrose, sucrose, sorbitol, mannitol, starch, gum arabic, calcium phosphate, alginates, tragacanth, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup and methylcellulose. The formulation may additionally include: lubricants, such as talc, magnesium stearate and mineral oil; wetting agents; emulsifiers and suspending agents; preservatives, such as methyl and propyl hydroxybenzoates; sweeteners; and flavoring agents. Other exemplary excipients are described in Handbook of Pharmaceutical Excipients, 6th edition, Rowe et al., eds., Pharmaceutical Press (2009).

[0353] These pharmaceutical compositions can be prepared in a conventional manner, for example, by conventional mixing, dissolving, granulating, making dragees, grinding, emulsifying, encapsulating, embedding or lyophilizing processes. Methods for preparing formulations well known in the art can be found, for example, in Remington: The Science and Practice of Pharmacy, 21st edition, Gennaro ed., Lippincott Williams & Wilkins (2005) and Encyclopedia of Pharmaceutical Technology, ed. J. Swarbrick and JC Boylan, 1988-1999, Marcel Dekker, New York. The appropriate formulation depends on the selected route of administration. The formulation and preparation of such compositions are well known to those skilled in the art of pharmaceutical formulation. In preparing the formulation, the active compound can be ground to provide a suitable particle size before combining with the other ingredients. If the active compound is substantially insoluble, it can be ground to a particle size of less than 200 mesh. If the active compound is substantially water-soluble, the particle size can be adjusted by grinding to provide a substantially uniform distribution in the formulation, for example 40 mesh.

[0354] dose

[0355] The dosage of the compound used in the methods described herein, or a pharmaceutically acceptable salt or prodrug thereof, or a pharmaceutical composition thereof, may depend on many factors, such as the following: the pharmacodynamic properties of the compound; the mode of administration; the age, health and weight of the recipient; the nature and extent of the symptoms; the frequency of treatment and the type of concurrent treatment (if any); and the clearance rate of the compound in the animal to be treated. A person skilled in the art can determine the appropriate dosage based on the above factors. The compound used in the methods described herein may be initially administered at a suitable dosage, which may be adjusted as necessary, depending on the clinical response. In general, the suitable daily dose of the compound of the present invention will be the amount of the lowest dose at which the compound effectively produces a therapeutic effect. Such an effective dosage generally depends on the above factors.

[0356] The compound of the present invention can be applied to the patient in a single dose or multiple doses. When multiple doses are applied, each dose can be separated from each other by, for example, 1-24 hours, 1-7 days, 1-4 weeks or 1-12 months. The compound can be applied according to the schedule, or the compound can be applied without a predetermined schedule. The active compound can be applied every day, every 2 days, 3 days, 4 days, 5 days or 6 days, for example, 1 time, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 11 times or 12 times, 1, 2, 3, 4, 5, 6 times or 7 times per week, 1 time, 2 times, 3 times, 4 times, 5 times or 6 times per month, or 1 time, 2 times, 3 times, 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 11 times or 12 times per year. It should be understood that for any particular subject, a specific dosage regimen should be adjusted over time according to the professional judgment of the person who needs to be applied or supervised to apply the composition.

[0357] Although the attending physician will ultimately decide the appropriate amount and dosing regimen, the effective amount of the compounds of the invention may be, for example, a total daily dose of any compound described herein, for example, between 0.05 mg and 3000 mg. Alternatively, the amount of the dose may be calculated using the patient's weight. Such dosage ranges may include, for example, between 0.05-1000 mg (e.g., 0.25-800 mg). In some embodiments, 0.05 mg, 0.1 mg, 0.25 mg, 0.5 mg, 1 mg, 2 mg, 3 mg, 4 mg, 5 mg, 10 mg, 15 mg, 20 mg, 25 mg, 30 mg, 35 mg, 40 mg, 45 mg, 50 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 950 mg, or 1000 mg of the compound is administered.

[0358] In the method of the present invention, the time period of the compound of the present invention of multiple doses is variable to the patient. For example, in some embodiments, the dosage of the compound of the present invention is applied to the patient in a time period of 1-7 days, 1-12 weeks or 1-3 months. In other embodiments, the compound is applied to the patient in a time period of, for example, 4-11 months or 1-30 years. In other embodiments, the compound is applied to the patient at the onset of symptoms. In any one of these embodiments, the amount of the compound applied can change during the application time period. When the compound is applied every day, application can occur, for example, once, twice or three times a day.

[0359] preparation

[0360] Compounds identified as being able to treat any of the disorders described herein using any of the methods described herein can be administered to a patient or animal in a unit dosage form together with a pharmaceutically acceptable diluent, carrier, or excipient. Compounds for such therapies can be produced and isolated by any standard techniques known to those skilled in the art of pharmaceutical chemistry. Conventional pharmaceutical practice can be used to provide suitable formulations or compositions to administer the identified compounds to subjects in need. Administration can begin before the patient develops symptoms.

[0361] Exemplary routes of administration of the compounds used in the present invention (e.g., compounds of the present invention) or their pharmaceutical compositions include oral, sublingual, buccal, transdermal, intradermal, intramuscular, parenteral, intravenous, intraarterial, intracranial, subcutaneous, intraorbital, intraventricular, intraspinal, intraperitoneal, intranasal, inhalation, and topical administration. Ideally, the compound is administered with a pharmaceutically acceptable carrier. Pharmaceutical preparations of the compounds described herein formulated for the treatment of the conditions described herein are also part of the present invention. Oral administration is a preferred route of administration in the methods of the present invention.

[0362] Preparations for oral administration

[0363] Pharmaceutical compositions contemplated by the present invention include those formulated for oral administration ("oral dosage forms"). Oral dosage forms may be in the form of tablets, capsules, liquid solutions or suspensions, powders, or liquid or solid crystals, containing the active ingredient in a mixture with non-toxic pharmaceutically acceptable excipients. These excipients can be, for example, inert diluents or fillers (e.g., sucrose, sorbitol, sugar, mannitol, microcrystalline cellulose, starch (including potato starch), calcium carbonate, sodium chloride, lactose, calcium phosphate, calcium sulfate or sodium phosphate); granulating and disintegrants (e.g., cellulose derivatives, including microcrystalline cellulose, starch (including potato starch), cross-linked sodium carboxymethyl cellulose, alginates or alginic acid); binders (e.g., sucrose, glucose, sorbitol, gum arabic, alginic acid, sodium alginate, gelatin, starch, pregelatinized starch, microcrystalline cellulose, magnesium aluminum silicate, sodium carboxymethyl cellulose, methylcellulose, hydroxypropyl methylcellulose, ethylcellulose, polyvinyl pyrrolidone or polyethylene glycol); and lubricants, glidants and anti-adherents (e.g., magnesium stearate, zinc stearate, stearic acid, silicon dioxide, hydrogenated vegetable oils or talc). Other pharmaceutically acceptable excipients may be colorants, flavoring agents, plasticizers, wetting agents, buffers and the like.

[0364] Preparations for oral administration can also be presented in the form of chewable tablets, hard gelatin capsules in which the active ingredient is mixed with an inert solid diluent (e.g., potato starch, lactose, microcrystalline cellulose, calcium carbonate, calcium phosphate or kaolin), or soft gelatin capsules in which the active ingredient is mixed with water or an oil medium (e.g., peanut oil, liquid paraffin or olive oil). Powders, granules and pills can be prepared using the ingredients mentioned above under tablets and capsules in a conventional manner using, for example, a mixer, fluidized bed equipment or spray drying equipment.

[0365] Controlled release compositions for oral use can be configured to release active drugs by controlling the dissolution and / or diffusion of active drug substances. Any of a variety of strategies can be used to obtain controlled release and target plasma concentration versus time curves. In an example, controlled release is obtained by appropriately selecting various formulation parameters and ingredients, including, for example, various types of controlled release compositions and coatings. Examples include single or multi-unit tablets or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, nanoparticles, patches, and liposomes. In certain embodiments, compositions include biodegradable, pH and / or temperature-sensitive polymer coatings.

[0366] The controlled release by dissolution or diffusion can be achieved by coating the tablet, capsule, pill or granule formulation of the compound appropriately, or by incorporating the compound into an appropriate matrix. The controlled release coating may include one or more of the coating materials mentioned above and / or, for example, shellac, beeswax, sugar wax, castor wax, carnauba wax, stearyl alcohol, glyceryl monostearate, glyceryl distearate, glyceryl palmitostearate, ethylcellulose, acrylic resin, dl-polylactic acid, cellulose acetate butyrate, polyvinyl chloride, polyvinyl acetate, vinyl pyrrolidone, polyethylene, polymethacrylate, methyl methacrylate, 2-hydroxy methacrylate, methacrylate hydrogel, 1,3-butylene glycol, ethylene glycol methacrylate and / or polyethylene glycol. In controlled release matrix formulations, the matrix material may also include, for example, hydrated methylcellulose, carnauba wax and stearyl alcohol, carbopol 934, silicone, tristearin, methyl acrylate-methyl methacrylate, polyvinyl chloride, polyethylene and / or halogenated fluorocarbons.

[0367] Liquid forms into which the compounds and compositions of the invention may be incorporated for oral administration include aqueous solutions, suitably flavored syrups, aqueous or oily suspensions, and flavored emulsions with edible oils such as cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as elixirs and similar pharmaceutical vehicles.

[0368] Preparations for parenteral administration

[0369] The compounds described herein used in the methods of the present invention may be administered in pharmaceutically acceptable parenteral (e.g., intravenous or intramuscular) formulations as described herein. Pharmaceutical preparations may also be administered parenterally (intravenously, intramuscularly, subcutaneously, etc.) in dosage forms or formulations containing conventional nontoxic pharmaceutically acceptable carriers and adjuvants. Specifically, preparations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions, which may contain antioxidants, buffers, antibacterial agents, and solutes that make the preparation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions that may include suspending agents and thickening agents. For example, in order to prepare such compositions, the compounds of the present invention may be dissolved or suspended in a parenterally acceptable liquid vehicle. Among acceptable vehicles and solvents, water, water adjusted to a suitable pH by adding an appropriate amount of hydrochloric acid, sodium hydroxide or a suitable buffer, 1,3-butanediol, Ringer's solution, and isotonic sodium chloride solution may be used. Aqueous formulations may also contain one or more preservatives, such as methylparaben, ethylparaben, or n-propylparaben.Additional information on parenteral formulations may be found, for example, in the United States Pharmacopeia-National Formulary (USP-NF), which is incorporated herein by reference.

[0370] Parenteral formulations may be any of the five general types of formulations identified by the USP-NF as suitable for parenteral administration:

[0371] (1) "Drug injection" means a liquid preparation of a drug substance (e.g., a compound of the present invention) or a solution thereof;

[0372] (2) "Injectable drug": a drug substance (e.g., a compound of the present invention) in dry solid form that is to be combined with an appropriate sterile vehicle for parenteral administration as a pharmaceutical injection;

[0373] (3) "Drug injectable emulsion": a liquid preparation in which the drug substance (e.g., a compound of the present invention) is dissolved or dispersed in a suitable emulsion medium;

[0374] (4) "Drug injectable suspension": a liquid preparation in which the drug substance (e.g., a compound of the invention) is suspended in a suitable liquid medium; and

[0375] (5) "Drugs for injectable suspensions": drug substances (eg, compounds of the invention) in dry solid form, which are to be combined with an appropriate sterile vehicle for parenteral administration as a pharmaceutical injectable suspension.

[0376] Preparations for parenteral administration include solutions of the compound prepared in water appropriately mixed with a surfactant (e.g., hydroxypropylcellulose). Dispersions can also be prepared in glycerol, liquid polyethylene glycol, DMSO, and mixtures thereof with or without alcohol and in oil. Under normal storage and use conditions, these preparations may contain preservatives to prevent microbial growth. Conventional procedures and ingredients for selecting and preparing suitable preparations are described in, for example, Remington: The Science and Practice of Pharmacy, 21st edition, Gennarα edited, Lippincott Williams & Wilkins (2005) and the United States Pharmacopeia: National Formulary (USP36NF31), published in 2013.

[0377] Preparations for parenteral administration may, for example, contain excipients, sterile water or saline, polyalkylene glycols (e.g., polyethylene glycol), oils of plant origin, or hydrogenated naphthalene. Biocompatible biodegradable lactide polymers, lactide / glycolide copolymers, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compound. Other potentially useful compound parenteral delivery systems include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Preparations for inhalation may contain excipients, such as lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycocholate, and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or may be gels.

[0378] Parenteral preparations can be formulated for rapid release or for sustained / extended release of the compound. Exemplary formulations for parenteral release of the compound include: aqueous solutions, powders for reconstitution, co-solvent solutions, oil / water emulsions, suspensions, oil-based solutions, liposomes, microspheres, and polymer gels.

[0379] The following examples are intended to illustrate the present invention. They are not intended to limit the present invention in any way.

[0380] Example

[0381] Example 1. ATR inhibition in STAG2-deficient cells

[0382] To evaluate the impact of STAG2 deficiency on ATRi response, RPE1-hTERT-ΔTP53 deficient in the gene was generated by knocking out STAG2 using CRISPR-Cas9. To avoid potential off-target effects, two different sgRNAs were used to generate each KO clone. Treatment with compound 121 induced significantly stronger proliferation inhibition in STAG2-KO cells compared to wild-type (WT) counterparts ( Figure 1A This phenotype was observed in a second assay that measured viability by the ability of surviving cells to form colonies ( Figure 1B ).

[0383] Because bladder cancer is a cancer in which STAG2-deficient tumors have been observed, we sought to reproduce our observations in a cell model derived from bladder cancer. Using a similar approach as before, STAG2-deficient T24 cells were generated. Interestingly, colony formation of T24-STAG2 KO cells was impaired after treatment with compound 121 ( Figure 2 ). Collectively, this confirms that STAG2 loss of function is a determinant of ATRi sensitivity. Those results suggest that STAG2 is a potential biomarker for treating patients with ATRi.

[0384] Example 2. ATR inhibition in SETD2-deficient tumor cells

[0385] To determine whether SETD2 inactivation contributes to ATRi sensitivity, SETD2 was depleted from two human cell lines, MCF10A and RPE1-hTERT-ΔTP53, using specific siRNAs. It was observed that SETD2 depletion sensitized these cells to compound 121 treatment to a similar extent as depletion of ATM, a known determinant of ATRi sensitivity ( Figure 3A and 3B). Notably, depletion of SETD2 from a third cell line, HeLa, did not result in ATRi sensitivity. However, in this cell line, even depletion of ATM did not induce sensitivity to compound 121, suggesting that the HeLa cell line may not be a relevant model for studying ATRi sensitivity to siRNA depletion ( Figure 3C ).

[0386] To investigate whether SETD2 deficiency contributes to ATRi sensitivity in a more clinically relevant context, a panel of six SETD2-proficient and three SETD2-deficient renal clear cell carcinoma and colorectal cancer cell lines was assembled ( Figure 4A ) and treated them with compound 121. It was observed that, on average, SETD2-deficient cell lines were more sensitive to compound 121 than SETD2-proficient cell lines ( Figure 4B ).

[0387] In addition, the monotherapy dose-escalation phase of the study (Module 1) is recruiting patients with advanced solid tumors with qualifying loss-of-function mutations in a predefined subset of genes associated with ATRi sensitivity (STEP2 gene). A variety of tumors and genomic alterations are represented, including 5 patients with SETD2 mutations. Three of these patients are still on study, with treatment duration ranging from approximately 23 weeks to 45 weeks. In addition, one of these patients has a confirmed partial response (RECIST v1.1). As of the most recent report, the clinical benefit rate (CBR) in SETD2 patients evaluable for response was 80%. This means that 4 of the 5 patients responded, or are on treatment and progression-free for ≥16 weeks. Patients with tumors with SETD2 alterations are being recruited.

[0388] Together, these data support SETD2 status as a biomarker of ATRi sensitivity in tumors.

[0389] Example 3. ATR inhibition in CDK12-deficient tumor cells

[0390] To assess the effect of CDK12 inactivation on ATRi sensitivity, isogenic cell line pairs were used in the RPE1-hTERT-ΔTP53 and DLD1 human cell line backgrounds, where clones carrying XRISPR / Cas9-generated CDK12 knockouts (CDK12- / -) were compared to parental CDK12-wild-type controls (CDK12+ / +). CDK12 deficiency was confirmed to result in increased sensitivity to compound 121 treatment in both cell line backgrounds ( Figure 5A and 5B ).

[0391] In an ongoing study, 7 CDK12 patients enrolled in Study M1 are evaluable for response, but none are still on study. One of these patients has a confirmed partial response (RECIST v1.1) and has remained on study for nearly 27 weeks. The clinical benefit rate (CBR) for CDK12 patients enrolled in Study Module 1 was 29%, meaning 2 of 7 patients responded or were on treatment and progression-free for ≥16 weeks. Patients with tumors that have CDK12 alterations are being recruited. Taken together, the data suggest that CDK12 status in the tumor is a determinant of ATRi sensitivity.

[0392] Example 4. ATR inhibition in RNASEH2A and RNASEH2B deficient tumor cells

[0393] The RNase H2 protein complex is composed of three subunits encoded by the RNASEH2A, RNASEH2B, and RNASEH2C genes in a manner where all three subunits are required for complex stability and activity. To determine whether RNase H2 deficiency would increase cellular sensitivity to ATRi, the RNASEH2B gene was inactivated in two human cell lines, RPE1-hTERT-ΔTP53 and 5637, using CRISPR / Cas9 (note that this results in a complete loss of the RNase H2 complex). In both cell backgrounds, RNase H2-deficient cells (RNASEH2B- / -) were more sensitive to compound 121 than the isogenic wild-type (RNASEH2B+ / +) cell lines ( Fig. 6A and 6B ).

[0394] To confirm that RNase H2 deficiency is also sensitive to ATRi treatment in vitro, isogenic 5637 RNASEH2B+ / + and RNASEH2B- / - bladder cancer cell lines were developed as subcutaneous xenografts in immunodeficient mice and treated with compound 121 or vehicle control. Although compound 121 showed no efficacy in RNASEH2B+ / + tumors, significant and dose-dependent tumor growth inhibition was observed in RNASEH2B- / - tumors after compound 121 treatment ( Fig. 7A and 7B ). In addition, a triple-negative breast cancer patient-derived xenograft (PDX) was identified that was RNase H2-deficient as confirmed by immunohistochemistry using an RNase H2-specific antibody. This model also responded to compound 121 treatment and showed tumor regression at the maximum tolerated dose ( Fig. 8A and 8B ).

[0395] Together, these data support the use of RNase H2 (RNASEH2B or RNASEH2A) alterations as a biomarker for ATRi sensitivity.

[0396] Example 5. ATR inhibition in RAD51B, RAD51C or RAD51D deficient tumor cells

[0397] To determine the effect of RAD51B, RAD51C, or RAD51D deficiency on ATRi sensitivity, these genes were inactivated separately in RPE1-hTERT-ΔTP53 cells expressing Cas9 using two independent sgRNAs per gene. It was observed that inactivation of any of the three genes (RAD51B, RAD51C, or RAD51D) sensitized cells to treatment with compound 121 to a comparable extent ( Fig. 9A , 9B , 9C).

[0398] In addition, three patients with RAD51C alterations enrolled in Study M1 are evaluable for response and all remain on study. One of these patients has a confirmed complete response (RECIST v1.1) and remains on study for 41 weeks. In addition, one patient had a CA-125 tumor marker response and remained on study for 43 weeks. The Clinical Benefit Rate (CBR) for RAD51C patients enrolled in Study Module 1 was 100%, meaning that 3 of 3 patients responded or are on treatment and progression-free for ≥16 weeks. Patients with tumors with RAD51C alterations are enrolling.

[0399] Together, these data support the conclusion that alterations in RAD51B, RAD51C, or RAD51D are biomarkers of ATRi sensitivity.

[0400] Example 6. ATR inhibition in ATRIP, RAD17, REV3L, FZR1 or CHTF8 deficient cells

[0401] To investigate whether defects in any of the ATRIP, RAD17, REV3L, FZR1, or CHTF8 genes lead to ATRi sensitivity, specific siRNAs were used to downregulate the expression of the genes in two or three human cell lines, RPE1-hTERT-ΔTP53, MCF10A, or HeLa. siRNAs targeting SETD2 or ATM were used as positive controls. It was confirmed that siRNA-mediated attenuation of ATRIP, RAD17, REV3L, FZR1, or CHTF8 sensitized at least one cell line to treatment with compound 121, reaching levels comparable to or higher than attenuation of ATM or SETD2 ( Fig. 10A , 10Band 10C). These data suggest that tumors harboring inactivating alterations of ATRIP, RAD17, REV3L, FZR1, or CHTF8 may be sensitive to ATRi treatment.

[0402] Example 7. Lack of ATRi sensitivity under ARID1A

[0403] In addition to the genes disclosed herein, the sensitivity of ATRi to loss of ARID1A, described as a bona fide biomarker of ATRi sensitivity in Williamson et al., Nat. Comms., 7:13837, 2016, was investigated. Three isogenic ARID1A wild-type (WT) and ARID1A-deficient (ARID1A- / -) human cell line pairs were employed: HCT116, MCF10A, and BEAS2B. In all cases, ARID1A deficiency did not result in sensitivity to ATR inhibition by AZD-6738, contrary to published data ( Fig.11A , 11B To strengthen this observation, a panel of tissue-matched cancer cell lines that were either ARID1A WT or carried deleterious ARID1A alterations (LOF) were assembled and their sensitivity to AZD-6738 was measured. Consistent with the isogenic cell line data, there was no significant trend toward higher ATRi sensitivity in ARID1A L0F cell lines compared to ARID1A WT ( Fig.12 ). In conclusion, it is believed that the genes named in this application present a list of true determinants of ATRi sensitivity rather than some biomarkers described in the scientific literature.

[0404] Other Implementations

[0405] Various modifications and variations of the described invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the present invention has been described in conjunction with specific embodiments, it should be understood that the claimed invention should not be unduly limited to such specific embodiments. In fact, various modifications to the described modes for implementing the present invention that are apparent to those skilled in the art are intended to be within the scope of the present invention.

[0406] Other embodiments are within the claims.

Claims

1. A method for treating cancer in a subject, the method comprising administering to the subject in need thereof a therapeutically effective amount of an ATR inhibitor, wherein the cancer has been previously identified as a cancer having loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B.

2. A method for treating cancer in a subject, the method comprising administering to the subject in need thereof a therapeutically effective amount of an ATR inhibitor, wherein the cancer has a loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B.

3. A method of treating cancer in a subject, the method comprising: (i) identifying the cancer as having loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B; and (ii) administering to said subject in need thereof a therapeutically effective amount of an ATR inhibitor.

4. The method according to any one of claims 1 to 3, wherein the administration route is oral administration.

5. A method for inducing cell death of abnormal cancer cells having loss of function of STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B, the method comprising contacting the cells with an effective amount of an ATR inhibitor, the effective amount being sufficient to induce cell death of the abnormal cancer cells.

6. A method for treating a cancer in a subject, wherein the cancer has a biallelic STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutation, the method comprising administering to the subject in need thereof an effective amount of an ATR inhibitor.

7. A method for treating cancer in a subject, the method comprising administering to the subject in need thereof an effective amount of an ATR inhibitor, wherein the cancer has been previously identified as having a biallelic STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutation.

8. A method of inducing cell death in cancer cells having a loss-of-function mutation in STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B, the method comprising contacting the cells with an ATR inhibitor.

9. The method of claim 8, wherein the cell is in a subject.

10. The method of any one of claims 6 to 9, wherein the method further comprises, prior to the administering step or the contacting step, identifying the cancer as having a biallelic STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutation.

11. The method of claim 10, wherein the identifying step comprises: determining an integer total copy number and / or two integer allele-specific copy numbers of a locus segment within a STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B gene region in a cancer cell from the subject or in the cancer cell from a plurality of read counts comprising homozygous and heterozygous single nucleotide variants (sNVs) obtained by sequencing a sample comprising the cancer cell and from a reference read count, wherein the cancer is identified as having biallelic STAG2, SETD2, CDK12, ATRIP, REV3L, RAD17, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B loss-of-function mutations, if at least one of said integer total copy number and said integer allele-specific copy number is 0, provided that the remaining STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD5 1B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B allele, if present, comprises an inactivating mutation, or If none of the integer allele-specific copy numbers is 0 and a STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B allele is present, then each of the alleles independently comprises an inactivating mutation.

12. The method of claim 11, wherein the determining step comprises: Determining a total copy number log ratio, an allele copy number log odds ratio, and a target coverage value for the SNV from the read counts and the reference read counts; Segmenting the total copy number log ratio and the allele copy number log odds ratio; estimating the sample purity and sample ploidy of the cancer cells from the total copy number log ratio and the target coverage value; as well as From the target coverage value, the sample purity, the sample ploidy, the total copy number log ratio and the allele copy number log odds ratio, an integer total copy number of a segment containing multiple SNVs within the STAG2, SETD2, CDK1 2, ATRIP, REV3L, RAD1 7, CHTF8, FZR1, RAD51B, RAD51C, RAD51D, PALB2, RNASEH2A or RNASEH2B gene region in the cancer cells and two integer allele-specific copy numbers of the segment are generated. The method of claim 12 , wherein the method further comprises adjusting a position offset ratio.

14. The method of any one of claims 11 to 13, wherein the plurality of SNVs comprises consistently covered SNVs.

15. The method of claim 14, wherein each of the consistently covered SNVs has an average coverage of at least 200x reads across a set of normal samples.

16. The method of any one of claims 11 to 15, wherein the plurality of SNVs comprises frequent SNVs having an allele frequency of 33% to 66% in humans.

17. The method of claim 16, wherein the plurality of SNVs comprises SNVs that are proximal to the frequent SNVs.

18. The method of any one of claims 11 to 16, wherein the plurality of SNVs comprises SNVs, each of the SNVs having a 5'-flanking sequence of at least 20 contiguous nucleobases comprising 25-75% GC content, wherein the 5'-flanking sequence is unique and does not comprise other SNVs.

19. The method of any one of claims 11 to 18, wherein the plurality of SNVs comprises at least 20 heterozygous SNVs.

20. The method of any one of claims 11 to 19, wherein the reference read counts are from a set of normal samples.

21. The method of any one of claims 11 to 19, wherein the gene region comprises flanking regions of up to 10 kilobases each.

22. The method of any one of claims 11 to 19, wherein the gene region comprises flanking regions of up to 5 kilobases each.

23. The method of any one of claims 11 to 19, wherein the gene region comprises - each - a flanking region of up to 2 kilobases.

24. The method of any one of claims 11 to 23, wherein the gene region is an exon region.

25. The method of any one of claims 11 to 23, wherein the genomic region is a total transcriptome region.

26. The method of any one of claims 11 to 23, wherein the gene region is a genomic region.

27. The method of any one of claims 6 to 26, wherein the biallelic loss-of-function mutation comprises at least one somatic mutation.

28. The method of any one of claims 6 to 27, wherein the biallelic loss-of-function mutation comprises at least one germline mutation.

29. The method of any one of claims 1 to 28, wherein the ATR inhibitor is a compound of formula (I): or a pharmaceutically acceptable salt thereof, in is a double bond, and each Y is independently N or CR 4 ;or is a single bond, and each Y is independently NR Y , carbonyl or C(R Y )2; where each R Y is independently H or optionally substituted C 1-6 alkyl; R 1 is optionally substituted C 1-6 Alkyl or H; R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, -N(R 5 )2.-OR 5 、-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or -QR 5B ; R 3 is optionally substituted C 1-9 heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl; Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl; Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A ; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group; Each R 5A is independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 Aryl; R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or optionally substituted alkoxy; Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group; Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and X is hydrogen or halogen.

30. The method of claim 29, wherein the ATR inhibitor is a compound of formula (II): or a pharmaceutically acceptable salt thereof, in Each Y is independently N or CR 4 ; R 1 is optionally substituted C 1-6 Alkyl or H; R 2 is optionally substituted C 2-9 Heterocyclyl, optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl, optionally substituted C 2-9 Heterocyclyl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, optionally substituted C 1-9 Heteroaryl C 1-6 Alkyl, halogen, -N(R 5 )2.-OR 5 、-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or -QR 5B ; R 3 is optionally substituted C 1-9 heteroaryl or optionally substituted C 1-9 Heteroaryl C 1-6 alkyl; Each R 4 are independently hydrogen, halogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkenyl or optionally substituted C 2-6 Alkynyl; Each R 5 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl or -SO2R 5A ; or two R 5 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group; Each R 5A is independently optionally substituted C 1-6 Alkyl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 6-10 Aryl; R 5B is hydroxy, optionally substituted C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 1-9 Heteroaryl, -N(R 5 )2.-CON(R 6 )2、-SO2N(R 6 2. -SO2R 5A or optionally substituted alkoxy; Each R 6 are independently hydrogen, optionally substituted C 1-6 Alkyl, optionally substituted C 2-6 Alkoxyalkyl, optionally substituted C 6-10 Aryl C 1-6 Alkyl, optionally substituted C 6-10 Aryl, optionally substituted C 3-8 Cycloalkyl or optionally substituted C 1-9 heteroaryl; or two R 6 Together with the atoms to which it is attached, it forms an optionally substituted C 2-9 Heterocyclic group; Q is optionally substituted C 2-9 Heterocyclylene, optionally substituted C 3-8 Cycloalkylene, optionally substituted C 1-9 Heteroarylene or optionally substituted C 6-10 an arylene group; and X is hydrogen or halogen.

31. The method of claim 29, wherein the ATR inhibitor is selected from the group consisting of compounds 43, 57, 62, 87, 93, 94, 95, 99, 100, 106, 107, 108, 109, 111, 112, 113, 114, 115, 116, 118, 119, 120, 121, 122, 123, 135, 147, 148 and pharmaceutically acceptable salts thereof.

32. The method of claim 31, wherein the ATR inhibitor is compound 43 or a pharmaceutically acceptable salt thereof.

33. The method of claim 29, wherein the ATR inhibitor is Compound 121 or a pharmaceutically acceptable salt thereof.

34. The method of claim 29, wherein the ATR inhibitor is Compound 122 or a pharmaceutically acceptable salt thereof.

35. The method of any one of claims 1 to 28, wherein the ATR inhibitor is or a pharmaceutically acceptable salt thereof.

36. The method of any one of claims 1 to 28, wherein the ATR inhibitor is or a pharmaceutically acceptable salt thereof.

37. The method of any one of claims 1 to 36, wherein the method does not comprise the step of administering or contacting with a PARP inhibitor.

38. The method of any one of claims 1 to 37, wherein the ATR inhibitor is administered as a monotherapy.

39. The method of any one of claims 1 to 36, wherein the cancer is renal cell carcinoma, mature B-cell neoplasm, endometrial cancer, ovarian cancer, fallopian tube cancer, primary peritoneal cancer, colorectal cancer, skin cancer, small intestine cancer, non-small cell lung cancer, melanoma, bladder cancer, pancreatic cancer, head and neck cancer, mesothelioma, glioma, prostate cancer, breast cancer, or esophageal and gastric cancer.

40. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of STAG2.

41. The method of claim 37, wherein the cancer is renal cell carcinoma, endometrial cancer, acute myeloid leukemia, bladder cancer, uterine cancer, or gastric cancer.

42. The method of any one of claims 1 to 36, wherein the loss of function is a loss of function of SETD2.

43. The method of claim 42, wherein the cancer is mesothelioma, renal clear cell carcinoma, renal papillary cell carcinoma, lung adenocarcinoma, bile duct carcinoma, uveal melanoma, bladder urothelial carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, invasive breast carcinoma, lung squamous cell carcinoma, esophageal cancer, head and neck squamous cell carcinoma, or ovarian serous cystadenocarcinoma.

44. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of CDK12.

45. The method of claim 44, wherein the cancer is prostate adenocarcinoma, ovarian serous cystadenocarcinoma, uterine corpus endometrial carcinoma, skin melanoma, lung adenocarcinoma, or invasive breast carcinoma.

46. ​​The method of any one of claims 1 to 36, wherein the loss of function is loss of function of ATRIP.

47. The method of claim 46, wherein the cancer is uveal melanoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, gastric adenocarcinoma, head and neck squamous cell carcinoma, or renal clear cell carcinoma.

48. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of REV3L.

49. The method of claim 48, wherein the cancer is uterine corpus endometrial carcinoma, gastric adenocarcinoma, prostate adenocarcinoma, lung squamous cell carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, skin melanoma, or lung adenocarcinoma.

50. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of RAD17.

51. The method of claim 50, wherein the cancer is gastric adenocarcinoma, prostate adenocarcinoma, or invasive breast carcinoma.

52. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of CHTF8.

53. The method of claim 52, wherein the cancer is prostate adenocarcinoma.

54. The method of any one of claims 1 to 36, wherein the loss of function is a loss of function of FZR1.

55. The method of claim 54, wherein the cancer is head and neck squamous cell carcinoma, skin melanoma, or renal papillary cell carcinoma.

56. The method of any one of claims 1 to 55, wherein the loss of function is loss of function of RAD51B.

57. The method of claim 56, wherein the cancer is uterine corpus endometrial carcinoma, renal papillary cell carcinoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, skin melanoma, or invasive breast carcinoma.

58. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of RAD51C.

59. The method of claim 58, wherein the cancer is cutaneous melanoma, uterine corpus endometrial carcinoma, ovarian serous cystadenocarcinoma, or invasive breast carcinoma.

60. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of RAD51D.

61. The method of claim 60, wherein the cancer is ovarian serous cystadenocarcinoma, gastric adenocarcinoma, or cutaneous melanoma.

62. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of PALB2.

63. The method of claim 62, wherein the cancer is prostate adenocarcinoma, lung adenocarcinoma, hepatocellular carcinoma, invasive breast carcinoma, uterine corpus endometrial carcinoma, lung squamous cell carcinoma, ovarian serous cystadenocarcinoma, or gastric adenocarcinoma.

64. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of RNASEH2A.

65. The method of any one of claims 1 to 36, wherein the loss of function is loss of function of RNASEH2B.

66. The method of claim 64 or 65, wherein the cancer is sarcoma, bladder urothelial carcinoma, chronic lymphocytic leukemia.

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