WO2021046178A1 - Composés et méthodes de traitement du cancer - Google Patents

Composés et méthodes de traitement du cancer Download PDF

Info

Publication number
WO2021046178A1
WO2021046178A1 PCT/US2020/049140 US2020049140W WO2021046178A1 WO 2021046178 A1 WO2021046178 A1 WO 2021046178A1 US 2020049140 W US2020049140 W US 2020049140W WO 2021046178 A1 WO2021046178 A1 WO 2021046178A1
Authority
WO
WIPO (PCT)
Prior art keywords
group
alkyl
optionally substituted
independently selected
cancer
Prior art date
Application number
PCT/US2020/049140
Other languages
English (en)
Inventor
Alan D'andrea
Brian S.J. Blagg
Rachel E. DAVIS
Jia Zhou
Original Assignee
Dana-Farber Cancer Institute, Inc.
University Of Kansas
University Of Notre Dame
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Dana-Farber Cancer Institute, Inc., University Of Kansas, University Of Notre Dame filed Critical Dana-Farber Cancer Institute, Inc.
Publication of WO2021046178A1 publication Critical patent/WO2021046178A1/fr

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents

Definitions

  • This disclosure relates to compounds useful in treating cancer, in particular to biphenyl or phenyl-cyclohexyl derivatives useful in treating cancer identified as having a homologous recombination (HR) deficiency.
  • HR homologous recombination
  • Cancer cells are often defective in one of the six major DNA repair pathways.
  • EOCs epithelial ovarian cancers
  • HR homologous recombination
  • PARPi poly(ADP-ribose) polymerase inhibitor
  • POLQ a translesion DNA polymerase that is involved in alternative end joining (Alt-EJ), regulates genomic stability in HR- deficient cancers.
  • Alt-EJ translesion DNA polymerase that is involved in alternative end joining
  • loss of POLQ-mediated DNA repair in HR-deficient ovarian cancer cells creates a synthetic lethality (Ceccaldi et al., 2015).
  • the present disclosure provides a method of treating a homologous recombination (HR)-deficient cancer or a POLQ-overexpressing cancer, the method comprising: (i) identifying a subject having an HR-deficient cancer or a POLQ-overexpressing cancer, or both; and (ii) after (i), administering to the subject a therapeutically effective amount of a compound of Formula (A), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has Formula (I), or a pharmaceutically acceptable salt thereof.
  • the gene regulating homologous recombination is BRCAl/2.
  • the cancer is selected from prostate cancer, colon cancer, lung cancer, liver cancer, sarcoma, melanoma, breast cancer, ovarian cancer, and pancreatic cancer.
  • the cancer has an acquired resistance to a PARP inhibitor.
  • the cancer has a de novo resistance to a PARP inhibitor.
  • the method further comprises administering to the subject a therapeutically effective amount of an additional anti-cancer agent.
  • the additional anti-cancer agent is a platinum-based anti-cancer agent.
  • the platinum-based anti-cancer agent is selected from carboplatin and cisplatin.
  • the additional anti-cancer agent is a PARP inhibitor.
  • the PARP inhibitor is selected from olaparib, veliparib, rucaparib, BGB-290 (pamiparib), talazoparib (BMN 673), and niraparib.
  • the present disclosure provides a method of killing a POLQ-overexpressing cancer cell, the method comprising (i) determining that a cancer cell is overexpressing POLQ, wherein POLQ overexpression is a predictive biomarker that the cancer cell is susceptible to killing by a POLQ inhibitor; and (ii) after (i), contacting the POLQ-overexpressing cancer cell with an effective amount of a compound of Formula (A), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has Formula (I), or a pharmaceutically acceptable salt thereof.
  • contacting the cancer cell with the compound of Formula (A), or a pharmaceutically acceptable salt thereof is carried out in vitro, in vivo, or ex vivo.
  • the present disclosure provides a method of treating a cancer having a de novo or an acquired resistance to a PARP inhibitor, the method comprising administering to a subject in need thereof a therapeutically effective amount of a compound of Formula (A), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has Formula (I), or a pharmaceutically acceptable salt thereof.
  • the method further comprises administering to the subject a therapeutically effective amount of an additional anti-cancer agent.
  • the additional anti-cancer agent is a PARP inhibitor.
  • the PARP inhibitor is selected from olaparib, veliparib, pamiparib (BGB-290), talazoparib (BMN 673), and niraparib.
  • the present disclosure provides a method of inhibiting DNA polymerase q (Ro ⁇ q) in a cancer cell, the method comprising contacting the cancer cell with an effective amount of a compound of Formula (A), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has Formula (I), or a pharmaceutically acceptable salt thereof.
  • the present disclosure provides a method of inhibiting heat shock protein 90 (Hsp90) in a cancer cell, the method comprising contacting the cancer cell with an effective amount of a compound of Formula (A), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has Formula (I), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A), or a pharmaceutically acceptable salt thereof selectively inhibits a C-terminal binding domain of the Hsp90.
  • the cancer cell is contacted in vitro. In some embodiments, the cancer cell is contacted in vivo. In some embodiments, the cancer cell is contacted ex vivo.
  • the present disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising a compound of Formula (A), or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
  • the compound of Formula (A) has Formula (I), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has formula: or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 8 , R 6 , R 7 , and ring A are as described herein.
  • ring A is selected from the group consisting of: C3-8 cycloalkyl and Ce-u aryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R A ;
  • R 8 is selected from -Ci-6 alkyl, optionally substituted with NR 5 R 6 , and a group of formula (i):
  • R A is selected from the group consisting of: H, halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6alkoxy, and Ci-6haloalkoxy;
  • R 1 is selected from the group consisting of: Cy 2 and Cy 2 -NR 6 -; each Cy 2 is independently selected from the group consisting of: Ce-u aryl and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R B ;
  • R B is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-CI-3 alkyl, amino, Ci-6 alkylamino, di(Ci-6 alkyl)amino, Cy 1 , Cy ⁇ Cm alkyl, and Cy ! -O-;
  • Cy 1 is C6-12 aryl, optionally substituted by 1, 2, 3, 4, or 5 substituents independently selected from R g ;
  • R g is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-Ci-3 alkyl, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino;
  • R al and R a2 are independently selected from the group consisting of: H, C1-3 alkyl, and C1-3 haloalkyl; and each R 6 is independently selected from the group consisting of: H and C1-3 alkyl.
  • the compound of Formula (I) has formula: or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and ring A are as described herein.
  • ring A is selected from the group consisting of: C3-6 cycloalkyl and Ce-u aryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R A ;
  • R A is selected from the group consisting of: H, halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, and Ci-6haloalkoxy;
  • R 1 is selected from the group consisting of: Ce-u aryl and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R B ;
  • R B is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, Ci-6 alkylamino, di(C 1-6 alky l)amino, Cy 1 , Cy ⁇ Cm alkyl, and Cy ⁇ O; Cy 1 is G.-I2 aryl, optionally substituted by 1, 2, 3, 4, or 5 substituents independently selected from R g ;
  • R g is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-C1-3 alkyl, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino;
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H, Cy 1 , Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, and Ci-6haloalkoxy;
  • R al and R a2 are independently selected from the group consisting of: H, C1-3 alkyl, and C1-3 haloalkyl;
  • R 6 is selected from the group consisting of: H and C1-3 alkyl.
  • R 8 is -Ci-6 alkyl, optionally substituted with NR 5 R 6 .
  • R 8 is -Ci-6 alkyl substituted with NR 5 R 6 .
  • ring A is C3-8 cycloalkyl.
  • ring A is C3-6 cycloalkyl.
  • ring A is selected from the group consisting of: cyclopentyl, cyclohexyl, and cycloheptyl.
  • ring A is cyclohexyl
  • the compound of Formula (A) is selected from any one of the following compounds:
  • the compound of Formula (I) has Formula (la): or a pharmaceutically acceptable salt thereof.
  • ring A is Ce-u aryl.
  • ring A is phenyl
  • the compound of Formula (I) has Formula (lb): or a pharmaceutically acceptable salt thereof. In some embodiments, the compound of Formula (I) has Formula (Ic): or a pharmaceutically acceptable salt thereof.
  • R 1 is Cy 2 -NR 6 .
  • Cy 2 is Ce-u aryl, optionally substituted with 1, 2, or 3 independently selected R B .
  • R 1 is Ce-u aryl, optionally substituted with 1, 2, or 3 independently selected R B .
  • R 1 is phenyl, optionally substituted with 1, 2, or 3 independently selected R B .
  • R 1 is 5-10 membered heteroaryl, optionally substituted with 1, 2, or 3 independently selected R B .
  • R 1 is triazole, optionally substituted with 1, 2, or 3 independently selected R B .
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, Cy 1 , and Cy CCi-3 alkyl.
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H and Cy 1 .
  • R 2 , R 3 , R 7 , and R 4 are each H.
  • R 2 , R 7 , and R 3 are each H; and R 4 is Cy 1 .
  • Cy 1 is Ce-12 aryl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, Ci-4 haloalkyl and Ci -6 alkoxy.
  • Cy 1 is phenyl, optionally substituted with Ci-6 alkoxy.
  • Cy 1 is phenyl, optionally substituted with halo or Ci-4 haloalkyl.
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OR al .
  • R al is selected from the group consisting of: H and C1-3 alkyl. In some embodiments, R 5 is H.
  • R 5 is Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy.
  • R 6 is H.
  • R 1 is selected from the group consisting of: Cy 2 -NR 6 -, Ce-12 aryl, and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, or 3 substituents independently selected from R B ;
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, Cy 1 , and Cy ⁇ Cm alkyl;
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H and Cy 1 ;
  • Cy 1 is Ce-12 aryl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, Ci-4 haloalkyl, and Ci-6 alkoxy;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy;
  • R 6 is H.
  • R 1 is selected from the group consisting of: CM 2 aryl and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, or 3 substituents independently selected from R B ;
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, Cy 1 , and CyCCm alkyl;
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H and Cy 1 ;
  • Cy 1 is Ce-12 aryl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, Ci-4 haloalkyl, and Ci-6 alkoxy;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy;
  • R 6 is H.
  • R 1 is Ce-12 aryl, optionally substituted with 1, 2, or 3 independently selected
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, and
  • Cy 1 is G.-I2 aryl, optionally substituted with Ci-6 alkoxy;
  • R 2 , R 3 , R 7 , and R 4 are each H;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy;
  • R 6 is H.
  • R 1 is 5-10 membered heteroaryl, optionally substituted with 1, 2, or 3 independently selected R B ;
  • R B is CykCm alkyl
  • Cy 1 is Ce-12 aryl, optionally substituted with Ci-4 alkoxy;
  • R 2 , R 7 , and R 3 are each H;
  • R 4 is Ce-12 aryl, optionally substituted with halo or Ci-4 haloalkyl;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy;
  • R 6 is H.
  • the compound of Formula (I) is selected from any one of the compounds described herein.
  • FIG. 1 A contains a bar graph showing ATPase activity of novobiocin and compounds 1-6.
  • FIG. IB contains a bar graph showing ATPase activity of novobiocin and compounds 7-10.
  • FIG. 1C contains a bar graph showing IC50 ratio for WT over BRCA1-KO for olaparib, novobiocin, and compounds 1 and 2.
  • FIG. 2 contains a line plot showing that compound 1 efficiently kills B40 cells.
  • FIG. 3 A contains a bar graph showing that compound 1 effectively kills
  • FIG. 3B contains a line plot showing that compound 1 effectively kills BRCA1 RPEl cells.
  • FIG. 4 contains a bar graph showing that compound 1 more effectively killed BRCA1 -mutated cancer cell lines (MDA-MB-436 and UWB1) than their WT counterparts (MDA-MB-436 + BRCA1 and UWB1 + BRCA1).
  • BRC A 1 -mutated parental MDA-MB-436
  • BRCA1 cDNA cells in presence of indicated test compounds (200 nM) or novobiocin (100 mM) were shown. Results from one experiment are shown.
  • FIG. 5A contains an image showing the results of the clonogenic survival assays performed with novobiocin, olaparib, and compound 1.
  • Compound 1 selectively killed BRCA1 null cells (RPE-P53 / BRCAl ).
  • FIG. 5B contains a bar graph showing the results of the survival assays performed with novobiocin, olaparib, compound 1, and compound 2. All tested compounds selectively killed BRCA1 null cells (RPE-P53 / BRCAl ).
  • FIG. 6 contains bar graph showing that compound 1 kills UWB1 (BRCA1 mutated) cells more efficiently than BRCA1 -complemented UWB1 cells.
  • FIG. 7 contains images showing that compound 1 killed MB436+EV cells more readily than MB436+BRCA1 (selective cell killing in the MB436 isogenic pair).
  • FIG. 8 contains bar graph showing that compounds 1 and 2 killed MB436+EV cells more readily than MB436+BRCA1 cells (selective cell killing in the MB436 isogenic pair).
  • FIG. 9A contains images showing that compound 1 killed MB436+EV cells more readily than MB436+BRCA1 cells (selective cell killing in the MB436 isogenic pair).
  • FIG. 9B contains a line plot showing that POLQ knockout (KO) RPE cells showed resistance to compound 1.
  • FIG. 10 contains an image of western blot of MCF7 lysate for compound 9, and anti-proliferative EC50 against MCF7 and SKBR3.
  • FIG. 11 contains an image of western blot of MCF7 lysate for compound 4, and anti-proliferative EC50 against MCF7 and SKBR3.
  • FIG. 12 contains an image of western blot of MCF7 lysate for compound 6, and anti-proliferative ECso against MCF7 and SKBR3.
  • FIG. 13 contains a bar graph showing ATPase activity for novobiocin and compound 1 compared to DMSO and no enzyme control.
  • FIG. 14 contains a bar graph showing fraction of clonogenic survival of RPE cells treated with olaparib, novobiocin, and compound 1.
  • FIG. 15 contains a bar graph showing fraction of clonogenic survival of MDA-MB-436 cells treated with olaparib, novobiocin, and compound 1.
  • FIG. 16 contains a table showing IC50 values for olaparib, novobiocin, and compound 1 in BRCAl (RPE) cells.
  • FIG. 17A provides results of CTG Glo assay (7 days) for compound 11.
  • FIG. 17B provides results of CTG Glo assay (7 days) for compound 12.
  • FIG. 17C provides results of CTG Glo assay (7 days) for compound 13.
  • FIG. 17D provides results of CTG Glo assay (7 days) for compound 14.
  • FIG. 18 contains a table showing IC50 values for compounds 11-14 on BRCA1 and WT RPE cells.
  • FIG. 19 contains a line plot showing that the BRCA1 RPE cells used in experiments are hypersensitive to olaparib.
  • FIG. 20 contains a line plot showing that the BRCA1 RPE cells used in experiments are sensitive to novobiocin.
  • the present disclosure provides a method of treating cancer, the method comprising administering to a subject (e.g., in need thereol) a therapeutically effective amount of a compound of Formula (A) or Formula (I) as described herein, or a pharmaceutically acceptable salt thereof.
  • a subject e.g., in need thereol
  • the cancer is homologous recombination (HR)-deficient.
  • the HR-deficiency in a cancer can be characterized by a lack of a functional homologous recombination (HR) DNA repair pathway, and can be correlated with mutation or alteration of one or more HR-associated genes, such as BRCA1, BRCA2, RAD50, RAD54, RAD51B, RED51C, RAD51D, CtlP (Choline Transporter-Like Protein), PALB2 (Partner and Localizer of BRCA2), XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells 2), RECQL4 (RecQ Protein- Like 4), BLM (Bloom syndrome, RecQ helicase-like), WRN (Wemer syndrome,
  • HR-associated genes such as BRCA1, BRCA2, RAD50, RAD54, RAD51B, RED51C, RAD51D, CtlP (Choline Transporter-Like Protein), PALB2 (Partner and Localizer of BRCA2), XRCC2 (X-ray repair complementing defective
  • FA and FA-like genes include FANCA/C/D2/E//F//GL, FANCA, FANCB, FANCC, FANCD1 (BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (BRIP1), FANCL, FANCM, FANCN (PALB2), FANCP (SLX4), FANCS (BRCA1), RAD51C, and XPF.
  • HR-associated genes include RECA, ARID1A, ATM, CHEKl/2, FAM175A, HDAC2, ERCC3, MRE11A, CDK12, CDKN1A/B/C, BAP1, MLL2, CDKN2A, NPM1, TP53, ATRX, BARDl, BRCAl/2, BRIP1, MRE11A, NBN,
  • a cancer known to have a mutation in at least one HR-associated gene is an HR-deficient cancer.
  • the mutation is a pathogenic somatic mutation.
  • the mutation is germline mutation.
  • an HR-deficient cancer has at least one mutated HR gene selected from PTEN, BRCA1, BRCA2, and ATM.
  • the HR-deficient cancer has a pathogenic mutation (not a benign variant) in an HR gene, including a pathogenic mutation in, e.g., the BRCA1,
  • the pathogenicity of the mutation can be determined by any suitable art-recognized method.
  • the cancer is characterized by one or more BRCA mutations. In some aspects of these embodiments, the cancer is characterized by BRCA1 mutation, BRCA2 mutation, or a mutation in both BRCA1 and BRCA2 genes.
  • BRCA1 Located on chromosome 17, BRCA1 is the first gene identified conferring increased risk for breast and ovarian cancer (Miki et al, Science, 266:66-71 (1994)).
  • the BRCA1 gene (Gene ID: 672) is divided into 24 separate exons. Exons 1 and 4 are noncoding, in that they are not part of the final functional BRCA1 protein product.
  • the BRCA1 coding region spans roughly 5600 base pairs (bp). Each exon consists of 200-400 bp, except for exon 11 which contains about 3600 bp.
  • BRCA2 gene by positional cloning of a region on chromosome 13ql2-ql3 implicated in Icelandic families with breast cancer.
  • Human BRCA2 (Gene ID: 675) gene contains 27 exons. Similar to BRCA1, BRCA2 gene also has a large exon 11, translational start sites in exon 2, and coding sequences that are AT-rich.
  • BRCA genes associated with cancer are described, for example, in Friend, S. et al, 1995, Nature Genetics 11: 238, US 2003/0235819, US 6083698, US 7250497, US 5747282, WO 1999028506, US 5837492, WO 2014160876; all of which are incorporated herein by reference.
  • DNA polymerase q (PolO, also referred to as POLQ; Gene ID No. 10721) is a family A DNA polymerase that also functions as a DNA-dependent ATPase (see, e.g., Seki et al. Nucl. Acids Res. (2003) 31 (21): 6117-6126).
  • HR-deficient cancers lack afunctional DNArepair pathway
  • an increase in the expression POLQ in HR-deficient cancer is believed to be compensatory, i.e., increased levels of POLQ regulate genomic stability and survival in these cancers. It is believed that HR-deficient tumors with repair deficiency, which often exhibit replication stress and collapsed replication forks, are hyper-dependent on alternative repair pathways and upregulate POLQ expression as a survival mechanism (See, e.g., Ceccaldi et al, 2015).
  • POLQ is implicated in a pathway required for the repair of double-stranded DNA breaks, referred to as the error-prone microhomology-mediated end-joining (MMEJ) pathway.
  • MMEJ microhomology-mediated end-joining
  • POLQ is also a translesion polymerase that is involved in alternative end joining (Alt-EJ) of double-stranded breaks (DSB) (Ceccaldi et al, 2015, Nature 518, 258-262; Mateos-Gomez et al, 2015, Nature 518, 254-257). Knockdown of POLQ was found to enhance cell death in HR-deficient cancers.
  • POLQ deletion in a HR-deficient background results in marked developmental disadvantage or synthetic embryonic lethality in mice (Ceccaldi et al, 2015, Nature 518, 258-262; Shima et al, 2004, Molecular and cellular biology 24, 10381-10389).
  • knockdown of POLQ in HR- proficient cells up-regulates HR activity and RAD51 nucleofilament assembly, while knockdown of POLQ in HR-deficient EOCs enhances cell death (See, e.g., Ceccaldi et al, Nature (2015) 518, 7538, 258-262).
  • the cancer e.g., HR-deficient cancer as described herein
  • POLQ overexpression in the cancer can be at least 2-fold, at least 3- fold, at least 4-fold, at least 5-fold, at least 10-fold, at least 20-fold, at least 50-fold, at least 100-fold, at least 500-fold, or at least 1000-fold greater, relative to POLQ expression in a control tissue (e.g., a non-cancer cells of the same type).
  • POLQ overexpression is a predictive biomarker that the cancer cell is susceptible to killing by a POLQ inhibitor.
  • the present disclosure provides a method of killing a POLQ-overexpressing cancer cell, the method comprising (i) determining that a cancer cell is overexpressing POLQ, wherein POLQ overexpression is a predictive biomarker that the cancer cell is susceptible to killing by a POLQ inhibitor; and (ii) after (i), contacting the POLQ-overexpressing cancer cell with an effective amount of a compound of Formula (A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof is an inhibitor of POLQ. That is, the compound of Formula(A) or Formula (I) reduces, slows, halts, and/or prevents POLQ activity in a cancer cell (e.g., HR-deficient cancer cell).
  • a cancer cell e.g., HR-deficient cancer cell
  • POLQ protein is structurally distinct from other polymerases with its three domains.
  • POLQ is a large protein containing an N-term helicase-like ATPase domain, a central linker domain, and a C-term polymerase domain.
  • the N-terminus of POLQ contains a helicase-like ATPase domain.
  • the central domain binds RAD51, displaces RPA proteins from DSBs and antagonizes HR repair in an ATP -hydrolysis dependent manner (Ceccaldi et al, 2015; Mateos-Gomez et al, 2015; Mateos-Gomez et al, 2017).
  • the POLQ C-terminal domain is an error-prone polymerase, which presumably fills in nucleotides during TLS and alt-EJ DNA repair. It has been shown that both the ATPase domain and the polymerase domain are required for POLQ- mediated Alt-EJ (Beagan et al, 2017, PLoS Genet 13, el006813).
  • the compound of Formula(A) or Formula (I) inhibits polymerase function, ATPase function, or both polymerase function and ATPase function of POLQ. In some embodiments, the compound of Formula(A) or Formula (I) disrupts POLQ-DNA interaction or antagonizes ATP. In some embodiments, the compound of Formula(A) or formula (I) selectively inhibits (e.g., reduces, slows, halts, and/or prevents) the ATPase activity of POLQ.
  • the compound of Formula(A) or Formula (I) selectively inhibits ATPase activity of POLQ and does not inhibit the polymerase activity of POLQ or disrupt POLQ-DNA interactions. In some embodiments, the compound of Formula(A) or Formula (I) selectively inhibits ATPase activity of POLQ and does not inhibit other ATPase enzymes in the cancer cell. In some embodiments, the compound of Formula(A) or Formula (I) targets and selectively inhibits ATPase domain of POLQ and therefore promotes lethality of cancers, such as HR-deficient cancers, while having little or no effect on healthy cells.
  • the present disclosure provides a method of inhibiting DNA polymerase q (Ro ⁇ q) in a cancer cell, the method comprising contacting the cancer cell with an effective amount of a compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • the cancer cell is HR-deficient as described herein.
  • the cancer cell is contacted in vitro, in vivo, or ex vivo.
  • POLQ is inhibited in a cancer cell of a patient after the compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof, is administered to the patient in need thereof.
  • the present disclosure provides a method of treating cancer characterized by overexpression of DNA polymerase q (Ro ⁇ q), the method comprising administering to a subject in need thereof a therapeutically effective amount of a compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • the cancer contains a mutation in at least one gene regulating homologous recombination (HR) (e.g., BRCA 1/2 gene), as described herein. Accordingly, aspects of the disclosure provide a method for treating cancer that is characterized by one or more HR-associated mutations and/or overexpressed POLQ. Determining or Identifying step
  • a method of treating cancer described herein comprises a step of identifying a cancer cell from a subject as a HR-deficient cancer cell.
  • a method of treating cancer described herein comprises the steps of: a) identifying a subject in need thereof having an HR-deficient cancer (e.g., by al) determining that the cancer contains a mutation or an alteration in a gene regulating homologous recombination (HR) and/or a2) determining that the cancer is overexpressing POLQ); and b) administering to the subject a therapeutically effective amount of a compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • the administering of step b) occurs after the determining of step a); or the administering of step b) occurs prior to the determining of step a).
  • the determining of step al) is conducted before the determining of step a2); or the determining of step al) is conducted after the determining of step a2).
  • a mutation in a gene regulating homologous recombination, or the overexpression of POLQ can be determined by any suitable art- recognized methods.
  • a mutation in a gene regulating homologous recombination, or the overexpression of POLQ can be determined without isolating a cancer cell from a subject.
  • a mutation can be identified by analyzing blood sample of the subject, or a sample of hair, urine, saliva, or feces of the subject for the presence of a cancer biomarker.
  • cancer biomarker refers to a substance or process that is indicative of the presence of cancer in the body of a subject.
  • a biomarker may be a molecule secreted by a tumor or a specific response of the subject’s body to the presence of a cancer.
  • a mutation can be identified be isolating a cancer cell from a subject.
  • a cancer cell for analysis of a mutation in an HR-associated gene or levels of expression of POLQ can be isolated from the subject by surgical means (e.g., laparoscopically).
  • an HR mutation or a level of POLQ expression is being identified in the cancer cell of the subject.
  • any of the methods, reagents, protocols and devices generally known in the art can be used to identify a mutation in a gene regulating HR or an overexpression of POLQ.
  • next generation sequencing, immunohistochemistry, fluorescence microscopy, break apart FISH analysis, Southern blotting, Western blotting, FACS analysis, Northern blotting, ELISA or ELISPOT, antibodies microarrays, or immunohistochemistry, and PCR-based amplification (e.g., RT-PCR and quantitative real-time RT-PCR) techniques can be used to identify the mutation or a POLQ status of cancer.
  • the assays are typically performed, e.g., with at least one labelled nucleic acid probe or at least one labelled antibody or antigen-binding fragment thereof.
  • Assays can utilize other detection methods known in the art for detecting a mutation in a HR-associated gene.
  • Any DNA sequencing platform for somatic mutations can be used.
  • Illumina MiSeq platform Illumina TruSeq Amplicon Cancer Hotspot panel, 47 gene
  • NextSeq Alent SureSelect XT, 592 gene selected based on COSMIC database
  • the sample can be a biological sample or a biopsy sample (e.g., a paraffin-embedded biopsy sample) from the patient.
  • the patient is a patient suspected of having a cancer having a mutation in a HR-associated gene (e.g., BRCAl/2 mutation in breast or ovarian cancer).
  • Exemplary methods for determining POLQ overexpressing cancers are described, e.g., in EP 2710142, which is incorporated herein by reference in its entirety. Exemplary methods to identify a BRCA mutation in cancer are described, for example, in WO1998043092 and WO 2013124740, both of which are incorporated herein by reference.
  • the compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof is an inhibitor of heat shock protein 90 (Hsp90). That is, the compound of Formula(A) or Formula (I) reduces, slows, halts, and/or prevents heat shock protein 90 (Hsp90) activity in a cancer cell (e.g., HR- deficient cancer cell).
  • a cancer cell e.g., HR- deficient cancer cell
  • Hsp90 heat shock protein 90
  • Hsp90-ai Hsp90-a2
  • Hsp90- isoform Hsp90-a2
  • Hsp90 protein consists of four structural domains: highly conserved N-terminal domain (NTD) of about 25 kDa, “charged linker” region, that connects the N-terminus with the middle domain, a middle domain (MD) of about 40 kDa, and a C-terminal domain (CTD) of about 12 kDa.
  • NTD N-terminal domain
  • MD middle domain
  • CCD C-terminal domain
  • Hsp90 is implicated in stabilizing a number of proteins (chaperones) associated with cancer. Without being bound by a theory, it is believed that inhibition of Hsp90 leads to apoptosis of the cancer cells.
  • Hsp90 protein is implicated in stabilizing mutant oncogenic proteins such as v-Src, Bcr/Abl, and p53.
  • Hsp90 is implicated in stabilizing several growth factors and signaling molecules, such as EGFR, PI3K, and AKT, which leads to promotion of growth factor signaling pathways and induction of VEGF, nitric oxide synthase, and the matrix metalloprotease MMP2. This induction promotes angiogenesis and metathesis of the cancerous cells.
  • Hsp90 stabilizes homologous recombination proteins such as BRCA1 and BRCA2 proteins. These proteins help repair damaged DNA in cancer cells, and are involved in the repair of chromosomal damage with an important role in the error-free repair of DNA double-strand breaks. If the stabilizing function of Hsp90 is disrupted (e.g., by an inhibitor compound of the present application), the damaged DNA is not repaired properly, which ultimately leads to the death of the cancer cell. In sum, many different cancer types and subtypes rely on pathways mediated by the Hsp90 protein for proliferation and tumor development. Hence, inhibitors of Hsp90 protein may be used to treat a wide variety of cancers (e.g., cancers described herein).
  • Hsp90 The cellular function of Hsp90 is independent of the cellular function of POLQ (as discussed above).
  • the Hsp90 and the POLQ proteins repair cellular DNA by completely different molecular mechanisms.
  • the compounds of the present disclosure are dual inhibitors (Hsp90 and POLQ inhibitors) that simultaneously exert their apoptotic effect on the cancer cells via two independent molecular mechanisms.
  • this leads to increased therapeutic potency of the claimed compounds for treating cancer.
  • the Hsp90 protein contains three domains: the ATP-binding, protein/nucleic acid-binding, and dimerizing domain, each of which play a crucial role in the function of the protein.
  • the region of the protein near the N-terminus has a high-affinity ATP-binding site.
  • the protein/nucleic acid-binding region of Hsp90 is located toward the C-terminus of the amino sequence. The ability of Hsp90 to clamp onto proteins/nucleic acids (by binding the proteins/nucleic acids in the binding region) allows Hsp90 to perform several functions including assisting folding, preventing aggregation, and facilitating transport.
  • Hsp90 plays a role in the maturation and stabilization of more than 200 protein substrates (Davis, et al, A scaffold merging approach to Hsp90 C-terminal inhibition: synthesis and evaluation of a chimeric library. MedChemComm 2017, 8, 593).
  • the compound of Formula(A) or Formula (I) inhibits the N-terminal ATP binding/ ATPase function of Hsp90, or the C-terminal protein/nucleic acid-binding function of Hsp90. In some embodiments, the compound of Formula Formula(A) or (I) selectively inhibits (e.g., reduces, slows, halts, and/or prevents) the protein/nucleic acid-binding function at the C-terminus of Hsp90. In some embodiments, the compound of Formula(A) or Formula (I) selectively inhibits C-terminal binding domain of Hsp90 while not inhibiting the N-terminal ATPase domain of Hsp90.
  • the present disclosure provides a method of inhibiting a heat shock protein 90 (Hsp90) in a cancer cell, the method comprising contacting the cell with an effective amount of a compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • the cancer cell is contacted in vitro.
  • the cancer cell is contacted in vivo.
  • the cancer cell in contacted ex vivo.
  • Hsp90 is inhibited in a cancer cell of a subject after the compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof, is administered to the subject in need thereof.
  • the present disclosure provides a method inhibiting a heat shock protein 90 (Hsp90) in a subject (e.g., in need thereof), the method comprising administering to the subject an effective amount of a compound of Formula(A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • inhibiting a heat shock protein 90 (Hsp90) in a subject results in treating or ameliorating symptoms of a cancer in the subject (e.g., any one of the cancers described herein).
  • cancers e.g., HR-deficient cancers
  • gynecologic cancer e.g., ovarian cancer, breast cancer, fallopian tube cancer, uterine leiomyoma
  • prostate cancer non-Hodgkin’s lymphoma, colon cancer, lipoma, basal cell skin carcinoma, squamous cell skin carcinoma, osteosarcoma, acute myelogenous leukemia (AML), and other cancers
  • AML acute myelogenous leukemia
  • BRCA1 and BRCA2 genes Genetic susceptibility to breast cancer has been linked to mutations of the BRCA1 and BRCA2 genes. It is postulated that a mutation causes a disruption in the protein which causes chromosomal instability in BRCA mutated cells thereby predisposing them to neoplastic transformation. Inherited mutations in the BRCA1 and BRCA2 genes account for approximately 7-10% of all breast cancer cases. Women with BRCA mutations have a lifetime risk of breast cancer between 56-87%, and a lifetime risk of ovarian cancer between 27-44%.
  • the present disclosure provides a method of treating breast cancer (e.g., HR-deficient breast cancer such as POLQ overexpressing breast cancer).
  • breast cancer e.g., HR-deficient breast cancer such as POLQ overexpressing breast cancer.
  • Suitable examples of breast cancer include lobular carcinoma in situ (LCIS), a ductal carcinoma in situ (DCIS), an invasive ductal carcinoma (IDC), inflammatory breast cancer, Paget disease of the nipple, Phyllodes tumor, Angiosarcoma, adenoid cystic carcinoma, low-grade adenosquamous carcinoma, medullary carcinoma, mucinous carcinoma, papillary carcinoma, tubular carcinoma, metaplastic carcinoma, micropapillary carcinoma, mixed carcinoma, and other types of breast cancer, including triple negative (TNBC), HER positive, neoadjuvant HER2 negative, estrogen receptor positive, progesterone receptor positive, HER and estrogen receptor positive, HER and progesterone receptor positive, estrogen and progesterone receptor
  • Epithelial ovarian cancer is the most lethal gynecologic malignancy and the fifth most lethal cancer type overall in women in the United States (Siegel et al, 2017, CA Cancer J Clin 67, 7-30). Ovarian cancers often present genome instability (Cancer Genome Atlas Research, 2011), with almost half of the ovarian cancers harbor defects in one or more DNA repair pathways, mostly in HR (Bast et al, 2009, Nature reviews Cancer 9, 415-428; Pal et al, 2005, Cancer 104, 2807- 2816).
  • Ovarian cancer cells are initially sensitive to chemotherapeutic drugs such as platinum analogues (carboplatin or cisplatin) but become resistant to these drugs over time (Pignata et al, 2011, Cancer letters 303, 73-83).
  • chemotherapeutic drugs such as platinum analogues (carboplatin or cisplatin) but become resistant to these drugs over time (Pignata et al, 2011, Cancer letters 303, 73-83).
  • the extract mechanism of this acquired resistance remains unclear but appears to be multifactorial, including enhanced DNA repair (Shen et al, 2012, Pharmacol Rev 64, 706-721). Therefore, inhibition of the enhanced DNA repair pathway can re-sensitize ovarian cancer cells to platinum analogues.
  • the present disclosure provides a method of treating ovarian cancer (e.g., HR-deficient ovarian cancer POLQ overexpressing ovarian cancer).
  • ovarian cancer include epithelial ovarian carcinomas (EOC), maturing teratomas, dysgerminomas, endodermal sinus tumors, granulosa- theca tumors, Sertoli-Leydig cell tumors, primary peritoneal carcinomas, small cell carcinoma of the ovary (SCCO), teratomas of the ovary, sex cord-stromal ovarian cancer, dysgerminoma ovarian germ cell cancer, choriocarcinomas, carcinosarcomas, adenosarcomas, leiomyosarcomas, fibrosarcomas, and Krukenberg tumor.
  • pancreatic cancer e.g., HR-deficient pancreatic cancer such as POLQ overexpressing pancreatic cancer
  • pancreatic cancer include tumors affecting the exocrine gland, exocrine tumors, endocrine tumors, islet cell tumors, neurendocrine tumors, cystic tumours, cancer of the acinar cells, insulinomas, somatostatinomas, gastrinomas, glucagonomas, adenocarcinoma of the pancreas, pancreatoblastoma, sarcomas of the pancreas, adenosquamous carcinomas, colloid carcinomas, hepatoid carcinomas, intraductal papillary mucinous neoplasms, mucinous cystic neoplasms, pancreatic intraepithelial neoplasia, pancreatoblastomas, serous cystadenomas,
  • the present disclosure provides a method of treating prostate cancer (e.g., HR-deficient prostate cancer such as POLQ overexpressing prostate cancer).
  • prostate cancer e.g., HR-deficient prostate cancer such as POLQ overexpressing prostate cancer.
  • Suitable examples of prostate cancer include prostate adenocarcinoma, acinar adenocarcinoma, ductal adenocarcinoma, transitional cell (or urothelial) cancer, squamous cell cancer, small cell prostate cancer, carcinoid, sarcomas, small cell carcinomas, neuroendocrine tumors, and transitional cell carcinomas.
  • the prostate cancer is advanced prostate cancer with germane to somatic homologous recombination deficiency.
  • lung cancer e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung
  • kidney cancer e.g., nephroblastoma, a.k.a.
  • Wilms tumor, renal cell carcinoma); acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma
  • myelofibrosis MF
  • chronic idiopathic myelofibrosis chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)
  • neuroblastoma e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis
  • neuroendocrine cancer e.g., gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoid tumor
  • osteosarcoma e.g., bone cancer
  • ovarian cancer e.g, cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma
  • papillary adenocarcinoma pancreatic cancer
  • pancreatic cancer e.g, pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors
  • penile cancer
  • HR-deficient cells e.g., BRCAl/2 mutated cells
  • SSBs DNA single-strand breaks
  • DSBs double-strand breaks
  • PARP inhibitors PARPi
  • PARPi examples include iniparib (BSI 201), talazoparib (BMN-673), niraparib, olaparib (AZD-2281, TOPARP-A), rucaparib (AG014699, PF-01367338), veliparib (ABT-888), CEP 9722, MK 4827, BGB-290 and 3-aminobenzamide, 4-amino- 1,8-napthalimide, benzamide, BGP- 15, BYK204165 , 3 ,4-Dihy dro-5- [4-( 1 -piperidiny l)butoxy 1] - 1 (2H)- isoquinolinone, DR2313, 1,5-Isoquinolinediol, MC2050, ME0328, PJ-34 hydrochloride hydrate, and UPF-1069.
  • BBI 201 iniparib
  • MN-673 talazoparib
  • niraparib
  • PARPI is the founding member of a large family of poly (ADP -ribose) polymerases with 17 members identified (Ame et ah, Bioessays 26:882-893, 2004). It is the primary enzyme catalyzing the transfer of ADP-ribose units fromNAD+ to target proteins including PARP1 itself. Under normal physiologic conditions, PARP1 facilitates the repair of DNAbase lesions by helping recruit base excision repair proteins XRCC1 and Ro ⁇ b (Dantzer et ah, Methods Enzymol. 409:493- 510, 2006).
  • any of the cancers described herein can be PARP inhibitor-resistant.
  • the present disclosure provides a method of treating a cancer having a de novo or an acquired resistance to a PARP inhibitor, the method comprising administering to a subject in need thereof a therapeutically effective amount of a compound of Formula (A) or Formula (I), or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) or Formula (I), or a pharmaceutically acceptable salt thereof can be administered to the subject in combination with a therapeutically effective amount of an additional anti cancer agent.
  • the additional anti-cancer agent is a PARP inhibitor (e.g., olaparib, veliparib, pamiparib (BGB-290), talazoparib (BMN 673), or niraparib).
  • a PARP inhibitor e.g., olaparib, veliparib, pamiparib (BGB-290), talazoparib (BMN 673), or niraparib.
  • POLQ channels HR repair by antagonizing HR and promoting PARP- dependent error-prone repair.
  • inhibition of POLQ is expected to enhance cell death of PARP inhibitor-resistant cancers.
  • the PARP enzyme cooperates with POLQ in the process of Alternative End-Joining Repair (Alt-EJ).
  • PARP is required to localize POLQ at the site of the double strand break (DSB) repair.
  • DSB double strand break
  • Human tumors can become resistant to PARP inhibitors; however, these tumors can still be sensitive to a POLQ inhibitor if POLQ can localize to the DSB in a PARP-independent manner. Accordingly, aspects of the disclosure provide methods for treating a cancer that is resistant to PARP inhibitor therapy.
  • a cancer that is resistant to a PARP inhibitor means that the cancer does not respond to such inhibitor, for example as evidenced by continued proliferation and increasing tumor growth and burden.
  • the cancer can have initially responded to treatment with such inhibitor (referred to herein as a previously administered therapy) but can have grown resistant after a treatment period. In some instances, the cancer can have never responded to treatment with such inhibitor at all.
  • Cancers resistant to PARP inhibitors can be identified using methods known in the art (see, e.g., WO 2014205105, US 8729048; incorporated herein by reference). Suitable examples of cancers resistant to PARP-inhibitors include breast cancer, ovarian cancer, lung cancer, bladder cancer, liver cancer, head and neck cancer, pancreatic cancer, gastrointestinal cancer, and colorectal cancer.
  • the present disclosure provides compounds useful in treating cancer (e.g., cancer having alterations in genes regulating homologous recombination (HR) repair or HR-deficient cancer, or POLQ-overexpressing cancer).
  • cancer e.g., cancer having alterations in genes regulating homologous recombination (HR) repair or HR-deficient cancer, or POLQ-overexpressing cancer.
  • such compounds include a compound of Formula (A): or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 8 , R 6 , R 7 , and ring A are as described herein.
  • ring A is selected from the group consisting of: C3-8 cycloalkyl and Ce-u aryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R A ;
  • R 8 is selected from -Ci-6 alkyl, optionally substituted with NR 5 R 6 , and a group of formula (i):
  • R A is selected from the group consisting of: H, halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6alkoxy, and Ci-6haloalkoxy;
  • R 1 is selected from the group consisting of: Cy 2 and Cy 2 -NR 6 -; each Cy 2 is independently selected from the group consisting of: Ce-u aryl and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R B ;
  • R B is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-CI-3 alkyl, amino, Ci-6 alkylamino, di(Ci-6 alkyl)amino, Cy 1 , Cy ⁇ Ci ⁇ alkyl, and Cy ! -O-;
  • Cy 1 is Ce-12 aryl, optionally substituted by 1, 2, 3, 4, or 5 substituents independently selected from R g ;
  • R g is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-Ci-3 alkyl, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino;
  • R al and R a2 are independently selected from the group consisting of: H, C1-3 alkyl, and C1-3 haloalkyl; and each R 6 is independently selected from the group consisting of: H and C1-3 alkyl.
  • the compound of Formula (A) include a compound of Formula (I): or a pharmaceutically acceptable salt thereof, wherein R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and ring A are as described herein.
  • ring A is selected from the group consisting of: C3-6 cycloalkyl and C6-12 aryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R A ;
  • R A is selected from the group consisting of: H, halo, Ci-6 alkyl, C14 haloalkyl, Ci-6 alkoxy, and Ci-6haloalkoxy;
  • R 1 is selected from the group consisting of: Ce-u aryl and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 substituents independently selected from R B ;
  • R B is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-CI-3 alkyl, amino, Ci-6 alkylamino, di(Ci-6 alkyl)amino, Cy 1 , Cy CC1-3 alkyl, and Cy ! -O-;
  • Cy 1 is C6-12 aryl, optionally substituted by 1, 2, 3, 4, or 5 substituents independently selected from R g ;
  • R g is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C2- 6 alkenyl, C2-6 alkynyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, cyano-Ci-3 alkyl, HO-Ci-3 alkyl, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino;
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H, Cy 1 , Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, and Ci-6haloalkoxy;
  • R al and R a2 are independently selected from the group consisting of: H, C1-3 alkyl, and C1-3 haloalkyl;
  • R 6 is selected from the group consisting of: H and C1-3 alkyl.
  • R 8 is -Ci-6 alkyl, optionally substituted withNR 5 R 6 . In some embodiments, R 8 is -Ci-6 alkyl substituted with NR 5 R 6 . In some embodiments, R 5 and R 6 are each independently selected from H and C1-3 alkyl. In some embodiments, R 5 and R 6 are each C1-3 alkyl.
  • R 8 is a group of formula (i):
  • ring A is C3-8 cycloalkyl, which is optionally substituted with 1, 2, or 3 substituents independently selected from R A . In some embodiments, ring A is C3-8 cycloalkyl. In some embodiments, ring A is C3-6 cycloalkyl, which is optionally substituted with 1, 2, or 3 substituents independently selected from R A . In some embodiments, ring A is C3-6 cycloalkyl.
  • ring A is selected from the group consisting of: cyclopentyl, cyclohexyl, and cycloheptyl, each of which is optionally substituted with 1, 2, or 3 substituents independently selected from R A .
  • ring A is selected from the group consisting of: cyclopentyl, cyclohexyl, and cycloheptyl.
  • ring A is cyclopentyl.
  • ring A is cyclohexyl.
  • ring A is cycloheptyl.
  • ring A is cyclohexyl, which is optionally substituted with 1, 2, or 3 substituents independently selected from R A . In some embodiments, ring A is cyclohexyl.
  • ring A is Ce-u aryl, which is optionally substituted with
  • ring A is C6-12 aryl.
  • ring A is phenyl, which is optionally substituted with 1,
  • ring A is phenyl
  • R A is selected from the group consisting of: H, halo, Ci-4 haloalkyl, and Ci-6haloalkoxy. In some embodiments, R A is selected from the group consisting of: H, Ci-6 alkyl, and Ci-6 alkoxy. In some embodiments, R A is selected from the group consisting of: H and Ci-6 alkyl.
  • the compound of Formula (A) has the following formula: or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) has the following formula:
  • the compound of Formula (A) has the following formula: or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (I) has Formula (la): or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (I) has Formula (lb): or a pharmaceutically acceptable salt thereof. In some embodiments, the compound of Formula (I) has Formula (Ic): or a pharmaceutically acceptable salt thereof.
  • R 1 is Cy 2 .
  • R 1 is Cy 2 -NR 6 -.
  • Cy 2 is Ce-u aryl, optionally substituted with 1, 2, or 3 independently selected R B . In some embodiments, Cy 2 is 5-10 membered heteroaryl, optionally substituted with 1, 2, or 3 independently selected R B .
  • R 6 is H. In some embodiments, R 6 is C1-3 alkyl.
  • R 1 is Ce-u aryl, optionally substituted with 1, 2, or 3 independently selected R B . In some embodiments, R 1 is Ce-n aryl, substituted with one R B . In some embodiments, R 1 is Ce-n aryl. In some embodiments, R 1 is phenyl, optionally substituted with 1, 2, or 3 independently selected R B . In some embodiments, R 1 is phenyl, substituted with one R B . In some embodiments, R 1 is phenyl.
  • R 1 is 5-10 membered heteroaryl, optionally substituted with 1, 2, or 3 independently selected R B . In some embodiments, R 1 is 5-10 membered heteroaryl, substituted with one R B . In some embodiments, R 1 is 5-10 membered heteroaryl. In some embodiments, R 1 is triazole, optionally substituted with 1, 2, or 3 independently selected R B . In some embodiments, R 1 is triazole, substituted with one R B . In some embodiments, R 1 is triazole.
  • R B is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, amino, Ci-6 alkylamino, di(C 1-6 alky l)amino, Cy 1 , and Cy CC1-3 alkyl.
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, Cy 1 , and Cy 1 -C 1 - alkyl. In some embodiments, R B is selected from the group consisting of: halo, Ci-6 alkyl, and Ci-6 alkoxy. In some embodiments, R B is selected from the group consisting of: Cy 1 and Cy ⁇ Cm alkyl. In some embodiments, R B is Cy 1 . In some embodiments, R B is Cy 1 -C 1 - alkyl. In some embodiments, R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H and Cy 1 . In some embodiments, R 2 , R 3 , R 7 , and R 4 are each H. In some embodiments, R 2 , R 7 , and R 3 are each H; and R 4 is Cy 1 .
  • Cy 1 is Ce-12 aryl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, Ci-4 haloalkyl and Ci-6 alkoxy. In some embodiments, Cy 1 is Ce-12 aryl. In some embodiments, Cy 1 is Ce-12 aryl, optionally substituted by halo, Ci-4 haloalkyl or Ci-6 alkoxy. In some embodiments, Cy 1 is phenyl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, Ci-4 haloalkyl and Ci-6 alkoxy. In some embodiments, Cy 1 is phenyl. In some embodiments, Cy 1 is phenyl, optionally substituted by halo, Ci-4 haloalkyl or Ci-6 alkoxy. In some embodiments,
  • Cy 1 is Ce-12 aryl, optionally substituted with Ci-6 alkoxy. In some embodiments, Cy 1 is Ce-12 aryl, optionally substituted with halo or Ci-4 haloalkyl. In some embodiments, Cy 1 is phenyl, optionally substituted with Ci-6 alkoxy. In some embodiments, Cy 1 is phenyl, optionally substituted with halo or Ci-4 haloalkyl.
  • R g is selected from the group consisting of: OH, NO2, CN, halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino. In some embodiments, R g is selected from the group consisting of: halo, Ci-6 alkyl, C14 haloalkyl, Ci-6 alkoxy, Ci-6haloalkoxy, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino.
  • R g is selected from the group consisting of: halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, Ci-6 haloalkoxy, amino, Ci-6 alkylamino, and di(Ci-6 alkyl)amino. In some embodiments,
  • R g is selected from the group consisting of: halo, Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, and C 1-6 haloalkoxy. In some embodiments, R g is selected from the group consisting of: Ci-6 alkyl, C1-4 haloalkyl, Ci-6 alkoxy, and Ci-6 haloalkoxy. In some embodiments, R g is selected from the group consisting of: Ci-6 alkyl and Ci-6 alkoxy.
  • R 5 is Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy.
  • R 5 is Ci-6 alkyl substituted with OH.
  • R 5 is Ci-6 alkyl substituted with Ci -6 alkoxy.
  • R al and R a2 are independently selected from the group consisting of: H and C1-3 alkyl.
  • R al is selected from the group consisting of: H and C1-3 alkyl.
  • R 32 is selected from the group consisting of: H and C1-3 alkyl.
  • R al is H.
  • R al is C1-3 alkyl.
  • R a2 is H.
  • R 32 is C1-3 alkyl.
  • R 1 is selected from the group consisting of: Cy 2 -NR 6 -, C6-12 aryl, and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, or 3 substituents independently selected from R B ;
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, Cy 1 , and CyCCi-3 alkyl;
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H and Cy 1 ;
  • Cy 1 is C6-12 aryl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, C1-4 haloalkyl, and Ci-6 alkoxy;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or C 1-6 alkoxy;
  • R 6 is H.
  • R 1 is selected from the group consisting of: C6-12 aryl and 5-10 membered heteroaryl, each of which is optionally substituted with 1, 2, or 3 substituents independently selected from R B ;
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, Cy 1 , and CyCCi-3 alkyl;
  • R 2 , R 3 , R 7 , and R 4 are each independently selected from the group consisting of: H and Cy 1 ;
  • Cy 1 is C6-12 aryl, optionally substituted by 1, 2, or 3 substituents independently selected from the group consisting of: halo, C1-4 haloalkyl, and Ci-6 alkoxy;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or C 1-6 alkoxy; and R 6 is H.
  • R 1 is Ce-12 aryl, optionally substituted with 1, 2, or 3 independently selected
  • R B is selected from the group consisting of: halo, Ci-6 alkyl, Ci-6 alkoxy, and
  • Cy 1 is 0,-1 aryl, optionally substituted with Ci-6 alkoxy;
  • R 2 , R 3 , R 7 , and R 4 are each H;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy; and R 6 is H.
  • R 1 is 5-10 membered heteroaryl, optionally substituted with 1, 2, or 3 independently selected R B ;
  • R B is CykCm alkyl;
  • Cy 1 is Ce-12 aryl, optionally substituted with CM alkoxy
  • R 2 , R 7 , and R 3 are each H;
  • R 4 is Ce-12 aryl, optionally substituted with halo or Ci-4 haloalkyl;
  • R 5 is selected from the group consisting of: H and Ci-6 alkyl, optionally substituted with OH or Ci-6 alkoxy; and R 6 is H.
  • the compound of Formula (A) or Formula (I) is selected from the group consisting of: or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) or Formula (I) is selected from the group consisting of : or a pharmaceutically acceptable salt thereof.
  • the compound of Formula (A) is selected from any one of the following compounds: or a pharmaceutically acceptable salt thereof.
  • Compounds of Formula (A) or Formula (I), including salts thereof, can be prepared using known organic synthesis techniques and can be synthesized according to any of numerous possible synthetic routes.
  • the compounds described herein can be prepared using methods and procedures similar to those described in Donnelly, A. et al, The Design, Synthesis, and Evaluation of Coumarin Ring Derivatives of the Novobiocin Scaffold that Exhibit Antiproliferative Activity,
  • the reactions for preparing the compounds provided herein can be carried out in suitable solvents which can be readily selected by one of skill in the art of organic synthesis.
  • suitable solvents can be substantially non-reactive with the starting materials (reactants), the intermediates, or products at the temperatures at which the reactions are carried out, e.g., temperatures which can range from the solvent's freezing temperature to the solvent's boiling temperature.
  • a given reaction can be carried out in one solvent or a mixture of more than one solvent.
  • suitable solvents for a particular reaction step can be selected by the skilled artisan.
  • Preparation of the compounds provided herein can involve the protection and deprotection of various chemical groups.
  • the need for protection and deprotection, and the selection of appropriate protecting groups, can be readily determined by one skilled in the art.
  • the chemistry of protecting groups can be found, for example, in P. G. M. Wuts and T. W. Greene, Protective Groups in Organic Synthesis, 4 th Ed., Wiley & Sons, Inc., New York (2006).
  • the compounds of Formula (A) or Formula (I) can be used in combination with anti-cancer therapies (e.g., anti-cancer agents, or therapies such as surgery, transplantation or radiotherapy).
  • anti-cancer therapies can show a synergistic effect in the treatment of cancers described herein (e.g., HR-deficient cancers, cancers resistant to poly (ADP-ribose) polymerase (PARP) inhibitor therapy, POLQ overexpressing cancers, and/or cancers characterized by one or more BRCA mutations and/or reduced expression of Fanconi (Fane) proteins).
  • PARP poly (ADP-ribose) polymerase
  • POLQ overexpressing cancers e.g., characterized by one or more BRCA mutations and/or reduced expression of Fanconi (Fane) proteins.
  • “synergistic” refers to the joint action of agents (e.g., pharmaceutically active agents), that when taken together increase each other's effectiveness.
  • a POLQ inhibitor in an HR-deficient cancer, POLQ-mediates Alt-EJ in the enhanced pathway.
  • a POLQ inhibitor can re-sensitize HR-deficient cancer (e.g., ovarian cancer) to a PARP inhibitor or a platinum analogue.
  • the anti-cancer therapy is selected from the group consisting of surgery, radiation therapy, chemotherapy, gene therapy, DNA therapy, viral therapy, RNA therapy, adjuvant therapy, and immunotherapy.
  • the chemotherapy comprises administering to the subject a cytotoxic agent in an amount effective to treat the HR-deficient cancer.
  • the cytotoxic agent is selected from the group consisting of a platinum agent, mitomycin C, a poly (ADP-ribose) polymerase (PARP) inhibitor (e.g., any one of PARP inhibitors described herein), a radioisotope, a vinca alkaloid, an antitumor alkylating agent, a monoclonal antibody and an antimetabolite.
  • the cytotoxic agent is an ataxia telangiectasia mutated (ATM) kinase inhibitor.
  • platinum agents include cisplatin, carboplatin, oxaliplatin, satraplatin, picoplatin, nedaplatin, triplatin, and lipoplatin.
  • cytotoxic radioisotopes include 67 Cu, 67 Ga, 90 Y, 1 1 1. 177 Lu, 186 Re, 188 Re, a-Particle emitter, 211 At, 213 Bi, 225 Ac, Auger-electron emitter, 125 I, 212 Pb, and m In.
  • antitumor alkylating agents include nitrogen mustards, cyclophosphamide, mechlorethamine or mustine (HN2), uramustine or uracil mustard, melphalan, chlorambucil, ifosfamide, bendamustine, nitrosoureas, carmustine, lomustine, streptozocin, alkyl sulfonates, busulfan, thiotepa, procarbazine, altretamine, triazenes, dacarbazine, mitozolomide, and temozolomide.
  • anti-cancer monoclonal antibodies include to necitumumab, dinutuximab, nivolumab, blinatumomab, pembrolizumab, ramucirumab, obinutuzumab, adotrastuzumab emtansine, pertuzumab, brentuximab, ipilimumab, ofatumumab, catumaxomab, bevacizumab, cetuximab, tositumomab-I 131 , ibritumomab tiuxetan, alemtuzumab, gemtuzumab ozogamicin, trastuzumab, and rituximab.
  • vinca alkaloids include vinblastine, vincristine, vindesine, vinorelbine, desoxyvincaminol, vincaminol, vinbumine, vincamajine,ieridine, vinbumine, and vinpocetine.
  • Suitable examples of antimetabolites include fluorouracil, cladribine, capecitabine, mercaptopurine, pemetrexed, fludarabine, gemcitabine, hydroxyurea, methotrexate, nelarbine, clofarabine, cytarabine, decitabine, pralatrexate, floxuridine, and thioguanine.
  • the anti-cancer therapy is an immunotherapy, such as cellular immunotherapy, antibody therapy or cytokine therapy.
  • immunotherapy such as cellular immunotherapy, antibody therapy or cytokine therapy.
  • POLQ inhibitors are expected to function in many ways similar to PARP inhibitors, and to synergize with immunotherapy.
  • Suitable examples of cellular immunotherapy include dendritic cell therapy and Sipuleucel-T.
  • Suitable examples of antibody therapy include alemtuzumab, ipilimumab, nivolumab, ofatumumab, pembrolizumab, and rituximab.
  • cytokine therapy examples include interferons (for example, IFNa, IRNb, IKNg, IFNri) and interleukins.
  • the immunotherapy comprises one or more immune checkpoint inhibitors.
  • immune checkpoint proteins include CTLA-4 and its ligands CD80 and CD86, PD-1 with its ligands PD-L1 and PD-L2, and 4-1BB.
  • anti-cancer therapies include abiraterone acetate (e.g ., ZYTIGA), ABVD, ABVE, ABVE-PC, AC, AC-T, ADE, ado-trastuzumab emtansine (e.g., KADCYLA), afatinib dimaleate (e.g., GILOTRIF), aldesleukin (e.g., PROLEUKIN), alemtuzumab (e.g., CAMPATH), anastrozole (e.g., ARIMIDEX), arsenic trioxide (e.g., TRISENOX), asparaginase erwinia chrysanthemi (e.g., ERWINAZE), axitinib (e.g, INLYTA), azacitidine (e.g, MYLOSAR, VIDAZA), BEACOPP, belinostat (e.g., BELEODAQ), bendabirater
  • the anti-cancer therapy is selected from the group consisting of epigenetic or transcriptional modulators (e.g., DNA methyltransferase inhibitors, histone deacetylase inhibitors (HD AC inhibitors), lysine methyltransferase inhibitors), antimitotic drugs (e.g., taxanes and vinca alkaloids), hormone receptor modulators (e.g., estrogen receptor modulators and androgen receptor modulators), cell signaling pathway inhibitors, modulators of protein stability (e.g., proteasome inhibitors),
  • epigenetic or transcriptional modulators e.g., DNA methyltransferase inhibitors, histone deacetylase inhibitors (HD AC inhibitors), lysine methyltransferase inhibitors
  • antimitotic drugs e.g., taxanes and vinca alkaloids
  • hormone receptor modulators e.g., estrogen receptor modulators and androgen receptor modulators
  • cell signaling pathway inhibitors e.g., modulators of protein stability (
  • a POLQ inhibitor can be independently administered in combination with an anti-cancer therapy including, e.g., surgery, radiation therapy, transplantation (e.g., stem cell transplantation, bone marrow transplantation), immunotherapy, and chemotherapy.
  • an anti-cancer therapy is a combination of paclitaxel and olaparib, paclitaxel and carboplatin, olaparib and trabectedin, or carboplatin and niraparib.
  • the anti-cancer therapy includes rucaparib, olaparib, prexasertib or nivolumab.
  • the additional anti-cancer agent is a PARP inhibitor.
  • the PARP inhibitor is selected from olaparib, veliparib, pamiparib (BGB-290), talazoparib (BMN 673), and niraparib.
  • the present application also provides pharmaceutical compositions comprising an effective amount of a compound of Formula (A) or Formula (I) disclosed herein, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
  • the pharmaceutical composition can also comprise at least one of any one of the additional therapeutic agents described herein.
  • the application also provides pharmaceutical compositions and dosage forms comprising any one the additional therapeutic agents described herein (e.g., in a kit).
  • the carrier(s) are “acceptable” in the sense of being compatible with the other ingredients of the formulation and, in the case of a pharmaceutically acceptable carrier, not deleterious to the recipient thereof in an amount used in the medicament.
  • Pharmaceutically acceptable carriers, adjuvants and vehicles that can be used in the pharmaceutical compositions of the present application include ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol, and wool fat.
  • ion exchangers alumina, aluminum stearate, lecithin
  • serum proteins such as human serum albumin
  • buffer substances such as phosphates, g
  • compositions or dosage forms can contain any one of the compounds and therapeutic agents described herein in the range of 0.005% to 100% with the balance made up from the suitable pharmaceutically acceptable excipients.
  • the contemplated compositions can contain 0.001%-100% (e.g., 0.1-95%, 75-85%, or 20-80%) of any one of the compounds and therapeutic agents provided herein, wherein the balance can be made up of any pharmaceutically acceptable excipient described herein, or any combination of these excipients.
  • compositions of the present application include those suitable for any acceptable route of administration.
  • Acceptable routes of administration include, buccal, cutaneous, endocervical, endosinusial, endotracheal, enteral, epidural, interstitial, intra-abdominal, intra-arterial, intrabronchial, intrabursal, intracerebral, intracistemal, intracoronary, intradermal, intraductal, intraduodenal, intradural, intraepidermal, intraesophageal, intragastric, intragingival, intraileal, intralymphatic, intramedullary, intrameningeal, intramuscular, intranasal, intraovarian, intraperitoneal, intraprostatic, intrapulmonary, intrasinal, intraspinal, intrasynovial, intratesticular, intrathecal, intratubular, intratumoral, intrauterine, intravascular, intravenous, nasal, nasogastric, oral, parenteral, percutaneous, perid
  • compositions and formulations described herein can conveniently be presented in a unit dosage form, e.g., tablets, capsules (e.g., hard or soft gelatin capsules), sustained release capsules, and in liposomes, and can be prepared by any methods well known in the art of pharmacy. See, for example, Remington: The Science and Practice of Pharmacy, Lippincott Williams & Wilkins, Baltimore, MD (20th ed. 2000). Such preparative methods include the step of bringing into association with the molecule to be administered ingredients such as the carrier that constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers, liposomes or finely divided solid carriers, or both, and then, if necessary, shaping the product.
  • compositions of the present application suitable for oral administration can be presented as discrete units such as capsules, sachets, granules or tablets each containing a predetermined amount (e.g., effective amount) of the active ingredient; a powder or granules; a solution or a suspension in an aqueous liquid or a non-aqueous liquid; an oil-in-water liquid emulsion; a water-in- oil liquid emulsion; packed in liposomes; or as a bolus, etc.
  • Soft gelatin capsules can be useful for containing such suspensions, which can beneficially increase the rate of compound absorption.
  • carriers that are commonly used include lactose, sucrose, glucose, mannitol, and silicic acid and starches.
  • Other acceptable excipients can include: a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite
  • useful diluents include lactose and dried com starch.
  • the active ingredient is combined with emulsifying and suspending agents.
  • certain sweetening and/or flavoring and/or coloring agents can be added.
  • Compositions suitable for oral administration include lozenges comprising the ingredients in a flavored basis, usually sucrose and acacia or tragacanth; and pastilles comprising the active ingredient in an inert basis such as gelatin and glycerin, or sucrose and acacia.
  • compositions suitable for parenteral administration include aqueous and non- aqueous sterile injection solutions or infusion solutions which can contain antioxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the intended recipient; and aqueous and non-aqueous sterile suspensions which can include suspending agents and thickening agents.
  • the formulations can be presented in unit-dose or multi-dose containers, for example, sealed ampules and vials, and can be stored in a freeze dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, saline (e.g., 0.9% saline solution) or 5% dextrose solution, immediately prior to use.
  • Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules and tablets.
  • the injection solutions can be in the form, for example, of a sterile injectable aqueous or oleaginous suspension.
  • This suspension can be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents.
  • the sterile injectable preparation can also be a sterile injectable solution or suspension in anon-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1, 3-butanediol.
  • acceptable vehicles and solvents that can be employed are mannitol, water, Ringer's solution and isotonic sodium chloride solution.
  • sterile, fixed oils are conventionally employed as a solvent or suspending medium.
  • any bland fixed oil can be employed including synthetic mono- or diglycerides.
  • Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their poly oxy ethylated versions.
  • These oil solutions or suspensions can also contain a long-chain alcohol diluent or dispersant.
  • compositions of the present disclosure can be administered in the form of suppositories for rectal administration.
  • These compositions can be prepared by mixing a compound of the present application with a suitable non-irritating excipient which is solid at room temperature but liquid at the rectal temperature and therefore will melt in the rectum to release the active components.
  • suitable non-irritating excipient include cocoa butter, beeswax, and polyethylene glycols.
  • compositions of the present disclosure can be administered by nasal aerosol or inhalation.
  • Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and can be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other solubilizing or dispersing agents known in the art. See, for example, U.S. Patent No. 6,803,031. Additional formulations and methods for intranasal administration are found in Ilium, L., J Pharm Pharmacol, 56:3-17, 2004 and Ilium, L., Eur J Pharm Sci 11:1-18, 2000.
  • the topical compositions of the present disclosure can be prepared and used in the form of an aerosol spray, cream, emulsion, solid, liquid, dispersion, foam, oil, gel, hydrogel, lotion, mousse, ointment, powder, patch, pomade, solution, pump spray, stick, towelette, soap, or other forms commonly employed in the art of topical administration and/or cosmetic and skin care formulation.
  • the topical compositions can be in an emulsion form. Topical administration of the pharmaceutical compositions of the present application is especially useful when the desired treatment involves areas or organs readily accessible by topical application.
  • the topical composition comprises a combination of any one of the compounds and therapeutic agents disclosed herein, and one or more additional ingredients, carriers, excipients, or diluents including absorbents, anti-irritants, anti acne agents, preservatives, antioxidants, coloring agents/pigments, emollients (moisturizers), emulsifiers, film-forming/holding agents, fragrances, leave-on exfoliants, prescription drugs, preservatives, scrub agents, silicones, skin- identical/repairing agents, slip agents, sunscreen actives, surfactants/detergent cleansing agents, penetration enhancers, and thickeners.
  • additional ingredients, carriers, excipients, or diluents including absorbents, anti-irritants, anti acne agents, preservatives, antioxidants, coloring agents/pigments, emollients (moisturizers), emulsifiers, film-forming/holding agents, fragrances, leave-on exfoliants, prescription drugs, preservatives, scrub agents, silicones
  • compositions for coating an implantable medical device such as prostheses, artificial valves, vascular grafts, stents, or catheters.
  • Suitable coatings and the general preparation of coated implantable devices are known in the art and are exemplified in U.S. Patent Nos. 6,099,562; 5,886,026; and 5,304,121.
  • the coatings are typically biocompatible polymeric materials such as a hydrogel polymer, polydimethylsiloxane, polycaprolactone, polyethylene glycol, polylactic acid, ethylene vinyl acetate, and mixtures thereof.
  • the coatings can optionally be further covered by a suitable topcoat of fluorosilicone, polysaccharides, polyethylene glycol, phospholipids or combinations thereof to impart controlled release characteristics in the composition.
  • Coatings for invasive devices are to be included within the definition of pharmaceutically acceptable carrier, adjuvant or vehicle, as those terms are used herein.
  • the present disclosure provides an implantable drug release device impregnated with or containing a compound or a therapeutic agent described herein, or a composition comprising a compound or a therapeutic agent described herein, such that said compound or therapeutic agent is released from said device and is therapeutically active.
  • a therapeutic compound is present in an effective amount (e.g., a therapeutically effective amount).
  • Effective doses can vary, depending on the diseases treated, the severity of the disease, the route of administration, the sex, age and general health condition of the subject, excipient usage, the possibility of co-usage with other therapeutic treatments such as use of other agents and the judgment of the treating physician.
  • an effective amount of a therapeutic compound can range, for example, from about 0.001 mg/kg to about 500 mg/kg (e.g., from about 0.001 mg/kg to about 200 mg/kg; from about 0.01 mg/kg to about 200 mg/kg; from about 0.01 mg/kg to about 150 mg/kg; from about 0.01 mg/kg to about 100 mg/kg; from about 0.01 mg/kg to about 50 mg/kg; from about 0.01 mg/kg to about 10 mg/kg; from about 0.01 mg/kg to about 5 mg/kg; from about 0.01 mg/kg to about 1 mg/kg; from about 0.01 mg/kg to about 0.5 mg/kg; from about 0.01 mg/kg to about 0.1 mg/kg; from about 0. 0.01 mg/kg to about 500 mg/kg (e.g., from about 0.001 mg/kg to about 200 mg/kg; from about 0.01 mg/kg to about 200 mg/kg; from about 0.01 mg/kg to about 150 mg/kg; from about 0.01 mg/kg to about 100 mg/kg;
  • an effective amount of a therapeutic compound is about 0.1 mg/kg, about 0.5 mg/kg, about 1 mg/kg, about 2 mg/kg, or about 5 mg/kg.
  • the foregoing dosages can be administered on a daily basis (e.g., as a single dose or as two or more divided doses, e.g., once daily, twice daily, thrice daily) or non-daily basis (e.g., every other day, every two days, every three days, once weekly, twice weekly, once every two weeks, once a month).
  • a daily basis e.g., as a single dose or as two or more divided doses, e.g., once daily, twice daily, thrice daily
  • non-daily basis e.g., every other day, every two days, every three days, once weekly, twice weekly, once every two weeks, once a month.
  • the compounds and compositions described herein can be administered to the subject in any order.
  • a first therapeutic agent such as a compound of Formula (A) or Formula (I)
  • a first therapeutic agent can be administered prior to or subsequent to (e.g., 5 minutes, 15 minutes, 30 minutes, 45 minutes, 1 hour, 2 hours, 4 hours, 6 hours, 12 hours, 24 hours, 48 hours, 72 hours, 96 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 8 weeks, or 12 weeks before or after), or concomitantly with the administration of a second therapeutic agent, such as an anti-cancer therapy described herein, to a subject in need of treatment.
  • the compound of Formula (A) or Formula (I), or a composition containing the compound can be administered separately, sequentially or simultaneously with the second therapeutic agent, such as a chemotherapeutic agent described herein.
  • the therapeutic agents can be administered in a single dosage form (e.g., tablet, capsule, or a solution for injection or infusion) or in separate dosage forms.
  • kits useful for example, in the treatment of disorders, diseases and conditions described herein, which include one or more containers containing a pharmaceutical composition comprising a therapeutically effective amount of a compound of the present disclosure.
  • kits can further include, if desired, one or more of various conventional pharmaceutical kit components, such as containers with one or more pharmaceutically acceptable carriers, additional containers, etc.
  • Instructions, either as inserts or as labels, indicating quantities of the components to be administered, guidelines for administration, and/or guidelines for mixing the components, can also be included in the kit.
  • the kit can optionally include directions to perform a test to determine a mutation (e.g., HR-associated mutation) in a cancer cell, and/or any of the reagents and device(s) to perform such tests.
  • a mutation e.g., HR-associated mutation
  • the kit can optionally include directions to perform a test to determine a POLQ overexpression in a cancer cell, and/or any of the reagents and device(s) to perform such tests.
  • the kit can also optionally include an additional therapeutic agent (e.g., PARP inhibitor or a platinum-based anticancer agent).
  • the term “about” means “approximately” (e.g., plus or minus approximately 10% of the indicated value).
  • the term “compound” as used herein is meant to include all stereoisomers, geometric isomers, tautomers, and isotopes of the structures named or depicted. Compounds herein identified by name or structure as one particular tautomeric form are intended to include other tautomeric forms unless otherwise specified.
  • pharmaceutical and “pharmaceutically acceptable” are employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • an ex vivo cell can be part of a tissue sample excised from an organism such as a mammal.
  • an in vitro cell can be a cell in a cell culture.
  • an in vivo cell is a cell living in an organism such as a mammal.
  • treating refers to 1) inhibiting the disease; for example, inhibiting a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., arresting further development of the pathology and/or symptomatology), or 2) ameliorating the disease; for example, ameliorating a disease, condition or disorder in an individual who is experiencing or displaying the pathology or symptomatology of the disease, condition or disorder (i.e., reversing the pathology and/or symptomatology).
  • preventing or “prevention” of a disease, condition or disorder refers to decreasing the risk of occurrence of the disease, condition or disorder in a subject or group of subjects (e.g., a subject or group of subjects predisposed to or susceptible to the disease, condition or disorder). In some embodiments, preventing a disease, condition or disorder refers to decreasing the possibility of acquiring the disease, condition or disorder and/or its associated symptoms. In some embodiments, preventing a disease, condition or disorder refers to completely or almost completely stopping the disease, condition or disorder from occurring.
  • the term “pharmaceutically acceptable salt” refers to a salt that is formed between an acid and a basic group of the compound, such as an amino functional group, or between a base and an acidic group of the compound, such as a carboxyl functional group.
  • the compound is a pharmaceutically acceptable acid addition salt.
  • acids commonly employed to form pharmaceutically acceptable salts of the therapeutic compounds described herein include inorganic acids such as hydrogen bisulfide, hydrochloric acid, hydrobromic acid, hydroiodic acid, sulfuric acid and phosphoric acid, as well as organic acids such as para-toluenesulfonic acid, salicylic acid, tartaric acid, bitartaric acid, ascorbic acid, maleic acid, besylic acid, fumaric acid, gluconic acid, glucuronic acid, formic acid, glutamic acid, methanesulfonic acid, ethanesulfonic acid, benzenesulfonic acid, lactic acid, oxalic acid, para- bromophenylsulfonic acid, carbonic acid, succinic acid, citric acid, benzoic acid and acetic acid, as well as related inorganic and organic acids.
  • inorganic acids such as hydrogen bisulfide, hydrochloric acid, hydrobromic acid, hydroiodic acid, sulfuric
  • Such pharmaceutically acceptable salts thus include sulfate, pyrosulfate, bisulfate, sulfite, bisulfite, phosphate, monohydrogenphosphate, dihydrogenphosphate, metaphosphate, pyrophosphate, chloride, bromide, iodide, acetate, propionate, decanoate, caprylate, acrylate, formate, isobutyrate, caprate, heptanoate, propiolate, oxalate, malonate, succinate, suberate, sebacate, fumarate, maleate, butyne-l,4-dioate, hexyne-l,6-dioate, benzoate, chlorobenzoate, methylbenzoate, dinitrobenzoate, hydroxybenzoate, methoxybenzoate, phthalate, terephthalate, sulfonate, xylene sulfonate, phenylacetate, phenylprop
  • bases commonly employed to form pharmaceutically acceptable salts of the therapeutic compounds described herein include hydroxides of alkali metals, including sodium, potassium, and lithium; hydroxides of alkaline earth metals such as calcium and magnesium; hydroxides of other metals, such as aluminum and zinc; ammonia, organic amines such as unsubstituted or hydroxyl- substituted mono-, di-, or tri-alkylamines, dicyclohexylamine; tributyl amine; pyridine; N-methyl, N-ethylamine; diethylamine; triethylamine; mono-, bis-, or tris- (2-OH-(Cl-C6)-alkylamine), such as N,N-dimethyl-N-(2-hydroxyethyl)amine or tri- (2-hydroxyethyl)amine; N-methyl-D-glucamine; morpholine; thiomorpholine; piperidine; pyrrolidine; and amino acids such as arginine
  • homologous recombination refers to the cellular process of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used for repairing double-stranded breaks in DNA.
  • Two primary models for how homologous recombination repairs double-strand breaks in DNA are the double-strand break repair (DSBR) pathway (sometimes called the double Holliday junction model) and the synthesis-dependent strand annealing (SDSA) pathway (See, e.g., Sung, P; Klein, H (October 2006). “Mechanism of homologous recombination: mediators and helicases take on regulatory functions”. Nature Reviews Molecular Cell Biology 7 (10): 739- 750, incorporated herein by reference).
  • subject or “patient” is intended to include humans and animals that are capable of suffering from or afflicted with a cancer or any disorder involving, directly or indirectly, a cancer.
  • subjects include mammals, e.g., humans, dogs, cows, horses, pigs, sheep, goats, cats, mice, rabbits, rats, and transgenic non-human animals.
  • subjects include companion animals, e.g. dogs, cats, rabbits, and rats.
  • subjects include livestock, e.g., cows, pigs, sheep, goats, and rabbits.
  • subjects include thoroughbred or show animals, e.g., horses, pigs, cows, and rabbits.
  • the subject is a human, e.g., a human having, at risk of having, or potentially capable of having cancer.
  • a “subject in need of treatment” is a subject identified as having cancer.
  • the subject in need of treatment is identified as having a homologous recombination (HR)-deficient cancer, i.e., the subject has been diagnosed by a physician (e.g., using methods well known in the art; see WO 2014/138101, incorporated herein by reference) as having aHR- deficient cancer.
  • the HR status of the cancer can be determined by, for example, a BRCA 1 -specific CGH classifier (Evers et al. Trends Pharmacol Sci. 2010 Aug;31(8):372-80), an assay that determines the capacity of primary cell cultures to form foci after PARP inhibition (Mukhopadhyay, A. et al. (2010) Clin. Cancer Res.
  • the HR-deficient cancer is resistant to treatment with a poly (ADP-ribose) polymerase (PARP) inhibitor alone (see, for example, Montoni et al. Front Pharmacol. 2013 Feb 27;4:18).
  • PARP poly (ADP-ribose) polymerase
  • the subject in need of treatment is a subject identified as having a cancer that is resistant to or at risk of developing resistance to PARP inhibitor therapy using methods well known in the art (see, e.g., WO 2014205105, WO 2015040378, WO 2011153345; incorporated herein by reference).
  • the PARP inhibitor-resistant cancer is deficient in homologous recombination (i.e., the cancer is characterized by a lack of a functional homologous recombination (HR) DNA repair pathway, and is resistant to PARP inhibitor therapy).
  • anti-cancer therapy refers to any agent, composition or medical technique (e.g., surgery, radiation treatment, etc.) useful for the treatment of cancer.
  • an anti-cancer agent can be a small molecule, antibody, peptide or antisense compound.
  • Suitable examples of antisense compounds include interfering RNAs (e.g., dsRNA, siRNA, shRNA, miRNA, and amiRNA) and antisense oligonucleotides (ASO).
  • inhibitor refers to the ability of a compound to reduce, slow, halt, and/or prevent activity of a particular biological process in a cell relative to vehicle.
  • “inhibit”, “block”, “suppress” or “prevent” means that the activity being inhibited, blocked, suppressed, or prevented is reduced by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% as compared to the activity of a control (e.g., activity in the absence of the inhibitor.
  • inhibitor means that the activity of the target of the inhibitor (e.g. the ATPase activity of POLQ) is reduced by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% as compared to a control (e.g., the ATPase activity of POLQ in the absence of the inhibitor).
  • a control e.g., the ATPase activity of POLQ in the absence of the inhibitor.
  • an “effective amount” refers to an amount sufficient to elicit the desired biological response, e.g., treating cancer or inhibiting a biological activity.
  • the effective amount of the compounds described herein can vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the condition being treated, the mode of administration, and the age and health of the subject, and the guidance of the treating physician.
  • An effective amount includes that amount necessary to slow, reduce, inhibit, ameliorate or reverse one or more symptoms associated with cancer. For example, in the treatment of cancer, such terms can refer to a reduction in the size of the tumor.
  • Cn-m alkyl refers to a saturated hydrocarbon group that can be straight-chain (linear) or branched, having n to m carbons.
  • alkyl moieties include chemical groups such as methyl, ethyl, «-propyl, isopropyl, «-butyl, tert- butyl, isobutyl, sec-butyl; higher homologs such as 2-methyl- 1 -butyl, «-pentyl, 3-pentyl, «- hexyl, 1 ,2,2-trimethylpropyl, and the like.
  • the alkyl group contains from 1 to 6 carbon atoms, from 1 to 4 carbon atoms, from 1 to 3 carbon atoms, or 1 to 2 carbon atoms.
  • Cn-m alkenyl refers to a linear or branched hydrocarbon group having one or more carbon-carbon double bonds and having n to m carbons.
  • Suitable example alkenyl groups include ethenyl, «-propenyl, isopropenyl, «-butenyl, ve -butenyl. and the like.
  • the alkenyl moiety contains 2 to 6, 2 to 4, or 2 to 3 carbon atoms.
  • Cn-m alkynyl means a straight or branched chain hydrocarbon group, containing n to m carbon atoms and containing at least one carbon-carbon triple bond, such as ethynyl, 1-propynyl, 1-butynyl, 2-butynyl, and the like.
  • alkynyl groups can either be unsubstituted or substituted with one or more substituents.
  • alkynyl groups will comprise 2 to 9 carbon atoms (for example, 2 to 6 carbon atoms, 2 to 4 carbon atoms, or 2 carbon atoms).
  • C n -m alkynylene refers to a divalent alkynyl group.
  • Cn-m alkoxy refers to a group of formula -O-Cn-m alkyl.
  • Suitable exemplary alkoxy groups include methoxy, ethoxy, propoxy (for example, «-propoxy and isopropoxy), butoxy (for example, «-butoxy and tert-butoxy), and the like.
  • the alkoxy group has 1 to 6, 1 to 4, or 1 to 3 carbon atoms.
  • halo refers to a halogen atom such as F, Cl, Br, or I. In some embodiments, a halo is F, Cl, or Br. In other embodiments, halo is F, Cl, or I. In other embodiments, halo is F, I, or Br.
  • Cn-mhaloalkyl refers to an alkyl group having from one halogen atom to 2s+l halogen atoms which can be the same or different, where “s” is the number of carbon atoms in the alkyl group, and the alkyl group has n to m carbon atoms.
  • the haloalkyl group is fluorinated only.
  • the alkyl group has 1 to 6, 1 to 4, or 1 to 3 carbon atoms.
  • Cn-mhaloalkoxy refers to a group of formula -O-haloalkyl having n to m carbon atoms.
  • An example haloalkoxy group is OCF3.
  • the haloalkoxy group is fluorinated only.
  • the alkyl group has 1 to 6, 1 to 4, or 1 to 3 carbon atoms.
  • aryl refers to an aromatic hydrocarbon group, which can be monocyclic or polycyclic (for example, having 2, 3 or 4 fused rings).
  • Cn-m aryl refers to an aryl group having from n to m ring carbon atoms.
  • Aryl groups include, for example, phenyl, naphthyl, anthracenyl, phenanthrenyl, indanyl, indenyl and the like.
  • aryl groups have from 6 to 20 carbon atoms, from 6 to 15 carbon atoms, or from 6 to 10 carbon atoms.
  • the aryl group is phenyl.
  • cycloalkyl refers to non-aromatic cyclic hydrocarbons including cyclized alkyl and/or alkenyl groups.
  • Cycloalkyl groups can include mono- or polycyclic (e.g., having 2, 3 or 4 fused rings) groups and spirocycles. Ring forming carbon atoms of a cycloalkyl group can be optionally substituted by 1 or 2 independently selected oxo or sulfide groups (e.g., C(O) or C(S)).
  • cycloalkyl moieties that have one or more aromatic rings fused (i.e., having a bond in common with) to the cycloalkyl ring, for example, benzo or thienyl derivatives of cyclopentane, cyclohexane, and the like.
  • a cycloalkyl group containing a fused aromatic ring can be attached through any ring-forming atom including a ring-forming atom of the fused aromatic ring.
  • Cycloalkyl groups can have 3, 4, 5, 6, 7, 8, 9, or 10 ring-forming carbons (C3-10).
  • the cycloalkyl is a C3-10 monocyclic or bicyclic cyclocalkyl.
  • the cycloalkyl is a C3-7 monocyclic cyclocalkyl.
  • Example cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclopentenyl, cyclohexenyl, cyclohexadienyl, cycloheptatrienyl, norbomyl, norpinyl, norcamyl, adamantyl, and the like.
  • cycloalkyl is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl.
  • heteroaryl refers to a monocyclic or polycyclic aromatic heterocycle having at least one heteroatom ring member selected from sulfur, oxygen, and nitrogen.
  • the heteroaryl ring has 1, 2, 3, or 4 heteroatom ring members independently selected from nitrogen, sulfur and oxygen.
  • any ring-forming N in a heteroaryl moiety can be an N-oxide.
  • the heteroaryl is a 5-10 membered monocyclic or bicyclic heteroaryl having 1, 2, 3 or 4 heteroatom ring members independently selected from nitrogen, sulfur and oxygen.
  • the heteroaryl is a 5-6 monocyclic heteroaryl having 1 or 2 heteroatom ring members independently selected from nitrogen, sulfur and oxygen.
  • the heteroaryl is a five- membered or six-membereted heteroaryl ring.
  • a five-membered heteroaryl ring is a heteroaryl with a ring having five ring atoms wherein one or more (e.g., 1, 2, or 3) ring atoms are independently selected fromN, O, and S.
  • Exemplary five-membered ring heteroaryls are thienyl, furyl, pyrrolyl, imidazolyl, thiazolyl, oxazolyl, pyrazolyl, isothiazolyl, isoxazolyl, 1,2,3-triazolyl, tetrazolyl, 1,2,3-thiadiazolyl, 1,2,3- oxadiazolyl, 1,2,4-triazolyl, 1 ,2,4-thiadiazolyl, 1,2,4-oxadiazolyl, 1,3,4-triazolyl, 1,3,4-thiadiazolyl, and 1,3,4-oxadiazolyl.
  • a six-membered heteroaryl ring is a heteroaryl with a ring having six ring atoms wherein one or more (e.g., 1, 2, or 3) ring atoms are independently selected fromN, O, and S.
  • Exemplary six-membered ring heteroaryls are pyridyl, pyrazinyl, pyrimidinyl, triazinyl and pyridazinyl.
  • Cn-m alkylamino refers to a group of formula -NH(alkyl), wherein the alkyl group has n to m carbon atoms. In some embodiments, the alkyl group has 1 to 6, 1 to 4, or 1 to 3 carbon atoms.
  • alkylamino groups include N-methylamino, N-ethylamino, N- propylamino (e.g., N-( «-propyl)amino andN-isopropylamino), N-butylamino (e.g., N- (/i-butyl)amino and N-(/er/-butyl)amino), and the like.
  • di Cn-m alkylamino refers to a group of formula -N(alkyl)2, wherein each alkyl group independently has n to m carbon atoms. In some embodiments, each alkyl group has 1 to 6, 1 to 4, or 1 to 3 carbon atoms. Suitable examples of dialkylamino groups include N,N-methylehtylamino, N,N- diethylamino, N,N-propylethylamino, N,N-butylisopropylamino, and the like.
  • a POLQ fragment (APol) containing the ATPase domain with a RAD51 binding site (amino acids 1 to 987) was cloned into pFastBac-C-Flag and purified from baculovirus-infected SF9 insect cells.
  • the POLQ-pFastBac-C-Flag vector was transformed into DHlObac E. coli, and bacteria were plated on an IPTG and X-Gal containing plates and recombinant bacmid DNA was purified using the Qiagen midiprep kit.
  • POLQ bacmid was transfected into the SF9 cells grown in Grace’s Insect Medium (FBS, penstrep, fungizone, and sparfloxacin) using the Cellfectin II reagent. Baculovirus excreted from the cells and the surrounding media were collected after three days (PI). Then, SF9 cells were grown to 90-100% confluence on 15 cm plates. 150 pi of PI virus was added to the plate covered with 25 mL Grace’s Insect Medium. The surrounding media containing P2 virus was collected after 3 days. Then, SF9 cells were grown in 1 L spinner flasks at a volume of 500 mL and a density of 1.5-2 million cells/mL.
  • Grace’s Insect Medium FBS, penstrep, fungizone, and sparfloxacin
  • the cell lysis was incubated with M2 Flag beads (Sigma) for 3 hours at 4C on a spinning wheel.
  • the M2 Flag beads were washed 3 times lysis buffer and POLQ protein was then eluted in lysis buffer supplemented with 0.2 mg/ml of Flag peptide (Sigma).
  • the protein was concentrated in lysis buffer using 10 kDa centrifugal filters (Amicon).
  • the protein was then quantified by staining intensity on Coomassie. Purified protein was flash-frozen in small aliquots in liquid nitrogen and stored at -80°C.
  • ATPase activity of a POLQ was studied using the ADP-Glo kinase assay (Promega).
  • a 10 m ⁇ mix containing 10 nM of POLQ-APol protein, 600 nM of 30mer single-stranded DNA substrate, 40 mM Tris-HCl buffer (pH 7.6), 20 mM MgC12, 0.1 mg/ml BSA, and 1 mM DTT was added to each reaction well in a black 384 well plate (Coming). Then, 100 nL of a chemical inhibitor or negative control (DMSO) was added to each well.
  • DMSO chemical inhibitor or negative control
  • the CellTiter-Glo luminescent cell viability assay kit (Promega) was used to measure cell viability after drug treatment.
  • the CellTiter-Glo kit determines the number of viable cells in culture based on quantitation of the ATP present, an indicator of metabolically active cells. 500 to 1000 cells per well were seeded in a 96- well plate in 100 pL media volume. 24 hours later, cells were treated with indicated drugs by adding 100 pL medium with 2* concentrated drug of desired final concentration. Cells were cultured in drug containing medium for 6 days, by then cell viability was determined by measuring the luminescent signal, following the manufacturer’s instructions. Survival fraction of drug-treated cells was normalized to DMSO-treated control. Survival, IC50, and statistics were determined by using the GraphPad Prism software.
  • POLQ protein (APol, aa 1-987) was pre-incubated with inhibitors and ssDNA for 30 minutes (min) in reaction buffer (20 mM HEPES-KOH (pH 7.6), 100 mM KC1, 5 mM MgC12, 0.25 pg/m ⁇ BSA, 0.05 mM EDTA, 0.5 mM DTT, 3% glycerol, and 0.01% NP-40).
  • the substrate ATP 500 mM cold ATP and 1 pCi of [g- 32 R]-ATR as a tracer was added to start reactions. The total volume of the reactions was 20 pi.
  • TSA Thermal Stability Assay
  • HEK293T cells overexpressing eGFP-POLQ were lysed in IP buffer (ThermoFisher Scientific, #87788) with PMSF, protease and phosphatase inhibitors. 50 pL of cell lysate was aliquoted to each tube and NVB or DMSO was added. The mixture was incubated for 15 min at room temperature, heated at indicated temperature (37 °C to 55 °C) for 3 min, and then at room temperature again for another 5 min. Next, the mixture was centrifuged at 20,000 g for 15 minutes. The supernatant was taken for Western blot analysis.
  • Human cells were maintained in culture media (DME-HG/F-12 for WT and knock outs RPEl cells; RMPI for MDA-MB-436; DMEM for U20S) supplemented with 10% FBS and 1% penicillin-streptomycin.
  • Full length POLQ was cloned by Gibson assembly in pCAG-GFP (Plasmid #11150) and co-transfected with Super PiggyBac Transposase Expression Vector (#PB210PA-1, System Biosciences) using Lipofectamine LTX with Plus Reagent in RPE-P53.
  • Cells were seeded, at 2 different concentrations, into each well of a 6-well plate (100 and 200 cells for WT RPE1; 500 and 1000 cells for HR-deficient cells). Next day, cells were treated with indicated of inhibitors. Cells were allowed to grow in drug-containing medium for 12 to 14 days. Cells were fixed and stained with 0.2% crystal violet in methanol for 30 min (Crystal Violet solution, Sigma HT90132), and rinsed with distilled water three times. The stained dishes were air-dried, and the number of colonies (>50 cells) was counted in each well.
  • TP53 knockouts were generated in RPE-1 cells knockout for TP53 (RPE-P53).
  • TP53 knockout was generated by co-transfection of Cas9 (pSpCas9(BB)-2A-GFP addgene #48138) (PX458) and TP53 sgRNA vectors (gRNA cloning vector Plasmid addgene #41824) by Lipofectamine LTX with Plus Reagent (ThermoFisher). Single colonies were screened by western blotting.
  • RPE1-P53 BRCA2 cells were obtained by co-transfection of Cas9 and two sgRNA vectors targeting introns flanking exon 2 of BRCA2 gene.
  • SgRNA sequences are the following (Tp53: GGCAGCTACGGTTTCCGTC; BRCA2-2: GGTAAAACTCAGAAGCGC; BRCA2- 3: GCAACACTGTGACGTACT).
  • PCR primers sequences used for genotyping are the following (Deletion PCR: seqBRCA2-For:
  • RPE1-P53 overexpressing eGFP-POLQ were plated in m-Dish 35 mm (Ibidi). The day after, DMSO, Rucaparib (1 mM) or Novobiocin (200 mM) were added on the cells for 24 hours. Microirradiations were performed with two photons laser (800 nm) on an inverted Laser Scanning Confocal Microscope with Spectral Detection and Multi-photon Laser (LSM880NLO/Mai Tai Laser - Zeiss/Spectra Physics) with Airyscan module. Images were then analyzed with Fiji and statistical analysis were performed using Prism7.
  • PARP inhibitors Olaparib and Rucaparib (Selleckchem) were dissolved in DMSO and kept in small aliquots at -20 °C.
  • Novobiocin (NVB) (Sigma) was dissolved in DMSO snap freeze by addition of liquid nitrogen in one-shot aliquots and stored at -80 °C. The remaining compounds were synthesized by methods known in the art, such as those disclosed in U.S. Patent No. 10,030,006, the contents of which are incorporated herein by reference in their entirety.
  • Example 1 - exemplified compounds are specific POLQ inhibitors
  • the effect of the exemplified compounds on the survival of HR-deficient cells was determined (See Figures 1-9B).
  • the compounds more effectively killed BRCAL versus WT RPE1 cells in luminescence-based cell viability assays and clonogenic assays.
  • the compounds also more effectively killed BRCAl-mutated cancer cell lines (MDA-MB-436 and UWB1) than their WT counterparts (MDA-MB-436 + BRCA1 and UWB1 + BRCA1), demonstrating that the compounds create a synthetic lethality with HR.
  • IC50 demonstrated that compound 1 was 200 times more potent than NVB (a control compound) in killing BRC A 1 RPEl cells (see Table 1).
  • compound 1 kills UWB1 (BRCA1 mutated) cells more efficiently than BRCAl-complemented UWB1 cells (See Figure 6). Additional results of testing compound 1, including results of ATPase activity assay and clonogenic survival assay in BRCA1-KO PRE cells, are shown in Figures 13-16. IC50 for the selected compounds against WT and BRCA1-KO cells (Retinal pigment cells, RPE1) are shown in Table 2.
  • Anti-proliferative IC50 (mM) for the exemplified compounds for the selected cancer cell types are shown in Table 4.
  • Cells were maintained in a 1 : 1 mixture of advanced DMEM/F12 (Gibco) supplemented with nonessential amino acids, L-glutamine (2 mM), streptomycin (500 pg/mL), penicillin (100 units/mL), and 10% FBS. Cells were grown to confluence in a humidified atmosphere (37 °C, 5% CCh), seeded (2000/well, 100 pL) in 96-well plates, and allowed to attach overnight. Compound or GDA at varying concentrations in DMSO (1% DMSO final concentration) was added.
  • MCF-7 cells were cultured as described above and treated with various concentrations of drug, GDA in DMSO (1% DMSO final concentration), or vehicle (DMSO) for 24 h.
  • Cells were harvested in cold PBS and lysed in RIPA lysis buffer containing 1 mM PMSF, 2 mM sodium orthovanadate, and protease inhibitors on ice for 1 h. Lysates were clarified at 14,000 g for 10 min at 4 °C. Protein concentrations were determined by using the Pierce BCA protein assay kit per the manufacturer’s instructions. Equal amounts of protein (20 pg) were electrophoresed under reducing conditions, transferred to a nitrocellulose membrane, and immunoblotted with the corresponding specific antibodies. Membranes were incubated with an appropriate horseradish peroxidase-labeled secondary antibody, developed with a chemiluminescent substrate, and visualized.
  • NVB was reported to function as a HSP90 inhibitor, through direct interaction with the protein (Marcu, et al. (2000). JBiol Chem 275, 37181-37186), although the cellular activity is poor (anti-proliferative IC50 in SKBR3 cells for novobiocin is about 700 mM).

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Organic Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Animal Behavior & Ethology (AREA)
  • General Health & Medical Sciences (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

La présente invention concerne, dans certains aspects, des procédés de traitement de cancers, tels que des cancers déficients en recombinaisons homologues (HR). Dans certains modes de réalisation, l'invention concerne un procédé de traitement du cancer par l'administration à un sujet d'un composé de formule (A), ou d'un sel pharmaceutiquement acceptable de celui-ci. Dans un premier aspect général, la présente invention concerne un procédé de traitement d'un cancer déficient en recombinaisons homologues (HR) ou d'un cancer surexprimant la POLQ, le procédé comprenant : (i) l'identification d'un sujet ayant un cancer déficient en HR ou un cancer surexprimant la POLQ, ou les deux; et (ii) après (i), l'administration au sujet d'une quantité thérapeutiquement efficace d'un composé de formule (A), ou d'un sel pharmaceutiquement acceptable de celui-ci. Dans certains modes de réalisation, le composé de formule (A) a la formule (I). L'invention concerne également un sel pharmaceutiquement acceptable de celui-ci.
PCT/US2020/049140 2019-09-04 2020-09-03 Composés et méthodes de traitement du cancer WO2021046178A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201962895823P 2019-09-04 2019-09-04
US62/895,823 2019-09-04

Publications (1)

Publication Number Publication Date
WO2021046178A1 true WO2021046178A1 (fr) 2021-03-11

Family

ID=74853024

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2020/049140 WO2021046178A1 (fr) 2019-09-04 2020-09-03 Composés et méthodes de traitement du cancer

Country Status (1)

Country Link
WO (1) WO2021046178A1 (fr)

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014138101A1 (fr) * 2013-03-04 2014-09-12 Board Of Regents, The University Of Texas System Signature génique pour prédire un cancer déficient pour la recombinaison homologue (rh)
US20160272584A1 (en) * 2013-11-07 2016-09-22 University Of Kansas Biphenylamide derivative hsp90 inhibitors
WO2017070198A1 (fr) * 2015-10-19 2017-04-27 Dana-Farber Cancer Institute, Inc. Polymérase q utilisée comme cible dans des cancers déficients en rh
US20170253582A1 (en) * 2014-06-13 2017-09-07 The University Of Kansas Triazole modified coumarin and biphenyl amide-based hsp90 inhibitors
WO2019079297A1 (fr) * 2017-10-16 2019-04-25 Dana-Farber Cancer Institute, Inc. Composés et procédés de traitement du cancer

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014138101A1 (fr) * 2013-03-04 2014-09-12 Board Of Regents, The University Of Texas System Signature génique pour prédire un cancer déficient pour la recombinaison homologue (rh)
US20160272584A1 (en) * 2013-11-07 2016-09-22 University Of Kansas Biphenylamide derivative hsp90 inhibitors
US20170253582A1 (en) * 2014-06-13 2017-09-07 The University Of Kansas Triazole modified coumarin and biphenyl amide-based hsp90 inhibitors
WO2017070198A1 (fr) * 2015-10-19 2017-04-27 Dana-Farber Cancer Institute, Inc. Polymérase q utilisée comme cible dans des cancers déficients en rh
WO2019079297A1 (fr) * 2017-10-16 2019-04-25 Dana-Farber Cancer Institute, Inc. Composés et procédés de traitement du cancer

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
FORSBERG LEAH K; DAVIS RACHEL E; WIMALASENA VIRANGIKA K; BLAGG BRIAN S J: "Exploiting Polarity and Chirality to Probe the Hsp90 C-terminus", BIOORG MED CHEM, vol. 26, no. 12, 23 July 2018 (2018-07-23), pages 3096 - 3110, XP085408674 *

Similar Documents

Publication Publication Date Title
CN107108637B (zh) 三唑并嘧啶化合物及其用途
AU2018352382B2 (en) Compounds and methods for treating cancer
JP6889101B2 (ja) グルタミナーゼ阻害剤の結晶形態
CN113811333B (zh) 靶向抗癌核激素受体的化合物
KR20160029076A (ko) 핵수송 조절인자 및 이의 용도
KR20200062386A (ko) 암 치료용 병용 요법
TW200424206A (en) Salts of tricyclic inhibitors of poly(ADP-ribose) polymerases
JP2017532312A (ja) 癌を治療するための併用療法
TW201121956A (en) Use of N-(4-((3-(2-amino-4-pyrimidinyl)-2-pyridinyl)oxy)phenyl)-4-(4-methyl-2-thienyl)-1-phthalazinamine in the treatment of antimitotic agent resistant cancer
US20190055563A1 (en) Polymerase q as a target in hr-deficient cancers
CN109715157A (zh) 用于治疗癌症的组合
JP7543278B2 (ja) 有機化合物
TW201636350A (zh) 作為激酶調節劑之三唑並嗒
WO2023172669A2 (fr) Polythérapies pour la modulation de la production de lipides
EP3125901B1 (fr) Dérivés de céphalosporines pour traiter le cancer
TW201343169A (zh) 使用奧諾拉（ａｕｒｏｒａ）激酶抑制劑治療癌症的方法
CN115998872A (zh) 一种含有抑制核酸内切酶功能的药物及其抗肿瘤的用途
KR20240122783A (ko) Fgfr 저해제 및 kras 저해제를 포함하는 병용 요법
WO2021046178A1 (fr) Composés et méthodes de traitement du cancer
WO2021046220A1 (fr) Composés et méthodes de traitement du cancer
TW202108570A (zh) 抗癌核荷爾蒙受體標靶化合物
KR20130130802A (ko) 보르트만닌 유사체의 결정질 형태의 조성물 및 이의 사용 방법
AU2019275453B2 (en) Organic compounds
TW202428280A (zh) 組合療法
JP2022023033A (ja) ガンの処置に有用なｔｉｅ２キナーゼの阻害方法

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 20861503

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 20861503

Country of ref document: EP

Kind code of ref document: A1