WO2022204720A1 - (furopyrimidin-4-yl)piperazine compounds and uses thereof - Google Patents
(furopyrimidin-4-yl)piperazine compounds and uses thereof Download PDFInfo
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- WO2022204720A1 WO2022204720A1 PCT/US2022/071344 US2022071344W WO2022204720A1 WO 2022204720 A1 WO2022204720 A1 WO 2022204720A1 US 2022071344 W US2022071344 W US 2022071344W WO 2022204720 A1 WO2022204720 A1 WO 2022204720A1
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- WIPO (PCT)
- Prior art keywords
- compound
- ring
- cancer
- pharmaceutically acceptable
- acceptable salt
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Classifications
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D491/00—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00
- C07D491/02—Heterocyclic compounds containing in the condensed ring system both one or more rings having oxygen atoms as the only ring hetero atoms and one or more rings having nitrogen atoms as the only ring hetero atoms, not provided for by groups C07D451/00 - C07D459/00, C07D463/00, C07D477/00 or C07D489/00 in which the condensed system contains two hetero rings
- C07D491/04—Ortho-condensed systems
- C07D491/044—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring
- C07D491/048—Ortho-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring the oxygen-containing ring being five-membered
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
- A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
- A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
- A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
Definitions
- RAD51 protein expression is elevated in immortalized cells as well as in a wide variety of human cancer cell lines (PMID: 11782381, 12712436). It was proposed that RAD51 overexpression results in an increased cellular resistance to radiation and some chemotherapeutic drugs, such as topoisomerase inhibitors or DNA crosslinking agents (PMID: 12712436, 12024032, 9611228). RAD51 overexpression has also been investigated in numerous tumor tissues using immunohistochemistry (IHC).
- IHC immunohistochemistry
- FIG.3D shows an example of the effect of Compound 3 dihydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4.
- FIG.3E shows an example of the effect of Compound 11 dihydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4.
- FIG.3F shows an example of the effect of Compound 4 dihydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4.
- FIG.3G shows an example of the effect of Compound 15 dihydrrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4.
- FIG.10B shows an example of the effect of Compound 5 hydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
- FIG.10C shows the effect of Compound 2 hydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
- FIG.10D shows an example of the effect of Compound 3 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
- FIG.10E shows an example of the effect of Compound 4 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
- FIG.10F shows an example of the effect of Compound 11 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
- FIG.10G shows an example of the effect of Compound 15 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
- DETAILED DESCRIPTION [0056] A description of example embodiments follows.
- Ring G is oxazolyl, phenyl, pyridinyl, dihydropyridinyl, indolyl, indolinyl, isoindolinyl, quinolinyl, isoquinolinyl, quinoxalinyl, tetrahydroquinolinyl, benzofuranyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, benzo[d][1,3]dioxolyl, dihydrobenzo[b][1,4]dioxinyl, cyclohexyl, tetrahydropyranyl, piperidinyl, piperazinyl or morpholinyl.
- Ring G is bicyclic fused (C 5 -C 15 )heterocyclyl. Values for the remaining variables are as described in the first embodiment, or first through ninth aspects thereof. [0068] In an eleventh aspect of the first embodiment, Ring G is indolinyl, isoindolinyl, dihydrobenzo[d]imidazolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, tetrahydroquinoxalinyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, benzo[d][1,3]dioxolyl, chromanyl, or dihydrobenzo[b][1,4]dioxinyl.
- R 1 is independently bromo or cyano. Values for the remaining variables are as described in the first embodiment, or first through sixteenth aspects thereof.
- R 2 is H or, together with an atom of Ring G and their intervening atoms, forms a three- to eight-membered ring that is spiro or fused to Ring G. Values for the remaining variables are as described in the first embodiment, or first through seventeenth aspects thereof.
- R 2 is H.
- n 0, 1 or 2.
- Values for the remaining variables are as described in the first embodiment, or first through fortieth aspects thereof. [0099] In a forty-second aspect of the first embodiment, p is 1. Values for the remaining variables are as described in the first embodiment, or first through forty-first aspects thereof. [00100] In a forty-third aspect of the first embodiment, p is 2. Values for the remaining variables are as described in the first embodiment, or first through forty-second aspects thereof.
- a fourth embodiment is a compound having the following structural formula: or a pharmaceutically acceptable salt thereof.
- a fifth embodiment is a compound having the following structural formula: or a pharmaceutically acceptable salt thereof, wherein A 2 is -C(H) 2 -, -N(H)- or -O-; and A 3 is >C(H)- or >N-.
- Values for the remaining variables e.g., R 1 , R 2 , R 3 , m, n, p and Ring G are as described in the first embodiment, or any aspect thereof.
- a second aspect of the fifth embodiment is -C(H) 2 - and A 3 is >C(H)-. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or fifth embodiment.
- a second aspect of the fifth embodiment A 2 is -O- and A 3 is >C(H)-. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or fifth embodiment, or first aspect thereof.
- a sixth embodiment is a compound having the following structural formula: or a pharmaceutically acceptable salt thereof.
- Hydroxyalkyl refers to an alkyl radical wherein one or more (e.g., one) hydrogen atoms is replaced by a hydroxy, wherein alkyl and hydroxy are as described herein.
- Hydro(C 1 -C 6 )alkyl refers to a (C 1 -C 6 )alkyl wherein one or more hydrogen atoms is replaced by a hydroxy. Examples of hydroxyalkyl include, but are not limited to, 2-hydroxyethyl.
- Cyano as used herein, means -C ⁇ N.
- (C 5 -C 8 )carbocyclyl means a carbocyclyl ring system having from 5 to 8 ring carbons.
- a carbocyclyl can be saturated (i.e., a cycloalkyl).
- a carbocyclyl can be unsaturated (i.e., contain at least one degree of unsaturation, as in at least one carbon-carbon double bond or triple bond).
- a carbocyclyl ring system may consist of monocyclic rings, fused rings, bridged rings and spirocyclic rings.
- cycloalkyl examples include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and norbornyl.
- Cycloalkoxy refers to a cycloalkyl ring system attached through an oxygen linking atom.
- (C 3 -C 7 )cycloalkoxy refers to a cycloalkoxy group in which a (C 3 - C 7 )cycloalkyl is attached through an oxygen linking atom.
- heterocyclyl examples include, but are not limited to, azetidinyl, oxetanyl, piperidinyl, piperazinyl, pyrrolyl, pyrrolidinyl, imidazolidinyl, imidazolinyl, morpholinyl, tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyranyl, 1,3- dioxolyl, 1,4-dioxanyl, 1,4-oxathianyl, dihydrobenzofuranyl, hexahydropyrimidinyl, 3- azabicyclo[3.1.0]hexanyl, azepanyl, 3-azabicyclo[3.2.2]nonanyl, decahydroisoquinolinyl, 2- azaspiro[3.3]heptanyl, 2-oxa-6-azaspiro[3.3]heptanyl, 2,
- the fused heterocyclyl is indoline, isoindoline, dihydrobenzo[d]imidazole, tetrahydroquinoline, tetrahydroisoquinoline, tetrahydroquinoxaline, dihydrobenzofuran, dihydroisobenzofuran, benzo[d][1,3]dioxole, chromane, or dihydrobenzo[b][1,4]dioxine.
- the fused heterocyclyl is 6,7-dihydro-5H-pyrrolo[3,4-b]pyridine or 5,6,7,8-tetrahydro-1,7-naphthyridine.
- the term “monocyclic” refers to a ring system consisting of a single ring. Examples of monocyclic rings include, but are not limited to, phenyl, pyridyl, piperazinyl, morpholino, tetrahydropyranyl, imidazole, and furanyl and thiophenyl. [00145]
- the term “bicyclic” refers to a ring system consisting of two rings. Examples of bicyclic rings include, but are not limited to, naphthyl, quinolinyl, indolyl and indoline.
- spirocyclic ring refers to a carbocyclyl or heterocyclyl, as described herein, which is attached to a second carbocyclyl or second heterocyclyl group by a single carbon atom.
- spirocyclic rings include, but are not limited to [00147]
- fused ring refers to any ring (e.g., an aryl ring, heteroaryl ring, carbocyclyl ring or heterocyclyl ring) that shares two adjacent atoms with a second ring (e.g., an aryl ring, heteroaryl ring, carbocyclyl ring or heterocyclyl ring).
- divalent radicals formed by removing one hydrogen atom from a parent group include, but are not limited to: carbocyclene, cycloalkylene, heterocyclylene, arylene, and heteroarylene, which are derived from carbocyclyl, cycloalkyl, heterocyclyl, aryl and heteroaryl, respectively.
- substituted means that at least one (e.g., one, two, three, four, five, six, etc., from one to five, from one to three, one or two) hydrogen atom is replaced with a non-hydrogen substituent, provided that normal valencies are maintained and that the substitution results in a stable compound.
- This disclosure is intended to cover all possible tautomers even when a structure depicts only one of them.
- the bicyclic ring containing X and Y is denoted with aromatic conjugation circles in formula I, and is understood to include the following resonance structures and when X is -O- and Y is -C(H)-; and the following resonance structures and when Y is -O- and X is -C(H)-.
- phrases “pharmaceutically acceptable” means that the substance or composition the phrase modifies must be, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. If a substance is part of a composition or formulation, the substance must also be compatible chemically and/or toxicologically with the other ingredients in the composition or formulation.
- the term “compounds of the present disclosure” refers to a compound of any structural formula depicted herein (e.g., a compound of Formula I, a subformula of a compound of Formula I), as well as isomers, such as stereoisomers (including diastereoisomers, enantiomers and racemates), geometrical isomers, conformational isomers (including rotamers and astropisomers), tautomers, isotopically labeled compounds (including deuterium substitutions), and inherently formed moieties (e.g., polymorphs and/or solvates, such as hydrates) thereof.
- isomers such as stereoisomers (including diastereoisomers, enantiomers and racemates), geometrical isomers, conformational isomers (including rotamers and astropisomers), tautomers, isotopically labeled compounds (including deuterium substitutions), and inherently formed moieties (e.g., polymorphs
- isomers refers to different compounds that have the same molecular formula but differ in arrangement and configuration of the atoms.
- Enantiomers are a pair of stereoisomers that are non-superimposable mirror images of each other.
- organic amines include, but are not limited to, isopropylamine, benzathine, cholinate, diethanolamine, diethylamine, lysine, meglumine, piperazine and tromethamine.
- a salt (e.g., pharmaceutically acceptable salt) of a compound of the present disclosure can be synthesized from the parent compound that contains a basic or acidic moiety by conventional chemical methods.
- a substituent in a compound of this present disclosure is denoted deuterium, such compound has an isotopic enrichment factor for each designated deuterium atom of at least 3500 (52.5% deuterium incorporation at each designated deuterium atom), at least 4000 (60% deuterium incorporation), at least 4500 (67.5% deuterium incorporation), at least 5000 (75% deuterium incorporation), at least 5500 (82.5% deuterium incorporation), at least 6000 (90% deuterium incorporation), at least 6333.3 (95% deuterium incorporation), at least 6466.7 (97% deuterium incorporation), at least 6600 (99% deuterium incorporation), or at least 6633.3 (99.5% deuterium incorporation).
- mutation refers to a change or difference in the genetic material of a cell as compared to a reference wildtype genetic sequence, e.g., a deletion, an insertion, a SNP, a gene rearrangement, and/or the introduction of a foreign gene or sequence.
- DNA damage can be identified directly through, for example, mutations, or indirectly through, for example, increased level and/or activity of a DNA damage process or DNA repair protein.
- the DNA repair protein is a DNA editing enzyme.
- DNA damaging agent refers to any agent that directly or indirectly damages DNA in such a way that homologous recombination could repair the damage.
- resistant cancer As used herein, “cancer is resistant” and “refractory cancer” refers to cancer that does not respond to a treatment. For example, the cancer may be resistant at the beginning of treatment, or it may become resistant during treatment.
- the treatment resistance can be occurred by different mechanisms and examples include individual genetic differences, multi-drug resistance, cell death inhibiting (apoptosis suppression), altering in the drug metabolism, epigenetic and drug targets, enhancing DNA repair and gene amplification.
- a therapeutically effective amount refers to an amount of a therapeutic agent, such as a compound of the present disclosure, that, when administered to a subject, such as a human, is sufficient to effect treatment.
- the pharmaceutical composition can be formulated for particular routes of administration such as oral administration, parenteral administration (e.g., intravenous administration) and rectal administration, etc.
- the pharmaceutical compositions of the present disclosure can be made up in a solid form (including, without limitation, capsules, tablets, pills, granules, powders or suppositories), or in a liquid form (including, without limitation, solutions, suspensions or emulsions).
- the pharmaceutical compositions can be subjected to conventional pharmaceutical operations, such as sterilization, and/or can contain conventional inert diluents, lubricating agents, or buffering agents, as well as adjuvants, such as preservatives, stabilizers, wetting agents, emulsifiers and buffers, etc.
- compositions intended for oral use are prepared according to any method known in the art for the manufacture of pharmaceutical compositions and such compositions can contain one or more agents selected from the group consisting of sweetening agents, flavoring agents, coloring agents and preserving agents in order to provide pharmaceutically elegant and palatable preparations.
- Tablets may contain the active ingredient in admixture with nontoxic pharmaceutically acceptable excipients which are suitable for the manufacture of tablets.
- excipients are, for example, inert diluents, such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch or alginic acid; binding agents, for example, starch, gelatin or acacia; and lubricating agents, for example magnesium stearate, stearic acid or talc.
- the tablets are uncoated or coated by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period.
- a time delay material such as glyceryl monostearate or glyceryl distearate can be employed.
- compositions comprise a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) in the form of an aqueous isotonic solution or suspension, and certain suppositories comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) are advantageously prepared from fatty emulsions or suspensions.
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- the present disclosure further provides anhydrous pharmaceutical compositions and dosage forms comprising a compound provided herein (e.g., a compound of Formula I, or a subformula thereof), or a pharmaceutically acceptable salt thereof, since water may facilitate the degradation of certain compounds.
- Anhydrous pharmaceutical compositions and dosage forms of the disclosure can be prepared using anhydrous or low moisture- containing ingredients and low moisture or low humidity conditions.
- An anhydrous pharmaceutical composition may be prepared and stored such that its anhydrous nature is maintained. Accordingly, anhydrous compositions are packaged using materials known to prevent exposure to water such that they can be included in suitable formulary kits.
- a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) is typically formulated into pharmaceutical dosage forms to provide an easily controllable dosage of the drug and to give the patient an elegant and easily handleable product.
- the dosage regimen for the compounds of the present disclosure will, of course, vary depending upon known factors, such as the pharmacodynamic characteristics of the particular agent and its mode and route of administration; the species, age, sex, health, medical condition, and weight of the recipient; the nature and extent of the symptoms; the kind of concurrent treatment; the frequency of treatment; the route of administration; the renal and hepatic function of the patient; and the effect desired.
- Compounds described herein may be administered in a single daily dose, or the total daily dosage may be administered in divided doses, e.g., two, three, or four times daily.
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- one or more therapeutically active agents e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- one or more therapeutically active agents e.g., independently selected from an anti-cancer agent (e.g., chemotherapeutic agent), anti-allergic agent, anti-emetic, pain reliever, immunomodulator and cytoprotective agent to treat cancer.
- an anti-cancer agent e.g., chemotherapeutic agent
- anti-allergic agent e.g., anti-allergic agent
- anti-emetic anti-emetic
- pain reliever e.g., immunomodulator and cytoprotective agent
- cytoprotective agent e.g., cytoprotective agent to treat cancer.
- combination therapy refers to the administration of two or more therapeutic agents to treat a disease, disorder or condition described herein. Such administration encompasses co-administration of the therapeutic agents in a substantially simultaneous manner, such as in a single capsule having
- a further embodiment is a pharmaceutical combination
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- a pharmaceutical combination can further comprise one or more pharmaceutically acceptable carriers, such as one or more of the pharmaceutically acceptable carriers described herein.
- Examples of therapies for use in combination with a compound of the present disclosure include standard of care therapies and/or regimens (e.g., standard of care agents), such as first-line standard of care therapies (e.g., chemotherapies) or last-line standard of care therapies (e.g., chemotherapies).
- Standard of care therapies are therapies that a clinician should use for a certain type of patient, illness and/or clinical circumstance.
- organizations such as National Comprehensive Cancer Network (NCCN) publish guidelines and/or treatment algorithms setting forth best practices for treatment of certain patients, illnesses and/or clinical circumstances. See nccn.org. These guidelines often establish, set forth and/or summarize standard of care therapies.
- NCCN National Comprehensive Cancer Network
- a compound of the present disclosure is administered in combination with a standard of care therapy for ovarian cancer.
- standard of care therapies for ovarian cancer include a platinum analogue (e.g., cisplatin, paclitaxel, carboplatin) or a combination including a platinum analogue (e.g., docetaxel and carboplatin; paclitaxel and carboplatin; carboplatin and liposomal doxorubicin (dox); paclitaxel, carboplatin and bevacizumab (bev); carboplatin and gemcitabine (gem)/(bev); carboplatin, liposomal dox and bev; carboplatin, paclitaxel and bev; cisplatin and gemcitabine; oxaliplatin); altretamine; capecitabine; ifosfamide; irinotecan; melphalan; paclitaxel (
- Non-limiting examples of standard of care therapies for ovarian cancer also include a targeted therapy, such as an antibody therapy (e.g., bevacizumab); a PARP inhibitor (e.g., olaparib, rucaparib, niraparib, veliparib, talazoparib); a tyrosine kinase inhibitor (TKI) (e.g, pazopanib); an immunotherapy; an immune checkpoint inhibitor (e.g., PD-1 or PD-L1 inhibitor); pembrolizumab; or a hormone therapy (e.g., tamoxifen, anastrozole, exemestane, letrozole,an LHRH agonist, such as leuprolide acetate, megestrol acetate).
- an antibody therapy e.g., bevacizumab
- PARP inhibitor e.g., olaparib, rucaparib, niraparib, veliparib,
- a compound of the present disclosure is administered in combination with a standard of care therapy for prostate cancer, including castration resistant prostrate cancer.
- standard of care therapies for prostate cancer include PARP inhibitors (e.g., olaparib, rucaparib, niraparib, veliparib, talazoparib), LHRH agonists (e.g., goserelin acetate, histrelin acetate, leuprolide acetate, and triptorelin pamoate); LHRH antagonists (e.g., degarelix); anti-androgen receptors (e.g., bicalutamide, flutamide, nilutamide, enzalutamide, apalutamide, darolutamide); corticosteroids (e.g., prednisone, methylprednisolone, hydrocortisone, dexamethasone); estrogens (e.g., dieth
- PARP inhibitors e.g.,
- brachytherapy refers to radiation therapy delivered by a spatially confined radioactive material inserted into the body at or near a tumor or other proliferative tissue disease site.
- the term is intended without limitation to include exposure to radioactive isotopes (e.g., At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, and radioactive isotopes of Lu).
- Suitable radiation sources for use as a cell conditioner of the present invention include both solids and liquids.
- a compound of the present disclosure can render abnormal cells more sensitive to treatment with radiation for purposes of killing and/or inhibiting the growth of such cells.
- some embodiments include a method for sensitizing abnormal cells in a mammal to treatment with radiation which comprises administering to the mammal an amount of a compound as described herein, which amount is effective insensitizing abnormal cells to treatment with radiation.
- the amount of a compound of the present disclosure in this method can be determined according to the means for ascertaining effective amounts of such compounds and salts described herein.
- standard of care therapy includes radiation therapy.
- DNA damaging agents can also be used in combination with a compound of the present disclosure.
- a further example is bortezomib.
- Yet further examples include gemcitabine, nabpaclitaxel, erlotinib, fluorouracil and FOLFIRINOX (a chemotherapy regimen made up of folinic acid, fluorouracil, irinotecan and oxaliplatin), or any combination of two or more of the foregoing, e.g., to treat pancreatic cancer (e.g., advanced pancreatic cancer, pancreatic ductal adenocarcinoma).
- pancreatic cancer e.g., advanced pancreatic cancer, pancreatic ductal adenocarcinoma
- Anti-cancer agents of particular interest for use in combination with the compounds of the present disclosure include: [00226] Topoisomerase inhibitors, including Type I topoisomerase inhibitors, such as irinotecan, topotecan, and camptothecin, and Type 2 topoisomerase inhibitors, such as etoposide, doxorubicin, and epirubicin. [00227] Poly(ADP-ribose) polymerase (PARP) inhibitors, such as olaparib, rucaparib, niraparib, talazoparib, veliparib, pamiparib and iniparib.
- PARP Poly(ADP-ribose) polymerase
- Anti-angiogenesis agents include, for example, MMP-2 (matrix-
- COX-II inhibitors examples include CELEBREXTM (alecoxib), valdecoxib, and rofecoxib.
- useful matrix metalloproteinase inhibitors are described in WO 96/33172 (published October 24,1996), WO 96/27583 (published March 7,1996), European Patent Application No.97304971.1 (filed July 8,1997), European Patent Application No.99308617.2 (filed October 29, 1999), WO 98/07697 (published February 26,1998), WO 98/03516 (published January 29,1998), WO 98/34918 (published August 13,1998), WO 98/34915 (published August 13,1998), WO 98/33768 (published August 6,1998), WO 98/30566 (published July 16, 1998), European Patent Publication 606,046 (published July 13,1994), European Patent Publication 931, 788 (published July 28,1999), WO 90/05719 (published May 31,1990), WO 99/52910 (published October 21,1999), WO 99/5
- Embodiments of MMP-2 and MMP-9 inhibitors include those that have little or no activity inhibiting MMP-1.
- MMP-2 and/or AMP-9 are those that selectively inhibit MMP-2 and/or AMP-9 relative to the other matrix-metalloproteinases (i.e., MAP-1, MMP-3, MMP-4, MMP-5, MMP-6, MMP- 7, MMP-8, MMP-10, MMP-ll, MMP-12, and MMP-13).
- MMP inhibitors useful in some embodiments are AG-3340, RO 323555, and RS 13-0830.
- Autophagy inhibitors include, but are not limited to chloroquine, 3-methyladenine, hydroxychloroquine (PlaquenilTM), bafilomycin A1, 5-amino-4-imidazole carboxamide riboside (AICAR), okadaic acid, autophagy-suppressive algal toxins which inhibit protein phosphatases of type 2A or type 1, analogues of cAMP, and drugs which elevate cAMP levels such as adenosine, LY204002, N6-mercaptopurine riboside, and vinblastine.
- antisense or siRNA that inhibits expression of proteins including but not limited to ATG5 (which are implicated in autophagy), may also be used.
- HDAC proteins may be grouped into classes based on homology to yeast HDAC proteins with Class I made up of HDAC1, HDAC2, HDAC3 and HDAC 8; Class IIa made up of HDAC4, HDAC5, HDAC7 and HDAC 9; Class IIb made up of HDAC6 and HDAC10; and Class IV made up of HDAC11.
- the HDAC inhibitor is trichostatin A, vorinostat (Proc. Natl. Acad. Sci. U.S.A.1998 Mar 17;95(6):3003- 7), givinostat, abexinostat (Mol. Cancer Ther.2006 May;5(5):1309-17), belinostat (Mol.
- Platelet-derived growth factor (PDGF) receptor inhibitors imatinib (Gleevec®); linifanib (N-[4-(3-amino-1H-indazol-4-yl)phenyl]-N'-(2-fluoro-5-methylphenyl)urea, also known as ABT 869, available from Genentech); sunitinib malate (Sutent®); quizartinib (AC220, CAS 950769-58-1); pazopanib (Votrient®); axitinib (Inlyta®); sorafenib (Nexavar®); vargatef (BIBF1120, CAS 928326-83-4); telatinib (BAY57-9352, CAS 332012-40-5); vatalanib dihydrochloride (PTK787, CAS 212141-51-0); and motesanib diphosphate (AMG706, CAS 857876-30-3,
- B-RAF inhibitors regorafenib (BAY73-4506, CAS 755037-03-7); tuvizanib (AV951, CAS 475108-18-0); vemurafenib (ZELBORAF®, PLX-4032, CAS 918504-65-1); encorafenib (also known as LGX818); 1-methyl-5-[[2-[5-(trifluoromethyl)-1H-imidazol-2- yl]-4-pyridinyl]oxy]-N-[4-(trifluoromethyl)phenyl-1H-benzimidazol-2-amine (RAF265, CAS 927880-90-8); 5-[1-(2-hydroxyethyl)-3-(pyridin-4-yl)-1H-pyrazol-4-yl]-2,3-dihydroinden-1- one oxime (GDC-0879, CAS 905281-76-7); 5-[2-[4-[2-(d
- chemotherapeutic agents include chemotherapeutic agents, cytotoxic agents, and non-peptide small molecules such as Gleevec® (Imatinib Mesylate), Velcade® (bortezomib), Casodex (bicalutamide), Iressa® (gefitinib), and Adriamycin as well as a host of chemotherapeutic agents.
- anti-cancer drugs include Herceptin®, Avastin®, Erbitux®, Rituxan®, Taxol®, Arimidex®, Taxotere®, ABVD, AVICINE, Abagovomab, Acridine carboxamide, Adecatumumab, 17-N-Allylamino-17- demethoxygeldanamycin, Alpharadin, Alvocidib, 3-Aminopyridine-2-carboxaldehyde thiosemicarbazone, Amonafide, Anthracenedione, Anti-CD22 immunotoxins, Antineoplastic, Antitumorigenic herbs, Apaziquone, Atiprimod, Azathioprine, Belotecan, Bendamustine, BIBW 2992, Biricodar, Brostallicin, Bryostatin, Buthionine sulfoximine, CBV (chemotherapy), Calyculin, cell-cycle nonspecific antine
- chemotherapeutic cell conditioners include anti-hormonal agents that act to regulate or inhibit hormone action on tumors such as anti-estrogens including for example tamoxifen, (NolvadexTM), raloxifene, aromatase inhibiting 4(5)- imidazoles, 4hydroxytamoxifen, trioxifene, keoxifene, LY 117018, onapristone, and toremifene (Fareston); and anti-androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine
- anti-estrogens
- Non-limiting examples of therapeutic agents that can be used in combinations with a compound as described herein are mTOR inhibitors.
- exemplary mTOR inhibitors include, e.g., temsirolimus; ridaforolimus (formally known as deferolimus, (1R,2R,4S)-4- [(2R)-2 [(1R,9S,12S,15R,16E,18R,19R,21R, 23S,24E,26E,28Z,30S,32S,35R)- 1,18- dihydroxy-19,30-dimethoxy-15,17,21,23, 29,35-hexamethyl-2,3,10,14,20-pentaoxo-11,36- dioxa-4- azatricyclo[30.3.1.0 4,9 ] hexatriaconta-16,24,26,28-tetraen-12-yl]propyl]-2- methoxycyclohexyl dimethylphosphinate, also known as AP
- WO 03/064383 everolimus (Afinitor® or RAD001); rapamycin (AY22989, Sirolimus®); simapimod (CAS 164301-51-3); emsirolimus, (5- ⁇ 2,4- Bis[(3S)-3-methylmorpholin-4-yl]pyrido[2,3-d]pyrimidin-7-yl ⁇ -2- methoxyphenyl)methanol (AZD8055); 2-Amino-8-[trans-4-(2-hydroxyethoxy)cyclohexyl]-6-(6- methoxy-3-pyridinyl)- 4-methyl-pyrido[2,3-d]pyrimidin-7(8H)-one (PF04691502, CAS 1013101-36-4); and N 2 - [1,4-dioxo-4-[[4-(4-oxo-8-phenyl-4H-1-benzopyran-2-yl)morpholinium-4- yl]methoxy]butyl]-L
- a compound of the present disclosure is administered to a subject in need thereof in combination with a PARP inhibitor, for example, to treat prostate cancer (e.g., castration-resistant prostate cancer).
- a compound of the present disclosure is administered to a subject in need thereof in combination with an androgen receptor inhibitor (e.g., enzalutamide), for example, to treat prostate cancer (e.g., castration- resistant prostate cancer).
- an androgen receptor inhibitor e.g., enzalutamide
- a compound of the present disclosure is administered to a subject in need thereof in combination with a proteasome inhibitor (e.g., bortezomib), for example, to treat multiple myeloma.
- anti-emetics can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) to prevent nausea (upper stomach) and vomiting.
- nivolumab also known as MDX-1106, MDX-1106-04, ONO-4538, BMS-936558, or OPDIVO®
- other anti-PD-1 antibodies as disclosed in US 8,008,449 and WO 2006/121168, incorporated by reference in their entirety
- cemiplimab LIBTAYO®
- spartalizumab PDR001
- pidilizumab CureTech
- MEDI0680 Medimmune
- cemiplimab REGN2810
- TSR-042 dostarlimab
- PF-06801591 sinitilimab
- toripalimab tislelizumab
- BGB-A317 camrelizumab
- anti-PD-1 antibody molecules include those described, e.g., in WO 2015/112800, WO 2016/092419, WO 2015/085847, WO 2014/179664, WO 2014/194302, WO 2014/209804, WO 2015/200119, US 8,735,553, US 7,488,802, US 8,927,697, US 8,993,731, and US 9,102,727, incorporated by reference in their entirety.
- the PD-1 inhibitor is an anti-PD-1 antibody molecule as described in US 2015/0210769, published on July 30, 2015, entitled “Antibody Molecules to PD-1 and Uses Thereof,” incorporated by reference in its entirety.
- Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure also include: PD-L1 inhibitors, such as atezolizumab (also known as MPDL3280A, RG7446, RO5541267, YW243.55.S70, or TECENTRIQ®) and other anti- PD-L1 antibodies as disclosed in US 8,217,149, incorporated by reference in its entirety, avelumab (BAVENCIO® also known as MSB0010718C) and other anti-PD-L1 antibodies as disclosed in WO 2013/079174, incorporated by reference in its entirety, durvalumab (IMFINZI® or MEDI4736) and other anti-PD-L1 antibodies as disclosed in US 8,779,108, incorporated by reference in its entirety), FAZ053 (Novartis), and BMS-936559 (Bristol- Myers Squibb).
- atezolizumab also known as MPDL3280A, RG7446, RO5541267
- the anti-PD-L1 antibody molecule is BMS-936559 (Bristol-Myers Squibb), also known as MDX-1105 or 12A4.
- BMS-936559 and other anti-PD-L1 antibodies are disclosed in US 7,943,743 and WO 2015/081158, incorporated by reference in their entirety.
- the immune checkpoint inhibitor aredrugs that target CTLA-4, such as ipilimumab (YERVOY®), tremelimumab, ALPN-202 (Alpine Immune Sciences), RP2 (Replimune), BMS-986249 (Bristol-Myers Squibb), BMS- 986218 (Bristol-Myers Squibb), zalifrelimab (Agenus, Ludwig Institute for Cancer Research, UroGen Pharma, Recepta Biopharma), BCD-217 (BIOCAD), Onc-392 (Pfizer, OncoImmune), IBI310 (Innovent Biologics), KN046 (Alphamab), MK-1308 (Merck & Co), REGN4659 (Regeneron Pharmaceuticals), XmAb20717 (Xencor), XmAb22841 (Xencor), Anti-CTLA-4 NF (Bristol-Myers Squibb), MEDI5752 (AstraZeneca), A
- the CTLA-4 inhibitor is ipilimumab. In other embodiments, the CTLA4 inhibitor is tremelimumab.
- Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure also include: LAG-3 inhibitors.
- the LAG-3 inhibitor is chosen from LAG525 (Novartis), BMS-986016 (Bristol-Myers Squibb), or TSR- 033 (Tesaro).
- the LAG-3 inhibitor is an anti-LAG-3 antibody molecule.
- the LAG-3 inhibitor is an anti-LAG-3 antibody molecule as disclosed in US 2015/0259420, published on September 17, 2015, entitled “Antibody Molecules to LAG- 3 and Uses Thereof,” incorporated by reference in its entirety.
- the anti- LAG-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP050-Clone I or BAP050-Clone J disclosed in US 2015/0259420.
- the anti-LAG-3 antibody molecule is BMS-986016 (Bristol-Myers Squibb), also known as BMS986016.
- the anti-LAG-3 antibody molecule is TSR-033 (Tesaro).
- the anti-LAG-3 antibody molecule is IMP731 or GSK2831781 (GSK and Prima BioMed).
- IMP731 and other anti-LAG-3 antibodies are disclosed in WO 2008/132601 and US 9,244,059, incorporated by reference in their entirety.
- the anti-LAG-3 antibody molecule is IMP761 (Prima BioMed).
- anti-LAG-3 antibodies include those described, e.g., in WO 2008/132601, WO 2010/019570, WO 2014/140180, WO 2015/116539, WO 2015/200119, WO 2016/028672, US 9,244,059, US 9,505,839, incorporated by reference in their entirety.
- the anti-LAG-3 inhibitor is a soluble LAG-3 protein, e.g., IMP321 (Prima BioMed), e.g., as disclosed in WO 2009/044273, incorporated by reference in its entirety.
- Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure also include: Tim-3 inhibitors.
- the TIM-3 inhibitor is MGB453 (Novartis) or TSR-022 (Tesaro). In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule. In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule as disclosed in US 2015/0218274, published on August 6, 2015, entitled “Antibody Molecules to TIM-3 and Uses Thereof,” incorporated by reference in its entirety. In one embodiment, the anti-TIM-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of ABTIM3-hum11 or ABTIM3-hum03 disclosed in US 2015/0218274.
- the anti-TIM-3 antibody molecule is TSR-022 (AnaptysBio/Tesaro). In one embodiment, the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or light chain sequence of APE5137 or APE5121. APE5137, APE5121, and other anti- TIM-3 antibodies are disclosed in WO 2016/161270, incorporated by reference in its entirety. In one embodiment, the anti-TIM-3 antibody molecule is the antibody clone F38-2E2.
- anti-TIM-3 antibodies include those described, e.g., in WO 2016/111947, WO 2016/071448, WO 2016/144803, US 8,552,156, US 8,841,418, and US 9,163,087, incorporated by reference in their entirety.
- RAD51 depletion leads to accumulation of self-DNA in cytoplasm and upregulation of innate immune response pathway genes (PMID: 28334891, the entire content of which is incorporated herein by reference).
- SCLC small cell lung cancer
- a compound of the present disclosure is administered in combination with an immune checkpoint inhibitor described herein and/or (e.g., or) an agent selected from gemcitabine, nabpaclitaxel, erlotinib, fluorouracil or FOLFIRINOX (a chemotherapy regimen made up of folinic acid, fluorouracil, irinotecan and oxaliplatin), or any combination of two or more of the foregoing, e.g., to treat pancreatic cancer (e.g., advanced pancreatic cancer, pancreatic ductal adenocarcinoma).
- an immune checkpoint inhibitor described herein and/or e.g., or an agent selected from gemcitabine, nabpaclitaxel, erlotinib, fluorouracil or FOLFIRINOX (a chemotherapy regimen made up of folinic acid, fluorouracil, irinotecan and oxaliplatin), or any combination of two or more of the foregoing, e
- an immune checkpoint inhibitor is selected from a PD-1 inhibitor, PD-L1 inhibitor, CTLA-4 inhibitor, LAG-3 inhibitor or TIM-3 inhibitor. In some embodiments, an immune checkpoint inhibitor is selected from a PD-1 inhibitor, PD-L1 inhibitor or CTLA-4 inhibitor. In some embodiments, an immune checkpoint inhibitor is a PD-1 inhibitor. In some embodiments, an immune checkpoint inhibitor is a PD-L1 inhibitor. In some embodiments, an immune checkpoint inhibitor is a CTLA-4 inhibitor.
- kits comprising two or more separate pharmaceutical compositions, at least one of which contains a compound of the present disclosure is provided.
- the kit comprises a pharmaceutical composition comprising a compound of the present disclosure and a pharmaceutical composition comprising an additional therapeutic agent identified herein for use in combination with a compound of the present disclosure.
- the kit comprises means for separately retaining said compositions, such as a container, divided bottle, or divided foil packet.
- kits of the present disclosure may be used for administering different dosage forms, for example, oral and parenteral, for administering the separate compositions at different dosage intervals, or for titrating the separate compositions against one another.
- the kit of the present disclosure typically comprises directions for administration, e.g., to treat a disease, disorder or condition described herein.
- a compound of the present disclosure may also be used to advantage in combination with known therapeutic processes, for example, the administration of hormones or especially radiation.
- a compound of the present disclosure may in particular be used as a radiosensitizer, especially for the treatment of tumors which exhibit poor sensitivity to radiotherapy.
- the compound of the present disclosure and the other therapeutic agent may be manufactured and/or formulated by the same or different manufacturers.
- the compound of the present disclosure and the other therapeutic agent may be brought together into a combination therapy: (i) prior to release of the combination product to physicians (e.g., in the case of a kit comprising the compound of the present disclosure and the other therapeutic agent); (ii) by the physician (or under the guidance of a physician) shortly before administration; (iii) in the patient themselves, e.g., during sequential administration of the compound of the present disclosure and the other therapeutic agent.
- the pharmaceutical composition (or formulation) for application may be packaged in a variety of ways depending upon the method used for administering the drug.
- an article for distribution includes a container having deposited therein the pharmaceutical formulation in an appropriate form.
- Suitable containers are well-known to those skilled in the art and include materials such as bottles (plastic and glass), sachets, ampoules, plastic bags, metal cylinders, and the like.
- the container may also include a tamper-proof assemblage to prevent indiscreet access to the contents of the package.
- the container has deposited thereon a label that describes the contents of the container. The label may also include appropriate warnings.
- the pharmaceutical composition or combination of the present disclosure can be in a unit dosage form, e.g., containing from about 1 to about 1000 mg of active ingredient(s) for a subject of from about 50 to about 70 kg, or from about 1 to about 500 mg, from about 1 to about 250 mg, from about 1 to about 150 mg, from about 0.5 to about 100 mg, or from about 1 to about 50 mg of active ingredient(s) for a subject of from about 50 to about 70 kg.
- the therapeutically effective dosage of a compound, pharmaceutical composition or pharmaceutical combination is dependent on the species of the subject, the body weight, age and individual condition of the subject, and the disease, disorder or condition or the severity thereof being treated.
- the above-cited dosage properties may be demonstrable in in vitro and in vivo tests using advantageously mammals, e.g., mice, rats, dogs, monkeys, or isolated organs, tissues and preparations thereof.
- the compounds of the present disclosure can be applied in vitro in the form of solutions, e.g., aqueous solutions, and in vivo either enterally, parenterally, advantageously intravenously, e.g., as a suspension or in aqueous solution.
- the dosage in vitro may range between about 10 -3 molar and 10 -9 molar concentrations.
- a therapeutically effective amount in vivo may range depending on the route of administration, among other things, between about 0.1 mg/kg to about 500 mg/kg, or between about 1 mg/kg to about 100 mg/kg.
- the concentration of one or more therapeutic agents provided in a pharmaceutical composition is less than 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19%, 18%, 17%, 16%, 15%,14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%,
- the concentration of one or more therapeutic agents provided in a pharmaceutical composition is greater than 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19.75%, 19.50%, 19.25% 19%, 18.75%, 18.50%, 18.25% 18%, 17.75%, 17.50%, 17.25% 17%, 16.75%, 16.50%, 16.25% 16%, 15.75%, 15.50%, 15.25% 15%, 14.75%, 14.50%, 14.25% 14%, 13.75%, 13.50%, 13.25% 13%, 12.75%, 12.50%, 12.25% 12%, 11.75%, 11.50%, 11.25% 11%, 10.75%, 10.50%, 10.25% 10%, 9.75%, 9.50%, 9.25% 9%, 8.75%, 8.50%, 8.25% 8%, 7.75%, 7.50%, 7.25% 7%, 6.75%, 6.50%, 6.25% 6%, 5.75%, 5.50%, 5.25% 5%, 4.75%,
- the concentration of one or more therapeutic agents provided in a pharmaceutical composition is in the range from about 0.0001% to about 50%, about 0.001% to about 40 %, about 0.01% to about 30%, about 0.02% to about 29%, about 0.03% to about 28%, about 0.04% to about 27%, about 0.05% to about 26%, about 0.06% to about 25%, about 0.07% to about 24%, about 0.08% to about 23%, about 0.09% to about 22%, about 0.1% to about 21%, about 0.2% to about 20%, about 0.3% to about 19%, about 0.4% to about 18%, about 0.5% to about 17%, about 0.6% to about 16%, about 0.7% to about 15%, about 0.8% to about 14%, about 0.9% to about 12%, about 1% to about 10% w/w, w/v or v/v.
- the concentration of one or more therapeutic agents provided in a pharmaceutical composition is in the range from about 0.001% to about 10%, about 0.01% to about 5%, about 0.02% to about 4.5%, about 0.03% to about 4%, about 0.04% to about 3.5%, about 0.05% to about 3%, about 0.06% to about 2.5%, about 0.07% to about 2%, about 0.08% to about 1.5%, about 0.09% to about 1%, about 0.1% to about 0.9% w/w, w/v or v/v.
- Methods of Use [00293] It has now been found that the compounds of the present disclosure decrease a level of RAD51.
- a cell e.g., a cell expressing RAD51; a cancer cell, such as a cancer cell expressing RAD51, including a cancer cell of any of the cancers described herein
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof.
- the cell is a cancer cell.
- the cell is in a subject, such as a human.
- the method further comprises contacting the cell (e.g., cancer cell) with one or more additional therapeutic agents.
- a cell e.g., cancer cell
- additional therapeutic agents e.g., a cell having a cancer, including any of the cancers described herein.
- methods of decreasing a level of RAD51 in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof).
- Also provided herein are methods of promoting endoplasmic reticulum (ER) stress in a cell comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof).
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof.
- ER stress can be caused by ROS.
- the ER stress is caused by ROS.
- promoting ER stress in a cell is inducing ER stress in the cell.
- promoting ER stress includes increasing a level of ROS in the cell, for example, by contacting the cell with an agent that increases levels of ROS in the cell.
- the cell is in a subject, such as a human.
- methods of promoting the Unfolded Protein Response (UPR) in a cell comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof).
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof.
- the promoting the UPR in a cell is activating the UPR in the cell.
- the UPR is induced by ER stress.
- the cell is in a subject, such as a human.
- Also provided herein are methods of promoting degradation of a DNA repair protein selected from RAD51, MGMT and/or MPG in a cell (e.g., a cell expressing RAD51, MGMT and/or MPG; a cancer cell, such as a cancer cell expressing RAD51, MGMT and/or MPG, including a cancer cell of any of the cancers described herein), comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof).
- a compound of the present disclosure e.g., a compound of Formula I, or a
- the cell is in a subject, such as a human.
- the DNA repair protein is RAD51.
- a method described herein comprises contacting a cell, such as a cancer cell, with a compound of the present disclosure, it will be understood that the method can be conducted in vitro, ex vivo or in vivo.
- some embodiments comprise contacting the cell in vitro.
- Some embodiments comprise contacting the cell ex vivo.
- Some embodiments comprise contacting the cell in vivo as, for example, when the cell is in a subject, such as a human.
- the following biomarkers relate to modulating (e.g., promoting) unfolded protein response, ER stress and/or degradation of DNA repair proteins, such as RAD51: phospho-eIF2a, XBP1 splicing, ATF4 expression, and gene expression signature driven by ATF4, CHOP, XBP1s, and ATF6 transcription factors.
- the method increases one or more of phosphorylation of eIF2a, levels of phospho-eIF2a, XBP1 splicing, ATF4 expression and gene expression signature driven by ATF4, CHOP, XBP1s, and ATF6 transcription factors.
- cancers are a solid tumor cancer.
- the cancer comprises a solid tumor (e.g., a colorectal, breast, prostate, lung, pancreatic, renal or ovarian tumor). Accordingly, in some embodiments, the cancer is a solid tumor cancer.
- the cancer is selected from one or more of a cancer of the pulmonary system, a brain cancer, a cancer of the gastrointestinal tract, a skin cancer, a genitourinary cancer, head and neck cancer, a sarcoma, a carcinoma, and a neuroendocrine cancer.
- the solid tumor cancer is breast cancer, bladder cancer, endometrial cancer, esophageal cancer, liver cancer, pancreatic cancer, lung cancer, cervical cancer, colon cancer, colorectal cancer, gastric cancer, kidney cancer, ovarian cancer, prostate cancer, testicular cancer, uterine cancer, a viral-induced cancer, melanoma or sarcoma.
- the cancer is bladder cancer.
- Hematologic cancers that can be treated according to the methods described herein include leukemias (e.g., acute leukemias, such as acute myeloid leukemia or acute lymphocytic leukemia; chronic leukemias, such as chronic myeloid leukemia or chronic lymphocytic leukemia), lymphomas (e.g., B-cell lymphoma, T- cell lymphoma) and multiple myeloma.
- the cancer is a leukemia.
- the cancer is an acute leukemia.
- the cancer is acute myeloid leukemia or acute lymphocytic leukemia.
- the cancer is a chronic leukemia.
- the cancer is chronic myeloid leukemia or chronic lymphocytic leukemia.
- the cancer is a lymphoma.
- the hematologic cancer is selected from multiple myeloma, myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), acute lymphocytic leukemia, lymphocytic lymphoma, mycosis fungoides, chronic lymphogenous leukemia, chronic lymphocytic leukemia (CLL), mantle cell lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma or myelofibrosis.
- MDS myelodysplastic syndrome
- AML acute myeloid leukemia
- ALL acute lymphoblastic leukemia
- CLL chronic lymphocytic leukemia
- mantle cell lymphoma diffuse large B-
- the cancer is selected from ovarian cancer, multiple myeloma, pancreatic cancer, prostate cancer, breast cancer, endometrial cancer, colorectal cancer or lymphoma.
- the cancer expresses a BRCA (e.g., BRCA1 and/or BRCA2) variant (e.g., mutant).
- the BRCA variant is a BRCA (loss- of-function) mutant resistant to PARP.
- the cancer is a pre-metastatic cancer. In some embodiments, the cancer is a metastatic cancer.
- the cancer is previously treated, e.g., the compound of the present disclosure is administered, alone or in combination with one or more additional therapies, as a subsequent therapy (e.g., a second-line therapy, a third-line therapy, a last-line therapy).
- a subsequent therapy e.g., a second-line therapy, a third-line therapy, a last-line therapy.
- the cancer is previously untreated as, for example, when the compound of the present disclosure is administered, alone or in combination with one or more additional therapies, as a first-line therapy.
- the method further comprises administering to the subject a subsequent therapy for the cancer (e.g., second-line therapy, third-line therapy, last-line therapy).
- the cancer is resistant.
- Examples of cancer treatable according to the methods described herein include, but are not limited to, adenocarcinoma of the breast, prostate, and colon; all forms of bronchogenic carcinoma of the lung; myeloid; melanoma; hepatoma; neuroblastoma; papilloma; apudoma; choristoma; branchioma; malignant carcinoid syndrome; carcinoid heart disease; and carcinoma (e.g., Walker, basal cell, basosquamous, Brown-Pearce, ductal, Ehrlich tumor, Krebs 2, merkel cell, mucinous, lung cancer (e.g., large cell lung cancer, such as squamous cell carcinoma, non-small cell lung), oat cell, papillary, scirrhous, bronchiolar, bronchogenic, squamous cell, and transitional cell).
- carcinoma e.g., Walker, basal cell, basosquamous, Brown-Pearce, ductal
- cancer treatable according to the methods described herein include, but are not limited to, histiocytic disorders; leukemia; histiocytosis malignant; Hodgkin's disease; hypereosinophilia, immunoproliferative small; non-Hodgkin's lymphoma; plasmacytoma; reticuloendotheliosis; melanoma; chondroblastoma; chondroma; chondrosarcoma; dermatofibrosarcoma protuberans, fibrotic cancer (myelofibrosis, pancreatic cancer (e.g., pancreatic ductal adenocarcinoma), kidney cancer, liver cancer, lung cancer (e.g., large cell lung cancer, such as squamous cell carcinoma), breast cancer (e.g., inflammatory breast cancer), ovarian cancer (e.g., high grade serious ovarian carcinoma), endometrial cancer, uterine cancer, uterine sarcom
- cancers are also contemplated as amenable to treatment: adenoma; cholangioma; cholesteatoma; cyclindroma; cystadenocarcinoma; cystadenoma; granulosa cell tumor; gynandroblastoma; hepatocellular cancer, hepatoma; hidradenoma; islet cell tumor; Leydig cell tumor; papilloma; sertoli cell tumor; theca cell tumor; leiomyoma; leiomyosarcoma; myoblastoma; myomma; myosarcoma; rhabdomyoma; rhabdomyosarcoma; ependymoma; ganglioneuroma; glioma; medulloblastoma; meningioma; neurilemmoma; neuroblastoma; neuroepithelioma; neurofibroma; neuroma
- cancers treatable according to the methods described herein include, but are not limited to, Acute Lymphoblastic Leukemia (ALL); Acute Myeloid Leukemia (AML); Adrenocortical Carcinoma; Adrenocortical Carcinoma, Childhood; AIDS- Related Cancer (e.g., Kaposi Sarcoma, AIDS-Related Lymphoma, Primary CNS Lymphoma); Cancer of the anal region; Anal Cancer; Appendix Cancer; Astrocytomas, Childhood; Atypical Teratoid/Rhabdoid Tumor, Childhood, Central Nervous System (CNS); Neoplasms of the CNS (e.g., primary CNS lymphoma, spinal axis tumors, medulloblastoma, brain stem gliomas or pituitary adenomas), Barrett’s esophagus (e.g., pre-malignant syndrome), and mycoses fungoides, Basal Cell Carcinoma of the Skin; Bile Du
- Metastases of the aforementioned cancers can also be treated in accordance with the methods described herein.
- RAD51 has also been implicated in suppression of innate immunity and immune signaling. See PMID: 28334891, the entire content of which is incorporated herein by reference.
- methods of treating an immune deficiency, including an autoimmune disease comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof).
- Non-limiting examples of immune deficiencies are Autoimmune Lymphoproliferative Syndrome (ALPS), Autoimmune polyglandular syndrome type 1 (APS- 1), BENTA Disease, Caspase Eight Deficiency State (CEDS), Chronic Granulomatous Disease (CGD), Common Variable Immunodeficiency (CVID), Congenital Neutropenia Syndromes, CTLA4 Deficiency, DOCKS Deficiency, GATA2 Deficiency, Glycosylation Disorders With Immunodeficiency, hyper-immunoglobulin E syndrome (HIES), Hyper- Immunoglobulin M (Hyper-IgM) Syndromes, Leukocyte adhesion deficiency (LAD), LRBA deficiency, PB Kinase disease, PLCG2-associated antibody deficiency and immune dysregulation (PLAID), severe combined immunodeficiency (SCID), STAT3 gain-of- function disease, warts, hypogammaglobulinemia, infections, and myeloka
- Double strand breaks and defective DNA damage response more broadly, are thought to underlie neurodegeneration. See PMID: 25033177, the entire content of which is incorporated herein by reference. Accordingly, also provided herein are methods of treating a neurodegenerative disorder in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof).
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof.
- Non-limiting examples of neurodegenerative disorders are multiple sclerosis, Parkinson's disease (PD), Alzheimer's disease (AD), Dentatorubropallidoluysian atrophy (DRPLA), Huntington's Disease (HD), Spinocerebellar ataxia Type 1 (SCAl), Spinocerebellar ataxia Type 2 (SCA2), Spinocerebellar ataxia Type 3 (SCA3), Spinocerebellar ataxia 6 (SCA6), Spinocerebellar ataxia Type 7 (SCA 7), Spinocerebellar ataxia Type 8 (SCA8), Spinocerebellar ataxia Type 12 (SCA12), Spinocerebellar ataxia Type 17 (SCAl 7), Spinobulbar Muscular Ataxia/Kennedy Disease (SBMA), Fragile X syndrome (FRAXA), Fragile XE mental retardation (FRAXE), and Myotonic dystrophy (DM).
- PD Parkinson's disease
- AD Alzheimer
- the method comprises determining whether a subject has an increased level of DNA damage; and administering to the subject a therapeutically effective amound of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) if it is determined that the subject has an increased level of DNA damage.
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- the method comprises providing a subject determined to have an an increased level of a DNA repair protein (e.g., RAD51); and administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing).
- a DNA repair protein e.g., RAD51
- a therapeutically effective amount of a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing.
- the increased level of the DNA repair protein results from the DNA repair protein being upregulated.
- the method comprises determining whether a subject has an increased level of a DNA repair protein (e.g., RAD51); and administering to the subject a therapeutically effective amound of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) if it is determined that the subject has an increased level of the DNA repair protein.
- a DNA repair protein e.g., RAD51
- a therapeutically effective amound of a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing
- the increased level of the DNA repair protein results from the DNA repair protein being upregulated.
- the method comprises providing a subject determined to have an an increased level of RAD51; and administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing).
- a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing.
- the increased level of RAD51 results from RAD51 being upregulated.
- the method comprises determining whether a subject has an increased level of RAD51; and administering to the subject a therapeutically effective amound of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) if it is determined that the subject has an increased level of RAD51.
- a therapeutically effective amound of a compound of the present disclosure e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing.
- the increased level of RAD51 results from RAD51 being upregulated.
- a therapeutically effective amount of a therapeutic agent (e.g., a compound of the present disclosure) to be administered to a subject in accordance with the methods described herein can be determined by a clinician of ordinary skill using the guidance provided herein and other methods known in the art.
- suitable dosages may range, depending on the route of administration, among other things, from about 0.1 mg/kg to about 500 mg/kg, or from about 1 mg/kg to about 100 mg/kg.
- a compound of the present disclosure can be administered via a variety of routes of administration, including, for example, oral, dietary, topical, transdermal, rectal, parenteral (e.g., intra-arterial, intravenous, intramuscular, subcutaneous injection, intradermal injection), intravenous infusion and inhalation (e.g., intrabronchial, intranasal or oral inhalation, intranasal drops) routes of administration, depending on the compound and the particular disease to be treated. Administration can be local or systemic as indicated. The preferred mode of administration can vary depending on the particular compound chosen. In some embodiments, the compound of the present disclosure is administered orally. In some embodiments, the compound of the present disclosure is administered intravenously.
- parenteral e.g., intra-arterial, intravenous, intramuscular, subcutaneous injection, intradermal injection
- intravenous infusion and inhalation e.g., intrabronchial, intranasal or oral inhalation, intranasal drops
- a method described herein further comprises administering to the subject a DNA damaging agent, for example, radiation, a topoisomerase inhibitor, a PARP inhibitor, a DNA crosslinking agent, or a standard of care agent that induces DNA damage, such as a DNA crosslinking agent.
- a method described herein further comprises administering to the subject a DNA damaging agent, for example, radiation, a topoisomerase inhibitor, a PARP inhibitor, a DNA crosslinking agent.
- a method described herein further comprises administering to the subject an agent that promotes (e.g., induces) ER stress, for example, an agent that increases levels of ROS or a proteasome inhibitor.
- a method described herein further comprises administering to the subject a standard of care agent, such as any of the standard of care agents described herein.
- a method described herein further comprises administering to the subject one or more of FOLFIRINOX, modified FOLFIRINOX regimen, gemcitabine and abraxane, gemcitibine and capecitabine, olaparib, gemcitabine and erlotinib, gemcitabine, docetaxel and capecitabine, larotrectinib or pembrolizumab, e.g., for the treatment of pancreatic cancer.
- the compound of the present disclosure can be administered before, after or concurrently with the other therapy (e.g., additional therapeutic agent(s)).
- the compound of the present disclosure and other therapeutic agent(s) can be in separate formulations or the same formulation.
- the compound of the present disclosure and other therapy can be administered sequentially (e.g., as separate compositions) within an appropriate time frame as determined by a skilled clinician (e.g., a time sufficient to allow an overlap of the pharmaceutical effects of the compound of the present disclosure and the other therapy).
- the compounds of the present disclosure in free form or in pharmaceutically acceptable salt form, exhibit valuable pharmacological properties, which can be demonstrated at least by using any one of the test procedures described herein.
- EXEMPLIFICATION [00333]
- the compounds of the present disclosure can be prepared in a number of ways known to one skilled in the art of organic synthesis in view of the methods, reaction schemes and examples provided herein.
- the compounds of the present disclosure can be synthesized using the methods described below, together with synthetic methods known in the art of synthetic organic chemistry, or by variations thereon, as appreciated by those skilled in the art. Preferred methods include, but are not limited to, those described below.
- the reactions are performed in a solvent or solvent mixture appropriate to the reagents and materials employed and suitable for the transformations being affected.
- Protecting groups incorporated in making of the compounds of the present disclosure may be shown as one regioisomer but may also exist as a mixture of regioisomers.
- the following abbreviations used hereinbelow have the corresponding meanings: ACN acetonitrile; Ac 2 O acetic anhydride; Aq aqueous; BSA bovine serum albumin; BINAP 2,2'-Bis(diphenylphosphino)-1,1'-binaphthyl; Boc tert-butyloxycarbonyl; C Celsius; CH 2 Cl 2 dichloromethane; Cs 2 CO 3 cesium carbonate; d doublet; dd doublet of doublets; DCE 1,2-dichloroethane; DCM dichloromethane; DIPEA/DIEA N,N-diisopropylethylamine; DMF N,N-dimethylformamide; DMSO dimethylsul
- a compound obtained in each step can be used in a subsequent reaction directly as a reaction solution or as a composition, the compound can also be isolated from a reaction mixture in accordance with a conventional method.
- the compound can be readily purified by separation means such as recrystallization, distillation, or chromatography. Unless specifically described otherwise, each instance of the same symbols in the compounds in the following reactions is defined the same.
- Manufacturing Methods Manufacturing Method A Manufacturing method of compounds of formula (I) and formula (Ia)
- a compound of formula (I) and/or (Ia) can be manufactured, for example, by the manufacturing method described below.
- LG a and LG b are independently leaving groups. Examples thereof include iodine, bromine, chlorine, triflate, alkoxy, sulfonyloxy, imidazole, and the like. LG a and LG b are preferably chlorine. [00344] This is a step for obtaining compound a3 by adding a2 to compound a1 in the presence of a base in a suitable solvent.
- the solvent used in this step is selected from the solvents exemplified below and the like.
- examples thereof include aprotic solvents, such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile, ether solvents, such as tetrahydrofuran and 1,4-dioxane, halogenated hydrocarbons, such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons, such as toluene and benzene, mixtures thereof, and the like.
- aprotic solvents such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile
- ether solvents such as tetrahydrofuran and 1,4-dioxane
- halogenated hydrocarbons such as dichlor
- the amount of base used is generally 2 to 20 equivalents, preferably 4 to 8 equivalents with respect to 1 equivalent of compound a1.
- the amount of a2 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound a1.
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 80 °C.
- Examples thereof include aprotic solvents, such as N,N-dimethylformamide, N-methyl-2- pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, and ethyl acetate, ether solvents, such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons, such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons, such as toluene and benzene, alcohol solvents, such as ethanol and methanol, mixtures thereof, and the like.
- aprotic solvents such as N,N-dimethylformamide, N-methyl-2- pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, and ethyl acetate
- ether solvents such as cyclopentyl
- Preferred examples thereof include cyclopentyl methyl ether, 1,4- dioxane, ethyl acetate, methanol, and mixtures thereof.
- the amount of acid used is generally 2 to 100 equivalents, preferably 2 to 20 equivalents with respect to 1 equivalent of compound a3.
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
- a basic salt such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride
- an aromatic amine such as pyridine, lutidine, 4-dimethylaminopyridine, or N,N-dimethylaniline
- a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N-methylpiperidine, N- methylpyrrolidine, or N-methylmorpholine, or the like
- N,N- diisopropylethylamine is particularly preferred.
- the solvent used in this step is selected from the solvents exemplified below and the like.
- examples thereof include aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, esters such as methyl acetate and ethyl acetate, mixtures thereof, and the like.
- aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile
- ether solvents such as cyclopentyl methyl ether and 1,
- Preferred examples thereof include chloroform and dichloromethane.
- the amount of a5 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound a4.
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
- an inorganic acid such as hydrochloric acid, sulfuric acid, nitric acid, or phosphoric acid, or an organic acid such as oxalic acid, citric acid, or acetic acid can be used.
- Hydrochloric acid is particularly preferred.
- the solvent used in this step is selected from the solvents exemplified below and the like.
- Examples thereof include aprotic solvents such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, ethyl acetate, and acetone, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2- dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, alcohol solvents such as ethanol and methanol, mixtures thereof, and the like.
- Preferred examples thereof include methanol, acetone, water, and mixtures thereof.
- the amount of acid used is generally 2 to 100 equivalents, preferably 20 to 40 equivalents with respect to 1 equivalent of compound of formula (I).
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
- Manufacturing Method B Manufacturing method of compounds of formula (I') or formula (I'a)
- a compound of formula (I') or formula (I'a) which is a compound represented by formula (I) wherein R 2 is a hydrogen atom, can be manufactured, for example, by the manufacturing method described below.
- HZ for each occurrence, independently represents acid, g is 0, 1 or 2 and q is 0, 1, 2 or 3. Values for the remaining variables (e.g., X, Y, Ring G, R 1 , R 3 , m, n and p) are as described in the first through ninth embodiments, or any aspect thereof.
- This is a step for obtaining compound of formula (I') by reacting compound a4 with compound b1 obtained by the manufacturing method described below in the presence of a base in a suitable solvent.
- a basic salt such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride
- an aromatic amine such as pyridine, lutidine, 4-dimethylaminopyridine, or N,N-dimethylaniline
- a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N-methylpiperidine, N- methylpyrrolidine, or N-methylmorpholine, or the like
- N,N- diisopropylethylamine is particularly preferred.
- the solvent used in this step is selected from the solvents exemplified below and the like.
- examples thereof include aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, esters such as methyl acetate and ethyl acetate, mixtures thereof, and the like.
- aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile
- ether solvents such as cyclopentyl methyl ether and 1,
- Preferred examples thereof include chloroform and dichloromethane.
- the amount of b5 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound a3.
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
- an inorganic acid such as hydrochloric acid, sulfuric acid, nitric acid, or phosphoric acid, or an organic acid such as oxalic acid, citric acid, or acetic acid can be used.
- Hydrochloric acid is particularly preferred.
- the solvent used in this step is selected from the solvents exemplified below and the like.
- Examples thereof include aprotic solvents such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, ethyl acetate, and acetone, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2- dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, alcohol solvents such as ethanol and methanol, mixtures thereof, and the like.
- Preferred examples thereof include methanol, acetone, water, and mixtures thereof.
- the amount of acid used is generally 2 to 100 equivalents, preferably 20 to 40 equivalents with respect to 1 equivalent of a compound of formula (I').
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
- Manufacturing Method C Manufacturing method of an intermediate a5
- a compound represented by a5 can be manufactured, for example, by the manufacturing method described below. wherein LG is a leaving group. Values for the remaining variables (e.g., Ring G, R 2 , R 3 , n and p) are as described in the first through eighth embodiments, or any aspect thereof.
- Each LG b is independently a leaving group. Examples thereof include iodine, bromine, chlorine, triflate, alkoxy, sulfonyloxy, imidazolyl, and the like. Each LG b is preferably the same. LG b is preferably chlorine.
- This is a step for obtaining compound a5 by reacting c2 with compound c1 in the presence of a base in a suitable solvent. As c2, carbonothioic diiodide, carbonothioic dibromide, or thiophosgene can be used, and thiophosgene is particularly preferred.
- a basic salt such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride
- an aromatic amine such as pyridine, lutidine, 4- dimethylaminopyridine, or N,N-dimethylaniline
- a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N- methylpiperidine, N-methylpyrrolidine, or N-methylmorpholine, or the like
- N,N-diisopropylethylamine is particularly preferable.
- the solvent used in this step is selected from the solvents exemplified below and the like.
- examples thereof include aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, and ethyl acetate, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2- dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, mixtures thereof, and the like.
- Preferred examples thereof include chloroform and dichloromethane.
- Each LG b is independently a leaving group. Examples thereof include iodine, bromine, chlorine, triflate, alkoxy, sulfonyloxy, imidazolyl, and the like. Each LG b is preferably the same. LG b is preferably chlorine. [00357] This is a step for obtaining b1 by reacting c2 with compound d1 in the presence of base in a suitable solvent.
- Preferred examples thereof include mixtures of water and dichloromethane and chloroform.
- the amount of c2 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound d1.
- the reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours.
- the reaction temperature is generally about -78 °C to about 180 °C, preferably about -20 °C to about 50 °C.
- a compound of interest can be obtained by protecting a portion other than the reaction point and deprotecting the protected portion after the completion of a reaction or a series of reactions, as needed if one of the functional groups other than the reaction point is altered under the described reaction condition or is unsuitable for performing the described method.
- a protecting group common protecting groups such as those described in a reference (e.g., Protective Groups in Organic Synthesis, 3rd ed., T. W. Greene, John Wiley & Sons Inc. (1999) or the like) can be used.
- alkali bicarbonates such as sodium bicarbonate and potassium bicarbonate
- alkali carbonates such as sodium carbonate and potassium carbonate
- metal hydrides such as sodium hydride and potassium hydride
- alkali metal hydroxides such as sodium hydroxide and potassium hydroxide
- alkali metal alkoxides such as sodium methoxide and sodium tert- butoxide
- organic metal bases such as butyl lithium and lithium diisopropylamide
- organic bases such as triethylamine, diisopropylethylamine, pyridine, 4- dimethylaminopyridine (DMAP), and 1,8-diazabicyclo[5.4.0]-7-undecene (DBU).
- the solvent used in each of the steps described above should be appropriately selected depending on the type of reaction or raw material compound or the like.
- examples thereof include alcohols such as methanol, ethanol, and isopropanol, ketones such as acetone and ethyl methyl ketone, halogenated hydrocarbons such as methylene chloride and chloroform, ethers such as tetrahydrofuran (THF) and dioxane, aromatic hydrocarbons such as toluene and benzene, aliphatic hydrocarbons such as hexane and heptane, esters such as ethyl acetate and propyl acetate, amides such as N,N-dimethylformamide (DMF) and N- methyl-2-pyrrolidone, sulfoxides such as dimethyl sulfoxide (DMSO), and nitriles such as acetonitrile.
- alcohols such as methanol, ethanol, and isopropan
- the compound of the invention represented by formula (1) or an intermediate thereof can be separated or purified by a method that is known to those skilled in the art. Examples thereof include extraction, partition, precipitation, column chromatography (e.g., silica gel chromatography, ion exchange chromatography, and preparative liquid chromatography), crystallization, and the like.
- crystallization solvents examples include alcohol solvents such as methanol, ethanol, and 2-propanol, ether solvents such as diethyl ether, ester solvents such as ethyl acetate, aromatic hydrocarbon solvents such as benzene and toluene, ketone solvents such as acetone, halogen solvents such as dichloromethane and chloroform, hydrocarbon solvents such as hexane, aprotic solvents such as dimethylformamide and acetonitrile, water, mixtures thereof, and the like.
- alcohol solvents such as methanol, ethanol, and 2-propanol
- ether solvents such as diethyl ether
- ester solvents such as ethyl acetate
- aromatic hydrocarbon solvents such as benzene and toluene
- ketone solvents such as acetone
- halogen solvents such as dichloromethane and chloroform
- hydrocarbon solvents such as hexane
- the molecular structure of the compound of the invention can be readily determined by a spectroscopic method such as nuclear magnetic resonance, infrared spectroscopy, or circular dichroism spectroscopy, or mass spectrometry by referring to the structure derived from each raw material compound.
- the intermediate or final product in the manufacturing method described above can lead to another compound encompassed by the present invention by appropriately converting the functional group thereof, extending various side changes based on especially an amino group, a hydroxyl group, a carbonyl group, halogen group, or the like, and, in doing so, applying protection and deprotection described above as needed.
- Reference Compound 1 tert-butyl 4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate [00370] Pyridine (27.0 g) was added to a 1,4-dioxane solution (171 mL) of 4- chlorofuro[2,3-d]pyrimidine (26.4g) and tert-butyl piperazine-1-carboxylate (33.4g), and the reaction solution was stirred for 4 hours at 80°C. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: hexane/ethyl acetate) to obtain Reference Compound 1 (20.0 g).
- Reference Compound 4 tert-butyl 4-(5-cyanofuro[2,3-d]pyrimidin-4-yl)piperazine-1- carboxylate
- Reference Compound 4 [00372] A DMF solution (5 mL) of tert-butyl 4-(5-bromofuro[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate (467 mg), tetrakis triphenylphosphine palladium (282 mg), and cyanated zinc (286 mg) was stirred under microwave irradiation (100°C, 1 hour). Ethyl acetate was added to the reaction solution, and the solution was washed with saturated sodium bicarbonate water and saturated saline.
- Reference Compound 9 6-(isothiocyanatomethyl)quinoxaline
- Thiophosgen (0.26 mL) was added to chloroform (10 mL) and saturated sodium bicarbonate water (10 mL) solution of quinoxalin-6-ylmethanamine (640mg) while being cooled with ice. The reaction mixture was stirred for 15 minutes being cooled with ice. The reaction mixture was separated and organic phase was dried with sodium sulfate, filtered, and concentrated under reduced pressure. The crude product was used for next reaction without further purification.
- Compound 75 4-(furo[2,3-d]pyrimidin-4-yl)-N-(4- (hydroxymethyl)benzyl)piperazine-1-carbothioamide C ompound 74
- Compound 75 [00394] A 4M lithium borohydride THF solution (0.03 mL) was added to a THF solution (10 mL) of methyl 4-((4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carbothioamide)methyl) benzoate (53 mg) while being cooled with ice, and the reaction solution was stirred for 12 hours at room temperature.
- a THF solution (5 mL) of 5-((2-(tert-butoxy)-2-oxoethyl)(tert-butoxycarbonyl)amino) pentanoate (76 mg), triethylamine (0.04 mL), and PyBOP (159 mg) was separately stirred for 1 hour at room temperature. After mixing the reaction solutions described above at room temperature, the reaction solution was stirred for 12 hours. The reaction solution was diluted with ethyl acetate, then washed with saturated sodium bicarbonate water and saturated saline. The organic phase was then dried with sodium sulfate, filtered, and concentrated under reduced pressure.
- Reagents.22Rv1, MDA-MB-231, and Ov56 cells were purchased from ATCC and cultured according to the manufacturer’s instructions.
- the CellTiter-Glo cell viability assay (G7570) was purchased from Promega and used according to the manufacturer’s protocol.
- Human RAD51/RECA (Sandwich ELISA) ELISA kit (LS-F6761) was purchased from Lifespan Bio (LSBio).
- Olaparib (S1060) and camptothecin (S1288) were purchased from Selleck chemicals.
- Antibodies Antibodies.
- the culture supernatant was removed and washed with PBS.
- the cells were lysed with RIPA buffer (radioimmunoprecipitation buffer), and the lysate was retrieved.
- the protein concentration of the retrieved lysate was measured, and the lysate was diluted with 0.1 ⁇ sample buffer such that the protein mass in 7 ⁇ L would be constant.3 ⁇ L of 5 ⁇ Fluorescence Mastar Mix was then added, and the mixture was heated for 5 minutes at 100°C with a heat block. The heated sample was dispensed on a plate in accordance with the protocol of Wes (SimpleProtein).
- Table 9 shows the IC 50 range for each assayed compound, wherein “A” denotes a compound having an IC 50 in the assay of less than 0.3 ⁇ M, “B” denotes a compound having an IC 50 in the assay of from 0.3 ⁇ M to 1 ⁇ M and “C” denotes a compound having an IC 50 in the assay of greater than 1 ⁇ M. [Table 9]
- ER stress-induced UPR is a cellular adaptive response that evolved to restore protein-folding homeostasis by reducing protein synthesis through phosphorylation of eIF2 ⁇ and by increasing the ER protein-folding and degradative capacities through transcriptional activation by XBP1 and ATF6 ⁇ .
- XBP1 and ATF6 ⁇ XBP1 and ATF6 ⁇ .
- Compound 1 was tested for efficacy in inducing ER stress, its ability to cause phosphorylation of eIF2 ⁇ and activate the ATF4 transcription factor using Western blot analysis in 22Rv1 cells.
- 22Rv1 cells were treated with 10 ⁇ M Compound 1.
- the cells were harvested after the periods of time indicated in FIG.1 by washing with ice-cold PBS and then lysed with ice- cold RIPA buffer (Cell Signaling Technologies, 9806S) containing 1% Halt protease and phosphatase inhibitor cocktail (ThermoFisher Scientific, 78444) on ice.
- Whole cell lysates were sonicated and centrifuged at 16,000 x g for 10 min at 4 ⁇ C, and the protein concentration of the supernatant was determined using a BCA Protein assay kit (ThermoScientific, 23225).
- transcription factor ATF4 also increased significantly after 2 hrs of treatment with Compound 1. This data demonstrates that Compound 1 induces ER stress leading to UPR in cancer cells.
- Assay Example 3 Gene expression analysis by quantitative real-time (qRT)–PCR [00417] The effectiveness Compound 1 and Compound 4 dihydrochloride in activating ATF4 were assessed by analyzing expression of ATF4 regulated genes, that is TRIB3, GADD34, ERO1 ⁇ , and ATF3, using RT-qPCR. Total RNA was isolated from cells using Quiagene RNAeasy kit.
- cDNA was synthesized from 500 ng of total RNA in a 20 ⁇ L reaction volume using the SuperScript III First-Strand Synthesis SuperMix Kit (Invitrogen) for 50 minutes at 50°C, followed by 85°C for 5 minutes.
- qPCR analysis of ATF3, TRIB3, GADD34, ERO1a, and GAPDH mRNA levels was conducted using the QuantStudio 3 system.
- Taqman real-time PCR assay probes were purchased from ThermoFisher Scientific.
- 22Rv1 cells were treated with the indicated compounds at concentrations ranging from 0 – 25 ⁇ M for 24 hrs. After 24 hrs of treatment, cells were harvested and lysed in ice- cold PBS containing Halt Protease and Phosphatase inhibitor cocktail. BCA assay was used to quantify the protein in the cell lysate. RAD51 levels were measured using the Human RAD51/RecA sandwich enzyme ⁇ linked immunosorbent assay (ELISA) kit (LSBio, Seattle, WA) according to the manufacturer’s protocol. [00420] As shown in the FIGs.3A-G, all the tested compounds demonstrated >35% reduction in levels of RAD51 protein as compared to vehicle control at 100 nM concentration after 24 hrs of treatment.
- ELISA Human RAD51/RecA sandwich enzyme ⁇ linked immunosorbent assay
- FIG.4 shows example fluorescent micrographs of control cells, camptothecin- treated cells, and cells treated with 0.1 ⁇ M or 1 ⁇ M of the indicated compound (Compound 1, Compound 2 hydrochloride, Compound 11 dihydrochloride, Compound 4 dihydrochloride, and Compound 15 dihydrochloride) in combination with 0.1 ⁇ M camptothecin.
- the indicated compound Compound 1, Compound 2 hydrochloride, Compound 11 dihydrochloride, Compound 4 dihydrochloride, and Compound 15 dihydrochloride
- FIGs.5A-C all the tested compounds demonstrated significant reduction in RAD51-foci formation after 72 hrs at 1 ⁇ M concentration.
- Compound 4 dihydrochloride and Compound 15 dihydrochloride demonstrated a significant reduction in RAD51-foci formation at 1 ⁇ M at all the time points tested.
- PARPi Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are effective in cancers with a defective HRR (PMID: 30934991). Cells with defects in the HRR, including those with deleterious variants in BRCA1 or BRCA2 (BRCA1/2) genes, are particularly sensitive to PARPi (PMID: 15829967, 15829966, 18971340). In breast cancer (BC), the efficacy results of the PARPi olaparib (Lynparza®) in metastatic patients carrying a germline BRCA1/2 (gBRCA) pathogenic variant have led to its recent approval by the Food and Drug Administration (PMID: 28578601).
- Cell viability for 22Rv1, Ov56, and MDA-MB-231 cells was assessed using a CellTiterGlo (Promega) assay according to the manufacturer’s protocol. Specifically, 300 cells were plated per well in a 384-well tissue culture treated plate (Greiner) in 20 ⁇ L of complete medium. Compounds of the present disclosure to be tested and olaparib were added using a Labcyte Echo acoustic dispensing device at desired concentration and the cells were incubated for 96 hours. Cell viability was assessed using CellTiterGlo (Promega) on an Envision (PerkinElmer) plate reader.
- 22Rv1 cell line xenografts were established in the flank of athymic mice (Charles River) as previously described (PMID: 31799745). Flank tumors were allowed to grow to a volume of approximately 200 mm 3 . Mice with established tumors were randomized into treatment groups. The mice in the treatment groups were treated with different doses of the tested compounds of the present disclosure or vehicle by oral gavage. After 24 hr of treatment, the mice were sacrificed and blood and tumor tissue were harvested for PK and PD analyses. PK blood samples were collected by heart puncture in EDTA tubes. Tumor tissues were flash frozen for PK and PD analyses. Blood and tumor concentrations of the tested compounds were determined by protein precipitation followed by LC/MS-MS analysis.
- FIGs.9A-E summarize the PK data for Compound 1, Compound 5 hydrochloride, Compound 3 dihydrochloride, Compound 11 dihydrochloride, and Compound 4 dihydrochloride.
- Compound 2 hydrochloride and Compound 15 dihydrochloride were not detected in plasma or tumor after 24 hr of treatment.
- Compound 4 dihydrochloride displayed the best PK properties, with the highest concentration of drug observed in the tumor and plasma after 24 hrs of exposure. As shown in FIGs.10A-G, all the tested compounds demonstrated decreased RAD51 levels in a tumor after 24 hrs of treatment.
- Compound 4 dihydrochloride and Compound 5 hydrochloride demonstrated a dose- dependent decrease in the levels of RAD51.
- Immunoblot analysis and gene expression analysis using RT-qPCR demonstrated that the indicated compounds induced ER stress and the UPR.
- RAD51 ELISA assay and RAD51 foci formation assay in vitro demonstrated that all tested compounds decreased the levels of RAD51 and suppressed the HRR.
- cell viability assays demonstrated that the tested compounds produced synergy with PARPi olaparib, and also showed cell line-specific effects as single agents.
- PK/PD studies revealed that all the compounds tested effectively decreased RAD51 levels in vivo after 24 hr exposure, with varied clearance times.
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Abstract
Provided herein are compounds of the following structural formula: (I), or a pharmaceutically acceptable salt thereof, wherein values for the variables (e.g., R1, R2, R3, X, Y, m, n,p, Ring G) are as described herein. Compounds of Formula I and pharmaceutically acceptable salts thereof, pharmaceutical compositions of either of the foregoing, and combinations of any of the foregoing can be used, e.g., to decrease a level of RAD51.
Description
(Furopyrimidin-4-yl)piperazine Compounds and Uses Thereof RELATED APPLICATION [0001] This application claims the benefit of U.S. Provisional Application No. 63/166,852, filed on March 26, 2021, the entire teachings of which are incorporated herein by reference. BACKGROUND [0002] DNA repair is essential for cells to maintain genome stability in an environment that constantly produces DNA damage (PMID: 33015624). Unrepaired DNA damage in a cell can result in genomic instability and ultimately lead to cancer. Cancer is a disease of abnormal cells that divide uncontrollably and have the ability to infiltrate and destroy normal body tissue. Cancer prevention depends on the maintenance of several DNA damage repair pathways, including homologous recombination repair (HRR). However, tumors that are deficient in HRR are sensitive to cancer therapeutics that interfere with DNA replication (PMID: 20598756). Therefore, induction of DNA damage repair proteins in cancer cells is associated with therapeutic resistance and even metastasis (PMID: 24397478). [0003] A key protein in the HRR pathway is RAD51. RAD51 belongs to the recA/RAD51 gene family that arose from a gene duplication of the archaeal RadA protein and is highly conserved throughout evolution (PMID: 10486005, 9021132, 16798872). In humans, RAD51 is a 339-amino acid protein that plays a major role in homologous recombination of DNA during double strand break (DSB) repair. RAD51 is regulated by a group of proteins that include BRCA1, BRCA2, PALB2 and the RAD51 paralogs (PMID: 25833843). Misregulation of RAD51, or one of its regulators, is associated with cancer as well as Fanconi anemia (FA)-like syndrome (PMID: 25833843, 30551670). While loss or reduction of RAD51 protein function can increase the risk of cancer, RAD51 upregulation in cancer can contribute to therapeutic resistance (PMID: 18243065, 32001312). Maintaining appropriate levels of RAD51 expression and activity is critical for HRR in both cancer prevention and cancer treatment. [0004] As part of HRR, RAD51 facilitates strand transfer between interrupted sequences and their undamaged homologies (PMID: 12778123). Several studies have shown that the level of RAD51 protein expression is elevated in immortalized cells as well as in a wide variety of human cancer cell lines (PMID: 11782381, 12712436). It was proposed that RAD51 overexpression results in an increased cellular resistance to radiation and some
chemotherapeutic drugs, such as topoisomerase inhibitors or DNA crosslinking agents (PMID: 12712436, 12024032, 9611228). RAD51 overexpression has also been investigated in numerous tumor tissues using immunohistochemistry (IHC). Overexpression of RAD51 has been observed in virtually all different types of cancer, including, but not limited to, neuroblastoma, breast, ovarian, pancreatic, head and neck, lung, colorectal, prostate, and esophageal squamous cell carcinomas, as well as multiple myeloma and gliomas (PMID: 10851081, 11093813, 15956972, 16596227, 17707537, 19545791, 20092964, 21744352, 23065657, 20002770, 32554304, 11782381, 31632548, 32577161, the entire contents of which are incorporated herein by reference). Therapeutically, RAD51 overexpression was also associated with poor patient prognosis in most of these cancer studies. [0005] One of the hallmarks of cancer cells is uncontrolled proliferation (PMID: 21376230). In order to cope with rapid proliferation, cancer cells require a greater amount of protein synthesis at a faster rate than non-cancer cells. Because of the high rate of protein synthesis in cancer cells, an enhanced capacity for protein folding is required, which puts a substantial demand on the protein folding machinery in the endoplasmic reticulum (ER) [PMID: 32457508]. When the unfolded or misfolded protein load in a cell exceeds the capacity of the ER to fold proteins, the cell is under a state of ER stress [PMID: 30996048]. In order to overcome ER stress, cancer cells exploit intrinsic adaptive mechanisms such as the unfolded protein response (UPR) [PMID: 32457508, 17565364]. ER stress and the associated UPR have been shown to participate in the development of cancer [PMID: 24823636]. Further, recent findings indicated that sustained level of high ER stress could provide therapeutic effect against cancer cell [PMID: 30863482, 27729194, 26555175, 27308392]. Indeed, ER stress-inducing drugs have been useful in treating cancers such as myeloma. [PMID: 23729400] When ER stress activates the UPR, a complex cellular response occurs including the upregulation of aberrant protein degradation in the ER, with the goal of resolving the ER stress. [PMID: 9891777] It has been demonstrated that ER stress- induced UPR leads to degradation of multiple DNA repair proteins including, but not limited to, RAD51, MGMT, and MPG. [PMID: 26951384, 24021650, 30996048, 32521270] Thus, therapeutic induction of ER stress and UPR could make cancer cells specifically vulnerable to DNA damage therapy by, for example, degrading RAD51. [0006] Accordingly, there is a need for compounds that decrease the level of RAD51 in cancer cells, e.g., by inducing ER stress and the UPR.
SUMMARY [0007] Provided herein are compounds that decrease the level of RAD51, pharmaceutically acceptable salts thereof, pharmaceutical compositions of either of the foregoing, and combinations of any of the foregoing. The compounds described herein can be used in methods of treating cancer, e.g., by administering to a subject in need thereof a therapeutically effective amount of the compound, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition or combination comprising the compound, or a pharmaceutically acceptable salt thereof. [0008] One aspect is a compound of Formula I:
or a pharmaceutically acceptable salt thereof, wherein values for the variables (e.g., X, Y, R1, R2, R3, m, n, p and Ring G) are as described herein. [0009] Another aspect is a pharmaceutical composition comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing), and one or more pharmaceutically acceptable carriers. [0010] Yet another aspect is a pharmaceutical combination comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing), and one or more additional therapeutic agents. [0011] Another aspect is a method of decreasing a level of RAD51 in a cell (e.g., cancer cell), comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing), for example, a therapeutically effective amount of a compound of the present disclosure. [0012] Another aspect is a method of decreasing RAD51 levels in a subject in need thereof (e.g., a subject having cancer), comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing).
[0013] Another aspect is a method of treating cancer, comprising administering to a subject in need thereof a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing). [0014] Another aspect is a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing), or a composition (e.g., pharmaceutical composition) described herein for use in treating a disorder, disease or condition described herein in a subject. Another aspect is use of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) for the manufacture of a medicament for treating a disorder, disease or condition described herein. BRIEF DESCRIPTION OF THE DRAWINGS [0015] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee. [0016] The foregoing will be apparent from the following more particular description of example embodiments. [0017] FIG.1 shows an example of an immunoblot analysis in 22Rv1 cells treated with Compound 1 according to Assay Example 2. [0018] FIG.2A shows an example of RT-qPCR analysis of ATF3 in 22Rv1 cells treated with Compound 1 or Compound 4 dihydrochloride according to Assay Example 3. [0019] FIG.2B shows an example of RT-qPCR analysis of GADD34 in 22Rv1 cells treated with Compound 1 or Compound 4 dihydrochloride according to Assay Example 3. [0020] FIG.2C shows an example of RT-qPCR analysis of ERO1α in 22Rv1 cells treated with Compound 1 or Compound 4 dihydrochloride according to Assay Example 3. [0021] FIG.2D shows an example of RT-qPCR analysis of TRIB3 in 22Rv1 cells treated with Compound 1 or Compound 4 dihydrochloride according to Assay Example 3. [0022] FIG.3A shows an example of the effect of Compound 1 on the concentration of RAD51in vitro as determined by an ELISA assay according to Assay Example 4. [0023] FIG.3B shows an example of the effect of Compound 5 hydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4.
[0024] FIG.3C shows an example of the effect of Compound 2 hydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4. [0025] FIG.3D shows an example of the effect of Compound 3 dihydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4. [0026] FIG.3E shows an example of the effect of Compound 11 dihydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4. [0027] FIG.3F shows an example of the effect of Compound 4 dihydrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4. [0028] FIG.3G shows an example of the effect of Compound 15 dihydrrochloride on the concentration of RAD51 in vitro as determined by an ELISA assay according to Assay Example 4. [0029] FIG.4 shows example images from the RAD51 Foci assay described in Assay Example 5 at 72h. [0030] FIG.5A shows an example of the quantitation of RAD51 Foci number at 24h for various compounds disclosed herein in Assay Example 5. [0031] FIG.5B shows an example of the quantitation of RAD51 Foci number at 48h for various compounds disclosed herein in Assay Example 5. [0032] FIG.5C shows an example of the quantitation of RAD51 Foci number at 72h for various compounds disclosed herein in Assay Example 5. [0033] FIG.6A shows example data from a combination study for 22Rv1 cells with Compound 1 and olaparib according to Assay Example 6. [0034] FIG.6B shows example data from a combination study for 22Rv1 cells with Compound 5 hydrochloride and olaparib according to Assay Example 6. [0035] FIG.6C shows example data from a combination study for 22Rv1 cells with Compound 2 hydrochloride and olaparib according to Assay Example 6. [0036] FIG.6D shows example data from a combination study for 22Rv1 cells with Compound 3 dihydrochloride and olaparib according to Assay Example 6. [0037] FIG.6E shows example data from a combination study for 22Rv1 cells with Compound 4 dihydrochloride and olaparib according to Assay Example 6.
[0038] FIG.6F shows example data from a combination study for 22Rv1 cells with Compound 11 dihydrochloride and olaparib according to Assay Example 6. [0039] FIG.6G shows example data from a combination study for 22Rv1 cells with Compound 15 dihydrochloride and olaparib according to Assay Example 6. [0040] FIG.7A shows an example of the single agent effect of various compounds disclosed herein against Ov56 cells in the assay described in Assay Example 6. [0041] FIG.7B shows an example of the single agent effect of various compounds disclosed herein against 22Rv1 cells in the assay described in Assay Example 6. [0042] FIG.7C shows an example of the single agent effect of various compounds disclosed herein in MDA-MB-231 cell lines in the assay described in Assay Example 6. [0043] FIG.8 is a schematic showing design of Pharmacokinetic (PK)/Pharmacodynamic (PD) Study 1. [0044] FIG.9A shows a summary of drug concentration in plasma and tumor after 24 h for Compound 1 in the study described in PK/PD Study 1. [0045] FIG.9B shows a summary of drug concentration in plasma and tumor after 24 h for Compound 5 hydrochloride in the study described in PK/PD Study 1. [0046] FIG.9C shows a summary of drug concentration in plasma and tumor after 24 h for Compound 3 dihydrochloride in the study described in PK/PD Study 1. [0047] FIG.9D shows a summary of drug concentration in plasma and tumor after 24 h for Compound 11 dihydrochloride in the study described in PK/PD Study 1. [0048] FIG.9E shows a summary of drug concentration in plasma and tumor after 24 h for Compound 4 dihydrochloride in the study described in PK/PD Study 1. [0049] FIG.10A shows an example of the effect of Compound 1 on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1. [0050] FIG.10B shows an example of the effect of Compound 5 hydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1. [0051] FIG.10C shows the effect of Compound 2 hydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1. [0052] FIG.10D shows an example of the effect of Compound 3 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1. [0053] FIG.10E shows an example of the effect of Compound 4 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1.
[0054] FIG.10F shows an example of the effect of Compound 11 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1. [0055] FIG.10G shows an example of the effect of Compound 15 dihydrochloride on the concentration of RAD51 in vivo as determined by ELISA assay according to PK/PD Study 1. DETAILED DESCRIPTION [0056] A description of example embodiments follows. Compounds [0057] A first embodiment is a compound having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein: X is -O- and Y is -C(H)-, or Y is -O- and X is -C(H)-; Ring G is (C6-C15)aryl, (C5-C15)heteroaryl, (C3-C15)carbocyclyl, monocyclic (C3- C10)heterocyclyl or bicyclic fused (C5-C15)heterocyclyl; R1, for each occurrence, is independently halo, cyano, hydroxy, (C1-C6)alkyl, (C1- C6)haloalkyl, (C1-C6)alkoxy or (C1-C6)haloalkoxy; R2 is H, (C1-C6)hydroxyalkyl, (C6-C15)aryl(C1-C6)alkyl or (C3-C15)heterocyclyl(C1- C6)alkyl or, together with an atom of Ring G and their intervening atoms, forms a three- to eight-membered ring that is spiro or fused to Ring G; R3, for each occurrence, is independently oxo or halo, cyano, hydroxy, (C1- C6)haloalkyl, (C1-C6)haloalkoxy, (C1-C6)hydroxyalkyl, (C1-C6)alkyl, (C1-C6)alkoxy, (C2- C12)alkoxyalkyl, -C(O)(C1-C6)alkyl, -C(O)-(C1-C6)alkylene-N(R5)2, -C(O)(OR4), - C(O)N(R5)2, -S(O)2N(R5), or -N(R5)2; R4, for each occurrence, is independently H or (C1-C6)alkyl; R5, for each occurrence, is independently H, (C1-C6)alkyl, (C6-C15)aryl, (C5- C15)heteroaryl, -C(O)(OR6) or -CH2C(O)(OR6); R6, for each occurrence, is independently H or (C1-C6)alkyl; m is 0, 1 or 2; n is 0, 1, 2 or 3; and p is 0, 1 or 2.
[0058] In a first aspect of the first embodiment, X is -O- and Y is -C(H)-. Values for the remaining variables are as described in the first embodiment. [0059] In a second aspect of the first embodiment, Y is -O- and X is -C(H)-. Values for the remaining variables are as described in the first embodiment, or first aspect thereof. [0060] In a third aspect of the first embodiment, Ring G is (C6-C10)aryl, (C5- C10)heteroaryl, (C6-C10)carbocyclyl, monocyclic (C5-C6)heterocyclyl or bicyclic fused (C6- C10)heterocyclyl. Values for the remaining variables are as described in the first embodiment, or first or second aspect thereof. [0061] In a fourth aspect of the first embodiment, Ring G is oxazolyl, phenyl, pyridinyl, dihydropyridinyl, indolyl, indolinyl, isoindolinyl, quinolinyl, isoquinolinyl, quinoxalinyl, tetrahydroquinolinyl, benzofuranyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, benzo[d][1,3]dioxolyl, dihydrobenzo[b][1,4]dioxinyl, cyclohexyl, tetrahydropyranyl, piperidinyl, piperazinyl or morpholinyl. Values for the remaining variables are as described in the first embodiment, or first through third aspects thereof. [0062] In a fifth aspect of the first embodiment, Ring G is (C6-15)aryl or (C5-15)heteroaryl (e.g., in some aspects, (C6-C15)aryl). Values for the remaining variables are as described in the first embodiment, or first through fourth aspects thereof. [0063] In a sixth aspect of the first embodiment, Ring G is phenyl. Values for the remaining variables are as described in the first embodiment, or first through fifth aspects thereof. [0064] In a seventh aspect of the first embodiment, Ring G is (C5-15)heteroaryl. Values for the remaining variables are as described in the first embodiment, or first through sixth aspects thereof. [0065] In an eighth aspect of the first embodiment, Ring G is pyridinyl, dihydropyridinyl, indolyl, quinolinyl, isoquinolinyl, quinoxalinyl or benzofuranyl. Values for the remaining variables are as described in the first embodiment, or first through seventh aspects thereof. [0066] In a ninth aspect of the first embodiment, Ring G is pyridinyl, indolyl, quinolinyl or quinoxalinyl. Values for the remaining variables are as described in the first embodiment, or first through eighth aspects thereof. [0067] In a tenth aspect of the first embodiment, Ring G is bicyclic fused (C5-C15)heterocyclyl. Values for the remaining variables are as described in the first embodiment, or first through ninth aspects thereof.
[0068] In an eleventh aspect of the first embodiment, Ring G is indolinyl, isoindolinyl, dihydrobenzo[d]imidazolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, tetrahydroquinoxalinyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, benzo[d][1,3]dioxolyl, chromanyl, or dihydrobenzo[b][1,4]dioxinyl. Values for the remaining variables are as described in the first embodiment, or first through tenth aspects thereof. [0069] In a twelth aspect of the first embodiment, Ring G is (C3-15)carbocyclyl or monocyclic (C5-15)heterocyclyl. Values for the remaining variables are as described in the first embodiment, or first through eleventh aspects thereof. [0070] In a tirteenth aspect of the first embodiment, Ring G is a saturated (C5- 8)carbocyclyl or a saturated monocyclic (C5-8)heterocyclyl. Values for the remaining variables are as described in the first embodiment, or first through twelth aspects thereof. [0071] In a fourteenth aspect of the first embodiment, Ring G is cyclohexyl, tetrahydropyranyl, piperidinyl, piperazinyl or morpholinyl. Values for the remaining variables are as described in the first embodiment, or first through thirteenth aspects thereof. [0072] In a fifteenth aspect of the first embodiment, R1, for each occurrence, is independently halo, cyano, (C1-C6)alkyl or (C1-C6)haloalkyl. Values for the remaining variables are as described in the first embodiment, or first through fourteenth aspects thereof. [0073] In a sixteenth aspect of the first embodiment, R1 is independently halo or cyano. Values for the remaining variables are as described in the first embodiment, or first through fifteenth aspects thereof. [0074] In a seventeenth aspect of the first embodiment, R1 is independently bromo or cyano. Values for the remaining variables are as described in the first embodiment, or first through sixteenth aspects thereof. [0075] In an eighteenth aspect of the first embodiment, R2 is H or, together with an atom of Ring G and their intervening atoms, forms a three- to eight-membered ring that is spiro or fused to Ring G. Values for the remaining variables are as described in the first embodiment, or first through seventeenth aspects thereof. [0076] In a nineteenth aspect of the first embodiment, R2 is H. Values for the remaining variables are as described in the first embodiment, or first through eighteenth aspects thereof. [0077] In a twentieth aspect of the first embodiment, R2, together with an atom of Ring G and their intervening atoms, forms a four- to six-membered ring that is spiro or fused to Ring G. Values for the remaining variables are as described in the first embodiment, or first through nineteenth aspects thereof.
[0078] In a twenty-first aspect of the first embodiment, R2, together with an atom of Ring G and their intervening atoms, forms a four- to six-membered ring that is spiro to Ring G. Values for the remaining variables are as described in the first embodiment, or first through twentieth aspects thereof. [0079] In a twenty-second aspect of the first embodiment, R2 and Ring G, together with their intervening atoms, form a 7-oxa-2-azaspiro[3.5]nonan-2-yl. Values for the remaining variables are as described in the first embodiment, or first through twenty-first aspects thereof. [0080] In a twenty-third aspect of the first embodiment, R2, together with an atom of Ring G and their intervening atoms, forms a four- to six-membered ring that is fused to Ring G. Values for the remaining variables are as described in the first embodiment, or first through twenty-second aspects thereof. [0081] In a twenty-fourth aspect of the first embodiment, R2 and Ring G, together with their intervening atoms, form a 5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl or 5,8-dihydro- 1,7-naphthyridin-7(6H)-yl. Values for the remaining variables are as described in the first embodiment, or first through twenty-third aspects thereof. [0082] In a twenty-fifth aspect of the first embodiment, R3, for each occurrence, is independently halo, (C1-C6)alkyl, cyano or (C1-C6)alkoxy. Values for the remaining variables are as described in the first embodiment, or first through twenty-fourth aspects thereof. [0083] In a twenty-sixth aspect of first embodiment, R3, for each occurrence, is independently -F, -Cl, -Br, or methoxy. Values for the remaining variables are as described in the first embodiment, or first through twenty-fifth aspects thereof. [0084] In a twenty-seventh aspect of first embodiment, R3, for each occurrence, is independently -C(O)-(C1-C6)alkylene-N(R5)2, -C(O)(OR4), -C(O)N(R5)2, -S(O)2N(R5), or -N(R5)2. Values for the remaining variables are as described in the first embodiment, or first through twenty-sixth aspects thereof. [0085] In a twenty-eighth aspect of the first embodiment, R4, for each occurrence, is independently (C1-C6)alkyl. Values for the remaining variables are as described in the first embodiment, or first through twenty-seventh aspects thereof. [0086] In a twenty-ninth aspect of the first embodiment, R4, for each occurrence, is H. Values for the remaining variables are as described in the first embodiment, or first through twenty-eighth aspects thereof.
[0087] In a thirteeth aspect of the first embodiment, R5, for each occurrence, is H, pyrimidinyl, tert-butoxycarbonyl, methyl tert-butoxycarbonyl or methyl carboxylate. Values for the remaining variables are as described in the first embodiment, or first through twenty- ninth aspects thereof. [0088] In a thirty-first aspect of the first embodiment, R5, for each occurrence, is independently -C(O)(OR6) or -CH2C(O)(OR6). Values for the remaining variables are as described in the first embodiment, or first through thirteeth aspects thereof. [0089] In a thirty-second aspect of the first embodiment, R6, for each occurrence, is independently (C1-C6)alkyl. Values for the remaining variables are as described in the first embodiment, or first through thirty-first aspects thereof. [0090] In a thirty-third aspect of the first embodiment, R6, for each occurrence, is H. Values for the remaining variables are as described in the first embodiment, or first through thirty-second aspects thereof. [0091] In a thirty-fourth aspect of the first embodiment, m is 0 or 1. Values for the remaining variables are as described in the first embodiment, or first through thirty-third aspects thereof. [0092] In a thirty-fifth aspect of the first embodiment, m is 0. Values for the remaining variables are as described in the first embodiment, or first through thirty-fourth aspects thereof. [0093] In a thirty-sixth aspect of the first embodiment, m is 1. Values for the remaining variables are as described in the first embodiment, or first through thirty-fifth aspects thereof. [0094] In a thirty-seventh aspect of the first embodiment, n is 0, 1 or 2. Values for the remaining variables are as described in the first embodiment, or first through thirty-sixth aspects thereof. [0095] In a thirty-eighth aspect of the first embodiment, n is 0 or 1. Values for the remaining variables are as described in the first embodiment, or first through thirty-seventh aspects thereof. [0096] In a thirty-ninth aspect of the first embodiment, n is 0. Values for the remaining variables are as described in the first embodiment, or first through thirty-eighth aspects thereof. [0097] In a fortieth aspect of the first embodiment, n is 1. Values for the remaining variables are as described in the first embodiment, or first through thirty-ninth aspects thereof.
[0098] In a forty-first aspect of the first embodiment, p is 0. Values for the remaining variables are as described in the first embodiment, or first through fortieth aspects thereof. [0099] In a forty-second aspect of the first embodiment, p is 1. Values for the remaining variables are as described in the first embodiment, or first through forty-first aspects thereof. [00100] In a forty-third aspect of the first embodiment, p is 2. Values for the remaining variables are as described in the first embodiment, or first through forty-second aspects thereof. [00101] A second embodiment is a compound having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein R7 is H, halo, cyano, hydroxy, (C1- C6)alkyl, (C1-C6)haloalkyl, (C1-C6)alkoxy or (C1-C6)haloalkoxy. Values for the remaining variables (e.g., R2, R3, n, p and Ring G) are as described in the first embodiment, or any aspect thereof. [00102] In a first aspect of the second embodiment, R7 is H, halo, cyano, (C1-C6)alkyl or (C1-C6)haloalkyl (e.g., in some aspects, H, halo, cyano or (C1-C6)haloalkyl). Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or the second embodiment. [00103] In a second aspect of the second embodiment, R7 is H, halo or cyano. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or the second embodiment, or first aspect thereof. [00104] In a third aspect of the second embodiment, R7 is H, bromo or cyano. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or the second embodiment, or first or second aspect thereof. [00105] In a fourth aspect of the second embodiment, R7 is H. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or the second embodiment, or first through third aspects thereof. [00106] A third embodiment is a compound having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein A1 is -C(H)- or -N-; and Z1 and Z2 are absent, or Z1 and Z2, taken together with their intervening atoms, form a 4-7-membered ring that optionally contains one, two or three independently selected heteroatoms. Values for the remaining variables (e.g., R1, R2, R3, m, n, p and Ring G) are as described in the first embodiment, or any aspect thereof. [00107] In a first aspect of the third embodiment, A1 is -C(H)-. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or third embodiment. [00108] In a second aspect of the third embodiment, A1 is -N-. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or third embodiment, or first aspect thereof. [00109] In a third aspect of the third embodiment, Z1 and Z2 are absent. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or third embodiment, or first or second aspect thereof. [00110] In a fourth aspect of the third embodiment, Z1 and Z2, taken together with their intervening atoms, form a 4-7-membered ring that optionally contains one, two or three independently selected heteroatoms. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or third embodiment, or first through third aspects thereof. [00111] In a fifth aspect of the third embodiment, Z1 and Z2, taken together with their intervening atoms, form a 5-6-membered ring that contains one or two heteroatoms independently selected from O and N. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or third embodiment, or first through fourth aspects thereof. [00112] A fourth embodiment is a compound having the following structural formula:
or a pharmaceutically acceptable salt thereof. Values for the variables (e.g., A1, Z1, Z2, R2, R3, R7, n, p and Ring G) are as described in the first through third embodiments, or any aspect of the foregoing. [00113] A fifth embodiment is a compound having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein A2 is -C(H)2-, -N(H)- or -O-; and A3 is >C(H)- or >N-. Values for the remaining variables (e.g., R1, R2, R3, m, n, p and Ring G) are as described in the first embodiment, or any aspect thereof. [00114] In a first aspect of the fifth embodiment, A2 is -C(H)2- and A3 is >C(H)-. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or fifth embodiment. [00115] In a second aspect of the fifth embodiment, A2 is -O- and A3 is >C(H)-. Values for the remaining variables are as described in the first embodiment, or any aspect thereof, or fifth embodiment, or first aspect thereof. [00116] A sixth embodiment is a compound having the following structural formula:
or a pharmaceutically acceptable salt thereof. Values for the variables (e.g., A2, A3, R2, R3, R7, n, p) are as described in the first, second or fifth embodiment, or any aspect of the foregoing. [00117] Specific examples of compounds of the present disclosure include those compounds depicted in Table A, and pharmaceutically acceptable salts thereof. Definitions [00118] For purposes of interpreting this specification, the following definitions will apply, and whenever appropriate, terms used in the singular will also include the plural. Terms used in the specification have the following meanings unless the context clearly indicates otherwise.
[00119] All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein is intended merely to better illuminate the present disclosure and does not pose a limitation on the scope of the present disclosure otherwise claimed. [00120] The terms “a,” “an,” “the” and similar terms used in the context of the present disclosure (especially in the context of the claims) are to be construed to cover both the singular and plural unless otherwise indicated herein or clearly contradicted by the context. [00121] As used herein, the term “heteroatom” refers to nitrogen (N), oxygen (O) or sulfur (S) atoms, in particular, nitrogen or oxygen. When one heteroatom is S, it can be optionally mono- or di-oxygenated (i.e., -S(O)- or -S(O)2-). Unless otherwise indicated, any heteroatom with unsatisfied valencies is assumed to have hydrogen atoms sufficient to satisfy the valencies. [00122] As used herein, the term “alkyl” refers to a branched or straight-chain, monovalent, hydrocarbon radical having the specified number of carbon atoms, and the general formula CnH2n+1. Thus, the term “(C1-C6)alkyl” refers to a branched or straight- chain, monovalent, hydrocarbon radical of the general formula CnH2n+1 wherein n is 1, 2, 3, 4, 5 or 6. Examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, i-propyl, n- butyl, i-butyl, s-butyl, t-butyl, n-pentyl, 1-methylbutyl, 2-methylbutyl, 3-methylbutyl, neopentyl, 3,3-dimethylpropyl, hexyl, 2-methylpentyl, and the like. [00123] The term “alkoxy,” as used herein, refers to an alkyl radical attached through an oxygen linking atom, wherein alkyl is as described herein. “(C1-C6)alkoxy” refers to an alkoxy group in which a (C1-C6)alkyl is attached through an oxygen linking atom. Examples of alkoxy groups include, but are not limited to, methoxy, ethoxy, propoxy (e.g., n-propoxy and iso-propoxy), and butoxy (e.g., t-butoxy). [00124] The term “alkoxyalkyl” as used herein, refers to an alkyl radical wherein one or more (e.g., one) hydrogen atoms is each independently replaced by an alkoxy, wherein alkyl and alkoxy are as described herein. “Alkoxy(C1-C6)alkyl” refers to a (C1-C6)alkyl wherein one or more hydrogen atoms is each replaced by an alkoxy. “(C2-C12)alkoxyalkyl” refers to the total carbon count in the alkoxyalkyl being 2-12 carbons. Examples of alkoxyalkyl include, but are not limited to, 2-methoxyethyl. [00125] “Halogen” and “halo,” as used herein, refer to fluorine, chlorine, bromine or iodine. In some embodiments, halogen is fluoro, chloro or bromo. In some embodiments,
halogen is fluoro or chloro. In some embodiments, halogen is chloro, bromo or iodo. In some embodiments, halogen is chloro or bromo. [00126] “Haloalkyl,” as used herein, refers to an alkyl radical wherein one or more hydrogen atoms is each independently replaced by a halogen, wherein alkyl and halogen are as described herein. “Haloalkyl” includes mono-, poly- and perhaloalkyl groups. “(C1- C6)haloalkyl” refers to a (C1-C6)alkyl wherein one or more hydrogen atoms is each independently replaced by a halogen. Examples of haloalkyl include, but are not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, trichloromethyl, pentafluoroethyl, pentachloroethyl, 2,2,2-trifluoroethyl, heptafluoropropyl, and heptachloropropyl. [00127] “Haloalkoxy,” as used herein, refers to a haloalkyl radical attached through an oxygen linking atom, wherein haloalkyl is as described herein. “(C1-C6)haloalkoxy” refers to a haloalkoxy group in which a (C1-C6)haloalkyl is attached through an oxygen linking atom. Examples of haloalkoxy include, but are not limited to, trifluoromethoxy, difluoromethoxy, 2,2,2-trifluoroethoxy, and pentafluoroethoxy. [00128] “Hydroxy,” as used herein, means -OH. [00129] “Hydroxyalkyl,” as used herein, refers to an alkyl radical wherein one or more (e.g., one) hydrogen atoms is replaced by a hydroxy, wherein alkyl and hydroxy are as described herein. “Hydroxy(C1-C6)alkyl” refers to a (C1-C6)alkyl wherein one or more hydrogen atoms is replaced by a hydroxy. Examples of hydroxyalkyl include, but are not limited to, 2-hydroxyethyl. [00130] “Cyano,” as used herein, means -C≡N. [00131] “Oxo,” as used herein, means =O. [00132] “Thiourea,” as used herein, means
A substituted thiourea has one or more of the hydrogens replaced with substituent(s). [00133] “Thioamide,” as used herein, means
A substituted thioamide has one or more of the hydrogens replaced with substituent(s). A “carbothioamide” also refers to “thioamide”. [00134] The term “carbocyclyl,” as used herein, refers to a saturated or unsaturated, non- aromatic, monocyclic or polycyclic (e.g., bicyclic, tricyclic) hydrocarbon ring system having the specified number of ring carbon atoms. Thus, “(C5-C8)carbocyclyl” means a carbocyclyl ring system having from 5 to 8 ring carbons. A carbocyclyl can be saturated (i.e., a
cycloalkyl). Alternatively, a carbocyclyl can be unsaturated (i.e., contain at least one degree of unsaturation, as in at least one carbon-carbon double bond or triple bond). A carbocyclyl ring system may consist of monocyclic rings, fused rings, bridged rings and spirocyclic rings. Examples of carbocyclyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, and norbornyl. [00135] The term “cycloalkyl,” as used herein, refers to a saturated, monocyclic or polycyclic (e.g., bicyclic, tricyclic), aliphatic, hydrocarbon ring system having the specified number of carbon atoms. Thus, “(C5-C8)cycloalkyl” means a cycloalkyl ring system having from 5 to 8 ring carbons. Examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and norbornyl. [00136] “Cycloalkoxy,” as used herein, refers to a cycloalkyl ring system attached through an oxygen linking atom. “(C3-C7)cycloalkoxy” refers to a cycloalkoxy group in which a (C3- C7)cycloalkyl is attached through an oxygen linking atom. Examples of cycloalkoxy groups include, but are not limited to, cyclopropyloxy, cyclobutyloxy, cyclopentyloxy and cyclohexyloxy. [00137] The term “aryl,” as used herein, refers to a monocyclic or polycyclic, aromatic, carbocyclic ring system having the specified number of ring atoms. Thus, “(C6)aryl” refers to an aryl ring system having six ring carbon atoms. Typically, aryl has 6 to 15, 6 to 10, 6 to 9, or 6 ring carbon atoms. An aryl ring system may consist of a single ring or a fused ring system. Examples of aryl include, but are not limited to, phenyl and napthyl. [00138] The term “arylalkyl” as used herein, refers to an alkyl radical wherein one or more (e.g., one) hydrogen atoms is each independently replaced by an aryl, wherein alkyl and aryl are as described herein. Examples of aralkyl include, but are not limited to, benzyl. [00139] The term “heteroaryl,” as used herein, refers to a monocyclic or polycyclic, aromatic, hydrocarbon ring system having the specified number of ring atoms, wherein at least one carbon atom in the ring has been replaced with a heteroatom. Thus, “(C5- C6)heteroaryl” refers to a heteroaryl ring system having five or six ring atoms. Typically, heteroaryl has 5 to 15, 5 to 10, 5 to 9, or 5 to 6 ring atoms. A heteroaryl ring system may consist of a single ring or a fused ring system. A typical monocyclic heteroaryl is a 5- to 6- membered ring containing one to three heteroatoms (e.g., one, two or three) independently selected from oxygen, sulfur and nitrogen, and a typical fused heteroaryl ring system is a 9- to 10-membered ring system containing one to four heteroatoms independently selected from oxygen, sulfur and nitrogen. The fused heteroaryl ring system may consist of two heteroaryl
rings fused together or a heteroaryl ring fused to an aryl ring (e.g., phenyl). Examples of heteroaryl include, but are not limited to, pyrrolyl, pyridyl, pyrazolyl, indolyl, indolinyl, isoindolinyl, indazolyl, thienyl, furanyl, benzofuranyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, oxazolyl, isoxazolyl, imidazolyl, triazolyl, tetrazolyl, triazinyl, pyrimidinyl, pyrazinyl, thiazolyl, purinyl, benzimidazolyl, quinolinyl, isoquinolinyl, quinoxalinyl, tetrahydroquinolinyl, benzofuranyl, benzopyranyl, benzothiophenyl, benzoimidazolyl, benzoxazolyl, 1H-benzo[d][1,2,3]triazolyl, and the like. [00140] The term “heterocyclyl,” as used herein, refers to a saturated or partially saturated, non-aromatic, monocyclic or polycyclic (e.g., bicyclic, tricyclic) ring system having the specified number of ring atoms, wherein at least one carbon atom in the ring system has been replaced with a heteroatom independently selected from oxygen, sulfur and nitrogen. Thus, “(C3-C7)heterocyclyl” means a heterocyclyl having from 3-7 ring atoms. “Heterocyclyl” includes monocyclic rings, fused rings, bridged rings and spirocyclic rings. In some embodiments, heterocyclyl is (C3-C7)heterocyclyl, (C5-C6)heterocyclyl, (C5)heterocyclyl or (C6)heterocyclyl. In some embodiments, heterocyclyl (e.g., (C3-C7)heterocyclyl) is a saturated heterocyclyl. [00141] Heterocyclyl can contain 1 to 7, 1 to 5, 1 to 3, 1 to 2, 1 or 2 heteroatoms. A heterocyclyl can be attached at a heteroatom or a carbon atom, as valencies permit. Examples of heterocyclyl include, but are not limited to, azetidinyl, oxetanyl, piperidinyl, piperazinyl, pyrrolyl, pyrrolidinyl, imidazolidinyl, imidazolinyl, morpholinyl, tetrahydrofuranyl, tetrahydrothiophenyl, tetrahydrothiopyranyl, tetrahydropyranyl, 1,3- dioxolyl, 1,4-dioxanyl, 1,4-oxathianyl, dihydrobenzofuranyl, hexahydropyrimidinyl, 3- azabicyclo[3.1.0]hexanyl, azepanyl, 3-azabicyclo[3.2.2]nonanyl, decahydroisoquinolinyl, 2- azaspiro[3.3]heptanyl, 2-oxa-6-azaspiro[3.3]heptanyl, 2,6-diazaspiro[3.3]heptanyl, 8-aza- bicyclo[3.2.1]octanyl, 3,8-diazabicyclo[3.2.1]octanyl, 3-oxa-8-aza-bicyclo[3.2.1]octanyl, 8- oxa-3-aza-bicyclo[3.2.1]octanyl, 2-oxa-5-aza-bicyclo[2.2.1]heptanyl, 2,5-diaza- bicyclo[2.2.1]heptanyl, 1,4-dioxa-8-aza-spiro[4.5]decanyl, 3-oxa-1,8-diazaspiro[4.5]decanyl, octahydropyrrolo[3,2-b]pyrrolyl, tetrahydro-2H-pyran, 1,2-dihydropyridine, 1,6- dihydropyridinyl, 1,3-dihydroisobenzofuranyl, and the like. [00142] The term “heterocyclylalkyl” as used herein, refers to an alkyl radical wherein one or more (e.g., one) hydrogen atoms is each independently replaced by a heterocyclyl, wherein alkyl and heterocyclyl are as described herein. “Heterocyclyl(C1-C6)alkyl” refers to a (C1- C6)alkyl wherein one or more hydrogen atoms is each independently replaced by a
heterocyclyl. Examples of heterocyclylalkyl include, but are not limited to, 2-morpholinoethyl (
[00143] The term “fused heterocyclyl” refers to a heterocyclyl, as defined above, which is fused to an aryl (e.g., phenyl) or a heteroaryl ring as defined above. Examples of such fused heterocyclyl include, but are not limited to, 1,2,3,4-tetrahydroisoquinoline, indoline, isoindoline, benzo[d][1,3]dioxole, 1,2,3,4-tetrahydro-2,7-naphthyridine, 5,6,7,8-tetrahydro- 1,7-naphthyridine, 1,2,3,4-tetrahydro-2,6-naphthyridine, 5,6,7,8-tetrahydro-1,6- naphthyridine, 2,3,4,5-tetrahydro-1H-benzo[d]azepine, 1,2,3,4-tetrahydro-1,4- epiminonaphthalene, 2,3-dihydrobenzofurane, 5,6,7,8-tetrahydropyrido[3,4-b]pyrazine, and the like. In some embodiments, the fused heterocyclyl is benzo[d][1,3]dioxole, optionally substituted indole, (e.g., 1H-indole, 1-methyl-1H-indole, di-tert-butyl 2,2'-((5-(1H-indol-1- yl)-5-oxopentyl)azanediyl)diacetate, tert-butyl indoline-1-carboxylate), quinoxaline, quinoline, isoquinoline, indoline, 1,3-dihydroisobenzofuran, 2,3-dihydrobenzofuran, optionally substituted 1,2,3,4-tetrahydroquinoline, (e.g., 1-methyl-1,2,3,4- tetrahydroquinoline, tert-butyl 3,4-dihydroquinoline-1(2H)-carboxylate, 1-(3,4- dihydroquinolin-1(2H)-yl)ethan-1-one). In some embodiments, the fused heterocyclyl is indoline, isoindoline, dihydrobenzo[d]imidazole, tetrahydroquinoline, tetrahydroisoquinoline, tetrahydroquinoxaline, dihydrobenzofuran, dihydroisobenzofuran, benzo[d][1,3]dioxole, chromane, or dihydrobenzo[b][1,4]dioxine. In some embodiments, the fused heterocyclyl is 6,7-dihydro-5H-pyrrolo[3,4-b]pyridine or 5,6,7,8-tetrahydro-1,7-naphthyridine. [00144] The term “monocyclic” refers to a ring system consisting of a single ring. Examples of monocyclic rings include, but are not limited to, phenyl, pyridyl, piperazinyl, morpholino, tetrahydropyranyl, imidazole, and furanyl and thiophenyl. [00145] The term “bicyclic” refers to a ring system consisting of two rings. Examples of bicyclic rings include, but are not limited to, naphthyl, quinolinyl, indolyl and indoline. [00146] The term “spirocyclic ring” or “spiro” refers to a carbocyclyl or heterocyclyl, as described herein, which is attached to a second carbocyclyl or second heterocyclyl group by a single carbon atom. Examples of such spirocyclic rings include, but are not limited to
[00147] The term “fused ring” or “fused” refers to any ring (e.g., an aryl ring, heteroaryl ring, carbocyclyl ring or heterocyclyl ring) that shares two adjacent atoms with a second ring (e.g., an aryl ring, heteroaryl ring, carbocyclyl ring or heterocyclyl ring). Examples of fused rings include, but are not limited to,
and
[00148] When “ene” is added after the “yl” at the end of any of the previously defined terms to form a new term, the new term refers to a radical formed by removing one hydrogen atom from the original term from which the new term is derived. For example, “alkylene” refers to a divalent radical formed by removing one hydrogen atom from an alkyl group, and “methylene” refers to a divalent radical, -CH2-, derived from removing one hydrogen atom from methyl. Other examples of divalent radicals formed by removing one hydrogen atom from a parent group include, but are not limited to: carbocyclene, cycloalkylene, heterocyclylene, arylene, and heteroarylene, which are derived from carbocyclyl, cycloalkyl, heterocyclyl, aryl and heteroaryl, respectively. [00149] The term “substituted,” as used herein, means that at least one (e.g., one, two, three, four, five, six, etc., from one to five, from one to three, one or two) hydrogen atom is replaced with a non-hydrogen substituent, provided that normal valencies are maintained and that the substitution results in a stable compound. Unless otherwise indicated, an “optionally substituted” group can have a substituent at each substitutable position of the group. In the compound of structural formula I:
, for example, it will be appreciated that any substitutable atom in the ring containing X and Y is optionally substituted because m is, in some embodiments, 0, 1 or 2. It will be further appreciated that X and Y, when they are -C(H)- and m is not 0, are each independently optionally substituted. For example, when X is -O- and Y is -C(H)-, Y is unsubstituted, as in the compound of
structural formula IV:
when R7 is hydrogen, or substituted, as in the compound of structural formula II when R7 is not hydrogen. Similarly, any substituted atom in the ring containing A1 in a compound of structural formula IIIa:
is optionally substituted because p is, in some embodiments, 0, 1 or 2, and, further, A1, when it is -C(H)- and p is not 0, is optionally substituted by R3. When more than one position in any given structure may be substituted with more than one substituent selected from a specified group (e.g., when m is 2, p is 2, or m is 1 and p is 1 or 2), the substituent can be the same or different at every position. Alternatively, an “optionally substituted group” can be unsubstituted (e.g., when m and/or p is 0). [00150] When a substituent is oxo, then two hydrogens on a single atom are replaced with the substituent. Oxo substituents are not present on aromatic moieties. [00151] When there is a nitrogen atom(s) on a compound of the present disclosure, the nitrogen atom(s) may be independently converted to N-oxides by treatment with an oxidizing agent (e.g., mCPBA and/or hydrogen peroxide) to afford other compounds of the present disclosure. Thus, shown and claimed nitrogen atoms are considered to cover both the shown nitrogen and its N-oxide (N ^O) derivative. [00152] When any variable occurs more than one time in any constituent or formula for a compound, its definition at each occurrence is independent of its definition at every other occurrence. Thus, for example, if a group is shown to be substituted with 0-3 substituents, then said group may be unsubstituted or substituted with up to three substituents, and each substituent is selected independently from the other substituent(s). [00153] When a bond to a substituent is shown to cross a bond connecting two atoms in a ring (as the bond to R1 in structural formula I) or to cross a circle denoting a ring (as the bond to R3 in structural formula I), then such substituent may be bonded to any substitutable atom in the ring. Further, when the ring the bond to the substituent crosses into is polycyclic (e.g., bicyclic, as in the ring system in structural formula I containing X and Y), the substituent
may be bonded to any substitutable atom of the ring or ring system the bond to the substituent crosses into. When a substituent is listed without indicating the atom to which such substituent is bonded to the rest of the compound of a given formula, then such substituent may be bonded via any atom in such substituent. [00154] Combinations of substituents and/or variables are permissible only if such combinations result in stable compounds. [00155] As a person of ordinary skill in the art would understand, for example, a ketone (-C(H)C(O)) group in a molecule may tautomerize to its enol form (-C=C(OH)). This disclosure is intended to cover all possible tautomers even when a structure depicts only one of them. [00156] The bicyclic ring containing X and Y is denoted with aromatic conjugation circles
in formula I, and is understood to include the following resonance structures
and
when X is -O- and Y is -C(H)-; and the following resonance structures
and
when Y is -O- and X is -C(H)-. [00157] The phrase “pharmaceutically acceptable” means that the substance or composition the phrase modifies must be, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. If a substance is part of a composition or formulation, the substance must also be compatible chemically and/or toxicologically with the other ingredients in the composition or formulation. [00158] Unless specified otherwise, the term “compounds of the present disclosure” refers to a compound of any structural formula depicted herein (e.g., a compound of Formula I, a subformula of a compound of Formula I), as well as isomers, such as stereoisomers (including diastereoisomers, enantiomers and racemates), geometrical isomers, conformational isomers (including rotamers and astropisomers), tautomers, isotopically labeled compounds (including deuterium substitutions), and inherently formed moieties (e.g.,
polymorphs and/or solvates, such as hydrates) thereof. When a moiety is present that is capable of forming a salt, then salts are included as well, in particular, pharmaceutically acceptable salts. [00159] Compounds of the present disclosure may have asymmetric centers, chiral axes, and chiral planes (e.g., as described in: E. L. Eliel and S. H. Wilen, Stereo-chemistry of Carbon Compounds, John Wiley & Sons, New York, 1994, pages 1119-1190), and occur as racemic mixtures, individual isomers (e.g., diastereomers, enantiomers, geometrical isomers, conformational isomers (including rotamers and atropisomers), tautomers) and intermediate mixtures, with all possible isomers and mixtures thereof being included in the present invention. [00160] As used herein, the term “isomers” refers to different compounds that have the same molecular formula but differ in arrangement and configuration of the atoms. [00161] “Enantiomers” are a pair of stereoisomers that are non-superimposable mirror images of each other. A 1:1 mixture of a pair of enantiomers is a “racemic” mixture. “Racemate” or “racemic” is used to designate a racemic mixture where appropriate. When designating the stereochemistry for the compounds of the present disclosure, a single stereoisomer with known relative and absolute configuration of the two chiral centers is designated using the conventional RS system (e.g., (1S,2S)); a single stereoisomer with known relative configuration but unknown absolute configuration is designated with stars (e.g., (1R*,2R*)); and a racemate with two letters (e.g., (1RS,2RS) as a racemic mixture of (1R,2R) and (1S,2S); (1RS,2SR) as a racemic mixture of (1R,2S) and (1S,2R)). [00162] “Diastereoisomers” are stereoisomers that have at least two asymmetric atoms, but which are not mirror-images of each other. The absolute stereochemistry is specified according to the Cahn-Ingold-Prelog R-S system. When a compound is a pure enantiomer, the stereochemistry at each chiral carbon may be specified by either R or S. Resolved compounds whose absolute configuration is unknown can be designated (+) or (–) depending on the direction (dextro- or levorotatory) which they rotate plane polarized light at the wavelength of the sodium D line. Alternatively, the resolved compounds can be defined by the respective retention times for the corresponding enantiomers/diastereomers via chiral HPLC. [00163] Geometric isomers may occur when a compound contains a double bond or some other feature that gives the molecule a certain amount of structural rigidity. If the compound contains a double bond, the double bond may be E- or Z-configuration. If the compound
contains a disubstituted cycloalkyl, the cycloalkyl substituent may have a cis- or trans- configuration. [00164] Conformational isomers (or conformers) are isomers that can differ by rotations about one or more bonds. Rotamers are conformers that differ by rotation about only a single bond. [00165] The term “atropisomer,” as used herein, refers to a structural isomer based on axial or planar chirality resulting from restricted rotation in the molecule. [00166] Optically active (R)- and (S)- isomers may be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques (e.g., separated on chiral SFC or HPLC chromatography columns, such as CHIRALPAK® and CHIRALCEL® columns available from DAICEL Corp. or other equivalent columns, using the appropriate solvent or mixture of solvents to achieve suitable separation). [00167] The compounds of the present disclosure can be isolated in optically active or racemic forms. Optically active forms may be prepared by resolution of racemic forms or by synthesis from optically active starting materials. All processes used to prepare compounds of the present disclosure and intermediates made therein are considered to be part of the present disclosure. When enantiomeric or diastereomeric products are prepared, they may be separated by conventional methods, for example, by chromatography or fractional crystallization. [00168] Depending on the process conditions, the end products of the present disclosure are obtained either in free (neutral) or salt form. Both the free form and the salts of these end products are within the scope of the present disclosure. If so desired, one form of a compound may be converted into another form. A free base or acid may be converted into a salt; a salt may be converted into the free compound or another salt; a mixture of isomeric compounds of the present disclosure may be separated into the individual isomers. [00169] The phrase “pharmaceutically acceptable” means that the substance or composition the phrase modifies must be, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. If a substance is part of a composition or formulation, the substance must also be compatible chemically and/or toxicologically with the other ingredients in the composition or formulation.
[00170] As used herein, “pharmaceutically acceptable salts” refers to salts derived from suitable inorganic and organic acids and inorganic and organic bases that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are preferred. However, other salts may be useful, e.g., in isolation or purification steps which may be employed during preparation, and thus, are contemplated to be within the scope of the present disclosure. [00171] Pharmaceutically acceptable acid addition salts can be formed from inorganic acids and organic acids. Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, toluenesulfonic acid, sulfosalicylic acid, and the like. Pharmaceutically acceptable acid addition salts include, but are not limited to, acetate, ascorbate, adipate, aspartate, benzoate, besylate, bromide/hydrobromide, bicarbonate/carbonate, bisulfate/sulfate, camphorsulfonate, caprate, chloride/hydrochloride, chlortheophyllonate, citrate, ethanedisulfonate, fumarate, gluceptate, gluconate, glucuronate, glutamate, glutarate, glycolate, hippurate, hydroiodide/iodide, isethionate, lactate, lactobionate, laurylsulfate, malate, maleate, malonate/hydroxymalonate, mandelate, mesylate, methylsulphate, mucate, naphthoate, napsylate, nicotinate, nitrate, octadecanoate, oleate, oxalate, palmitate, pamoate, phenylacetate, phosphate/hydrogen phosphate/dihydrogen phosphate, polygalacturonate, propionate, salicylates, stearate, succinate, sulfamate, sulfosalicylate, tartrate, tosylate, trifluoroacetate and xinafoate salts. [00172] Pharmaceutically acceptable base addition salts can be formed from inorganic and organic bases. Inorganic bases from which salts can be derived include, for example, ammonium salts and metals from columns I to XII of the periodic table. In certain embodiments, a base addition salt is derived from sodium, potassium, ammonium, calcium, magnesium, iron, silver, zinc, or copper; particularly suitable base addition salts include ammonium, potassium, sodium, calcium and magnesium salts. Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion-exchange
resins, and the like. Examples of organic amines include, but are not limited to, isopropylamine, benzathine, cholinate, diethanolamine, diethylamine, lysine, meglumine, piperazine and tromethamine. [00173] A salt (e.g., pharmaceutically acceptable salt) of a compound of the present disclosure can be synthesized from the parent compound that contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, nonaqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are preferred. [00174] It will be understood that when the compound of the present disclosure contains more than one basic moiety or more than one acidic moiety, each such moiety can independently be involved in forming an acid addition salt form or base addition salt form, with all possible salt forms being included in this disclosure. Further, when two or more moieties of a compound of the present disclosure are in salt form, the anions or cations forming the two or more salt forms can be the same or different. Typically, the anions or cations forming the two or more salt forms are the same. Typical molar ratios of an anion or cation in a salt of a compound of the present disclosure to the compound of the present disclosure are 3:1, 2:1, 1:1, 2:1, 3:1, 4:1 and 5:1. In some embodiments, the molar ratio of an anion or cation (e.g., anion) in a salt of a compound of the present disclosure to the compound of the present disclosure is 1:1 (e.g., as in the monohydrochloride salt of Compound 6). In some embodiments, the molar ratio of an anion or cation (e.g., anion) in a salt of a compound of the present disclosure to the compound of the present disclosure is 2:1 (e.g., as in the dihydrochloride salt of Compound 4). [00175] Lists of suitable salts are found in Allen, L.V., Jr., ed., Remington: The Science and Practice of Pharmacy, 22nd Edition, Pharmaceutical Press, London, UK (2012), the relevant disclosure of which is hereby incorporated by reference in its entirety. [00176] Compounds described herein are also provided, and can be administered, as a free base. [00177] Any formula given herein is also intended to represent unlabeled forms as well as isotopically labeled forms of the compounds. lsotopically labeled compounds have structures depicted by the formulas given herein except that one or more atoms are replaced by an atom having a selected atomic mass or mass number. Examples of isotopes that can be
incorporated into compounds of the present disclosure include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine and iodine, such as 2H, 3H, 11C, 13C, 14C, 15N, 18F, 31P, 32P, 35S, 36Cl, 123I, 124I and 125I, respectively. The present disclosure includes various isotopically labeled compounds as defined herein, for example those into which radioactive isotopes, such as 3H and 14C, or those into which non-radioactive isotopes, such as 2H and 13C are present. Such isotopically labelled compounds are useful in metabolic studies (with 14C), reaction kinetic studies (with, for example 2H or 3H), detection or imaging techniques, such as positron emission tomography (PET) or single-photon emission computed tomography (SPECT) including drug or substrate tissue distribution assays, or in radioactive treatment of patients. In particular, an 18F or labeled compound may be particularly desirable for PET or SPECT studies. [00178] Further, substitution with heavier isotopes, particularly deuterium (i.e., 2H or D) may afford certain therapeutic advantages resulting from greater metabolic stability, for example, increased in vivo half-life or reduced dosage requirements or an improvement in therapeutic index. It is understood that deuterium in this context is regarded as a substituent of a compound of the present disclosure. The concentration of such a heavier isotope, specifically deuterium, may be defined by the isotopic enrichment factor. The term “isotopic enrichment factor,” as used herein, means the ratio between the isotopic abundance and the natural abundance of a specified isotope. If a substituent in a compound of this present disclosure is denoted deuterium, such compound has an isotopic enrichment factor for each designated deuterium atom of at least 3500 (52.5% deuterium incorporation at each designated deuterium atom), at least 4000 (60% deuterium incorporation), at least 4500 (67.5% deuterium incorporation), at least 5000 (75% deuterium incorporation), at least 5500 (82.5% deuterium incorporation), at least 6000 (90% deuterium incorporation), at least 6333.3 (95% deuterium incorporation), at least 6466.7 (97% deuterium incorporation), at least 6600 (99% deuterium incorporation), or at least 6633.3 (99.5% deuterium incorporation). [00179] Isotopically labeled compounds of the present disclosure can generally be prepared by conventional techniques known to those skilled in the art or by processes disclosed in the schemes or in the examples and preparations described below (or analogous processes to those described hereinbelow), by substituting an appropriate or readily available isotopically labeled reagent for a non-isotopically labeled reagent otherwise employed. Such compounds have a variety of potential uses, e.g., as standards and reagents in determining the
ability of a potential pharmaceutical compound to bind to target proteins or receptors, or for imaging compounds of this disclosure bound to biological receptors in vivo or in vitro. [00180] The term “solvate” means a physical association of a compound of the present disclosure with one or more solvent molecules, whether organic or inorganic. This physical association includes hydrogen bonding. In certain instances, the solvate will be capable of isolation, for example, when one or more solvent molecules are incorporated in the crystal lattice of a crystalline solid. The solvent molecules in the solvate may be present in a regular arrangement and/or a non-ordered arrangement. The solvate may comprise either a stoichiometric or nonstoichiometric amount of the solvent molecules. “Solvate” encompasses both solution phase and solid phase solvates. Examples of solvates include, but are not limited to, hydrates, ethanolates, methanolates, and isopropanolates. Methods of solvation are generally known in the art. [00181] Compounds of the present disclosure can be provided as amorphous solids or crystalline solids. Lyophilization can be employed to provide the compounds of the present disclosure as a solid. [00182] A “pharmaceutically acceptable carrier” refers to media generally accepted in the art for the delivery of biologically active agents to animals, in particular, mammals, including, generally recognized as safe (GRAS) solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drug stabilizers, binders, buffering agents (e.g., maleic acid, tartaric acid, lactic acid, citric acid, acetic acid, sodium bicarbonate, sodium phosphate, and the like), disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, and the like, and combinations thereof, as would be known to those skilled in the art (see, for example, Allen, L.V., Jr. et al., Remington: The Science and Practice of Pharmacy (2 Volumes), 22nd Edition, Pharmaceutical Press (2012). [00183] The term “increased level of DNA damage” is DNA damage occurring in one or more cells relative to a reference level. [00184] The term “DNA damage” refers to breaks, nicks, and mutations of DNA present in a cell. For example, DNA damage can include one or more of single-strand breaks (e.g., nicks), double strand breaks (DSBs), and mutations. DNA damage can be caused, for example, by exposure to a DNA damaging agent, as well as environmental shock, e.g., hyperthermia.
[00185] The term “mutation” refers to a change or difference in the genetic material of a cell as compared to a reference wildtype genetic sequence, e.g., a deletion, an insertion, a SNP, a gene rearrangement, and/or the introduction of a foreign gene or sequence. DNA damage can be identified directly through, for example, mutations, or indirectly through, for example, increased level and/or activity of a DNA damage process or DNA repair protein. In some embodiments, the DNA repair protein is a DNA editing enzyme. [00186] The term “DNA damaging agent” refers to any agent that directly or indirectly damages DNA in such a way that homologous recombination could repair the damage. Non- limiting examples of DNA damaging agents are DNA damaging chemicals, chemotherapeutic agents, radiochemotherapy and ionizing or ultraviolet radiation. Non- limiting examples of DNA damaging chemotherapeutic agents include alkylating agents, nitrosoureas, anti-metabolites, plant alkaloids, plant extracts and radioisotopes. Non-limiting examples of DNA damaging chemotherapeutic agents also include DNA-damaging drugs, for example, 5-fluorouracil (5-FU), capecitabine, S-1 (Tegafur, 5-chloro-2,4-dihydroxypyridine and oxonic acid), 5-ethynyluracil, arabinosylcytosine (ara-C), 5-azacytidine (5-AC), 2' ,2' - difluoro-2' -deoxycytidine (dFdC), purine antimetabolites (mercaptopurine, azathiopurine, thioguanine), gemcitabine hydrochlorine (Gemzar), pentostatin, allopurinol, 2-fluoro- arabinosyl-adenine (2F-ara-A), hydroxyurea, sulfur mustard (bischloroetyhylsulfide), mechlorethamine, melphalan, chlorambucil, cyclophosphamide, ifosfamide, thiotepa, AZQ, mitomycin C, dianhydrogalactitol, dibromoducitol, alkyl sulfonate (busulfan), nitrosoureas (BCNU, CCNU, 4-methyl CCNU or ACNU), procarbazine, decarbazine, rebeccamycin, anthracyclins such as doxorubicin (adriamycin; ADR), daunorubicin (Cerubicine), idarubicin (Idamycin) and epirubicin (Ellence), anthracyclin analogs such as mitoxantrone, actinimycin D, non-intercalating topoisomerase inhibitors such as epipodophyllotoxins (etoposide or VP16, teniposide or VM-26), podophylotoxin, bleomycin (Blea), pepleomycin, compounds that form adducts with nucleic acid including platinum derivatives, e.g., cisplatin (CDDP), trans analog of cisplatin, carboplatin, iproplatin, tetraplatin and oxaliplatin, as well as camptothecin, topotecan, irinotecan (CPT-11), and SN-38. Radiation e.g., ultraviolet (UV), infrared (IR), or α-, β-, or γ-radiation, is also a DNA damaging agent. [00187] The terms “malignancy” and “cancer” are used interchangeably herein, and refer to diseases in which abnormal cells divide without control and can invade nearby tissues. Malignant cells can also spread to other parts of the body through the blood and lymph systems. There are several main types of malignancy. Carcinoma is a malignancy that begins
in the skin or in tissues that line or cover internal organs. Sarcoma is a malignancy that begins in bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. Leukemia is a malignancy that starts in blood-forming tissue, such as the bone marrow, and causes large numbers of abnormal blood cells to be produced and enter the blood. Lymphoma and multiple myeloma are malignancies that begin in the cells of the immune system. Central nervous system cancers are malignancies that begin in the tissues of the brain and spinal cord. [00188] The term “solid tumor,” as used herein, refers to malignancies/cancers formed of abnormal masses of tissue that usually do not contain cysts or liquid areas. Solid tumors are named/classified according to the tissue/cells of origin. Examples include, but are not limited to, sarcomas and carcinomas. [00189] The term “leukemia,” as used herein, refers to hematologic or blood cell malignancies/cancers that begin in blood-forming tissue, such as the bone marrow. Examples include, but are not limited to, chronic leukemia, acute leukemia, acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphocytic leukemia (ALL), acute lymphoblastic leukemia (e.g., B-cell, T-cell) and chronic lymphocytic leukemia (CLL). [00190] The term “lymphoma,” as used herein, refers to lymphatic cell malignancies/cancers that begin in the cells of the immune system. Examples include, but are not limited to, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma and multiple myeloma. [00191] The term “immune deficiency” refers to a condition in which a portion or some portions of cell components constituting an immune system of a subject are defective, dysfunctional or absent. “Immune deficiency” includes deficiencies in which congenital immunity and/or acquired immunity are suppressed and/or decreased. In some embodiments, a subject having an immune deficiency is an immunocompromised subject. Non-limiting examples of immune deficiencies are AIDS, hypogammaglobulinemia, agammaglobulinemia, granulocyte deficiency, chronic granulomatous disease, asplenia, SCID, complement deficiency, and sickle cell anemia. [00192] A “subject” to which administration is contemplated refers to a human (i.e., male or female of any age group, e.g., pediatric subject (e.g., infant, child, or adolescent) or adult subject (e.g., young adult, middle-aged adult, or senior adult)) or non-human animal. In certain embodiments, the non-human animal is a mammal (e.g., primate (e.g., cynomolgus monkey or rhesus monkey), commercially relevant mammal (e.g., cattle, pig, horse, sheep, goat, cat, or dog)), or bird (e.g., commercially relevant bird, such as chicken, duck, goose, or turkey). In certain embodiments, the non-human animal is a fish, reptile, or amphibian. The
non-human animal may be a male or female at any stage of development. The non-human animal may be a transgenic animal or genetically engineered animal. The term “patient” refers to a human subject in need of treatment of a disease. [00193] As used herein, a subject (e.g., a human) is “in need of” a treatment if such subject would benefit biologically, medically or in quality of life from such treatment. [00194] The term “administer,” “administering,” or “administration” refers to implanting, absorbing, ingesting, injecting, inhaling, or otherwise introducing a compound, or a pharmaceutically acceptable salt thereof, or a composition of the foregoing, in or on a subject. [00195] “Treat,” “treating” and “treatment,” as used herein, refer to the administration of a medication or medical care to a subject, such as a human, having a disease or condition of interest, e.g., a cancer, and includes: (i) preventing the disease or condition from occurring in a subject, in particular, when such subject is predisposed to the condition but has not yet been diagnosed as having it; (ii) inhibiting the disease or condition, e.g., arresting its development; (iii) relieving the disease or condition, e.g., causing regression of the disease or condition; and/or (iv) relieving the symptoms resulting from the disease or condition (e.g., pain, weight loss, cough, fatigue, weakness, etc.). [00196] As used herein, “first-line therapy” refers to the first therapy given for a disease or condition. [00197] As used herein, “subsequent therapy” refers to any therapy given after a first-line therapy for a disease or condition. When a first-line therapy includes therapeutic agent(s), a subsequent therapy comprises one or more therapeutic agent(s) that are different from the therapeutic agent(s) of a first-line therapy. In some embodiments, the subsequent therapy is a second-line therapy (i.e., the second therapy given for a disease or condition). In some embodiments, the subsequent therapy is a third-line therapy (i.e., the third therapy given for a disease or condition). In some embodiments, the subsequent therapy is a last-line therapy. [00198] As used herein, “resistant cancer”, “cancer is resistant” and “refractory cancer” refers to cancer that does not respond to a treatment. For example, the cancer may be resistant at the beginning of treatment, or it may become resistant during treatment. The treatment resistance can be occurred by different mechanisms and examples include individual genetic differences, multi-drug resistance, cell death inhibiting (apoptosis suppression), altering in the drug metabolism, epigenetic and drug targets, enhancing DNA repair and gene amplification.
[00199] The term “a therapeutically effective amount,” as used herein, refers to an amount of a therapeutic agent, such as a compound of the present disclosure, that, when administered to a subject, such as a human, is sufficient to effect treatment. The amount of a therapeutic agent that constitutes an “effective amount” will vary depending on the therapeutic agent, the condition being treated and its severity, the manner of administration, the duration of treatment, or the subject to be treated (e.g., age, weight, fitness of the subject), but can be determined routinely by one of ordinary skill in the art based on his own knowledge and this disclosure. In embodiments, an “effective amount” effects treatment as measured by a statistically significant change in one or more indications, symptoms, signs, diagnostic tests, vital signs, and the like. In other embodiments, an “effective amount” manages or prevents a condition as measured by a lack of a statistically significant change in one or more indications, symptoms, signs, diagnostic tests, vital signs, and the like. [00200] The regimen of administration can affect what constitutes a therapeutically effective amount. A compound of the present disclosure can be administered to the subject either prior to or after the onset of a cancer condition. Further, several divided dosages, as well as staggered dosages, can be administered daily or sequentially, or the dose can be continuously infused, or can be a bolus injection. Further, the dosages of the compound(s) of the present disclosure can be proportionally increased or decreased as indicated by the exigencies of the therapeutic or prophylactic situation. Pharmaceutical Compositions and Combinations [00201] Compounds of the present disclosure are typically used in a pharmaceutical composition (e.g., a pharmaceutical composition comprising a compound of the present disclosure, or a pharmaceutically acceptable salt thereof, and one or more pharmaceutically acceptable carriers). A “pharmaceutically acceptable carrier” refers to media generally accepted in the art for the delivery of biologically active agents to animals, in particular, mammals, including, generally recognized as safe (GRAS) solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drug stabilizers, binders, buffering agents (e.g., maleic acid, tartaric acid, lactic acid, citric acid, acetic acid, sodium bicarbonate, sodium phosphate, and the like), disintegration agents, lubricants, sweetening agents, flavoring agents, dyes, and the like, and combinations thereof, as would be known to those skilled in the art (see, for example, Allen, L.V., Jr. et al., Remington: The Science and Practice of Pharmacy (2 Volumes), 22nd Edition, Pharmaceutical Press (2012).
[00202] In one aspect, provided herein is a pharmaceutical composition comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) (e.g., a therapeutically effective amount of a compound of the present disclosure), and a pharmaceutically acceptable carrier. In a further embodiment, the composition comprises at least two pharmaceutically acceptable carriers, such as those described herein. For purposes of the present disclosure, unless designated otherwise, solvates are generally considered compositions. Preferably, pharmaceutically acceptable carriers are sterile. The pharmaceutical composition can be formulated for particular routes of administration such as oral administration, parenteral administration (e.g., intravenous administration) and rectal administration, etc. In addition, the pharmaceutical compositions of the present disclosure can be made up in a solid form (including, without limitation, capsules, tablets, pills, granules, powders or suppositories), or in a liquid form (including, without limitation, solutions, suspensions or emulsions). The pharmaceutical compositions can be subjected to conventional pharmaceutical operations, such as sterilization, and/or can contain conventional inert diluents, lubricating agents, or buffering agents, as well as adjuvants, such as preservatives, stabilizers, wetting agents, emulsifiers and buffers, etc. Typically, the pharmaceutical compositions are tablets or gelatin capsules comprising the active ingredient together with one or more of: a) diluents, e.g., lactose, dextrose, sucrose, mannitol, sorbitol, cellulose and/or glycine; b) lubricants, e.g., silica, talcum, stearic acid, its magnesium or calcium salt and/or polyethyleneglycol; c) binders, e.g., magnesium aluminum silicate, starch paste, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose and/or polyvinylpyrrolidone; d) disintegrants, e.g., starches, agar, alginic acid or its sodium salt, or effervescent mixtures; and e) absorbents, colorants, flavors and sweeteners. Tablets may be either film-coated or enteric-coated according to methods known in the art. [00203] Suitable compositions for oral administration include a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) in the form of tablets, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsion, hard or soft capsules, or syrups or elixirs. Compositions intended for oral use are prepared according to any method known in the art
for the manufacture of pharmaceutical compositions and such compositions can contain one or more agents selected from the group consisting of sweetening agents, flavoring agents, coloring agents and preserving agents in order to provide pharmaceutically elegant and palatable preparations. Tablets may contain the active ingredient in admixture with nontoxic pharmaceutically acceptable excipients which are suitable for the manufacture of tablets. These excipients are, for example, inert diluents, such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch or alginic acid; binding agents, for example, starch, gelatin or acacia; and lubricating agents, for example magnesium stearate, stearic acid or talc. The tablets are uncoated or coated by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monostearate or glyceryl distearate can be employed. Formulations for oral use can be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, for example, calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example, peanut oil, liquid paraffin or olive oil. [00204] Certain injectable compositions comprise a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) in the form of an aqueous isotonic solution or suspension, and certain suppositories comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) are advantageously prepared from fatty emulsions or suspensions. Said compositions may be sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers. In addition, they may also contain other therapeutically valuable substances. Said compositions are prepared according to conventional mixing, granulating or coating methods, respectively, and contain about 0.1-75%, or contain about 1-50%, of the active ingredient. [00205] Suitable compositions for transdermal application include a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) with a suitable carrier. Carriers suitable for transdermal delivery include absorbable pharmacologically acceptable solvents to assist passage through the skin of the host. For example, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with
carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin. [00206] Suitable compositions comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) for topical application, e.g., to the skin and eyes, include aqueous solutions, suspensions, ointments, creams, gels or sprayable formulations, e.g., for delivery by aerosol or the like. Such topical delivery systems will, in particular, be appropriate for dermal application, e.g., for the treatment of skin cancer, e.g., for prophylactic use in sun creams, lotions, sprays and the like. They are thus particularly suited for use in topical, including cosmetic, formulations well-known in the art. Such may contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives. [00207] As used herein, a topical application may also pertain to an inhalation or to an intranasal application. A composition suitable for inhalation or intranasal administration may be conveniently delivered in the form of a dry powder (either alone, as a mixture, for example a dry blend with lactose, or a mixed component particle, for example, with phospholipids) from a dry powder inhaler, or an aerosol spray presentation from a pressurised container, pump, spray, atomizer or nebuliser, with or without the use of a suitable propellant. [00208] The present disclosure further provides anhydrous pharmaceutical compositions and dosage forms comprising a compound provided herein (e.g., a compound of Formula I, or a subformula thereof), or a pharmaceutically acceptable salt thereof, since water may facilitate the degradation of certain compounds. Anhydrous pharmaceutical compositions and dosage forms of the disclosure can be prepared using anhydrous or low moisture- containing ingredients and low moisture or low humidity conditions. An anhydrous pharmaceutical composition may be prepared and stored such that its anhydrous nature is maintained. Accordingly, anhydrous compositions are packaged using materials known to prevent exposure to water such that they can be included in suitable formulary kits. Examples of suitable packaging include, but are not limited to, hermetically sealed foils, plastics, unit dose containers (e.g., vials), blister packs, and strip packs. [00209] The present disclosure further provides pharmaceutical compositions and dosage forms that comprise one or more agents that reduce the rate by which the compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) as an active ingredient will decompose.
Such agents, which are referred to herein as “stabilizers,” include, but are not limited to, antioxidants such as ascorbic acid, pH buffers, or salt buffers, etc. [00210] A compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) is typically formulated into pharmaceutical dosage forms to provide an easily controllable dosage of the drug and to give the patient an elegant and easily handleable product. The dosage regimen for the compounds of the present disclosure will, of course, vary depending upon known factors, such as the pharmacodynamic characteristics of the particular agent and its mode and route of administration; the species, age, sex, health, medical condition, and weight of the recipient; the nature and extent of the symptoms; the kind of concurrent treatment; the frequency of treatment; the route of administration; the renal and hepatic function of the patient; and the effect desired. Compounds described herein (e.g., a compound of Formula I, or a subformula thereof), or a pharmaceutically acceptable salt thereof, may be administered in a single daily dose, or the total daily dosage may be administered in divided doses, e.g., two, three, or four times daily. [00211] In certain instances, it may be advantageous to administer a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) in combination with one or more therapeutically active agents. For example, it may be advantageous to administer a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) in combination with one or more therapeutically active agents, e.g., independently selected from an anti-cancer agent (e.g., chemotherapeutic agent), anti-allergic agent, anti-emetic, pain reliever, immunomodulator and cytoprotective agent to treat cancer. [00212] The term “combination therapy” refers to the administration of two or more therapeutic agents to treat a disease, disorder or condition described herein. Such administration encompasses co-administration of the therapeutic agents in a substantially simultaneous manner, such as in a single capsule having a fixed ratio of active ingredients. Alternatively, such administration encompasses co-administration in multiple, or in separate containers (e.g., capsules, powders, and liquids) for each active ingredient. Such administration also encompasses use of each type of therapeutic agent in a sequential manner, either at approximately the same time or at different times. A compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically
acceptable salt of the foregoing) and an additional therapeutic agent(s) can be administered via the same administration route or via different administration routes. Powders and/or liquids may be reconstituted or diluted to a desired dose prior to administration. Typically, the treatment regimen will provide beneficial effects of the drug combination in treating the diseases, conditions or disorders described herein. [00213] In some embodiments, the methods for combination therapies described herein provides an agent known to modulate other pathways, or other components of the same pathway, or even overlapping sets of target enzymes when used in combination with a compound as described herein. In one aspect, such therapy includes but is not limited to the combination of a compound as described herein with chemotherapeutic agents, therapeutic antibodies, and radiation treatment, to provide a synergistic or additive therapeutic effect. [00214] Compositions for use in combination therapies will either be formulated together as a pharmaceutical combination, or provided for separate administration (e.g., associated in a kit). Accordingly, a further embodiment is a pharmaceutical combination comprising a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) (e.g., a therapeutically effective amount of a compound of the present disclosure), and one or more other therapeutic agents (e.g., a therapeutically effective amount of one or more other therapeutic agents). A pharmaceutical combination can further comprise one or more pharmaceutically acceptable carriers, such as one or more of the pharmaceutically acceptable carriers described herein. [00215] Examples of therapies for use in combination with a compound of the present disclosure (e.g., in combination therapy, in a pharmaceutical combination) include standard of care therapies and/or regimens (e.g., standard of care agents), such as first-line standard of care therapies (e.g., chemotherapies) or last-line standard of care therapies (e.g., chemotherapies). Standard of care therapies are therapies that a clinician should use for a certain type of patient, illness and/or clinical circumstance. Often, organizations such as National Comprehensive Cancer Network (NCCN) publish guidelines and/or treatment algorithms setting forth best practices for treatment of certain patients, illnesses and/or clinical circumstances. See nccn.org. These guidelines often establish, set forth and/or summarize standard of care therapies. [00216] In some embodiments, a compound of the present disclosure is administered in combination with a standard of care therapy for ovarian cancer. For example, non-limiting examples of standard of care therapies for ovarian cancer include a platinum analogue (e.g.,
cisplatin, paclitaxel, carboplatin) or a combination including a platinum analogue (e.g., docetaxel and carboplatin; paclitaxel and carboplatin; carboplatin and liposomal doxorubicin (dox); paclitaxel, carboplatin and bevacizumab (bev); carboplatin and gemcitabine (gem)/(bev); carboplatin, liposomal dox and bev; carboplatin, paclitaxel and bev; cisplatin and gemcitabine; oxaliplatin); altretamine; capecitabine; ifosfamide; irinotecan; melphalan; paclitaxel (e.g., albumin-bound paclitaxel); pemetrexed; or vinorelbine. Non-limiting examples of standard of care therapies for ovarian cancer also include a targeted therapy, such as an antibody therapy (e.g., bevacizumab); a PARP inhibitor (e.g., olaparib, rucaparib, niraparib, veliparib, talazoparib); a tyrosine kinase inhibitor (TKI) (e.g, pazopanib); an immunotherapy; an immune checkpoint inhibitor (e.g., PD-1 or PD-L1 inhibitor); pembrolizumab; or a hormone therapy (e.g., tamoxifen, anastrozole, exemestane, letrozole,an LHRH agonist, such as leuprolide acetate, megestrol acetate). Non-limiting examples of standard of care therapies for ovarian cancer further include a hormone therapy (e.g., anastrozole, exemestane, letrozole, leuprolide acetate, megestrol acetate, tamoxifen). Non- limiting examples of standard of care therapies for ovarian cancer additionally include cyclophosphamide; etoposide; sorafenib; or vinorelbine. [00217] In some embodiments, a compound of the present disclosure is administered in combination with a standard of care therapy for pancreatic cancer. Non-limiting examples of standard of care therapies for pancreatic cancer include FOLFIRINOX (a chemotherapy regimen made up of folinic acid, bolus fluorouracil, irinotecan and oxaliplatin); modified FOLFIRINOX regimen (a chemotherapy regimen made up of folinic acid, continuous infusion fluorouracil, irinotecan and oxaliplatin); gemcitabine and abraxane; gemcitibine and capecitabine; olaparib; emcitabine and erlotinib; gemcitabine, docetaxel and capecitabine; larotrectinib; pembrolizumab; gemcitabine; and the triple combination of nab-paclitaxel, gemcitabine and cisplatin. [00218] In some embodiments, a compound of the present disclosure is administered in combination with a standard of care therapy for prostate cancer, including castration resistant prostrate cancer. Non-limiting examples of standard of care therapies for prostate cancer include PARP inhibitors (e.g., olaparib, rucaparib, niraparib, veliparib, talazoparib), LHRH agonists (e.g., goserelin acetate, histrelin acetate, leuprolide acetate, and triptorelin pamoate); LHRH antagonists (e.g., degarelix); anti-androgen receptors (e.g., bicalutamide, flutamide, nilutamide, enzalutamide, apalutamide, darolutamide); corticosteroids (e.g., prednisone, methylprednisolone, hydrocortisone, dexamethasone); estrogens (e.g., diethylstilbestrol);
androgen synthesis inhibitors (e.g., ketoconazole, abiraterone acetate); and androgen deprivation therapies. [00219] In some embodiments, a compound of the present disclosure is administered in combination with a standard of care therapy for multiple myeloma. Non-limiting examples of standard of care therapies for multiple myeloma include proteasome inhibitors such as bortezomib, carfilzomib and marizomib. [00220] Radiation therapy can be administered in combination with a compound of the present disclosure in some embodiments. Exemplary radiation therapies include external- beam therapy, internal radiation therapy, implant radiation, stereotactic radiosurgery, systemic radiation therapy, radiotherapy and permanent or temporary interstitial brachytherapy. The term “brachytherapy,” as used herein, refers to radiation therapy delivered by a spatially confined radioactive material inserted into the body at or near a tumor or other proliferative tissue disease site. The term is intended without limitation to include exposure to radioactive isotopes (e.g., At211, I131, I125, Y90, Re186, Re188, Sm153, Bi212, P32, and radioactive isotopes of Lu). Suitable radiation sources for use as a cell conditioner of the present invention include both solids and liquids. By way of non-limiting example, the radiation source can be a radionuclide, such as I125, I131, Yb169, Ir192 as a solid source, I125 as a solid source, or other radionuclides that emit photons, beta particles, gamma radiation, or other therapeutic rays. The radioactive material can also be a fluid made from any solution of radionuclide(s), e.g., a solution of I125 or I131, or a radioactive fluid can be produced using a slurry of a suitable fluid containing small particles of solid radionuclides, such as Au198, Y90. Moreover, the radionuclide(s) can be embodied in a gel or radioactive micro spheres. [00221] Without being limited by any theory, a compound of the present disclosure can render abnormal cells more sensitive to treatment with radiation for purposes of killing and/or inhibiting the growth of such cells. Accordingly, some embodiments include a method for sensitizing abnormal cells in a mammal to treatment with radiation which comprises administering to the mammal an amount of a compound as described herein, which amount is effective insensitizing abnormal cells to treatment with radiation. The amount of a compound of the present disclosure in this method can be determined according to the means for ascertaining effective amounts of such compounds and salts described herein. In some embodiments, standard of care therapy includes radiation therapy.
[00222] DNA damaging agents can also be used in combination with a compound of the present disclosure. Non-limiting examples of DNA damaging agents include radiation, topoisomerase inhibitors, PARP inhibitors, DNA crosslinking agents and standard of care agents that induce DNA damage, such as DNA crosslinking agents. Particular non-limiting examples of DNA damaging agents include gemcitabine and temozolomide. [00223] Agents that induce endoplasmic reticulum (ER) stress can also be used in combination with a compound of the present disclosure. Non-limiting examples of agents that induce ER stress include agents that increase levels of reactive oxygen species (ROS) (e.g., napabucasin), chaperone inhibitors, HSP90 inhibitors, HSP70 inhibitors, PDI inhibitors and proteasome inhibitors. Further non-limiting examples of agents that induce ER stress include GSK2606414, GSK2656157, STF-083010, tyrosine kinase inhibitor (e.g., sorafenib), phosphor-eif2α phosphatase (e.g., Sal003), diindolylmethane derivatives, proteasome inhibitors (e.g., bortezomib), levistolide A, andrographolide, tolfenamic acid, cantharidin, carnosic acid, casticin, cryptotanshinone, curcumin, flavokawain B, fucoidan, 2-3,4- dihydroxyphenylethanol, 7-dimethoxyflavone, SMIP004 (N-(4-butyl-2-methyl- phenylacetamide), licochalcone A, neferine, paeonol, pardaxin, parthenolide, piperine, polyphenon E, polyphyllin D, resveratrol, dehydrocostuslactone, γ-tocotrienol, Ω- hydroxyundec-9-enoic acid, ampelopsin, ardisianone, genistein, guttiferone H, guggulsterone, marchantin M, sarsasapogenin, saxifragifolin, prodigiosin, quercetin, honokiol, brefeldin A, A-tocopheryl succinate, verrucarin A, vitamin E succinate, ultrafine and zerumbone. See, for example, Walczak, A., et al. Oxidative Medicine and Cellular Longevity Volume 2019, Article ID 5729710, the entire content of which is incorporated herein by reference. [00224] Non-limiting examples of chemotherapeutic agents for use in combination with a compound of the present disclosure (e.g., in combination therapy, in a pharmaceutical combination) include capecitabine (Xeloda®), N4-pentoxycarbonyl-5-deoxy-5- fluorocytidine, carboplatin (Paraplatin®), cisplatin (Platinol®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®), dacarbazine (DTIC-Dome®), doxorubicin hydrochloride (Adriamycin®, Rubex®), fludarabine phosphate (Fludara®), 5-fluorouracil (Adrucil®, Efudex®), gemcitabine (difluorodeoxycitidine), irinotecan (Camptosar®), L- asparaginase (ELSPAR®), 6-mercaptopurine (Purinethol®), methotrexate (Folex®), pentostatin, 6-thioguanine, thiotepa, and topotecan hydrochloride for injection (Hycamptin®). A further example is bortezomib. Yet further examples include gemcitabine,
nabpaclitaxel, erlotinib, fluorouracil and FOLFIRINOX (a chemotherapy regimen made up of folinic acid, fluorouracil, irinotecan and oxaliplatin), or any combination of two or more of the foregoing, e.g., to treat pancreatic cancer (e.g., advanced pancreatic cancer, pancreatic ductal adenocarcinoma). [00225] Anti-cancer agents of particular interest for use in combination with the compounds of the present disclosure include: [00226] Topoisomerase inhibitors, including Type I topoisomerase inhibitors, such as irinotecan, topotecan, and camptothecin, and Type 2 topoisomerase inhibitors, such as etoposide, doxorubicin, and epirubicin. [00227] Poly(ADP-ribose) polymerase (PARP) inhibitors, such as olaparib, rucaparib, niraparib, talazoparib, veliparib, pamiparib and iniparib. [00228] DNA crosslinking agents, such as cisplatin, carboplatin and oxaliplatin. [00229] Agents that increase levels of reactive oxygen species (ROS), such as napabucasin. [00230] PARP inhibitors such as olaparib, rucaparib, niraparib, veliparib and talazoparib. [00231] Purine antimetabolites and/or inhibitors of de novo purine synthesis: pemetrexed (Alimta®), gemcitabine (Gemzar®), 5-fluorouracil (Adrucil®, Carac® and Efudex®), methotrexate (Trexall®), capecitabine (Xeloda®), floxuridine (FUDR®), decitabine (Dacogen®), azacitidine (Vidaza® and Azadine®), 6-mercaptopurine (Purinethol®), cladribine (Leustatin®, Litak® and Movectro®), fludarabine (Fludara®), pentostatin (Nipent®), nelarabine (Arranon®), clofarabine (Clolar® and Evoltra®), and cytarabine (Cytosar®).Anti-angiogenesis agents include, for example, MMP-2 (matrix- metalloproteinase 2) inhibitors, rapamycin, temsirolimus (CCI-779), everolimus (RAD001), sorafenib, sunitinib, and bevacizumab. Examples of useful COX-II inhibitors include CELEBREX™ (alecoxib), valdecoxib, and rofecoxib. Examples of useful matrix metalloproteinase inhibitors are described in WO 96/33172 (published October 24,1996), WO 96/27583 (published March 7,1996), European Patent Application No.97304971.1 (filed July 8,1997), European Patent Application No.99308617.2 (filed October 29, 1999), WO 98/07697 (published February 26,1998), WO 98/03516 (published January 29,1998), WO 98/34918 (published August 13,1998), WO 98/34915 (published August 13,1998), WO 98/33768 (published August 6,1998), WO 98/30566 (published July 16, 1998), European Patent Publication 606,046 (published July 13,1994), European Patent Publication 931, 788 (published July 28,1999), WO 90/05719 (published May 31,1990), WO 99/52910 (published
October 21,1999), WO 99/52889 (published October 21, 1999), WO 99/29667 (published June 17,1999), PCT International Application No. PCT/IB98/01113 (filed July 21,1998), European Patent Application No.99302232.1 (filed March 25,1999), Great Britain Patent Application No.9912961.1 (filed June 3, 1999), United States Provisional Application No. 60/148,464 (filed August 12,1999), United States Patent 5,863, 949 (issued January 26,1999), United States Patent 5,861, 510 (issued January 19,1999), and European Patent Publication 780,386 (published June 25, 1997), all of which are incorporated herein in their entireties by reference. Embodiments of MMP-2 and MMP-9 inhibitors include those that have little or no activity inhibiting MMP-1. Other embodiments include those that selectively inhibit MMP-2 and/or AMP-9 relative to the other matrix-metalloproteinases (i.e., MAP-1, MMP-3, MMP-4, MMP-5, MMP-6, MMP- 7, MMP-8, MMP-10, MMP-ll, MMP-12, and MMP-13). Some specific examples of MMP inhibitors useful in some embodiments are AG-3340, RO 323555, and RS 13-0830. [00232] Autophagy inhibitors include, but are not limited to chloroquine, 3-methyladenine, hydroxychloroquine (Plaquenil™), bafilomycin A1, 5-amino-4-imidazole carboxamide riboside (AICAR), okadaic acid, autophagy-suppressive algal toxins which inhibit protein phosphatases of type 2A or type 1, analogues of cAMP, and drugs which elevate cAMP levels such as adenosine, LY204002, N6-mercaptopurine riboside, and vinblastine. In addition, antisense or siRNA that inhibits expression of proteins including but not limited to ATG5 (which are implicated in autophagy), may also be used. [00233] In other embodiments, agents useful in methods for combination therapy with a compound as described herein include, but are not limited to: erlotinib, afatinib, gefitinib, GDC0941, MLN1117, BYL719 (alpelisib), BKM120 (buparlisib), CYT387, GLPG0634, baricitinib, lestaurtinib, momelotinib, pacritinib, ruxolitinib, TG101348, crizotinib, tivantinib, AMG337, cabozantinib, foretinib, onartuzumab, NVP-AEW541, dasatinib, ponatinib, saracatinib, bosutinib, trametinib, selumetinib, cobimetinib, PD0325901, RO5126766, axitinib, bevacizumab, cetuximab, fostamatinib, imatinib, lapatinib, lenvatinib, ibrutinib, nilotinib, panitumumab, pazopanib, pegaptanib, ranibizumab, sorafenib, sunitinib, SU6656, trastuzumab, tofacitinib, vandetanib, vemurafenib, irinotecan, Taxol, docetaxel, rapamycin or MLN0128. [00234] B-cell lymphoma 2 (BCL-2) inhibitors: venetoclax. [00235] B-cell receptor signaling antagonists (e.g., a Bruton’s tyrosine kinase (BTK) inhibitors): ibrutinib.
[00236] Bromodomain inhibitors. A bromodomain inhibitor inhibits at least one bromodomain protein, such as Brd2, Brd3, Brd4 and/or BrdT, for example Brd4. In some of these embodiments, the bromodomain inhibitor is JQ-1 (Nature 2010 Dec 23;468(7327):1067-73), BI2536 (ACS Chem. Biol.2014 May 16;9(5):1160-71; Boehringer Ingelheim), TG101209 (ACS Chem. Biol.2014 May 16;9(5):1160-71), OTX015 (Mol. Cancer Ther. November 201312; C244; Oncoethix), IBET762 (J Med Chem.2013 Oct 10;56(19):7498-500; GlaxoSmithKline), IBET151 (Bioorg. Med. Chem. Lett.2012 Apr 15;22(8):2968-72; GlaxoSmithKline), PFI-1 (J. Med. Chem.2012 Nov 26;55(22):9831-7; Cancer Res.2013 Jun 1;73(11):3336-46; Structural Genomics Consortium) of CPI-0610 (Constellation Pharmaceuticals). In some embodiments, the bromodomain inhibitor is TG101209, BI2536, OTX015, C244, IBET762, IBET151, or PFI-1. [00237] Histone deacetylase (HDAC) inhibitors. A HDAC inhibitor inhibits at least one HDAC protein. HDAC proteins may be grouped into classes based on homology to yeast HDAC proteins with Class I made up of HDAC1, HDAC2, HDAC3 and HDAC 8; Class IIa made up of HDAC4, HDAC5, HDAC7 and HDAC 9; Class IIb made up of HDAC6 and HDAC10; and Class IV made up of HDAC11. In some of these embodiments, the HDAC inhibitor is trichostatin A, vorinostat (Proc. Natl. Acad. Sci. U.S.A.1998 Mar 17;95(6):3003- 7), givinostat, abexinostat (Mol. Cancer Ther.2006 May;5(5):1309-17), belinostat (Mol. Cancer Ther.2003 Aug;2(8):721-8), panobinostat (Clin. Cancer Res.2006 Aug 1;12(15):4628-35), resminostat (Clin. Cancer Res.2013 Oct 1;19(19):5494-504), quisinostat (Clin. Cancer Res.2013 Aug 1;19(15):4262-72), depsipeptide (Blood.2001 Nov 1;98(9):2865-8), entinostat (Proc. Natl. Acad. Sci. U.S.A.1999 Apr 13;96(8):4592-7), mocetinostat (Bioorg. Med. Chem. Lett.2008 Feb 1;18(3):106771) or valproic acid (EMBO J.2001 Dec 17;20(24):6969-78). For example, in some embodiments the HDAC inhibitor is panobinostat, vorinostat, MS275, belinostat, or LBH589. In some embodiments, the HDAC inhibitor is panobinostat or SAHA. [00238] In embodiments, a compound as described herein is administered in combination with an epidermal growth factor receptor tyrosine kinase (EGFR) inhibitor. Examples of EGFR inhibitors include erlotinib, osimertinib, cetuximab, gefitinib, necitumumab, lapatinib, neratinib, panitumumab, vandetanib, and necitumumab. A combination of a compound as described herein and an EGFR inhibitor may be useful, for example, in the treatment of cancers that are related to EGFR dysregulation, such as non-small-cell lung cancer (NSCLC), pancreatic cancer, breast cancer, and colon cancer. EGFR may be dysregulated, for example,
due to activating mutations in exons 18, 19, 20, or 21. In particular embodiments, the EGFR inhibitor is erlotinib or osimertinib. In particular embodiments, the combination of a compound as described herein and an EGFR inhibitor is used to treat EGFR-mutated NSCLC. In particular embodiments, the combination of a compound as described herein and an EGFR inhibitor is used to treat an EGFR inhibitor-resistant cancer, and the compound as described herein sensitized the cancer to the EGFR inhibitor. [00239] EGFR antibodies: cetuximab (Erbitux®). [00240] MTAP inhibitors: (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)- 4-((methylthio)methyl)pyrrolidin-3-ol (MT-DADMe-Immucillin-A, CAS 653592-04-2). [00241] Methylthioadenosine: ((2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5- ((methylthio)methyl)tetrahydrofuran-3,4-diol, CAS 2457-80-9). [00242] Epidermal growth factor receptor (EGFR) inhibitors: erlotinib hydrochloride (Tarceva®) and gefitnib (Iressa®). [00243] EGFR antibodies: cetuximab (Erbitux®). [00244] MET inhibitors: capmatinib (INC280, CAS 1029712-80-8). [00245] Platelet-derived growth factor (PDGF) receptor inhibitors: imatinib (Gleevec®); linifanib (N-[4-(3-amino-1H-indazol-4-yl)phenyl]-N'-(2-fluoro-5-methylphenyl)urea, also known as ABT 869, available from Genentech); sunitinib malate (Sutent®); quizartinib (AC220, CAS 950769-58-1); pazopanib (Votrient®); axitinib (Inlyta®); sorafenib (Nexavar®); vargatef (BIBF1120, CAS 928326-83-4); telatinib (BAY57-9352, CAS 332012-40-5); vatalanib dihydrochloride (PTK787, CAS 212141-51-0); and motesanib diphosphate (AMG706, CAS 857876-30-3, N-(2,3-dihydro-3,3-dimethyl-1H-indol-6-yl)-2- [(4-pyridinylmethyl)amino]-3-pyridinecarboxamide, described in PCT Publication No. WO 02/066470). [00246] Phosphoinositide 3-kinase (PI3K) inhibitors: 4-[2-(1H-Indazol-4-yl)-6-[[4- (methylsulfonyl)piperazin-1-yl]methyl]thieno[3,2-d]pyrimidin-4-yl]morpholine (also known as GDC 0941 and described in PCT Publication Nos. WO 09/036082 and WO 09/055730); 4-(trifluoromethyl)-5-(2,6-dimorpholinopyrimidin-4-yl)pyridin-2-amine (also known as BKM120 or NVP-BKM120, and described in PCT Publication No. WO 2007/084786); alpelisib (BYL719): (5Z)-5-[[4-(4-Pyridinyl)-6-quinolinyl]methylene]-2,4-thiazolidinedione (GSK1059615, CAS 958852-01-2); 5-[8-methyl-9-(1-methylethyl)-2-(4-morpholinyl)-9H- purin-6-yl]-2-pyrimidinamine (VS-5584, CAS 1246560-33-7) and everolimus (AFINITOR®).
[00247] Cyclin-dependent kinase (CDK) inhibitors: ribociclib (LEE011, CAS 1211441- 98-3); aloisine A; alvocidib (also known as flavopiridol or HMR-1275, 2-(2-chlorophenyl)- 5,7-dihydroxy-8-[(3S,4R)-3-hydroxy-1-methyl-4-piperidinyl]-4-chromenone, and described in U.S. Patent No.5,621,002); crizotinib (PF-02341066, CAS 877399-52-5); 2-(2- chlorophenyl)-5,7-dihydroxy-8-[(2R,3S)-2-(hydroxymethyl)-1-methyl-3-pyrrolidinyl]- 4H-1- benzopyran-4-one, hydrochloride (P276-00, CAS 920113-03-7); 1-methyl-5-[[2-[5- (trifluoromethyl)-1H-imidazol-2-yl]-4-pyridinyl]oxy]-N-[4-(trifluoromethyl)phenyl]-1H- benzimidazol-2-amine (RAF265, CAS 927880-90-8); indisulam (E7070); roscovitine (CYC202); 6-acetyl-8-cyclopentyl-5-methyl-2-(5-piperazin-1-yl-pyridin-2-ylamino)-8H- pyrido[2,3-d]pyrimidin-7-one, hydrochloride (PD0332991); dinaciclib (SCH727965); N-[5- [[(5-tert-butyloxazol-2-yl)methyl]thio]thiazol-2-yl]piperidine-4-carboxamide (BMS 387032, CAS 345627-80-7); 4-[[9-chloro-7-(2,6-difluorophenyl)-5H-pyrimido[5,4-d][2]benzazepin-2- yl]amino]-benzoic acid (MLN8054, CAS 869363-13-3); 5-[3-(4,6-difluoro-1H-benzimidazol- 2-yl)-1H-indazol-5-yl]-N-ethyl-4-methyl-3-pyridinemethanamine (AG-024322, CAS 837364- 57-5); 4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxylic acid N-(piperidin-4-yl)amide (AT7519, CAS 844442-38-2); 4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]-N-[4- (methylsulfonyl)phenyl]-2-pyrimidinamine (AZD5438,CAS 602306-29-6); palbociclib (PD- 0332991); and (2R,3R)-3-[[2-[[3-[[S(R)]-S-cyclopropylsulfonimidoyl]-phenyl]amino]-5- (trifluoromethyl)-4-pyrimidinyl]oxy]-2-butanol (BAY 10000394). [00248] p53-MDM2 inhibitors: (S)-1-(4-chloro-phenyl)-7-isopropoxy-6-methoxy-2-(4- {methyl-[4-(4-methyl-3-oxo-piperazin-1-yl)-trans-cyclohexylmethyl]-amino}-phenyl)-1,4- dihydro-2H-isoquinolin-3-one, (S)-5-(5-chloro-1-methyl-2-oxo-1,2-dihydro-pyridin-3-yl)-6- (4-chloro-phenyl)-2-(2,4-dimethoxy-pyrimidin-5-yl)-1-isopropyl-5,6-dihydro-1H- pyrrolo[3,4-d]imidazol-4-one, [(4S,5R)-2-(4-tert-butyl-2-ethoxyphenyl)-4,5-bis(4- chlorophenyl)-4,5-dimethylimidazol-1-yl]-[4-(3-methylsulfonylpropyl)piperazin-1- yl]methanone (RG7112), 4-[[(2R,3S,4R,5S)-3-(3-chloro-2-fluorophenyl)-4-(4-chloro-2- fluorophenyl)-4-cyano-5-(2,2-dimethylpropyl)pyrrolidine-2-carbonyl]amino]-3- methoxybenzoic acid (RG7388), SAR299155, 2-((3R,5R,6S)-5-(3-chlorophenyl)-6-(4- chlorophenyl)-1-((S)-1-(isopropylsulfonyl)-3-methylbutan-2-yl)-3-methyl-2-oxopiperidin-3- yl)acetic acid (AMG232), {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2- hydroxy-3-pentanyl]-3-methyl-2-oxo-3-piperidinyl}acetic acid (AM-8553), (±)-4-[4,5-bis(4- chlorophenyl)-2-(2-isopropoxy-4-methoxy-phenyl)-4,5-dihydro-imidazole-1-carbonyl]- piperazin-2-one (Nutlin-3), 2-methyl-7-[phenyl(phenylamino)methyl]-8-quinolinol (NSC
66811), 1-N-[2-(1H-indol-3-yl)ethyl]-4-N-pyridin-4-ylbenzene-1,4-diamine (JNJ-26854165), 4-[4,5-bis(3,4-chlorophenyl)-2-(2-isopropoxy-4-methoxy-phenyl)-4,5-dihydro-imidazole-1- carboxyl]-piperazin-2-one (Caylin-1), 4-[4,5-bis(4-trifluoromethyl-phenyl)-2-(2-isopropoxy- 4-methoxy-phenyl)-4,5-dihydro-imidazole-1-carboxyl]-piperazin-2-one (Caylin-2), 5-[[3- dimethylamino)propyl]amino]-3,10-dimethylpyrimido[4,5-b]quinoline-2,4(3H,10H)-dione dihydrochloride (HLI373) and trans-4-iodo-4′-boranyl-chalcone (SC204072). [00249] Mitogen-activated protein kinase (MEK) inhibitors: XL-518 (also known as GDC-0973, CAS No.1029872-29-4, available from ACC Corp.); selumetinib (5-[(4-bromo- 2-chlorophenyl)amino]-4-fluoro-N-(2-hydroxyethoxy)-1-methyl-1H-benzimidazole-6- carboxamide, also known as AZD6244 or ARRY 142886, described in PCT Publication No. WO 2003/077914); 2-[(2-chloro-4-iodophenyl)amino]-N-(cyclopropylmethoxy)-3,4-difluoro- benzamide (also known as CI-1040 or PD184352 and described in PCT Publication No. WO 2000/035436); N-[(2R)-2,3-dihydroxypropoxy]-3,4-difluoro-2-[(2-fluoro-4- iodophenyl)amino]- benzamide (also known as PD0325901 and described in PCT Publication No. WO 2002/006213); 2,3-bis[amino[(2-aminophenyl)thio]methylene]-butanedinitrile (also known as U0126 and described in U.S. Patent No.2,779,780); N-[3,4-difluoro-2-[(2-fluoro- 4-iodophenyl)amino]-6-methoxyphenyl]-1-[(2R)-2,3-dihydroxypropyl]- cyclopropanesulfonamide (also known as RDEA119 or BAY869766 and described in PCT Publication No. WO 2007/014011); (3S,4R,5Z,8S,9S,11E)-14-(ethylamino)-8,9,16- trihydroxy-3,4-dimethyl-3,4,9; 19-tetrahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione] (also known as E6201 and described in PCT Publication No. WO 2003/076424); 2'-amino-3'- methoxyflavone (also known as PD98059 available from Biaffin GmbH & Co., KG, Germany); (R)-3-(2,3-dihydroxypropyl)-6-fluoro-5-(2-fluoro-4-iodophenylamino)-8- methylpyrido[2,3-d]pyrimidine-4,7(3H,8H)-dione (TAK-733, CAS 1035555-63-5); pimasertib (AS-703026, CAS 1204531-26-9); trametinib dimethyl sulfoxide (GSK-1120212, CAS 1204531-25-80); 2-(2-fluoro-4-iodophenylamino)-N-(2-hydroxyethoxy)-1,5-dimethyl- 6-oxo-1,6-dihydropyridine-3-carboxamide (AZD 8330); 3,4-difluoro-2-[(2-fluoro-4- iodophenyl)amino]-N-(2-hydroxyethoxy)-5-[(3-oxo-[1,2]oxazinan-2-yl)methyl]benzamide (CH 4987655 or Ro 4987655); and 5-[(4-bromo-2-fluorophenyl)amino]-4-fluoro-N-(2- hydroxyethoxy)-1-methyl-1H-benzimidazole-6-carboxamide (MEK162). [00250] B-RAF inhibitors: regorafenib (BAY73-4506, CAS 755037-03-7); tuvizanib (AV951, CAS 475108-18-0); vemurafenib (ZELBORAF®, PLX-4032, CAS 918504-65-1); encorafenib (also known as LGX818); 1-methyl-5-[[2-[5-(trifluoromethyl)-1H-imidazol-2-
yl]-4-pyridinyl]oxy]-N-[4-(trifluoromethyl)phenyl-1H-benzimidazol-2-amine (RAF265, CAS 927880-90-8); 5-[1-(2-hydroxyethyl)-3-(pyridin-4-yl)-1H-pyrazol-4-yl]-2,3-dihydroinden-1- one oxime (GDC-0879, CAS 905281-76-7); 5-[2-[4-[2-(dimethylamino)ethoxy]phenyl]-5-(4- pyridinyl)-1H-imidazol-4-yl]-2,3-dihydro-1H-inden-1-one oxime (GSK2118436 or SB590885); (+/-)-methyl (5-(2-(5-chloro-2-methylphenyl)-1-hydroxy-3-oxo-2,3-dihydro-1H- isoindol-1-yl)-1H-benzimidazol-2-yl)carbamate (also known as XL-281 and BMS908662), dabrafenib (TAFINLAR®), and N-(3-(5-chloro-1H-pyrrolo[2,3-b]pyridine-3-carbonyl)-2,4- difluorophenyl)propane-1-sulfonamide (also known as PLX4720). [00251] ALK inhibitors: crizotinib (XALKORI®). [00252] PIM kinase inhibitors: or a pharmaceutically
acceptable salt thereof. [00253] Proteasome inhibitors: bortezomib (VELCADE®), N-5-benzyloxycarbonyl-Ile- Glu(O-tert-butyl)-Ala-leucinal (PSI), carfilzomib and ixazomib, marizomib (NPI-0052), delanzomib (CEP-18770), and O-methyl-N-[(2-methyl-5- thiazolyl)carbonyl]-L-seryl-O- methyl-N-[(1S)-2-[(2R)-2-methyl-2-oxiranyl]-2-oxo-1-(phenylmethyl)ethyl]-L-serinamide (oprozomib, ONX-0912, PR-047) (e.g., bortezomib). An RNAi screen identified TNK1 as a potential modulator of proteasome inhibitor sensitivity in myeloma. Zhu et al., Blood (2011) 117 (14): 3847-3857. In some embodiments, a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) is administered in combination with a proteasome inhibitor described herein, such as bortezomib, e.g., for the treatment of multiple myeloma. [00254] Further non-limiting examples of therapeutic agents that can be used in combinations with a compound as described herein are chemotherapeutic agents, cytotoxic agents, and non-peptide small molecules such as Gleevec® (Imatinib Mesylate), Velcade® (bortezomib), Casodex (bicalutamide), Iressa® (gefitinib), and Adriamycin as well as a host of chemotherapeutic agents. Non-limiting examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide (CYTOXAN®); alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphaoramide and
trimethylolomelamine; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimustine; antibiotics such as aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, calicheamicin, carabicin, carminomycin, carzinophilin, Casodex®, chromomycins, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L- norleucine, doxorubicin, epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine, androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfomithine; elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidamine; mitoguazone; mitoxantrone; mopidamol; nitracrine; pentostatin; phenamet; pirarubicin; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK.RTM.; razoxane; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2',2''- trichlorotriethylamine; urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); cyclophosphamide; thiotepa; taxanes, e.g., paclitaxel (TAXOLTM , Bristol-Myers Squibb Oncology, Princeton, N.J.), docetaxel (TAXOTERETM, Rhone-Poulenc Rorer, Antony, France) and cabazitaxel (JEVTANA, Sanofi Genzyme); retinoic acid; esperamicins; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. [00255] In some embodiments, the chemotherapeutic is selected from the group consisting of mitotic inhibitors (e.g., paclitaxel, nab-paclitaxel), alkylating agents, anti-metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, biological response modifiers, anti-hormones, angiogenesis inhibitors, and anti-androgens.
[00256] More non-limiting examples of chemotherapeutic agents for use in combination with a compound of the present disclosure (e.g., in combination therapy, in a pharmaceutical combination) include capecitabine (Xeloda®), N4-pentoxycarbonyl-5-deoxy-5- fluorocytidine, carboplatin (Paraplatin®), cisplatin (Platinol®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®), dacarbazine (DTIC-Dome®), doxorubicin hydrochloride (Adriamycin®, Rubex®), fludarabine phosphate (Fludara®), 5-fluorouracil (Adrucil®, Efudex®), gemcitabine (difluorodeoxycitidine), irinotecan (Camptosar®), L- asparaginase (ELSPAR®), 6-mercaptopurine (Purinethol®), methotrexate (Folex®), pentostatin, 6-thioguanine, thiotepa, and topotecan hydrochloride for injection (Hycamptin®). [00257] Further non-limiting examples of commonly prescribed anti-cancer drugs include Herceptin®, Avastin®, Erbitux®, Rituxan®, Taxol®, Arimidex®, Taxotere®, ABVD, AVICINE, Abagovomab, Acridine carboxamide, Adecatumumab, 17-N-Allylamino-17- demethoxygeldanamycin, Alpharadin, Alvocidib, 3-Aminopyridine-2-carboxaldehyde thiosemicarbazone, Amonafide, Anthracenedione, Anti-CD22 immunotoxins, Antineoplastic, Antitumorigenic herbs, Apaziquone, Atiprimod, Azathioprine, Belotecan, Bendamustine, BIBW 2992, Biricodar, Brostallicin, Bryostatin, Buthionine sulfoximine, CBV (chemotherapy), Calyculin, cell-cycle nonspecific antineoplastic agents, Dichloroacetic acid, Discodermolide, Elsamitrucin, Enocitabine, Epothilone, Eribulin, Everolimus, Exatecan, Exisulind, Ferruginol, Forodesine, Fosfestrol, ICE chemotherapy regimen, IT-101, Imexon, Imiquimod, Indolocarbazole, Irofulven, Laniquidar, Larotaxel, Lenalidomide, Lucanthone, Lurtotecan, Mafosfamide, Mitozolomide, Nafoxidine, Nedaplatin, Olaparib, Ortataxel, PAC- 1, Pawpaw, Pixantrone, Proteasome inhibitor, Rebeccamycin, Resiquimod, Rubitecan, SN- 38, Salinosporamide A, Sapacitabine, Stanford V, Swainsonine, Talaporfin, Tariquidar, Tegafur-uracil, Temodar, Tesetaxel, Triplatin tetranitrate, Tris(2-chloroethyl)amine, Troxacitabine, Uramustine, Vadimezan, Vinflunine, ZD6126 or Zosuquidar. [00258] Also included as suitable chemotherapeutic cell conditioners are anti-hormonal agents that act to regulate or inhibit hormone action on tumors such as anti-estrogens including for example tamoxifen, (NolvadexTM), raloxifene, aromatase inhibiting 4(5)- imidazoles, 4hydroxytamoxifen, trioxifene, keoxifene, LY 117018, onapristone, and toremifene (Fareston); and anti-androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine;
methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine; navelbine; novantrone; teniposide; daunomycin; aminopterin; xeloda; ibandronate; camptothecin-11 (CPT-11); topoisomeRASe inhibitor RFS 2000; difluoromethylornithine (DMFO). [00259] Non-limiting examples of therapeutic agents that can be used in combinations with a compound as described herein are mTOR inhibitors. Exemplary mTOR inhibitors include, e.g., temsirolimus; ridaforolimus (formally known as deferolimus, (1R,2R,4S)-4- [(2R)-2 [(1R,9S,12S,15R,16E,18R,19R,21R, 23S,24E,26E,28Z,30S,32S,35R)- 1,18- dihydroxy-19,30-dimethoxy-15,17,21,23, 29,35-hexamethyl-2,3,10,14,20-pentaoxo-11,36- dioxa-4- azatricyclo[30.3.1.04,9] hexatriaconta-16,24,26,28-tetraen-12-yl]propyl]-2- methoxycyclohexyl dimethylphosphinate, also known as AP23573 and MK8669, and described in PCT Publication No. WO 03/064383); everolimus (Afinitor® or RAD001); rapamycin (AY22989, Sirolimus®); simapimod (CAS 164301-51-3); emsirolimus, (5-{2,4- Bis[(3S)-3-methylmorpholin-4-yl]pyrido[2,3-d]pyrimidin-7-yl}-2- methoxyphenyl)methanol (AZD8055); 2-Amino-8-[trans-4-(2-hydroxyethoxy)cyclohexyl]-6-(6- methoxy-3-pyridinyl)- 4-methyl-pyrido[2,3-d]pyrimidin-7(8H)-one (PF04691502, CAS 1013101-36-4); and N2- [1,4-dioxo-4-[[4-(4-oxo-8-phenyl-4H-1-benzopyran-2-yl)morpholinium-4- yl]methoxy]butyl]-L- arginylglycyl-L-α-aspartylL-serine- inner salt (SEQ ID NO: 1482) (SF1126, CAS 936487-67-1), and XL765. [00260] In certain other embodiments, a method for treating cancer is provided, the method comprising administering an effective amount of a compound as described herein and a CDK inhibitor to a subject in need thereof. [00261] In embodiments, the CDK inhibitor is a CDK2, CDK4, CDK6, CDK7, CDK8, CDK9, CDK10, and/or CDK11 inhibitor. In some embodiments, the CDK inhibitor is a CDK7, CDK9 inhibitor, or both. In some embodiments, the CDK inhibitor is dinaciclib (ACS Med. Chem. Lett.2010 May 17;1(5):204-8; Mol. Cancer Ther.2010 Aug;9(8):2344-53; Merck, Sharp and Dohme), AT7519 (J. Med. Chem.2008 Aug 28;51(16):4986-99; Astex Pharmaceutical) or palbociclib (J. Med. Chem.2005 Apr 7;48(7):2388-406; Pfizer).In certain embodiments, the CDK inhibitor is a CDK9 inhibitor, such as alvocidib. The alvocidib may be administered as the free bases, as a pharmaceutically acceptable salt or as a prodrug. In certain embodiments, the CDK9 inhibitor is alvocidib. in other embodiments, the CDK9 inhibitor is a pharmaceutically acceptable salt of alvocidib. In other embodiments, the CDK9
inhibitor is a prodrug of alvocidib. Prodrugs of alvocidib include those disclosed in WO 2016/187316, the full disclosure of which is hereby incorporated by reference in its entirety. [00262] In one embodiment, a compound as described herein is administered to a subject in need thereof in combination with an ATR inhibitor, such as AZD6738 or VX-970. The administration may be before, concurrently or after administration of the ATR inhibitor. In one specific embodiment, a compound as described herein is administered to a subject in need thereof in combination with an ATR inhibitor, such as AZD6738 or VX-970 for treatment of non-small cell lung cancer. In a related specific embodiment, a pharmaceutically acceptable salt of a compound as described herein is administered to a subject in need thereof in combination with an ATR inhibitor, such as AZD6738 or VX-970 for treatment of non- small cell lung cancer. In some of the foregoing embodiments, the salt is a tartrate salt. In some of the foregoing embodiments, the ATR inhibitor is AZD6738. In some of the foregoing embodiments, the ATR inhibitor is VX-970. In some embodiments, the salt is a tartrate salt and the ATR inhibitor is AZD6738. In some embodiments, the salt is a tartrate salt and the ATR inhibitor is VX-970. In some of the foregoing embodiments, the ATR inhibitor is a combination of AZD6738 and VX-970. [00263] In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with one or more of the following additional therapeutic agents or combinations of additional therapeutic agents: a platinum analogue (e.g., cisplatin, paclitaxel, carboplatin) or a combination including a platinum analogue (e.g., docetaxel and carboplatin; paclitaxel and carboplatin; carboplatin and liposomal doxorubicin (dox); paclitaxel, carboplatin and bevacizumab (bev); carboplatin and gemcitabine (gem)/(bev); carboplatin, liposomal dox and bev; carboplatin, paclitaxel and bev; cisplatin and gemcitabine; oxaliplatin); altretamine; capecitabine; ifosfamide; irinotecan; melphalan; paclitaxel (e.g., albumin-bound paclitaxel); pemetrexed; or vinorelbine, for example, to treat ovarian cancer. In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with one or more of the following additional therapeutic agents or combinations of additional therapeutic agents:; a targeted therapy, such as an antibody therapy (e.g., bevacizumab); a PARP inhibitor (e.g., olaparib, rucaparib, niraparib); a tyrosine kinase inhibitor (TKI) (e.g, pazopanib); an immunotherapy; an immune checkpoint inhibitor (e.g., PD-1 or PD-L1 inhibitor); pembrolizumab; or a hormone therapy (e.g., tamoxifen, anastrozole, exemestane, letrozole,an LHRH agonist, such as leuprolide acetate, megestrol acetate), for example, to treat ovarian cancer. In certain embodiments, a
compound of the present disclosure is administered to a subject in need thereof in combination with a hormone therapy (e.g., anastrozole, exemestane, letrozole, leuprolide acetate, megestrol acetate, tamoxifen), for example, to treat ovarian cancer. In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with one or more of the following additional therapeutic agents: cyclophosphamide; etoposide; sorafenib; or vinorelbine, for example, to treat ovarian cancer. [00264] In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with one or more of the following additional therapeutic agents or combinations of additional therapeutic agents: FOLFIRINOX; modified FOLFIRINOX regimen; gemcitabine and abraxane; gemcitibine and capecitabine; olaparib; emcitabine and erlotinib; emcitabine, docetaxel and capecitabine; larotrectinib; or pembrolizumab, for example, to treat pancreatic cancer. In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with protein-bound paclitaxel, gemcitabine and cisplatin, for example, to treat pancreatic cancer. [00265] In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with one or more of the following additional therapeutic agents: an LHRH agonist (e.g., goserelin acetate, histrelin acetate, leuprolide acetate, and triptorelin pamoate); an LHRH antagonist (e.g., degarelix); an anti-androgen (e.g., bicalutamide, flutamide, nilutamide, enzalutamide, apalutamide, darolutamide); a corticosteroid (e.g., prednisone, methylprednisolone, hydrocortisone, dexamethasone); an estrogen (e.g., diethylstilbestrol); an androgen synthesis inhibitor (e.g., ketoconazole, abiraterone acetate); or an androgen deprivation therapy, for example, to treat prostate cancer. In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with a PARP inhibitor, for example, to treat prostate cancer (e.g., castration-resistant prostate cancer). In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with an androgen receptor inhibitor (e.g., enzalutamide), for example, to treat prostate cancer (e.g., castration- resistant prostate cancer). [00266] In certain embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with a proteasome inhibitor (e.g., bortezomib), for example, to treat multiple myeloma.
[00267] Some patients may experience allergic reactions to compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) during or after administration. Therefore, anti-allergic agents can be administered in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) to minimize the risk of an allergic reaction. Suitable anti-allergic agents include corticosteroids (Knutson, S., et al., PLoS One, DOI:10.1371/journal.pone.0111840 (2014)), such as dexamethasone (e.g., DECADRON®), beclomethasone (e.g., BECLOVENT®), hydrocortisone (also known as cortisone, hydrocortisone sodium succinate, hydrocortisone sodium phosphate, sold under the tradenames ALA-CORT®, hydrocortisone phosphate, SOLU-CORTEF®, HYDROCORT ACETATE® and LANACORT®), prednisolone (sold under the tradenames DELTA-CORTEL®, ORAPRED®, PEDIAPRED® and PRELONE®), prednisone (sold under the tradenames DELTASONE®, LIQUID RED®, METICORTEN® and ORASONE®), methylprednisolone (also known as 6-methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, sold under the tradenames DURALONE®, MEDRALONE®, MEDROL®, M-PREDNISOL® and SOLU- MEDROL®); antihistamines, such as diphenhydramine (e.g., BENADRYL®), hydroxyzine, and cyproheptadine; and bronchodilators, such as the beta-adrenergic receptor agonists, albuterol (e.g., PROVENTIL®), and terbutaline (BRETHINE®). [00268] Some patients may experience nausea during and after administration of the compounds described herein and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)). Therefore, anti-emetics can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)) to prevent nausea (upper stomach) and vomiting. Suitable anti-emetics include aprepitant (EMEND®), ondansetron (ZOFRAN®), granisetron HCl (KYTRIL®), lorazepam (ATIVAN®, dexamethasone (DECADRON®), prochlorperazine (COMPAZINE®), casopitant (REZONIC® and ZUNRISA®), and combinations thereof. [00269] Medication to alleviate the pain experienced during the treatment period is often prescribed to make the patient more comfortable. Common over-the-counter analgesics, such TYLENOL®, can also be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)). Opioid analgesic drugs such as hydrocodone/paracetamol or hydrocodone/acetaminophen (e.g., VICODIN®), morphine (e.g., ASTRAMORPH® or AVINZA®), oxycodone (e.g., OXYCONTIN® or PERCOCET®), oxymorphone hydrochloride (OPANA®), and fentanyl (e.g.,
DURAGESIC®) can be useful for moderate or severe pain, and can be used in combination with compounds of the present disclosure and/or other therapeutic agent(s) (e.g., anti-cancer agent(s)). [00270] Immunomodulators (e.g., immunooncology agents) of particular interest for use in combination with compounds of the present disclosure include: afutuzumab (available from ROCHE®); pegfilgrastim (NEULASTA®); lenalidomide (CC-5013, REVLIMID®); thalidomide (THALOMID®); actimid (CC4047); and IRX-2 (mixture of human cytokines including interleukin 1, interleukin 2, and interferon γ, CAS 951209-71-5, available from IRX Therapeutics). [00271] Chimeric antigen receptor T-cell (CAR-T) therapies of particular interest for use in combination with compounds of the present disclosure include: tisagenlecleucel (Novartis), axicabtagene ciloleucel (Kite), and tocilizumab (atlizumab; Roche). [00272] Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure include: PD-1 inhibitors, such as pembrolizumab (also known as Lambrolizumab, MK-3475, MK03475, SCH-900475, or KEYTRUDA®) and other anti-PD-1 antibodies (as disclosed in Hamid, O. et al.(2013) New England Journal of Medicine 369 (2): 134–44, US 8,354,509, and WO 2009/114335, incorporated by reference in their entirety), nivolumab (also known as MDX-1106, MDX-1106-04, ONO-4538, BMS-936558, or OPDIVO®) and other anti-PD-1 antibodies (as disclosed in US 8,008,449 and WO 2006/121168, incorporated by reference in their entirety), cemiplimab (LIBTAYO®), spartalizumab (PDR001), pidilizumab (CureTech), MEDI0680 (Medimmune), cemiplimab (REGN2810), dostarlimab (TSR-042), PF-06801591 (Pfizer), sinitilimab, toripalimab, tislelizumab (BGB-A317), camrelizumab (INCSHR1210, SHR-1210), AMP-224 (Amplimmune), CBT-501 (CBT Pharmaceuticals), CBT-502 (CBT Pharmaceuticals), JS001 (Junshi Biosciences), IBI308 (Innovent Biologics), INCSHR1210 (Incyte), also known as SHR-1210 (Hengrui Medicine), BGBA317 (Beigene), BGB-108 (Beigene), BAT-I306 (Bio- Thera Solutions), GLS-010 (Gloria Pharmaceuticals; WuXi Biologics), AK103, AK104, AK105 (Akesio Biopharma; Hangzhou Hansi Biologics; Hanzhong Biologics), LZM009 (Livzon), HLX-10 (Henlius Biotech), MEDI0680 (Medimmune), PDF001 (Novartis), PF- 06801591 (Pfizer), Pidilizumab (CureTech) also known as CT-011 and other anti-PD-1 antibodies (as disclosed in Rosenblatt, J. et al. (2011) J Immunotherapy 34(5): 409-18, US 7,695,715, US 7,332,582, and US 8,686,119, incorporated by reference in their entirety), REGN2810 (Regeneron), TSR-042 (Tesaro) also known as ANB011, or CS1003 (CStone
Pharmaceuticals). MEDI0680 (Medimmune), is also known as AMP-514. MEDI0680 and other anti- PD-1 antibodies are disclosed in US 9,205,148 and WO 2012/145493, incorporated by reference in their entirety. Further known anti-PD-1 antibody molecules include those described, e.g., in WO 2015/112800, WO 2016/092419, WO 2015/085847, WO 2014/179664, WO 2014/194302, WO 2014/209804, WO 2015/200119, US 8,735,553, US 7,488,802, US 8,927,697, US 8,993,731, and US 9,102,727, incorporated by reference in their entirety. In one embodiment, the PD-1 inhibitor is an anti-PD-1 antibody molecule as described in US 2015/0210769, published on July 30, 2015, entitled “Antibody Molecules to PD-1 and Uses Thereof,” incorporated by reference in its entirety. In one embodiment, the anti-PD-1 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP049-Clone-E or BAP049-Clone-B disclosed in US 2015/0210769. The antibody molecules described herein can be made by vectors, host cells, and methods described in US 2015/0210769, incorporated by reference in its entirety. In one embodiment, the PD-1 inhibitor is a peptide that inhibits the PD-1 signaling pathway, e.g., as described in US 8,907,053, incorporated by reference in its entirety. In one embodiment, the PD-1 inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PD-L1 or PD-L2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence). In one embodiment, the PD-1 inhibitor is AMP-224 (B7-DCIg (Amplimmune), e.g., disclosed in WO 2010/027827 and WO 2011/066342, incorporated by reference in their entirety). [00273] Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure also include: PD-L1 inhibitors, such as atezolizumab (also known as MPDL3280A, RG7446, RO5541267, YW243.55.S70, or TECENTRIQ®) and other anti- PD-L1 antibodies as disclosed in US 8,217,149, incorporated by reference in its entirety, avelumab (BAVENCIO® also known as MSB0010718C) and other anti-PD-L1 antibodies as disclosed in WO 2013/079174, incorporated by reference in its entirety, durvalumab (IMFINZI® or MEDI4736) and other anti-PD-L1 antibodies as disclosed in US 8,779,108, incorporated by reference in its entirety), FAZ053 (Novartis), and BMS-936559 (Bristol- Myers Squibb). In certain embodiments, the PD-L1 inhibitor is KN035 (Alphamab; 3DMed; Ascletis Pharma), Envafolimab (TRACON Pharmaceuticals), BMS 936559 (Bristol-Myers Squibb), CS1001 (CStone Pharmaceuticals, Ligand Pharmaceuticals), CX-072 (CytomX Therapeutics), FAZ053 (Novartis), SHR-1316 (Hengrui Medicine), TQB2450 (Chiatai Tianqing), STI-A1014 (Zhaoke Pharm; Lee's Pharm, Lonza, Sorrento Therapeutics,
NantWorks), LYN00102 (Lynkcell), A167 (Harbour BioMed, Kelun Group), BGB-A333 (Beigene), MSB2311 (Mabspace Biosciences), or HLX-20 (Henlius Biotech). In one embodiment, the anti-PD-L1 antibody molecule is BMS-936559 (Bristol-Myers Squibb), also known as MDX-1105 or 12A4. BMS-936559 and other anti-PD-L1 antibodies are disclosed in US 7,943,743 and WO 2015/081158, incorporated by reference in their entirety. In certain embodiments, the PD-L1 inhibitor is Cosibelimab (Fortress Biotech), LY3300054 or Iodapolimab (Eli Lilly), GS-4224 (Gilead Sciences), STI-A1015 (Yuhan, Sorrento Therapeutics), BCD-135 (BIOCAD), Cosibelimab (Dana-Farber Cancer Institute, TG Therapeutics), APL-502 (Apollomics), AK106 (Akeso Biopharma), MSB2311 (Transcenta Holding), TG-1501 (TG Therapeutics), FAZ053 (Novartis). In certain embodiments, the PD- L1 inhibitor is MT-6035 (Molecular Templates), Icaritin and ZKAB001 (Lonza, Lee’s Pharmaceutical Holdings, Sorrento Therapeutics, Shenogen Pharma Group), TRIDENT Antibody (MacroGenics, Zai Lab), YBL-007 (Anh-Gook Pharmaceutical, Y-Biologics), HTI- 1316 (Hengrui Therapeutics), PD-L1 Oncology Project (Weizmann Institute of Sciences), JS003 (Shanghai Junshi Biosciences), ND021 (Numab Therapeutics, CStone Pharmaceuticals), Toca 521 (Tocagen), STT01 (STCube). In certain embodiments, the PD- L1 inhibitor is DB004 (DotBio), MT-5050 (Molecular Templates), KD036 (Kadmon). In one embodiment, the PD-L1 inhibitor is an anti-PD-L1 antibody molecule. In one embodiment, the PD-L1 inhibitor is an anti-PD-L1 antibody molecule as disclosed in US 2016/0108123, published on April 21, 2016, entitled “Antibody Molecules to PD-L1 and Uses Thereof,” incorporated by reference in its entirety. In one embodiment, the anti-PD-L1 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP058- Clone O or BAP058-Clone N disclosed in US 2016/0108123. [00274] Further known anti-PD-L1 antibodies include those described, e.g., in WO 2015/181342, WO 2014/100079, WO 2016/000619, WO 2014/022758, WO 2014/055897, WO 2015/061668, WO 2013/079174, WO 2012/145493, WO 2015/112805, WO 2015/109124, WO 2015/195163, US 8,168,179, US 8,552,154, US 8,460,927, and US 9,175,082, incorporated by reference in their entirety. [00275] In some embodiments, the immune checkpoint inhibitor is a cytotoxic T- lymphocyte-associated modulator. In some embodiments, the immune checkpoint inhibitor aredrugs that target CTLA-4, such as ipilimumab (YERVOY®), tremelimumab, ALPN-202 (Alpine Immune Sciences), RP2 (Replimune), BMS-986249 (Bristol-Myers Squibb), BMS- 986218 (Bristol-Myers Squibb), zalifrelimab (Agenus, Ludwig Institute for Cancer Research,
UroGen Pharma, Recepta Biopharma), BCD-217 (BIOCAD), Onc-392 (Pfizer, OncoImmune), IBI310 (Innovent Biologics), KN046 (Alphamab), MK-1308 (Merck & Co), REGN4659 (Regeneron Pharmaceuticals), XmAb20717 (Xencor), XmAb22841 (Xencor), Anti-CTLA-4 NF (Bristol-Myers Squibb), MEDI5752 (AstraZeneca), AGEN1181 (Agenus), MGD019 (MacroGenics), ATOR-1015 (Alligator Bioscience), BCD-145 (BIOCAD), PSB205 (Sound Biologics), CS1002 (CStone Pharmaceuticals), ADU-1604 (Aduro Biotech), PF-06753512 (Pfizer), BioInvent-Transgene Research Program (Transgene), AGEN2041 (Agenus, Recepta Biopharam), ATOR-1144 (Alligator Bioscience), CTLA-4 Research Project (Sorrento Therapeutics), PD-L1/CTLA-4 Research Project (Sorrento Therapeutics), HLX13 (Shanghai Henlius Biotech), ISA203 (ISA Pharmaceuticals), PRS-300 Series A (Pieris Pharmaceuticals), BA3071 (BioAtla), CTLA4 Cancer Research Program (Biosortia Pharmaceuticals), RP3 (Replimune), CG0161 (Cold Genesys), APL-509 (Apollomics, JSR), AGEN2041 (Ludwig Institute for Cancer Research), APC 101 (Advanced Proteome), CTLA- 4 Inhibitor (Advanced Proteome), BA3071 (BeiGene), BPI-002 (BeyondSpring Pharmaceuticals), CTLA-4 Antibody (Tikcro Technologies), Immuno-Oncology Research Program II (OliPass), PBP1701 (Prestige BioPharma), DB002 (DotBio), DB003 (DotBio), OR-2299 (OncoResponse), NK044 (Alphamab). In certain embodiments, the CTLA-4 inhibitor is ipilimumab. In other embodiments, the CTLA4 inhibitor is tremelimumab. [00276] Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure also include: LAG-3 inhibitors. In some embodiments, the LAG-3 inhibitor is chosen from LAG525 (Novartis), BMS-986016 (Bristol-Myers Squibb), or TSR- 033 (Tesaro). In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule. In one embodiment, the LAG-3 inhibitor is an anti-LAG-3 antibody molecule as disclosed in US 2015/0259420, published on September 17, 2015, entitled “Antibody Molecules to LAG- 3 and Uses Thereof,” incorporated by reference in its entirety. In one embodiment, the anti- LAG-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of BAP050-Clone I or BAP050-Clone J disclosed in US 2015/0259420. In one embodiment, the anti-LAG-3 antibody molecule is BMS-986016 (Bristol-Myers Squibb), also known as BMS986016. BMS-986016 and other anti-LAG-3 antibodies are disclosed in WO 2015/116539 and US 9,505,839, incorporated by reference in their entirety. In one embodiment, the anti-LAG-3 antibody molecule is TSR-033 (Tesaro). In one embodiment, the anti-LAG-3 antibody molecule is IMP731 or GSK2831781 (GSK and Prima BioMed). IMP731 and other anti-LAG-3 antibodies are disclosed in WO 2008/132601 and US
9,244,059, incorporated by reference in their entirety. In one embodiment, the anti-LAG-3 antibody molecule is IMP761 (Prima BioMed). Further known anti-LAG-3 antibodies include those described, e.g., in WO 2008/132601, WO 2010/019570, WO 2014/140180, WO 2015/116539, WO 2015/200119, WO 2016/028672, US 9,244,059, US 9,505,839, incorporated by reference in their entirety. In one embodiment, the anti-LAG-3 inhibitor is a soluble LAG-3 protein, e.g., IMP321 (Prima BioMed), e.g., as disclosed in WO 2009/044273, incorporated by reference in its entirety. [00277] Immune checkpoint inhibitors of interest for use in combination with compounds of the present disclosure also include: Tim-3 inhibitors. In some embodiments, the TIM-3 inhibitor is MGB453 (Novartis) or TSR-022 (Tesaro). In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule. In one embodiment, the TIM-3 inhibitor is an anti-TIM-3 antibody molecule as disclosed in US 2015/0218274, published on August 6, 2015, entitled “Antibody Molecules to TIM-3 and Uses Thereof,” incorporated by reference in its entirety. In one embodiment, the anti-TIM-3 antibody molecule comprises the CDRs, variable regions, heavy chains and/or light chains of ABTIM3-hum11 or ABTIM3-hum03 disclosed in US 2015/0218274. In one embodiment, the anti-TIM-3 antibody molecule is TSR-022 (AnaptysBio/Tesaro). In one embodiment, the anti-TIM-3 antibody molecule comprises one or more of the CDR sequences (or collectively all of the CDR sequences), the heavy chain or light chain variable region sequence, or the heavy chain or light chain sequence of APE5137 or APE5121. APE5137, APE5121, and other anti- TIM-3 antibodies are disclosed in WO 2016/161270, incorporated by reference in its entirety. In one embodiment, the anti-TIM-3 antibody molecule is the antibody clone F38-2E2. Further known anti-TIM-3 antibodies include those described, e.g., in WO 2016/111947, WO 2016/071448, WO 2016/144803, US 8,552,156, US 8,841,418, and US 9,163,087, incorporated by reference in their entirety. [00278] RAD51 depletion leads to accumulation of self-DNA in cytoplasm and upregulation of innate immune response pathway genes (PMID: 28334891, the entire content of which is incorporated herein by reference). In small cell lung cancer (SCLC) tissues, increased RAD51 staining correlated with decreased CD8+ lymphocyte infiltration (PMID: 34620176, the entire content of which is incorporated herein by reference). These reports suggest that RAD51 is involved in immune signaling, and that compounds of the present disclosure could enhance the efficacy of immune checkpoint inhibitors, e.g., in the treatment of lung cancer, such as SCLC.
[00279] In some embodiments, a compound of the present disclosure is administered to a subject in need thereof in combination with an immunooncology agent, such as an immune checkpoint inhibitor. In some embodiments, a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) is administered in combination with an immune checkpoint inhibitor described herein, e.g., to treat pancreatic cancer (e.g., pancreatic ductal adenocarcinoma). In some embodiments, a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) is administered in combination with an immune checkpoint inhibitor described herein and/or (e.g., or) an agent selected from gemcitabine, nabpaclitaxel, erlotinib, fluorouracil or FOLFIRINOX (a chemotherapy regimen made up of folinic acid, fluorouracil, irinotecan and oxaliplatin), or any combination of two or more of the foregoing, e.g., to treat pancreatic cancer (e.g., advanced pancreatic cancer, pancreatic ductal adenocarcinoma). In some embodiments, an immune checkpoint inhibitor is selected from a PD-1 inhibitor, PD-L1 inhibitor, CTLA-4 inhibitor, LAG-3 inhibitor or TIM-3 inhibitor. In some embodiments, an immune checkpoint inhibitor is selected from a PD-1 inhibitor, PD-L1 inhibitor or CTLA-4 inhibitor. In some embodiments, an immune checkpoint inhibitor is a PD-1 inhibitor. In some embodiments, an immune checkpoint inhibitor is a PD-L1 inhibitor. In some embodiments, an immune checkpoint inhibitor is a CTLA-4 inhibitor. [00280] In an effort to protect normal cells from treatment toxicity and to limit organ toxicities, cytoprotective agents (such as neuroprotectants, free-radical scavengers, cardioprotectors, anthracycline extravasation neutralizers, nutrients and the like) may be used as an adjunct therapy in combination with compounds of the present disclosure. Suitable cytoprotective agents include amifostine (ETHYOL®), glutamine, dimesna (TAVOCEPT®), mesna (MESNEX®), dexrazoxane (ZINECARD® or TOTECT®), xaliproden (XAPRILA®), and leucovorin (also known as calcium leucovorin, citrovorum factor and folinic acid). [00281] The structure of the active compounds identified by code numbers, generic or trade names may be taken from the actual edition of the standard compendium “The Merck Index” or from databases, e.g., Patents International (e.g., IMS World Publications). [00282] In another aspect of the present disclosure, a kit comprising two or more separate pharmaceutical compositions, at least one of which contains a compound of the present disclosure is provided. In some embodiments, the kit comprises a pharmaceutical composition comprising a compound of the present disclosure and a pharmaceutical
composition comprising an additional therapeutic agent identified herein for use in combination with a compound of the present disclosure. In one embodiment, the kit comprises means for separately retaining said compositions, such as a container, divided bottle, or divided foil packet. An example of such a kit is a blister pack, as typically used for the packaging of tablets, capsules and the like. [00283] The kit of the present disclosure may be used for administering different dosage forms, for example, oral and parenteral, for administering the separate compositions at different dosage intervals, or for titrating the separate compositions against one another. To assist compliance, the kit of the present disclosure typically comprises directions for administration, e.g., to treat a disease, disorder or condition described herein. [00284] A compound of the present disclosure may also be used to advantage in combination with known therapeutic processes, for example, the administration of hormones or especially radiation. A compound of the present disclosure may in particular be used as a radiosensitizer, especially for the treatment of tumors which exhibit poor sensitivity to radiotherapy. [00285] In the combination therapies of the present disclosure, the compound of the present disclosure and the other therapeutic agent may be manufactured and/or formulated by the same or different manufacturers. Moreover, the compound of the present disclosure and the other therapeutic agent may be brought together into a combination therapy: (i) prior to release of the combination product to physicians (e.g., in the case of a kit comprising the compound of the present disclosure and the other therapeutic agent); (ii) by the physician (or under the guidance of a physician) shortly before administration; (iii) in the patient themselves, e.g., during sequential administration of the compound of the present disclosure and the other therapeutic agent. [00286] The pharmaceutical composition (or formulation) for application may be packaged in a variety of ways depending upon the method used for administering the drug. Generally, an article for distribution includes a container having deposited therein the pharmaceutical formulation in an appropriate form. Suitable containers are well-known to those skilled in the art and include materials such as bottles (plastic and glass), sachets, ampoules, plastic bags, metal cylinders, and the like. The container may also include a tamper-proof assemblage to prevent indiscreet access to the contents of the package. In addition, the container has deposited thereon a label that describes the contents of the container. The label may also include appropriate warnings.
[00287] The pharmaceutical composition or combination of the present disclosure can be in a unit dosage form, e.g., containing from about 1 to about 1000 mg of active ingredient(s) for a subject of from about 50 to about 70 kg, or from about 1 to about 500 mg, from about 1 to about 250 mg, from about 1 to about 150 mg, from about 0.5 to about 100 mg, or from about 1 to about 50 mg of active ingredient(s) for a subject of from about 50 to about 70 kg. The therapeutically effective dosage of a compound, pharmaceutical composition or pharmaceutical combination is dependent on the species of the subject, the body weight, age and individual condition of the subject, and the disease, disorder or condition or the severity thereof being treated. A physician, clinician or veterinarian of ordinary skill can readily determine the therapeutically effective amount of each of the active ingredients necessary to prevent or treat the progress of the disease, disorder or condition. [00288] The above-cited dosage properties may be demonstrable in in vitro and in vivo tests using advantageously mammals, e.g., mice, rats, dogs, monkeys, or isolated organs, tissues and preparations thereof. The compounds of the present disclosure can be applied in vitro in the form of solutions, e.g., aqueous solutions, and in vivo either enterally, parenterally, advantageously intravenously, e.g., as a suspension or in aqueous solution. The dosage in vitro may range between about 10-3 molar and 10-9 molar concentrations. A therapeutically effective amount in vivo may range depending on the route of administration, among other things, between about 0.1 mg/kg to about 500 mg/kg, or between about 1 mg/kg to about 100 mg/kg. [00289] In some embodiments, the concentration of one or more therapeutic agents provided in a pharmaceutical composition is less than 100%, 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19%, 18%, 17%, 16%, 15%,14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002%, or 0.0001% w/w, w/v or v/v. [00290] In some embodiments, the concentration of one or more therapeutic agents provided in a pharmaceutical composition is greater than 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 19.75%, 19.50%, 19.25% 19%, 18.75%, 18.50%, 18.25% 18%, 17.75%, 17.50%, 17.25% 17%, 16.75%, 16.50%, 16.25% 16%, 15.75%, 15.50%, 15.25% 15%, 14.75%, 14.50%, 14.25% 14%, 13.75%, 13.50%, 13.25% 13%, 12.75%, 12.50%, 12.25% 12%, 11.75%, 11.50%, 11.25% 11%, 10.75%, 10.50%, 10.25% 10%, 9.75%, 9.50%, 9.25% 9%,
8.75%, 8.50%, 8.25% 8%, 7.75%, 7.50%, 7.25% 7%, 6.75%, 6.50%, 6.25% 6%, 5.75%, 5.50%, 5.25% 5%, 4.75%, 4.50%, 4.25%, 4%, 3.75%, 3.50%, 3.25%, 3%, 2.75%, 2.50%, 2.25%, 2%, 1.75%, 1.50%, 125% , 1%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.09%, 0.08%, 0.07%, 0.06%, 0.05%, 0.04%, 0.03%, 0.02%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0009%, 0.0008%, 0.0007%, 0.0006%, 0.0005%, 0.0004%, 0.0003%, 0.0002%, or 0.0001% w/w, w/v, or v/v. [00291] In some embodiments, the concentration of one or more therapeutic agents provided in a pharmaceutical composition is in the range from about 0.0001% to about 50%, about 0.001% to about 40 %, about 0.01% to about 30%, about 0.02% to about 29%, about 0.03% to about 28%, about 0.04% to about 27%, about 0.05% to about 26%, about 0.06% to about 25%, about 0.07% to about 24%, about 0.08% to about 23%, about 0.09% to about 22%, about 0.1% to about 21%, about 0.2% to about 20%, about 0.3% to about 19%, about 0.4% to about 18%, about 0.5% to about 17%, about 0.6% to about 16%, about 0.7% to about 15%, about 0.8% to about 14%, about 0.9% to about 12%, about 1% to about 10% w/w, w/v or v/v. [00292] In some embodiments, the concentration of one or more therapeutic agents provided in a pharmaceutical composition is in the range from about 0.001% to about 10%, about 0.01% to about 5%, about 0.02% to about 4.5%, about 0.03% to about 4%, about 0.04% to about 3.5%, about 0.05% to about 3%, about 0.06% to about 2.5%, about 0.07% to about 2%, about 0.08% to about 1.5%, about 0.09% to about 1%, about 0.1% to about 0.9% w/w, w/v or v/v. Methods of Use [00293] It has now been found that the compounds of the present disclosure decrease a level of RAD51. Accordingly, provided herein are methods of decreasing levels of RAD51 in a cell (e.g., a cell expressing RAD51; a cancer cell, such as a cancer cell expressing RAD51, including a cancer cell of any of the cancers described herein), comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). In some embodiments, the cell is a cancer cell. In some embodiments, the cell is in a subject, such as a human. In some embodiments, the method further comprises contacting the cell (e.g., cancer cell) with one or more additional therapeutic agents.
[00294] Also provided herein are methods of decreasing a level of RAD51 in a subject in need thereof (e.g., a subject having a cancer, including any of the cancers described herein), comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). Without being bound to theory, possible mechanisms of decreasing a level of RAD51 include inhibiting expression of RAD51 in a cell, inhibiting transfer of RAD51 from one location in a cell to another location in the cell (including the transfer of RAD51 between the nucleus and cytoplasm), and promoting degradation of RAD51 in a cell. [00295] Also provided herein are methods of promoting endoplasmic reticulum (ER) stress in a cell (e.g., a cancer cell, such as a cancer cell of any of the cancers described herein), comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). ER stress can be caused by ROS. Thus, in some embodiments, the ER stress is caused by ROS. In some embodiments, promoting ER stress in a cell is inducing ER stress in the cell. In some embodiments, promoting ER stress includes increasing a level of ROS in the cell, for example, by contacting the cell with an agent that increases levels of ROS in the cell. In some embodiments, the cell is in a subject, such as a human. [00296] Also provided herein are methods of promoting the Unfolded Protein Response (UPR) in a cell (e.g., a cancer cell, including a cancer cell of any of the cancers described herein), comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). In some embodiments, the promoting the UPR in a cell is activating the UPR in the cell. In some embodiments the UPR is induced by ER stress. In some embodiments, the cell is in a subject, such as a human. [00297] Also provided herein are methods of promoting degradation of a DNA repair protein selected from RAD51, MGMT and/or MPG in a cell (e.g., a cell expressing RAD51, MGMT and/or MPG; a cancer cell, such as a cancer cell expressing RAD51, MGMT and/or MPG, including a cancer cell of any of the cancers described herein), comprising contacting the cell with a compound of the present disclosure (e.g., a compound of Formula I, or a
subformula thereof, or a pharmaceutically acceptable salt thereof, such as a therapeutically effective amount of a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). In some embodiments, the cell is in a subject, such as a human. In some embodiments, the DNA repair protein is RAD51. [00298] When a method described herein comprises contacting a cell, such as a cancer cell, with a compound of the present disclosure, it will be understood that the method can be conducted in vitro, ex vivo or in vivo. Thus, some embodiments comprise contacting the cell in vitro. Some embodiments comprise contacting the cell ex vivo. Some embodiments comprise contacting the cell in vivo as, for example, when the cell is in a subject, such as a human. [00299] Without wishing to be bound by any particular theory, it is believed that the following biomarkers relate to modulating (e.g., promoting) unfolded protein response, ER stress and/or degradation of DNA repair proteins, such as RAD51: phospho-eIF2a, XBP1 splicing, ATF4 expression, and gene expression signature driven by ATF4, CHOP, XBP1s, and ATF6 transcription factors. Accordingly, in some embodiments of any of the methods described herein, the method increases one or more of phosphorylation of eIF2a, levels of phospho-eIF2a, XBP1 splicing, ATF4 expression and gene expression signature driven by ATF4, CHOP, XBP1s, and ATF6 transcription factors. [00300] Also provided herein are methods of treating a cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). [00301] A wide variety of cancers, including solid tumors, leukemias, lymphomas, and myelomas are amenable to the methods disclosed herein. In some embodiments, the cancer is a solid tumor cancer. In some embodiments, the cancer comprises a solid tumor (e.g., a colorectal, breast, prostate, lung, pancreatic, renal or ovarian tumor). Accordingly, in some embodiments, the cancer is a solid tumor cancer. In some embodiments, the cancer is selected from one or more of a cancer of the pulmonary system, a brain cancer, a cancer of the gastrointestinal tract, a skin cancer, a genitourinary cancer, head and neck cancer, a sarcoma, a carcinoma, and a neuroendocrine cancer. In various embodiments, the solid tumor cancer is breast cancer, bladder cancer, endometrial cancer, esophageal cancer, liver cancer, pancreatic cancer, lung cancer, cervical cancer, colon cancer, colorectal cancer, gastric cancer, kidney cancer, ovarian cancer, prostate cancer, testicular cancer, uterine
cancer, a viral-induced cancer, melanoma or sarcoma. In some embodiments, the cancer is bladder cancer. In some embodiments, the cancer is lung cancer (e.g., non-small cell lung cancer). In other embodiments, the cancer is liver cancer. In some embodiments, the cancer is a sarcoma, bladder cancer or renal cancer. In some embodiments, the cancer is prostate cancer (e.g., castration-resistant prostate cancer, castration-sensitive prostate cancer). In other embodiments, the cancer is bladder cancer, pancreatic cancer, colorectal cancer, glioblastoma, kidney cancer, non-small cell lung carcinoma, prostate cancer, sarcoma, skin cancer, thyroid cancer, testicular cancer or vulvar cancer. In some embodiments, the cancer is endometrial cancer, pancreatic cancer, testicular cancer, renal cancer, melanoma, colorectal cancer, thyroid cancer, bladder cancer, pancreatic cancer, vulvar cancer, sarcoma, prostate cancer, lung cancer or anal cancer. In some embodiments, the cancer is a sarcoma. In some embodiments, the cancer is a renal cell carcinoma. [00302] In some embodiments, the cancer is a non-solid tumor cancer. In some embodiments, the cancer is a hematologic cancer. Hematologic cancers that can be treated according to the methods described herein include leukemias (e.g., acute leukemias, such as acute myeloid leukemia or acute lymphocytic leukemia; chronic leukemias, such as chronic myeloid leukemia or chronic lymphocytic leukemia), lymphomas (e.g., B-cell lymphoma, T- cell lymphoma) and multiple myeloma. In some embodiments, the cancer is a leukemia. In some embodiments, the cancer is an acute leukemia. In some embodiments, the cancer is acute myeloid leukemia or acute lymphocytic leukemia. In some embodiments, the cancer is a chronic leukemia. In some embodiments, the cancer is chronic myeloid leukemia or chronic lymphocytic leukemia. In some embodiments, the cancer is a lymphoma. In some embodiments, the hematologic cancer is selected from multiple myeloma, myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), acute lymphocytic leukemia, lymphocytic lymphoma, mycosis fungoides, chronic lymphogenous leukemia, chronic lymphocytic leukemia (CLL), mantle cell lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, Hodgkin’s lymphoma, non-Hodgkin’s lymphoma or myelofibrosis. [00303] In some embodiments, the cancer is selected from ovarian cancer, multiple myeloma, pancreatic cancer, prostate cancer, breast cancer, endometrial cancer, colorectal cancer or lymphoma.
[00304] In some embodiments, the cancer expresses a BRCA (e.g., BRCA1 and/or BRCA2) variant (e.g., mutant). In some embodiments, the BRCA variant is a BRCA (loss- of-function) mutant resistant to PARP. [00305] In some embodiments, the cancer is a pre-metastatic cancer. In some embodiments, the cancer is a metastatic cancer. [00306] In some embodiments, the cancer is previously treated, e.g., the compound of the present disclosure is administered, alone or in combination with one or more additional therapies, as a subsequent therapy (e.g., a second-line therapy, a third-line therapy, a last-line therapy). [00307] In some embodiments, the cancer is previously untreated as, for example, when the compound of the present disclosure is administered, alone or in combination with one or more additional therapies, as a first-line therapy. In further embodiments, the method further comprises administering to the subject a subsequent therapy for the cancer (e.g., second-line therapy, third-line therapy, last-line therapy). [00308] In some embodiments, the cancer is resistant. [00309] Examples of cancer treatable according to the methods described herein include, but are not limited to, adenocarcinoma of the breast, prostate, and colon; all forms of bronchogenic carcinoma of the lung; myeloid; melanoma; hepatoma; neuroblastoma; papilloma; apudoma; choristoma; branchioma; malignant carcinoid syndrome; carcinoid heart disease; and carcinoma (e.g., Walker, basal cell, basosquamous, Brown-Pearce, ductal, Ehrlich tumor, Krebs 2, merkel cell, mucinous, lung cancer (e.g., large cell lung cancer, such as squamous cell carcinoma, non-small cell lung), oat cell, papillary, scirrhous, bronchiolar, bronchogenic, squamous cell, and transitional cell). Additional examples of cancer treatable according to the methods described herein include, but are not limited to, histiocytic disorders; leukemia; histiocytosis malignant; Hodgkin's disease; hypereosinophilia, immunoproliferative small; non-Hodgkin's lymphoma; plasmacytoma; reticuloendotheliosis; melanoma; chondroblastoma; chondroma; chondrosarcoma; dermatofibrosarcoma protuberans, fibrotic cancer (myelofibrosis, pancreatic cancer (e.g., pancreatic ductal adenocarcinoma), kidney cancer, liver cancer, lung cancer (e.g., large cell lung cancer, such as squamous cell carcinoma), breast cancer (e.g., inflammatory breast cancer), ovarian cancer (e.g., high grade serious ovarian carcinoma), endometrial cancer, uterine cancer, uterine sarcoma (e.g., uterine leiomyosarcoma), renal cell cancer, sarcoma (e.g., soft tissue sarcoma), malignant fibrous histiocytoma, fibrosarcoma (e.g., dermatofibrosarcoma protuberans) and
hepatocellular carcinoma); fibroma; fibrosarcoma; giant cell tumors; histiocytoma; lipoma; liposarcoma; mesothelioma; myxoma; myxosarcoma; osteoma; osteosarcoma; pediatric malignancy, chordoma; craniopharyngioma; dysgerminoma; hamartoma; mesenchymoma; mesonephroma; myosarcoma; ameloblastoma; cementoma; odontoma; teratoma; thymoma; trophoblastic tumor. Further, the following types of cancers are also contemplated as amenable to treatment: adenoma; cholangioma; cholesteatoma; cyclindroma; cystadenocarcinoma; cystadenoma; granulosa cell tumor; gynandroblastoma; hepatocellular cancer, hepatoma; hidradenoma; islet cell tumor; Leydig cell tumor; papilloma; sertoli cell tumor; theca cell tumor; leiomyoma; leiomyosarcoma; myoblastoma; myomma; myosarcoma; rhabdomyoma; rhabdomyosarcoma; ependymoma; ganglioneuroma; glioma; medulloblastoma; meningioma; neurilemmoma; neuroblastoma; neuroepithelioma; neurofibroma; neuroma; paraganglioma; paraganglioma nonchromaffin. Yet more examples of cancer treatable according to the methods described herein include, but are not limited to, angiokeratoma; angiolymphoid hyperplasia with eosinophilia; angioma sclerosing; angiomatosis; glomangioma; hemangioendothelioma; hemangioma; hemangiopericytoma; hemangiosarcoma; lymphangioma; lymphangiomyoma; lymphangiosarcoma; pinealoma; carcinosarcoma; chondrosarcoma; cystosarcoma phyllodes; fibrosarcoma; hemangiosarcoma; leiomyosarcoma; leukosarcoma; liposarcoma; lymphangiosarcoma; myosarcoma; myxosarcoma; ovarian carcinoma; rhabdomyosarcoma; sarcoma; neoplasms; nerofibromatosis; and cervical dysplasia. [00310] Further examples of cancers treatable according to the methods described herein include, but are not limited to, Acute Lymphoblastic Leukemia (ALL); Acute Myeloid Leukemia (AML); Adrenocortical Carcinoma; Adrenocortical Carcinoma, Childhood; AIDS- Related Cancer (e.g., Kaposi Sarcoma, AIDS-Related Lymphoma, Primary CNS Lymphoma); Cancer of the anal region; Anal Cancer; Appendix Cancer; Astrocytomas, Childhood; Atypical Teratoid/Rhabdoid Tumor, Childhood, Central Nervous System (CNS); Neoplasms of the CNS (e.g., primary CNS lymphoma, spinal axis tumors, medulloblastoma, brain stem gliomas or pituitary adenomas), Barrett’s esophagus (e.g., pre-malignant syndrome), and mycoses fungoides, Basal Cell Carcinoma of the Skin; Bile Duct Cancer; Bladder Cancer; Bladder Cancer, Childhood; Bone Cancer (including Ewing Sarcoma, Osteosarcoma and Malignant Fibrous Histiocytoma); Brain Tumors/Cancer; Breast Cancer; Burkitt Lymphoma; Carcinoid Tumor (Gastrointestinal); Carcinoid Tumor, Childhood; Cardiac (Heart) Tumors, Childhood; Embryonal Tumors, Childhood; Germ Cell Tumor,
Childhood; Primary CNS Lymphoma; Cervical Cancer; Childhood Cervical Cancer; Cholangiocarcinoma; Chordoma, Childhood; Chronic Lymphocytic Leukemia (CLL); Chronic Myelogenous Leukemia (CML); Chronic Myeloproliferative Neoplasms; Colorectal Cancer; Childhood Colorectal Cancer; Craniopharyngioma, Childhood; Cutaneous T-Cell Lymphoma (e.g., Mycosis Fungoides and Sézary Syndrome); Ductal Carcinoma In Situ (DCIS); Embryonal Tumors, Central Nervous System, Childhood; Cancer of the Endocrine system (e.g., cancer of the thyroid, pancreas, parathyroid or adrenal glands), Endometrial Cancer (Uterine Cancer); Ependymoma, Childhood; Esophageal Cancer; Childhood Esophageal Cancer; Esthesioneuroblastoma; Ewing Sarcoma; Extracranial Germ Cell Tumor, Childhood; Extragonadal Germ Cell Tumor; Eye Cancer; Childhood Intraocular Melanoma; Intraocular Melanoma; Retinoblastoma; Fallopian Tube Cancer; Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma; Gallbladder Cancer; Gastric (Stomach) Cancer; Childhood Gastric (Stomach) Cancer; Gastrointestinal Carcinoid Tumor; Gastrointestinal Stromal Tumors (GIST); Childhood Gastrointestinal Stromal Tumors; Germ Cell Tumors; Childhood Central Nervous System Germ Cell Tumors (e.g., Childhood Extracranial Germ Cell Tumors, Extragonadal Germ Cell Tumors, Ovarian Germ Cell Tumors, Testicular Cancer); Gestational Trophoblastic Disease; Gynecologic Tumors ((e.g., uterine sarcomas, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina or carcinoma of the vulva), Hairy Cell Leukemia; Head and Neck Cancer; Heart Tumors, Childhood; Hepatocellular (Liver) Cancer; Histiocytosis, Langerhans Cell; Hodgkin Lymphoma; Hypopharyngeal Cancer; Cutaneous or Intraocular Melanoma; Childhood Intraocular Melanoma; Islet Cell Tumors, Pancreatic Neuroendocrine Tumors; Kaposi Sarcoma; Kidney (Renal Cell) Cancer; Langerhans Cell Histiocytosis; Laryngeal Cancer; Leukemia; Lip and Oral Cavity Cancer; Liver Cancer; Lung Cancer (Non-Small Cell and Small Cell); Childhood Lung Cancer; Lymphoma; Male Breast Cancer; Malignant Fibrous Histiocytoma of Bone and Osteosarcoma; Melanoma; Childhood Melanoma; Melanoma, Intraocular (Eye); Childhood Intraocular Melanoma; Merkel Cell Carcinoma; Mesothelioma, Malignant; Childhood Mesothelioma; Metastatic Cancer; Metastatic Squamous Neck Cancer with Occult Primary; Midline Tract Carcinoma With NUT Gene Changes; Mouth Cancer; Multiple Endocrine Neoplasia Syndromes; Multiple Myeloma/Plasma Cell Neoplasms; Mycosis Fungoides; Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasms; Myelogenous Leukemia, Chronic (CML); Myeloid Leukemia, Acute (AML); Myeloproliferative Neoplasms, Chronic; Nasal Cavity and
Paranasal Sinus Cancer; Nasopharyngeal Cancer; Neuroblastoma; Non-Hodgkin Lymphoma; Non-Small Cell Lung Cancer; Oral Cancer, Lip and Oral Cavity Cancer and Oropharyngeal Cancer; Osteosarcoma and Malignant Fibrous Histiocytoma of Bone; Ovarian Cancer; Childhood Ovarian Cancer; Pancreatic Cancer; Childhood Pancreatic Cancer; Pancreatic Neuroendocrine Tumors; Papillomatosis (Childhood Laryngeal); Paraganglioma; Childhood Paraganglioma; Paranasal Sinus and Nasal Cavity Cancer; Parathyroid Cancer; Penile Cancer; Pharyngeal Cancer; Pheochromocytoma; Childhood Pheochromocytoma; Pituitary Tumor; Plasma Cell Neoplasm/Multiple Myeloma; Pleuropulmonary Blastoma; Pregnancy and Breast Cancer; Primary Central Nervous System (CNS) Lymphoma; Primary Peritoneal Cancer; Prostate Cancer; Rectal Cancer; Recurrent Cancer; Renal Cell (Kidney) Cancer; Retinoblastoma; Rhabdomyosarcoma, Childhood; Salivary Gland Cancer; Sarcoma (e.g., Childhood Rhabdomyosarcoma, Childhood Vascular Tumors, Ewing Sarcoma, Kaposi Sarcoma, Osteosarcoma (Bone Cancer), Soft Tissue Sarcoma, Uterine Sarcoma); Sézary Syndrome; Skin Cancer; Childhood Skin Cancer; Small Cell Lung Cancer; Small Intestine Cancer; Soft Tissue Sarcoma; Squamous Cell Carcinoma of the Skin; Squamous Neck Cancer with Occult Primary, Metastatic; Stomach (Gastric) Cancer; Childhood Stomach (Gastric) Cancer; T-Cell Lymphoma, Cutaneous (e.g., Mycosis Fungoides and Sèzary Syndrome); Testicular Cancer; Childhood Testicular Cancer; Throat Cancer (e.g., Nasopharyngeal Cancer, Oropharyngeal Cancer, Hypopharyngeal Cancer); Thymoma and Thymic Carcinoma; Thyroid Cancer; Transitional Cell Cancer of the Renal Pelvis and Ureter; Ureter and Renal Pelvis (e.g., renal cell carcinoma, carcinoma of the renal pelvis), benign prostatic hypertrophy, parathyroid cancer, Transitional Cell Cancer; Urethral Cancer; Uterine Cancer, Endometrial; Uterine Sarcoma; Vaginal Cancer; Childhood Vaginal Cancer; Vascular Tumors; Vulvar Cancer; and Wilms Tumor and Other Childhood Kidney Tumors. [00311] Metastases of the aforementioned cancers can also be treated in accordance with the methods described herein. [00312] RAD51 has also been implicated in suppression of innate immunity and immune signaling. See PMID: 28334891, the entire content of which is incorporated herein by reference. Thus, also provided herein are methods of treating an immune deficiency, including an autoimmune disease, in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). Non-limiting examples of immune deficiencies are Autoimmune
Lymphoproliferative Syndrome (ALPS), Autoimmune polyglandular syndrome type 1 (APS- 1), BENTA Disease, Caspase Eight Deficiency State (CEDS), Chronic Granulomatous Disease (CGD), Common Variable Immunodeficiency (CVID), Congenital Neutropenia Syndromes, CTLA4 Deficiency, DOCKS Deficiency, GATA2 Deficiency, Glycosylation Disorders With Immunodeficiency, hyper-immunoglobulin E syndrome (HIES), Hyper- Immunoglobulin M (Hyper-IgM) Syndromes, Leukocyte adhesion deficiency (LAD), LRBA deficiency, PB Kinase disease, PLCG2-associated antibody deficiency and immune dysregulation (PLAID), severe combined immunodeficiency (SCID), STAT3 gain-of- function disease, warts, hypogammaglobulinemia, infections, and myelokathexis syndrome (WHIMS), X-Linked agammaglobulinemia (XLA), X-linked lymphoproliferative disease (XLP), and XMEN disease; lupus erythematosus; Wiskott-Aldrich syndrome; autoimmune lymphoproliferative syndrome; myasthenia gravis; rheumatoid arthritis (RA); lupus nephritis; multiple sclerosis; systemic lupus erythematosis; discoid lupus; subacute cutaneous lupus erythematosus; cutaneous lupus erythematosus including chilblain lupus erythematosus; chronic arthritis; Sjogren's syndrome; inflammatory chronic rhinosinusitis; colitis; celiac disease; inflammatory bowel disease; Barrett's esophagus; inflammatory gastritis; autoimmune nephritis; autoimmune vasculitis; autoimmune hepatitis; autoimmune carditis; autoimmune encephalitis; autoimmune diabetes; autoimmune diabetes nephritis; psoriasis; Graft-versus-host disease (GvHD); and autoimmune mediated hematological disease. [00313] Double strand breaks and defective DNA damage response more broadly, are thought to underlie neurodegeneration. See PMID: 25033177, the entire content of which is incorporated herein by reference. Accordingly, also provided herein are methods of treating a neurodegenerative disorder in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt thereof). Non-limiting examples of neurodegenerative disorders are multiple sclerosis, Parkinson's disease (PD), Alzheimer's disease (AD), Dentatorubropallidoluysian atrophy (DRPLA), Huntington's Disease (HD), Spinocerebellar ataxia Type 1 (SCAl), Spinocerebellar ataxia Type 2 (SCA2), Spinocerebellar ataxia Type 3 (SCA3), Spinocerebellar ataxia 6 (SCA6), Spinocerebellar ataxia Type 7 (SCA 7), Spinocerebellar ataxia Type 8 (SCA8), Spinocerebellar ataxia Type 12 (SCA12), Spinocerebellar ataxia Type 17 (SCAl 7), Spinobulbar Muscular Ataxia/Kennedy Disease (SBMA), Fragile X syndrome (FRAXA), Fragile XE mental retardation (FRAXE), and Myotonic dystrophy (DM).
[00314] In some embodiments of any of the methods disclosed herein, the method comprises providing a subject determined to have an increased level of DNA damage; and administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing). [00315] In some embodiments of any of the methods disclosed herein, the method comprises determining whether a subject has an increased level of DNA damage; and administering to the subject a therapeutically effective amound of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) if it is determined that the subject has an increased level of DNA damage. [00316] In some embodiments of any of the methods disclosed herein, the method comprises providing a subject determined to have an an increased level of a DNA repair protein (e.g., RAD51); and administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing). In some embodiments, the increased level of the DNA repair protein results from the DNA repair protein being upregulated. [00317] In some embodiments of any of the methods disclosed herein, the method comprises determining whether a subject has an increased level of a DNA repair protein (e.g., RAD51); and administering to the subject a therapeutically effective amound of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) if it is determined that the subject has an increased level of the DNA repair protein. In some embodiments, the increased level of the DNA repair protein results from the DNA repair protein being upregulated. [00318] In some embodiments of any of the methods disclosed herein, the method comprises providing a subject determined to have an an increased level of RAD51; and administering to the subject a therapeutically effective amount of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing). In some embodiments, the increased level of RAD51 results from RAD51 being upregulated. [00319] In some embodiments of any of the methods disclosed herein, the method comprises determining whether a subject has an increased level of RAD51; and administering
to the subject a therapeutically effective amound of a compound of the present disclosure (e.g., a compound of Formula I, or a subformula thereof, or a pharmaceutically acceptable salt of the foregoing) if it is determined that the subject has an increased level of RAD51. In some embodiments, the increased level of RAD51 results from RAD51 being upregulated. [00320] A therapeutically effective amount of a therapeutic agent (e.g., a compound of the present disclosure) to be administered to a subject in accordance with the methods described herein can be determined by a clinician of ordinary skill using the guidance provided herein and other methods known in the art. For example, suitable dosages may range, depending on the route of administration, among other things, from about 0.1 mg/kg to about 500 mg/kg, or from about 1 mg/kg to about 100 mg/kg. [00321] A compound of the present disclosure can be administered via a variety of routes of administration, including, for example, oral, dietary, topical, transdermal, rectal, parenteral (e.g., intra-arterial, intravenous, intramuscular, subcutaneous injection, intradermal injection), intravenous infusion and inhalation (e.g., intrabronchial, intranasal or oral inhalation, intranasal drops) routes of administration, depending on the compound and the particular disease to be treated. Administration can be local or systemic as indicated. The preferred mode of administration can vary depending on the particular compound chosen. In some embodiments, the compound of the present disclosure is administered orally. In some embodiments, the compound of the present disclosure is administered intravenously. [00322] A compound of the present disclosure can also be administered in combination with one or more other therapies (e.g., a chemotherapy, such as a chemotherapeutic agent; an immunotherapy, such as an immunotherapeutic agent, an immunooncology agent; radiation therapy). In some embodiments, the methods further comprise administering to the subject one or more additional therapeutic agents (e.g., a therapeutically effective amount of one or more additional therapeutic agents). Suitable additional therapeutic agents for use in the methods disclosed herein include those discussed herein in connection with combination therapy and pharmaceutical combinations. [00323] In some embodiments, a method described herein further comprises administering to the subject a DNA damaging agent, for example, radiation, a topoisomerase inhibitor, a PARP inhibitor, a DNA crosslinking agent, or a standard of care agent that induces DNA damage, such as a DNA crosslinking agent. In some embodiments, a method described herein further comprises administering to the subject a DNA damaging agent, for example, radiation, a topoisomerase inhibitor, a PARP inhibitor, a DNA crosslinking agent.
[00324] In some embodiments, a method described herein further comprises administering to the subject an agent that promotes (e.g., induces) ER stress, for example, an agent that increases levels of ROS or a proteasome inhibitor. [00325] In some embodiments, a method described herein further comprises administering to the subject a standard of care agent, such as any of the standard of care agents described herein. [00326] In some embodiments, a method described herein further comprises administering to the subject one or more of FOLFIRINOX, modified FOLFIRINOX regimen, gemcitabine and abraxane, gemcitibine and capecitabine, olaparib, gemcitabine and erlotinib, gemcitabine, docetaxel and capecitabine, larotrectinib or pembrolizumab, e.g., for the treatment of pancreatic cancer. In some embodiments, a method described herein further comprises administering to the subject nab-paclitaxel, gemcitabine and cisplatin, e.g., for the treatment of pancreatic cancer. [00327] In some embodiments, a method described herein further comprises administering to the subject one or more of a platinum analogue, a combination comprising a platinum analogue, altretamine, capecitabine, ifosfamide, irinotecan, melphalan, paclitaxel, pemetrexed, vinorelbine, a targeted therapy, a PARP inhibitor, a tyrosine kinase inhibitor (TKI), an immunotherapy, an immune checkpoint inhibitor, pembrolizumab, a hormone therapy, cyclophosphamide, etoposide, sorafenib or vinorelbine, e.g., for the treatment of ovarian cancer. [00328] In some embodiments, a method described herein further comprises administering to the subject one or more of an LHRH agonist; an LHRH antagonist, an anti-androgen, a corticosteroid, an estrogen, an androgen synthesis inhibitor or an androgen deprivation therapy, e.g., for the treatment of prostate cancer. [00329] In some embodiments, a method described herein further comprises administering to the subject a proteasome inhibitor, e.g., for the treatment of multiple myeloma. [00330] In some embodiments, a method described herein further comprises administering to the subject an immunooncology agent, such as an immune checkpoint inhibitor. [00331] When administered in combination with another therapy, the compound of the present disclosure can be administered before, after or concurrently with the other therapy (e.g., additional therapeutic agent(s)). When two or more therapeutic agents are co- administered simultaneously (e.g., concurrently), the compound of the present disclosure and other therapeutic agent(s) can be in separate formulations or the same formulation.
Alternatively, the compound of the present disclosure and other therapy can be administered sequentially (e.g., as separate compositions) within an appropriate time frame as determined by a skilled clinician (e.g., a time sufficient to allow an overlap of the pharmaceutical effects of the compound of the present disclosure and the other therapy). [00332] The compounds of the present disclosure in free form or in pharmaceutically acceptable salt form, exhibit valuable pharmacological properties, which can be demonstrated at least by using any one of the test procedures described herein. EXEMPLIFICATION [00333] The compounds of the present disclosure can be prepared in a number of ways known to one skilled in the art of organic synthesis in view of the methods, reaction schemes and examples provided herein. The compounds of the present disclosure can be synthesized using the methods described below, together with synthetic methods known in the art of synthetic organic chemistry, or by variations thereon, as appreciated by those skilled in the art. Preferred methods include, but are not limited to, those described below. The reactions are performed in a solvent or solvent mixture appropriate to the reagents and materials employed and suitable for the transformations being affected. It will be understood by those skilled in the art of organic synthesis that the functionality present on the molecule should be consistent with the transformations proposed. This will sometimes require a judgment to modify the order of the synthetic steps or to select one particular process scheme over another in order to obtain a desired compound of the disclosure. [00334] The starting materials are generally available from commercial sources such as Sigma Aldrich or other commercial vendors, or are prepared as described in this disclosure, or are readily prepared using methods well known to those skilled in the art (e.g., prepared by methods generally described in Louis F. Fieser and Mary Fieser, Reagents for Organic Synthesis, v.1-19, Wiley, New York (1967-1999 ed.), Larock, R.C., Comprehensive Organic Transformations, 2nd ed., Wiley-VCH Weinheim, Germany (1999), or Beilsteins Handbuch der organischen Chemie, 4, Aufl. ed. Springer-Verlag, Berlin, including supplements (also available via the Beilstein online database). [00335] For illustrative purposes, the reaction schemes depicted below provide potential routes for synthesizing the compounds of the present disclosure as well as key intermediates. Those skilled in the art will appreciate that other synthetic routes may be used to synthesize the compounds of the present disclosure. Although specific starting materials and reagents are depicted in the schemes and discussed below, other starting materials and reagents can be
easily substituted to provide a variety of derivatives and/or reaction conditions. In addition, many of the compounds prepared by the methods described below can be further modified in view of this disclosure using conventional chemistry well known to those skilled in the art. [00336] In the preparation of compounds of the present disclosure, protection of remote functionality of intermediates may be necessary. The need for such protection will vary depending on the nature of the remote functionality and the conditions of the preparation methods. The need for such protection is readily determined by one skilled in the art. For a general description of protecting groups and their use, see Greene, T.W. et al., Protecting Groups in Organic Synthesis, 4th Ed., Wiley (2007). Protecting groups incorporated in making of the compounds of the present disclosure, such as the trityl protecting group, may be shown as one regioisomer but may also exist as a mixture of regioisomers. [00337] The following abbreviations used hereinbelow have the corresponding meanings: ACN acetonitrile; Ac2O acetic anhydride; Aq aqueous; BSA bovine serum albumin; BINAP 2,2'-Bis(diphenylphosphino)-1,1'-binaphthyl; Boc tert-butyloxycarbonyl; C Celsius; CH2Cl2 dichloromethane; Cs2CO3 cesium carbonate; d doublet; dd doublet of doublets; DCE 1,2-dichloroethane; DCM dichloromethane; DIPEA/DIEA N,N-diisopropylethylamine; DMF N,N-dimethylformamide; DMSO dimethylsulfoxide; EDC 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide; EtOAc ethyl acetate; EtOH ethanol; g gram; h hour(s); HATU 2-(1H-7-azabenzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate; HOAt 1-hydroxy-7-azabenzotriazole; HPLC high pressure liquid chromatography; IBX 2-iodoxybenzoic acid; kg kilogram; L liter; LC liquid chromatography; LCMS liquid chromatography and mass spectrometry; LiOH Lithium hydroxide; MeOH methanol; MS mass spectrometry; M molar;
m multiplet; min minutes; mL milliliter(s); µM micromolar; m/z mass to charge ratio; nm nanometer; nM nanomolar; N normal; NMP N-methylpyrrolidone; NMR nuclear magnetic resonance; Pd(OAc)2 palladium(II) acetate; PS polymer-supported; PG protecting group; pTsOH p-toluenesulfonic acid; rac racemic; s singlet; sat. saturated; t triplet; TEA trimethylamine; TFA trifluoroacetic acid; TFE trifluoroethanol; THF tetrahydrofuran; TLC thin layer chromatography. [00338] Manufacturing methods of the compounds according to the present invention are described below. The compounds of the invention represented by formula (I) or pharmaceutically acceptable salts thereof can be manufactured from known compounds, for example, by the following manufacturing methods A, B, and C and similar methods thereto, or an appropriately combination of synthesis methods that are well known to those skilled in the art. [00339] A compound in a reaction includes cases where a salt is formed. Examples of such a salt that is used include those that are similar to the salt in formula (Ia) such as Compound 2 hydrochloride. [00340] While a compound obtained in each step can be used in a subsequent reaction directly as a reaction solution or as a composition, the compound can also be isolated from a reaction mixture in accordance with a conventional method. The compound can be readily purified by separation means such as recrystallization, distillation, or chromatography. Unless specifically described otherwise, each instance of the same symbols in the compounds in the following reactions is defined the same. Manufacturing Methods Manufacturing Method A (Manufacturing method of compounds of formula (I) and formula (Ia)) [00341] A compound of formula (I) and/or (Ia) can be manufactured, for example, by the manufacturing method described below.
wherein each LG is independently a leaving group, PG is a protecting group, HZ, for each occurrence, independently represents acid, g is 0, 1 or 2 and q is 0, 1, 2 or 3. Values for the remaining variables (e.g., X, Y, Ring G, R1, R2, R3, m, n and p) are as described in the first through eighth embodiments, or any aspect thereof. [00342] As the protecting group PGa, the protecting groups described as a protecting group of an amino group in Protecting Groups in Organic Synthesis (authored by Theodora W. Greene, Peter G. M. Wuts, published by John Wiley & Sons, Inc., 1999) can be used. [00343] LGa and LGb are independently leaving groups. Examples thereof include iodine, bromine, chlorine, triflate, alkoxy, sulfonyloxy, imidazole, and the like. LGa and LGb are preferably chlorine.
[00344] This is a step for obtaining compound a3 by adding a2 to compound a1 in the presence of a base in a suitable solvent. As the base used in this step, a basic salt, such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride, an aromatic amine, such as pyridine, lutidine, 4-dimethylaminopyridine, or N,N-dimethylaniline, a tertiary amine, such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N-methylpiperidine, N-methylpyrrolidine, or N-methylmorpholine, or the like can be used, and pyridine is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents, such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile, ether solvents, such as tetrahydrofuran and 1,4-dioxane, halogenated hydrocarbons, such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons, such as toluene and benzene, mixtures thereof, and the like. Preferred examples thereof include 1,4-dioxane. The amount of base used is generally 2 to 20 equivalents, preferably 4 to 8 equivalents with respect to 1 equivalent of compound a1. The amount of a2 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound a1. The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 80 °C.
[00345] This is a step for obtaining compound a4 by reacting a suitable acid with compound a3 in a suitable solvent. The acid is, for example, hydrochloric acid, sulfuric acid, nitric acid, trifluoroacetate, or formic acid, and hydrochloric acid is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents, such as N,N-dimethylformamide, N-methyl-2- pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, and ethyl acetate, ether solvents, such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons, such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons, such as toluene and benzene, alcohol solvents, such as ethanol and methanol, mixtures
thereof, and the like. Preferred examples thereof include cyclopentyl methyl ether, 1,4- dioxane, ethyl acetate, methanol, and mixtures thereof. The amount of acid used is generally 2 to 100 equivalents, preferably 2 to 20 equivalents with respect to 1 equivalent of compound a3. The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
[00346] This is a step for obtaining a compound of formula (I) by reacting compound a4 with compound a5 obtained by the manufacturing method described below in the presence of a base in a suitable solvent. As the base, a basic salt such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride, an aromatic amine such as pyridine, lutidine, 4-dimethylaminopyridine, or N,N-dimethylaniline, a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N-methylpiperidine, N- methylpyrrolidine, or N-methylmorpholine, or the like can be used, and N,N- diisopropylethylamine is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, esters such as methyl acetate and ethyl acetate, mixtures thereof, and the like. Preferred examples thereof include chloroform and dichloromethane. The amount of a5 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound a4. The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
[00347] This is a step for obtaining a compound of formula (Ia) by reacting an acid represented by HZ with a compound of formula (I) in a suitable solvent. As the acid, an inorganic acid such as hydrochloric acid, sulfuric acid, nitric acid, or phosphoric acid, or an organic acid such as oxalic acid, citric acid, or acetic acid can be used. Hydrochloric acid is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, ethyl acetate, and acetone, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2- dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, alcohol solvents such as ethanol and methanol, mixtures thereof, and the like. Preferred examples thereof include methanol, acetone, water, and mixtures thereof. The amount of acid used is generally 2 to 100 equivalents, preferably 20 to 40 equivalents with respect to 1 equivalent of compound of formula (I). The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C. Manufacturing Method B (Manufacturing method of compounds of formula (I') or formula (I'a)) [00348] A compound of formula (I') or formula (I'a), which is a compound represented by formula (I) wherein R2 is a hydrogen atom, can be manufactured, for example, by the manufacturing method described below.
[00349] HZ, for each occurrence, independently represents acid, g is 0, 1 or 2 and q is 0, 1, 2 or 3. Values for the remaining variables (e.g., X, Y, Ring G, R1, R3, m, n and p) are as described in the first through ninth embodiments, or any aspect thereof.
[00350] This is a step for obtaining compound of formula (I') by reacting compound a4 with compound b1 obtained by the manufacturing method described below in the presence of a base in a suitable solvent. As the base, a basic salt such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride, an aromatic amine such as pyridine, lutidine, 4-dimethylaminopyridine, or N,N-dimethylaniline, a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N-methylpiperidine, N- methylpyrrolidine, or N-methylmorpholine, or the like can be used, and N,N- diisopropylethylamine is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, and propionitrile, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, esters such as methyl acetate and ethyl acetate, mixtures thereof, and the like. Preferred examples thereof include chloroform and
dichloromethane. The amount of b5 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound a3. The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C.
[00351] This is a step for obtaining a compound of formula (I'a) by reacting an acid represented by HZ with a compound of formula (I') in a suitable solvent. As the acid, an inorganic acid such as hydrochloric acid, sulfuric acid, nitric acid, or phosphoric acid, or an organic acid such as oxalic acid, citric acid, or acetic acid can be used. Hydrochloric acid is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, ethyl acetate, and acetone, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2- dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, alcohol solvents such as ethanol and methanol, mixtures thereof, and the like. Preferred examples thereof include methanol, acetone, water, and mixtures thereof. The amount of acid used is generally 2 to 100 equivalents, preferably 20 to 40 equivalents with respect to 1 equivalent of a compound of formula (I'). The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C. Manufacturing Method C (Manufacturing method of an intermediate a5) [00352] A compound represented by a5 can be manufactured, for example, by the manufacturing method described below.
wherein LG is a leaving group. Values for the remaining variables (e.g., Ring G, R2, R3, n and p) are as described in the first through eighth embodiments, or any aspect thereof. [00353] Each LGb is independently a leaving group. Examples thereof include iodine, bromine, chlorine, triflate, alkoxy, sulfonyloxy, imidazolyl, and the like. Each LGb is preferably the same. LGb is preferably chlorine. [00354] This is a step for obtaining compound a5 by reacting c2 with compound c1 in the presence of a base in a suitable solvent. As c2, carbonothioic diiodide, carbonothioic dibromide, or thiophosgene can be used, and thiophosgene is particularly preferred. As the base, a basic salt such as sodium carbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride, an aromatic amine such as pyridine, lutidine, 4- dimethylaminopyridine, or N,N-dimethylaniline, a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N- methylpiperidine, N-methylpyrrolidine, or N-methylmorpholine, or the like can be used, and N,N-diisopropylethylamine is particularly preferable. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, and ethyl acetate, ether solvents such as cyclopentyl methyl ether and 1,4-dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2- dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, mixtures thereof, and the like. Preferred examples thereof include chloroform and dichloromethane. The amount of acid used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound c1. The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -20 °C to about 180 °C, preferably about 0 °C to about 50 °C. Manufacturing Method D (Manufacturing method of an intermediate b1) [00355] A compound represented by b1 can be manufactured, for example, by the manufacturing method described below.
wherein LG is a leaving group. Values for the remaining variables (e.g., Ring G, R3, n and p) are as described in the first through eighth embodiments, or any aspect thereof.
[00356] Each LGb is independently a leaving group. Examples thereof include iodine, bromine, chlorine, triflate, alkoxy, sulfonyloxy, imidazolyl, and the like. Each LGb is preferably the same. LGb is preferably chlorine. [00357] This is a step for obtaining b1 by reacting c2 with compound d1 in the presence of base in a suitable solvent. As the base, a basic salt such as sodium carbonate, sodium bicarbonate, potassium carbonate, cesium carbonate, sodium acetate, sodium hydride, or calcium hydride, an aromatic amine such as pyridine, lutidine, 4-dimethylaminopyridine, or N,N-dimethylaniline, a tertiary amine such as triethylamine, tripropylamine, tributylamine, cyclohexyldimethylamine, N,N-diisopropylethylamine, N-methylpiperidine, N- methylpyrrolidine, or N-methylmorpholine can be used, and sodium bicarbonate is particularly preferred. The solvent used in this step is selected from the solvents exemplified below and the like. Examples thereof include aprotic solvents such as N,N- dimethylformamide, N-methyl-2-pyrrolidone, dimethyl sulfoxide, acetonitrile, propionitrile, methyl acetate, and ethyl acetate, ether solvents such as cyclopentyl methyl ether and 1,4- dioxane, halogenated hydrocarbons such as dichloromethane, chloroform, 1,2-dichloroethane, and chlorobenzene, hydrocarbons such as toluene and benzene, water, mixtures thereof, and the like. Preferred examples thereof include mixtures of water and dichloromethane and chloroform. The amount of c2 used is generally 1 to 10 equivalents, preferably 1 to 3 equivalents with respect to 1 equivalent of compound d1. The reaction time is generally about 0.5 hours to about 48 hours, preferably about 0.5 hours to about 2 hours. The reaction temperature is generally about -78 °C to about 180 °C, preferably about -20 °C to about 50 °C. [00358] Even without an explicit description of specific use of a protecting group in each reaction of the manufacturing methods described above, a compound of interest can be obtained by protecting a portion other than the reaction point and deprotecting the protected portion after the completion of a reaction or a series of reactions, as needed if one of the functional groups other than the reaction point is altered under the described reaction condition or is unsuitable for performing the described method. [00359] As a protecting group, common protecting groups such as those described in a reference (e.g., Protective Groups in Organic Synthesis, 3rd ed., T. W. Greene, John Wiley & Sons Inc. (1999) or the like) can be used. More specifically, examples of protecting groups of an amino group include benzyloxylcarbonyl, tert-butoxycarbonyl, acetyl, benzyl, and the like.
Examples of protecting groups of a hydroxyl group include trialkylsilyl groups such as trimethylsilyl and tert-butyldimethylsilyl, acetyl, benzyl, and the like. [00360] A protecting group can be introduced or removed by a method that is commonly used in organic synthetic chemistry (see, for example, the aforementioned Protective Groups in Organic Synthesis) or a similar method thereto. [00361] The base used in each of the steps described above should be appropriately selected depending on the type of reaction or raw material compound or the like. Examples thereof include alkali bicarbonates such as sodium bicarbonate and potassium bicarbonate, alkali carbonates such as sodium carbonate and potassium carbonate, metal hydrides such as sodium hydride and potassium hydride, alkali metal hydroxides such as sodium hydroxide and potassium hydroxide, alkali metal alkoxides such as sodium methoxide and sodium tert- butoxide, organic metal bases such as butyl lithium and lithium diisopropylamide, and organic bases such as triethylamine, diisopropylethylamine, pyridine, 4- dimethylaminopyridine (DMAP), and 1,8-diazabicyclo[5.4.0]-7-undecene (DBU). [00362] The solvent used in each of the steps described above should be appropriately selected depending on the type of reaction or raw material compound or the like. Examples thereof include alcohols such as methanol, ethanol, and isopropanol, ketones such as acetone and ethyl methyl ketone, halogenated hydrocarbons such as methylene chloride and chloroform, ethers such as tetrahydrofuran (THF) and dioxane, aromatic hydrocarbons such as toluene and benzene, aliphatic hydrocarbons such as hexane and heptane, esters such as ethyl acetate and propyl acetate, amides such as N,N-dimethylformamide (DMF) and N- methyl-2-pyrrolidone, sulfoxides such as dimethyl sulfoxide (DMSO), and nitriles such as acetonitrile. These solvents can be used alone or as a mixture of two or more solvents. An organic base can be used as a solvent depending on the type of reaction. [00363] The compound of the invention represented by formula (1) or an intermediate thereof can be separated or purified by a method that is known to those skilled in the art. Examples thereof include extraction, partition, precipitation, column chromatography (e.g., silica gel chromatography, ion exchange chromatography, and preparative liquid chromatography), crystallization, and the like. Examples of crystallization solvents that can be used include alcohol solvents such as methanol, ethanol, and 2-propanol, ether solvents such as diethyl ether, ester solvents such as ethyl acetate, aromatic hydrocarbon solvents such as benzene and toluene, ketone solvents such as acetone, halogen solvents such as dichloromethane and chloroform, hydrocarbon solvents such as hexane, aprotic solvents such
as dimethylformamide and acetonitrile, water, mixtures thereof, and the like. The methods described in Jikken Kagaku Koza [Experimental Chemistry] (Ed. by The Chemical Society of Japan, Maruzen) Vol.1 and the like can be used as other purification methods. [00364] The molecular structure of the compound of the invention can be readily determined by a spectroscopic method such as nuclear magnetic resonance, infrared spectroscopy, or circular dichroism spectroscopy, or mass spectrometry by referring to the structure derived from each raw material compound. [00365] The intermediate or final product in the manufacturing method described above can lead to another compound encompassed by the present invention by appropriately converting the functional group thereof, extending various side changes based on especially an amino group, a hydroxyl group, a carbonyl group, halogen group, or the like, and, in doing so, applying protection and deprotection described above as needed. Conversion of a functional group and extension of side chains can be performed using a common method that is routinely used (see, for example, Comprehensive Organic Transformations, R. C. Larock, John Wiley & Sons Inc. (1999). [00366] Hereinafter, the present invention is described more specifically with the Reference Compounds, Compounds, and Assay Examples, but the present invention is not limited thereto. Compounds were identified by an elemental analysis value, a mass spectrum, a high performance liquid chromatography mass spectrometry system; LC-MS, IR spectroscopy, NMR spectroscopy, high performance liquid chromatography (HPLC), or the like. The compound names denoted in the following Reference Compounds and Compounds are not necessarily in accordance with the IUPAC nomenclature. While abbreviations are sometimes used to simplify a description, these abbreviations are defined the same as the above descriptions. [00367] NMR and MS data in Reference Compounds and Compounds use the following abbreviations. Me: methyl group tert: tertiary DMF: N,N-dimethylformamide DMSO: dimethyl sulfoxide THF: tetrahydrofuran DIPEA: N,N-diisopropylethylamine CPME: cyclopentyl methyl ether
TFA: trifluoroacetate PyBOP: (benzotriazol-1-yloxy)tripyrrolidinophosphonium hexafluorophosphate s: singlet brs: broad singlet d: doublet dd: double doublet t: triplet q: quartet m: multiplet br: broad J: coupling constant Hz: Hertz CDCl3: deuterated chloroform DMSO-d6: deuterated dimethyl sulfoxide CD3OD: deuterated methanol [00368] High performance liquid chromatography-mass spectrometer; measurement conditions of LC-MS are as follows. The observed mass spectrometry value [MS (m/z)] is indicated by [M+H]+, [M+2H]2+, [M+Na]+, or [M+2Na]2+, and time of retention is indicated by Rt (min). [00369] Measurement conditions Detector: ACQUITY® SQ detector (Waters) HPLC: ACQUITY UPLC® system Column: Waters ACQUITY UPLC® BEH C18 (1.7 um, 2.1 mm X 30 mm) Solvent: solution A: 0.06% formic acid/H2O, solution B: 0.06% formic acid/MeCN Gradient condition: 0.0-1.3 min Linear gradient from B 2% to 96% Flow rate: 0.8 mL/min UV: 220 nm and 254 nm Synthetic Examples Table A.
Reference Compound 1: tert-butyl 4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate
[00370] Pyridine (27.0 g) was added to a 1,4-dioxane solution (171 mL) of 4- chlorofuro[2,3-d]pyrimidine (26.4g) and tert-butyl piperazine-1-carboxylate (33.4g), and the reaction solution was stirred for 4 hours at 80°C. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: hexane/ethyl acetate) to obtain Reference Compound 1 (20.0 g). (LC-MS: [M+H]+/Rt (min)) = 305.3 [M+H]+/0.977 [00371] The compounds shown in Table 1 were obtained using a corresponding commercially available raw material by the same method as Reference Compound 1. [Table 1]
Reference Compound 4: tert-butyl 4-(5-cyanofuro[2,3-d]pyrimidin-4-yl)piperazine-1- carboxylate
Reference Compound 4 [00372] A DMF solution (5 mL) of tert-butyl 4-(5-bromofuro[2,3-d]pyrimidin-4- yl)piperazine-1-carboxylate (467 mg), tetrakis triphenylphosphine palladium (282 mg), and cyanated zinc (286 mg) was stirred under microwave irradiation (100°C, 1 hour). Ethyl acetate was added to the reaction solution, and the solution was washed with saturated sodium bicarbonate water and saturated saline. The organic phase was dried with sodium sulfate, filtered, and concentrated under reduced pressure. The resulting raw product was purified by silica gel chromatography (mobile phase: hexane/ethyl acetate) to obtain Reference Compound 4 (363 mg). LC-MS: [M+H]+/Rt (min) = 330.3 [M+H]+/0.897 Reference Compound 5: 4-(piperazin-1-yl)furo[2,3-d]pyrimidine
[00373] 4M hydrochloride ethyl acetate (400 mL) was added to a methanol solution (400 mL) of tert-butyl 4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carboxylate (19.97 g) while being cooled with ice. The reaction solution was then stirred overnight at room temperature. The generated solid was filtered out and washed with ethyl acetate and then dried under reduce pressure to obtain the dihydrochloride salt of Reference Compound 5 (17.7 g). (LC-MS: [M+H]+/Rt (min)) = 205.2 [M+H]+/0.373 [00374] Salts of the compounds shown in Table 2 were obtained from a corresponding raw material by the same method as Reference Compound 5. [
Reference Compound 9: 6-(isothiocyanatomethyl)quinoxaline
Reference Compound 9 [00375] Thiophosgen (0.26 mL) was added to chloroform (10 mL) and saturated sodium bicarbonate water (10 mL) solution of quinoxalin-6-ylmethanamine (640mg) while being cooled with ice. The reaction mixture was stirred for 15 minutes being cooled with ice. The reaction mixture was separated and organic phase was dried with sodium sulfate, filtered, and concentrated under reduced pressure. The crude product was used for next reaction without further purification. LC-MS: [M+H]+/Rt(min) = 202.1[M+H]+/0.803 [00376] The compounds shown in Table 3 were obtained from a corresponding raw material by the same method as Reference Compound 9.
Compound 1: N-((1H-indol-6-yl)methyl)-4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1- carbothioamide
Compound 1 [00377] A chloroform solution (100 mL) of (1H-indol-6-yl)methanamine (3.22 g), DIPEA (7.6 g), and thiophosgene (2.53 g) was stirred for 30 minutes while being cooled with ice. A chloroform solution (50 mL) of 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (3.0 g) and DIPEA (7.6 g) was added to the reaction solution, and the reaction solution was stirred for 2 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 1 (3.0 g).1H-NMR (DMSO-d6) δ: 10.98 (1H, s), 8.30 (1H, s), 8.23 (1H, t, J = 5.6 Hz), 7.88 (1H, d, J = 2.4 Hz), 7.44 (1H, d, J = 8.0 Hz), 7.35 (1H, s), 7.27 (1H, t, J = 2.8 Hz), 7.23 (1H, d, J = 2.4 Hz), 6.99 (1H, d, J = 7.6 Hz), 6.36 (1H, brs), 4.89 (2H, d, J = 5.6 Hz), 4.05-3.98 (8H, m). (LC-MS: [M+H]+/Rt (min)) = 398.0 [M+H]+/0.810 Compound 2: N-(3,4-dimethoxybenzyl)-4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1- carbothioamide
Compound 2 [00378] A chloroform solution (3 mL) of 3,4-dimethoxybenzylamine (0.07 mL), DIPEA (0.16 mL) and thiophosgene (0.04 mL) was stirred for 30 minutes while being cooled with ice. A chloroform solution (3 mL) of 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (84 mg) and DIPEA (0.16 mL) was added to the reaction solution, and the reaction solution was stirred for 2 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 2 (73 g).1H-NMR (CDCl3) δ: 8.34 (1H, s), 7.49 (1H, d, J = 2.4 Hz), 6.88-6.76 (4H, m), 5.69 (1H, brs), 4.78 (2H, d, J = 5.6 Hz), 4.11 (8H, s), 3.84 (6H, s). (LC-MS: [M+H]+/Rt (min)) = 414.4 [M+H]+/0.753 Compound 3: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(quinoxalin-6-ylmethyl)piperazine-1- carbothioamide
Compound 3 [00379] A chloroform solution (10 mL) of quinoxalin-6-ylmethanamine hydrochloride (106 mg), DIPEA (0.38 mL), and thiophosgene (0.04 mL) was stirred for 30 minutes while being cooled with ice. A chloroform solution (10 mL) of 4-(piperazin-1-yl)furo[2,3- d]pyrimidine dihydrochloride (100 mg) and DIPEA (0.38 mL) was added to the reaction solution, and the reaction solution was stirred for 2 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by
silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 3 (64 g).1H-NMR (CDCl3) δ: 8.86 (2H, s), 8.40 (1H, s), 8.13 (1H, d, J = 9.2 Hz), 8.04 (1H, d, J = 1.2 Hz), 7.83 (1H, dd, J = 1.6, 8.4 Hz), 7.34 (2H, d, J = 2.4 Hz), 6.81 (2H, d, J = 2.4 Hz), 4.23-4.17 (8H, m), 6.02 (1H, brs), 5.24 (2H, d, J = 5.6 Hz), 4.23-4.17 (8H, m). (LC-MS: [M+H]+/Rt (min)) = 406.3 [M+H]+/0.675 [00380] Compound 3 was also synthesized by the following method. Compound 3: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(quinoxalin-6-ylmethyl)piperazine-1- carbothioamide
Compound 3 [00381] Triethyl amine (1.52 mL) was added to a chloroform solution (10 mL) of 6- (isothiocyanatomethyl)quinoxaline (0.65 g) and 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (0.81 g) was stirred for 2 hours while being cooled with ice. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 3 (1.37 g).1H-NMR (CDCl3) δ: 8.86 (2H, s), 8.40 (1H, s), 8.13 (1H, d, J = 9.2 Hz), 8.04 (1H, d, J = 1.2 Hz), 7.83 (1H, dd, J = 1.6, 8.4 Hz), 7.34 (2H, d, J = 2.4 Hz), 6.81 (2H, d, J = 2.4 Hz), 4.23-4.17 (8H, m), 6.02 (1H, brs), 5.24 (2H, d, J = 5.6 Hz), 4.23-4.17 (8H, m). LC-MS: [M+H]+/Rt (min) = 406.3 [M+H]+/0.675[0058]. Compound 4: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(quinolin-7-ylmethyl)piperazine-1- carbothioamide
Compound 4
[00382] Triethyl amine (1.28 mL) was added to a chloroform solution (10 mL) of 7- (isothiocyanatomethyl)quinoline (240 mg) and 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (316 mg) was stirred for 1 hours while being cooled with ice. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 4 (306 mg).1H-NMR (CDCl3) δ: 8.81 (1H, dd, J = 2.0, 4.8 Hz), 8.29 (1H, s), 8.17 (1H, d, J= 8.4 Hz), 8.04 (1H, s), 7.75 (1H, d, J = 8.8 Hz), 7.56 (1H, dd, J = 1.2, 8.4 Hz), 7.43 (1H, d, J = 2.0 Hz), 7.38 (1H, dd, J = 4.8, 8.4 Hz), 6.71 (1H, d, J = 2.4 Hz), 6.53 (1H, brs), 5.11 (2H, d, J = 4.8 Hz), 4.15-4.04 (8H, m). (LC-MS: [M+2H]2+/Rt (min)) = 203.2 [M+H]+/0.596 Compound 4 di-TFA salt: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(quinolin-7-ylmethyl)piperazine- 1-carbothioamide di-TFA salt
Compound 4 di-TFA salt [00383] A chloroform solution (3 mL) of (quinolin-7-yl)methanamine (0.07 mL), DIPEA (0.16 mL), and thiophosgene (0.04 mL) was stirred for 30 minutes while being cooled with ice. A chloroform solution (3 mL) of 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (84 mg) and DIPEA (0.16 mL) was added to the reaction solution, and the reaction solution was stirred for 2 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by reversed-phase HPLC (mobile phase: 0.035% TFA solution/acetonitrile) to obtain Compound 4 di-TFA salt (52 g).1H-NMR (DMSO-d6) δ: 9.04 (1H, dd, J = 1.2, 5.2 Hz), 7.68 (1H, d, J = 7.6 Hz), 8.49 (1H, t, J = 5.2 Hz), 8.31 (1H, s), 8.09 (1H, d, J = 8.0 Hz), 7.97 (1H, s), 7.89 (1H, d, J = 2.8 Hz), 7.74-7.70 (2H, m), 7.25 (1H, d, J = 2.4 Hz), 5.06 (2H, d,J = 5.6 Hz), 4.09-4.03 (8H, m). (LC-MS: [M+2H]2+/Rt (min)) = 203.2 [M+H]+/0.596 [00384] Compound 4 was also synthesized by the following method. Compound 4: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(quinolin-7-ylmethyl)piperazine-1- carbothioamide
Compound 4 di-TFA salt Compound 4 [00385] 4-(furo[2,3-d]pyrimidin-4-yl)-N-(quinolin-7-ylmethyl)piperazine-1- carbothioamide di-TFA salt (40 mg) was suspended in chloroform (40 mL). After adding saturated sodium bicarbonate water and stirring, the organic phase and the aqueous phase were separated. The organic phase was dried with sodium sulfate and then filtered and concentrated under reduced pressure to obtain Compound 4 (20 mg).1H-NMR (CDCl3) δ: 8.81 (1H, dd, J = 2.0, 4.8 Hz), 8.29 (1H, s), 8.17 (1H, d, J= 8.4 Hz), 8.04 (1H, s), 7.75 (1H, d, J = 8.8 Hz), 7.56 (1H, dd, J = 1.2, 8.4 Hz), 7.43 (1H, d, J = 2.0 Hz), 7.38 (1H, dd, J = 4.8, 8.4 Hz), 6.71 (1H, d, J = 2.4 Hz), 6.53 (1H, brs), 5.11 (2H, d, J = 4.8 Hz), 4.15-4.04 (8H, m). (LC-MS: [M+2H]2+/Rt (min)) = 203.2 [M+H]+/0.596 Compound 5: 4-(furo[2,3-d]pyrimidin-4-yl)-N-((tetrahydro-2H-pyran-4- yl)methyl)piperazine-1-carbothioamide
Compound 5 [00386] A DMF solution (3 mL) of 4-aminomethyltetrahydropyran (0.04mL), triethylamine (0.15 mL), and thiophosgene (0.03 mL) was stirred for 4 hours while being cooled with ice.4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (100 mg) was added to the reaction solution, and the reaction solution was stirred for 12 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain
Compound 5 (43 mg).1H-NMR (CDCl3) δ: 8.39 (1H, s), 7.53 (1H, dd, J = 2.4, 8.8 Hz), 6.78 (1H, d, J = 2.8 Hz), 5.74 (1H, brs), 4.14 (8H, s), 3.97 (2H, dd, J = 3.2, 11.2 Hz), 3.60 (2H, t, J = 4.4 Hz), 3.36 (2H, dt, J = 2.4, 12.0 Hz), 2.06-1.96 (1H, m), 1.64 (2H, dd, J = 2.0, 13.2 Hz), 1.39-1.28 (2H, m). (LC-MS: [M+H]+/Rt (min)) = 362.2 [M+H]+/0.670 Compound 15: N-((6-chloropyridin-2-yl)methyl)-4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1- carbothioamide
Compound 15 [00387] A chloroform solution (3 mL) of (6-chloropyridin-2-yl)methanamine (318 mg), DIPEA (0.65 mL), and thiophosgene (0.11 mL) was stirred for 30 minutes while being cooled with ice. A chloroform solution (3 mL) of 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (409 mg) and DIPEA (0.65 mL) was added to the reaction solution, and the reaction solution was stirred for 2 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 15 (207 mg).1H-NMR (CDCl3) δ: 8.39 (1H, s), 7.63 (1H, t, J = 7.6 Hz), 7.51 (1H, d, J = 2.0 Hz), 7.23 (2H, d, J = 8.8 Hz), 7.10 (1H ,brs), 6.78 (2H, d, J = 2.8 Hz), 4.19-4.13 (8H, m). (LC-MS: [M+H]+/Rt (min)) = 389.2 [M+H]+/0.823 Compound 17: N-(benzo[d] [1,3]dioxolo-5-ylmethyl)-4-(furo[2,3-d]pyrimidin-4- yl)piperazine-1-carbothioamide
Compound 17 [00388] A DMF solution (1 mL) of 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (61 mg), 3,4-methylenedioxybenzylisothiocyanate (64 mg), and DIPEA (170 mg) was stirred for 20 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography (mobile phase: hexane/ethyl acetate) to obtain Compound 17 (83 mg).1H-NMR (DMSO-d6) δ: 8.30 (1H, d, J = 4.4 Hz), 8.17 (1H, s), 7.88 (1H, d, J = 2.8 Hz), 7.23 (1H, d,J = 2.8 Hz), 6.91 (1H, d, J = 1.2 Hz), 6.84-6.77 (2H, m), 5.96 (2H, s), 4.70 (2H, d, J = 5.6 Hz), 4.08-3.98 (8H, m). (LC-MS: [M+H]+/Rt (min)) = 398.0 [M+H]+/0.810 Compound 36: tert-butyl 5((4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1- carbothioamide)methyl)indoline-1-carboxylate
Compound 36 [00389] A chloroform solution (3 mL) of tert-butyl 5-(aminomethyl)indoline-1- carboxylate (90 mg) and thiophosgene (0.03 mL) was stirred for 30 minutes while being cooled with ice. A chloroform solution (3 mL) of 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (50 mg) and DIPEA (0.19 mL) was added to the reaction solution, and the reaction solution was stirred for 2 hours at room temperature. After concentrating the reaction solution under reduced pressure, the resultant was purified by silica gel chromatography
(mobile phase: chloroform/methanol) to obtain Compound 5 (48 mg). (LC-MS: [M+H]+/Rt (min)) = 495.4 [M+H]+/1.009 [00390] Compound 36 was also synthesized by the following method. Compound 36: tert-butyl 5((4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1- carbothioamide)methyl)indoline-1-carboxylate
Compound 36 [00391] A chloroform solution (50 mL) of tert-butyl 5-(isothiocyanatomethyl)indoline-1- carboxylate (3.51 g) was dropwisely added over 30 minitues to a chloroform solution (100 mL) of triethyl amine (9.62 mL) and 4-(piperazin-1-yl)furo[2,3-d]pyrimidine dihydrochloride (3.51 g) was stirred for 4 hours while being cooled with ice. After concentrating the reaction solution under reduced pressure, the reaction mixture was dissolved in chloroform and washed with saturated sodium bicarbonate water (50 mL) for 3 times. The organic phase was dried with sodium sulfate, filtered, and concentrated in reduced pressure. Amino silica gel was added to the EtOAc (50 mL) of resultant and stirred at room temperature. The raction mixture was filtrated and concentrated in reduced pressure to give Compound 36 (5.84 g).1H- NMR(CDCl3) δ: 8.40(1H, s), 7.56 (1H, d, J = 2.4 Hz), 7.14-7.10 (2H, m), 6.82 (1H, d, J = 2.4 Hz), 4.78 (2H, d, J = 4.4 Hz), 4.16 (8H, brs), 3.95 (2H, t, J = 8.4 Hz), (2H, d, J = 8.4 Hz) (LC-MS: [M+H]+/Rt(min)) = 495.3[M+H]+/1.021 [00392] The compounds shown in Table 4 were obtained from a corresponding raw material by the same method as Compound 1. Compounds purified by silica gel chromatography were obtained as a free form, and compounds purified by reverse-phase HPLC were obtained as a TFA salt. [
[00393] Compound 75: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(4- (hydroxymethyl)benzyl)piperazine-1-carbothioamide
Compound 74 Compound 75 [00394] A 4M lithium borohydride THF solution (0.03 mL) was added to a THF solution (10 mL) of methyl 4-((4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carbothioamide)methyl) benzoate (53 mg) while being cooled with ice, and the reaction solution was stirred for 12 hours at room temperature. The reaction solution was quenched with an aqueous saturated ammonium chloride solution and then diluted with ethyl acetate, and washed with water and saturated saline. The reaction solution was then dried with sodium sulfate, filtered, and concentrated under reduced pressure. The resultant was purified by silica gel chromatography (mobile phase: chloroform/methanol) to obtain Compound 75 (48 mg). LC-MS: [M+H]+/Rt (min) = 384.3 [M+H]+/0.654. Compound 76: 4-((4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carbothioamide)methyl) benzoate
Compound 74 Compound 76 mono-TFA salt [00395] Lithium hydroxide (6 mg) was added to a THF solution (5 mL) of methyl 4-((4- (furo[2,3-d]pyrimidin-4-yl)piperazine-1-carbothioamide)methyl) benzoate (20 mg) while being cooled with ice, and the reaction solution was stirred for 12 hours at room temperature. After concentrating the reaction solution, the resultant was purified by reversed-phase HPLC (mobile phase: 0.035% TFA solution/acetonitrile) to obtain the mono-TFA salt of Compound 76 (3 mg). (LC-MS: [M+H]+/Rt(min)) = 396.3 [M+H]+/0.638 Compound 78: tert-butyl N-(tert―butoxycarbonyl)-N-(5-(6-((4-(furo[2,3-d]pyrimidin-4- yl)piperazine-1-carbothioamide)methyl)-1H-indol-1-yl)-5-oxopentyl)glycinate
[00396] Sodium hydride (27 mg) was added to a THF solution (5 mL) of N-((1H-indol-6- yl)methyl)-4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carbothioamide (60 mg) while being cooled, and then the reaction solution was stirred for 30 minutes at room temperature. A THF solution (5 mL) of 5-((2-(tert-butoxy)-2-oxoethyl)(tert-butoxycarbonyl)amino) pentanoate (76 mg), triethylamine (0.04 mL), and PyBOP (159 mg) was separately stirred for 1 hour at room temperature. After mixing the reaction solutions described above at room temperature, the reaction solution was stirred for 12 hours. The reaction solution was diluted with ethyl acetate, then washed with saturated sodium bicarbonate water and saturated saline. The
organic phase was then dried with sodium sulfate, filtered, and concentrated under reduced pressure. The resulting raw product was purified by silica gel chromatography (mobile phase: hexane/ethyl acetate) to obtain Compound 78 (108 mg). LC-MS: [M+H]+/Rt (min) = 706.7 [M+H]+/1.177. Compound 44: 4-(furo[2,3-d]pyrimidin-4-yl)-N-((1-methylindolin-5-yl)methyl)piperazine-1- carbothioamide
Compound 44 Compound 11 dihydrochloride [00397] Triacetoxyborohydride (50 mg) was added to a methanol solution (1 mL) of 4- (furo[2,3-d]pyrimidin-4-yl)-N-(indolin-5-ylmethyl)piperazine-1-carbothioamide dihydrochloride (11 mg), formalin (1 mL), and acetic acid (0.6 μL), and then the reaction solution was stirred for 12 hours at room temperature. The reaction solution was diluted with ethyl acetate, then washed with saturated sodium bicarbonate water and saturated saline. The organic phase was then dried with sodium sulfate, filtered, and concentrated under reduced pressure. The resulting raw product was purified by reversed-phase HPLC (mobile phase: 0.035% TFA solution/acetonitrile) to obtain Compound 44 di-TFA salt (3 mg). (LC-MS: [M+H]+/Rt (min)) = 409.4 [M+H]+/0.712 [00398] Salts of the compounds shown in Table 5 were obtained from a corresponding raw material by the same method as Compound 44 di-TFA salt. [
[00399] Compound 87: 4-(furo[2,3-d]pyrimidin-4-yl)-N-((1-methylindolin-5- yl)methyl)piperazine-1-carbothioamide
Compound 11 dihydrochloride Compound 87 [00400] Acetic anhydride (8.9 μL) was added to a THF solution (2 mL) of 4-(furo[2,3- d]pyrimidin-4-yl)-N-(indolin-5-ylmethyl)piperazine-1-carbothioamide dihydrochloride (11 mg) and pyridine (7.6 μL), and then the reaction solution was stirred for 2 hours at room temperature. The reaction solution was diluted with ethyl acetate, then washed with saturated sodium bicarbonate water and saturated saline. The organic phase was then dried with sodium sulfate, filtered, and concentrated under reduced pressure. The resulting raw product was purified by reversed-phase HPLC (mobile phase: 0.035% TFA solution/acetonitrile). The resulting compound was then dissolved into ethyl acetate, then washed with saturated sodium
bicarbonate water. The organic phase was then dried with sodium sulfate, filtered, and concentrated under reduced pressure to obtain Compound 87 (4 mg). LC-MS: [M+H]+/Rt (min) = 437.4 [M+H]+/0.716. [00401] The compound shown in Table 6 was obtained from a corresponding raw material by the same method as Compound 87. [Table 6]
[00402] Compound 2: N-(3,4-dimethoxybenzyl)-4-(furo[2,3-d]pyrimidin-4-yl)piperazine- 1-carbothioamide monohydrochloride
Compound 2 Compound 2 monohydrochloride [00403] Concentrated hydrochloric acid (0.09 mL) was added to an acetone solution (5 mL) of N-(3,4-dimethoxybenzyl)-4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1-carbothioamide (73 mg), and the reaction solution was stirred for 20 hours at room temperature. The resulting solid was filtered out, washed with acetone, and dried under reduced pressure to obtain Compound 2 monohydrochloride (52 mg).1 H-NMR (400 MHz, DMSO-d6) δ: 8.28-8.34 (1H, m), 8.13-8.22 (1H, m), 7.86-7.93 (1H, m), 7.20-7.27 (1H, m), 6.94-7.02 (1H, m), 6.80-6.91
(2H, m), 4.67-4.77 (2H, m), 3.92-4.08 (8H, m), 3.71 (6H, s). (LC-MS: [M+H]+/Rt (min)) = 414.3 [M+H]+/0.759 [00404] Salts of the compounds shown in Table 7 were obtained from a corresponding raw material by the same method as Compound 2 monohydrochloride. [Table 7]
[00405] Compound 11: 4-(furo[2,3-d]pyrimidin-4-yl)-N-(indolin-5-ylmethyl)piperazine-1- carbothioamide
[00406] tert-butyl 5((4-(furo[2,3-d]pyrimidin-4-yl)piperazine-1- carbothioamide)methyl)indoline-1-carboxylate (Compound 36, 19 mg) was stirred for 6 hours at room temperature in 4 M hydrochloric acid in CPME (5 mL). The reaction solution was concentrated. The resulting solid was suspended in ethyl acetate and stirred for 1 hours, and then filtered out to obtain Compound 11 dihydrochloride (18 mg).1 H-NMR (400 MHz, CD3CD―d4) δ: 8.42 (1H, s), 7.87 (1H, d, J = 2.8 Hz), 7.50 (1H, s), 7.42 (2H, s), 7.28 (1H, d, J = 2.8 Hz), 4.94 (2H, s), 4.84 (8H, s), 4.20 (2H, s), 3.85 (2H, t, J = 7.2 Hz), 3.34 (2H, s). (LC-MS: [M+2H]2+/Rt (min)) = 198.2 [M+2H]2+/0.356 [00407] Salts of the compounds shown in Table 8 were obtained from a corresponding raw material by the same method as Compound 11 dihydrochloride. [Table 8]
Assay Examples Materials and Methods [00408] Reagents.22Rv1, MDA-MB-231, and Ov56 cells were purchased from ATCC and cultured according to the manufacturer’s instructions. The CellTiter-Glo cell viability assay (G7570) was purchased from Promega and used according to the manufacturer’s protocol. Human RAD51/RECA (Sandwich ELISA) ELISA kit (LS-F6761) was purchased from Lifespan Bio (LSBio). Olaparib (S1060) and camptothecin (S1288) were purchased from Selleck chemicals. [00409] Antibodies. Rabbit monoclonal antibody to RAD51(ab133534, 1:800) and mouse monoclonal antibody to Geminin (ab104306, 1:250) were purchased from Abcam. Rabbit monoclonal antibodies to ATF4 (cat # 11815, 1:1000) and Phospho eIF2a (cat# 3398) were purchased from Cell Signaling Technology. Goat anti-rabbit 488 (A27035, 1:1000) and goat anti-mouse 647 (A28181, 1:1000) secondary antibodies were purchased from ThermoFisher Scientific. The GAPDH (sc-365062; 1:1000-2000) antibody was purchased from Santa Cruz Technologies. Nuclear stain Hoechst 33342 (cat# 62249) was also purchased from ThermoFisher Scientific.
Assay Example 1: Assay for decrease of RAD51 levels in FaDu cells [00410] An assay was conducted to assess the ability of certain compounds disclosed herein to decrease RAD51 levels in FaDu cells. The results are reported as an IC50 range for each assayed compound. [00411] FaDu cells were obtained from the American Type Culture Collection (ATCC). The cells were cultured in an MEM medium containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in the presence of 5% CO2. The cells were seeded at 2 x 105 cells per well in a 12-well plate, and the compound to be evaluated was added such that the final concentration of DMSO would be 0.1%, and the cells were cultured for 24 hours. After the completion of culturing, the culture supernatant was removed and washed with PBS. The cells were lysed with RIPA buffer (radioimmunoprecipitation buffer), and the lysate was retrieved. [00412] The protein concentration of the retrieved lysate was measured, and the lysate was diluted with 0.1× sample buffer such that the protein mass in 7 μL would be constant.3 μL of 5× Fluorescence Mastar Mix was then added, and the mixture was heated for 5 minutes at 100°C with a heat block. The heated sample was dispensed on a plate in accordance with the protocol of Wes (SimpleProtein). Ladders and samples were dispensed in column A, blocking buffer was dispensed in column B, primary antibodies (anti-RAD51 antibodies (CST, #8875, 1:100) and anti-tubulin antibodies (CST, #3873S, 1:1000)) were dispensed in column C, HRP (horseradish peroxidase) labeled secondary antibodies (mixture of equal amounts of anti- mouse antibodies and anti-rabbit antibodies) were dispensed in column D, and an HRP substrate mixture was dispensed in column E. Capillary electrophoresis was applied in accordance with the standard protocol of Wes to obtain quantitative data. [00413] Table 9 shows the IC50 range for each assayed compound, wherein “A” denotes a compound having an IC50 in the assay of less than 0.3 µM, “B” denotes a compound having an IC50 in the assay of from 0.3 µM to 1 µM and “C” denotes a compound having an IC50 in the assay of greater than 1 µM. [Table 9]
Assay Example 2: Immunoblot Analysis [00414] ER stress-induced UPR is a cellular adaptive response that evolved to restore protein-folding homeostasis by reducing protein synthesis through phosphorylation of eIF2α and by increasing the ER protein-folding and degradative capacities through transcriptional activation by XBP1 and ATF6α. [PMID: 22116877] If the UPR cannot resolve the protein- folding defect, cells undergo apoptosis through ATF4 and CHOP activation. [PMID: 23624402]. Compound 1 was tested for efficacy in inducing ER stress, its ability to cause phosphorylation of eIF2α and activate the ATF4 transcription factor using Western blot analysis in 22Rv1 cells. [00415] 22Rv1 cells were treated with 10 µM Compound 1. The cells were harvested after the periods of time indicated in FIG.1 by washing with ice-cold PBS and then lysed with ice- cold RIPA buffer (Cell Signaling Technologies, 9806S) containing 1% Halt protease and
phosphatase inhibitor cocktail (ThermoFisher Scientific, 78444) on ice. Whole cell lysates were sonicated and centrifuged at 16,000 x g for 10 min at 4˚C, and the protein concentration of the supernatant was determined using a BCA Protein assay kit (ThermoScientific, 23225). Equal amounts of protein lysates (30 μg/lane and 10 µg/lane only for Histone H3 immunoblots) were fractionated on a NuPAGE Novex 4%–12% Bis-Tris Protein Gel (Thermo Fisher Scientific, NP0335BOX) and transferred onto a low fluorescence PVDF membrane (Millipore, IPFL07810). Subsequently, the membranes were blocked with 5% BSA for 1 hour at room temperature and then treated with the appropriate antibody at 4°C overnight. Goat anti-rabbit IgG conjugated to IRDye 700 (926-68171) or 800 (827-08365) and goat anti-mouse IgG conjugated to IRDye 700 (926-68170) or 800 (827-08364) secondary antibodies were purchased from Li-Cor Biosciences and used at 1:20000 in 5% BSA in TBST (TBS-Tween 20; Genesee Scientific, 18-235B). Protein expression was visualized with Li-Cor Odyssey CLX imaging system. Li-Cor Image Studio software was used for western blot analysis and quantification. [00416] As shown in FIG.1, treatment of the cells with 10 µM Compound 1 significantly increased phosphorylation of eIF2α after 15 minutes of treatment. Additionally, expression of transcription factor ATF4 also increased significantly after 2 hrs of treatment with Compound 1. This data demonstrates that Compound 1 induces ER stress leading to UPR in cancer cells. Assay Example 3: Gene expression analysis by quantitative real-time (qRT)–PCR [00417] The effectiveness Compound 1 and Compound 4 dihydrochloride in activating ATF4 were assessed by analyzing expression of ATF4 regulated genes, that is TRIB3, GADD34, ERO1α, and ATF3, using RT-qPCR. Total RNA was isolated from cells using Quiagene RNAeasy kit. cDNA was synthesized from 500 ng of total RNA in a 20 µL reaction volume using the SuperScript III First-Strand Synthesis SuperMix Kit (Invitrogen) for 50 minutes at 50°C, followed by 85°C for 5 minutes. qPCR analysis of ATF3, TRIB3, GADD34, ERO1a, and GAPDH mRNA levels was conducted using the QuantStudio 3 system. Taqman real-time PCR assay probes were purchased from ThermoFisher Scientific. As shown in FIGs.2A-D, treatment of 22Rv1 cells with Compound 1 or Compound 4 dihydrochloride led to a significant increase in expression of the selected genes (TRIB3, GADD34, ERO1α, and ATF3) after 6 hr of treatment. Assay Example 4: RAD51 ELISA Assay [00418] In order to test the efficacy of Compound 1, Compound 5 hydrochloride, Compound 2 hydrochloride, Compound 3 dihydrochloride, Compound 11 dihydrochloride,
Compound 4 dihydrochloride, and Compound 15 dihydrochloride, their ability to decrease levels of RAD51 in vitro was assessed at the protein level by a commercially available ELISA assay. [00419] 22Rv1 cells were treated with the indicated compounds at concentrations ranging from 0 – 25 µM for 24 hrs. After 24 hrs of treatment, cells were harvested and lysed in ice- cold PBS containing Halt Protease and Phosphatase inhibitor cocktail. BCA assay was used to quantify the protein in the cell lysate. RAD51 levels were measured using the Human RAD51/RecA sandwich enzyme‐linked immunosorbent assay (ELISA) kit (LSBio, Seattle, WA) according to the manufacturer’s protocol. [00420] As shown in the FIGs.3A-G, all the tested compounds demonstrated >35% reduction in levels of RAD51 protein as compared to vehicle control at 100 nM concentration after 24 hrs of treatment. In particular, Compound 15 dihydrochloride, Compound 4 dihydrochloride, Compound 11 dihydrochloride, and Compound 3 dihydrochloride demonstrated higher (>50%) reduction in RAD51 levels at a 100 nM concentration, which was 61.84%, 61.66%, 54.60%, and 53.00% reduction in RAD51 levels, respectively. Assay Example 5: RAD51 Foci Assay [00421] It is well established that RAD51 plays a critical role in HRR (PMID: 12778123). To assess the effect of the disclosed compounds on the functional status of HRR, RAD51 foci-positive tumor cells (22Rv1) in S/G2-phase of the cell cycle (geminin-positive) were evaluated using fluorescence microscopy. [00422] 22Rv1 cells were treated with the indicated compounds at concentrations ranging from 0 – 1 µM for 24/48/72 hrs in combination with 0.1 µM camptothecin. After each incubation, cells were fixed at room temperature for 20 min using 4% performaldehyde (PFA), followed by permeabilization with 0.3% Triton X-100 in PBS. Before addition of primary antibodies, cells were blocked with blocking buffer (PBS + 3% goat serum) overnight at 4 ºC. Primary antibodies were diluted in PBS (anti-RAD51 at a 1:800 dillution and anti-Geminin at a 1:250 dilution) and incubated with the cells overnight at 4 ºC. Secondary antibodies were diluted in PBS (Goat anti-rabbit 488 and Goat anti-mouse 647 at a 1:1000 dilution) and incubated with the cells for 3 hrs at room temperature. After the staining steps, nuclei were counterstained with Hoechst 405. Imaging was performed using high content screening microscope, GE IN Cell Analyzer 6500 with 40X/0.95 NA Nikon objective, 12 fields/well binning 1x1. Images were acquired using 3-channels in confocal mode (Hoechst: Channel 1 Ex.405 Em. (445/58), RAD51: Channel 2 Ex.488 Em. (524/48),
and Geminin: Channel 3 Ex.642 Em. (682/60)) Maximum intensity projection (5 Z-slices, 1.5 µm step size) was used for the analysis of RAD51 Foci. Image quantification analysis was done using Thermo Fisher HCS Studio 6.6.1, Cellomics Scan. The Cellomics Spot Detector BioApplication algorithms were used for image quantification, and unbiased automated outlier rejection Phyton scripts were applied. [00423] FIG.4 shows example fluorescent micrographs of control cells, camptothecin- treated cells, and cells treated with 0.1 µM or 1 µM of the indicated compound (Compound 1, Compound 2 hydrochloride, Compound 11 dihydrochloride, Compound 4 dihydrochloride, and Compound 15 dihydrochloride) in combination with 0.1 µM camptothecin. As shown in FIGs.5A-C all the tested compounds demonstrated significant reduction in RAD51-foci formation after 72 hrs at 1 µM concentration. Compound 4 dihydrochloride and Compound 15 dihydrochloride demonstrated a significant reduction in RAD51-foci formation at 1 µM at all the time points tested. Assay Example 6: Cell Viability Assay [00424] Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are effective in cancers with a defective HRR (PMID: 30934991). Cells with defects in the HRR, including those with deleterious variants in BRCA1 or BRCA2 (BRCA1/2) genes, are particularly sensitive to PARPi (PMID: 15829967, 15829966, 18971340). In breast cancer (BC), the efficacy results of the PARPi olaparib (Lynparza®) in metastatic patients carrying a germline BRCA1/2 (gBRCA) pathogenic variant have led to its recent approval by the Food and Drug Administration (PMID: 28578601). Similarly, use of PARPi could be extended beyond gBRCA to a wider group of cancer patients if HRR deficiency is induced therapeutically, such as by UPR modulation. Compound 1, Compound 5 hydrochloride, Compound 2 hydrochloride, Compound 3 dihydrochloride, Compound 11 dihydrochloride, Compound 4 dihydrochloride, and Compound 15 dihydrochloride at a concentration of 0.125 µM, 0.25 µM, 1 µM or 5 µM were evaluated in vitro for their ability to demonstrate synergy with olaparib against 22Rv1 cells. [00425] Cell viability for 22Rv1, Ov56, and MDA-MB-231 cells was assessed using a CellTiterGlo (Promega) assay according to the manufacturer’s protocol. Specifically, 300 cells were plated per well in a 384-well tissue culture treated plate (Greiner) in 20 μL of complete medium. Compounds of the present disclosure to be tested and olaparib were added using a Labcyte Echo acoustic dispensing device at desired concentration and the cells were incubated for 96 hours. Cell viability was assessed using CellTiterGlo (Promega) on an
Envision (PerkinElmer) plate reader. Synergy analysis was performed according to Chou- Talalay method (PMID: 20068163). [00426] As shown in FIGs.6A-6G, all the tested compounds except Compound 5 hydrochloride demonstrated some synergy with olaparib. In particular, Compound 3 dihydrochloride demonstrated synergy with olaparib at all tested concentrations. The efficacy of certain indicated compounds as a single agent against 22Rv1, Ov56, and MDA-MB-231 cell lines was also evaluated. As shown in FIGs.7A-C, Ov56 was the most sensitive to the tested compounds followed by 22Rv1 and MDA-MB-231, respectively. These results suggest that Ov56 cells may be more dependent on RAD51-driven HRR for efficient cell cycle progression as compared to 22Rv1 and MDA-MB-231 cells. Pharmacokinetic/Pharmacodynamic (PK/PD) Study 1 [00427] The efficacy of the certain disclosed compounds in decreasing RAD51 levels in vivo was evaluated. A cell line-derived xenograft (CDX) of 22Rv1 cells were grown in athymic nude mice and utilized for pharmacokinetic (PK) and phrmacodynamic (PD) evaluation as outlined in FIG.8. Tumor and plasma from each mouse were collected after 24 hrs of treatment and assessed for amount of drug present (PK) and RAD51 protein levels (PD). [00428] 22Rv1 cell line xenografts were established in the flank of athymic mice (Charles River) as previously described (PMID: 31799745). Flank tumors were allowed to grow to a volume of approximately 200 mm3. Mice with established tumors were randomized into treatment groups. The mice in the treatment groups were treated with different doses of the tested compounds of the present disclosure or vehicle by oral gavage. After 24 hr of treatment, the mice were sacrificed and blood and tumor tissue were harvested for PK and PD analyses. PK blood samples were collected by heart puncture in EDTA tubes. Tumor tissues were flash frozen for PK and PD analyses. Blood and tumor concentrations of the tested compounds were determined by protein precipitation followed by LC/MS-MS analysis. PD effect of tested compounds on tumor tissue was assessed using a RAD51 ELISA assay as described above in Assay Example 4. [00429] FIGs.9A-E summarize the PK data for Compound 1, Compound 5 hydrochloride, Compound 3 dihydrochloride, Compound 11 dihydrochloride, and Compound 4 dihydrochloride. Compound 2 hydrochloride and Compound 15 dihydrochloride were not detected in plasma or tumor after 24 hr of treatment. Compound 4 dihydrochloride displayed the best PK properties, with the highest concentration of drug observed in the tumor and
plasma after 24 hrs of exposure. As shown in FIGs.10A-G, all the tested compounds demonstrated decreased RAD51 levels in a tumor after 24 hrs of treatment. In particular, Compound 4 dihydrochloride and Compound 5 hydrochloride demonstrated a dose- dependent decrease in the levels of RAD51. [00430] Immunoblot analysis and gene expression analysis using RT-qPCR demonstrated that the indicated compounds induced ER stress and the UPR. RAD51 ELISA assay and RAD51 foci formation assay in vitro demonstrated that all tested compounds decreased the levels of RAD51 and suppressed the HRR. Further, cell viability assays demonstrated that the tested compounds produced synergy with PARPi olaparib, and also showed cell line-specific effects as single agents. Finally, PK/PD studies revealed that all the compounds tested effectively decreased RAD51 levels in vivo after 24 hr exposure, with varied clearance times. In view of these results, Compound 3 dihydrochloride, Compound 11 dihydrochloride, and Compound 4 dihydrochloride demonstrated superior efficacies in decreasing the level of RAD51 in vitro and in vivo. [00431] The teachings of all patents, published applications and references cited herein are incorporated by reference in their entirety. [00432] While example embodiments have been particularly shown and described, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the embodiments encompassed by the appended claims.
Claims
CLAIMS What is claimed is: 1. A compound having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein: X is -O- and Y is -C(H)-, or Y is -O- and X is -C(H)-; Ring G is (C6-C15)aryl, (C5-C15)heteroaryl, (C3-C15)carbocyclyl, monocyclic (C3- C10)heterocyclyl or bicyclic fused (C5-C15)heterocyclyl; R1, for each occurrence, is independently halo, cyano, hydroxy, (C1-C6)alkyl, (C1- C6)haloalkyl, (C1-C6)alkoxy or (C1-C6)haloalkoxy; R2 is H, (C1-C6)hydroxyalkyl, (C6-C15)aryl(C1-C6)alkyl or (C3-C15)heterocyclyl(C1- C6)alkyl or, together with an atom of Ring G and their intervening atoms, forms a three- to eight-membered ring that is spiro or fused to Ring G; R3, for each occurrence, is independently oxo or halo, cyano, hydroxy, (C1- C6)haloalkyl, (C1-C6)haloalkoxy, (C1-C6)hydroxyalkyl, (C1-C6)alkyl, (C1- C6)alkoxy, (C2-C12)alkoxyalkyl, -C(O)(C1-C6)alkyl, -C(O)-(C1-C6)alkylene- N(R5)2, -C(O)(OR4), -C(O)N(R5)2, -S(O)2N(R5), or -N(R5)2; R4, for each occurrence, is independently H or (C1-C6)alkyl; R5, for each occurrence, is independently H, (C1-C6)alkyl, (C6-C15)aryl, (C5- C15)heteroaryl, -C(O)(OR6) or -CH2C(O)(OR6); R6, for each occurrence, is independently H or (C1-C6)alkyl; m is 0, 1 or 2; n is 0, 1, 2 or 3; and p is 0, 1 or 2.
2. The compound of claim 1, wherein X is -O- and Y is -C(H)-.
3. The compound of claim 1, wherein Y is -O- and X is -C(H)-.
4. The compound of any one of claims 1-3, wherein Ring G is (C6-C10)aryl, (C5- C10)heteroaryl, (C6-C10)carbocyclyl, monocyclic (C5-C6)heterocyclyl or bicyclic fused (C6-C10)heterocyclyl.
5. The compound of any one of claims 1-4, wherein Ring G is oxazolyl, phenyl, pyridinyl, dihydropyridinyl, indolyl, indolinyl, isoindolinyl, quinolinyl, isoquinolinyl, quinoxalinyl, tetrahydroquinolinyl, benzofuranyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, benzo[d][1,3]dioxolyl, dihydrobenzo[b][1,4]dioxinyl, cyclohexyl, tetrahydropyranyl, piperidinyl, piperazinyl or morpholinyl.
6. The compound of any one of claims 1-3, wherein Ring G is (C6-15)aryl or (C5-15)heteroaryl.
7. The compound of claim 6, wherein Ring G is (C6-C15)aryl.
8. The compound of claim 7, wherein Ring G is phenyl.
9. The compound of claim 6, wherein Ring G is (C5-C15)heteroaryl.
10. The compound of claim 9, wherein Ring G is pyridinyl, dihydropyridinyl, indolyl, quinolinyl, isoquinolinyl, quinoxalinyl or benzofuranyl.
11. The compound of any one of claims 1-3, wherein Ring G is bicyclic fused (C5-C15)heterocyclyl.
12. The compound of claim 11, wherein Ring G is indolinyl, isoindolinyl, dihydrobenzo[d]imidazolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, tetrahydroquinoxalinyl, dihydrobenzofuranyl, dihydroisobenzofuranyl, benzo[d][1,3]dioxolyl, chromanyl, or dihydrobenzo[b][1,4]dioxinyl.
13. The compound of any one of claims 1-3, wherein Ring G is (C3-15)carbocyclyl or monocyclic (C5-15)heterocyclyl.
14. The compound of claim 13, wherein Ring G is a saturated (C5-8)carbocyclyl or a saturated monocyclic (C5-8)heterocyclyl.
15. The compound of claim 13 or 14, wherein Ring G is cyclohexyl, tetrahydropyranyl, piperidinyl, piperazinyl or morpholinyl.
16. The compound of any one of claims 1-15, wherein R1, for each occurrence, is independently halo, cyano, (C1-C6)alkyl or (C1-C6)haloalkyl.
17. The compound of claim 16, wherein R1 is independently halo or cyano.
18. The compound of claim 17, wherein R1 is independently bromo or cyano.
19. The compound of any one of claims 1-18, wherein R2 is H or, together with an atom of Ring G and their intervening atoms, forms a three- to eight-membered ring that is spiro or fused to Ring G.
20. The compound of claim 19, wherein R2 is H.
21. The compound of claim 19, wherein R2, together with an atom of Ring G and their intervening atoms, forms a four- to six-membered ring that is spiro or fused to Ring G.
22. The compound of claim 21, wherein R2, together with an atom of Ring G and their intervening atoms, forms a four- to six-membered ring that is spiro to Ring G.
23. The compound of claim 22, wherein R2 and Ring G, together with their intervening atoms, form a 7-oxa-2-azaspiro[3.5]nonan-2-yl.
24. The compound of claim 21, wherein R2, together with an atom of Ring G and their intervening atoms, forms a four- to six-membered ring that is fused to Ring G.
25. The compound of claim 24, wherein R2 and Ring G, together with their intervening atoms form a 5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl or 5,8-dihydro-1,7- naphthyridin-7(6H)-yl.
26. The compound of any one of claims 1-25, wherein R3, for each occurrence, is independently halo, (C1-C6)alkyl, cyano or (C1-C6)alkoxy.
27. The compound of claim 26, wherein R3, for each occurrence, is independently -F, -Cl, -Br, or methoxy.
28. The compound of claim 1-25, wherein R3, for each occurrence, is independently - C(O)-(C1-C6)alkylene-N(R5)2, -C(O)(OR4), -C(O)N(R5)2, -S(O)2N(R5) or -N(R5)2.
29. The compound of any one of claims 1-25 and 28, wherein R4, for each occurrence, is independently (C1-C6)alkyl.
30. The compound of any one of claims 1-25 and 28, wherein R4, for each occurrence, is H.
31. The compound of any one of claims 1-25 and 28-30, wherein R5, for each occurrence, is independently H, pyrimidinyl, tert-butoxycarbonyl, methyl tert-butoxycarbonyl or methyl carboxylate.
32. The compound of claim 1-25 and 28-30, wherein R5, for each occurrence, is independently -C(O)(OR6) or -CH2C(O)(OR6).
33. The compound of any one of claims 1-25, 28-30 and 32, wherein R6, for each occurrence, is independently (C1-C6)alkyl.
34. The compound of any one of claims 1-25, 28-30 and 32, wherein R6, for each occurrence, is H.
35. The compound of any one of claims 1-34, wherein m is 0 or 1.
36. The compound of claim 35, wherein m is 0.
37. The compound of claim 35, wherein m is 1.
38. The compound of any one of claims 1-37, wherein n is 0, 1 or 2.
39. The compound of claim 38, wherein n is 0 or 1.
40. The compound of claim 39, wherein n is 0.
41. The compound of claim 39, wherein n is 1.
42. The compound of any one of claims 1-41, wherein p is 0.
43. The compound of any one of claims 1-41, wherein p is 1.
44. The compound of any one of claims 1-41, wherein p is 2.
46. The compound of any one of claims 1-3 and 16-44, having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein: A1 is -C(H)- or -N-; and Z1 and Z2 are absent, or Z1 and Z2, taken together with their intervening atoms, form a 4-7-membered ring that optionally contains one, two or three independently selected heteroatoms.
47. The compound of any one of claims 1, 2, 19-34 and 38-45, having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein: R7 is H, halo, cyano, hydroxy, (C1-C6)alkyl, (C1-C6)haloalkyl, (C1-C6)alkoxy or (C1- C6)haloalkoxy; A1 is -C(H)- or -N-; and
Z1 and Z2 are absent, or Z1 and Z2, taken together with their intervening atoms, form a 4-7-membered ring that optionally contains one, two or three independently selected heteroatoms.
48. The compound of claim 46 or 47, wherein A1 is -C(H)-.
49. The compound of claim 46 or 47, wherein A1 is -N-.
50. The compound of any one of claims 46-49, wherein Z1 and Z2 are absent.
51. The compound of any one of claims 46-49, wherein Z1 and Z2, taken together with their intervening atoms, form a 4-7-membered ring that optionally contains one, two or three independently selected heteroatoms.
52. The compound of claim 51, wherein Z1 and Z2, taken together with their intervening atoms, form a 5-6-membered ring that contains one or two heteroatoms independently selected from O and N.
54. The compound of any one of claims 1, 2, 19-34 and 38-45, having the following structural formula:
or a pharmaceutically acceptable salt thereof, wherein:
R7 is -H, halo, cyano, hydroxy, (C1-C6)alkyl, (C1-C6)haloalkyl, (C1-C6)alkoxy or (C1- C6)haloalkoxy; A2 is -C(H)2-, -N(H)- or -O-; and A3 is >C(H)- or >N-.
55. The compound of claim 53 or 54, wherein A2 is -C(H)2- and A3 is >C(H)-.
56. The compound of claim 53 or 54, wherein A2 is -O- and A3 is >C(H)-.
57. The compound of any one of claims 45, 47-52 and 54-56, wherein R7 is H, halo, cyano, (C1-C6)alkyl or (C1-C6)haloalkyl.
58. The compound of claim 57, wherein R7 is: (a) H, halo or cyano; (b) H, bromo or cyano; or (c) H.
60. The compound of claim 1, wherein the compound has one of the following structural formulas:
69. A pharmaceutical composition, comprising a compound of any one of claims 1-68, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
70. A method of decreasing a level of RAD51 in a cell, comprising contacting the cell with a compound of any one of claims 1-68, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of claim 69.
71. The method of claim 70, further comprising contacting the cell with one or more additional therapeutic agents.
72. A method of decreasing a level of RAD51 in a subject having a cancer, comprising administering to the subject a therapeutically effective amount of a compound of any one of claims 1-68, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition of claim 69.
73. The method of claim 72, further comprising administering to the subject one or more additional therapeutic agents.
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US7220856B2 (en) * | 2002-06-27 | 2007-05-22 | Schering Aktiengesellschaft | Substituted quinoline CCR5 receptor antagonists |
US20080051414A1 (en) * | 2003-10-14 | 2008-02-28 | Arizona Board Of Regents On Behalf Of The University Of Arizona | Protein Kinase Inhibitors |
US20080226747A1 (en) * | 2007-03-01 | 2008-09-18 | Supergen, Inc. | Pharmaceutical formulations comprising salts of a protein kinase inhibitor and methods of using same |
WO2013072694A1 (en) * | 2011-11-15 | 2013-05-23 | Xention Limited | Thieno- and furo - pyrimidines and pyridines, useful as potassium channel inhibitors |
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US7220856B2 (en) * | 2002-06-27 | 2007-05-22 | Schering Aktiengesellschaft | Substituted quinoline CCR5 receptor antagonists |
US20080051414A1 (en) * | 2003-10-14 | 2008-02-28 | Arizona Board Of Regents On Behalf Of The University Of Arizona | Protein Kinase Inhibitors |
US20080226747A1 (en) * | 2007-03-01 | 2008-09-18 | Supergen, Inc. | Pharmaceutical formulations comprising salts of a protein kinase inhibitor and methods of using same |
WO2013072694A1 (en) * | 2011-11-15 | 2013-05-23 | Xention Limited | Thieno- and furo - pyrimidines and pyridines, useful as potassium channel inhibitors |
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