Classifications

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  • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
  • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
  • C07D403/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
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  • C07D239/02—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings
  • C07D239/24—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members
  • C07D239/28—Heterocyclic compounds containing 1,3-diazine or hydrogenated 1,3-diazine rings not condensed with other rings having three or more double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, directly attached to ring carbon atoms
  • C07D239/46—Two or more oxygen, sulphur or nitrogen atoms
  • C07D239/48—Two nitrogen atoms
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/4164—1,3-Diazoles
  • A61K31/4184—1,3-Diazoles condensed with carbocyclic rings, e.g. benzimidazoles
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  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/4353—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems
  • A61K31/437—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems the heterocyclic ring system containing a five-membered ring having nitrogen as a ring hetero atom, e.g. indolizine, beta-carboline
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  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
  • A61K31/4427—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems
  • A61K31/4439—Non condensed pyridines; Hydrogenated derivatives thereof containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. omeprazole
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  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
  • A61K31/445—Non condensed piperidines, e.g. piperocaine
  • A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/47—Quinolines; Isoquinolines
  • A61K31/475—Quinolines; Isoquinolines having an indole ring, e.g. yohimbine, reserpine, strychnine, vinblastine
• • A—HUMAN NECESSITIES
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  • 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
  • A61K31/496—Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene or sparfloxacin
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  • 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
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  • 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
  • A61K31/506—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim not condensed and containing further heterocyclic rings
• • A—HUMAN NECESSITIES
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  • 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
  • A61K31/513—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim having oxo groups directly attached to the heterocyclic ring, e.g. cytosine
• • A—HUMAN NECESSITIES
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  • 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
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
  • A61K31/5375—1,4-Oxazines, e.g. morpholine
  • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
  • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
  • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
• • A—HUMAN NECESSITIES
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  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
  • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
  • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
  • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
  • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
  • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
  • A61P35/04—Antineoplastic agents specific for metastasis
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  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D213/00—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members
  • C07D213/02—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
  • C07D213/04—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
  • C07D213/60—Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
  • C07D213/72—Nitrogen atoms
  • C07D213/74—Amino or imino radicals substituted by hydrocarbon or substituted hydrocarbon radicals
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  • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
  • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
  • C07D401/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings linked by a chain containing hetero atoms as chain links
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  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
  • C07D401/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing three or more hetero rings
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  • C07D403/14—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing three or more hetero rings
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  • C07D413/14—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing three or more hetero rings
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
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Definitions

• Mutant Ras proteins drive approximately 30 percent of all human cancers - including 95 percent of pancreatic cancers and 45 percent of colorectal cancers, and treatment of these mutant Ras cancers is currently an area of high unmet medical need. Mutant Ras cancers are highly proliferative and depend on basal levels of autophagy for survival, suggesting that inhibition of autophagy in these“autophagy addicted” cancers is a viable therapeutic approach.
• ULKl inhibits autophagy in cancer cells, relieving FOX3 A turn-over and upregulation of the pro-apoptotic protein PUMA.
• ULKl kinase activity has been shown to be required for Bcl-2-L-13 mediated mitophagy (autophagy of damaged mitochondria).
• ULKl and ULK2 kinases have also been demonstrated to rewire cancer cell glucose metabolism. ULK inhibitors may also find utility in blocking these noncanonical protumoral activities of ULK.
• LRRK2 is present in antigen-presenting cells including dendritic cells. LRRK2 activity has been shown to be important in Dectin-1 mediated innate immune responses, including an activation of the NFkB pathway and increased TNF-alpha production in dendritic cells of patients with Crohn’s disease.
• Inhibitors of LRRK2 are sought for the treatment of neurodegenerative diseases including Parkinson’s disease, and also are sought for the treatment of
• gastrointestinal diseases including Crohn’s disease, ulcerative colitis, and inflammatory bowel disease.
• compositions and their use as agents in the treatment of disorders such as cancer, processes for their preparation, and pharmaceutical compositions containing them as an active ingredient.
• Such pharmaceutical compositions may comprise the compound as the sole active agent or in combination with other active agents in the presence of a
• A is selected from the group consisting of phenyl and a 5 or 6-member or heteroaryl; W is CH or N; R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and C 3 - Cscycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine; R 2 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, C 3 -C 6 cycloalkyl, Ci-Csalkenyl, C 2 -Csalkynyl, Ci-Csalkoxy, and Ci-Csalkoxy-Ci-Csalkyl, wherein each Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 -C
• W is CH or N;
• X is CH or N;
• Y is C(R 33 ) or N;
• R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and Cs-Cscycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine;
• R 2 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 - Csalkenyl, C 2 -Csalkynyl, Ci-Csalkoxy, and Ci-C 5 alkoxy-C 2 -C 5 alkyl, wherein each Ci- Csalkyl, C 3 -C 6 cycloalkyl, C 2 -Csalkeny
• ring DD is selected from the group consisting of
• W is CH or N;
• R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and C 3 -C 5 cycloalkyl, wherein Ci-Csalkyl and C 3 -C 5 cycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine;
• R 2 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 -Csalkenyl, C 2 -Csalkynyl, Ci- Csalkoxy, and Ci-Csalkoxy-Ci-Csalkyl, wherein each Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 - C alkenyl, Cri-C alkynyl, and C i -Csalkoxy may be optionally substituted by one, two, or three independent occurrences of flu
• alkyl refers to a saturated straight or branched hydrocarbon.
• exemplary alkyl groups include, but are not limited to, straight or branched hydrocarbons of 1-6, 1-5, 1-4, 1-3, or 1-2 carbon atoms, referred to herein as Ci-C 6 alkyl, Ci- Csalkyl, Ci-C4alkyl, Ci-C3alkyl, and Ci-C 2 alkyl, respectively.
• Exemplary alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, 2-methyl -1 -butyl, 3-methyl-2- butyl, 2-methyl-l-pentyl, 3 -methyl- 1 -pentyl, 4-methyl- 1 -pentyl, 2-methyl-2 -pentyl, 3-methyl- 2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl -1 -butyl, 3,3-dimethyl-l-butyl, 2-ethyl- 1 -butyl, butyl, isobutyl, t-butyl, pentyl, isopentyl, neopentyl, hexyl, etc.
• alkenyl refers to an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond.
• alkenyl groups include, but are not limited to, a straight or branched group of 2-6 or 3-4 carbon atoms, referred to herein as C2-C6alkenyl, and C3-C4alkenyl, respectively.
• alkenyl groups include, but are not limited to, vinyl, allyl, butenyl, pentenyl, etc.
• alkoxy refers to a straight or branched alkyl group attached to oxygen (alkyl-O-).
• exemplary alkoxy groups include, but are not limited to, alkoxy groups of 1-6 or 2-6 carbon atoms, referred to herein as Ci-C 6 alkoxy, and C2- C 6 alkoxy, respectively.
• Exemplary alkoxy groups include, but are not limited to methoxy, ethoxy, isopropoxy, etc.
• alkoxyalkyl groups include, but are not limited to methoxymethyl, 2-methoxy ethyl, 1 -methoxy ethyl, 2-methoxypropyl, ethoxymethyl, 2- isopropoxy ethyl etc.
• alkynyl refers to an unsaturated straight or branched hydrocarbon having at least one carbon-carbon triple bond.
• exemplary alkynyl groups include, but are not limited to, straight or branched groups of 2-6, or 3-6 carbon atoms, referred to herein as C2-C6alkynyl, and C3-C6alkynyl, respectively.
• exemplary alkynyl groups include, but are not limited to, ethynyl, propynyl, butynyl, pentynyl, hexynyl,
• cycloalkyl or a“carbocyclic group” as used herein refers to a saturated or partially unsaturated hydrocarbon group of, for example, 3-6, or 4-6 carbons, referred to herein as C3-C6cycloalkyl or C4-C6cycloalkyl, respectively.
• exemplary cycloalkyl groups include, but are not limited to, cyclohexyl, cyclopentyl, cyclopentenyl, cyclobutyl or cyclopropyl.
• cycloalkoxy refers to a cycloalkyl group attached to oxygen (cycloalkyl-O-).
• exemplary cycloalkoxy groups include, but are not limited to, cycloalkoxy groups of 3-6 carbon atoms, referred to herein as C3-C6cycloalkoxy groups.
• Exemplary cycloalkoxy groups include, but are not limited to, cyclopropoxy, cyclobutoxy, cyclopentoxy, cyclohexyloxy, etc.
• halo or“halogen” as used herein refer to F, Cl, Br, or I.
• heteroaryl refers to a monocyclic aromatic 5 or 6 membered ring system containing one or more heteroatoms, for example one to three heteroatoms, such as nitrogen, oxygen, and sulfur. Where possible, said heteroaryl ring may be linked to the adjacent radical though carbon or nitrogen. Examples of heteroaryl rings include but are not limited to furan, thiophene, pyrrole, thiazole, oxazole, isothiazole, isoxazole, imidazole, pyrazole, triazole, pyridine or pyrimidine etc.
• heterocyclyl or“heterocyclic group” are art-recognized and refer to saturated or partially unsaturated, 4-10 membered ring structures, including monocyclic, bridged or fused rings, and whose ring structures include one to three heteroatoms, such as nitrogen, oxygen, and sulfur. Where possible, heterocyclyl rings may be linked to the adjacent radical through carbon or nitrogen. Examples of heterocyclyl groups include, but are not limited to, pyrrolidine, piperidine, morpholine, thiomorpholine, piperazine, oxetane, azetidine, tetrahydrofuran or dihydrofuran etc.
• A“combination therapy” is a treatment that includes the administration of two or more therapeutic agents, e.g ., a compound of Formula I and a MAPKAP pathway inhibitor, to a patient in need thereof.
• “Individual,”“patient,” or“subject” are used interchangeably and include any animal, including mammals, preferably mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, and most preferably humans.
• the compounds described herein can be administered to a mammal, such as a human, but can also be administered to other mammals such as an animal in need of veterinary treatment, e.g, domestic animals (e.g., dogs, cats, and the like), farm animals ( e.g. , cows, sheep, pigs, horses, and the like) and laboratory animals (e.g, rats, mice, guinea pigs, and the like).
• A“MAPKAP pathway inhibitor” is an inhibitor of the MAP kinase signaling pathway. Inhibitors of this pathway include Ras inhibitors (e.g. AMG-510, MRTX 849),
• RAF inhibitors e.g. dabrafenib, vemurafenib, LY3009120
• MEK inhibitors e.g. trametinib, binimetinib, selumetinib, cobimetinib
• ERK inhibitors e.g. ulixertinib, SCH772984, LY3214996.
• the terms“MAPKAP pathway inhibitor” and“MAPKAP kinase inhibitor are used interchangeably herein.
• “Pharmaceutically or pharmacologically acceptable” include molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or a human, as appropriate.
• preparations should meet sterility, pyrogenicity, and general safety and purity standards as required by FDA Office of Biologies standards.
• compositions may also contain other active compounds providing supplemental, additional, or enhanced therapeutic functions.
• composition refers to a composition comprising at least one compound as disclosed herein formulated together with one or more pharmaceutically acceptable carriers.
• pharmaceutically acceptable salt(s) refers to salts of acidic or basic groups that may be present in compounds used in the compositions.
• compositions that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids.
• the acids that may be used to prepare pharmaceutically acceptable acid addition salts of such basic compounds are those that form non-toxic acid addition salts, i.e., salts containing pharmacologically acceptable anions, including, but not limited to, malate, oxalate, chloride, bromide, iodide, nitrate, sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate, lactate, salicylate, citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulf
• compositions that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations.
• examples of such salts include alkali metal or alkaline earth metal salts, particularly calcium, magnesium, sodium, lithium, zinc, potassium, and iron salts.
• Compounds included in the present compositions that include a basic or acidic moiety may also form pharmaceutically acceptable salts with various amino acids.
• the compounds of the disclosure may contain both acidic and basic groups; for example, one amino and one carboxylic acid group. In such a case, the compound can exist as an acid addition salt, a zwitterion, or a base salt.
• the compounds of the disclosure may contain one or more chiral centers and, therefore, exist as stereoisomers.
• stereoisomers when used herein consist of all enantiomers or diastereomers. These compounds may be designated by the symbols“(+),”“(- ),”“R” or“S,” depending on the configuration of substituents around the stereogenic carbon atom, but the skilled artisan will recognize that a structure may denote a chiral center implicitly.
• the presently described compounds encompasses various stereoisomers of these compounds and mixtures thereof. Mixtures of enantiomers or diastereomers may be designated“( ⁇ )” in nomenclature, but the skilled artisan will recognize that a structure may denote a chiral center implicitly.
• the term“therapeutically effective amount” means the amount of the subject compound that will elicit the biological or medical response of a tissue, system or animal, (e.g. mammal or human) that is being sought by the researcher, veterinarian, medical doctor or other clinician.
• the compounds described herein are administered in therapeutically effective amounts to treat a disorder.
• Treating includes any effect, e.g., lessening, reducing, modulating, or eliminating, that results in the improvement of the condition, disease, disorder and the like.
• the disclosure also embraces isotopically labeled compounds which are identical to those recited herein, except that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number usually found in nature.
• isotopes that can be incorporated into compounds of the invention include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur, fluorine and chlorine, such as 2 H, 3 ⁇ 4, 13 C, 14 C, 15 N, 18 0, 17 0, 31 P, 32 P, 35 S, 18 F, and 36 C1, respectively.
• a compound of the disclosure may have one or more H atom replaced with deuterium.
• Stereoselective syntheses a chemical or enzymatic reaction in which a single reactant forms an unequal mixture of stereoisomers during the creation of a new stereocenter or during the transformation of a pre-existing one, are well known in the art. Stereoselective syntheses encompass both enantio- and
• A is selected from the group consisting of phenyl and a 5 or 6-member or heteroaryl; W is CH or N; R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and C 3 - C 5 cycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine; R 2 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 -Csalkenyl, C 2 -Csalkynyl, Ci-Csalkoxy, and Ci-C 5 alkoxy-C 2 -C 5 alkyl, wherein each Ci-Csalkyl, C 3 -C 6 cycloalkyl, C
• each Ci-C 6 alkyl and C 3 -C 6 cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine;
• U is N or CR 13 ;
• V is selected from the group consisting of oxygen, C(R 34 ) 2 , and NR 6 ;
• r is 0, 1, or 2;
• q is 1, 2, or 3;
• R 11 is selected from the group consisting of H, Ci-C 3 alkyl, and C 3 -C 5 cycloalkyl, wherein Ci-C 3 alkyl and C 3 -C 5 cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine;
• R 12 is selected from the group consisting of H, Ci-C 3 alkyl, and C 3 -C 5 cycloalkyl, wherein Ci-C 3 alkyl and C 3 - C 5 cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine;
• W is CH or N;
• X is CH or N;
• Y is C(R 33 ) or N;
• R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and Cs-Cscycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine;
• R 2 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 - Csalkenyl, C 2 -Csalkynyl, Ci-Csalkoxy, and Ci-C 5 alkoxy-C 2 -C 5 alkyl, wherein each Ci- Csalkyl, C 3 -C 6 cycloalkyl, C 2 -Csalkeny
• C 3 -C 6 cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine;
• U is N or CR 13 ;
• V is selected from the group consisting of oxygen, C(R 34 ) 2 , and NR 6 ;
• r is 0, 1, or 2;
• q is 1, 2, or 3;
• R 11 is selected from the group consisting of H, Ci-C 3 alkyl, and C3-C5cycloalkyl, wherein Ci-C3alkyl and C3-C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine;
• R 12 is selected from the group consisting of H, Ci-C3alkyl, and C3-C5cycloalkyl, wherein Ci-C3alkyl and C3-C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine;
• R 13 is selected from H and Ci-C3alkyl;
• W is N.
• X is CH and Y is N.
• X is CH and Y is C(R 33 ).
• R 4 is B.
• R 4 is selected from the group consisting of:
• R 4 is selected from the group consisting of:
• R 4 is selected from the group consisting of:
• R 1 is selected from the group consisting of halogen, Ci- Csalkyl, and Cs-Cscycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted with one, two, or three independent occurrences of fluorine.
• the compound is represented by Formula IB:
• n 2, 3, or 4
• R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and Cs-Cscycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine
• R 2 is selected from the group consisting of Ci-C 2 alkyl and C 3 - C 4 cycloalkyl, and halogen, wherein Ci-C 2 alkyl and C 3 -C 4 cycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine
• R 3 is selected from the group consisting of H, Ci-C 3 alkyl, and C 3 -C 5 cycloalkyl, wherein Ci-C 3 alkyl and C 3 - C 5 cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine
• R 4 is selected from the group consisting of
• each Ci-C 6 alkyl and C 3 -C 6 cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine;
• U is N or CR 13 ;
• V is selected from the group consisting of oxygen, C(R 34 ) 2 , and NR 6 ;
• r is 0, 1, or 2;
• q is 1, 2, or 3;
• R 1 1 is selected from the group consisting of H, Ci- C 3 alkyl, and C 3 -C 5 cycloalky
• R 1 is selected from the group consisting of halogen, Ci- Csalkyl and C 3 -C 5 cycloalkyl, wherein Ci-Csalkyl and C 3 -C 5 cycloalkyl may be optionally substituted with one, two, or three independent occurrences of fluorine, and C 3 -C 5 cycloalkyl.
• R 1 is CF 3.
• R 1 is CF 2 H.
• R 1 is selected from the group consisting of chloro, bromo, and fluoro.
• R 1 is bromo.
• R 1 is cyclopropyl.
• R 2 is selected from the group consisting of C 3 - C 4 cycloalkyl, Ci-Csalkyl, and halogen. In some embodiments, R 2 is selected from the group consisting of Ci-C 2 alkyl, C 3 -C 4 cycloalkyl, and bromo. [00064] In some embodiments, R 3 is selected from the group consisting of H and Ci- Csalkyl, wherein Ci-C3alkyl may be optionally substituted by one or more independent occurrences of fluorine.
• R 4 is selected from the group consisting of:
• R 4 is selected from the group consisting of:
• each R 6 and R 9 is independently selected from the group consisting of H, Ci-C 6 alkyl, and C3-C6cycloalkyl, wherein Ci-C 6 alkyl and C3- C 6 cycloalkyl is optionally substituted by one or more independent occurrences of fluorine.
• R 7 is H.
• R L is selected from the group consisting of Ci-C 6 alkyl and C3-C6cycloalkyl, wherein Ci-C 6 alkyl and C3-C6cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine.
• R L is cyclobutyl. In some embodiments R L is NR U R 12 .
• R is , wherein each Ci-C 6 alkyl and
• C3-C6cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine; U is N or CR 13 ; V is selected from the group consisting of oxygen, C(R 34 )2, and NR 6 ; r is 0, 1, or 2; q is 1, 2, or 3; R 13 is selected from H and Ci-C3alkyl; and each occurrence of R 34 is independently selected from H, Ci-C3alkyl, and Cs-Cscycloalkyl, wherein Ci-C3alkyl and C3-C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine, or two R 34 are joined together with the carbon to which they are attached to form a C3-C6cycloalkyl; provided that when r is 0 and q is 1, then U is not CR 13 and V is not O, and when r or q is 1, then U is not N and V is not O or NR 6 .
• -N(R 3 )-C(0)-R L is selected from the group consisting of:
• -N(R 3 )-C(0)-R L is selected from the group consisting of:
• the compound is represented by a formula selected from the group consisting of:
• each occurrence of R 1 is CF 3 ; each occurrence of R 2 is independently selected from Ci-C 2 alkyl, C 3 -C 4 cycloalkyl, bromo, and chloro; each occurrence of R 3 is independently selected from the group consisting of H, and Ci-C 2 alkyl; each occurrence of R 9 is independently selected from H and Ci-C 3 alkyl; each occurrence of R 34 is independently selected from the group consisting of H, Ci-C 3 alkyl, and C 3 - Cscycloalkyl; and n is 3.
• each occurrence of R 1 is CF 2 H; each occurrence of R 2 is independently selected from Ci-C 2 alkyl, C 3 -C 4 cycloalkyl, bromo, and chloro; each occurrence of R 3 is independently selected from the group consisting of H, and Ci-C 2 alkyl; each occurrence of R 9 is independently selected from H and Ci-C 3 alkyl; each occurrence of R 34 is independently selected from the group consisting of H, Ci-C 3 alkyl, and C 3 - Cscycloalkyl; and n is 3.
• the compound is represented by a formula selected from the group consisting of:
• each occurrence of R 1 is CF 3 ; each occurrence of R 2 is independently selected from Ci-C 2 alkyl, C 3 -C 4 cycloalkyl, bromo, and chloro; each occurrence of R 3 is independently selected from the group consisting of H, and Ci-C 2 alkyl; each occurrence of R 9 is independently selected from H and Ci-C 3 alkyl; and n is 3.
• each occurrence of R 1 is CF 2 H; each occurrence of R 2 is independently selected from Ci-C 2 alkyl, C 3 -C 4 cycloalkyl, bromo, and chloro; each occurrence of R 3 is independently selected from the group consisting of H, and Ci-C 2 alkyl; each occurrence of R 9 is independently selected from H and Ci-C 3 alkyl; and n is 3.
• the compound is represented by a formula selected from the group consisting of:
• each occurrence of R 1 is CF 3 ; each occurrence of R 2 is independently selected from Ci-C 2 alkyl, C 3 -C 4 cycloalkyl, bromo, and chloro; each occurrence of R 3 is independently selected from the group consisting of H, and Ci-C 2 alkyl; each occurrence of R 9 is independently selected from H and Ci-C 3 alkyl; and n is 3.
• the compound is represented by Formula IC:
• ring DD is selected from the group consisting of
• W is CH or N;
• R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and C 3 -C 5 cycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine;
• R 2 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, C 3 -C 6 cycloalkyl, Ci-Csalkenyl, C 2 -Csalkynyl, Ci- Csalkoxy, and Ci-Csalkoxy-Ci-Csalkyl, wherein each Ci-Csalkyl, C 3 -C 6 cycloalkyl, C 2 - C alkenyk Cri-C alkynyl, and C i-C alkoxy may be optionally substituted by one, two, or three independent occurrences of fluorine or cyano;
• each Ci-C 6 alkyl and C3-C6cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine
• U is N or CR 13
• V is selected from the group consisting of oxygen, C(R 34 ) 2 , and NR 6
• r is 0, 1, or 2
• q is 1, 2, or 3
• R 11 is selected from the group consisting of H, Ci-C3alkyl, and C3-C5cycloalkyl, wherein Ci-C3alkyl and C3-C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine
• R 12 is selected from the group consisting of H, Ci-C3alkyl, and C3-C5cycloalkyl, wherein Ci-C3alkyl and C3- C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine
• R 13 is selected from H and Ci-C3alkyl; each
• W is N. In some embodiments W is CH.
• ring DD is selected from the group consisting of:
• ring DD is selected from the group consisting of:
• R 4 is selected from the group consisting of:
• L is -(CH2) m .
• m is 0.
• m is 1.
• m is 2.
• m is 3.
• R 4 is D and m is 0. In some embodiments R 4 is D and m is 1. In some embodiments, R 4 is selected from D and B and m is 2. In some
• R 4 is selected from D and B and m is 3.
• R 1 is selected from the group consisting of halogen, Ci-
• R 3 is selected from the group consisting of H, Ci-C3alkyl, and C3- Cscycloalkyl wherein Ci-C3alkyl and C3-C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine.
• C3-C6cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine; U is N or CR 13 ; V is selected from the group consisting of oxygen, C(R 34 )2, and NR 6 ; r is 0, 1, or 2; q is 1, 2, or 3; R 13 is selected from H and Ci-C3alkyl; and each occurrence of R 34 is independently selected from H, Ci-C3alkyl, and C3-C5cycloalkyl, wherein Ci-C3alkyl and C3-C5cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine, or two R 34 are joined together with the carbon to which they are attached to form a C 3 -C 6 cycloalkyl; provided that when r is 0 and q is 1, then U is not CR 13 and V is not O, and when r or q is 1, then U is not N and V is not O or NR 6 .
• n 3.
• the compound is represented by Formula IE:.
• ring DD is selected from the group consisting of:
• each Ci-C 6 alkyl and C 3 -C 6 cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine;
• U is N or CR 13 ;
• V is selected from the group consisting of oxygen, C(R 34 ) 2 , and NR 6 ;
• r is 0, 1, or 2;
• q is 1, 2, or 3;
• R 1 1 is selected from the group consisting of H, Ci- C 3 alkyl, and C 3 -C 5 cycloalky
• ring DD is taken from the group consisting of: [000134]
• R 1 is selected from the group consisting of halogen, Ci- Csalkyl, and Cs-Cscycloalkyl, wherein Ci-Csalkyl and Cs-Cscycloalkyl may be optionally substituted with one, two, or three independent occurrences of fluorine.
• R 1 is CF 3 . In some embodiments, R 1 is CF2H. In some embodiments, R 1 is selected from the group consisting of chloro, bromo, and fluoro. In some embodiments, R 1 is bromo. In some embodiments, R 1 is cyclopropyl.
• R 2 is selected from the group consisting of C3- C4cycloalkyl, Ci-Csalkyl, and halogen. In some embodiments, R 2 is selected from the group consisting of Ci-C2alkyl, C3-C4cycloalkyl, and bromo.
• R 3 is selected from the group consisting of H and Ci- C3alkyl, wherein Ci-C3alkyl may be optionally substituted by one or more independent occurrences of fluorine.
• R 4 is D.
• each R 6 and R 9 is independently selected from the group consisting of H, Ci-C 6 alkyl, and C3-C6cycloalkyl, wherein Ci-C 6 alkyl and C3- C 6 cycloalkyl is optionally substituted by one or more independent occurrences of fluorine.
• R 7 is H.
• R L is selected from the group consisting of Ci-C 6 alkyl and C3-C6cycloalkyl, wherein Ci-C 6 alkyl and C3-C6cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine.
• R L is cyclobutyl. In some embodiments R L is NR U R 12 .
• R L is , wherein each Ci-C 6 alkyl and
• m is 0. In some embodiments m is 1. In some embodiments, m is 2. In some embodiments, m is 3.
• -N(R 3 )-C(0)-R L is selected from the group consisting of:
• n 3.
• the compound is represented by a formula selected from the group consisting of:
• the compound is represented by a formula selected from the group consisting of:
• the compound is represented by Formula IE.4 as defined above. In some embodiments, the compound is represented a formula selected from the group consisting of Formula IE.5, and Formula IE.6 as defined above.
• the compound is represented by a formula selected from the group consisting of:
• each occurrence of R 1 is CF 3 ; each occurrence of R 2 is independently selected from Ci-C 2 alkyl and C 3 -C 4 cycloalkyl; each occurrence of R 3 is independently selected from the group consisting of H and Ci-C 2 alkyl; each occurrence of R 6 is independently selected from the group consisting of H, Ci-C 6 alkyl and C 3 -C 6 cycloalkyl; each occurrence of R 9 is selected from H and Ci-C 3 alkyl; each occurrence of R 34 is independently selected from H, Ci-C 3 alkyl, C 3 -C 5 cycloalkyl; and n is 3.
• the compound is represented by Formula IE.7 as defined above. In some embodiments, the compound is represented a formula selected from the group consisting of Formula IE.8, and Formula IE.9 as defined above.
• the compound is taken from Formula IF:
• ring DD is selected from the group consisting of:
• n 2, 3, or 4;
• R 1 is selected from the group consisting of halogen, cyano, Ci-Csalkyl, and C 3 -C 5 cycloalkyl, wherein Ci-Csalkyl and C 3 -C 5 cycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine;
• R 2 is selected from the group consisting of Ci-C 2 alkyl and C 3 -C 4 cycloalkyl, and halogen, wherein Ci-C 2 alkyl and C 3 - C 4 cycloalkyl may be optionally substituted by one, two or three independent occurrences of fluorine;
• R 3 is selected from the group consisting of H, Ci-C 3 alkyl, and C 3 -C 5 cycloalkyl, wherein Ci-C 3 alkyl and C 3 -C 5 cycloalkyl may be optionally substituted by one or more independent occurrences of fluorine;
• R 4
• ring DD is taken from the group consisting of:
• R 1 is selected from the group consisting of halogen, Ci-
• Ci-Csalkyl and C3-C5cycloalkyl may be optionally substituted with one, two, or three independent occurrences of fluorine.
• R 2 is selected from the group consisting of C3- C4cycloalkyl, Ci-Csalkyl, and halogen. In some embodiments, R 2 is selected from the group consisting of Ci-C2alkyl, C3-C4cycloalkyl, and bromo.
• R 3 is selected from the group consisting of H and Ci- C3alkyl, wherein Ci-C3alkyl may be optionally substituted by one or more independent occurrences of fluorine.
• R 4 is D. [000165] In some embodiments, R 4 is selected from the group consisting of:
• R 4 is selected from the group consisting of:
• R 7 is H.
• R L is selected from the group consisting of Ci-C 6 alkyl and C3-C6cycloalkyl, wherein Ci-C 6 alkyl and C3-C6cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine.
• C 6 cycloalkyl may be optionally substituted by 1, 2, or 3 independent occurrences of fluorine; U is N or CR 13 ; V is selected from the group consisting of oxygen, C(R 34 )2, and NR 6 ; r is 0, 1, or 2; q is 1, 2, or 3; R 13 is selected from H and Ci-C3alkyl; and each occurrence of R 34 is independently selected from H, Ci-C3alkyl, and C3-C5cycloalkyl, wherein Ci-C3alkyl and C3- Cscycloalkyl may be optionally substituted by one or more independent occurrences of fluorine, or two R 34 are joined together with the carbon to which they are attached to form a C3-C6cycloalkyl; provided that when r is 0 and q is 1, then U is not CR 13 and V is not O, and when r or q is 1, then U is not N and V is not O or NR 6 .
• m is 0. In some embodiments m is 1. In some embodiments, m is 2. In some embodiments, m is 3. [000172] In some embodiments, -N(R 3 )-C(0)-R L is selected from the group consisting of:
• -N(R 3 )-C(0)-R L is selected from the group consisting of:
• n 3.
• the compound is represented by a formula selected from the group consisting of:
• each occurrence of R 1 is CF 3 ; each occurrence of R 2 is independently selected from Ci-C 2 alkyl and C 3 -C 4 cycloalkyl; each occurrence of R 3 is independently selected from the group consisting of H and Ci-C 2 alkyl; each occurrence of R 6 is independently selected from the group consisting of H, Ci-C 6 alkyl and C 3 -C 6 cycloalkyl; each occurrence of R 7 is independently selected from the group consisting of H, C 1 -C 6 alkyl, C 3 -C 6 cycloalkyl; each occurrence of R 9 is selected from H and Ci-C 3 alkyl; each occurrence of R 34 is independently selected from H, Ci-C 3 alkyl, C 3 -C 5 cycloalkyl; and n is 3.
• the compound is represented by Formula IF.1 as defined above.
• the compound is represented a formula selected from the group consisting of Formula IF.2, and Formula IF.3 as defined above.
• the compound is represented by a formula selected from the group consisting of:
• Compounds described herein can act as inhibitors of autophagy useful in the treatment of a disorder in a patient in need thereof.
• the disorder for example, can be a tumor, e.g. a solid tumor.
• the disorder may also be cancer.
• Exemplary disorders also include gastrointestinal stromal tumors, esophageal cancer, gastric cancer, melanomas, gliomas, glioblastomas, ovarian cancer, bladder cancer, pancreatic cancer, prostate cancer, lung cancers, breast cancers, renal cancers, hepatic cancers, osteosarcomas, multiple myelomas, cervical carcinomas, cancers that are metastatic to bone, papillary thyroid carcinoma, non-small cell lung cancer, and colorectal cancers.
• a cancer treated by the methods described herein may be a metastatic cancer.
• the compounds described herein are useful for the treatment of cancers caused by RAS mutation.
• the cancer is caused by a KRAS mutation.
• the cancer has additional mutations in tumor suppressor proteins, including mutations in TP53, PTEN, CDN2A/INK4A, pl6, or STAG2.
• these additional mutations occur in one or more of TP53, PTEN, CDN2A/INK4A, pi 6, or STAG2.
• the cancer is pancreatic ductal adenocarcinoma.
• the cancer is lung cancer.
• the cancer is colorectal.
• autophagosomes for instance by measurement of fluorescent puncta with the autophagosome marker Cyto-ID.
• cellular inhibition of ULK kinase by compounds described herein is determined by inhibition of phosphorylation of cellular ULK substrates including ATG13, ATG14, Beclin 1, or STING either in tumor cells or in non-tumor host tissues. In some embodiments, cellular inhibition of ULK kinase by compounds described herein is determined in host tissues including immune cells.
• inhibition of autophagy and anti-tumor activity by compounds described herein are evaluated in syngeneic murine genetically engineered models (GEMs) of mutant RAS cancers.
• GEMs murine genetically engineered models
• inhibition of autophagy and anti-tumor activity by compounds described herein are evaluated in the murine GEM syngeneic orthotopic pancreatic cancer model known as the KPC model (LSL- Kras G12D/+ ;LSL-Trp53 R172H/+ ;Pdx-l-Cre) or variants of the KPC model.
• the immunomodulatory component of ULK inhibition is an enhanced anti-tumor activity of Natural Killer cells. In some embodiments, the immunomodulatory component of ULK inhibition is an enhanced activity of effector T Cells, including cytotoxic T Cells.
• a contemplated method comprises optionally contacting a sample obtained from the patient (including but not limited to a tumor, blood, saliva, or tissue) prior to administration of the compound with a phospho- ATG13 antibody ELISA assay, and comparing the level of phospho-ATG13 in the sample obtained prior to administration with the level of phospho-ATG13 in the sample obtained during or after the course of administration.
• the phospho-ATG13 is p- S318ATG13.
• a contemplated method comprises optionally contacting a sample obtained from the patient (including but not limited to a tumor, blood, saliva, or tissue) prior to administration of the compound with a pBeclin antibody ELISA assay, and comparing the level of pBeclin in the sample obtained prior to administration with the level of pBeclin in the sample obtained during or after the course of administration.
• the compounds provided herein may be administered to patients (animals and humans) in need of such treatment in dosages that will provide optimal pharmaceutical efficacy. It will be appreciated that the dose required for use in any particular application will vary from patient to patient, not only with the particular compound or composition selected, but also with the route of administration, the nature of the condition being treated, the age and condition of the patient, concurrent medication or special diets then being followed by the patient, and other factors which those skilled in the art will recognize, with the appropriate dosage ultimately being at the discretion of the attendant physician.
• a compound provided herein may be administered orally, subcutaneously, topically, parenterally, by inhalation spray or rectally in dosage unit formulations containing conventional non-toxic pharmaceutically acceptable carriers, adjuvants and vehicles.
• Parenteral administration may include subcutaneous injections, intravenous or intramuscular injections or infusion techniques.
• Treatment can be continued for as long or as short a period as desired.
• the compositions may be administered on a regimen of, for example, one to four or more times per day.
• a suitable treatment period can be, for example, at least about one week, at least about two weeks, at least about one month, at least about six months, at least about 1 year, or indefinitely.
• a treatment period can terminate when a desired result is achieved.
• Compounds described herein can be administered in combination with one or more additional therapeutic agents to treat a disorder described herein, such as cancer.
• a pharmaceutical composition comprising a compound described herein, e.g. , a compound of Formula I as defined herein, one or more additional therapeutic agents, and a pharmaceutically acceptable excipient.
• a compound of Formula I as defined herein and one additional therapeutic agent is administered.
• a compound of Formula I as defined herein and two additional therapeutic agents are administered.
• a compound of Formula I as defined herein and three additional therapeutic agents are administered.
• Combination therapy can be achieved by administering two or more therapeutic agents, each of which is formulated and administered separately.
• a compound of Formula I as defined herein and an additional therapeutic agent can be formulated and administered separately.
• Combination therapy can also be achieved by administering two or more therapeutic agents in a single formulation, for example a pharmaceutical composition comprising a compound of Formula I as one therapeutic agent and one or more additional therapeutic agents such as a MAPKAP pathway inhibitor or chemotherapeutic agent.
• a compound of Formula I as defined herein and an additional therapeutic agent can be administered in a single formulation.
• Other combinations are also encompassed by combination therapy. While the two or more agents in the combination therapy can be administered simultaneously, they need not be.
• administration of a first agent can precede administration of a second agent (or combination of agents) by minutes, hours, days, or weeks.
• the two or more agents can be administered within minutes of each other or within 1, 2, 3, 6, 9, 12, 15, 18, or 24 hours of each other or within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14 days of each other or within 2, 3, 4, 5, 6, 7, 8, 9, or weeks of each other. In some cases, even longer intervals are possible. While in many cases it is desirable that the two or more agents used in a combination therapy be present in within the patient's body at the same time, this need not be so.
• Combination therapy can also include two or more administrations of one or more of the agents used in the combination using different sequencing of the component agents. For example, if agent X and agent Y are used in a combination, one could administer them sequentially in any combination one or more times, e.g., in the order X-Y-X, X-X-Y, Y- X-Y, Y-Y-X, X-X-Y- Y, etc.
• the one or more additional therapeutic agents that may be administered in combination with a compound provided herein can be a MAPKAP pathway inhibitor.
• MAPKAP pathway inhibitors include, for example, MEK inhibitors, ERK inhibitors, RAF inhibitors, and Ras inhibitors.
• Exemplary MEK inhibitors include, but are not limited to, trametinib, selumetinib, cobimetinib, binimetinib, and pharmaceutically acceptable salts thereof.
• Exemplary ERK inhibitors include, but are not limited to, include, but are not limited to, ulixertinib, SCH772984, LY3214996, ravoxertinib, VX-l le, and pharmaceutically acceptable salts thereof.
• Exemplary RAF inhibitors include, but are not limited to, LY3009120,
• Ras inhibitors include, but are not limited to, AMG-510, MRTX849, and pharmaceutically acceptable salts thereof.
• the additional therapeutic agents can be chemotherapeutic agents including but not limited to an anti-tubulin agents (for example, paclitaxel, paclitaxel protein-bound particles for injectable suspension including nab- paclitaxel, eribulin, docetaxel, ixabepilone, vincristine, auristatins, or maytansinoids), vinorelbine, DNA-alkylating agents (including cisplatin, carboplatin, oxaliplatin,
• an anti-tubulin agents for example, paclitaxel, paclitaxel protein-bound particles for injectable suspension including nab- paclitaxel, eribulin, docetaxel, ixabepilone, vincristine, auristatins, or maytansinoids
• vinorelbine DNA-alkylating agents (including cisplatin, carboplatin, oxaliplatin,
• the additional therapeutic agents can be immunomodulatory agents including but not limited to anti-PD-lor anti-PDL-1 therapeutics including pembrolizumab, nivolumab, atezolizumab, durvalumab, BMS-936559, or avelumab, anti-TIM3 (anti-HAVcr2) therapeutics including but not limited to TSR-022 or MBG453, anti-LAG3 therapeutics including but not limited to relatlimab, LAG525, or TSR- 033, anti-4-lBB (anti-CD37, anti-TNFRSF9), CD40 agonist therapeutics including but not limited to SGN-40, CP-870,893 or R07009789, anti-CD47 therapeutics including but not limited to Hu5F9-G4, anti-CD20 therapeutics, anti-CD38 therapeutics, STING agonists including but not limited to ADU-S100, MK-1454, ASA404, or amidobenzimidazoles, anthracyclines including
• metoclopramide metoclopramide, lorazepam, alprazolam, haloperidol, droperidol, dronabinol, dexamethasone, methylprednisolone, prochlorperazine, granisetron, ondansetron, dolasetron, tropisetron, spegfilgrastim, erythropoietin, epoetin alfa and darbepoetin alfa, ipilumumab, vemurafenib, and mixtures thereof.
• the principal active ingredient may be mixed with a pharmaceutical carrier, e.g., conventional tableting ingredients such as corn starch, lactose, sucrose, sorbitol, talc, stearic acid, magnesium stearate, dicalcium phosphate or gums, and other pharmaceutical diluents, e.g., water, to form a solid preformulation composition containing a homogeneous mixture of a compound provided herein, or a non-toxic pharmaceutically acceptable salt thereof.
• a pharmaceutical carrier e.g., conventional tableting ingredients such as corn starch, lactose, sucrose, sorbitol, talc, stearic acid, magnesium stearate, dicalcium phosphate or gums, and other pharmaceutical diluents, e.g., water
• a pharmaceutical carrier e.g., conventional tableting ingredients such as corn starch, lactose, sucrose, sorbitol, talc, stearic acid, magnesium stea
• the subject composition is mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as, for example,
• compositions may also comprise buffering agents.
• Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.
• the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, com, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, cyclodextrins and mixtures thereof.
• inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl a
• Suspensions in addition to the subject composition, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
• suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
• the active component may be mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants which may be required.
• Powders and sprays may contain, in addition to a subject composition, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances.
• Sprays may additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.
• Exemplary enteric materials include cellulose acetate phthalate (CAP), hydroxypropyl methylcellulose phthalate (HPMCP), polyvinyl acetate phthalate (PVAP), hydroxypropyl methylcellulose acetate succinate (HPMCAS), cellulose acetate trimellitate, hydroxypropyl methylcellulose succinate, cellulose acetate succinate, cellulose acetate hexahydrophthalate, cellulose propionate phthalate, cellulose acetate maleate, cellulose acetate butyrate, cellulose acetate propionate, copolymer of methylmethacrylic acid and methyl methacrylate, copolymer of methyl acrylate, methylmethacrylate and methacrylic acid, copolymer of methylvinyl ether and maleic anhydride (Gantrez ES series), ethyl methyacrylate-methylmethacrylate- chlorotrimethylammonium ethyl acrylate copolymer, natural resins such
• hexafluorophosphate “H2” is hydrogen gas
• “HC1” is hydrochloric acid
• “Hex” is hexane
• “H2O” is water
• “HOBt” is Hydroxybenzotriazole“IC50” is half maximal inhibitory concentration
• “K2CO3” is potassium carbonate
• “K3PO4” is potassium phosphate
• “LiMHDS” is lithium bis(trimethylsilyl)amide
• “MeCN” is acetonitrile
• “MeOH” is methanol
• “MeABuXPhos” is di-tert-butyl(2',4',6'-triisopropyl-3,4,5,6-tetramethyl-[l, r- biphenyl]-2-yl)phosphine
• “MgS0 4 ” is magnesium sulfate
• “MHz” is megahertz
• “min” is minute or minutes
• “MS” mass spectrometry
• “MTBE” is methyl /er/-butyl ether
• “NADH” is nicotinamide adenine dinucleotide
• “NaH” is sodium hydride
• “NaHCCE” is sodium bicarbonate
• “bfeSCE” sodium sulfate
• “NH4CI” is ammonium chloride
• Scheme 1 illustrates an exemplary preparation of amines D-I-i, D-I-ii, and D- I-iii.
• A-I Treatment of A-I with amine R 4 -H, which can be aliphatic or heterocyclic, in the presence of a base (e.g. CS2CO3 or K2CO3) affords compound B-I.
• a base e.g. CS2CO3 or K2CO3
• Intermediate C-I may be selectively converted to amine D-I-i where R 2b is alkenyl, alkynyl, or cycloalkyl by mild reducing conditions for example, zinc or iron metal with ammonium chloride.
• Intermediate C-I can be fully reduced to D-I-iii by palladium catalyzed hydrogenation.
• Intermediate B-I where R 2a is Cl, Br, alkyl, CN or alkoxy may be reduced to D-I-ii by mild reducing conditions for example, zinc or iron metal with
• examples of X include N and CH
• examples of Y include N, CH, and C-F where X and Y are not both N
• examples of R 2 include alkyl and cycloalkyl
• examples of R 4 include an N-linked alkyl and N-linked heterocylcyl with suitable optional substituents as exemplified by the tables of intermediates below.
• Intermediate C-II can be fully reduced to D-II-iii by palladium catalyzed hydrogenation.
• Intermediate B-II where R 2a is Cl, Br, alkyl, CN or alkoxy may be reduced to D-II-ii by mild reducing conditions for example, zinc or iron metal with ammonium chloride.
• examples of X include N and CH
• examples of Y include N, CH, and C-F where X and Y are not both N
• examples of R 2 include alkyl and cycloalkyl
• examples of R 4 include an N-linked alkyl and N-linked heterocyclyl with suitable optional substituents as exemplified by the tables of intermediates below.
• Scheme 3 illustrates an exemplary preparation of amine D-III-i, D-III-ii and D-III-iii., wherein L is -CH 2 -CH 2 -.
• Reduction of A-III-i with reducing reagents such as DIBAL affords aldehyde A-III-ii.
• Another way to prepare A-III-ii is reduction of A-III-i to the corresponding alcohol followed by mild oxidation conditions such as using MnC .
• examples of X include N and CH
• examples of Y include N, CH, and C-F where X and Y are not both N
• examples of R include methyl and ethyl
• examples of R 2 include alkyl and cycloalkyl
• examples of R 4 include an N-linked alkyl and N-linked heterocyclyl with suitable optional substituents as exemplified by the tables of intermediates below
• examples of LG include mesylate and tosylate.
• R Me or Et reduction reduction
• examples of X include N and CH
• examples of Y include N, CH, and C-F where X and Y are not both N
• examples of R include methyl and ethyl
• examples of R 2 include alkyl and cycloalkyl
• examples of R 4 include -(CH 2 ) m -C(0)-B and -(CH2) m - C(0)-N(R5)R 6 , where m is 0,1, or 2.
• general pyrazole-amines D-VII-i or D-VII-ii are prepared by the two methods shown in Scheme 7.
• examples of R 4 -L-linked 7- 1 or 7-2 are shown.
• One method involves alkylation of B-VII (readily available to those skilled in art) with commercially available 7-1 to provide nitro-pyrazole C-VII-i and/or C- Vll-ii in the presence of base (e.g. potassium carbonate, cesium carbonate or sodium hydride) and a polar aprotic solvent (dimethyl sulfoxide, dimethylformamide, tetrahydrofuran or the like), at temperatures between ambient and 150 °C.
• base e.g. potassium carbonate, cesium carbonate or sodium hydride
• a polar aprotic solvent dimethyl sulfoxide, dimethylformamide, tetrahydrofuran or the like
• examples of LG include Cl and Br
• examples of R 2 include alkyl, cycloalkyl, alkoxy, halogen, and CN, where alkyl, cycloalkyl, or alkoxy can be optionally fluorinated
• examples of R 4 include heterocyclyl with suitable optional substituents as exemplified by the tables of interemediates below, C(0)NR 6 R 9 , and NR 6 R 9 , where each of R 6 and R 9 can independently be H or an alkyl group
• examples of L include -(CH2) m - where m can be 0, 1, 2, or 3, and when m is 0, R 4 is C-linked to the pyrazole, when m is 1, R 4 is C- linked to L, and when m is 2 or 3, R 4 is N-linked or C-linked to L.
• alkyl cycloalkyl, branchedalkyl, halogen, CN, or alkoxy. All optionally fluorinated.
• Scheme 17 describes the synthesis of substituted oxazoles D-XV as reported in WO2014078378, the content of which are hereby incorporated by reference in its entirety.
• Various acid chlorides A-XV-i react with R 2 substituted aminoalkyl nitriles 17-1 (readily available to those skilled in the art) to furnish A-XV-ii.
• A-XV-ii is converted oxazole-amines D-XV under acidic conditions such as acetic acid, sulfuric acid or hydrochloric acid.
• examples of R 2 can be alkyl, cycloalkyl, or alkoxy, where alkyl, cycloalkyl, or alkoxy can be optionally fluorinated, and examples of R 4 include heterocyclyl with suitable optional substituents as exemplified by the tables of intermediates below and NR 6 R 9 , where each of R 6 and R 9 can independently be an alkyl group, where each of R 6 and R 9 can independently be an alkyl group.
• triazole-amines D-XVIII-i and D-XVIII-ii are prepared as shown in Scheme 20.
• examples of R 4 -L-linked 7-1 or 7-2 are shown.
• Triazoles B-XVIII are prepared from dinitro-esters A-XVIII-i by reaction with aldehydes 20-1 (readily available to those skilled in the art) using the procedure described in Asian J. of Chem, 2014, 26, 4744 and Hanneng Cailliao, 2008, 16, 49, the contents of which are hereby incorporated by reference in their entireties.
• B-XVIII may be prepared by nitration of A-XVIII-ii.
• examples of R 4 include alkyl, cycloalkyl, and heterocyclyl with suitable optional substituents as exemplified by the tables of intermediates below and examples of L include -(CH2) m - where m can be 0, 1, 2, or 3 and when m is 0, R 4 is C-linked to the boronate ester, when m is 1, then R 4 is C-linked to L, and when m is 2, or 3 then R 4 is N-linked or C-linked to L.
• R 1 can be cycloalkyl.
• Treatment of commercially available 5-bromo-2-chloro-6- (methylthio)pyrimidine with boronic esters/boronic acids/trifluoroborates in the presence of a palladium catalyst (Suzuki coupling) afford R 1 -substituted thiopyrimidines L-III (t 0).
• Examples of R 1 in this scheme include cycloalkyl such as cyclopropyl.
• Scheme 24 illustrates the general preparation of H-I.
• E-I acyl chloride
• DIEA base
• Many acyl chlorides (F-I) are commercially available and those that are not can be readily prepared from the corresponding carboxylic acids F-I-l with SOCh in a presence of base (EfoN or DIEA).
• the Boc protecting group of G-I may be removed upon exposure to acid, for example HC1 or TFA.
• examples of R L can include alkyl and cycloalkyl (e.g., cyclobutyl).
• Scheme 25 illustrates the general preparation of H-II.
• Compound G-II can be prepared by reaction of amine E-II with commercially available isocyanate F-II. Many isocyanate are commercially available and those that are not can be readily prepared from the corresponding carboxylic acids or amines (see scheme 27).
• the Boc protecting group of G- II may be removed upon exposure to acid, for example HC1 or TFA.
• examples of R 9 can include alkyl and cycloalkyl (e.g., cyclobutyl) and examples of R 6 can include H and alkyl.
• Scheme 26 illustrates the general preparation of H-III.
• Compound G-III can be prepared by reaction of amine E-III with 2,2,2-trichloroethyl carbamate F-III which can be prepared from amines and acids (see scheme 27). The Boc protecting group of G-III may be removed upon exposure to acid, for example HC1 or TFA.
• examples of R 9 can include alkyl and cycloalkyl (e.g., cyclobutyl) and examples of R 6 can include H and alkyl.
• Scheme 27 illustrate the general preparation of isocyanates F-II and carbamates F-III.
• Non-commercial isocyanates F-II can be prepared from amines or carboxylic acids. Reaction of amine with phosgene, or a phosgene equivalent such as diphosgene, triphosgene, or N,N’-dicarbonylimidazole provides isocyanate F-II.
• isocyanate F-II can be obtained directly from carboxylic acid via Curtius rearrangement: the mixing of acid with diphenylphosphoryl azide in a solvent such as 1,4- dioxane or dimethylformamide in the presence of base, such as tri ethyl amine, and raising the temperature of the reaction to about 80-120 °C.
• Certain carbamates F-III can also be prepared via Curtius rearrangement in the presence of an appropriate alcohol such as trichloroethanol.
• Trichloroethyl carbamates F-III are also readily prepared from amines by acylation with trichloroethyl chloroformate by standard conditions.
• . alkyl, branchedalkyl, or cycloalkyl
• Scheme 28 illustrates the general preparation of key intermediates J and K.
• Key intermediate J can be prepared from H (either free base or salt) and thiopyrimidine L-I in the presence of an organic base (e. g. triethylamine or DIEA) with optional heating to provide key intermediate J.
• organic base e. g. triethylamine or DIEA
• key intermediate K can be prepared from H by reaction with either L-II or L-III.
• Scheme 29 illustrates the general preparation of key intermediate M.
• an aprotic solvent e. g. DME, DMF, DMSO, or NMP
• Scheme 30 illustrates general preparations of compounds of Formula 1-1 from substituted D.
• the preparation of Formula 1-1 can be accomplished from key intermediates K and J.
• the first nucleophilic substitution reaction of K with amines of the formula D is typically performed in a polar solvent at temperatures ranging from ambient temp to 150 °C, in some embodiments with microwave heating, optionally in the presence of an acid for example 4 N HC1 in 1,4-dioxane to provide the Formula 1-1.
• Compounds D which are not commercially available, can be readily prepared (see schemes 1-20).
• Formula I-A free base or salt
• sodium cyanoborohydride or sodium triacetoxyborohydride and an aldehyde or ketone in the presence of a catalytic amount of acetic acid in polar solvents such as MeOH (reductive amination conditions) affords Formula 1-1 wherein R 4 contains a nitrogen substituted with alkyl or cycloalkyl.
• the free amine (or salt) can be treated with commercially available acyl chloride or sulfonyl chloride to afford Formula 1-1 wheein R 4 contains a nitrogen substituted with acyl or sulonfyl.
• Scheme 31 illustrates the general preparation of compounds of Formula 1-2
• the preparation of Formula 1-2 can be accomplished by a Buchwald-Hartwig coupling reaction between D and M. Many amines D which are not commercially available can be readily prepared (see schemes 1-12).
• reductive alkylation, acylation and sulfonylation can be performed to provide Formula 1-2 after deprotection of Formula 1-2 that contains a nitrogen protecting group such as a Boc group.
• reaction mixture was diluted with water (100 mL) and the solution was extracted with EtOAc (2 x 50 mL), The combined organics were evaporated under reduced pressure and the crude was purified by silica gel column chromatography (2 % MeOH/DCM, 10 CV’s) to give l-(3-bromo-4-nitrophenyl)-4-methylpiperazin-2-one (3.1 g, 76 % yield) as a yellow solid.
• the mixture was extracted with EtOAc (3 x 30 mL) and the combined organic extracts were dried over anhydrous Na2S04, filtered and concentrated under the reduced pressure to obtain the crude.
• the crude was purified by silica gel column chromatography (hexane/EtOAc) l-(3- (methoxymethyl)-4-nitrophenyl)-4-methylpiperazine (0.76 g, 72 % yield).
• the resulting reaction mixture was heated at 100 °C 16 h.
• the reaction was diluted with water and extracted with DCM (4 x 25 mL).
• the organics were combined and dried over anhydrous NaiSCE, filtered and concentrated to dryness under vacuum to afford a black oil.
• the black oil was purified using silica gel (0 to 15 % MeOH/DCM, 15 CV's) to obtain l-methyl-4-(3-methyl-4-nitrophenyl)-lH-imidazole (0.31 g, 47 % yield).
• the reaction mixture was diluted with water (200 mL) and extracted with EtOAc (3 x 300 mL). The combined organic extracts were washed with brine (200 mL), dried over anhydrous INfeSCL, filtered and concentrated under reduced pressure.
• the crude was purified by silica gel column chromatography (0 tol0% EtOAc/hexane) to obtain 2-chloro-5-cyclopropyl-4-(methylthio) pyrimidine (14.0 g, 66 % yield) as a yellow oil.
• Example L2 4-chloro-2-(methylthio)-5-(trifluoromethyl)pyrimidine.
• the reaction mixture was diluted with water (20 mL) and extracted with DCM (3 x 10 mL). The combined organic extracts were dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure.
• the crude product was purified by silica gel column chromatography (0 to 3 % DCM/MeOH, 15 CV’s) to obtain N-(3-((2-chloro-5- (trifluoromethyl)pyridin-4-yl)amino)propyl)cyclobutanecarboxamide (0.2 g, 18 % yield) as a yellow solid.
• Example 21 N-(3 -((2-((3 -methyl - 1 -(piperidin-4-yl)- 1 H-pyrazol -4-yl)amino)-5 - (trifluoromethyl)pyrimidin-4-yl)amino)propyl)cyclobutanecarboxamide.
• reaction mixture was stirred at rt for 24 h.
• the solution was quenched with sat. NaElCCh solution (40 mL) and extracted with EtOAc (3 x 20 mL).
• EtOAc 3 x 20 mL
• the combined organic extracts were washed with brine, dried over anhydrous Na 2 S0 4 , filtered, concentrated under reduced pressure.
• the reaction mixture was purged with nitrogen gas for 15 min and then X-Phos (0.1 g, 0.17 mmol) and Pd 2 (dba) 3 (0.081 g, 0.08 mmol) were added.
• the reaction mixture was heated at 90 °C for 16 h. and then cooled to rt.
• the reaction mixture was diluted with water (5 mL) and extracted with DCM (3 x 10 mL). The combined organic extracts were dried over anhydrous INfeSCL, filtered and concentrated under reduced pressure.
• the crude obtained was purified by silica gel column chromatography (0 to 5 % DCM/MeOH, 15 CV’s) to obtain N-(3-((2-((4-methyl-6-(4-methylpiperazin-l-yl)pyridin-3- yl)amino)-5-(trifluoromethyl)pyridin-4-yl)amino)propyl)-cyclobutanecarboxamide (0.08 g, 19 % yield) as brown solid.
• Inhibition of ULK1 was measured by adding serial diluted test compound (final assay concentration of 1% DMSO). A decrease in absorption at 340 nm was monitored continuously for 6 hours at 30 °C on a multi-mode microplate reader (BioTek). The reaction rate was calculated using the 2-3 h time frame. The reaction rate at each concentration of compound was converted to percent inhibition using controls (i.e. reaction with no test compound and reaction with a known inhibitor) and IC50 values were calculated by fitting a four-parameter sigmoidal curve to the data using Prism (GraphPad software).
• Assays were conducted in 384-well plates (100 uL final volume) using 0.1 nM ULK1 (from Beryllium), 0.075 mM peptide substrate ( Y ANWL AASIYLDGKKK (SEQ ID NO: 5)), 1.5 units pyruvate kinase, 2.1 units lactate dehydrogenase, 1 mM phosphoenol pyruvate, 0.28 mM NADH and 1 mM ATP in assay buffer (100 mM Tris, pH 7.5, 15 mM MgCh, 0.5 mM DTT, 0.004% (w/v) BSA, and 0.004% Triton X-100).
• Inhibition of ULK1 was measured by adding serial diluted test compound (final assay concentration of 1% DMSO). A decrease in absorption at 340 nm was monitored continuously for 6 hours at 30 °C on a multi-mode microplate reader (BioTek). The reaction rate was calculated using the 2-3 h time frame. The reaction rate at each concentration of compound was converted to percent inhibition using controls ⁇ i.e. reaction with no test compound and reaction with a known inhibitor) and IC50 values were calculated using software routines in Prism (GraphPad software).
• Assays were conducted in 384-well plates (100 uL final volume) using 9.7 nM ULK2 (Eurofms CAT# 14-772), 0.25 mg/mL myelin basic protein, 1.5 units pyruvate kinase, 2.1 units lactate dehydrogenase, 1 mM phosphoenol pyruvate, 0.28 mM NADH and 1 mM ATP in assay buffer (100 mM Tris, pH 7.5, 15 mM MgCh, 0.5 mM DTT, 0.1 % octyl-glucoside, 0.002% (w/v) BSA, and 0.002% Triton X-100).
• A549 (KRAS mutant) human lung cancer cells (6,000 cells/well) were added to a 384-well tissue-culture treated plate in 50 pL of pre-warmed DMEM medium
• Dulbecco Phosphate Buffered Saline (Gibco). Cells were lysed using MPER lysis buffer (Pierce, Rockford, IL) containing Halt Phosphatase and Protease Inhibitors (Pierce, Rockford, IL) and Phosphatase inhibitor cocktail 2 (Sigma, St. Louis, MO) at 4 °C for 10 minutes with shaking.
• MPER lysis buffer Pierce, Rockford, IL
• Halt Phosphatase and Protease Inhibitors Pierford, IL
• Phosphatase inhibitor cocktail 2 Sigma, St. Louis, MO
• Example 35 pATG13 levels of mutant KRas MiaPaCa-2 cells after treatment with ULK inhibitors in combination with Trametinib
• MiaPaCa-2 human pancreatic cancer cells (10000 cells/well) were added to a 384-well tissue-culture treated plate in 50 pL of pre-warmed DMEM medium supplemented with 10% characterized fetal bovine serum (Invitrogen, Carlsbad, CA), 100 units/mL penicillin G, 100 pg/mL streptomycin, and 2.5% Horse Serum and allowed to grow overnight at 37 °C, 5% C02, and 95% humidity. The following day, 10 pL of media containing trametinib or DMSO as a control was added to wells. The final concentration of trametinib in wells was 250 nM.
• a dose response of a test compound (0.6 pL per well) was added.
• DMSO (0.6 pL) was added to control wells.
• the plate was briefly shaken to mix wells and then incubated at 37 °C overnight. The next day, the media was aspirated and cells were washed with Dulbecco’s Phosphate Buffered Saline (Gibco).
• Cells were lysed using MPER lysis buffer (Pierce, Rockford, IL) containing Halt Phosphatase and Protease Inhibitors (Pierce, Rockford, IL) and Phosphatase inhibitor cocktail 2 (Sigma, St. Louis, MO) at 4 °C for 10 minutes with shaking.
• Assays were conducted in 384-well plates (100 uL final volume) using 26.4 nM LRRK2 (Thermo Fisher), 0.1 mM peptide substrate (RLGRDKYKTLRQIRQ (SEQ ID NO: 6)), 1.5 units pyruvate kinase, 2.1 units lactate dehydrogenase, 1 mM phosphoenol pyruvate, 0.28 mM NADH and 1 mM ATP in assay buffer (100 mM Tris, pH 7.5, 15 mM MgCh, 0.5 mM DTT, 0.004% (w/v) BSA, and 0.004% Triton X-100).
• Inhibition of LRRK2 was measured by adding serial diluted test compound (final assay concentration of 1% DMSO). A decrease in absorption at 340 nm was monitored continuously for 6 hours at 30 °C on a multi-mode microplate reader (BioTek). The reaction rate was calculated using the 2-3 h time frame. The reaction rate at each concentration of compound was converted to percent inhibition using controls (i.e. reaction with no test compound and reaction with a known inhibitor) and IC 50 values were calculated using software routines in Prism (GraphPad software).
• LRRK2 protein sequence (residues 970-2528; SEQ. ID NO. 4)
• + refers to an IC50 greater than 300 nM and less than or equal to 600 nM; and“+ + + +” refers to an IC50 greater than 600 nM and less than 20,000 nM.
• Example 37 Evaluation of ULK inhibitors in pancreatic ductal adenocarcinoma (PD AC) in vitro and in vivo
• PD AC pancreatic ductal adenocarcinoma
• ULK inhibitors will be evaluated in PD AC flux assays, and the IC50 of the compounds in a panel of multiple PD AC cell lines, including cells derived from primary tumors of a Trp53 lox/+ , LSL-Kras G12D , Rosa-rtTA LSL , p48Cre + ) will be determined using a clonogenicity 2D assay and a 3D organoid assay, in the absence or the presence of trametinib.
• the therapeutic efficacy of ULK inhibitors in PD AC models will be evaluated by (i) assessing the tumor kinetics of PD AC subcutaneously; (ii) assessing the tumor kinetics of PD AC (KPC implanted C57 black mice) orthotopically in the pancreas in syngeneic models; (iii) assessing tumor growth kinetics in syngeneic models with ULK inhibitors and MEK inhibitors; (iv) assessing the compounds in the PD AC autochthonous model; (v) assessing histological changes in the tumor microenvironment; (vi) assessing the changes in the immune cell infiltrates in the tumors upon inhibition by ULK inhibitors; (vii) assessing the efficacy of ULK inhibitors in combination with immune checkpoint blockade.

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