WO2021127328A1 - Trpml modulators - Google Patents
Trpml modulators Download PDFInfo
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- WO2021127328A1 WO2021127328A1 PCT/US2020/065839 US2020065839W WO2021127328A1 WO 2021127328 A1 WO2021127328 A1 WO 2021127328A1 US 2020065839 W US2020065839 W US 2020065839W WO 2021127328 A1 WO2021127328 A1 WO 2021127328A1
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- HAHYXYKFMHJMIE-UHFFFAOYSA-N C1C2NCC1C2 Chemical compound C1C2NCC1C2 HAHYXYKFMHJMIE-UHFFFAOYSA-N 0.000 description 1
- WXXRWYRZLBAERW-UHFFFAOYSA-N C1CB1c1ccccc1 Chemical compound C1CB1c1ccccc1 WXXRWYRZLBAERW-UHFFFAOYSA-N 0.000 description 1
- NCIQNWYJLAAFAH-UHFFFAOYSA-N CC(C)(C)OC(N(CC1)CCN1C(Cl)=O)=O Chemical compound CC(C)(C)OC(N(CC1)CCN1C(Cl)=O)=O NCIQNWYJLAAFAH-UHFFFAOYSA-N 0.000 description 1
- JIVGSHFYXPRRSZ-UHFFFAOYSA-N COc(cccc1C=O)c1OC Chemical compound COc(cccc1C=O)c1OC JIVGSHFYXPRRSZ-UHFFFAOYSA-N 0.000 description 1
- PPGYWCNAQGFSIL-UHFFFAOYSA-N O=C(N1C(C2)CC2C1)N1CCNCC1 Chemical compound O=C(N1C(C2)CC2C1)N1CCNCC1 PPGYWCNAQGFSIL-UHFFFAOYSA-N 0.000 description 1
- ISDBWOPVZKNQDW-UHFFFAOYSA-N O=Cc(cc1)ccc1-c1ccccc1 Chemical compound O=Cc(cc1)ccc1-c1ccccc1 ISDBWOPVZKNQDW-UHFFFAOYSA-N 0.000 description 1
- ZRYZBQLXDKPBDU-UHFFFAOYSA-N O=Cc(cc1)ccc1Br Chemical compound O=Cc(cc1)ccc1Br ZRYZBQLXDKPBDU-UHFFFAOYSA-N 0.000 description 1
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- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
- C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
- C07D471/10—Spiro-condensed systems
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P17/00—Drugs for dermatological disorders
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P21/00—Drugs for disorders of the muscular or neuromuscular system
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P25/00—Drugs for disorders of the nervous system
- A61P25/14—Drugs for disorders of the nervous system for treating abnormal movements, e.g. chorea, dyskinesia
- A61P25/16—Anti-Parkinson drugs
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- C—CHEMISTRY; METALLURGY
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- C07D—HETEROCYCLIC COMPOUNDS
- C07D257/00—Heterocyclic compounds containing rings having four nitrogen atoms as the only ring hetero atoms
- C07D257/02—Heterocyclic compounds containing rings having four nitrogen atoms as the only ring hetero atoms not condensed with other rings
- C07D257/04—Five-membered rings
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- 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
- C07D401/02—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
- C07D401/06—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 carbon chain containing only aliphatic carbon atoms
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- 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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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- 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
- C07D403/06—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 carbon chain containing only aliphatic carbon atoms
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- 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
- C07D403/14—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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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D405/00—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom
- C07D405/14—Heterocyclic compounds containing both one or more hetero rings having oxygen atoms as the only ring hetero atoms, and one or more rings having nitrogen as the only ring hetero atom containing three or more hetero rings
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
- C07D413/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings
- C07D413/06—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07D—HETEROCYCLIC COMPOUNDS
- C07D413/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and oxygen atoms as the only ring hetero atoms
- 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
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- C—CHEMISTRY; METALLURGY
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- C07D—HETEROCYCLIC COMPOUNDS
- C07D417/00—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00
- C07D417/02—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings
- C07D417/06—Heterocyclic compounds containing two or more hetero rings, at least one ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for by group C07D415/00 containing two hetero rings linked by a carbon chain containing only aliphatic carbon atoms
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- 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
- C07D491/10—Spiro-condensed systems
- C07D491/107—Spiro-condensed systems with only one oxygen atom as ring hetero atom in the oxygen-containing ring
Definitions
- Transient Receptor Potential Mucolipin-1 (also known as TRPML1 or MLl) is a Ca 2+ channel in the lysosome that regulates certain aspects of lysosome trafficking, including autophagy.
- TRPML1 is an inwardly rectifying current channel that transports cations from the lumen of the lysosome to the cytosol.
- the present disclosure provides, among other things, technologies for regulating (e.g., up- regulating) autophagy.
- the present disclosure demonstrates effectiveness of certain approaches to TRPMLl modulation (e.g., TRPMLl agonism) in enhancing autophagy.
- TRPMLl modulation e.g., TRPMLl agonism
- the present disclosure demonstrates that targeting TRPMLl as described herein can enhance autophagy.
- the present disclosure also provides certrain technologies for use in medicine, and in particular for treating certain diseases, disorders or conditions and/or for identifying, characterizing, and/or manufacturing certain agents and/or compositions or that comprise or deliver them that are useful in treating such diseases, disorders or conditions.
- modulating e.g., agonizing
- TRPLM1 e.g., agonizing
- TRPMLl modulators useful for promoting autophagy and/or treating certain diseases, disorders, or conditions.
- TRPMLl. jOO09
- the present application provides compounds having a structure as set forth in Formula I:
- A is wherein A is substituted with 0, 1, 2, 3 or 4 R a ;
- Cy is absent or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S, Ci- 6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of L 1 is absent, -NR 3 -, -0-, -S-, Ci- 6 alkylenyl, C2-6 alkynylenyl, -NR 3 -C I-6 alkylenyl, -O-Ci- 6 alkylenyl, -C(0)Co- 6 alkylenyl; -C(0)NR 3 -, or -C(0)-C(0)-;
- L 2 is absent, -(NR 3 ) s -S(0)-Co- 6 alkylenyl-, -(NR 3 ) s -S(0)2-Co- 6 alkylenyl-, -(NR 3 ) s -S(0)(NR 3 )-, -S(0) 2 -NR 3 -, -NR 3 -C I-6 haloalkylenyl, -(NR 3 ) s -P(0)(R 3 )-, -Ci-e alkylenyl-S(O)-, -Ci- 6 alkylenyl-S(0)2-, -C(0)-(NR 3 ) s -, -(NR 3 ) s -C(0)-, or an optionally substituted 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S;
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
- Y is H or an optionally substituted group selected from Ci- 6 aliphatic, O-Ci- 6 aliphatic, C3-12 cycloalkyl, Ci- 6 alkyl ene-R b , C3-6 cycloalkyl -R b , and 4- to 6- atom heterocyclyl -R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from CH, CR a , or N, wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci- 6 aliphatic, 2- to 10-membered heteroaliphatic, P(0)(R 3 )2, -C(0)Ci- 6 aliphatic, C(0)N(R 3 )2, C6-12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently halo, oxo, or optionally substituted Ci- 6 aliphatic;
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl; each R 2 is independently selected from halo, CN, C(0)0H, and an optionally substituted group selected from Ci- 6 aliphatic, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic; each R 3 is independently selected from H and optionally substituted Ci- 6 aliphatic; each R 5 is independently selected from Ci- 6 alkyl, -N(R 3 )2, -O-Ci- 6 alky
- Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci- 6 aliphatic, or C 3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- V is selected from C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising
- Y is H or an optionally substituted group selected from Ci- 6 aliphatic, O-Ci- 6 aliphatic, C 3-12 cycloalkyl, Ci- 6 alkyl ene-R b , C 3-6 cycloalkyl -R b , and 4- to 6- atom heterocyclyl -R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from CH, CR a , or N,.
- X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R 3 )2, -C(0)Ci- 6 aliphatic, C(0)N(R 3 )2, Cr,.
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci- 6 alkyl, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic; each R 3 is independently selected from H and optionally substituted Ci- 6 aliphatic; each R 5 is independently selected from Ci- 6 alkyl, -N(C I-6 alkyl )2, -O-Ci
- the present application provides compounds having a structure as set forth in Formula G : r or a pharmaceutically acceptable salt thereof, wherein Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- L 1 is absent, -NR 3 -Co-6 alkylenyl-, -O-Co-6 alkylenyl, Ci-6 alkyl enyl, -C(0)-Co-6 alkylenyl, - C(0)0-Co- 6 alkylenyl, -
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
- Y is Ci- 6 aliphatic, -S(0)2-Ci- 6 aliphatic, -O-Ci- 6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from C, CR a , S, O, orN, as valency permits, wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R 3 )2, C6-12 aryl, C 3 . 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently hydrogen, halo, or optionally substituted Ci- 6 aliphatic, or when L 1 and Cy are absent, R a comes together with Z to form a Ci- 6 alkenyl;
- R b is an optionally substituted group selected from -NR 3 -C(0)-CI- 6 aliphatic, -C(0)-Ci- 6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12- membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci-6 aliphatic and N(R 3 )-C(0)-Ci-6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci- 6 aliphatic, C(0)Ci- 6 alipha
- Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci- 6 aliphatic, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
- Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R 3 )2, C6-12 aryl, C3- 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently hydrogen, halo, or optionally substituted Ci- 6 aliphatic, or when L 1 and Cy are absent, R a comes together with Z to form a Ci- 6 alkenyl;
- R b is an optionally substituted group selected from -NR3-C(0)-C 1-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci-6 aliphatic and N(R 3 )-C(0)-Ci-6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O
- the term “agonist” generally refers to an agent whose presence or level correlates with elevated level or activity of a target, as compared with that observed absent the agent (or with the agent at a different level).
- an agonist is one whose presence or level correlates with a target level or activity that is comparable to or greater than a particular reference level or activity (e.g., that observed under appropriate reference conditions, such as presence of a known agonist, e.g., a positive control).
- an agonist may be a direct agonist in that it exerts its influence directly on (e.g., interacts directly with) the target; in some embodiments, an agonist may be an indirect agonist in that it exerts its influence indirectly (e.g., by acting on, such as interacting with, a regulator of the target, or with some other component or entity.
- Aliphatic refers to a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as “cycloaliphatic”), that has a single point or more than one points of attachment to the rest of the molecule.
- aliphatic groups contain 1-12 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-6 aliphatic carbon atoms (e.g., Ci- 6 ).
- aliphatic groups contain 1-5 aliphatic carbon atoms (e.g., Ci- 5). In other embodiments, aliphatic groups contain 1-4 aliphatic carbon atoms (e.g., C1-4). In still other embodiments, aliphatic groups contain 1-3 aliphatic carbon atoms (e.g., C1-3), and in yet other embodiments, aliphatic groups contain 1-2 aliphatic carbon atoms (e.g., C1-2).
- cycloaliphatic refers to a monocyclic C3-8 hydrocarbon or a bicyclic C7-10 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point or more than one points of attachment to the rest of the molecule.
- Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkylenyl, alkenyl, alkenylenyl, alkynyl, or alkynylenyl groups and hybrids thereof.
- a preferred aliphatic group is Ci- 6 alkyl.
- aliphatic is multivalent (i.e., has multiple points of attachment to the rest of the molecule). In some embodiments, aliphatic is bivalent (i.e., has two points of attachment to the rest of the molecule).
- An example bivalent aliphatic group can be referred to as “alkylenyl”.
- alkyl refers to a saturated, optionally substituted straight or branched chain or cyclic hydrocarbon group having (unless otherwise specified) 1-12, 1-10, 1-8, 1-6, 1-4, 1-3, or 1-2 carbon atoms (e.g., Ci-12, Ci-10, Ci- 8 , Ci- 6, Ci- 4 , Ci- 3 , or C1-2).
- exemplary alkyl groups include methyl, ethyl, propyl, butyl, pentyl, hexyl, and heptyl.
- cycloalkyl refers to an optionally substituted saturated ring system of about 3 to about 10 ring carbon atoms.
- exemplary monocyclic cycloalkyl rings include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.
- alkylene is a bivalent straight or branched alkyl group.
- an "alkylene chain” is a polymethylene group, i.e., -(CtfcV, wherein n is a positive integer, e.g., from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, or from 2 to 3.
- An optionally substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms is optionally replaced with a substituent.
- Suitable substituents include those described below for a substituted aliphatic group and also include those described in the specification herein. It will be appreciated that two substituents of the alkylene group may be taken together to form a ring system. In certain embodiments, two substituents can be taken together to form a 3- to 7-membered ring. The substituents can be on the same or different atoms.
- haloalkylenyl refers to an straight-chain or branched alkylenyl group substituted by one or more halogen atoms (e.g., one, two, three or four halo, such as fluoro, iodo, bromo, or chi or o).
- alkenyl refers to an optionally substituted straight or branched chain or cyclic hydrocarbon group having at least one double bond and having (unless otherwise specified) 2-12, 2-10, 2-8, 2-6, 2-4, or 2-3 carbon atoms(e.g., C2-12, C2-10, C2-8, C2-6, C2-4, or C2-3).
- alkenyl groups include ethenyl, propenyl, butenyl, pentenyl, hexenyl, and heptenyl.
- cycloalkenyl refers to an optionally substituted non-aromatic monocyclic or multicyclic ring system containing at least one carbon-carbon double bond and having about 3 to about 10 carbon atoms.
- Exemplary monocyclic cycloalkenyl rings include cyclopentenyl, cyclohexenyl, and cycloheptenyl.
- alkenyl ene and “alkenyl enyl” are used interchangeably and refers to a bivalent alkenyl group.
- alkenylene is a bivalent straight or branched alkenyl group.
- Alkynyl refers to an optionally substituted straight or branched chain hydrocarbon group having at least one triple bond and having (unless otherwise specified) 2-12, 2-10, 2-8, 2-6, 2-4, or 2-3 carbon atoms (e.g., C2-12, C2-10, C2-8, C2-6, C2-4, or C2-3).
- exemplary alkynyl groups include ethynyl, propynyl, butynyl, pentynyl, hexynyl, and heptynyl.
- Alkynylene The term “alkynylene” and “alkynylenyl” are used interchangeably and refers to a bivalent alkynyl group. In some embodiments, “alkynylene” is a bivalent straight or branched alkynyl group.
- an analog refers to a substance that shares one or more particular structural features, elements, components, or moieties with a reference substance. Typically, an “analog” shows significant structural similarity with the reference substance, for example sharing a core or consensus structure, but also differs in certain discrete ways.
- an analog is a substance that can be generated from the reference substance, e.g., by chemical manipulation of the reference substance. In some embodiments, an analog is a substance that can be generated through performance of a synthetic process substantially similar to (e.g., sharing a plurality of steps with) one that generates the reference substance. In some embodiments, an analog is or can be generated through performance of a synthetic process different from that used to generate the reference substance.
- an antagonist generally refers to an agent whose presence or level correlates with decreased level or activity of a target, as compared with that observed absent the agent (or with the agent at a different level).
- an antagonist is one whose presence or level correlates with a target level or activity that is comparable to or less than a particular reference level or activity (e.g., that observed under appropriate reference conditions, such as presence of a known antagonist, e.g., a positive control).
- an antagonist may be a direct antagonist in that it exerts its influence directly on (e.g., interacts directly with) the target; in some embodiments, an antagonist may be an indirect antagonist in that it exerts its influence indirectly (e.g., by acting on, such as interacting with, a regulator of the target, or with some other component or entity.
- Aryl refers to monocyclic and bicyclic ring systems having a total of five to fourteen ring members (e.g., C5-14), wherein at least one ring in the system is aromatic and wherein each ring in the system contains three to seven ring members.
- an “aryl” group contains between six and twelve total ring members (e.g., C6-12).
- the term “aryl” may be used interchangeably with the term “aryl ring”.
- “aryl” refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, anthracyl and the like, which may bear one or more substituents.
- “aryl” groups are hydrocarbons.
- an “aryl” ring system is an aromatic ring (e.g., phenyl) that is fused to a non-aromatic ring (e.g., cycloalkyl). Examples of aryl rings include that are fused include , , .
- Two events or entities are “associated” with one another, as that term is used herein, if the presence, level and/or form of one is correlated with that of the other.
- a particular entity e.g., polypeptide, genetic signature, metabolite, microbe, etc
- two or more entities are physically “associated” with one another if they interact, directly or indirectly, so that they are and/or remain in physical proximity with one another.
- two or more entities that are physically associated with one another are covalently linked to one another; in some embodiments, two or more entities that are physically associated with one another are not covalently linked to one another but are non-covalently associated, for example by means of hydrogen bonds, van der Waals interaction, hydrophobic interactions, magnetism, and combinations thereof.
- biological sample typically refers to a sample obtained or derived from a biological source (e.g., a tissue or organism or cell culture) of interest, as described herein.
- a source of interest comprises an organism, such as an animal or human.
- a biological sample is or comprises biological tissue or fluid.
- a biological sample may be or comprise bone marrow; blood; blood cells; ascites; tissue or fine needle biopsy samples; cell-containing body fluids; free floating nucleic acids; sputum; saliva; urine; cerebrospinal fluid, peritoneal fluid; pleural fluid; feces; lymph; gynecological fluids; skin swabs; vaginal swabs; oral swabs; nasal swabs; washings or lavages such as a ductal lavages or broncheoalveolar lavages; aspirates; scrapings; bone marrow specimens; tissue biopsy specimens; surgical specimens; feces, other body fluids, secretions, and/or excretions; and/or cells therefrom, etc.
- a biological sample is or comprises cells obtained from an individual.
- obtained cells are or include cells from an individual from whom the sample is obtained.
- a sample is a “primary sample” obtained directly from a source of interest by any appropriate means.
- a primary biological sample is obtained by methods selected from the group consisting of biopsy (e.g., fine needle aspiration or tissue biopsy), surgery, collection of body fluid (e.g., blood, lymph, feces etc.), etc.
- sample refers to a preparation that is obtained by processing (e.g., by removing one or more components of and/or by adding one or more agents to) a primary sample. For example, filtering using a semi-permeable membrane.
- processing e.g., by removing one or more components of and/or by adding one or more agents to
- a primary sample For example, filtering using a semi-permeable membrane.
- Such a “processed sample” may comprise, for example, nucleic acids or proteins extracted from a sample or obtained by subjecting a primary sample to techniques such as amplification or reverse transcription of mRNA, isolation and/or purification of certain components, etc. 0026] Biomarker.
- biomarker is used herein, consistent with its use in the art, to refer to a to an entity (or form thereof) whose presence, or level, correlates with a particular biological event or state of interest, so that it is considered to be a “marker” of that event or state.
- a biomarker may be or comprise a marker for a particular disease state, or for likelihood that a particular disease, disorder or condition may develop, occur, or reoccur.
- a biomarker may be or comprise a marker for a particular disease or therapeutic outcome, or likelihood thereof.
- a biomarker is predictive, in some embodiments, a biomarker is prognostic, in some embodiments, a biomarker is diagnostic, of the relevant biological event or state of interest.
- Carrier refers to a diluent, adjuvant, excipient, or vehicle with which a composition is administered.
- carriers can include sterile liquids, such as, for example, water and oils, including oils of petroleum, animal, vegetable or synthetic origin, such as, for example, peanut oil, soybean oil, mineral oil, sesame oil and the like.
- carriers are or include one or more solid components.
- Combination therapy refers to those situations in which a subject is simultaneously exposed to two or more therapeutic regimens (e.g., two or more therapeutic agents or modality(ies)).
- the two or more regimens may be administered simultaneously; in some embodiments, such regimens may be administered sequentially (e.g., all “doses” of a first regimen are administered prior to administration of any doses of a second regimen); in some embodiments, such agents are administered in overlapping dosing regimens.
- “administration” of combination therapy may involve administration of one or more agent(s) or modality(ies) to a subject receiving the other agent(s) or modality(ies) in the combination.
- combination therapy does not require that individual agents be administered together in a single composition (or even necessarily at the same time), although in some embodiments, two or more agents, or active moieties thereof, may be administered together in a combination composition, or even in a combination compound (e.g., as part of a single chemical complex or covalent entity).
- Comparable refers to two or more agents, entities, situations, sets of conditions, etc., that may not be identical to one another but that are sufficiently similar to permit comparison therebetween so that one skilled in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed.
- comparable sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in the art will understand, in context, what degree of identity is required in any given circumstance for two or more such agents, entities, situations, sets of conditions, etc. to be considered comparable.
- composition may be used to refer to a discrete physical entity that comprises one or more specified components.
- a composition may be of any form - e.g., gas, gel, liquid, solid, etc.
- Dosage form or unit dosage form may be used to refer to a physically discrete unit of an active agent (e.g., a therapeutic or diagnostic agent) for administration to a subject.
- an active agent e.g., a therapeutic or diagnostic agent
- each such unit contains a predetermined quantity of active agent.
- such quantity is a unit dosage amount (or a whole fraction thereof) appropriate for administration in accordance with a dosing regimen that has been determined to correlate with a desired or beneficial outcome when administered to a relevant population (/. ., with a therapeutic dosing regimen).
- the total amount of a therapeutic composition or agent administered to a particular subject is determined by one or more attending physicians and may involve administration of multiple dosage forms.
- Dosing regimen or therapeutic regimen may be used to refer to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time.
- a given therapeutic agent has a recommended dosing regimen, which may involve one or more doses.
- a dosing regimen comprises a plurality of doses each of which is separated in time from other doses.
- individual doses are separated from one another by a time period of the same length; in some embodiments, a dosing regimen comprises a plurality of doses and at least two different time periods separating individual doses.
- all doses within a dosing regimen are of the same unit dose amount. In some embodiments, different doses within a dosing regimen are of different amounts. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount different from the first dose amount. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount same as the first dose amount. In some embodiments, a dosing regimen is correlated with a desired or beneficial outcome when administered across a relevant population (/. ., is a therapeutic dosing regimen).
- Engineered refers to the aspect of having been manipulated by the hand of man.
- a small molecule may be considered to be engineered if its structure and/or production is designed and/or implemented by the hand ot man.
- a polynucleotide may be considered to be “engineered” when two or more sequences, that are not linked together in that order in nature, are manipulated by the hand of man to be directly linked to one another in the engineered polynucleotide.
- an engineered polynucleotide comprises a regulatory sequence that is found in nature in operative association with a first coding sequence but not in operative association with a second coding sequence, is linked by the hand of man so that it is operatively associated with the second coding sequence.
- a cell or organism is considered to be “engineered” if it has been manipulated so that its genetic information is altered (e.g ., new genetic material not previously present has been introduced, for example by transformation, mating, somatic hybridization, transfection, transduction, or other mechanism, or previously present genetic material is altered or removed, for example by substitution or deletion mutation, or by mating protocols).
- excipient refers to a non-therapeutic agent that may be included in a pharmaceutical composition, for example, to provide or contribute to a desired consistency or stabilizing effect.
- Suitable pharmaceutical excipients include, for example, starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
- heteroaliphatic or “heteroaliphatic group”, as used herein, denotes an optionally substituted hydrocarbon moiety having, in addition to carbon atoms, from one to five heteroatoms, that may be straight-chain ( i.e unbranched), branched, or cyclic (“heterocyclic”) and may be completely saturated or may contain one or more units of unsaturation, but which is not aromatic.
- heteroatom refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen.
- nitrogen also includes a substituted nitrogen.
- heteroaliphatic groups contain 1-10 carbon atoms wherein 1-3 carbon atoms are optionally and independently replaced with heteroatoms selected from oxygen, nitrogen, and sulfur. In some embodiments, heteroaliphatic groups contain 1-4 carbon atoms, wherein 1-2 carbon atoms are optionally and independently replaced with heteroatoms selected from oxygen, nitrogen, and sulfur. In yet other embodiments, heteroaliphatic groups contain 1-3 carbon atoms, wherein 1 carbon atom is optionally and independently replaced with a heteroatom selected from oxygen, nitrogen, and sulfur. Suitable heteroaliphatic groups include, but are not limited to, linear or branched, heteroalkyl, heteroalkenyl, and heteroalkynyl groups. For example, a 1- to 10 atom heteroaliphatic group includes the following exemplary groups: -O-CH3, -CH2-O-CH3, -O-CH2- CH2-O-CH2-CH2-O-CH3, and the like.
- Heteroaryl and “heteroar-”, used alone or as part of a larger moiety, e.g., “heteroaralkyl”, or “heteroaralkoxy”, refer to monocyclic or bicyclic ring groups having 5 to 12 ring atoms (e.g., 5- to 6- membered monocyclic heteroaryl or 9- to 12-membered bicyclic heteroaryl); having 6, 10, or 14 p-electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms.
- heteroatom refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quatemized form of a basic nitrogen.
- Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, pteridinyl, imidazo[l,2-a]pyrimidinyl, imidazo[l,2-a]pyridyl, imidazo[4,5-b]pyridyl, imidazo[4,5-c]pyridyl,
- heteroaryl and “heteroar-”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring (i.e., a bicyclic heteroaryl ring having 1 to 3 heteroatoms).
- Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzotriazolyl, benzothiazolyl, benzothiadiazolyl, benzoxazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, AH quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, pyrido[2,3-b]-l,4-oxazin-3(4H)-one, and benzoisoxazolyl.
- heteroaryl group may be mono- or bicyclic.
- heteroaryl may be used interchangeably with the terms “heteroaryl ring”, “heteroaryl group”, or “heteroaromatic”, any of which terms include rings that are optionally substituted.
- heteroarylkyl refers to an alkyl group substituted by a heteroaryl, wherein the alkyl and heteroaryl portions independently are optionally substituted.
- heteroatom refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quatemized form of a basic nitrogen.
- Heterocycle As used herein, the terms “heterocycle”, “heterocyclyl”, “heterocyclic radical”, and “heterocyclic ring” are used interchangeably and refer to a stable 3- to 8-membered monocyclic, a 7- to 12-membered bicyclic, or a 10- to 16-membered polycyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, such as one to four, heteroatoms, as defined above.
- nitrogen When used in reference to a ring atom of a heterocycle, the term "nitrogen” includes a substituted nitrogen.
- the nitrogen in a saturated or partially unsaturated ring having 0-3 heteroatoms selected from oxygen, sulfur or nitrogen, the nitrogen may be N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or NR + (as in N-substituted pyrrolidinyl).
- a heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted.
- saturated or partially unsaturated heterocyclic radicals include, without limitation, azetidinyl, oxetanyl, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, piperidinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and thiamorpholinyl.
- a heterocyclyl group may be mono-, bi-, tri-, or polycyclic, preferably mono-, bi-, or tricyclic, more preferably mono- or bicyclic.
- heterocyclylalkyl refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.
- a bicyclic heterocyclic ring also includes groups in which the heterocyclic ring is fused to one or more aryl rings.
- bicyclic heterocyclic groups include indolinyl, isoindolinyl, benzodioxolyl, 1,3- dihydroisobenzofuranyl, 2,3-dihydrobenzofuranyl, tetrahydroquinolinyl,
- a bicyclic heterocyclic ring can also be a spirocyclic ring system (e.g., 7- to 11-membered spirocyclic fused heterocyclic ring having, in addition to carbon atoms, one or more heteroatoms as defined above (e.g., one, two, three or four heteroatoms)).
- a bicyclic heterocyclic ring can also be a bridged ring system (e.g., 7- to 11-membered bridged heterocyclic ring having one, two, or three bridging atoms.
- Exemplary bridged ring systems include /y ⁇ and .
- Exemplary polycyclic heterocyclic ring systems that are spirocyclic include
- oral administration and “administered orally” as used herein have their art-understood meaning referring to administration by mouth of a compound or composition.
- 004OJ Parenteral The phrases “parenteral administration” and “administered parenterally” as used herein have their art-understood meaning referring to modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intramuscular, intra-arterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticulare, subcapsular, subarachnoid, intraspinal, and intrasternal injection and infusion.
- Partially unsaturated refers to a ring moiety that includes at least one double or triple bond between ring atoms.
- the term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic (e.g., aryl or heteroaryl) moieties, as herein defined.
- a patient refers to any organism to which a provided composition is or may be administered, e.g., for experimental, diagnostic, prophylactic, cosmetic, and/or therapeutic purposes. Typical patients or subjects include animals (e.g, mammals such as mice, rats, rabbits, non-human primates, and/or humans). In some embodiments, a patient is a human. In some embodiments, a patient or a subject is suffering from or susceptible to one or more disorders or conditions. In some embodiments, a patient or subject displays one or more symptoms of a disorder or condition. In some embodiments, a patient or subject has been diagnosed with one or more disorders or conditions. In some embodiments, a patient or a subject is receiving or has received certain therapy to diagnose and/or to treat a disease, disorder, or condition.
- animals e.g., mammals such as mice, rats, rabbits, non-human primates, and/or humans.
- a patient is a human.
- a patient or a subject is suffering from or susceptible to one or more disorders or conditions.
- composition refers to an active agent, formulated together with one or more pharmaceutically acceptable carriers.
- the active agent is present in unit dose amount appropriate for administration in a therapeutic or dosing regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population.
- compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin, lungs, or oral cavity; intravaginally or intrarectally, for example, as a pessary, cream, or foam; sublingually; ocularly; transdermally; or nasally, pulmonary, and to other mucosal surfaces.
- oral administration for example, drenches (aqueous or non-aqueous solutions or suspension
- compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
- composition or vehicle means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body.
- Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.
- materials which can serve as pharmaceutically-acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, com oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline;
- compositions that are appropriate for use in pharmaceutical contexts, i.e., salts which 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 well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences , 66: 1-19 (1977).
- pharmaceutically acceptable salts include, but are not limited to, nontoxic acid addition salts, which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
- nontoxic acid addition salts which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
- pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, di gluconate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2- hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate
- Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
- pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate.
- polycyclic refers to a saturated or unsaturated ring system having two or more rings (for example, heterocyclyl rings, heteroaryl rings, cycloalkyl rings, or aryl rings), having between 7 and 20 atoms, in which one or more carbon atoms are common to two adjacent rings.
- the rings in a polycyclic ring system may be fused (i.e., bicyclic or tricyclic), spirocyclic, or a combination thereof.
- Exemplary polyclic systems include
- Prevent or prevention when used in connection with the occurrence of a disease, disorder, and/or condition, refer to reducing the risk of developing the disease, disorder and/or condition and/or to delaying onset of one or more characteristics or symptoms of the disease, disorder or condition. Prevention may be considered complete when onset of a disease, disorder or condition has been delayed for a predefined period of time.
- Reference As used herein describes a standard or control relative to which a comparison is performed. For example, in some embodiments, an agent, animal, individual, population, sample, sequence or value of interest is compared with a reference or control agent, animal, individual, population, sample, sequence or value.
- a reference or control is tested and/or determined substantially simultaneously with the testing or determination of interest.
- a reference or control is a historical reference or control, optionally embodied in a tangible medium.
- a reference or control is determined or characterized under comparable conditions or circumstances to those under assessment. Those skilled in the art will appreciate when sufficient similarities are present to justify reliance on and/or comparison to a particular possible reference or control.
- Sample typically refers to an aliquot of material obtained or derived from a source of interest.
- a source of interest is a biological or environmental source.
- a source of interest may be or comprise a cell, tissue, or organism, such as a microbe, a plant, or an animal (e.g., a human).
- a source of interest is or comprises biological tissue or fluid.
- a source of interest may be or comprise a preparation generated in a production run.
- a sample is a “primary sample” obtained directly from a source of interest by any appropriate means.
- the term “sample” refers to a preparation that is obtained by processing (e.g., by removing one or more components of and/or by adding one or more agents to) a primary sample.
- ⁇ 0051 ⁇ Specific: The term “specific”, when used herein with reference to an agent having an activity, is understood by those skilled in the art to mean that the agent discriminates between potential target entities or states. For example, in some embodiments, an agent is said to bind “specifically” to its target if it binds preferentially with that target in the presence of one or more competing alternative targets. In many embodiments, specific interaction is dependent upon the presence of a particular structural feature of the target entity (e.g., an epitope, a cleft, a binding site). It is to be understood that specificity need not be absolute. In some embodiments, specificity may be evaluated relative to that of the binding agent for one or more other potential target entities (e.g., competitors).
- specificity is evaluated relative to that of a reference specific binding agent. In some embodiments, specificity is evaluated relative to that of a reference non-specific binding agent. In some embodiments, the agent or entity does not detectably bind to the competing alternative target under conditions of binding to its target entity. In some embodiments, a binding agent binds with higher on-rate, lower off-rate, increased affinity, decreased dissociation, and/or increased stability to its target entity as compared with the competing alternative target(s).
- substituted or optionally substituted As described herein, compounds of the invention may contain “optionally substituted” moieties.
- the term “substituted,” whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. “Substituted” applies to one or more hydrogens that are either explicit or implicit from the structure (e.g., refers to at least Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position.
- Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds.
- stable refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes provided herein.
- Groups described as being “substituted” preferably have between 1 and 4 substituents, more preferably 1 or 2 substituents.
- Groups described as being “optionally substituted” may be unsubstituted or be “substituted” as described above.
- Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; -(CH2)o-4R°; -(CH2)o-40R°; -0(CH2)o-4R°, -O-
- Suitable monovalent substituents on R° are independently halogen, -(CH 2 )o- 2 R*, -(haloR*), -(CH 2 ) O-2 OH, -(CH 2 ) O-2 OR*, -(CH 2 ) O-2 CH(OR*) 2 , -0(haloR*), -CN, -N 3 , -(CH 2 ) 0- 2 C(0)R ⁇ , -(CH 2 ) O-2 C(0)OH, -(CH 2 ) O-2 C(0)OR ⁇ , -(CH 2 ) O-2 SR*, -(CH 2 ) O-2 SH, -(CH 2 ) O-2 NH 2 , - (CH 2 ) O-2 NHR ⁇ , -(CH 2 ) O-2 NR* 2 , -N0 2 , -SiR* 3 , -OSiR
- Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: -0(CR * 2 ) 2-3 0-, wherein each independent occurrence of R * is selected from hydrogen, Ci- 6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
- Suitable substituents on the aliphatic group of R * include halogen, R*, -(haloR*), -OH, - OR*, -0(haloR*), -CN, -C(0)0H, -C(0)0R*, -NH 2 , NHR*, -NR* 2 , or -N0 2 , wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Ci- 4 aliphatic, -CH 2 Ph, -0(CH 2 )o-iPh, or a 5- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
- Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include -R ⁇ , -NR ⁇ 2 , -C(0)R ⁇ , -C(0)0R ⁇ , -C(0)C(0)R ⁇ ,
- each R is independently hydrogen, Ci- 6 aliphatic which may be substituted as defined below, unsubstituted -OPh, or an unsubstituted 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R ⁇ , taken together with their intervening atom(s) form an unsubstituted 3- to 12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
- Suitable substituents on the aliphatic group of R are independently halogen, - R*, -(haloR*), -OH, -OR*, -0(haloR*), -CN, -C(0)OH, -C(0)OR*, -NH 2 , -NHR*, -NR* 2 , or -N0 2 , wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Ci- 4 aliphatic, -CH 2 Ph, -0(CH 2 )o-iPh, or a 3- to 6- membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
- small molecule means a low molecular weight organic and/or inorganic compound.
- a “small molecule” is a molecule that is less than about 5 kilodaltons (kD) in size.
- a small molecule is less than about 4 kD, 3 kD, about 2 kD, or about 1 kD.
- the small molecule is less than about 800 daltons (D), about 600 D, about 500 D, about 400 D, about 300 D, about 200 D, or about 100 D.
- a small molecule is less than about 2000 g/mol, less than about 1500 g/mol, less than about 1000 g/mol, less than about 800 g/mol, or less than about 500 g/mol. In some embodiments, a small molecule is not a polymer.
- a small molecule does not include a polymeric moiety.
- a small molecule is not and/or does not comprise a protein or polypeptide (e.g., is not an oligopeptide or peptide).
- a small molecule is not and/or does not comprise a polynucleotide (e.g., is not an oligonucleotide).
- a small molecule is not and/or does not comprise a polysaccharide; for example, in some embodiments, a small molecule is not a glycoprotein, proteoglycan, glycolipid, etc.). In some embodiments, a small molecule is not a lipid.
- a small molecule is a modulating agent (e.g., is an inhibiting agent or an activating agent).
- a small molecule is biologically active.
- a small molecule is detectable (e.g., comprises at least one detectable moiety).
- a small molecule is a therapeutic agent.
- small molecule compounds have structures that can exist in one or more steroisomeric forms.
- such a small molecule may be utilized in accordance with the present disclosure in the form of an individual enantiomer, diastereomer or geometric isomer, or may be in the form of a mixture of stereoisomers; in some embodiments, such a small molecule may be utilized in accordance with the present disclosure in a racemic mixture form.
- ⁇ 6Q64J Those of skill in the art will appreciate that certain small molecule compounds have structures that can exist in one or more tautomeric forms. In some embodiments, such a small molecule may be utilized in accoradance with the present disclosure in the form of an individual tautomer, or in a form that interconverts between tautomeric forms.
- small molecule compounds have structures that permit isotopic substitution (e.g., 2 H or 3 ⁇ 4 for H;, U C, 13 C or 14 C for 12C; , 13 N or 15 N for 14N; 17 0 or 18 0 for 160; 36 C1 for XXC; 18 F for XXF; 1311 for XXXI; etc).
- such a small molecule may be utilized in accordance with the present disclosure in one or more isotopically modified forms, or mixtures thereof.
- reference to a particular small molecule compound may relate to a specific form of that compound.
- a particular small molecule compound may be provided and/or utilized in a salt form (e.g., in an acid-addition or base-addition salt form, depending on the compound); in some such embodiments, the salt form may be a pharmaceutically acceptable salt form.
- In some embodiments, where a small molecule compound is one that exists or is found in nature, that compound may be provided and/or utilized in accordance in the present disclosure in a form different from that in which it exists or is found in nature.
- a preparation of a particular small molecule compound that contains an absolute or relative amount of the compound, or of a particular form thereof, that is different from the absolute or relative (with respect to another component of the preparation including, for example, another form of the compound) amount of the compound or form that is present in a reference preparation of interest is distinct from the compound as it exists in the reference preparation or source.
- a preparation of a single stereoisomer of a small molecule compound may be considered to be a different form of the compound than a racemic mixture of the compound; a particular salt of a small molecule compound may be considered to be a different form from another salt form of the compound; a preparation that contains only a form of the compound that contains one conformational isomer ((Z) or (E)) of a double bond may be considered to be a different form of the compound from one that contains the other conformational isomer ((E) or (Z)) of the double bond; a preparation in which one or more atoms is a different isotope than is present in a reference preparation may be considered to be a different form; etc.
- a bond designated as ⁇ in a small molecule structure refers to a bond that, in some embodiments, is a single (e.g., saturated) bond, and in some embodiments, is a double (e.g., unsaturated) bond.
- the following structure is intended to encompass both an fO069 j
- the symbol /vw refers to a point of attachment between two atoms.
- Therapeutic agent in general refers to any agent that elicits a desired pharmacological effect when administered to an organism.
- an agent is considered to be a therapeutic agent if it demonstrates a statistically significant effect across an appropriate population.
- the appropriate population may be a population of model organisms.
- an appropriate population may be defined by various criteria, such as a certain age group, gender, genetic background, preexisting clinical conditions, etc.
- a therapeutic agent is a substance that can be used to alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition.
- a “therapeutic agent” is an agent that has been or is required to be approved by a government agency before it can be marketed for administration to humans.
- a “therapeutic agent” is an agent for which a medical prescription is required for administration to humans.
- 007tj Treat As used herein, the terms “treat,” “treatment,” or “treating” refer to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition. Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and/or condition. In some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and/or condition, for example, for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and/or condition.
- Autophagy is a mechanism of the cell that degrades cytoplasmic material and organelles.
- autophagy There are multiple types of autophagy: (1) macroautophagy (generally referred to as autophagy); (2) microautophagy; and (3) chaperone-mediateed autophagy. See Eskelinen & Saftig, Biochimica et Biophysica Acta - Mol. Cell Res., 1793(4):664-673 (2009).
- macroautophagy the autophagosome engulfs waste materials in the cytoplasm and fuses to the lysosome, where materials are delivered for degradation.
- the lysosome is as a subcellular organelle containing more than 50 soluble acid hydrolases useful for digesting cellular components.
- TRPMLl Transient Receptor Potential Mucolipin-1
- PNAS E1373-E1381 (March 2, 2015).
- TRPMLl is an inwardly rectifying current channel that transports cations from the lumen of the lysosome to the cytosol.
- autophagy upregulation of autophagy is beneficial to patients suffering from a number of diseases and disorders. For example, it has been reported that inducing autophagy promotes clearance of hepatotoxic alpha- 1 -anti -trypsin (ATZ) in the liver. See Pastore, et al., EMBO Mol. Med. 5(3): 397-412 (Mar. 2013). Moreover, autophagy was recently found to be useful in the treatment of neurodegenerative disorders, cancer, and heart disease. See Pierzynowska, et al, Metab. Brain Dis., 33(4); 989-1008 (2016) (discussing neurodegenerative disorders); Nelson & Shacka, Curr. Pathobiol.
- AZA hepatotoxic alpha- 1 -anti -trypsin
- TRPMLl TRPMLl modulators useful for promoting autophagy and/or treating certain diseases, disorders, or conditions.
- TRMPLl may represent a particularly desirable target that, among other things, may permit modulation (e.g., enhancement) of autophagy in certain contexts.
- TRMPL1 modulators that are small molecule compounds having a chemical structure as indicated below in Formula I:
- A is wherein A is substituted with 0, 1, 2, 3 or 4 R a ;
- Cy is absent or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S, Ci- 6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of
- L 1 is absent, -NR 3 -, -0-, -S-, Ci- 6 alkylenyl, C2-6 alkynylenyl, -NR 3 -C I-6 alkyl enyl,-0-Ci- 6 alkylenyl, -C(0)Co- 6 alkylenyl; -C(0)NR 3 -, or -C(0)-C(0)-;
- L 2 is absent, -(NR 3 ) s -S(0)-Co-6 alkylenyl-, -(NR 3 ) s -S(0)2-Co-6 alkylenyl-, -(NR 3 ) s -S(0)(NR 3 )-, -S(0) 2 -NR 3 -, -NR 3 -C I-6 haloalkylenyl, -(NR 3 ) s -P(0)(R 3 )-, -Ci- 6 alkylenyl-S(O)-,
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
- Z is Ci- 6 aliphatic, 2- to 10-membered heteroaliphatic, P(0)(R 3 )2, -C(0)Ci- 6 aliphatic, C(0)N(R 3 )2, C6-12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently halo, oxo, or optionally substituted Ci- 6 aliphatic;
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl; each R 2 is independently selected from halo, CN, C(0)0H, and an optionally substituted group selected from Ci- 6 aliphatic, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic; each R 3 is independently selected from H and optionally substituted Ci- 6 aliphatic; each R 5 is independently selected from Ci- 6 alkyl, -N(R 3 )2, -O-Ci- 6 alky
- A is substituted with 0, 1, 2, 3, or 4 R a .
- A is unsubstituted (i.e, is substituted with 0 R a ).
- A is substituted with 1 R a .
- A is substituted with 2 R a .
- A is substituted with 3 R a .
- A is substituted with 4 R a .
- the compound of formula I is:
- the compound of formula I is:
- the present application provides compounds having a structure as set forth in Formula G :
- Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- L 1 is absent, -NR 3 -Co-6 alkylenyl-, -O-Co-6 alkylenyl, Ci-6 alkyl enyl, -C(0)-Co-6 alkylenyl, - C(0)0-Co- 6 alkylenyl, -C(0)-NR 3 -, -NR 3 -C(0)-;
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
- Y is Ci- 6 aliphatic, -S(0)2-Ci- 6 aliphatic, -O-Ci- 6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from C, CR a , S, O, orN, as valency permits, wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R 3 )2, C6-12 aryl, C 3 . 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently hydrogen, halo, or optionally substituted Ci- 6 aliphatic, or when L 1 and Cy are absent, R a comes together with Z to form a Ci- 6 alkenyl;
- R b is an optionally substituted group selected from -NR 3 -C(0)-CI- 6 aliphatic, -C(0)-Ci- 6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12- membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci-6 aliphatic and N(R 3 )-C(0)-Ci-6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic,
- the present application provides compounds having a structure as set forth in Formula IF : or a pharmaceutically acceptable salt thereof, wherein
- Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci- 6 aliphatic, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
- Y is H, Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Y is optionally substituted with one or more instances of R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from C, CR a , S, O, orN, as valency permits, wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y; Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R 3 )2, C6-12 aryl, C3- 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N,
- R b is an optionally substituted group selected from -NR3-C(0)-C 1-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci-6 aliphatic and N(R 3 )-C(0)-Ci-6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O
- each of X 1 , X 2 , X 3 , and X 4 is independently selected from C, CR a , S, O, NH, or N, as valency permits, wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y .
- X 1 , X 2 , X 3 , and X 4 are each N or NH.
- X 1 , X 2 , X 3 , and X 4 are each CR a or C.
- X 1 , X 2 , and X 3 are N and X 4 is CR a or C. In some embodiments, X 1 , X 3 , and X 4 are N and X 2 is CR a or C . In some embodiments, X 1 , X 2 , and X 4 are N and X 3 is CR a or C . In some embodiments, X 2 , X 3 , and X 4 are N and X 1 is CR a or C . In some embodiments, X 1 and X 2 are N and X 3 and X 4 are each independently CR a or C .
- X 1 and X 3 are N and X 2 and X 4 are each independently CR a or C . In some embodiments, X 1 and X 4 are N and X 2 and X 3 are each independently CR a or C . In some embodiments, X 2 and X 3 are N and X 1 and X 4 are each independently CR a or C . In some embodiments, X 2 and X 4 are N and X 1 and X 3 are each independently CR a or C . In some embodiments, X 3 and X 4 are N and X 1 and X 2 are each independently CR a or C .
- X 1 is N and X 2 , X 3 , and X 4 are each independently CR a or C .
- X 2 is N and X 1 , X 3 , and X 4 are each independently CR a or C .
- X 3 is N and X 1 , X 2 , and X 4 are each independently CR a or C .
- X 4 is N and X 1 , X 2 , and X 3 are each independently CR a or C .
- a compound of Formula G or IF is selected from:
- each R a is hydrogen, halo, oxo, or optionally substituted Ci- 6 aliphatic, or when L 1 and Cy are absent, R a comes together with Z to form a Ci- 6 alkenyl.
- each R a is hydrogen, halo, oxo, or optionally substituted Ci- 6 aliphatic.
- R a is Ci- 6 alkyl.
- R a is C1-3 alkyl.
- R a is methyl. ⁇ 0085J
- R a is halo.
- R a is bromo, chloro, fluoro, or iodo.
- R a is bromo.
- R a is chloro.
- R a is fluoro.
- R a is iodo.
- R a is oxo
- R a comes together with Z to form Ci- 6 alkenyl. In some embodiments, when L 1 and Cy are absent, R a comes together with Z to form:
- Y is Ci-6 aliphatic, -S(0)2-Ci-6 aliphatic, -O-Ci-6 aliphatic, C3- 12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of R b .
- Y is Ci- 6 aliphatic optionally substituted with one or more instances of R b .
- Y is Ci- 6 alkyl optionally substituted with one or more instances of R b .
- Y is C1-3 alkyl optionally substituted with one or more instances of R b .
- Y is methyl.
- Y is ethyl.
- Y is isopropyl.
- Y is tert-butyl.
- Y is n-butyl.
- Y is Ci- 6 aliphatic substituted with one or more instances of R b .
- Y is methyl substituted with R b .
- Y is ethyl substituted with R b .
- Y is propyl substituted with R b .
- Y is O-Ci- 6 aliphatic optionally substituted with one or more instances of R b .
- Y is O-Ci- 6 alkyl optionally substituted with one or more instances of R b .
- Y is O-C1-3 alkyl.
- Y is O-methyl optionally substituted with one or more instances of R b .
- Y is C3-12 cycloalkyl optionally substituted with one or more instances of R b . In some embodiments, Y is C3-6 cycloalkyl optionally substituted with one or more instances of R b . In some embodiments, Y is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In some embodiments, Y is cyclopropyl. In some embodiments, Y is cyclobutyl. In some embodiments, Y is cyclopentyl. In some embodiments, Y is cyclohexyl.
- Y is 4- to 6- atom heterocyclyl optionally substituted with one or more instances of R b . .
- azetidinyl optionally substituted with one or more instances of R b .
- Y is pyrrolidinyl optionally substituted with one or more instances of R b .
- Y is piperdinyl optionally substituted with one or more instances of R b .
- R b is an optionally substituted group selected from -NR. 3 -C(0)- Ci-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- R b is optionally substituted -NR3-C(0)-C I -6 aliphatic.
- R b is -NH-C(0)-CI-6 aliphatic.
- R b is -N(CH3)-C(0)-CI-6 aliphatic.
- R b is optionally substituted C6-12 aryl. In some embodiments, R b is optionally substituted phenyl. In some embodiments, R b is phenyl substituted with halogen or - (CH2) O -4R°. In some embodiments, R b is unsubstituted phenyl.
- R b is optionally substituted -C(0)-Ci- 6 aliphatic. In some embodiments, R b is -0(0)-(03 ⁇ 4)3.
- R b is optionally substituted Ci- 6 aliphatic. In some embodiments, R b is methyl, ethyl, propyl, butyl, pentyl, or hexyl.
- R b is optionally substituted 2- to 10-atom heteroaliphatic. In some embodiments, R b is 3- to 6-atom heteroaliphatic. In some embodiments, R b is -(CH 2 ) I-4 -0-CH 3 . In some embodiments, some embodiments, R b is -CH2-O-CH3. In some embodiments, R b is - CH2-CH2-O-CH3. In some embodiments, R b is -CH2-CH2-CH2-O-CH3. In some embodiments, R b is -(CH 2 )I-4-N(CH3).
- R b is optionally substituted -C(0)-C6-i2 aryl
- R b is optionally substituted 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, R b is optionally substituted 4- to 6-membered heterocyclyl comprising 1 to 3 heteroatoms selected from N, O, and S. In some embodiments, R b is optionally substituted 4- membered heterocyclyl comprising 1 heteroatom selected from N, O, and S. In some embodiments, R b is optionally substituted 5-membered heterocyclyl comprising 1 to 3 heteroatoms selected from N, O, and S.
- R b is optionally substituted 6-membered heterocyclyl comprising 1 to 3 heteroatoms selected from N, O, and S.
- R b is 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S optionally substituted with -(CH 2 )o- 4 N(R°)C(0)R°, -C(0)R°, -(O1 ⁇ 4)o- 4 R°, or -(CH 2 )O-40R°.
- R b is or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, R b is pyridinyl.
- Cy is absent or a bivalent moiety selected from 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S, Ci- 6 aliphatic, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more R 1 .
- Cy is optionally substituted with one or more R 1 , i.e., is substituted with 0, 1, 2, 3, or 4 R 1 .
- Cy is unsubstituted (i.e., is substituted with 0 R 1 ).
- Cy is substituted with 1, 2, 3, or 4 R 1 .
- Cy is substituted with 1 R 1 .
- Cy is substituted with 2 R 1 .
- Cy is substituted with 3 R 1 .
- Cy is substituted with 4 R 1 .
- Cy is absent.
- Cy is 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Cy is 4- to 6- membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 4-membered monocyclic heterocyclic comprising 1 heteroatom selected from N, O, P, and S. In some embodiments, Cy is 5-membered monocyclic heterocyclic comprising 1 to 2 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 6- membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, P, and S.
- Cy is azetidinyl, pyrrolidinyl, piperdinyl, or piperazinyl. ⁇ 01091 In some embodiments, Cy is azetidinyl, optionally substituted with one or more R 1 .
- Cy is piperdinyl optionally substituted with one or more R 1 . In some embodiments, Cy is unsubstituted piperdinyl. In some embodiments, Cy is piperdinyl substituted with one or more R 1 .
- Cy is piperazinyl optionally substituted with one or more R 1 . In some embodiments, Cy is unsubstituted piperazinyl. In some embodiments, Cy is piperazinyl substituted with one or more R 1 ..
- Cy is 7- to 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 10- to 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 10- membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 11- membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S.
- Cy is 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 5- or 6- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Cy is 5-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Cy is 6-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- Cy is 7- to 12-membered bicyclic heteroaryl comprising comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 9- to 12-membered bicyclic heteroaryl comprising comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 9-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 10-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S.
- Cy is 11-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. 0115J In some embodiments, Cy is Ci- 6 aliphatic. In some embodiments, Cy is Ci- 6 alkylenyl. [0116
- each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl.
- R 1 is N(R 3 )2.
- R 1 is NH2.
- R 1 is N(H)(CH3).
- R 1 is N(03 ⁇ 4) 2.
- R 1 is OH.
- R 1 is CN.
- R 1 is C(0)NHR 3 . In some embodiments, R 1 is C(0)NH 2. In some embodiments, R 1 is optionally substituted Ci- 6 aliphatic. In some embodiments, R 1 is optionally substituted Ci- 6 alkyl. In some embodiments, R 1 is optionally substituted C1-4 alkyl. In some embodiments, R 1 is optionally substituted Ci alkyl. In some embodiments, N(R 3 )-C(0)-CI- 6 aliphatic. In some embodiments, N(R 3 )-C(0)-CI- 6 alkyl. [Q119J In some embodiments, a substituent on an optionally substituted carbon atom of an optionally substituted R 1 group is selected from: halo, OH, NH2, and oxo.
- Cy is selected from Table Cy:
- L 1 is absent, -NR 3 -Co- 6 alkylenyl-, -O-Co- 6 alkylenyl, Ci- 6 alkylenyl, -C(0)-Co-e alkylenyl, -C(0)0-Co-e alkylenyl, -C(0)-NR 3 -, -NR 3 -C(0)-.
- L 1 is absent, -NR 3 -, -0-, -S-, Ci- 6 alkylenyl, C2-6 alkynylenyl, -NR 3 - Ci-6 alkylenyl, -O-C 1-6 alkylenyl, -C(0)Co-6 alkylenyl, -C(0)NR 3 -, or -C(0)-C(0)-.
- L 1 is -NR 3 -Co- 6 alkylenyl. In some embodiments, -NR 3 -. In some embodiments, L 1 is -NR 3 -C I-6 alkylenyl. In some embodiments, L 1 is -N(03 ⁇ 4)-. In some embodiments, L 1 is -NH-.
- L 1 is -O-Co- 6 alkylenyl. In some embodiments, L 1 is -0-. In some embodiments, L 1 is -O-Ci- 6 alkylenyl. In some embodiments, L 1 is -O-C 1-6 alkyl. In some embodiments, L 1 is -O-C1-3 alkyl. In some embodiments, L 1 is -O-CH2-.
- L 1 is -S-.
- L 1 is Ci- 6 alkylenyl. In some embodiments, L 1 is Ci- 6 alkyl. In some embodiments, L 1 is -CH2-. In some embodiments, L 1 is C2-6 alkynylenyl. In some embodiments,
- L 1 is -C(0)Co- 6 alkyl enyl.
- L 1 is -C(0)0-Co- 6 alkylenyl.
- L 1 is -C(0)-NR 3 -.
- L 1 is -NR 3 -C(0)-.
- L 1 is -C(0)-C(0)-.
- Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R 3 )2, C6-12 aryl, C3-12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q .
- Z is Ci- 6 aliphatic, 2- to 10-membered heteroaliphatic, P(0)(R 3 ) 2 , - C(0)Ci- 6 aliphatic, C(0)N(R 3 )2, C6-12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12- membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q .
- Z is substituted with (R 2 ) q .
- q is 0, 1, 2, 3, or 4. That is, in some embodiments, Z is substituted with 0, 1, 2, 3, or 4 R 2 .
- Z is unsubstituted (i.e., q is 0).
- q is 1.
- q is 2.
- q is 3.
- q is 4.
- Z is Ci- 6 aliphatic. In some embodiments, Z is Ci- 6 alkyl. In some embodiments, Z is C1-3 alkyl. In some embodiments, Z is methyl. In some embodiments, Z is ethyl. jO137 ⁇ In some embodiments, Z is 2- to 10-membered heteroaliphatic. In some embodiments, Z is 2- to 5-membered heteroaliphatic. In some embodiments, Z is 3-membered heteroaliphatic. In some embodiments, Z is -O-CH3, -CH2-O-CH3, -O-CH2-CH2-O-CH2-CH2-O-CH3. In some embodiments, Z is -O-CH 3 . In some embodiments, Z is -CH 2 -O-CH 3 . In some embodiments, Z is -O-CH2-CH2-O-CH2-CH2-O-CH3.
- Z is -C(0)Ci- 6 aliphatic. In some embodiments, Z is -C(0)-Ci- 6 alkyl. In some embodiments, Z is -C(0)-CH3. In some embodiments, Z is -C(0)-(CH3)3.
- Z is -C(0)N(R 3 )2. In some embodiments, Z is -C(0)NH2. In some embodiments, Z is -C(0)N(CH3)2.
- Z is C6-12 aryl. In some embodiments, Z is phenyl substituted with (R 2 ) q . In some embodiments, Z is phenyl substituted with 0, 1, 2, 3, or 4 R 2 . In some embodiments, Z is unsubstituted phenyl. In some embodiments, Z is phenyl substituted with 1, 2, 3, or 4 R 2 . In some embodiments, Z is phenyl substituted with 1 or 2 R 2 . In some emboidments, Z is phenyl substituted with 1 or 2 halo.
- Z is C3-12 monocyclic or polycyclic cycloalkyl. In some embodiments, Z is cyclobutyl. In some embodiments, Z is cyclopentyl. In some embodiments, Z is cyclohexyl. [0142] In some embodiments, Z is 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 4- to 6- membered monocyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 4-membered monocyclic heterocyclyl comprising 1 heteroatom selected from N, O, and S.
- Z is 5-membered monocyclic heterocyclyl comprising 1-2 heteroatoms selected from N, O, and S. In some embodiments, Z is 6-membered monocyclic heterocyclyl comprising 1-4 heteroatoms selected from N, O, and S.
- Z is 10- to 12-membered bicyclic heterocyclyl. In some embodiments, Z is 10- to 12-membered fused bicyclic heterocyclyl. In some embodiments, Z is 10- to 12-membered bridged bicyclic heterocyclyl.
- Z is 10- to 16-membered polycyclic heterocyclyl. In some embodiments, Z is 10-membered polycyclic heterocyclyl. In some embodiments, Z is 11- membered polycyclic heterocyclyl. In some embodiments, Z is 12-membered polycyclic heterocyclyl. In some embodiments, Z is 13-membered polycyclic heterocyclyl. In some embodiments, Z is 14-membered polycyclic heterocyclyl. In some embodiments, Z is 15- membered polycyclic heterocyclyl. In some embodiments, Z is 16-membered polycyclic heterocyclyl. In some embodiments, a polycyclic Z moiety is a spirocyclic and fused tricyclic moiety.
- Z is 9- to 12-membered spirocyclic heterocyclyl. In some embodiments, Z is 9-membered spirocyclic heterocyclyl. In some embodiments, Z is 10- membered spirocyclic heterocyclyl. In some embodiments, Z is 11-membered spirocyclic heterocyclyl. In some embodiments, Z is 12-membered spirocyclic heterocyclyl.
- Z is 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 5- to 6- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 5-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 6-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- Z is 8- to 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 8-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 9-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 10-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 11-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 12-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- each R 2 is independently selected from halo, CN, C(0)0H, and an optionally substituted group selected from Ci- 6 aliphatic, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic.
- R 2 is halo.
- R 2 is selected from fluoro, chloro, bromo, and iodo.
- R 2 is CN.
- R 2 is an optionally substituted Ci- 6 aliphatic.
- R 2 is optionally substituted Ci- 6 alkyl.
- R 2 is optionally substituted Ci-4 alkyl.
- R 2 is optionally substituted C1-2 alkyl. In some embodiments, R 2 is methyl. In some embodiments, R 2 is ethyl. In some embodiments, R 2 is an optionally substituted O-Ci- 6 aliphatic. In some embodiments, R 2 is optionally substituted O-Ci- 6 alkyl. In some embodiments, R 2 is optionally substituted O-C1-4 alkyl. In some embodiments, R 2 is optionally substituted O-C1-2 alkyl. In some embodiments, R 2 is O-methyl. In some embodiments, R 2 is O-ethyl.
- a substituent on an optionally substituted carbon atom of an optionally substituted R 2 group is halo (e.g., bromo, chloro, fluoro, iodo).
- each R 3 is independently selected from H and optionally substituted group selected from Ci- 6 aliphatic, C3-12 cycloalkyl, and 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- R 3 is H.
- R 3 is an optionally substituted Ci- 6 aliphatic. In some embodiments, R 3 is optionally substituted Ci- 6 alkyl. In some embodiments, R 3 is optionally substituted C1-4 alkyl. In some embodiments, R 3 is optionally substituted C1-2 alkyl. In some embodiments, R 3 is methyl. In some embodiments, R 3 is ethyl.
- R 3 is C3-12 cycloalkyl.
- R 3 is 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S
- a substituent on an optionally substituted carbon atom of an optionally substituted R 3 group is halo (e.g., bromo, chloro, fluoro, iodo).
- 01561 In some embodiments, Z is selected from Table Z:
- L 2 is absent, -(NR 3 ) s -S(0)-Co-6 alkylenyl-, -(NR 3 ) s -S(0)2-Co-6 alkylenyl-, -(NR 3 ) s -S(0)(NR 3 )-, -S(0) 2 -NR 3 -, -NR 3 -C I-6 haloalkylenyl, -(NR 3 ) s -P(0)(R 3 )-, -Ci- 6 alkylenyl-S(O)-, -Ci-6 alkylenyl-S(0)2-, -C(0)-(NR 3 ) s -, -(NR 3 ) s -C(0)-, or an optionally sbustituted 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatom
- L 2 is absent.
- L 2 is -(NR 3 ) s -S(0)-Co- 6 alkylenyl. In some embodiments, L 2 is - (NR 3 ) S -S(0)-CH2-. In some embodiments, L 2 is -(NR 3 ) s -S(0)-. In some embodiments, L 2 is - S(O)-. In some embodiments, L 2 is -NR 3 -S(0)-. In some embodiments, L 2 is -NH-S(O)-. In some embodiments, L 2 is -N(CH 3 )-S(0)-.
- L 2 is -(NR 3 ) s -S(0) 2 - Co- 6 alkylenyl.
- L 2 is - (NR 3 ) S -S(0)2-CH2-.
- L 2 is -(NR 3 ) s -S(0) 2 -.
- L 2 is - S(0) 2 -.
- L 2 is -NR 3 -S(0)2-.
- L 2 is -NH-S(0)2-.
- L 2 is -N(CH3)-S(0)2-.
- L 2 is -(NR 3 ) s -S(0)(NR 3 )-. In some embodiments, L 2 is -S(0)(NH)- . In some embodiments, L 2 is -(NR 3 )-S(0)(NR 3 )-. In some embodiments, L 2 is -NH-S(0)(NH)-. In some embodiments, L 2 is -N(CH 3 )-S(0)(NH)-.
- L 2 is -S(0) 2 -NR 3 -. In some embodiments, L 2 is -S(0) 2 -NH-. In some embodiments, L 2 is -S(0) 2 -N(CH 3 )-.
- L 2 is -NR 3 -C I-6 haloalkylenyl.
- L 2 is -(NR 3 ) s -P(0)(R 3 )-. In some embodiments, L 2 is -P(0)(R 3 ). In some embodiments, L 2 is -(NR 3 )-P(0)(R 3 )-. In some embodiments, L 2 is -P(0)(CH 3 )-. In some embodiments, L 2 is -NH-P(0)(CH 3 )-.
- L 2 is -C(0)-(NR 3 ) s -.
- L2 is -C(0)NH-.
- L 2 is -C(O)-.
- L 2 is -N(R 3 )-C(0)-.
- L 2 is -NH-C(O)-.
- L 2 is -Ci- 6 alkylenyl-S(O)-. In some embodiments, L 2 is -CH2- S(O)-.
- L 2 is -Ci-6 alkylenyl-S(0)2-. In some embodiments, L 2 is -CH2- S(0) 2 .
- L 2 is -(NR 3 ) s -C(0)-.
- L 2 is optionally substituted -NR 3 -Ci- 6 alkylenyl. In some embodiments, L 2 is optionally substituted -NR 3 -Ci-3alkylenyl. In some embodiments, L 2 is optionally substituted -NR 3 -C I alkylenyl. In some embodiments, L 2 is -NH-CH2-. In some embodiments, L 2 is -NH-CH(CF3)-.
- L 2 is optionally substituted -Ci- 6 alkylenyl-S(O)-. In some embodiments, L 2 is optionally substituted -C1-3 alkylenyl-S(O)-. In some embodiments, L 2 is optionally substituted -Ci alkylenyl-S(O)-. In some embodiments, L 2 is -CH 2 -S(0)-.
- L 2 is optionally substituted -Ci-6 alkylenyl-S(0)2-. In some embodiments, L 2 is optionally substituted -C1-3 alkylenyl-S(0)2-. In some embodiments, L 2 is optionally substituted -Ci alkylenyl-S(0)2-. In some embodiments, L 2 is -CH2-S(0)2-.
- L 2 is optionally substituted 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- L 2 is a 4- to 6-membered monocyclic heterocyclcyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- L 2 is a 4-membered monocyclic heterocyclcyl comprising 1 heteroatom selected from N, O, and S.
- L 2 is a 5-membered monocyclic heterocyclcyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- L 2 is a 6-membered monocyclic heterocyclcyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- L 2 is optionally substituted 8- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L 2 is optionally substituted 8-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L 2 is optionally substituted 9-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L 2 is optionally substituted 10-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- L 2 is optionally substituted 11-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L 2 is optionally substituted 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- a substituent on an optionally substituted carbon atom of an optionally substituted L 2 group is halo (e.g., bromo, chloro, fluoro, iodo) or Ci- 6 alkyl.
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from
- V is substituted with (R 6 ) m .
- m is
- V is substituted with 0, 1, 2, 3, or 4 R 6 .
- V is unsubstituted (i.e., m is 0).
- m is 1.
- m is 2.
- m is 3.
- m is 4.
- V is Ci- 6 aliphatic. In some embodiments, V is is Ci- 6 alkyl. In some embodiments, V is selected from methyl, ethyl, propyl, butyl, propyl, and hexyl. j0179
- V is 4-membered heterocyclic comprising 1 heteroatom selected from N, O, and S. In some embodiments, V is 5-membered heterocyclic comprising 1 to 4 heteroatom selected from N, O, and S. In some embodiments, V is 6-membered heterocyclic comprising 1 to 4 heteroatom selected from N, O, and S. In some embodiments, V is morpholinyl.
- V is 7- to 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 7-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 8-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 9-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 10-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- V is 11-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- V is 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- In some embodiments, V is C6-12 aryl. In some embodiments, V is phenyl. jj0183J In some embodiments, V is 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 5- to 6- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- V is 5- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 6-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is pyridyl. [0184J In some embodiments, V is 7- to 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 7- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
- V is 8- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 9- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 10- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 11- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is indolyl.
- V is C3-12 cycloalkyl. In some embodiments, V is C3-6 cycloalkyl. In some embodiments, V is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In some embodiments, V is cyclopropyl. In some embodiments, V is cyclobutyl. In some embodiments, V is cyclopentyl. In some embodiments, V is cyclohexyl.
- each R 6 is halo, -CN or an optionally substituted group selected from O-Ci- 6 aliphatic, Ci- 6 aliphatic, and C6-12 aryl. j0187
- R 6 is halo. In some embodiments, R 6 is chloro, fluoro, bromo, or iodo. In some embodiments, R 6 is fluoro. In some embodiments, R 6 is chloro. In some embodiments, R 6 is bromo. In some embodiments, R 6 is iodo. ⁇ 0190J In some embodiments, R 6 is -S(0)-R 5 . In some embodiments, R 6 is -S(0)-CH 3 .
- R 6 is -S(0) 2 -R 5 . In some embodiments, R 6 is -S(0) 2 -Ci- 6 alkyl. In some embodiments, R 6 is -S(0) 2 -CH 3 . In some embodiments, R 6 is -S(0) 2 -CH 2 CH 3 . In some embodiments, R 6 is -S(0)2-CHF2. In some embodiments, R 6 is -S(0)2-CF3.
- R 6 is -S(0) 2 -N(C I-6 alkyl)2. In some embodiments, R 6 is -S(0) 2 - N(CH 3 ) 2.
- R 6 is S(0)(NH)-R 5 . In some embodiments, R 6 is -S(0)(NH)-CH 3 . 0194
- R 6 is -C(0)-R 5 . In some embodiments, R 6 is -C(0)-CH 3 . In some embodiments, R 6 is -C(0)-CF 3 . In some embodiments, R 6 is -C(0)-pyrolidinyl.
- R 6 is -C(0)0-R 5 . In some embodiments, R 6 is -C(0)0-Ci- 6 alkyl. In some embodiments, R 6 is -C(0)0-CH 3 . In some embodiments, R 6 is -C(0)0-CH 2 CH 3 .
- R 6 is -C(0)-NH(R 5 ). In some embodiments, R 6 is -C(0)-NH(CH 3 ). In some embodiments, R 6 is -C(0)-NH-cyclopropyl.
- R 6 is -C(0)-N(R 5 )2. In some embodiments, R 6 is -0(0)-N(03 ⁇ 4)2. [ ( ⁇ 199
- R 6 is optionally substituted O-Ci- 6 alkyl. In some embodiments, R 6 is O-CH 3 . In some embodiments, R 6 is O-CH 2 CH 3 . In some embodiments, R 6 is O-CF 3.
- R 6 is optionally substituted Ci- 6 aliphatic.
- R 6 is C 1-6 alkyl. In some embodiments, R 6 is C 1-4 alkyl. In some embodiments, R 6 is methyl. In some embodiments, R 6 is ethyl. In some embodiments, R 6 is propyl. In some embodiments, R 6 is butyl. In some embodimetns, R 6 is tert-butyl. In some embodiments, R 6 is -CH 2 F. In some embodiments, R 6 is -CHF 2 . In some embodiments, R 6 is CF 3 .
- R 6 is optionally substituted C6-12 aryl.
- a substituent on an optionally substituted carbon atom of an optionally substituted R 6 is halo (e.g., bromo, chloro, fluoro, iodo), Ci- 6 alkyl, OH, or oxo.
- each R 5 is independently selected from Ci-6 alkyl, -N(R 3 ) 2 , - O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R 5 is optionally substituted with one or more substituents selected from halo and OH.
- R 5 is Ci-6 alkyl.
- R 5 is -N(R 3 ) 2 .
- R 5 is -NH 2 .
- R 5 is -NH(C I-6 aliphatic). In some embodiments, R 5 is -NH(03 ⁇ 4). In some embodiments, R 5 is -O-Ci- 6 alkyl. In some embodiments, R 5 is C(0)-Ci- 6 alkyl. In some embodiments, R 5 is P(0)(Ci- 6 alkyl)2. In some embodiments, R 5 is C3-12 cycloalkyl. In some embodiments, R 5 is 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R 5 is optionally substituted with one or more substituents selected from halo and OH. j
- the present application provides compounds having a structure as set forth in Formula II:
- the present application provides compounds having a structure as set forth in Formula II:
- Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci- 6 aliphatic, or C 3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- V is selected from C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein Vis substituted with (R 6 ) m ;
- Y is H or an optionally substituted group selected from Ci- 6 aliphatic, O-Ci- 6 aliphatic, C3-12 cycloalkyl, Ci- 6 alkyl ene-R b , C3-6 cycloalkyl -R b , and 4- to 6- atom heterocyclyl-R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from CH, CR a , or N,. wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci- 6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R 3 )2, -C(0)Ci- 6 aliphatic, C(0)N(R 3 )2, Ce- 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently halo, oxo, or optionally substituted Ci- 6 aliphatic;
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci- 6 alkyl, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic; each R 3 is independently selected from H and optionally substituted Ci- 6 aliphatic; each R 5 is independently selected from Ci- 6 alkyl, -N(C I-6 alkyl )2, -O-Ci
- the present application provides a compound of formula lib: lib or a pharmaceutically acceptable salt thereof, wherein Z, R 6 , Y, and m are defined herein.
- a compound of the present disclosure i.e., a compound of formula I, G, II, IG, and other formulae provided herein
- Table A a compound of formula I, G, II, IG, and other formulae provided herein
- a compound of the present invention e.g., a compound of formula I, G, II, IG, and other formulae provided herein
- Table B a compound of formula I, G, II, IG, and other formulae provided herein
- the present disclosure describes one or more characteristics of certain TRPMLl modulators provided by and/or useful in the practice of the present disclosure.
- the present disclosure provides technologies for assessing one or more relevant characteristics and/or for identifying, selecting, prioritizing, and/or characterizing one or more useful TRPMLl modulators.
- the present disclosure provides certain biological and/or chemical assays (e.g., that facilitate and/or permit assessment of one or more feature(s) of TRMPL1 expression and/or activity, and/or of impact of TRPMLl modulator(s) on such expression and/or activity.
- the present disclosure provides technologies for identifying and/or characterizing one or more aspects of biological pathway(s) (e.g., autophagy pathway(s)) involving TRMPL1, and thus permits identification and/or characterization of additional useful targets within such pathway(s) and/or of modulator(s) that impact such pathway(s) (whether or not targeting TRPMLl itself).
- the present disclosure provides and/or utilizes a composition that comprises and/or delivers a compound as described herein (e.g., together with one or more other components).
- compositions that comprise and/or deliver compounds reported herein (e.g., compounds of Formula I-II), or an intermediate, degradant, or an active metabolite thereof, e.g., when contacted with or otherwise administered to a system or environment e.g., which system or environment may include TRPMLl activity; in some embodiments, administration of such a composition to the system or environment achieves the regulation of autophagy and lysosomal biogenesis as described herein.
- compounds reported herein e.g., compounds of Formula I-II
- an intermediate, degradant, or an active metabolite thereof e.g., when contacted with or otherwise administered to a system or environment e.g., which system or environment may include TRPMLl activity
- administration of such a composition to the system or environment achieves the regulation of autophagy and lysosomal biogenesis as described herein.
- a provided composition as described herein may be a pharmaceutical composition in that it comprises an active agent (e.g., a compound of Formula I-II or an active metabolite thereof) and one or more pharmaceutically acceptable excipients (e.g., one or more pharmaceutically acceptable adjuvants, carriers, excipients, and/or vehicles); in some such embodiments, a provided pharmaceutical composition comprises and/or delivers a compound described herein (e.g., a compound of Formula I- II), or an active metabolite thereof to a relevant system or environment (e.g., to a subject in need thereof) as described herein.
- an active agent e.g., a compound of Formula I-II or an active metabolite thereof
- pharmaceutically acceptable excipients e.g., one or more pharmaceutically acceptable adjuvants, carriers, excipients, and/or vehicles
- a provided pharmaceutical composition comprises and/or delivers a compound described herein (e.g., a compound of Formula I- II),
- a provided composition (e.g., a pharmaceutical composition) includes a compound (e.g., as described herein) in a salt form such as a pharmaceutically acceptable salt form.
- a provided composition may be formulated for administration to a subject (e.g., a human) according to a particular route (e.g., orally, parenterally, by inhalation or nasal spray, topically (e.g., as by powders, ointments, or drops), rectally, buccally, intravaginally, intraperitoneally, intracistemally or via an implanted reservoir, etc).
- a particular route e.g., orally, parenterally, by inhalation or nasal spray, topically (e.g., as by powders, ointments, or drops), rectally, buccally, intravaginally, intraperitoneally, intracistemally or via an implanted reservoir, etc).
- a provided composition (e.g., a pharmaceutical composition) comprises or delivers an amount of a compound as described herein (or an active metabolite thereof) that is effective to measurably modulate TRPMLl activity, and/or to induce autophagy and/or lysosomal biogenesis in a biological sample or in a subject, when administered in accordance with a therapeutic regimen.
- a provided compound or composition is formulated for administration to a patient in need of such composition.
- a compound or composition as described herein may be administered in a dose amount and/or by a route of administration effective for treating or lessening the severity of a disease or disorder described herein.
- a composition e.g., a pharmaceutical composition
- a composition as described herein may be formulated in unit form (e.g., which may offer ease of administration and/or uniformity of dosage).
- an appropriate dosage level may be within a range of about 0.01 mg/kg to about 50 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
- the present disclosure provides technologies for modulating TRPML1 activty.
- the present application relates to a method of modulating TRPMLl activty in a subject comprising administering to the subject a provided compound, or a composition as described herein.
- compositions as described herein may be useful in medicine (e.g., in the treatment of one or more diseases, disorders, or conditions).
- targeting e.g., agonizing
- TRPMLl may be a particularly effective strategy for modulating (e.g., enhancing) autophagy and/or lysosomal biogenesis.
- a disease, disorder or condition that may be treated as described herein may be or comprise a disease, disorder or condition associated with TRPMLl deficiency.
- the present disclosure identifies that TRMPL1 deficiency is associated with particular diseases, disorders or conditions, some or all of which may be treated in accordance with the present disclosure.
- treatment provided herein involves administration of a TRMPLl modulator as described herein in an amount effective to modulate TRMPLl activity in a lysosome and/or increase autophagy.
- a disease, disorder, or condition amenable to treatment as described herein is or comprises a liver disease, a neurodegenerative disorder, cancer, or a heart disease.
- a disease, disorder, or condition amenable to treatment as described herein is or comprises a lysosomal storage disease, such as Niemann-Pick C (NPC) disease, Gaucher disease, and Pompe disease.
- NPC Niemann-Pick C
- a disease, disorder, or condition amenable to treatment as described herein is an age-related common neurodegenerative disease, such as Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease.
- a disease, disorder, or condition amenable to treatment as described herein is a type IV Mucolipidosis (ML4) neurodegenerative lysosomal storage disease caused by mutations in TRPML1.
- ML4 Mucolipidosis
- a disease, disorder, or condition amenable to treatment as described herein is related to reactive oxygen species or oxidative stress.
- the present application relates to use of a compound and/or composition described herein for use in the manufacture of a medicament e.g., for modulation of TRPMLl activity.
- the present application relates to use of a compound and/or composition described herein for use in the manufacture of a medicament for treating a disease, disorder or condition, e.g., through modulation of TRPMLl activity; in some emebodiments, the disease, disorder, or condition is a liver disease, a neurodegenerative disorder, cancer, or a heart disease.
- the disease, disorder, or condition is a muscular disease, a liver disease, a metabolic disease, an atherosclerotic disease, an inflammatory bowel disease, an atherosclerotic disease, a neurodegenerative disease, an oncological disease, or an infectious disease.
- the disease, disorder, or condition is a muscular disease.
- the muscular disease is a muscular dystrophy.
- the muscular dystrophy is Duchenne muscular dystrophy.
- the disease, disorder, or condition is an infectious disease.
- the infectious disease is an infection of Heliobacter pylori or Mycobacterium tuberculosis. ⁇ 0245J In some embodiments, the infectious disease is tuberculosis.
- A is wherein A is substituted with 0, 1, 2, 3 or 4 R a ;
- Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci- 6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- L 1 is absent, -NR 3 -, -0-, -S-, Ci- 6 alkylenyl, C2-6 alkynylenyl, -NR 3 -C I-6 alkyl enyl,-0-Ci- 6 alkylenyl,
- L 2 is absent, -(NR 3 ) s -S(0)-Co-6 alkylenyl-, -(NR 3 ) s -S(0)2-Co-6 alkylenyl-, -(NR 3 ) s -S(0)(NR 3 )-, - S(0) 2 -NR 3 -, -NR 3 -CI-6 haloalkylenyl, -(NR 3 ) s -P(0)(R 3 )-, -Ci- 6 alkylenyl-S(O)-, -Ci- 6 alkylenyl-S(0)2-, -C(0)-(NR 3 ) s -, -(NR 3 ) s -C(0)-, or an optionally substituted 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S;
- V is selected from Ci- 6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R 6 ) m ;
- Y is H or an optionally substituted group selected from Ci- 6 aliphatic, O-Ci- 6 aliphatic, C3-12 cycloalkyl, Ci- 6 alkyl ene-R b , C3-6 cycloalkyl -R b , and 4- to 6- atom heterocyclyl-R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from CH, CR a , or N,. wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci- 6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R 3 )2, -C(0)Ci- 6 aliphatic, C(0)N(R 3 )2, Ce- 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently halo, oxo, or optionally substituted Ci- 6 aliphatic;
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci- 6 alkyl, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic; each R 3 is independently selected from H and optionally substituted Ci- 6 aliphatic; each R 5 is independently selected from Ci- 6 alkyl, -N(C I-6 alkyl )2, -O-Ci
- R b or 4- to 6- atom heterocyclyl-R b .
- R b is C6-12 aryl or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
- Cy is 4- to 6- membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, and S. 16. The compound of any one of the preceding embodiments, wherein Cy is piperdinyl or piperzinyl.
- R 2 is halo.
- Z is selected from halo (e g., bromo, chloro, fluoro, iodo), -C3 ⁇ 4, -CH2CH3, -O-CH3, -CH2-O-CH3, -O-CH2-CH2-O-CH2- CH2-O-CH3,
- V is C6-12 aryl or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. 33.
- V is C6-12 aryl.
- Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci- 6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R 1 ;
- V is selected from C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising
- Y is H or an optionally substituted group selected from Ci- 6 aliphatic, O-Ci- 6 aliphatic, C3-12 cycloalkyl, Ci- 6 alkyl ene-R b , C3-6 cycloalkyl -R b , and 4- to 6- atom heterocyclyl -R b ; each of X 1 , X 2 , X 3 , and X 4 is independently selected from CH, CR a , or N,. wherein X 1 , X 2 , X 3 , and X 4 are selected from C and N when bound to Y;
- Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R 3 )2, -C(0)Ci-6 aliphatic, C(0)N(R 3 )2, Ce- 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R 2 ) q ; each R a is independently halo, oxo, or optionally substituted Ci- 6 aliphatic;
- R b is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R 1 is independently selected from N(R 3 )2, OH, CN, C(0)NHR 3 , and an optionally substituted group selected from Ci- 6 aliphatic andN(R 3 )-C(0)-Ci- 6 alkyl; each R 2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci- 6 alkyl, C(0)Ci- 6 aliphatic, and O-Ci- 6 aliphatic; each R 3 is independently selected from H and optionally substituted Ci- 6 aliphatic; each R 5 is independently selected from Ci- 6 alkyl, -N(C I-6 alkyl )2, -O-Ci
- a pharmaceutical composition comprising a compound of any one of the preceding embodiments and a pharmaceutically acceptable carrier, adjuvant, or vehicle.
- a method of modulating TRPMLl comprising administering to a subject a compound of any one of the preceding embodiments.
- a method of treating a disease, disorder, or condition in a subject comprising administering a compound of any one of the preceding embodiments.
- lysosomal storage disorder is selected from Niemann-Pick C disease, Gaucher disease, and Pompe disease.
- the disease, disorder, or condition is age-related common neurodegenerative disease.
- invention 57 The method of embodiment 57, wherein the disease, disorder, or condition is selected from Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease.
- Step-1 Synthesis of l-(2,3-dimethoxyphenyl)ethan-l-ol: 0249J
- THF 2,3-dimethoxybenzaldehyde
- Step-2 Synthesis of l-(2,3-dimethoxyphenyl)ethan-l-one:
- Step-1 Synthesis of 1 -methyl- lH-indole-4-carbaldehyde :
- Tetrakis(triphenylphosphine)palladium(0) (0.1 eq) was added to then reaction under an argon atmosphere and purged the reaction mixture with argon for 15 min. The tube was then fitted with a screw cap and the reaction was stirred at 90 °C for 3 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture cooled to room temperature, filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with water and extracted ethyl acetate. The combine organic layers were washed with water and brine, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure.
- Step-2 General procedure for synthesis of l-Boc-4-arylpiperidine derivatives:
- Step-1 Synthesis of tert-butyl (E)-4-((hydroxyimino)methyl)piperidine-l-carboxylate:
- Step-2 Synthesis of tert-butyl (Z)-4-(chloro(hydroxyimino)methyl)piperidine-l-carboxylate:
- Step-3 Synthesis of tert-butyl 4-(5-(trimethylsilyl)isoxazol-3-yl)piperidine-l-carboxylate: j0261
- tert-butyl (Z)-4-(chloro(hy droxyimino)m ethyl )piperi dine- 1- carboxylate 1.7 g, 6.4 mmol, 1 eq
- ethynyltrimethylsilane 3.14 g, 32 mmol, 5 eq
- triethyl amine (1.24 g, 9.6 mmol, 1.5 eq) were added at 0 °C.
- Step-4 Synthesis of tert-butyl 4-(isoxazol-3-yl)piperidine-l-carboxylate: f 262J
- tert-butyl 4-(5-(trimethylsilyl)isoxazol-3-yl)piperidine-l- carboxylate 1. g, 4.3 mmol, 1 eq
- potassium bifluoride 33 mg, 0.43 mmol, 0.1 eq
- Step 1 Synthesis of 3-formyl-2-hydroxybenzonitrile: f 264J
- 2-hydroxybenzonitrile (1 g, 8.39 mmol, 1 eq) in acetic acid (10 mL)
- hexamethylenetetramine (1.8 g, 12.59 mmol, 1.5 eq) was added.
- the reaction was stirred at 120 °C for 2 h.
- the progress of the reaction was monitored by TLC.
- the reaction mixture was cooled to room temperature and concentrated under reduced pressure.
- the residue was dissolved in ethyl acetate and washed with water.
- the organic layer was dried over anhydrous Na2S04, filtered and concentrated under reduced pressure.
- Step 1 0267 A pyrex tube was charged with a solution of 4-bromobenzaldehyde (1.86 g, 10.06 mmol, 1.2 eq), phenylboronic acid (1 g, 8.38 mmol, 1 eq) and K3PO4 (4.44 g, 20.9 mmol, 2.5 eq) in water (3 mL) and 1,4-dioxane (6 mL).
- the tube was sealed with a septum and the reaction mixture was purged with argon via an argon balloon for 15 min.
- PdCl2(dppf) (183 mg, 0.25 mmol, 0.03 eq) was then added to the reaction under an argon atmosphere and the purging with argon was continued for 5 min.
- the tube was then sealed with a screw cap and the reaction was heated at 100 °C for 12 h. The progress of the reaction was monitored by TLC.
- the reaction was cooled to room temperature and the reaction mixture was filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with ethyl acetate and washed with water and brine.
- Step-1 Synthesis of 4-chloro-3-methoxypyridine: f0269
- CMBP cyanomethyltributylphosphorane
- Step-2 Synthesis of 4-chloro-5-methoxynicotinaldehyde:
- Step-3 Synthesis of 4,5-dimethoxynicotinaldehyde:
- Step-1 Synthesis of tert-butyl 4-(4-chlorophenyl)-3,6-dihydropyridine-l(2H)-carboxylate
- Step-2 Synthesis of tert-butyl 4-(4-chlorophenyl)piperidine-l-carboxylate
- Step-3 Synthesis of 4-(4-chlorophenyl)piperidine f0275J
- DCM DCM
- trifluoroacetic acid 5 mL
- the reaction was warmed to room temperature and stirred for 2 h.
- the progress of the reaction was monitored by TLC.
- the reaction mixture was concentrated under reduced pressure.
- the residue was dissolved in saturated aqueous NaHCCh solution and extracted with DCM.
- the combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure.
- the crude product was purified by column chromatography on silica gel to afford the titled compound 4-(4-chlorophenyl)piperidine (600 g, 91.6%).
- LCMS 196.10 [M+H] + .
- Step-1 Procedure for synthesis of 1 -(tert-butyl) 3-methyl pyrrolidine- 1 ,3-dicarboxylate 0276J
- l-(tert-butoxycarbonyl)pyrrolidine-3-carboxylic acid 5 g, 23.23 mmol, 1 eq
- cesium carbonate 15.14 g, 46.46 mmol, 2 eq
- iodomethane 4.9 g, 34.85 mmol, 1.5 eq
- Step-2 Procedure for synthesis of tert-butyl 3-(hydroxymethyl)pyrrolidine- 1 -carboxylate :
- Step-3 Procedure for synthesis of tert-butyl 3-(((methylsulfonyl)oxy)methyl)pyrrolidine-l- carboxylate:
- Example Cl Synthetic scheme for synthesis of l'-((2,3-dimethoxyphenyl)(l-phenethyl-lH- tetrazol-5-yl)methyl)-6-fluoro-l-methylspiro[indoline-3,4'-piperidine] (C-1):
- Step 3 Synthesis of tetrazole compounds
- Tert-butylamine (0.18 g, 2.46 mmol) was added in one portion and the resulting mixture was stirred for 12 h at room temperature. After, water (10 mL) was added and organic layer was separated. Aqueous phase was extracted with DCM (10 mL x 2) and organic layers were combined, washed with 10% NaHSCri aq solution (20 mL), saturated NaHCCh aq solution (20 mL) and brine (20 mL), dried over sodium sulfate, filtered and evaporated to afford tert-butyl 4-(tert-butylcarbamoyl)-4-methylpiperidine-l- carboxylate (0.7 g, 1.16 mmol, 50% purity, 57.1% yield) that was used in the next step without further purification.
- Example C5 Synthesis of l- ⁇ l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l, 2,3,4- tetrazol-5-yl]methyl]piperidin-4-yl ⁇ -2,2-dimethylpropan-l-one, C-141
- Step 1 Step 2 C-141 ⁇ 0299[ Step 1. Synthesis of 4-pi valoylpiperi din- 1-ium chloride
- tert-butyl 4-pivaloylpiperidine-l-carboxylate (0.2 g, 0.742 mmol) was dissolved in 1M MeOH*HCl (10 mL). The reaction mixture was stirred for lh, then evaporated under reduced pressure and ether (10 mL) was added to precipitate the product. The solid was filtered-off, washed with ether (10 mL) and dried on air to give 2,2-dimethyl-l-(piperidin-4-yl)propan-l-one hydrochloride (0.145 g, 0.708 mmol, 90% purity, 85.5% yield) that was used in next step without further purification.
- Step 2 Synthesis of l- ⁇ l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl]methyl]piperidin-4-yl ⁇ -2,2-dimethylpropan- 1 -one j0302
- reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC (deionized water/HPLC -grade methanol) that afforded l- ⁇ l-[(2,3-dimethoxyphenyl)[l-(2- phenyl ethyl)- 1H- 1 ,2,3 ,4-tetrazol-5-yl]methyl]piperidin-4-yl ⁇ -2,2-dimethyl propan- 1 -one, C- 141.
- HPLC deionized water/HPLC -grade methanol
- Step 1 Step 2 C-140 ⁇ 0303! Step 1.
- Example Cl Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl]methyl]-4-(l-methoxycyclohexanecarbonyl)piperazine, C-128: 0307J Step 1. Synthesis of tert-butyl 4-(l-methoxycyclohexanecarbonyl)piperazine-l- carboxylate
- Step 1 Synthesis of tert-butyl 4- ⁇ 2-azabicyclo[2.1.1]hexane-2-carbonyl ⁇ piperazine-l- carboxylate
- Step 2 Synthesis of 2-(piperazine-l-carbonyl)-2-azabicyclo[2.1.1]hexane ⁇ 03161 tert-butyl 4- ⁇ 2-azabicyclo[2.1.1]hexane-2-carbonyl ⁇ piperazine-l-carboxylate (1.2 g, 4.06 mmol) was dissolved in 1M MeOH*HCl (10 mL). The reaction mixture was stirred for lh, evaporated and ether (15 mL) was added to precipitate the product. White solid was filtered-off, washed with ether (15 mL) and dried on air.
- reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC (deionized water/HPLC -grade acetonitrile) that afforded l-[(2,3-dimethoxyphenyl)[l-(2- phenylethyl)-lH-l,2,3,4-tetrazol-5-yl]methyl]-4-(l-methoxycyclobutanecarbonyl)piperazine C- 160.
- HPLC deionized water/HPLC -grade acetonitrile
- Example Cll Synthesis of ((3r,5r,7r)-adamantan-l-yl)(4-((2,3-dimethoxyphenyl)(l- phenethyl-lH-tetrazol-5-yl)methyl)piperazin-l-yl)methanone, C-173
- Step-1 Procedure for the synthesis of tert-butyl 4-((2,3-dimethoxyphenyl)(l-phenethyl- lH-tetrazol-5-yl)methyl)piperazine-l-carboxylate 11.4:
- Step-2 Procedure for the synthesis of l-((2,3-dimethoxyphenyl)(l-phenethyl-lH-tetrazol- 5-yl)methyl)piperazine 11.5:
- Example 02 Synthesis of l-(4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)methyl)-lH-tetrazol-l-yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one, C-158 and 1- (4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-2H-tetrazol-2- yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one, C-156:
- Step-1 & 2 Procedure for the synthesis of 1 -((2,3-dimethoxyphenyl)( 1 //-tetrazol-5- yl)methyl)-4-phenylpiperidine 12.5:
- Step-3 Procedure for the synthesis of l-(4-(2-(5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl)methyl)- lH-tetrazol- 1 -yl)ethyl)piperazin- 1 -yl)-2,2-dimethylpropan- 1 -one, and l-(4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-2H-tetrazol-2- yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one: 0345j Method A: To a stirred solution of l-((2,3-dimethoxyphenyl)(lH-tetrazol-5-yl)methyl)-4- phenylpiperidine 12.5 (450 mg, 1.18 mmol, 1 eq) and 2-
- reaction mixture was cooled to room temperature, diluted with water and extracted with 10% methanol in DCM. The combined organic layers were dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure to dryness.
- Example C13 synthesis of A-((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)methyl)-l//-tetrazol-l-yl)methyl)cyclohexyl)-/V-methylpivalamide, C-177 0350J Step-1: Procedure for the synthesis of ((lr,4r)-4-((tert- butoxycarbonyl)amino)cyclohexyl)methyl methanesulfonate (13.2):
- Step-6 Procedure for the synthesis of /er/-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl (methyl )-l //-tetrazol- 1 -yl (methyl )cyclohexyl)carbamate (13.9):
- Step-7 Procedure for the synthesis of /er/-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperi din- l-yl)m ethyl)- l/7-tetrazol-l-yl)methyl)cyclohexyl)(methyl)carbamate (10):
- reaction mixture was allowed to attain ambient temperature and stirred for 3 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the titled fe/7-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl )m ethyl)- 1/7-tetrazol- 1 -yl)methyl)cyclohexyl)(methyl)carbamate 13.10 (0.08 g, crude) as an off-white solid.
- Step-8 Procedure for the synthesis of (lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperi din- l-yl)m ethyl)- li7-tetrazol-l-yl)methyl)-/V-m ethyl cy cl ohexan-1 -amine (13.11): [03651 To a stirred solution of te/7-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl )m ethyl)- 177-tetrazol- 1 -yl)methyl)cyclohexyl)(methyl)carbamate 13.10 (0.08 g, 0.132 mmol, 1 eq) in DCM (2.0 mL) was
- reaction mixture was warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with DCM and basified with saturated aqueous NaHCCb solution and separated layers. The combined organic layers were dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness to afford (lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)m ethyl)- liT-tetrazol-l-yl)methyl)-/V-m ethyl cy cl ohexan-1 -amine 13.11 (0.06 g, crude) as off white solid. This compound was used in the next step without further purification.
- Example C14 synthesis of l-(4-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)- l//-tetrazol-l-yl)piperidin-l-yl)-2,2-dimethylpropan-l-one C-148 and l-(4-(5-((2,3- dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-2 -tetrazol-2-yl)piperidin-l-yl)-2,2- dimethylpropan-l-one, C-150:
- Step-1 & 2 Procedure for the synthesis of l-((2,3-dimethoxyphenyl)(l-(piperidin-4-yl)- lH-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 & l-((2,3-dimethoxyphenyl)(2-(piperidin-4- yl)-2H-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 A: 0370J To a stirred solution of l-((2,3-dimethoxyphenyl)(lH-tetrazol-5-yl)methyl)-4- phenylpiperidine 14.1 (3.0 g, 7.9 mmol, 1 eq) and tert-butyl 4-bromopiperidine-l-carboxylate 14.2 (2.5 g, 9.4 mmol, 1.2 eq) in DMF (30 mL) was added K2CO3 (2.18 g,
- Step-3 Procedure for the synthesis of l-(4-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin- 1 -yl)m ethyl)- l//-tetrazol- 1 -yl)piperidin- 1 -yl)-2,2-dimethylpropan- 1 -one and 1 -(4-(5-((2,3- dimethoxyphenyl)(4-phenylpiperidin- l -yl)methyl)-2//-tetrazol-2-yl)piperidin-l -yl)-2,2- dimethylpropan- 1 -one :
- reaction mixture was stirred at RT for 16 h. After completion of reaction, the reaction mixture was quenched with cold water and extracted with DCM. The combined organic layers were washed with water, dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure to dryness.
- Example C15 Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl] methyl]-4-(2-methoxyethyl)-4-methylpiperidine, C- 198 :
- Step 4 Step 5 Step 6 c'198 0375J Step 1. Synthesis of tert-butyl 4-[methoxy(methyl)carbamoyl]-4-methylpiperidine-l- carboxylate
- HeLa wt or HeLa TRPML1 KO cells were plated at 2700 cells/well into black- walled, 384-well Cell carrier Ultra tissue culture treated plates in complete media and incubated overnight. The next day, cells are treated for 2 hrs with compounds and incubated at 37 °C. Cells were then fixed for 30 minutes at room temperature in 4% final PFA and washed five times with 90 pL PBS. PBS is aspirated from the wells and the cells are blocked with 7.5 pL blocking buffer (1:1 PBS/Odyssey block buffer containing 0.1% triton x-100 and 1% goat serum).
- Table 1 shows the activity of selected compounds of this invention in TFEB assays.
- the compound numbers correspond to the compound numbers above in Table A.
- Compounds having an activity designated as “++++” provided an AC50 of ⁇ 2.00 mM; compounds having an activity designated as “+++” provided an AC50 of 2.01-8.00 mM; compounds having an activity designated as “++” provided an AC50 of 8.01-9.99 mM; and compounds having an activity designated as "+” provided an AC50 of > 10.00 mM.
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Abstract
The present invention provides compounds, pharmaceutically acceptable compositions thereof, and methods of using the same.
Description
TRPML MODULATORS
CROSS-REFERENCE TO RELATED APPLICATIONS
[00(111 The present application claims priority to U.S. Provisional Application No. 63/119,907, filed December 1, 2020; U.S. Provisional Application No. 62/950,818, filed December 19, 2019; and U.S. Provisional Application No. 62/950,807, filed December 19, 2019, each of which is incorporated herein in its entirety.
BACKGROUND
[0002) Transient Receptor Potential Mucolipin-1 (also known as TRPML1 or MLl) is a Ca2+ channel in the lysosome that regulates certain aspects of lysosome trafficking, including autophagy. See Wang, et al., PNAS, E1373-E1381 (March 2, 2015). In particular, TRPML1 is an inwardly rectifying current channel that transports cations from the lumen of the lysosome to the cytosol. See Di Paolda, et ah, Cell Calcium 69:112-121 (2018). Release of Ca2+ from the lysosome via TRPMLl modulates transcription factor EB activity. See Medina, et ah, Nat. Cell. Biol., 17(3):288-299 (2015).
SUMMARY
[0003) It has recently been discovered that upregulation of autophagy is beneficial to patients suffering from a number of diseases and disorders. For example, it has been reported that inducing autophagy promotes clearance of hepatotoxic alpha- 1 -anti -trypsin (ATZ) in the liver. See Pastore, et ah, EMBO Mol. Med. 5(3): 397-412 (Mar. 2013). Moreover, autophagy was recently found to be useful in the treatment of neurodegenerative disorders, cancer, and heart disease. See Pierzynowska, et ah, Metab. Brain Dis., 33(4); 989-1008 (2018) (discussing neurodegenerative disorders); Nelson & Shacka, Curr. Pathobiol. Rep., 1(4): 239-245 (2013) (discussing cancer); Sciaretta, et ah, Annual Review of Physiology, 80:1-26 (2018) (discussing heart disease); Maiuri & Kroemer, Cell Death & Differentiation, 26: 680-689 (2019) (discussing therapeutic applications of autophagy, generally).
{O0O4J The present disclosure provides, among other things, technologies for regulating (e.g., up- regulating) autophagy. For example, in some embodiments, the present disclosure demonstrates effectiveness of certain approaches to TRPMLl modulation (e.g., TRPMLl agonism) in enhancing
autophagy. Thus, among other things, the present disclosure demonstrates that targeting TRPMLl as described herein can enhance autophagy. j0005f The present disclosure also provides certrain technologies for use in medicine, and in particular for treating certain diseases, disorders or conditions and/or for identifying, characterizing, and/or manufacturing certain agents and/or compositions or that comprise or deliver them that are useful in treating such diseases, disorders or conditions. j|0006J In some embodiments, the present disclosure demonstrates that modulating (e.g., agonizing) TRPLM1 and/or otherwise enhancing autophagy is useful in the treatment of certain diseases, disorders or conditions.
{OO07J It is, therefore, desirable to identify methods and modes of promoting autophagy. Given TRPMLL s role in autophagy, described herein are TRPMLl modulators useful for promoting autophagy and/or treating certain diseases, disorders, or conditions.
[0008) In particular, the present application provides technologies useful for modulating
TRPMLl. jOO09| In some embodiments, the present application provides compounds having a structure as set forth in Formula I:
Z-L^Cy-A-L^V
I or a pharmaceutically acceptable salt thereof, wherein
Cy is absent or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of
L1 is absent, -NR3-, -0-, -S-, Ci-6 alkylenyl, C2-6 alkynylenyl, -NR3-CI-6 alkylenyl, -O-Ci-6 alkylenyl, -C(0)Co-6 alkylenyl; -C(0)NR3-, or -C(0)-C(0)-;
L2 is absent, -(NR3)s-S(0)-Co-6 alkylenyl-, -(NR3)s-S(0)2-Co-6 alkylenyl-, -(NR3)s-S(0)(NR3)-, -S(0)2-NR3-, -NR3-CI-6 haloalkylenyl, -(NR3)s-P(0)(R3)-, -Ci-e alkylenyl-S(O)-, -Ci-6 alkylenyl-S(0)2-, -C(0)-(NR3)s-, -(NR3)s-C(0)-, or an optionally substituted 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is H or an optionally substituted group selected from Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, Ci-6 alkyl ene-Rb, C3-6 cycloalkyl -Rb, and 4- to 6- atom heterocyclyl -Rb; each of X1, X2, X3, and X4 is independently selected from CH, CRa, or N, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-membered heteroaliphatic, P(0)(R3)2, -C(0)Ci-6 aliphatic, C(0)N(R3)2, C6-12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently halo, oxo, or optionally substituted Ci-6 aliphatic;
Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and optionally substituted Ci-6 aliphatic;
each R5 is independently selected from Ci-6 alkyl, -N(R3)2, -O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH; each R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), - C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1. jOOlOJ In some embodiments, the present application provides compounds having a structure as set forth in Formula II:
II or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
V is selected from C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising
1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein Vis substituted with (R6)m;
Y is H or an optionally substituted group selected from Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, Ci-6 alkyl ene-Rb, C3-6 cycloalkyl -Rb, and 4- to 6- atom heterocyclyl -Rb; each of X1, X2, X3, and X4 is independently selected from CH, CRa, or N,. wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R3)2, -C(0)Ci-6 aliphatic, C(0)N(R3)2, Cr,. 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently halo, oxo, or optionally substituted Ci-6 aliphatic;
Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 alkyl, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and optionally substituted Ci-6 aliphatic; each R5 is independently selected from Ci-6 alkyl, -N(CI-6 alkyl )2, -O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH; each R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), - C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-12 aryl; m is 0, 1, 2, 3, or 4; and q is 0, 1, 2, 3, or 4.
{00111 In some embodiments, the present application provides compounds having a structure as set forth in Formula G :
r or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
L1 is absent, -NR3-Co-6 alkylenyl-, -O-Co-6 alkylenyl, Ci-6 alkyl enyl, -C(0)-Co-6 alkylenyl, - C(0)0-Co-6 alkylenyl, -
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is Ci-6 aliphatic, -S(0)2-Ci-6 aliphatic, -O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of Rb; each of X1, X2, X3, and X4 is independently selected from C, CRa, S, O, orN, as valency permits, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3. 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently hydrogen, halo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl;
Rb is an optionally substituted group selected from -NR3-C(0)-CI-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12- membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic and N(R3)-C(0)-Ci-6 alkyl;
each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and an optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S; each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1. j0012J In some embodiments, the present application provides compounds having a structure as set forth in Formula IF :
II’ or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is H, Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Y is optionally substituted with one or more instances of Rb; each of X1, X2, X3, and X4 is independently selected from C, CRa, S, O, orN, as valency permits, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3- 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently hydrogen, halo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl;
Rb is an optionally substituted group selected from -NR3-C(0)-C 1-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic and N(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and an optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S; each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1.
DEFINITIONS
|00!3| Agonist. As will be understood by those skilled in the art, the term “agonist” generally refers to an agent whose presence or level correlates with elevated level or activity of a target, as compared with that observed absent the agent (or with the agent at a different level). In some embodiments, an agonist is one whose presence or level correlates with a target level or activity that is comparable to or greater than a particular reference level or activity (e.g., that observed under appropriate reference conditions, such as presence of a known agonist, e.g., a positive control). In some embodiments, an agonist may be a direct agonist in that it exerts its influence directly on (e.g., interacts directly with) the target; in some embodiments, an agonist may be an indirect agonist in that it exerts its influence indirectly (e.g., by acting on, such as interacting with, a regulator of the target, or with some other component or entity.
[0014] Aliphatic: The term “aliphatic” refers to a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as “cycloaliphatic”), that has a single point or more than one points of attachment to the rest of the molecule. Unless otherwise specified, aliphatic groups contain 1-12 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-6 aliphatic carbon atoms (e.g., Ci-6). In some embodiments, aliphatic groups contain 1-5 aliphatic carbon atoms (e.g., Ci- 5). In other embodiments, aliphatic groups contain 1-4 aliphatic carbon atoms (e.g., C1-4). In still other embodiments, aliphatic groups contain 1-3 aliphatic carbon atoms (e.g., C1-3), and in yet other embodiments, aliphatic groups contain 1-2 aliphatic carbon atoms (e.g., C1-2). In some embodiments, “cycloaliphatic” refers to a monocyclic C3-8 hydrocarbon or a bicyclic C7-10 hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point or more than one points of attachment to the rest of the molecule. Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkylenyl, alkenyl, alkenylenyl, alkynyl, or alkynylenyl groups and hybrids thereof. A preferred aliphatic group is Ci-6 alkyl. In some embodiments, aliphatic is multivalent (i.e., has multiple points of attachment to the rest of the molecule). In some
embodiments, aliphatic is bivalent (i.e., has two points of attachment to the rest of the molecule). An example bivalent aliphatic group can be referred to as “alkylenyl”. jOOlSJ Alkyl: The term “alkyl”, used alone or as part of a larger moiety, refers to a saturated, optionally substituted straight or branched chain or cyclic hydrocarbon group having (unless otherwise specified) 1-12, 1-10, 1-8, 1-6, 1-4, 1-3, or 1-2 carbon atoms (e.g., Ci-12, Ci-10, Ci-8, Ci- 6, Ci-4, Ci-3, or C1-2). Exemplary alkyl groups include methyl, ethyl, propyl, butyl, pentyl, hexyl, and heptyl. The term “cycloalkyl” refers to an optionally substituted saturated ring system of about 3 to about 10 ring carbon atoms. Exemplary monocyclic cycloalkyl rings include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.
{0016| Alkylene: The term "alkyl ene" and “alkylenyl” are used interchangeably and refers to a bivalent alkyl group. In some embodiments, “alkylene” is a bivalent straight or branched alkyl group. In some embodiments, an "alkylene chain" is a polymethylene group, i.e., -(CtfcV, wherein n is a positive integer, e.g., from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, or from 2 to 3. An optionally substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms is optionally replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group and also include those described in the specification herein. It will be appreciated that two substituents of the alkylene group may be taken together to form a ring system. In certain embodiments, two substituents can be taken together to form a 3- to 7-membered ring. The substituents can be on the same or different atoms. The term “haloalkylenyl” refers to an straight-chain or branched alkylenyl group substituted by one or more halogen atoms (e.g., one, two, three or four halo, such as fluoro, iodo, bromo, or chi or o).
{0017J Alkenyl: The term “alkenyl”, used alone or as part of a larger moiety, refers to an optionally substituted straight or branched chain or cyclic hydrocarbon group having at least one double bond and having (unless otherwise specified) 2-12, 2-10, 2-8, 2-6, 2-4, or 2-3 carbon atoms(e.g., C2-12, C2-10, C2-8, C2-6, C2-4, or C2-3). Exemplary alkenyl groups include ethenyl, propenyl, butenyl, pentenyl, hexenyl, and heptenyl. The term “cycloalkenyl” refers to an optionally substituted non-aromatic monocyclic or multicyclic ring system containing at least one carbon-carbon double bond and having about 3 to about 10 carbon atoms. Exemplary monocyclic cycloalkenyl rings include cyclopentenyl, cyclohexenyl, and cycloheptenyl.
{00181 Alkenylene: The term "alkenyl ene" and “alkenyl enyl” are used interchangeably and refers to a bivalent alkenyl group. In some embodiments, “alkenylene” is a bivalent straight or branched alkenyl group.
{0019! Alkynyl: The term “alkynyl”, used alone or as part of a larger moiety, refers to an optionally substituted straight or branched chain hydrocarbon group having at least one triple bond and having (unless otherwise specified) 2-12, 2-10, 2-8, 2-6, 2-4, or 2-3 carbon atoms (e.g., C2-12, C2-10, C2-8, C2-6, C2-4, or C2-3). Exemplary alkynyl groups include ethynyl, propynyl, butynyl, pentynyl, hexynyl, and heptynyl.
[0020 j Alkynylene : The term "alkynylene" and “alkynylenyl” are used interchangeably and refers to a bivalent alkynyl group. In some embodiments, “alkynylene” is a bivalent straight or branched alkynyl group.
[002TJ Analog: As used herein, the term “analog” refers to a substance that shares one or more particular structural features, elements, components, or moieties with a reference substance. Typically, an “analog” shows significant structural similarity with the reference substance, for example sharing a core or consensus structure, but also differs in certain discrete ways. In some embodiments, an analog is a substance that can be generated from the reference substance, e.g., by chemical manipulation of the reference substance. In some embodiments, an analog is a substance that can be generated through performance of a synthetic process substantially similar to (e.g., sharing a plurality of steps with) one that generates the reference substance. In some embodiments, an analog is or can be generated through performance of a synthetic process different from that used to generate the reference substance.
[0O22J Antagonist. As will be understood by those skilled in the art, the term “antagonist” generally refers to an agent whose presence or level correlates with decreased level or activity of a target, as compared with that observed absent the agent (or with the agent at a different level). In some embodiments, an antagonist is one whose presence or level correlates with a target level or activity that is comparable to or less than a particular reference level or activity (e.g., that observed under appropriate reference conditions, such as presence of a known antagonist, e.g., a positive control). In some embodiments, an antagonist may be a direct antagonist in that it exerts its influence directly on (e.g., interacts directly with) the target; in some embodiments, an antagonist may be an indirect antagonist in that it exerts its influence indirectly (e.g., by acting on, such as interacting with, a regulator of the target, or with some other component or entity.
{0O23J Aryl: The term “aryl” refers to monocyclic and bicyclic ring systems having a total of five to fourteen ring members (e.g., C5-14), wherein at least one ring in the system is aromatic and wherein each ring in the system contains three to seven ring members. In some embodiments, an “aryl” group contains between six and twelve total ring members (e.g., C6-12). The term “aryl” may be used interchangeably with the term “aryl ring”. In certain embodiments of the present invention, “aryl” refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, anthracyl and the like, which may bear one or more substituents. Unless otherwise specified, “aryl” groups are hydrocarbons. In some embodiments, an “aryl” ring system is an aromatic ring (e.g., phenyl) that is fused to a non-aromatic ring (e.g., cycloalkyl). Examples of aryl rings include that are fused include
, , .
[0024) Associated: Two events or entities are “associated” with one another, as that term is used herein, if the presence, level and/or form of one is correlated with that of the other. For example, a particular entity (e.g., polypeptide, genetic signature, metabolite, microbe, etc) is considered to be associated with a particular disease, disorder, or condition, if its presence, level and/or form correlates with incidence of and/or susceptibility to the disease, disorder, or condition (e.g., across a relevant population). In some embodiments, two or more entities are physically “associated” with one another if they interact, directly or indirectly, so that they are and/or remain in physical proximity with one another. In some embodiments, two or more entities that are physically associated with one another are covalently linked to one another; in some embodiments, two or more entities that are physically associated with one another are not covalently linked to one another but are non-covalently associated, for example by means of hydrogen bonds, van der Waals interaction, hydrophobic interactions, magnetism, and combinations thereof.
|()Q25| Biological sample: As used herein, the term “biological sample” typically refers to a sample obtained or derived from a biological source (e.g., a tissue or organism or cell culture) of interest, as described herein. In some embodiments, a source of interest comprises an organism, such as an animal or human. In some embodiments, a biological sample is or comprises biological tissue or fluid. In some embodiments, a biological sample may be or comprise bone marrow; blood; blood cells; ascites; tissue or fine needle biopsy samples; cell-containing body fluids; free floating nucleic acids; sputum; saliva; urine; cerebrospinal fluid, peritoneal fluid; pleural fluid; feces; lymph; gynecological fluids; skin swabs; vaginal swabs; oral swabs; nasal swabs; washings
or lavages such as a ductal lavages or broncheoalveolar lavages; aspirates; scrapings; bone marrow specimens; tissue biopsy specimens; surgical specimens; feces, other body fluids, secretions, and/or excretions; and/or cells therefrom, etc. In some embodiments, a biological sample is or comprises cells obtained from an individual. In some embodiments, obtained cells are or include cells from an individual from whom the sample is obtained. In some embodiments, a sample is a “primary sample” obtained directly from a source of interest by any appropriate means. For example, in some embodiments, a primary biological sample is obtained by methods selected from the group consisting of biopsy (e.g., fine needle aspiration or tissue biopsy), surgery, collection of body fluid (e.g., blood, lymph, feces etc.), etc. In some embodiments, as will be clear from context, the term “sample” refers to a preparation that is obtained by processing (e.g., by removing one or more components of and/or by adding one or more agents to) a primary sample. For example, filtering using a semi-permeable membrane. Such a “processed sample” may comprise, for example, nucleic acids or proteins extracted from a sample or obtained by subjecting a primary sample to techniques such as amplification or reverse transcription of mRNA, isolation and/or purification of certain components, etc. 0026] Biomarker. The term “biomarker” is used herein, consistent with its use in the art, to refer to a to an entity (or form thereof) whose presence, or level, correlates with a particular biological event or state of interest, so that it is considered to be a “marker” of that event or state. To give but a few examples, in some embodiments, a biomarker may be or comprise a marker for a particular disease state, or for likelihood that a particular disease, disorder or condition may develop, occur, or reoccur. In some embodiments, a biomarker may be or comprise a marker for a particular disease or therapeutic outcome, or likelihood thereof. Thus, in some embodiments, a biomarker is predictive, in some embodiments, a biomarker is prognostic, in some embodiments, a biomarker is diagnostic, of the relevant biological event or state of interest.
[0027] Carrier: As used herein, the term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which a composition is administered. In some exemplary embodiments, carriers can include sterile liquids, such as, for example, water and oils, including oils of petroleum, animal, vegetable or synthetic origin, such as, for example, peanut oil, soybean oil, mineral oil, sesame oil and the like. In some embodiments, carriers are or include one or more solid components.
[0028] Combination therapy: As used herein, the term “combination therapy” refers to those situations in which a subject is simultaneously exposed to two or more therapeutic regimens (e.g.,
two or more therapeutic agents or modality(ies)). In some embodiments, the two or more regimens may be administered simultaneously; in some embodiments, such regimens may be administered sequentially (e.g., all “doses” of a first regimen are administered prior to administration of any doses of a second regimen); in some embodiments, such agents are administered in overlapping dosing regimens. In some embodiments, “administration” of combination therapy may involve administration of one or more agent(s) or modality(ies) to a subject receiving the other agent(s) or modality(ies) in the combination. For clarity, combination therapy does not require that individual agents be administered together in a single composition (or even necessarily at the same time), although in some embodiments, two or more agents, or active moieties thereof, may be administered together in a combination composition, or even in a combination compound (e.g., as part of a single chemical complex or covalent entity).
[0029J Comparable. As used herein, the term “comparable” refers to two or more agents, entities, situations, sets of conditions, etc., that may not be identical to one another but that are sufficiently similar to permit comparison therebetween so that one skilled in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed. In some embodiments, comparable sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small number of varied features. Those of ordinary skill in the art will understand, in context, what degree of identity is required in any given circumstance for two or more such agents, entities, situations, sets of conditions, etc. to be considered comparable. For example, those of ordinary skill in the art will appreciate that sets of circumstances, individuals, or populations are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under or with different sets of circumstances, individuals, or populations are caused by or indicative of the variation in those features that are varied. 003OJ Composition: Those skilled in the art will appreciate that the term “composition” may be used to refer to a discrete physical entity that comprises one or more specified components. In general, unless otherwise specified, a composition may be of any form - e.g., gas, gel, liquid, solid, etc.
[003 Tj Dosage form or unit dosage form: Those skilled in the art will appreciate that the term “dosage form” may be used to refer to a physically discrete unit of an active agent (e.g., a
therapeutic or diagnostic agent) for administration to a subject. Typically, each such unit contains a predetermined quantity of active agent. In some embodiments, such quantity is a unit dosage amount (or a whole fraction thereof) appropriate for administration in accordance with a dosing regimen that has been determined to correlate with a desired or beneficial outcome when administered to a relevant population (/. ., with a therapeutic dosing regimen). Those of ordinary skill in the art appreciate that the total amount of a therapeutic composition or agent administered to a particular subject is determined by one or more attending physicians and may involve administration of multiple dosage forms.
[0032 j Dosing regimen or therapeutic regimen: Those skilled in the art will appreciate that the terms “dosing regimen” and “therapeutic regimen” may be used to refer to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time. In some embodiments, a given therapeutic agent has a recommended dosing regimen, which may involve one or more doses. In some embodiments, a dosing regimen comprises a plurality of doses each of which is separated in time from other doses. In some embodiments, individual doses are separated from one another by a time period of the same length; in some embodiments, a dosing regimen comprises a plurality of doses and at least two different time periods separating individual doses. In some embodiments, all doses within a dosing regimen are of the same unit dose amount. In some embodiments, different doses within a dosing regimen are of different amounts. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount different from the first dose amount. In some embodiments, a dosing regimen comprises a first dose in a first dose amount, followed by one or more additional doses in a second dose amount same as the first dose amount. In some embodiments, a dosing regimen is correlated with a desired or beneficial outcome when administered across a relevant population (/. ., is a therapeutic dosing regimen). [0033] Engineered: In general, the term “engineered” refers to the aspect of having been manipulated by the hand of man. For example, in some embodiments, a small molecule may be considered to be engineered if its structure and/or production is designed and/or implemented by the hand ot man. Analogously, in some embodiments, a polynucleotide may be considered to be “engineered” when two or more sequences, that are not linked together in that order in nature, are manipulated by the hand of man to be directly linked to one another in the engineered polynucleotide. For example, in some embodiments of the present invention, an engineered
polynucleotide comprises a regulatory sequence that is found in nature in operative association with a first coding sequence but not in operative association with a second coding sequence, is linked by the hand of man so that it is operatively associated with the second coding sequence. Comparably, a cell or organism is considered to be “engineered” if it has been manipulated so that its genetic information is altered ( e.g ., new genetic material not previously present has been introduced, for example by transformation, mating, somatic hybridization, transfection, transduction, or other mechanism, or previously present genetic material is altered or removed, for example by substitution or deletion mutation, or by mating protocols). As is common practice and is understood by those in the art, expression products of an engineered polynucleotide, and/or progency of an engineered polynucleotide or cell are typically still referred to as “engineered” even though the actual manipulation was performed on a prior entity. 0034f Excipient: As used herein, the term “excipient” refers to a non-therapeutic agent that may be included in a pharmaceutical composition, for example, to provide or contribute to a desired consistency or stabilizing effect. Suitable pharmaceutical excipients include, for example, starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like.
[0035 j Heteroaliphatic. The term “heteroaliphatic” or “heteroaliphatic group”, as used herein, denotes an optionally substituted hydrocarbon moiety having, in addition to carbon atoms, from one to five heteroatoms, that may be straight-chain ( i.e unbranched), branched, or cyclic (“heterocyclic”) and may be completely saturated or may contain one or more units of unsaturation, but which is not aromatic. The term “heteroatom” refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen. The term “nitrogen” also includes a substituted nitrogen. Unless otherwise specified, heteroaliphatic groups contain 1-10 carbon atoms wherein 1-3 carbon atoms are optionally and independently replaced with heteroatoms selected from oxygen, nitrogen, and sulfur. In some embodiments, heteroaliphatic groups contain 1-4 carbon atoms, wherein 1-2 carbon atoms are optionally and independently replaced with heteroatoms selected from oxygen, nitrogen, and sulfur. In yet other embodiments, heteroaliphatic groups contain 1-3 carbon atoms, wherein 1 carbon atom is optionally and independently replaced with a heteroatom selected from oxygen, nitrogen, and sulfur. Suitable heteroaliphatic groups include, but are not limited to, linear or
branched, heteroalkyl, heteroalkenyl, and heteroalkynyl groups. For example, a 1- to 10 atom heteroaliphatic group includes the following exemplary groups: -O-CH3, -CH2-O-CH3, -O-CH2- CH2-O-CH2-CH2-O-CH3, and the like.
[0036) Heteroaryl: The terms “heteroaryl” and “heteroar-”, used alone or as part of a larger moiety, e.g., “heteroaralkyl”, or “heteroaralkoxy”, refer to monocyclic or bicyclic ring groups having 5 to 12 ring atoms (e.g., 5- to 6- membered monocyclic heteroaryl or 9- to 12-membered bicyclic heteroaryl); having 6, 10, or 14 p-electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms. The term “heteroatom” refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quatemized form of a basic nitrogen. Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, pteridinyl, imidazo[l,2-a]pyrimidinyl, imidazo[l,2-a]pyridyl, imidazo[4,5-b]pyridyl, imidazo[4,5-c]pyridyl, pyrrolopyridyl, pyrrolopyrazinyl, thienopyrimidinyl, triazolopyridyl, and benzoisoxazolyl. The terms “heteroaryl” and “heteroar-”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring (i.e., a bicyclic heteroaryl ring having 1 to 3 heteroatoms). Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzotriazolyl, benzothiazolyl, benzothiadiazolyl, benzoxazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, AH quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, pyrido[2,3-b]-l,4-oxazin-3(4H)-one, and benzoisoxazolyl. A heteroaryl group may be mono- or bicyclic. The term “heteroaryl” may be used interchangeably with the terms “heteroaryl ring”, “heteroaryl group”, or “heteroaromatic”, any of which terms include rings that are optionally substituted. The term “heteroaralkyl” refers to an alkyl group substituted by a heteroaryl, wherein the alkyl and heteroaryl portions independently are optionally substituted.
|(MB7| Heteroatom: The term “heteroatom” as used herein refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quatemized form of a basic nitrogen. 0038J Heterocycle: As used herein, the terms “heterocycle”, “heterocyclyl”, “heterocyclic radical”, and “heterocyclic ring” are used interchangeably and refer to a stable 3- to 8-membered
monocyclic, a 7- to 12-membered bicyclic, or a 10- to 16-membered polycyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, such as one to four, heteroatoms, as defined above. When used in reference to a ring atom of a heterocycle, the term "nitrogen" includes a substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0-3 heteroatoms selected from oxygen, sulfur or nitrogen, the nitrogen may be N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or NR+ (as in N-substituted pyrrolidinyl). A heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted. Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, azetidinyl, oxetanyl, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, piperidinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and thiamorpholinyl. A heterocyclyl group may be mono-, bi-, tri-, or polycyclic, preferably mono-, bi-, or tricyclic, more preferably mono- or bicyclic. The term “heterocyclylalkyl” refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted. A bicyclic heterocyclic ring also includes groups in which the heterocyclic ring is fused to one or more aryl rings. Exemplary bicyclic heterocyclic groups include indolinyl, isoindolinyl, benzodioxolyl, 1,3- dihydroisobenzofuranyl, 2,3-dihydrobenzofuranyl, tetrahydroquinolinyl,
A bicyclic heterocyclic ring can also be a spirocyclic ring system (e.g., 7- to 11-membered spirocyclic fused heterocyclic ring having, in addition to carbon atoms, one or more heteroatoms as defined above (e.g., one, two, three or four heteroatoms)). A bicyclic heterocyclic ring can also be a bridged ring system (e.g., 7- to 11-membered bridged heterocyclic ring having one, two, or three bridging atoms. Exemplary bridged ring systems include
/y\ and . Exemplary polycyclic heterocyclic ring systems that are spirocyclic include
|0039| Oral: The phrases “oral administration” and “administered orally” as used herein have their art-understood meaning referring to administration by mouth of a compound or composition. 004OJ Parenteral: The phrases “parenteral administration” and “administered parenterally” as used herein have their art-understood meaning referring to modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intramuscular, intra-arterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticulare, subcapsular, subarachnoid, intraspinal, and intrasternal injection and infusion. fOMIj Partially unsaturated: As used herein, the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond between ring atoms. The term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic (e.g., aryl or heteroaryl) moieties, as herein defined.
[0042J Patient or subject: As used herein, the term “patient” or “subject” refers to any organism to which a provided composition is or may be administered, e.g., for experimental, diagnostic, prophylactic, cosmetic, and/or therapeutic purposes. Typical patients or subjects include animals (e.g, mammals such as mice, rats, rabbits, non-human primates, and/or humans). In some embodiments, a patient is a human. In some embodiments, a patient or a subject is suffering from or susceptible to one or more disorders or conditions. In some embodiments, a patient or subject displays one or more symptoms of a disorder or condition. In some embodiments, a patient or subject has been diagnosed with one or more disorders or conditions. In some embodiments, a
patient or a subject is receiving or has received certain therapy to diagnose and/or to treat a disease, disorder, or condition.
[0043j Pharmaceutical composition: As used herein, the term “pharmaceutical composition” refers to an active agent, formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, the active agent is present in unit dose amount appropriate for administration in a therapeutic or dosing regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin, lungs, or oral cavity; intravaginally or intrarectally, for example, as a pessary, cream, or foam; sublingually; ocularly; transdermally; or nasally, pulmonary, and to other mucosal surfaces. j0944{ Pharmaceutically acceptable: As used herein, the phrase “pharmaceutically acceptable” refers to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
[0045} Pharmaceutically acceptable carrier: As used herein, the term “pharmaceutically acceptable carrier” means a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, or solvent encapsulating material, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically-acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt;
gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, com oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer’s solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and/or polyanhydrides; and other non toxic compatible substances employed in pharmaceutical formulations.
[004 j Pharmaceutically acceptable salt: The term “pharmaceutically acceptable salt”, as used herein, refers to salts of such compounds that are appropriate for use in pharmaceutical contexts, i.e., salts which 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 well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences , 66: 1-19 (1977). In some embodiments, pharmaceutically acceptable salts include, but are not limited to, nontoxic acid addition salts, which are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. In some embodiments, pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, di gluconate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2- hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, / oluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. In some embodiments, pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations
formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate. j0047f Polycyclic: As used herein, the term “polycyclic” refers to a saturated or unsaturated ring system having two or more rings (for example, heterocyclyl rings, heteroaryl rings, cycloalkyl rings, or aryl rings), having between 7 and 20 atoms, in which one or more carbon atoms are common to two adjacent rings. The rings in a polycyclic ring system may be fused (i.e., bicyclic or tricyclic), spirocyclic, or a combination thereof. Exemplary polyclic systems include
[0048J Prevent or prevention: As used herein, the terms “prevent” or “prevention”, when used in connection with the occurrence of a disease, disorder, and/or condition, refer to reducing the risk of developing the disease, disorder and/or condition and/or to delaying onset of one or more characteristics or symptoms of the disease, disorder or condition. Prevention may be considered complete when onset of a disease, disorder or condition has been delayed for a predefined period of time. j0ft49| Reference: As used herein describes a standard or control relative to which a comparison is performed. For example, in some embodiments, an agent, animal, individual, population, sample, sequence or value of interest is compared with a reference or control agent, animal, individual, population, sample, sequence or value. In some embodiments, a reference or control is tested and/or determined substantially simultaneously with the testing or determination of interest. In some embodiments, a reference or control is a historical reference or control, optionally
embodied in a tangible medium. Typically, as would be understood by those skilled in the art, a reference or control is determined or characterized under comparable conditions or circumstances to those under assessment. Those skilled in the art will appreciate when sufficient similarities are present to justify reliance on and/or comparison to a particular possible reference or control. {0050} Sample: As used herein, the term “sample” typically refers to an aliquot of material obtained or derived from a source of interest. In some embodiments, a source of interest is a biological or environmental source. In some embodiments, a source of interest may be or comprise a cell, tissue, or organism, such as a microbe, a plant, or an animal (e.g., a human). In some embodiments, a source of interest is or comprises biological tissue or fluid. In some embodiments, a source of interest may be or comprise a preparation generated in a production run. In some embodiments, a sample is a “primary sample” obtained directly from a source of interest by any appropriate means. In some embodiments, as will be clear from context, the term “sample” refers to a preparation that is obtained by processing (e.g., by removing one or more components of and/or by adding one or more agents to) a primary sample.
{0051} Specific: The term “specific”, when used herein with reference to an agent having an activity, is understood by those skilled in the art to mean that the agent discriminates between potential target entities or states. For example, in some embodiments, an agent is said to bind “specifically” to its target if it binds preferentially with that target in the presence of one or more competing alternative targets. In many embodiments, specific interaction is dependent upon the presence of a particular structural feature of the target entity (e.g., an epitope, a cleft, a binding site). It is to be understood that specificity need not be absolute. In some embodiments, specificity may be evaluated relative to that of the binding agent for one or more other potential target entities (e.g., competitors). In some embodiments, specificity is evaluated relative to that of a reference specific binding agent. In some embodiments, specificity is evaluated relative to that of a reference non-specific binding agent. In some embodiments, the agent or entity does not detectably bind to the competing alternative target under conditions of binding to its target entity. In some embodiments, a binding agent binds with higher on-rate, lower off-rate, increased affinity, decreased dissociation, and/or increased stability to its target entity as compared with the competing alternative target(s).
[0052 j Substituted or optionally substituted: As described herein, compounds of the invention may contain “optionally substituted” moieties. In general, the term “substituted,” whether
preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. “Substituted” applies to one or more hydrogens that are either explicit or implicit from the structure (e.g.,
refers to at least
Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds. The term “stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes provided herein. Groups described as being “substituted” preferably have between 1 and 4 substituents, more preferably 1 or 2 substituents. Groups described as being “optionally substituted” may be unsubstituted or be “substituted” as described above.
|0QS3j Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; -(CH2)o-4R°; -(CH2)o-40R°; -0(CH2)o-4R°, -O-
(CH2)O-4C(0)OR°; -(CH2)O-4CH(OR°)2; -(CH2)O-4SR°; -(CH2)o-4Ph, which may be substituted with R°; -(CH2)o-40(CH2)o-iPh which may be substituted with R°; -CH=CHPh, which may be substituted with R°; -(CH2)o-40(CH2)o-i-pyridyl which may be substituted with R°; -NO2; -CN; -N3; -(CH2)O-4N(R°)2; -(CH2)O-4N(R°)C(0)R°; -N(R°)C(S)R°; -(CH2)O-
4N(R0)C(0)NR°2; -N(R°)C(S)NR°2; -(CH2)O-4N(R°)C(0)OR°;
N(R°)N(R°)C(0)R°; -N(R°)N(R0)C(0)NR0 2; -N(R°)N(R°)C(0)0R°; -(CH2)o-4C(0)R°; C(S)R°; -(CH2)O-4C(0)OR°; -(CH2)O-4C (O) SR° ; -(CH2)o-4C(0)OSiR0 3; -(CH2)o-40C(0)R°; -
OC(0)(CH2)O-4 SR° ; -(CH2)o-4 SC (0)R° ; -(CH2)o-4C(0)NR°2; -C(S)NR°2; -C(S)SR°; -
SC(S)SR°, -(CH2)O-40C(0)NR°2; -C(0)N(0R°)R°; -C(0)C(0)R°; -C(0)CH2C(0)R°; -
C(NOR°)R°; -(CH2)O-4SSR°; -(CH2)O-4S(0)2R°; -(CH2)0- S(O)2ORo; -(CH2)0- OS(O)2Ro; - S(0)2NR°2; -(CH2)O-4S(0)R°; -N(R°)S(0)2NR°2; -N(R°)S(0)2R°; -N(OR°)R°; -C(NH)NR°2; - P(0)2R°; -P(0)R°2; -0P(0)R°2; -0P(0)(0R°)2; SiR°3; -(C1-4 straight or branched alkylene)0- N(R°)2; or —(Ci— 4 straight or branched alkylene)C(0)0-N(R°)2, wherein each R° may be substituted as defined below and is independently hydrogen, Ci-6 aliphatic, -CH2Ph, -0(CH2)o- iPh, -CH2-(5- to 6-membered heteroaryl ring), or a 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R°, taken together with their intervening atom(s), form a 3- to 12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below. 0054J Suitable monovalent substituents on R° (or the ring formed by taking two independent occurrences of R° together with their intervening atoms), are independently halogen, -(CH2)o-2R*, -(haloR*), -(CH2)O-2OH, -(CH2)O-2OR*, -(CH2)O-2CH(OR*)2, -0(haloR*), -CN, -N3, -(CH2)0- 2C(0)R·, -(CH2)O-2C(0)OH, -(CH2)O-2C(0)OR·, -(CH2)O-2SR*, -(CH2)O-2SH, -(CH2)O-2NH2, - (CH2)O-2NHR·, -(CH2)O-2NR*2, -N02, -SiR*3, -OSiR*3, -C(0)SR* -(Ci_4 straight or branched alkylene)C(0)OR*, or -SSR* wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently selected from Ci-4 aliphatic, - CH2Ph, -0(CH2)o-iPh, or a 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R° include =0 and =S. fOOSSJ Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: =0 (“oxo”), =S, =NNR%, =NNHC(0)R*, =NNHC(0)0R*, =NNHS(0)2R*, =NR*, =NOR*, -0(C(R* 2))2-30-, or -S(C(R* 2))2-3S-, wherein each independent occurrence of R* is selected from hydrogen, Ci-6 aliphatic which may be substituted as defined below, or an unsubstituted 5- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: -0(CR* 2)2-30-, wherein each independent occurrence of R* is selected from hydrogen, Ci-6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered
saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. 0056j Suitable substituents on the aliphatic group of R* include halogen, R*, -(haloR*), -OH, - OR*, -0(haloR*), -CN, -C(0)0H, -C(0)0R*, -NH2, NHR*, -NR*2, or -N02, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Ci-4 aliphatic, -CH2Ph, -0(CH2)o-iPh, or a 5- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[0057J Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include -R†, -NR† 2, -C(0)R†, -C(0)0R†, -C(0)C(0)R†,
C(0)CH2C(0)R†, -S(0)2R†, -S(0)2NR† 2, -C(S)NR† 2, -C(NH)NR† 2, or -N(R†)S(0)2R†; wherein each R: is independently hydrogen, Ci-6 aliphatic which may be substituted as defined below, unsubstituted -OPh, or an unsubstituted 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R†, taken together with their intervening atom(s) form an unsubstituted 3- to 12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
{0058} Suitable substituents on the aliphatic group of R: are independently halogen, - R*, -(haloR*), -OH, -OR*, -0(haloR*), -CN, -C(0)OH, -C(0)OR*, -NH2, -NHR*, -NR*2, or -N02, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Ci-4 aliphatic, -CH2Ph, -0(CH2)o-iPh, or a 3- to 6- membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. j|0059| Small molecule: As used herein, the term “small molecule” means a low molecular weight organic and/or inorganic compound. In general, a “small molecule” is a molecule that is less than about 5 kilodaltons (kD) in size. In some embodiments, a small molecule is less than about 4 kD, 3 kD, about 2 kD, or about 1 kD. In some embodiments, the small molecule is less than about 800 daltons (D), about 600 D, about 500 D, about 400 D, about 300 D, about 200 D, or about 100 D. In some embodiments, a small molecule is less than about 2000 g/mol, less than about 1500 g/mol,
less than about 1000 g/mol, less than about 800 g/mol, or less than about 500 g/mol. In some embodiments, a small molecule is not a polymer.
[0060J In some embodiments, a small molecule does not include a polymeric moiety. In some embodiments, a small molecule is not and/or does not comprise a protein or polypeptide (e.g., is not an oligopeptide or peptide). In some embodiments, a small molecule is not and/or does not comprise a polynucleotide (e.g., is not an oligonucleotide). In some embodiments, a small molecule is not and/or does not comprise a polysaccharide; for example, in some embodiments, a small molecule is not a glycoprotein, proteoglycan, glycolipid, etc.). In some embodiments, a small molecule is not a lipid.
{00611 In some embodiments, a small molecule is a modulating agent (e.g., is an inhibiting agent or an activating agent). In some embodiments, a small molecule is biologically active. In some embodiments, a small molecule is detectable (e.g., comprises at least one detectable moiety). In some embodiments, a small molecule is a therapeutic agent.
[0062] Those of ordinary skill in the art, reading the present disclosure, will appreciate that certain small molecule compounds described herein may be provided and/or utilized in any of a variety of forms such as, for example, crystal forms (e.g., polymorphs, solvates, etc), salt forms, protected forms, pro-drug forms, ester forms, isomeric forms (e.g., optical and/or structural isomers), isotopic forms, etc.
{00631 Those of ordinary skill in the art will appreciate that certain small molecule compounds have structures that can exist in one or more steroisomeric forms. In some embodiments, such a small molecule may be utilized in accordance with the present disclosure in the form of an individual enantiomer, diastereomer or geometric isomer, or may be in the form of a mixture of stereoisomers; in some embodiments, such a small molecule may be utilized in accordance with the present disclosure in a racemic mixture form.
{6Q64J Those of skill in the art will appreciate that certain small molecule compounds have structures that can exist in one or more tautomeric forms. In some embodiments, such a small molecule may be utilized in accoradance with the present disclosure in the form of an individual tautomer, or in a form that interconverts between tautomeric forms.
{6065J Those of skill in the art will appreciate that certain small molecule compounds have structures that permit isotopic substitution (e.g., 2H or ¾ for H;, UC, 13C or 14C for 12C; , 13N or 15N for 14N; 170 or 180 for 160; 36C1 for XXC; 18F for XXF; 1311 for XXXI; etc). In some
embodiments, such a small molecule may be utilized in accordance with the present disclosure in one or more isotopically modified forms, or mixtures thereof.
[0066] In some embodiments, reference to a particular small molecule compound may relate to a specific form of that compound. In some embodiments, a particular small molecule compound may be provided and/or utilized in a salt form (e.g., in an acid-addition or base-addition salt form, depending on the compound); in some such embodiments, the salt form may be a pharmaceutically acceptable salt form. O <i7| In some embodiments, where a small molecule compound is one that exists or is found in nature, that compound may be provided and/or utilized in accordance in the present disclosure in a form different from that in which it exists or is found in nature. Those of ordinary skill in the art will appreciate that, in some embodiments, a preparation of a particular small molecule compound that contains an absolute or relative amount of the compound, or of a particular form thereof, that is different from the absolute or relative (with respect to another component of the preparation including, for example, another form of the compound) amount of the compound or form that is present in a reference preparation of interest (e.g., in a primary sample from a source of interest such as a biological or environmental source) is distinct from the compound as it exists in the reference preparation or source. Thus, in some embodiments, for example, a preparation of a single stereoisomer of a small molecule compound may be considered to be a different form of the compound than a racemic mixture of the compound; a particular salt of a small molecule compound may be considered to be a different form from another salt form of the compound; a preparation that contains only a form of the compound that contains one conformational isomer ((Z) or (E)) of a double bond may be considered to be a different form of the compound from one that contains the other conformational isomer ((E) or (Z)) of the double bond; a preparation in which one or more atoms is a different isotope than is present in a reference preparation may be considered to be a different form; etc.
[0068] Those skilled in the art will appreciate that a bond designated as ~ in a small molecule structure, as used herein, refers to a bond that, in some embodiments, is a single (e.g., saturated) bond, and in some embodiments, is a double (e.g., unsaturated) bond. For example, the following structure:
is intended to encompass both
an fO069 j Those skilled in the art will further appreciate that, in small molecule structures, the symbol/vw , as used herein, refers to a point of attachment between two atoms. j0070f Therapeutic agent: As used herein, the phrase “therapeutic agent” in general refers to any agent that elicits a desired pharmacological effect when administered to an organism. In some embodiments, an agent is considered to be a therapeutic agent if it demonstrates a statistically significant effect across an appropriate population. In some embodiments, the appropriate population may be a population of model organisms. In some embodiments, an appropriate population may be defined by various criteria, such as a certain age group, gender, genetic background, preexisting clinical conditions, etc. In some embodiments, a therapeutic agent is a substance that can be used to alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition. In some embodiments, a “therapeutic agent” is an agent that has been or is required to be approved by a government agency before it can be marketed for administration to humans. In some embodiments, a “therapeutic agent” is an agent for which a medical prescription is required for administration to humans. j|007tj Treat: As used herein, the terms “treat,” “treatment,” or “treating” refer to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and/or reduce incidence of one or more symptoms or features of a disease, disorder, and/or condition. Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and/or condition. In some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and/or condition, for example, for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and/or condition.
DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS
TRPML1 andAutophagy
|()Q72j Autophagy is a mechanism of the cell that degrades cytoplasmic material and organelles. There are multiple types of autophagy: (1) macroautophagy (generally referred to as autophagy);
(2) microautophagy; and (3) chaperone-mediateed autophagy. See Eskelinen & Saftig, Biochimica et Biophysica Acta - Mol. Cell Res., 1793(4):664-673 (2009). In macroautophagy, the autophagosome engulfs waste materials in the cytoplasm and fuses to the lysosome, where materials are delivered for degradation. The lysosome is as a subcellular organelle containing more than 50 soluble acid hydrolases useful for digesting cellular components. Fusion of the lysosome to the autophagosome is activated, in part, by release of ions through ion channels in the membrane of the lysome, including Ca2+. See Cao, etal, J. Bio. Chem., 292(20)8424-8435 (2017). [0073] Transient Receptor Potential Mucolipin-1 (also known as TRPMLl or MLl) is a Ca2+ channel in the lysosome that regulates autophagy. See Wang, etal. , PNAS, E1373-E1381 (March 2, 2015). In particular, TRPMLl is an inwardly rectifying current channel that transports cations from the lumen of the lysosome to the cytosol. See Di Paolda, et al, Cell Calcium 69:112-121 (2018). Release of Ca2+ from the lysosome via TRPMLl modulates transcription factor EB activity via local calcineurin activation, which ultimately induces autophagy and lysosomal biogenesis. See Medina, et al., Nat. Cell. Biol., 17(3):288-299 (2015).
[0074] It has recently been discovered that upregulation of autophagy is beneficial to patients suffering from a number of diseases and disorders. For example, it has been reported that inducing autophagy promotes clearance of hepatotoxic alpha- 1 -anti -trypsin (ATZ) in the liver. See Pastore, et al., EMBO Mol. Med. 5(3): 397-412 (Mar. 2013). Moreover, autophagy was recently found to be useful in the treatment of neurodegenerative disorders, cancer, and heart disease. See Pierzynowska, et al, Metab. Brain Dis., 33(4); 989-1008 (2018) (discussing neurodegenerative disorders); Nelson & Shacka, Curr. Pathobiol. Rep., 1(4): 239-245 (2013) (discussing cancer); Sciaretta, et al, Annual Review of Physiology, 80:1-26 (2018) (discussing heart disease); Maiuri & Kroemer, Cell Death & Differentiation, 26: 680-689 (2019) (discussing therapeutic applications of autophagy, generally). It is, therefore, desirable to identify methods and modes of promoting autophagy. Given TRPMLl ’ s role in autophagy, described herein are TRPMLl modulators useful for promoting autophagy and/or treating certain diseases, disorders, or conditions.
[0075] The present disclosure provides the insight that TRMPLl may represent a particularly desirable target that, among other things, may permit modulation (e.g., enhancement) of autophagy in certain contexts.
TRPML1 Modulators
Structure
[00761 In some embodiments, the present disclosure provides and/or utilizes TRMPL1 modulators that are small molecule compounds having a chemical structure as indicated below in Formula I:
Z-ΐ qg-A-ΐ n
I or a pharmaceutically acceptable salt thereof, wherein
Cy is absent or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of
L1 is absent, -NR3-, -0-, -S-, Ci-6 alkylenyl, C2-6 alkynylenyl, -NR3-CI-6 alkyl enyl,-0-Ci-6 alkylenyl, -C(0)Co-6 alkylenyl; -C(0)NR3-, or -C(0)-C(0)-;
L2 is absent, -(NR3)s-S(0)-Co-6 alkylenyl-, -(NR3)s-S(0)2-Co-6 alkylenyl-, -(NR3)s-S(0)(NR3)-, -S(0)2-NR3-, -NR3-CI-6 haloalkylenyl, -(NR3)s-P(0)(R3)-, -Ci-6 alkylenyl-S(O)-,
-Ci-6 alkylenyl-S(0)2-, -C(0)-(NR3)s-, -(NR3)s-C(0)-, or an optionally substituted 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is H or an optionally substituted group selected from Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, Ci-6 alkyl ene-Rb, C3-6 cycloalkyl -Rb, and 4- to 6- atom heterocyclyl-Rb; each of X1, X2, X3, and X4 is independently selected from CH, CRa, or N,. wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-membered heteroaliphatic, P(0)(R3)2, -C(0)Ci-6 aliphatic, C(0)N(R3)2, C6-12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently halo, oxo, or optionally substituted Ci-6 aliphatic;
Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and optionally substituted Ci-6 aliphatic; each R5 is independently selected from Ci-6 alkyl, -N(R3)2, -O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH; each R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), - C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1. 0077J As defined generally above, A is
wherein X1, X2, X3, and X4 are as defined generally above, and A is substituted with 0, 1, 2, 3 or 4 Ra.
{0078J As defined generally above, A is substituted with 0, 1, 2, 3, or 4 Ra. In some embodiments, A is unsubstituted (i.e, is substituted with 0 Ra). In some embodiments, A is substituted with 1 Ra. In some embodiments, A is substituted with 2 Ra. In some embodiments, A is substituted with 3 Ra. In some embodiments, A is substituted with 4 Ra.
{0080J In some embodiments, the present application provides compounds having a structure as set forth in Formula G :
G or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered
monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
L1 is absent, -NR3-Co-6 alkylenyl-, -O-Co-6 alkylenyl, Ci-6 alkyl enyl, -C(0)-Co-6 alkylenyl, - C(0)0-Co-6 alkylenyl, -C(0)-NR3-, -NR3-C(0)-;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is Ci-6 aliphatic, -S(0)2-Ci-6 aliphatic, -O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of Rb; each of X1, X2, X3, and X4 is independently selected from C, CRa, S, O, orN, as valency permits, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3. 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently hydrogen, halo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl;
Rb is an optionally substituted group selected from -NR3-C(0)-CI-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12- membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic and N(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic;
each R3 is independently selected from H and an optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S; each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1.
{00811 In some embodiments, the present application provides compounds having a structure as set forth in Formula IF :
or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is H, Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Y is optionally substituted with one or more instances of Rb; each of X1, X2, X3, and X4 is independently selected from C, CRa, S, O, orN, as valency permits, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3- 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently hydrogen, halo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl;
Rb is an optionally substituted group selected from -NR3-C(0)-C 1-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic and N(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and an optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S; each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1.
[0082] As defined generally above, in some embodiments, each of X1, X2, X3, and X4 is independently selected from C, CRa, S, O, NH, or N, as valency permits, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y . In some embodiments, X1, X2, X3, and X4 are each N or NH. In some embodiments, X1, X2, X3, and X4 are each CRa or C. In some embodiments, X1, X2, and X3 are N and X4 is CRa or C. In some embodiments, X1, X3, and X4 are N and X2 is CRa or C . In some embodiments, X1, X2, and X4 are N and X3 is CRa or C . In some
embodiments, X2, X3, and X4 are N and X1 is CRa or C . In some embodiments, X1 and X2 are N and X3 and X4 are each independently CRa or C . In some embodiments, X1 and X3 are N and X2 and X4 are each independently CRa or C . In some embodiments, X1 and X4 are N and X2 and X3 are each independently CRa or C . In some embodiments, X2 and X3 are N and X1 and X4 are each independently CRa or C . In some embodiments, X2 and X4 are N and X1 and X3 are each independently CRa or C . In some embodiments, X3 and X4 are N and X1 and X2 are each independently CRa or C . In some embodiments, X1 is N and X2, X3, and X4 are each independently CRa or C . In some embodiments, X2 is N and X1, X3, and X4 are each independently CRa or C . In some embodiments, X3 is N and X1, X2, and X4 are each independently CRa or C . In some embodiments, X4 is N and X1, X2, and X3 are each independently CRa or C . 0083] In some embodiments, a compound of Formula G or IF is selected from:
|0 84| As defined generally above, each Ra is hydrogen, halo, oxo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl. In some embodiments, each Ra is hydrogen, halo, oxo, or optionally substituted Ci-6 aliphatic. In some embodiments, Ra is Ci-6 alkyl. In some embodiments, Ra is C1-3 alkyl. In some embodiments, Ra is methyl.
{0085J In some embodiments, Ra is halo. In some embodiments, Ra is bromo, chloro, fluoro, or iodo. In some embodiments, Ra is bromo. In some embodiments, Ra is chloro. In some embodiments, Ra is fluoro. In some embodiments, Rais iodo.
[O086J In some embodiments, Ra is oxo.
{00871 In some embodiments, when L1 and Cy are absent, Ra comes together with Z to form Ci-6 alkenyl. In some embodiments, when L1 and Cy are absent, Ra comes together with Z to form:
{008SJ As defined generally above, Y is Ci-6 aliphatic, -S(0)2-Ci-6 aliphatic, -O-Ci-6 aliphatic, C3- 12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of Rb.
[O089J In some embodiments, Y is Ci-6 aliphatic optionally substituted with one or more instances of Rb. In some embodiments, Y is Ci-6 alkyl optionally substituted with one or more instances of Rb. In some embodiments, Y is C1-3 alkyl optionally substituted with one or more instances of Rb. In some embodiments, Y is methyl. In some embodiments, Y is ethyl. In some embodiments, Y is isopropyl. In some embodiments, Y is tert-butyl. In some embodiments, Y is n-butyl.
[0090| In some embodiments, Y is Ci-6 aliphatic substituted with one or more instances of Rb. In some embodiments, Y is methyl substituted with Rb. In some embodiments, Y is ethyl substituted with Rb. In some embodiments, Y is propyl substituted with Rb. j0091[ In some embodiments, Y is O-Ci-6 aliphatic optionally substituted with one or more instances of Rb. In some embodiments, Y is O-Ci-6 alkyl optionally substituted with one or more instances of Rb. In some embodiments, Y is O-C1-3 alkyl. In some embodiments, Y is O-methyl optionally substituted with one or more instances of Rb.
{0Q92J In some embodiments, Y is C3-12 cycloalkyl optionally substituted with one or more instances of Rb. In some embodiments, Y is C3-6 cycloalkyl optionally substituted with one or more instances of Rb. In some embodiments, Y is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In some embodiments, Y is cyclopropyl. In some embodiments, Y is cyclobutyl. In some embodiments, Y is cyclopentyl. In some embodiments, Y is cyclohexyl.
[0093] In some embodiments, Y is 4- to 6- atom heterocyclyl optionally substituted with one or more instances of Rb. . In some embodiments, azetidinyl optionally substituted with one or more instances of Rb. In some embodiments, Y is pyrrolidinyl optionally substituted with one or more instances of Rb . In some embodiments, Y is piperdinyl optionally substituted with one or more instances of Rb .
[0094] As defined generally above, Rb is an optionally substituted group selected from -NR.3-C(0)- Ci-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0095] In some embodiments, Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. [0096] In some embodiments, Rb is optionally substituted -NR3-C(0)-CI-6 aliphatic. In some embodiments, Rb is -NH-C(0)-CI-6 aliphatic. In some embodiments, Rb is -N(CH3)-C(0)-CI-6 aliphatic.
[0097] In some embodiments, Rb is optionally substituted C6-12 aryl. In some embodiments, Rb is optionally substituted phenyl. In some embodiments, Rb is phenyl substituted with halogen or - (CH2)O-4R°. In some embodiments, Rb is unsubstituted phenyl.
[0098] In some embodiments, Rb is optionally substituted -C(0)-Ci-6 aliphatic. In some embodiments, Rb is -0(0)-(0¾)3.
[0099] In some embodiments, Rb is optionally substituted Ci-6 aliphatic. In some embodiments, Rb is methyl, ethyl, propyl, butyl, pentyl, or hexyl.
[0100] In some embodiments, Rb is optionally substituted 2- to 10-atom heteroaliphatic. In some embodiments, Rb is 3- to 6-atom heteroaliphatic. In some embodiments, Rb is -(CH2)I-4-0-CH3. In some embodiments, some embodiments, Rb is -CH2-O-CH3. In some embodiments, Rb is - CH2-CH2-O-CH3. In some embodiments, Rb is -CH2-CH2-CH2-O-CH3. In some embodiments, Rb is -(CH2)I-4-N(CH3).
[0101] In some embodiments, Rb is optionally substituted -C(0)-C6-i2 aryl
[0192] In some embodiments, Rb is optionally substituted 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some
embodiments, Rb is optionally substituted 4- to 6-membered heterocyclyl comprising 1 to 3 heteroatoms selected from N, O, and S. In some embodiments, Rb is optionally substituted 4- membered heterocyclyl comprising 1 heteroatom selected from N, O, and S. In some embodiments, Rb is optionally substituted 5-membered heterocyclyl comprising 1 to 3 heteroatoms selected from N, O, and S. In some embodiments, Rb is optionally substituted 6-membered heterocyclyl comprising 1 to 3 heteroatoms selected from N, O, and S. In some embodiments, Rb is 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S optionally substituted with -(CH2)o-4N(R°)C(0)R°, -C(0)R°, -(O¼)o- 4R°, or -(CH2)O-40R°.
[0103] In some embodiments, Rb is or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Rb is pyridinyl. |O104[ In some embodiments, Y is selected from Table Y:
[01051 As defined generally above, Cy is absent or a bivalent moiety selected from 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S, Ci-6 aliphatic, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more R1.
[0ίb6| In some embodiments, Cy is optionally substituted with one or more R1, i.e., is substituted with 0, 1, 2, 3, or 4 R1. In some embodiments, Cy is unsubstituted (i.e., is substituted with 0 R1). In some embodiments, Cy is substituted with 1, 2, 3, or 4 R1. In some embodiments, Cy is substituted with 1 R1. In some embodiments, Cy is substituted with 2 R1. In some embodiments, Cy is substituted with 3 R1. In some embodiments, Cy is substituted with 4 R1.
[01071 In some embodiments, Cy is absent.
[0108] In some embodiments, Cy is 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Cy is 4- to 6- membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 4-membered monocyclic heterocyclic comprising 1 heteroatom selected from N, O, P, and S. In some embodiments, Cy is 5-membered monocyclic heterocyclic comprising 1 to 2 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 6- membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is azetidinyl, pyrrolidinyl, piperdinyl, or piperazinyl.
{01091 In some embodiments, Cy is azetidinyl, optionally substituted with one or more R1.
{01101 In some embodiments, Cy is piperdinyl optionally substituted with one or more R1. In some embodiments, Cy is unsubstituted piperdinyl. In some embodiments, Cy is piperdinyl substituted with one or more R1.
{01 II I In some embodiments, Cy is piperazinyl optionally substituted with one or more R1. In some embodiments, Cy is unsubstituted piperazinyl. In some embodiments, Cy is piperazinyl substituted with one or more R1..
[0112J In some embodiments, Cy is 7- to 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 10- to 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 10- membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 11- membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S.
|0113| In some embodiments, Cy is 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 5- or 6- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Cy is 5-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Cy is 6-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. 0114J In some embodiments, Cy is 7- to 12-membered bicyclic heteroaryl comprising comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 9- to 12-membered bicyclic heteroaryl comprising comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 9-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 10-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 11-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. In some embodiments, Cy is 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, P, and S. 0115J In some embodiments, Cy is Ci-6 aliphatic. In some embodiments, Cy is Ci-6 alkylenyl. [0116| In some embodiments, Cy is C6-12 aryl. In some embodiments, Cy is phenyl.
{01171 In some embodiments, Cy is C3-12 cycloalkyl. In some embodiments, Cy is cycobutyl, cyclopentyl, or cyclohexyl. In some embodiments, Cy is cyclobutyl. In some embodiments, Cy is cyclopentyl. In some embodiments, Cy is cyclohexyl. 011 | As defined generally above, each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl. In some embodiments, R1 is N(R3)2. In some embodiments, R1 is NH2. In some embodiments, R1 is N(H)(CH3). In some embodiments, R1 is N(0¾)2. In some embodiments, R1 is OH. In some embodiments, R1 is CN. In some embodiments, R1 is C(0)NHR3. In some embodiments, R1 is C(0)NH2. In some embodiments, R1 is optionally substituted Ci-6 aliphatic. In some embodiments, R1 is optionally substituted Ci-6 alkyl. In some embodiments, R1 is optionally substituted C1-4 alkyl. In some embodiments, R1 is optionally substituted Ci alkyl. In some embodiments, N(R3)-C(0)-CI-6 aliphatic. In some embodiments, N(R3)-C(0)-CI-6 alkyl. [Q119J In some embodiments, a substituent on an optionally substituted carbon atom of an optionally substituted R1 group is selected from: halo, OH, NH2, and oxo.
{01201 In some embodiments, Cy is selected from Table Cy:
-i-NOCN-i-
{01211 As defined generally above, L1 is absent, -NR3-Co-6 alkylenyl-, -O-Co-6 alkylenyl, Ci-6 alkylenyl, -C(0)-Co-e alkylenyl, -C(0)0-Co-e alkylenyl, -C(0)-NR3-, -NR3-C(0)-. j0122| In some embodiments, L1 is absent, -NR3-, -0-, -S-, Ci-6 alkylenyl, C2-6 alkynylenyl, -NR3- Ci-6 alkylenyl, -O-C 1-6 alkylenyl, -C(0)Co-6 alkylenyl, -C(0)NR3-, or -C(0)-C(0)-.
| I23| In some embdiments, LMS absent.
{0I24J In some embodiments, L1 is -NR3-Co-6 alkylenyl. In some embodiments, -NR3-. In some embodiments, L1 is -NR3-CI-6 alkylenyl. In some embodiments, L1 is -N(0¾)-. In some embodiments, L1 is -NH-.
[0125J In some embodiments, L1 is -O-Co-6 alkylenyl. In some embodiments, L1 is -0-. In some embodiments, L1 is -O-Ci-6 alkylenyl. In some embodiments, L1 is -O-C 1-6 alkyl. In some embodiments, L1 is -O-C1-3 alkyl. In some embodiments, L1 is -O-CH2-.
[0126J In some embodiments, L1 is -S-.
[0127J In some embodiments, L1 is Ci-6 alkylenyl. In some embodiments, L1 is Ci-6 alkyl. In some embodiments, L1 is -CH2-. In some embodiments, L1 is C2-6 alkynylenyl. In some embodiments,
{0128J In some embodiments, L1 is -C(0)Co-6 alkyl enyl.
[0129J In some embodiments, L1 is -C(0)0-Co-6 alkylenyl.
|0I30| In some embodiments, L1 is -C(0)-NR3-.
[0131] In some embodiments, L1 is -NR3-C(0)-.
[0132] In some embodiments, L1 is -C(0)-C(0)-.
[0133] As defined generally above, Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3-12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S,
or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q.
[61341 In some embodiments, Z is Ci-6 aliphatic, 2- to 10-membered heteroaliphatic, P(0)(R3)2, - C(0)Ci-6 aliphatic, C(0)N(R3)2, C6-12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12- membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q.
[0135| In some embodiments, Z is substituted with (R2)q. As defined generally above, q is 0, 1, 2, 3, or 4. That is, in some embodiments, Z is substituted with 0, 1, 2, 3, or 4 R2. In some embodiments, Z is unsubstituted (i.e., q is 0). In some embodiments, q is 1. In some embodiments, q is 2. In some embodiments, q is 3. In some embodiments, q is 4.
[01361 In some embodiments, Z is Ci-6 aliphatic. In some embodiments, Z is Ci-6 alkyl. In some embodiments, Z is C1-3 alkyl. In some embodiments, Z is methyl. In some embodiments, Z is ethyl. jO137} In some embodiments, Z is 2- to 10-membered heteroaliphatic. In some embodiments, Z is 2- to 5-membered heteroaliphatic. In some embodiments, Z is 3-membered heteroaliphatic. In some embodiments, Z is -O-CH3, -CH2-O-CH3, -O-CH2-CH2-O-CH2-CH2-O-CH3. In some embodiments, Z is -O-CH3. In some embodiments, Z is -CH2-O-CH3. In some embodiments, Z is -O-CH2-CH2-O-CH2-CH2-O-CH3.
[61381 In some embodiments, Z is -C(0)Ci-6 aliphatic. In some embodiments, Z is -C(0)-Ci-6 alkyl. In some embodiments, Z is -C(0)-CH3. In some embodiments, Z is -C(0)-(CH3)3.
[6139[ In some embodiments, Z is -C(0)N(R3)2. In some embodiments, Z is -C(0)NH2. In some embodiments, Z is -C(0)N(CH3)2.
{01401 In some embodiments, Z is C6-12 aryl. In some embodiments, Z is phenyl substituted with (R2)q. In some embodiments, Z is phenyl substituted with 0, 1, 2, 3, or 4 R2. In some embodiments, Z is unsubstituted phenyl. In some embodiments, Z is phenyl substituted with 1, 2, 3, or 4 R2. In some embodiments, Z is phenyl substituted with 1 or 2 R2. In some emboidments, Z is phenyl substituted with 1 or 2 halo.
[61411 In some embodiments, Z is C3-12 monocyclic or polycyclic cycloalkyl. In some embodiments, Z is cyclobutyl. In some embodiments, Z is cyclopentyl. In some embodiments, Z is cyclohexyl.
[0142] In some embodiments, Z is 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 4- to 6- membered monocyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 4-membered monocyclic heterocyclyl comprising 1 heteroatom selected from N, O, and S. In some embodiments, Z is 5-membered monocyclic heterocyclyl comprising 1-2 heteroatoms selected from N, O, and S. In some embodiments, Z is 6-membered monocyclic heterocyclyl comprising 1-4 heteroatoms selected from N, O, and S.
[0143] In some embodiments, Z is 10- to 12-membered bicyclic heterocyclyl. In some embodiments, Z is 10- to 12-membered fused bicyclic heterocyclyl. In some embodiments, Z is 10- to 12-membered bridged bicyclic heterocyclyl.
[0144] In some embodiments, Z is 10- to 16-membered polycyclic heterocyclyl. In some embodiments, Z is 10-membered polycyclic heterocyclyl. In some embodiments, Z is 11- membered polycyclic heterocyclyl. In some embodiments, Z is 12-membered polycyclic heterocyclyl. In some embodiments, Z is 13-membered polycyclic heterocyclyl. In some embodiments, Z is 14-membered polycyclic heterocyclyl. In some embodiments, Z is 15- membered polycyclic heterocyclyl. In some embodiments, Z is 16-membered polycyclic heterocyclyl. In some embodiments, a polycyclic Z moiety is a spirocyclic and fused tricyclic moiety.
[0145] In some embodiments, Z is 9- to 12-membered spirocyclic heterocyclyl. In some embodiments, Z is 9-membered spirocyclic heterocyclyl. In some embodiments, Z is 10- membered spirocyclic heterocyclyl. In some embodiments, Z is 11-membered spirocyclic heterocyclyl. In some embodiments, Z is 12-membered spirocyclic heterocyclyl.
[0146] In some embodiments, Z is 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 5- to 6- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 5-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 6-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0147] In some embodiments, Z is 8- to 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 8-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 9-membered
heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 10-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 11-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, Z is 12-membered heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0148] As defined generally above, each R2 is independently selected from halo, CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic. In some embodiments, R2 is halo. In some embodiments, R2 is selected from fluoro, chloro, bromo, and iodo. In some embodiments, R2 is CN. In some embodiments, R2 is an optionally substituted Ci-6 aliphatic. In some embodiments, R2 is optionally substituted Ci-6 alkyl. In some embodiments, R2 is optionally substituted Ci-4 alkyl. In some embodiments, R2 is optionally substituted C1-2 alkyl. In some embodiments, R2 is methyl. In some embodiments, R2 is ethyl. In some embodiments, R2 is an optionally substituted O-Ci-6 aliphatic. In some embodiments, R2 is optionally substituted O-Ci-6 alkyl. In some embodiments, R2 is optionally substituted O-C1-4 alkyl. In some embodiments, R2 is optionally substituted O-C1-2 alkyl. In some embodiments, R2 is O-methyl. In some embodiments, R2 is O-ethyl.
[0149] In some embodiments, a substituent on an optionally substituted carbon atom of an optionally substituted R2 group is halo (e.g., bromo, chloro, fluoro, iodo).
{0150} As defined generally above, each R3 is independently selected from H and optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, and 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0151] In some embodiments, R3 is H.
{0152] In some embodiments, R3 is an optionally substituted Ci-6 aliphatic. In some embodiments, R3 is optionally substituted Ci-6 alkyl. In some embodiments, R3 is optionally substituted C1-4 alkyl. In some embodiments, R3 is optionally substituted C1-2 alkyl. In some embodiments, R3 is methyl. In some embodiments, R3 is ethyl.
[0153] In some embodiments, R3 is C3-12 cycloalkyl.
{0154} In some embodiments, R3 is 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S
[0155! In some embodiments, a substituent on an optionally substituted carbon atom of an optionally substituted R3 group is halo (e.g., bromo, chloro, fluoro, iodo).
|01561 In some embodiments, Z is selected from Table Z:
Table Z halo (e g., bromo, chloro, fluoro, iodo), -CH3, -CH2CH3, -O-CH3, -CH2-O-CH3, -O-CH2-CH2-O-
CH2-CH2-O-CH3, -CH2-OH,
[0157] As defined generally above, L2 is absent, -(NR3)s-S(0)-Co-6 alkylenyl-, -(NR3)s-S(0)2-Co-6 alkylenyl-, -(NR3)s-S(0)(NR3)-, -S(0)2-NR3-, -NR3-CI-6 haloalkylenyl, -(NR3)s-P(0)(R3)-, -Ci-6 alkylenyl-S(O)-, -Ci-6 alkylenyl-S(0)2-, -C(0)-(NR3)s-, -(NR3)s-C(0)-, or an optionally sbustituted 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0158] In some embodiments, L2 is absent.
[0159] In some embodiments, L2 is -(NR3)s-S(0)-Co-6 alkylenyl. In some embodiments, L2 is - (NR3)S-S(0)-CH2-. In some embodiments, L2 is -(NR3)s-S(0)-. In some embodiments, L2 is - S(O)-. In some embodiments, L2 is -NR3-S(0)-. In some embodiments, L2 is -NH-S(O)-. In some embodiments, L2 is -N(CH3)-S(0)-.
[0160] In some embodiments, L2 is -(NR3)s-S(0)2- Co-6 alkylenyl. In some embodiments, L2 is - (NR3)S-S(0)2-CH2-. In some embodiments, L2 is -(NR3)s-S(0)2-. In some embodiments, L2 is - S(0)2-. In some embodiments, L2 is -NR3-S(0)2-. In some embodiments, L2 is -NH-S(0)2-. In some embodiments, L2 is -N(CH3)-S(0)2-.
[0161] In some embodiments, L2 is -(NR3)s-S(0)(NR3)-. In some embodiments, L2 is -S(0)(NH)- . In some embodiments, L2 is -(NR3)-S(0)(NR3)-. In some embodiments, L2 is -NH-S(0)(NH)-. In some embodiments, L2 is -N(CH3)-S(0)(NH)-.
{0162} In some embodiments, L2 is -S(0)2-NR3-. In some embodiments, L2 is -S(0)2-NH-. In some embodiments, L2 is -S(0)2-N(CH3)-.
[0163] In some embodiments, L2 is -NR3-CI-6 haloalkylenyl.
[0164] In some embodiments, L2 is -(NR3)s-P(0)(R3)-. In some embodiments, L2 is -P(0)(R3). In some embodiments, L2 is -(NR3)-P(0)(R3)-. In some embodiments, L2 is -P(0)(CH3)-. In some embodiments, L2 is -NH-P(0)(CH3)-.
[0165] In some embodiments, L2 is -C(0)-(NR3)s-. In some embodiments, L2 is -C(0)NH-. In some embodiments, L2 is -C(O)-. In some embodiments, L2 is -N(R3)-C(0)-. In some embodiments, L2 is -NH-C(O)-.
{0166} In some embodiments, L2 is -Ci-6 alkylenyl-S(O)-. In some embodiments, L2 is -CH2- S(O)-.
[0167} In some embodiments, L2 is -Ci-6 alkylenyl-S(0)2-. In some embodiments, L2 is -CH2- S(0)2.
|01681 In some embodiments, L2 is -C(0)-(NR3)s-. In some embodiments, L2 is -C(0)-NH-. In some embodiments, L2 is -0(0)-N(0¾)-.
[01691 In some embodiments, L2 is -(NR3)s-C(0)-.
[6170J In some embodiments, L2 is optionally substituted -NR3-Ci-6alkylenyl. In some embodiments, L2 is optionally substituted -NR3-Ci-3alkylenyl. In some embodiments, L2 is optionally substituted -NR3-CI alkylenyl. In some embodiments, L2 is -NH-CH2-. In some embodiments, L2 is -NH-CH(CF3)-.
[01711 In some embodiments, L2 is optionally substituted -Ci-6 alkylenyl-S(O)-. In some embodiments, L2 is optionally substituted -C1-3 alkylenyl-S(O)-. In some embodiments, L2 is optionally substituted -Ci alkylenyl-S(O)-. In some embodiments, L2 is -CH2-S(0)-.
[01721 In some embodiments, L2 is optionally substituted -Ci-6 alkylenyl-S(0)2-. In some embodiments, L2 is optionally substituted -C1-3 alkylenyl-S(0)2-. In some embodiments, L2 is optionally substituted -Ci alkylenyl-S(0)2-. In some embodiments, L2 is -CH2-S(0)2-.
[01731 In some embodiments, L2 is optionally substituted 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is a 4- to 6-membered monocyclic heterocyclcyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is a 4-membered monocyclic heterocyclcyl comprising 1 heteroatom selected from N, O, and S. In some embodiments, L2 is a 5-membered monocyclic heterocyclcyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is a 6-membered monocyclic heterocyclcyl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0174J In some embodiments, L2 is optionally substituted 8- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is optionally substituted 8-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is optionally substituted 9-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is optionally substituted 10-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is optionally substituted 11-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, L2 is optionally
substituted 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
[0175] In some embodiments, a substituent on an optionally substituted carbon atom of an optionally substituted L2 group is halo (e.g., bromo, chloro, fluoro, iodo) or Ci-6 alkyl.
|0I76| As defined generally above, V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from
N, O, and S, C6-12 aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m.
[ 177] As defined generally above, V is substituted with (R6)m. As defined generally above, m is
O, 1, 2, 3, or 4. That is, in some embodiments, V is substituted with 0, 1, 2, 3, or 4 R6. In some embodiments, V is unsubstituted (i.e., m is 0). In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4.
[0178J In some embodiments, V is Ci-6 aliphatic. In some embodiments, V is is Ci-6 alkyl. In some embodiments, V is selected from methyl, ethyl, propyl, butyl, propyl, and hexyl. j0179| In some embodiments, V is C6-12 aryl. In some embodiments, V is phenyl. 0180] In some embodiments, V is 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 4- to 6- membered monocyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 4-membered heterocyclic comprising 1 heteroatom selected from N, O, and S. In some embodiments, V is 5-membered heterocyclic comprising 1 to 4 heteroatom selected from N, O, and S. In some embodiments, V is 6-membered heterocyclic comprising 1 to 4 heteroatom selected from N, O, and S. In some embodiments, V is morpholinyl.
[01811 In some embodiments, V is 7- to 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 7-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 8-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 9-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 10-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 11-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 12-membered bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
|b!82| In some embodiments, V is C6-12 aryl. In some embodiments, V is phenyl. jj0183J In some embodiments, V is 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 5- to 6- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 5- membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 6-membered monocyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is pyridyl. [0184J In some embodiments, V is 7- to 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 7- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 8- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 9- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 10- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 11- membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is 12-membered bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S. In some embodiments, V is indolyl.
[0185J In some embodiments, V is C3-12 cycloalkyl. In some embodiments, V is C3-6 cycloalkyl. In some embodiments, V is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl. In some embodiments, V is cyclopropyl. In some embodiments, V is cyclobutyl. In some embodiments, V is cyclopentyl. In some embodiments, V is cyclohexyl.
[018fiJ As defined generally above, each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl. j0187| In some embodiments, each R6 is independently selected from halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), -C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-i2 aryl. 0188J In some embodiments, each R6 is independently selected from S(0)-R5, S(0)2-R5, or an optionally substituted Ci-6 alkyl.
[0189J In some embodiments, R6 is halo. In some embodiments, R6 is chloro, fluoro, bromo, or iodo. In some embodiments, R6 is fluoro. In some embodiments, R6 is chloro. In some embodiments, R6 is bromo. In some embodiments, R6 is iodo.
{0190J In some embodiments, R6 is -S(0)-R5. In some embodiments, R6 is -S(0)-CH3.
[0191] In some embodiments, R6 is -S(0)2-R5. In some embodiments, R6 is -S(0)2-Ci-6 alkyl. In some embodiments, R6 is -S(0)2-CH3. In some embodiments, R6 is -S(0)2-CH2CH3. In some embodiments, R6 is -S(0)2-CHF2. In some embodiments, R6 is -S(0)2-CF3.
[0I92| In some embodiment, R6 is -S(0)2-N(CI-6 alkyl)2. In some embodiments, R6 is -S(0)2- N(CH3)2.
[0193] In some embodiments, R6 is S(0)(NH)-R5. In some embodiments, R6 is -S(0)(NH)-CH3. 0194| In some embodiments, R6 is -CN.
[0195J In some embodiments, R6 is -C(0)-R5. In some embodiments, R6 is -C(0)-CH3. In some embodiments, R6 is -C(0)-CF3. In some embodiments, R6 is -C(0)-pyrolidinyl.
[0196] In some embodiments, R6 is -C(0)0-R5. In some embodiments, R6 is -C(0)0-Ci-6 alkyl. In some embodiments, R6 is -C(0)0-CH3. In some embodiments, R6 is -C(0)0-CH2CH3.
[01 7] In some embodiments, R6 is -C(0)-NH(R5). In some embodiments, R6 is -C(0)-NH(CH3). In some embodiments, R6 is -C(0)-NH-cyclopropyl.
[0198] In some embodiments, R6 is -C(0)-N(R5)2. In some embodiments, R6 is -0(0)-N(0¾)2. [(}199| In some embodiments, R6 is -P(0)(R5)2. In some embodiments, R6 is -P(0)(CH3)2.
[0200] In some embodiments, R6 is optionally substituted O-Ci-6 alkyl. In some embodiments, R6 is O-CH3. In some embodiments, R6 is O-CH2CH3. In some embodiments, R6 is O-CF3.
[0201] In some embodiments, R6 is optionally substituted Ci-6 aliphatic. In some embodiments, R6 is C 1-6 alkyl. In some embodiments, R6 is C1-4 alkyl. In some embodiments, R6 is methyl. In some embodiments, R6 is ethyl. In some embodiments, R6 is propyl. In some embodiments, R6 is butyl. In some embodimetns, R6 is tert-butyl. In some embodiments, R6 is -CH2F. In some embodiments, R6 is -CHF2. In some embodiments, R6 is CF3.
[0202] In some embodiments, R6 is optionally substituted C6-12 aryl.
[0203] In some embodiments, a substituent on an optionally substituted carbon atom of an optionally substituted R6 is halo (e.g., bromo, chloro, fluoro, iodo), Ci-6 alkyl, OH, or oxo.
[0294] As defined generally above, each R5 is independently selected from Ci-6 alkyl, -N(R3)2, - O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH. In some embodiments, R5 is Ci-6 alkyl. In some embodiments, R5 is -N(R3)2. In some embodiments, R5 is -NH2. In some
embodiments, R5 is -NH(CI-6 aliphatic). In some embodiments, R5 is -NH(0¾). In some embodiments, R5 is -O-Ci-6 alkyl. In some embodiments, R5 is C(0)-Ci-6 alkyl. In some embodiments, R5 is P(0)(Ci-6 alkyl)2. In some embodiments, R5 is C3-12 cycloalkyl. In some embodiments, R5 is 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH. j|O205J In some embodiments, V is selected from Table V:
Table V
-CH2CH2CH3,
0206J In some embodiments, the present application provides compounds having a structure as set forth in Formula II:
II or a pharmaceutically acceptable salt thereof, wherein X1, X2, X3, X4, Y, Z, Cy, and V are as described generally above.
[0207J In some embodiments, the present application provides compounds having a structure as set forth in Formula II:
II or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
V is selected from C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic
heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein Vis substituted with (R6)m;
Y is H or an optionally substituted group selected from Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, Ci-6 alkyl ene-Rb, C3-6 cycloalkyl -Rb, and 4- to 6- atom heterocyclyl-Rb; each of X1, X2, X3, and X4 is independently selected from CH, CRa, or N,. wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R3)2, -C(0)Ci-6 aliphatic, C(0)N(R3)2, Ce- 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently halo, oxo, or optionally substituted Ci-6 aliphatic;
Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 alkyl, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and optionally substituted Ci-6 aliphatic; each R5 is independently selected from Ci-6 alkyl, -N(CI-6 alkyl )2, -O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH; each R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), - C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-12 aryl; m is 0, 1, 2, 3, or 4; and q is 0, 1, 2, 3, or 4. 0208J In some embodiments, the present application provides a compound of formula Ila:
Ila or a pharmaceutically acceptable salt thereof, wherein Z, R6, Y, and m are defined herein. j|O209J In some embodiments, the present application provides a compound of formula lib:
lib or a pharmaceutically acceptable salt thereof, wherein Z, R6, Y, and m are defined herein.
[0210J It is to be understood that the above embodiments may be combined together, as if each and every combination were specifically and individually listed.
[0211] In some embodiments, a compound of the present disclosure (i.e., a compound of formula I, G, II, IG, and other formulae provided herein) is selected from Table A:
0212] In some embodiments, a compound of the present invention (e.g., a compound of formula I, G, II, IG, and other formulae provided herein) is selected from Table B:
Table B
Characteristics j|0213J Among other things, in some embodiments, the present disclosure describes one or more characteristics of certain TRPMLl modulators provided by and/or useful in the practice of the present disclosure.
{0214} In some embodiments, the present disclosure provides technologies for assessing one or more relevant characteristics and/or for identifying, selecting, prioritizing, and/or characterizing one or more useful TRPMLl modulators.
[0215J In some embodiments, the present disclosure provides certain biological and/or chemical assays (e.g., that facilitate and/or permit assessment of one or more feature(s) of TRMPL1 expression and/or activity, and/or of impact of TRPMLl modulator(s) on such expression and/or activity. Alternatively or additionally, the present disclosure provides technologies for identifying and/or characterizing one or more aspects of biological pathway(s) (e.g., autophagy pathway(s)) involving TRMPL1, and thus permits identification and/or characterization of additional useful targets within such pathway(s) and/or of modulator(s) that impact such pathway(s) (whether or not targeting TRPMLl itself).
Compositions
{0216} In some embodiments, the present disclosure provides and/or utilizes a composition that comprises and/or delivers a compound as described herein (e.g., together with one or more other components).
!02i7J In some embodiments, the present disclosure provides compositions that comprise and/or deliver compounds reported herein (e.g., compounds of Formula I-II), or an intermediate, degradant, or an active metabolite thereof, e.g., when contacted with or otherwise administered to a system or environment e.g., which system or environment may include TRPMLl activity; in some embodiments, administration of such a composition to the system or environment achieves the regulation of autophagy and lysosomal biogenesis as described herein.
{0218} In some embodiments, a provided composition as described herein may be a pharmaceutical composition in that it comprises an active agent (e.g., a compound of Formula I-II or an active metabolite thereof) and one or more pharmaceutically acceptable excipients (e.g., one or more pharmaceutically acceptable adjuvants, carriers, excipients, and/or vehicles); in some such embodiments, a provided pharmaceutical composition comprises and/or delivers a compound
described herein (e.g., a compound of Formula I- II), or an active metabolite thereof to a relevant system or environment (e.g., to a subject in need thereof) as described herein.
[0219] In some embodiments, a provided composition (e.g., a pharmaceutical composition) includes a compound (e.g., as described herein) in a salt form such as a pharmaceutically acceptable salt form.
[0220] Is some embodiments, a provided composition (e.g., a pharmaceutical composition) may be formulated for administration to a subject (e.g., a human) according to a particular route (e.g., orally, parenterally, by inhalation or nasal spray, topically (e.g., as by powders, ointments, or drops), rectally, buccally, intravaginally, intraperitoneally, intracistemally or via an implanted reservoir, etc).
[0221] In some embodiments, a provided composition (e.g., a pharmaceutical composition) comprises or delivers an amount of a compound as described herein (or an active metabolite thereof) that is effective to measurably modulate TRPMLl activity, and/or to induce autophagy and/or lysosomal biogenesis in a biological sample or in a subject, when administered in accordance with a therapeutic regimen. 0222] In certain embodiments, a provided compound or composition is formulated for administration to a patient in need of such composition. In some embodiments, a compound or composition as described herein may be administered in a dose amount and/or by a route of administration effective for treating or lessening the severity of a disease or disorder described herein.
[0223] In some embodiments, a composition (e.g., a pharmaceutical composition) as described herein may be formulated in unit form (e.g., which may offer ease of administration and/or uniformity of dosage).
[0224 j Those skilled in the art will appreciate that effective dose amounts may vary from subject to subject, for example depending on a variety of factors, including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed and its route of administration; the species, age, body weight, sex and diet of the patient; the general condition of the subject; the time of administration; the rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and the like.
{0225J In some embodiments, an appropriate dosage level may be within a range of about 0.01 mg/kg to about 50 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
Applications and Uses
| 226j The present application provides a variety of uses and applications for compounds and/or compositions as described herein, for example in light of their activities and/or characteristics as described herein. In some embodiments, such uses may include therapeutic and/or diagnostic uses. Alternatively, in some embodiments such uses may include research, production, and/or other technological uses.
|0227j Among other things, in some embodiments, the present disclosure provides technologies for modulating TRPML1 activty. In some embodiments, the present application relates to a method of modulating TRPMLl activty in a subject comprising administering to the subject a provided compound, or a composition as described herein.
Diseases, Disorders, and Conditions
[0228] The present disclosure demonstrates that compounds and/or compositions as described herein may be useful in medicine (e.g., in the treatment of one or more diseases, disorders, or conditions).
[0229] Among other things, as described herein, the present disclosure provides an insight that targeting (e.g., agonizing) TRPMLl may be a particularly effective strategy for modulating (e.g., enhancing) autophagy and/or lysosomal biogenesis.
[0230] In some embodiments, a disease, disorder or condition that may be treated as described herein may be or comprise a disease, disorder or condition associated with TRPMLl deficiency. Furthermore, in some embodiments, the present disclosure identifies that TRMPL1 deficiency is associated with particular diseases, disorders or conditions, some or all of which may be treated in accordance with the present disclosure.
[0231] In some embodiments, treatment provided herein involves administration of a TRMPLl modulator as described herein in an amount effective to modulate TRMPLl activity in a lysosome and/or increase autophagy.
{0232J In some embodiments, a disease, disorder, or condition amenable to treatment as described herein is or comprises a liver disease, a neurodegenerative disorder, cancer, or a heart disease. [0233] In some embodiments, a disease, disorder, or condition amenable to treatment as described herein is or comprises a lysosomal storage disease, such as Niemann-Pick C (NPC) disease, Gaucher disease, and Pompe disease.
[0234] In some embodiments, a disease, disorder, or condition amenable to treatment as described herein is an age-related common neurodegenerative disease, such as Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease.
[0235] In some embodiments, a disease, disorder, or condition amenable to treatment as described herein is a type IV Mucolipidosis (ML4) neurodegenerative lysosomal storage disease caused by mutations in TRPML1.
[0236] In some embodiments, a disease, disorder, or condition amenable to treatment as described herein is related to reactive oxygen species or oxidative stress.
[0237] In some embodiments, the present application relates to use of a compound and/or composition described herein for use in the manufacture of a medicament e.g., for modulation of TRPMLl activity.
[0238] In some embodiments, the present application relates to use of a compound and/or composition described herein for use in the manufacture of a medicament for treating a disease, disorder or condition, e.g., through modulation of TRPMLl activity; in some emebodiments, the disease, disorder, or condition is a liver disease, a neurodegenerative disorder, cancer, or a heart disease.
[0239] In some embodiments, the disease, disorder, or condition is a muscular disease, a liver disease, a metabolic disease, an atherosclerotic disease, an inflammatory bowel disease, an atherosclerotic disease, a neurodegenerative disease, an oncological disease, or an infectious disease.
[0240] In some embodiments, the disease, disorder, or condition is a muscular disease.
[0241] In some embodiments, the muscular disease is a muscular dystrophy.
[0242] In some embodiments, the muscular dystrophy is Duchenne muscular dystrophy.
[0243] In some embodiments, the disease, disorder, or condition is an infectious disease.
[0244] In some embodiments, the infectious disease is an infection of Heliobacter pylori or Mycobacterium tuberculosis.
{0245J In some embodiments, the infectious disease is tuberculosis.
Exemplary Embodiments
[0246J The following numbered embodiments, while non-limiting, are exemplary of certain aspects of the disclosure:
1. A compound of F ormula I
Z-ΐ ϋg-A-ΐ U
I or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
L1 is absent, -NR3-, -0-, -S-, Ci-6 alkylenyl, C2-6 alkynylenyl, -NR3-CI-6 alkyl enyl,-0-Ci-6 alkylenyl,
-C(0)Co-6 alkylenyl; -C(0)NR3-, -C(0)-C(0)-;
L2 is absent, -(NR3)s-S(0)-Co-6 alkylenyl-, -(NR3)s-S(0)2-Co-6 alkylenyl-, -(NR3)s-S(0)(NR3)-, - S(0)2-NR3-, -NR3 -CI-6 haloalkylenyl, -(NR3)s-P(0)(R3)-, -Ci-6 alkylenyl-S(O)-, -Ci-6 alkylenyl-S(0)2-, -C(0)-(NR3)s-, -(NR3)s-C(0)-, or an optionally substituted 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is H or an optionally substituted group selected from Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, Ci-6 alkyl ene-Rb, C3-6 cycloalkyl -Rb, and 4- to 6- atom heterocyclyl-Rb; each of X1, X2, X3, and X4 is independently selected from CH, CRa, or N,. wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R3)2, -C(0)Ci-6 aliphatic, C(0)N(R3)2, Ce- 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently halo, oxo, or optionally substituted Ci-6 aliphatic;
Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 alkyl, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and optionally substituted Ci-6 aliphatic; each R5 is independently selected from Ci-6 alkyl, -N(CI-6 alkyl )2, -O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH; each R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), - C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1.
2. The compound of embodiment 1, wherein X1, X2, X3, and X4 are each N.
4. The compound of any one of the preceding embodiments, wherein Y is H or Ci-6 alkylene-Rb.
5. The compound of any one of the preceding embodiments, wherein Y is H.
6. The compound of any one of the preceding embodiments, wherein Y is Ci-6 alkylene-Rb.
7. The compound of any one of the preceding embodiments, wherein Y is C3-6 cycloalkyl-
Rb or 4- to 6- atom heterocyclyl-Rb.
8. The compound of any one of the preceding embodiments, wherein Rb is C6-12 aryl or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
9. The compound of any one of the preceding embodiments, wherein Rb is phenyl.
10. The compound of any one of the preceding embodiments, wherein Y is selected from:
11. The compound of any one of the preceding embodiments, wherein Cy is absent or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from
N, O, and S.
12. The compound of any one of the preceding embodiments, wherein Cy is absent.
13. The compound of any one of the preceding embodiments, wherein Cy is 4- to 12- membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N,
O, and S.
15. The compound of any one of the preceding embodiments, wherein Cy is 4- to 6- membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, and S.
16. The compound of any one of the preceding embodiments, wherein Cy is piperdinyl or piperzinyl.
18. The compound of any one of the preceding embodiments, wherein L1 is absent, -NR3-, or Ci-6 alkyl enyl.
19. The compound of any one of the preceding embodiments, wherein L1 is absent.
20. The compound of any one of the preceding embodiments, wherein L1 is-NR3-.
21. The compound of any one of the preceding embodiments, wherein L2 is absent, -(NR3)S- S(0)-Co-6 alkyl enyl, or -(NR3)s-S(0)2-Co-6 alkyl enyl.
22. The compound of any one of the preceding embodiments, wherein L2 is absent, -(NR3)S- S(O)-, or -(NR3)s-S(0)2-.
23. The compound of any one of the preceding embodiments, wherein L2 is absent or -(NR3)s-S(0)2-.
24. The compound of any one of the preceding embodiments, wherein L2 is -NR3-S(0)2-.
25. The compound of any one of the preceding embodiments, wherein L2 is -NH-S(0)2-.
26. The compound of any one of the preceding embodiments, wherein Z is Ce-u aryl, 2- to 10 atom heteroaliphatic, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q.
27. The compound of any one of the preceding embodiments, wherein Z is Ce-u aryl or 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
28. The compound of any one of the preceding embodiments, wherein Z is Ce-u aryl.
29. The compound of any one of the preceding embodiments, wherein Z is Ce-u aryl substituted with 1, 2, 3, or 4 R2.
30. The compound of any one of the preceding embodiments, wherein R2 is halo.
31. The compound of any one of the preceding embodiments, wherein Z is selected from halo (e g., bromo, chloro, fluoro, iodo), -C¾, -CH2CH3, -O-CH3, -CH2-O-CH3, -O-CH2-CH2-O-CH2- CH2-O-CH3,
The compound of any one of the preceding embodiments, wherein V is C6-12 aryl or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
33. The compound of any one of the preceding embodiments, wherein V is C6-12 aryl.
34. The compound of any one of the preceding embodiments, wherein V is C6-12 aryl substituted with 1, 2, 3, or 4 R6.
35. The compound of any one of the preceding embodiments, wherein R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, or an optionally substituted O-Ci-6 alkyl.
36. The compound of any one of the preceding embodiments, wherein R6 is S(0)-R5, S(0)2-R5, or an optionally substituted Ci-6 alkyl.
37. The compound of any one of the preceding embodiments, wherein R6 is halo.
38. The compound of any one of the preceding embodiments, wherein R6 is fluoro or chloro.
39. The compound of any one of the preceding embodiments, wherein R6 is S(0)2-R5.
40. The compound of any one of the preceding embodiments, wherein R6 is -S(0)2-Ci-6 alkyl.
41. The compound of any one of the preceding embodiments, wherein R6 is -S(0)2-CH3.
42. The compound of any one of the preceding embodiments, wherein R6 is -S(0)2-N(CI-6 alkyl )2.
43. The compound of any one of the preceding embodiments, wherein R6 is -S(0)2-N(CH3)2.
44. The compound of any one of the preceding embodiments, wherein V is selected from - CH2CH2CH3,
II or a pharmaceutically acceptable salt thereof.
II or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
V is selected from C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising
1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein Vis substituted with (R6)m;
Y is H or an optionally substituted group selected from Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, Ci-6 alkyl ene-Rb, C3-6 cycloalkyl -Rb, and 4- to 6- atom heterocyclyl -Rb; each of X1, X2, X3, and X4 is independently selected from CH, CRa, or N,. wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, P(0)(R3)2, -C(0)Ci-6 aliphatic, C(0)N(R3)2, Ce- 12 aryl, C3-12 cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic
or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently halo, oxo, or optionally substituted Ci-6 aliphatic;
Rb is C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 alkyl, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and optionally substituted Ci-6 aliphatic; each R5 is independently selected from Ci-6 alkyl, -N(CI-6 alkyl )2, -O-Ci-6 alkyl, C(0)-Ci-6 alkyl, P(0)(Ci-6 alkyl)2, C3-12 cycloalkyl, and 5- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein R5 is optionally substituted with one or more substituents selected from halo and OH; each R6 is halo, S(0)-R5, S(0)2-R5, S(0)(NH)-R5, -CN, -C(0)-R5, -C(0)0-R5, -C(0)-NH(R5), - C(0)-N(R5)2, -P(0)(R5)2, or an optionally substituted group selected from O-Ci-6 alkyl, Ci-6 alkyl, and C6-12 aryl; m is 0, 1, 2, 3, or 4; and q is 0, 1, 2, 3, or 4.
Ila
or a pharmaceutically acceptable salt thereof.
48. The compound of any one of the preceding embodiments, wherein the compound is of formula lib:
lib or a pharmaceutically acceptable salt thereof.
49. A compound selected from Table A.
50. A compound selected from Table B.
51. A pharmaceutical composition comprising a compound of any one of the preceding embodiments and a pharmaceutically acceptable carrier, adjuvant, or vehicle.
52. A method of modulating TRPMLl comprising administering to a subject a compound of any one of the preceding embodiments.
53. A method of treating a disease, disorder, or condition in a subject comprising administering a compound of any one of the preceding embodiments.
54. The method of embodiment 54, wherein the disease, disorder, or condition is a lysosomal storage disorder.
55. The method of embodiment 55, wherein the lysosomal storage disorder is selected from Niemann-Pick C disease, Gaucher disease, and Pompe disease.
56. The method of embodiment 54, wherein the disease, disorder, or condition is age-related common neurodegenerative disease.
57. The method of embodiment 57, wherein the disease, disorder, or condition is selected from Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease.
58. The method of embodiment 54, wherein the disease, disorder, or condition is a type IV Mucolipidosis (ML4) neurodegenerative lysosomal storage disease caused by mutations in TRPMLl.
EXEMPLIFICATION
[ 247J The present teachings include descriptions provided in the Examples that are not intended to limit the scope of any claim. Unless specifically presented in the past tense, inclusion in the Examples is not intended to imply that the experiments were actually performed. The following non-limiting examples are provided to further illustrate the present teachings. Those of skill in the art, in light of the present application, will appreciate that many changes can be made in the specific embodiments that are provided herein and still obtain a like or similar result without departing from the spirit and scope of the present teachings
Ill
Synthetic Examples 0248] As depicted in the Examples below, in certain exemplary embodiments, compounds are prepared according to the following general procedures. It will be appreciated that, although the general methods depict the synthesis of certain compounds of the present invention, the following general methods, and other methods known to one of ordinary skill in the art, can be applied to all compounds and subclasses and species of each of these compounds, as described herein.
A. Certain Synthetic Intermediates
Scheme 1:
Step-1: Synthesis of l-(2,3-dimethoxyphenyl)ethan-l-ol: 0249J To a stirred solution of 2,3-dimethoxybenzaldehyde (1 g, 6.01 mmol, 1 eq) in THF (20 mL) was added dropwise a 3 M solution of methyl magnesium bromide in diethyl ether (3ml, 9.03 mmol, 1.5 eq) at 0° C. The reaction mixture was stirred at RT for overnight. The progress of the reaction was monitored by TLC. After completion, the reaction mixture was diluted with water and extracted with ethyl acetate. The organic layers were washed with water, brine, dried over anhydrous sodium sulfate and evaporated under reduced pressure. The crude product was purified by silica gel column chromatography to afford the titled compound l-(2,3- dimethoxyphenyl)ethan-l-ol (0.7 g, 64%). LCMS: 183.09 [M+H]+.
Step-2: Synthesis of l-(2,3-dimethoxyphenyl)ethan-l-one:
[0250] To a stirred mixture of l-(2,3-dimethoxyphenyl)ethan-l-ol (0.8 g, 4.39 mmol, 1 eq) in acetone (20 mL), was added 2 M Jones reagent in aq. H2SO4 (6.6 mL, 13.18 mmol, 3 eq) at RT. The reaction mixture was stirred at RT for 30 min. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was quenched with isopropanol and concentrated under reduced pressure. The crude product was purified by column chromatography
to afford the desired product l-(2,3-dimethoxyphenyl)ethan-l-one (0.6 g, 76%). LCMS: 181.08 [M+l]+.
Step-1: Synthesis of 1 -methyl- lH-indole-4-carbaldehyde :
{02511 To a stirred solution of lH-indole-4-carbaldehyde (1 g, 6.8 mmol, 1 eq) in DMF (10 mL) was added NaH (0.130 g, 7.4 mmol, 1.1 eq) at 0 °C under the nitrogen atmosphere followed by addition of methyl iodide (1.06 g, 7.5 mmol, 1.1 eq). The reaction mixture was stirred at 0°C for 1 hour. The progress of the reaction was monitored by TLC. After completion, the reaction mixture was quenched with water and extracted with ethyl acetate. The organic layers were washed with water, brine, dried over anhydrous sodium sulfate and evaporated under reduced pressure. The crude product was purified by column chromatography to afford the titled compound 1- methyl-lH-indole-4-carbaldehyde (0.90 g, 82.56%). LCMS: 160.07 [M+H]+.
[0252) Method A (Ar=a/c/f): A pyrex tube was charged with respective aryl halides (1.1 eq), tert-butyl 4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-3,6-dihydropyridine-l(2H)- carboxylate (1 eq), 2 M NaiCCb solution (3 eq) in a mixture of 1,4 dioxane:H20 (4:1, 10 vol) and the reaction mixture was purged with argon for 15 min. Tetrakis(triphenylphosphine)palladium(0) (0.1 eq) was added to then reaction under an argon atmosphere and purged the reaction mixture with argon for 15 min. The tube was then fitted with a screw cap and the reaction was stirred at 90 °C for 3 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture cooled to room temperature, filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with water and extracted ethyl acetate. The combine organic layers were washed with water and brine, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford respective l-Boc-4-aryl-3,6-dihydropyridine derivative. 0253J Method B (Ar=b/e/g): A pyrex tube was charged with respective aryl halide (1.1 eq), tert-butyl 4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-3,6-dihydropyridine-l(2H)- carboxylate (1 eq), potassium carbonate (2 eq) in a mixture of DMEvThO (5:1, 10 vol) and the reaction mixture was purged with argon for 10 min. [1,1'- Bis(diphenylphosphino)ferrocene]dichloropalladium(II) (0.1 eq) was then added to the reaction under an argon atmosphere and purged the reaction mixture with argon for 5 min. The tube was then fitted with a screw cap and the reaction was stirred at 80 °C for 16 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was cooled to room temperature, filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with water and extracted ethyl acetate. The combine organic layers were washed with water and brine, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford respective l-Boc-4-aryl-3,6-dihydropyridine derivative.
[0254J Method C (Ar=d): A pyrex tube was charged with respective aryl halide (1.1 eq), tert- butyl 4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-3,6-dihydropyridine-l(2H)-carboxylate (1 eq), cesium carbonate (2 eq) in a mixture of 1,4 dioxane:H20 (4:1, 10 vol) and the reaction mixture
was purged with argon for 10 min. Diehl orobis(triphenylphosphine)palladium(II) (0.1 eq) was then added to the reaction under an argon atmosphere and purged the reaction mixture with argon for 15 min. The tube was then fitted with a screw cap and the reaction was stirred at 80 °C for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture cooled to room temperature, filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with water and extracted ethyl acetate. The combine organic layers were washed with water and brine, dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford respective l-Boc-4-aryl-3,6-dihydropyridine derivative.
Step-2: General procedure for synthesis of l-Boc-4-arylpiperidine derivatives:
[0255) Method A (Ar=a/b): A solution of respective l-Boc-4-aryl-3,6-dihydropyridine (1 eq) in ethyl acetate was purged with nitrogen for 10 min. Platinum(IV) oxide (10% w/w) was added to the reaction under a nitrogen atmosphere at room temperature. The reaction mixture was purged with hydrogen for 2 - 3 minutes and stirred at room temperature for 3 h under an atmosphere of hydrogen (100 Psi pressure). The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was concentrated under reduced pressure to dryness to afford respective l-Boc-4-arylpiperidine derivative. The crude product was used in the next step without further purification.
[0256J Method B (Ar=c/d/e/f/g): A solution of respective l-Boc-4-aryl-3,6-dihydropyridine (1 eq) in methanol was purged with nitrogen for 10 min. 10-20% Palladium on carbon (10% w/w) was added to the reaction under nitrogen atmosphere at room temperature. The reaction mixture was purged with hydrogen for 2-3 minutes and stirred at room temperature for 12 h under an atmosphere of hydrogen under balloon pressure. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was filtered through a pad of Celite and the Celite pad was washed with methanol. The filtrate was concentrated under reduced pressure to dryness to afford respective l-Boc-4-arylpiperidine derivative. The crude product was used in the next step without further purification.
Step-3: General procedure for synthesis of 4-arylpiperidine derivatives:
[0257) Method A (Ar=a/c/e/f/g): To stirred solution of respective l-Boc-4-arylpiperidine (1 eq) in DCM (5 vol), a 50% solution of trifluoroacetic acid solution in DCM (5 Vol) was added dropwise at 0 °C. The reaction mixture was warmed to room temperature and stirred for 2 to 16 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was quenched with saturated aqueous NaHCCb solution and extracted with DCM. The combined organic layers were washed with water and brine, dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure to dryness to afford the respective 4-arylpiperidine derivative. The crude product was used in the next step without further purification.
[0258J Method B (Ar=b/d): To a stirred solution of respective l-Boc-4-arylpiperidine (1 eq) in 1,4-dioxane (10 vol), a 4 M solution of HC1 in 1,4-dioxane (5 vol) was added at 5 to 10 °C. The reaction mixture was warmed to room temperature and stirred for 4 to 16 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure, the residue was dissolve in saturated aqueous NaHCCh solution and extracted with DCM. The combined organic layers were washed with water and brine, dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the respective 4-arylpiperidine derivative. The crude product was used in the next step without further purification.
Synthesis of 3-(piperidin-4-yl)isoxazole
Step-1: Synthesis of tert-butyl (E)-4-((hydroxyimino)methyl)piperidine-l-carboxylate:
{0259J To a stirred solution of tert-butyl 4-formylpiperidine-l-carboxylate (1 g, 4.6 mmol, 1 eq) in water (10 mL) in methanol (10 mL), hydroxyl amine hydrochloride (390 mg, 5.6 mmol, 1.2 eq) followed by NaiCCb (248 mg, 2.3 mmol, 0.5 eq) were added. The reaction mixture was stirred at room temperature for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were washed with water and brine, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness to afford the titled compound tert-butyl (E)-4-((hydroxyimino)methyl)piperidine-l-carboxylate (The reaction was repeated on 1 g scale) (1.9 g, crude, combined yields from 1 g x 2 batches). This compound was used in the next step without further purification. LCMS: 229.15 [M+H]+.
Step-2: Synthesis of tert-butyl (Z)-4-(chloro(hydroxyimino)methyl)piperidine-l-carboxylate:
[0260] To a stirred solution of tert-butyl (E)-4-((hydroxyimino)m ethyl )piperi dine- 1- carboxylate (1 g, 4.4 mmol, 1 eq) in DMF (3 mL), N-chlorosuccinimide (0.59 g, 4.4 mmol, 1 eq) was added. The reaction mixture was stirred at room temperature for overnight. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water, the resulting solid was filtered out and dried under reduced pressure to afford
the titled compound tert-butyl (Z)-4-(chloro(hydroxyimino)methyl)piperidine-l-carboxylate (1 g, Crude). This compound was used in the next step without further purification. LCMS: 263.11 [M+H]+.
Step-3: Synthesis of tert-butyl 4-(5-(trimethylsilyl)isoxazol-3-yl)piperidine-l-carboxylate: j0261| To a stirred solution of tert-butyl (Z)-4-(chloro(hy droxyimino)m ethyl )piperi dine- 1- carboxylate (1.7 g, 6.4 mmol, 1 eq) in ethyl acetate (100 mL), ethynyltrimethylsilane (3.14 g, 32 mmol, 5 eq) followed by triethyl amine (1.24 g, 9.6 mmol, 1.5 eq) were added at 0 °C. The reaction mixture was warmed to room temperature and stirred for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was filtered and the filtrate was concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound tert-butyl 4-(5-(trimethylsilyl)isoxazol- 3-yl)piperidine-l-carboxylate (2 g, 96%). LCMS: 325.19 [M+H]+.
Step-4: Synthesis of tert-butyl 4-(isoxazol-3-yl)piperidine-l-carboxylate: f 262J To a stirred solution of tert-butyl 4-(5-(trimethylsilyl)isoxazol-3-yl)piperidine-l- carboxylate (1.4 g, 4.3 mmol, 1 eq) in a mixture of water (1 mL) and methanol (10 mL), potassium bifluoride (33 mg, 0.43 mmol, 0.1 eq) was added. The reaction mixture was stirred at room temperature for 6 days. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure and the residue was dissolved in ethyl acetate. The organic layer was washed with water and brine, dried over anhydrous NaiSCL and concentrated under reduced pressure to afford the titled compound tert- butyl 4-(isoxazol-3-yl)piperidine-l-carboxylate (1 g, crude). This compound was used in the next step without further purification. LCMS: 253.15 [M+H]+.
Step-5: Synthesis of 3-(piperidin-4-yl)isoxazole:
[0263J To a stirred solution of tert-butyl 4-(isoxazol-3-yl)piperidine-l-carboxylate (1 g, 4 mmol, 1 eq) in DCM (20 mL), trifluoroacetic acid (10 mL) was added dropwise at 0 °C. The reaction mixture was warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated
under reduced pressure to dryness to afford the titled compound 3-(piperidin-4-yl)isoxazole (1 g. crude). This compound was used in the next step without further purification. LCMS: 153.09 [M+H]+.
Step 1: Synthesis of 3-formyl-2-hydroxybenzonitrile: f 264J To a stirred solution of 2-hydroxybenzonitrile (1 g, 8.39 mmol, 1 eq) in acetic acid (10 mL), hexamethylenetetramine (1.8 g, 12.59 mmol, 1.5 eq) was added. The reaction was stirred at 120 °C for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was cooled to room temperature and concentrated under reduced pressure. The residue was dissolved in ethyl acetate and washed with water. The organic layer was dried over anhydrous Na2S04, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound 3- formyl-2-hydroxybenzonitrile (105 mg, 8.5%) and 5-formyl-2-hydroxybenzonitrile (330 mg, 27%). LCMS: No ionization.
Step 2: Synthesis of 3-formyl-2-methoxybenzonitrile:
[02(>5J To a stirred solution of 3 -formyl -2-hydroxybenzonitrile (100 mg, 0.68 mmol, 1 eq) in DMF (2 mL), potassium carbonate (188 mg, 1.36 mmol, 2 eq) followed by iodomethane (145 mg, 1.02 mmol, 1.5 eq) were added. The reaction was stirred at room temperature for 5 h. The progress of the reaction was monitored by TLC. After completion of the reaction, water was added to the reaction mixture and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the titled
compound 3-formyl-2-methoxybenzonitrile (100 mg, crude). This compound was used in the next step without further purification. LCMS: No ionization.
Step 1
General procedure for synthesis of (pyridin-2-ylmethoxy)henzaldehyde derivatives:
{0206J To a stirred solution of respective hydroxybenzaldehyde (1 eq) in DMF (10 vol), potassium carbonate (3 eq) followed by 2-(chloromethyl)pyridine hydrochloride (1.1 eq) were added. The reaction was stirred at 80 °C for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was cooled to room temperature; ice-cold water was added and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the respective (pyridin-2- ylmethoxy)benzaldehyde derivative.
Synthesis of [l,l'-biphenyl]-4-carbaldehyde
Step 1 0267] A pyrex tube was charged with a solution of 4-bromobenzaldehyde (1.86 g, 10.06 mmol, 1.2 eq), phenylboronic acid (1 g, 8.38 mmol, 1 eq) and K3PO4 (4.44 g, 20.9 mmol, 2.5 eq) in water (3 mL) and 1,4-dioxane (6 mL). The tube was sealed with a septum and the reaction mixture was purged with argon via an argon balloon for 15 min. PdCl2(dppf) (183 mg, 0.25 mmol, 0.03 eq) was then added to the reaction under an argon atmosphere and the purging with argon was continued for 5 min. The tube was then sealed with a screw cap and the reaction was heated at 100 °C for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was cooled to room temperature and the reaction mixture was filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with ethyl acetate and washed with water and brine. The organic layer was dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness to afford the titled compound [l,l'-biphenyl]-4-carbaldehyde (500 mg, crude). This compound was used in the next without further purification. LCMS: No ionization.
{0268J To a stirred solution of 3,4-dimethoxypyridine (250 mg, 1.79 mmol, 1 eq) in THF (5 mL), 1.6 M solution of n-BuLi in hexane (1.2 mL, 1.97 mmol, 1.1 eq) was added dropwise at -78 °C under an argon atmosphere. The reaction was stirred at the same temperature for 30 min. DMF (0.31 mL, 3.95 mmol, 2.2 eq) was then added to the reaction at -78 °C under an argon atmosphere. The reaction was stirred at the same temperature for 30 min under an argon atmosphere. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was quenched with saturated aqueous NH4CI solution and extracted with ethyl acetate. The combined
organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound 3,4-dimethoxypicolinaldehyde (62 mg, 20.6%). LCMS: 168.10 [M+H]+.
Step 2
Step-1: Synthesis of 4-chloro-3-methoxypyridine: f0269| To a stirred solution of 4-chl oropyri din-3 -ol (1 g, 7.71 mmol, 1 eq) in toluene (10 mL), a solution of cyanomethyltributylphosphorane (CMBP) 1 M in toluene (23.1 mL, 23.1 mmol, 3 eq) followed by methanol (0.93 mL, 23.1 mmol, 3 eq) were added at 0 °C. The reaction was warmed to room temperature and stirred for 3 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were washed with brine, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound 4-chl oro-3-methoxypyri dine (280 mg, 25.45%). LCMS: 144.00 [M+H]+.
Step-2: Synthesis of 4-chloro-5-methoxynicotinaldehyde:
[0270) A stirred solution of 4-chl oro-3-methoxypyri dine (180 mg, 1.25 mmol, 1 eq) in THF (5 mL) was cooled to -78 °C and to which a 2 M solution of LDA in THF (1.25 mL, 2.51 mmol, 2 eq) was added. The reaction was stirred at the same temperature for 30 min. N,N- Dimethylformamide (0.19 mL, 2.51 mmol, 2 eq) was then added to the reaction at -78 °C. The reaction was gradually warmed to room temperature and stirred for 2.5 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was cooled to 0 °C, quenched with saturated aqueous MLCl solution and extracted with ethyl acetate. The combined organic layers were washed with brine, dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the titled compound 4-chloro-5-
methoxynicotinaldehyde (210 mg, crude). This compound was used in the next step without further purification. LCMS: 172.00 [M+H]+.
Step-3: Synthesis of 4,5-dimethoxynicotinaldehyde:
|02711 To a stirred solution 4-chloro-5-methoxynicotinaldehyde (200 mg, 1.16 mmol, 1 eq) in methanol (5 mL), sodium methoxide (126 mg, 2.33 mmol, 2 eq) was added and the reaction was stirred at 60 °C for 5 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was cooled to room temperature, diluted with water and extracted with ethyl acetate. The combined organic layers were washed with brine, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness. The crude product was purified by column chromatography on silica gel to afford the titled compound 4,5- dimethoxynicotinaldehyde (83 mg, 43%). LCMS: 168.10 [M+H]+.
[0272J To a stirred solution of 2,3-dimethoxypyridine (1 g, 7.18 mmol, 1 eq) in THF, 2.5 M solution of n-BuLi in hexane (6.33 mL, 15.7 mmol, 2.2 eq) was added dropwise at -78 °C under an argon atmosphere. The reaction was warmed to 0 °C and stirred for 1 h. DMF (2.4 mL, 31.4 mmol, 4.38 eq) was then added dropwise to the reaction at -78 °C under an argon atmosphere. The reaction was warmed to 0 °C and stirred for 30 min under an argon atmosphere. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was quenched with saturated aqueous MLCl solution and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound 2,3-dimethoxyisonicotinaldehyde (250 mg, 20.83%). LCMS: 168.00 [M+H]+.
Synthesis of 4-(4-chlorophenyl)piperidine
Step-1: Synthesis of tert-butyl 4-(4-chlorophenyl)-3,6-dihydropyridine-l(2H)-carboxylate
( 273J A pyrex tube was charged with a solution of l-bromo-4-chlorobenzene (2 g, 10.44 mmol, 1 eq), tert-butyl 4-(4,4,5,5-tetramethyl-l,3,2-dioxaborolan-2-yl)-3,6-dihydropyridine- l(2H)-carboxylate (3.87 g, 12.53 mmol, 1.2 eq) and potassium carbonate (2.8 g, 20.6 mmol, 2.5 eq) in a mixture of water (4 mL) and DMF (20 mL). The tube was sealed with a septum and the reaction mixture was purged with argon via an argon balloon for 15 min. [1,T- Bis(diphenylphosphino)ferrocene]palladium(II) dichloride (752 mg, 1.04 mmol, 0.1 eq) was then added to the reaction under an argon atmosphere and the purging with argon was continued for 5 min. The tube was then sealed with a screw cap and the reaction was heated at 80 °C for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was cooled to room temperature and the reaction mixture was filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was diluted with ethyl acetate and washed with water and brine. The organic layer was dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound tert-butyl 4-(4-chlorophenyl)-3,6-dihydropyridine- 1 (2H)-carboxylate (1.5 g, 49%). LCMS: 294.10 [M+H]+.
Step-2: Synthesis of tert-butyl 4-(4-chlorophenyl)piperidine-l-carboxylate
(02741 To a stirred solution of tert-butyl 4-(4-chlorophenyl)-3,6-dihydropyridine-l(2H)- carboxylate (1 g, 3.4 mmol, 1 eq) in ethyl acetate (20 mL), the reaction mixture was purged with nitrogen for 5 min and platinum(IV) oxide (150 mg, 15% w/w) was added under an atmosphere of nitrogen. The reaction mixture was then purged with hydrogen for 2 min and stirred at room temperature for 3 h under an atmosphere of hydrogen via hydrogen balloon. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was filtered through a pad of Celite and the Celite pad was washed with ethyl acetate. The filtrate was
concentrated under reduced pressure to dryness to afford the titled compound tert-butyl 4-(4- chlorophenyl)piperidine-l-carboxylate (900 mg, crude). This compound was used in the next step without further purification. LCMS: 296.10 [M+H]+.
Step-3: Synthesis of 4-(4-chlorophenyl)piperidine f0275J To a stirred solution of tert-butyl 4-(4-chlorophenyl)piperidine-l-carboxylate (990 mg, 3.35 mmol, 1 eq) in DCM (5 mL), trifluoroacetic acid (5 mL) was added dropwise at 0 °C. The reaction was warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure. The residue was dissolved in saturated aqueous NaHCCh solution and extracted with DCM. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound 4-(4-chlorophenyl)piperidine (600 g, 91.6%). LCMS: 196.10 [M+H]+.
Step-1: Procedure for synthesis of 1 -(tert-butyl) 3-methyl pyrrolidine- 1 ,3-dicarboxylate 0276J To a stirred solution of l-(tert-butoxycarbonyl)pyrrolidine-3-carboxylic acid (5 g, 23.23 mmol, 1 eq) in acetone (20 mL), cesium carbonate (15.14 g, 46.46 mmol, 2 eq) followed by iodomethane (4.9 g, 34.85 mmol, 1.5 eq) were added. The reaction was stirred at room temperature for 4 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure. The residue was dissolve in water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the titled compound l-(tert-
butyl) 3-methyl pyrrolidine- 1, 3 -dicarboxylate (3 g, crude). This compound was used in the next step without further purification. LCMS: 230.15 [M+H]+.
Step-2: Procedure for synthesis of tert-butyl 3-(hydroxymethyl)pyrrolidine- 1 -carboxylate :
|0277J To a stirred solution of 1 -(tert-butyl) 3-methyl pyrrolidine- 1, 3 -dicarboxylate (3 g,
13.33 mmol, 1 eq) in methanol (10 mL), sodium borohydride (1.5 g, 39.99 mmol, 3 eq) was added in portions at 0 °C. The reaction was warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was quenched with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure. The crude product was purified by column chromatography on silica gel to afford the titled compound tert-butyl 3-
(hydroxymethyl)pyrrolidine-l -carboxylate (1 g, 50%). LCMS: 202.15 [M+H]+.
Step-3: Procedure for synthesis of tert-butyl 3-(((methylsulfonyl)oxy)methyl)pyrrolidine-l- carboxylate:
[0278] To a stirred solution of tert-butyl 3 -(hydroxymethyl)pyrrolidine-l -carboxylate (500 mg, 2.53 mmol, 1 eq), triethyl amine (0.71 mL, 5.07 mmol, 2 eq) and DMAP (31 mg, 0.025 mmol, 0.01 eq) in DCM (5 mL), methanesulfonyl chloride (0.24 mL, 3.04 mmol, 1.2 eq) was added dropwise at 0 °C. The reaction was warmed to room temperature and stirred for 4 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction was quenched with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the titled compound tert-butyl 3-(((methylsulfonyl)oxy)methyl)pyrrolidine-l-carboxylate (600 mg, crude). This compound was used in the next step without further purification.
Example Cl: Synthetic scheme for synthesis of l'-((2,3-dimethoxyphenyl)(l-phenethyl-lH- tetrazol-5-yl)methyl)-6-fluoro-l-methylspiro[indoline-3,4'-piperidine] (C-1):
C-1
[0279) To a stirred solution of 6-fluoro-l-methylspiro[indoline-3,4'-piperidine] (Cl .1) (85 mg, 0.386 mmol, 1 eq) in methanol (1.7 mL), 2,3-dimethoxybenzaldehyde (Cl.2) (70.6 mg, 0.425 mmol, 1.1 eq) and (2-isocyanoethyl)benzene (Cl.3) (55.7 mg, 0.425 mmol, 1.1 eq) were added, and followed by the addition of azidotrimethyl silane (0.056 mL, 0.425 mmol, 1.1 eq) at room temperature and the reaction mixture was stirred for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure. The crude product was purified by Combiflash chromatography on silica gel. The compound was further triturated with n-pentane, the solids were filtered out and dried under reduced pressure to afford T-((2,3-dimethoxyphenyl)(l-phenethyl-lH-tetrazol-5-yl)methyl)-6- fluoro-l-methylspiro[indoline-3,4'-piperidine] (C-1). Yield: 61 mg, 29%; Appearance: White solid; ¾NMR (400 MHz, DMSO-de) d 7.32 - 7.20 (m, 3H), 7.16 - 6.99 (m, 5H), 6.96 - 6.91 (m, 1H), 6.33 - 6.25 (m, 2H), 5.29 (s, 1H), 4.74 - 4.56 (m, 2H), 3.81 (s, 3H), 3.73 (s, 3H), 3.11 (s, 2H), 3.13 - 3.03 (m, 2H), 2.69 (s, 3H), 2.72 - 2.66 (m, 2H), 2.08 - 1.97 (m, 2H), 1.74 - 1.64 (m, 2H), 1.54 - 1.44 (m, 2H); HPLC purity: 99.73%; LCMS Calculated for C31H35FN6O2: 542.28; Observed: 543.40 [M+H]+.
Example C2: General synthesis of certain tetrazole compounds:
[0280] Step 1. Synthesis of N-(2 -phenyl ethyl)formamide
{02811 The mixture of 2 -phenyl ethan-1 -amine (30 g, 247 mmol) and formic acid (366 g, 7950 mmol, 300mL) was refluxed for 30 hours followed by cooling to room temperature and evaporation of formic acid excess under reduced pressure. The residue was partitioned between water/ethyl acetate mixture (300 mL/300 mL). The organic layer was separated, dried over sodium sulfate, filtered and evaporated under reduced pressure to afford N-(2-phenylethyl)formamide (8.5 g, 56.9 mmol, 90% purity, 20.7%) that was used in next step without further purification.
{0282] Step 2. Synthesis of (2 isocyanoethyl)benzene
[0283] Phosphoroyl trichloride (9.6 g, 62.6 mmol) was added dropwise at -15 °C to a solution of N-(2-phenylethyl)formamide (8 g, 53.6 mmol) and triethylamine (17.3 g, 170 mmol) in DCM (100 mL) and the mixture was stirred for 1 h and poured into saturated aq NaiCCh solution (200 mL). The organic layer was separated, dried over sodium sulfate, filtered and evaporated under reduced pressure to afford (2 isocyanoethyl)benzene as an yellow oil (4 g, 30.4 mmol, 95% purity, 54.0% yield).
[0284] Step 3: Synthesis of tetrazole compounds
[0285] 2-isocyanoethyl)benzene (1 eq.), 2,3-dimethoxybenzaldehyde (1 eq.) and azidotrimethylsilane (1 eq.) were added to a stirred solution of amine (0.9 - 1 eq.) in MeOH (10 mL). The reaction mixture was stirred at room temperature for 12 hours and evaporated under reduced pressure. The residue was subjected to HPLC (deionized water/HPLC-grade methanol or acetonitrile) or normal phase column chromatography.
[0286] The following examples were prepared using standard chemical manipulations and procedures similar to those used for the preparation of the previous example as indicated in the table below:
Example C3: Synthesis of N-tert-butyl-l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH- l,2,3,4-tetrazol-5-yl]methyl]-N-methylpiperidine-4-carboxamide, C-124:
Step 3
[0287J Step 1. Synthesis of benzyl 4-(tert-butyl(methyl)carbamoyl)piperidine-l-carboxylate [0288J HATU (0.946 g, 2.49 mmol) was added to a stirred solution of l- [(benzyloxy)carbonyl]piperidine-4-carboxylic acid (0.6 g, 2.27 mmol) and DIPEA (0.439 g, 3.4 mmol) in dry DCM (10 mL). The mixture was stirred for 10 min and cooled to 0 °C. tert- Butylmethylamine (0.237 g, 2.72 mmol) was added in one portion and resulting mixture was stirred for 12 h at room temperature. After, water (10 mL) was added, and organic layer was separated. Aqueous phase was extracted with DCM (10 mL x 2) and organic layers were combined, washed with 10% NaHSCri aq solution (20 mL), saturated NaHCCh aq solution (20 mL) and brine (20 mL), dried over NaiSCL, filtered and evaporated. The residue (1 g, ca 50% purity) was purified by column chromatography (chloroform/acetonitrile) to obtain benzyl 4-(tert- butyl(methyl)carbamoyl)-piperidine-l-carboxylate (0.5 g, 1.5 mmol, 95% purity, 62.9% yield).
{0289J Step 2. Synthesis of N-(tert-butyl)-N-methylpiperidine-4-carboxamide
|()290J Benzyl 4-[tert-butyl(methyl)carbamoyl]piperidine-l-carboxylate (0.5 g, 1.5 mmol) was dissolved in methanol (10 mL) and treated with 10% Pd/C (0.05 g). The resulting mixture was hydrogenated at 1 atm and room temperature until the reaction was completed (TLC control). The catalyst was filtered off and the filtrate was evaporated to afford N-(tert-butyl)-N- methylpiperidine-4-carboxamide (0.25 g, 1.26 mmol, 95% purity, 79.7% yield). jj029t| Step 3. Synthesis ofN-tert-butyl-l-[(2, 3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l, 2,3,4- tetrazol-5-yl]methyl]-N-methylpiperidine-4-carboxamide
[0292J (2-isocyanoethyl)benzene (0.181 g, 1.38 mmol), 2,3 -dimethoxybenzaldehyde (0.229 g,
I.38 mmol), and azidotrimethylsilane (0.158 g, 1.38 mmol) were added to a stirred solution of N- tert-butyl-N-methylpiperidine-4-carboxamide (0.25 g, 1.26 mmol) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC purification (deionized water/HPLC -grade methanol, ammonia) that afforded N-tert-butyl-l-[(2,3- dimethoxyphenyl)[l -(2 -phenyl ethyl)- 1H- 1,2,3, 4-tetrazol-5-yl]methyl]-N-methylpiperidine-4- carboxamide, C-124. Yield: 45.8 mg, 6.63 %; Appearance: Beige solid; ¾ NMR (400 MHz, DMSO- e) d 7.20 (dd, J= 16.5, 7.1 Hz, 3H), 7.14 - 7.05 (m, 2H), 7.01 (dt, J= 14.3, 7.9 Hz, 2H), 6.89 (d, J= 7.7 Hz, 1H), 5.30 (s, 1H), 4.73 - 4.60 (m, 1H), 4.56 (q, J= 7.3, 6.9 Hz, 1H), 3.76 (s, 3H), 3.62 (s, 3H), 3.02 (d, J= 6.7 Hz, 2H), 2.79 (s, 3H), 2.71 (d, J= 11.0 Hz, 1H), 2.58 (d, J =
I I.6 Hz, 1H), 2.39 (s, 1H), 2.03 (s, 1H), 1.93 (s, 1H), 1.48 (s, 4H), 1.26 (s, 9H); HPLC purity: 98.38%; LCMS Calculated for C29H40N6O3: 520.68; Observed: 521.4 [M+H]+.
Example C4: Synthesis of N-tert-butyl-l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH- l,2,3,4-tetrazol-5-yl]methyl]-4-methylpiperidine-4-carboxamide, C-143:
|0293| Step 1. Synthesis of tert-butyl 4-(tert-butylcarbamoyl)-4-methylpiperidine-l-carboxylate {0294J HATU (0.86 g, 2.26 mmol) was added to a stirred solution of l-[(tert-butoxy)carbonyl]-4- methylpiperidine-4-carboxylic acid (0.5 g, 2.05 mmol) and DIPEA (0.8162 g, 6.31 mmol) in dry DCM (10 mL). The mixture was stirred for 10 min and cooled to 0 °C. Tert-butylamine (0.18 g, 2.46 mmol) was added in one portion and the resulting mixture was stirred for 12 h at room temperature. After, water (10 mL) was added and organic layer was separated. Aqueous phase was extracted with DCM (10 mL x 2) and organic layers were combined, washed with 10% NaHSCri aq solution (20 mL), saturated NaHCCh aq solution (20 mL) and brine (20 mL), dried over sodium sulfate, filtered and evaporated to afford tert-butyl 4-(tert-butylcarbamoyl)-4-methylpiperidine-l- carboxylate (0.7 g, 1.16 mmol, 50% purity, 57.1% yield) that was used in the next step without further purification. j()295| Step 2. Synthesis of N-tert-butyl-4-methylpiperidine-4-carboxamide hydrochloride
{02961 Acetyl chloride (1.54 g, 19.6 mmol) was added dropwise to a cooled stirred methanol (10 mL). After 15 min tert-butyl 4-(tert-butylcarbamoyl)-4-methylpiperidine-l-carboxylate (0.7 g, 1.16 mmol, 50% purity) was added in one portion and the solution was left with stirring for 3 h. Solvent was evaporated and the residue was treated with acetone (10 mL), crude solid was filtered and air-dried to afford N-tert-butyl-4-methylpiperidine-4-carboxamide hydrochloride (0.31 g, 1.32 mmol, 95% purity, 82.5% yield).
{02971 Step 3. Synthesis ofN-tert-butyl-l-[(2, 3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l, 2,3,4- tetrazol-5-yl]methyl]-4-methylpiperidine-4-carboxamide
{0298J (2-isocyanoethyl)benzene (0.19 g, 1.44 mmol), 2,3-dimethoxybenzaldehyde (0.24 g, 1.44 mmol), triethylamine (0.1488 g, 1.46 mmol) and azidotrimethylsilane (0.17 g, 1.47 mmol) were added to a stirred solution of N-tert-butyl-4-methylpiperidine-4-carboxamide hydrochloride (0.31 g, 1.32 mmol) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC purification (deionized water/HPLC -grade acetonitrile) that afforded for N-tert-butyl-1 -[(2,3-dimethoxyphenyl)[ 1 -(2-phenylethyl)- 1H- 1 ,2,3,4-tetrazol-5- yl]methyl]-4-methylpiperidine-4-carboxamide, C-143. Yield: 21.8 mg, 3.01 %; Appearance: Beige solid; NMR (600 MHz, DMSO -d6) d 7.24 (t, J= 7.4 Hz, 2H), 7.19 (t, J= 7.2 Hz, 1H), 7.08 (d, J= 7.4 Hz, 2H), 7.03 (d, J= 8.0 Hz, 1H), 7.02 - 6.95 (m, 1H), 6.92 (d, J= 7.7 Hz, 1H), 6.51 (s, 1H), 5.20 (s, 1H), 4.63 (dt, J= 14.0, 7.0 Hz, 1H), 4.55 (dt, J= 14.4, 7.6 Hz, 1H), 3.77 (s, 3H), 3.63 (s, 3H), 3.01 (t, J= 7.4 Hz, 2H), 2.38 (s, 1H), 2.26 (s, 1H), 2.16 (d, J= 10.5 Hz, 1H), 2.04 (t, J= 10.0 Hz, 1H), 1.89 (s, 2H), 1.26 (dd, J= 16.8, 7.0 Hz, 2H), 1.17 (s, 9H), 0.96 (s, 3H); HPLC purity: 100%; LCMS Calculated for CiiHtoNeCb: 520.68; Observed: 521 4 [M+H]+
Example C5: Synthesis of l-{l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l, 2,3,4- tetrazol-5-yl]methyl]piperidin-4-yl}-2,2-dimethylpropan-l-one, C-141
Step 1 Step 2 C-141
{0299[ Step 1. Synthesis of 4-pi valoylpiperi din- 1-ium chloride
[0300] tert-butyl 4-pivaloylpiperidine-l-carboxylate (0.2 g, 0.742 mmol) was dissolved in 1M MeOH*HCl (10 mL). The reaction mixture was stirred for lh, then evaporated under reduced pressure and ether (10 mL) was added to precipitate the product. The solid was filtered-off, washed with ether (10 mL) and dried on air to give 2,2-dimethyl-l-(piperidin-4-yl)propan-l-one hydrochloride (0.145 g, 0.708 mmol, 90% purity, 85.5% yield) that was used in next step without further purification.
[0301] Step 2. Synthesis of l-{ l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl]methyl]piperidin-4-yl } -2,2-dimethylpropan- 1 -one j0302| (2-isocyanoethyl)benzene (0.102 g, 0.769 mmol), 2,3 -dimethoxybenzaldehyde (0.13 g, 0.782 mmol), azidotrimethylsilane (0.09 g, 0.781 mmol) were added to a stirred solution of 2,2- dimethyl- l-(piperidin-4-yl)propan-l -one hydrochloride (0.145 g, 0.708 mmol) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC (deionized water/HPLC -grade methanol) that afforded l-{l-[(2,3-dimethoxyphenyl)[l-(2- phenyl ethyl)- 1H- 1 ,2,3 ,4-tetrazol-5-yl]methyl]piperidin-4-yl } -2,2-dimethyl propan- 1 -one, C- 141. Yield: 59.9 mg, 15.0 %; Appearance: Yellow solid; ¾ NMR (600 MHz, DMSO- e) d 7.26 (d, J = 7.5 Hz, 2H), 7.24 - 7.16 (m, 1H), 7.15 - 7.07 (m, 2H), 7.05 (d, J= 8.0 Hz, 1H), 7.03 - 6.98 (m, 1H), 6.91 (dd, J= 7.7, 1.6 Hz, 1H), 5.32 (s, 1H), 4.63 (ddd, J= 14.0, 8.0, 6.2 Hz, 1H), 4.55 (dt, J = 14.2, 7.6 Hz, 1H), 3.78 (s, 3H), 3.64 (s, 3H), 3.03 (qt, J= 13.8, 7.2 Hz, 2H), 2.80 (dt, 7= 10.3, 5.3 Hz, 1H), 2.75 (d, J= 12.0 Hz, 1H), 2.61 (d, J= 11.5 Hz, 1H), 2.05 (td, J= 11.0, 4.3 Hz, 1H), 1.95 (td, J= 10.8, 4.8 Hz, 1H), 1.45 (d, J= 8.8 Hz, 4H), 1.02 (s, 9H); HPLC purity: 97.34%; LCMS Calculated for C28H37N5O3: 491.64; Observed: 492.2 [M+H]+.
Example C6: tert-butyl({l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5- yl]methyl]piperidin-4-yl}methyl)amine, C-140
Step 1 Step 2 C-140
{0303! Step 1. Synthesis of N-(tert-butyl)-l-((2,3-dimethoxyphenyl)(l-phenethyl-lH-tetrazol-5- yl)methyl)piperidine-4-carboxamide
[0304j (2-isocyanoethyl)benzene (0.131 g, 0.998 mmol), 2, 3-dimethoxybenzaldehyde (0.167 g, 0.998 mmol), azidotrimethylsilane (0.115 g, 0.998 mmol), triethylamine (0.0918 g, 0.909 mmol) were added to a stirred solution of N-tert-butylpiperidine-4-carboxamide hydrochloride (0.2 g, 0.906 mmol) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (TLC control), the reaction mixture was diluted with methanol (10 mL), filtered and the obtained solid was triturated with pentane (15 mL) and dried under reduced pressure. The crude product was purified by HPLC (deionized water/HPLC -grade methanol) to afford N-tert- butyl-l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5-yl]methyl]-piperidine- 4-carboxamide (0.25 g, 0.493 mmol, 95% purity, 46.9% yield).
[0305j Step 2. Synthesis of tert-butyl({l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l, 2,3,4- tetrazol-5-yl]methyl]piperidin-4-yl}methyl)amine
[0306J 2M Borane dimethyl sulfide complex THF solution (0.5 mL) was added to a stirred solution of N-(tert-butyl)-l-((2,3-dimethoxyphenyl)(l-phenethyl-lH-tetrazol-5-yl)methyl)piperidine-4- carboxamide (0.25 g, 0.493 mmol) in THF (15 mL) at room temperature under argon. The reaction mixture was heated at 40° C under a reflux condenser under argon for 16 h. After cooling to room temperature, methanol (10 mL) was added dropwise slowly. The resulting clear colorless reaction mixture was stirred vigorously and heated at 65°C under a reflux condenser under argon for 6 h. After completion, the reaction mixture was cooled to room temperature the solvent was removed under reduced pressure to give crude product that was purified by HPLC (deionized water/HPLC- grade methanol, ammonia) to afford tert-butyl({l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH- l,2,3,4-tetrazol-5-yl]methyl]piperidin-4-yl}methyl)amine C-140. Yield: 109.0 mg, 42.9 %; Appearance: Light brown oil; Ή NMR (600 MHz, DMSO -d6) d 7.40 - 7.24 (m, 2H), 7.24 - 7.18 (m, 1H), 7.12 (d, 7= 7.3 Hz, 2H), 7.06 (td, 7 = 7.9, 1.6 Hz, 1H), 7.01 (dt, 7= 8.2, 1.7 Hz, 1H), 6.96 (dt, 7= 7.6, 1.7 Hz, 1H), 5.27 (d, 7= 1.5 Hz, 1H), 4.63 (dp, 7= 29.2, 7.3 Hz, 2H), 3.80 (d, 7= 1.6 Hz, 3H), 3.68 (d, 7= 1.6 Hz, 3H), 3.05 (t, 7= 7.5 Hz, 2H), 2.71 (d, 7= 11.0 Hz, 1H), 2.56 (s, 1H), 2.28 (s, 2H), 1.91 (dt, 7= 27.0, 10.7 Hz, 2H), 1.61 (s, 2H), 1.10 (d, 7= 8.8 Hz, 4H), 0.97 (d, 7 = 1 6 Hz, 9H); HPLC purity: 100%; LCMS Calculated for CisHtoNeCh 492.67; Observed: 493 4 [M+H]+.
Example Cl: Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl]methyl]-4-(l-methoxycyclohexanecarbonyl)piperazine, C-128:
0307J Step 1. Synthesis of tert-butyl 4-(l-methoxycyclohexanecarbonyl)piperazine-l- carboxylate
[0308J 1-methoxycyclohexane-l -carboxylic acid (0.5 g, 3.16 mmol) was added to a solution of HATU (1.31 g, 3.47 mmol) and DIPEA (1.22 g, 9.48 mmol) inDCM (15 mL) and the mixture was stirred at room temperature for 15 min. tert-butyl piperazine- 1-carboxylate (0.6 g, 3.22 mmol) was added to the reaction mixture. The mixture was stirred overnight, then poured into water (20 mL) and extracted with EtOAc (25 mL x 2). The organic layer was washed with brine (50 mL), dried over NaiSCL, filtered and evaporated in vacuum to give tert-butyl 4-(l- methoxycyclohexanecarbonyl)piperazine- 1-carboxylate (0.7 g, 2.14 mmol, 67% purity, 45.4% yield) that was used in next step without further purification. 0309J Step 2. Synthesis of l-(l-methoxycyclohexanecarbonyl)piperazine hydrochloride [0310J tert-butyl 4-(l-methoxycyclohexanecarbonyl)piperazine-l-carboxylate (0.7 g, 2.14 mmol, 67% purity) was dissolved in 1M MeOH*HCl (10 mL). The reaction mixture was stirred for lh, then evaporated and ether (10 mL) was added to precipitate the product. The solid was filtered- off, washed with ether (10 mL) and dried on air to give 1-(1- methoxycyclohexanecarbonyl)piperazine hydrochloride (0.4 g, 1.52 mmol, 70% purity, 49.8% yield) that was used in next step without additional purification.
[03111 Step 3. Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5- yl]methyl]-4-(l-methoxycyclohexanecarbonyl)piperazine
[0312J (2-isocyanoethyl)benzene (0.253 g, 1.93 mmol), 2,3-dimethoxybenzaldehyde (0.320 g, 1.93 mmol), azidotrimethylsilane (0.222 g, 1.93 mmol) were added to a stirred solution of 1-(1- methoxycyclohexanecarbonyl)piperazine hydrochloride (0.4 g, 1.52 mmol, 70% purity) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected
to HPLC (deionized water/HPLC -grade acetonitrile) that afforded l-[(2,3-dimethoxyphenyl)[l-(2- phenylethyl)-lH-l,2,3,4-tetrazol-5-yl]methyl]-4-(l-methoxycyclohexanecarbonyl)piperazine, C- 128. Yield: 364.7 mg, 35.8 %; Appearance: Yellow solid; Ή NMR (600 MHz, DMSO -d6) d 7.24 (t, J= 7.5 Hz, 2H), 7.17 (t, J= 7.4 Hz, 1H), 7.06 (d, J= 7.7 Hz, 2H), 7.02 (dd, J= 17.6, 7.9 Hz, 2H), 6.89 (d, J= 7.7 Hz, 1H), 5.26 (s, 1H), 4.60 (dt, J= 13.7, 6.8 Hz, 1H), 4.51 (dt, J= 14.4, 7.7 Hz, 1H), 3.88 (d, J= 21.7 Hz, 1H), 3.78 (s, 3H), 3.75 (s, 1H), 3.70 (s, 3H), 3.48 (d, J= 29.6 Hz, 1H), 3.36 (s, 1H), 3.02 (s, 3H), 2.98 (dd, J= 15.0, 7.5 Hz, 2H), 2.35 (s, 2H), 2.20 (d, J= 28.6 Hz, 2H), 1.78 (d, J= 13.8 Hz, 2H), 1.60 - 1.45 (m, 3H), 1.42 (p, J= 4.9, 4.2 Hz, 4H), 1.24 - 1.07 (m, 1H); HPLC purity: 100%; LCMS Calculated for C30H40N6O4: 548.69; Observed: 5494 [M+H]+.
Example C8: Synthesis of 2-{4-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4- tetrazol-5-yl] methyl] piperazine- l-carbonyl}-2-azabicyclo [2.1.1] hexane, C- 168
[0313] Step 1. Synthesis of tert-butyl 4-{2-azabicyclo[2.1.1]hexane-2-carbonyl}piperazine-l- carboxylate
[0314] Ethylbis(propan-2-yl)amine (2.15 g, 16.7 mmol) was added to a stirred solution of tert- butyl 4-(carbonochloridoyl)piperazine-l-carboxylate (1.55 g, 6.27 mmol) and 2- azabicyclo[2.1.1]hexane hydro-chloride (0.5 g, 4.18 mmol) in dry DCM (20 mL). The mixture was stirred at room temperature until the reaction completion (TLC control). Then the reaction mixture was poured into water (20 mL) and the product was extracted with EtOAc (25 mL x 2). The combined organic layers were washed with brine (50 mL), dried over NaiSCL, filteres and evaporated in vacuum to give crude tert-butyl 4-{2-azabicyclo[2.1.1]hexane-2- carbonyl (piperazine- 1-carboxylate (1.2 g, 4.06 mmol, 90.7% purity, 87.8% yield) that was used in next step without further purification.
[0315] Step 2. Synthesis of 2-(piperazine-l-carbonyl)-2-azabicyclo[2.1.1]hexane
{03161 tert-butyl 4-{2-azabicyclo[2.1.1]hexane-2-carbonyl}piperazine-l-carboxylate (1.2 g, 4.06 mmol) was dissolved in 1M MeOH*HCl (10 mL). The reaction mixture was stirred for lh, evaporated and ether (15 mL) was added to precipitate the product. White solid was filtered-off, washed with ether (15 mL) and dried on air. The crude product was purified by HPLC (deionized water/ HPLC-grade methanol, ammonia) to give 2-(piperazine-l-carbonyl)-2- azabicyclo[2.1.1]hexane (0.12 g, 0.614 mmol, 100% purity, 15.1% yield).
{03171 Step 3. Synthesis of 2-{4-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl]methyl]piperazine-l-carbonyl}-2-azabicyclo[2.1.1]hexane
{0318| (2-isocyanoethyl)benzene (0.88 g, 0.664 mmol), 2,3-dimethoxybenzaldehyde (0.11 g, 0.664 mmol), triethylamine (0.211 g, 2.08mmol) and azidotrimethyl silane (0.077 g, 0.664 mmol) were added to a stirred solution of 2-(piperazine-l-carbonyl)-2-azabicyclo[2.1.1]hexane (0.119 g, 0.614 mmol) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC (deionized water/HPLC -grade acetonitrile) that afforded a 2-{4- [(2,3 -dimethoxyphenyl)[ 1 -(2 -phenyl ethyl)- 1H- 1 ,2,3 ,4-tetrazol-5-yl]methyl]piperazine- 1 - carbonyl}-2-azabicyclo[2.1.1]hexane C-168. Yield: 123.8 mg, 37.5 %; Appearance: Beige solid;
NMR (400 MHz, DMSO -d6) d 7.28 (t, J= 7.3 Hz, 2H), 7.21 (t, J= 7.2 Hz, 1H), 7.15 - 7.09 (m, 2H), 7.08 - 6.99 (m, 2H), 6.95 (dd, J= 7.5, 1.9 Hz, 1H), 5.32 (s, 1H), 4.67 (dd, J= 14.0, 6.9 Hz, 1H), 4.56 (dt, J = 14.3, 7.6 Hz, 1H), 4.01 (d, J= 6.9 Hz, 1H), 3.81 (s, 3H), 3.72 (s, 3H), 3.26 (d, 7= 10.1 Hz, 4H), 3.17 (d, J= 17.7 Hz, 2H), 3.05 (hept, J= 7.3 Hz, 2H), 2.74 (dd, J= 6.8, 3.4 Hz, 1H), 2.37 (dt, J= 10.5, 4.9 Hz, 2H), 2.22 (dt, J= 10.6, 4.8 Hz, 2H), 1.77 (s, 2H), 1.17 (dd, J = 44, 1 9 Hz, 2H); HPLC purity: 100%; LCMS Calculated for C28H35N7O3: 517.63; Observed: 518.4 [M+H]+.
Example C9: Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5- yl]methyl]-4-(l-methoxycyclobutanecarbonyl)piperazine, C-160:
C-160
[0319J Step 1. Synthesis of tert-butyl 4-{2-azabicyclo[2.1.1]hexane-2-carbonyl}piperazine-l- carboxylate
[0320J 1-methoxycyclobutane-l -carboxylic acid (0.348 g, 2.68 mmol) was added to a solution of l-(lH-imidazole-l -carbonyl)- lH-imidazole (0.52 g, 3.21 mmol) in THF (15 mL) and the mixture was stirred at room temperature for 15 min. After tert-butyl piperazine- 1-carboxylate (0.5 g, 2.68 mmol) was added to the reaction mixture and it was stirred until reaction completion (overnight, NMR control). Then the reaction mixture was poured into water (20 mL) and the product was extracted with EtOAc (25 mL x 2). The combined organic layers were washed with brine (50 mL), dried over NaiSCL, filtered and evaporated in vacuum to give tert-butyl 4-(l- methoxycyclobutanecarbonyl)piperazine- 1-carboxylate (0.63 g, 2.11 mmol, 100% purity, 78.8% yield).
[03211 Step 2. Synthesis of 2-(piperazine-l-carbonyl)-2-azabicyclo[2.1.1]hexane [0322| tert-butyl 4-(l-methoxycyclobutanecarbonyl)piperazine-l-carboxylate (0.62 g, 2.11 mmol) was dissolved in 1M MeOH*HCl (10 mL). The reaction mixture was stirred for lh, evaporated and ether (15 mL) was added to precipitate the product. White solid was filtered-off, washed with ether (15 mL) and dried on air to give l-(l-methoxycyclobutanecarbonyl)piperazine hydrochloride (0.4 g, 1.7 mmol, 100% purity, 82.4% yield).
{0323J Step 3. Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5- yl]methyl]-4-(l-methoxycyclobutanecarbonyl)piperazine 0324j (2-isocyanoethyl)benzene (0.097 g, 0.608 mmol), 2,3-dimethoxybenzaldehyde (0.101 g, 0.608 mmol), azidotrimethylsilane (0.070 g, 0.608 mmol) were added to a stirred solution of 1-(1- methoxycyclobutanecarbonyl)piperazine hydrochloride (0.130 g, 0.553 mmol) in MeOH (5 mL). The reaction mixture was stirred at RT for 12 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC (deionized water/HPLC -grade acetonitrile) that afforded l-[(2,3-dimethoxyphenyl)[l-(2- phenylethyl)-lH-l,2,3,4-tetrazol-5-yl]methyl]-4-(l-methoxycyclobutanecarbonyl)piperazine C- 160. Yield: 148.2 mg, 48.7 %; Appearance: White solid;
NMR (400 MHz, DMSO -d6) d 7.26 (dd, J = 8.1, 6.4 Hz, 2H), 7.24 - 7.16 (m, 1H), 7.13 - 7.06 (m, 2H), 7.07 - 6.97 (m, 2H), 6.91 (dd, J= 7.4, 2.0 Hz, 1H), 5.30 (s, 1H), 4.63 (dt, J= 13.7, 6.7 Hz, 1H), 4.54 (dt, J= 14.3, 7.7 Hz, 1H), 3.81 (s, 3H), 3.72 (s, 3H), 3.56 - 3.37 (m, 4H), 3.02 (q, J= 6.7, 6.0 Hz, 2H), 2.97 (s, 3H), 2.41 (q, J= 12.9, 11.0 Hz, 4H), 2.21 (s, 2H), 2.03 (q, 7= 10.0 Hz, 2H), 1.72 (tt, 7= 9.9, 5.5 Hz, 1H), 1.49 (p, J = 8.9 Hz, 1H); HPLC purity: 100%; LCMS Calculated for CisHseNeCL: 520.63; Observed: 521.4 [M+H]+.
[ 325j Step-1: General procedure for synthesis of formamide derivatives 10.2:
{0326J A stirred solution of amine 10.1 (1 eq) in methyl formate (2.5 - 3 eq) in a pyrex tube sealed with a screw cap was stirred at reflux for 12 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was cooled to room temperature and concentrated under reduced pressure to dryness to afford formamide 10.2. This compound was used in the next step without further purification.
|0327j Step-2: General procedure for synthesis of isocyanide derivative 10.3:
|()328j To a stirred solution of formamide 10.2 (1 eq) in pyridine (10 vol), / oluenesulfonyl chloride (2.5 eq) was added at 0 °C. The reaction mixture was gradually warmed to room
temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of reaction, water was added to the reaction mixture and extracted with ethyl acetate. The combined organic layers were washed with water, dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to afford isocyanide 10.3. This compound was used in the next step without further purification. 0329] Step-3: General procedure for synthesis of tetrazole derivatives C-176:
[0330] To a stirred solution of substituted piperidine 10.4 (1 eq), 2,3-dimethoxy benzaldehyde 10.5 (1.1 eq) and isocyanide 10.3 (1.1 eq) in methanol (10 vol), azidotrimethylsilane (1.1 eq) was added dropwise at 0 °C. The reaction was warmed to room temperature and stirred for 12 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was concentrated under reduced pressure. The crude product was purified by column chromatography followed by reverse phase preparative HPLC to afford the tetrazole derivative C- 176.
[0331] Yield: 150 mg, 29%; Appearance: Off white solid; ¾ NMR (400 MHz, DMSOe) d 7.30 - 7.24 (m, 2H), 7.22 - 7.08 (m, 6H), 7.08 - 7.00 (m, 2H), 7.00 - 6.94 (m, 3H), 5.32 - 5.22 (m, 2H), 3.82 (s, 3H), 3.61 (s, 3H), 3.15 (dd, J= 6.4, 14.0 Hz, 1H), 3.00 (dd, J= 8.0, 13.2 Hz, 1H), 2.83 (d, J = 10.4 Hz, 1H), 2.73 (d, J= 10.8 Hz, 1H), 2.42 - 2.32 (m, 1H), 2.17 (t, J= 8.8 Hz, 1H), 2.07 (t, J = 10.4 Hz, 1H), 1.74 - 1.54 (m, 4H), 1.53 (d, J = 6.4 Hz, 3H); HPLC purity: 97.76%; LCMS calculated for C30H35N5O2: 497.28; Observed: 498.13 [M+H]+.
[0332] The following examples were prepared using standard chemical manipulations and procedures similar to those used for the example above:
Example Cll: Synthesis of ((3r,5r,7r)-adamantan-l-yl)(4-((2,3-dimethoxyphenyl)(l- phenethyl-lH-tetrazol-5-yl)methyl)piperazin-l-yl)methanone, C-173
[0333) Step-1: Procedure for the synthesis of tert-butyl 4-((2,3-dimethoxyphenyl)(l-phenethyl- lH-tetrazol-5-yl)methyl)piperazine-l-carboxylate 11.4:
{0334J To a stirred solution of 2,3-dimethoxy benzaldehyde 11.1 (5 g, 30.1 mmol, 1 eq), N-Boc piperazine 11.2 (6.26 g, 33.1 mmol, 1.1 eq) and isocyanide 11.3 (4.6 mL, 33.1 mmol, 1.1 eq) in methanol (100 mL) was added trimethyl silyl azide (4.4 mL, 33.1 mmol, 1.1 eq) dropwise at room temperature and the reaction mixture was stirred at ambient temperature for 5 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was concentrated under reduced pressure. The crude product was purified by combiflash chromatography on silica gel to afford the phenethyl tetrazole 11.4 (14.5 g, 94.8%). LCMS: 509.30 [M+H]+.
[0335) Step-2: Procedure for the synthesis of l-((2,3-dimethoxyphenyl)(l-phenethyl-lH-tetrazol- 5-yl)methyl)piperazine 11.5:
[Q336) To a stirred solution of phenethyl tetrazole 11.4 (14.5 g, 28.5 mmol, 1 eq) in DCM (72.5 mL) was added trifluoroacetic acid (72.5 mL) dropwise at 0 °C. The reaction mixture was warmed to room temperature and stirred for 12 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was concentrated under reduced pressure to dryness and triturated with diethyl ether. The residue was dissolved in saturated aqueous NaHCCh solution and extracted with ethyl acetate. The combined organic layers were dried over anhydrous
Na2SC>4, filtered and concentrated under reduced pressure to dryness to afford piperazine 11.5 (8 g, crude). This compound was used in the next step without further purification. LCMS: 409.23 [M+H]+. 0337J Step-3: Method A: Procedure for the synthesis of ((3r,5r,7r)-adamantan-l-yl)(4-((2,3- dimethoxyphenyl)(l-phenethyl-lH-tetrazol-5-yl)methyl)piperazin-l-yl)methanone, C-173:
[033SJ To a stirred solution of piperazine 11.5 (250 mg, 0.612 mmol, 1 eq) in DCM (5 mL) was added triethyl amine (0.17 mL, 1.22 mmol, 2 eq) at 0 °C. (3r,5r,7r)-adamantane-l-carbonyl chloride 11.6 (146 mg, 0.735 mmol, 1.2 eq) was then added dropwise to the reaction mixture at 0 °C. The reaction mixture was warmed to room temperature and stirred for 4 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with DCM. The combined organic layers were dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness. The crude product was purified by combiflash chromatography on silica gel to afford ((3r,5r,7r)-adamantan-l-yl)(4-((2,3- dimethoxyphenyl)(l-phenethyl-lH-tetrazol-5-yl)methyl)piperazin-l-yl)methanone C-173.
[0339[ Yield: 130 mg, 37.2%; Appearance: White solid; ¾NMR (400 MHz, DMSO-de) d 7.30 - 7.24 (m, 2H), 7.22 - 7.17 (m, 1H), 7.12 - 7.00 (m, 4H), 6.93 (d, J= 7.6 Hz, 1H), 5.27 (s, 1H), 4.70 - 4.50 (m, 2H), 3.80 (s, 3H), 3.72 (s, 3H), 3.57 - 3.45 (m, 4H), 3.30 - 3.26 (m, 1H), 3.09 - 2.98 (m, 2H), 2.38 - 2.30 (m, 2H), 2.22 - 2.14 (m, 2H), 1.94 (bs, 3H), 1.88 - 1.78 (m, 5H), 1.70 - 1.59 (m, 6H); HPLC purity: 98.74%; LCMS calculated for C33H42N6O3: 570.33; Observed: 571.40 [M+H]+. 0340J Method B: To a stirred solution of acid 11.6a (100 mg, 0.694 mmol, 1 eq) in DMF (4 mL) were added DIPEA (0.24 mL, 1.38 mmol, 2 eq) and HATU (316 mg, 0.832 mmol, 1.2 eq) and the reaction mixture was stirred at room temperature for 10 min. Piperazine 1 (283 mg, 0.694 mmol, 1 eq) was then added to the reaction mixture and stirred at room temperature for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness. The crude product was purified by reverse phase preparative HPLC to afford the titled compound.
[0341J The following examples were prepared using standard chemical manipulations and procedures similar to those used for the preparation of the example above:
Example 02: Synthesis of l-(4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)methyl)-lH-tetrazol-l-yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one, C-158 and 1- (4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-2H-tetrazol-2- yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one, C-156:
[0342) Step-1 & 2: Procedure for the synthesis of 1 -((2,3-dimethoxyphenyl)( 1 //-tetrazol-5- yl)methyl)-4-phenylpiperidine 12.5:
|0343| To a stirred solution of 2,3-dimethoxybenzaldehyde 12.1 (4.5 g, 27.1 mmol, 1.1 eq), 4- phenylpiperidine 12.2 (4.0 g, 24.84 mmol, 1.0 eq) and 2-isocyano-2-methylpropane 12.3 (2.2 g, 27.32 mmol, 1.1 eq) in MeOH (100 mL), was added azidotrimethylsilane (3.1 g, 27.32 mmol, 1.1 eq) at 0 °C. The reaction mixture was stirred at RT for 4 h. After completion of the reaction, the solid obtained was filtered and washed with methanol, dried and refluxed with aq. HCL (70 mL). The reaction mixture was allowed to cool to room temperature and neutralized by aqueous NaHCCh solution. The solid so obtained was filtered, dried under reduced pressure to afford 1- ((2,3-dimethoxyphenyl)(lH-tetrazol-5-yl)methyl)-4-phenylpiperidine 12.5 (4.5 g, 48.3%).
[0344J Step-3: Procedure for the synthesis of l-(4-(2-(5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl)methyl)- lH-tetrazol- 1 -yl)ethyl)piperazin- 1 -yl)-2,2-dimethylpropan- 1 -one,
and l-(4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-2H-tetrazol-2- yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one: 0345j Method A: To a stirred solution of l-((2,3-dimethoxyphenyl)(lH-tetrazol-5-yl)methyl)-4- phenylpiperidine 12.5 (450 mg, 1.18 mmol, 1 eq) and 2-(4-pivaloylpiperazin-l-yl)ethyl methanesulfonate 12.6 (415 mg, 1.42 mmol, 1.2 eq) in DMF (10 mL), cesium carbonate/K2C03 (770 mg, 2.36 mmol, 2 eq) was added and the reaction mixture was heated at 80 °C for 12 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was cooled to room temperature, diluted with water and extracted with 10% methanol in DCM. The combined organic layers were dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure to dryness. The crude product was purified by column chromatography on silica gel followed by reverse phase preparative HPLC to afford the titled compound l-(4-(2-(5-((2,3- dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-lH-tetrazol-l-yl)ethyl)piperazin-l-yl)-2,2- dimethylpropan-l-one C-158 and l-(4-(2-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)methyl)-2H-tetrazol-2-yl)ethyl)piperazin-l-yl)-2,2-dimethylpropan-l-one C-156.
I0346J C-158: Yield: 15 mg, 2.2%; Appearance: Off-white solid; Ή NMR (400 MHz, DMSO- de) d 7.30 - 7.00 (m, 8H), 5.62 (s, 1H), 4.64 - 4.45 (m, 2H), 3.81 (s, 3H), 3.76 (s, 3H), 3.45 - 3.35 (m, 4H), 3.04 - 2.95 (m, 1H), 2.90 - 2.82 (m, 1H), 2.78 - 2.63 (m, 2H), 2.42 - 2.26 (m, 6H), 2.23
- 2.12 (m, 1H), 1.79 - 1.60 (m, 4H), 1.16 (s, 9H); HPLC purity: 99.82%; LCMS calculated for C32H45N7O3: 575.36; Observed: 576.40 [M+H]+.
[03471 C-156 Yield: 30 mg, 4.4%; Appearance: Off-white solid; Ή NMR (400 MHz, DMSO- de) d 7.34 - 7.13 (m, 6H), 7.12 - 7.04 (m, 1H), 6.99 - 6.92 (m, 1H), 5.31 (s, 1H), 4.83 - 4.75 (m, 2H), 3.78 (s, 3H), 3.66 (s, 3H), 3.00 - 2.84 (m, 3H), 2.76 - 2.68 (m, 1H), 2.37 - 2.28 (m, 4H), 2.15
- 2.03 (m, 2H), 1.74 - 1.56 (m, 4H), 1.13 (s, 9H), (5H merged with the solvent /moisture peak); HPLC purity: 99 64%; LCMS calculated for C32H45N7O3: 575.36; Observed: 576.30 [M+H]+ [0348J Method B: To a stirred solution of l-((2,3-dimethoxyphenyl)(lH-tetrazol-5-yl)methyl)-4- phenylpiperidine 12.5 (400 mg, 1.05 mmol, 1 eq), alcohol 12.6 (449 mg, 2.11 mmol, 2 eq) and TPP (553 mg, 2.11 mmol, 2 eq) in THF (8 mL) was added DEAD (0.33 mL, 2.11 mmol, 2 eq) and the reaction mixture was stirred for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and
concentrated under reduced pressure. The crude product was purified and isolated by Combiflash chromatography followed by reverse phase preparative HPLC to afford the desired product. 0349j The following examples were prepared using standard chemical manipulations and procedures similar to those used for the preparation of the example above.
Example C13: synthesis of A-((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)methyl)-l//-tetrazol-l-yl)methyl)cyclohexyl)-/V-methylpivalamide, C-177
0350J Step-1: Procedure for the synthesis of ((lr,4r)-4-((tert- butoxycarbonyl)amino)cyclohexyl)methyl methanesulfonate (13.2):
[0351J To a stirred solution of tert-butyl ((lr,4r)-4-(hydroxymethyl)cyclohexyl)carbamate 13.1 (0.5 g, 2.18 mmol, 1 eq) in DCM (10 mL), triethyl amine (0.36 mL, 2.62 mmol, 1.2 eq) followed by methanesulfonyl chloride (0.17 mL, 2.18 mmol, 1 eq) were added at 0 °C. The reaction mixture was warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was quenched with saturated NaHCCb and extracted with DCM (2 X 20 mL). The combined organic layer was washed with water (20 mL) dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford ((lr,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)methyl methanesulfonate 2 (0.6 g, crude). This compound was used in the next step without further purification. LCMS: Desired product mass was not observed. 0352J Step-2: Procedure for the synthesis of tert- butyl ((lr,4r)-4-
(azidomethyl)cyclohexyl)carbamate (13.3):
[0353! A stirred solution of respective ((lr,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)methyl methanesulfonate 13.2 (0.6 g, 1.95 mmol, 1 eq) in DMF (12 mL) was added NalNri (0.254 g, 3.91 mmol, 2 eq). The reaction mixture was stirred at 80 °C for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was allowed to cool to
RT and quenched with cold water (30 mL). The solid so obtained was filtered, washed with water and dried to afford tert-butyl ((lr,4r)-4-(azidomethyl)cyclohexyl)carbamate 13.3 (0.45 g, crude) as a white solid. This compound was used in the next step without further purification. LCMS: Desired product mass was not observed. f0354| Step-3: Procedure for the synthesis of tert-butyl ((lr,4r)-4-
(aminomethyl)cyclohexyl)carbamate (13.4):
[03S5J To a stirred solution of respective tert- butyl ((lr,4r)-4-(azidomethyl)cyclohexyl)carbamate 13.3 (0.45 g, 1.77 mmol, 1 eq) in THF:H20 (4.5 mL:0.45 mL) was added TPP (0.56 g, 2.12 mmol, 1.2 eq). The reaction mixture was stirred at reflux temperature for 2 h. The progress of the reaction was monitored by TLC. After completion of reaction, the reaction mixture was concentrated under reduced pressure, acidified using 2N HC1 and extracted with diethyl ether (3X25 mL). The aqueous layer was basified using aqueous NaHCCb and extracted using 10% MeOH: DCM (3 X 40 mL). The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to afford the corresponding /ert-butyl ((lr,4r)-4- (aminomethyl)cyclohexyl)carbamate 4 (0.250 g, crude) as a brown semisolid. This compound was used in the next step without further purification. LCMS: Desired product mass was not observed. [0356) Step-4: Procedure for the synthesis of tert-butyl ((lr,4r)-4-
(formamidomethyl)cyclohexyl)carbamate (13.5): j0357j A solution of tert- butyl ((lr,4r)-4-(aminomethyl)cyclohexyl)carbamate 13.4 (0.25 g, 1.1 mmol, 1 eq) in methyl formate (1.25 mL, 5 vol) was stirred at RT for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure to dryness to afford tert-butyl ((lr,4r)-4- (formamidomethyl)cyclohexyl)carbamate 13.5 (0.28 g, crude). This compound was used in the next step without further purification. LCMS: Desired product mass was not observed. 0358J Step-5: Procedure for the synthesis of tert- butyl ((lr,4r)-4-
(isocyanomethyl)cyclohexyl)carbamate (13.6):
[0359J To a stirred solution of respective tert-butyl ((lr,4r)-4- (formamidomethyl)cyclohexyl)carbamate 13.5 (0.13 g, 0.51 mmol, 1 eq) in pyridine (2.5 L), p- toluenesulfonyl chloride (0.15 g, 0.76 mmol, 1.5 eq) was added portion wise at 0 °C. The reaction mixture was gradually warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, water was added to the reaction mixture
and extracted with ethyl acetate. The combined organic layers were washed with water, dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure. The crude product was purified by combiflash chromatography on silica gel using (EtOAc/n-Hexane: 10-15%) as eluent to afford /er/-butyl ((lr,4r)-4-(isocyanomethyl)cyclohexyl)carbamate 6 (0.1 g, 82.7%) as a white solid. LCMS: 239.10 [M+H]+. 0360] Step-6: Procedure for the synthesis of /er/-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl (methyl )-l //-tetrazol- 1 -yl (methyl )cyclohexyl)carbamate (13.9):
[0361] To a stirred solution of ter/-butyl ((lr,4r)-4-(isocyanomethyl)cyclohexyl)carbamate 13.6 (0.098 g, 0.41 mmol, 1.05 eq), 4-phenylpiperidine 13.7 (0.07 g, 33.1 mmol, 1.1 eq) and 2,3- dimethoxybenzaldehyde 8 (0.065, 0.39 mmol, 1 eq) in methanol (1.5 mL) was added trimethyl silyl azide (0.057 mL, 0.43 mmol, 1.1 eq) dropwise at room temperature and the reaction mixture was stirred at ambient temperature for 12 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure. The crude product was purified by combiflash chromatography on silica gel using (EtOAc/n-Hexane: 45-55%) as eluent to afford /er/-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl )m ethyl)- l/7-tetrazol-l-yl)methyl)cy cl ohexyl)carbamate 9 (0.11 g, 47.6%). LCMS: 591.1 [M+H]+.
[0362] Step-7: Procedure for the synthesis of /er/-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperi din- l-yl)m ethyl)- l/7-tetrazol-l-yl)methyl)cyclohexyl)(methyl)carbamate (10):
[0363] To a stirred solution of ter/-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin-1 -yl)methyl)-l //-tetrazol- 1 -yl)methyl)cyclohexyl)carbamate 13.9 (0.11 g, 0.19 mmol, 1 eq) in DMF (2.5 mL), was added NaH (50%, 0.011 g, 0.28 mmol, 1.5 eq) at 0 °C, the reaction mixture was stirred at the same temperature for 10 minutes and to this was added Mel (0.014 mL, 0.223 mmol, 1.2 eq). The reaction mixture was allowed to attain ambient temperature and stirred for 3 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness to afford the titled fe/7-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl )m ethyl)- 1/7-tetrazol- 1 -yl)methyl)cyclohexyl)(methyl)carbamate 13.10 (0.08 g, crude) as an off-white solid. This compound was used in the next step without further purification.
{0304J Step-8: Procedure for the synthesis of (lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperi din- l-yl)m ethyl)- li7-tetrazol-l-yl)methyl)-/V-m ethyl cy cl ohexan-1 -amine (13.11): [03651 To a stirred solution of te/7-butyl ((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperidin- 1 -yl )m ethyl)- 177-tetrazol- 1 -yl)methyl)cyclohexyl)(methyl)carbamate 13.10 (0.08 g, 0.132 mmol, 1 eq) in DCM (2.0 mL) was added trifluoroacetic acid (0.4 mL) dropwise at 0 °C. The reaction mixture was warmed to room temperature and stirred for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with DCM and basified with saturated aqueous NaHCCb solution and separated layers. The combined organic layers were dried over anhydrous Na2SC>4, filtered and concentrated under reduced pressure to dryness to afford (lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl)m ethyl)- liT-tetrazol-l-yl)methyl)-/V-m ethyl cy cl ohexan-1 -amine 13.11 (0.06 g, crude) as off white solid. This compound was used in the next step without further purification.
[0366J Step-9: Procedure for the synthesis of /V-((lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4- phenylpiperi din- l-yl)m ethyl)- li7-tetrazol-l-yl)methyl)cy cl ohexyl)-/V-methylpivalamide (C-177): [03671 To a stirred solution of (lr,4r)-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l- yl )m ethyl)- li7-tetrazol-l-yl)methyl)-/V-m ethyl cyclohexan-1 -amine 11 (0.06 g, 0.12 mmol, 1 eq) in DCM (1.5 mL), was added TEA (0.033 mL, 0.24 mmol, 2 eq) and pivaloyl chloride (0.017 g, 0.14 mmol, 1.2 eq) at 0 °C. The reaction mixture was stirred at RT for 2 h. After completion of the reaction, the reaction mixture was quenched with water (6 mL) and extracted with DCM (3 X 2 mL). The combined organic layers were dried over anhydrous NaiSCL, filtered and concentrated under reduced pressure to dryness. The crude was purified by preparative HPLC to afford N- ((!/, 4/ )-4-((5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l -yl)methyl)-l //-tetrazol-1 - yl [methyl )cycl ohexyl )-A-methyl pi val amide C-177.
I0368J Yield: 19 mg, 27%; Appearance: Off white solid; ¾ NMR (400 MHz, DMSOe) d 7.29 - 7.15 (m, 5H), 7.11 - 7.05 (m, 3H), 5.57 (s, 1H), 4.27 (d, 7= 3.2 Hz, 2H), 3.9 (m, 1H), 3.82 (s, 3H), 3.75 (s, 3H), 3.02 (d, J= 10 Hz, 1H), 2.86 (d, J= 8.8 Hz, 1H), 2.67 (s, 2H), 2.37 (t, 7= 12 Hz, 1H), 2.18 (t, J= 10.8 Hz, 1H), 1.73 - 1.63 (m, 5H), 1.56-1.41 (m, 4H), 1.41-1.35 (m, 1H), 1.17 (s, 9H), 1.12 - 0.9 (m, 2H), 3H (merged in solvent peak);; HPLC purity: 97.33%; LCMS calculated for C34H48N6O3: 588.38; Observed: 589.40 [M+H]+.
Example C14: synthesis of l-(4-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)- l//-tetrazol-l-yl)piperidin-l-yl)-2,2-dimethylpropan-l-one C-148 and l-(4-(5-((2,3- dimethoxyphenyl)(4-phenylpiperidin-l-yl)methyl)-2 -tetrazol-2-yl)piperidin-l-yl)-2,2- dimethylpropan-l-one, C-150:
C-148 C-150
|0369| Step-1 & 2: Procedure for the synthesis of l-((2,3-dimethoxyphenyl)(l-(piperidin-4-yl)- lH-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 & l-((2,3-dimethoxyphenyl)(2-(piperidin-4- yl)-2H-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 A: 0370J To a stirred solution of l-((2,3-dimethoxyphenyl)(lH-tetrazol-5-yl)methyl)-4- phenylpiperidine 14.1 (3.0 g, 7.9 mmol, 1 eq) and tert-butyl 4-bromopiperidine-l-carboxylate 14.2 (2.5 g, 9.4 mmol, 1.2 eq) in DMF (30 mL) was added K2CO3 (2.18 g, 15.8 mmol, 2 eq) and the reaction mixture was stirred at 90 °C for 16 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was diluted with water and extracted with ethyl acetate. The combined organic layers were dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure to dryness. The crude product was purified by combiflash chromatography to afford an off-white solid product (3.3 g, 74.32%). LCMS: 563.15 [M+H]+. To a stirred solution of the obtained solid product (3.3 g, 5.87 mmol, 1 eq) in DCM (40 mL) was added TFA (10 mL) at 0 °C. The reaction mixture was stirred at room temperature for 2 h. The progress of the reaction was monitored by TLC. After completion of the reaction, the reaction mixture was concentrated under reduced pressure and triturated with diethyl ether to afford 1-
((2,3-dimethoxyphenyl)(l-(piperidin-4-yl)-lH-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 & l-((2,3-dimethoxyphenyl)(2-(piperidin-4-yl)-2H-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 A (1.2 g, 44.28%) as an off white solid. This compound was used in the next step without further purification. LCMS: 463.15 [M+H]+.
|0371| Step-3: Procedure for the synthesis of l-(4-(5-((2,3-dimethoxyphenyl)(4-phenylpiperidin- 1 -yl)m ethyl)- l//-tetrazol- 1 -yl)piperidin- 1 -yl)-2,2-dimethylpropan- 1 -one and 1 -(4-(5-((2,3- dimethoxyphenyl)(4-phenylpiperidin- l -yl)methyl)-2//-tetrazol-2-yl)piperidin-l -yl)-2,2- dimethylpropan- 1 -one :
[ 372J To a stirred solution of mixture of l-((2,3-dimethoxyphenyl)(l-(piperidin-4-yl)-lH- tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3 & l-((2,3-dimethoxyphenyl)(2-(piperidin-4-yl)- 2H-tetrazol-5-yl)methyl)-4-phenylpiperidine 14.3A (0.3 g, 0.64 mmol, 1 eq) in DCM (20 mL), were added DIPEA (0.22 mL, 1.28 mmol, 2 eq) at RT and pivaloyl chloride (0.117 g, 0.97 mmol, 1.5 eq) at 0 °C. The reaction mixture was stirred at RT for 16 h. After completion of reaction, the reaction mixture was quenched with cold water and extracted with DCM. The combined organic layers were washed with water, dried over anhydrous NaiSCri, filtered and concentrated under reduced pressure to dryness. The crude product was purified by reverse phase preparative HPLC to afford 1 -(4-(5-((2,3 -dimethoxyphenyl)(4-phenylpiperidin- 1 -yl)methyl)- l//-tetrazol- 1 - yl)piperidin-l-yl)-2,2-dimethylpropan-l-one C-148 and l-(4-(5-((2,3-dimethoxyphenyl)(4- phenylpiperidin-1 -yl)methyl)-2//-tetrazol-2-yl)piperidin-l -yl)-2,2-dimethylpropan-l -one C-150. [03731 C-148: Yield: 10 mg, 4%; Appearance: Off white solid; ¾ NMR (400 MHz, DMSOe) d 7.3 - 7.11 (m, 7H), 7.04 - 7.02 (m, 1H), 5.58 (s, 1H), 5.08-5.06 (m, 1H), 4.43 (t, J= 17.2 Hz, 2H), 3.80 (s, 3H), 3.67 (s, 3H), 3.05-2.99 (m, 3H), 2.78 (d, 7= 12 Hz, 1H), 2.24-2.13 (m, 2H), 2.02- 1.93 (m, 2H), 1.81 - 1.67 (m, 6H), 1.22 (s, 9H) 1H (merged in solvent peak); HPLC purity: 99.67%; LCMS calculated for C31H42N6O3: 546.33; Observed: 547.30 [M+H]+.
[0374J C-150: Yield: 23 mg, 8%; Appearance: Off white solid; 'H NMR (400 MHz, DMS06) d 7.3 - 7.14 (m, 6H), 7.08 (t, J= 7.6 Hz, 1H), 6.96 (d, J= 7.6 Hz, 1H), 5.34 (s, 1H), 5.14-5.09 (m, 1H), 4.28 (d, 7 = 14 Hz, 2H), 3.78 (s, 3H), 3.67 (s, 3H), 3.10 (t, 7 = 12.4 Hz, 2H), 2.96 (d, 7 = 10 Hz, 1H), 2.72 (d, 7= 13.6 Hz, 1H), 2.49 (m, 1H), 2.24 (d, 7 = 12.8 Hz, 2H), 2.08 (q, 7 = 10.4 Hz, 2H), 1.86 (q, 7 = 12 Hz, 2H), 1.69 - 1.61 (m, 4H), 1.20 (s, 9H); HPLC purity: 97.35%; LCMS calculated for C31H42N6O3: 546.33; Observed: 547.15 [M+H]+.
Example C15: Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol- 5-yl] methyl]-4-(2-methoxyethyl)-4-methylpiperidine, C- 198 :
Step 4 Step 5 Step 6 c'198 0375J Step 1. Synthesis of tert-butyl 4-[methoxy(methyl)carbamoyl]-4-methylpiperidine-l- carboxylate
[0376J A solution of l-[(tert-butoxy)carbonyl]-4-methylpiperidine-4-carboxylic acid (10 g, 41.1 mmol), methoxy(methyl)amine hydrochloride (4 g, 41.1 mmol), (3- {[(ethylimino)methylidene]amino}propyl)dimethylamine hydrochloride (7.9 g, 41.2 mmol), 1H- 1,2,3-benzotriazol-l-ol and ethylbis(propan-2-yl)amine (5.55 g, 41.1 mmol) in dry DMF (100 mL) was stirred at room temperature for 16 h and concentrated under the reduced pressure. The residue was dissolved in ethyl acetate (100 mL), washed with water (100 mL), brine (100 mL), dried over sodium sulfate, filtered and concentrated under reduced pressure to afford tert-butyl 4- [methoxy(methyl)carbamoyl]-4-methylpiperidine-l-carboxylate (10.8 g, 37.7 mmol, 74.65% purity, 68.8% yield) that was used in next step without further purification.
|0377[ Step 2. Synthesis of tert-butyl 4-formyl-4-methylpiperidine-l-carboxylate as a colorless oil [0378! Lithium aluminum hydride (0.451 g, 11.9 mmol) was added portionwise to the solution of tert-butyl 4-[methoxy(methyl)carbamoyl]-4-methylpiperidine-l-carboxylate (3.15 g, 10.9 mmol)
in dry THF (50 mL). The reaction mixture was stirred at room temperature for 0.5 h and quenched with an 20% aqueous solution of sodium hydroxide (25 mL). Solids were removed by filtration and washed with ethyl acetate (20 mL x 2). The combined organic layers were washed with brine (50 mL), dried over sodium sulfate, filtered and evaporated under reduced pressure to afford tert- butyl 4-formyl-4-methylpiperidine-l-carboxylate as a colorless oil (1.9 g, 8.35 mmol, 85% purity, 65.1% yield) that was used in the next step without further purification.
[0379J Step 3. Synthesis of tert-butyl 4-[(lE)-2-methoxyethenyl]-4-methylpiperidine-l- carboxylate
[0380J Potassium tert-butoxide (2.8 g, 25 mmol) was added to a solution of methoxymethyltriphenylphosphomum chloride (8.57 g, 25 mmol) in dry THF (60 mL) at 0 oC. After 30 minutes a solution of tert-butyl 4-formyl-4-methylpiperidine-l-carboxylate (1.9 g, 8.35 mmol) in dry THF (20 mL) was added to this mixture at 0 °C. The reaction mixture was allowed to warm up to room temperature and stir overnight. After, the mixture was evaporated under reduced pressure to dryness. A residue was treated with mixture water/ethyl acetate (50mL/50 mL). The organic phase was separated, washed with brine (50 mL), dried over sodium sulfate, filtered and evaporated under reduced pressure. The residue was purified by HPLC (deionized water/HPLC -grade acetonitrile) to afford tert-butyl 4-[(lE)-2-methoxyethenyl]-4- methylpiperidine-l-carboxylate (0.53 g, 2.07 mmol, 100% purity, 24.8% yield).
{0381} Step 4. Synthesis of tert-butyl 4-(2-methoxyethyl)-4-methylpiperidine-l-carboxylate [0382J tert-butyl 4-[(lE)-2-methoxyethenyl]-4-methylpiperidine-l-carboxylate (0.53 g, 2.07 mmol) was dissolved in methanol (5 mL) and treated with 10% Pd/C (0.05 g). The resulting mixture was hydrogenated at ambient pressure and room temperature until the reaction was completed. The catalyst was filtered off and the filtrate was evaporated to afford tert-butyl 4-(2- methoxyethyl)-4-methylpiperidine-l-carboxylate (0.5 g, 1.94 mmol, 90.38% purity, 84.7% yield) that was used in next step without further purification.
[0383J Step 5. Synthesis of 4-(2-methoxyethyl)-4-methylpiperidine hydrochloride [0384} Acetyl chloride (3.3 g, 0.042 mmol) was added to methanol (10 mL) at 0 °C and the mixture was stirred for lh at this temperature. Tert-butyl 4-(2 -m ethoxy ethyl)-4-methylpiperidine-l- carboxylate (0.5 g, 1.94 mmol) was then added portionwise and the reaction mixture was allowed to warm up and stir at room temperature overnight. After, the solvent was evaporated under
reduced pressure to afford 4-(2-methoxyethyl)-4-methylpiperidine hydrochloride (0.37 g, 1.9 mmol, 91.89% purity, 90.4% yield) that was used in next step without further purification.
[0385J Step 6. Synthesis of l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5- yl]methyl]-4-(2-methoxyethyl)-4-methylpiperidine
|0386| (2-isocyanoethyl)benzene (0.126 g, 0.964 mmol), 2,3-dimethoxybenzaldehyde (0.160 g, 0.964 mmol), and azidotrimethylsilane (0.303 g, 2.63 mmol) were added to a stirred solution of 4- (2-methoxyethyl)-4-methylpiperidine hydrochloride (0.17 g, 0.877 mmol) and triethylamine (0.0887 g, 0.877 mmol) in methanol (5 mL). The reaction mixture was stirred at room temperature for 16 h. After completion of the reaction (control by TLC), the reaction mixture was evaporated under reduced pressure. The residue was subjected to HPLC purification (deionized water/HPLC- grade methanol) to afford l-[(2,3-dimethoxyphenyl)[l-(2-phenylethyl)-lH-l,2,3,4-tetrazol-5- yl]methyl]-4-(2-methoxyethyl)-4-methyl-piperidine C-198. Yield: 3.9 mg, 0.88 %; Appearance: Yellow oil; NMR (600 MHz, DMSO -d6) d 7.24 (dd, J= 8.1, 6.7 Hz, 2H), 7.22 - 7.16 (m, 1H), 7.09 (dd, J= 6.9, 1.6 Hz, 2H), 7.03 (t, J= 8.0 Hz, 1H), 6.98 (dd, J= 8.2, 1.6 Hz, 1H), 6.93 (dd, J = 7.8, 1.6 Hz, 1H), 5.22 (s, 1H), 4.64 (dt, J= 13.8, 6.8 Hz, 1H), 4.60 - 4.52 (m, 1H), 3.77 (s, 3H), 3.67 (s, 3H), 3.15 (s, 3H), 3.03 (td, J= 7.0, 6.4, 2.8 Hz, 2H), 2.19 (dd, J= 19.2, 6.8 Hz, 2H), 2.14 - 2.04 (m, 1H), 1.38 (dd, J= 8.0, 6.5 Hz, 2H), 1.31 (td, 7= 10.6, 9.1, 3.5 Hz, 2H), 1.19 (d, 7= 13.3 Hz, 2H), 0.78 (s, 3H).); HPLC purity: 100%; LCMS Calculated for C27H37N5O3: 479.6; Observed: 480.4 [M+H]+.
Biological Activity
[0387J For the TFEB nuclear translocation assay, HeLa wt or HeLa TRPML1 KO cells were plated at 2700 cells/well into black- walled, 384-well Cell carrier Ultra tissue culture treated plates in complete media and incubated overnight. The next day, cells are treated for 2 hrs with compounds and incubated at 37 °C. Cells were then fixed for 30 minutes at room temperature in 4% final PFA and washed five times with 90 pL PBS. PBS is aspirated from the wells and the cells are blocked with 7.5 pL blocking buffer (1:1 PBS/Odyssey block buffer containing 0.1% triton x-100 and 1% goat serum). After 30-60 minutes of block, 7.5 pL of primary anti-TFEB (rabbit) antibody is added for a final dilution of 1:200 antibody in 15 pL blocking buffer. Plates are incubated overnight at 4 °C. The following day, plates are washed again into PBS, 90 pL with 5 washes, all PBS is aspirated from the wells and the cells are incubated for 1 hr in 1 : 1000 goat-anti rabbit Alexa
488 secondary antibody, also containing 10 pg/mL Hoechst 33342. After the 1 hr RT incubation, plates are washed a final time into PBS, sealed with foil and imaged with an automated epifluorescence microscopy (PerkinElmer Operetta CLS). Four different fields were imaged per well using x20 magnification for DAPI and FITC filter sets. Images were quantified using PerkinElmer Harmony software, briefly: apply Hatfield correction (basic/ advanced) for input images. Use the Find Nuclei building block with channel set at Hoechst to find the nuclei. Use the Find cytoplasm building block with channel set to Alexa 488 to find the cytoplasm. Use select cell region with Channel set at Alexa 488 and region of interest as Nuclei and define outer border at 0 pm and inner at 45 pm to cover complete nuclei. Use select cell region with Channel set at Alexa 488 and region of interest as ring region and define outer border at -5 pm and inner at 0 pm to define a ring around the nucleus. Use the find calculate intensity parameter to calculate intensity of the nuclear region and the ring region. Define results as Number of nuclei and ratio of A/B where A is Intensity of Nuclei and B is intensity of the ring region.
Analytical Instrumentation and Purification:
{0388J NMR Instrument Details: : Varian 400MHz, Probe-1: Auto XID Probe 2: ATB. 0389J LCMS Instrument Details: ShimadzuLCMS-2010EV system coupled to SPD-M20 A PDA and ELS detectors. Softa model 400.
|b390| LCMS Method 1 - Acidic conditions
Column: X-Select C18 CSH (3.0*50) mm 2.5p; Make: Waters
Mobile Phase A: 0.05% formic acid in water: Acetonitrile ( 95:5); pH= 3.5
Mobile Phase B: 0.05% formic acid in Acetonitrile
Column oven temperature: 50 C
Flow rate: 1.2 mL/minute
PDA: 210nm Maxplot
Gradient program :
Time(min) A% B%
0.0 100 0
2.0 2 98
3.0 2 98
3.2 100 0
4.0 100 0
MS Parameters Mode: Dual (+/-)
Detector voltage: 1.5KV Scan rang: 80-2000amu Scan speed: 2000
[0391f LCMS Method 2 - Basic conditions
Column: X-Select C18 CSH (3.0*50) mm 2.5pm ; Make: Waters
Mobile Phase A : 5mM Ammonium Bicarb; pH= 8.8
Mobile Phase B: Acetonitrile
Column oven temperature: 50 C
Flow rate: 1.2 mL/minute
PDA: 210nm Maxplot
Gradient program :
Time(min) A% B%
0.0 100 0
2.0 2 98
3.0 2 98
3.2 100 0
4.0 100 0
MS Parameters Mode: Dual (+/-) Detector voltage: 1.5KV Scan rang: 80-2000amu Scan speed: 2000
[0392| HPLC Method 1 - Acidic Conditions
Column : X-Select CSH C18 (4.6*150) mm; 5p; Make: Waters Mobile Phase: A - 0.1% Formic acid in water : Acetonitrile(95:05) ; pH=3.5 B - Acetonitrile
Flow Rate: 1.0. mL/minute PDA : 210nm maxplot Gradient program : Time(min) A% B%
0.0 95 5
1.0 95 5
8.0 0 100
12.0 0 100
14.0 95 5
18.0 95 5
{03931 HPLC Method 2 - Basic Conditions
Column : Xbridge Cl 8 (4.6*150) mm, 5m; Make: Waters Mobile Phase A - 0.1% NH3 in water; pH=9.5 B - Acetonitrile Flow Rate: 1.2. mL/minute PDA : 210nm maxplot Gradient program :
Time(min) A% B%
0.0 98 2
6.0 0 85
8.0 0 85
9.0 0 100
12.0 0 100
14.0 98 2
18.0 98 2
|0394J Table 1 shows the activity of selected compounds of this invention in TFEB assays. The compound numbers correspond to the compound numbers above in Table A. Compounds having an activity designated as “++++” provided an AC50 of < 2.00 mM; compounds having an activity
designated as “+++” provided an AC50 of 2.01-8.00 mM; compounds having an activity designated as “++” provided an AC50 of 8.01-9.99 mM; and compounds having an activity designated as "+" provided an AC50 of > 10.00 mM.
Claims
Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, C6-12 aryl, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
L1 is absent, -NR3-Co-6 alkylenyl-, -O-Co-6 alkylenyl, Ci-6 alkyl enyl, -C(0)-Co-6 alkylenyl, - C(0)0-Co-6 alkylenyl, -
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, C6-12 aryl, and C3-12 cycloalkyl, wherein Vis substituted with (R6)m;
Y is Ci-6 aliphatic, -S(0)2-Ci-6 aliphatic, -O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or C6-12 aryl, wherein Y is optionally substituted with one or more instances of Rb; each of X1, X2, X3, and X4 is independently selected from C, CRa, S, O, orN, as valency permits, wherein X1, X2, X3, and X4 are selected from C and N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3. 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently hydrogen, halo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl;
Rb is an optionally substituted group selected from -NR3-C(0)-CI-6 aliphatic, -C(0)-Ci-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12- membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or polycyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic; each R3 is independently selected from H and an optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S; each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1.
2. The compound of claim 1, wherein X1, X2, X3, and X4 are each N.
4. The compound of any one of claims 1-3, wherein Y is C3-6 cycloalkyl substituted with Rb, 4- to 6- atom heterocyclyl substituted with Rb, or Ci-6 aliphatic substituted with Rb.
5. The compound of claim 4, wherein Y is Ci-6 aliphatic substituted with Rb.
6. The compound of claim 4, wherein Y is C3-6 cycloalkyl substituted with Rb or 4- to 6- atom heterocyclyl substituted with Rb.
7. The compound of any one of claims 1-6, wherein Rb is C6-12 aryl or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
8. The compound of claim 7, wherein Rb is phenyl.
9. The compound of claim 1, wherein Y is selected from Table Y.
10. The compound of any one of claims 1-9, wherein Cy is absent or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
11. The compound of claim 10, wherein Cy is absent.
12. The compound of claim 10, wherein Cy is 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
13. The compound of claim 12, wherein Cy is 4- to 6-membered monocyclic heterocyclic comprising 1 to 3 heteroatoms selected from N, O, and S.
14. The compound of claim 13, wherein Cy is piperdinyl or piperzinyl.
15. The compound of claim 1, wherein Cy is selected from Table Cy.
16. The compound of any one of claim 1-15, wherein L1 is absent, -NR3-, or Ci-6 alkylenyl.
17. The compound of claim 16, wherein L1 is absent.
18. The compound of claim 16, wherein L1 is-NR3-.
19. The compound of any one of claims 1-18, wherein Z is C6-12 aryl, 2- to 10 atom heteroaliphatic, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q.
20. The compound of claim 19, wherein Z is C6-12 aryl or 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
21. The compound of claim 20, wherein Z is C6-12 aryl.
22. The compound of claim 21, wherein Z is C6-12 aryl substituted with 1, 2, 3, or 4 R2.
23. The compound of any one of claims 1-22, wherein R2 is halo.
24. The compound of claim 1, wherein Z is selected from Table Z.
25. The compound of any one of 1-24, wherein V is C6-12 aryl or 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S.
26. The compound of claim 25, wherein V is C6-12 aryl.
27. The compound of claim 26, wherein V is C6-12 aryl substituted with 1, 2, 3, or 4 R6.
28. The compound of any one of claims 1-27, wherein R6 is halo, Ci-6 aliphatic, or an optionally substituted O-Ci-6 aliphatic.
29. The compound of claim 28, wherein R6 is halo or an optionally substituted O-Ci-6 aliphatic.
30. The compound of claim 29, wherein R6 is halo.
31. The compound of claim 30, wherein R6 is fluoro or chloro.
32. The compound of claim 29, wherein R6 is an optionally substituted O-Ci-6 aliphatic.
33. The compound of claim 32, wherein R6 is -O-CH3.
34. The compound of claim 1, wherein V is selected from Table V.
II’ or a pharmaceutically acceptable salt thereof, wherein
Cy is absent, or a bivalent moiety selected from 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, P, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, Ci-6 aliphatic, or C3-12 cycloalkyl, wherein Cy is optionally substituted with one or more of R1;
V is selected from Ci-6 aliphatic, C6-12 aryl, 4- to 12-membered monocyclic or bicyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S,
5- to 12-membered monocyclic of bicyclic aryl, and C3-12 cycloalkyl, wherein V is substituted with (R6)m;
Y is Ci-6 aliphatic, O-Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membered heterocyclyl comprising
1 to 4 heteroatoms selected from N, O, and S, wherein Y is optionally substituted with one or more instances of Rb; each of X1, X2, X3, and X4 is independently selected from CRaN, S, or O,. wherein X1, X2, X3, and X4 are selected from N when bound to Y;
Z is Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)Ci-6 aliphatic, -C(0)N(R3)2, C6-12 aryl, C3- 12 monocyclic or polycyclic cycloalkyl, 4- to 16-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S, wherein Z is substituted with (R2)q; each Ra is independently hydrogen, halo, or optionally substituted Ci-6 aliphatic, or when L1 and Cy are absent, Ra comes together with Z to form a Ci-6 alkenyl;
Rb is an optionally substituted group selected from -N(R3)2-, -NR3-C(0)-CI-6 aliphatic, -C(O)- C1-6 aliphatic, Ci-6 aliphatic, 2- to 10-atom heteroaliphatic, -C(0)-C6-i2 aryl, C6-12 aryl, 4- to 12-membered monocyclic or polycyclic heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S, or 5- to 12-membered monocyclic or bicyclic heteroaryl comprising 1 to 4 heteroatoms selected from N, O, and S; each R1 is independently selected from N(R3)2, OH, CN, C(0)NHR3, and an optionally substituted group selected from Ci-6 aliphatic andN(R3)-C(0)-Ci-6 alkyl; each R2 is independently selected from halo, -CN, C(0)0H, and an optionally substituted group selected from Ci-6 aliphatic, C(0)Ci-6 aliphatic, and O-Ci-6 aliphatic;
each R3 is independently selected from H and an optionally substituted group selected from Ci-6 aliphatic, C3-12 cycloalkyl, 3- to 12-membetered heterocyclyl comprising 1 to 4 heteroatoms selected from N, O, and S; each R6 is halo, -CN or an optionally substituted group selected from O-Ci-6 aliphatic, Ci-6 aliphatic, and C6-12 aryl; m is 0, 1, 2, 3, or 4; n is 0 or 1; q is 0, 1, 2, 3, or 4; and s is 0 or 1.
Ila or a pharmaceutically acceptable salt thereof.
39. A compound selected from Table A.
40. A compound selected from Table B.
41. A pharmaceutical composition comprising a compound of any one of claims 1-40 and a pharmaceutically acceptable carrier, adjuvant, or vehicle.
42. A method of modulating TRPMLl comprising administering to a subject a compound of any one claims 1-40.
43. A method of treating a disease, disorder, or condition in a subject comprising administering a compound of any one of claims 1-40.
44. The method of claim 43, wherein the disease, disorder, or condition is a lysosomal storage disorder.
45. The method of claim 44, wherein the lysosomal storage disorder is selected from Niemann- Pick C disease, Gaucher disease, and Pompe disease.
46. The method of claim 43, wherein the disease, disorder, or condition is age-related common neurodegenerative disease.
47. The method of claim 46, wherein the disease, disorder, or condition is selected from Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease.
48. The method of claim 43, wherein the disease, disorder, or condition is a type IV Mucolipidosis (ML4) neurodegenerative lysosomal storage disease caused by mutations in TRPMLl.
49. The method of claim 43, wherein the disease, disorder, or condition is a muscular disease, a liver disease, a metabolic disease, an atherosclerotic disease, an inflammatory bowel disease, an
atherosclerotic disease, a neurodegenerative disease, an oncological disease, or an infectious disease.
50. The method of claim 49, wherein the disease, disorder, or condition is a muscular disease.
51. The method of claim 50, wherein the muscular disease is a muscular dystrophy.
52. The method of claim 53, wherein the muscular dystrophy is Duchenne muscular dystrophy.
53. The method of claim 49, wherein the disease, disorder, or condition is an infectious disease.
54. The method of claim 53, wherein the infectious disease is an infection of Heliobacter pylori or Mycobacterium tuberculosis.
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