IP Library › Granted Patent US 9,676,785

Granted Patent B2

US 9,676,785 · App. 14/331,161 · Granted Jun 13, 2017

HCV protease inhibitors and uses thereof

Inventors: Deqiang Niu (Lexington, MA); Russell C. Petter (Stow, MA); Juswinder Singh (Ashland, MA); Arthur F. Kluge (Lincoln, MA); Lixin Qiao (Tewksbury, MA)

Assignee: Celgene CAR LLC

C07D487/16 A61K31/407 A61K31/4035 A61K31/506 A61K45/06 C07D403/12 C07D403/14 C07D487/04 C07K5/06165 C07K5/0806 C07K5/0812 C07K5/0827 A61K38/00

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Quick Facts

Patent No.: US 9,676,785
App. No.: 14/331,161
Granted: Jun 13, 2017
Kind: B2

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Abstract

The present invention provides compounds, pharmaceutically acceptable compositions thereof, and methods of using the same.

Claims (211)

1. A method for treating hepatitis C viral infection in a patient, comprising the step of administering to a patient in need thereof a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

R 1 and R 1 , are independently hydrogen or optionally substituted C 1-6 aliphatic, or R 1 and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring;

R 2a is —OH or —NHSO 2 R 2 ;

R 2 is —N(R) 2 or an optionally substituted group selected from C 3-7 cycloalkyl, a bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

each R is independently hydrogen, optionally substituted C 1-6 aliphatic, or:

two R on the same nitrogen atom are taken together with the nitrogen to form a 4-7membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 3 is -L-Y, wherein -L-Y is selected from the following:

(a) L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and one or two methylene units of L are independently replaced by —NRC(O)—, —C(O)NR—, —N(R)SO 2 —, —SO 2 N(R)—, —S(O)—, —SO 2 —, —OC(O)—, —C(O)O, or —C(O)—; and Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN; or

(b) L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO 2 —, —SO 2 N(R)—, —S(O)—, —SO 2 —, —OC(O)—, or —C(O)O—, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—; and Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN; or

(c) L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—; and Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN; or

(h) L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one alkylidenyl double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO 2 —, —SO 2 N(R)—, —S(O)—, —SO 2 —, —OC(O)—, or —C(O)O—, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—; and Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN;

or R 3 and R 1 are taken together with their intervening atoms to form an optionally substituted saturated or unsaturated 12-18 membered ring having 2-6 heteroatoms independently selected from nitrogen oxygen, or sulfur, wherein the ring formed thereby comprises -L-Y; or

R 3 and a ring formed by R 1 and R 1 , are taken together with their intervening atoms to form an optionally substituted saturated or unsaturated 12-18 membered ring having 2-6 heteroatoms independently selected from nitrogen oxygen, or sulfur, wherein the ring formed thereby comprises -L-Y;

R 4 is H, —NHC(O)R 5 , —NHC(O)OR 6 ,

or a natural or unnatural amino acid side-chain group;

each R 5 is independently —N(R) 2 or an optionally substituted group selected from C 1-6 aliphatic, a bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 6 is an optionally substituted group selected from C 1-6 aliphatic, a bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; and

R 7 is an optionally substituted group selected from C 1-6 aliphatic, a bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; and

R z is

or R 4 and R z are taken together with their intervening atoms to form an optionally substituted, saturated or unsaturated 16-22 membered ring having 2-6 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

wherein the 16-22 membered ring is optionally substituted with (R m ) p , wherein:

p is an integer from 1 to 6, inclusive;

each occurrence of R m is independently halogen, —OR° , —CN, —N(R° ) 2 , or an optionally substituted group selected from C 1-6 aliphatic or C 3-7 cycloalkyl; and

each occurrence of R y is independently selected from halogen, —OR° , —CN, —NO 2 , —N(R° ) 2 , or optionally substituted C 1-4 aliphatic;

each R° of R m and R y is independently optionally substituted C 1-6 aliphatic; and

m is an integer from 0 to 4, inclusive;

s is an integer from 0 to 4, inclusive;

t is an integer from 0 to 4, inclusive;

wherein the sum of s and t is non-zero.

2. The method according to claim 1 , wherein:

L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and one or two methylene units of L are independently replaced by —NRC(O)—, —C(O)NR—, —N(R)SO 2 —, —SO 2 N(R)—, —S(O)—, —SO 2 —, —OC(O)—, —C(O)O, or —C(O)—; and

Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN.

3. The method according to claim 1 , wherein:

L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO 2 —, —SO 2 N(R)—, —S(O)—, —SO 2 —, —OC(O)—, or —C(O)O—, and one additional methylene unit of L is optionally replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—; and

Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN.

4. The method according to claim 3 , wherein L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, and one additional methylene unit of L is optionally replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—.

5. The method according to claim 3 , wherein L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —OC(O)—.

6. The method according to claim 1 , wherein L is —NRC(O)CH═CH—, —NRC(O)CH═CHCH 2 N(CH 3 )—, —NRC(O)CH═CHCH 2 O—, —CH 2 NRC(O)CH═CH—, —NRSO 2 CH═CH—, —NRSO 2 CH═CHCH 2 1 —, or —NRC(O)C(═CH 2 )CH 2 —; wherein the R group of L is H or optionally substituted C 1-6 aliphatic; and Y is hydrogen or C 1-6 aliphatic optionally substituted with oxo, halogen, NO 2 , or CN.

7. The method according to claim 6 , wherein L is —NHC(O)CH═CH—, —NHC(O)CH═CHCH 2 N(CH 3 )—, —NHC(O)CH═CHCH 2 O—, —CH 2 NHC(O)CH═CH—, —NHSO 2 CH═CH—, —NHSO 2 CH═CHCH 2 —, or —NHC(O)C(═CH 2 )CH 2 —.

8. The method according to claim 1 , wherein L is a bivalent C 2-8 straight or branched, hydrocarbon chain wherein L has at least one alkylidenyl double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO 2 —, —SO 2 N(R)—, —S(O)—, —SO 2 —, —OC(O)—, or —C(O)O—, and one additional methylene unit of L is optionally replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—.

9. A method for treating hepatitis C infection in a patient, comprising the step of administering to a patient in need thereof a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

R 1 and R 1 , are independently hydrogen or optionally substituted C 1-6 aliphatic, or R 1 and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring;

R 2a is —OH or —NHSO 2 R 2 ;

each R is independently hydrogen, optionally substituted C 1-6 aliphatic, or:

two R on the same nitrogen atom are taken together with the nitrogen to form a 4-7 membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 3 is -L-Y, wherein:

L is a covalent bond, —C(O)—, —N(R)C(O)—, a bivalent C 1-8 saturated or unsaturated, straight or branched, hydrocarbon chain, —CH 2 —, —NH—, —CH 2 NH—, —NHCH 2 —, —NHC(O)—, —NHC(O)CH 2 OC(O)—, —CH 2 NHC(O)—, —NHSO 2 —, —NHSO 2 CH 2 —, or —SO 2 NH—; and

Y is selected from:

wherein each R e is independently selected from halogen;

R 4 is H, —NHC(O)R 5 , —NHC(O)OR 6 ,

or a natural or unnatural amino acid side-chain group;

R z is

wherein the 16-22 membered ring is optionally substituted with (R m ) p , wherein:

p is an integer from 1 to 6, inclusive;

each occurrence of R m is independently halogen, —OR∘ , —CN, —N(R∘ ) 2 , or an optionally substituted group selected from C 1-6 aliphatic or C 3-7 cycloalkyl; and

each occurrence of R y is independently selected from halogen, —OR∘ , —CN, —NO 2 , —N(R∘ ) 2 , or optionally substituted C 1-4 aliphatic;

each R∘ of R m and R y is independently optionally substituted C 1-6 aliphatic; and

m is an integer from 0 to 4, inclusive;

s is an integer from 0 to 4, inclusive;

t is an integer from 0 to 4, inclusive;

wherein the sum of s and t is non-zero.

10. The method according to claim 1 , wherein said compound is of formula II-a or II-b:

or a pharmaceutically acceptable salt thereof.

11. A method for treating an HCV protease-mediated disorder in a patient, comprising the step of administering to a patient in need thereof a compound selected from the group consisting of:

or a pharmaceutically acceptable salt thereof.

12. A method for inhibiting HCV protease, or a mutant thereof, activity comprising the step of administering to a patient in need thereof a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

R 1 and R 1 , are independently hydrogen or optionally substituted C 1-6 aliphatic, or R l and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring;

R 2a is —OH or —NHSO 2 R 2 ;

each R is independently hydrogen, optionally substituted C 1-6 aliphatic, or:

two R on the same nitrogen atom are taken together with the nitrogen to form a 4-7membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 3 is -L-Y, wherein -L-Y is selected from the following:

R 3 and a ring formed by R l and R 1 , are taken together with their intervening atoms to form an optionally substituted saturated or unsaturated 12-18 membered ring having 2-6 heteroatoms independently selected from nitrogen oxygen, or sulfur, wherein the ring formed thereby comprises -L-Y;

R 4 is H, —NHC(O)R 5 , —NHC(O)OR 6 ,

or a natural or unnatural amino acid side-chain group;

R z is

wherein the 16-22 membered ring is optionally substituted with (R m ) p , wherein:

p is an integer from 1 to 6, inclusive;

each occurrence of R m is independently halogen, —OR∘ , —CN, —N(R∘ ) 2 , or an optionally substituted group selected from C 1-6 aliphatic or C 3-7 cycloalkyl;

each occurrence of R m is independently selected from halogen, —OR∘ , —CN, —NO 2 , —N(R∘ ) 2 , or optionally substituted C 1-4 aliphatic;

each R∘ of R m or R y is independently optionally substituted C 1-6 aliphatic; and

m is an integer from 0 to 4, inclusive;

s is an integer from 0 to 4, inclusive;

t is an integer from 0 to 4, inclusive;

wherein the sum of s and t is non-zero.

13. The method according to claim 12 , wherein the HCV protease, or a mutant thereof, activity is inhibited irreversibly by covalently modifying a cysteine residue of HCV protease, wherein the cysteine is Cys159 or at an equivalent position to Cys159 of HCV protease subtype 1b.

14. The method according to claim 12 , wherein the HCV protease, or a mutant thereof, activity is inhibited irreversibly by covalently modifying Cys159 of HCV protease.

15. The method according to claim 12 , wherein the HCV protease, or a mutant thereof, activity is inhibited irreversibly by covalently modifying Cys16 of HCV protease.

16. The method of claim 1 , wherein the step of administering occurs once daily.

17. The method according to claim 1 , wherein the disorder is hepatitis C.

18. The method of claim 1 comprising the step of irreversibly inhibiting HCV protease by covalently modifying a cysteine residue of HCV protease, wherein the cysteine is Cys159 or at an equivalent position to Cys159 of HCV protease subtype 1b.

19. The method of claim 18 , wherein the HCV protease genotype or subtype is selected from the group consisting of 1a, 1b, 1c, 2a, 2b, 2c, 2i, 2k, 3a, 3b, 3k, 4a, 4d, 4f, 5a, 6a, 6b, 6c, 6d, 6e, 6f, 6g, 6h, 6i, 6j, 6k, 6l, 6m, 6n, 6o, 6p, 6q, 6t, and 7a.

20. The method of claim 19 , wherein the HCV protease genotype or subtype is 1a, 1b, 2a, or 3a.

21. The method according to claim 1 , comprising the step of irreversibly inhibiting HCV protease by covalently modifying Cys159 of HCV protease.

22. The method according to claim 1 , comprising the step of irreversibly inhibiting HCV protease by covalently modifying Cys16 of HCV protease.

23. The method according to claim 1 , wherein R z is

24. The method according to claim 1 , wherein R 4 and R z are taken together with their intervening atoms to form an optionally substituted, saturated or unsaturated 16-22 membered ring having 2-6 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

25. The method according to claim 24 , wherein the compound is of formula I-e or I-f:

or a pharmaceutically acceptable salt thereof;

wherein:

p is an integer from 1 to 6, inclusive; and

each occurrence of R m is independently halogen, —OR∘ , —CN, —N(R∘ ) 2 , or an optionally substituted group selected from the group consisting of C 1-6 aliphatic and C 3-7 cycloalkyl; and

R∘ is an optionally substituted group selected from C 1-6 aliphatic.

26. The method according to claim 1 , wherein R 1 and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring.

27. The method according to claim 26 , wherein R 1 and R 1 , are taken together to form:

wherein R∘ is an optionally substituted group selected from C 1-6 aliphatic.

28. The method according to claim 27 , wherein R∘ is vinyl.

29. The method according to claim 27 , wherein R∘ is ethyl.

30. A method for inhibiting HCV protease, or a mutant thereof, activity comprising the step of administering to a patient in need thereof a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

R 1 and R 1 , are independently hydrogen or optionally substituted C 1-6 aliphatic, or R 1 and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring;

R 2a is —OH or —NHSO 2 R 2 ;

each R is independently hydrogen, optionally substituted C 1-6 aliphatic, or:

two R on the same nitrogen atom are taken together with the nitrogen to form a 4-7membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 3 is -L-Y, wherein:

Y is selected from:

wherein each R e is independently selected from halogen;

R 3 and R 1 are taken together with their intervening atoms to form an optionally substituted saturated or unsaturated 12-18 membered ring having 2-6 heteroatoms independently selected from nitrogen oxygen, or sulfur, wherein the ring formed thereby comprises -L-Y; or

R 4 is H, —NHC(O)R 5 , —NHC(O)OR 6 ,

or a natural or unnatural amino acid side-chain group;

R z is

wherein the 16-22 membered ring is optionally substituted with (R m ) p , wherein:

p is an integer from 1 to 6, inclusive;

each occurrence of R m is independently halogen, —OR∘ , —CN, —N(R∘ ) 2 , or an optionally substituted group selected from C 1-6 aliphatic or C 3-7 cycloalkyl; and

each occurrence of R y is independently selected from halogen, —OR∘ , —CN, —NO 2 , —N(R∘ ) 2 , or optionally substituted C 1-4 aliphatic;

each R∘ of R m or R y is independently optionally substituted C 1-6 aliphatic; and

m is an integer from 0 to 4, inclusive;

s is an integer from 0 to 4, inclusive;

t is an integer from 0 to 4, inclusive;

wherein the sum of s and t is non-zero.

31. A method for treating hepatitis C infection in a patient, comprising the step of administering to a patient in need thereof a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

R 1 and R 1 , are independently hydrogen or optionally substituted C 1-6 aliphatic, or R 1 and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring;

R 2a is —OH or —NHSO 2 R 2 ;

each R is independently hydrogen, optionally substituted C 1-6 aliphatic, or:

two R on the same nitrogen atom are taken together with the nitrogen to form a 4-7membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 3 is -L-Y, wherein -L-Y is selected from:

R 4 is H, —NHC(O)R 5 , —NHC(O)OR 6 ,

or a natural or unnatural amino acid side-chain group;

R z is

wherein the 16-22 membered ring is optionally substituted with (R m ) p , wherein:

p is an integer from 1 to 6, inclusive;

each occurrence of R m is independently halogen, —OR∘ , —CN, —N(R∘ ) 2 , or an optionally substituted group selected from C 1-6 aliphatic or C 3-7 cycloalkyl; and

each occurrence of R y is independently selected from halogen, —OR∘ , —CN, —NO 2 , —N(R∘ ) 2 , or optionally substituted C 1-4 aliphatic;

each R∘ of R m or R m is independently optionally substituted C 1-6 aliphatic; and

m is an integer from 0 to 4, inclusive;

s is an integer from 0 to 4, inclusive;

t is an integer from 0 to 4, inclusive;

wherein the sum of s and t is non-zero.

32. A method for inhibiting HCV protease, or a mutant thereof, activity comprising the step of administering to a patient in need thereof a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

R 1 and R 1 , are independently hydrogen or optionally substituted C 1-6 aliphatic, or R 1 and R 1 , are taken together to form an optionally substituted 3-7 membered carbocyclic ring;

R 2a is —OH or —NHSO 2 R 2 ;

each R is independently hydrogen, optionally substituted C 1-6 aliphatic, or:

two R on the same nitrogen atom are taken together with the nitrogen to form a 4-7membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur;

R 3 is -L-Y, wherein -L-Y is selected from:

R 4 is H, —NHC(O)R 5 , —NHC(O)OR 6 ,

or a natural or unnatural amino acid side-chain group;

R z is

wherein the 16-22 membered ring is optionally substituted with (R m ) p , wherein:

p is an integer from 1 to 6, inclusive;

each occurrence of R m is independently halogen, —OR∘ , —CN, —N(R∘ ) 2 , or an optionally substituted group selected from C 1-6 aliphatic or C 3-7 cycloalkyl; and

each occurrence of R y is independently selected from halogen, —OR∘ , —CN, —NO 2 , —N(R∘ ) 2 , or optionally substituted C 1-4 aliphatic;

each R∘ of R m or R y is independently optionally substituted C 1-6 aliphatic; and

m is an integer from 0 to 4, inclusive;

s is an integer from 0 to 4, inclusive;

t is an integer from 0 to 4, inclusive;

wherein the sum of s and t is non-zero.

Assignments (3)

MERGER AND CHANGE OF NAME Recorded Apr 12, 2017

From: CELGENE AVILOMICS RESEARCH, INC.; CELGENE CAR LLC

To: CELGENE CAR LLC

Reel/Frame 041979/0447 →

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 15, 2016

From: NIU, DEQIANG; PETTER, RUSSELL C.; SINGH, JUSWINDER; KLUGE, ARTHUR F.; QIAO, LIXIN

To: AVILA THERAPEUTICS, INC.

Reel/Frame 038293/0683 →

CHANGE OF NAME Recorded Apr 15, 2016

From: AVILA THERAPEUTICS, INC.

To: CELGENE AVILOMICS RESEARCH, INC.

Reel/Frame 038445/0480 →

Continuity (6)

Division 12339770 · Dec 19, 2008

Provisional Application 61016110 · Dec 21, 2007

Provisional Application 61016473 · Dec 23, 2007

Provisional Application 61075001 · Jun 23, 2008

Provisional Application 61098675 · Sep 19, 2008

Related Publication 20140323465A1 · Oct 30, 2014