Sonic hedgehog modulators
The present invention relates to macrocyclic small molecule inhibitors of the Sonic Hedgehog signaling pathway, syntheses thereof, and intermediates thereto. Such small molecule modulators of the Sonic Hedgehog signaling pathway are useful in the treatment of proliferative diseases (e.g., basal cell carcinoma, Gorlin syndrome, medulloblastoma, or pancreatic cancer), pulmonary diseases (e.g., interstitial pnuemonitis or interstitial pulmonary fibrosis), and developmental disorders (e.g., phocomelia or cyclopia). Novel non-natural macrocycles are provided that inhibit Sonic Hedgehog induced-protein transcription.
1. A compound of formula I:
or a pharmaceutically acceptable salt thereof, wherein:
designates a single or double bond;
X 1 is —O—;
X 2 is —NR—;
Y 1 , Y 2 , and Y 3 are each ═O;
Z is —NR 4 R 5 or —OR 5 ;
T is a covalent bond or a bivalent C 1-12 saturated or unsaturated, straight or branched, aliphatic chain;
j is 1;
k is 1;
m is an integer from 0 to 2, inclusive;
n is an integer from 0 to 2, inclusive;
each occurrence of R 1 is independently hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or
two R 1 groups may be taken together with their intervening atoms to form a 3-8-membered ring; or
when X 2 is —NR—, R 1 and the R of —NR— may be taken together with their intervening atoms to form a 3-8-membered ring;
each occurrence of R 2 is independently hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or
two R 2 groups may be taken together with their intervening atoms to form a 3-8-membered ring;
R 3 is hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur;
R 4 is hydrogen;
R 5 is hydrogen or —C(R 6 ) 3 ;
each occurrence of R 6 is independently hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or
two occurrences of R 6 may be taken together with their intervening atoms to form a 3-8-membered ring; and
each R is independently hydrogen, a protecting group, —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 7-15 arylalkyl moiety, C 1-12 aliphatic moiety, 6-10-membered aryl moiety, 5-10-membered heteroaryl moiety having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or C 1-12 heteroaliphatic moiety; or:
two R on the same nitrogen atom may be taken with the nitrogen to form a 4-7-membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur;
wherein when a group is substituted, the group is substituted with one or more substituents independently selected from the group consisting of aliphatic, heteroaliphatic, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy, aryloxy, heteroalkoxy, heteroaryloxy, alkylthio, arylthio, heteroalkylthio, heteroarylthio, —F, —Cl, —Br, —I, —OH, —NO 2 , —CN, —CF 3 —CH 2 CF 3 , —CHCl 2 , —CH 2 OH, —CH 2 CH 2 OH, —CH 2 NH 2 , —CH 2 SO 2 CH 3 , —C(O)R x1 , —CO 2 (R x1 ), —CON(R x1 ) 2 , —OC(O)R x1 , —OCO 2 R x1 , —OCON(R x1 ) 2 , —N(R x1 ) 2 , —S(O) 2 R x1 , and —NR x1 (CO)R x1 , wherein each occurrence of R x1 is independently selected from the group consisting of aliphatic, heteroaliphatic, aryl, heteroaryl, arylalkyl, and heteroarylalkyl;
with the proviso that R 6 is not —CH 2 OH or —CH 2 OCH 2 CH 2 OH.
2. The compound according to claim 1 , wherein T is —CH 2 —.
3. The compound according to claim 1 , wherein R 1 is hydrogen.
4. The compound according to claim 1 , wherein R 2 is optionally substituted 6-10-membered aryl.
5. The compound according to claim 4 , wherein R 2 is phenyl.
6. The compound according to claim 1 , wherein R 3 is hydrogen.
7. The compound according to claim 1 , wherein Z is —NR 4 R 5 .
8. The compound according to claim 1 , wherein R 5 is —C(R 6 ) 3 .
9. The compound according to claim 8 , wherein:
each occurrence of R 6 is independently hydrogen or an optionally substituted group selected from the group consisting of C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, 6-10-membered aryl; or
two occurrences of R 6 may be taken together with their intervening atoms to form a 3-8-membered ring.
10. The compound according to claim 9 , wherein each occurrence of R 6 is independently hydrogen or an optionally substituted group selected from C 1-6 aliphatic and 6-10-membered aryl.
11. The compound according to claim 10 , wherein one occurrence of R 6 is optionally substituted 6-membered aryl.
12. The compound according to claim 11 , wherein one occurrence of R 6 is 4-chlorophenyl.
13. The compound according to claim 1 , wherein designates a double bond.
14. The compound according to claim 13 , wherein designates a trans double bond.
15. The compound according to claim 1 , wherein the compound is of the formula:
16. The compound according to claim 15 , wherein the compound is of the formula:
17. The compound according to claim 16 , wherein the compound is of the formula:
18. The compound according to claim 15 , wherein the compound is selected from:
19. The compound according to claim 15 , wherein the compound is of the formula:
20. The compound according to claim 16 , wherein the compound is of the formula:
wherein,
s is an integer from 1 to 5, inclusive; and
each R x is independently selected from hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, and an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
21. The compound according to claim 20 , wherein the compound is of the formula:
v is an integer from 1 to 10, inclusive;
t is an integer from 1 to 5, inclusive; and
each R y is independently selected from hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, and an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur.
22. The compound according to claim 1 , wherein the compound is selected from:
23. The compound according to claim 1 , wherein the compound is:
24. A pharmaceutical composition comprising a compound according to claim 1 and a pharmaceutically acceptable carrier.
25. A method of treating Gorlin syndrome, medulloblastoma, basal cell carcinoma, or pancreatic cancer in a subject suffering therefrom, the method comprising administering to the subject a therapeutically effective amount of a compound of formula I:
or a pharmaceutically acceptable salt thereof, wherein:
designates a single or double bond;
X 1 is —O—;
X 2 is —NR—;
Y 1 , Y 2 , and Y 3 are each ═O;
Z is —NR 4 R 5 or —OR 5 ;
T is a covalent bond or a bivalent C 1-12 saturated or unsaturated, straight or branched, aliphatic chain;
j is 1;
k is 1;
m is an integer from 0 to 2, inclusive;
n is an integer from 0 to 2, inclusive;
each occurrence of R 1 is independently hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or
two R 1 groups may be taken together with their intervening atoms to form a 3-8-membered ring; or
when X 2 is —NR—, R 1 and the R of —NR— may be taken together with their intervening atoms to form a 3-8-membered ring;
each occurrence of R 2 is independently hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or
two R 2 groups may be taken together with their intervening atoms to form a 3-8-membered ring;
R 3 is hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur;
R 4 is hydrogen;
R 5 is hydrogen or —C(R 6 ) 3 ;
each occurrence of R 6 is independently hydrogen, halogen, —CN, —SCN, —NO 2 , —CO 2 R, —SOR, —SO 2 R, —NR 2 , —OR, —SR, or an optionally substituted group selected from the group consisting of —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 1-12 aliphatic, C 1-12 heteroaliphatic, C 7-15 arylalkyl, C 3-15 heteroarylalkyl, 6-10-membered aryl, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur; and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur; or
two occurrences of R 6 may be taken together with their intervening atoms to form a 3-8-membered ring; and
each R is independently hydrogen, a protecting group, —C(═O)-alkyl, —C(═O)-alkenyl, —C(═O)-alkynyl, —C(═O)-aryl, —C(═O)-carbocyclic, —C(═O)-heterocyclic, —C(═O)-(aromatic heterocyclic), C 7-15 arylalkyl moiety, C 1-12 aliphatic moiety, 6-10-membered aryl moiety, 5-10-membered heteroaryl moiety having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or C 1-12 heteroaliphatic moiety; or:
two R on the same nitrogen atom may be taken with the nitrogen to form a 4-7-membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur;
wherein when a group is substituted, the group is substituted with one or more substituents independently selected from the group consisting of aliphatic, heteroaliphatic, aryl, heteroaryl, arylalkyl, heteroarylalkyl, alkoxy, aryloxy, heteroalkoxy, heteroaryloxy, alkylthio, arylthio, heteroalkylthio, heteroarylthio, —F, —Cl, —Br, —I, —OH, —NO 2 , —CN, —CF 3 , —CH 2 CF 3 , —CHCl 2 , —CH 2 OH, —CH 2 CH 2 OH, —CH 2 NH 2 , —CH 2 SO 2 CH 3 , —C(O)R x1 , —CO 2 (R x1 ), —CON(R x1 ) 2 , —OC(O)R x1 , —OCO 2 R x1 , —OCON(R x1 ) 2 , —N(R x1 ) 2 , —S(O) 2 R x1 , and —NR x1 (CO)R x1 , wherein each occurrence of R x1 is independently selected from the group consisting of aliphatic, heteroaliphatic, aryl, heteroaryl, arylalkyl, and heteroarylalkyl.
26. The compound according to claim 1 , wherein R 2 is hydrogen.
27. The compound according to claim 1 , wherein Z is —OR 5 .
28. The compound according to claim 1 , wherein R 5 is hydrogen.
29. The compound according to claim 8 , wherein two occurrences of R 6 are hydrogen.
30. The compound according to claim 8 , wherein one occurrence of R 6 is an optionally substituted group selected from the group consisting of C 1-6 aliphatic group, 5-10-membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, and 4-7-membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, and sulfur.