Spirocyclic degronimers for target protein degradation
This invention provides compounds that have spirocyclic E3 Ubiquitin Ligase targeting moieties (Degrons), which can be used as is or linked to a targeting ligand for a protein that has been selected for in vivo degradation, and methods of use and compositions thereof as well as methods for their preparation.
1. A Degronimer consisting of a Degron covalently linked to a Targeting Ligand, wherein the Degronimer is of Formula:
or a pharmaceutically acceptable salt or N-oxide thereof;
wherein:
W 1 is CR 1 R 2 , C═O, C═S, C═CH 2 , SO 2 , S(O), P(O)Oalkyl, P(O)NHalkyl, P(O)N(alkyl) 2 , P(O)alkyl, P(O)OH, or P(O)NH 2 ;
W 2 is CR 3 R 4 , C═O, C═S, C═CH 2 , SO 2 , S(O), P(O)Oalkyl, P(O)NHalkyl, P(O)N(alkyl) 2 , P(O)alkyl, P(O)OH, or P(O)NH 2 ;
X is independently NH, NR 12 , CH 2 , CHR 12 , C(R 12 ) 2 , O, or S;
n is 0, 1, 2, or 3;
is a single or double bond;
Y and Z are each independently selected from CH 2 , CHR 12 , C(R 12 ) 2 , C(O), N, NH, NR 13 , O, S, and S(O) as permitted by valency;
R 1 , R 2 , R 3 , R 4 , R 7 , and R 8 , are independently selected from hydrogen, alkyl, aliphatic, heteroaliphatic, aryl, heteroaryl, carbocyclic, hydroxyl, alkoxy, amine, —NHalkyl, or —Nalkyl 2 ;
or R 1 and R 2 form a 3-, 4-, 5-, or 6-membered spirocarbocycle, or a 4-, 5-, or 6-membered spiroheterocycle comprising 1 or 2 heteroatoms selected from N and O;
or R 3 and R 4 form a 3-, 4-, 5-, or 6-membered spirocarbocycle, or a 4-, 5-, or 6-membered spiroheterocycle comprising 1 or 2 heteroatoms selected from N and O;
or R 7 and R 8 form a 3-, 4-, 5-, or 6-membered spirocarbocycle, or a 4-, 5-, or 6-membered spiroheterocycle comprising 1 or 2 heteroatoms selected from N and O;
or R 1 and R 3 form a 1, 2, 3 or 4 carbon bridged ring;
or R 1 and R 7 form a 1, 2, 3 or 4 carbon bridged ring;
or R 3 and R 7 form a 1, 2, 3, or 4 carbon bridged ring;
R 5 is selected at each instance from: alkyl, alkene, alkyne, halogen, hydroxyl, alkoxy, azide, amino, cyano, aryl, heteroaryl, heteroaliphatic, hetercyclic, —NHalkyl, —N(alkyl) 2 , —NHSO 2 alkyl, —N(alkyl)SO 2 alkyl, —NHSO 2 aryl, aliphatic, —N(alkyl)SO 2 aryl, —NHSO 2 alkenyl, —N(alkyl)SO 2 alkenyl, —NHSO 2 alkynyl, —N(alkyl)SO 2 alkynyl, and haloalkyl;
or two R 5 substituents together with the carbon atom(s) to which they are bound can form a 3, 4, 5 or 6 membered ring;
R 6 is a bond wherein Y or Z is substituted with R 10 ;
or R 6 is a divalent moiety attached to Y and Z that contains 1 to 5 contiguous carbon atoms that form a 3 to 8-membered ring wherein 1, 2, or 3 carbon atoms can be replaced with a nitrogen, oxygen or sulfur atom wherein one of the ring atoms is substituted with R 10 and the others are optionally substituted with R 11 ;
wherein the contiguous atoms of R 6 can be attached through a single or double bond;
or
forms a bicyclic moiety which is substituted with R 10 and optionally substituted with one or more groups independently selected from R 11 and oxo;
R 10 is Linker-Targeting Ligand;
R 11 is selected at each instance from: hydrogen, alkyl, alkenyl, alkynyl, aliphatic, heteroaliphatic, carbocyclic, halogen, hydroxyl, amino, cyano, alkoxy, aryl, heteroaryl, heterocyclic, carbocyclic, alkylamino, alkylhydroxyl, and haloalkyl;
R 12 is selected from alkyl, alkene, alkyne, halogen, hydroxyl, alkoxy, azide, amino, —C(O)H, —C(O)OH, —C(O)(aliphatic), —C(O)O(aliphatic), —NH(aliphatic), —N(independently aliphatic) 2 , —NHSO 2 alkyl, —N(alkyl)SO 2 alkyl, —NHSO 2 aryl, —N(alkyl)SO 2 aryl, —NHSO 2 alkenyl, —N(alkyl)SO 2 alkenyl, —NHSO 2 alkynyl, —N(alkyl)SO 2 alkynyl, aliphatic, heteroaliphatic, aryl, heteroaryl, hetercyclic, carbocyclic, cyano, nitro, nitroso, —SH, —Salkyl, and haloalkyl;
R 13 is selected from alkyl, alkenyl, alkynyl, —C(O)H, —C(O)OH, —C(O)alkyl, and —C(O)Oalkyl;
Linker is a chemical group that covalently attaches the Degron to the Targeting Ligand;
and Targeting Ligand is a moiety that is capable of binding to or binds to a Targeted Protein, wherein the Targeted Protein is selected from ABL, BRD4, BRD9, CBP, DOT1L, ERK1, ERK2, EZH2, FGFR3, FGFR4, FKBP, IRAK4, JAK2, MDM2, NTRK1, RET, the glucocorticoid receptor, the androgen receptor, and the estrogen receptor.
2. A pharmaceutical composition comprising a compound of claim 1 and a pharmaceutically acceptable excipient.
3. The compound of claim 1 , wherein W 1 is C═O, C═S, or C═CH 2 .
4. The compound of claim 1 , wherein W 2 is C═O, C═S, or C═CH 2 .
5. The compound of claim 1 , wherein X is NH or NR 3 and R 3 is alkyl.
6. The compound of claim 1 , wherein n is 0.
7. The compound of claim 1 , wherein R 7 and R 8 are hydrogen.
8. The compound of claim 1 , wherein R 6 is a divalent moiety attached to Y and Z that contains 1 to 5 contiguous carbon atoms that form a 3 to 8-membered ring wherein 1, 2, or 3 carbon atoms can be replaced with a nitrogen, oxygen or sulfur atom wherein one of the ring atoms is substituted with R 10 and the others are optionally substituted with R 11 ; wherein the contiguous atoms of R 6 can be attached through a single or double bond.
9. The compound of claim 1 , wherein
forms a bicyclic moiety which is substituted with R 10 and optionally substituted with one or more groups independently selected from R 11 and oxo.
10. The compound of claim 9 , wherein
is selected from:
11. The compound of claim 1 , wherein W 1 is C═O, W 2 is C═O, X is NH, and n=0.
12. The compound of claim 1 , wherein the Targeted Protein is the androgen receptor.
13. The compound of claim 1 , wherein the Targeted Protein is the estrogen receptor.
14. The compound of claim 1 , wherein the compound is selected from:
15. The compound of claim 1 , wherein the compound is selected from:
16. The compound of claim 1 , wherein the compound is selected from:
17. The compound of claim 1 , wherein the Targeted Protein is the glucocorticoid receptor.
18. The compound of claim 1 , wherein the compound is selected from:
19. The compound of claim 1 , wherein the compound is selected from:
20. The compound of claim 1 , wherein Linker is selected from:
wherein:
X 1 and X 2 are independently selected from bond, NH, NR 25 , CH 2 , CHR 25 , C(R 25 ) 2 , O, and S;
R 20 , R 21 , R 22 , R 23 , and R 24 are independently selected from heteroarylalkyl, aryl, arylalkyl, heterocycle, aliphatic, heteroaliphatic, heteroaryl, polypropylene glycol, lactic acid, glycolic acid, carbocycle, bond, alkyl, —C(O)— —C(O)O—, —OC(O)—, —C(O)alkyl, —C(O)Oalkyl, —C(S)—, —SO 2 —, —S(O)—, —C(S)—, —C(O)NH—, —NHC(O)—, —N(alkyl)C(O)—, —C(O)N(alkyl)-, —O—, —S—, —NH—, —N(alkyl)-, —CH(—O—R 26 )—, —CH(—NHR 25 )—, —CH(—NH 2 )—, —CH(—NR 25 2 )—, —C(—O—R 26 )alkyl-, —C(—NHR 25 )alkyl-, —C(—NH 2 )alkyl-, —C(—NR 25 2 )alkyl-, -alkyl(R 27 )-alkyl(R 28 )—, —C(R 27 R 28 )—, —P(O)(OR 26 )O—, —P(O)(OR 26 )—, —NHC(O)NH—, —N(R 25 )C(O)N(R 25 )—, —N(H)C(O)N(R 25 )—, polyethylene glycol, poly(lactic-co-glycolic acid), alkene, haloalkyl, alkoxy, and alkyne,
R 25 is selected at each instance from alkyl, —C(O)H, —C(O)OH, —C(O)alkyl, —C(O)Oalkyl, alkenyl, and alkynyl;
R 26 is hydrogen, alkyl, arylalkyl, heteroarylalkyl, alkene, alkyne, aryl, heteroaryl, heterocyclic, aliphatic, or heteroaliphatic; and
R 27 and R 28 are independently selected from hydrogen, alkyl, amine, or together with the carbon atom to which they are attached, form C(O), C(S), C═CH 2 , a C 3 -C 6 spirocarbocycle, or a 4-, 5-, or 6-membered spiroheterocycle comprising 1 or 2 heteroatoms selected from N and O.
21. The compound of claim 20 , wherein
is selected from:
22. The compound of claim 21 , wherein R 7 and R 8 are hydrogen.
23. The compound of claim 22 , wherein W 1 is C═O, W 2 is C═O, X is NH, and n=0.
24. The compound of claim 20 , wherein the compound is selected from:
25. The compound of claim 20 , wherein the compound is selected from:
26. The compound of claim 20 , wherein the compound is selected from:
27. The compound of claim 20 , wherein the compound is selected from:
28. The compound of claim 20 , wherein the compound is selected from:
29. The compound of claim 1 , wherein the Targeted Protein is selected from BRD4 and BRD9.
30. The compound of claim 1 , wherein the Targeted Protein is selected from FGFR3 and FGFR4.
31. The compound of claim 1 , wherein the Targeted Protein is selected from ERK 1 and ERK2.
32. The compound of claim 1 , wherein the Targeted Protein is JAK2.
33. The compound of claim 1 , wherein the Targeted Protein is selected from DOT1l, NTRK1, and RET.
34. The compound of claim 1 , wherein the Targeted Protein is selected from ABL, FKBP, and MDM2.
35. The compound of claim 1 , wherein the Targeted Protein is selected from EZH2 and IRAK4.