IP Library › Granted Patent US 8,912,204

Granted Patent B2

US 8,912,204 · App. 13/411,919 · Granted Dec 16, 2014

Compounds and methods for kinase modulation, and indications therefor

Inventors: Prabha N. Ibrahim (Mountain View, CA); Ryan Bremer (Oakland, CA); Jiazhong Zhang (Foster City, CA); Marika Nespi (Berkeley, CA); Hanna Cho (San Francisco, CA)

Assignee: Plexxikon Inc.

C07D487/04

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Quick Facts

Patent No.: US 8,912,204
App. No.: 13/411,919
Granted: Dec 16, 2014
Kind: B2

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Abstract

Compounds of Formula I: and salts thereof, formulations thereof, conjugates thereof, derivatives thereof, forms thereof and uses thereof are described. In certain aspects and embodiments, the described compounds or salts thereof, formulations thereof, conjugates thereof, derivatives thereof, forms thereof are active on at least one of Fms protein kinase or Kit protein kinase. Also described are methods of use thereof to treat diseases and conditions, including diseases and conditions associated with activity of Fms protein kinases and/or Kit protein kinases, including rheumatoid arthritis, osteoarthritis, osteoporosis, peri-prosthetic osteolysis, systemic sclerosis, demyelinating disorders, multiple sclerosis, Charcot Marie Tooth syndrome, amyotrophic lateral sclerosis, Alzheimer's disease, Parkinson's disease, ulcerative colitis, Crohn's disease, immune thrombocytopenic purpura, myelopreparation for autologous transplantation, transplant rejection, nephritis, nephropathy, type I diabetes, acute pain, inflammatory pain, neuropathic pain, breast cancer, prostate cancer, pancreatic cancer, lung cancer, ovarian cancer, gliomas, glioblastomas, neurofibromatosis, osteolytic bone metastases, and giant cell tumors.

Claims (125)

1. A compound having the chemical structure of Formula I,

or a salt, a tautomer or a stereoisomer thereof,

wherein:

L 1 is selected from the group consisting of —C(R 7 R 8 )—, —C(O)—, —C(S)—, —N(R 9 )—, —O—, —S—, —S(O)—, and —S(O) 2 —;

Ar is selected from the group consisting of:

wherein

indicates the point of attachment of Ar to L 1 of Formula I;

R 2 is selected from the group consisting of —[C(R 10 R 11 )] r —R 19 , —[C(R 10 R 11 )] p —N(R 18 )—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —O—[C(R 10 R 11 )] q —R 19 , —[O—[C(R 10 R 11 )] 2 ] a —R 21 , —[C(R 10 R 11 )] p —S—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —C(O)—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —C(S)—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —S(O)—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —S(O) 2 —[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —C(O)—N(R 18 )—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —C(S)—N(R 18 )—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —S(O)—N(R 18 )—[C(R 10 R 11 )] q —R 19 , —[C(R 10 R 11 )] p —S(O) 2 —N(R 18 )—[C(R 10 R 11 )] q R 19 , and —N(R 18 )—R 20 ;

a is 1 or 2;

p, q and r are independently 0, 1, 2, or 3;

s is 1, 2, or 3;

R 4 is selected from the group consisting of hydrogen, optionally substituted lower alkyl, optionally substituted lower alkenyl, optionally substituted lower alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —NO 2 , —O—R 22 , —S—R 24 , —N(R 22 )—R 23 , —C(O)—R 24 , —C(S)—R 24 , —C(O)—N(R 22 )—R 23 , —C(S)—N(R 22 )—R 23 , —C(O)—N(R 25 )—OR 22 , —C(S)—N(R 25 )—OR 22 , —C(O)—N(R 25 )—S(O) 2 —R 24 , —C(S)—N(R 25 )—S(O) 2 —R 24 , —C(O)—O—R 22 , —S(O)—R 24 , —S(O) 2 —R 24 , —S(O)—N(R 22 )—R 23 , —S(O) 2 —N(R 22 )—R 23 , —S(O) 2 —N(R 25 )—C(O)R 24 , —S(O) 2 —N(R 25 )—C(S)R 24 , —N(R 25 )—C(O)—R 24 , —N(R 25 )—C(S)—R 24 , —N(R 25 )—S(O)—R 24 , —N(R 25 )—S(O) 2 —R 24 , —N(R 25 )—C(O)—N(R 22 )—R 23 , —N(R 25 )—C(S)—N(R 22 )—R 23 , and —N(R 25 )—S(O) 2 —N(R 22 )—R 23 ;

R 5 is selected from the group consisting of hydrogen, optionally substituted lower alkyl, optionally substituted lower alkenyl, optionally substituted lower alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —NO 2 , —O—R 28 , —S—R 28 , —C(O)—R 28 , —C(S)—R 28 , —C(O)—N(R 26 )—R 27 , —C(S)—N(R 26 )—R 27 , —C(O)—N(R 29 )—OR 26 , —C(S)—N(R 29 )—OR 26 , —C(O)—N(R 29 )—S(O) 2 —R 28 , —C(S)—N(R 29 )—S(O) 2 —R 28 , —C(O)—O—R 26 , —S(O)—R 28 , —S(O) 2 —R 28 , —S(O)—N(R 26 )—R 27 , —S(O) 2 —N(R 26 )—R 27 , —S(O) 2 —N(R 29 )—C(O)R 28 , —S(O) 2 —N(R 29 )—C(S)R 28 , —N(R 29 )—C(O)—R 28 , —N(R 29 )—C(S)—R 28 , —N(R 29 )—S(O)—R 28 , —N(R 29 )—S(O) 2 —R 28 , —N(R 29 )—C(O)—N(R 26 )—R 27 , —N(R 29 )—C(S)—N(R 26 )—R 27 , and —N(R 29 )—S(O) 2 —N(R 26 )—R 27 ;

R 6 is selected from the group consisting of hydrogen, halogen, optionally substituted lower alkyl, optionally substituted lower alkenyl, optionally substituted lower alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, —CN, —NO 2 , —O—R 30 , —S—R 32 , —N(R 30 )—R 31 , —C(O)—R 32 , —C(S)—R 32 , —C(O)—N(R 30 )—R 31 , —C(S)—N(R 30 )—R 31 , —C(O)—N(R 33 )—OR 30 , —C(S)—N(R 33 )—OR 30 , —C(O)—N(R 33 )—S(O) 2 —R 32 , —C(S)—N(R 33 )—S(O) 2 —R 32 , —C(O)—O—R 30 , —S(O)—R 32 , —S(O) 2 —R 32 , —S(O)—N(R 30 )—R 31 , —S(O) 2 —N(R 30 )—R 31 , —S(O) 2 —N(R 33 )—C(O)R 32 , —S(O) 2 —N(R 33 )—C(S)R 32 , —N(R 33 )—C(O)—R 32 , —N(R 33 )—C(S)—R 32 , —N(R 33 )—S(O)—R 32 , —N(R 33 )—S(O) 2 —R 32 , —N(R 33 )—C(O)—N(R 30 )—R 31 , —N(R 33 )—C(S)—N(R 30 )—R 31 , and —N(R 33 )—S(O) 2 —N(R 30 )—R 31 ;

R 7 , R 8 , R 10 , and R 11 , at each occurrence, are independently selected from the group consisting of hydrogen, fluoro, —OH, —NH 2 , lower alkyl, lower alkoxy, lower alklylthio, mono-alkylamino, di-alkylamino, and —N(R 34 )—R 35 , wherein the alkyl chain(s) of lower alkyl, lower alkoxy, lower alkylthio, mono-alkylamino, or di-alkylamino are optionally substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino; or

R 7 and R 8 , or any two of R 10 and R 11 on the same or different carbons, combine to form a 3-7 membered monocyclic cycloalkyl or 5-7 membered monocyclic heterocycloalkyl and any others of R 10 and R 11 are independently selected from the group consisting of hydrogen, fluoro, —OH, —NH 2 , lower alkyl, lower alkoxy, lower alklylthio, mono-alkylamino, di-alkylamino, and —N(R 34 )—R 35 , wherein the alkyl chain(s) of lower alkyl, lower alkoxy, lower alkylthio, mono-alkylamino, or di-alkylamino are optionally substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino, and wherein the 3-7 membered monocyclic cycloalkyl or 5-7 membered monocyclic heterocycloalkyl are optionally substituted with one or more substituents selected from the group consisting of halogen, —OH, —NH 2 , lower alkyl, fluoro substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino;

R 9 , R 25 , R 29 , and R 33 are independently selected from the group consisting of hydrogen, optionally substituted lower alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, —C(O)—R 36 , —C(S)—R 36 , —S(O)—R 36 , —S(O) 2 —R 36 , —C(O)—N(H)—R 36 , —C(S)—N(H)—R 36 , and —S(O) 2 —N(H)—R 36 ;

R 15 and R 16 are independently selected from the group consisting of hydrogen, halogen, optionally substituted lower alkyl, —N(R 37 )—R 38 , —O—R 37 , and —S—R 39 ;

R 18 at each occurrence is independently hydrogen, lower alkyl, or lower alkyl substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 25 lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, fluoro substituted mono-alkylamino, di-alkylamino, fluoro substituted di-alkylamino, and —N(R 34 )—R 35 ;

R 19 is selected from the group consisting of optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl;

R 20 is selected from the group consisting of optionally substituted lower alkyl, optionally substituted lower alkenyl, and optionally substituted lower alkynyl;

R 21 is selected from the group consisting of hydrogen, optionally substituted lower alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and —O—R 40 ;

R 24 , R 28 and R 32 are independently selected from the group consisting of optionally substituted lower alkyl, optionally substituted lower alkenyl, optionally substituted lower alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl;

R 22 , R 23 , R 26 , R 27 , R 30 and R 31 are independently selected from the group consisting of hydrogen, optionally substituted lower alkyl, optionally substituted lower alkenyl, optionally substituted lower alkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl;

R 34 and R 35 at each occurrence combine with the nitrogen to which they are attached to form a 5-7 membered heterocycloalkyl optionally substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkyl, fluoro substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, and fluoro substituted lower alkylthio;

R 36 at each occurrence is independently selected from the group consisting of optionally substituted lower alkyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl;

R 37 and R 38 at each occurrence are independently hydrogen or optionally substituted lower alkyl; and

R 39 and R 40 at each occurrence are independently optionally substituted lower alkyl.

2. The compound of claim 1 , wherein:

R 20 is selected from the group consisting of lower alkyl, lower alkenyl, and lower alkynyl, wherein lower alkyl, lower alkenyl or lower alkynyl are optionally substituted with one or more substituents R 74 ;

R 21 is selected from the group consisting of hydrogen, lower alkyl optionally substituted with one or more substituents R 74 , cycloalkyl, heterocycloalkyl, aryl, heteroaryl, and —O—R 73 , wherein cycloalkyl, heterocycloalkyl, aryl or heteroaryl are optionally substituted with one or more substituents R 75 ;

R 19 is selected from the group consisting of cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl or heteroaryl are optionally substituted with one or more substituents R 75 ;

R 73 is lower alkyl optionally substituted with one or more substituents R 74 ;

R 74 at each occurrence is independently selected from the group consisting of —OH, —NH 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 76 , —S—R 76 , —N(R 77 )—R 76 , —N(R 77 )—C(O)—R 76 , —N(R 77 )—S(O)—R 76 , —N(R 77 )—S(O) 2 —R 76 , —C(O)—N(R 77 )—R 76 , —C(O)—O—R 76 , —C(O)—R 76 , —S(O)—N(R 77 )—R 76 , —S(O) 2 —N(R 77 )—R 76 , —S(O)—R 76 , —S(O) 2 —R 76 , fluoro, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl and heteroaryl are optionally substituted with one or more substituents R 75 ;

R 75 at each occurrence is independently selected from the group consisting of —OH, —NH 2 , —NO 2 , —CN, —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 76 , —S—R 76 , —N(R 77 )—R 76 , —N(R 77 )—C(O)—R 76 , —N(R 77 )—S(O)—R 76 , —N(R 77 )—S(O) 2 —R 76 , —S(O)—R 76 , —S(O) 2 —R 76 , —C(O)—R 76 , —C(O)—O—R 76 , —C(O)—N(R 77 )—R 76 , —S(O)—N(R 77 )—R 76 , —S(O) 2 —N(R 77 )—R 76 , halogen, lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, and wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 75 , or as substituents of lower alkyl, are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —NO 2 , —CN, —C(O)—OH, —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 78 , —S—R 78 , —N(R 77 )—R 78 , —N(R 77 )—C(O)—R 78 , —N(R 77 )—S(O) 2 —R 78 , —S(O)—R 78 , —S(O) 2 —R 78 , —C(O)—R 78 , —C(O)—O—R 78 , —C(O)—N(R 77 )—R 78 , —S(O) 2 —N(R 77 )—R 78 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 76 at each occurrence is independently selected from the group consisting of lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, and wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 76 or as substituents of lower alkyl are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 80 , —S—R 80 , —N(R 79 )—R 80 , —N(R 79 )—C(O)—R 80 , —N(R 79 )—S(O) 2 —R 80 , —C(O)—R 80 , —S(O)—R 80 , —S(O) 2 —R 80 , —C(O)—O—R 80 , —C(O)—N(R 79 )—R 80 , —S(O) 2 —N(R 79 )—R 80 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 77 and R 79 at each occurrence are independently hydrogen, lower alkyl, or lower alkyl substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, fluoro substituted mono-alkylamino, di-alkylamino, fluoro substituted di-alkylamino, and cycloalkylamino; and

R 78 and R 80 at each occurrence are independently selected from the group consisting of lower alkyl, heterocycloalkyl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino, and wherein heterocycloalkyl and heteroaryl are optionally substituted with one or more substituents selected from the group consisting of halogen, —CN, lower alkyl, fluoro substituted lower alkyl, lower alkoxy and fluoro substituted lower alkoxy.

3. The compound of claim 2 , wherein:

R 75 at each occurrence is independently selected from the group consisting of —OH, —NH 2 , —NO 2 , —CN, —O—R 76 , —S—R 76 , —N(R 77 )—R 76 , —N(R 77 )—C(O)—R 76 , —N(R 77 )—S(O)—R 76 , —N(R 77 )—S(O) 2 —R 76 , —C(O)—R 76 , —S(O)—R 76 , —S(O) 2 —R 76 , halogen, lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, and wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 75 , or as substituents of lower alkyl, are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —NO 2 , —CN, —O—R 78 , —S—R 78 , —N(R 77 )—R 78 , —N(R 77 )—C(O)—R 78 , —N(R 77 )—S(O) 2 —R 78 , —S(O)—R 78 , —S(O) 2 —R 78 , —C(O)—R 78 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 76 at each occurrence is independently selected from the group consisting of lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, and wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 76 or as substituents of lower alkyl are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 80 , —S—R 80 , —N(R 79 )—R 80 , —N(R 79 )—C(O)—R 80 , —N(R 79 )—S(O) 2 —R 80 , —C(O)—R 80 , —S(O)—R 80 , —S(O) 2 —R 80 , —C(O)—O—R 80 , —C(O)—N(R 79 )—R 80 , —S(O) 2 —N(R 79 )R 80 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

4. The compound of claim 3 , wherein:

R 4 is selected from the group consisting of hydrogen, —CN, —O—R 100 , —S—R 100 , —N(R 101 )—R 100 , and lower alkyl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino;

R 5 is selected from the group consisting of hydrogen, —CN, —O—R 100 , —S—R 100 , and lower alkyl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino;

R 6 is hydrogen;

R 100 is lower alkyl optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino; and

R 101 is hydrogen or lower alkyl optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino.

5. A compound having the chemical structure of Formula Ia,

or a salt, a tautomer or a stereoisomer thereof,

wherein:

L 2 is selected from the group consisting of —C(R 44 R 45 )—, —C(O)—, —C(S)—, —N(R 46 )—, —O—, —S—, —S(O)—, and —S(O) 2 —;

Ar 1 is

wherein

indicates the point of attachment of Ar 1 to L 2 of Formula Ia;

R 47 is selected from the group consisting of a bond, —C(R 49 R 50 )—R 58 , —[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—C(R 49 R 50 )—R 58 , —N(R 51 )—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—[C(R 49 R 50 )] 3 —R 58 , —C(R 49 R 50 )—N(R 51 )—R 58 , —O—, —O—C(R 49 R 50 )—R 58 , —O—[C(R 49 R 50 )] 2 —R 58 , —O—[C(R 49 R 50 )] 3 —R 58 , —C(R 49 R 50 )—O—R 58 , —S—R 58 , —S—C(R 49 R 50 )—R 58 , —S—[C(R 49 R 50 )] 2 —R 58 , —S—[C(R 49 R 50 )] 3 —R 58 , —C(R 49 R 50 )—S—R 58 , —C(O)—N(R 51 )—R 58 , —C(O)—N(R 51 )—C(R 49 R 50 )—R 58 , —C(O)—N(R 51 )—[C(R 49 R 50 )] 2 —R 58 , —C(S)—N(R 51 )—R 58 , —C(S)—N(R 51 )—C(R 49 R 50 )—R 58 , —C(S)—N(R 51 )—[C(R 49 R 50 )] 2 —R 58 , —S(O)—N(R 51 )—R 58 , —S(O)—N(R 51 )—C(R 49 R 50 )—R 58 , —S(O)—N(R 51 )—[C(R 49 R 50 )] 2 —R 58 , —S(O) 2 —N(R 51 )—R 58 , —S(O) 2 —N(R 51 )—C(R 49 R 50 )—R 58 , —S(O) 2 —N(R 51 ))—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—C(O)—R 58 , —N(R 51 )—C(O)—C(R 49 R 50 )—R 58 , —N(R 51 )—C(O)—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—C(S)—R 58 , —N(R 51 )—C(S)—C(R 49 R 50 )—R 58 , —N(R 51 )—C(S)—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—S(O)—R 58 , —N(R 51 )—S(O)—C(R 49 R 50 )—R 58 , —N(R 51 )—S(O)—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—S(O) 2 —R 58 , —N(R 51 )—S(O) 2 —C(R 49 R 50 )—R 58 , —N(R 51 )—S(O) 2 —[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—C(O)—N(R 51 )—R 58 , —N(R 51 )—C(O)—N(R 51 )—C(R 49 R 50 )—R 58 , —N(R 51 )—C(O)—N(R 51 )—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—C(S)—N(R 51 )—R 58 , —N(R 51 )—C(S)—N(R 51 )—C(R 49 R 50 )—R 58 , —N(R 51 )—C(S)—N(R 51 )—[C(R 49 R 50 )] 2 —R 58 , —N(R 51 )—S(O) 2 —N(R 51 )—R 58 , —N(R 51 )—S(O) 2 —N(R 51 )—)C(R 49 R 50 )—R 58 , and —N(R 51 )—S(O) 2 —N(R 51 )—[C(R 49 R 50 ] 2 —R 58 ;

R 41 is selected from the group consisting of hydrogen, —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 59 , —S—R 59 , —N(R 60 )—R 59 , —N(R 60 )—C(O)—R 59 , —N(R 60 )—S(O)—R 59 , —N(R 60 )—S(O) 2 —R 59 , —C(O)—N(R 60 )—R 59 , —C(O)—O—R 59 , —C(O)—R 59 , —S(O)—N(R 60 )—R 59 , —S(O) 2 —N(R 60 )—R 59 , —S(O)—R 59 , —S(O) 2 —R 59 , lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 41 or as substituents of lower alkyl are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 61 , —S—R 61 , —N(R 60 )—R 61 , —N(R 60 )—C(O)—R 61 , —N(R 60 )—S(O)—R 61 , —N(R 60 )—S(O) 2 —R 61 , —C(O)—R 61 , —S(O)—R 61 , —S(O) 2 R 61 , —C(O)—O—R 61 , —C(O)—N(R 60 )R 61 , —S(O)—N(R 60 )—R 61 , —S(O) 2 —N(R 60 )—R 61 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 42 is selected from the group consisting of hydrogen, —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 62 , —S—R 62 , —N(R 63 )—C(O)—R 62 , —N(R 63 )—S(O)—R 62 , —N(R 63 )—S(O) 2 —R 62 , —C(O)—N(R 63 )—R 62 , —C(O)—O—R 62 , —C(O)—R 62 , —S(O)—N(R 63 )—R 62 , —S(O) 2 —N(R 63 )—R 62 , —S(O)—R 62 , —S(O) 2 —R 62 , lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 42 or as substituents of lower alkyl are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 64 , —S—R 64 , —N(R 63 )—R 64 , —N(R 63 )—C(O)—R 64 , —N(R 63 )—S(O)—R 64 , —N(R 63 )—S(O) 2 —R 64 , —C(O)—R 64 , —S(O)—R 64 , —S(O) 2 —R 64 , —C(O)—O—R 64 , —C(O)—N(R 63 )—R 64 , —S(O)—N(R 63 )—R 64 , —S(O) 2 —N(R 63 )—R 64 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 43 is independently selected from the group consisting of hydrogen, —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 65 , —S—R 65 , —N(R 66 )—R 65 , —N(R 66 )—C(O)—R 65 , —N(R 66 )—S(O)—R 65 , —N(R 66 )—S(O) 2 —R 65 , —C(O)—N(R 66 )—R 65 , —C(O)—O—R 65 , —C(O)—R 65 , —S(O)—N(R 66 )—R 65 , —S(O) 2 —N(R 66 )—R 65 , —S(O)—R 65 , —S(O) 2 —R 65 , halogen, lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 43 or as substituents of lower alkyl are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 67 , —S—R 67 , —N(R 66 )—R 67 , —N(R 66 )—C(O)—R 67 , —N(R 66 )—S(O)—R 67 , —N(R 66 )—S(O) 2 —R 67 , —C(O)—R 67 , —S(O)—R 67 , —S(O) 2 —R 67 , —C(O)—O—R 67 , —C(O)—N(R 66 )—R 67 , —S(O)—N(R 66 )—R 67 , —S(O) 2 —N(R 66 )—R 67 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 58 is selected from the group consisting of optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl or optionally substituted heteroaryl;

R 44 , R 45 , R 49 and R 50 at each occurrence are independently selected from the group consisting of hydrogen, fluoro, lower alkyl, fluoro substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino; or

R 44 and R 45 , or any two of R 49 and R 50 on the same or different carbons, combine to form a 3-7 membered monocyclic cycloalkyl or 5-7 membered monocyclic heterocycloalkyl, and any others of R 49 and R 50 are independently selected from the group consisting of hydrogen, fluoro, lower alkyl, fluoro substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino, wherein the 3-7 membered monocyclic cycloalkyl or 5-7 membered monocyclic heterocycloalkyl is optionally substituted with one or more substituents selected from the group consisting of halogen, —OH, —NH 2 , lower alkyl, fluoro substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino;

R 52 , and R 56 are independently selected from the group consisting of halogen, lower alkyl, —N(R 70 )—R 71 , —O—R 70 , and —S—R 72 , wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, fluoro substituted mono-alkylamino, di-alkylamino, fluoro substituted di-alkylamino, and cycloalkylamino;

R 59 , R 62 , and R 65 are independently selected from the group consisting of lower alkyl, cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, and wherein cycloalkyl, heterocycloalkyl, aryl, and heteroaryl as R 59 , R 62 , or R 65 or as substituents of lower alkyl are optionally substituted with one or more substituents selected from the group consisting of —OH, —NH 2 , —CN, —NO 2 , —C(O)—OH, —S(O)—NH 2 , —S(O) 2 —NH 2 , —C(O)—NH 2 , —O—R 69 , —S—R 69 , —N(R 68 )—R 69 , —N(R 68 )—C(O)—R 69 , —N(R 68 )—S(O)—R 69 , —N(R 68 )—S(O) 2 —R 69 , —C(O)—R 69 , —S(O)—R 69 , —S(O) 2 —R 69 , —C(O)—O—R 69 , —C(O)—N(R 68 )—R 69 , —S(O)—N(R 68 )—R 69 , —S(O) 2 —N(R 68 )—R 69 , halogen, lower alkyl, fluoro substituted lower alkyl, and cycloalkylamino;

R 46 , R 51 , R 60 , R 63 , R 66 and R 68 at each occurrence are independently hydrogen, lower alkyl, or lower alkyl substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, fluoro substituted mono-alkylamino, di-alkylamino, fluoro substituted di-alkylamino, and cycloalkylamino;

R 61 , R 64 , R 67 and R 69 at each occurrence are independently selected from the group consisting of lower alkyl, heterocycloalkyl and heteroaryl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino, and wherein heterocycloalkyl and heteroaryl are optionally substituted with one or more substituents selected from the group consisting of halogen, —CN, lower alkyl, fluoro substituted lower alkyl, lower alkoxy and fluoro substituted lower alkoxy;

R 70 and R 71 at each occurrence are independently hydrogen, lower alkyl or lower alkyl substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, fluoro substituted mono-alkylamino, di-alkylamino, fluoro substituted di-alkylamino, and cycloalkylamino; and

R 72 at each occurrence is lower alkyl or lower alkyl substituted with one or more substituents selected from the group consisting of fluoro, —OH, —NH 2 , lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, fluoro substituted mono-alkylamino, di-alkylamino, fluoro substituted di-alkylamino, and cycloalkylamino.

6. The compound of claim 5 , wherein:

R 58 is selected from the group consisting of cycloalkyl, heterocycloalkyl, aryl and heteroaryl, wherein cycloalkyl, heterocycloalkyl, aryl or heteroaryl are optionally substituted with one or more substituents R 75 ;

7. The compound of claim 6 , wherein:

8. The compound of claim 7 , wherein:

R 41 is selected from the group consisting of hydrogen, —CN, —O—R 100 , —S—R 100 , —N(R 101 )—R 100 , and lower alkyl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino;

R 42 is selected from the group consisting of hydrogen, —CN, —O—R 100 , —S—R 100 , and lower alkyl, wherein lower alkyl is optionally substituted with one or more substituents selected from the group consisting of fluoro, lower alkoxy, fluoro substituted lower alkoxy, lower alkylthio, fluoro substituted lower alkylthio, mono-alkylamino, di-alkylamino, and cycloalkylamino;

R 43 is hydrogen;

9. The compound of claim 8 , wherein:

Ar 1 is

R 52 , and R 56 are independently halogen, lower alkyl, fluoro substituted lower alkyl, —N(R 82 )—R 81 , —O—R 81 , or —S—R 83 ;

R 81 and R 82 are independently hydrogen, lower alkyl, or fluoro substituted lower alkyl; and

R 83 is lower alkyl or fluoro substituted lower alkyl.

10. A compound having the chemical structure of Formula Ia,

or a salt, a tautomer or a stereoisomer thereof,

wherein:

X is N;

R 84 is hydrogen, lower alkyl, fluoro substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, or cycloalkyl;

R 85 is fluoro, lower alkyl or lower alkoxy;

R 87 is hydrogen or lower alkyl; and R 88 is phenyl, pyridinyl or pyrimidinyl, wherein phenyl, pyridinyl or pyrimidinyl are optionally substituted with 1, 2 or 3 substituents independently selected from the group consisting of —CN, fluoro, chloro, bromo, lower alkyl, fluoro substituted lower alkyl, methoxy substituted lower alkyl, lower alkoxy, fluoro substituted lower alkoxy, cycloalkyloxy, alkylsulfonyl, mono-alkylamino, di-alkylamino, or cycloalkylamino.

11. A compound selected from the group consisting of:

(6-Methoxy-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0015),

(5-Fluoro-2-methoxy-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0022),

(5-Fluoro-6-methoxy-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0024),

(5-Fluoro-2-methoxy-pyridin-4-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0025),

Pyridin-2-ylmethyl-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0028),

(6-Chloro-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0029),

[5-(7H-Pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-(6-trifluoromethyl-pyridin-3-ylmethyl)-amine (P-0030),

(6-Morpholin-4-yl-pyridin-2-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0031),

(6-Pyrrolidin-1-yl-pyridin-2-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0032),

(5-Ethyl-pyridin-2-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0033),

(3-Methyl-pyridin-4-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0034),

(2-Methyl-pyridin-4-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0035),

(2-Morpholin-4-yl-pyridin-4-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0036),

(2-Methoxy-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0084),

(2-Ethoxy-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0085),

(2-Cyclopentyloxy-pyridin-3-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0086),

(2-Cyclopentyloxy-pyridin-4-ylmethyl)-[5-(7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0087),

(5-Fluoro-6-methoxy-pyridin-3-ylmethyl)-[5-(4-methoxy-7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0092),

(5-Fluoro-2-methoxy-pyridin-3-ylmethyl)-[5-(4-methoxy-7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0093),

(5-Fluoro-pyridin-3-ylmethyl)-[5-(4-methoxy-7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-amine (P-0098) and

[5-(4-Methoxy-7H-pyrrolo[2,3-d]pyrimidin-5-ylmethyl)-pyrimidin-2-yl]-(6-trifluoromethyl-pyridin-3-ylmethyl)-amine (P-0102),

or a salt, a tautomer or a stereoisomer thereof.

12. A composition comprising a pharmaceutically acceptable carrier; and a compound according to claim 1 .

13. A composition comprising a pharmaceutically acceptable carrier; and a compound according to claim 5 .

14. A composition comprising a pharmaceutically acceptable carrier; and a compound according to claim 10 .

15. A composition comprising a pharmaceutically acceptable carrier; and a compound according to claim 12 .

Assignments (2)

CORRECTIVE ASSIGNMENT TO CORRECT THE NAME OF 5TH CONVEYING PARTY PREVIOUSLY RECORDED ON REEL 032353 FRAME 0957. ASSIGNOR(S) HEREBY CONFIRMS THE NAME OF THE 5TH CONVEYING PARTY AS HANNA CHO. Recorded Mar 6, 2014

From: IBRAHIM, PRABHA N.; BREMER, RYAN; ZHANG, JIAZHONG; NESPI, MARIKA; CHO, HANNA

To: PLEXXIKON INC.

Reel/Frame 032399/0488 →

ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 5, 2014

From: IBRAHIM, PRABHA N.; BREMER, RYAN; ZHANG, JIAZHONG; NESPI, MARIKA; 06/10/2009, HANNA CHO

To: PLEXXIKON INC.

Reel/Frame 032353/0957 →

Continuity (3)

Division 12467194 · May 15, 2009

Provisional Application 61054451 · May 19, 2008

Related Publication 20120165329A1 · Jun 28, 2012