U.S. patent application number 14/391369 was filed with the patent office on 2015-03-26 for compositions and methods for treating cancer.
The applicant listed for this patent is The Regents of the University of California. Invention is credited to Jonathan Ostrem, Ulf Peters, Kevan M. Shokat.
Application Number | 20150087628 14/391369 |
Document ID | / |
Family ID | 49328138 |
Filed Date | 2015-03-26 |
United States Patent
Application |
20150087628 |
Kind Code |
A1 |
Ostrem; Jonathan ; et
al. |
March 26, 2015 |
COMPOSITIONS AND METHODS FOR TREATING CANCER
Abstract
K-Ras is the most frequently mutated oncogene in human cancer.
Disclosed herein are compositions and methods for modulating K-Ras
and treating cancer.
Inventors: |
Ostrem; Jonathan; (San
Francisco, CA) ; Peters; Ulf; (San Francisco, CA)
; Shokat; Kevan M.; (San Francisco, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Regents of the University of California |
Oakland |
CA |
US |
|
|
Family ID: |
49328138 |
Appl. No.: |
14/391369 |
Filed: |
April 10, 2013 |
PCT Filed: |
April 10, 2013 |
PCT NO: |
PCT/US2013/036031 |
371 Date: |
October 8, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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61622507 |
Apr 10, 2012 |
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61728145 |
Nov 19, 2012 |
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61794956 |
Mar 15, 2013 |
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Current U.S.
Class: |
514/210.18 ;
435/184; 435/188; 514/316; 514/322; 514/323; 514/326; 514/329;
514/330; 514/407; 514/412; 546/189; 546/199; 546/201; 546/210;
546/223; 546/224; 546/226; 548/365.7; 548/409; 548/453 |
Current CPC
Class: |
C07D 401/12 20130101;
A61P 35/00 20180101; C07D 211/58 20130101; C07D 211/62 20130101;
C12Q 2600/156 20130101; C07D 487/10 20130101; C07D 487/04 20130101;
C07D 471/10 20130101; A61P 43/00 20180101; C07D 405/12 20130101;
C07C 235/20 20130101; C07D 401/06 20130101; C07D 409/04 20130101;
C12Y 306/05002 20130101; C07C 317/08 20130101; C12Q 1/6886
20130101; G01N 2500/04 20130101; C07D 295/26 20130101; A61P 35/02
20180101; C07D 295/185 20130101; A61K 38/1709 20130101; C07D 417/12
20130101; C07D 231/40 20130101; C07D 401/04 20130101; C12N 9/14
20130101; C07D 207/14 20130101; C07D 413/12 20130101; C12Q 2600/158
20130101; C07D 495/04 20130101 |
Class at
Publication: |
514/210.18 ;
514/316; 514/322; 514/323; 514/326; 514/329; 514/330; 514/407;
514/412; 546/189; 546/199; 546/201; 546/210; 546/223; 546/224;
546/226; 548/365.7; 548/409; 548/453; 435/184; 435/188 |
International
Class: |
C07D 487/04 20060101
C07D487/04; C07D 401/12 20060101 C07D401/12; C12N 9/14 20060101
C12N009/14; C07D 211/62 20060101 C07D211/62; C07D 409/04 20060101
C07D409/04; C07D 401/06 20060101 C07D401/06; C07D 211/58 20060101
C07D211/58 |
Claims
1. A compound having the formula: R.sup.1-L.sup.1-L.sup.2-L.sup.3-E
wherein, R.sup.1 is a Switch 2-Binding Pocket binding moiety;
L.sup.1 is a bond or a divalent radical chemical linker; L.sup.2 is
a bond or a divalent radical chemical linker; L.sup.3 is a bond or
a divalent radical chemical linker; E is an electrophilic chemical
moiety capable of forming a covalent bond with a K-Ras cysteine
residue or a K-Ras aspartate residue.
2. The compound of claim 1, wherein R.sup.1 is hydrogen,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl.
3.-6. (canceled)
7. The compound of claim 1, wherein R.sup.1 is: ##STR00314##
##STR00315## wherein, R.sup.3 is independently hydrogen, oxo,
halogen, --CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8, N(O).sub.m,
--NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; X is independently --Cl, --Br, --I, or --F; e2 is independently
an integer from 0 to 2; e3 is independently an integer from 0 to 3;
e4 is independently an integer from 0 to 4; e5 is independently an
integer from 0 to 5; e6 is independently an integer from 0 to 6; e7
is independently an integer from 0 to 7.
8. The compound of claim 1, wherein R.sup.1 is R.sup.3-substituted
pyridinyl, R.sup.3-substituted pyrimidinyl, R.sup.3-substituted
thiophenyl, R.sup.3-substituted furanyl, R.sup.3-substituted
indolyl, R.sup.3-substituted benzoxadiazolyl, R.sup.3-substituted
benzodioxolyl, R.sup.3-substituted benzodioxanyl,
R.sup.3-substituted thianaphthanyl, R.sup.3-substituted
pyrrolopyridinyl, R.sup.3-substituted indazolyl,
R.sup.3-substituted quinolinyl, R.sup.3-substituted quinoxalinyl,
R.sup.3-substituted pyridopyrazinyl, R.sup.3-substituted
quinazolinonyl, R.sup.3-substituted benzoisoxazolyl,
R.sup.3-substituted imidazopyridinyl, R.sup.3-substituted
benzofuranyl, R.sup.3-substituted benzothiophenyl,
R.sup.3-substituted phenyl, R.sup.3-substituted naphthyl,
R.sup.3-substituted biphenyl, R.sup.3-substituted pyrrolyl,
R.sup.3-substituted pyrazolyl, R.sup.3-substituted imidazolyl,
R.sup.3-substituted pyrazinyl, R.sup.3-substituted oxazolyl,
R.sup.3-substituted isoxazolyl, R.sup.3-substituted thiazolyl,
R.sup.3-substituted furylthienyl, R.sup.3-substituted pyridyl,
R.sup.3-substituted pyrimidyl, R.sup.3-substituted benzothiazolyl,
R.sup.3-substituted purinyl, R.sup.3-substituted benzimidazolyl,
R.sup.3-substituted isoquinolyl, R.sup.3-substituted thiadiazolyl,
R.sup.3-substituted oxadiazolyl, R.sup.3-substituted pyrrolyl,
R.sup.3-substituted diazolyl, R.sup.3-substituted triazolyl,
R.sup.3-substituted tetrazolyl, R.sup.3-substituted
benzothiadiazolyl, R.sup.3-substituted isothiazolyl,
R.sup.3-substituted pyrazolopyrimidinyl, R.sup.3-substituted
pyrrolopyrimidinyl, R.sup.3-substituted benzotriazolyl, or
R.sup.3-substituted quinolyl; R.sup.3 is independently hydrogen,
oxo, halogen, --CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8,
--N(O).sub.m, --NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7 and
R.sup.8 substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; X is independently --Cl, --Br, --I, or --F.
9. (canceled)
10. The compound of claim 1, wherein L.sup.1, L.sup.2 and L.sup.3
are independently a bond, --NR.sup.2C--, --O--, --S--, --C(O)--,
--S(O)--, --S(O).sub.2--, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene; or a substituted or
unsubstituted spirocyclic linker; R.sup.2C is independently
hydrogen, oxo, halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; Two adjacent
R.sup.2C substituents may optionally be joined to form a
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two R.sup.2C
substituents bonded to the same atom may optionally be joined to
form a substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.7c, R.sup.8c, R.sup.9c and
R.sup.10c are independently hydrogen, halogen, --CF.sub.3, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7c and R.sup.8c substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m1,
m3, v1, and v3 are independently an integer from 1 to 2; n1 and n3
are independently an integer from 0 to 4; X.sup.c is independently
--Cl, --Br, --I, or --F.
11. The compound of claim 1, wherein L.sup.1, L.sup.2 and L.sup.3
are independently --CR.sup.2AR.sup.2B--, ##STR00316## R.sup.2A and
R.sup.2B are independently hydrogen, oxo, halogen,
--CX.sup.a.sub.3, --CN, --SO.sub.2Cl, --SO.sub.n1R.sup.10a,
--SO.sub.v1NR.sup.7aR.sup.8a, --NHNH.sub.2, --ONR.sup.7aR.sup.8a,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7aR.sup.8a,
--N(O).sub.m1, --NR.sup.7aR.sup.8a, --C(O)R.sup.9a,
--C(O)--OR.sup.9a, --C(O)NR.sup.7aR.sup.8a, --OR.sup.10a,
--NR.sup.7aSO.sub.2R.sup.10a, --NR.sup.7aC.dbd.(O)R.sup.9a,
--NR.sup.7aC(O)--OR.sup.9a, --NR.sup.7aOR.sup.9a,
--OCX.sup.a.sub.3, --OCHX.sup.a.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.2A and R.sup.2B substituent
bonded to the same atom may optionally be joined to form a
substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.2C is independently hydrogen,
oxo, halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCHX.sup.c.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; R.sup.7a, R.sup.8a,
R.sup.9a and R.sup.10a are independently hydrogen, halogen,
--CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl;
R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7c and
R.sup.8c substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; z is
independently an integer from 0 to 10; m1, m3, v1, and v3 are
independently an integer from 1 to 2; n1 and n3 are independently
an integer from 0 to 4; X.sup.a and X.sup.c are independently --Cl,
--Br, --I, or --F.
12.-14. (canceled)
15. The compound of claim 1, wherein E comprises ##STR00317##
##STR00318## ##STR00319## ##STR00320## ##STR00321## ##STR00322##
##STR00323## ##STR00324## ##STR00325## ##STR00326## ##STR00327##
##STR00328## R.sup.13 is independently hydrogen, oxo, halogen,
--CX.sup.b.sub.3, --CN, --SO.sub.2Cl, --SO.sub.rR.sup.17,
--SO.sub.pNR.sup.14R.sup.15, NHNH.sub.2, --ONR.sup.14R.sup.15,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.14R.sup.15,
--N(O).sub.q, --NR.sup.14R.sup.15, --C(O)R.sup.16,
--C(O)--OR.sup.16, --C(O)NR.sup.14R.sup.15, --OR.sup.17,
--NR.sup.14SO.sub.2R.sup.17, --NR.sup.14C.dbd.(O)R.sup.16,
--NR.sup.14C(O)--OR.sup.16, --NR.sup.14OR.sup.16,
--OCX.sup.b.sub.3, --OCHX.sup.b.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; Two adjacent R.sup.13 substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl; Two R.sup.13 substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.14, R.sup.15, R.sup.16, and R.sup.17 are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.14 and
R.sup.15 substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; p is
independently 1 or 2; q is independently an integer from 1 to 2; r
is independently an integer from 0 to 4; X.sup.b is independently
--Cl, --Br, --I, or --F.
16. The compound of claim 1, wherein E comprises a substituted or
unsubstituted vinyl sulfone moiety, substituted or unsubstituted
vinyl sulfonamide moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
17. (canceled)
18. A pharmaceutical composition comprising a pharmaceutically
acceptable excipient and a compound of claim 1.
19. A method of treating a disease in a patient in need of such
treatment, said method comprising administering a therapeutically
effective amount of a compound of claim 1 to said patient.
20. The method of claim 19, wherein said disease is cancer.
21. (canceled)
22. (canceled)
23. (canceled)
24. A method of modulating the activity of a K-Ras protein, said
method comprising contacting said K-Ras protein with an effective
amount of a compound of claim 1.
25.-37. (canceled)
38. A K-Ras protein covalently bound to a compound of claim 1,
wherein said compound is covalently bound to a cysteine residue of
said K-Ras protein.
39.-46. (canceled)
47. A K-Ras protein covalently bound to a compound of claim 1,
wherein said compound is covalently bound to an aspartate residue
of said K-Ras protein.
48.-64. (canceled)
65. A method of selectively modulating a Ras protein, said method
comprising contacting said Ras protein with a compound which
contacts at least one amino acid residue forming a Switch 2 binding
pocket of said Ras protein, wherein said at least one amino acid
residue is selected from valine-7, valine-9, glycine-10,
proline-34, threonine-58, glycine-60, glutamine-61, glutamate-62,
glutamate-63, arginine-68, tyrosine-71, methionine-72, tyrosine-96,
glutamine-99 and isoleucine-100 of said Ras protein, and wherein
said compound covalently reacts with an amino acid residue of said
Ras protein.
66.-73. (canceled)
74. A compound having molecular dimensions compatible with the
shape of a K-Ras Switch 2 binding pocket wherein the compound, when
present in an aqueous solution comprising 200 .mu.M of the compound
and 4 .mu.M K-Ras, covalently binds to at least 50% of K-Ras
proteins present in solution after 24 hours.
75. A compound of Formula: ##STR00329## or a pharmaceutically
acceptable salt thereof, wherein: e5 is an integer from 0 to 5; X'
is --O--, --NH--, or --S--; R.sup.2A and R.sup.2B are independently
hydrogen, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.2A and R.sup.2B substituent bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.3 is independently hydrogen, oxo, halogen, --CX.sub.3, --CN,
--SO.sub.2Cl, --SO.sub.nR.sup.10, --SO.sub.vNR.sup.7R.sup.8,
--NHNH.sub.2, --ONR.sup.7R.sup.8, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7R.sup.8, N(O).sub.m, --NR.sup.7R.sup.8,
--C(O)R.sup.9, --C(O)--OR.sup.9, --C(O)NR.sup.7R.sup.8,
--OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; L.sup.2 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; L.sup.3 is independently
R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; E is an electrophilic chemical
moiety capable of forming a covalent bond with a cysteine or
aspartate residue; R.sup.2C is independently hydrogen, oxo,
halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)NR.sup.7cR.sup.8c, --OR.sup.10c,
--NR.sup.7cSO.sub.2R.sup.10c, --NR.sup.7cC.dbd.(O)R.sup.9c,
--NR.sup.7cC(O)--OR.sup.9c, --NR.sup.7cOR.sup.9c,
--OCX.sup.c.sub.3, --OCHX.sup.c.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; two adjacent R.sup.2C substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl; two R.sup.2C substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a,
R.sup.8a, R.sup.9a and R.sup.10a are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl;
R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; m, m1, m3, v, v1, and v3 are
independently 1 or 2; n, n1, and n3 are independently an integer
from 0 to 4; X, X.sup.a and X.sup.c are independently --Cl, --Br,
--I, or --F.
76. The compound of claim 75, wherein E comprises a substituted or
unsubstituted vinyl sulfone moiety, substituted or unsubstituted
vinyl sulfonamide moiety, substituted or unsubstituted peroxide
moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
77.-83. (canceled)
84. A method of treating a disorder in a subject in need thereof,
comprising: a. determining the presence or absence of a K-Ras
mutation in a malignant or neoplastic cell isolated from the
subject; and b. if a K-Ras mutation is determined to be present in
the subject, administering to the subject a therapeutically
effective amount of a compound or pharmaceutically acceptable salt
of claim 1.
85. (canceled)
86. (canceled)
87. A method of treating cancer in a human subject in need thereof,
comprising administering to said subject at least one compound or
pharmaceutically acceptable salt of claim 1, wherein said subject
has a K-Ras mutation.
88. (canceled)
89. (canceled)
90. The compound, or a pharmaceutically acceptable salt thereof, of
claim 1, wherein said compound modulates the binding of GDP or GTP
to a K-Ras protein.
91.-114. (canceled)
Description
RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional
Patent Application Nos. 61/622,507, filed Apr. 10, 2012;
61/728,145, filed Nov. 19, 2012; and 61/794,956, filed Mar. 15,
2013, which are all incorporated herein by reference in their
entirety and for all purposes.
REFERENCE TO A "SEQUENCE LISTING," A TABLE, OR A COMPUTER PROGRAM
LISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE
[0002] The Sequence Listing written in file 84850-869921_ST25.TXT,
created on Apr. 9, 2013, 28,573 bytes, machine format IBM-PC,
MS-Windows operating system, is hereby incorporated by
reference.
BACKGROUND OF THE INVENTION
[0003] K-Ras is the most frequently mutated oncogene in human
cancer. However, past attempts to directly target this enzyme with
reversible inhibitors have been almost entirely unsuccessful.
[0004] Ras proteins are small guanine nucleotide-binding proteins
that act as molecular switches by cycling between active GTP-bound
and inactive GDP-bound conformations. Ras signaling is regulated
through a balance between activation by guanine nucleotide exchange
factors (GEFs), most commonly son of sevenless (SOS), and
inactivation by GTPase-activating proteins (GAPs) such as
neurofibromin or p120GAP (see FIG. 1). The Ras proteins play a
critical role in the regulation of cell proliferation,
differentiation, and survival. Dysregulation of the Ras signaling
pathway is almost invariably associated with disease.
Hyper-activating somatic mutations in Ras are among the most common
lesions found in human cancer. Most of these mutations have been
shown to decrease the sensitivity of Ras to GAP stimulation and
decrease its intrinsic GTPase activity, leading to an increase in
the active GTP-bound population. Although mutation of any one of
the three Ras isoforms (K-Ras, N-Ras, or H-Ras) has been shown to
lead to oncogenic transformation, K-Ras mutations are by far the
most common in human cancer. For example, K-Ras mutations are known
to be often associated with pancreatic, colorectal and
non-small-cell lung carcinomas. Similarly, H-Ras mutations are
common in cancers such as papillary thyroid cancer, lung cancers
and skin cancers. Finally, N-Ras mutations occur frequently in
hepatocellular carcinoma.
[0005] The structural basis for the Ras cycle and Ras
hyperactivation are well understood. Over 40 crystal structures of
H-Ras have been solved, including both wild-type and mutants bound
to GDP or analogs of GTP. Likewise, the structures of H-Ras in
complex with many of its binding partners are known. The
nucleotide-binding pocket is bordered by four main regions: the
phosphate-binding loop (P-loop, residues 10-17), Switch 1 (residues
30-40), Switch 2 (residues 60-76), and the base-binding loops
(residues 116-120 and 145-147), (Hall et al. PNAS, 2002, 19,
12138-12142 and Vetter 2001 Science). The Switch regions govern
interactions between Ras and its binding partners by adopting
different conformations when bound to GTP or GDP. Threonine-35 and
glycine-60 make key hydrogen bonds with the .gamma.-phosphate of
GTP, holding the Switch 1 and Switch 2 regions in the active
conformation, respectively. Upon hydrolysis of GTP and release of
phosphate, these two regions are free to relax into the inactive
GDP conformation.
[0006] The regions bordering the nucleotide pocket also contain the
most common sites of Ras mutation in cancer. The vast majority of
oncogenic mutations occur at residues 12 or 13 in the P-loop, or
residue 61 in Switch 2. Structural data suggest that mutation of
glycine-12 or glycine-13 would sterically occlude the critical
arginine residue of the GAP and thus prohibit inactivation of Ras
signaling. Mutation of glutamine-61 similarly impairs GAP-mediated
Ras inactivation.
[0007] Thus, there is a need in the art for effective Ras
inhibitors and anticancer compounds. The present invention provides
solutions to these and other problems in the art.
BRIEF SUMMARY OF THE INVENTION
[0008] Described herein, inter alia, is the use of covalent (e.g.
reversible or irreversible) chemistry to target a Ras protein,
including but not limited to chemically tractable oncogenic mutants
such as K-RasG12C. Also described herein, inter alia, are the first
small molecules which specifically target the human oncogene
(K-RasG12C) and do not bind to the proto-oncogenic form of the
protein (K-Ras).
[0009] In a first aspect, a compound having the formula
R.sup.1-L.sup.1-L.sup.2-L.sup.3-E is provided. R.sup.1 is a Switch
2-Binding Pocket binding moiety. L.sup.1 is a bond or a divalent
radical chemical linker. L.sup.2 is a bond or a divalent radical
chemical linker. L.sup.3 is a bond or a divalent radical chemical
linker. E is an electrophilic chemical moiety capable of forming a
covalent bond with a Ras (e.g. K-Ras) cysteine residue or a Ras
(e.g. K-Ras) aspartate residue.
[0010] In a second aspect, a pharmaceutical composition including a
pharmaceutically acceptable excipient and a compound described
herein (including embodiments, examples, and in Table 1, 2, 3, 4,
or 5) is provided.
[0011] In a third aspect, a method of treating a disease in a
patient in need of such treatment is provided. The method including
administering a therapeutically effective amount of a compound
described herein (including embodiments, examples, and in Table 1,
2, 3, 4, or 5) to the patient.
[0012] In a fourth aspect, a method of modulating the activity of a
K-Ras protein is provided. The method including contacting the
K-Ras protein with an effective amount of a compound described
herein (including embodiments, examples, and in Table 1, 2, 3, 4,
or 5).
[0013] In a fifth aspect, a method of modulating a K-Ras protein is
provided. The method including contacting the K-Ras protein with an
effective amount of a compound described herein (including
embodiments, examples, and in Table 1, 2, 3, 4, or 5).
[0014] In a sixth aspect, a K-Ras protein covalently bonded to a
compound, such as, for example, a compound described herein
(including modulators, inhibitors, embodiments, examples, and in
Table 1, 2, 3, 4, or 5) is provided. The compound is covalently
bonded to a cysteine residue of the K-Ras protein.
[0015] In a seventh aspect, a K-Ras protein covalently bonded to a
compound, such as, for example, a compound described herein
((including modulators, inhibitors, embodiments, examples, and in
Table 1, 2, 3, 4, or 5) is provided. The compound is covalently
bonded to an aspartate residue of the K-Ras protein.
[0016] In an eighth aspect, a method of identifying a covalent
inhibitor of K-Ras protein is provided. The method including
contacting a K-Ras protein with a K-Ras inhibitor test compound,
allowing the K-Ras inhibitor test compound to covalently inhibit
the K-Ras protein, and detecting the level of covalent inhibition
of the K-Ras protein, thereby identifying a covalent inhibitor of
K-Ras protein.
[0017] In some embodiments, provided is a compound having the
formula:
R.sup.1-L.sup.1-L.sup.2-L.sup.3-E
wherein, R.sup.1 is a Switch 2-Binding Pocket binding moiety;
L.sup.1 is a bond or a divalent radical chemical linker; L.sup.2 is
a bond or a divalent radical chemical linker; L.sup.3 is a bond or
a divalent radical chemical linker; and E is an electrophilic
chemical moiety capable of forming a covalent bond with a K-Ras
cysteine residue or a K-Ras aspartate residue. In some embodiments,
R.sup.1 is hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. For example, R.sup.1 is substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; or R.sup.1 is substituted or
unsubstituted aryl or substituted or unsubstituted heteroaryl, such
as substituted or unsubstituted fused ring aryl or substituted or
unsubstituted fused ring heteroaryl. In some embodiments, R.sup.1
is R.sup.3-substituted or unsubstituted aryl or R.sup.3-substituted
or unsubstituted heteroaryl, wherein R.sup.3 is independently
hydrogen, oxo, halogen, --CX.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.nR.sup.10, --SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2,
--ONR.sup.7R.sup.8, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7R.sup.8, --N(O).sub.m, --NR.sup.7R.sup.8,
--C(O)R.sup.9, --C(O)--OR.sup.9, --C(O)NR.sup.7R.sup.8,
--OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; and X is independently Cl, --Br, --I, or --F.
[0018] In some embodiments, R.sup.1 is:
##STR00001## ##STR00002##
wherein, R.sup.3 is independently hydrogen, oxo, halogen,
--CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8,
--N(O).sub.m, --NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; X is independently --Cl, --Br, --I, or --F; e2 is independently
an integer from 0 to 2; e3 is independently an integer from 0 to 3;
e4 is independently an integer from 0 to 4; e5 is independently an
integer from 0 to 5; e6 is independently an integer from 0 to 6;
and e7 is independently an integer from 0 to 7.
[0019] In some embodiments, R.sup.1 is R.sup.3-substituted
pyridinyl, R.sup.3-substituted pyrimidinyl, R.sup.3-substituted
thiophenyl, R.sup.3-substituted furanyl, R.sup.3-substituted
indolyl, R.sup.3-substituted benzoxadiazolyl, R.sup.3-substituted
benzodioxolyl, R.sup.3-substituted benzodioxanyl,
R.sup.3-substituted thianaphthanyl, R.sup.3-substituted
pyrrolopyridinyl, R.sup.3-substituted indazolyl,
R.sup.3-substituted quinolinyl, R.sup.3-substituted quinoxalinyl,
R.sup.3-substituted pyridopyrazinyl, R.sup.3-substituted
quinazolinonyl, R.sup.3-substituted benzoisoxazolyl,
R.sup.3-substituted imidazopyridinyl, R.sup.3-substituted
benzofuranyl, R.sup.3-substituted benzothiophenyl,
R.sup.3-substituted phenyl, R.sup.3-substituted naphthyl,
R.sup.3-substituted biphenyl, R.sup.3-substituted pyrrolyl,
R.sup.3-substituted pyrazolyl, R.sup.3-substituted imidazolyl,
R.sup.3-substituted pyrazinyl, R.sup.3-substituted oxazolyl,
R.sup.3-substituted isoxazolyl, R.sup.3-substituted thiazolyl,
R.sup.3-substituted furylthienyl, R.sup.3-substituted pyridyl,
R.sup.3-substituted pyrimidyl, R.sup.3-substituted benzothiazolyl,
R.sup.3-substituted purinyl, R.sup.3-substituted benzimidazolyl,
R.sup.3-substituted isoquinolyl, R.sup.3-substituted thiadiazolyl,
R.sup.3-substituted oxadiazolyl, R.sup.3-substituted pyrrolyl,
R.sup.3-substituted diazolyl, R.sup.3-substituted triazolyl,
R.sup.3-substituted tetrazolyl, R.sup.3-substituted
benzothiadiazolyl, R.sup.3-substituted isothiazolyl,
R.sup.3-substituted pyrazolopyrimidinyl, R.sup.3-substituted
pyrrolopyrimidinyl, R.sup.3-substituted benzotriazolyl, or
R.sup.3-substituted quinolyl; where R.sup.3 is independently
hydrogen, oxo,
halogen, --CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8,
--N(O).sub.m, --NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; and X is independently --Cl, --Br, --I, or --F.
[0020] In other embodiments, R.sup.1 is unsubstituted pyridinyl,
unsubstituted pyrimidinyl, unsubstituted thiophenyl, unsubstituted
furanyl, unsubstituted indolyl, unsubstituted benzoxadiazolyl,
unsubstituted benzodioxolyl, unsubstituted benzodioxanyl,
unsubstituted thianaphthanyl, unsubstituted pyrrolopyridinyl,
unsubstituted indazolyl, unsubstituted quinolinyl, unsubstituted
quinoxalinyl, unsubstituted pyridopyrazinyl, unsubstituted
quinazolinonyl, unsubstituted benzoisoxazolyl, unsubstituted
imidazopyridinyl, unsubstituted benzofuranyl, unsubstituted
benzothiophenyl, unsubstituted phenyl, unsubstituted naphthyl,
unsubstituted biphenyl, unsubstituted pyrrolyl, unsubstituted
pyrazolyl, unsubstituted imidazolyl, unsubstituted pyrazinyl,
unsubstituted oxazolyl, unsubstituted isoxazolyl, unsubstituted
thiazolyl, unsubstituted furylthienyl, unsubstituted pyridyl,
unsubstituted pyrimidyl, unsubstituted benzothiazolyl,
unsubstituted purinyl, unsubstituted benzimidazolyl, unsubstituted
isoquinolyl, unsubstituted thiadiazolyl, unsubstituted oxadiazolyl,
unsubstituted pyrrolyl, unsubstituted diazolyl, unsubstituted
triazolyl, unsubstituted tetrazolyl, unsubstituted
benzothiadiazolyl, unsubstituted isothiazolyl, unsubstituted
pyrazolopyrimidinyl, unsubstituted pyrrolopyrimidinyl,
unsubstituted benzotriazolyl, or unsubstituted quinolyl.
[0021] In some embodiments, L.sup.1, L.sup.2 and L.sup.3 are
independently a bond, --NR.sup.2C--, --O--, --S--, --C(O)--,
--S(O)--, --S(O).sub.2--, substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene; or a substituted or
unsubstituted spirocyclic linker; R.sup.2C is independently
hydrogen, oxo,
halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; Two adjacent
R.sup.2C substituents may optionally be joined to form a
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two R.sup.2C
substituents bonded to the same atom may optionally be joined to
form a substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.7c, R.sup.8c, R.sup.9c and
R.sup.10c are independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.7c and R.sup.8c substituents
bonded to the same nitrogen atom may optionally be joined to form a
substituted or unsubstituted heterocycloalkyl or substituted or
unsubstituted heteroaryl; m1, m3, v1, and v3 are independently an
integer from 1 to 2; n1 and n3 are independently an integer from 0
to 4; and X.sup.c is independently --Cl, --Br, --I, or --F.
[0022] In some embodiments, L.sup.1, L.sup.2 and L.sup.3 are
independently --CR.sup.2AR.sup.2B--,
##STR00003##
R.sup.2A and R.sup.2B are independently hydrogen, oxo, halogen,
--CX.sup.a.sub.3, --CN, --SO.sub.2Cl, --SO.sub.n1R.sup.10a,
--SO.sub.v1NR.sup.7aR.sup.8a, --NHNH.sub.2, --ONR.sup.7aR.sup.8a,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7aR.sup.8a,
--N(O).sub.m1, --NR.sup.7aR.sup.8a, --C(O)R.sup.9a,
--C(O)--OR.sup.9a, --C(O)NR.sup.7aR.sup.8a, --OR.sup.10a,
--NR.sup.7aSO.sub.2R.sup.10a, --NR.sup.7aC.dbd.(O)R.sup.9a,
--NR.sup.7aC(O)--OR.sup.9a, --NR.sup.7aOR.sup.9a,
--OCX.sup.a.sub.3, --OCHX.sup.a.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.2A and R.sup.2B substituent
bonded to the same atom may optionally be joined to form a
substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.2C is independently hydrogen,
oxo, halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a,
R.sup.8a, R.sup.9a and R.sup.10a are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl;
R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7c and
R.sup.8c substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; z is
independently an integer from 0 to 10; m1, m3, v1, and v3 are
independently an integer from 1 to 2; n1 and n3 are independently
an integer from 0 to 4; and X.sup.a and X.sup.c are independently
--Cl, --Br, --I, or --F.
[0023] In some embodiments, L.sup.1 is independently substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene, or substituted or
unsubstituted spirocyclic linker; or L.sup.2 is independently
substituted or unsubstituted cycloalkylene, substituted or
unsubstituted heterocycloalkylene, substituted or unsubstituted
arylene, substituted or unsubstituted heteroarylene, or substituted
or unsubstituted spirocyclic linker; or L.sup.3 is independently
substituted or unsubstituted cycloalkylene, substituted or
unsubstituted heterocycloalkylene, substituted or unsubstituted
arylene, substituted or unsubstituted heteroarylene, or substituted
or unsubstituted spirocyclic linker. In some embodiments, L.sup.1
is independently R.sup.2C-substituted or unsubstituted
cycloalkylene, R.sup.2C-substituted or unsubstituted
heterocycloalkylene, R.sup.2C-substituted or unsubstituted arylene,
R.sup.2C-substituted or unsubstituted heteroarylene, or
R.sup.2C-substituted or unsubstituted spirocyclic linker; or
L.sup.2 is independently R.sup.2C-substituted or unsubstituted
cycloalkylene, R.sup.2C-substituted or unsubstituted
heterocycloalkylene, R.sup.2C-substituted or unsubstituted arylene,
R.sup.2C-substituted or unsubstituted heteroarylene, or
R.sup.2C-substituted or unsubstituted spirocyclic linker; or
L.sup.3 is independently R.sup.2C-substituted or unsubstituted
cycloalkylene, R.sup.2C-substituted or unsubstituted
heterocycloalkylene, R.sup.2C-substituted or unsubstituted arylene,
R.sup.2C-substituted or unsubstituted heteroarylene, or
R.sup.2C-substituted or unsubstituted spirocyclic linker.
[0024] In some embodiments, L.sup.1 is independently
##STR00004## ##STR00005## ##STR00006## ##STR00007## ##STR00008##
##STR00009##
L.sup.2 is independently
##STR00010## ##STR00011## ##STR00012## ##STR00013## ##STR00014##
##STR00015##
L.sup.3 is independently
##STR00016## ##STR00017## ##STR00018## ##STR00019## ##STR00020##
##STR00021##
and wherein f2 is independently an integer from 0 to 2; f6 is
independently an integer from 0 to 6; f7 is independently an
integer from 0 to 7; f8 is independently an integer from 0 to 8; f9
is independently an integer from 0 to 9; f10 is independently an
integer from 0 to 10; f12 is independently an integer from 0 to 12;
f14 is independently an integer from 0 to 14.
[0025] In some embodiments, E comprises
##STR00022## ##STR00023## ##STR00024## ##STR00025## ##STR00026##
##STR00027## ##STR00028## ##STR00029## ##STR00030## ##STR00031##
##STR00032##
wherein R.sup.13 is independently hydrogen, oxo, halogen,
--CX.sup.b.sub.3, --CN, --SO.sub.2Cl, --SO.sub.rR.sup.17,
--SO.sub.pNR.sup.14R.sup.15, --NHNH.sub.2, --ONR.sup.14R.sup.15,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.14R.sup.15,
--N(O).sub.q, --NR.sup.14R.sup.15, --C(O)R.sup.16,
--C(O)--OR.sup.16, --C(O)NR.sup.14R.sup.15, --OR.sup.17,
--NR.sup.14SO.sub.2R.sup.17, --NR.sup.14C.dbd.(O)R.sup.16,
--NR.sup.14C(O)--OR.sup.16, --NR.sup.14OR.sup.16,
--OCX.sup.b.sub.3, --OCHX.sup.b.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; two adjacent R.sup.13 substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl; Two R.sup.13 substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.14, R.sup.15, R.sup.16, and R.sup.17 are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.14 and
R.sup.15 substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; p is
independently 1 or 2; q is independently an integer from 1 to 2; r
is independently an integer from 0 to 4; and X.sup.b is
independently --Cl, --Br, --I, or --F.
[0026] In some embodiments, E may comprise a substituted or
unsubstituted vinyl sulfone moiety, substituted or unsubstituted
vinyl sulfonamide moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
[0027] In some embodiments, E comprises an unsubstituted vinyl
sulfone moiety, unsubstituted vinyl sulfonamide moiety,
unsubstituted fluoro(C.sub.1-C.sub.4)alkylketone moiety,
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
unsubstituted acrylamide moiety, unsubstituted disulfide moiety,
unsubstituted thiol moiety, unsubstituted phosphonate moiety,
unsubstituted aldehyde moiety, unsubstituted enone moiety,
unsubstituted diazomethylketone moiety, unsubstituted
diazomethylamide moiety, unsubstituted cyanocyclopropyl carboxamide
moiety, unsubstituted epoxide moiety, unsubstituted epoxyketone
moiety, unsubstituted epoxyamide moiety, unsubstituted aryl
aldehyde moiety, unsubstituted aryl dialdehyde moiety,
unsubstituted dialdehyde moiety, unsubstituted nitrogen mustard
moiety, unsubstituted propargyl moiety, or unsubstituted
propargylamide moiety.
[0028] In some embodiments, the compound is a compound of
Formula:
##STR00033##
or a pharmaceutically acceptable salt thereof, wherein: e5 is an
integer from 0 to 5; X' is --O--, --NH--, or --S--; R.sup.2A and
R.sup.2B are independently hydrogen, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.2A and R.sup.2B substituent
bonded to the same atom may optionally be joined to form a
substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.3 is independently hydrogen,
oxo, halogen, --CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8,
--N(O).sub.m, --NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; L.sup.2 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; L.sup.3 is independently
R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; E is an electrophilic chemical
moiety capable of forming a covalent bond with a cysteine or
aspartate residue; R.sup.2C is independently hydrogen, oxo,
halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; two adjacent R.sup.2C substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl; two R.sup.2C substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a,
R.sup.8a, R.sup.9a and R.sup.10a are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl;
R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; m, m1, m3, v, v1,
and v3 are independently 1 or 2; n, n1, and n3 are independently an
integer from 0 to 4; X, X.sup.a and X.sup.c are independently --Cl,
--Br, --I, or --F.
[0029] In some embodiments, E comprises a substituted or
unsubstituted vinyl sulfone moiety, substituted or unsubstituted
vinyl sulfonamide moiety, substituted or unsubstituted peroxide
moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
[0030] In some embodiments, L.sup.2 is independently
R.sup.2C-substituted or unsubstituted heterocycloalkylene or
R.sup.2C-substituted or unsubstituted spirocyclic linker and
L.sup.3 is a bond. For example, L.sup.2 is monocyclic 4, 5, or
6-membered heterocycloalkylene; or L.sup.2 is unsubstituted
piperazino or unsubstituted piperidino; or L.sup.2 is bicyclic
fused heterocycloalkylene; or L.sup.2 is an unsubstituted
spirocyclic linker.
[0031] In some embodiments, E is a substituted or unsubstituted
vinyl sulfone moiety, substituted or unsubstituted vinyl
sulfonamide moiety, or a substituted or unsubstituted acrylamide
moiety.
[0032] Further provided herein are pharmaceutical compositions
comprising a pharmaceutically acceptable excipient and a compound
of the invention.
[0033] Also provided is a method of treating a disease in a patient
in need of such treatment, said method comprising administering a
therapeutically effective amount of a compound of any one of the
compounds disclosed herein. In some embodiments, the disease is
cancer, including but not limited to colon cancer, colorectal
cancer, pancreatic cancer, breast cancer, leukemia, or lung cancer
(including non-small cell lung cancer).
[0034] Also provided are methods of modulating the activity of a
Ras protein, including a H-Ras, N-Ras, or K-Ras protein, comprising
contacting said Ras protein with an effective amount of a compound
disclosed herein. The activity is, for example, GTPase activity,
nucleotide exchange, effector protein binding, effector protein
activation, guanine exchange factor (GEF) binding, GEF-facilitated
nucleotide exchange, phosphate release, nucleotide release,
nucleotide binding, Ras (e.g. K-Ras) subcellular localization, Ras
(e.g. K-Ras) post-translational processing, or Ras (e.g. K-Ras)
post-translational modifications. Said modulating can be increasing
the activity of said Ras (e.g. K-Ras) protein or reducing it. Said
Ras (e.g. K-Ras) protein can be a human K-Ras protein. For example,
a human K-Ras protein contains a G12C, G12D, G13C, or G13D
mutation.
[0035] In some embodiments, a method of modulating a K-Ras protein
is provided, said method comprising contacting said K-Ras protein
with an effective amount of a compound described herein. Said
modulating is, for example, modulation of K-Ras subcellular
localization, K-Ras post-translational processing, or a K-Ras
post-translational modification. Said K-Ras protein is, for
example, a human K-Ras protein. In some embodiments, said human
K-Ras protein contains a G12C, G12D, G13C, or G13D mutation.
[0036] In some embodiments, said Ras (e.g. K-Ras) protein is within
a biological cell, for example a biological cell which forms part
of an organism.
[0037] Provided herein is also a Ras (e.g. K-Ras) protein
covalently bound to a compound as disclosed herein, wherein said
compound is covalently bound to a cysteine residue of said Ras
(e.g. K-Ras) protein. Said covalently modified Ras protein may have
a modulated activity relative to a control, wherein said activity
is selected from GTPase activity, nucleotide exchange, effector
protein binding, effector protein activation, guanine exchange
factor (GEF) binding, GEF-facilitated nucleotide exchange,
phosphate release, nucleotide release, nucleotide binding, Ras
subcellular localization, Ras post-translational processing, and
Ras post-translational modifications. In some embodiments, said Ras
protein is a K-Ras protein which contains a G12C mutation. The
covalently bonded compound can be bonded to cysteine residue 12. In
other embodiments, the covalently modified Ras protein is a K-Ras
protein which contains a G13C mutation. The covalently bonded
compound can be bonded to cysteine residue 13.
[0038] In other embodiments, a Ras (e.g. K-Ras) protein is provided
which is covalently bound to a compound disclosed herein, wherein
said compound is covalently bound to an aspartate residue of said
Ras protein. Said covalently modified Ras protein may have a
modulated activity relative to a control, wherein said activity is
selected from GTPase activity, nucleotide exchange, effector
protein binding, effector protein activation, guanine exchange
factor (GEF) binding, GEF-facilitated nucleotide exchange,
phosphate release, nucleotide release, nucleotide binding, Ras
subcellular localization, Ras post-translational processing, and
Ras post-translational modifications. In some embodiments, said Ras
protein is a K-Ras protein which contains a G12D mutation. The
covalently bonded compound can be bonded to aspartate residue 12.
In other embodiments, the covalently modified Ras protein is a
K-Ras protein which contains a G13D mutation. The covalently bonded
compound can be bonded to aspartate residue 13.
[0039] Further provided herein is a method of identifying a
covalent inhibitor of K-Ras protein comprising: contacting a K-Ras
protein with a K-Ras inhibitor test compound; allowing said K-Ras
inhibitor test compound to covalently inhibit said K-Ras protein;
and detecting the level of covalent inhibition of said K-Ras
protein thereby identifying a covalent inhibitor of K-Ras protein.
In some embodiments, the K-Ras inhibitor test compound is a Switch
2-Binding Pocket covalent inhibitor test compound and said K-Ras
protein is a G12C mutant K-Ras protein. The method may also
comprise the steps of: contacting a wildtype K-Ras protein with
said Switch 2-Binding Pocket covalent inhibitor test compound;
allowing said Switch 2-Binding Pocket covalent inhibitor test
compound to inhibit said wildtype K-Ras protein; detecting the
level of inhibition of said wildtype K-Ras protein; comparing the
level of inhibition of said wildtype K-Ras protein to the level of
covalent inhibition of said G12C mutant K-Ras protein, wherein a
higher level of covalent inhibition of said G12C mutant K-Ras
indicates said Switch 2-Binding Pocket covalent inhibitor test
compound is specific for said G12C mutant K-Ras protein.
[0040] In some embodiments, said K-Ras inhibitor test compound is a
Switch 2-Binding Pocket covalent inhibitor test compound and said
K-Ras protein is a G12D mutant K-Ras protein. The method of
identifying may also comprise the steps of: contacting a wildtype
K-Ras protein with said Switch 2-Binding Pocket covalent inhibitor
test compound; allowing said Switch 2-Binding Pocket covalent
inhibitor test compound to inhibit said wildtype K-Ras protein;
detecting the level of inhibition of said wildtype K-Ras protein;
comparing the level of inhibition of said wildtype K-Ras protein to
the level of covalent inhibition of said G12D mutant K-Ras protein,
wherein a higher level of covalent inhibition of said G12D mutant
K-Ras indicates said Switch 2-Binding Pocket covalent inhibitor
test compound is specific for said G12D mutant K-Ras protein.
[0041] In some embodiments, said K-Ras inhibitor test compound is a
Switch 2-Binding Pocket covalent inhibitor test compound and said
K-Ras protein is a G13C mutant K-Ras protein. The method of
identifying may also comprise the steps of: contacting a wildtype
K-Ras protein with said Switch 2-Binding Pocket covalent inhibitor
test compound; allowing said Switch 2-Binding Pocket covalent
inhibitor test compound to inhibit said wildtype K-Ras protein;
detecting the level of inhibition of said wildtype K-Ras protein;
comparing the level of inhibition of said wildtype K-Ras protein to
the level of covalent inhibition of said G13C mutant K-Ras protein,
wherein a higher level of covalent inhibition of said G13C mutant
K-Ras indicates said Switch 2-Binding Pocket covalent inhibitor
test compound is specific for said G13C mutant K-Ras protein.
[0042] In some embodiments, said K-Ras inhibitor test compound is a
Switch 2-Binding Pocket covalent inhibitor test compound and said
K-Ras protein is a G13D mutant K-Ras protein. The method of
identifying may also comprise the steps of: contacting a wildtype
K-Ras protein with said Switch 2-Binding Pocket covalent inhibitor
test compound; allowing said Switch 2-Binding Pocket covalent
inhibitor test compound to inhibit said wildtype K-Ras protein;
detecting the level of inhibition of said wildtype K-Ras protein;
comparing the level of inhibition of said wildtype K-Ras protein to
the level of covalent inhibition of said G13D mutant K-Ras protein,
wherein a higher level of covalent inhibition of said G13D mutant
K-Ras indicates said Switch 2-Binding Pocket covalent inhibitor
test compound is specific for said G13D mutant K-Ras protein.
[0043] Provided herein is a method of selectively modulating a Ras
protein, said method comprising contacting said Ras protein with a
compound which contacts at least one amino acid residue forming a
Switch 2 binding pocket of said Ras protein, wherein said at least
one amino acid residue is selected from valine-7, valine-9,
glycine-10, proline-34, threonine-58, glycine-60, glutamine-61,
glutamate-62, glutamate-63, arginine-68, tyrosine-71,
methionine-72, tyrosine-96, glutamine-99 and isoleucine-100 of said
Ras protein, and wherein said compound covalently reacts with an
amino acid residue of said Ras protein. In some embodiments, the
compound binds to a K-Ras protein with a higher binding affinity as
compared to a H-Ras protein. In some embodiments, said compound
interacts with at least one of glycine-60, glutamate-62, or
glutamate-63. In some embodiments, said interacting between said
amino acid residue and said compound involves hydrogen bonding, van
der Waals interaction, ionic bonding, covalent bonding, or
hydrophobic interaction. In some embodiments, said compound fills
space within said Switch 2 binding pocket. In some embodiments,
said compound inhibits K-Ras as measured by the fraction of protein
covalently labeled by the compound, wherein the compound is present
in 50-fold excess and wherein the fraction of protein covalently
labeled is determined by mass spectrometry. In some embodiments,
said compound covalently reacts with an amino acid residue of said
Ras (e.g. K-ras) protein. In some embodiments, said amino acid
residue is cysteine-12 of K-Ras G12C mutant protein.
[0044] Further provided is a method of designing a compound which
covalently binds to a Switch 2 binding pocket of a K-Ras protein,
the method comprising the steps of: [0045] a. providing a
structural model of a reference compound bound to the Switch 2
binding pocket of the K-Ras protein, wherein the reference compound
is non-covalently bound to said Switch 2 binding pocket; [0046] b.
identifying a cysteine, aspartate, lysine, tyrosine or glutamate
residue located in proximity to said Switch 2 binding pocket when
said reference compound is bound to said Switch 2 binding pocket;
[0047] c. generating at least one additional structural model of a
test compound bound to said Switch 2 binding pocket, wherein said
test compound comprises an electrophilic moiety; and [0048] d.
selecting said test compound if said electrophilic moiety is
located within bonding distance of said cysteine residue when said
test compound is bound to said Switch 2 binding pocket.
[0049] Compounds are also provided having molecular dimensions
compatible with the shape of a K-Ras Switch 2 binding pocket
wherein the compound, when present in an aqueous solution
comprising 200 .mu.M of the compound and 4 .mu.M K-Ras, covalently
binds to at least 50% of K-Ras proteins present in solution after
24 hours.
BRIEF DESCRIPTION OF THE DRAWINGS
[0050] FIG. 1. Ras cycles from inactive GDP-bound state to active
GTP-bound state. In the active conformation, Ras may interact with
downstream effector proteins. PI3K is unusual amongst effectors in
that it makes critical contacts with the Switch 2 region of Ras.
Structural data suggest that other effectors, including Raf, only
make direct contacts with the Switch 1 region.
[0051] FIG. 2: Structural insights into nucleotide binding by Ras.
(A) The conformation of Ras undergoes significant changes upon
binding to different nucleotides. Especially affected are two
regions of the protein, termed switch 1 (residue 30-40, black) and
Switch 2 (residue 60-76, dark gray), that are involved in binding
downstream effectors. Shown here are structures of wild-type Ras
bound to GDP (PDB code: 4q21 (Milburn M V, Tong L, deVos A M,
Brunger A, Yamaizumi Z, Nishimura S, Kim S H. Science. 1990 Feb.
23; 247(4945):939-45), inactive conformation) and GMPPCP (PDB code:
121p (Krengel, U., Thesis, Heidelberg, 1991), active conformation);
sequence legend SEQ ID NO:1 left, SEQ ID NO:2 right. (B) Detailed
view of the nucleotide binding pocket of the G12C mutant of Ras.
This structure was solved in the Shokat lab to 2.4 .ANG.
resolution. Labeled residues are either known to play important
roles in the biological function of Ras (oncogenic mutations often
occur in G12, G13 and Q61) (Forbes, S. et al. Cosmic 2005. Br J
Cancer 94, 318-22 (2006)), can serve as potential sites for
cysteine mutant for covalent attachment (C12, G13, S17, A18, Q30)
or show lysine residues that may serve as additional nucleophiles
for divalent probes (K16, K117, K147). The nucleophilic sulfur of
cysteine-12 is in close proximity to the terminal phosphate group
of GDP, supporting the idea of using this cysteine as nucleophilic
anchor for covalent (e.g. reversible, irreversible) modification;
sequence legend SEQ ID NO:3.
[0052] FIG. 3. Tethering to identify drug-like fragments that bind
to K-Ras G12C; Tethering depends on a complex equilibrium of
disulfide exchange between compounds and reducing agent. K-RasG12C
may exchange with compounds binding in the nucleotide-binding
pocket (square) or allosteric pocket (circle); mass
spectrometry-based; reversible covalent interaction based on
complex equilibrium of disulfides; semi-high throughput; identify
low-affinity drug-like fragments to use as scaffolds; based on
binding, not inhibition of activity.
[0053] FIG. 4. Compound (JO-01-189cbut) binding to Switch 2-Binding
Pocket of K-Ras. (A) Binding of JO-01-189cbut to the Switch
2-Binding Pocket induces changes in the protein structure,
including to the adjacent Switch 2 region. For comparison wild-type
Ras bound to GDP (PDB code: 4q21.sup.2, inactive conformation) and
GMPPCP (PDB code: 121p.sup.3, active conformation) are shown.
Switch 1 (residue 30-40, black) and Switch 2 (residue 60-76, dark
gray) are colored for clarity; sequence legend SEQ ID NO:1 left,
SEQ ID NO:2 right, SEQ ID NO:4 bottom. (B) JO-01-189cbut binding to
the Switch 2-Binding Pocket is shown in three-dimensional detail
with interacting amino acids labeled; sequence legend SEQ ID
NO:4.
[0054] FIG. 5. Two hits from screen of disulfide containing
compounds. Percentages represent the amount of modified Ras in the
presence of 100 .mu.M each of compound and BME. The screening hits
all showed selectivity for the mutant cysteine, causing minimal
modification of wild-type K-Ras. Addition of GDP had no significant
effect on modification of K-RasG12C by 6H05. Results from 2E07 show
that it is possible to achieve some selectivity for K-RasG12C over
H-RasG12C. These screens were carried out using K-RasG12C truncated
and K-Ras wild-type truncated.
[0055] FIG. 6. Structure and DR50 of 6H05 analogues. Compound
JO-148A is slightly more potent than the related screening hit.
[0056] FIG. 7. Compound(ligand):protein contacts/interactions of
Rasmed-055:G12C K-Ras, sequence legend (SEQ ID NO:4).
[0057] FIG. 8. Compound(ligand):protein contacts/interactions of
JO-01-189cbut:G12C K-Ras; sequence legend (SEQ ID NO:4).
[0058] FIGS. 9. (A and B) Protein sequences for human H-Ras and
K-Ras (including splice variants and mutants); in some embodiments,
a Ras protein may contain one or more amino acids at the amino
terminus due to the design of expression constructs (e.g. GAMGS may
be in embodiments of H-Ras G12C truncation or G in embodiments of
K-Ras constructs), however, amino acid numbering follows the
physiological amino acid numbering not including construct
introduced amino terminus extra amino acids.
[0059] FIGS. 10. (A and B) K-Ras*mant-d-GDP exchange with unlabeled
GDP, half-life (single exponential) shown (stop-flow experiment
with low magnesium).
[0060] FIGS. 11. (A and B) K-Ras*mant-d-GDP exchange with unlabeled
GDP or GTP, half-life (single exponential) shown (stop-flow
experiment with low magnesium).
[0061] FIG. 12. Ras-079 shows same conformation in two different
space groups (C2 vs. P212121); P212121 has switch 1 ordered in
unseen conformation, metal present as well in K-Ras sequence legend
(SEQ ID NO:4).
[0062] FIG. 13. Unusual metal coordination in new P212121 space
group (Tyr-32) of K-Ras, sequence legend (SEQ ID NO:4).
[0063] FIGS. 14. (A and B) Labeling of H-Ras G12C; labeling
successful (>1 day, EDTA, 250 micM); only single labeling
visible despite high conc.; Potential degradation products.
[0064] FIG. 15. Evidence of compound in H-Ras; 1 sigma 2fo-fc map
shown, H-Ras*GDP*055, 1.18 A resolution, 0.1791 Rfree, sequence
legend (SEQ ID NO:3).
[0065] FIG. 16. Compound is out of the pocket in H-Ras compared to
K-Ras; H-Ras*GDP*055 (light gray), K-Ras*GDP*055 (dark gray);
sequence legend light gray (SEQ ID NO:3), dark gray (SEQ ID
NO:4).
[0066] FIG. 17. Co-crystal structures show novel pocket, sequence
legend (SEQ ID NO:4).
[0067] FIG. 18. Co-crystal structures show novel pocket; new polar
interactions in optimized compounds; inhibitors bind behind Switch
II and disrupt both Switches; bind much more slowly to KrasGTP;
switch conformations are critical for activation downstream; may
interfere with GTP binding; sequence legend (SEQ ID NO:4).
[0068] FIG. 19. G60A in Switch II is dominant negative, glycine-60
to alanine mutation is dominant negative; small changes in Switch
II can have huge consequences for function; top Kras-G12C with
Ras-055; bottom Kras-WT truncated; sequence legend top (SEQ ID
NO:4), bottom (SEQ ID NO:16).
[0069] FIG. 20. Ras nucleotide exchange and protein
interactions.
[0070] FIG. 21 Inhibitors block Ras activation "OFF exchange";
similar inhibition seen in [a-32P]GTP "ON exchange"; working on
plate-based assay to test relative nucleotide affinities.
[0071] FIG. 22. Ras nucleotide exchange and protein
interactions.
[0072] FIG. 23. Raf1-RBD pull-downs; inhibitors decrease Raf
binding, especially in GTP-GDP mixtures; suggest inhibitors change
relative affinity for nucleotides.
[0073] FIG. 24. H358 (G12C) cells less sensitive in high serum; 24
hr treatment in 0.5% FBS followed by proliferation in 10% FBS;
larger difference at lower cell density.
[0074] FIG. 25. Proliferation of human lung cancer cell lines; 24
hr treatment in 0.5% FBS followed by proliferation in 10% FBS.
[0075] FIG. 26. Induction of pERK after treatment in G12C cells; in
Braf melanoma cells, Kras siRNA induces pERK.
[0076] FIGS. 27. (A and B) Phosphosignaling after treatment with
Ras-083.
[0077] FIG. 28. Proliferation of human lung cancer cell lines;
2,000 cells/well; 24 hr treatment, 48 hr washout all in 10%
FBS.
[0078] FIG. 29. Proliferation of human lung cancer cell lines; 24
hr treatment (0.5% FBS), 48 hr washout (10% FBS); now both G12C
cell lines look significantly more sensitive to Ras-083.
[0079] FIG. 30. Proliferation of human lung cancer cell lines;
4,000 cells/well; 24 hr treatment, 48 hr washout all at 10% FBS; 1
uM lapatinib.
[0080] FIG. 31. Raf1-RBD pull-downs; Ras-083 impairs binding of
RasGTP to Raf1-RBD after EDTA-catalyzed exchange; Adding a mixture
of GTP and GDP allows preferential binding to GDP even when GTP is
in excess (10:1 and 7:1); experiment performed as described
herein.
[0081] FIG. 32. Compound binding to K-Ras alters affinities for GTP
and GppNp (GNP), (competition experiments with mant-dGDP).
[0082] FIG. 33. IC50 of different nucleotides competing with
mant-d-GDP (.about.1 micM); IC50 ratios (representative of relative
affinities) shift greatly towards GDP over GTP in case of the
compound bound K-Ras.
[0083] FIGS. 34. (A and B) Compound binding to K-Ras reduces
SOS-mediated exchange (association of mant-d-GDP monitored).
[0084] FIGS. 35. (A and B) Compound binding to K-Ras reduces
SOS-mediated exchange (association of mant-d-GppNp monitored).
[0085] FIGS. 36. (A, B, C, and D) Compound binding to K-Ras reduces
SOS-mediated exchange (dissociation of mant-d-GDP monitored).
[0086] FIG. 37. Labeling of K-Ras G12C loaded with GDP or GTP
analog; fragments bind to GDP-loaded K-Ras G12C but not GTP-loaded
K-Ras G12C; % modification with 100 .mu.M fragment and 200 .mu.M
.beta.ME; figure legend SEQ ID NO:15.
[0087] FIG. 38. Concentration of fragment necessary for 50%
modification of K-RasG12C in presence of 100 .mu.M .beta.ME, figure
legend SEQ ID NO:15; several rounds of inhibitor optimization lead
to improved labeling at 200 .mu.M .beta.ME. This series shows the
effect of linker changes on labeling.
[0088] FIG. 39. 189Cbu selectively slows GEF-catalyzed nucleotide
exchange by K-Ras G12C without affecting wild type K-Ras, figure
legend SEQ ID NO:10 and SEQ ID NO:11.
[0089] FIG. 40. Inhibitors induce formation of a pocket behind
switch II; switch II is modeled from active (GMPPNP.sctn.) and
inactive (GDP.sctn.) structures into the 189Cbu complex left; the
model shows a steric clash between the inhibitor and residues from
switch II in the active conformation, suggesting these compounds
may disrupt the active state of Ras and impair downstream
signaling; left panel K-Ras G12C bound to 189Cbu; .sctn.Model,
switch II mapped onto 189Cu structure; figure legend SEQ ID
NO:4.
[0090] FIG. 41. Ras cycles between an inactive GDP-bound state and
an active GTP-bound state; in the active conformation, Ras
interacts with downstream effector proteins such as Raf and PI3K;
effectors interact with Ras-GTP through switch I and switch II,
which differ structurally between nucleotide states; oncogenic
mutations in Ras (most frequently at positions 12, 13, or 61)
disrupt GAP-facilitated GTP hydrolysis, kinetically locking Ras in
the GTP-bound "on" state.
[0091] FIG. 42. Targeted glycine-12 to cysteine (G12C) mutant of
K-Ras by taking advantage of the high nucleophilicity of the mutant
residue; most common K-Ras mutation in lung cancer (.about.9%
NSCLC, COSMIC); adjacent to nucleotide site and switches; covalent
handle enhances selectivity and potency.
[0092] FIG. 43. Screened 480-compound library at 100 .mu.M .beta.ME
and 100 .mu.M fragment; compounds modifying K-Ras G12C at >50%
were considered hits; of 17 hit compounds, none caused >10%
modification of wild type K-Ras, which contains a surface exposed
cysteine (C118); two hits shown; fragments bind to GDP-loaded K-Ras
but not GTP-loaded K-Ras; left panel % modification with 100 .mu.M
fragment and 100 .mu.M .beta.ME; right panel % modification with
100 .mu.M fragment and 200 .mu.M .beta.ME.
DETAILED DESCRIPTION OF THE INVENTION
I. Definitions
[0093] The abbreviations used herein have their conventional
meaning within the chemical and biological arts. The chemical
structures and formulae set forth herein are constructed according
to the standard rules of chemical valency known in the chemical
arts.
[0094] Where substituent groups are specified by their conventional
chemical formulae, written from left to right, they equally
encompass the chemically identical substituents that would result
from writing the structure from right to left, e.g., --CH.sub.2O--
is equivalent to --OCH.sub.2--.
[0095] The term "alkyl," by itself or as part of another
substituent, means, unless otherwise stated, a straight (i.e.,
unbranched) or branched carbon chain (or carbon), or combination
thereof, which may be fully saturated, mono- or polyunsaturated and
can include mono-, di- and multivalent radicals, having the number
of carbon atoms designated (i.e., C.sub.1-C.sub.10 means one to ten
carbons). Examples of saturated hydrocarbon radicals include, but
are not limited to, groups such as methyl, ethyl, n-propyl,
isopropyl, n-butyl, t-butyl, isobutyl, sec-butyl,
(cyclohexyl)methyl, homologs and isomers of, for example, n-pentyl,
n-hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkyl
group is one having one or more double bonds or triple bonds.
Examples of unsaturated alkyl groups include, but are not limited
to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl),
2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1- and 3-propynyl,
3-butynyl, and the higher homologs and isomers. An alkoxy is an
alkyl attached to the remainder of the molecule via an oxygen
linker (--O--).
[0096] The term "alkylene," by itself or as part of another
substituent, means, unless otherwise stated, a divalent radical
derived from an alkyl, as exemplified, but not limited by,
--CH.sub.2CH.sub.2CH.sub.2CH.sub.2--. Typically, an alkyl (or
alkylene) group will have from 1 to 24 carbon atoms, with those
groups having 10 or fewer carbon atoms being preferred in the
present invention. A "lower alkyl" or "lower alkylene" is a shorter
chain alkyl or alkylene group, generally having eight or fewer
carbon atoms. The term "alkenylene," by itself or as part of
another substituent, means, unless otherwise stated, a divalent
radical derived from an alkene.
[0097] The term "heteroalkyl," by itself or in combination with
another term, means, unless otherwise stated, a stable straight or
branched chain, or combinations thereof, including at least one
carbon atom and at least one heteroatom selected from the group
consisting of O, N, P, Si, and S, and wherein the nitrogen and
sulfur atoms may optionally be oxidized, and the nitrogen
heteroatom may optionally be quaternized. The heteroatom(s) O, N,
P, S, B, As, and Si may be placed at any interior position of the
heteroalkyl group or at the position at which the alkyl group is
attached to the remainder of the molecule. Examples include, but
are not limited to: --CH.sub.2--CH.sub.2--O--CH.sub.3,
--CH.sub.2--CH.sub.2--NH--CH.sub.3,
--CH.sub.2--CH.sub.2--N(CH.sub.3)--CH.sub.3,
--CH.sub.2--S--CH.sub.2--CH.sub.3, --CH.sub.2--CH.sub.2,
--S(O)--CH.sub.3, --CH.sub.2--CH.sub.2--S(O).sub.2--CH.sub.3,
--CH.dbd.CH--O--CH.sub.3, --Si(CH.sub.3).sub.3,
--CH.sub.2--CH.dbd.N--OCH.sub.3,
--CH.dbd.CH--N(CH.sub.3)--CH.sub.3, --O--CH.sub.3,
--O--CH.sub.2--CH.sub.3, and --CN. Up to two or three heteroatoms
may be consecutive, such as, for example, --CH.sub.2--NH--OCH.sub.3
and CH.sub.2--O--Si(CH.sub.3).sub.3.
[0098] Similarly, the term "heteroalkylene," by itself or as part
of another substituent, means, unless otherwise stated, a divalent
radical derived from heteroalkyl, as exemplified, but not limited
by, --CH.sub.2--CH.sub.2--S--CH.sub.2--CH.sub.2-- and
--CH.sub.2--S--CH.sub.2--CH.sub.2--NH--CH.sub.2--. For
heteroalkylene groups, heteroatoms can also occupy either or both
of the chain termini (e.g., alkyleneoxy, alkylenedioxy,
alkyleneamino, alkylenediamino, and the like). Still further, for
alkylene and heteroalkylene linking groups, no orientation of the
linking group is implied by the direction in which the formula of
the linking group is written. For example, the formula
--C(O).sub.2R'-- represents both --C(O).sub.2R'-- and
--R'C(O).sub.2--. As described above, heteroalkyl groups, as used
herein, include those groups that are attached to the remainder of
the molecule through a heteroatom, such as --C(O)R', --C(O)NR',
--NR'R'', --OR', --SR', and/or --SO.sub.2R'. Where "heteroalkyl" is
recited, followed by recitations of specific heteroalkyl groups,
such as --NR'R'' or the like, it will be understood that the terms
heteroalkyl and --NR'R'' are not redundant or mutually exclusive.
Rather, the specific heteroalkyl groups are recited to add clarity.
Thus, the term "heteroalkyl" should not be interpreted herein as
excluding specific heteroalkyl groups, such as --NR'R'' or the
like.
[0099] The terms "cycloalkyl" and "heterocycloalkyl," by themselves
or in combination with other terms, mean, unless otherwise stated,
cyclic versions of "alkyl" and "heteroalkyl," respectively.
Additionally, for heterocycloalkyl, a heteroatom can occupy the
position at which the heterocycle is attached to the remainder of
the molecule. Examples of cycloalkyl include, but are not limited
to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,
1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples
of heterocycloalkyl include, but are not limited to,
1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl,
3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl,
tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl,
1-piperazinyl, 2-piperazinyl, and the like. A "cycloalkylene" and a
"heterocycloalkylene," alone or as part of another substituent,
means a divalent radical derived from a cycloalkyl and
heterocycloalkyl, respectively.
[0100] The terms "halo" or "halogen," by themselves or as part of
another substituent, mean, unless otherwise stated, a fluorine,
chlorine, bromine, or iodine atom. Additionally, terms such as
"haloalkyl" are meant to include monohaloalkyl and polyhaloalkyl.
For example, the term "halo(C.sub.1-C.sub.4)alkyl" includes, but is
not limited to, fluoromethyl, difluoromethyl, trifluoromethyl,
2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the
like.
[0101] The term "acyl" means, unless otherwise stated, --C(O)R
where R is a substituted or unsubstituted alkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl.
[0102] The term "aryl" means, unless otherwise stated, a
polyunsaturated, aromatic, hydrocarbon substituent, which can be a
single ring or multiple rings (preferably from 1 to 3 rings) that
are fused together (i.e., a fused ring aryl) or linked covalently.
A fused ring aryl refers to multiple rings fused together wherein
at least one of the fused rings is an aryl ring. The term
"heteroaryl" refers to aryl groups (or rings) that contain at least
one heteroatom such as N, O, or S, wherein the nitrogen and sulfur
atoms are optionally oxidized, and the nitrogen atom(s) are
optionally quaternized. Thus, the term "heteroaryl" includes fused
ring heteroaryl groups (i.e., multiple rings fused together wherein
at least one of the fused rings is a heteroaromatic ring). A
5,6-fused ring heteroarylene refers to two rings fused together,
wherein one ring has 5 members and the other ring has 6 members,
and wherein at least one ring is a heteroaryl ring. Likewise, a
6,6-fused ring heteroarylene refers to two rings fused together,
wherein one ring has 6 members and the other ring has 6 members,
and wherein at least one ring is a heteroaryl ring. And a 6,5-fused
ring heteroarylene refers to two rings fused together, wherein one
ring has 6 members and the other ring has 5 members, and wherein at
least one ring is a heteroaryl ring. A heteroaryl group can be
attached to the remainder of the molecule through a carbon or
heteroatom. Non-limiting examples of aryl and heteroaryl groups
include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1-pyrrolyl,
2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl,
pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl,
3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl,
5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl,
3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl,
purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl,
2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl.
Substituents for each of the above noted aryl and heteroaryl ring
systems are selected from the group of acceptable substituents
described below. An "arylene" and a "heteroarylene," alone or as
part of another substituent, mean a divalent radical derived from
an aryl and heteroaryl, respectively. A heteroaryl group
substituent may be a --O-- bonded to a ring heteroatom
nitrogen.
[0103] A fused ring heterocyloalkyl-aryl is an aryl fused to a
heterocycloalkyl. A fused ring heterocycloalkyl-heteroaryl is a
heteroaryl fused to a heterocycloalkyl. A fused ring
heterocycloalkyl-cycloalkyl is a heterocycloalkyl fused to a
cycloalkyl. A fused ring heterocycloalkyl-heterocycloalkyl is a
heterocycloalkyl fused to another heterocycloalkyl. Fused ring
heterocycloalkyl-aryl, fused ring heterocycloalkyl-heteroaryl,
fused ring heterocycloalkyl-cycloalkyl, or fused ring
heterocycloalkyl-heterocycloalkyl may each independently be
unsubstituted or substituted with one or more of the substitutents
described herein. Spirocyclic rings are two or more rings wherein
adjacent rings are attached through a single atom. The individual
rings within spirocyclic rings may be identical or different.
Individual rings in spirocyclic rings may be substituted or
unsubstituted and may have different substituents from other
individual rings within a set of spirocyclic rings. Possible
substituents for individual rings within spirocyclic rings are the
possible substituents for the same ring when not part of
spirocyclic rings (e.g. substitutents for cycloalkyl or
heterocycloalkyl rings). Spirocylic rings may be substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkyl or
substituted or unsubstituted heterocycloalkylene and individual
rings within a spirocyclic ring group may be any of the immediately
previous list, including having all rings of one type (e.g. all
rings being substituted heterocycloalkylene wherein each ring may
be the same or different substituted heterocycloalkylene). When
referring to a spirocyclic ring system, heterocyclic spirocyclic
rings means a spirocyclic rings wherein at least one ring is a
heterocyclic ring and wherein each ring may be a different ring.
When referring to a spirocyclic ring system, substituted
spirocyclic rings means that at least one ring is substituted and
each substituent may optionally be different.
[0104] The term "oxo," as used herein, means an oxygen that is
double bonded to a carbon atom.
[0105] The term "alkylsulfonyl," as used herein, means a moiety
having the formula --S(O.sub.2)--R', where R' is a substituted or
unsubstituted alkyl group as defined above. R' may have a specified
number of carbons (e.g., "C.sub.1-C.sub.4 alkylsulfonyl").
[0106] Each of the above terms (e.g., "alkyl," "heteroalkyl,"
"aryl," and "heteroaryl") includes both substituted and
unsubstituted forms of the indicated radical. Preferred
substituents for each type of radical are provided below.
[0107] Substituents for the alkyl and heteroalkyl radicals
(including those groups often referred to as alkylene, alkenyl,
heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl,
heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one
or more of a variety of groups selected from, but not limited to,
--OR', .dbd.O, .dbd.NR', .dbd.N--OR', --NR'R'', --SR', -halogen,
--SiR'R''R''', --OC(O)R', --C(O)R', --CO.sub.2R', --CONR'R'',
--OC(O)NR'R'', --NR''C(O)R', --NR'--C(O)NR''R''',
--NR''C(O).sub.2R', --NR--C(NR'R''R''').dbd.NR'''',
--NR--C(NR'R'').dbd.NR''', --S(O)R', --S(O).sub.2R',
--S(O).sub.2NR'R'', --NRSO.sub.2R', NR'NR''R''', ONR'R'',
NR'C.dbd.(O)NR''NR'''R'''', --CN, --NO.sub.2, --NR'SO.sub.2R'',
--NR'C.dbd.(O)R'', --NR'C(O)--OR'', --NR'OR'', in a number ranging
from zero to (2m'+1), where m' is the total number of carbon atoms
in such radical. R, R', R'', R''', and R'''' each preferably
independently refer to hydrogen, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl (e.g., aryl substituted with 1-3 halogens), substituted or
unsubstituted heteroaryl, substituted or unsubstituted alkyl,
alkoxy, or thioalkoxy groups, or arylalkyl groups. When a compound
of the invention includes more than one R group, for example, each
of the R groups is independently selected as are each R', R'',
R''', and R'''' group when more than one of these groups is
present. When R' and R'' are attached to the same nitrogen atom,
they can be combined with the nitrogen atom to form a 4-, 5-, 6-,
or 7-membered ring. For example, --NR'R'' includes, but is not
limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above
discussion of substituents, one of skill in the art will understand
that the term "alkyl" is meant to include groups including carbon
atoms bound to groups other than hydrogen groups, such as haloalkyl
(e.g., --CF.sub.3 and --CH.sub.2CF.sub.3) and acyl (e.g.,
--C(O)CH.sub.3, --C(O)CF.sub.3, --C(O)CH.sub.2OCH.sub.3, and the
like).
[0108] Similar to the substituents described for the alkyl radical,
substituents for the aryl and heteroaryl groups are varied and are
selected from, for
example: --OR', --NR'R'', --SR', -halogen, --SiR'R''R''',
--OC(O)R', --C(O)R', --CO.sub.2R', --CONR'R'', --OC(O)NR'R'',
--NR''C(O)R', --NR'--C(O)NR''R''', --NR''C(O).sub.2R',
--NR--C(NR'R''R''').dbd.NR'''', --NR--C(NR'R'').dbd.NR''',
--S(O)R', --S(O).sub.2R', --S(O).sub.2NR'R'', --NRSO.sub.2R',
NR'NR''R''', ONR'R'', NR'C.dbd.(O)NR''NR'''R'''', --CN, --NO.sub.2,
--R', --N.sub.3, --CH(Ph).sub.2, fluoro(C.sub.1-C.sub.4)alkoxy, and
fluoro(C.sub.1-C.sub.4)alkyl, --NR'SO.sub.2R'', --NR'C.dbd.(O)R'',
--NR'C(O)--OR'', --NR'OR'', in a number ranging from zero to the
total number of open valences on the aromatic ring system; and
where R', R'', R''', and R'''' are preferably independently
selected from hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, and
substituted or unsubstituted heteroaryl. When a compound of the
invention includes more than one R group, for example, each of the
R groups is independently selected as are each R', R'', R''', and
R'''' groups when more than one of these groups is present.
[0109] Substituents for rings (e.g. cycloalkyl, heterocycloalkyl,
aryl, heteroaryl, cycloalkylene, heterocycloalkylene, arylene, or
heteroarylene) may be depicted as substituents on the ring rather
than on a specific atom of a ring (commonly referred to as a
floating substituent). In such a case, the substituent may be
attached to any of the ring atoms (obeying the rules of chemical
valency) and in the case of fused rings or spirocyclic rings, a
substituent depicted as associated with one member of the fused
rings or spirocyclic rings (a floating substituent on a single
ring), may be a substituent on any of the fused rings or
spirocyclic rings (a floating substituent on multiple rings). When
a substituent is attached to a ring, but not a specific atom (a
floating substituent), and a subscript for the substituent is an
integer greater than one, the multiple substituents may be on the
same atom, same ring, different atoms, different fused rings,
different spirocyclic rings, and each substituent may optionally be
different. Where a point of attachment of a ring to the remainder
of a molecule is not limited to a single atom (a floating
substituent), the attachment point may be any atom of the ring and
in the case of a fused ring or spirocyclic ring, any atom of any of
the fused rings or spirocyclic rings while obeying the rules of
chemical valency. Where a ring, fused rings, or spirocyclic rings
contain one or more ring heteroatoms and the ring, fused rings, or
spirocyclic rings are shown with one more more floating
substituents (including, but not limited to, points of attachment
to the remainder of the molecule), the floating substituents may be
bonded to the heteroatoms. Where the ring heteroatoms are shown
bound to one or more hydrogens (e.g. a ring nitrogen with two bonds
to ring atoms and a third bond to a hydrogen) in the structure or
formula with the floating substituent, when the heteroatom is
bonded to the floating substituent, the substituent will be
understood to replace the hydrogen, while obeying the rules of
chemical valency.
[0110] Two or more substituents may optionally be joined to form
aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups. Such
so-called ring-forming substituents are typically, though not
necessarily, found attached to a cyclic base structure. In one
embodiment, the ring-forming substituents are attached to adjacent
members of the base structure. For example, two ring-forming
substituents attached to adjacent members of a cyclic base
structure create a fused ring structure. In another embodiment, the
ring-forming substituents are attached to a single member of the
base structure. For example, two ring-forming substituents attached
to a single member of a cyclic base structure create a spirocyclic
structure. In yet another embodiment, the ring-forming substituents
are attached to non-adjacent members of the base structure.
[0111] Two of the substituents on adjacent atoms of the aryl or
heteroaryl ring may optionally form a ring of the formula
-T-C(O)--(CRR').sub.q--U--, wherein T and U are independently
--NR--, --O--, --CRR'--, or a single bond, and q is an integer of
from 0 to 3. Alternatively, two of the substituents on adjacent
atoms of the aryl or heteroaryl ring may optionally be replaced
with a substituent of the formula -A-(CH.sub.2).sub.r--B--, wherein
A and B are independently --CRR'--, --O--, --NR--, --S--, --S(O)--,
--S(O).sub.2--, --S(O).sub.2NR'--, or a single bond, and r is an
integer of from 1 to 4. One of the single bonds of the new ring so
formed may optionally be replaced with a double bond.
Alternatively, two of the substituents on adjacent atoms of the
aryl or heteroaryl ring may optionally be replaced with a
substituent of the formula
--(CRR').sub.s--X'--(C''R''R''').sub.d--, where s and d are
independently integers of from 0 to 3, and X' is --O--, --NR'--,
--S--, --S(O)--, --S(O).sub.2--, or --S(O).sub.2NR'--. The
substituents R, R', R'', and R''' are preferably independently
selected from hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, and
substituted or unsubstituted heteroaryl.
[0112] As used herein, the terms "heteroatom" or "ring heteroatom"
are meant to include, oxygen (O), nitrogen (N), sulfur (S),
phosphorus (P), Boron (B), Arsenic (As), and silicon (Si).
[0113] A "substituent group," as used herein, means a group
selected from the following moieties: [0114] (A) oxo, halogen,
--CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted
cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl,
unsubstituted heteroaryl, and [0115] (B) alkyl, heteroalkyl,
cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, substituted
with at least one substituent selected from: [0116] (i) oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted
cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl,
unsubstituted heteroaryl, and [0117] (ii) alkyl, heteroalkyl,
cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, substituted
with at least one substituent selected from: [0118] (a) oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, NHNH.sub.2, ONH.sub.2, NHC.dbd.(O)NHNH.sub.2,
NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, unsubstituted alkyl,
unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted
heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, and
[0119] (b) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl,
or heteroaryl, substituted with at least one substituent selected
from: oxo, [0120] halogen, --CF.sub.3, --CN, --OH, --NH.sub.2,
--COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, NHNH.sub.2, ONH.sub.2,
NHC.dbd.(O)NHNH.sub.2, NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted
cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, and
unsubstituted heteroaryl.
[0121] A "size-limited substituent" or "size-limited substituent
group," as used herein, means a group selected from all of the
substituents described above for a "substituent group," wherein
each substituted or unsubstituted alkyl is a substituted or
unsubstituted C.sub.1-C.sub.20 alkyl, each substituted or
unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20
membered heteroalkyl, each substituted or unsubstituted cycloalkyl
is a substituted or unsubstituted C.sub.4-C.sub.8 cycloalkyl, and
each substituted or unsubstituted heterocycloalkyl is a substituted
or unsubstituted 4 to 8 membered heterocycloalkyl.
[0122] A "lower substituent" or "lower substituent group," as used
herein, means a group selected from all of the substituents
described above for a "substituent group," wherein each substituted
or unsubstituted alkyl is a substituted or unsubstituted
C.sub.1-C.sub.8 alkyl, each substituted or unsubstituted
heteroalkyl is a substituted or unsubstituted 2 to 8 membered
heteroalkyl, each substituted or unsubstituted cycloalkyl is a
substituted or unsubstituted C.sub.3-C.sub.7 cycloalkyl, and each
substituted or unsubstituted heterocycloalkyl is a substituted or
unsubstituted 3 to 7 membered heterocycloalkyl.
[0123] In some embodiments, each substituted group described in the
compounds herein is substituted with at least one substituent
group. More specifically, in some embodiments, each substituted
alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
heterocycloalkyl, substituted aryl, substituted heteroaryl,
substituted alkylene, substituted heteroalkylene, substituted
cycloalkylene, substituted heterocycloalkylene, substituted
arylene, and/or substituted heteroarylene described in the
compounds herein are substituted with at least one substituent
group. In other embodiments, at least one or all of these groups
are substituted with at least one size-limited substituent group.
In other embodiments, at least one or all of these groups are
substituted with at least one lower substituent group.
[0124] In other embodiments of the compounds herein, each
substituted or unsubstituted alkyl may be a substituted or
unsubstituted C.sub.1-C.sub.20 alkyl, each substituted or
unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20
membered heteroalkyl, each substituted or unsubstituted cycloalkyl
is a substituted or unsubstituted C.sub.3-C.sub.8 cycloalkyl,
and/or each substituted or unsubstituted heterocycloalkyl is a
substituted or unsubstituted 3 to 8 membered heterocycloalkyl. In
some embodiments of the compounds herein, each substituted or
unsubstituted alkylene is a substituted or unsubstituted
C.sub.1-C.sub.20 alkylene, each substituted or unsubstituted
heteroalkylene is a substituted or unsubstituted 2 to 20 membered
heteroalkylene, each substituted or unsubstituted cycloalkylene is
a substituted or unsubstituted C.sub.3-C.sub.8 cycloalkylene,
and/or each substituted or unsubstituted heterocycloalkylene is a
substituted or unsubstituted 3 to 8 membered
heterocycloalkylene.
[0125] In some embodiments, each substituted or unsubstituted alkyl
is a substituted or unsubstituted C.sub.1-C.sub.8 alkyl, each
substituted or unsubstituted heteroalkyl is a substituted or
unsubstituted 2 to 8 membered heteroalkyl, each substituted or
unsubstituted cycloalkyl is a substituted or unsubstituted
C.sub.5-C.sub.7 cycloalkyl, and/or each substituted or
unsubstituted heterocycloalkyl is a substituted or unsubstituted 5
to 7 membered heterocycloalkyl. In some embodiments, each
substituted or unsubstituted alkylene is a substituted or
unsubstituted C.sub.1-C.sub.8 alkylene, each substituted or
unsubstituted heteroalkylene is a substituted or unsubstituted 2 to
8 membered heteroalkylene, each substituted or unsubstituted
cycloalkylene is a substituted or unsubstituted C.sub.5-C.sub.7
cycloalkylene, and/or each substituted or unsubstituted
heterocycloalkylene is a substituted or unsubstituted 5 to 7
membered heterocycloalkylene.
[0126] The term "pharmaceutically acceptable salts" is meant to
include salts of the active compounds that are prepared with
relatively nontoxic acids or bases, depending on the particular
substituents found on the compounds described herein. When
compounds of the present invention contain relatively acidic
functionalities, base addition salts can be obtained by contacting
the neutral form of such compounds with a sufficient amount of the
desired base, either neat or in a suitable inert solvent. Examples
of pharmaceutically acceptable base addition salts include sodium,
potassium, calcium, ammonium, organic amino, or magnesium salt, or
a similar salt. When compounds of the present invention contain
relatively basic functionalities, acid addition salts can be
obtained by contacting the neutral form of such compounds with a
sufficient amount of the desired acid, either neat or in a suitable
inert solvent. Examples of pharmaceutically acceptable acid
addition salts include those derived from inorganic acids like
hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic,
phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,
monohydrogensulfuric, hydriodic, or phosphorous acids and the like,
as well as the salts derived from relatively nontoxic organic acids
like acetic, propionic, isobutyric, maleic, malonic, benzoic,
succinic, suberic, fumaric, lactic, mandelic, phthalic,
benzenesulfonic, p-tolylsulfonic, citric, tartaric, oxalic,
methanesulfonic, and the like. Also included are salts of amino
acids such as arginate and the like, and salts of organic acids
like glucuronic or galactunoric acids and the like (see, for
example, Berge et al., "Pharmaceutical Salts", Journal of
Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds
of the present invention contain both basic and acidic
functionalities that allow the compounds to be converted into
either base or acid addition salts.
[0127] Thus, the compounds of the present invention may exist as
salts, such as with pharmaceutically acceptable acids. The present
invention includes such salts. Examples of such salts include
hydrochlorides, hydrobromides, sulfates, methanesulfonates,
nitrates, maleates, acetates, citrates, fumarates, tartrates (e.g.,
(+)-tartrates, (-)-tartrates, or mixtures thereof including racemic
mixtures), succinates, benzoates, and salts with amino acids such
as glutamic acid. These salts may be prepared by methods known to
those skilled in the art.
[0128] The neutral forms of the compounds are preferably
regenerated by contacting the salt with a base or acid and
isolating the parent compound in the conventional manner. The
parent form of the compound differs from the various salt forms in
certain physical properties, such as solubility in polar
solvents.
[0129] In addition to salt forms, the present invention provides
compounds, which are in a prodrug form. Prodrugs of the compounds
described herein are those compounds that readily undergo chemical
changes under physiological conditions to provide the compounds of
the present invention. Additionally, prodrugs can be converted to
the compounds of the present invention by chemical or biochemical
methods in an ex vivo environment. For example, prodrugs can be
slowly converted to the compounds of the present invention when
placed in a transdermal patch reservoir with a suitable enzyme or
chemical reagent.
[0130] Certain compounds of the present invention can exist in
unsolvated forms as well as solvated forms, including hydrated
forms. In general, the solvated forms are equivalent to unsolvated
forms and are encompassed within the scope of the present
invention. Certain compounds of the present invention may exist in
multiple crystalline or amorphous forms. In general, all physical
forms are equivalent for the uses contemplated by the present
invention and are intended to be within the scope of the present
invention.
[0131] As used herein, the term "salt" refers to acid or base salts
of the compounds used in the methods of the present invention.
Illustrative examples of acceptable salts are mineral acid
(hydrochloric acid, hydrobromic acid, phosphoric acid, and the
like) salts, organic acid (acetic acid, propionic acid, glutamic
acid, citric acid and the like) salts, quaternary ammonium (methyl
iodide, ethyl iodide, and the like) salts.
[0132] Certain compounds of the present invention possess
asymmetric carbon atoms (optical or chiral centers) or double
bonds; the enantiomers, racemates, diastereomers, tautomers,
geometric isomers, stereoisometric forms that may be defined, in
terms of absolute stereochemistry, as (R)- or (S)- or, as (D)- or
(L)- for amino acids, and individual isomers are encompassed within
the scope of the present invention. The compounds of the present
invention do not include those which are known in art to be too
unstable to synthesize and/or isolate. The present invention is
meant to include compounds in racemic and optically pure forms.
Optically active (R)- and (S)-, or (D)- and (L)-isomers may be
prepared using chiral synthons or chiral reagents, or resolved
using conventional techniques. When the compounds described herein
contain olefinic bonds or other centers of geometric asymmetry, and
unless specified otherwise, it is intended that the compounds
include both E and Z geometric isomers.
[0133] As used herein, the term "isomers" refers to compounds
having the same number and kind of atoms, and hence the same
molecular weight, but differing in respect to the structural
arrangement or configuration of the atoms.
[0134] The term "tautomer," as used herein, refers to one of two or
more structural isomers which exist in equilibrium and which are
readily converted from one isomeric form to another.
[0135] It will be apparent to one skilled in the art that certain
compounds of this invention may exist in tautomeric forms, all such
tautomeric forms of the compounds being within the scope of the
invention.
[0136] Unless otherwise stated, structures depicted herein are also
meant to include all stereochemical forms of the structure; i.e.,
the R and S configurations for each asymmetric center. Therefore,
single stereochemical isomers as well as enantiomeric and
diastereomeric mixtures of the present compounds are within the
scope of the invention.
[0137] Unless otherwise stated, structures depicted herein are also
meant to include compounds which differ only in the presence of one
or more isotopically enriched atoms. For example, compounds having
the present structures except for the replacement of a hydrogen by
a deuterium or tritium, or the replacement of a carbon by .sup.13C-
or .sup.14C-enriched carbon are within the scope of this
invention.
[0138] The compounds of the present invention may also contain
unnatural proportions of atomic isotopes at one or more of the
atoms that constitute such compounds. For example, the compounds
may be radiolabeled with radioactive isotopes, such as for example
tritium (.sup.3H), iodine-125 (.sup.125I), or carbon-14 (.sup.14C).
All isotopic variations of the compounds of the present invention,
whether radioactive or not, are encompassed within the scope of the
present invention.
[0139] The symbol "" denotes the point of attachment of a chemical
moiety to the remainder of a molecule or chemical formula.
[0140] It should be noted that throughout the application that
alternatives are written in Markush groups, for example, each amino
acid position that contains more than one possible amino acid. It
is specifically contemplated that each member of the Markush group
should be considered separately, thereby comprising another
embodiment, and the Markush group is not to be read as a single
unit.
[0141] A combinatorial chemical library is a collection of diverse
chemical compounds generated by either chemical synthesis or
biological synthesis, by combining a number of chemical "building
blocks" such as reagents. For example, a linear combinatorial
chemical library such as a polypeptide library is formed by
combining a set of chemical building blocks (amino acids) in every
possible way for a given compound length (i.e., the number of amino
acids in a polypeptide compound). Millions of chemical compounds
can be synthesized through such combinatorial mixing of chemical
building blocks.
[0142] Preparation and screening of combinatorial chemical
libraries is well known to those of skill in the art. Such
combinatorial chemical libraries include, but are not limited to,
peptide libraries (see, e.g., U.S. Pat. No. 5,010,175, Furka, Int.
J. Pept. Prot. Res. 37:487-493 (1991) and Houghton et al., Nature
354:84-88 (1991)). Other chemistries for generating chemical
diversity libraries can also be used. Such chemistries include, but
are not limited to: peptoids (e.g., PCT Publication No. WO
91/19735), encoded peptides (e.g., PCT Publication WO 93/20242),
random bio-oligomers (e.g., PCT Publication No. WO 92/00091),
benzodiazepines (e.g., U.S. Pat. No. 5,288,514), diversomers such
as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc.
Nat. Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides
(Hagihara et al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidal
peptidomimetics with glucose scaffolding (Hirschmann et al., J.
Amer. Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses
of small compound libraries (Chen et al., J. Amer. Chem. Soc.
116:2661 (1994)), oligocarbamates (Cho et al., Science 261:1303
(1993)), and/or peptidyl phosphonates (Campbell et al., J. Org.
Chem. 59:658 (1994)), nucleic acid libraries (see Ausubel, Berger
and Sambrook, all supra), peptide nucleic acid libraries (see,
e.g., U.S. Pat. No. 5,539,083), antibody libraries (see, e.g.,
Vaughn et al., Nature Biotechnology, 14(3):309-314 (1996) and
PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et al.,
Science, 274:1520-1522 (1996) and U.S. Pat. No. 5,593,853). The
methods above may be used to synthesize single molecular
species.
[0143] The terms "a" or "an," as used in herein means one or more.
In addition, the phrase "substituted with a[n]," as used herein,
means the specified group may be substituted with one or more of
any or all of the named substituents. For example, where a group,
such as an alkyl or heteroaryl group, is "substituted with an
unsubstituted C.sub.1-C.sub.20 alkyl, or unsubstituted 2 to 20
membered heteroalkyl," the group may contain one or more
unsubstituted C.sub.1-C.sub.20 alkyls, and/or one or more
unsubstituted 2 to 20 membered heteroalkyls. Moreover, where a
moiety is substituted with an R substituent, the group may be
referred to as "R-substituted." Where a moiety is R-substituted,
the moiety is substituted with at least one R substituent and each
R substituent is optionally different.
[0144] Description of compounds of the present invention is limited
by principles of chemical bonding known to those skilled in the
art. Accordingly, where a group may be substituted by one or more
of a number of substituents, such substitutions are selected so as
to comply with principles of chemical bonding and to give compounds
which are not inherently unstable and/or would be known to one of
ordinary skill in the art as likely to be unstable under ambient
conditions, such as aqueous, neutral, and several known
physiological conditions. For example, a heterocycloalkyl or
heteroaryl is attached to the remainder of the molecule via a ring
heteroatom in compliance with principles of chemical bonding known
to those skilled in the art thereby avoiding inherently unstable
compounds.
[0145] The terms "treating" or "treatment" refers to any indicia of
success in the treatment or amelioration of an injury, disease,
pathology or condition, including any objective or subjective
parameter such as abatement; remission; diminishing of symptoms or
making the injury, pathology or condition more tolerable to the
patient; slowing in the rate of degeneration or decline; making the
final point of degeneration less debilitating; improving a
patient's physical or mental well-being. The treatment or
amelioration of symptoms can be based on objective or subjective
parameters; including the results of a physical examination,
neuropsychiatric exams, and/or a psychiatric evaluation. For
example, the certain methods presented herein successfully treat
cancer by decreasing the incidence of cancer and or causing
remission of cancer. In some embodiments of the compositions or
methods described herein, treating cancer includes slowing the rate
of growth or spread of cancer cells, reducing metastasis, or
reducing the growth of metastatic tumors. The term "treating" and
conjugations thereof, include prevention of an injury, pathology,
condition, or disease.
[0146] An "effective amount" is an amount sufficient for a compound
to accomplish a stated purpose relative to the absence of the
compound (e.g. achieve the effect for which it is administered,
treat a disease, reduce enzyme activity, increase enzyme activity,
reduce signaling pathway, reduce one or more symptoms of a disease
or condition (e.g. reduce GTPase activity in a cell, increase
GTPase activity, reduce signaling pathway stimulated by GTP bound
Ras (e.g. K-Ras), reduce the signaling pathway activity of Ras,
reduce the signaling pathway activity of K-Ras, reduce the
signaling pathway activity of K-Ras4A, reduce the signaling pathway
activity of K-Ras4B, reduce the signaling pathway activity of
H-Ras, reduce the signaling pathway activity of N-Ras, reduce the
signaling pathway activity of K-Ras G12C, reduce the signaling
pathway activity of K-Ras G13C, reduce the signaling pathway
activity of K-Ras G13D, reduce the signaling pathway activity of
K-Ras G12D, reduce the signaling pathway activity of a mutant
K-Ras, increase the activity of Ras, increase the activity of
K-Ras, increase the activity of K-Ras4A, increase the activity of
K-Ras4B, increase the activity of H-Ras, increase the activity of
N-Ras, increase the activity of K-Ras G12C, increase the activity
of K-Ras G13C, increase the activity of K-Ras G12D, increase the
activity of K-Ras G13D, increase the activity of a mutant K-Ras,
inhibit the binding of K-Ras to SOS, inhibit the binding of K-Ras
to a GEF, inhibit nucleotide exchange). An example of an "effective
amount" is an amount sufficient to contribute to the treatment,
prevention, or reduction of a symptom or symptoms of a disease,
which could also be referred to as a "therapeutically effective
amount." A "reduction" of a symptom or symptoms (and grammatical
equivalents of this phrase) means decreasing of the severity or
frequency of the symptom(s), or elimination of the symptom(s). A
"prophylactically effective amount" of a drug is an amount of a
drug that, when administered to a subject, will have the intended
prophylactic effect, e.g., preventing or delaying the onset (or
reoccurrence) of an injury, disease, pathology or condition, or
reducing the likelihood of the onset (or reoccurrence) of an
injury, disease, pathology, or condition, or their symptoms. The
full prophylactic effect does not necessarily occur by
administration of one dose, and may occur only after administration
of a series of doses. Thus, a prophylactically effective amount may
be administered in one or more administrations. An "activity
decreasing amount," as used herein, refers to an amount of
antagonist required to decrease the activity of an enzyme relative
to the absence of the antagonist. A "function disrupting amount,"
as used herein, refers to the amount of antagonist required to
disrupt the function of an enzyme or protein relative to the
absence of the antagonist (e.g. disrupt the protein-protein
interaction between K-Ras and a signaling pathway binding protein
such as PI3K, disrupt the interaction of K-Ras and GEF, disrupt the
interaction of K-Ras and SOS, disrupt the interaction of K-Ras with
Raf). The exact amounts will depend on the purpose of the
treatment, and will be ascertainable by one skilled in the art
using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage
Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of
Pharmaceutical Compounding (1999); Pickar, Dosage Calculations
(1999); and Remington: The Science and Practice of Pharmacy, 20th
Edition, 2003, Gennaro, Ed., Lippincott, Williams &
Wilkins).
[0147] "Control" or "control experiment" is used in accordance with
its plain ordinary meaning and refers to an experiment in which the
subjects or reagents of the experiment are treated as in a parallel
experiment except for omission of a procedure, reagent, or variable
of the experiment. In some instances, the control is used as a
standard of comparison in evaluating experimental effects. In some
embodiments, a control is the measurement of the activity (e.g.
GTPase activity, protein-protein interaction, signaling pathway) of
a protein (e.g. Ras, K-Ras, mutant K-Ras, K-Ras G12C, K-Ras G12D,
K-Ras G13C, K-Ras G13D) in the absence of a compound as described
herein (including embodiments, examples, Table 1, 2, 3, 4, or
5).
[0148] "Contacting" is used in accordance with its plain ordinary
meaning and refers to the process of allowing at least two distinct
species (e.g. chemical compounds including biomolecules, or cells)
to become sufficiently proximal to react, interact or physically
touch. It should be appreciated; however, the resulting reaction
product can be produced directly from a reaction between the added
reagents or from an intermediate from one or more of the added
reagents which can be produced in the reaction mixture.
[0149] The term "contacting" may include allowing two species to
react, interact, or physically touch, wherein the two species may
be a compound as described herein and a protein or enzyme (e.g.
Ras, K-Ras, H-Ras, N-Ras, K-Ras4A, K-Ras4B, mutant Ras, mutant
K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D). In some
embodiments, the protein may be K-Ras. In some embodiments, the
protein may be a mutant K-Ras (e.g. K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D). In some embodiments, the protein may be K-Ras4A.
In some embodiments, the protein may be K-Ras4B. In some
embodiments contacting includes allowing a compound described
herein to interact with a protein or enzyme that is involved in a
signaling pathway. In some embodiments contacting includes allowing
a compound described herein to interact with a Switch 2-Binding
Pocket.
[0150] As defined herein, the term "inhibition", "inhibit",
"inhibiting" and the like in reference to a protein-inhibitor
interaction means negatively affecting (e.g. decreasing) the
activity or function of the protein (e.g. decreasing the signaling
pathway stimulated by GTP bound Ras (e.g. K-Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D), nucleotide exchange, effector
protein binding, effector protein activation, guanine exchange
factor (GEF) binding, SOS binding, GEF-facilitated nucleotide
exchange, phosphate release, nucleotide release, nucleotide
binding) relative to the activity or function of the protein in the
absence of the inhibitor (e.g. mutant K-Ras inhibitor, activitated
K-Ras inhibitor). In some embodiments inhibition refers to
reduction of a disease or symptoms of disease. In some embodiments,
inhibition refers to a reduction in the activity of a signal
transduction pathway or signaling pathway (e.g. reduction of a
pathway involving GTP bound Ras (e.g. K-Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D), reduction of a pathway involving
mutant K-Ras (e.g. K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D)). Thus, inhibition includes, at least in part, partially or
totally blocking stimulation, decreasing, preventing, or delaying
activation, or inactivating, desensitizing, or down-regulating the
signaling pathway or enzymatic activity or the amount of a protein
(e.g. K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D). In
some embodiments, inhibition refers to inhibition of interactions
of Ras (K-Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) with
signaling pathway binding partners (e.g. PI3K, SOS, Raf). In some
embodiments, inhibition refers to inhibition of interactions of Ras
with a GEF (e.g. SOS).
[0151] The term "modulator" refers to a composition that increases
or decreases the level of a target molecule or the function (e.g.
GTPase activity, nucleotide exchange, effector protein binding,
effector protein activation, guanine exchange factor (GEF) binding,
SOS binding, GEF-facilitated nucleotide exchange, phosphate
release, nucleotide release, nucleotide binding) of a target
molecule or the physical state (e.g. Ras subcellular localization,
Ras post-translational processing, Ras post-translational
modifications) of the target of the molecule (e.g. a target may be
K-Ras and the function may be to hydrolyze GTP or activate a
signaling pathway that is activated by GTP bound K-Ras, interaction
of K-Ras with protein binding partners (e.g. PI3K, SOS, Raf)). In
some embodiments, a GTPase modulator is a compound that reduces the
activity of a GTPase in a cell. In some embodiments, a GTPase
modulator is a compound that increases the activity of a GTPase in
a cell. In some embodiments, a GTPase modulator is a compound that
reduces the signaling pathway in a cell that is activated by the
GTP bound form of Ras. In some embodiments, a GTPase modulator is a
compound that increases the signaling pathway in a cell that is
activated by the GTP bound form of Ras. In some embodiments, a
K-Ras disease modulator is a compound that reduces the severity of
one or more symptoms of a disease associated with K-Ras (e.g.
cancer, metastatic cancer). A K-Ras modulator is a compound that
increases or decreases the activity or function or level of
activity or level of function of K-Ras or level of K-Ras or level
of K-Ras in a particular physical state. A mutant K-Ras modulator
is a compound that that increases or decreases the activity or
function or level of activity or level of function of mutant K-Ras
or level of mutant K-Ras or level of mutant K-Ras in a particular
physical state. A K-Ras G12C modulator, K-Ras G12D modulator, K-Ras
G13C modulator, or K-Ras G13D modulator is a compound that
increases or decreases the activity or function or level of
activity or level of function of that particular mutant K-Ras or
level of that particular mutant K-Ras or level of that particular
mutant K-Ras in a particular physical state. A K-Ras inhibitor is a
compound that decreases the activity or function or level of
activity or level of function of K-Ras or level of K-Ras or level
of K-Ras in a particular physical state. A mutant K-Ras inhibitor
is a compound that that decreases the activity or function or level
of activity or level of function of mutant K-Ras or level of mutant
K-Ras or level of mutant K-Ras in a particular physical state. A
K-Ras G12C inhibitor, K-Ras G12D inhibitor, K-Ras G13C inhibitor,
or K-Ras G13D inhibitor is a compound that decreases the activity
or function or level of activity or level of function of that
particular mutant K-Ras or level of that particular mutant K-Ras or
level of that particular mutant K-Ras in a particular physical
state.
[0152] The term "modulate" is used in accordance with its plain
ordinary meaning and refers to the act of changing or varying one
or more properties. "Modulation" refers to the process of changing
or varying one or more properties. For example, as applied to the
effects of a modulator on a target protein, to modulate means to
change by increasing or decreasing a property or function of the
target molecule or the amount of the target molecule.
[0153] "Patient" or "subject in need thereof" refers to a living
organism suffering from or prone to a disease or condition that can
be treated by administration of a pharmaceutical composition as
provided herein. Non-limiting examples include humans, other
mammals, bovines, rats, mice, dogs, monkeys, goat, sheep, cows,
deer, and other non-mammalian animals. In some embodiments, a
patient is human.
[0154] "Disease" or "condition" refer to a state of being or health
status of a patient or subject capable of being treated with the
compounds or methods provided herein. In some embodiments, the
disease is a disease related to (e.g. caused by) a mutant Ras. In
some embodiments, the disease is a disease related to (e.g. caused
by) a mutant K-Ras (e.g. K-Ras G12C, G13C, G12D, or G13D) or
aberrant K-Ras signaling pathway activity (e.g. lung cancer, breast
cancer, colon cancer, colorectal cancer, pancreatic cancer,
leukemia). Examples of diseases, disorders, or conditions include,
but are not limited to cancer. Examples of diseases, disorders, or
conditions include, but are not limited to MYH-associated
polyposis. In some instances, "disease" or "condition" refers to
cancer. In some instances, "disease" or "condition" refers to
MYH-associated polyposis. In some further instances, "cancer"
refers to human cancers and carcinomas, sarcomas, adenocarcinomas,
lymphomas, leukemias, etc., including solid and lymphoid cancers,
kidney, breast, lung, bladder, colon, ovarian, prostate, pancreas,
stomach, brain, head and neck, skin, uterine, testicular, glioma,
esophagus, and liver cancer, including hepatocarcinoma, lymphoma,
including B-acute lymphoblastic lymphoma, non-Hodgkin's lymphomas
(e.g., Burkitt's, Small Cell, and Large Cell lymphomas), Hodgkin's
lymphoma, leukemia (including AML, ALL, and CML), or multiple
myeloma.
[0155] As used herein, the term "cancer" refers to all types of
cancer, neoplasm or malignant tumors found in mammals (e.g.
humans), including leukemia, carcinomas and sarcomas. Exemplary
cancers that may be treated with a compound or method provided
herein include cancer of the thyroid, endocrine system, brain,
breast, cervix, colon, head & neck, liver, kidney, lung,
non-small cell lung, melanoma, mesothelioma, ovary, sarcoma,
stomach, uterus, Medulloblastoma, colorectal cancer, pancreatic
cancer. Additional examples include, Hodgkin's Disease,
Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, glioma,
glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, primary
thrombocytosis, primary macroglobulinemia, primary brain tumors,
cancer, malignant pancreatic insulanoma, malignant carcinoid,
urinary bladder cancer, premalignant skin lesions, testicular
cancer, lymphomas, thyroid cancer, neuroblastoma, esophageal
cancer, genitourinary tract cancer, malignant hypercalcemia,
endometrial cancer, adrenal cortical cancer, neoplasms of the
endocrine or exocrine pancreas, medullary thyroid cancer, medullary
thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid
cancer, hepatocellular carcinoma, or prostate cancer.
[0156] The term "leukemia" refers broadly to progressive, malignant
diseases of the blood-forming organs and is generally characterized
by a distorted proliferation and development of leukocytes and
their precursors in the blood and bone marrow. Leukemia is
generally clinically classified on the basis of (1) the duration
and character of the disease-acute or chronic; (2) the type of cell
involved; myeloid (myelogenous), lymphoid (lymphogenous), or
monocytic; and (3) the increase or non-increase in the number
abnormal cells in the blood-leukemic or aleukemic (subleukemic).
Exemplary leukemias that may be treated with a compound or method
provided herein include, for example, acute nonlymphocytic
leukemia, chronic lymphocytic leukemia, acute granulocytic
leukemia, chronic granulocytic leukemia, acute promyelocytic
leukemia, adult T-cell leukemia, aleukemic leukemia, a
leukocythemic leukemia, basophylic leukemia, blast cell leukemia,
bovine leukemia, chronic myelocytic leukemia, leukemia cutis,
embryonal leukemia, eosinophilic leukemia, Gross' leukemia,
hairy-cell leukemia, hemoblastic leukemia, hemocytoblastic
leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic
leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic
leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid
leukemia, lymphosarcoma cell leukemia, mast cell leukemia,
megakaryocytic leukemia, micromyeloblastic leukemia, monocytic
leukemia, myeloblastic leukemia, myelocytic leukemia, myeloid
granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia,
plasma cell leukemia, multiple myeloma, plasmacytic leukemia,
promyelocytic leukemia, Rieder cell leukemia, Schilling's leukemia,
stem cell leukemia, subleukemic leukemia, or undifferentiated cell
leukemia.
[0157] The term "sarcoma" generally refers to a tumor which is made
up of a substance like the embryonic connective tissue and is
generally composed of closely packed cells embedded in a fibrillar
or homogeneous substance. Sarcomas that may be treated with a
compound or method provided herein include a chondrosarcoma,
fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma,
osteosarcoma, Abemethy's sarcoma, adipose sarcoma, liposarcoma,
alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma,
chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor
sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma,
fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma,
granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple
pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells,
lymphoma, immunoblastic sarcoma of T-cells, Jensen's sarcoma,
Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma,
malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic
sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, or
telangiectaltic sarcoma.
[0158] The term "melanoma" is taken to mean a tumor arising from
the melanocytic system of the skin and other organs. Melanomas that
may be treated with a compound or method provided herein include,
for example, acral-lentiginous melanoma, amelanotic melanoma,
benign juvenile melanoma, Cloudman's melanoma, S91 melanoma,
Harding-Passey melanoma, juvenile melanoma, lentigo maligna
melanoma, malignant melanoma, nodular melanoma, subungal melanoma,
or superficial spreading melanoma.
[0159] The term "carcinoma" refers to a malignant new growth made
up of epithelial cells tending to infiltrate the surrounding
tissues and give rise to metastases. Exemplary carcinomas that may
be treated with a compound or method provided herein include, for
example, medullary thyroid carcinoma, familial medullary thyroid
carcinoma, acinar carcinoma, acinous carcinoma, adenocystic
carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum,
carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell
carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid
carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma,
bronchiolar carcinoma, bronchogenic carcinoma, cerebriform
carcinoma, cholangiocellular carcinoma, chorionic carcinoma,
colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform
carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical
carcinoma, cylindrical cell carcinoma, duct carcinoma, carcinoma
durum, embryonal carcinoma, encephaloid carcinoma, epiermoid
carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma,
carcinoma ex ulcere, carcinoma fibrosum, gelatiniforni carcinoma,
gelatinous carcinoma, giant cell carcinoma, carcinoma
gigantocellulare, glandular carcinoma, granulosa cell carcinoma,
hair-matrix carcinoma, hematoid carcinoma, hepatocellular
carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypernephroid
carcinoma, infantile embryonal carcinoma, carcinoma in situ,
intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's
carcinoma, Kulchitzky-cell carcinoma, large-cell carcinoma,
lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma,
lymphoepithelial carcinoma, carcinoma medullare, medullary
carcinoma, melanotic carcinoma, carcinoma molle, mucinous
carcinoma, carcinoma muciparum, carcinoma mucocellulare,
mucoepidermoid carcinoma, carcinoma mucosum, mucous carcinoma,
carcinoma myxomatodes, nasopharyngeal carcinoma, oat cell
carcinoma, carcinoma ossificans, osteoid carcinoma, papillary
carcinoma, periportal carcinoma, preinvasive carcinoma, prickle
cell carcinoma, pultaceous carcinoma, renal cell carcinoma of
kidney, reserve cell carcinoma, carcinoma sarcomatodes,
schneiderian carcinoma, scirrhous carcinoma, carcinoma scroti,
signet-ring cell carcinoma, carcinoma simplex, small-cell
carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle
cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous
cell carcinoma, string carcinoma, carcinoma telangiectaticum,
carcinoma telangiectodes, transitional cell carcinoma, carcinoma
tuberosum, tuberous carcinoma, verrucous carcinoma, or carcinoma
villosum.
[0160] "Ras associated cancer" (also referred to herein as "Ras
related cancer") refers to a cancer caused by aberrant Ras activity
or signaling. A "cancer associated with aberrant K-Ras activity"
(also referred to herein as "K-Ras related cancer") is a cancer
caused by aberrant K-Ras activity or signaling (e.g. a mutant
K-Ras). K-Ras related cancers may include lung cancer, non-small
cell lung cancer, breast cancer, leukemia, pancreatic cancer, colon
cancer, colorectal cancer. Other cancers that are associated with
aberrant activity of one or more of Ras, K-Ras, H-Ras, N-Ras,
mutant K-Ras (including K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D mutants), mutant N-Ras, and mutant H-Ras are well known in the
art and determining such cancers are within the skill of a person
of skill in the art.
[0161] "Pharmaceutically acceptable excipient" and
"pharmaceutically acceptable carrier" refer to a substance that
aids the administration of an active agent to and absorption by a
subject and can be included in the compositions of the present
invention without causing a significant adverse toxicological
effect on the patient. Non-limiting examples of pharmaceutically
acceptable excipients include water, NaCl, normal saline solutions,
lactated Ringer's, normal sucrose, normal glucose, binders,
fillers, disintegrants, lubricants, coatings, sweeteners, flavors,
salt solutions (such as Ringer's solution), alcohols, oils,
gelatins, carbohydrates such as lactose, amylose or starch, fatty
acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, and
colors, and the like. Such preparations can be sterilized and, if
desired, mixed with auxiliary agents such as lubricants,
preservatives, stabilizers, wetting agents, emulsifiers, salts for
influencing osmotic pressure, buffers, coloring, and/or aromatic
substances and the like that do not deleteriously react with the
compounds of the invention. One of skill in the art will recognize
that other pharmaceutical excipients are useful in the present
invention.
[0162] The term "preparation" is intended to include the
formulation of the active compound with encapsulating material as a
carrier providing a capsule in which the active component with or
without other carriers, is surrounded by a carrier, which is thus
in association with it. Similarly, cachets and lozenges are
included. Tablets, powders, capsules, pills, cachets, and lozenges
can be used as solid dosage forms suitable for oral
administration.
[0163] As used herein, the term "administering" means oral
administration, administration as a suppository, topical contact,
intravenous, intraperitoneal, intramuscular, intralesional,
intrathecal, intranasal or subcutaneous administration, or the
implantation of a slow-release device, e.g., a mini-osmotic pump,
to a subject. Administration is by any route, including parenteral
and transmucosal (e.g., buccal, sublingual, palatal, gingival,
nasal, vaginal, rectal, or transdermal). Parenteral administration
includes, e.g., intravenous, intramuscular, intra-arteriole,
intradermal, subcutaneous, intraperitoneal, intraventricular, and
intracranial. Other modes of delivery include, but are not limited
to, the use of liposomal formulations, intravenous infusion,
transdermal patches, etc. By "co-administer" it is meant that a
composition described herein is administered at the same time, just
prior to, or just after the administration of one or more
additional therapies, for example cancer therapies such as
chemotherapy, hormonal therapy, radiotherapy, or immunotherapy. The
compounds of the invention can be administered alone or can be
coadministered to the patient. Coadministration is meant to include
simultaneous or sequential administration of the compounds
individually or in combination (more than one compound). Thus, the
preparations can also be combined, when desired, with other active
substances (e.g. to reduce metabolic degradation). The compositions
of the present invention can be delivered by transdermally, by a
topical route, formulated as applicator sticks, solutions,
suspensions, emulsions, gels, creams, ointments, pastes, jellies,
paints, powders, and aerosols.
[0164] The term "administer (or administering) a Ras inhibitor"
means administering a compound that inhibits the activity or level
(e.g. amount) or level of a signaling pathway of one or more Ras
proteins (e.g. a Ras inhibitor, K-Ras inhibitor, N-Ras inhibitor,
H-Ras inhibitor, mutant K-Ras inhibitor, K-Ras G12C inhibitor,
K-Ras G13C inhibitor, K-Ras G12D inhibitor, K-Ras G13D inhibitor)
to a subject. Administration may include, without being limited by
mechanism, allowing sufficient time for the Ras inhibitor to reduce
the activity of one or more Ras proteins or for the Ras inhibitor
to reduce one or more symptoms of a disease (e.g. cancer, wherein
the Ras inhibitor may arrest the cell cycle, slow the cell cycle,
reduce DNA replication, reduce cell replication, reduce cell
growth, reduce metastasis, or cause cell death). The term
"administer (or administering) a K-Ras inhibitor" means
administering a compound that inhibits the activity or level (e.g.
amount) or level of a signaling pathway of one or more K-Ras
proteins (K-Ras, mutant K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G13C,
K-Ras G13D).
[0165] The term "associated" or "associated with" in the context of
a substance or substance activity or function associated with a
disease (e.g. a protein associated disease, a cancer associated
with aberrant Ras activity, K-Ras associated cancer, mutant K-Ras
associated cancer, activated K-Ras associated cancer, K-Ras G12C
associated cancer, K-Ras G13C associated cancer, K-Ras G12D
associated cancer, K-Ras G13D associated cancer) means that the
disease (e.g. cancer) is caused by (in whole or in part), or a
symptom of the disease is caused by (in whole or inpart) the
substance or substance activity or function. For example, a cancer
associated with aberrant Ras activity or function may be a cancer
that results (entirely or partially) from aberrant Ras activity or
function (e.g. enzyme activity, protein-protein interaction,
signaling pathway) or a cancer wherein a particular symptom of the
disease is caused (entirely or partially) by aberrant Ras activity
or function. As used herein, what is described as being associated
with a disease, if a causative agent, could be a target for
treatment of the disease. For example, a cancer associated with
aberrant Ras activity or function or a Ras associated cancer, may
be treated with a Ras modulator or Ras inhibitor, in the instance
where increased Ras activity or function (e.g. signaling pathway
activity) causes the cancer. For example, a cancer associated with
K-Ras G12C may be a cancer that a subject with K-Ras G12C is at
higher risk of developing as compared to a subject without K-Ras
G12C.
[0166] The term "aberrant" as used herein refers to different from
normal. When used to describe enzymatic activity, aberrant refers
to activity that is greater or less than a normal control or the
average of normal non-diseased control samples. Aberrant activity
may refer to an amount of activity that results in a disease,
wherein returning the aberrant activity to a normal or
non-disease-associated amount (e.g. by administering a compound or
using a method as described herein), results in reduction of the
disease or one or more disease symptoms.
[0167] The term "electrophilic chemical moiety" is used in
accordance with its plain ordinary chemical meaning and refers to a
monovalent chemical group that is electrophilic.
[0168] The term "Ras" refers to one or more of the family of human
Ras GTPase proteins (e.g. K-Ras, H-Ras, N-Ras). The term "K-Ras"
refers to the nucleotide sequences or proteins of human K-Ras (e.g.
human K-Ras4A (NP.sub.--203524.1), human K-Ras4B
(NP.sub.--004976.2), or both K-Ras4A and K-Ras4B). The term "K-Ras"
includes both the wild-type form of the nucleotide sequences or
proteins as well as any mutants thereof. In some embodiments,
"K-Ras" is wild-type K-Ras. In some embodiments, "K-Ras" is one or
more mutant forms. The term "K-Ras" XYZ refers to a nucleotide
sequence or protein of a mutant K-Ras wherein the Y numbered amino
acid of K-Ras that has an X amino acid in the wildtype instead has
a Z amino acid in the mutant (e.g. K-Ras G12C has a G in wildtype
protein but a C in the K-Ras G12C mutant protein). In some
embodiments K-Ras refers to K-Ras4A and K-Ras4B. In some
embodiments, K-Ras refers to K-Ras4A. In some embodiments, K-Ras
refers to K-Ras4B.
[0169] The term "Ras inhibitor test compound" as used herein refers
to a compound that is being characterized in an assay for the
ability to inhibit an activity, function, or level (e.g. amount) of
a Ras protein. The term "K-Ras inhibitor test compound" as used
herein refers to a compound that is being characterized in an assay
for the ability to inhibit an activity, function, or level (e.g.
amount) of K-Ras protein. A "Switch 2-Binding Pocket covalent
inhibitor test compound" is a Ras inhibitor test compound that
binds to a Ras Switch 2-Binding Pocket and is being tested for the
ability to covalently inhibit an activity, function, or level (e.g.
amount) of a Ras protein.
[0170] The term "signaling pathway" as used herein refers to a
series of interactions between cellular and optionally
extra-cellular components (e.g. proteins, nucleic acids, small
molecules, ions, lipids) that conveys a change in one component to
one or more other components, which in turn may convey a change to
additional components, which is optionally propogated to other
signaling pathway components. For example, binding of a K-Ras with
a compound as described herein may result in a change in one or
more protein-protein interactions of the K-Ras, resulting in
changes in cell growth, proliferation, or survival.
[0171] An amino acid residue in a protein "corresponds" to a given
residue when it occupies the same essential structural position
within the protein as the given residue. For example, a selected
residue in a selected protein corresponds to Gly 12 of Human
K-Ras4A or Human K-Ras 4B or both when the selected residue
occupies the same essential spatial or other structural
relationship as Gly 12 in Human K-Ras4A or Human K-Ras 4B or both.
In some embodiments, where a selected protein is aligned for
maximum homology with the Human K-Ras4A or Human K-Ras 4B protein,
the position in the aligned selected protein aligning with Gly 12
is said to correspond to Gly 12. Instead of a primary sequence
alignment, a three dimensional structural alignment can also be
used, e.g., where the structure of the selected protein is aligned
for maximum correspondence with the Human K-Ras4A or Human K-Ras 4B
protein and the overall structures compared. In this case, an amino
acid that occupies the same essential position as Gly 12 in the
structural model is said to correspond to the Gly 12 residue.
[0172] The terms "unsubstituted vinyl sulfone moiety",
"unsubstituted vinyl sulfonamide moiety", "unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety", "unsubstituted
chloro(C.sub.1-C.sub.4)alkylketone moiety", "unsubstituted
acrylamide moiety", "unsubstituted disulfide moiety",
"unsubstituted thiol moiety", "unsubstituted phosphonate moiety",
"unsubstituted aldehyde moiety", "unsubstituted enone moiety",
"unsubstituted diazomethylketone moiety", "unsubstituted
diazomethylamide moiety", "unsubstituted cyanocyclopropyl
carboxamide moiety", "unsubstituted epoxide moiety", "unsubstituted
epoxyketone moiety", "unsubstituted epoxyamide moiety",
"unsubstituted aryl aldehyde moiety", "unsubstituted aryl
dialdehyde moiety", "unsubstituted dialdehyde moiety",
"unsubstituted nitrogen mustard moiety", "unsubstituted propargyl
moiety", or "unsubstituted propargylamide moiety" are used
according to their plain ordinary chemical meaning and refer to
those monovalent chemical groups named having the lowest molecular
weight for each such group while obeying the rules of chemical
valency. A substituted form of one of the named groups may be
substituted with one or more of any of the substituent groups
described herein while obeying the rules of chemical valency.
[0173] "Switch 2," as used herein, refers to a protein domain of a
Ras protein (e.g. K-Ras) formed by residues corresponding to
residues 60-76 of K-Ras (e.g. K-Ras Switch 2 refers to residues
60-76 of K-Ras). A "Switch 2 Binding Region" is a region of a Ras
protein (e.g. K-Ras) that is formed by amino acid residues that
contact at least a portion of Switch 2 when Ras is bound to GTP. A
"Switch 2-Binding Pocket" or "S2BP" is a cavity bound (the limits
or boundaries of which are made), at least in part, by the amino
acid residues that form Switch 2 and the Switch 2 Binding Region.
In some embodiments, a "Switch 2-Binding Pocket" or "S2BP" is a
cavity, in the GDP bound form of Ras (e.g. K-Ras), bound (the
limits or boundaries of which are made), at least in part, by the
amino acid residues that form Switch 2 and the Switch 2 Binding
Region.
[0174] In some embodiments, the Switch 2-Binding Pocket is bound at
least in part by one or more of V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and/or I100 of K-Ras or
equivalent residues in homologous, related (e.g. H-Ras, N-Ras), or
mutant Ras proteins. In some embodiments, the S2BP is bound at
least in part by an amino acid residue shown to be interacting with
the JO-01-189cbut compound in FIG. 4B or contributing to the
surface contacting the JO-01-189cbut compound in FIG. 4A. In some
embodiments, the S2BP is bound at least in part by the left portion
of the proximity contour in FIG. 7 or 8. A compound as described
herein (including embodiments, examples, and compounds of Table 1,
2, 3, 4, or 5), which binds to amino acids that form or contacts
amino acids that form the Switch 2-Binding Pocket is a "Switch
2-Binding Pocket binding compound" and a moiety of a compound that
binds to amino acids that form or contacts amino acids that form
the Switch 2-Binding Pocket is a "Switch 2-Binding Pocket binding
moiety".
[0175] In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts one amino acid that forms the Switch 2-Binding Pocket. In
some embodiments, a Switch 2-Binding Pocket binding compound or
Switch 2-Binding Pocket binding moiety binds or contacts multiple
amino acids that form the Switch 2-Binding Pocket. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts one K-Ras amino
acid selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68,
Y71, M72, Y96, Q99, and I100. In some embodiments, a Switch
2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts multiple K-Ras amino acids
selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71,
M72, Y96, Q99, and I100. In some embodiments, a Switch 2-Binding
Pocket binding compound or Switch 2-Binding Pocket binding moiety
binds or contacts two K-Ras amino acids selected from V7, V9, G10,
P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In
some embodiments, a Switch 2-Binding Pocket binding compound or
Switch 2-Binding Pocket binding moiety binds or contacts three
K-Ras amino acids selected from V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts four K-Ras amino acids selected
from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96,
Q99, and I100. In some embodiments, a Switch 2-Binding Pocket
binding compound or Switch 2-Binding Pocket binding moiety binds or
contacts five K-Ras amino acids selected from V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts six K-Ras amino
acids selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68,
Y71, M72, Y96, Q99, and I100. In some embodiments, a Switch
2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts seven K-Ras amino acids selected
from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96,
Q99, and I100. In some embodiments, a Switch 2-Binding Pocket
binding compound or Switch 2-Binding Pocket binding moiety binds or
contacts eight K-Ras amino acids selected from V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts nine K-Ras amino
acids selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68,
Y71, M72, Y96, Q99, and I100. In some embodiments, a Switch
2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts ten K-Ras amino acids selected
from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96,
Q99, and I100. In some embodiments, a Switch 2-Binding Pocket
binding compound or Switch 2-Binding Pocket binding moiety binds or
contacts eleven K-Ras amino acids selected from V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts twelve K-Ras
amino acids selected from V7, V9, G10, P34, T58, G60, Q61, E62,
E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts thirteen K-Ras amino acids
selected from V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71,
M72, Y96, Q99, and I100. In some embodiments, a Switch 2-Binding
Pocket binding compound or Switch 2-Binding Pocket binding moiety
binds or contacts fourteen K-Ras amino acids selected from V7, V9,
G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and
I100. In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts fifteen K-Ras amino acids selected from V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100.
[0176] In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts one amino acid selected from amino acids in a mutant
K-Ras, related Ras (H-Ras, N-Ras), or homolog of K-Ras
corresponding to K-Ras residues V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts multiple K-Ras amino acids
selected from amino acids in a mutant K-Ras, related Ras (H-Ras,
N-Ras), or homolog of K-Ras corresponding to K-Ras residues V7, V9,
G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and
I100. In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts two K-Ras amino acids selected from amino acids in a
mutant K-Ras, related Ras (H-Ras, N-Ras), or homolog of K-Ras
corresponding to K-Ras residues V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts three K-Ras amino acids selected
from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras), or
homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts four K-Ras amino
acids selected from amino acids in a mutant K-Ras, related Ras
(H-Ras, N-Ras), or homolog of K-Ras corresponding to K-Ras residues
V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99,
and I100. In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts five K-Ras amino acids selected from amino acids in a
mutant K-Ras, related Ras (H-Ras, N-Ras), or homolog of K-Ras
corresponding to K-Ras residues V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts six K-Ras amino acids selected
from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras), or
homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts seven K-Ras amino
acids selected from amino acids in a mutant K-Ras, related Ras
(H-Ras, N-Ras), or homolog of K-Ras corresponding to K-Ras residues
V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99,
and I100. In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts eight K-Ras amino acids selected from amino acids in a
mutant K-Ras, related Ras (H-Ras, N-Ras), or homolog of K-Ras
corresponding to K-Ras residues V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts nine K-Ras amino acids selected
from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras), or
homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts ten K-Ras amino
acids selected from amino acids in a mutant K-Ras, related Ras
(H-Ras, N-Ras), or homolog of K-Ras corresponding to K-Ras residues
V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99,
and I100. In some embodiments, a Switch 2-Binding Pocket binding
compound or Switch 2-Binding Pocket binding moiety binds or
contacts eleven K-Ras amino acids selected from amino acids in a
mutant K-Ras, related Ras (H-Ras, N-Ras), or homolog of K-Ras
corresponding to K-Ras residues V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts twelve K-Ras amino acids selected
from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras), or
homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some
embodiments, a Switch 2-Binding Pocket binding compound or Switch
2-Binding Pocket binding moiety binds or contacts thirteen K-Ras
amino acids selected from amino acids in a mutant K-Ras, related
Ras (H-Ras, N-Ras), or homolog of K-Ras corresponding to K-Ras
residues V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72,
Y96, Q99, and I100. In some embodiments, a Switch 2-Binding Pocket
binding compound or Switch 2-Binding Pocket binding moiety binds or
contacts fourteen K-Ras amino acids selected from amino acids in a
mutant K-Ras, related Ras (H-Ras, N-Ras), or homolog of K-Ras
corresponding to K-Ras residues V7, V9, G10, P34, T58, G60, Q61,
E62, E63, R68, Y71, M72, Y96, Q99, and I100. In some embodiments, a
Switch 2-Binding Pocket binding compound or Switch 2-Binding Pocket
binding moiety binds or contacts fifteen K-Ras amino acids selected
from amino acids in a mutant K-Ras, related Ras (H-Ras, N-Ras), or
homolog of K-Ras corresponding to K-Ras residues V7, V9, G10, P34,
T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and I100.
II. Compounds
[0177] In a first aspect is provided a compound which is capable of
reacting with an amino acid residue of a Ras protein (including
K-Ras, N-Ras and H-Ras proteins). For example, the compound may
contact a residue of a Ras protein Switch 2 binding pocket. For
example, where the residue of the Switch 2 binding pocket that
contacts the compound may be V7, V9, G10, P34, T58, G60, Q61, E62,
E63, R68, Y71, M72, Y96, Q99, or I100. In some embodiments, the
compound interacts with at least one of G60, E62, or E63.
[0178] In some embodiments, the compound covalently reacts with an
amino acid residue of the Ras protein to form a covalent bond (e.g.
reversible or irreversible). For example the amino acid residue is
a cysteine, aspartate, lysine, tyrosine or glutamate residue of the
Ras protein. In some embodiments, the amino acid residue is a
cysteine residue, for example a G12C or G13C residue of a K-Ras
protein. In some embodiments, the amino acid residue is an
aspartate residue, for example a G12D or G13D residue of a K-Ras
protein.
[0179] In some embodiments, a compound having the formula
R.sup.1-L.sup.1-L.sup.2-L.sup.3-E is provided. R.sup.1 is a Switch
2-Binding Pocket binding moiety. L.sup.1 is a bond or a divalent
radical chemical linker. L.sup.2 is a bond or a divalent radical
chemical linker. L.sup.3 is a bond or a divalent radical chemical
linker. E is an electrophilic chemical moiety capable of forming a
covalent bond with a Ras cysteine residue or a Ras aspartate
residue. In some embodiments, Ras is a K-Ras. In some embodiments,
the compound contacts a residue of K-Ras Switch 2. In some
embodiments, wherein the compound contacts K-Ras, R.sup.1 contacts
V7, V9, G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99,
or I100. For example, R.sup.1 contacts at least one of G60, E62, or
E63. In some embodiments, the compound does not contact the
residues of K-Ras that contact GTP. In some embodiments, the
compound does not contact the residues of K-Ras that contact the
guanine of GTP or GDP. In some embodiments, the compound does not
contact the residues of K-Ras that contact GDP. In some
embodiments, the compound forms an irreversible covalent bond with
a K-Ras cysteine residue. In some embodiments, the compound forms a
reversible covalent bond with a K-Ras cysteine residue. In some
embodiments, the compound forms an irreversible covalent bond with
a K-Ras aspartate residue. In some embodiments, the compound forms
a reversible covalent bond with a K-Ras aspartate residue. In some
embodiments, R.sup.1 contacts residues that contact Switch 2 in the
GTP bound form of K-Ras. In some embodiments, R.sup.1 contacts
residues that contact Switch 2 in the GDP bound form of K-Ras. In
some embodiments, R.sup.1 is hydrogen, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. In some embodiments, R.sup.1 is
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl. In some embodiments,
R.sup.1 is substituted or unsubstituted aryl or substituted or
unsubstituted heteroaryl. In some embodiments, R.sup.1 is
R.sup.3-substituted or unsubstituted aryl or R.sup.3-substituted or
unsubstituted heteroaryl. In some embodiments, R.sup.1 is
R.sup.3-substituted or unsubstituted fused ring aryl. In some
embodiments, R.sup.1 is R.sup.3-substituted or unsubstituted fused
ring heteroaryl.
[0180] In some embodiments, R.sup.1 is
##STR00034## ##STR00035##
[0181] In some embodiments R.sup.1 is R.sup.3-substituted
pyridinyl, R.sup.3-substituted pyrimidinyl, R.sup.3-substituted
thiophenyl, R.sup.3-substituted furanyl, R.sup.3-substituted
indolyl, R.sup.3-substituted benzoxadiazolyl, R.sup.3-substituted
benzodioxolyl, R.sup.3-substituted benzodioxanyl,
R.sup.3-substituted thianaphthanyl, R.sup.3-substituted
pyrrolopyridinyl, R.sup.3-substituted indazolyl,
R.sup.3-substituted quinolinyl, R.sup.3-substituted quinoxalinyl,
R.sup.3-substituted pyridopyrazinyl, R.sup.3-substituted
quinazolinonyl, R.sup.3-substituted benzoisoxazolyl,
R.sup.3-substituted imidazopyridinyl, R.sup.3-substituted
benzofuranyl, R.sup.3-substituted benzothiophenyl,
R.sup.3-substituted phenyl, R.sup.3-substituted naphthyl,
R.sup.3-substituted biphenyl, R.sup.3-substituted pyrrolyl,
R.sup.3-substituted pyrazolyl, R.sup.3-substituted imidazolyl,
R.sup.3-substituted pyrazinyl, R.sup.3-substituted oxazolyl,
R.sup.3-substituted isoxazolyl, R.sup.3-substituted thiazolyl,
R.sup.3-substituted furylthienyl, R.sup.3-substituted pyridyl,
R.sup.3-substituted pyrimidyl, R.sup.3-substituted benzothiazolyl,
R.sup.3-substituted purinyl, R.sup.3-substituted benzimidazolyl,
R.sup.3-substituted isoquinolyl, R.sup.3-substituted thiadiazolyl,
R.sup.3-substituted oxadiazolyl, R.sup.3-substituted pyrrolyl,
R.sup.3-substituted diazolyl, R.sup.3-substituted triazolyl,
R.sup.3-substituted tetrazolyl, R.sup.3-substituted
benzothiadiazolyl, R.sup.3-substituted isothiazolyl,
R.sup.3-substituted pyrazolopyrimidinyl, R.sup.3-substituted
pyrrolopyrimidinyl, R.sup.3-substituted benzotriazolyl, or
R.sup.3-substituted quinolyl. In some embodiments R.sup.1 is
substituted pyridinyl, substituted pyrimidinyl, substituted
thiophenyl, substituted furanyl, substituted indolyl, substituted
benzoxadiazolyl, substituted benzodioxolyl, substituted
benzodioxanyl, substituted thianaphthanyl, substituted
pyrrolopyridinyl, substituted indazolyl, substituted quinolinyl,
substituted quinoxalinyl, substituted pyridopyrazinyl, substituted
quinazolinonyl, substituted benzoisoxazolyl, substituted
imidazopyridinyl, substituted benzofuranyl, substituted
benzothiophenyl, substituted phenyl, substituted naphthyl,
substituted biphenyl, substituted pyrrolyl, substituted pyrazolyl,
substituted imidazolyl, substituted pyrazinyl, substituted
oxazolyl, substituted isoxazolyl, substituted thiazolyl,
substituted furylthienyl, substituted pyridyl, substituted
pyrimidyl, substituted benzothiazolyl, substituted purinyl,
substituted benzimidazolyl, substituted isoquinolyl, substituted
thiadiazolyl, substituted oxadiazolyl, substituted pyrrolyl,
substituted diazolyl, substituted triazolyl, substituted
tetrazolyl, substituted benzothiadiazolyl, substituted
isothiazolyl, substituted pyrazolopyrimidinyl, substituted
pyrrolopyrimidinyl, substituted benzotriazolyl, or substituted
quinolyl.
[0182] In some embodiments R.sup.1 is unsubstituted pyridinyl,
unsubstituted pyrimidinyl, unsubstituted thiophenyl, unsubstituted
furanyl, unsubstituted indolyl, unsubstituted benzoxadiazolyl,
unsubstituted benzodioxolyl, unsubstituted benzodioxanyl,
unsubstituted thianaphthanyl, unsubstituted pyrrolopyridinyl,
unsubstituted indazolyl, unsubstituted quinolinyl, unsubstituted
quinoxalinyl, unsubstituted pyridopyrazinyl, unsubstituted
quinazolinonyl, unsubstituted benzoisoxazolyl, unsubstituted
imidazopyridinyl, unsubstituted benzofuranyl, unsubstituted
benzothiophenyl, unsubstituted phenyl, unsubstituted naphthyl,
unsubstituted biphenyl, unsubstituted pyrrolyl, unsubstituted
pyrazolyl, unsubstituted imidazolyl, unsubstituted pyrazinyl,
unsubstituted oxazolyl, unsubstituted isoxazolyl, unsubstituted
thiazolyl, unsubstituted furylthienyl, unsubstituted pyridyl,
unsubstituted pyrimidyl, unsubstituted benzothiazolyl,
unsubstituted purinyl, unsubstituted benzimidazolyl, unsubstituted
isoquinolyl, unsubstituted thiadiazolyl, unsubstituted oxadiazolyl,
unsubstituted pyrrolyl, unsubstituted diazolyl, unsubstituted
triazolyl, unsubstituted tetrazolyl, unsubstituted
benzothiadiazolyl, unsubstituted isothiazolyl, unsubstituted
pyrazolopyrimidinyl, unsubstituted pyrrolopyrimidinyl,
unsubstituted benzotriazolyl, or unsubstituted quinolyl.
[0183] R.sup.3 is independently hydrogen, oxo, halogen, --CX.sub.3,
--CN, --SO.sub.2Cl, --SO.sub.nR.sup.10, --SO.sub.vNR.sup.7R.sup.8,
--NHNH.sub.2, --ONR.sup.7R.sup.8, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7R.sup.8, --N(O).sub.m, --NR.sup.7R.sup.8,
--C(O)R.sup.9, --C(O)--OR.sup.9, --C(O)NR.sup.7R.sup.8,
--OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl. In some embodiments,
R.sup.3 is independently hydrogen, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two adjacent R.sup.3 substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl. Two R.sup.3 substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl. In
some embodiments, R.sup.3 is methyl, --Cl, --NH.sub.2, --I, --CCH,
--CH.sub.2CH.sub.2OH, --OCH.sub.2CCH, --CF.sub.3, --OCH.sub.3,
--OH, --CH.sub.2CH.sub.3, --NHS(O).sub.2CH.sub.3,
--CH.sub.2NH.sub.2, --Br, isoxazolyl, --NHC(O)OC(CH.sub.3).sub.3,
p-chlorophenyl, thiophenyl, --F, pyrazolyl, --CH.sub.2OH,
--C(O)NHCH.sub.2CH.sub.2OH, --OCH.sub.2CH.sub.2OH,
--S(O).sub.2NH.sub.2, tetrazolyl, --CHCH.sub.3OH, --C(O)CH.sub.3,
--C(O)H, --OCH.sub.3, --C(O)OH, --C(O)OCH.sub.3, --C(O)NH.sub.2,
--N(CH.sub.3).sub.2, --CH.sub.2NH.sub.2, --CH.sub.2NHC(O)CH.sub.3,
pyrrolidinyl, --OCH.sub.2CH.sub.2NH.sub.2, --C(O)N(CH.sub.3).sub.2,
NHCH.sub.3, --NHC(O)CH.sub.3, --CN, --C(O)OCH.sub.3, or
##STR00036##
[0184] R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl. In some
embodiments, R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. R.sup.7 and R.sup.8 substituents
bonded to the same nitrogen atom may optionally be joined to form a
substituted or unsubstituted heterocycloalkyl or substituted or
unsubstituted heteroaryl.
[0185] The symbol m is independently 1 or 2. The symbol v is
independently 1 or 2. The symbol n is independently an integer from
0 to 4. The symbol X is independently Cl, --Br, --I, or --F. In
some embodiments v is 1. In other embodiments, v is 2. In some
embodiments m is 1. In some embodiments m is 2. In some embodiments
n is 0. In some embodiments n is 1. In some embodiments n is 2. In
some embodiments n is 3. In some embodiments n is 4. In some
embodiments, X is --Cl. In some embodiments, X is --Br. In some
embodiments, X is --I. In some embodiments, X is --F.
[0186] The symbol e2 is independently an integer from 0 to 2. The
symbol e3 is independently an integer from 0 to 3. The symbol e4 is
independently an integer from 0 to 4. The symbol e5 is
independently an integer from 0 to 5. The symbol e6 is
independently an integer from 0 to 6. The symbol e7 is
independently an integer from 0 to 7. The symbol f2 is
independently an integer from 0 to 2. The symbol f6 is
independently an integer from 0 to 6. The symbol f7 is
independently an integer from 0 to 7. The symbol f8 is
independently an integer from 0 to 8. The symbol f9 is
independently an integer from 0 to 9. The symbol f10 is
independently an integer from 0 to 10. The symbol f12 is
independently an integer from 0 to 12. The symbol f14 is
independently an integer from 0 to 14.
[0187] L.sup.1, L.sup.2 and L.sup.3 are independently a bond,
--NR.sup.2C--, --O--, --S--, C(O)--, --S(O)--, --S(O).sub.2--,
substituted or unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, substituted or unsubstituted heteroarylene;
or a substituted or unsubstituted spirocyclic linker. In some
embodiments, L.sup.1 is a bond. In some embodiments, L.sup.2 is a
bond. In some embodiments, L.sup.3 is a bond. In some embodiments,
L.sup.1 is substituted or unsubstituted alkylene, substituted or
unsubstituted heteroalkylene, substituted or unsubstituted
cycloalkylene, substituted or unsubstituted heterocycloalkylene,
substituted or unsubstituted arylene, substituted or unsubstituted
heteroarylene; or a substituted or unsubstituted spirocyclic
linker. In some embodiments, L.sup.2 is substituted or
unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, substituted or unsubstituted heteroarylene;
or a substituted or unsubstituted spirocyclic linker. In some
embodiments, L.sup.3 is substituted or unsubstituted alkylene,
substituted or unsubstituted heteroalkylene, substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene; or a substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.1 is
--NR.sup.2C--. In some embodiments, L.sup.1 is --O--. In some
embodiments, L.sup.1 is --S--. In some embodiments, L.sup.1 is
--C(O)--. In some embodiments, L.sup.1 is --S(O)--. In some
embodiments, L.sup.1 is --S(O).sub.2--. In some embodiments,
L.sup.2 is --NR.sup.2C--. In some embodiments, L.sup.2 is --O--. In
some embodiments, L.sup.2 is --S--. In some embodiments, L.sup.2 is
--C(O)--. In some embodiments, L.sup.2 is --S(O)--. In some
embodiments, L.sup.2 is --S(O).sub.2--. In some embodiments,
L.sup.3 is --NR.sup.2C--. In some embodiments, L.sup.3 is --O--. In
some embodiments, L.sup.3 is --S--. In some embodiments, L.sup.3 is
--C(O)--. In some embodiments, L.sup.3 is --S(O)--. In some
embodiments, L.sup.3 is --S(O).sub.2--. In some embodiments,
L.sup.1 is independently CR.sup.2AR.sup.2B--. In some embodiments,
L.sup.2 is independently --CR.sup.2AR.sup.2B--. In some
embodiments, L.sup.3 is independently --CR.sup.2AR.sup.2B--. In
some embodiments, L.sup.1 is independently
##STR00037##
In some embodiments, L.sup.2 is independently
##STR00038##
In some embodiments, L.sup.3 is independently
##STR00039##
In some embodiments, L.sup.1 is independently
##STR00040##
In some embodiments, L.sup.2 is independently
##STR00041##
In some embodiments, L.sup.3 is independently
##STR00042##
In some embodiments, L.sup.1 is independently
##STR00043##
In some embodiments, L.sup.2 is independently
##STR00044##
In some embodiments, L.sup.3 is independently
##STR00045##
[0188] In some embodiments, L.sup.1 is independently substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene, or substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.1 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.1 is
independently
##STR00046##
In some embodiments, L.sup.2 is independently substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene, or substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.2 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.2 is
independently
##STR00047##
[0189] In some embodiments, L.sup.3 is independently substituted or
unsubstituted cycloalkylene, substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted arylene,
substituted or unsubstituted heteroarylene, or substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.3 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker. In some embodiments, L.sup.3 is
independently
##STR00048##
[0190] In some embodiments, L.sup.2 is independently a bond,
L.sup.3 is independently a bond, and L.sup.1 is independently
##STR00049## ##STR00050## ##STR00051## ##STR00052## ##STR00053##
##STR00054##
In some embodiments, L.sup.1 is independently
##STR00055## ##STR00056## ##STR00057## ##STR00058## ##STR00059##
##STR00060##
In some embodiments, L.sup.2 is independently
##STR00061## ##STR00062## ##STR00063## ##STR00064## ##STR00065##
##STR00066##
In some embodiments, L.sup.3 is independently
##STR00067## ##STR00068## ##STR00069## ##STR00070## ##STR00071##
##STR00072##
[0191] R.sup.2A and R.sup.2B are independently hydrogen, oxo,
halogen, --CX.sup.a.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n1R.sup.10a, --SO.sub.v1NR.sup.7aR.sup.8a, --NHNH.sub.2,
--ONR.sup.7aR.sup.8a, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7aR.sup.8a, --N(O).sub.m1, --NR.sup.7aR.sup.8a,
--C(O)R.sup.9a, --C(O)--OR.sup.9a, --C(O)NR.sup.7aR.sup.8a,
OR.sup.10a, --NR.sup.7aSO.sub.2R.sup.10a,
--NR.sup.7aC.dbd.(O)R.sup.9a, --NR.sup.7aC(O)--OR.sup.9a,
--NR.sup.7aOR.sup.9a, --OCX.sup.a.sub.3, --OCHX.sup.a.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl. R.sup.2A and
R.sup.2B substituents bonded to the same atom may optionally be
joined to form a substituted or unsubstituted cycloalkyl or
substituted or unsubstituted heterocycloalkyl. In some embodiments,
R.sup.2A is independently hydrogen, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. In some embodiments, R.sup.2B is
independently hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl.
[0192] R.sup.7a, R.sup.8a, R.sup.9a and R.sup.10a are independently
hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl. R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl. In
some embodiments, R.sup.7a, R.sup.8a, R.sup.9a and R.sup.10a are
independently hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl.
[0193] R.sup.2C is independently hydrogen, oxo,
halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl. Two adjacent
R.sup.2C substituents may optionally be joined to form a
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl. Two R.sup.2C
substituents bonded to the same atom may optionally be joined to
form a substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl. In some embodiments, R.sup.2C is
independently hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl.
[0194] R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, NHNH.sub.2, ONH.sub.2,
NHC.dbd.(O)NHNH.sub.2, NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl. R.sup.7c and
R.sup.8c substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl. In
some embodiments, R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are
independently hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl.
[0195] The symbols m1, m3, v1, and v3 are independently an integer
from 1 to 2. The symbols n1 and n3 are independently an integer
from 0 to 4. The symbols X.sup.a and X.sup.c are independently
--Cl, --Br, --I, or --F. The symbol v1 is independently 1 or 2. In
some embodiments, v1 is 1. In some embodiments, v1 is 2. The symbol
m1 is independently an integer from 1 to 2. In some embodiments, m1
is 1. In some embodiments, m1 is 2. The symbol n1 is independently
an integer from 0 to 4. In some embodiments, n1 is 0. In some
embodiments, n1 is 1. In some embodiments, n1 is 2. In some
embodiments, n1 is 3. In some embodiments, n1 is 4. X.sup.a is
independently --Cl, --Br, --I, or --F. In some embodiments, X.sup.a
is --Cl. In some embodiments, X.sup.a is --Br. In some embodiments,
X.sup.a is --I. In some embodiments, X.sup.a is --F. The symbol v3
is independently 1 or 2. In some embodiments, v3 is 1. In some
embodiments, v3 is 2. The symbol m3 is independently an integer
from 1 to 2. In some embodiments, m3 is 1. In some embodiments, m3
is 2. The symbol n3 is independently an integer from 0 to 4. In
some embodiments, n3 is 0. In some embodiments, n3 is 1. In some
embodiments, n3 is 2. In some embodiments, n3 is 3. In some
embodiments, n3 is 4. X.sup.c is independently --Cl, --Br, --I, or
--F. In some embodiments, X.sup.c is --Cl. In some embodiments,
X.sup.c is --Br. In some embodiments, X.sup.c is --I. In some
embodiments, X.sup.c is --F. The symbol z is independently an
integer from 0 to 10. In some embodiments, z is 0. In some
embodiments, z is 1. In some embodiments, z is 2. In some
embodiments, z is 3. In some embodiments, z is 4. In some
embodiments, z is 5. In some embodiments, z is 6. In some
embodiments, z is 7. In some embodiments, z is 8. In some
embodiments, z is 9. In some embodiments, z is 10.
[0196] In some embodiments, E is an electrophilic chemical moiety
capable of forming a covalent bond with a K-Ras cysteine residue.
In some embodiments, E is an electrophilic chemical moiety capable
of forming a covalent bond with a K-Ras aspartate residue. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras cysteine sidechain. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras aspartate sidechain. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras cysteine sulfur. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras aspartate sidechain oxygen. In
some embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras residue 12 cysteine. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras residue 12 asparate. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras residue 13 cysteine. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras residue 13 asparate. In some
embodiments, E is an electrophilic chemical moiety capable of
forming a covalent bond with a K-Ras residue near the Switch
2-Binding Pocket in the folded protein. In some embodiments, E is
an electrophilic chemical moiety capable of forming a covalent bond
with a K-Ras residue in the Switch 2-Binding Pocket in the folded
protein. In some embodiments, E is an electrophilic chemical moiety
capable of forming an irreversible covalent bond with a K-Ras
residue. In some embodiments, E is an electrophilic chemical moiety
capable of forming a reversible covalent bond with a K-Ras
residue.
[0197] In some embodiments, E comprises a substituted or
unsubstituted vinyl sulfone moiety, substituted or unsubstituted
vinyl sulfonamide moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety,
##STR00073## ##STR00074## ##STR00075## ##STR00076## ##STR00077##
##STR00078## ##STR00079## ##STR00080## ##STR00081## ##STR00082##
##STR00083## ##STR00084## ##STR00085##
[0198] In some embodiments, E is a substituted or unsubstituted
vinyl sulfone moiety, substituted or unsubstituted vinyl
sulfonamide moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety,
##STR00086## ##STR00087## ##STR00088## ##STR00089## ##STR00090##
##STR00091## ##STR00092## ##STR00093## ##STR00094## ##STR00095##
##STR00096##
[0199] In some embodiments, E comprises an unsubstituted vinyl
sulfone moiety, unsubstituted vinyl sulfonamide moiety,
unsubstituted fluoro(C.sub.1-C.sub.4)alkylketone moiety,
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
unsubstituted acrylamide moiety, unsubstituted disulfide moiety,
unsubstituted thiol moiety, unsubstituted phosphonate moiety,
unsubstituted aldehyde moiety, unsubstituted enone moiety,
unsubstituted diazomethylketone moiety, unsubstituted
diazomethylamide moiety, unsubstituted cyanocyclopropyl carboxamide
moiety, unsubstituted epoxide moiety, unsubstituted epoxyketone
moiety, unsubstituted epoxyamide moiety, unsubstituted aryl
aldehyde moiety, unsubstituted aryl dialdehyde moiety,
unsubstituted dialdehyde moiety, unsubstituted nitrogen mustard
moiety, unsubstituted propargyl moiety, or unsubstituted
propargylamide moiety. In some embodiments, E is an unsubstituted
vinyl sulfone moiety, unsubstituted vinyl sulfonamide moiety,
unsubstituted fluoro(C.sub.1-C.sub.4)alkylketone moiety,
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
unsubstituted acrylamide moiety, unsubstituted disulfide moiety,
unsubstituted thiol moiety, unsubstituted phosphonate moiety,
unsubstituted aldehyde moiety, unsubstituted enone moiety,
unsubstituted diazomethylketone moiety, unsubstituted
diazomethylamide moiety, unsubstituted cyanocyclopropyl carboxamide
moiety, unsubstituted epoxide moiety, unsubstituted epoxyketone
moiety, unsubstituted epoxyamide moiety, unsubstituted aryl
aldehyde moiety, unsubstituted aryl dialdehyde moiety,
unsubstituted dialdehyde moiety, unsubstituted nitrogen mustard
moiety, unsubstituted propargyl moiety, or unsubstituted
propargylamide moiety.
[0200] R.sup.13 is independently hydrogen, oxo, halogen,
--CX.sup.b.sub.3, --CN, --SO.sub.2Cl, --SO.sub.rR.sup.17,
--SO.sub.pNR.sup.14R.sup.15, --NHNH.sub.2, --ONR.sup.14R.sup.15,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.14R.sup.15,
--N(O).sub.q, --NR.sup.14R.sup.15, --C(O)R.sup.16,
--C(O)--OR.sup.16, --C(O)NR.sup.14R.sup.15, OR.sup.17,
--NR.sup.14SO.sub.2R.sup.17, NR.sup.14C(O)R.sup.16,
--NR.sup.14C(O)--OR.sup.16, --NR.sup.14OR.sup.16,
--OCX.sup.b.sub.3, --OCHX.sup.b.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two adjacent R.sup.13 substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl. Two R.sup.13 substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl. In
some embodiments, R.sup.13 is hydrogen. In some embodiments,
R.sup.13 is methyl. In some embodiments, R.sup.13 is ethyl. In some
embodiments, R.sup.13 is --CN. In some embodiments, R.sup.13 is
--NO.sub.2.
[0201] R.sup.14, R.sup.15, R.sup.16, and R.sup.17 are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl. R.sup.14 and
R.sup.15 substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl. In
some embodiments, R.sup.14, R.sup.15, R.sup.16, and R.sup.17 are
independently hydrogen, substituted or unsubstituted alkyl,
substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. The symbol p is independently 1 or 2.
In some embodiments, p is 1. In some embodiments, p is 2. The
symbol q is independently an integer from 1 to 2. In some
embodiments, q is 1. In some embodiments, q is 2. The symbol r is
independently an integer from 0 to 4. In some embodiments, r is 0.
In some embodiments, r is 1. In some embodiments, r is 2. In some
embodiments, r is 3. In some embodiments, r is 4. X.sup.b is
independently --Cl, --Br, --I, or --F. In some embodiments, X.sup.b
is --Cl. In some embodiments, X.sup.b is --Br. In some embodiments,
X.sup.b is --I. In some embodiments, X.sup.b is --F.
[0202] In some embodiments of the compounds provided herein,
R.sup.1 is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.20-substituted or
unsubstituted alkyl, R.sup.20-substituted or unsubstituted
heteroalkyl, R.sup.20-substituted or unsubstituted cycloalkyl,
R.sup.20-substituted or unsubstituted heterocycloalkyl,
R.sup.20-substituted or unsubstituted aryl, or R.sup.20-substituted
or unsubstituted heteroaryl.
[0203] R.sup.20 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.21-substituted or unsubstituted alkyl, R.sup.21-substituted
or unsubstituted heteroalkyl, R.sup.21-substituted or unsubstituted
cycloalkyl, R.sup.21-substituted or unsubstituted heterocycloalkyl,
R.sup.21-substituted or unsubstituted aryl, or R.sup.21-substituted
or unsubstituted heteroaryl.
[0204] R.sup.21 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.22-substituted or unsubstituted alkyl, R.sup.22-substituted
or unsubstituted heteroalkyl, R.sup.22-substituted or unsubstituted
cycloalkyl, R.sup.22-substituted or unsubstituted heterocycloalkyl,
R.sup.22-substituted or unsubstituted aryl, or R.sup.22-substituted
or unsubstituted heteroaryl.
[0205] In some embodiments of the compounds provided herein,
R.sup.2 is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.23-substituted or
unsubstituted alkyl, R.sup.23-substituted or unsubstituted
heteroalkyl, R.sup.23-substituted or unsubstituted cycloalkyl,
R.sup.23-substituted or unsubstituted heterocycloalkyl,
R.sup.23-substituted or unsubstituted aryl, or R.sup.23-substituted
or unsubstituted heteroaryl.
[0206] R.sup.23 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.24-substituted or unsubstituted alkyl, R.sup.24-substituted
or unsubstituted heteroalkyl, R.sup.24-substituted or unsubstituted
cycloalkyl, R.sup.24-substituted or unsubstituted heterocycloalkyl,
R.sup.24-substituted or unsubstituted aryl, or R.sup.24-substituted
or unsubstituted heteroaryl.
[0207] R.sup.24 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.25-substituted or unsubstituted alkyl, R.sup.25-substituted
or unsubstituted heteroalkyl, R.sup.25-substituted or unsubstituted
cycloalkyl, R.sup.25-substituted or unsubstituted heterocycloalkyl,
R.sup.25-substituted or unsubstituted aryl, or R.sup.25-substituted
or unsubstituted heteroaryl.
[0208] In some embodiments of the compounds provided herein,
R.sup.2A is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.23A-substituted or
unsubstituted alkyl, R.sup.23A-substituted or unsubstituted
heteroalkyl, R.sup.23A-substituted or unsubstituted cycloalkyl,
R.sup.23A-substituted or unsubstituted heterocycloalkyl,
R.sup.23A-substituted or unsubstituted aryl, or
R.sup.23A-substituted or unsubstituted heteroaryl.
[0209] R.sup.23A is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.24A-substituted or unsubstituted alkyl, R.sup.24A-substituted
or unsubstituted heteroalkyl, R.sup.24A-substituted or
unsubstituted cycloalkyl, R.sup.24A-substituted or unsubstituted
heterocycloalkyl, R.sup.24A-substituted or unsubstituted aryl, or
R.sup.24A-substituted or unsubstituted heteroaryl.
[0210] R.sup.24A is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.25A-substituted or unsubstituted alkyl, R.sup.25A-substituted
or unsubstituted heteroalkyl, R.sup.25A-substituted or
unsubstituted cycloalkyl, R.sup.25A-substituted or unsubstituted
heterocycloalkyl, R.sup.25A-substituted or unsubstituted aryl, or
R.sup.25A-substituted or unsubstituted heteroaryl.
[0211] In some embodiments of the compounds provided herein,
R.sup.2B is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.23B-substituted or
unsubstituted alkyl, R.sup.23B-substituted or unsubstituted
heteroalkyl, R.sup.23B-substituted or unsubstituted cycloalkyl,
R.sup.23B-substituted or unsubstituted heterocycloalkyl,
R.sup.23B-substituted or unsubstituted aryl, or
R.sup.23B-substituted or unsubstituted heteroaryl.
[0212] R.sup.23B is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.24B-substituted or unsubstituted alkyl, R.sup.24B-substituted
or unsubstituted heteroalkyl, R.sup.24B-substituted or
unsubstituted cycloalkyl, R.sup.24B-substituted or unsubstituted
heterocycloalkyl, R.sup.24B-substituted or unsubstituted aryl, or
R.sup.24B-substituted or unsubstituted heteroaryl.
[0213] R.sup.24B is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.25B-substituted or unsubstituted alkyl, R.sup.25B-substituted
or unsubstituted heteroalkyl, R.sup.25B-substituted or
unsubstituted cycloalkyl, R.sup.25B-substituted or unsubstituted
heterocycloalkyl, R.sup.25B-substituted or unsubstituted aryl, or
R.sup.25B-substituted or unsubstituted heteroaryl.
[0214] In some embodiments of the compounds provided herein,
R.sup.2C is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.23C-substituted or
unsubstituted alkyl, R.sup.23C-substituted or unsubstituted
heteroalkyl, R.sup.23C-substituted or unsubstituted cycloalkyl,
R.sup.23C-substituted or unsubstituted heterocycloalkyl,
R.sup.23C-substituted or unsubstituted aryl, or
R.sup.23C-substituted or unsubstituted heteroaryl.
[0215] R.sup.23C is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.24C-substituted or unsubstituted alkyl, R.sup.24C-substituted
or unsubstituted heteroalkyl, R.sup.24C-substituted or
unsubstituted cycloalkyl, R.sup.24C-substituted or unsubstituted
heterocycloalkyl, R.sup.24C-substituted or unsubstituted aryl, or
R.sup.24C-substituted or unsubstituted heteroaryl.
[0216] R.sup.24C is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.25C-substituted or unsubstituted alkyl, R.sup.25C-substituted
or unsubstituted heteroalkyl, R.sup.25C-substituted or
unsubstituted cycloalkyl, R.sup.25C-substituted or unsubstituted
heterocycloalkyl, R.sup.25C-substituted or unsubstituted aryl, or
R.sup.25C-substituted or unsubstituted heteroaryl.
[0217] In some embodiments of the compounds provided herein,
R.sup.3 is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.26-substituted or
unsubstituted alkyl, R.sup.26-substituted or unsubstituted
heteroalkyl, R.sup.26-substituted or unsubstituted cycloalkyl,
R.sup.26-substituted or unsubstituted heterocycloalkyl,
R.sup.26-substituted or unsubstituted aryl, or R.sup.26-substituted
or unsubstituted heteroaryl.
[0218] R.sup.26 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.27-substituted or unsubstituted alkyl, R.sup.27-substituted
or unsubstituted heteroalkyl, R.sup.27-substituted or unsubstituted
cycloalkyl, R.sup.27substituted or unsubstituted heterocycloalkyl,
R.sup.27-substituted or unsubstituted aryl, or R.sup.27-substituted
or unsubstituted heteroaryl.
[0219] R.sup.27 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.28-substituted or unsubstituted alkyl, R.sup.28-substituted
or unsubstituted heteroalkyl, R.sup.28-substituted or unsubstituted
cycloalkyl, R.sup.28-substituted or unsubstituted heterocycloalkyl,
R.sup.28-substituted or unsubstituted aryl, or R.sup.28-substituted
or unsubstituted heteroaryl.
[0220] In some embodiments of the compounds provided herein,
L.sup.1 is independently a bond, --NH--, --O--, --S--, --C(O)--,
--S(O)--, --S(O).sub.2--, R.sup.29-substituted or unsubstituted
alkylene, R.sup.29-substituted or unsubstituted heteroalkylene,
R.sup.29-substituted or unsubstituted cycloalkylene,
R.sup.29-substituted or unsubstituted heterocycloalkylene,
R.sup.29-substituted or unsubstituted arylene, or
R.sup.29-substituted or unsubstituted heteroarylene.
[0221] R.sup.29 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.30-substituted or unsubstituted alkyl, R.sup.30-substituted
or unsubstituted heteroalkyl, R.sup.30-substituted or unsubstituted
cycloalkyl, R.sup.30substituted or unsubstituted heterocycloalkyl,
R.sup.30-substituted or unsubstituted aryl, or R.sup.30-substituted
or unsubstituted heteroaryl.
[0222] R.sup.30 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.31-substituted or unsubstituted alkyl, R.sup.31-substituted
or unsubstituted heteroalkyl, R.sup.31-substituted or unsubstituted
cycloalkyl, R.sup.31-substituted or unsubstituted heterocycloalkyl,
R.sup.31-substituted or unsubstituted aryl, or R.sup.31-substituted
or unsubstituted heteroaryl.
[0223] In some embodiments of the compounds provided herein,
L.sup.2 is independently a bond, --NH--, --O--, --S--, --C(O)--,
--S(O)--, --S(O).sub.2--, R.sup.32-substituted or unsubstituted
alkylene, R.sup.32-substituted or unsubstituted heteroalkylene,
R.sup.32-substituted or unsubstituted cycloalkylene,
R.sup.32-substituted or unsubstituted heterocycloalkylene,
R.sup.32-substituted or unsubstituted arylene, or
R.sup.32-substituted or unsubstituted heteroarylene.
[0224] R.sup.32 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.33-substituted or unsubstituted alkyl, R.sup.33-substituted
or unsubstituted heteroalkyl, R.sup.33-substituted or unsubstituted
cycloalkyl, R.sup.33substituted or unsubstituted heterocycloalkyl,
R.sup.33-substituted or unsubstituted aryl, or R.sup.33-substituted
or unsubstituted heteroaryl.
[0225] R.sup.33 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.34-substituted or unsubstituted alkyl, R.sup.34-substituted
or unsubstituted heteroalkyl, R.sup.34-substituted or unsubstituted
cycloalkyl, R.sup.34-substituted or unsubstituted heterocycloalkyl,
R.sup.34-substituted or unsubstituted aryl, or R.sup.34-substituted
or unsubstituted heteroaryl.
[0226] In some embodiments of the compounds provided herein,
L.sup.3 is independently a bond, --NH--, --O--, --S--, --C(O)--,
--S(O)--, --S(O).sub.2--, R.sup.35-substituted or unsubstituted
alkylene, R.sup.35-substituted or unsubstituted heteroalkylene,
R.sup.35-substituted or unsubstituted cycloalkylene,
R.sup.35-substituted or unsubstituted heterocycloalkylene,
R.sup.35-substituted or unsubstituted arylene, or
R.sup.35-substituted or unsubstituted heteroarylene.
[0227] R.sup.35 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.36-substituted or unsubstituted alkyl, R.sup.36-substituted
or unsubstituted heteroalkyl, R.sup.36-substituted or unsubstituted
cycloalkyl, R.sup.36substituted or unsubstituted heterocycloalkyl,
R.sup.36-substituted or unsubstituted aryl, or R.sup.36-substituted
or unsubstituted heteroaryl.
[0228] R.sup.36 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.37-substituted or unsubstituted alkyl, R.sup.37-substituted
or unsubstituted heteroalkyl, R.sup.37-substituted or unsubstituted
cycloalkyl, R.sup.37-substituted or unsubstituted heterocycloalkyl,
R.sup.37-substituted or unsubstituted aryl, or R.sup.37-substituted
or unsubstituted heteroaryl.
[0229] In some embodiments of the compounds provided herein,
R.sup.7 is independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, R.sup.38-substituted or unsubstituted alkyl,
R.sup.38-substituted or unsubstituted heteroalkyl,
R.sup.38-substituted or unsubstituted cycloalkyl,
R.sup.38-substituted or unsubstituted heterocycloalkyl,
R.sup.38-substituted or unsubstituted aryl, or R.sup.38-substituted
or unsubstituted heteroaryl.
[0230] R.sup.38 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
--S(O).sub.2CHCH.sub.2, --NHS(O).sub.2CHCH.sub.2,
R.sup.39-substituted or unsubstituted alkyl, R.sup.39-substituted
or unsubstituted heteroalkyl, R.sup.39-substituted or unsubstituted
cycloalkyl, R.sup.39substituted or unsubstituted heterocycloalkyl,
R.sup.39-substituted or unsubstituted aryl, or R.sup.39-substituted
or unsubstituted heteroaryl.
[0231] R.sup.39 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
--S(O).sub.2CHCH.sub.2, --NHS(O).sub.2CHCH.sub.2,
R.sup.40-substituted or unsubstituted alkyl, R.sup.40-substituted
or unsubstituted heteroalkyl, R.sup.40-substituted or unsubstituted
cycloalkyl, R.sup.40-substituted or unsubstituted heterocycloalkyl,
R.sup.40-substituted or unsubstituted aryl, or R.sup.40-substituted
or unsubstituted heteroaryl.
[0232] In some embodiments of the compounds provided herein,
R.sup.8 is independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, R.sup.41-substituted or unsubstituted alkyl,
R.sup.41-substituted or unsubstituted heteroalkyl,
R.sup.41-substituted or unsubstituted cycloalkyl,
R.sup.41-substituted or unsubstituted heterocycloalkyl,
R.sup.41-substituted or unsubstituted aryl, or R.sup.41-substituted
or unsubstituted heteroaryl.
[0233] R.sup.41 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
--S(O).sub.2CHCH.sub.2, --NHS(O).sub.2CHCH.sub.2,
R.sup.42-substituted or unsubstituted alkyl, R.sup.42-substituted
or unsubstituted heteroalkyl, R.sup.42-substituted or unsubstituted
cycloalkyl, R.sup.42 substituted or unsubstituted heterocycloalkyl,
R.sup.42-substituted or unsubstituted aryl, or R.sup.42-substituted
or unsubstituted heteroaryl.
[0234] R.sup.42 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
--S(O).sub.2CHCH.sub.2, --NHS(O).sub.2CHCH.sub.2,
R.sup.43-substituted or unsubstituted alkyl, R.sup.43-substituted
or unsubstituted heteroalkyl, R.sup.43-substituted or unsubstituted
cycloalkyl, R.sup.43-substituted or unsubstituted heterocycloalkyl,
R.sup.43-substituted or unsubstituted aryl, or R.sup.43-substituted
or unsubstituted heteroaryl.
[0235] In some embodiments of the compounds provided herein,
R.sup.9 is independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, R.sup.n-substituted or unsubstituted alkyl,
R.sup.44-substituted or unsubstituted heteroalkyl,
R.sup.44-substituted or unsubstituted cycloalkyl,
R.sup.44-substituted or unsubstituted heterocycloalkyl,
R.sup.44-substituted or unsubstituted aryl, or R.sup.44-substituted
or unsubstituted heteroaryl.
[0236] R.sup.44 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.45-substituted or unsubstituted alkyl, R.sup.45-substituted
or unsubstituted heteroalkyl, R.sup.45-substituted or unsubstituted
cycloalkyl, R.sup.45 substituted or unsubstituted heterocycloalkyl,
R.sup.45-substituted or unsubstituted aryl, or R.sup.45-substituted
or unsubstituted heteroaryl.
[0237] R.sup.45 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.46-substituted or unsubstituted alkyl, R.sup.46-substituted
or unsubstituted heteroalkyl, R.sup.46-substituted or unsubstituted
cycloalkyl, R.sup.46-substituted or unsubstituted heterocycloalkyl,
R.sup.46-substituted or unsubstituted aryl, or R.sup.46-substituted
or unsubstituted heteroaryl.
[0238] In some embodiments of the compounds provided herein,
R.sup.10 is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.47-substituted or
unsubstituted alkyl, R.sup.47-substituted or unsubstituted
heteroalkyl, R.sup.47-substituted or unsubstituted cycloalkyl,
R.sup.47-substituted or unsubstituted heterocycloalkyl,
R.sup.47-substituted or unsubstituted aryl, or R.sup.47-substituted
or unsubstituted heteroaryl.
[0239] R.sup.47 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.48-substituted or unsubstituted alkyl, R.sup.48-substituted
or unsubstituted heteroalkyl, R.sup.48-substituted or unsubstituted
cycloalkyl, R.sup.48 substituted or unsubstituted heterocycloalkyl,
R.sup.48-substituted or unsubstituted aryl, or R.sup.48-substituted
or unsubstituted heteroaryl.
[0240] R.sup.48 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.49-substituted or unsubstituted alkyl, R.sup.49-substituted
or unsubstituted heteroalkyl, R.sup.49-substituted or unsubstituted
cycloalkyl, R.sup.49-substituted or unsubstituted heterocycloalkyl,
R.sup.49-substituted or unsubstituted aryl, or R.sup.49-substituted
or unsubstituted heteroaryl.
[0241] In some embodiments of the compounds provided herein,
R.sup.13 is independently hydrogen, oxo, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.56-substituted or
unsubstituted alkyl, R.sup.56-substituted or unsubstituted
heteroalkyl, R.sup.56-substituted or unsubstituted cycloalkyl,
R.sup.56-substituted or unsubstituted heterocycloalkyl,
R.sup.56-substituted or unsubstituted aryl, or R.sup.56-substituted
or unsubstituted heteroaryl.
[0242] R.sup.56 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.57-substituted or unsubstituted alkyl, R.sup.57-substituted
or unsubstituted heteroalkyl, R.sup.57-substituted or unsubstituted
cycloalkyl, R.sup.57substituted or unsubstituted heterocycloalkyl,
R.sup.57-substituted or unsubstituted aryl, or R.sup.57-substituted
or unsubstituted heteroaryl.
[0243] R.sup.57 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.58-substituted or unsubstituted alkyl, R.sup.58-substituted
or unsubstituted heteroalkyl, R.sup.58-substituted or unsubstituted
cycloalkyl, R.sup.58-substituted or unsubstituted heterocycloalkyl,
R.sup.58-substituted or unsubstituted aryl, or R.sup.58-substituted
or unsubstituted heteroaryl.
[0244] In another embodiment of the compounds provided herein,
R.sup.14 is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.59-substituted or
unsubstituted alkyl, R.sup.59-substituted or unsubstituted
heteroalkyl, R.sup.59-substituted or unsubstituted cycloalkyl,
R.sup.59-substituted or unsubstituted heterocycloalkyl,
R.sup.59-substituted or unsubstituted aryl, or R.sup.59-substituted
or unsubstituted heteroaryl.
[0245] R.sup.59 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.60-substituted or unsubstituted alkyl, R.sup.60-substituted
or unsubstituted heteroalkyl, R.sup.60-substituted or unsubstituted
cycloalkyl, R.sup.60-substituted or unsubstituted heterocycloalkyl,
R.sup.60-substituted or unsubstituted aryl, or R.sup.60-substituted
or unsubstituted heteroaryl.
[0246] R.sup.60 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.61-substituted or unsubstituted alkyl, R.sup.61-substituted
or unsubstituted heteroalkyl, R.sup.61-substituted or unsubstituted
cycloalkyl, R.sup.61-substituted or unsubstituted heterocycloalkyl,
R.sup.61-substituted or unsubstituted aryl, or R.sup.61-substituted
or unsubstituted heteroaryl.
[0247] In a further embodiment of the compounds provided herein,
R.sup.15 is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.62-substituted or
unsubstituted alkyl, R.sup.62-substituted or unsubstituted
heteroalkyl, R.sup.62-substituted or unsubstituted cycloalkyl,
R.sup.62-substituted or unsubstituted heterocycloalkyl,
R.sup.62-substituted or unsubstituted aryl, or R.sup.62-substituted
or unsubstituted heteroaryl.
[0248] R.sup.62 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.63-substituted or unsubstituted alkyl, R.sup.63-substituted
or unsubstituted heteroalkyl, R.sup.63-substituted or unsubstituted
cycloalkyl, R.sup.63-substituted or unsubstituted heterocycloalkyl,
R.sup.63-substituted or unsubstituted aryl, or R.sup.63-substituted
or unsubstituted heteroaryl.
[0249] R.sup.63 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.64-substituted or unsubstituted alkyl, R.sup.64-substituted
or unsubstituted heteroalkyl, R.sup.64-substituted or unsubstituted
cycloalkyl, R.sup.64-substituted or unsubstituted heterocycloalkyl,
R.sup.64-substituted or unsubstituted aryl, or R.sup.64-substituted
or unsubstituted heteroaryl.
[0250] In some embodiments of the compounds provided herein,
R.sup.16 is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.65-substituted or
unsubstituted alkyl, R.sup.65-substituted or unsubstituted
heteroalkyl, R.sup.65-substituted or unsubstituted cycloalkyl,
R.sup.65-substituted or unsubstituted heterocycloalkyl,
R.sup.65-substituted or unsubstituted aryl, or R.sup.65-substituted
or unsubstituted heteroaryl.
[0251] R.sup.65 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.66-substituted or unsubstituted alkyl, R.sup.66-substituted
or unsubstituted heteroalkyl, R.sup.66-substituted or unsubstituted
cycloalkyl, R.sup.66-substituted or unsubstituted heterocycloalkyl,
R.sup.66-substituted or unsubstituted aryl, or R.sup.66-substituted
or unsubstituted heteroaryl.
[0252] R.sup.66 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.67-substituted or unsubstituted alkyl, R.sup.67-substituted
or unsubstituted heteroalkyl, R.sup.67-substituted or unsubstituted
cycloalkyl, R.sup.67-substituted or unsubstituted heterocycloalkyl,
R.sup.67-substituted or unsubstituted aryl, or R.sup.67-substituted
or unsubstituted heteroaryl.
[0253] In some embodiments of the compounds provided herein,
R.sup.17 is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.68-substituted or
unsubstituted alkyl, R.sup.68-substituted or unsubstituted
heteroalkyl, R.sup.68-substituted or unsubstituted cycloalkyl,
R.sup.68-substituted or unsubstituted heterocycloalkyl,
R.sup.68-substituted or unsubstituted aryl, or R.sup.68-substituted
or unsubstituted heteroaryl.
[0254] R.sup.68 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.69-substituted or unsubstituted alkyl, R.sup.69-substituted
or unsubstituted heteroalkyl, R.sup.69-substituted or unsubstituted
cycloalkyl, R.sup.69-substituted or unsubstituted heterocycloalkyl,
R.sup.69-substituted or unsubstituted aryl, or R.sup.69-substituted
or unsubstituted heteroaryl.
[0255] R.sup.69 is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.70-substituted or unsubstituted alkyl, R.sup.70-substituted
or unsubstituted heteroalkyl, R.sup.70-substituted or unsubstituted
cycloalkyl, R.sup.70-substituted or unsubstituted heterocycloalkyl,
R.sup.70-substituted or unsubstituted aryl, or R.sup.70-substituted
or unsubstituted heteroaryl.
[0256] In some embodiments of the compounds provided herein,
R.sup.7a is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.38a-substituted or
unsubstituted alkyl, R.sup.38a-substituted or unsubstituted
heteroalkyl, R.sup.38a-substituted or unsubstituted cycloalkyl,
R.sup.38a-substituted or unsubstituted heterocycloalkyl,
R.sup.38a-substituted or unsubstituted aryl, or
R.sup.38a-substituted or unsubstituted heteroaryl.
[0257] R.sup.38a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.39a-substituted or unsubstituted alkyl, R.sup.39a-substituted
or unsubstituted heteroalkyl, R.sup.39a-substituted or
unsubstituted cycloalkyl, R.sup.39asubstituted or unsubstituted
heterocycloalkyl, R.sup.39a-substituted or unsubstituted aryl, or
R.sup.39a-substituted or unsubstituted heteroaryl.
[0258] R.sup.39a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.40a-substituted or unsubstituted alkyl, R.sup.40a-substituted
or unsubstituted heteroalkyl, R.sup.40a-substituted or
unsubstituted cycloalkyl, R.sup.40a-substituted or unsubstituted
heterocycloalkyl, R.sup.40a-substituted or unsubstituted aryl, or
R.sup.40a-substituted or unsubstituted heteroaryl.
[0259] In some embodiments of the compounds provided herein,
R.sup.8a is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.41a-substituted or
unsubstituted alkyl, R.sup.41a-substituted or unsubstituted
heteroalkyl, R.sup.41a-substituted or unsubstituted cycloalkyl,
R.sup.41a-substituted or unsubstituted heterocycloalkyl,
R.sup.41a-substituted or unsubstituted aryl, or R.sup.41a
substituted or unsubstituted heteroaryl.
[0260] R.sup.41a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.42a-substituted or unsubstituted alkyl, R.sup.42a-substituted
or unsubstituted heteroalkyl, R.sup.42a-substituted or
unsubstituted cycloalkyl, R.sup.42asubstituted or unsubstituted
heterocycloalkyl, R.sup.42a-substituted or unsubstituted aryl, or
R.sup.42a-substituted or unsubstituted heteroaryl.
[0261] R.sup.42a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.43a-substituted or unsubstituted alkyl, R.sup.43a-substituted
or unsubstituted heteroalkyl, R.sup.43a-substituted or
unsubstituted cycloalkyl, R.sup.43a-substituted or unsubstituted
heterocycloalkyl, R.sup.43a-substituted or unsubstituted aryl, or
R.sup.43a-substituted or unsubstituted heteroaryl.
[0262] In some embodiments of the compounds provided herein,
R.sup.9a is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.44a-substituted or
unsubstituted alkyl, R.sup.44a-substituted or unsubstituted
heteroalkyl, R.sup.44a-substituted or unsubstituted cycloalkyl,
R.sup.44a-substituted or unsubstituted heterocycloalkyl,
R.sup.44a-substituted or unsubstituted aryl, or
R.sup.44a-substituted or unsubstituted heteroaryl.
[0263] R.sup.44a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.45a-substituted or unsubstituted alkyl, R.sup.45a-substituted
or unsubstituted heteroalkyl, R.sup.45a-substituted or
unsubstituted cycloalkyl, R.sup.45asubstituted or unsubstituted
heterocycloalkyl, R.sup.45a-substituted or unsubstituted aryl, or
R.sup.45a-substituted or unsubstituted heteroaryl.
[0264] R.sup.45a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.46a-substituted or unsubstituted alkyl, R.sup.46a-substituted
or unsubstituted heteroalkyl, R.sup.46a-substituted or
unsubstituted cycloalkyl, R.sup.46a-substituted or unsubstituted
heterocycloalkyl, R.sup.46a-substituted or unsubstituted aryl, or
R.sup.46a-substituted or unsubstituted heteroaryl.
[0265] In some embodiments of the compounds provided herein,
R.sup.10a is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.47a-substituted or
unsubstituted alkyl, R.sup.47a-substituted or unsubstituted
heteroalkyl, R.sup.47a-substituted or unsubstituted cycloalkyl,
R.sup.47a-substituted or unsubstituted heterocycloalkyl,
R.sup.47a-substituted or unsubstituted aryl, or
R.sup.47a-substituted or unsubstituted heteroaryl.
[0266] R.sup.47a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.48a-substituted or unsubstituted alkyl, R.sup.48a-substituted
or unsubstituted heteroalkyl, R.sup.48a-substituted or
unsubstituted cycloalkyl, R.sup.48asubstituted or unsubstituted
heterocycloalkyl, R.sup.48a-substituted or unsubstituted aryl, or
R.sup.48a-substituted or unsubstituted heteroaryl.
[0267] R.sup.48a is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.49a-substituted or unsubstituted alkyl, R.sup.49a-substituted
or unsubstituted heteroalkyl, R.sup.49a-substituted or
unsubstituted cycloalkyl, R.sup.49a-substituted or unsubstituted
heterocycloalkyl, R.sup.49a-substituted or unsubstituted aryl, or
R.sup.49a-substituted or unsubstituted heteroaryl.
[0268] In some embodiments of the compounds provided herein,
R.sup.7c is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.38c-substituted or
unsubstituted alkyl, R.sup.38c-substituted or unsubstituted
heteroalkyl, R.sup.38c-substituted or unsubstituted cycloalkyl,
R.sup.38c-substituted or unsubstituted heterocycloalkyl,
R.sup.38c-substituted or unsubstituted aryl, or
R.sup.38c-substituted or unsubstituted heteroaryl.
[0269] R.sup.38c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.39c-substituted or unsubstituted alkyl, R.sup.39c-substituted
or unsubstituted heteroalkyl, R.sup.39c-substituted or
unsubstituted cycloalkyl, R.sup.39c-substituted or unsubstituted
heterocycloalkyl, R.sup.39c-substituted or unsubstituted aryl, or
R.sup.39c-substituted or unsubstituted heteroaryl.
[0270] R.sup.39c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.40c-substituted or unsubstituted alkyl, R.sup.40c-substituted
or unsubstituted heteroalkyl, R.sup.40c-substituted or
unsubstituted cycloalkyl, R.sup.40c-substituted or unsubstituted
heterocycloalkyl, R.sup.40c-substituted or unsubstituted aryl, or
R.sup.40c-substituted or unsubstituted heteroaryl.
[0271] In some embodiments of the compounds provided herein,
R.sup.8c is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.41c-substituted or
unsubstituted alkyl, R.sup.41c-substituted or unsubstituted
heteroalkyl, R.sup.41c-substituted or unsubstituted cycloalkyl,
R.sup.41c-substituted or unsubstituted heterocycloalkyl,
R.sup.41c-substituted or unsubstituted aryl, or
R.sup.41c-substituted or unsubstituted heteroaryl.
[0272] R.sup.41c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.42c-substituted or unsubstituted alkyl, R.sup.42c-substituted
or unsubstituted heteroalkyl, R.sup.42c-substituted or
unsubstituted cycloalkyl, R.sup.42c-substituted or unsubstituted
heterocycloalkyl, R.sup.42c-substituted or unsubstituted aryl, or
R.sup.42c-substituted or unsubstituted heteroaryl.
[0273] R.sup.42c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.43c-substituted or unsubstituted alkyl, R.sup.43c-substituted
or unsubstituted heteroalkyl, R.sup.43c-substituted or
unsubstituted cycloalkyl, R.sup.43c-substituted or unsubstituted
heterocycloalkyl, R.sup.43c-substituted or unsubstituted aryl, or
R.sup.43c-substituted or unsubstituted heteroaryl.
[0274] In some embodiments of the compounds provided herein,
R.sup.9c is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.44c-substituted or
unsubstituted alkyl, R.sup.44c-substituted or unsubstituted
heteroalkyl, R.sup.44csubstituted or unsubstituted cycloalkyl,
R.sup.44c-substituted or unsubstituted heterocycloalkyl,
R.sup.44c-substituted or unsubstituted aryl, or
R.sup.44c-substituted or unsubstituted heteroaryl.
[0275] R.sup.44c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.45c-substituted or unsubstituted alkyl, R.sup.45c-substituted
or unsubstituted heteroalkyl, R.sup.45c-substituted or
unsubstituted cycloalkyl, R.sup.45c-substituted or unsubstituted
heterocycloalkyl, R.sup.45c-substituted or unsubstituted aryl, or
R.sup.45c-substituted or unsubstituted heteroaryl.
[0276] R.sup.45c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.46c-substituted or unsubstituted alkyl, R.sup.46c-substituted
or unsubstituted heteroalkyl, R.sup.46c-substituted or
unsubstituted cycloalkyl, R.sup.46c-substituted or unsubstituted
heterocycloalkyl, R.sup.46c-substituted or unsubstituted aryl, or
R.sup.46c-substituted or unsubstituted heteroaryl.
[0277] In some embodiments of the compounds provided herein,
R.sup.10c is independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, R.sup.47c-substituted or
unsubstituted alkyl, R.sup.47c-substituted or unsubstituted
heteroalkyl, R.sup.47c-substituted or unsubstituted cycloalkyl,
R.sup.47c-substituted or unsubstituted heterocycloalkyl,
R.sup.47c-substituted or unsubstituted aryl, or
R.sup.47c-substituted or unsubstituted heteroaryl.
[0278] R.sup.47c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.48c-substituted or unsubstituted alkyl, R.sup.48c-substituted
or unsubstituted heteroalkyl, R.sup.48c-substituted or
unsubstituted cycloalkyl, R.sup.48c-substituted or unsubstituted
heterocycloalkyl, R.sup.48c-substituted or unsubstituted aryl, or
R.sup.48c-substituted or unsubstituted heteroaryl.
[0279] R.sup.48c is independently oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
R.sup.49c-substituted or unsubstituted alkyl, R.sup.49c-substituted
or unsubstituted heteroalkyl, R.sup.49c-substituted or
unsubstituted cycloalkyl, R.sup.49c-substituted or unsubstituted
heterocycloalkyl, R.sup.49c-substituted or unsubstituted aryl, or
R.sup.49c-substituted or unsubstituted heteroaryl.
[0280] In some embodiments of the compounds provided herein,
R.sup.22, R.sup.25, R.sup.25A, R.sup.25B, R.sup.25C, R.sup.28,
R.sup.31, R.sup.34, R.sup.37, R.sup.40, R.sup.43, R.sup.46,
R.sup.49, R.sup.58, R.sup.61, R.sup.64, R.sup.67, R.sup.70,
R.sup.40a, R.sup.43a, R.sup.46a, R.sup.49a, R.sup.40c, R.sup.43c,
R.sup.46c, R.sup.49c, are independently hydrogen, oxo,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted
cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or
unsubstituted heteroaryl.
[0281] In some embodiments, the compound has the Formula:
##STR00097##
R.sup.3, e5, R.sup.2A, R.sup.2B, L.sup.2, L.sup.3, and E are as
described herein and above (including embodiments). X' is --O--,
--NH--, or --S--. E is an electrophilic chemical moiety capable of
forming a covalent bond with a cysteine or aspartate residue;
R.sup.2C is independently hydrogen, oxo, halogen, --CX.sup.c.sub.3,
--CN, --SO.sub.2Cl, --SO.sub.n3R.sup.10c,
--SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2, --ONR.sup.7cR.sup.8c,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7cR.sup.8c,
--N(O).sub.m3, --NR.sup.7cR.sup.8c, --C(O)R.sup.9c,
--C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c, --OR.sup.10c,
--NR.sup.7cSO.sub.2R.sup.10c, --NR.sup.7c C.dbd.(O)R.sup.9c,
--NR.sup.7cC(O)--OR.sup.9c, --NR.sup.7cOR.sup.9c,
--OCX.sup.c.sub.3, --OCHX.sup.c.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; two adjacent R.sup.2C substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl; two R.sup.2C substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a,
R.sup.8a, R.sup.9a and R.sup.10a are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl;
R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; m, m1, m3, v, v1,
and v3 are independently 1 or 2; n, n1, and n3 are independently an
integer from 0 to 4; X, X.sup.a and X.sup.c are independently --Cl,
--Br, --I, or --F.
[0282] In some embodiments, E comprises a substituted or
unsubstituted vinyl sulfone moiety, substituted or unsubstituted
vinyl sulfonamide moiety, substituted or unsubstituted peroxide
moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety. In some embodiments, E is a
substituted or unsubstituted vinyl sulfone moiety, substituted or
unsubstituted vinyl sulfonamide moiety, substituted or
unsubstituted peroxide moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
[0283] In some embodiments, L.sup.2 is independently
R.sup.2C-substituted or unsubstituted heterocycloalkylene or
R.sup.2C-substituted or unsubstituted spirocyclic linker and
L.sup.3 is a bond. For example, L.sup.2 is monocyclic 4, 5, or
6-membered heterocycloalkylene. In some embodiments, L.sup.2 is
unsubstituted piperazino or unsubstituted piperidino. In other
embodiments, L.sup.2 is bicyclic fused heterocycloalkylene. In yet
other embodiments, L.sup.2 is an unsubstituted spirocyclic
linker.
[0284] In some embodiments of the above compounds, E comprises a
substituted or unsubstituted vinyl sulfone moiety, substituted or
unsubstituted vinyl sulfonamide moiety, or a substituted or
unsubstituted acrylamide moiety. In some embodiments of the above
compounds, E is a substituted or unsubstituted vinyl sulfone
moiety, substituted or unsubstituted vinyl sulfonamide moiety, or a
substituted or unsubstituted acrylamide moiety.
[0285] In some embodiments, the compound has the Formula:
##STR00098##
[0286] In some embodiments, the compound binds Ras (e.g. K-Ras,
H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D) behind Switch II. In embodiments, the compound modulates the
conformation of Switch II. In embodiments, the compound modulates
the conformation of Switch I. In embodiments, the compound
modulates the conformation of Switch I and Switch II. In
embodiments, the compound inhibits (e.g. by about 0.1, 0.2, 0.3,
0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0,
8.0, 9.0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35,
40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400,
500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000,
8000, 9000, 10000 fold or more) Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
nucleotide exchange (e.g. GDP for GTP or GTP for GDP) relative to
the absence of the compound. In embodiments, the compound inhibits
release of GDP from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,
K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the
absence of the compound. In embodiments, the compound inhibits
binding of GDP to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the absence
of the compound. In embodiments, the compound inhibits binding of
GTP to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) relative to the absence of the
compound. In embodiments, the compound increases (e.g. by about
0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, 3.0, 4.0,
5.0, 6.0, 7.0, 8.0, 9.0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,
100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000,
4000, 5000, 6000, 7000, 8000, 9000, 10000 fold or more) Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) nucleotide exchange (e.g. GDP for GTP or GTP for
GDP) relative to the absence of the compound. In embodiments, the
compound increases release of GDP from Ras (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound increases release of GTP from Ras (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound increases binding of GDP to Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound inhibits binding of GTP to Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound inhibits binding of a GTP analog (e.g. mant-dGTP) to Ras
(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) relative to the absence of the compound. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid that contacts GTP in the absence of
the compound. In embodiments, the compound modulates the
conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid that contacts
GDP in the absence of the compound. In embodiments, the compound
modulates the conformation of a plurality of Ras (e.g. K-Ras,
H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D) amino acids that contact GTP in the absence of the compound.
In embodiments, the compound modulates the conformation of a
plurality of Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acids that contact GDP in
the absence of the compound. In embodiments, the compound modulates
the binding of GTP and/or GDP to Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
compared to binding in the absence of the compound. In embodiments,
the compound modulates the release of GTP and/or GDP from Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) compared to release in the absence of the
compound. In embodiments, the compound modulates the ratio of the
binding of GTP and GDP to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant
Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) compared to
the ratio in the absence of the compound. In embodiments, the
compound modulates the ratio of the rate of release of GTP and GDP
from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) compared to the ratio in the absence
of the compound. In embodiments, the compound modulates the
conformation of a Ras amino acid that contacts the gamma phosphate
of GTP when GTP is bound to Ras. In embodiments, the compound
inhibits the binding of the gamma phosphate of GTP relative to the
binding in the absence of the compound. In embodiments, the
compound binds Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) protein bound to GDP and,
after release of the GDP, modulates the subsequent binding of GDP
or GTP to the Ras bound to the compound. In embodiments, the
compound binds Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) protein bound to GDP and,
after release of the GDP, modulates the subsequent binding of GDP
to the Ras bound to the compound. In embodiments, the compound
binds Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) protein bound to GDP and after
release of the GDP, modulates the subsequent binding of GTP to the
Ras bound to the compound.
[0287] In embodiments, the compound inhibits proliferation of
cancer cells under nutrient deficient conditions relative to the
absence of the compound. In embodiments, the compound inhibits
growth of cancer cells under nutrient deficient conditions relative
to the absence of the compound. In embodiments, the compound
inhibits growth of cancer cells under nutrient deficient conditions
relative to the absence of the compound. In embodiments, the
compound inhibits growth of cancer cells under serum deprivation
conditions relative to the absence of the compound. In embodiments,
the compound inhibits proliferation of cancer cells under serum
deprivation conditions relative to the absence of the compound. In
embodiments, the compound inhibits growth of cancer cells under
conditions (e.g. local cell environment in a patient) mimicking
serum deprivation relative to the absence of the compound. In
embodiments, the compound inhibits proliferation of cancer cells
under conditions (e.g. local cell environment in a patient)
mimicking serum deprivation relative to the absence of the
compound.
[0288] In embodiments, the compound modulates the conformation of
the amino acid corresponding to amino acid 60 in human K-Ras in a
Ras protein. In embodiments, the compound modulates the distance
between the alpha carbon of the amino acid corresponding to amino
acid 12 in human K-Ras and the alpha carbon of the amino acid
corresponding to amino acid 60 in human K-Ras, in a Ras protein
(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D). In embodiments the compound increases the
distance between the alpha carbon of the amino acid corresponding
to amino acid 12 in human K-Ras and the alpha carbon of the amino
acid corresponding to amino acid 60 in human K-Ras, in a Ras
protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D). In embodiments the compound
increases the distance (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,
0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9,
2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2,
3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5,
4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,
5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1,
7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4,
8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7,
9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8,
10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9,
12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,
13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1,
14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,
15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3,
17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4,
18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5,
19.6, 19.7, 19.8, 19.9, 20.0, or more angstroms) between the alpha
carbon of the amino acid corresponding to amino acid 12 in human
K-Ras and the alpha carbon of the amino acid corresponding to amino
acid 60 in human K-Ras, in a Ras protein (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments the
compound increases the distance (e.g. by about 0.1, 0.2, 0.3, 0.4,
0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7,
1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0,
3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3,
4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6,
5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9,
7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2,
8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5,
9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7,
10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8,
11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9,
13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0,
14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1,
15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2,
17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3,
18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4,
19.5, 19.6, 19.7, 19.8, 19.9, 20.0, or more angstroms) between the
alpha carbon of the amino acid corresponding to amino acid 12 in
human K-Ras and the alpha carbon of the amino acid corresponding to
amino acid 60 in human K-Ras, in a Ras protein (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
when bound to GDP, relative to the absence of the compound. In
embodiments the compound increases the distance (e.g. by about 0.1,
0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4,
1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7,
2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0,
4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3,
5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6,
6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9,
8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2,
9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4,
10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5,
11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6,
12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7,
13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8,
14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9,
17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0,
18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1,
19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0, or more
angstroms) between the alpha carbon of the amino acid corresponding
to amino acid 12 in human K-Ras and the alpha carbon of the amino
acid corresponding to amino acid 60 in human K-Ras, in a Ras
protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) when bound to GTP, compared to the
distance in the absence of the compound. In embodiments, upon
binding to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) the compound (e.g. a compound
described herein, including embodiments and including a compound
described in a table, example, or figure) modulates the distance
between the alpha carbon of the amino acid corresponding to amino
acid 12 in human K-Ras and the alpha carbon of the amino acid
corresponding to amino acid 60 in human K-Ras, in the Ras protein
(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) to be about 4.9 angstroms or greater (e.g.
about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0, 5.1,
5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4,
6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,
7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0,
9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2,
10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3,
11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4,
12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5,
13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6,
14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7,
15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8,
17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9,
19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0
angstroms, or greater). In embodiments, upon binding to Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) the compound (e.g. a compound described herein,
including embodiments and including a compound described in a
table, example, or figure) modulates the distance between the alpha
carbon of the amino acid corresponding to amino acid 12 in human
K-Ras and the alpha carbon of the amino acid corresponding to amino
acid 60 in human K-Ras, in the Ras protein (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
to be greater than about 4.9 angstroms (e.g. greater than about
5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0, 5.1, 5.2,
5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5,
6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8,
7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1,
9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3,
10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4,
11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5,
12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6,
13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7,
14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8,
15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9,
18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0,
19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0
angstroms, or greater). In embodiments, upon binding to Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) the compound (e.g. a compound described herein,
including embodiments and including a compound described in a
table, example, or figure) modulates the distance between the alpha
carbon of the amino acid corresponding to amino acid 12 in human
K-Ras and the alpha carbon of the amino acid corresponding to amino
acid 60 in human K-Ras, in the Ras protein (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
to be 4.9 angstroms or greater (e.g. 5.0, 5.1, 5.2, 5.3, 5.4, 5.5,
5.6, 5.7, 5.8, 5.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,
5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1,
7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4,
8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7,
9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8,
10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9,
12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,
13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1,
14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,
15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3,
17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4,
18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5,
19.6, 19.7, 19.8, 19.9, 20.0 angstroms, or greater). In
embodiments, upon binding to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant
Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) the compound
(e.g. a compound described herein, including embodiments and
including a compound described in a table, example, or figure)
modulates the distance between the alpha carbon of the amino acid
corresponding to amino acid 12 in human K-Ras and the alpha carbon
of the amino acid corresponding to amino acid 60 in human K-Ras, in
the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) to be greater than 4.9
angstroms (e.g. greater than 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6,
5.7, 5.8, 5.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9,
6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2,
7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5,
8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8,
9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9,
11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0,
12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1,
13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2,
14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3,
15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4,
17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5,
18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6,
19.7, 19.8, 19.9, 20.0 angstroms, or greater).
[0289] In embodiments, the compound increases the flexibility of
Switch I relative to the absence of the compound. In embodiments,
the compound increases the disorder of Switch I relative to the
absence of the compound. In embodiments, the compound inhibits the
binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) to another protein. In
embodiments, the compound inhibits the binding of Ras ((e.g. K-Ras,
H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D) to another protein, wherein the binding is dependent on Ras
binding to GTP. In embodiments, the compound inhibits the binding
of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) to another protein, wherein the
binding is dependent on Ras binding to GDP. In embodiments, the
compound inhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to Raf
(e.g. Raf1). In embodiments, the compound inhibits the binding of
Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) to SOS. In embodiments, the compound
inhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras)
to a GEF. In embodiments, the compound inhibits the binding of Ras
((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) to PI3K. In embodiments, the compound
modulates metal binding near the nucleotide binding site. In
embodiments, the compound modulates the conformation of the Ras
metal binding site near the nucleotide binding site. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid relative to the conformation in the
absence of the compound, wherein the Ras amino acid conformation is
also modulated by a Ras G60 mutation. In embodiments, the compound
modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino
acid relative to the conformation in the absence of the compound,
wherein the Ras amino acid conformation is also modulated by a Ras
G60A mutation. In embodiments, the compound modulates the
conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid relative to
the conformation in the absence of the compound, wherein the Ras
amino acid conformation is also modulated by a Ras T35 mutation. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid relative to the conformation in the
absence of the compound, wherein the Ras amino acid conformation is
also modulated by a Ras T35S mutation. In embodiments, the compound
modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino
acid relative to the conformation in the absence of the compound,
wherein the Ras amino acid conformation is also modulated by a
mutation of the Ras amino acid corresponding to K-Ras G60. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid relative to the conformation in the
absence of the compound, wherein the Ras amino acid conformation is
also modulated by a mutation of the Ras amino acid corresponding to
K-Ras T35.
[0290] The crystal structures of Hras and Kras bound to GTP show a
contact between the gamma phosphate and the backbone amide of
glycine-60 in switch II. This contact is known to be critical for
orienting the switches for binding to downstream effectors. This
conformation required for binding downstream effectors is called
state 2. Mutation of glycine-60 to alanine (G60A) prevents proper
rotation of residue-60 upon GTP binding, and induces an alternate
conformation called state 1. In this conformation, the gamma
phosphate of GTP forms a water-mediated hydrogen bond to
alanine-60, which likely acts to maintain GTP affinity. Similarly,
direct contacts between the gamma phosphate and switch I are
replaced by water-mediated contacts. The complete loss of these
contacts to the gamma phosphate would be likely to decrease the
affinity of Ras for GTP, having less effect on the affinity for
GDP.
[0291] The state 1 conformation can also be stabilized by mutating
threonine-35 to serine (T35S), and the GTP-bound crystal structure
of this mutant is known. A crystal structure of the wild-type
protein in state 1 has also been solved. We noticed that the
conformation of Ras (state 1 or state 2) could be predicted by
measuring the distance between the alpha carbon of residue-60 and
the alpha carbon of residue-12. If this distance is 3.9 .ANG. or
less, direct contacts between the gamma phosphate and the switches
are possible and the protein adopts state 2. If this distance is
4.9 .ANG. or greater, these direct contacts are no longer possible
and the protein adopts state 1.
[0292] When bound to GDP, the conformation of the protein is
unaffected by the G60A mutation or the T35S mutation. In both
cases, as with the wild-type, the distance between position 12 and
position 60 is approximately 8 .ANG.. In crystal structures we have
solved with our inhibitors (e.g. a compound selected from the
compounds described herein) bound to KrasG12C, the structures show
distances between residue-12 and residue-60 of more than 8 .ANG. in
the GDP-bound state. Unlike the wild-type, G60A and T35S, when our
inhibitor (e.g. a compound selected from the compounds described
herein) is bound this distance cannot decrease to below 5 .ANG.
upon GTP-binding due to a steric clash that would occur between our
inhibitor and switch II. Therefore, our inhibitors (e.g. a compound
selected from the compounds described herein) will prevent switch
II from forming contacts with the gamma phosphate and, when they
increase the distance between these two residues enough (>11
.ANG.), even cause disordering of switch I.
[0293] Based on these observations, our compounds (e.g. a compound
selected from the compounds described herein) are likely to have a
deleterious effect on GTP binding. Due to the critical contacts
from the gamma phosphate to switch II, some of our compounds (e.g.
a compound selected from the compounds described herein) will have
a greater effect on GTP binding than on GDP binding.
[0294] In some embodiments, the compound is any one of the
compounds in Table 1, 2, 3, 4, or 5.
[0295] In some embodiments, a compound as described herein may
include multiple instances of R.sup.3, R.sup.7, R.sup.8, R.sup.9,
R.sup.10, R.sup.2A, R.sup.7a, R.sup.8a, R.sup.9a, R.sup.10a,
R.sup.2B, R.sup.2C, R.sup.7c, R.sup.8c, R.sup.9c, R.sup.10c, X,
X.sup.a, X.sup.c, m, n, v, m1, n1, v1, m3, n3, v3, and/or other
variables. In such embodiments, each variable may optional be
different and be appropriately labeled to distinguish each group
for greater clarity. For example, where each R.sup.3, R.sup.7,
R.sup.8, R.sup.9, R.sup.10, R.sup.2A, R.sup.7a, R.sup.8a, R.sup.9a,
R.sup.10a, R.sup.2B, R.sup.2C, R.sup.7c, R.sup.8c, R.sup.9c,
R.sup.10c, X, X.sup.a, X.sup.c, m, n, v, m1, n1, v1, m3, n3, and/or
v3, is different, they may be referred to, for example, as
R.sup.3.1, R.sup.3.2, R.sup.3.3, R.sup.3.4, R.sup.3.5, R.sup.3.6,
R.sup.3.7, R.sup.7.1, R.sup.7.2, R.sup.7.3, R.sup.7.4, R.sup.7.5,
R.sup.7.6, R.sup.7.7, R.sup.8.1, R.sup.8.2, R.sup.8.3, R.sup.8.4,
R.sup.8.5, R.sup.8.6, R.sup.8.7, R.sup.9.1, R.sup.9.2, R.sup.9.3,
R.sup.9.4, R.sup.9.5, R.sup.9.6, R.sup.9.7, R.sup.10.1, R.sup.10.2,
R.sup.10.3, R.sup.10.4, R.sup.10.5, R.sup.10.6, R.sup.10.7,
R.sup.2A.1, R.sup.2A.2, R.sup.2A.3, R.sup.7a.1, R.sup.7a.2,
R.sup.7a.3, R.sup.7a.4, R.sup.7a.5, R.sup.7a.6, R.sup.8a.1,
R.sup.8a.2, R.sup.8a.3, R.sup.8a.4, R.sup.8a.5, R.sup.8a.6,
R.sup.9a.1, R.sup.9a.2, R.sup.9a.3, R.sup.9a.4, R.sup.9a.5,
R.sup.9a.6, R.sup.10a.1, R.sup.10a.2, R.sup.10a.3, R.sup.10a.4,
R.sup.10a.5, R.sup.10a.6, R.sup.2B.1, R.sup.2B.2, R.sup.2B.3,
R.sup.2C.1, R.sup.2C.2, R.sup.2C.3, R.sup.2C.4, R.sup.2C.5,
R.sup.2C.6, R.sup.2C.7, R.sup.2C.8, R.sup.2C.9, R.sup.2C.10,
R.sup.2C.11, R.sup.2C.12, R.sup.2C.13, R.sup.2C.14, R.sup.2C.15,
R.sup.2C.16, R.sup.2C.17, R.sup.2C.18, R.sup.2C.19, R.sup.2C.20,
R.sup.2C.21, R.sup.2C.22, R.sup.2C.23, R.sup.2C.24, R.sup.2C.25,
R.sup.2C.26, R.sup.2C.27, R.sup.2C.28, R.sup.2C.29, R.sup.2C.30,
R.sup.2C.31, R.sup.2C.32, R.sup.2C.33, R.sup.2C.34, R.sup.2C.35,
R.sup.2C.36, R.sup.2C.37, R.sup.2C.38, R.sup.2C.39, R.sup.2C.40,
R.sup.2C.41, R.sup.2C.42, R.sup.7c.1, R.sup.7c.2, R.sup.7c.3,
R.sup.7c.4, R.sup.7c.5, R.sup.7c.6, R.sup.7c.7, R.sup.7c.8,
R.sup.7c.9, R.sup.7c.10, R.sup.7c.11, R.sup.7c.12, R.sup.7c.13,
R.sup.7c.14, R.sup.7c.15, R.sup.7c.16, R.sup.7c.17, R.sup.7c.18,
R.sup.7c.19, R.sup.7c.20, R.sup.7c.21, R.sup.7c.22, R.sup.7c.23,
R.sup.7c.24, R.sup.7c.25, R.sup.7c.26, R.sup.7c.27, R.sup.7c.28,
R.sup.7c.29, R.sup.7c.30, R.sup.7c.31, R.sup.7c.32, R.sup.7c.33,
R.sup.7c.34, R.sup.7c.35, R.sup.7c.36, R.sup.7c.37, R.sup.7c.38,
R.sup.7c.39, R.sup.7c.40, R.sup.7c.41, R.sup.7c.42, R.sup.8c.1,
R.sup.8c.2, R.sup.8c.3, R.sup.8c.4, R.sup.8c.5, R.sup.8c.6,
R.sup.8c.7, R.sup.8c.8, R.sup.8c.9, R.sup.8c.10, R.sup.8c.11,
R.sup.8c.12, R.sup.8c.13, R.sup.8c.14, R.sup.8c.15, R.sup.8c.16,
R.sup.8c.17, R.sup.8c.18, R.sup.8c.19, R.sup.8c.20, R.sup.8c.21,
R.sup.8c.22, R.sup.8c.23, R.sup.8c.24, R.sup.8c.25, R.sup.8c.26,
R.sup.8c.27, R.sup.8c.28, R.sup.8c.29, R.sup.8c.30, R.sup.8c.31,
R.sup.8c.32, R.sup.8c.33, R.sup.8c.34, R.sup.8c.35, R.sup.8c.36,
R.sup.8c.37, R.sup.8c.38, R.sup.8c.39, R.sup.8c.40, R.sup.8c.41,
R.sup.8c.42, R.sup.9c.1, R.sup.9c.2, R.sup.9c.3, R.sup.9c.4,
R.sup.9c.5, R.sup.9c.6, R.sup.9c.7, R.sup.9c.8, R.sup.9c.9,
R.sup.9c.10, R.sup.9c.11, R.sup.9c.12, R.sup.9c.13, R.sup.9c.14,
R.sup.9c.15, R.sup.9c.16, R.sup.9c.17, R.sup.9c.18, R.sup.9c.19,
R.sup.9c.20, R.sup.9c.21, R.sup.9c.22, R.sup.9c.23, R.sup.9c.24,
R.sup.9c.25, R.sup.9c.26, R.sup.9c.27, R.sup.9c.28, R.sup.9c.29,
R.sup.9c.30, R.sup.9c.31, R.sup.9c.32, R.sup.9c.33, R.sup.9c.34,
R.sup.9c.35, R.sup.9c.36, R.sup.9c.37, R.sup.9c.38, R.sup.9c.39,
R.sup.9c.40, R.sup.9c.41, R.sup.9c.42, R.sup.10c.1, R.sup.10c.2,
R.sup.10c.3, R.sup.10c.4, R.sup.10c.5, R.sup.10c.6, R.sup.10c.7,
R.sup.10c.8, R.sup.10c.9, R.sup.10c.10, R.sup.10c.11, R.sup.10c.12,
R.sup.10c.13, R.sup.10c.14, R.sup.10c.15, R.sup.10c.16,
R.sup.10c.17, R.sup.10c.18, R.sup.10c.19, R.sup.10c.20,
R.sup.10c.21, R.sup.10c.22, R.sup.10c.23, R.sup.10c.24,
R.sup.10c.25, R.sup.10c.26, R.sup.10c.27, R.sup.10c.28,
R.sup.10c.29, R.sup.10c.30, R.sup.10c.31, R.sup.10c.32,
R.sup.10c.33, R.sup.10c.34, R.sup.10c.35, R.sup.10c.36,
R.sup.10c.37, R.sup.10c.38, R.sup.10c.39, R.sup.10c.40,
R.sup.10c.41, R.sup.10c.42, X.sup.1, X.sup.2, X.sup.3, X.sup.4,
X.sup.5, X.sup.6, X.sup.7, X.sup.a1, X.sup.a2, X.sup.a3, X.sup.a4,
X.sup.a5, X.sup.a6, X.sup.c1, X.sup.c2, X.sup.c3, X.sup.c4,
X.sup.c5, X.sup.c6, X.sup.c7, X.sup.c8, X.sup.c9, X.sup.c10,
X.sup.c11, X.sup.c12, X.sup.c13, X.sup.c14, X.sup.c15, X.sup.c16,
X.sup.c17, X.sup.c18, X.sup.c19, X.sup.c20, X.sup.c21, X.sup.c22,
X.sup.c23, X.sup.c24, X.sup.c25, X.sup.c26, X.sup.c27, X.sup.c28,
X.sup.c29, X.sup.c30, X.sup.c31, X.sup.c32, X.sup.c33, X.sup.c34,
X.sup.c35, X.sup.c36, X.sup.c37, X.sup.c38, X.sup.c39, X.sup.c40,
X.sup.c41, X.sup.c42, m.sup.1, m.sup.2, m.sup.3, m.sup.4, m.sup.5,
m.sup.6, m.sup.7, n.sup.1, n.sup.2, n.sup.3, n.sup.4, n.sup.5,
n.sup.6, n.sup.7, v.sup.1, v.sup.2, v.sup.3, v.sup.4, v.sup.5,
v.sup.6, v.sup.7, m1.sup.1, m1.sup.2, m1.sup.3, m1.sup.4, m1.sup.5,
m1.sup.6, n1.sup.1, n1.sup.2, n1.sup.3, n1.sup.4, n1.sup.5,
n1.sup.6, v1.sup.1, v1.sup.2, v1.sup.3, v1.sup.4, v1.sup.5,
v1.sup.6, m3.sup.1, m3.sup.2, m3.sup.3, m3.sup.4, m3.sup.5,
m3.sup.6, m3.sup.7, m3.sup.8, m3.sup.9, m3.sup.10, m3.sup.11,
m3.sup.12, m3.sup.13, m3.sup.14, m3.sup.15, m3.sup.16, m3.sup.17,
m3.sup.18, m3.sup.19, m3.sup.20, m3.sup.21, m3.sup.22, m3.sup.23,
m3.sup.24, m3.sup.25, m3.sup.26, m3.sup.22, m3.sup.28, m3.sup.29,
m3.sup.30, m3.sup.31, m3.sup.32, m3.sup.33, m3.sup.34, m3.sup.35,
m3.sup.36, m3.sup.37, m3.sup.38, m3.sup.39, m3.sup.40, m3.sup.41,
m3.sup.42, n3.sup.1, n3.sup.2, n3.sup.3, n3.sup.4, n3.sup.5,
n3.sup.6, n3.sup.7, n3.sup.8, n3.sup.9, n3.sup.10, n3.sup.11,
n3.sup.12, n3.sup.13, n3.sup.14, n3.sup.15, n3.sup.16, n3.sup.17,
n3.sup.18, n3.sup.19, n3.sup.20, n3.sup.21, n3.sup.22, n3.sup.23,
n3.sup.24, n3.sup.25, n3.sup.26, n3.sup.27, n3.sup.28, n3.sup.29,
n3.sup.30, n3.sup.31, n3.sup.32, n3.sup.33, n3.sup.34, n3.sup.35,
n3.sup.36, n3.sup.37, n3.sup.38, n3.sup.39, n3.sup.40, n3.sup.41,
n3.sup.42, v3.sup.1, v3.sup.2, v3.sup.3, v3.sup.4, v3.sup.5,
v3.sup.6, v3.sup.7, v3.sup.8, v3.sup.9, v3.sup.10, v3.sup.11,
v3.sup.12, v3.sup.13, v3.sup.14, v3.sup.15, v3.sup.16, v3.sup.17,
v3.sup.18, v3.sup.19, v3.sup.20, v3.sup.21, v3.sup.22, v3.sup.23,
v3.sup.24, v3.sup.25, v3.sup.26, v3.sup.27, v3.sup.28, v3.sup.29,
v3.sup.30, v3.sup.31, v3.sup.32, v3.sup.33, v3.sup.34, v3.sup.35,
v3.sup.36, v3.sup.37, v3.sup.38, v3.sup.39, v3.sup.40, v3.sup.41,
v3.sup.42, respectively, wherein the definition of R.sup.3 is
assumed by R.sup.3.1, R.sup.3.2, R.sup.3.3, R.sup.3.4, R.sup.3.5,
R.sup.3.6, R.sup.3.7, the definition of R.sup.7 is assumed by
R.sup.7.1, R.sup.7.2, R.sup.7.3, R.sup.7.4, R.sup.7.5, R.sup.7.6,
R.sup.7.7, the definition of R.sup.8 is assumed by R.sup.8.1,
R.sup.8.2, R.sup.8.3, R.sup.8.4, R.sup.8.5, R.sup.8.6, R.sup.8.7,
the definition of R.sup.9 is assumed by R.sup.9.1, R.sup.9.2,
R.sup.9.3, R.sup.9.4, R.sup.9.5, R.sup.9.6, R.sup.9.7, the
definition of R.sup.10 is assumed by R.sup.10.1, R.sup.10.2,
R.sup.10.3, R.sup.10.4, R.sup.10.5, R.sup.10.6, R.sup.10.7, the
definition of R.sup.2A is assumed by R.sup.2A.1, R.sup.2A.2,
R.sup.2A.3, the definition of R.sup.7a is assumed by R.sup.7a.1,
R.sup.7a.2, R.sup.7a.3, R.sup.7a.4, R.sup.7a.5, R.sup.7a.6, the
definition of R.sup.8a is assumed by R.sup.8a.1, R.sup.8a.2,
R.sup.8a.3, R.sup.8a.4, R.sup.8a.5, R.sup.8a.6, the definition of
R.sup.9a is assumed by R.sup.9a.1, R.sup.9a.2, R.sup.9a.3,
R.sup.9a.4, R.sup.9a.5, R.sup.9a.6, the definition of R.sup.10a is
assumed by R.sup.10a.1, R.sup.10a.2, R.sup.10a.3, R.sup.10a.4,
R.sup.10a.5, R.sup.10a.6, the definition of R.sup.2B is assumed by
R.sup.2B.1, R.sup.2B.2, R.sup.2B.3, the definition of R.sup.2C is
assumed by R.sup.2C.1, R.sup.2C.2, R.sup.2C.3, R.sup.2C.4,
R.sup.2C.5, R.sup.2C.6, R.sup.2C.7, R.sup.2C.8, R.sup.2C.9,
R.sup.2C.10, R.sup.2C.11, R.sup.2C.12, R.sup.2C.13, R.sup.2C.14,
R.sup.2C.15, R.sup.2C.16, R.sup.2C.17, R.sup.2C.18, R.sup.2C.19,
R.sup.2C.20, R.sup.2C.21, R.sup.2C.22, R.sup.2C.23, R.sup.2C.24,
R.sup.2C.25, R.sup.2C.26, R.sup.2C.27, R.sup.2C.28, R.sup.2C.29,
R.sup.2C.30, R.sup.2C.31, R.sup.2C.32, R.sup.2C.33, R.sup.2C.34,
R.sup.2C.35, R.sup.2C.36, R.sup.2C.37, R.sup.2C.38, R.sup.2C.39,
R.sup.2C.40, R.sup.2C.41, R.sup.2C.42, the definition of R.sup.7c
is assumed by R.sup.7c.1, R.sup.7c.2, R.sup.7c.3, R.sup.7c.4,
R.sup.7c.5, R.sup.7c.6, R.sup.7c.7, R.sup.7c.8, R.sup.7c.9,
R.sup.7c.10, R.sup.7c.11, R.sup.7c.12, R.sup.7c.13, R.sup.7c.14,
R.sup.7c.15, R.sup.7c.16, R.sup.7c.17, R.sup.7c.18, R.sup.7c.19,
R.sup.7c.20, R.sup.7c.21, R.sup.7c.22, R.sup.7c.23, R.sup.7c.24,
R.sup.7c.25, R.sup.7c.26, R.sup.7c.27, R.sup.7c.28, R.sup.7c.29,
R.sup.7c.30, R.sup.7c.31, R.sup.7c.32, R.sup.7c.33, R.sup.7c.34,
R.sup.7c.35, R.sup.7c.36, R.sup.7c.37, R.sup.7c.38, R.sup.7c.39,
R.sup.7c.40, R.sup.7c.41, R.sup.7c.42, the definition of R.sup.8c
is assumed by R.sup.8c.1, R.sup.8c.2, R.sup.8c.3, R.sup.8c.4,
R.sup.8c.5, R.sup.8c.6, R.sup.8c.7, R.sup.8c.8, R.sup.8c.9,
R.sup.8c.10, R.sup.8c.11, R.sup.8c.12, R.sup.8c.13, R.sup.8c.14,
R.sup.8c.15, R.sup.8c.16, R.sup.8c.17, R.sup.8c.18, R.sup.8c.19,
R.sup.8c.20, R.sup.8c.21, R.sup.8c.22, R.sup.8c.23, R.sup.8c.24,
R.sup.8c.25, R.sup.8c.26, R.sup.8c.27, R.sup.8c.28, R.sup.8c.29,
R.sup.8c.30, R.sup.8c.31, R.sup.8c.32, R.sup.8c.33, R.sup.8c.34,
R.sup.8c.35, R.sup.8c.36, R.sup.8c.37, R.sup.8c.38, R.sup.8c.39,
R.sup.8c.40, R.sup.8c.41, R.sup.8c.42, the definition of R.sup.9c
is assumed by R.sup.9c.1, R.sup.9c.2, R.sup.9c.3, R.sup.9c.4,
R.sup.9c.5, R.sup.9c.6, R.sup.9c.7, R.sup.9c.8, R.sup.9c.9,
R.sup.9c.10, R.sup.9c.11, R.sup.9c.12, R.sup.9c.13, R.sup.9c.14,
R.sup.9c.15, R.sup.9c.16, R.sup.9c.17, R.sup.9c.18, R.sup.9c.19,
R.sup.9c.20, R.sup.9c.21, R.sup.9c.22, R.sup.9c.23, R.sup.9c.24,
R.sup.9c.25, R.sup.9c.26, R.sup.9c.27, R.sup.9c.28, R.sup.9c.29,
R.sup.9c.30, R.sup.9c.31, R.sup.9c.32, R.sup.9c.33, R.sup.9c.34,
R.sup.9c.35, R.sup.9c.36, R.sup.9c.37, R.sup.9c.38, R.sup.9c.39,
R.sup.9c.40, R.sup.9c.41, R.sup.9c.42, the definition of R.sup.10c
is assumed by R.sup.10c.1, R.sup.10c.2, R.sup.10c.3, R.sup.10c.4,
R.sup.10c.5, R.sup.10c.6, R.sup.10c.7, R.sup.10c.8, R.sup.10c.9,
R.sup.10c.10, R.sup.10c.11, R.sup.10c.12, R.sup.10c.13,
R.sup.10c.14, R.sup.10c.15, R.sup.10c.16, R.sup.10c.17,
R.sup.10c.18, R.sup.10c.19, R.sup.10c.20, R.sup.10c.21,
R.sup.10c.22, R.sup.10c.23, R.sup.10c.24, R.sup.10c.25,
R.sup.10c.26, R.sup.10c.27, R.sup.10c.28, R.sup.10c.29,
R.sup.10c.30, R.sup.10c.31, R.sup.10c.32, R.sup.10c.33,
R.sup.10c.34, R.sup.10c.35, R.sup.10c.36, R.sup.10c.37,
R.sup.10c.38, R.sup.10c.39, R.sup.10c.40, R.sup.10c.41,
R.sup.10c.42, the definition of X is assumed by X.sup.1, X.sup.2,
X.sup.3, X.sup.4, X.sup.5, X.sup.6, X.sup.7, the definition of
X.sup.a is assumed by X.sup.a1, X.sup.a2, X.sup.a3, X.sup.a4,
X.sup.a5, X.sup.a6, the definition of X.sup.c is assumed by
X.sup.c1, X.sup.c2, X.sup.c3, X.sup.c4, X.sup.c5, X.sup.c6,
X.sup.c7, X.sup.c8, X.sup.c9, X.sup.c10, X.sup.c11, X.sup.c12,
X.sup.c13, X.sup.c14, X.sup.c15, X.sup.c16, X.sup.c17, X.sup.c18,
X.sup.c19, X.sup.c20, X.sup.c21, X.sup.c22, X.sup.c23, X.sup.c24,
X.sup.c25, X.sup.c26, X.sup.c27, X.sup.c28, X.sup.c29, X.sup.c30,
X.sup.c31, X.sup.c32, X.sup.c33, X.sup.c34, X.sup.c35, X.sup.c36,
X.sup.c37, X.sup.c38, X.sup.c39, X.sup.c40, X.sup.c41, X.sup.c42,
the definition of m is assumed by m.sup.1, m.sup.2, m.sup.3,
m.sup.4, m.sup.5, m.sup.6, m.sup.7, the definition of n is assumed
by n.sup.1, n.sup.2, n.sup.3, n.sup.4, n.sup.5, n.sup.6, n.sup.7,
the definition of v is assumed by v.sup.1, v.sup.2, v.sup.3,
v.sup.4, v.sup.5, v.sup.6, v.sup.7, the definition of m1 is assumed
by m1.sup.1, m1.sup.2, m1.sup.3, m1.sup.4, m1.sup.5, m1.sup.6, the
definition of n1 is assumed by n1.sup.1, n1.sup.2, n1.sup.3,
n1.sup.4, n1.sup.5, n1.sup.6, the definition of v1 is assumed by
v1.sup.1, v1.sup.2, v1.sup.3, v1.sup.4, v1.sup.5, v1.sup.6, the
definition of m3 is assumed by m3.sup.1, m3.sup.2, m3.sup.3,
m3.sup.4, m3.sup.5, m3.sup.6, m3.sup.7, m3.sup.8, m3.sup.9,
m3.sup.10, m3.sup.11, m3.sup.12, m3.sup.13, m3.sup.14, m3.sup.15,
m3.sup.16, m3.sup.17, m3.sup.18, m3.sup.19, m3.sup.20, m3.sup.21,
m3.sup.22, m3.sup.23, m3.sup.24, m3.sup.25, m3.sup.26, m3.sup.27,
m3.sup.28, m3.sup.29 m3.sup.30, m3.sup.31, m3.sup.32, m3.sup.33,
m3.sup.34, m3.sup.35, m3.sup.36, m3.sup.37, m3.sup.38, m3.sup.39,
m3.sup.40, m3.sup.41, m3.sup.42, the definition of n3 is assumed by
n3.sup.1, n3.sup.2, n3.sup.3, n3.sup.4, n3.sup.5, n3.sup.6,
n3.sup.7, n3.sup.8, n3.sup.9, n3.sup.9, n3.sup.10, n3.sup.11,
n3.sup.12, n3.sup.13, n3.sup.14, n3.sup.15, n3.sup.16, n3.sup.17,
n3.sup.18, n3.sup.19, n3.sup.20, n3.sup.21, n3.sup.22, n3.sup.23,
n3.sup.24, n3.sup.25, n3.sup.26, n3.sup.27, n3.sup.28, n3.sup.29,
n3.sup.30, n3.sup.31, n3.sup.32, n3.sup.33, n3.sup.34, n3.sup.35,
n3.sup.36, n3.sup.37, n3.sup.38, n3.sup.39, n3.sup.40, n3.sup.41,
n3.sup.42, the definition of v3 is assumed by v3.sup.1, v3.sup.2,
v3.sup.3, v3.sup.4, v3.sup.5, v3.sup.6, v3.sup.7, v3.sup.8,
v3.sup.9, v3.sup.10, v3.sup.11, v3.sup.12, v3.sup.13, v3.sup.14,
v3.sup.15, v3.sup.16, v3.sup.17, v3.sup.18, v3.sup.19, v3.sup.20,
v3.sup.21, v3.sup.22, v3.sup.23, v3.sup.24, v3.sup.25, v3.sup.26,
v3.sup.27, v3.sup.28, v3.sup.29, v3.sup.30, v3.sup.31, v3.sup.32,
v3.sup.33, v3.sup.34, v3.sup.35, v3.sup.36, v3.sup.37, v3.sup.38,
v3.sup.39, v3.sup.40, v3.sup.41, v3.sup.42.
[0296] The variables used within a definition of R.sup.3, R.sup.7,
R.sup.8, R.sup.9, R.sup.10, R.sup.2A, R.sup.7a, R.sup.8a, R.sup.9a,
R.sup.10a, R.sup.2B, R.sup.2C, R.sup.7c, R.sup.8c, R.sup.9c,
R.sup.10c, X, X.sup.a, X.sup.c, m, n, v, m1, n1, v1, m3, n3, v3,
and/or other variables that appear at multiple instances and are
different may similarly be appropriately labeled to distinguish
each group for greater clarity.
III. Pharmaceutical Compositions and Methods
[0297] In a second aspect, a pharmaceutical composition including a
pharmaceutically acceptable excipient and a compound described
herein (including embodiments, examples, and any compound in Table
1, 2, 3, 4, or 5) is provided.
[0298] In a third aspect, a method of treating a disease in a
patient in need of such treatment is provided. The method including
administering a therapeutically effective amount of a compound
described herein (including embodiments, examples, and any compound
in Table 1, 2, 3, 4, or 5) to the patient. In some embodiments, the
disease is cancer. In some embodiments, the cancer is lung cancer,
colorectal cancer, colon cancer, pancreatic cancer, breast cancer,
or leukemia. In some embodiments, the cancer is lung cancer. In
some embodiments, the cancer is non-small cell lung cancer. In some
embodiments, the cancer is colon cancer. In some embodiments, the
cancer is colorectal cancer. In some embodiments, the cancer is
breast cancer. In some embodiments, the cancer is leukemia. In some
embodiments, the cancer is pancreatic cancer. In some embodiments,
the cancer is a cancer associated with aberrant K-Ras. In some
embodiments, the cancer is a cancer associated with a mutant K-Ras.
In some embodiments, the cancer is a cancer associated with K-Ras
G12C. In some embodiments, the cancer is a cancer associated with
K-Ras G12D. In some embodiments, the cancer is a cancer associated
with K-Ras G13C. In some embodiments, the cancer is a cancer
associated with K-Ras G13D.
[0299] In some embodiments, a method of treating a disorder in a
subject in need thereof is provided, comprising a) determining the
presence or absence of a mutation in a Ras protein (such as in a
K-Ras, N-Ras, or H-Ras protein) in a malignant or neoplastic cell
isolated from the subject and b) if the mutation is determined to
be present in the subject, administering to the subject a
therapeutically effective amount of a compound or pharmaceutically
acceptable salt of the invention. In some embodiments, the disorder
is cancer.
[0300] Various methods are suitable for determining the presence of
absence of a mutation in a Ras protein in a cell isolated from a
subject. As used herein, the term "mutation" is used to refer to
deletions, insertions and/or substitutions as indicated. For
example, assays can be performed to determine the presence of a
nucleic acid sequence in the cell, where the nucleic acid sequence
or a fragment thereof encodes the Ras protein. In some embodiments,
nucleic acid detection comprises the use of a hybridization assay.
Generally, a hybridization assay involves hybridization between
complimentary sequences of one or more pairs of polynucleotides,
such as between an oligonucleotide and an extracted or amplified
genomic DNA. Non-limiting examples of hybridization assays for
genotyping SNPs include polymerase chain reaction (PCR) assays,
blotting assays, TaqMan assays (Life Technologies; Carlsbad,
Calif.), mass spectroscopy assays, sequencing assays, gel
electrophoresis, ELISA, MALDI-TOF mass spectrometry hybridization,
primer extension, fluorescence detection, fluorescence resonance
energy transfer (FRET), fluorescence polarization, microchannel
electrophoresis, microarray, southern blot, northern blot, slot
blot, dot blot, single primer linear nucleic acid amplification, as
described in U.S. Pat. No. 6,251,639, SNP-IT, GeneChips
(Affymetrix; Santa Clara, Calif.), HuSNP (Affymetrix; Santa Clara,
Calif.), BeadArray (Illumina; San Diego, Calif.), Invader assay
(Hologic; Bedford, Mass.), MassEXTEND (Sequenom; San Diego Calif.),
MassCLEAVE (hMC) method (Sequenom; San Diego Calif.), and others.
PCR assays include any assays utilizing a PCR amplification
process. In some embodiments, the PCR assay comprises the use of
oligonucleotide primers that hybridize only to the variant or wild
type allele (e.g., to the region of polymorphism or mutation) of a
diallelic SNP. PCR assays may also combine amplification with probe
hybridization, such as in a TaqMan assay (see e.g., U.S. Pat. Nos.
5,962,233 and 5,538,848, each of which is herein incorporated by
reference) where the assay is performed during a PCR reaction.
Alternatively, detection of one or more mutations may utilize a
SNP-IT primer extension assay (Orchid Cellmark, Burlington, N.C.;
See e.g., U.S. Pat. Nos. 5,952,174 and 5,919,626, each of which is
herein incorporated by reference). In other embodiments, a mass
spectroscopy-based assay is used, such as a MassARRAY system
(Sequenom; San Diego Calif.). See for example U.S. Pat. Nos.
6,043,031; 5,777,324; and 5,605,798, incorporated herein by
reference. Detection of one or more mutations may also utilize an
array of probes (also referred to as a "DNA chip" assay, e.g. a
GeneChip assay--Affymetrix, Santa Clara, Calif.). See e.g., U.S.
Pat. Nos. 6,045,996; 5,925,525; and 5,858,659; each of which is
herein incorporated by reference. In still other embodiments, a DNA
microchip containing electronically captured probes is used (see
e.g. U.S. Pat. Nos. 6,017,696; 6,068,818; and 6,051,380; each
incorporated herein by reference). In yet other embodiments,
detection of mutations is performed using a "bead array" (Illumina,
San Diego, Calif.; See e.g., PCT Publications WO 99/67641 and WO
00/39587; each incorporated herein by reference). In other
embodiments, a sample comprising nucleic acid obtained from a cell
is sequenced to determine the presence of a mutation. Any method
known in the art may be used, for instance as described in US
2011/0319290 and US 2009/0298075, each incorporated herein by
reference. Sequencing may involve, for example, precipitation of
the nucleic acid followed by resuspension and sequencing using
Maxam-Gilbert sequencing, chain-termination sequencing,
pyrosequencing, polony sequencing, or nanopore sequencing.
[0301] In some embodiments, a method of treating a disorder in a
subject is provided, comprising determining the presence or absence
of a Ras mutation (e.g. K-Ras mutation) in a malignant or
neoplastic cell isolated from the subject, in connection with the
prescription an effective amount of a compound or pharmaceutically
acceptable salt of the invention, and, if the mutation is
determined to be present in the subject, an alert is provided to a
third party which may be, for example, a caregiver/care provider
(e.g. a medical professional such as a physician, including an
oncologist, a hospital, or clinic), care manager, other health
professional, a third-party payor, an insurance company or a
government office. For example, the third party is a caregiver who
is a physician. The alert may comprise providing a report in any
suitable form, such as in electronic or paper form. For example,
providing the alert is performed with the aid of a processor, for
example using a computer system executing instructions contained in
computer-readable media. One or more steps of methods described
here may be implemented and/or executed, in hardware or software.
Software may be stored, for example, in memory or in any other
computer readable medium and executed using a processor. Such
processors may be associated with one or more controllers,
calculation units, and/or other units of a computer system or
implanted in firmware. Computer readable media and memory include
RAM, ROM, flash memory, magnetic disks, laser disks, or other
media. Software or alerts may be delivered to a computing device or
between computing devices via any known delivery method, including,
for example, a communication channel such as a telephone line, the
internet, a wireless connection, or via a transportable medium such
as a computer readable disk, flash drive etc. Computing devices
include PCs, workstations, smartphones, tablets, PDAs or any other
devices comprising processors.
[0302] Reports can comprise output from the detection method such
as the presence and/or nature of the mutation. The alert may
further comprise information regarding prognosis, resistance, or
potential or suggested therapeutic options. The alert can comprise
information on the likely effectiveness of a therapeutic option,
the acceptability of a therapeutic option, or the advisability of
applying the therapeutic option to a patient having a mutation
identified in the test. The alert can include information, or a
recommendation on, the administration of a drug, e.g., the
administration at a preselected dosage or in a preselected
treatment regimen, and/or in combination with other drugs, to the
patient. In some embodiments, the subject is alerted if a subject
is designated as having a cancer in which aberrant Ras (e.g. H-Ras,
N-Ras, or K-Ras) expression or activity is involved. For example, a
subject is alerted if the subject is determined to have a mutated
version of Ras, e.g. K-Ras. In one embodiment, an alert is provided
if the subject is determined to have a G12C mutation.
[0303] In a fourth aspect, a method of modulating the activity of a
K-Ras protein is provided. The method including contacting the
K-Ras protein with an effective amount of a compound described
herein (including embodiments, examples, and any compound in Table
1, 2, 3, 4, or 5). In some embodiments, the activity of the K-Ras
protein is it's GTPase activity, nucleotide exchange, differential
GDP or GTP binding, effector protein binding, effector protein
activation, guanine exchange factor (GEF) binding, GEF-facilitated
nucleotide exchange, phosphate release, nucleotide release,
nucleotide binding, K-Ras subcellular localization, K-Ras
post-translational processing, K-Ras post-translational
modifications, or a GTP bound K-Ras signaling pathway. In some
embodiments, the activity of the K-Ras protein is its GTPase
activity, nucleotide exchange, effector protein binding, effector
protein activation, guanine exchange factor (GEF) binding,
GEF-facilitated nucleotide exchange, phosphate release, nucleotide
release, nucleotide binding, or the activity of a GTP bound K-Ras
signaling pathway. In some embodiments, the modulating of the
activity of the K-Ras protein includes modulating the binding
affinity of K-Ras for GDP. In some embodiments, the modulating of
the activity of the K-Ras protein includes the binding affinity of
K-Ras for GTP. In some embodiments, the modulating of the activity
of the K-Ras protein includes modulating the relative binding
affinity of K-Ras for GTP vs. GDP. In some embodiments, the
activity of the K-Ras protein is the activity of a signaling
pathway activated by GTP bound K-Ras. In some embodiments, the
modulating is increasing the activity of said K-Ras protein. In
some embodiments, the modulating is reducing the activity of said
K-Ras protein. In some embodiments, the K-Ras protein is a human
K-Ras protein. In some embodiments, the human K-Ras protein
contains a G12C mutation. In some embodiments, the human K-Ras
protein contains a G12D mutation. In some embodiments, the human
K-Ras protein contains a G13C mutation. In some embodiments, the
human K-Ras protein contains a G13D mutation. In some embodiments,
the K-Ras protein is a human K-Ras4A protein. In some embodiments,
the K-Ras protein is a human K-Ras4B protein. In some embodiments,
the K-Ras protein is a mutant K-Ras protein. In some embodiments,
the K-Ras protein is an activated K-Ras protein. In some
embodiments, the K-Ras protein is within a biological cell. In some
embodiments, the biological cell forms part of an organism. In some
embodiments of the method of modulating the activity of a K-Ras
protein including contacting the K-Ras protein with an effective
amount of a compound described herein (including embodiments,
examples, and any compound in Table 1, 2, 3, 4, or 5), the compound
is less effective at modulating the activity of an H-Ras protein.
In some embodiments of the method, the compound modulates the
activity of K-Ras at least two-fold more than it modulates the
activity of H-Ras. In some embodiments of the method, the compound
modulates the activity of K-Ras at least five-fold more than it
modulates the activity of H-Ras. In some embodiments of the method,
the compound modulates the activity of K-Ras at least ten-fold more
than it modulates the activity of H-Ras. In some embodiments of the
method, the compound modulates the activity of K-Ras at least
fifty-fold more than it modulates the activity of H-Ras. In some
embodiments of the method of modulating the activity of a K-Ras
protein including contacting the K-Ras protein with an effective
amount of a compound described herein (including embodiments,
examples, and any compound in Table 1, 2, 3, 4, or 5), the compound
is less effective at modulating the activity of an N-Ras protein.
In some embodiments of the method, the compound modulates the
activity of K-Ras at least two-fold more than it modulates the
activity of N-Ras. In some embodiments of the method, the compound
modulates the activity of K-Ras at least five-fold more than it
modulates the activity of N-Ras. In some embodiments of the method,
the compound modulates the activity of K-Ras at least ten-fold more
than it modulates the activity of N-Ras. In some embodiments of the
method, the compound modulates the activity of K-Ras at least
fifty-fold more than it modulates the activity of N-Ras.
[0304] In a fifth aspect, a method of modulating a K-Ras protein is
provided. The method including contacting the K-Ras protein with an
effective amount of a compound described herein (including
embodiments, examples, and in Table 1, 2, 3, 4, or 5). In some
embodiments, the K-Ras protein is modulated in K-Ras subcellular
localization, K-Ras post-translational processing, K-Ras
post-translational modifications, or a GTP bound K-Ras signaling
pathway. In some embodiments, the modulating is increasing the
post-translational processing or modifications of the K-Ras
protein. In some embodiments, the modulating is reducing the
post-translational processing or modifications of the K-Ras
protein. In some embodiments, the K-Ras protein is a human K-Ras
protein. In some embodiments, the human K-Ras protein contains a
G12C mutation. In some embodiments, the human K-Ras protein
contains a G12D mutation. In some embodiments, the human K-Ras
protein contains a G13C mutation. In some embodiments, the human
K-Ras protein contains a G13D mutation. In some embodiments, the
K-Ras protein is a human K-Ras4A protein. In some embodiments, the
K-Ras protein is a human K-Ras4B protein. In some embodiments, the
K-Ras protein is a mutant K-Ras protein. In some embodiments, the
K-Ras protein is an activated K-Ras protein. In some embodiments,
the K-Ras protein is within a biological cell. In some embodiments,
the biological cell forms part of an organism.
[0305] In a sixth aspect, a K-Ras protein covalently bonded to a
compound, for example a compound as described herein (including
modulators, inhibitors, embodiments, examples, and any compound in
Table 1, 2, 3, 4, or 5), is provided. The compound is covalently
bonded to a cysteine residue of the K-Ras protein. In some
embodiments, the covalently modified K-Ras protein has a modulated
activity relative to a control, wherein the activity is selected
from GTPase activity, nucleotide exchange, effector protein
binding, effector protein activation, guanine exchange factor (GEF)
binding, GEF-facilitated nucleotide exchange, phosphate release,
nucleotide release, nucleotide binding, K-Ras subcellular
localization, K-Ras post-translational processing, and K-Ras
post-translational modifications. In some embodiments, the
covalently modified K-Ras protein is modulated in K-Ras subcellular
localization, K-Ras post-translational processing, or K-Ras
post-translational modifications. In some embodiments, the
covalently modified K-Ras protein contains a G12C mutation. In some
embodiments, the compound is covalently bonded to cysteine residue
12. In some embodiments, the covalently modified K-Ras protein
contains a G13C mutation. In some embodiments, the compound is
covalently bonded to cysteine residue 13. In some embodiments, the
K-Ras protein is bonded to a K-Ras inhibitor, a mutant K-Ras
inhibitor, a K-Ras G12C inhibitor, or a K-Ras G13C inhibitor. In
some embodiments, the K-Ras protein is bonded to a K-Ras modulator,
a mutant K-Ras modulator, a K-Ras G12C modulator, or a K-Ras G13C
modulator.
[0306] In a seventh aspect, a K-Ras protein covalently bonded to a
compound, for example a compound as described herein (including
modulators, inhibitors, embodiments, examples, and in Table 1, 2,
3, 4, or 5), is provided. The compound is covalently bonded to an
aspartate residue of the K-Ras protein. In some embodiments, the
covalently modified K-Ras protein has a modulated activity relative
to a control, wherein the activity is selected from GTPase
activity, nucleotide exchange, effector protein binding, effector
protein activation, guanine exchange factor (GEF) binding,
GEF-facilitated nucleotide exchange, phosphate release, nucleotide
release, nucleotide binding, K-Ras subcellular localization, K-Ras
post-translational processing, and K-Ras post-translational
modifications. In some embodiments, the covalently modified K-Ras
protein is modulated in K-Ras subcellular localization, K-Ras
post-translational processing, or K-Ras post-translational
modifications. In some embodiments, the covalently modified K-Ras
protein contains a G12D mutation. In some embodiments, the compound
is covalently bonded to aspartate residue 12. In some embodiments,
the covalently modified K-Ras protein contains a G13D mutation. In
some embodiments, the compound is covalently bonded to aspartate
residue 13. In some embodiments, the K-Ras protein is bonded to a
K-Ras inhibitor, a mutant K-Ras inhibitor, a K-Ras G12D inhibitor,
or a K-Ras G13D inhibitor. In some embodiments, the K-Ras protein
is bonded to a K-Ras modulator, a mutant K-Ras modulator, a K-Ras
G12D modulator, or a K-Ras G13D modulator.
[0307] In an eighth aspect, a method of identifying a covalent
inhibitor of K-Ras protein is provided. The method including
contacting a K-Ras protein with a K-Ras inhibitor test compound,
allowing the K-Ras inhibitor test compound to covalently inhibit
the K-Ras protein, detecting the level of covalent inhibition of
the K-Ras protein, and thereby identifying a covalent inhibitor of
K-Ras protein. In some embodiments of the method, the K-Ras
inhibitor test compound is a Switch 2-Binding Pocket covalent
inhibitor test compound. In some embodiments, the K-Ras protein is
a G12C mutant K-Ras protein. In some embodiments, the K-Ras protein
is a G13C mutant K-Ras protein. In some embodiments, the K-Ras
protein is a G12D mutant K-Ras protein. In some embodiments, the
K-Ras protein is a G13D mutant K-Ras protein. In some embodiments
of the method, wherein the K-Ras protein contacting the Switch
2-Binding Pocket covalent inhibitor test compound is a mutant K-Ras
(e.g. K-Ras G12C, G12D, G13C, G13D), the method further includes
contacting a wildtype K-Ras protein with the Switch 2-Binding
Pocket covalent inhibitor test compound, allowing the Switch
2-Binding Pocket covalent inhibitor test compound to inhibit the
wildtype K-Ras protein, detecting the level of inhibition of the
wildtype K-Ras protein, comparing the level of inhibition of the
wildtype K-Ras protein to the level of covalent inhibition of the
mutant K-Ras protein (e.g. K-Ras G12C, G12D, G13C, G13D), wherein a
higher level of covalent inhibition of the mutant K-Ras protein
indicates the Switch 2-Binding Pocket covalent inhibitor test
compound is specific for the mutant K-Ras protein. In some
embodiments, the K-Ras inhibitor test compound is a Switch
2-Binding Pocket covalent inhibitor test compound and the K-Ras
protein is a G12C mutant K-Ras protein. In some embodiments, the
K-Ras inhibitor test compound is a Switch 2-Binding Pocket covalent
inhibitor test compound and the K-Ras protein is a G12D mutant
K-Ras protein. In some embodiments, the K-Ras inhibitor test
compound is a Switch 2-Binding Pocket covalent inhibitor test
compound and the K-Ras protein is a G13C mutant K-Ras protein. In
some embodiments, the K-Ras inhibitor test compound is a Switch
2-Binding Pocket covalent inhibitor test compound and the K-Ras
protein is a G13D mutant K-Ras protein. In some embodiments of the
method, the Switch 2-Binding Pocket covalent test inhibitor
compound does not covalently inhibit the wildtype K-Ras
protein.
[0308] In some embodiments of the above aspects, the compound binds
Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) behind Switch II. In embodiments, the
compound modulates the conformation of Switch II. In embodiments,
the compound modulates the conformation of Switch I. In
embodiments, the compound modulates the conformation of Switch I
and Switch II. In embodiments, the compound inhibits (e.g. by about
0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 2.0, 3.0, 4.0,
5.0, 6.0, 7.0, 8.0, 9.0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95,
100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000,
4000, 5000, 6000, 7000, 8000, 9000, 10000 fold or more) Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) nucleotide exchange (e.g. GDP for GTP or GTP for
GDP) relative to the absence of the compound. In embodiments, the
compound inhibits release of GDP from Ras (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound inhibits binding of GDP to Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound inhibits binding of GTP to Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments, the
compound increases (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,
0.7, 0.8, 0.9, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60,
65, 70, 75, 80, 85, 90, 95, 100, 200, 300, 400, 500, 600, 700, 800,
900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000
fold or more) Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) nucleotide exchange (e.g.
GDP for GTP or GTP for GDP) relative to the absence of the
compound. In embodiments, the compound increases release of GDP
from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) relative to the absence of the
compound. In embodiments, the compound increases release of GTP
from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) relative to the absence of the
compound. In embodiments, the compound increases binding of GDP to
Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) relative to the absence of the compound. In
embodiments, the compound inhibits binding of GTP to Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) relative to the absence of the compound. In
embodiments, the compound inhibits binding of a GTP analog (e.g.
mant-dGTP) to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) relative to the absence
of the compound. In embodiments, the compound modulates the
conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid that contacts
GTP in the absence of the compound. In embodiments, the compound
modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino
acid that contacts GDP in the absence of the compound. In
embodiments, the compound modulates the conformation of a plurality
of Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) amino acids that contact GTP in the
absence of the compound. In embodiments, the compound modulates the
conformation of a plurality of Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino
acids that contact GDP in the absence of the compound. In
embodiments, the compound modulates the binding of GTP and/or GDP
to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) compared to binding in the absence of
the compound. In embodiments, the compound modulates the release of
GTP and/or GDP from Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras,
K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) compared to release
in the absence of the compound. In embodiments, the compound
modulates the ratio of the binding of GTP and GDP to Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) compared to the ratio in the absence of the
compound. In embodiments, the compound modulates the ratio of the
rate of release of GTP and GDP from Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
compared to the ratio in the absence of the compound. In
embodiments, the compound modulates the conformation of a Ras amino
acid that contacts the gamma phosphate of GTP when GTP is bound to
Ras. In embodiments, the compound inhibits the binding of the gamma
phosphate of GTP relative to the binding in the absence of the
compound. In embodiments, the compound binds Ras (e.g. K-Ras,
H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D) protein bound to GDP and, after release of the GDP, modulates
the subsequent binding of GDP or GTP to the Ras bound to the
compound. In embodiments, the compound binds Ras (e.g. K-Ras,
H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D) protein bound to GDP and, after release of the GDP, modulates
the subsequent binding of GDP to the Ras bound to the compound. In
embodiments, the compound binds Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) protein
bound to GDP and, after release of the GDP, modulates the
subsequent binding of GTP to the Ras bound to the compound.
[0309] In embodiments, the compound inhibits proliferation of
cancer cells under nutrient deficient conditions relative to the
absence of the compound. In embodiments, the compound inhibits
growth of cancer cells under nutrient deficient conditions relative
to the absence of the compound. In embodiments, the compound
inhibits growth of cancer cells under nutrient deficient conditions
relative to the absence of the compound. In embodiments, the
compound inhibits growth of cancer cells under serum deprivation
conditions relative to the absence of the compound. In embodiments,
the compound inhibits proliferation of cancer cells under serum
deprivation conditions relative to the absence of the compound. In
embodiments, the compound inhibits growth of cancer cells under
conditions (e.g. local cell environment in a patient) mimicking
serum deprivation relative to the absence of the compound. In
embodiments, the compound inhibits proliferation of cancer cells
under conditions (e.g. local cell environment in a patient)
mimicking serum deprivation relative to the absence of the
compound.
[0310] In embodiments, the compound modulates the conformation of
the amino acid corresponding to amino acid 60 in human K-Ras in a
Ras protein. In embodiments, the compound modulates the distance
between the alpha carbon of the amino acid corresponding to amino
acid 12 in human K-Ras and the alpha carbon of the amino acid
corresponding to amino acid 60 in human K-Ras, in a Ras protein
(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D). In embodiments the compound increases the
distance between the alpha carbon of the amino acid corresponding
to amino acid 12 in human K-Ras and the alpha carbon of the amino
acid corresponding to amino acid 60 in human K-Ras, in a Ras
protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D). In embodiments the compound
increases the distance (e.g. by about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,
0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9,
2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2,
3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5,
4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,
5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1,
7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4,
8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7,
9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8,
10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9,
12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,
13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1,
14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,
15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3,
17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4,
18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5,
19.6, 19.7, 19.8, 19.9, 20.0, or more angstroms) between the alpha
carbon of the amino acid corresponding to amino acid 12 in human
K-Ras and the alpha carbon of the amino acid corresponding to amino
acid 60 in human K-Ras, in a Ras protein (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
relative to the absence of the compound. In embodiments the
compound increases the distance (e.g. by about 0.1, 0.2, 0.3, 0.4,
0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7,
1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0,
3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3,
4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6,
5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9,
7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2,
8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5,
9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7,
10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8,
11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9,
13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0,
14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1,
15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2,
17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3,
18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4,
19.5, 19.6, 19.7, 19.8, 19.9, 20.0, or more angstroms) between the
alpha carbon of the amino acid corresponding to amino acid 12 in
human K-Ras and the alpha carbon of the amino acid corresponding to
amino acid 60 in human K-Ras, in a Ras protein (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
when bound to GDP, relative to the absence of the compound. In
embodiments the compound increases the distance (e.g. by about 0.1,
0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4,
1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7,
2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0,
4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3,
5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6,
6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9,
8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2,
9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4,
10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5,
11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6,
12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7,
13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8,
14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9,
17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0,
18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1,
19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0, or more
angstroms) between the alpha carbon of the amino acid corresponding
to amino acid 12 in human K-Ras and the alpha carbon of the amino
acid corresponding to amino acid 60 in human K-Ras, in a Ras
protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) when bound to GTP, compared to the
distance in the absence of the compound. In embodiments, upon
binding to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) the compound (e.g. a compound
described herein, including embodiments and including a compound
described in a table, example, or figure) modulates the distance
between the alpha carbon of the amino acid corresponding to amino
acid 12 in human K-Ras and the alpha carbon of the amino acid
corresponding to amino acid 60 in human K-Ras, in the Ras protein
(e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) to be about 4.9 angstroms or greater (e.g.
about 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0, 5.1,
5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4,
6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7,
7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0,
9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2,
10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3,
11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4,
12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5,
13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6,
14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7,
15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8,
17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9,
19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0
angstroms, or greater). In embodiments, upon binding to Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) the compound (e.g. a compound described herein,
including embodiments and including a compound described in a
table, example, or figure) modulates the distance between the alpha
carbon of the amino acid corresponding to amino acid 12 in human
K-Ras and the alpha carbon of the amino acid corresponding to amino
acid 60 in human K-Ras, in the Ras protein (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
to be greater than about 4.9 angstroms (e.g. greater than about
5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 5.0, 5.1, 5.2,
5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5,
6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8,
7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1,
9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3,
10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4,
11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5,
12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6,
13.7, 13.8, 13.9, 14.0, 14.1, 14.2, 14.3, 14.4, 14.5, 14.6, 14.7,
14.8, 14.9, 15.0, 15.1, 15.2, 15.3, 15.4, 15.5, 15.6, 15.7, 15.8,
15.9, 17.0, 17.1, 17.2, 17.3, 17.4, 17.5, 17.6, 17.7, 17.8, 17.9,
18.0, 18.1, 18.2, 18.3, 18.4, 18.5, 18.6, 18.7, 18.8, 18.9, 19.0,
19.1, 19.2, 19.3, 19.4, 19.5, 19.6, 19.7, 19.8, 19.9, 20.0
angstroms, or greater). In embodiments, upon binding to Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) the compound (e.g. a compound described herein,
including embodiments and including a compound described in a
table, example, or figure) modulates the distance between the alpha
carbon of the amino acid corresponding to amino acid 12 in human
K-Ras and the alpha carbon of the amino acid corresponding to amino
acid 60 in human K-Ras, in the Ras protein (e.g. K-Ras, H-Ras,
N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D)
to be 4.9 angstroms or greater (e.g. 5.0, 5.1, 5.2, 5.3, 5.4, 5.5,
5.6, 5.7, 5.8, 5.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,
5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1,
7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4,
8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7,
9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8,
10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9,
12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0,
13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1,
14.2, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2,
15.3, 15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3,
17.4, 17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4,
18.5, 18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5,
19.6, 19.7, 19.8, 19.9, 20.0 angstroms, or greater). In
embodiments, upon binding to Ras (e.g. K-Ras, H-Ras, N-Ras, mutant
Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) the compound
(e.g. a compound described herein, including embodiments and
including a compound described in a table, example, or figure)
modulates the distance between the alpha carbon of the amino acid
corresponding to amino acid 12 in human K-Ras and the alpha carbon
of the amino acid corresponding to amino acid 60 in human K-Ras, in
the Ras protein (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) to be greater than 4.9
angstroms (e.g. greater than 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6,
5.7, 5.8, 5.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9,
6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7.0, 7.1, 7.2,
7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5,
8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8,
9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9,
11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0,
12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1,
13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0, 14.1, 14.2,
14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.0, 15.1, 15.2, 15.3,
15.4, 15.5, 15.6, 15.7, 15.8, 15.9, 17.0, 17.1, 17.2, 17.3, 17.4,
17.5, 17.6, 17.7, 17.8, 17.9, 18.0, 18.1, 18.2, 18.3, 18.4, 18.5,
18.6, 18.7, 18.8, 18.9, 19.0, 19.1, 19.2, 19.3, 19.4, 19.5, 19.6,
19.7, 19.8, 19.9, 20.0 angstroms, or greater).
[0311] In embodiments, the compound increases the flexibility of
Switch I relative to the absence of the compound. In embodiments,
the compound increases the disorder of Switch I relative to the
absence of the compound. In embodiments, the compound inhibits the
binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C,
K-Ras G13C, K-Ras G12D, K-Ras G13D) to another protein. In
embodiments, the compound inhibits the binding of Ras ((e.g. K-Ras,
H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras
G13D) to another protein, wherein the binding is dependent on Ras
binding to GTP. In embodiments, the compound inhibits the binding
of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras
G13C, K-Ras G12D, K-Ras G13D) to another protein, wherein the
binding is dependent on Ras binding to GDP. In embodiments, the
compound inhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) to Raf
(e.g. Raf1). In embodiments, the compound inhibits the binding of
Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) to SOS. In embodiments, the compound
inhibits the binding of Ras ((e.g. K-Ras, H-Ras, N-Ras, mutant Ras)
to a GEF. In embodiments, the compound inhibits the binding of Ras
((e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C,
K-Ras G12D, K-Ras G13D) to PI3K. In embodiments, the compound
modulates metal binding near the nucleotide binding site. In
embodiments, the compound modulates the conformation of the Ras
metal binding site near the nucleotide binding site. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid relative to the conformation in the
absence of the compound, wherein the Ras amino acid conformation is
also modulated by a Ras G60 mutation. In embodiments, the compound
modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino
acid relative to the conformation in the absence of the compound,
wherein the Ras amino acid conformation is also modulated by a Ras
G60A mutation. In embodiments, the compound modulates the
conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras
G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino acid relative to
the conformation in the absence of the compound, wherein the Ras
amino acid conformation is also modulated by a Ras T35 mutation. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid relative to the conformation in the
absence of the compound, wherein the Ras amino acid conformation is
also modulated by a Ras T35S mutation. In embodiments, the compound
modulates the conformation of a Ras (e.g. K-Ras, H-Ras, N-Ras,
mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras G12D, K-Ras G13D) amino
acid relative to the conformation in the absence of the compound,
wherein the Ras amino acid conformation is also modulated by a
mutation of the Ras amino acid corresponding to K-Ras G60. In
embodiments, the compound modulates the conformation of a Ras (e.g.
K-Ras, H-Ras, N-Ras, mutant Ras, K-Ras G12C, K-Ras G13C, K-Ras
G12D, K-Ras G13D) amino acid relative to the conformation in the
absence of the compound, wherein the Ras amino acid conformation is
also modulated by a mutation of the Ras amino acid corresponding to
K-Ras T35.
[0312] The pharmaceutical compositions include optical isomers,
diastereomers, or pharmaceutically acceptable salts of the
modulators disclosed herein. The compound included in the
pharmaceutical composition may be covalently attached to a carrier
moiety, as described above. Alternatively, the compound included in
the pharmaceutical composition is not covalently linked to a
carrier moiety.
[0313] In a ninth aspect, a Ras protein (e.g. K-Ras, N-Ras, H-Ras,
or another Ras protein described herein) covalently bonded (e.g.
reversibly or irreversibly) to a compound, for example a compound
as described herein (including modulators, inhibitors, embodiments,
examples, and any compound in Table 1, 2, 3, 4, or 5), is provided.
In some embodiments, the compound is covalently bonded to a
cysteine, aspartate, lysine, tyrosine or glutamate residue of the
Ras protein (e.g. K-Ras, N-Ras, H-Ras, or another Ras protein
described herein). In some embodiments, the compound is a
modulator. In some embodiments, the compound is a modulator such as
an inhibitor. In some embodiments, the compound is a Ras modulator.
In some embodiments, the compound is a Ras inhibitor.
[0314] The compounds of the invention (i.e. compounds described
herein, including embodiments, examples, compounds of Table 1, 2,
3, 4, or 5) can be administered alone or can be coadministered to
the patient. Coadministration is meant to include simultaneous or
sequential administration of the compounds individually or in
combination (more than one compound). Thus, the preparations can
also be combined, when desired, with other active substances (e.g.
to reduce metabolic degradation).
[0315] The compounds of the present invention can be prepared and
administered in a wide variety of oral, parenteral and topical
dosage forms. Oral preparations include tablets, pills, powder,
dragees, capsules, liquids, lozenges, cachets, gels, syrups,
slurries, suspensions, etc., suitable for ingestion by the patient.
The compounds of the present invention can also be administered by
injection, that is, intravenously, intramuscularly,
intracutaneously, subcutaneously, intraduodenally, or
intraperitoneally. Also, the compounds described herein can be
administered by inhalation, for example, intranasally.
Additionally, the compounds of the present invention can be
administered transdermally. It is also envisioned that multiple
routes of administration (e.g., intramuscular, oral, transdermal)
can be used to administer the compounds of the invention.
Accordingly, the present invention also provides pharmaceutical
compositions comprising a pharmaceutically acceptable excipient and
one or more compounds of the invention.
[0316] For preparing pharmaceutical compositions from the compounds
of the present invention, pharmaceutically acceptable carriers can
be either solid or liquid. Solid form preparations include powders,
tablets, pills, capsules, cachets, suppositories, and dispersible
granules. A solid carrier can be one or more substances, that may
also act as diluents, flavoring agents, binders, preservatives,
tablet disintegrating agents, or an encapsulating material.
[0317] In powders, the carrier is a finely divided solid in a
mixture with the finely divided active component (e.g. a compound
provided herein). In tablets, the active component is mixed with
the carrier having the necessary binding properties in suitable
proportions and compacted in the shape and size desired. The
powders and tablets preferably contain from 5% to 70% of the active
compound.
[0318] Suitable solid excipients include, but are not limited to,
magnesium carbonate; magnesium stearate; talc; pectin; dextrin;
starch; tragacanth; a low melting wax; cocoa butter; carbohydrates;
sugars including, but not limited to, lactose, sucrose, mannitol,
or sorbitol, starch from corn, wheat, rice, potato, or other
plants; cellulose such as methyl cellulose,
hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose;
and gums including arabic and tragacanth; as well as proteins
including, but not limited to, gelatin and collagen. If desired,
disintegrating or solubilizing agents may be added, such as the
cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt
thereof, such as sodium alginate.
[0319] Dragee cores are provided with suitable coatings such as
concentrated sugar solutions, which may also contain gum arabic,
talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol,
and/or titanium dioxide, lacquer solutions, and suitable organic
solvents or solvent mixtures. Dyestuffs or pigments may be added to
the tablets or dragee coatings for product identification or to
characterize the quantity of active compound (i.e., dosage).
Pharmaceutical preparations of the invention can also be used
orally using, for example, push-fit capsules made of gelatin, as
well as soft, sealed capsules made of gelatin and a coating such as
glycerol or sorbitol.
[0320] For preparing suppositories, a low melting wax, such as a
mixture of fatty acid glycerides or cocoa butter, is first melted
and the active component is dispersed homogeneously therein, as by
stirring. The molten homogeneous mixture is then poured into
convenient sized molds, allowed to cool, and thereby to
solidify.
[0321] Liquid form preparations include solutions, suspensions, and
emulsions, for example, water or water/propylene glycol solutions.
For parenteral injection, liquid preparations can be formulated in
solution in aqueous polyethylene glycol solution.
[0322] When parenteral application is needed or desired,
particularly suitable admixtures for the compounds of the invention
are injectable, sterile solutions, preferably oily or aqueous
solutions, as well as suspensions, emulsions, or implants,
including suppositories. In particular, carriers for parenteral
administration include aqueous solutions of dextrose, saline, pure
water, ethanol, glycerol, propylene glycol, peanut oil, sesame oil,
polyoxyethylene-block polymers, and the like. Ampules are
convenient unit dosages. The compounds of the invention can also be
incorporated into liposomes or administered via transdermal pumps
or patches. Pharmaceutical admixtures suitable for use in the
present invention are well-known to those of skill in the art and
are described, for example, in Pharmaceutical Sciences (17th Ed.,
Mack Pub. Co., Easton, Pa.) and WO 96/05309, the teachings of both
of which are hereby incorporated by reference.
[0323] Aqueous solutions suitable for oral use can be prepared by
dissolving the active component (e.g. compounds described herein,
including embodiments, examples, compounds of Table 1, 2, 3, 4, or
5) in water and adding suitable colorants, flavors, stabilizers,
and thickening agents as desired. Aqueous suspensions suitable for
oral use can be made by dispersing the finely divided active
component in water with viscous material, such as natural or
synthetic gums, resins, methylcellulose, sodium
carboxymethylcellulose, hydroxypropylmethylcellulose, sodium
alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia, and
dispersing or wetting agents such as a naturally occurring
phosphatide (e.g., lecithin), a condensation product of an alkylene
oxide with a fatty acid (e.g., polyoxyethylene stearate), a
condensation product of ethylene oxide with a long chain aliphatic
alcohol (e.g., heptadecaethylene oxycetanol), a condensation
product of ethylene oxide with a partial ester derived from a fatty
acid and a hexitol (e.g., polyoxyethylene sorbitol mono-oleate), or
a condensation product of ethylene oxide with a partial ester
derived from fatty acid and a hexitol anhydride (e.g.,
polyoxyethylene sorbitan mono-oleate). The aqueous suspension can
also contain one or more preservatives such as ethyl or n-propyl
p-hydroxybenzoate, one or more coloring agents, one or more
flavoring agents and one or more sweetening agents, such as
sucrose, aspartame or saccharin. Formulations can be adjusted for
osmolarity.
[0324] Also included are solid form preparations that are intended
to be converted, shortly before use, to liquid form preparations
for oral administration. Such liquid forms include solutions,
suspensions, and emulsions. These preparations may contain, in
addition to the active component, colorants, flavors, stabilizers,
buffers, artificial and natural sweeteners, dispersants,
thickeners, solubilizing agents, and the like.
[0325] Oil suspensions can contain a thickening agent, such as
beeswax, hard paraffin or cetyl alcohol. Sweetening agents can be
added to provide a palatable oral preparation, such as glycerol,
sorbitol or sucrose. These formulations can be preserved by the
addition of an antioxidant such as ascorbic acid. As an example of
an injectable oil vehicle, see Minto, J. Pharmacol. Exp. Ther.
281:93-102, 1997. The pharmaceutical formulations of the invention
can also be in the form of oil-in-water emulsions. The oily phase
can be a vegetable oil or a mineral oil, described above, or a
mixture of these. Suitable emulsifying agents include
naturally-occurring gums, such as gum acacia and gum tragacanth,
naturally occurring phosphatides, such as soybean lecithin, esters
or partial esters derived from fatty acids and hexitol anhydrides,
such as sorbitan mono-oleate, and condensation products of these
partial esters with ethylene oxide, such as polyoxyethylene
sorbitan mono-oleate. The emulsion can also contain sweetening
agents and flavoring agents, as in the formulation of syrups and
elixirs. Such formulations can also contain a demulcent, a
preservative, or a coloring agent.
[0326] The pharmaceutical preparation is preferably in unit dosage
form. In such form the preparation is subdivided into unit doses
containing appropriate quantities of the active component. The unit
dosage form can be a packaged preparation, the package containing
discrete quantities of preparation, such as packeted tablets,
capsules, and powders in vials or ampoules. Also, the unit dosage
form can be a capsule, tablet, cachet, or lozenge itself, or it can
be the appropriate number of any of these in packaged form.
[0327] The quantity of active component in a unit dose preparation
may be varied or adjusted from 0.1 mg to 10000 mg, more typically
1.0 mg to 1000 mg, most typically 10 mg to 500 mg, according to the
particular application and the potency of the active component. The
composition can, if desired, also contain other compatible
therapeutic agents.
[0328] Some compounds may have limited solubility in water and
therefore may require a surfactant or other appropriate co-solvent
in the composition. Such co-solvents include: Polysorbate 20, 60
and 80; Pluronic F-68, F-84 and P-103; cyclodextrin; polyoxyl 35
castor oil; or other agents known to those skilled in the art. Such
co-solvents are typically employed at a level between about 0.01%
and about 2% by weight.
[0329] Viscosity greater than that of simple aqueous solutions may
be desirable to decrease variability in dispensing the
formulations, to decrease physical separation of components of a
suspension or emulsion of formulation and/or otherwise to improve
the formulation. Such viscosity building agents include, for
example, polyvinyl alcohol, polyvinyl pyrrolidone, methyl
cellulose, hydroxy propyl methylcellulose, hydroxyethyl cellulose,
carboxymethyl cellulose, hydroxy propyl cellulose, chondroitin
sulfate and salts thereof, hyaluronic acid and salts thereof,
combinations of the foregoing, and other agents known to those
skilled in the art. Such agents are typically employed at a level
between about 0.01% and about 2% by weight. Determination of
acceptable amounts of any of the above adjuvants is readily
ascertained by one skilled in the art.
[0330] The compositions of the present invention may additionally
include components to provide sustained release and/or comfort.
Such components include high molecular weight, anionic mucomimetic
polymers, gelling polysaccharides and finely-divided drug carrier
substrates. These components are discussed in greater detail in
U.S. Pat. Nos. 4,911,920; 5,403,841; 5,212,162; and 4,861,760. The
entire contents of these patents are incorporated herein by
reference in their entirety for all purposes.
[0331] Pharmaceutical compositions provided by the present
invention include compositions wherein the active ingredient (e.g.
compounds described herein, including embodiments, examples,
compounds of Table 1, 2, 3, 4, or 5) is contained in a
therapeutically effective amount, i.e., in an amount effective to
achieve its intended purpose. The actual amount effective for a
particular application will depend, inter alia, on the condition
being treated. When administered in methods to treat a disease,
such compositions will contain an amount of active ingredient
effective to achieve the desired result, e.g., modulating the
activity of a target molecule (e.g. a Ras, K-Ras, K-Ras G12C, K-Ras
G12D, K-Ras G13C, K-Ras G13D, a mutant K-Ras, an activated K-Ras),
and/or reducing, eliminating, or slowing the progression of disease
symptoms (e.g. cancer growth or metastasis). Determination of a
therapeutically effective amount of a compound of the invention is
well within the capabilities of those skilled in the art,
especially in light of the detailed disclosure herein.
[0332] The dosage and frequency (single or multiple doses)
administered to a mammal can vary depending upon a variety of
factors, for example, whether the mammal suffers from another
disease, and its route of administration; size, age, sex, health,
body weight, body mass index, and diet of the recipient; nature and
extent of symptoms of the disease being treated (e.g. lung cancer,
NSCL cancer, colon cancer, colorectal cancer, breast cancer,
pancreatic cancer, leukemia), kind of concurrent treatment,
complications from the disease being treated or other
health-related problems. Other therapeutic regimens or agents can
be used in conjunction with the methods and compounds of
Applicants' invention. Adjustment and manipulation of established
dosages (e.g., frequency and duration) are well within the ability
of those skilled in the art.
[0333] For any compound described herein, the therapeutically
effective amount can be initially determined from cell culture
assays. Target concentrations will be those concentrations of
active compound(s) that are capable of achieving the methods
described herein, as measured using the methods described herein or
known in the art.
[0334] As is well known in the art, therapeutically effective
amounts for use in humans can also be determined from animal
models. For example, a dose for humans can be formulated to achieve
a concentration that has been found to be effective in animals. The
dosage in humans can be adjusted by monitoring compounds
effectiveness and adjusting the dosage upwards or downwards, as
described above. Adjusting the dose to achieve maximal efficacy in
humans based on the methods described above and other methods is
well within the capabilities of the ordinarily skilled artisan.
[0335] Dosages may be varied depending upon the requirements of the
patient and the compound being employed. The dose administered to a
patient, in the context of the present invention should be
sufficient to effect a beneficial therapeutic response in the
patient over time. The size of the dose also will be determined by
the existence, nature, and extent of any adverse side-effects.
Determination of the proper dosage for a particular situation is
within the skill of the practitioner. Generally, treatment is
initiated with smaller dosages which are less than the optimum dose
of the compound. Thereafter, the dosage is increased by small
increments until the optimum effect under circumstances is reached.
In one embodiment, the dosage range is 0.001% to 10% w/v. In
another embodiment, the dosage range is 0.1% to 5% w/v.
[0336] Dosage amounts and intervals can be adjusted individually to
provide levels of the administered compound effective for the
particular clinical indication being treated. This will provide a
therapeutic regimen that is commensurate with the severity of the
individual's disease state.
[0337] Utilizing the teachings provided herein, an effective
prophylactic or therapeutic treatment regimen can be planned that
does not cause substantial toxicity and yet is effective to treat
the clinical symptoms demonstrated by the particular patient. This
planning should involve the careful choice of active compound by
considering factors such as compound potency, relative
bioavailability, patient body weight, presence and severity of
adverse side effects, preferred mode of administration and the
toxicity profile of the selected agent.
[0338] The ratio between toxicity and therapeutic effect for a
particular compound is its therapeutic index and can be expressed
as the ratio between LD.sub.50 (the amount of compound lethal in
50% of the population) and ED.sub.50 (the amount of compound
effective in 50% of the population). Compounds that exhibit high
therapeutic indices are preferred. Therapeutic index data obtained
from cell culture assays and/or animal studies can be used in
formulating a range of dosages for use in humans. The dosage of
such compounds preferably lies within a range of plasma
concentrations that include the ED.sub.50 with little or no
toxicity. The dosage may vary within this range depending upon the
dosage form employed and the route of administration utilized. See,
e.g. Fingl et al., In: THE PHARMACOLOGICAL BASIS OF
T.sup.HERAPEUTICS, Ch. 1, p. 1, 1975. The exact formulation, route
of administration and dosage can be chosen by the individual
physician in view of the patient's condition and the particular
method in which the compound is used.
IV. Administration
[0339] The compositions of the present invention can be delivered
by transdermally, by a topical route, formulated as applicator
sticks, solutions, suspensions, emulsions, gels, creams, ointments,
pastes, jellies, paints, powders, and aerosols. For therapeutic
applications, the compounds or drugs of the present invention can
be administered alone or co-administered in combination with
conventional chemotherapy, radiotherapy, hormonal therapy, and/or
immunotherapy.
[0340] The compositions of the present invention can also be
delivered as microspheres for slow release in the body. For
example, microspheres can be administered via intradermal injection
of drug-containing microspheres, which slowly release
subcutaneously (see Rao, J. Biomater Sci. Polym. Ed. 7:623-645,
1995; as biodegradable and injectable gel formulations (see, e.g.,
Gao Pharm. Res. 12:857-863, 1995); or, as microspheres for oral
administration (see, e.g., Eyles, J. Pharm. Pharmacol. 49:669-674,
1997). Both transdermal and intradermal routes afford constant
delivery for weeks or months.
[0341] The pharmaceutical compositions of the present invention can
be provided as a salt and can be formed with many acids, including
but not limited to hydrochloric, sulfuric, acetic, lactic,
tartaric, malic, succinic, etc. Pharmaceutical compositions
described herein may be salts of a compound or composition which
are prepared with relatively nontoxic acids or bases, depending on
the particular substituents found on the compounds described
herein. When compounds of the present invention contain relatively
acidic functionalities, base addition salts can be obtained by
contacting the neutral form of such compounds with a sufficient
amount of the desired base, either neat or in a suitable inert
solvent. Examples of pharmaceutically acceptable base addition
salts include sodium, potassium, calcium, ammonium, organic amino,
or magnesium salt, or a similar salt. When compounds of the present
invention contain relatively basic functionalities, acid addition
salts can be obtained by contacting the neutral form of such
compounds with a sufficient amount of the desired acid, either neat
or in a suitable inert solvent. Examples of pharmaceutically
acceptable acid addition salts include those derived from inorganic
acids like hydrochloric, hydrobromic, nitric, carbonic,
monohydrogencarbonic, phosphoric, monohydrogenphosphoric,
dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or
phosphorous acids and the like, as well as the salts derived from
relatively nontoxic organic acids like acetic, propionic,
isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric,
lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic,
citric, tartaric, methanesulfonic, and the like. Also included are
salts of amino acids such as arginate and the like, and salts of
organic acids like glucuronic or galactunoric acids and the like
(see, e.g., Berge et al., Journal of Pharmaceutical Science 66:1-19
(1977)). Certain specific compounds of the present invention
contain both basic and acidic functionalities that allow the
compounds to be converted into either base or acid addition salts.
Other pharmaceutically acceptable carriers known to those of skill
in the art are suitable for the present invention. Salts tend to be
more soluble in aqueous or other protonic solvents that are the
corresponding free base forms. In other cases, the preparation may
be a lyophilized powder in 1 mM-50 mM histidine, 0.1%-2% sucrose,
2%-7% mannitol at a pH range of 4.5 to 5.5, that is combined with
buffer prior to use.
[0342] The neutral forms of the compounds may be regenerated by
contacting the salt with a base or acid and isolating the parent
compound in the conventional manner. The parent form of the
compound differs from the various salt forms in certain physical
properties, such as solubility in polar solvents, but otherwise the
salts are equivalent to the parent form of the compound for the
purposes of the present invention.
[0343] Certain compositions described herein or Ras inhibitor
compounds of the present invention can exist in unsolvated forms as
well as solvated forms, including hydrated forms. In general, the
solvated forms are equivalent to unsolvated forms and are intended
to be encompassed within the scope of the present invention.
Certain Ras inhibitor compounds of the present invention may exist
in multiple crystalline or amorphous forms. In general, all
physical forms are equivalent for the uses contemplated by the
present invention and are intended to be within the scope of the
present invention.
[0344] In another embodiment, the compositions of the present
invention are useful for parenteral administration, such as
intravenous (IV) administration or administration into a body
cavity or lumen of an organ. The formulations for administration
will commonly comprise a solution of the compositions of the
present invention dissolved in a pharmaceutically acceptable
carrier. Among the acceptable vehicles and solvents that can be
employed are water and Ringer's solution, an isotonic sodium
chloride. In addition, sterile fixed oils can conventionally be
employed as a solvent or suspending medium. For this purpose any
bland fixed oil can be employed including synthetic mono- or
diglycerides. In addition, fatty acids such as oleic acid can
likewise be used in the preparation of injectables. These solutions
are sterile and generally free of undesirable matter. These
formulations may be sterilized by conventional, well known
sterilization techniques. The formulations may contain
pharmaceutically acceptable auxiliary substances as required to
approximate physiological conditions such as pH adjusting and
buffering agents, toxicity adjusting agents, e.g., sodium acetate,
sodium chloride, potassium chloride, calcium chloride, sodium
lactate and the like. The concentration of the compositions of the
present invention in these formulations can vary widely, and will
be selected primarily based on fluid volumes, viscosities, body
weight, and the like, in accordance with the particular mode of
administration selected and the patient's needs. For IV
administration, the formulation can be a sterile injectable
preparation, such as a sterile injectable aqueous or oleaginous
suspension. This suspension can be formulated according to the
known art using those suitable dispersing or wetting agents and
suspending agents. The sterile injectable preparation can also be a
sterile injectable solution or suspension in a nontoxic
parenterally-acceptable diluent or solvent, such as a solution of
1,3-butanediol.
[0345] In another embodiment, the formulations of the compositions
of the present invention can be delivered by the use of liposomes
which fuse with the cellular membrane or are endocytosed, i.e., by
employing receptor ligands attached to the liposome, that bind to
surface membrane protein receptors of the cell resulting in
endocytosis. By using liposomes, particularly where the liposome
surface carries receptor ligands specific for target cells, or are
otherwise preferentially directed to a specific organ, one can
focus the delivery of the compositions of the present invention
into the target cells in vivo. (See, e.g., Al-Muhammed, J.
Microencapsul. 13:293-306, 1996; Chonn, Curr. Opin. Biotechnol.
6:698-708, 1995; Ostro, Am. J. Hosp. Pharm. 46:1576-1587,
1989).
[0346] The compounds described herein can be used in combination
with one another, with other active agents known to be useful in
treating a disease associated with cells expressing a particular
Ras, K-Ras, mutant K-Ras (e.g. cancer), or with adjunctive agents
that may not be effective alone, but may contribute to the efficacy
of the active agent.
[0347] In some embodiments, co-administration includes
administering one active agent within 0.5, 1, 2, 4, 6, 8, 10, 12,
16, 20, or 24 hours of a second active agent. Co-administration
includes administering two active agents simultaneously,
approximately simultaneously (e.g., within about 1, 5, 10, 15, 20,
or 30 minutes of each other), or sequentially in any order. In some
embodiments, co-administration can be accomplished by
co-formulation, i.e., preparing a single pharmaceutical composition
including both active agents. In other embodiments, the active
agents can be formulated separately. In another embodiment, the
active and/or adjunctive agents may be linked or conjugated to one
another.
[0348] As a non-limiting example, the compounds described herein
can be co-administered with conventional chemotherapeutic agents
including alkylating agents (e.g., cyclophosphamide, ifosfamide,
chlorambucil, busulfan, melphalan, mechlorethamine, uramustine,
thiotepa, nitrosoureas, etc.), anti-metabolites (e.g.,
5-fluorouracil, azathioprine, methotrexate, leucovorin,
capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine,
pemetrexed, raltitrexed, etc.), plant alkaloids (e.g., vincristine,
vinblastine, vinorelbine, vindesine, podophyllotoxin, paclitaxel,
docetaxel, etc.), topoisomerase inhibitors (e.g., irinotecan,
topotecan, amsacrine, etoposide (VP16), etoposide phosphate,
teniposide, etc.), antitumor antibiotics (e.g., doxorubicin,
adriamycin, daunorubicin, epirubicin, actinomycin, bleomycin,
mitomycin, mitoxantrone, plicamycin, etc.), platinum-based
compounds (e.g. cisplatin, oxaloplatin, carboplatin, etc.), and the
like.
[0349] The compounds described herein can also be co-administered
with conventional hormonal therapeutic agents including, but not
limited to, steroids (e.g., dexamethasone), finasteride, aromatase
inhibitors, tamoxifen, and gonadotropin-releasing hormone agonists
(GnRH) such as goserelin.
[0350] Additionally, the compounds described herein can be
co-administered with conventional immunotherapeutic agents
including, but not limited to, immunostimulants (e.g., Bacillus
Calmette-Guerin (BCG), levamisole, interleukin-2, alpha-interferon,
etc.), monoclonal antibodies (e.g., anti-CD20, anti-HER2,
anti-CD52, anti-HLA-DR, and anti-VEGF monoclonal antibodies),
immunotoxins (e.g., anti-CD33 monoclonal antibody-calicheamicin
conjugate, anti-CD22 monoclonal antibody-pseudomonas exotoxin
conjugate, etc.), and radioimmunotherapy (e.g., anti-CD20
monoclonal antibody conjugated to .sup.111In, .sup.90Y, or
.sup.131I, etc.).
[0351] In a further embodiment, the compounds described herein can
be co-administered with conventional radiotherapeutic agents
including, but not limited to, radionuclides such as .sup.47Sc,
.sup.64Cu, .sup.67Cu, .sup.89Sr, .sup.86Y, .sup.87Y, .sup.90Y,
.sup.105Rh .sup.111Ag, .sup.111In, .sup.117mSn, .sup.149Pm,
.sup.153Sm, .sup.166Ho, .sup.177Lu, .sup.186Re, .sup.188Re,
.sup.211At, and .sup.212Bi, optionally conjugated to antibodies
directed against tumor antigens.
[0352] The pharmaceutical compositions of the present invention may
be sterilized by conventional, well-known sterilization techniques
or may be produced under sterile conditions. Aqueous solutions can
be packaged for use or filtered under aseptic conditions and
lyophilized, the lyophilized preparation being combined with a
sterile aqueous solution prior to administration. The compositions
can contain pharmaceutically acceptable auxiliary substances as
required to approximate physiological conditions, such as pH
adjusting and buffering agents, tonicity adjusting agents, wetting
agents, and the like, e.g., sodium acetate, sodium lactate, sodium
chloride, potassium chloride, calcium chloride, sorbitan
monolaurate, and triethanolamine oleate.
[0353] Formulations suitable for oral administration can comprise:
(a) liquid solutions, such as an effective amount of a packaged
compound or drug suspended in diluents, e.g., water, saline, or PEG
400; (b) capsules, sachets, or tablets, each containing a
predetermined amount of a Ras inhibitor compound or drug, as
liquids, solids, granules or gelatin; (c) suspensions in an
appropriate liquid; and (d) suitable emulsions. Tablet forms can
include one or more of lactose, sucrose, mannitol, sorbitol,
calcium phosphates, corn starch, potato starch, microcrystalline
cellulose, gelatin, colloidal silicon dioxide, talc, magnesium
stearate, stearic acid, and other excipients, colorants, fillers,
binders, diluents, buffering agents, moistening agents,
preservatives, flavoring agents, dyes, disintegrating agents, and
pharmaceutically compatible carriers. Lozenge forms can comprise a
Ras inhibitor compound or drug in a flavor, e.g., sucrose, as well
as pastilles comprising the Ras inhibitor compound in an inert
base, such as gelatin and glycerin or sucrose and acacia emulsions,
gels, and the like, containing, in addition to the Ras inhibitor,
carriers known in the art.
[0354] The compound of choice, alone or in combination with other
suitable components, can be made into aerosol formulations (i.e.,
they can be "nebulized") to be administered via inhalation. Aerosol
formulations can be placed into pressurized acceptable propellants,
such as dichlorodifluoromethane, propane, nitrogen, and the
like.
[0355] Suitable formulations for rectal administration include, for
example, suppositories, which comprises an effective amount of a
packaged Ras inhibitor compound or drug with a suppository base.
Suitable suppository bases include natural or synthetic
triglycerides or paraffin hydrocarbons. In addition, it is also
possible to use gelatin rectal capsules which contain a combination
of the Ras inhibitor compound or drug of choice with a base,
including, for example, liquid triglycerides, polyethylene glycols,
and paraffin hydrocarbons.
[0356] Formulations suitable for parenteral administration, such
as, for example, by intraarticular (in the joints), intravenous,
intramuscular, intratumoral, intradermal, intraperitoneal, and
subcutaneous routes, include aqueous and non-aqueous, isotonic
sterile injection solutions, which can contain antioxidants,
buffers, bacteriostats, and solutes that render the formulation
isotonic with the blood of the intended recipient, and aqueous and
non-aqueous sterile suspensions that can include suspending agents,
solubilizers, thickening agents, stabilizers, and preservatives.
Injection solutions and suspensions can also be prepared from
sterile powders, granules, and tablets. In the practice of the
present invention, compositions can be administered, for example,
by intravenous infusion, orally, topically, intraperitoneally,
intravesically, or intrathecally. Parenteral administration, oral
administration, and intravenous administration are the preferred
methods of administration. The formulations of compounds can be
presented in unit-dose or multi-dose sealed containers, such as
ampoules and vials.
[0357] The pharmaceutical preparation is preferably in unit dosage
form. In such form the preparation is subdivided into unit doses
containing appropriate quantities of the active component, e.g., a
Ras inhibitor compound. The unit dosage form can be a packaged
preparation, the package containing discrete quantities of
preparation, such as packeted tablets, capsules, and powders in
vials or ampoules. Also, the unit dosage form can be a capsule,
tablet, cachet, or lozenge itself, or it can be the appropriate
number of any of these in packaged form. The composition can, if
desired, also contain other compatible therapeutic agents.
[0358] In therapeutic use for the treatment of cancer, compound
utilized in the pharmaceutical compositions of the present
invention may be administered at the initial dosage of about 0.001
mg/kg to about 1000 mg/kg daily. A daily dose range of about 0.01
mg/kg to about 500 mg/kg, or about 0.1 mg/kg to about 200 mg/kg, or
about 1 mg/kg to about 100 mg/kg, or about 10 mg/kg to about 50
mg/kg, can be used. The dosages, however, may be varied depending
upon the requirements of the patient, the severity of the condition
being treated, and the compound or drug being employed. For
example, dosages can be empirically determined considering the type
and stage of cancer diagnosed in a particular patient. The dose
administered to a patient, in the context of the present invention,
should be sufficient to affect a beneficial therapeutic response in
the patient over time. The size of the dose will also be determined
by the existence, nature, and extent of any adverse side-effects
that accompany the administration of a compound in a particular
patient. Determination of the proper dosage for a particular
situation is within the skill of the practitioner. Generally,
treatment is initiated with smaller dosages which are less than the
optimum dose of the compound. Thereafter, the dosage is increased
by small increments until the optimum effect under circumstances is
reached. For convenience, the total daily dosage may be divided and
administered in portions during the day, if desired.
[0359] The compounds described herein can be used in combination
with one another, with other active agents known to be useful in
treating cancer or with adjunctive agents that may not be effective
alone, but may contribute to the efficacy of the active agent.
Kits/Articles of Manufacture
[0360] For use in the methods and/or applications (e.g. therapeutic
applications) described herein, kits and articles of manufacture
are also provided. In some embodiments, such kits comprise a
carrier, package, or container that is compartmentalized to receive
one or more containers such as vials, tubes, and the like, each of
the container(s) comprising one of the separate elements to be used
in a method described herein. Suitable containers include, for
example, bottles, vials, syringes, and test tubes. The containers
are formed from a variety of materials such as glass or
plastic.
[0361] The articles of manufacture provided herein contain
packaging materials. Packaging materials for use in packaging
pharmaceutical products include those found in, e.g., U.S. Pat.
Nos. 5,323,907, 5,052,558 and 5,033,252. Examples of pharmaceutical
packaging materials include, but are not limited to, blister packs,
bottles, tubes, inhalers, pumps, bags, vials, containers, syringes,
bottles, and any packaging material suitable for a selected
formulation and intended mode of administration and treatment. For
example, the container(s) includes one or more compounds described
herein, optionally in a composition or in combination with another
agent as disclosed herein. The container(s) optionally have a
sterile access port (for example the container is an intravenous
solution bag or a vial having a stopper pierceable by a hypodermic
injection needle). Such kits optionally comprising a compound with
an identifying description or label or instructions relating to its
use in the methods described herein.
[0362] For example, a kit may include one or more additional
containers, each with one or more of various materials (such as
reagents, optionally in concentrated form, and/or devices)
desirable from a commercial and user standpoint for use of a
compound described herein. Non-limiting examples of such materials
include, but not limited to, buffers, diluents, filters, needles,
syringes; carrier, package, container, vial and/or tube labels
listing contents and/or instructions for use, and package inserts
with instructions for use. A set of instructions may also be
included. A label is optionally on or associated with the
container. For example, a label is on a container when letters,
numbers or other characters forming the label are attached, molded
or etched into the container itself, a label is associated with a
container when it is present within a receptacle or carrier that
also holds the container, e.g., as a package insert. In addition, a
label may be used to indicate that the contents are to be used for
a specific therapeutic application. In addition, the label may
indicate directions for use of the contents, such as in the methods
described herein. In certain embodiments, the pharmaceutical
compositions is presented in a pack or dispenser device which
contains one or more unit dosage forms containing a compound
provided herein. The pack for example contains metal or plastic
foil, such as a blister pack. Or, the pack or dispenser device may
be accompanied by instructions for administration. Or, the pack or
dispenser may be accompanied with a notice associated with the
container in form prescribed by a governmental agency regulating
the manufacture, use, or sale of pharmaceuticals, which notice is
reflective of approval by the agency of the form of the drug for
human or veterinary administration. Such notice, for example, is
the labeling approved by the U.S. Food and Drug Administration for
prescription drugs, or the approved product insert. In some
embodiments, compositions containing a compound provided herein
formulated in a compatible pharmaceutical carrier are prepared,
placed in an appropriate container, and labeled for treatment of an
indicated condition.
V. Additional Embodiments
[0363] 1. A compound having the formula:
R.sup.1-L.sup.1-L.sup.2-L.sup.3-E wherein, R.sup.1 is a Switch
2-Binding Pocket binding moiety; L.sup.1 is a bond or a divalent
radical chemical linker; L.sup.2 is a bond or a divalent radical
chemical linker; L.sup.3 is a bond or a divalent radical chemical
linker; E is an electrophilic chemical moiety capable of forming a
covalent bond with a K-Ras cysteine residue or a K-Ras aspartate
residue.
[0364] 2. The compound of embodiment 1, wherein R.sup.1 is
hydrogen, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl.
[0365] 3. The compound of embodiment 1, wherein R.sup.1 is
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl.
[0366] 4. The compound of embodiment 1, wherein R.sup.1 is
substituted or unsubstituted aryl or substituted or unsubstituted
heteroaryl.
[0367] 5. The compound of embodiment 1, wherein R.sup.1 is
substituted or unsubstituted fused ring aryl or substituted or
unsubstituted fused ring heteroaryl.
[0368] 6. The compound of embodiment 1, wherein R.sup.1 is
R.sup.3-substituted or unsubstituted aryl or R.sup.3-substituted or
unsubstituted heteroaryl; wherein, R.sup.3 is independently
hydrogen, oxo, halogen, --CX.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.nR.sup.10, --SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2,
--ONR.sup.7R.sup.8, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7R.sup.8, --N(O).sub.m, --NR.sup.7R.sup.8,
--C(O)R.sup.9, --C(O)--OR.sup.9, --C(O)NR.sup.7R.sup.8,
--OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.2C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; X is independently --Cl, --Br, --I, or --F.
[0369] 7. The compound of embodiment 1, wherein R.sup.1 is:
##STR00099## ##STR00100##
wherein, R.sup.3 is independently hydrogen, oxo, halogen,
--CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8,
--N(O).sub.m, --NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; X is independently --Cl, --Br, --I, or --F; e2 is independently
an integer from 0 to 2; e3 is independently an integer from 0 to 3;
e4 is independently an integer from 0 to 4; e5 is independently an
integer from 0 to 5; e6 is independently an integer from 0 to 6; e7
is independently an integer from 0 to 7.
[0370] 8. The compound of embodiment 1, wherein R.sup.1 is
R.sup.3-substituted pyridinyl, R.sup.3-substituted pyrimidinyl,
R.sup.3-substituted thiophenyl, R.sup.3-substituted furanyl,
R.sup.3-substituted indolyl, R.sup.3-substituted benzoxadiazolyl,
R.sup.3-substituted benzodioxolyl, R.sup.3-substituted
benzodioxanyl, R.sup.3-substituted thianaphthanyl,
R.sup.3-substituted pyrrolopyridinyl, R.sup.3-substituted
indazolyl, R.sup.3-substituted quinolinyl, R.sup.3-substituted
quinoxalinyl, R.sup.3-substituted pyridopyrazinyl,
R.sup.3-substituted quinazolinonyl, R.sup.3-substituted
benzoisoxazolyl, R.sup.3-substituted imidazopyridinyl,
R.sup.3-substituted benzofuranyl, R.sup.3-substituted
benzothiophenyl, R.sup.3-substituted phenyl, R.sup.3-substituted
naphthyl, R.sup.3-substituted biphenyl, R.sup.3-substituted
pyrrolyl, R.sup.3-substituted pyrazolyl, R.sup.3-substituted
imidazolyl, R.sup.3-substituted pyrazinyl, R.sup.3-substituted
oxazolyl, R.sup.3-substituted isoxazolyl, R.sup.3-substituted
thiazolyl, R.sup.3-substituted furylthienyl, R.sup.3-substituted
pyridyl, R.sup.3-substituted pyrimidyl, R.sup.3-substituted
benzothiazolyl, R.sup.3-substituted purinyl, R.sup.3-substituted
benzimidazolyl, R.sup.3-substituted isoquinolyl,
R.sup.3-substituted thiadiazolyl, R.sup.3-substituted oxadiazolyl,
R.sup.3-substituted pyrrolyl, R.sup.3-substituted diazolyl,
R.sup.3-substituted triazolyl, R.sup.3-substituted tetrazolyl,
R.sup.3-substituted benzothiadiazolyl, R.sup.3-substituted
isothiazolyl, R.sup.3-substituted pyrazolopyrimidinyl,
R.sup.3-substituted pyrrolopyrimidinyl, R.sup.3-substituted
benzotriazolyl, or R.sup.3-substituted quinolyl; R.sup.3 is
independently hydrogen, oxo, halogen, --CX.sub.3, --CN,
--SO.sub.2Cl, --SO.sub.nR.sup.10, --SO.sub.vNR.sup.7R.sup.8,
--NHNH.sub.2, --ONR.sup.7R.sup.8, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7R.sup.8, --N(O).sub.m, --NR.sup.7R.sup.8,
--C(O)R.sup.9, --C(O)--OR.sup.9, --C(O)NR.sup.7R.sup.8,
--OR.sup.10, --NR.sup.7SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two adjacent R.sup.3
substituents may optionally be joined to form a substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl. Two R.sup.3 substituents bonded to the
same atom may optionally be joined to form a substituted or
unsubstituted cycloalkyl or substituted or unsubstituted
heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and R.sup.10 are
independently hydrogen, halogen, --CF.sub.3, --CN, --OH,
--NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl,
--SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2,
--ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2,
--NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3,
--OCHF.sub.2, substituted or unsubstituted alkyl, substituted or
unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,
substituted or unsubstituted heterocycloalkyl, substituted or
unsubstituted aryl, or substituted or unsubstituted heteroaryl;
R.sup.7 and R.sup.8 substituents bonded to the same nitrogen atom
may optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; m and
v are independently 1 or 2; n is independently an integer from 0 to
4; X is independently --Cl, --Br, --I, or --F.
[0371] 9. The compound of embodiment 1, wherein R.sup.1 is
unsubstituted pyridinyl, unsubstituted pyrimidinyl, unsubstituted
thiophenyl, unsubstituted furanyl, unsubstituted indolyl,
unsubstituted benzoxadiazolyl, unsubstituted benzodioxolyl,
unsubstituted benzodioxanyl, unsubstituted thianaphthanyl,
unsubstituted pyrrolopyridinyl, unsubstituted indazolyl,
unsubstituted quinolinyl, unsubstituted quinoxalinyl, unsubstituted
pyridopyrazinyl, unsubstituted quinazolinonyl, unsubstituted
benzoisoxazolyl, unsubstituted imidazopyridinyl, unsubstituted
benzofuranyl, unsubstituted benzothiophenyl, unsubstituted phenyl,
unsubstituted naphthyl, unsubstituted biphenyl, unsubstituted
pyrrolyl, unsubstituted pyrazolyl, unsubstituted imidazolyl,
unsubstituted pyrazinyl, unsubstituted oxazolyl, unsubstituted
isoxazolyl, unsubstituted thiazolyl, unsubstituted furylthienyl,
unsubstituted pyridyl, unsubstituted pyrimidyl, unsubstituted
benzothiazolyl, unsubstituted purinyl, unsubstituted
benzimidazolyl, unsubstituted isoquinolyl, unsubstituted
thiadiazolyl, unsubstituted oxadiazolyl, unsubstituted pyrrolyl,
unsubstituted diazolyl, unsubstituted triazolyl, unsubstituted
tetrazolyl, unsubstituted benzothiadiazolyl, unsubstituted
isothiazolyl, unsubstituted pyrazolopyrimidinyl, unsubstituted
pyrrolopyrimidinyl, unsubstituted benzotriazolyl, or unsubstituted
quinolyl.
[0372] 10. The compound of any one of embodiments 1 to 9, wherein
L.sup.1, L.sup.2 and L.sup.3 are independently a bond,
--NR.sup.2C--, --O--, --S--, --C(O)--, --S(O)--, --S(O).sub.2--,
substituted or unsubstituted alkylene, substituted or unsubstituted
heteroalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, substituted or unsubstituted heteroarylene;
or a substituted or unsubstituted spirocyclic linker; R.sup.2C is
independently hydrogen, oxo, halogen, --CX.sup.c.sub.3, --CN,
--SO.sub.2Cl, --SO.sub.2R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c,
--NHNH.sub.2, --ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, --NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; Two adjacent
R.sup.2C substituents may optionally be joined to form a
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; Two R.sup.2C
substituents bonded to the same atom may optionally be joined to
form a substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.7c, R.sup.8c, R.sup.9c and
R.sup.10c are independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.7c and R.sup.8c substituents
bonded to the same nitrogen atom may optionally be joined to form a
substituted or unsubstituted heterocycloalkyl or substituted or
unsubstituted heteroaryl; m1, m3, v1, and v3 are independently an
integer from 1 to 2; n1 and n3 are independently an integer from 0
to 4; X.sup.c is independently --Cl, --Br, --I, or --F.
[0373] 11. The compound of any one of embodiments 1 to 9, wherein
L.sup.1, L.sup.2 and L.sup.3 are independently
--CR.sup.2AR.sup.2B--,
##STR00101##
R.sup.2A and R.sup.2B are independently hydrogen, oxo, halogen,
--CX.sup.a.sub.3, --CN, --SO.sub.2Cl, --SO.sub.n1R.sup.10a,
--SO.sub.v1NR.sup.7aR.sup.8a, --NHNH.sub.2, --ONR.sup.7aR.sup.8a,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7aR.sup.8a,
--N(O).sub.m1, --NR.sup.7aR.sup.8a, --C(O)R.sup.9a,
--C(O)--OR.sup.9a, --C(O)NR.sup.7aR.sup.8a, --OR.sup.10a,
--NR.sup.7aSO.sub.2R.sup.10a, --NR.sup.7aC.dbd.(O)R.sup.9a,
--NR.sup.7aC(O)--OR.sup.9a, --NR.sup.7aOR.sup.9a,
--OCX.sup.a.sub.3, --OCHX.sup.a.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.2A and R.sup.2B substituent
bonded to the same atom may optionally be joined to form a
substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.2C is independently hydrogen,
oxo, halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a,
R.sup.8a, R.sup.9a and R.sup.10a are independently hydrogen,
halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH, --CONH.sub.2,
--NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H,
--SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7a and
R.sup.8a substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl;
R.sup.7c, R.sup.8c, R.sup.9c and R.sup.10c are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.7c and
R.sup.8c substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; z is
independently an integer from 0 to 10; m1, m3, v1, and v3 are
independently an integer from 1 to 2; n1 and n3 are independently
an integer from 0 to 4; X.sup.a and X.sup.c are independently --Cl,
--Br, --I, or --F.
[0374] 12. The compound of embodiment 10, wherein L.sup.1 is
independently substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, substituted or unsubstituted heteroarylene,
or substituted or unsubstituted spirocyclic linker; or L.sup.2 is
independently substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, substituted or unsubstituted heteroarylene,
or substituted or unsubstituted spirocyclic linker; or L.sup.3 is
independently substituted or unsubstituted cycloalkylene,
substituted or unsubstituted heterocycloalkylene, substituted or
unsubstituted arylene, substituted or unsubstituted heteroarylene,
or substituted or unsubstituted spirocyclic linker.
[0375] 13. The compound of embodiment 10, wherein L.sup.1 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; or L.sup.2 is independently
R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; or L.sup.3 is independently
R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker.
[0376] 14. The compound of embodiment 10, wherein L.sup.1 is
independently
##STR00102## ##STR00103## ##STR00104## ##STR00105## ##STR00106##
##STR00107## ##STR00108## ##STR00109## ##STR00110## ##STR00111##
##STR00112## ##STR00113##
or L.sup.3 is independently
##STR00114## ##STR00115## ##STR00116## ##STR00117## ##STR00118##
##STR00119## ##STR00120##
and wherein, f2 is independently an integer from 0 to 2; f6 is
independently an integer from 0 to 6; f7 is independently an
integer from 0 to 7; f8 is independently an integer from 0 to 8; f9
is independently an integer from 0 to 9; f10 is independently an
integer from 0 to 10; f12 is independently an integer from 0 to 12;
f14 is independently an integer from 0 to 14.
[0377] 15. The compound of any one of embodiments 1 to 14, wherein
E comprises
##STR00121## ##STR00122## ##STR00123## ##STR00124## ##STR00125##
##STR00126## ##STR00127## ##STR00128## ##STR00129## ##STR00130##
##STR00131## ##STR00132##
R.sup.13 is independently hydrogen, oxo, halogen, --CX.sup.b.sub.3,
--CN, --SO.sub.2Cl, --SO.sub.rR.sup.17,
--SO.sub.pNR.sup.14R.sup.15, --NHNH.sub.2, --ONR.sup.14R.sup.15,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.14R.sup.15,
--N(O).sub.q, --NR.sup.14R.sup.15, --C(O)R.sup.16,
--C(O)--OR.sup.16, --C(O)NR.sup.14R.sup.15, --OR.sup.17,
--NR.sup.14SO.sub.2R.sup.17, --NR.sup.14C.dbd.(O)R.sup.16,
--NR.sup.14C(O)--OR.sup.16, --NR.sup.14OR.sup.16,
--OCX.sup.b.sub.3, --OCHX.sup.b.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; Two adjacent R.sup.13 substituents may
optionally be joined to form a substituted or unsubstituted
cycloalkyl, substituted or unsubstituted heterocycloalkyl,
substituted or unsubstituted aryl, or substituted or unsubstituted
heteroaryl; Two R.sup.13 substituents bonded to the same atom may
optionally be joined to form a substituted or unsubstituted
cycloalkyl or substituted or unsubstituted heterocycloalkyl;
R.sup.14, R.sup.15, R.sup.16, and R.sup.17 are independently
hydrogen, halogen, --CF.sub.3, --CN, --OH, --NH.sub.2, --COOH,
--CONH.sub.2, --NO.sub.2, --SH, --SO.sub.2Cl, --SO.sub.3H,
--SO.sub.4H, --SO.sub.2NH.sub.2, --NHNH.sub.2, --ONH.sub.2,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H,
--NHC.dbd.(O)H, --NHC(O)--OH, --NHOH, --OCF.sub.3, --OCHF.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; R.sup.14 and
R.sup.15 substituents bonded to the same nitrogen atom may
optionally be joined to form a substituted or unsubstituted
heterocycloalkyl or substituted or unsubstituted heteroaryl; p is
independently 1 or 2; q is independently an integer from 1 to 2; r
is independently an integer from 0 to 4; X.sup.b is independently
--Cl, --Br, --I, or --F.
[0378] 16. The compound of any one of embodiments 1 to 14, wherein
E comprises a substituted or unsubstituted vinyl sulfone moiety,
substituted or unsubstituted vinyl sulfonamide moiety, substituted
or unsubstituted fluoro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted chloro(C.sub.1-C.sub.4)alkylketone
moiety, substituted or unsubstituted acrylamide moiety, substituted
or unsubstituted disulfide moiety, substituted or unsubstituted
thiol moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
[0379] 17. The compound of any one of embodiments 1 to 14, wherein
E comprises an unsubstituted vinyl sulfone moiety, unsubstituted
vinyl sulfonamide moiety, unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, unsubstituted
chloro(C.sub.1-C.sub.4)alkylketone moiety, unsubstituted acrylamide
moiety, unsubstituted disulfide moiety, unsubstituted thiol moiety,
unsubstituted phosphonate moiety, unsubstituted aldehyde moiety,
unsubstituted enone moiety, unsubstituted diazomethylketone moiety,
unsubstituted diazomethylamide moiety, unsubstituted
cyanocyclopropyl carboxamide moiety, unsubstituted epoxide moiety,
unsubstituted epoxyketone moiety, unsubstituted epoxyamide moiety,
unsubstituted aryl aldehyde moiety, unsubstituted aryl dialdehyde
moiety, unsubstituted dialdehyde moiety, unsubstituted nitrogen
mustard moiety, unsubstituted propargyl moiety, or unsubstituted
propargylamide moiety.
[0380] 18. A pharmaceutical composition comprising a
pharmaceutically acceptable excipient and a compound of any one of
embodiments 1 to 17.
[0381] 19. A method of treating a disease in a patient in need of
such treatment, said method comprising administering a
therapeutically effective amount of a compound of any one of
embodiments 1 to 17 to sa id patient.
[0382] 20. The method of embodiment 19, wherein said disease is
cancer.
[0383] 21. The method of embodiment 20, wherein said cancer is
colon cancer, colorectal cancer, pancreatic cancer, breast cancer,
or leukemia.
[0384] 22. The method of embodiment 20, wherein said cancer is lung
cancer.
[0385] 23. The method of embodiment 22, wherein said lung cancer is
non-small cell lung cancer.
[0386] 24. A method of modulating the activity of a K-Ras protein,
said method comprising contacting said K-Ras protein with an
effective amount of a compound of any one of embodiments 1 to
17.
[0387] 25. The method of embodiment 24, wherein said modulating of
said activity comprises modulating GTPase activity, nucleotide
exchange, differential GDP or GTP binding, effector protein
binding, effector protein activation, guanine exchange factor (GEF)
binding, GEF-facilitated nucleotide exchange, phosphate release,
nucleotide release, nucleotide binding, K-Ras subcellular
localization, K-Ras post-translational processing, or K-Ras
post-translational modifications.
[0388] 26. The method of embodiment 24, wherein said modulating is
increasing the activity of said K-Ras protein.
[0389] 27. The method of embodiment 24, wherein said modulating is
reducing the activity of said K-Ras protein.
[0390] 28. The method of embodiment 24, wherein said K-Ras protein
is a human K-Ras protein.
[0391] 29. The method of embodiment 28, wherein said human K-Ras
protein contains a G12C, G12D, G13C, or G13D mutation.
[0392] 30. The method of embodiment 28, wherein said human K-Ras
protein contains a G12C mutation.
[0393] 31. A method of modulating a K-Ras protein, said method
comprising contacting said K-Ras protein with an effective amount
of a compound of any one of embodiments 1 to 17.
[0394] 32. The method of embodiment 31, wherein said modulating is
of K-Ras subcellular localization, K-Ras post-translational
processing, or a K-Ras post-translational modification.
[0395] 33. The method of embodiment 31, wherein said K-Ras protein
is a human K-Ras protein.
[0396] 34. The method of embodiment 33, wherein said human K-Ras
protein contains a G12C, G12D, G13C, or G13D mutation.
[0397] 35. The method of embodiment 33, wherein said human K-Ras
protein contains a G12C mutation.
[0398] 36. The method of any one of embodiments 24 to 35, wherein
said K-Ras protein is within a biological cell.
[0399] 37. The method of embodiment 36, wherein said biological
cell forms part of an organism.
[0400] 38. A K-Ras protein covalently bound to a compound of any
one of embodiments 1 to 17, wherein said compound is covalently
bound to a cysteine residue of said K-Ras protein.
[0401] 39. The covalently modified K-Ras protein of embodiment 38,
wherein said compound is reversibly covalently bound to a cysteine
residue of said K-Ras protein.
[0402] 40. The covalently modified K-Ras protein of embodiment 38,
wherein said compound is irreversibly covalently bound to a
cysteine residue of said K-Ras protein.
[0403] 41. The covalently modified K-Ras protein of any one of
embodiments 38 to 40, wherein said covalently modified K-Ras
protein has a modulated activity relative to a control, wherein
said activity is selected from GTPase activity, nucleotide
exchange, differential GDP or GTP binding, effector protein
binding, effector protein activation, guanine exchange factor (GEF)
binding, GEF-facilitated nucleotide exchange, phosphate release,
nucleotide release, nucleotide binding, K-Ras subcellular
localization, K-Ras post-translational processing, and K-Ras
post-translational modifications.
[0404] 42. The covalently modified K-Ras protein of any one of
embodiments 38 to 40, wherein said covalently modified K-Ras
protein is modulated in K-Ras subcellular localization, K-Ras
post-translational processing, or K-Ras post-translational
modification.
[0405] 43. The covalently modified K-Ras protein of any one of
embodiments 38 to 40, wherein said K-Ras protein contains a G12C
mutation.
[0406] 44. The covalently modified K-Ras protein of embodiment 43,
wherein said compound is covalently bonded to cysteine residue
12.
[0407] 45. The covalently modified K-Ras protein of any one of
embodiments 38 to 40, wherein said K-Ras protein contains a G13C
mutation.
[0408] 46. The covalently modified K-Ras protein of embodiment 45,
wherein said compound is covalently bonded to cysteine residue
13.
[0409] 47. A K-Ras protein covalently bound to a compound of any
one of embodiments 1 to 17, wherein said compound is covalently
bound to an aspartate residue of said K-Ras protein.
[0410] 48. The covalently modified K-Ras protein of embodiment 47,
wherein said compound is reversibly covalently bound to an
aspartate residue of said K-Ras protein.
[0411] 49. The covalently modified K-Ras protein of embodiment 47,
wherein said compound is irreversibly covalently bound to an
aspartate residue of said K-Ras protein.
[0412] 50. The covalently modified K-Ras protein of any one of
embodiments 47 to 49, wherein said covalently modified K-Ras
protein has a modulated activity relative to a control, wherein
said activity is selected from GTPase activity, nucleotide
exchange, differential GDP or GTP binding, effector protein
binding, effector protein activation, guanine exchange factor (GEF)
binding, GEF-facilitated nucleotide exchange, phosphate release,
nucleotide release, nucleotide binding, K-Ras subcellular
localization, K-Ras post-translational processing, and K-Ras
post-translational modifications.
[0413] 51. The covalently modified K-Ras protein of any one of
embodiments 47 to 49, wherein said covalently modified K-Ras
protein is modulated in K-Ras subcellular localization, K-Ras
post-translational processing, or K-Ras post-translational
modification.
[0414] 52. The covalently modified K-Ras protein of any one of
embodiments 47 to 49, wherein said K-Ras protein contains a G12D
mutation.
[0415] 53. The covalently modified K-Ras protein of embodiment 52,
wherein said compound is covalently bonded aspartate residue
12.
[0416] 54. The covalently modified K-Ras protein of any one of
embodiments 47 to 49, wherein said K-Ras protein contains a G13D
mutation.
[0417] 55. The covalently modified K-Ras protein of embodiment 54,
wherein said compound is covalently bonded to aspartate residue
13.
[0418] 56. A method of identifying a covalent inhibitor of K-Ras
protein comprising: contacting a K-Ras protein with a K-Ras
inhibitor test compound; allowing said K-Ras inhibitor test
compound to covalently inhibit said K-Ras protein; detecting the
level of covalent inhibition of said K-Ras protein thereby
identifying a covalent inhibitor of K-Ras protein.
[0419] 57. The method of embodiment 56, wherein said K-Ras
inhibitor test compound is a Switch 2-Binding Pocket covalent
inhibitor test compound and said K-Ras protein is a G12C mutant
K-Ras protein.
[0420] 58. The method of embodiment 57 further comprising the steps
of: contacting a wildtype K-Ras protein with said Switch 2-Binding
Pocket covalent inhibitor test compound; allowing said Switch
2-Binding Pocket covalent inhibitor test compound to inhibit said
wildtype K-Ras protein; detecting the level of inhibition of said
wildtype K-Ras protein; comparing the level of inhibition of said
wildtype K-Ras protein to the level of covalent inhibition of said
G12C mutant K-Ras protein, wherein a higher level of covalent
inhibition of said G12C mutant K-Ras indicates said Switch
2-Binding Pocket covalent inhibitor test compound is specific for
said G12C mutant K-Ras protein.
[0421] 59. The method of embodiment 56, wherein said K-Ras
inhibitor test compound is a Switch 2-Binding Pocket covalent
inhibitor test compound and said K-Ras protein is a G12D mutant
K-Ras protein.
[0422] 60. The method of embodiment 59 further comprising the steps
of: contacting a wildtype K-Ras protein with said Switch 2-Binding
Pocket covalent inhibitor test compound; allowing said Switch
2-Binding Pocket covalent inhibitor test compound to inhibit said
wildtype K-Ras protein; detecting the level of inhibition of said
wildtype K-Ras protein; comparing the level of inhibition of said
wildtype K-Ras protein to the level of covalent inhibition of said
G12D mutant K-Ras protein, wherein a higher level of covalent
inhibition of said G12D mutant K-Ras indicates said Switch
2-Binding Pocket covalent inhibitor test compound is specific for
said G12D mutant K-Ras protein.
[0423] 61. The method of embodiment 56, wherein said K-Ras
inhibitor test compound is a Switch 2-Binding Pocket covalent
inhibitor test compound and said K-Ras protein is a G13C mutant
K-Ras protein.
[0424] 62. The method of embodiment 61 further comprising the steps
of: contacting a wildtype K-Ras protein with said Switch 2-Binding
Pocket covalent inhibitor test compound; allowing said Switch
2-Binding Pocket covalent inhibitor test compound to inhibit said
wildtype K-Ras protein; detecting the level of inhibition of said
wildtype K-Ras protein; comparing the level of inhibition of said
wildtype K-Ras protein to the level of covalent inhibition of said
G13C mutant K-Ras protein, wherein a higher level of covalent
inhibition of said G13C mutant K-Ras indicates said Switch
2-Binding Pocket covalent inhibitor test compound is specific for
said G13C mutant K-Ras protein.
[0425] 63. The method of embodiment 56, wherein said K-Ras
inhibitor test compound is a Switch 2-Binding Pocket covalent
inhibitor test compound and said K-Ras protein is a G13D mutant
K-Ras protein.
[0426] 64. The method of embodiment 59 further comprising the steps
of: contacting a wildtype K-Ras protein with said Switch 2-Binding
Pocket covalent inhibitor test compound; allowing said Switch
2-Binding Pocket covalent inhibitor test compound to inhibit said
wildtype K-Ras protein; detecting the level of inhibition of said
wildtype K-Ras protein; comparing the level of inhibition of said
wildtype K-Ras protein to the level of covalent inhibition of said
G13D mutant K-Ras protein, wherein a higher level of covalent
inhibition of said G13D mutant K-Ras indicates said Switch
2-Binding Pocket covalent inhibitor test compound is specific for
said G13D mutant K-Ras protein.
[0427] 65. A method of selectively modulating a Ras protein, said
method comprising contacting said Ras protein with a compound which
contacts at least one amino acid residue forming a Switch 2 binding
pocket of said Ras protein, wherein said at least one amino acid
residue is selected from valine-7, valine-9, glycine-10,
proline-34, threonine-58, glycine-60, glutamine-61, glutamate-62,
glutamate-63, arginine-68, tyrosine-71, methionine-72, tyrosine-96,
glutamine-99 and isoleucine-100 of said Ras protein, and wherein
said compound covalently reacts with an amino acid residue of said
Ras protein.
[0428] 66. The method of embodiment 65, wherein said compound binds
to a K-Ras protein with a higher binding affinity as compared to a
H-Ras protein.
[0429] 67. The method of embodiment 65, wherein said compound
interacts with at least one of glycine-60, glutamate-62, or
glutamate-63.
[0430] 68. The method of embodiment 65, wherein said interacting
between said amino acid residue and said compound involves hydrogen
bonding, van der Waals interaction, ionic bonding, covalent
bonding, or hydrophobic interaction.
[0431] 69. The method of embodiment 65, wherein said compound fills
space within said Switch 2 binding pocket.
[0432] 70. The method of embodiment 65, wherein said compound
inhibits K-Ras as measured by the fraction of protein covalently
labeled by the compound, wherein the compound is present in 50-fold
excess and wherein the fraction of protein covalently labeled is
determined by mass spectrometry.
[0433] 71. The method of embodiment 65, wherein said compound
covalently reacts with an amino acid residue of said K-ras
protein.
[0434] 72. The method of embodiment 71, wherein said amino acid
residue is cysteine-12 of K-Ras G12C mutant protein.
[0435] 73. A method of designing a compound which covalently binds
to a Switch 2 binding pocket of a K-Ras protein, the method
comprising the steps of: providing a structural model of a
reference compound bound to the Switch 2 binding pocket of the
K-Ras protein, wherein the reference compound is non-covalently
bound to said Switch 2 binding pocket; identifying a cysteine,
aspartate, lysine, tyrosine or glutamate residue located in
proximity to said Switch 2 binding pocket when said reference
compound is bound to said Switch 2 binding pocket; generating at
least one additional structural model of a test compound bound to
said Switch 2 binding pocket, wherein said test compound comprises
an electrophilic moiety; and selecting said test compound if said
electrophilic moiety is located within bonding distance of said
cysteine residue when said test compound is bound to said Switch 2
binding pocket.
[0436] 74. A compound having molecular dimensions compatible with
the shape of a K-Ras Switch 2 binding pocket wherein the compound,
when present in an aqueous solution comprising 200 .mu.M of the
compound and 4 .mu.M K-Ras, covalently binds to at least 50% of
K-Ras proteins present in solution after 24 hours.
[0437] 75. A compound of Formula:
##STR00133##
or a pharmaceutically acceptable salt thereof, wherein: e5 is an
integer from 0 to 5; X' is --O--, --NH--, or --S--; R.sup.2A and
R.sup.2B are independently hydrogen, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.2A and R.sup.2B substituent
bonded to the same atom may optionally be joined to form a
substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.3 is independently hydrogen,
oxo, halogen, --CX.sub.3, --CN, --SO.sub.2Cl, --SO.sub.nR.sup.10,
--SO.sub.vNR.sup.7R.sup.8, --NHNH.sub.2, --ONR.sup.7R.sup.8,
--NHC.dbd.(O)NHNH.sub.2, --NHC.dbd.(O)NR.sup.7R.sup.8,
--N(O).sub.m, --NR.sup.7R.sup.8, --C(O)R.sup.9, --C(O)--OR.sup.9,
--C(O)NR.sup.7R.sup.8, --OR.sup.10, --NR.sup.2SO.sub.2R.sup.10,
--NR.sup.7C.dbd.(O)R.sup.9, --NR.sup.7C(O)--OR.sup.9,
--NR.sup.7OR.sup.9, --OCX.sub.3, --OCHX.sub.2, substituted or
unsubstituted alkyl, substituted or unsubstituted heteroalkyl,
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; L.sup.2 is
independently R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; L.sup.3 is independently
R.sup.2C-substituted or unsubstituted cycloalkylene,
R.sup.2C-substituted or unsubstituted heterocycloalkylene,
R.sup.2C-substituted or unsubstituted arylene, R.sup.2C-substituted
or unsubstituted heteroarylene, or R.sup.2C-substituted or
unsubstituted spirocyclic linker; E is an electrophilic chemical
moiety capable of forming a covalent bond with a cysteine or
aspartate residue; R.sup.2C is independently hydrogen, oxo,
halogen, --CX.sup.c.sub.3, --CN, --SO.sub.2Cl,
--SO.sub.n3R.sup.10c, --SO.sub.v3NR.sup.7cR.sup.8c, --NHNH.sub.2,
--ONR.sup.7cR.sup.8c, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NR.sup.7cR.sup.8c, --N(O).sub.m3, --NR.sup.7cR.sup.8c,
--C(O)R.sup.9c, --C(O)--OR.sup.9c, --C(O)NR.sup.7cR.sup.8c,
--OR.sup.10c, NR.sup.7cSO.sub.2R.sup.10c,
--NR.sup.7cC.dbd.(O)R.sup.9c, --NR.sup.7cC(O)--OR.sup.9c,
--NR.sup.7cOR.sup.9c, --OCX.sup.c.sub.3, --OCHX.sup.c.sub.2,
substituted or unsubstituted alkyl, substituted or unsubstituted
heteroalkyl, substituted or unsubstituted cycloalkyl, substituted
or unsubstituted heterocycloalkyl, substituted or unsubstituted
aryl, or substituted or unsubstituted heteroaryl; two adjacent
R.sup.2C substituents may optionally be joined to form a
substituted or unsubstituted cycloalkyl, substituted or
unsubstituted heterocycloalkyl, substituted or unsubstituted aryl,
or substituted or unsubstituted heteroaryl; two R.sup.2C
substituents bonded to the same atom may optionally be joined to
form a substituted or unsubstituted cycloalkyl or substituted or
unsubstituted heterocycloalkyl; R.sup.7, R.sup.8, R.sup.9, and
R.sup.10 are independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.7a, R.sup.8a, R.sup.9a and
R.sup.10a are independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; R.sup.7a and R.sup.8a substituents
bonded to the same nitrogen atom may optionally be joined to form a
substituted or unsubstituted heterocycloalkyl or substituted or
unsubstituted heteroaryl; R.sup.7c, R.sup.8c, R.sup.9c and
R.sup.10c are independently hydrogen, halogen, --CF.sub.3, --CN,
--OH, --NH.sub.2, --COOH, --CONH.sub.2, --NO.sub.2, --SH,
--SO.sub.2Cl, --SO.sub.3H, --SO.sub.4H, --SO.sub.2NH.sub.2,
--NHNH.sub.2, --ONH.sub.2, --NHC.dbd.(O)NHNH.sub.2,
--NHC.dbd.(O)NH.sub.2, --NHSO.sub.2H, --NHC.dbd.(O)H, --NHC(O)--OH,
--NHOH, --OCF.sub.3, --OCHF.sub.2, substituted or unsubstituted
alkyl, substituted or unsubstituted heteroalkyl, substituted or
unsubstituted cycloalkyl, substituted or unsubstituted
heterocycloalkyl, substituted or unsubstituted aryl, or substituted
or unsubstituted heteroaryl; m, m1, m3, v, v1, and v3 are
independently 1 or 2; n, n1, and n3 are independently an integer
from 0 to 4; X, X.sup.a and X.sup.c are independently --Cl, --Br,
--I, or --F.
[0438] 76. The compound of embodiment 75, wherein E comprises a
substituted or unsubstituted vinyl sulfone moiety, substituted or
unsubstituted vinyl sulfonamide moiety, substituted or
unsubstituted peroxide moiety, substituted or unsubstituted
fluoro(C.sub.1-C.sub.4)alkylketone moiety, substituted or
unsubstituted chloro(C.sub.1-C.sub.4)alkylketone moiety,
substituted or unsubstituted acrylamide moiety, substituted or
unsubstituted disulfide moiety, substituted or unsubstituted thiol
moiety, substituted or unsubstituted phosphonate moiety,
substituted or unsubstituted aldehyde moiety, substituted or
unsubstituted enone moiety, substituted or unsubstituted
diazomethylketone moiety, substituted or unsubstituted
diazomethylamide moiety, substituted or unsubstituted
cyanocyclopropyl carboxamide moiety, substituted or unsubstituted
epoxide moiety, substituted or unsubstituted epoxyketone moiety,
substituted or unsubstituted epoxyamide moiety, substituted or
unsubstituted aryl aldehyde moiety, substituted or unsubstituted
aryl dialdehyde moiety, substituted or unsubstituted dialdehyde
moiety, substituted or unsubstituted nitrogen mustard moiety,
substituted or unsubstituted propargyl moiety, substituted or
unsubstituted propargylamide moiety.
[0439] 77. The compound or pharmaceutically acceptable salt of
embodiment 75, wherein L.sup.2 is independently
R.sup.2C-substituted or unsubstituted heterocycloalkylene or
R.sup.2C-substituted or unsubstituted spirocyclic linker and
L.sup.3 is a bond.
[0440] 78. The compound or pharmaceutically acceptable salt of
embodiment 75, wherein L.sup.2 is monocyclic 4, 5, or 6-membered
heterocycloalkylene.
[0441] 79. The compound or pharmaceutically acceptable salt of
embodiment 75, wherein L.sup.2 is unsubstituted piperazino or
unsubstituted piperidino.
[0442] 80. The compound or pharmaceutically acceptable salt of
embodiment 75, wherein L.sup.2 is bicyclic fused
heterocycloalkylene.
[0443] 81. The compound or pharmaceutically acceptable salt of
embodiment 75, wherein L.sup.2 is an unsubstituted spirocyclic
linker.
[0444] 82. The compound or pharmaceutically acceptable salt of
embodiment 75, wherein E is a substituted or unsubstituted vinyl
sulfone moiety, substituted or unsubstituted vinyl sulfonamide
moiety, or a substituted or unsubstituted acrylamide moiety.
[0445] 83. The compound or pharmaceutically acceptable salt of
embodiment 75, having the formula:
##STR00134##
[0446] 84. A method of treating a disorder in a subject in need
thereof, comprising: determining the presence or absence of a K-Ras
mutation in a malignant or neoplastic cell isolated from the
subject; and if a K-Ras mutation is determined to be present in the
subject, administering to the subject a therapeutically effective
amount of a compound or pharmaceutically acceptable salt of any one
of embodiments 1-17 and 74-83.
[0447] 85. A method of treating a disorder in a subject in need
thereof, comprising: determining the presence or absence of a K-Ras
mutation in a malignant or neoplastic cell isolated from the
subject, in connection with the prescription of an effective amount
of a compound or pharmaceutically acceptable salt of any one of
embodiments 1-17 and 74-83 to said subject; and if a K-Ras mutation
is determined to be present in the subject, providing an alert to a
caregiver of said subject.
[0448] 86. The method of embodiment 84 or 85, wherein the disorder
is cancer.
[0449] 87. A method of treating cancer in a human subject in need
thereof, comprising administering to said subject at least one
compound or pharmaceutically acceptable salt of any one of
embodiments 1-17 and 74-83, wherein said subject has a K-Ras
mutation.
[0450] 88. The method of any one of embodiments 84 to 87, wherein
the K-Ras mutation is selected from the group consisting of G12C,
G13C, G12D, and G13D.
[0451] 89. The method of embodiment 88, wherein the K-Ras mutation
is G12C.
[0452] 90. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound modulates the binding of GDP or GTP to a K-Ras
protein.
[0453] 91. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound inhibits the binding of GDP or GTP to a K-Ras protein.
[0454] 92. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound increases the binding of GDP or GTP to a K-Ras
protein.
[0455] 93. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound inhibits the binding of GTP to a K-Ras protein.
[0456] 94. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound increases the binding of GDP to a K-Ras protein.
[0457] 95. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound inhibits the release of GDP from a K-Ras protein.
[0458] 96. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound increases the release of GDP or GTP from a K-Ras
protein.
[0459] 97. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound increases the release of GDP from a K-Ras protein.
[0460] 98. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound increases the release of GTP from a K-Ras protein.
[0461] 99. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound modulates the binding of a K-Ras protein to Raf.
[0462] 100. The compound, or a pharmaceutically acceptable salt
thereof, of any one of embodiments 1-17 and 74-83, wherein said
compound inhibits the binding of a K-Ras protein to Raf.
[0463] 101. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound modulates the binding of GDP or GTP to
a K-Ras protein.
[0464] 102. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound inhibits the binding of GDP or GTP to
a K-Ras protein.
[0465] 103. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound increases the binding of GDP or GTP to
a K-Ras protein.
[0466] 104. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound inhibits the binding of GTP to a K-Ras
protein.
[0467] 105. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound increases the binding of GDP to a
K-Ras protein.
[0468] 106. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound inhibits the release of GDP from a
K-Ras protein.
[0469] 107. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound increases the release of GDP or GTP
from a K-Ras protein.
[0470] 108. The method of any one of embodiments 19-37, 65-72, and
84-89, w herein said compound increases the release of GDP from a
K-Ras protein.
[0471] 109. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound increases the release of GTP from a
K-Ras protein.
[0472] 110. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound modulates the binding of a K-Ras
protein to Raf.
[0473] 111. The method of any one of embodiments 19-37, 65-72, and
84-89, wherein said compound inhibits the binding of a K-Ras
protein to Raf.
[0474] 112. The method of any one of embodiments 19-37, 65-72,
84-89, and 101-111, wherein said compound binds a GDP bound K-Ras
protein.
[0475] 113. The compound of any one of embodiments 1-17, 74-83, and
90-100, wherein said compound binds a GDP bound K-Ras protein.
[0476] 114. A pharmaceutical composition comprising a
pharmaceutically acceptable excipient and a compound of any one of
embodiments 74-83, 90-100, and 113.
VI. Examples
[0477] The following examples are meant to illustrate certain
embodiments of the invention and not to limit the scope of the
invention described herein. Activating mutations in K-Ras are among
the most common lesions found in human cancer, and such mutations
are generally associated with poor prognosis. Despite numerous
efforts in academia and industry, small molecule inhibitors that
directly target K-Ras remain elusive. Even more highly desired are
molecules that selectively target mutant K-Ras while sparing the
wild type protein. We have used a fragment-based screen to discover
oncogenic mutant-specific inhibitors of K-Ras. Crystallographic
studies with multiple inhibitors in complex with K-Ras reveal that
the compounds bind in a novel hydrophobic pocket that is not
apparent in any published crystal structure of Ras. These
inhibitors disrupt the conformations of Switch I and Switch II,
domains that are essential for the association and activation of
downstream signaling partners. Our medicinal chemistry effort has
greatly improved potency, showing that this pocket is particularly
amenable to chemical optimization. In vitro biochemical
characterization of these inhibitors confirms that they block Ras
function. Our discovery of a new druggable pocket in K-Ras, and a
set of inhibitors that bind to it in a mutant-specific fashion,
provides a promising new avenue for the direct pharmacological
inhibition of oncogenic Ras. In embodiments, inhibitors bind to an
allosteric pocket behind Switch II, selectively bind to GDP-bound
state and not to GTP-bound state, the structure of inhibitor-Ras
complex suggests potential to block formation of proper GTP-bound
conformation and impair effector activation, and/or inhibitors slow
GEF-catalyzed nucleotide exchange, suggesting they might trap Ras
in the inactive state.
A. Compound Binding to K-Ras
[0478] In some embodiments, compounds described herein are divided
into three distinct parts: a terminal portion (e.g. R.sup.1 above),
a linker portion (e.g. L1-L2-L3- above) and a chemically reactive
portion (e.g. E above). In some embodiments, the terminal portion
is a hydrophobic moiety and may comprise a phenyl ring. In some
further embodiments the hydrophobic moiety is substituted with at
least one halogen atom. In some embodiments the linker portion is a
flexible linker portion. The linker portion may include a
substituted or unsubstituted saturated heterocycloalkylene. In some
embodiments, the chemically reactive portion forms a covalent bond
with a thiol of the oncogenic G12C mutant of K-Ras.
[0479] In some embodiments of the compounds described herein, the
hydrophobic terminal portion (e.g. R.sup.1) binds the K-Ras protein
in a deep pocket that is not apparent in structures of the protein
without a compound. In some embodiments, the deep pocket is formed
by compound binding. As shown in ligand interaction maps (FIGS. 7
and 8), this binding pocket includes the following amino acids:
valine-7, valine-9, threonine-58, arginine-68, tyrosine-71,
methionine-72, tyrosine-96. In some embodiments of the compounds,
having a hydrophobic terminal portion, the pocket may form a
hydrophobic counterpart to the compounds. In some embodiments,
several of the interacting amino acids (e.g. residues contacting a
compound) are integral parts of Switch-2, a flexible region of
K-Ras involved in effector binding and downstream signaling. In
some embodiments of K-Ras bound to a compound as disclosed herein,
Switch 2 looks distinct from the active conformation of Switch 2 in
GTP-bound K-Ras. In some embodiments, the changes in Switch-2 upon
compound binding may be how the compounds described herein
(including embodiments) modulate K-Ras, K-Ras activity, and/or
K-Ras function (e.g. decreasing the binding affinity of compound
bound K-Ras for a signaling pathway interacting protein (e.g.
PI3K)).
[0480] In some embodiments, the linker portion of compounds
described herein (e.g. L.sup.1, L.sup.2, and L.sup.3) shows
interactions with the K-Ras protein. In some embodiments of the
compounds described herein, the linker portion is more solvent
exposed than the terminal portion. In some embodiments, the linker
portion of the compounds described herein contacts amino acid
residues of Switch-2. In some embodiments, a Switch 2 residue
contacted by the linker portion is glycine-60, glutamate-62 or
glutamate-63. In some embodiments, the linker portion contacts all
three residues. In some embodiments, contact between the compound
linker portion and K-Ras provides stabilization of the unusual
protein conformation that may be induced by compound binding. In
some embodiments of the compounds described herein, the linker
portion of the compounds described herein have flexibility in
regard to chemical composition, while still providing modulation of
K-Ras.
[0481] In some embodiments of the compounds, several groups have
been found to be effective as the reactive portion of the compounds
(e.g. E, the electrophilic moiety, thiol reactive, aspartate
reactive). In some embodiments, the compounds are disulfide based
compounds to link the compound to K-Ras cysteine-12. X-ray crystal
structures (e.g. JO-01-189cbut) show clear electron density for the
disulfide linkage. Due to the possible instability of disulfide
linkages in the reducing environment of cells we developed
compounds with different reactive portions (e.g. electrophilic
moieties) that can covalently (e.g. reversibly, irreversibly) bind
to cysteine and aspartate. In some embodiments, the electrophilic
moiety E is selected from vinyl sulfones, acrylamides and epoxides.
In some embodiments, crystal structures for compounds containing
the electrophilic moiety vinyl sulfone show interactions of the
sulfone oxygens with either the protein directly or with ordered
water molecules. In some embodiments of the compounds, compounds
containing sulfones are sterically more demanding than disulfide
containing compounds. In some embodiments, the electrophilic moiety
E (e.g. vinyl sulfones) can modulate the conformation of Switch-1.
In some embodiments, the modulation of Switch 1 by compound binding
may modulate K-Ras activity or function (e.g. effector binding, for
example Raf or PI3K). In some embodiments, the compound binding to
K-Ras may modulate K-Ras metal binding by modulating Switch 1
structure or function (e.g. partially disordering Switch-1 relative
to the Switch 1 conformation in K-Ras that is not bound to a
compound as described herein). In some embodiments, the
electrophilic group E contributes to the binding of compound to
K-Ras by contacting K-Ras residues. In some embodiments, the
electrophilic group E contributes to the binding of compound to
K-Ras by covalently bonding to K-Ras through a cysteine or
aspartate at residues 12 or 13. The right balance between
chemically reactivity, sterical demands and favorable interactions
with the protein needs to be achieved for the best reactive group
to link the compound to oncogenic cysteine-12.
[0482] In some embodiments, the compounds described herein
(including embodiments, examples and compounds of Table 1, 2, 3, 4,
or 5) provide interactions with K-Ras through a novel complementary
pocket and the terminal portion including R.sup.1, that leads to a
previously unknown conformation of Switch-2, and a covalent link of
the compound to the oncogenic mutant K-Ras (e.g. G12C, G12D, G13C,
G13D), through the reactive portion containing E. In some
embodiments, E can contribute to K-Ras binding through interactions
beyond the covalent bond formation and can modulate Switch-1
conformation and stability. In some embodiments, by utilizing both
features with the described compounds, K-Ras G12C or G12D or G13C
or G13D can be selectively targeted.
B. Structure-Activity Relationships of Compound Examples
[0483] In some embodiments, where the terminal portion includes a
phenyl (e.g. R.sup.1 includes a phenyl ring), a hydrophobic group
is preferred in the 2-position on the phenyl ring, ortho to the O,
S, or N linking to the rest of the molecule (e.g. L.sup.1, L.sup.2,
or L.sup.3). In some embodiments, the terminal portion includes a
phenyl substituted with a larger halogen. In some embodiments,
R.sup.1 is a phenyl substituted with a substituted or unsubstituted
aryl or substituted or unsubstituted heteroaryl at the ortho
position to the bond to the linker portion. In some embodiments,
R.sup.1 is a phenyl substituted with a substituted or unsubstituted
fused ring aryl or substituted or unsubstituted fused ring
heteroaryl at the ortho position to the bond to the linker portion.
In some embodiments, these hydrophobic substituents (e.g.
substituted or unsubstituted aryl or substituted or unsubstituted
heteroaryl) on R.sup.1 (e.g. phenyl ring) ortho to the bond to the
linker portion, point toward the same affinity pocket in K-Ras. In
some embodiments, bulky substituents are well tolerated at the
5-position of phenyl relative to the bond to the linker portion. In
some embodiments, this position may accommodate bulky groups such
as a propargyl group, without compromising affinity. In some
embodiments, the 6 position on an R.sup.1 phenyl group (relative to
the ortho at the 2 position described previously in this paragraph)
is a non-hydrophobic group. In some embodiments, the terminal
portion includes a fused ring such as a fused ring aryl or fused
ring heteroaryl.
[0484] In some embodiments of the compounds, the linker portion is
bonded to the S2BP moiety through a secondary amine. In some
embodiments of the compounds linker portion is bonded to the S2BP
moiety through an ether or thioether. In some embodiments, the
linker portion is not a rigid moiety. In some embodiments, the
linker includes a ring (e.g. substituted or unsubstituted
heterocycloalkylene, substituted or unsubstituted cycloalkylene,
substituted or unsubstituted arylene. substituted or unsubstituted
heteroarylene substituted or unsubstituted fused rings, substituted
or unsubstituted spirocyclic rings). In some embodiments, the
linker portion includes a diamine. In some embodiments the linker
portion positions the S2BP binding moiety R.sup.1 and the
electrophilic moiety E for optimal contact with the S2BP and a
cysteine or asparate respectively.
[0485] In some embodiments, the electrophilic moiety E may have
flexibility. In some embodiments, optimization of the electrophile
positioning and angle of attack may provide compounds with greater
binding and potency.
C. The Switch 2-Binding Pocket
[0486] In some embodiments, the S2BP binding moiety or S2BP binding
compound interact with one or more of amino acid residues V7, V9,
G10, P34, T58, G60, Q61, E62, E63, R68, Y71, M72, Y96, Q99, and
I100 of K-Ras or the equivalent (i.e. corresponding) amino acids
present in mutants or homologs of K-Ras. In some embodiments, the
S2BP binding moiety or S2BP binding compound displace one or more
amino acids in Switch 2 of K-Ras that interact, in the GTP bound
form, with one or more of the amino acids of the Switch 2 Binding
Region of K-Ras, or the equivalent (i.e. corresponding) amino acids
present in mutants or homologs of K-Ras. In some embodiments, the
S2BP binding moiety or S2BP binding compound displace one or more
amino acids in the Switch 2 Binding Region of K-Ras that interact,
in the GTP bound form, with one or more of the Switch 2 residues of
K-Ras, or the equivalent (i.e. corresponding) amino acids present
in mutants or homologs of K-Ras.
[0487] In some embodiments, the Switch 2-Binding Pocket binding
moiety additionally interacts (e.g. bonds) with an amino acid that
forms part of the Switch 2-Binding Pocket. In some related
embodiments, the interaction is a hydrogen bond, van der Waals
interaction, ionic bond, covalent bond (e.g. disulfide bond) or
hydrophobic interaction.
D. Switch 2-Binding Pocket Binding Moieties that Interact with the
Switch 2-Binding Pocket
[0488] In some embodiments, to determine whether the Switch
2-Binding Pocket binding moiety or Switch 2-Binding Pocket binding
compound contacts and/or fills space within the Switch 2-Binding
Pocket, computer modeling techniques are employed. In some
embodiments, a query Switch 2-Binding Pocket binding compound (i.e.
a test or reference compound) is fit into a structural model, such
as a computer image, of Ras (e.g. K-Ras). In some embodiments, the
structural model is derived from one or more of the solved
co-crystal structures of human K-Ras bound to a compound as
described herein. The PyMOL Molecular Graphics System may be
employed to generate the image. Examples are presented in FIG. 7 or
8, wherein two compounds are built into the computer image of
K-Ras, derived from their respective co-crystal structures with
K-Ras.
[0489] The computer models are typically analyzed to prevent any
gross steric clashes and to satisfy key hydrogen bonds between the
query Switch 2-Binding Pocket binding compound and the K-Ras
protein. In some embodiments, energy minimization calculations are
performed to optimize binding energy. Using these techniques, one
skilled in the art can easily determine whether a query Switch
2-Binding Pocket binding compound includes a Switch 2-Binding
Pocket binding moiety that fills space within the Switch 2-Binding
Pocket.
[0490] In some embodiments, the query Switch 2-Binding Pocket
binding compound is analyzed to determine whether at least one bond
(e.g. a hydrogen bond) is formed between the query Switch 2-Binding
Pocket binding compound and an amino acid that forms part of the
Switch 2-Binding Pocket. In some embodiments, using a computer
modeling technique as described above, the distance between one or
more amino acids that form part of the Switch 2-Binding Pocket and
a potential contact point on the Switch 2-Binding Pocket binding
moiety is determined. In some embodiments, based on this distance,
one skilled in the art may determine whether at least one bond is
formed between one or more amino acids that form part of the Switch
2-Binding Pocket and a Switch 2-Binding Pocket binding moiety.
E. Identification of Covalent K-Ras Inhibitors
[0491] The invention further provides a method of designing a
compound which covalently binds to a Switch 2 binding pocket of a
K-Ras protein, the method comprising the steps of: a) providing a
structural model of a reference compound bound to the Switch 2
binding pocket of the K-Ras protein, wherein the reference compound
is covalently or non-covalently bound to said Switch 2 binding
pocket; b) identifying a cysteine, aspartate, lysine, tyrosine or
glutamate residue located in proximity to said Switch 2 binding
pocket when said reference compound is bound to said Switch 2
binding pocket; c) generating at least one additional structural
model of a test compound bound to said Switch 2 binding pocket,
wherein said test compound comprises an electrophilic moiety; and
d) selecting said test compound if said electrophilic moiety is
located within bonding distance of said cysteine, aspartate,
lysine, tyrosine or glutamate residue when said test compound is
bound to said Switch 2 binding pocket.
[0492] A structural model of a reference compound bound to a Switch
2 binding pocket of a Ras protein (such as K-Ras, N-Ras, or H-Ras)
may be provided as described above. Any suitable structural model
of a reference compound bound covalently or non-covalently to the
Ras protein can be used. For example, a three-dimensional computer
model or a representation thereof (e.g. a computer image) is used.
In some embodiments, an X-Ray crystal structure is used. For
example, one of the solved co-crystal structures of human K-Ras can
be used. In some embodiments, a structural model of a Switch 2
binding pocket of a K-Ras protein is used. Structural models can be
obtained from public databases, including but not limited to the
RCSB Protein Data Bank, available online at pdb.org and rcsb.orb.
Alternatively, structural models can also be obtained and
manipulated by computer modeling, including homology modeling and
folding studies.
[0493] Suitable reactive amino acid residues can be identified by
analyzing the sequence of the protein in conjunction with the
structural model to which the reference compound is bound. Putative
reactive amino acid residues which are cysteine, aspartate, lysine,
tyrosine or glutamate may be identified in proximity to the
reference compound. For example, cysteine residues in proximity to
the reference compound are identified. Once an amino acid residue
in the structural model has been identified, the intermolecular
distance between the reference compound and the putative reactive
amino acid may be noted. In some embodiments, the distance between
the putative reactive amino acid and at least one atom of the
reactive compound is less than or equal to 15, 12, 10, 8, 6, or 4
angstroms.
[0494] Test compounds comprising an electrophilic moiety may
subsequently used to generate additional structural models in which
the position of the electrophilic moiety relative to one or more of
the identified putative reactive amino acid residues is noted. The
bonding distance between the test compound and one of such residues
may be calculated based on the structural model, and a
determination may be made regarding the potential bonding distance
between the test compound (e.g. the electrophilic moiety) and the
putative reactive residue. Test compounds which appear to provide a
suitable bonding distance likely to result in the formation of a
covalent bond may then be chosen for further development. When
making such determinations, factors such as steric hindrance and
orientation of each chemical moiety may be taken into account. Test
compounds which are initially rejected may also be further modified
in order to improve the likelihood that they will form a covalent
bond with the target protein.
[0495] In some embodiments, the compounds described herein target a
mutant of K-Ras, glycine-12 to cysteine (G12C). This is the most
common Ras mutation in lung cancer (Forbes et al. 2006 Br J Cancer)
and the only known transforming mutation found in a recent
comparative sequencing study of a human lung tumor (Lee et al. 2010
Nature). 100% of K-Ras mutations in MYH-associated polyposis
(familial colon cancer syndrome) are K-RasG12C (Jones, S., Lambert,
S., Williams, G. T., Best, J. M., Sampson, J. R., & Cheadle, J.
P. (2004). Increased frequency of the k-ras G12C mutation in MYH
polyposis colorectal adenomas. British Journal of Cancer, 90(8),
1591-1593. doi:10.1038/sj.bjc.6601747) G12C places a nucleophilic
sulfhydryl group between the nucleotide-binding site and the
allosteric site. Since the regions surrounding both sites are
involved in interactions with effectors and GEFs, binding of
compounds (e.g. antagonists, inhibitors, small molecules) at either
site has the potential to disrupt downstream signaling. In some
embodiments, the location and nucleophilicity of this mutant
residue allows development of covalent (e.g. reversible,
irreversible) inhibitors of oncogenic K-Ras that bind in either the
active site or the cleft behind Switch 2 or the Switch 2-Binding
Pocket.
[0496] In some embodiments, a library of disulfide compounds may be
screened against a cysteine-containing protein in the presence of a
reducing agent such as .beta.-mercaptoethanol (BME). Compounds with
complementary binding interactions with a region of the protein
near the cysteine may shift the disulfide exchange equilibrium away
from BME modification of the cysteine thiol and enhance the ratio
of the hit ligand bound to the cysteine (see FIG. 3). The resulting
mass change of the protein can be readily detected by mass
spectrometry, and the percentage of modified protein can be used as
a measure of potency. Compounds which exchange with the cysteine
without conferring affinity should exchange with reducing agent
equally well and will not shift the equilibrium toward protein
modification. The potency of various compounds at a given
concentration of BME may be compared by calculating the
dose-response 50 (DR50), which is the concentration of compound at
which the protein becomes 50% modified.
[0497] In some embodiments, screening is for inhibitors of K-Ras
G12C, a naturally occurring, oncogenic form of the target does not
require removal of the mutant cysteine residue.
[0498] The crystal structure of the complex between H-Ras and SOS
(Margarit et al. 2003 Cell) shows that a deep nucleotide pocket has
been pried open, and the interface between Ras and SOS creates two
new clefts on either side of Ras residue 12.
[0499] The Switch 1 and Switch 2 areas of Ras show significant
structural differences between the GDP- and GTP-bound states.
Moreover, these regions are involved in interactions with all known
Ras binding partners, including effectors, GEFs and GAPs (See FIG.
1). In some embodiments, the compounds described herein covalently
modify cysteine-12 thereby altering the conformation of either
switch region affecting GEF binding or effector protein binding.
Multiple modes of compound (e.g. small molecule, antagonist,
inhibitor) interruption of Ras function can be employed.
[0500] In some embodiments, the compounds provided herein effect
the Ras binding to Raf or PI3K. In some embodiments, binding of the
compounds provided herein to K-Ras modulates K-Ras binding to Raf.
In some embodiments, binding of the compounds provided herein to
K-Ras modulates K-Ras binding to PI3K. In some embodiments, binding
of the compounds provided herein to K-Ras modulates K-Ras binding
to PI3K but not K-Ras binding to Raf. In some embodiments, binding
of the compounds provided herein to K-Ras reduces K-Ras binding to
PI3K but not K-Ras binding to Raf. In some embodiments, binding of
the compounds provided herein to K-Ras modulates K-Ras binding to
Raf but not K-Ras binding to PI3K. In some embodiments, binding of
the compounds provided herein to K-Ras reduces K-Ras binding to Raf
but not K-Ras binding to PI3K. In other embodiments, the compounds
provided herein alter intrinsic or GEF-enhanced nucleotide
exchange. In other embodiments, the compounds provided herein alter
Ras binding to SOS. In other embodiments, the compounds provided
herein modulate SOS-enhanced nucleotide exchange. In some
embodiments, the compounds provided herein increase the intrinsic
or GAP-stimulated rate of GTP hydrolysis. In some embodiments, the
compounds provided herein decrease the intrinsic affinity of K-Ras
for nucleotide. In some embodiments, the compounds provided herein
decrease the intrinsic affinity of K-Ras for GTP. In some
embodiments, the compounds provided herein decrease the intrinsic
affinity of K-Ras for GDP.
[0501] Residue 12 of K-Ras lies between the nucleotide-binding site
and an allosteric pocket. In some embodiments, the compounds
provided herein bind to either site or both sites. In some
embodiments, compound binding to the allosteric pocket alters
K-Ras-effector interactions. In some embodiments, compound binding
to the S2BP alters K-Ras-effector interactions. In some
embodiments, compound binding to the nucleotide-binding site alters
K-Ras-effector interactions. In some embodiments, simultaneous
compound binding to the allosteric pocket and the
nucleotide-binding site alters K-Ras-effector interactions. In some
embodiments, simultaneous compound binding to the S2BP and the
nucleotide-binding site alters K-Ras-effector interactions. In some
embodiments, compound binding to the allosteric pocket, S2BP,
and/or nucleotide-binding site alters the activity of the K-Ras
protein, it's GTPase activity, nucleotide exchange, effector
protein binding, effector protein activation, guanine exchange
factor (GEF) binding, GEF-facilitated nucleotide exchange,
phosphate release, nucleotide release, nucleotide binding, K-Ras
subcellular localization, K-Ras post-translational processing,
K-Ras post-translational modifications, or GTP bound K-Ras
signaling pathway.
[0502] In some embodiments, the compounds described herein afford a
covalent yet reversible handle.
F. Determining Intrinsic and GEF Mediated Nucleotide Exchange Rates
for Compound-Bound K-RasG12C
[0503] GEF-mediated nucleotide exchange assays were carried out
using full-length recombinant human K-Ras G12C and WT containing an
N-terminal hexahistidine tag and the catalytic domain of SOS
(residues 566-1049), also containing a hexahistidine tag, in the
presence of .alpha.-.sup.32P-labeled GTP. K-Ras WT and G12C were
treated with 250 .mu.M inhibitor overnight at 4 C in the following
buffer: 20 mM HEPES [pH 7.5], 150 mM NaCl, 10 mM EDTA. The percent
modification was determined by mass spectrometry (Waters Acquity
TQD). The proteins were then run over NAP-5 columns, eluting with
Buffer A (20 mM HEPES [pH 7.5], 150 mM NaCl, 20 mM MgCl.sub.2),
following the manufacturer's instructions. Reaction mixes were
prepared containing 4 .mu.M K-Ras and 1 .mu.M SOS in Buffer A with
1 mg/mL BSA. Separately, a solution of [.alpha.-.sup.32P] GTP (160
pCi/mL, 2 .mu.M total GTP) was prepared. The reactions were
initiated by adding 25 .mu.L GTP solution to 25 .mu.L of each
reaction mixture. Exchange was measured by blotting the reaction
onto nitrocellulose, washing with Buffer A, then visualizing by
phosphorimager.
G. Recombinant Protein Expression of K-Ras
[0504] Hexahistidine-tagged recombinant human K-Ras (isoform 2,
residues 1-169, based on construct used for pdb entry 3GFT) was
transformed into Escherichia coli (BL21 (DE)). After the bacterial
growth to an OD(600) of 0.4-0.6 in Terrific Broth containing 30
mg/L kanamycin at 37 C, induction was carried out at 18 C using 0.5
mM IPTG and growth was continued at 18.degree. C. for about 18 h.
The bacteria were harvested by centrifugation and the obtained
pellet either stored at -80 C or used freshly for the subsequent
steps.
[0505] The pellet was resuspended in lysis buffer (500 mM NaCl, 20
mM TRIS pH=8, 5 mM imidazole) containing protease inhibitor
cocktail (Roche complete EDTA free), the bacteria were lysed by
microfluidizer, 2 mM BME (final) was added and cell debris was
removed by ultracentrifugation. The supernatant was incubated for 1
h with Co-affinity beads (Clontech, .about.2 mL bed volume per 1 L
initial culture), the loaded beads then washed with lysis buffer
containing 2 mM BME and the protein eluded with buffer containing
125-250 mM imidazole. The hexahistidine tag was then cleaved using
Hexahistidine-tagged TEV-protease (1 mg recombinant TEV per 25 mg
crude K-Ras, 1 mg GDP added per 20 mg crude K-Ras) while dialyzing
against a buffer containing 300 mM NaCl, 20 mM TRIS pH=8, 5 mM
imidazole, 1 mM DTT, 0.5 mM EDTA. The cleaved protein was then
diluted 5-fold with low salt buffer (50 mM NaCl, 20 mM TRIS pH=8),
incubated with Ni-agarose beads (Qiagen) to remove uncleaved
protein and protease, and 5 mM MgCl2 and GDP was added to fully
load the metal and nucleotide site of K-Ras.
[0506] The crude protein was then purified by ion exchange
chromatography (HiTrap Q HP column, salt gradient from 50 to 500 mM
NaCl) to give the partially purified protein, commonly in following
buffer (.about.230 mM NaCl, 20 mM TRIS pH=8, small amounts of
GDP).
[0507] At this point the partially purified protein was either
fully labeled with the desired compound (incubation overnight with
an excess of compound at 4 C, labeling checked by massspec
analysis), frozen down and stored at -80 C, or used for further
purification.
[0508] The last purification step for the labeled or unlabeled
protein was gel-filtration using a Superdex 200 column (10/300 GL)
with the following buffer: 20 mM HEPES pH=7.5, 150 mM NaCl and 1 mM
DTT (for the unlabeled proteins). The freshly prepared and purified
protein was then concentrated to 5-20 mg/mL and used for the X-ray
crystallography trays.
H. X-Ray Crystallography
[0509] Sequences for the different K-Ras constructs were generally
codon-optimized and synthesized by DNA2.0 using the pJexpress411
vector. For the X-ray structures of compound labeled K-Ras G12C a
special cysteine-light mutant was used (G12C, C51S, C80L, C118S) to
enable more uniformly labeled species.
[0510] For X-ray crystallography 1 mM magnesium chloride and 40
microM GDP (final) were added to the freshly purified protein.
After high speed centrifugation hanging drop crystallization
conditions were set up by mixing 1:1 protein and precipitation
solutions. Common successful reservoir conditions were: 28-32%
PEG3000, 200 mM NaCl, 100 mM Tris pH=7; 1.8-2.2M 2:3
NaH2PO4:K2HPO4, 0.1M NaAc; 28-32% PEG4000, 200 mM NH4CH3COO, 100 mM
Na-citrate pH=5.6; 18-22% PEG8000, 100 mM CaCl2, 100 mM Tris
pH=7.5; 18-22% PEG3350, 0.2M CaCl2, pH=7.5. After a varying amount
of time, commonly several days, at 20 C three dimensional crystals
were observed. If necessary crystals were cryoprotected in the
crystallization solution supplemented with glycerol, flash frozen
and stored in liquid nitrogen prior to obtaining diffraction data
at beamlines 8.2.1/8.2.2 (100 K nitrogen stream) at the Berkeley
Lab Advanced Light Source. Data was initially processed with
HKL2000 (HKL Research, Inc., scaling) and then solved by molecular
replacement and refined to the indicated statistics using Phenix
(Adams et al.).
I. Mass Spectrometric Screen for Extent of Covalent Labeling
[0511] Un-tagged recombinant K-Ras G12C (1-169) at 4 .mu.M in
Buffer A was reacted with inhibitors at 200 .mu.M or 10 .mu.M (2%
DMSO final). At 2, 6, and 24 hrs, 10 .mu.L aliquots were removed
and the reactions were stopped by addition of 1 .mu.L 2% formic
acid. The extent of modification was determined by mass
spectrometry.
J. Disulfide Library Screen
[0512] We screened a library of disulfide compounds for covalent
modification of K-RasG12C (1-169) as determined by mass
spectrometry. Hit compounds will be defined as those causing
>50% modification of Ras at a concentration of 100 .mu.M while
in the presence of 100 .mu.M BME. It has been shown previously that
EDTA increases the nucleotide exchange rate of both H-Ras (Hattori
et al. 1987 Mol Cell Biol) and K-Ras (Hara et al. 1988 Oncogene
Res). The EDTA chelates Mg.sup.2+ and destabilizes the nucleotide
bound state of Ras. To enhance the possibility of finding molecules
which bind to the GTP site. The screen was carried out in the
presence of EDTA. Once hits have been identified, compound
titrations will be carried out in the presence of 200 .mu.M BME to
determine their DR50. These compounds will also be counter-screened
against wild-type K-Ras to verify that they modify the mutant
cysteine and not one of the three cysteines already present in the
wild-type sequence. While treatment of Ras with EDTA increases the
rate of nucleotide exchange by two orders of magnitude, nucleotide
exchange factors can increase the rate by a factor of 10.sup.5.
With a higher rate of exchange, we may be more likely to identify
compounds binding in the GTP site.
[0513] We have screened a library of 480 tethering compounds at 100
.mu.M each against K-RasG12C (1-169) in the presence of 100 .mu.M
BME and 10 mM EDTA. From this screen we have identified 17
molecules which reach >50% modification of Ras. A disulfide
containing hit (6H05) reached 95% modification, and titration
experiments gave a DR50 of 31 .mu.M. None of our hit compounds from
this library screen caused greater than 10% modification of
wild-type K-Ras, suggesting they are specifically tethering to the
mutant cysteine. When the entire library was screened against
H-RasG12C only 6H05 exhibited greater than 50% modification (see
FIG. 5).
[0514] All disulfide hit compounds identified in this screen were
less potent in the absence of EDTA, including 6H05. However, when
GDP and non-hydrolyzable GTP (GMPPNP) were each titrated up to 0.8
mM in the presence of EDTA, there was no detectable effect on
modification. This result strongly suggests that 6H05 does not
share a binding site with nucleotide.
[0515] To begin understanding the structure-activity relationship
of 6H05, we designed and synthesized a family of 10 analogues (see
FIG. 6). One of these analogues, JO-148A, showed slightly increased
potency over 6H05 with a DR50 of 27 .mu.M in the presence of EDTA.
In addition, this analogue retained a DR50 of 63 .mu.M in the
presence of 10 mM MgCl.sub.2 and 100 .mu.M GMPPNP. Under these
conditions, over the course of the experiment essentially no
nucleotide exchange is expected to occur.
K. Determining Intrinsic GTPase and GAP Mediated Activity of
Compound-Bound K-Ras G12C
[0516] The assays will be carried out as described previously
(Schubbert et al., Mol. Cell Biol. 2007, 7765-70). 200 nM of each
recombinant K-Ras protein (G12C, compound loaded G12C, G12D, WT)
that had been preloaded with [.gamma.-.sup.32P]GTP is incubated
without (intrinsic GTPase activity assay) or with (GAP assays)
GAP-related domain (GRD) proteins (neurofibromin or p120 GAP) at
room temperature. The hydrolyzed and released radioactive phosphate
is extracted and detected by liquid scintillation counting at
defined time points. Recombinant K-Ras and GRD proteins are
produced in Escherichia coli.
L. Determining Occupancy of the Pocket by Click Chemistry
[0517] Lysate from Calu-1 (G12C), NCI H-1792 (G12C), or HEK cells
is treated with 10 .mu.M inhibitor or DMSO for 24 hrs at 4.degree.
C. Ras is then immunoprecipitated with anti-Ras antibody on
magnetic beads Immobilized Ras is then treated with 200 .mu.M
Ras-069 (propargyl) for 24 hrs at 4 C. Rhodamine-azide or
biotin-azide is then attached to the propargyl group of Ras-069 by
Cu-catalyzed click reaction. Following elution of the proteins, the
extent of modification by Ras-069 is visualized by Western blot
(biotin) or fluorescence imager (rhodamine), and reveals the extent
of K-RasG12C with an unoccupied allosteric pocket after inhibitor
treatment. Thus, the extent of inhibitor modification is
anti-correlated with Western or fluorescence signal.
M. Initial Stop Flow Experiments
[0518] Conditions: 1 micM protein, buffer: 20 mM HEPES pH=7.5, 150
mM NaCl, 1 mM DTT, 2 mM unlabeled GDP if indicated, 1 micM SOS if
indicated, 2.5 mM EDTA if indicated, no added free Mg in buffer,
protein loaded with mant-dGDP, (1 h r.t. incubation with 2 mM EDTA,
NAP-5 purification), protein pre-labeled with compounds and frozen,
experiment at 20 C. Results: fast intrinsic bleaching/exchange,
larger drop in fluorescence due to EDTA treatment with compound,
acceleration of exchange in presence of SOS.
N. Continued Stop Flow Experiments
[0519] Conditions: 1 micM protein (same), buffer (changed): 40 mM
HEPES pH=7.5, 10 mM MgCl2, 1 mM DTT, 0.1 mM unlabeled GDP if
indicated (changed), 0.1 mM unlabeled GTP if indicated (new), 1
micM SOS if indicated (same concentration), 15 mM EDTA if indicated
(changed), now contains free Mg in buffer (s.a.), protein loaded
with mant-dGDP. (1 h r.t. incubation with 2 mM EDTA, NAP-5
purification), protein pre-labeled with compounds and frozen,
experiment at 20 C. Results: lowered intrinsic exchange, less
effect of EDTA, initial drop (may need more?), basically no SOS
acceleration. Ongoing experiments comparing GDP vs. GTP.
O. Crystallization Screen
[0520] Carried out screen for .about.500 conditions with labeled
protein loaded with either nucleotide. Found large number (>10
conditions) that showed crystallization with either form, more for
GDP, some overlap in conditions. Followed up on conditions: 9 for
GDP, 6 for GppNp (same for all 3 compounds). Reproduced fairly well
(about 1/2 of conditions)
P. Compound Binding Perturbs Nucleotide Binding (GTP vs. GDP)
[0521] More than 15 co-crystal structures confirm novel pocket
behind Switch II with strong SAR. Inhibitors block nucleotide
exchange and decrease Raf binding. It is possible to specifically
inhibit proliferation of KrasG12C-driven cancer cell lines by
treating under serum deprivation. Experiments being conducted to
obtain more complete signaling data, including for control
compound. FIGS. 12, 13, and 15 to 19 show modulation of K-ras
conformation by compound binding, which modulates nucleotide
binding site (e.g. GTP binding) and show novel binding pocket.
Q. Compound Binding to K-Ras Alters Affinities for GTP and GppNp
(GNP), (See FIGS. 34 to 36 and Tables 6 to 8)
[0522] The corresponding recombinantly expressed, full-length K-Ras
protein (wild type, G12C-mutant, G12C-mutant labeled fully with
either compound 055 (Ras-055) or 083 (Ras-083)) at about 10 micM
(micromolar) concentration was incubated with 200 micM mant-d-GDP
in the presence of 2.5 M EDTA. After one hour at room temperature
MgCl.sub.2 to a final concentration of 10 mM was added. The protein
was then run through a NAP-5 column to remove free nucleotide. The
concentration of the obtained protein was determined by Bradford
assay and the protein was then used in the described plate-based
assay. For the assay 10 micL of the prepared protein in reaction
buffer (20 mM HEPES pH=7.5, 150 mM NaCl, 1 mM DTT, 1 mM MgCl.sub.2)
was added to a well of a low volume black bottom plate (Corning,
#3676). The fluorescence intensity was measured on a spectramax M5
plate reader (Molecular devices, 360 nm excitation, 440 nm
emission) to provide a value used in later normalization. Then 5
micL of an EDTA solution with the indicated nucleotide (GDP, GTP,
or GppNp) was added to each well and the reaction mix was allowed
to equilibrate for two hours at room temperature. Measurement of
the fluorescent intensity at this time provided the end point.
Samples were measured in duplicates for each experiment. In the
final mix the concentrations were the following: protein (1 micM),
EDTA (5 mM), nucleotide (as indicated, titrated in 2.5-fold
dilution series, 15-points). Curves show results from one
representative experiment, the column-graph shows the averaged data
from three experiments with standard deviation shown as error. For
the determination of IC50 for each nucleotide a sigmoidal curve fit
was used (Prism-software).
[0523] Compound binding to K-Ras reduces SOS-mediated exchange
(dissociation of mant-d-GDP monitored). The corresponding
recombinantly expressed, full-length K-Ras protein (wild type,
G12C-mutant, G12C-mutant labeled fully with either compound 055 or
083) at about 10 micM concentration was incubated with 200 micM
mant-d-GDP in the presence of 2.5 M EDTA. After one hour at room
temperature MgCl.sub.2 to a final concentration of 10 mM was added.
The protein was then run through a NAP-5 column to remove free
nucleotide. The concentration of the obtained protein was
determined by Bradford assay and the protein was then used in the
described plate-based assay. Concentration of recombinantly
expressed SOS-protein was determined by Bradford assay as well. For
the assay 10 micL of the prepared protein in reaction buffer (20 mM
HEPES pH=7.5, 150 mM NaCl, 1 mM DTT, 1 mM MgCl.sub.2) was added to
a well of a low volume black bottom plate (Corning, #3676). Then 5
micL of either buffer (for intrinsic rate), SOS-solution, or
EDTA-solution containing the indicated nucleotide (GDP, GTP, or
GppNp) was added to each well. The fluorescence intensity of each
reaction was followed on a spectramax M5 plate reader (Molecular
devices, 360 nm excitation, 440 nm emission) over five hours (18000
seconds) at one minute intervals. Samples were measured in
triplicate for each experiment. In the final mix the concentrations
were the following: protein (1 micM), EDTA (if present: 5 mM), SOS
(if present: 1 micM), nucleotide (as indicated: 200 micM, excess).
Curves show results from one representative experiment, the table
shows the averaged data from three experiments with standard
deviation shown as error. For the determination of half-lives a
one-phase exponential decay model was used (Prism-software).
[0524] Compound binding to K-Ras reduces SOS-mediated exchange
(association of mant-d-GDP or mant-d-GppNp monitored). Protein
concentrations of freshly thawed, recombinantly expressed,
GDP-loaded full-length K-Ras protein (wild type, G12C-mutant,
G12C-mutant labeled fully with either compound 055 or 083) and SOS
were determined by Bradford assay. Then a K-Ras solution containing
varying amount of SOS in reaction buffer (20 mM HEPES pH=7.5, 150
mM NaCl, 1 mM DTT, 1 mM MgCl.sub.2) was prepared and 10 micL were
added to each well of a low volume black bottom plate (Corning,
#3676). The exchange reaction was started by addition of either 5
micL of a mant-d-GDP or mant-d-GppNp solution in reaction buffer.
The fluorescence intensity of each reaction was followed on a
spectramax M5 plate reader (Molecular devices, 360 nm excitation,
440 nm emission) over five hours (18000 seconds) at one minute
intervals. Samples were measured in triplicate for each experiment.
In the final mix the concentrations were the following: K-Ras (1
micM), SOS (0 (intrinsic), 0.25-4 micM, 2-fold dilution series),
mant-d-GDP/mant-d-GppNp (1 micM). Curves show results from one
representative experiment, the table shows the averaged data from
three experiments with standard deviation shown as error. For the
determination of half-lives a one-phase association model was used
(Prism software).
TABLE-US-00001 TABLE 1 Obtained structures (Electrophiles) ordered
by increasing potency: Labeling percentage + <=5%, 5% < ++
<=20%, 20%< +++ <=40%, 40%< ++++ <=60%, 60% <
+++++ Labeling % Resolution/ (10 micM) Space group R-free/
Structure Compound 24 h Unit cell R-work JO-02-112D ##STR00135##
+++ (plate) 3 sets 1.35A 1.35A 1.40A C121 (72,40,55A) (90,105,90)
0.1806/ 0.1504 0.1809/ 0.1577 0.1937/ 0.1537 JO-02-172 ##STR00136##
+ (plate) 2.09 A C121 (71,83,87A) (90,109,90) Diff. orient. 0.2285/
0.1897 JO-02-31A ##STR00137## ++ (plate) 1.70 A C121 (68,83,85A)
(90,111,90) 0.2106/ 0.1763 JO-02-56A ##STR00138## ++++ (plate) 2.30
A P22121 (93,108, 121A) (90,90,90) 0.2218/ 0.1809 Ras-028
##STR00139## +++ (plate) 1.55 A C121 (68,84,86A) (90,111,90)
0.1966/ 0.1814 Ras 055 (C2) ##STR00140## +++++ (plate) 1.57 A C121
(68,84,87A) (90,111,90) 0.1931/ 0.1584 Ras 055 (P1) ##STR00141##
+++++ (plate) 1.49 A P1 (33,40,62A) (77,82,78) 0.2122/ 0.1752
Ras-059 ##STR00142## +++++ (single) 1.58A C121 (68,84,87A)
(90,111,90) 0.1913/ 0.1740 Ras-062 ##STR00143## +++ (single) 1.94A
C121 (68,84,87A) (90,111,90) 0.2351/ 0.1948 UP-I-177C ##STR00144##
++++ (plate) 1.57 A C121 (68,84,86A) (90,111,90) 0.2087/ 0.1837
UP-I-185a ##STR00145## +++++ (single) 1.81A C121 (68,84,87A)
(90,111,90) 0.2038/ 0.1801
TABLE-US-00002 TABLE 2 Obtained structures (Disulfides) ordered by
increasing potency: Labeling percentage + <=5micromolar, 5
micromolar < ++ <=20 micromolar, 20 micromolar < +++
<=40 micromolar, 40 micromolar < ++++ <=60 micromolar, 60
micromolar < +++++ Resolution/ Potency/ Space group R-free/
Structure Compound Labeling Unit cell R-work JO-01-148 ##STR00146##
++++ (EC50 at 200 micM BME) Tethering 1.50 A P1 (33,39,63A)
(77,81,77) 0.1977/ 0.1639 JO-01-189 Cbut ##STR00147## ++ (EC50 at
200 micM BME) Tethering 1.29 A P1 (33,39,62A) (78,82,78) 0.1723/
0.1591
TABLE-US-00003 TABLE 3 Eletrophilic K-Ras Modulators (e.g. covalent
S2BP binding compounds). Percent reduction in activity of compound
at 10 micromolar relative to control (no compound): + <=5%, 5%
< ++ <=20%, 20% < +++ <=40%, 40% < ++++ <=60%,
60% < +++++. Structure Name Mol Weight 2 hrs 6 hrs 24 hrs
##STR00148## Ras-001 396.268 + + + ##STR00149## Ras-002 391.677 + +
+ ##STR00150## Ras-003 312.366 + + + ##STR00151## Ras-004 312.366 +
+ + ##STR00152## Ras-005 326.393 + + + ##STR00153## Ras-006 326.393
+ + + ##STR00154## Ras-007 414.326 + + + ##STR00155## Ras-008
427.73 + + + ##STR00156## Ras-009 348.42 + + + ##STR00157## Ras-010
362.447 + + + ##STR00158## Ras-011 461.283 + + +++ ##STR00159##
Ras-012 362.447 + + + ##STR00160## Ras-013 418.295 + + ++
##STR00161## Ras-014 348.42 + + + ##STR00162## Ras-015 437.736 + +
+++ ##STR00163## Ras-016 415.892 + + + ##STR00164## Ras-017 376.831
+ + + ##STR00165## Ras-018 372.867 + + +++ ##STR00166## Ras-019
408.3 + + ++ ##STR00167## Ras-020 416.876 + + + ##STR00168##
Ras-021 383.85 + + + ##STR00169## Ras-022 450.337 + + +
##STR00170## Ras-023 401.865 + + + ##STR00171## Ras-024 422.327 + +
+ ##STR00172## Ras-025 429.918 + + + ##STR00173## Ras-026 436.353 +
+ ++ ##STR00174## Ras-027 452.353 + + + ##STR00175## Ras-028
392.301 + + +++ ##STR00176## Ras-029 427.945 + + + ##STR00177##
Ras-030 484.737 + + ++++ ##STR00178## Ras-031 429.918 + + +
##STR00179## Ras-032 387.882 + + + ##STR00180## Ras-033 373.855 + +
+ ##STR00181## Ras-034 401.908 + + + ##STR00182## Ras-035 436.31 +
+ + ##STR00183## Ras-036 519.182 + ++ ++++ ##STR00184## Ras-037
451.321 + + ++ ##STR00185## Ras-038 437.295 + + + ##STR00186##
Ras-039 409.285 + + ++ ##STR00187## Ras-040 472.181 + + +++
##STR00188## Ras-041 388.866 + + ++ ##STR00189## Ras-042 386.85 + +
++ ##STR00190## Ras-043 435.322 + + + ##STR00191## Ras-044 437.338
+ + ++ ##STR00192## Ras-045 461.323 + + + ##STR00193## Ras-046
575.098 + + + ##STR00194## Ras-047 472.364 + + + ##STR00195##
Ras-048 453.337 + + ++ ##STR00196## Ras-049 480.363 + + +
##STR00197## Ras-050 423.311 + + ++ ##STR00198## Ras-051 388.866 +
+ ++ ##STR00199## Ras-052 532.224 + + ++ ##STR00200## Ras-053
519.182 + ++ ++++ ##STR00201## Ras-054 422.327 + +++ +++++
##STR00202## Ras-055 408.3 ++ +++ +++++ ##STR00203## Ras-056
459.347 + + + ##STR00204## Ras-057 920.597 + ++ ++++ ##STR00205##
JO-01-171 357.232 + + + ##STR00206## JO-01-172 343.205 + + +
##STR00207## JO-02-26 409.351 + + ++ ##STR00208## JO-02-31A 393.285
+ + ++ ##STR00209## JO-02-31B 388.933 + + ++ ##STR00210## JO-02-31C
424.965 + + +++ ##STR00211## JO-02-31D 409.351 + + + ##STR00212##
JO-02-36A 353.222 + + + ##STR00213## JO-02-36B 367.248 + + +
##STR00214## JO-02-37A 317.168 + + + ##STR00215## JO-02-37B 331.194
+ + + ##STR00216## JO-02-38B 255.317 + + + ##STR00217## JO-02-49A
367.85 + + + ##STR00218## JO-02-49B 351.396 + + + ##STR00219##
JO-02-49C 363.431 + + + ##STR00220## JO-02-74A 405.296 + + +++
##STR00221## JO-02-74B 419.323 + + ++ ##STR00222## JO-02-74C
405.296 + + ++ ##STR00223## JO-02-72 373.231 + + + ##STR00224##
JO-02-77A 359.248 + + + ##STR00225## JO-02-55 393.285 + + ++
##STR00226## JO-02-56A 450.337 + + ++++ ##STR00227## JO-02-56B
450.337 + + ++ ##STR00228## JO-02-112A 419.323 + + ++ ##STR00229##
JO-02-112B 433.349 + + ++ ##STR00230## JO-02-112C 407.312 + + +
##STR00231## JO-02-112D 379.259 + + +++ ##STR00232## JO-02-115A
358.84 + + + ##STR00233## JO-02-115B 407.312 + + + ##STR00234##
JO-02-115C 407.312 + + + ##STR00235## JO-02- 115D 427.73 + + +++
##STR00236## JO-02-116A 441.757 + + + ##STR00237## JO-02-116B
428.719 + + + ##STR00238## JO-02-125 312.368 + + +++ ##STR00239##
JO-02-139E 340.785 + + + ##STR00240## JO-02-144 518.197 + ++ +++++
##STR00241## JO-02-152 498.143 + + +++ ##STR00242## UP-I-162B
508.416 + + + ##STR00243## UP-I-164A 362.491 + + + ##STR00244##
UP-I-164B 346.426 + + + ##STR00245## UP-I-164C 345.441 + + +
##STR00246## UP-I-165B 460.332 + + + ##STR00247## UP-I-165C 366.396
+ + + ##STR00248## UP-I-165D 361.503 + + + ##STR00249## UP-I-177C
465.348 + ++ ++++ ##STR00250## UP-I-177D 554.25 + + +++++
##STR00251## UP-I-177E 648.251 + + +++++ ##STR00252## JO-02-155
468.117 + ++ ++++ ##STR00253## Ras-058 422.327 + + + ##STR00254##
Ras-059 420.354 + ++ +++++ ##STR00255## Ras-060 538.23 + + +
##STR00256## Ras-061 486.39 + + + ##STR00257## Ras-062 372.246 + +
+++ ##STR00258## UP-I-154B 407.55 + + + ##STR00259## UP-I-160B
394.512 + + + ##STR00260## JO-02-157A (R) 468.117 + + +
##STR00261## JO-02-1578 (S) 468.117 + + ++ ##STR00262## Ras-063
409.285 + ++ +++ ##STR00263## Ras-064 417.908 + + +++ ##STR00264##
Ras-065 455.88 + ++ +++ ##STR00265## Ras-066 405.799 + + ++
##STR00266## Ras-067 426.838 + + ++ ##STR00267## Ras-068 518.197 +
+ + ##STR00268## Ras-069 447.333 + ++ +++++
##STR00269## Ras-070 437.338 + + +++ ##STR00270## Ras-071 417.307 +
+ ++++ ##STR00271## Ras-072 538.23 + + + ##STR00272## UP-I-185a
450.363 ++ +++ +++++ ##STR00273## UP-I-185b 408.3 + + ++
##STR00274## UP-I-187 434.298 + + +++ ##STR00275## UP-I-154A
444.332 + + + ##STR00276## UP-I-154K 412.55 + + + ##STR00277##
Ras-073 +++ +++++ ##STR00278## Ras-074 ++++ ##STR00279## Ras-075 _
##STR00280## Ras-076 - ##STR00281## Ras-077 ++ +++++ ##STR00282##
Ras-078 - ##STR00283## JO-02-31A +++ ##STR00284## Ras-079 +++ +++++
+++++ ##STR00285## Ras-080 +++ ##STR00286## Ras-081 +++ ++++ +++++
##STR00287## Ras-082 +++ +++++ ##STR00288## Ras-083 +++ +++++
##STR00289## Ras-084 +++ +++++ +++++ ##STR00290## Ras-085 ++ +++
+++++ ##STR00291## Ras-086 ++++ ##STR00292## Ras-087
TABLE-US-00004 TABLE 4 Modulation of Ras by compound binding.
12C.alpha. to 60C.alpha. GDP-bound distance (.ANG.) Switch I Metal
ion WT 8 Mg Hras G60A 8.1 Mg (1XJ0) JO-02-172 8.3 Mg JO-02-112D 8.4
Mg JO-02-56A 8.5 Mg Chain D JO-02-56A 8.6 Mg Chain E JO-01-148 9 Ca
JO-01-189 9.1 Ca Ras-055_P1 9.5 Ca (Ras-055 in P1) Ras-028 11.1
disordered -- JO-02-56A 11.2 disordered Mg Chain C JO-02-31A 11.6
disordered -- JO-02-56A 11.7 disordered -- Chain A Ras-055_C2 11.9
disordered -- (Ras-055 in C2) UP-I-185a 12 disordered -- Ras-059
12.6 disordered -- UP-I-177C 12.8 disordered -- JO-02-56A no
density disordered -- Chain B Ras-062 no density disordered -- Hras
G12C 3.8 Mg Kras WT state 3.9 Mg state 2 (3GFT) Rap1A 3.9 Mg
(RafRBD) (1C1Y) Hras T35S state 3.9 Mg 2 (2KKM) Hras T35S state 4.9
low affinity state Mg 1 (3KKN) Kras WT state 1 4.9 low affinity
state Mg (4EFL) Hras G60A 5.2 low affinity state Mg (1XCM)
TABLE-US-00005 TABLE 5 Labeling % Resolution/ (10 micM) Space group
R-free/ Structure Compound 24 h Unit cell R-work JO-02-112D
##STR00293## +++ (plate) 3 sets 1.35A 1.35A 1.40A C121 (72, 40,
55A) (90, 105, 90) 0.1806/ 0.1504 0.1809/ 0.1577 0.1937/ 0.1537
JO-02-172 ##STR00294## + (plate) 2.09 A C121 (71, 83, 87A) (90,
109, 90) Diff. orient. 0.2285/ 0.1897 JO-02-31A ##STR00295## ++
(plate) 1.70 A C121 (68, 83, 85A) (90, 111, 90) 0.2106/ 0.1763
JO-02-56A ##STR00296## ++++ (plate) 2.30 A P22121 (93, 108, 121A)
(90, 90, 90) 0.2218/ 0.1809 Ras-028 ##STR00297## +++ (plate) 1.55 A
C121 (68, 84, 86A) (90, 111, 90) 0.1966/ 0.1814 Ras 055 (C2)
##STR00298## +++++ (plate) 1.57 A C121 (68, 84, 87A) (90, 111, 90)
0.1931/ 0.1584 Ras 055 (P1) ##STR00299## +++++ (plate) 1.49 A PI
(33, 40, 62A) (77, 82, 78) 0.2122/ 0.1752 Ras-059 ##STR00300##
+++++ (single) 1.58A C121 (68.84.87A) (90, 111, 90) 0.1913/ 0.1740
Ras-062 ##STR00301## +++ (single) 1.94A C121 (68, 84, 87A) (90,
111, 90) 0.2351/ 0.1948 UP-I-177C ##STR00302## ++++ (plate) 1.57 A
C121 (68, 84, 86A) (90, 111, 90) 0.2087/ 0.1837 UP-I-185a
##STR00303## +++++ (single) 1.81A C121 (68, 84, 87A) (90, 111, 90)
0.2038/ 0.1801 UP-I-185a (update, delete the old one) ##STR00304##
+++++ (single) 1.49A C121 (68, 84, 86A) (90, 111, 90) 0.1908/
0.1689 Ras-069 ##STR00305## +++ (single) 1.74A C121 (69, 85, 87A)
(90, 111, 90) 0.2098/ 0.1849 Ras-079 (C2) ##STR00306## +++++
(single) 1.37A C121 (68, 84, 84A) (90, 111, 90) 0.1918/ 0.1652
Ras-079 (P212121) ##STR00307## +++++ (single) 1.93A P212121 (39,
43, 88A) (90, 90, 90) 0.2086/ 0.1736 Ras-081 ##STR00308## +++++
(single) 2.04A C121 (68, 84, 86A) (90, 110, 90) 0.2169/ 0.1836
UP-I-177E ##STR00309## ++++ (plate) 2.27 A C121 (68, 85, 86A) (90,
111, 90) 0.2340/ 0.1857 UP-I-187 ##STR00310## +++ (single) 1.59A
C121 (68, 84, 87A) (90, 111, 90) 0.2004/ 0.1753
TABLE-US-00006 TABLE 6 Calculated/estimated half-lives from
experiments in FIG. 34. mant-dGDP Calculated/Estimated Half-lives
mant-dGDP intrinsic SOS, 4 .mu.M SOS, 2 .mu.M SOS, 1 .mu.M SOS, 0.5
.mu.M SOS, 0.25 .mu.M WT >18000 s 350 .+-. 40 s 420 .+-. 40 s
1030 .+-. 130 s 1850 .+-. 200 s 4500 .+-. 800 s G12C >18000 s
580 .+-. 70 s 810 .+-. 80 s 2100 .+-. 400 s 3700 .+-. 300 s 10700
.+-. 3000 s G12C-055 >18000 s 11300 .+-. 2500 s 10500 .+-. 4200
s >18000 s >18000 s >18000 s G12C-083 >18000 s 8200
.+-. 2400 s >18000 s >18000 s >18000 s >18000 s
TABLE-US-00007 TABLE 7 Calculated/estimated half-lives from
experiments in FIG. 35. mant-dGppNp Calculated/Estimated Half-lives
mant-dGppNp intrinsic SOS, 4 .mu.M SOS, 2 .mu.M SOS, 1 .mu.M SOS,
0.5 .mu.M SOS, 0.25 .mu.M WT >18000 s 610 .+-. 70 s 940 .+-. 100
s 2000 .+-. 150 s 3300 .+-. 140 s 7000 .+-. 500 s G12C >18000 s
1160 .+-. 70 s 1780 .+-. 70 s 3860 .+-. 730 s 4480 .+-. 80 s 16300
.+-. 1500 s G12C-055 no reliable data obtained G12C-083 no reliable
data obtained
TABLE-US-00008 TABLE 8 Calculated/estimated half-lives from
experiments in FIG. 36. Calculated/Estimated Half-lives SOS/GDP
SOS/GTP SOS/GppNp EDTA/GDP EDTA/GTP EDTA/GppNp WT 2080 .+-. 140 s
1010 .+-. 50 s 1120 .+-. 70 s 117 .+-. 6 s 112 .+-. 3 s 107 .+-. 2
s G12C 3640 .+-. 340 s 1560 .+-. 320 s 1640 .+-. 160 s 157 .+-. 5 s
151 .+-. 4 s 143 .+-. 5 s G12C-055 >18000 s >18000 s
>18000 s 247 .+-. 14 s 232 .+-. 13 s 197 .+-. 10 s G12C-083
>18000 s >18000 s >18000 s 370 .+-. 7 s 334 .+-. 7 s 304
.+-. 11 s
##STR00311##
##STR00312## ##STR00313##
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[0546] It is understood that the examples and embodiments described
herein are for illustrative purposes only and that various
modifications or changes in light thereof will be suggested to
persons skilled in the art and are to be included within the spirit
and purview of this application and scope of the appended claims.
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purposes.
Sequence CWU 1 SEQUENCE LISTING <160> NUMBER OF SEQ ID
NOS: 17 <210> SEQ ID NO 1 <211> LENGTH: 189 <212>
TYPE: PRT <213> ORGANISM: Homo sapiens <400> SEQUENCE:
1 Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1
5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu
Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val
Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala
Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg
Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr
Lys Ser Phe Glu Asp Ile His Gln Tyr 85 90 95 Arg Glu Gln Ile Lys
Arg Val Lys Asp Ser Asp Asp Val Pro Met Val 100 105 110 Leu Val Gly
Asn Lys Cys Asp Leu Ala Ala Arg Thr Val Glu Ser Arg 115 120 125 Gln
Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Tyr Ile Glu Thr 130 135
140 Ser Ala Lys Thr Arg Gln Gly Val Glu Asp Ala Phe Tyr Thr Leu Val
145 150 155 160 Arg Glu Ile Arg Gln His Lys Leu Arg Lys Leu Asn Pro
Pro Asp Glu 165 170 175 Ser Gly Pro Gly Cys Met Ser Cys Lys Cys Val
Leu Ser 180 185 <210> SEQ ID NO 2 <211> LENGTH: 166
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide of truncated H-Ras WT <400> SEQUENCE: 2 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His Gln Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Asp Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Ala Ala Arg Thr Val Glu Ser Arg 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Tyr Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Gln His 165 <210> SEQ ID NO 3
<211> LENGTH: 166 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide of truncated H-Ras G12C
<400> SEQUENCE: 3 Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala
Cys Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln
Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser
Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu
Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met
Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val
Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His Gln Tyr 85 90
95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Asp Asp Val Pro Met Val
100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Ala Ala Arg Thr Val Glu
Ser Arg 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro
Tyr Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Gly Val Glu Asp
Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Gln His 165
<210> SEQ ID NO 4 <211> LENGTH: 169 <212> TYPE:
PRT <213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Synthetic polypeptide of truncated
K-Ras G12C <400> SEQUENCE: 4 Met Thr Glu Tyr Lys Leu Val Val
Val Gly Ala Cys Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln
Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile
Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr
Ser Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60
Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Leu 65
70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His
His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp
Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Ser Asp Leu Pro Ser
Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser
Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln
Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile
Arg Lys His Lys Glu Lys 165 <210> SEQ ID NO 5 <211>
LENGTH: 189 <212> TYPE: PRT <213> ORGANISM: Homo
sapiens <400> SEQUENCE: 5 Met Thr Glu Tyr Lys Leu Val Val Val
Gly Ala Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu
Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu
Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys
Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser
Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70
75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His
Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val
Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg
Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr
Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Arg
Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg
Gln Tyr Arg Leu Lys Lys Ile Ser Lys Glu Glu Lys 165 170 175 Thr Pro
Gly Cys Val Lys Ile Lys Lys Cys Ile Ile Met 180 185 <210> SEQ
ID NO 6 <211> LENGTH: 189 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Synthetic polypeptide <400> SEQUENCE: 6
Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala Cys Gly Val Gly Lys 1 5
10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu
Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val
Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala
Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg
Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr
Lys Ser Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys
Arg Val Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly
Asn Lys Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln
Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135
140 Ser Ala Lys Thr Arg Gln Arg Val Glu Asp Ala Phe Tyr Thr Leu Val
145 150 155 160 Arg Glu Ile Arg Gln Tyr Arg Leu Lys Lys Ile Ser Lys
Glu Glu Lys 165 170 175 Thr Pro Gly Cys Val Lys Ile Lys Lys Cys Ile
Ile Met 180 185 <210> SEQ ID NO 7 <211> LENGTH: 189
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide <400> SEQUENCE: 7 Met Thr Glu Tyr Lys Leu Val Val
Val Gly Ala Asp Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln
Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile
Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr
Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60
Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65
70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His
His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp
Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser
Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser
Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln
Arg Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile
Arg Gln Tyr Arg Leu Lys Lys Ile Ser Lys Glu Glu Lys 165 170 175 Thr
Pro Gly Cys Val Lys Ile Lys Lys Cys Ile Ile Met 180 185 <210>
SEQ ID NO 8 <211> LENGTH: 189 <212> TYPE: PRT
<213> ORGANISM: Artificial Sequence <220> FEATURE:
<223> OTHER INFORMATION: Synthetic polypeptide <400>
SEQUENCE: 8 Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala Gly Cys Val
Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe
Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys
Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu
Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln
Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile
Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu
Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110
Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115
120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu
Thr 130 135 140 Ser Ala Lys Thr Arg Gln Arg Val Glu Asp Ala Phe Tyr
Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Gln Tyr Arg Leu Lys Lys
Ile Ser Lys Glu Glu Lys 165 170 175 Thr Pro Gly Cys Val Lys Ile Lys
Lys Cys Ile Ile Met 180 185 <210> SEQ ID NO 9 <211>
LENGTH: 189 <212> TYPE: PRT <213> ORGANISM: Artificial
Sequence <220> FEATURE: <223> OTHER INFORMATION:
Synthetic polypeptide <400> SEQUENCE: 9 Met Thr Glu Tyr Lys
Leu Val Val Val Gly Ala Gly Asp Val Gly Lys 1 5 10 15 Ser Ala Leu
Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp
Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40
45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr
50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe
Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp
Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser
Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu
Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala
Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr
Arg Gln Arg Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg
Glu Ile Arg Gln Tyr Arg Leu Lys Lys Ile Ser Lys Glu Glu Lys 165 170
175 Thr Pro Gly Cys Val Lys Ile Lys Lys Cys Ile Ile Met 180 185
<210> SEQ ID NO 10 <211> LENGTH: 188 <212> TYPE:
PRT <213> ORGANISM: Homo sapiens <400> SEQUENCE: 10 Met
Thr Glu Tyr Lys Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10
15 Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr
20 25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile
Asp Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly
Gln Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr
Gly Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys
Ser Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg
Val Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn
Lys Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala
Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140
Ser Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145
150 155 160 Arg Glu Ile Arg Lys His Lys Glu Lys Met Ser Lys Asp Gly
Lys Lys 165 170 175 Lys Lys Lys Lys Ser Lys Thr Lys Cys Val Ile Met
180 185 <210> SEQ ID NO 11 <211> LENGTH: 188
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide <400> SEQUENCE: 11 Met Thr Glu Tyr Lys Leu Val
Val Val Gly Ala Cys Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile
Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr
Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu
Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55
60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys
65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His
His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp
Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser
Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser
Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln
Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile
Arg Lys His Lys Glu Lys Met Ser Lys Asp Gly Lys Lys 165 170 175 Lys
Lys Lys Lys Ser Lys Thr Lys Cys Val Ile Met 180 185 <210> SEQ
ID NO 12 <211> LENGTH: 188 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Synthetic polypeptide <400> SEQUENCE: 12
Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala Asp Gly Val Gly Lys 1 5
10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu
Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val
Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala
Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg
Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr
Lys Ser Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys
Arg Val Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly
Asn Lys Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln
Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135
140 Ser Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val
145 150 155 160 Arg Glu Ile Arg Lys His Lys Glu Lys Met Ser Lys Asp
Gly Lys Lys 165 170 175 Lys Lys Lys Lys Ser Lys Thr Lys Cys Val Ile
Met 180 185 <210> SEQ ID NO 13 <211> LENGTH: 188
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide <400> SEQUENCE: 13 Met Thr Glu Tyr Lys Leu Val
Val Val Gly Ala Gly Cys Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile
Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr
Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu
Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55
60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys
65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His
His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp
Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser
Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser
Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln
Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile
Arg Lys His Lys Glu Lys Met Ser Lys Asp Gly Lys Lys 165 170 175 Lys
Lys Lys Lys Ser Lys Thr Lys Cys Val Ile Met 180 185 <210> SEQ
ID NO 14 <211> LENGTH: 188 <212> TYPE: PRT <213>
ORGANISM: Artificial Sequence <220> FEATURE: <223>
OTHER INFORMATION: Synthetic polypeptide <400> SEQUENCE: 14
Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala Gly Asp Val Gly Lys 1 5
10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu
Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val
Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala
Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg
Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr
Lys Ser Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys
Arg Val Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly
Asn Lys Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln
Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135
140 Ser Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val
145 150 155 160 Arg Glu Ile Arg Lys His Lys Glu Lys Met Ser Lys Asp
Gly Lys Lys 165 170 175 Lys Lys Lys Lys Ser Lys Thr Lys Cys Val Ile
Met 180 185 <210> SEQ ID NO 15 <211> LENGTH: 169
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide <400> SEQUENCE: 15 Met Thr Glu Tyr Lys Leu Val
Val Val Gly Ala Cys Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile
Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr
Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu
Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55
60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys
65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His
His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp
Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser
Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser
Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln
Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile
Arg Lys His Lys Glu Lys 165 <210> SEQ ID NO 16 <211>
LENGTH: 169 <212> TYPE: PRT <213> ORGANISM: Artificial
Sequence <220> FEATURE: <223> OTHER INFORMATION:
Synthetic polypeptide <400> SEQUENCE: 16 Met Thr Glu Tyr Lys
Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu
Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp
Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40
45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr
50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe
Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp
Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser
Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu
Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala
Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr
Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg
Glu Ile Arg Lys His Lys Glu Lys 165 <210> SEQ ID NO 17
<211> LENGTH: 169 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 17 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Ser Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Leu 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Ser Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Lys His Lys Glu Lys 165
1 SEQUENCE LISTING <160> NUMBER OF SEQ ID NOS: 17 <210>
SEQ ID NO 1 <211> LENGTH: 189 <212> TYPE: PRT
<213> ORGANISM: Homo sapiens <400> SEQUENCE: 1 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His Gln Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Asp Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Ala Ala Arg Thr Val Glu Ser Arg 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Tyr Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Gln His Lys Leu Arg Lys Leu Asn Pro Pro Asp
Glu 165 170 175 Ser Gly Pro Gly Cys Met Ser Cys Lys Cys Val Leu Ser
180 185 <210> SEQ ID NO 2 <211> LENGTH: 166 <212>
TYPE: PRT <213> ORGANISM: Artificial Sequence <220>
FEATURE: <223> OTHER INFORMATION: Synthetic polypeptide of
truncated H-Ras WT <400> SEQUENCE: 2 Met Thr Glu Tyr Lys Leu
Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr
Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro
Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45
Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50
55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu
Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile
His Gln Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Asp
Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Ala
Ala Arg Thr Val Glu Ser Arg 115 120 125 Gln Ala Gln Asp Leu Ala Arg
Ser Tyr Gly Ile Pro Tyr Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg
Gln Gly Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu
Ile Arg Gln His 165 <210> SEQ ID NO 3 <211> LENGTH: 166
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide of truncated H-Ras G12C <400> SEQUENCE: 3 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Cys Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His Gln Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Asp Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Ala Ala Arg Thr Val Glu Ser Arg 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Tyr Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Gln His 165 <210> SEQ ID NO 4
<211> LENGTH: 169 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide of truncated K-Ras G12C
<400> SEQUENCE: 4 Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala
Cys Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln
Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser
Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Ser Leu Leu
Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met
Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Leu 65 70 75 80 Val
Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85 90
95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met Val
100 105 110 Leu Val Gly Asn Lys Ser Asp Leu Pro Ser Arg Thr Val Asp
Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro
Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Gly Val Asp Asp
Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Lys His Lys
Glu Lys 165 <210> SEQ ID NO 5 <211> LENGTH: 189
<212> TYPE: PRT <213> ORGANISM: Homo sapiens
<400> SEQUENCE: 5 Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala
Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln
Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser
Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu
Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met
Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val
Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85 90
95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met Val
100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val Asp
Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro
Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Arg Val Glu Asp
Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Gln Tyr Arg
Leu Lys Lys Ile Ser Lys Glu Glu Lys 165 170 175 Thr Pro Gly Cys Val
Lys Ile Lys Lys Cys Ile Ile Met 180 185 <210> SEQ ID NO 6
<211> LENGTH: 189 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 6 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Cys Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80
Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85
90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met
Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val
Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile
Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Arg Val Glu
Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Gln Tyr
Arg Leu Lys Lys Ile Ser Lys Glu Glu Lys 165 170 175 Thr Pro Gly Cys
Val Lys Ile Lys Lys Cys Ile Ile Met 180 185 <210> SEQ ID NO 7
<211> LENGTH: 189 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 7 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Asp Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Arg Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Gln Tyr Arg Leu Lys Lys Ile Ser Lys Glu Glu
Lys 165 170 175 Thr Pro Gly Cys Val Lys Ile Lys Lys Cys Ile Ile Met
180 185 <210> SEQ ID NO 8 <211> LENGTH: 189 <212>
TYPE: PRT <213> ORGANISM: Artificial Sequence <220>
FEATURE: <223> OTHER INFORMATION: Synthetic polypeptide
<400> SEQUENCE: 8 Met Thr Glu Tyr Lys Leu Val Val Val Gly Ala
Gly Cys Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile Gln
Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp Ser
Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu Leu
Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala Met
Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80 Val
Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85 90
95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met Val
100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val Asp
Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro
Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Arg Val Glu Asp
Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Gln Tyr Arg
Leu Lys Lys Ile Ser Lys Glu Glu Lys 165 170 175 Thr Pro Gly Cys Val
Lys Ile Lys Lys Cys Ile Ile Met 180 185 <210> SEQ ID NO 9
<211> LENGTH: 189 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 9 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Gly Asp Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Arg Val Glu Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Gln Tyr Arg Leu Lys Lys Ile Ser Lys Glu Glu
Lys 165 170 175 Thr Pro Gly Cys Val Lys Ile Lys Lys Cys Ile Ile Met
180 185 <210> SEQ ID NO 10 <211> LENGTH: 188
<212> TYPE: PRT <213> ORGANISM: Homo sapiens
<400> SEQUENCE: 10 Met Thr Glu Tyr Lys Leu Val Val Val Gly
Ala Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile
Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp
Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu
Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala
Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80
Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85
90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met
Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val
Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile
Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Gly Val Asp
Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Lys His
Lys Glu Lys Met Ser Lys Asp Gly Lys Lys 165 170 175 Lys Lys Lys Lys
Ser Lys Thr Lys Cys Val Ile Met 180 185 <210> SEQ ID NO 11
<211> LENGTH: 188 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 11 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Cys Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Lys His Lys Glu Lys Met Ser Lys Asp Gly Lys
Lys 165 170 175 Lys Lys Lys Lys Ser Lys Thr Lys Cys Val Ile Met 180
185 <210> SEQ ID NO 12
<211> LENGTH: 188 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 12 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Asp Gly Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Lys His Lys Glu Lys Met Ser Lys Asp Gly Lys
Lys 165 170 175 Lys Lys Lys Lys Ser Lys Thr Lys Cys Val Ile Met 180
185 <210> SEQ ID NO 13 <211> LENGTH: 188 <212>
TYPE: PRT <213> ORGANISM: Artificial Sequence <220>
FEATURE: <223> OTHER INFORMATION: Synthetic polypeptide
<400> SEQUENCE: 13 Met Thr Glu Tyr Lys Leu Val Val Val Gly
Ala Gly Cys Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile
Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp
Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu
Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala
Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80
Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85
90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met
Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val
Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile
Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Gly Val Asp
Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Lys His
Lys Glu Lys Met Ser Lys Asp Gly Lys Lys 165 170 175 Lys Lys Lys Lys
Ser Lys Thr Lys Cys Val Ile Met 180 185 <210> SEQ ID NO 14
<211> LENGTH: 188 <212> TYPE: PRT <213> ORGANISM:
Artificial Sequence <220> FEATURE: <223> OTHER
INFORMATION: Synthetic polypeptide <400> SEQUENCE: 14 Met Thr
Glu Tyr Lys Leu Val Val Val Gly Ala Gly Asp Val Gly Lys 1 5 10 15
Ser Ala Leu Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20
25 30 Asp Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp
Gly 35 40 45 Glu Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln
Glu Glu Tyr 50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly
Glu Gly Phe Leu Cys 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser
Phe Glu Asp Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val
Lys Asp Ser Glu Asp Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys
Cys Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln
Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser
Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150
155 160 Arg Glu Ile Arg Lys His Lys Glu Lys Met Ser Lys Asp Gly Lys
Lys 165 170 175 Lys Lys Lys Lys Ser Lys Thr Lys Cys Val Ile Met 180
185 <210> SEQ ID NO 15 <211> LENGTH: 169 <212>
TYPE: PRT <213> ORGANISM: Artificial Sequence <220>
FEATURE: <223> OTHER INFORMATION: Synthetic polypeptide
<400> SEQUENCE: 15 Met Thr Glu Tyr Lys Leu Val Val Val Gly
Ala Cys Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile Gln Leu Ile
Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr Ile Glu Asp
Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu Thr Cys Leu
Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55 60 Ser Ala
Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys 65 70 75 80
Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His His Tyr 85
90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp Val Pro Met
Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser Arg Thr Val
Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile
Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln Gly Val Asp
Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Lys His
Lys Glu Lys 165 <210> SEQ ID NO 16 <211> LENGTH: 169
<212> TYPE: PRT <213> ORGANISM: Artificial Sequence
<220> FEATURE: <223> OTHER INFORMATION: Synthetic
polypeptide <400> SEQUENCE: 16 Met Thr Glu Tyr Lys Leu Val
Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu Thr Ile
Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp Pro Thr
Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40 45 Glu
Thr Cys Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr 50 55
60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe Leu Cys
65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp Ile His
His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser Glu Asp
Val Pro Met Val 100 105 110 Leu Val Gly Asn Lys Cys Asp Leu Pro Ser
Arg Thr Val Asp Thr Lys 115 120 125 Gln Ala Gln Asp Leu Ala Arg Ser
Tyr Gly Ile Pro Phe Ile Glu Thr 130 135 140 Ser Ala Lys Thr Arg Gln
Gly Val Asp Asp Ala Phe Tyr Thr Leu Val 145 150 155 160 Arg Glu Ile
Arg Lys His Lys Glu Lys 165 <210> SEQ ID NO 17 <211>
LENGTH: 169 <212> TYPE: PRT <213> ORGANISM: Artificial
Sequence <220> FEATURE: <223> OTHER INFORMATION:
Synthetic polypeptide <400> SEQUENCE: 17 Met Thr Glu Tyr Lys
Leu Val Val Val Gly Ala Gly Gly Val Gly Lys 1 5 10 15 Ser Ala Leu
Thr Ile Gln Leu Ile Gln Asn His Phe Val Asp Glu Tyr 20 25 30 Asp
Pro Thr Ile Glu Asp Ser Tyr Arg Lys Gln Val Val Ile Asp Gly 35 40
45 Glu Thr Ser Leu Leu Asp Ile Leu Asp Thr Ala Gly Gln Glu Glu Tyr
50 55 60 Ser Ala Met Arg Asp Gln Tyr Met Arg Thr Gly Glu Gly Phe
Leu Leu 65 70 75 80 Val Phe Ala Ile Asn Asn Thr Lys Ser Phe Glu Asp
Ile His His Tyr 85 90 95 Arg Glu Gln Ile Lys Arg Val Lys Asp Ser
Glu Asp Val Pro Met Val 100 105 110
Leu Val Gly Asn Lys Ser Asp Leu Pro Ser Arg Thr Val Asp Thr Lys 115
120 125 Gln Ala Gln Asp Leu Ala Arg Ser Tyr Gly Ile Pro Phe Ile Glu
Thr 130 135 140 Ser Ala Lys Thr Arg Gln Gly Val Asp Asp Ala Phe Tyr
Thr Leu Val 145 150 155 160 Arg Glu Ile Arg Lys His Lys Glu Lys
165
* * * * *