CERTAIN CHEMICAL ENTITIES, COMPOSITIONS AND METHODS

1 - 59 . (canceled)

60 . A compound of Formula I:

or a pharmaceutically acceptable salt thereof, wherein:

W a 1 is CR 3 ;

W a 2 is CR 5 ;

W a 3 is CR 6 ;

W a 4 is N;

W b 5 is CR 8 , CHR 8 , or N;

W d is

R a is hydrogen, halo, phosphate, urea, carbonate, alkyl, alkenyl, alkynyl, cycloalkyl, heteroalkyl, or heterocycloalkyl;

R 11 is hydrogen, alkyl, halo, amino, amido, hydroxy, or alkoxy;

R 12 is hydrogen, alkyl, cyano, alkynyl, alkenyl, halo, aryl, heteroaryl, heterocycloalkyl, cycloalkyl, amino, carboxylic acid, alkoxycarbonyl, or amido;

B is alkyl, amino, heteroalkyl, cycloalkyl, heterocycloalkyl, or a moiety of Formula II:

W c is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl;

q is an integer of 0, 1, 2, 3, or 4;

X is absent or is —(CH(R 9 )) z — and each instance of z is independently an integer of 1, 2, 3, or 4;

Y is absent, —O—, —S—, —S(═O)—, —S(═O) 2 —, —N(R 9 )—, —C(═O)(CHR 9 ) z —, —C(═O)—, —N(R 9 )C(═O)NH—, or —N(R 9 )C(R 9 ) 2 —, wherein when W b 5 is N, no more than one of X or Y is absent;

R 1 is hydrogen, alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy, nitro, phosphate, urea, or carbonate;

R 2 is alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy or nitro;

R 3 is hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamide, halo, cyano, hydroxyl, nitro, aryl, or heteroaryl;

R 5 , R 6 , and R 8 are independently hydrogen, C 1 -C 4 alkyl, C 2 -C 5 alkenyl, C 2 -C 5 alkynyl, C 3 -C 5 cycloalkyl, C 1 -C 4 heteroalkyl, C 1 -C 4 alkoxy, C 1 -C 4 amido, amino, acyl, C 1 -C 4 acyloxy, C 1 -C 4 sulfonamido, halo, cyano, hydroxy or nitro; and

each instance of R 9 is independently hydrogen, C 1 -C 10 alkyl, C 3 -C 7 cycloalkyl, or C 2 -C 10 heteroalkyl.

61 . The compound of claim 60 , wherein the compound is a compound of Formula VIII-A:

or a pharmaceutically acceptable salt thereof.

62 . The compound of claim 60 , wherein the compound is a compound of Formula VII:

or a pharmaceutically acceptable salt thereof.

63 . The compound of claim 60 , wherein W c is aryl or heterocycloalkyl.

64 . The compound of claim 60 , wherein R 3 is alkyl.

65 . The compound of claim 60 , wherein R 5 , R 6 , and R 8 are hydrogen.

66 . The compound of claim 60 , wherein X is —(CH(R 9 )) z — and z is an integer of 1.

67 . The compound of claim 60 , wherein Y is absent.

68 . The compound of claim 60 , wherein R 12 is iodo, bromo,

69 . The compound of claim 60 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

70 . The compound of claim 60 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

71 . The compound of claim 60 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

72 . A compound of Formula 6-A:

or a pharmaceutically acceptable salt thereof, wherein:

R 12 is hydrogen, alkyl, cyano, alkynyl, alkenyl, halo, aryl, heteroaryl, heterocycloalkyl, cycloalkyl, amino, carboxylic acid, alkoxycarbonyl, or amido;

B is alkyl, amino, heteroalkyl, cycloalkyl, heterocycloalkyl, or a moiety of Formula II:

W c is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl;

q is an integer of 0, 1, 2, 3, or 4;

R 1 is hydrogen, alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy, nitro, phosphate, urea, or carbonate;

R 2 is alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy or nitro; and

R 3 is hydrogen or alkyl.

73 . The compound of claim 72 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

74 . A compound of Formula IX:

or a pharmaceutically acceptable salt thereof.

W a 1 and W a 2 are independently CR 5 , S, N, or NR 4 ,

W a 4 is independently CR 7 , S, N, or NR 4 ;

wherein no more than two adjacent ring atoms are nitrogen or sulfur, and when W a 1 is S, one of W a 2 and W a 4 is N or NR 4 ;

W b 5 is CR 8 , N, or NR 8 ;

B is alkyl, amino, heteroalkyl, cycloalkyl, heterocycloalkyl, or a moiety of Formula II;

W c is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl;

q is an integer of 0, 1, 2, 3, or 4;

W d is a heterocycloalkyl, aryl or heteroaryl moiety;

X is —(CH(R 9 )) z —;

each instance of z independently is an integer of 1;

Y is absent;

R 1 is hydrogen, alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy or nitro;

R 2 is alkyl, heteroalkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, aryl, arylalkyl, heteroaryl, heteroarylalkyl, alkoxy, amido, amino, acyl, acyloxy, alkoxycarbonyl, sulfonamido, halo, cyano, hydroxy, nitro, phosphate, urea, or carbonate;

R 4 is hydrogen, acyl, C 1 -C 4 alkyl, C 2 -C 5 alkenyl, C 2 -C 5 alkynyl, C 3 -C 5 cycloalkyl, or C 1 -C 4 heteroalkyl;

R 5 , R 7 , and R 8 are independently hydrogen, C 1 -C 4 alkyl, C 2 -C 5 alkenyl, C 2 -C 5 alkynyl, C 3 -C 5 cycloalkyl, C 1 -C 4 heteroalkyl, acyl, C 1 -C 4 alkoxy, C 1 -C 4 amido, amino, C 1 -C 4 acyloxy, C 1 -C 4 sulfonamido, halo, cyano, hydroxy or nitro; and

each instance of R 9 is independently hydrogen, C 1 -C 10 alkyl, C 3 -C 7 cycloalkyl, or C 2 -C 10 heteroalkyl.

75 . The compound of claim 74 , wherein the compound is a compound of Formula XIII or Formula X:

or a pharmaceutically acceptable salt thereof, wherein

B is a moiety of Formula II;

wherein W c is aryl, heteroaryl, heterocycloalkyl, or cycloalkyl, and

q is an integer of 0, 1, or 2;

W d is:

X is (CH 2 ) z ;

Y is absent;

z is 1;

R 1 is hydrogen, fluoro, chloro, cyano, methyl, isopropyl, —CF 3 , methoxy, or nitro;

R 2 is halo, hydroxy, cyano, or nitro;

R 4 is hydrogen or methyl;

R 5 is hydrogen or methyl;

R 7 is hydrogen or methyl;

R 11 is amino; and

R 12 is hydrogen, alkyl, alkynyl, alkenyl, halo, aryl, heteroaryl, heterocycloalkyl, or cycloalkyl.

76 . The compound of claim 74 , wherein R 12 is iodo, bromo,

77 . The compound of claim 74 , wherein the compound is:

or a pharmaceutically acceptable salt thereof.

78 . A pharmaceutical composition comprising a compound of claim 60 , or a pharmaceutically acceptable salt thereof, and one or more pharmaceutically acceptable excipients.

79 . A pharmaceutical composition comprising a compound of claim 74 , or a pharmaceutically acceptable salt thereof, and one or more pharmaceutically acceptable excipients.

80 . A method of treating a disorder comprising administering an effective amount of a compound of claim 60 to a subject suffering from the disorder, wherein the disorder is selected from cancer, bone disorder, inflammatory disease, immune disease, nervous system disease, metabolic disease, respiratory disease, thrombosis, and cardiac disease.

81 . A method of treating a disorder comprising administering an effective amount of a compound of claim 74 to a subject suffering from the disorder, wherein the disorder is selected from cancer, bone disorder, inflammatory disease, immune disease, nervous system disease, metabolic disease, respiratory disease, thrombosis, and cardiac disease.