# Patent

## Title
Substituted 6,5-fused bicyclic heteroaryl compounds

## Abstract

The present invention relates to azole bicyclic heteroaryl compounds. The present invention also relates to pharmaceutical compositions containing these compounds and methods of treating cancer by administering these compounds and pharmaceutical compositions to subjects in need thereof. The present invention also relates to the use of such compounds for research or other non-therapeutic purposes.

## Background
RELATED APPLICATIONS
This application is a U.S. National Phase application, filed under 35 U.S.C. §371, of International Application No. PCT/US2014/029285, filed Mar. 14, 2014, which claims priority to, and the benefit of, U.S. provisional application Nos. 61/798,113, filed Mar. 15, 2013 and 61/856,625, filed Jul. 19, 2013, the entire contents of each of which are incorporated herein by reference in their entireties.


INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING
The contents of the text file named “EPIZ-019N01US-ST25.txt”, which was created on Sep. 9, 2015 and is 2 KB in size, are hereby incorporated by reference in their entireties.
BACKGROUND OF THE INVENTION
There is an ongoing need for new agents as inhibitors of EZH2 mutants, which can be used for treating an EZH2-mediated disorder (e.g., cancer).
SUMMARY OF THE INVENTION
In one aspect, the present invention features an azole bicyclic heteroaryl compound of Formula (I) below or a pharmaceutically acceptable salt thereof.




wherein

    
    
        X1 is NR7 or CR7;
        X2 is N, NR8, CR8, O, or S;
        X3 is NR8, CR8, O, or S;
        X4 is C or N;
        Y1 is N or CH;
        Y2 is N or CR6;
        Y3 is N or CR11;
        each of R5, R9, and R10, independently, is H or C1-C6 alkyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl;
        each R6 independently is H, halo, ORa, —NRaRb, —C(O)Ra, —C(O)ORa, —C(O)NRaRb, —NRbC(O)Ra, —S(O)2Ra, —S(O)2NRaRb, or RS2, in which each of Ra and Rb, independently is H or RS3 and each of RS2 and RS3 independently is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl; or, when applicable, Ra and Rb, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom; and each of RS2, RS3, and the 4 to 7-membered heterocycloalkyl ring containing Ra and Rb, is optionally substituted with one or more -Q2-T2, wherein Q2 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T2 is H, halo, cyano, —ORc, —NRcRd, —(NRcRdRd′)+A−, —C(O)Rc, —C(O)ORc, —C(O)NRcRd, —NRaC(O)Rc, —NRdC(O)ORc, —S(O)2Rc, —S(O)2NRcRd, or RS4, in which each of Rc, Rd, and Rd′, independently is H or RS5, A− is a pharmaceutically acceptable anion, each of RS4 and RS5, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, or Rc and Rd, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom, and each of RS4, RS5, and the 4 to 7-membered heterocycloalkyl ring containing Rc and Rd, is optionally substituted with one or more -Q3-T3, wherein Q3 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T3 is selected from the group consisting of H, halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 6-membered heteroaryl, ORe, COORe, —S(O)2Re, —NReRf, and —C(O)NReRf, each of Re and Rf independently being H or C1-C6 alkyl optionally substituted with OH, O—C1-C6 alkyl, or NH—C1-C6 alkyl; or -Q3-T3 is oxo; or -Q2-T2 is oxo; or any two neighboring -Q2-T2, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl; provided that -Q2-T2 is not H;
        each R7 independently is -Q4-T4, in which Q4 is a bond, C1-C4 alkyl linker, or C2-C4 alkenyl linker, each linker optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T4 is H, halo, cyano, NRgRh, —ORg, —C(O)Rg, —C(O)ORg, —C(O)NRgRh, —C(O)NRgORh, —NRgC(O)Rh, —S(O)2Rg, or RS6, in which each of Rg and Rh, independently is H or RS7, each of RS6 and RS7, independently is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and each of RS6 and RS7 is optionally substituted with one or more -Q5-T5, wherein Q5 is a bond, C(O), C(O)NRk, NRkC(O), NRk, S(O)2, NRkS(O)2, or C1-C3 alkyl linker, Rk being H or C1-C6 alkyl, and T5 is H, halo, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, hydroxyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 12-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl, and T5 is optionally substituted with one or more substituents selected from the group consisting of halo, C1-C6 alkyl, hydroxyl, cyano, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C5 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl except when T5 is H, halo, hydroxyl, or cyano; or -Q5-T5 is oxo; provided that -Q4-T4 is not H; and
        each of R8 and R11, independently, is H, halo, hydroxyl, COOH, cyano, RS8, ORS8, or COORS8, in which RS8 is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, and RS8 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, and di-C1-C6 alkylamino;
        X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
        n is 0, 1, 2, 3, 4, or 5;
        provided that at most one of X2 and X3 is O or S, at least one of X1, X2, X3, X4, Y1, Y2, and Y3 is N or NR7, and X1, X2, X3, X4, Y1, Y2, and Y3 are assigned such that the
    
    






moiety in Formula (I) is a bicyclic heteroaryl system.

In one subset of the compounds of Formula (I) features that X is azole or a bicyclic ring containing an azole moiety. In one embodiment, X is not 5-methoxy-1H-pyrrolo[3,2-b]pyridin-7(4H)-one, 5-methoxy-1H-pyrazolo[4,3-b]pyridin-7(4H)-one, 5-methoxy-1H-imidazo[4,5-b]pyridin-7(4H)-one, 5-methoxy-2-methyl-1H-imidazo[4,5-b]pyridin-7(4H)-one, or 5-methoxy-3-methyl-1H-pyrazolo[4,3-b]pyridin-7(4H)-one.
In one subset of the compounds of Formula (I), at least one of Y1, Y3, and X4 is N and when X4 is C, Y1 is N, Y2 is CR6, and Y3 is CR11, then X2 is CR8.
One subset of the compounds of Formula (I) includes those of Formula (Ia):




    
    
        wherein R7 is -Q4-T4, wherein Q4 is a bond or methyl linker, T4 is optionally substituted C1-C6 alkyl, optionally substituted C3-C8 cycloalkyl or optionally substituted 4- to 14-membered heterocycloalkyl. In some compounds, R7 is tetrahydropyranyl, piperidine substituted by 1, 2, or 3 C1-4 alkyl groups, or cyclohexyl substituted by N(C1-4 alkyl)2 wherein one or both of the C1-4 alkyl is optionally substituted with C1-6 alkoxyl.
    
    


The compounds of Formulae (I) and (Ia) can include one or more of the following features:
X4 is C.
X2 is N or CH.
X3 is CR8.
Y3 is CR11.
R6 is phenyl substituted with one or more -Q2-T2.
R6 is 5 to 6-membered heteroaryl containing 1-3 heteroatoms selected from N, O, and S and optionally substituted with one or more -Q2-T2, provided that the heteroaryl is not thiophenyl.
R6 is pyridinyl, pyrazolyl, pyrimidinyl, or furyl, each of which is optionally substituted with one or more -Q2-T2.
R6 is phenyl or 5- or 6-membered heteroaryl substituted with O—C1-6 alkyl or NH—C1-6 alkyl, each of which is optionally substituted with hydroxyl, O—C1-3 alkyl or NH—C1-3 alkyl, each of the O—C1-3 alkyl and NH—C1-3 alkyl being optionally further substituted with O—C1-3 alkyl or NH—C1-3 alkyl.
R6 is




R6 is halo, C1-C3 alkyl optionally substituted with one or more -Q2-T2, C2-C6 alkenyl optionally substituted with one or more -Q2-T2, C4-C6 cycloalkyl optionally substituted with one or more -Q2-T2, C(O)H, ORa, or —C(O)Ra, in which Ra is C1-C6 alkyl optionally substituted with one or more -Q2-T2 or 4 to 7-membered heterocycloalkyl optionally substituted with one or more -Q2-T2.
R6 is 4 to 7-membered heterocycloalkyl optionally substituted with one or more -Q2-T2, in which -Q2-T2 is oxo or Q2 is a bond and T2 is —ORc, —NRcRd, —C(O)Rc, —C(O)ORc, —S(O)2Rc, C1-C6 alkyl, or 4 to 7-membered heterocycloalkyl, each of which is optionally substituted with one or more -Q3-T3 when Rc or Rd is not H.
R6 is piperidinyl, 2,2,6,6-tetramethyl-piperidinyl, 1,2,3,6-tetrahydropyridinyl, 2,2,6,6-tetramethyl-1,2,3,6-tetrahydropyridinyl, piperazinyl, morpholinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, or pyrrolidinyl, each of which is optionally substituted with one or more -Q2-T2.
Q3 is a bond or C1-C3 alkyl linker and T3 is selected from the group consisting of C1-C3 alkyl, halo, ORe, —S(O)2Re, —NReRf, and —C(O)NReRf.
R7 is C1-C6 alkyl, C2-C4 alkenyl, C4-C6 cycloalkyl, 4 to 7-membered heterocycloalkyl, or C6-C10 aryl, each optionally substituted with one or more -Q5-T5.
R7 is cyclopentyl.
R7 is unsubstituted C1-C6 alkyl.
R7 is isopropyl or sec-butyl.
R7 is 5 to 6-membered heterocycloalkyl optionally substituted with one or more -Q5-T5.
R7 is piperidinyl optionally substituted with one -Q5-T5.
R7 is




R7 is




R7 is




R7 is




R7 is




R7 is




T5 is H, halo, C1-C6 alkyl, C1-C6 alkoxyl, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl.
T5 is C1-C6 alkyl or C1-C6 alkoxyl, each optionally substituted with halo, hydroxyl, cyano, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, or C3-C8 cycloalkyl.
Q5 is a bond and T5 is C1-C6 alkyl, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl.
Q5 is a bond or NRk and T5 is H, C1-C6 alkyl, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 12-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, C1-C6 alkylene-5- or 6-membered heteroaryl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, T5 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, and C3-C8 cycloalkyl.
Q5 is a bond or NRk and T5 is C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 5- or 6-membered heteroaryl, C1-C6 alkylene-5- or 6-membered heteroaryl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, T5 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, and C3-C8 cycloalkyl.
Q5 is CO and T5 is C1-C6 alkyl, C1-C6 alkoxyl, C3-C8 cycloalkyl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, or C1-C6 alkylene-4 to 12-membered heterocycloalkyl.
Q5 is C1-C3 alkyl linker and T5 is H or C6-C10 aryl, or C1-C6 alkylene-C6-C10 aryl.
R11 is H.
Each of R2 and R4, independently is H or C1-C6 alkyl optionally substituted with amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, or C6-C10 aryl.
Each of R2 and R4, independently is C1-C3 alkyl optionally substituted with C1-C6 alkoxyl.
Each of R2 and R4 is methyl.
R1 is H.
R8 is H, methyl, or ethyl.
R3 is H.
In some compounds of this invention,




is selected from the group consisting of indolyl, isoindolyl, indolizinyl, benzofuryl, isobenzofuryl, benzo[b]thienyl, benzoxazolyl, benzthiazolyl, benzimidazolyl, benzotriazolyl, benzoxadiazolyl, benzothiadiazolyl, purinyl, indazolyl, pyrrolopyridinyl, imidazopyridinyl, pyrazolopyridinyl, pyrrolopyrazinyl, imidazopyrazinyl, pyrazolopyrazinyl, pyrrolopyrimidinyl, pyrazolopyrimidinyl, pyrrolopyridazinyl, imidazopyridazinyl, pyrazolopyridazinyl, furopyridinyl, thienopyridinyl, furopyrazinyl, thienopyrazinyl, oxazolopyridinyl, isoxazolopyridinyl, thiazolopyridinyl, isothiazolopyridinyl, oxadiazolopyridinyl, thiadiazolopyridinyl, triazolopyridinyl, oxazolopyrazinyl, isoxazolopyrazinyl, thiazolopyrazinyl, isothiazolopyrazinyl, oxadiazolopyrazinyl, thiadiazolopyrazinyl, triazolopyrazinyl, furopyrimidinyl, thienopyrimidinyl, furopyridazinyl, thienopyridazinyl, oxazolopyrimidinyl, isoxazolopyrimidinyl, thiazolopyrimidinyl, isothiazolopyrimidinyl, oxadiazolopyrimidinyl, thiadiazolopyrimidinyl, triazolopyrimidinyl, oxazolopyridazinyl, isoxazolopyridazinyl, thiazolopyridazinyl, isothiazolopyridazinyl, oxadiazolopyridazinyl, thiadiazolopyridazinyl, triazolopyridazinyl, and imidazotriazinyl.

In some compounds of this invention,




is selected from the group consisting of





is selected from the group consisting of





In some compounds of this invention,




is selected from the group consisting of





In another aspect, the present invention features an azole bicyclic heteroaryl compound of Formula (II) below or a pharmaceutically acceptable salt thereof.




wherein,

    
    
        Z1 is N or CR7′,
        Z2 is N or CR2′, provided when Z1 is N, Z2 is N,
        R1′ is (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, unsubstituted or substituted (C3-C8)cycloalkyl, unsubstituted or substituted (C3-C8)cycloalkyl-(C1-C8)alkyl or —(C2-C8)alkenyl, unsubstituted or substituted (C5-C8)cycloalkenyl, unsubstituted or substituted (C5-C8)cycloalkenyl-(C1-C8)alkyl or —(C2-C8)alkenyl, unsubstituted or substituted (C6-C10)bicycloalkyl, unsubstituted or substituted heterocycloalkyl or —(C2-C8)alkenyl, unsubstituted or substituted heterocycloalkyl-(C1-C8)alkyl, unsubstituted or substituted aryl, unsubstituted or substituted aryl-(C1-C8)alkyl or —(C2-C8)alkenyl, unsubstituted or substituted heteroaryl, unsubstituted or substituted heteroaryl-(C1-C8)alkyl or —(C2-C8)alkenyl, —CORa′, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′;
        R2′ is hydrogen, (C1-C8)alkyl, trifluoromethyl, alkoxy, or halo, in which said (C1-C8)alkyl is optionally substituted with one to two groups selected from amino and (C1-C3)alkylamino;
        R7′ is hydrogen, (C1-C3)alkyl, or alkoxy;
        R3′ is hydrogen, (C1-C8)alkyl, cyano, trifluoromethyl, —NRa′Rb′, or halo;
        R6′ is selected from the group consisting of hydrogen, halo, (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, unsubstituted or substituted (C3-C8)cycloalkyl, unsubstituted or substituted (C3-C8)cycloalkyl-(C1-C8)alkyl, unsubstituted or substituted (C5-C8)cycloalkenyl, unsubstituted or substituted (C5-C8)cycloalkenyl-(C1-C8)alkyl, (C6-C10)bicycloalkyl, unsubstituted or substituted heterocycloalkyl, unsubstituted or substituted heterocycloalkyl-(C1-C8)alkyl, unsubstituted or substituted aryl, unsubstituted or substituted aryl-(C1-C8)alkyl, unsubstituted or substituted heteroaryl, unsubstituted or substituted heteroaryl-(C1-C8)alkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRaRb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —NRa′NRa′C(O)NRa′Rb′, —NRa′NRa′C(O)ORa′, —ORa′, —OC(O)Ra′, —OC(O)NRa′Rb′;
        wherein any (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, cycloalkyl, cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl group is optionally substituted by 1, 2 or 3 groups independently selected from the group consisting of —O(C1-C6)alkyl(Rc′)1-2, —S(C1-C6)alkyl(Rc′)1-2, —(C1-C6)alkyl(Rc′)1-2, —(C1-C8)alkyl-heterocycloalkyl, (C3-C8)cycloalkyl-heterocycloalkyl, halo, (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRaSO2Rb, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, OC(O)NRa′Rb′, heterocycloalkyl, aryl, heteroaryl, aryl(C1-C4)alkyl, and heteroaryl(C1-C4)alkyl;
        wherein any aryl or heteroaryl moiety of said aryl, heteroaryl, aryl(C1-C4)alkyl, or heteroaryl(C1-C4)alkyl is optionally substituted by 1, 2 or 3 groups independently selected from the group consisting of halo, (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRaRb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra, and —OC(O)NRa′Rb′;
        Ra′ and Rb′ are each independently hydrogen, (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C6-C10)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein said (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, cycloalkyl, cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl group is optionally substituted by 1, 2 or 3 groups independently selected from halo, hydroxyl, (C1-C4)alkoxy, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, —CO2H, —CO2 (C1-C4)alkyl, —CONH2, —CONH(C1-C4)alkyl, —CON((C1-C4)alkyl)((C1-C4)alkyl), —SO2 (C1-C4)alkyl, —SO2NH2, —SO2NH(C1-C4)alkyl, and SO2N((C1-C4)alkyl)((C1-C4)alkyl);
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 5-8 membered saturated or unsaturated ring, optionally containing an additional heteroatom selected from oxygen, nitrogen, and sulfur, wherein said ring is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C4)alkyl, (C1-C4)haloalkyl, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, hydroxyl, oxo, (C1-C4)alkoxy, and (C1-C4)alkoxy(C1-C4)alkyl, wherein said ring is optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 6- to 10-membered bridged bicyclic ring system optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;
        each Rc′ is independently (C1-C4)alkylamino, —NRa′SO2Rb′, —SORa′, —SO2Ra′, —NRa′C(O)ORa′, —NRa′Rb′, or —CO2Ra′;
        X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
        n is 0, 1, 2, 3, 4, or 5;
        provided that at most one of X2 and X3 is O or S and X1, X2, X3, X4, Y1, Y2, and Y3 are assigned such that the
    
    






moiety in Formula (I) is a bicyclic heteroaryl system.

One subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structure, each of D1, D2, and D3, independently, is CR901 or N, provided that at least one of D1, D2, and D3 is N. D4 is O, S, or NR902. Each R901 and R902, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, D1 is N, each of D2 and D3, independently, is CR901, and D4 is NR902. In other compounds, each of D1 and D2, independently, is CR901, D3 is N, and D4 is NR902. In still some compounds, each of D1 and D2 is N, D3 is CR901, and D4 is NR902. In yet some compounds, each of D1 and D3 is, independently, CR901, D2 is N, and D4 is NR902. In further some compounds, D1 is N, each of D2 and D3, independently, is CR901, and D4 is O or S.
Another subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structure, each of E1, E2, and E4, independently, is CR903 or N, provided that at least one of E1, E2, and E4 is N. E3 is O, S, or NR904. Each R903 and R904, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, E1 is N, each of E2 and E4, independently, is CR903, and E3 is NR904. In other compounds, each of E1 and E4, independently, is CR903, E2 is N, and E3 is NR904. In still other compounds, each of E1 and E2, independently, is CR903, E3 is NR904, and E4 is N. In yet other compounds, each of E1 and E2, independently, is CR903, E3 is O, and E4 is N.
Another subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structures, G1 is O, S, or NR907. Each of G2, G3, and G4, independently, is N or CR908, provided that at least one of G2, G3, and G4 is N. Each of R905, R906, R907, and R908, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, G1 is NR907, G2 is CR908, and each of G3 and G4, if present, is N. In other compounds, G1 is NR907, each of G2 and G4, if present, independently, is CR908 and G3 is N. In still other compounds, G1 is NR907, each of G2 and G4, if present, is N, and G3 is CR908. In yet other compounds, G1 is NR907, G2 is N, and each of G3 and G4, if present, independently, is CR908.
Another subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structures, each of J1, J2, J3, and J4, independently, is N or CR911, provided that at least one of J1, J2, J3, and J4 is N. Each of R909, R910, and R911, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, J1, if present, is N, and each of J2, J3, and J4, independently, is CR19. In some embodiments, X is




in which each of J2 and J3 is N and J4 is CR911.

Another subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structure, each of K1, K2, K3, and K4, independently, is N or CR914, provided that at least one of K1, K2, K3, and K4 is N. Each of R912, R913, and R914, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, K1 is N; and each of K2, K3, and K4, independently, is CR914. In some compounds, each of K1 and K4 is N and each of K2 and K3 independently is CR914.
Another subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structure, each of U1, U3, and U4, independently, is N or CR917, provided that at least one of U1, U3, and U4 is N. U2 is O, S, or NR918. Each of R915, R916, R917 and R918, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, U1 is N; U2 is NR918; and each of U3 and U4, independently, is CR917.
Another subset of the compounds of Formula (I), (Ia), or (II) features X being




In the above structure, each of V1 and V2, independently, is N or CR919, provided that at least one of V1 and V2 is N. V3 is O, S, or NR920. Each of V4, V5, and V6 is O, S, or NR921, or CR922R923. Each of R919, R920, R921, R922, and R923, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.
Another subset of the compounds of Formula (I), (Ia), or (II) features X being imidazole-2-yl, imidazol-4-yl, triazol-3-yl, 3H-imidazo[4,5-c]pyridin-7-yl, 1H-benzo[d]imidazol-4-yl, 1H-indazol-7-yl, isoxazol-3-yl, thiazol-2-yl, 1H-pyrazolo[4,3-c]pyridine-7-yl, imidazo[1,2-a]pyridine-8-yl, imidazo[1,2-c]pyrimidin-8-yl, 1,4,6,7-tetrahydropyrano[4,3-c]pyrazol-7-yl, 1,4,6,7-tetrahydropyrano[3,4-]imidazole-7-yl, 4,5,6,7-tetrahydro-1H-benzo[d]imidazole-4-yl, 7H-pyrrolo[2,3-d]pyrimidine-4-yl, 9H-purine-6-yl, 7-methyl-[1,2,4]triazolo[4,3-a]pyridin-5-ol-6-yl, [1,2,4]triazolo[4,3-a]pyridin-6-yl, 3-fluoro-1,5-dimethyl-1H-pyrazol-4-yl, or 5-fluoro-1,3-dimethyl-1H-pyrazol-4-yl.
The present invention also provides pharmaceutical compositions comprising one or more pharmaceutically acceptable carriers and one or more compounds selected from those of any of the Formulae described herein.
Another aspect of this invention is a method of treating or preventing an EZH2-mediated disorder. The method includes administering to a subject in need thereof a therapeutically effective amount of one or more compounds selected from those of any of the Formulae described herein. The EZH2-mediated disorder is a disease, disorder, or condition that is mediated at least in part by the activity of EZH2. In one embodiment, the EZH2-mediated disorder is related to an increased EZH2 activity. In one embodiment, the EZH2-mediated disorder is a cancer. The EZH2-mediated cancer may be lymphoma, leukemia or melanoma, for example, diffuse large B-cell lymphoma (DLBCL), non-Hodgkin's lymphoma (NHL), follicular lymphoma, chronic myelogenous leukemia (CML), acute myeloid leukemia, acute lymphocytic leukemia, mixed lineage leukemia, or myelodysplastic syndromes (MDS). In one embodiment the EZH2-mediated cancer may be a malignant rhabdoid tumor or INI1-deficient tumor. The histologic diagnosis of malignant rhabdoid tumor depends on identification of characteristic rhabdoid cells (large cells with eccentrically located nuclei and abundant, eosinophilic cytoplasm) and immunohistochemistry with antibodies to vimentin, keratin and epithelial membrane antigen. In most malignant rhabdoid tumors, the SMARCB1/INI1 gene, located in chromosome band 22q11.2, is inactivated by deletions and/or mutations. In one embodiment, the malignant rhabdoid tumors may be INI1-deficient tumors.
Unless otherwise stated, any description of a method of treatment includes use of the compounds to provide such treatment or prophylaxis as is described herein, as well as use of the compounds to prepare a medicament to treat or prevent such condition. The treatment includes treatment of human or non-human animals including rodents and other disease models. Methods described herein may be used to identify suitable candidates for treating or preventing EZH2-mediated disorders. For example, the invention also provides methods of identifying an inhibitor of a wild-type EZH2, a mutant EZH2 (e.g., a Y641, A677, and/or A687 mutant EZH2), or both.
For example, the method comprises the step of administering to a subject having a cancer with aberrant H3-K27 methylation an effective amount of one or more compounds of Formulae described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer. Examples of aberrant H3-K27 methylation may include a global increase in and/or altered distribution of H3-K27 di or tri-methylation within the cancer cell chromatin.
For example, the cancer is selected from the group consisting of cancers that overexpress EZH2 or other PRC2 subunits, contain loss-of-function mutations in H3-K27 demethylases such as UTX, or overexpress accessory proteins such as PHF19/PCL3 capable of increasing and or mislocalizing EZH2 activity (see references in Sneeringer et al. Proc Natl Acad Sci USA 107(49):20980-5, 2010).
For example, the method comprises the step of administering to a subject having a cancer overexpressing EZH2 a therapeutically effective amount of one or more compounds of Formulae described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer.
For example, the method comprises the step of administering to a subject having a cancer with a loss-of-function mutation in the H3-K27 demethylase UTX a therapeutically effective amount of one or more compounds of Formulae described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer.
For example, the method comprises the step of administering to a subject having a cancer overexpressing an accessory component(s) of the PRC2, such as PHF19/PCL3, a therapeutically effective amount of one or more compounds of Formulae described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer.
In still another aspect, this invention relates to a method of modulating the activity of the wild-type EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono-through tri-methylation of lysine 27 on histone H3 (H3-K27). For example, the present invention relates to a method of inhibiting the activity of EZH2 in a cell. This method can be conducted either in vitro or in vivo.
In yet another aspect, this invention features to a method of inhibiting in a subject conversion of H3-K27 to trimethylated H3-K27. The method comprises administering to a subject a therapeutically effective amount of one or more of the compounds of Formulae described herein to inhibit histone methyltransferase activity of EZH2, thereby inhibiting conversion of H3-K27 to trimethylated H3-K27 in the subject.
For example, the method comprises the step of administering to a subject having a cancer expressing a mutant EZH2 (e.g., a Y641, A677, and/or A687 mutant of EZH2) a therapeutically effective amount of one or more compounds of Formulae described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer.
For example, the cancer is selected from the group consisting of follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) of germinal center B cell-like (GCB) subtype. For example, the cancer is lymphoma, leukemia or melanoma. Preferably, the lymphoma is non-Hodgkin's lymphoma (NHL), follicular lymphoma or diffuse large B-cell lymphoma. Alternatively, the leukemia is chronic myelogenous leukemia (CML), acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
For example, the precancerous condition is myelodysplastic syndromes (MDS, formerly known as preleukemia).
For example, the cancer is a hematological cancer.
For example, the cancer is selected from the group consisting of brain and central nervous system (CNS) cancer, head and neck cancer, kidney cancer, ovarian cancer, pancreatic cancer, leukemia, lung cancer, lymphoma, myeloma, sarcoma, breast cancer, and prostate cancer. Preferably, a subject in need thereof is one who had, is having or is predisposed to developing brain and CNS cancer, kidney cancer, ovarian cancer, pancreatic cancer, leukemia, lymphoma, myeloma, and/or sarcoma. Exemplary brain and central CNS cancer includes medulloblastoma, oligodendroglioma, atypical teratoid/rhabdoid tumor, choroid plexus carcinoma, choroid plexus papilloma, ependymoma, glioblastoma, meningioma, neuroglial tumor, oligoastrocytoma, oligodendroglioma, and pineoblastoma. Exemplary ovarian cancer includes ovarian clear cell adenocarcinoma, ovarian endomethrioid adenocarcinoma, and ovarian serous adenocarcinoma. Exemplary pancreatic cancer includes pancreatic ductal adenocarcinoma and pancreatic endocrine tumor. Exemplary sarcoma includes chondrosarcoma, clear cell sarcoma of soft tissue, ewing sarcoma, gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma, and not otherwise specified (NOS) sarcoma. Alternatively, cancers to be treated by the compounds of the present invention are non NHL cancers.
For example, the cancer is selected from the group consisting of medulloblastoma, oligodendroglioma, ovarian clear cell adenocarcinoma, ovarian endomethrioid adenocarcinoma, ovarian serous adenocarcinoma, pancreatic ductal adenocarcinoma, pancreatic endocrine tumor, malignant rhabdoid tumor, astrocytoma, atypical teratoid/rhabdoid tumor, choroid plexus carcinoma, choroid plexus papilloma, ependymoma, glioblastoma, meningioma, neuroglial tumor, oligoastrocytoma, oligodendroglioma, pineoblastoma, carcinosarcoma, chordoma, extragonadal germ cell tumor, extrarenal rhabdoid tumor, schwannoma, skin squamous cell carcinoma, chondrosarcoma, clear cell sarcoma of soft tissue, ewing sarcoma, gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma, and not otherwise specified (NOS) sarcoma. Preferably, the cancer is medulloblastoma, ovarian clear cell adenocarcinoma, ovarian endomethrioid adenocarcinoma, pancreatic ductal adenocarcinoma, malignant rhabdoid tumor, atypical teratoid/rhabdoid tumor, choroid plexus carcinoma, choroid plexus papilloma, glioblastoma, meningioma, pineoblastoma, carcinosarcoma, extrarenal rhabdoid tumor, schwannoma, skin squamous cell carcinoma, chondrosarcoma, ewing sarcoma, epithelioid sarcoma, renal medullary carcinoma, diffuse large B-cell lymphoma, follicular lymphoma and/or NOS sarcoma. More preferably, the cancer is malignant rhabdoid tumor, medulloblastoma and/or atypical teratoid/rhabdoid tumor. Malignant rhabdoid tumors are high-grade neoplasms of the central nervous system (CNS), kidneys and soft tissue that usually occur in children. The histologic diagnosis of malignant rhabdoid tumor depends on identification of characteristic rhabdoid cells (large cells with eccentrically located nuclei and abundant, eosinophilic cytoplasm) and immunohistochemistry with antibodies to vimentin, keratin and epithelial membrane antigen. In most malignant rhabdoid tumors, the SMARCB1/INI1 gene, located in chromosome band 22q11.2, is inactivated by deletions and/or mutations. In one embodiment, the malignant rhabdoid tumors are INI1-deficient tumor.
For example, the method comprises the step of administering to a subject having a cancer expressing a mutant EZH2 (e.g., a Y641, A677, and/or A687 mutant of EZH2) a therapeutically effective amount of one or more compounds of Formulae described herein, wherein the compound(s) inhibits activity (e.g., histone methyltransferase activity) of the mutant EZH2, the wild-type EZH2, or both, thereby treating the cancer.
For example, the method further comprises the steps of performing an assay to detect a mutant EZH2 in a sample comprising cancer cells from a subject in need thereof.
In another aspect, the invention features a method of selecting a therapy for a patient having a disease associated with EZH2-mediated protein methylation. The method includes the steps of determining the presence of gene mutation in the EZH2 gene of the subject; and selecting, based on the presence of a gene mutation in the EZH2 gene a therapy for treating the disease. In one embodiment, the therapy includes the administration of one or more of the compounds of the invention. In one embodiment, the method further includes administrating one or more of the compounds of the invention to the subject. In one embodiment, the disease is cancer and the mutation is a Y641, A677, and/or A687 mutation.
In yet another aspect, a method of treatment is provided for a patient in need thereof, the method comprising the steps of determining the presence of gene mutation in the EZH2 gene and treating the patient in need thereof, based on the presence of a gene mutation in the EZH2 gene, with a therapy that includes the administration of the compounds of the invention. In one embodiment, the patient is a cancer patient and the mutation is a Y641, A677, and/or A687 mutation.
In still another aspect, this invention relates to a method of modulating the activity of the wild-type and mutant histone methyltransferase EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono- through tri-methylation of lysine 27 on histone H3 (H3-K27). For example, the present invention relates to a method of inhibiting the activity of certain mutant forms of EZH2 in a cell. The mutant forms of EZH2 include a substitution of another amino acid residue for tyrosine 641 (Y641, also Tyr641) of wild-type EZH2. The method includes contacting the cell with an effective amount of one or more of the compounds of any Formula described herein. This method can be conducted either in vitro or in vivo.
In yet another aspect, this invention features to a method of inhibiting in a subject conversion of H3-K27 to trimethylated H3-K27. The method comprises administering to a subject expressing a mutant EZH2 (e.g., a Y641, A677, and/or A687 mutant of EZH2) a therapeutically effective amount of one or more of the compounds of any Formula described herein to inhibit histone methyltransferase activity of EZH2, thereby inhibiting conversion of H3-K27 to trimethylated H3-K27 in the subject. For example, the histone methyltransferase activity inhibited is that of the Y641 mutant of EZH2. For example, the compound of this invention selectively inhibits histone methyltransferase activity of the Y641 mutant of EZH2. For example, the Y641 mutant of EZH2 is selected from the group consisting of Y641C, Y641F, Y641H, Y641N, and Y641S.
The method of inhibiting in a subject conversion of H3-K27 to trimethylated H3-K27 may also comprise performing an assay to detect a mutant EZH2 (e.g., a Y641, A677, and/or A687 mutant of EZH2) in a sample from a subject before administering to the subject expressing a mutant EZH2 a therapeutically effective amount of one or more of the compounds of any Formula described herein. For example, performing the assay to detect the mutant EZH2 includes whole-genome resequencing or target region resequencing that detects a nucleic acid encoding the mutant EZH2. For example, performing the assay to detect the mutant EZH2 includes contacting the sample with an antibody that binds specifically to a polypeptide or fragment thereof characteristic of the mutant EZH2. For example, performing the assay to detect the mutant EZH2 includes contacting the sample under highly stringent conditions with a nucleic acid probe that hybridizes to a nucleic acid encoding a polypeptide or fragment thereof characteristic of the mutant EZH2.
Further, the invention also relates to a method of identifying an inhibitor of a mutant EZH2, the wild-type EZH2, or both. The method comprises the steps of combining an isolated EZH2 with a histone substrate, a methyl group donor, and a test compound, wherein the histone substrate comprises a form of H3-K27 selected from the group consisting of unmethylated H3-K27, monomethylated H3-K27, dimethylated H3-K27, and any combination thereof; and performing an assay to detect methylation of H3-K27 (e.g., formation of trimethylated H3-K27) in the histone substrate, thereby identifying the test compound as an inhibitor of the EZH2 when methylation of H3-K27 (e.g., formation of trimethylated H3-K27) in the presence of the test compound is less than methylation of H3-K27 (e.g., formation of trimethylated H3-K27) in the absence of the test compound.
In one embodiment, performing the assay to detect methylation of H3-K27 in the histone substrate comprises measuring incorporation of labeled methyl groups.
In one embodiment, the labeled methyl groups are isotopically labeled methyl groups.
In one embodiment, performing the assay to detect methylation of H3-K27 in the histone substrate comprises contacting the histone substrate with an antibody that binds specifically to trimethylated H3-K27.
Also within the scope of the invention is a method of identifying a selective inhibitor of a mutant EZH2. The method comprises the steps of combining an isolated mutant EZH2 with a histone substrate, a methyl group donor, and a test compound, wherein the histone substrate comprises a form of H3-K27 selected from the group consisting of monomethylated H3-K27, dimethylated H3-K27, and a combination of monomethylated H3-K27 and dimethylated H3-K27, thereby forming a test mixture; combining an isolated wild-type EZH2 with a histone substrate, a methyl group donor, and a test compound, wherein the histone substrate comprises a form of H3-K27 selected from the group consisting of monomethylated H3-K27, dimethylated H3-K27, and a combination of monomethylated H3-K27 and dimethylated H3-K27, thereby forming a control mixture; performing an assay to detect trimethylation of the histone substrate in each of the test mixture and the control mixture; calculating the ratio of (a) trimethylation with the mutant EZH2 and the test compound (M+) to (b) trimethylation with the mutant EZH2 without the test compound (M−); calculating the ratio of (c) trimethylation with wild-type EZH2 and the test compound (WT+) to (d) trimethylation with wild-type EZH2 without the test compound (WT−); comparing the ratio (a)/(b) with the ratio (c)/(d); and identifying the test compound as a selective inhibitor of the mutant EZH2 when the ratio (a)/(b) is less than the ratio (c)/(d).
The present invention further provides a method of identifying a subject as a candidate for treatment with one or more compounds of the invention. The method comprises the steps of performing an assay to detect a mutant EZH2 in a sample from a subject; and identifying a subject expressing a mutant EZH2 as a candidate for treatment with one or more compounds of the invention, wherein the compound(s) inhibits histone methyltransferase activity of EZH2.
In one embodiment, the method comprises: (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least one primer that specifically hybridizes to a nucleic acid sequence of EZH2, or a complement thereof, characterized with nucleotides encoding a mutation that increases EZH2 trimethylation of H3-K27; (iii) detecting the presence of the mutation in the nucleic acid sample by detecting the presence of a nucleic acid characterized with nucleotides encoding a mutation that increases EZH2 trimethylation of H3-K27; and (iv) identifying the subject as a candidate for treatment. The method can further comprise (v) administering a therapeutically effective amount of an EZH2 inhibitor to the subject identified in step (iv), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27.
In one embodiment, the method comprises: (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least two primers that specifically hybridize to a nucleic acid sequence of EZH2, or a complement thereof, characterized with nucleotides encoding a mutation that increases EZH2 trimethylation of H3-K27; (iii) amplifying the nucleic acid sequence, or the complement thereof, characterized with nucleotides encoding the mutation that increases EZH2 trimethylation of H3-K27; (iv) detecting the presence of the mutation by detecting the presence of the amplified nucleic acid; and (v) identifying the subject as a candidate for treatment. The method can further comprise (vi) administering a therapeutically effective amount of an EZH2 inhibitor to the subject identified in step (v), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27.
In one embodiment, the method comprises: (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least one primer that specifically hybridizes to a nucleic acid sequence, or a complement thereof, characterized with nucleotides encoding a mutation at the position Tyr641 (Y641), A677, and/or A687 of EZH2, wherein the mutation increases EZH2 trimethylation of H3-K27; (iii) detecting the presence of the mutation at the nucleotides encoding Y641, A677, and/or A687 in the nucleic acid sample by detecting the presence of a nucleic acid encoding the mutation at Y641, A677, and/or A687; and (iv) identifying the subject as a candidate for treatment. The method can further comprise (v) selecting a therapy that includes the administration of a therapeutically effective amount of an EZH2 inhibitor to the subject identified in step (iv), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27.
In one embodiment, the method comprises: (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least two primers that specifically hybridize to a nucleic acid sequence, or a complement thereof, characterized with nucleotides encoding a mutation at the position Y641, A677, and/or A687 of EZH2, wherein the mutation increases EZH2 trimethylation of H3-K27; (iii) amplifying the nucleic acid sequence, or the complement thereof, characterized with the mutation at the nucleotides encoding position Y641, A677, and/or A687; (iv) detecting the presence of the mutation at the nucleotides encoding Y641, A677, and/or A687 by detecting the presence of the amplified nucleic acid; and (v) identifying the subject as a candidate for treatment. The method can further comprise (vi) selecting a therapy that includes the administration of a therapeutically effective amount of an EZH2 inhibitor to the subject identified in step (v), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27.
Still another aspect of the invention is a method of inhibiting conversion of H3-K27 to trimethylated H3-K27. The method comprises the step of contacting a mutant EZH2, the wild-type EZH2, or both, with a histone substrate comprising H3-K27 and an effective amount of a compound of the present invention, wherein the compound inhibits histone methyltransferase activity of EZH2, thereby inhibiting conversion of H3-K27 to trimethylated H3-K27.
Further, the compounds or methods described herein can be used for research (e.g., studying epigenetic enzymes) and other non-therapeutic purposes.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In the specification, the singular forms also include the plural unless the context clearly dictates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents and other references mentioned herein are incorporated by reference. The references cited herein are not admitted to be prior art to the claimed invention. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods and examples are illustrative only and are not intended to be limiting. In the case of conflict between the chemical structures and names of the compounds disclosed herein, the chemical structures will control.
Other features and advantages of the invention will be apparent from the following detailed description and claims.


DETAILED DESCRIPTION OF THE INVENTION
The present invention provides novel azole bicyclic heteroaryl compounds, synthetic methods for making the compounds, pharmaceutical compositions containing them and various uses of the compounds.
The present invention provides the compounds of Formula (I):




In this formula:

    
    
        X1 is NR7 or CR7;
        X2 is N, NR8, CR8, O, or S;
        X3 is NR8, CR8, O, or S;
        X4 is C or N;
        Y1 is N or CH;
        Y2 is N or CR6;
        Y3 is N, or CR11;
        each of R5, R9, and R10, independently, is H or C1-C6 alkyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl;
        each R6 independently is H, halo, ORa, —NRaRb, —C(O)Ra, —C(O)ORa, —C(O)NRaRb, —NRbC(O)Ra, —S(O)2Ra, —S(O)2NRaRb, or RS2, in which each of Ra and Rb, independently is H or RS3 and each of RS2 and RS3, independently is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl; or Ra and Rb, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom; and each of RS2, RS3, and the 4 to 7-membered heterocycloalkyl ring containing Ra and Rb, is optionally substituted with one or more -Q2-T2, wherein Q2 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T2 is H, halo, cyano, —ORc, —NRcRd, —(NRcRdRd′)+A−, —C(O)Rc, —C(O)ORc, —C(O)NRcRd, —NRdC(O)Rc, —NRdC(O)ORc, —S(O)2Rc, —S(O)2NRcRd, or RS4, in which each of Rc, Rd, and Rd′, independently is H or RS5, A− is a pharmaceutically acceptable anion, each of RS4 and RS5, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, or Rc and Rd, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom, and each of RS4, RS5, and the 4 to 7-membered heterocycloalkyl ring containing Rc and Rd, is optionally substituted with one or more -Q3-T3, wherein Q3 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T3 is selected from the group consisting of H, halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 6-membered heteroaryl, ORe, COORe, —S(O)2Re, —NReRf, and —C(O)NReRf, each of Re and Rf independently being H or C1-C6 alkyl optionally substituted with OH, O—C1-C6 alkyl, or NH—C1-C6 alkyl; or -Q3-T3 is oxo; or -Q2-T2 is oxo; or any two neighboring -Q2-T2, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl; provided that -Q2-T2 is not H;
        each R7 independently is -Q4-T4, in which -Q4 is a bond, C1-C4 alkyl linker, or C2-C4 alkenyl linker, each linker optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T4 is H, halo, cyano, NRgRh, —ORg, —C(O)Rg, —C(O)ORg, —C(O)NRgRh, —C(O)NRgORh, —NRgC(O)Rh, —S(O)2Rg, or RS6, in which each of Rg and Rh, independently is H or RS7, each of RS6 and RS7, independently is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and each of RS6 and RS7 is optionally substituted with one or more -Q5-T5, wherein Q5 is a bond, C(O), C(O)NRk, NRkC(O), NRk, S(O)2, NRkS(O)2, or C1-C3 alkyl linker, Rk being H or C1-C6 alkyl, and T5 is H, halo, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, hydroxyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl, and T5 is optionally substituted with one or more substituents selected from the group consisting of halo, C1-C6 alkyl, hydroxyl, cyano, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C5 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl except when T5 is H, halo, hydroxyl, or cyano; or -Q5-T5 is oxo; provided that -Q4-T4 is not H; and
        each of R8 and R11, independently, is H, halo, hydroxyl, COOH, cyano, RS8, ORS8, or COORS8, in which RS8 is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, and RS8 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, and di-C1-C6 alkylamino;
        X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
        n is 0, 1, 2, 3, 4, or 5;
        provided that at most one of X2 and X3 is O or S, at least one of X1, X2, X3, X4, Y1, Y2, and Y3 is N or NR7 as applicable, and X1, X2, X3, X4, Y1, Y2, and Y3 are assigned such that the
    
    






moiety in Formula (I) is a bicyclic heteroaryl system.

The compounds of Formula (I) can have one or more of the following features:
For example, n is 1.
For example, n is 2.
For example, n is 0.
For example, at least one of Y1, Y3, and X4 is N and when X4 is C, Y1 is N, Y2 is CR6, and Y3 is CR11, then X2 is CR8.
For example,




For example, X4 is C.
For example, X2 is N or CH.
For example, X3 is CR8.
For example, Y3 is CR11.
For example, R6 is phenyl substituted with one or more -Q2-T2.
For example, R6 is 5 to 6-membered heteroaryl containing 1-3 heteroatoms selected from N, O, and S and optionally substituted with one or more -Q2-T2, provided that the heteroaryl is not thiophenyl.
For example, R6 is pyridinyl, pyrazolyl, pyrimidinyl, or furyl, each of which is optionally substituted with one or more -Q2-T2.
For example, R6 is phenyl or 5- or 6-membered heteroaryl substituted with O—C1-6 alkyl or NH—C1-6 alkyl, each of which is optionally substituted with hydroxyl, O—C1-3 alkyl or NH—C1-3 alkyl, each of the O—C1-3 alkyl and NH—C1-3 alkyl being optionally further substituted with O—C1-3 alkyl or NH—C1-3 alkyl.
For example, R6 is




For example, R6 is ethynyl.
For example, R6 is ethynyl substituted with one or more -Q2-T2, in which Q2 is a bond or C1-C3 alkyl linker and T2 is C1-C6 alkyl, C3-C6 cycloalkyl, or 4 to 7-membered heterocycloalkyl (e.g., azetidinyl, oxetanyl, thietanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, tetrahydro-2H-thiopyranyl, 1,4-diazepanyl, 1,4-oxazepanyl, 2-oxa-5-azabicyclo[2.2.1]heptanyl, 2,5-diazabicyclo[2.2.1]heptanyl, and morpholinyl, and the like) optionally substituted with one or more -Q3-T3.
For example, R6 is




For example, R6 is halo (e.g., fluorine, chlorine, bromine, and iodine).
For example, R6 is C1-C3 alkyl substituted with one or more -Q2-T2.
For example, R6 is C2-C6 alkenyl or C4-C6 cycloalkyl each optionally substituted with one or more -Q2-T2.
For example, R6 is C(O)H.
For example, R6 is ORa or —C(O)Ra.
For example, Ra is C1-C6 alkyl or 4 to 7-membered heterocycloalkyl (e.g., azetidinyl, oxetanyl, thietanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, and morpholinyl, and the like), which is optionally substituted with one or more -Q2-T2.
For example, R6 is —NRaRb, —C(O)Ra, —C(O)ORa, —C(O)NRaRb, —NRbC(O)Ra, —S(O)2Ra, or —S(O)2NRaRb.
For example, each of Ra and Rb, independently is H or C1-C6 alkyl optionally substituted with one or more -Q2-T2.
For example, one of Ra and Rb is H.
For example, Ra and Rb, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom (e.g., azetidinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, and morpholinyl, and the like) and the ring is optionally substituted with one or more -Q2-T2.
For example, R6 is 4 to 7-membered heterocycloalkyl (e.g., azetidinyl, oxetanyl, thietanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, and morpholinyl, and the like) optionally substituted with one or more -Q2-T2.
For example, R6 is piperidinyl, 2,2,6,6-tetramethyl-piperidinyl, 1,2,3,6-tetrahydropyridinyl, 2,2,6,6-tetramethyl-1,2,3,6-tetrahydropyridinyl, piperazinyl, morpholinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, or pyrrolidinyl, each of which is optionally substituted with one or more -Q2-T2.
For example, R6 is 4 to 7-membered heterocycloalkyl optionally substituted with one or more -Q2-T2, and -Q2-T2 is oxo or -Q2 is a bond and T2 is —ORc, —NRcRd, —C(O)Rc, —C(O)ORc, —S(O)2Rc, C1-C6 alkyl, or 4 to 7-membered heterocycloalkyl, each of which is optionally substituted with one or more -Q3-T3 when Rc or Rd is not H.
For example, -Q2-T2 is oxo.
For example, Q2 is a bond.
For example, Q2 is an unsubstituted C1-C3 alkyl linker.
For example, T2 is C1-C6 alkyl or C6-C10 aryl, each optionally substituted with one or more -Q3-T3.
For example, T2 is an unsubstituted substituted straight chain C1-C6 or branched C3-C6 alkyl, including but not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl and n-hexyl.
For example, T2 is phenyl.
For example, T2 is halo (e.g., fluorine, chlorine, bromine, and iodine).
For example, T2 is 4 to 7-membered heterocycloalkyl (e.g., azetidinyl, oxetanyl, thietanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, and morpholinyl, and the like) optionally substituted with one or more -Q3-T3.
For example, T2 is —ORc, —NRcRd, —C(O)Rc, —C(O)ORc, or —S(O)2Rc.
For example, T2 is —(NRcRdRd′)+A−, —C(O)NRcRd, —NRdC(O)Rc, —NRdC(O)ORc, or —S(O)2NRcRd.
For example, Q2 is a bond or methyl linker and T2 is H, halo, —ORc, —NRcRd, —(NRcRdRd′)+A−, or —S(O)2NRcRd.
For example, Rc is C1-C6 alkyl or 4 to 7-membered heterocycloalkyl (e.g., azetidinyl, oxetanyl, thietanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, and morpholinyl, and the like), which is optionally substituted with one or more -Q3-T3.
For example, each of Rc and Rd, independently is H or C1-C6 alkyl optionally substituted with one or more -Q3-T3.
For example, Rc is H.
For example, Rd is H.
For example, Rc and Rd, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom (e.g., azetidinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, and morpholinyl, and the like) and the ring is optionally substituted with one or more -Q3-T3.
For example, Q2 is a bond and T2 is —ORc, —NRcRd, —C(O)Rc, —C(O)ORc, —S(O)2Rc, C1-C6 alkyl, or 4 to 7-membered heterocycloalkyl, each of which is optionally substituted with one or more -Q-T3 when Rc or Rd is not H.
For example, -Q3-T3 is oxo.
For example, T2 is 4 to 7-membered heterocycloalkyl or C3-C8 cycloalkyl and one or more -Q-T3 are oxo.
For example, Q3 is a bond or unsubstituted or substituted C1-C3 alkyl linker.
For example, T3 is H, halo, 4 to 7-membered heterocycloalkyl, C1-C3 alkyl, ORc, COORe, —S(O)2Re, —NReRf, or —C(O)NReRf.
For example, one of Rd and Re is H.
For example, Q3 is a bond or C1-C3 alkyl linker and T3 is selected from the group consisting of C1-C3 alkyl, halo, ORe, —S(O)2Re, —NReRf, and —C(O)NReRf.
For example, Re is H.
For example, Rf is H.
For example, R6 is selected from the group consisting of CH3, OCH3,










For example, R7 is C1-C6 alkyl optionally substituted with one or more -Q5-T5.
For example, R7 is C3-C8 cycloalkyl optionally substituted with one or more -Q5-T5.
For example, R7 is 4 to 7-membered heterocycloalkyl (e.g., azetidinyl, oxetanyl, thietanyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, tetrahyrofuranyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl, piperazinyl, tetrahydro-2H-pyranyl, 3,6-dihydro-2H-pyranyl, and morpholinyl, and the like) optionally substituted with one or more -Q5-T5.
For example, R7 is cyclopentyl.
For example, R7 is isopropyl or sec-butyl.
For example, R7 is 5 to 6-membered heterocycloalkyl optionally substituted with one or more -Q5-T5.
For example, R7 is piperidinyl optionally substituted with one -Q5-T5.
For example, R7 is tetrahydropyran cm




For example, R7 is




For example, R7 is




For example, R7 is




For example, R7 is




For example, R7 is




For example, R7 is




For example, R7 is




For example, R7 is




For example, R7 is




wherein R100 is phenyl, 5- or 6-membered heteroaryl, or 4 to 12-membered heterocycloalkyl, each optionally substituted with one or more T5a in which each T5a is independently C1-C6 alkoxyl or O—C1-C4 alkylene-C1-C4 alkoxy, and R101 is H or C1-C4 alkyl.

For example, R7 is










wherein each T5a is independently C1-C3 alkoxyl or O—C1-C3 alkylene-C1-C2 alkoxy.

For example, R7 is Q4-T4, Q4 is a bond and T4 is 4 to 7-membered heterocycloalkyl or C3-C8 cycloalkyl substituted with one or more -Q5-T5.
For example, -Q5-T5 is oxo.
For example, T5 is H, halo, C1-C6 alkyl, C1-C6 alkoxyl, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl.
For example, Q5 is a bond and T5 is C1-C6 alkyl, C3-C8 cycloalkyl, or 4 to 7-membered heterocycloalkyl.
For example, Q5 is a bond or NRk and T5 is H, C1-C6 alkyl, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 12-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, C1-C6 alkylene-5- or 6-membered heteroaryl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, T5 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, and C3-C8 cycloalkyl.
For example, Q5 is a bond or NRk and T5 is C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 5- or 6-membered heteroaryl, C1-C6 alkylene-5- or 6-membered heteroaryl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, T5 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, and C3-C8 cycloalkyl.
For example, Q5 is CO and T5 is C1-C6 alkyl, C1-C6 alkoxyl, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 7-membered heterocycloalkyl, 5- or 6-membered heteroaryl, C1-C6 alkylene-5- or 6-membered heteroaryl.
For example, T5 is C1-C6 alkyl optionally substituted with halo, hydroxyl, cyano, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, or C3-C8 cycloalkyl.
For example, Q5 is C1-C3 alkyl linker and T5 is H or C6-C10 aryl.
For example, Q5 is C1-C3 alkyl linker and T5 is C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 7-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl, T5 being optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxy, and C3-C8 cycloalkyl.
For example, X is azole or a bicyclic ring containing an azole moiety.
For example, X is not 5-methoxy-1H-pyrrolo[3,2-b]pyridin-7(4H)-one, 5-methoxy-1H-pyrazolo[4,3-b]pyridin-7(4H)-one, 5-methoxy-1H-imidazo[4,5-b]pyridin-7(4H)-one, 5-methoxy-2-methyl-1H-imidazo[4,5-b]pyridin-7(4H)-one, or 5-methoxy-3-methyl-1H-pyrazolo[4,3-b]pyridin-7(4H)-one.
For example, X is imidazol-2-yl, imidazol-4-yl, triazol-3-yl, 3H-imidazo[4,5-c]pyridin-7-yl, 1H-benzo[d]imidazol-4-yl, 1H-indazol-7-yl, isoxazol-3-yl, thiazol-2-yl, 1H-pyrazolo[4,3-c]pyridin-7-yl, imidazo[1,2-a]pyridin-8-yl, imidazo[1,2-c]pyrimidin-8-yl, 1,4,6,7-tetrahydropyrano[4,3-c]pyrazol-7-yl, 1,4,6,7-tetrahydropyrano[3,4]-imidazol-7-yl, 4,5,6,7-tetrahydro-1H-benzo[d]imidazol-4-yl, 7H-pyrrolo[2,3-d]pyrimidine-4-yl, 9H-purine-6-yl, 7-methyl-[1,2,4]triazolo[4,3-a]pyridin-5-ol-6-yl, [1,2,4]triazolo[4,3-a]pyridin-6-yl, 3-fluoro-1,5-dimethyl-1H-pyrazol-4-yl, or 5-fluoro-1,3-dimethyl-1H-pyrazol-4-yl.
For example,




is selected from indolyl, isoindolyl, indolizinyl, benzofuryl, isobenzofuryl, benzo[b]thienyl, benzoxazolyl, benzthiazolyl, benzimidazolyl, benzotriazolyl, benzoxadiazolyl, benzothiadiazolyl, purinyl, indazolyl, pyrrolopyridinyl, imidazopyridinyl, pyrazolopyridinyl, pyrrolopyrazinyl, imidazopyrazinyl, pyrazolopyrazinyl, pyrrolopyrimidinyl, pyrazolopyrimidinyl, pyrrolopyridazinyl, imidazopyridazinyl, pyrazolopyridazinyl, furopyridinyl, thienopyridinyl, furopyrazinyl, thienopyrazinyl, oxazolopyridinyl, isoxazolopyridinyl, thiazolopyridinyl, isothiazolopyridinyl, oxadiazolopyridinyl, thiadiazolopyridinyl, triazolopyridinyl, oxazolopyrazinyl, isoxazolopyrazinyl, thiazolopyrazinyl, isothiazolopyrazinyl, oxadiazolopyrazinyl, thiadiazolopyrazinyl, triazolopyrazinyl, furopyrimidinyl, thienopyrimidinyl, furopyridazinyl, thienopyridazinyl, oxazolopyrimidinyl, isoxazolopyrimidinyl, thiazolopyrimidinyl, isothiazolopyrimidinyl, oxadiazolopyrimidinyl, thiadiazolopyrimidinyl, triazolopyrimidinyl, oxazolopyridazinyl, isoxazolopyridazinyl, thiazolopyridazinyl, isothiazolopyridazinyl, oxadiazolopyridazinyl, thiadiazolopyridazinyl, triazolopyridazinyl, and imidazotriazinyl.

For example,




is selected from





For example,




is selected from





For example,




is selected from





For example, X is




In the above structure, each of D1, D2, and D3, independently, is CR901 or N, provided that at least one of D1, D2, and D3 is N. D4 is O, S, or NR902. Each R901 and R902, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, each of D2 and D3, independently, is CR901 and D4 is NR902. In other compounds, each of D1 and D2, independently, is CR901, D3 is N, and D4 is NR902. In other compounds, each of D1 and D2 is N, D3 is CR901, and D4 is NR902. In still other compounds, each of D1 and D3 is, independently, CR901, D2 is N, and D4 is NR902. In further other compounds, D1 is N, each of D2 and D3, independently, is CR901, and D4 is O or S.
For example, X is




In the above structure, each of E1, E2, and E4, independently, is CR903 or N, provided that at least one of E1, E2, and E4 is N. E3 is O, S, or NR904. Each R903 and R904, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, Et is N, each of E2 and E4, independently, is CR903, and E3 is NR904. In other compounds, each of Et and E4, independently, is CR903, E2 is N, and E3 is NR904. In still other compounds, each of E1 and E2, independently, is CR903, E3 is NR904, and E4 is N. In further other compounds, each of E1 and E2, independently, is CR903, E3 is O, and E4 is N.
For example, X is




In the above structures, G1 is O, S, or NR907. Each of G2, G3, and G4, independently, is N or CR908, provided that at least one of G2, G3, and G4 is N. Each of R905, R906, R907, and R908, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, G1 is NR907, G2 is CR908, and each of G3 and G4, if present, is N. In other compounds, G1 is NR907, each of G2 and G4, if present, independently, is CR908 and G3 is N. In still other compounds, G1 is NR907, each of G2 and G4, if present, is N, and G3 is CR908. In yet other compounds, G1 is NR907, G2 is N, and each of G3 and G4, if present, independently, is CR908.
For example, X is




In the above structures, each of J1, J2, J3, and J4, independently, is N or CR911, provided that at least one of J1, J2, J3, and J4 is N. Each of R909, R910, and R911, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, J1, if present, is N, and each of J2, J3, and J4, independently, is CR911. In some embodiments, X is




in which each of J2 and J3 is N and J4 is CR911.

For example, X is




In the above structure, each of K1, K2, K3, and K4, independently, is N or CR914, provided that at least one of K1, K2, K3, and K4 is N. Each of R912, R913, and R914, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, K1 is N and each of K2, K3, and K4, independently, is CR914. In other compounds, each of K1 and K4 is N and each of K2 and K3 independently, is CR914.
For example, X is




In the above structure, each of U1, U3, and U4, independently, is N or CR917, provided that at least one of U1, U3, and U4 is N. U2 is O, S, or NR918. Each of R915, R916, R917, and R918, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, U1 is N, U2 is NR918, and each of U3 and U4, independently, is CR917.
For example, X is




In the above structure, each of V1 and V2, independently, is N or CR919, provided that at least one of V1 and V2 is N. V3 is O, S, or NR920. Each of V4, V5, and V6 is O, S, or NR921, or CR922R923; and each of R919, R920, R921, R922, and R923, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.
One subset of the compounds of Formula (I) includes those of Formula (Ia):




wherein R7 is -Q4-T4, wherein Q4 is a bond or methyl linker, T4 is optionally substituted C1-C6 alkyl, optionally substituted C3-C8 cycloalkyl or optionally substituted 4- to 14-membered heterocycloalkyl; and R6, each of X2, X3, X4, Y1, Y3, X, and n is as defined herein for Formula (I). In some compounds, R7 is tetrahydropyranyl, piperidine substituted by 1, 2, or 3 C1-4 alkyl groups, or cyclohexyl substituted by N(C1-4 alkyl)2 wherein one or both of the C1-4 alkyl is optionally substituted with C1-6 alkoxyl.

In addition to the above-described features of the compounds of this invention, where applicable, the compounds of Formula (Ia) can include one or more of the following features:
For example, T4 is alkyl such as i-propyl.
For example, T4 is




For example, T4 is




in which R′′′ is T5, —C(O)T5, or S(O)2T5, T5 being as defined herein for Formula (I).

For example, the compounds of Formula (I) include those of Formula (Ib):




or a pharmaceutically acceptable salt thereof; wherein

    
    
        n5 is 0, 1, or 2;
        R501 is C(H) or N;
        R506 is C1-C6 alkyl, piperidine substituted by 1, 2, or 3 R707 groups, or cyclohexyl substituted by N(R707)2 wherein each R707 is independently C1-4 alkyl that is optionally substituted with (i) C1-6 alkoxyl, (ii) 4 to 12-membered heterocycloalkyl, (iii) C6-C10 aryl that is optionally further substituted with C1-C6 alkoxyl or O—C1-C4 alkylene-C1-C4 alkoxy, or (iv) 5- or 6-membered heteroaryl that is optionally further substituted with C1-C6 alkoxyl or O—C1-C4 alkylene-C1-C4 alkoxy;
        R507 is morpholine, piperazine, piperidine, diazepane, pyrrolidine, azetidine, O—C1-6 alkyl, NH—C1-6 alkyl, or O-heterocycle, wherein the heterocycle is a 4-7 membered heterocycle containing an oxygen or nitrogen, or both, and wherein the nitrogen can optionally be substituted with C1-3 alkyl; wherein the piperazine, piperidine, diazepane, pyrrolidine or azetidine groups can be optionally further substituted with OH, C1-6 alkyl, or O—C1-3 alkyl; and wherein each of the O—C1-6 alkyl and NH—C1-6 alkyl is optionally substituted with hydroxyl, O—C1-3 alkyl or NH—C1-3 alkyl, each of the O—C1-3 alkyl and NH—C1-3 alkyl being optionally further substituted with O—C1-3 alkyl or NH—C1-3 alkyl; and
        each of X2, X3, X4, Y1, Y3, X and n is as defined herein for Formula (I).
    
    


In addition to the above-described features of the compounds of this invention, where applicable, the compounds of Formula (Ib) can include one or more of the following features.
For example, R501 is C(H), and R507 is piperidine; diazepane; pyrrolidine; azetidine; O—C1-6 alkyl; or O-heterocycle, wherein the heterocycle is a 4-7 membered heterocycle containing an oxygen or nitrogen, or both, and wherein the nitrogen can optionally be substituted with C1-3 alkyl; wherein the piperidine, diazepane, pyrrolidine or azetidine groups can be optionally further substituted with OH, C1-6 alkyl, or O—C1-3 alkyl.
For example, R501 is C(H) and R507 is piperidine, diazepane, pyrrolidine, azetidine or O—C1-6 alkyl, wherein the piperidine, diazepane, pyrrolidine or azetidine groups can be optionally further substituted with OH or C1-6 alkyl.
For example, R501 is C(H), R507 is piperazine optionally further substituted with C1-6 alkyl, and R506 is piperidine substituted by 1, 2, or 3 C1-4 alkyl groups.
For example, R501 is N, and R507 is morpholine, piperidine, piperazine, diazepane, pyrrolidine, azetidine or O—C1-6 alkyl, wherein the piperidine, piperazine, diazepane, pyrrolidine or azetidine groups can be optionally further substituted with OH or C1-6 alkyl.
For example, R1 is H, methyl, or ethyl, and R2 is halo, cyano, C1-C6 alkoxyl optionally substituted with C1-C6 alkoxyl, C1-C3 alkyl optionally substituted with C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, optionally substituted 4 to 6-membered heterocycloalkyl (e.g., pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl), optionally substituted phenyl, or optionally substituted 5- or 6-membered heteroaryl (e.g., pyridinyl, pyrazolyl, pyrimidinyl, quinolinyl, tetrazolyl, oxazolyl, isoxazolyl, thiazolyl, isothiazolyl, furyl, or thienyl).
For example, R506 is C1-C6 alkyl such as i-propyl.
For example, R506 is




For example, R506 is




For example, R506 is




For example, R506 is




For example, R506 is




For example, R506 is




For example, when R501 is C(H), R507 is piperidine or diazepane, which are substituted with OH or C1-6 alkyl, or when R501 is N, R507 is piperidine, piperazine, or diazepane, which are optionally further substituted with OH or C1-6 alkyl.
For example, when R501 is C(H), R507 is piperidine substituted with C1-6 alkyl, or when R501 is N, R507 is piperidine substituted with OH or piperazine substituted with C1-6 alkyl.
For example, when R501 is N, R507 is unsubstituted piperazine.
For example, n5 is 0 or 1.
For example, when R501 is C(H) or N, R507 is O—C1-6 alkyl or O-heterocycle, and n5 is 1.
For example, when R501 is C(H), R507 is unsubstituted piperazine and R506 is piperidine substituted by 1, 2, or 3 C1-4 alkyl groups.
For example, R507 is O—C2-3 alkyl substituted with O—C1-2 alkyl, e.g., —OCH2CH2OCH3.
For example, n is 0, 1, or 2.
For example, n is 1.
For example, n is 2.
For example, n is 0.
For example, the compounds of Formula (I) include those of Formula (Ic):




or a pharmaceutically acceptable salt thereof;

wherein

    
    
        n6 is 0, 1 or 2;
        R606 is C1-C6 alkyl, piperidine substituted by 1, 2, or 3 R707 groups, or cyclohexyl substituted by N(R707)2 wherein each R707 is independently C1-4 alkyl that is optionally substituted with (i) C1-6 alkoxyl, (ii) 4 to 12-membered heterocycloalkyl, (iii) C6-C10 aryl that is optionally further substituted with C1-C6 alkoxyl or O—C1-C4 alkylene-C1-C4 alkoxy, or (iv) 5- or 6-membered heteroaryl that is optionally further substituted with C1-C6 alkoxyl or O—C1-C4 alkylene-C1-C4 alkoxy;
        R607 is morpholine, piperidine, piperazine, pyrrolidine, diazepane, oxetane, azetidine or O—C1-6 alkyl, wherein the piperidine, diazepane, oxetane or azetidine groups can be optionally further substituted with one or more C1-6 alkyl, C1-6 haloalkyl, C3-8 cycloalkyl, or 4 to 6-membered heterocycloalkyl; and
        each of X2, X3, X4, Y1, Y3, X and n is as defined herein for Formula (I).
    
    


In addition to the above-described features of the compounds of this invention, where applicable, the compounds of Formula (Ic) can include one or more of the following features:
For example, R606 is C1-C6 alkyl such as i-propyl.
For example, R606 is




For example, R606 is




For example, R606 is




For example, R606 is




For example, R606 is




For example, R606 is




For example, R607 is piperidine or oxetane, each of which is substituted with C1-6 alkyl.
For example, R607 is piperidine substituted with CH2CF3, cyclopropyl, cyclobutyl, or oxetane.
For example, n6 is 0 or 1.
For example, n is 0, 1, or 2.
The compounds of formula (Ia), (Ib), and (Ic) may further include the following features:
For example, X is




In the above structure, each of D1, D2, and D3, independently, is CR901 or N, provided that at least one of D1, D2, and D3 is N. D4 is O, S, or NR902. Each R901 and R902, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, each of D2 and D3, independently, is CR901 and D4 is NR902. In other compounds, each of D1 and D2, independently, is CR901, D3 is N and D4 is NR902. In other compounds, each of D1 and D2 is N, D3 is CR901, and D4 is NR902. In still other compounds, each of D1 and D3 is, independently, CR901, D2 is N, and D4 is NR902. In further other compounds, D1 is N, each of D2 and D3, independently, is CR901 and D4 is O or S.
For example, X is




In the above structure, each of E1, E2, and E4, independently, is CR903 or N, provided that at least one of E1, E2, and E4 is N. E3 is O, S, or NR904. Each R903 and R904, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, E1 is N, each of E2 and E4, independently, is CR903, and E3 is NR904. In other compounds, each of E1 and E4, independently, is CR903, E2 is N, and E3 is NR904. In still other compounds, each of E1 and E2, independently, is CR903, E3 is NR904, and E4 is N. In further other compounds, each of E1 and E2, independently, is CR903, E3 is O, and E4 is N.
For example, X is




In the above structures, G1 is O, S, or NR907. Each of G2, G3, and G4, independently, is N or CR908, provided that at least one of G2, G3, and G4 is N. Each of R905, R906, R907, and R908, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, G1 is NR907, G2 is CR908, and each of G3 and G4, if present, is N. In other compounds, G1 is NR907, each of G2 and G4, if present, independently, is CR908 and G3 is N. In still other compounds, G1 is NR907, each of G2 and G4, if present, is N, and G3 is CR908. In yet other compounds, G1 is NR907, G2 is N, and each of G3 and G4, if present, independently, is CR908.
For example, X is




In the above structures, each of J1, J2, J3, and J4, independently, is N or CR911, provided that at least one of J1, J2, J3, and J4 is N. Each of R909, R910, and R911, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, J1, if present, is N and each of J2, J3, and J4, independently, is CR911. In some embodiments, X is




in which each of J2 and J3 is N and J4 is CR911.

For example, X is




In the above structure, each of K1, K2, K3, and K4, independently, is N or CR914, provided that at least one of K1, K2, K3, and K4 is N. Each of R912, R913, and R914, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, K1 is N and each of K2, K3, and K4, independently, is CR914. In other compounds, each of K1 and K4 is N and each of K2 and K3, independently, is CR914.
For example, X is




In the above structure, each of U1, U3, and U4, independently, is N or CR917, provided that at least one of U1, U3, and U4 is N. U2 is O, S, or NR918. Each of R915, R916, R917, and R918, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl. In some compounds, U1 is N, U2 is NR918 and each of U3 and U4, independently, is CR917.
For example, X is




In the above structure, each of V1 and V2, independently, is N or CR919, provided that at least one of V1 and V2 is N. V3 is O, S, or NR920. Each of V4, V5, and V6 is O, S, or NR921, or CR922R923. Each of R919, R920, R921, R922, and R923, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.
For example, X is imidazol-2-yl, imidazol-4-yl, triazol-3-yl, 3H-imidazo[4,5-c]pyridin-7-yl, 1H-benzo[d]imidazol-4-yl, 1H-indazol-7-yl, isoxazol-3-yl, thiazol-2-yl, 1H-pyrazolo[4,3-c]pyridin-7-yl, imidazo[1,2-a]pyridin-8-yl, imidazo[1,2-c]pyrimidin-8-yl, 1,4,6,7-tetrahydropyrano[4,3-c]pyrazol-7-yl, 1,4,6,7-tetrahydropyrano[3,4]-imidazol-7-yl, 4,5,6,7-tetrahydro-1H-benzo[d]imidazol-4-yl, 7H-pyrrolo[2,3-d]pyrimidine-4-yl, 9H-purine-6-yl, 7-methyl-[1,2,4]triazolo[4,3-a]pyridin-5-ol-6-yl, [1,2,4]triazolo[4,3-a]pyridin-6-yl, 3-fluoro-1,5-dimethyl-1H-pyrazol-4-yl, or 5-fluoro-1,3-dimethyl-1H-pyrazol-4-yl.
The compounds of this invention also include those of Formula (II) or pharmaceutically acceptable salts thereof:




wherein,

    
    
        Z1 is N or CR7′,
        Z2 is N or CR2′, provided that when Z1 is N, Z2 is N,
        R1′ is (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, unsubstituted or substituted (C3-C8)cycloalkyl, unsubstituted or substituted (C3-C8)cycloalkyl-(C1-C8)alkyl or —(C2-C8)alkenyl, unsubstituted or substituted (C5-C8)cycloalkenyl, unsubstituted or substituted (C5-C8)cycloalkenyl-(C1-C8)alkyl or —(C2-C8)alkenyl, unsubstituted or substituted (C6-C10)bicycloalkyl, unsubstituted or substituted heterocycloalkyl or —(C2-C8)alkenyl, unsubstituted or substituted heterocycloalkyl-(C1-C8)alkyl, unsubstituted or substituted aryl, unsubstituted or substituted aryl-(C1-C8)alkyl or —(C2-C8)alkenyl, unsubstituted or substituted heteroaryl, unsubstituted or substituted heteroaryl-(C1-C8)alkyl or —(C2-C8)alkenyl, —CORa′, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′;
        R2′ is hydrogen, (C1-C8)alkyl, trifluoromethyl, alkoxy, or halo, in which said (C1-C8)alkyl is optionally substituted with one to two groups selected from amino and (C1-C3)alkylamino;
        R7′ is hydrogen, (C1-C3)alkyl, or alkoxy;
        R3′ is hydrogen, (C1-C8)alkyl, cyano, trifluoromethyl, —NRa′Rb′, or halo;
        R6′ is selected from the group consisting of hydrogen, halo, (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, unsubstituted or substituted (C3-C8)cycloalkyl, unsubstituted or substituted (C3-C8)cycloalkyl-(C1-C8)alkyl, unsubstituted or substituted (C5-C8)cycloalkenyl, unsubstituted or substituted (C5-C8)cycloalkenyl-(C1-C8)alkyl, (C6-C10)bicycloalkyl, unsubstituted or substituted heterocycloalkyl, unsubstituted or substituted heterocycloalkyl-(C1-C8)alkyl, unsubstituted or substituted aryl, unsubstituted or substituted aryl-(C1-C8)alkyl, unsubstituted or substituted heteroaryl, unsubstituted or substituted heteroaryl-(C1-C8)alkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —NRa′NRa′C(O)NRa′Rb′, —NRa′NRa′C(O)ORa′, —ORa, —OC(O)Ra′, —OC(O)NRa′Rb′;
        wherein any (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, cycloalkyl, cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl group is optionally substituted by 1, 2 or 3 groups independently selected from the group consisting of —O(C1-C6)alkyl(Rc′)1-2, —S(C1-C6)alkyl(Rc′)1-2, —(C1-C6)alkyl(Rc′)1-2, —(C1-C8)alkyl-heterocycloalkyl, (C3-C8)cycloalkyl-heterocycloalkyl, halo, (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, OC(O)NRa′Rb′, heterocycloalkyl, aryl, heteroaryl, aryl(C1-C4)alkyl, and heteroaryl(C1-C4)alkyl;
        wherein any aryl or heteroaryl moiety of said aryl, heteroaryl, aryl(C1-C4)alkyl, or heteroaryl(C1-C4)alkyl is optionally substituted by 1, 2 or 3 groups independently selected from the group consisting of halo, (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRaRb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′;
        Ra′ and Rb′ are each independently hydrogen, (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C6-C10)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein said (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, cycloalkyl, cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl group is optionally substituted by 1, 2 or 3 groups independently selected from halo, hydroxyl, (C1-C4)alkoxy, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, —CO2H, —CO2(C1-C4)alkyl, —CONH2, —CONH(C1-C4)alkyl, —CON((C1-C4)alkyl)((C1-C4)alkyl), —SO2(C1-C4)alkyl, —SO2NH2, —SO2NH(C1-C4)alkyl, and SO2N((C1-C4)alkyl)((C1-C4)alkyl);
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 5-8 membered saturated or unsaturated ring, optionally containing an additional heteroatom selected from oxygen, nitrogen, and sulfur, wherein said ring is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C4)alkyl, (C1-C4)haloalkyl, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, hydroxyl, oxo, (C1-C4)alkoxy, and (C1-C4)alkoxy(C1-C4)alkyl, wherein said ring is optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 6- to 10-membered bridged bicyclic ring system optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;
        each Rc′ is independently (C1-C4)alkylamino, —NRa′SO2Rb′, —SORa′, —SO2Ra′, —NRa′C(O)ORa′, —NRa′Rb′, or —CO2Ra′;
        X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnKr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
        n is 0, 1, 2, 3, 4, or 5.

Subgroup A of Formula (II)

        R1′ is selected from the group consisting of (C1-C8)alkyl, (C3-C8)cycloalkyl, heterocycloalkyl, aryl, and heteroaryl;
        R2′ is hydrogen, (C1-C8)alkyl, trifluoromethyl, alkoxy, or halo, in which said (C1-C8)alkyl is optionally substituted with one to two groups selected from amino and (C1-C3)alkylamino;
        R7′ is hydrogen, (C1-C3)alkyl, or alkoxy;
        R3′ is selected from the group consisting of hydrogen, (C1-C8)alkyl, cyano, trifluoromethyl, —NRa′Rb′, and halo;
        R6′ is selected from the group consisting of hydrogen, halo, cyano, trifluoromethyl, amino, (C1-C8)alkyl, (C3-C8)cycloalkyl; aryl, heteroaryl, acylamino; (C2-C8)alkynyl, arylalkynyl, heteroarylalkynyl; —SO2Ra′; —SO2NRa′Rb′ and —NRa′SO2Rb′; wherein any (C1-C8)alkyl, (C3-C8)cycloalkyl, (C2-C8)alkynyl, arylalkynyl, heteroarylalkynyl group is optionally substituted by 1, 2 or 3 groups independently selected from —O(C1-C6)alkyl(Rc′)1-2, —S(C1-C6)alkyl(Rc′)1-2, —(C1-C6)alkyl(Rc′)1-2, —(C1-C8)alkyl-heterocycloalkyl, (C3-C8)cycloalkyl-heterocycloalkyl, halo, (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, —OC(O)NRa′Rb′, heterocycloalkyl, aryl, heteroaryl, aryl(C1-C4)alkyl, and heteroaryl(C1-C4)alkyl;
        Ra′ and Rb′ are each independently hydrogen, (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C6-C10)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein said (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, cycloalkyl, cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl group is optionally substituted by 1, 2 or 3 groups independently selected from halo, hydroxyl, (C1-C4)alkoxy, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, —CO2H, —CO2(C1-C4)alkyl, —CONH2, —CONH(C1-C4)alkyl, —CON((C1-C4)alkyl)((C1-C4)alkyl), —SO2(C1-C4)alkyl, —SO2NH2, —SO2NH(C1-C4)alkyl, and —SO2N((C1-C4)alkyl)((C1-C4)alkyl);
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 5-8 membered saturated or unsaturated ring, optionally containing an additional heteroatom selected from oxygen, nitrogen, and sulfur, wherein said ring is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C4)alkyl, (C1-C4)haloalkyl, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, hydroxyl, oxo, (C1-C4)alkoxy, and (C1-C4)alkoxy(C1-C4)alkyl, wherein said ring is optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 6- to 10-membered bridged bicyclic ring system optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring. An aryl or heteroaryl group in this particular subgroup A is selected independently from the group consisting of furan, thiophene, pyrrole, oxazole, thiazole, imidazole, pyrazole, oxadiazole, thiadiazole, triazole, tetrazole, benzofuran, benzothiophene, benzoxazole, benzothiazole, phenyl, pyridine, pyridazine, pyrimidine, pyrazine, triazine, tetrazine, quinoline, cinnoline, quinazoline, quinoxaline, and naphthyridine or another aryl or heteroaryl group as follows:
    
    






wherein in (1),

    
    
        A is O, NH, or S; B is CH or N, and C is hydrogen or C1-C8 alkyl; or
    
    






wherein in (2),

    
    
        D is N or C optionally substituted by hydrogen or C1-C8 alkyl; or
    
    






wherein in (3),

    
    
        E is NH or CH2; F is O or CO; and G is NH or CH2; or
    
    






wherein in (4),

    
    
        J is O, S or CO; or
    
    






wherein in (5),

    
    
        Q is CH or N;
        M is CH or N; and
        L/(5) is hydrogen, halo, amino, cyano, (C1-C8)alkyl, (C3-C8)cycloalkyl, —CORa′, —CO2Ra, —CONRa′Rb′, —CONRa′NRa′Rb′, —SO2Ra′, —SO2NRa′Rb′, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —NRa′NRa′C(O)NRa′Rb′, or —ORa′,
        wherein any (C1-C8)alkyl or (C3-C8)cycloalkyl group is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′; wherein Ra′ and Rb′ are defined as above; or
    
    






wherein in (6),

    
    
        L/(6) is NH or CH2; or
    
    






wherein in (7),

    
    
        M/(7) is hydrogen, halo, amino, cyano, (C1-C8)alkyl, (C3-C8)cycloalkyl, heterocycloalkyl, —CORa, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′, —SO2Ra′, —SO2NRa′Rb′, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —NRa′NRa′C(O)NRa′Rb′, or —ORa′,
        wherein any (C1-C8)alkyl, (C3-C8)cycloalkyl, or heterocycloalkyl group is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′; wherein Ra′ and Rb′ are defined as above; or
    
    






wherein in (8),

    
    
        P is CH2, NH, O, or S; Q/(8) is CH or N; and n is 0-2; or
    
    






wherein in (9),

    
    
        S/(9) and T/(9) are C, or S/(9) is C and T/(9) is N, or S/(9) is N and T/(9) is C;
        R is hydrogen, amino, methyl, trifluoromethyl, or halo;
        U is hydrogen, halo, amino, cyano, nitro, trifluoromethyl, (C1-C8)alkyl, (C3-C8)cycloalkyl, —CORa′, —CO2Ra′, —CONRa′Rb′, —SO2Ra′, —SO2NRa′Rb′, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —ORa′, or 4-(1H-pyrazol-4-yl),
        wherein any (C1-C8)alkyl or (C3-C8)cycloalkyl group is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′; wherein Ra′ and Rb′ are defined as above.

Subgroup B of Formula (II)

        R1′ is (C1-C8)alkyl, (C3-C8)cycloalkyl, or heterocycloalkyl;
        R2′ is hydrogen, (C1-C3)alkyl, or halo, in which said (C1-C3)alkyl is optionally substituted with one to two groups selected from amino and (C1-C3)alkylamino;
        R7′ is hydrogen, (C1-C3)alkyl, or alkoxy;
        R3′ is hydrogen, (C1-C8)alkyl or halo;
        R6′ is hydrogen, halo, cyano, trifluoromethyl, amino, (C1-C8)alkyl, (C3-C8)cycloalkyl, aryl, heteroaryl, acylamino; (C2-C8)alkynyl, arylalkynyl, heteroarylalkynyl, —SO2Ra′, —SO2NRa′Rb′, or —NRa′SO2Rb′;
        wherein any (C1-C8)alkyl, (C3-C8)cycloalkyl, (C2-C8)alkynyl, arylalkynyl, or heteroarylalkynyl group is optionally substituted by 1, 2 or 3 groups independently selected from halo, (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, —OC(O)NRa′Rb′, heterocycloalkyl, aryl, heteroaryl, aryl(C1-C4)alkyl, and heteroaryl(C1-C4)alkyl;
        Ra′ and Rb′ are each independently hydrogen, (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C6-C10)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, wherein said (C1-C8)alkyl, (C2-C8)alkenyl, (C2-C8)alkynyl, cycloalkyl, cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl group is optionally substituted by 1, 2 or 3 groups independently selected from halo, hydroxyl, (C1-C4)alkoxy, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, —CO2H, —CO2(C1-C4)alkyl, —CONH2, —CONH(C1-C4)alkyl, —CON((C1-C4)alkyl)((C1-C4)alkyl), —SO2(C1-C4)alkyl, —SO2NH2, —SO2NH(C1-C4)alkyl, and —SO2N((C1-C4)alkyl)((C1-C4)alkyl);
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 5-8 membered saturated or unsaturated ring, optionally containing an additional heteroatom selected from oxygen, nitrogen, and sulfur, wherein said ring is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C4)alkyl, (C1-C4)haloalkyl, amino, (C1-C4)alkylamino, ((C1-C4)alkyl)((C1-C4)alkyl)amino, hydroxyl, oxo, (C1-C4)alkoxy, and (C1-C4)alkoxy(C1-C4)alkyl, wherein said ring is optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;
        or Ra′ and Rb′ taken together with the nitrogen to which they are attached represent a 6- to 10-membered bridged bicyclic ring system optionally fused to a (C3-C8)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring. Aryl and heteroaryl in this definition are selected from the group consisting of furan, thiophene, pyrrole, oxazole, thiazole, imidazole, pyrazole, oxadiazole, thiadiazole, triazole, tetrazole, benzofuran, benzothiophene, benzoxazole, benzothiazole, phenyl, pyridine, pyridazine, pyrimidine, pyrazine, triazine, tetrazine, quinoline, cinnoline, quinazoline, quinoxaline, and naphthyridine or a compound of another aryl or heteroaryl group as follows:
    
    






wherein in (1),

    
    
        A is O, NH, or S; B is CH or N, and C is hydrogen or C1-C8 alkyl; or
    
    






wherein in (2),

    
    
        D is N or C optionally substituted by hydrogen or C1-C8 alkyl; or
    
    






wherein in (3),

    
    
        E is NH or CH2; F is O or CO; and G is NH or CH2; or
    
    






wherein in (4),

    
    
        J is O, S or CO; or
    
    






wherein in (5),

    
    
        Q is CH or N;
        M is CH or N; and
        L/(5) is hydrogen, halo, amino, cyano, (C1-C8)alkyl, (C3-C8)cycloalkyl, —CORa′, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′, —SO2Ra′, —SO2NRa′Rb′, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —NRa′NRa′C(O)NRa′Rb′, or —ORa′,
        wherein any (C1-C8)alkyl, (C3-C8)cycloalkyl, group is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′,
        wherein Ra′ and Rb′ are defined as above; or
    
    






wherein in (6),

    
    
        L/(6) is NH or CH2; or
    
    






wherein in (7),

    
    
        M/(7) is hydrogen, halo, amino, cyano, (C1-C8)alkyl, (C3-C8)cycloalkyl, heterocycloalkyl, —CORa′, —CO2Ra′, —CONRa′Rb′, —CONRa′NRa′Rb′, —SO2Ra, —SO2NRa′Rb′, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —NRa′NRa′C(O)NRa′Rb′, or —ORa′,
        wherein any (C1-C8)alkyl, (C3-C8)cycloalkyl, heterocycloalkyl group is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SRa′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′; wherein Ra′ and Rb′ are defined as above; or
    
    






wherein in (8),

    
    
        P is CH2, NH, O, or S; Q/(8) is CH or N; and n is 0-2; or
    
    






wherein in (9),

    
    
        S/(9) and T/(9) are C, or S/(9) is C and T/(9) is N, or S/(9) is N and T/(9) is C;
        R is hydrogen, amino, methyl, trifluoromethyl, halo;
        U is hydrogen, halo, amino, cyano, nitro, trifluoromethyl, (C1-C8)alkyl, (C3-C8)cycloalkyl, —CORa, —CO2Ra′, —CONRa′Rb′, —SO2Ra′, —SO2NRa′Rb′, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —NRa′NRa′Rb′, —NRa′NRa′C(O)Rb′, —ORa′, or 4-(1H-pyrazol-4-yl),
        wherein any (C1-C8)alkyl, or (C3-C8)cycloalkyl group is optionally substituted by 1, 2 or 3 groups independently selected from (C1-C6)alkyl, (C3-C8)cycloalkyl, (C5-C8)cycloalkenyl, (C1-C6)haloalkyl, cyano, —CORa′, —CO2Ra′, —CONRa′Rb′, —SORa′, —SO2Ra′, —SO2NRa′Rb′, nitro, —NRa′Rb′, —NRa′C(O)Rb′, —NRa′C(O)NRa′Rb′, —NRa′C(O)ORa′, —NRa′SO2Rb′, —NRa′SO2NRa′Rb′, —ORa′, —OC(O)Ra′, and —OC(O)NRa′Rb′, wherein Ra′ and Rb′ are defined as above.

Subgroup C of Formula (II)

    
    


R1′ is isopropyl, tert-butyl, cyclobutyl, cyclopentyl, cyclohexyl, (1-methylethyl)cyclopropyl, 1,1-dioxo-tetrahydrothiophene-3-yl, 1-Me-piperidin-4-yl, tetrahydrofuran-3-yl, tetrahydropyran-4-yl, N,N-dimethyl-1-propanaminyl, benzyl, or 4-pyridyl;

    
    
        R2′ is hydrogen, (C1-C3)alkyl, or halo, in which said (C1-C3)alkyl is optionally substituted with one to two groups selected from amino and (C1-C3)alkylamino;
        R7′ is hydrogen, (C1-C3)alkyl, or alkoxy;
        R3′ is H, methyl, or Br; and
        R6′ is methyl, bis(1,1-dimethylethyl), bis(1-methylethyl), cyclopropyl, propyl, dimethylamino, ethylamino, (2-hydroxyethyl)amino, 2-propen-1-ylamino, 1-piperazinyl, 1-piperidinyl, 4-morpholinyl, 4-piperidinylamino, tetrahydro-2H-pyran-4-ylamino, phenylamino, (phenylmethyl)amino, (4-pyridinylmethyl)amino, [2-(2-pyridinylamino)ethyl]amino, 2-(dimethylamino)ethyl]amino, 4-pyridinylamino, 4-(aminocarbonyl)phenyl]amino, 3-hydroxy-3-methyl-1-butyn-1-yl, 4-pyridinylethynyl, phenylethynyl, 2-furanyl, 3-thienyl; 1H-pyrazol-4-yl, 1H-pyrazol-5-yl, 1H-indazol-6-yl, 3-methyl-1H-indazol-5-yl, 1H-1,2,3-benzotriazol-5-yl, 2-oxo-2,3-dihydro-1H-benzimidazol-5-yl, 2-oxo-2,3-dihydro-1H-indol-5-yl, 2-oxo-2,3-dihydro-1H-indol-6-yl, 2,1,3-benzoxadiazol-5-yl, 2-amino-6-quinazolinyl, 2,4-dioxo-1,2,3,4-tetrahydro-5-pyrimidinyl, 2-amino-5-pyrimidinyl, 7-oxo-1,5,6,7-tetrahydro-1,8-naphthyridin-3-yl, phenyl, 2-methylphenyl, 2-nitrophenyl, 2-phenylethyl, 3-aminophenyl, 4-aminophenyl, 4-chlorophenyl, 4-fluorophenyl, 4-(methyloxy)phenyl, 3-(acetylamino)phenyl, 4-(acetylamino)phenyl, 4-(aminocarbonyl)phenyl, 4-(1H-pyrazol-4-yl)phenyl, 4-(aminosulfonyl)phenyl, 4-(methylsulfonyl)phenyl, 4-[(dimethylamino)sulfonyl]phenyl, 4-[(methylamino)carbonyl]phenyl, 4-[(methylamino)sulfonyl]phenyl, 4-[(methylsulfonyl)amino]phenyl, 3-pyridinyl, 4-pyridinyl, 2-(4-morpholinyl)-4-pyridinyl, 2-amino-4-pyridinyl, 5-(methyloxy)-3-pyridinyl, 5-(methylsulfonyl)-3-pyridinyl, 5-[(cyclopropylsulfonyl)amino]-6-(methyloxy)-3-pyridinyl, 5-[(phenylsulfonyl)amino]-3-pyridinyl, 6-(4-methyl-1-piperazinyl)-3-pyridinyl, 6-(4-morpholinyl)-3-pyridinyl, 6-(acetylamino)-3-pyridinyl, 6-(dimethylamino)-3-pyridinyl, 6-(methyloxy)-3-pyridinyl, 6-[(methylamino)carbonyl]-3-pyridinyl, 6-[(methylamino)sulfonyl]-3-pyridinyl, 6-methyl-3-pyridinyl, or 4-pyridinyloxy.
    
    


Representative compounds of the present invention include compounds listed in Tables 1-3. In Table 1, X1 through X4 and Y1 through Y3 are as defined herein for Formula (I). In Table 2, except for n, R6 and R7, variables such as X2 through X4, X, Y1, Y3, Q3, T3, R1, and R2 are as defined herein for Formula (I). In Table 3, R′′′ is T5, —C(O)T5, or S(O)2T5, and the other variables except for n and R7, such as X2 through X4, X, Y1, Y3, R1, R2, R6, T5 and T5a are as defined herein for Formula (I).







TABLE 1











 


Structure of Z













 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 






















TABLE 2











 


Structure of R6













 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 


Cl


Br


OCH3


CH3


 














n is 0, 1, or 2













TABLE 3











 


Structure of R7







sec-butyl


cyclopentyl


isopropyl


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 











n is 0, 1, or 2






For example, compounds having Z from Table 1 also can or may have R6 from Table 2 and/or have R7 from Table 3.
As used herein, “alkyl”, “C1, C2, C3, C4, C5 or C6 alkyl” or “C1-C6 alkyl” is intended to include C1, C2, C3, C4, C5 or C6 straight chain (linear) saturated aliphatic hydrocarbon groups and C3, C4, C5 or C6 branched saturated aliphatic hydrocarbon groups. For example, C1-C6 alkyl is intended to include C1, C2, C3, C4, C5 and C6 alkyl groups. Examples of alkyl include, moieties having from one to six carbon atoms, such as, but not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, s-butyl, t-butyl, n-pentyl, s-pentyl or n-hexyl.
In certain embodiments, a straight chain or branched alkyl has six or fewer carbon atoms (e.g., C1-C6 for straight chain, C3-C6 for branched chain), and in another embodiment, a straight chain or branched alkyl has four or fewer carbon atoms.
As used herein, the term “cycloalkyl” refers to a saturated or unsaturated nonaromatic hydrocarbon mono- or multi-ring (e.g., fused, bridged, or spiro rings) system having 3 to 30 carbon atoms (e.g., C3-C10). Examples of cycloalkyl include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, and adamantyl. The term “heterocycloalkyl” refers to a saturated or unsaturated nonaromatic 3-8 membered monocyclic, 7-12 membered bicyclic (fused, bridged, or spiro rings), or 11-14 membered tricyclic ring system (fused, bridged, or spiro rings) having one or more heteroatoms (such as O, N, S, or Se), unless specified otherwise. Examples of heterocycloalkyl groups include, but are not limited to, piperidinyl, piperazinyl, pyrrolidinyl, dioxanyl, tetrahydrofuranyl, isoindolinyl, indolinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl, triazolidinyl, oxiranyl, azetidinyl, oxetanyl, thietanyl, 1,2,3,6-tetrahydropyridinyl, tetrahydropyranyl, dihydropyranyl, pyranyl, morpholinyl, tetrahydrothiopyranyl, 1,4-diazepanyl, 1,4-oxazepanyl, 2-oxa-5-azabicyclo[2.2.1]heptanyl, 2,5-diazabicyclo[2.2.1]heptanyl, 2-oxa-6-azaspiro[3.3]heptanyl, 2,6-diazaspiro[3.3]heptanyl, 1,4-dioxa-8-azaspiro[4.5]decanyl, 1,4-dioxaspiro[4.5]decanyl, 1-oxaspiro[4.5]decanyl, 1-azaspiro[4.5]decanyl, 3′H-spiro[cyclohexane-1,1′-isobenzofuran]-yl, 7′H-spiro[cyclohexane-1,5′-furo[3,4-b]pyridin]-yl, 3′H-spiro[cyclohexane-1,1′-furo[3,4-c]pyridin]-yl, and the like.
The term “optionally substituted alkyl” refers to unsubstituted alkyl or alkyl having designated substituents replacing one or more hydrogen atoms on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
An “arylalkyl” or an “aralkyl” moiety is an alkyl substituted with an aryl (e.g., phenylmethyl (benzyl)). An “alkylaryl” moiety is an aryl substituted with an alkyl (e.g., methylphenyl).
As used herein, “alkyl linker” is intended to include C1, C2, C3, C4, C5 or C6 straight chain (linear) saturated divalent aliphatic hydrocarbon groups and C3, C4, C5 or C6 branched saturated aliphatic hydrocarbon groups. For example, C1-C6 alkyl linker is intended to include C1, C2, C3, C4, C5 and C6 alkyl linker groups. Examples of alkyl linker include, moieties having from one to six carbon atoms, such as, but not limited to, methyl (—CH2—), ethyl (—CH2CH2—), n-propyl (—CH2CH2CH2—), i-propyl (—CHCH3CH2—), n-butyl (—CH2CH2CH2CH2—), s-butyl (—CHCH3CH2CH2—), i-butyl (—C(CH3)2CH2—), n-pentyl (—CH2CH2CH2CH2CH2—), s-pentyl (—CHCH3CH2CH2CH2—) or n-hexyl (—CH2CH2CH2CH2CH2CH2—).
“Alkenyl” includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double bond. For example, the term “alkenyl” includes straight chain alkenyl groups (e.g., ethenyl, propenyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl), and branched alkenyl groups.
In certain embodiments, a straight chain or branched alkenyl group has six or fewer carbon atoms in its backbone (e.g., C2-C6 for straight chain, C3-C6 for branched chain). The term “C2-C6” includes alkenyl groups containing two to six carbon atoms. The term “C3-C6” includes alkenyl groups containing three to six carbon atoms.
The term “optionally substituted alkenyl” refers to unsubstituted alkenyl or alkenyl having designated substituents replacing one or more hydrogen atoms on one or more hydrocarbon backbone carbon atoms. Such substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
“Alkynyl” includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but which contain at least one triple bond. For example, “alkynyl” includes straight chain alkynyl groups (e.g., ethynyl, propynyl, butyryl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl), and branched alkynyl groups. In certain embodiments, a straight chain or branched alkynyl group has six or fewer carbon atoms in its backbone (e.g., C2-C6 for straight chain, C3-C6 for branched chain). The term “C2-C6” includes alkynyl groups containing two to six carbon atoms. The term “C3-C6” includes alkynyl groups containing three to six carbon atoms.
The term “optionally substituted alkynyl” refers to unsubstituted alkynyl or alkynyl having designated substituents replacing one or more hydrogen atoms on one or more hydrocarbon backbone carbon atoms. Such substituents can include, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
Other optionally substituted moieties (such as optionally substituted cycloalkyl, heterocycloalkyl, aryl, or heteroaryl) include both the unsubstituted moieties and the moieties having one or more of the designated substituents. For example, substituted heterocycloalkyl includes those substituted with one or more alkyl groups, such as 2,2,6,6-tetramethyl-piperidinyl and 2,2,6,6-tetramethyl-1,2,3,6-tetrahydropyridinyl.
“Aryl” includes groups with aromaticity, including “conjugated,” or multicyclic systems with at least one aromatic ring and do not contain any heteroatom in the ring structure. Examples include phenyl, benzyl, 1,2,3,4-tetrahydronaphthalenyl, etc.
“Heteroaryl” groups are aryl groups, as defined above, except having from one to four heteroatoms in the ring structure, and may also be referred to as “aryl heterocycles” or “heteroaromatics.” As used herein, the term “heteroaryl” is intended to include a stable 5-, 6-, or 7-membered monocyclic or 7-, 8-, 9-, 10-, 11- or 12-membered bicyclic aromatic heterocyclic ring which consists of carbon atoms and one or more heteroatoms, e.g., 1 or 1-2 or 1-3 or 1-4 or 1-5 or 1-6 heteroatoms, or e.g., 1, 2, 3, 4, 5, or 6 heteroatoms, independently selected from the group consisting of nitrogen, oxygen and sulfur. The nitrogen atom may be substituted or unsubstituted (i.e., N or NR wherein R is H or other substituents, as defined). The nitrogen and sulfur heteroatoms may optionally be oxidized (i.e., N→O and S(O)p, where p=1 or 2). It is to be noted that total number of S and O atoms in the aromatic heterocycle is not more than 1.
Examples of heteroaryl groups include pyrrole, furan, thiophene, thiazole, isothiazole, imidazole, triazole, tetrazole, pyrazole, oxazole, isoxazole, pyridine, pyrazine, pyridazine, pyrimidine, and the like.
Furthermore, the terms “aryl” and “heteroaryl” include multicyclic aryl and heteroaryl groups, e.g., tricyclic, bicyclic, e.g., naphthalene, benzoxazole, benzodioxazole, benzothiazole, benzoimidazole, benzothiophene, quinoline, isoquinoline, naphthrydine, indole, benzofuran, purine, benzofuran, deazapurine, indolizine.
In the case of multicyclic aromatic rings, only one of the rings needs to be aromatic (e.g., 2,3-dihydroindole), although all of the rings may be aromatic (e.g., quinoline). The second ring can also be fused or bridged.
The cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring can be substituted at one or more ring positions (e.g., the ring-forming carbon or heteroatom such as N) with such substituents as described above, for example, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkoxy, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, alkylaminocarbonyl, aralkylaminocarbonyl, alkenylaminocarbonyl, alkylcarbonyl, arylcarbonyl, aralkylcarbonyl, alkenylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylthiocarbonyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety. Aryl and heteroaryl groups can also be fused or bridged with alicyclic or heterocyclic rings, which are not aromatic so as to form a multicyclic system (e.g., tetralin, methylenedioxyphenyl, such as benzo[d][1,3]dioxole-5-yl).
As used herein, “carbocycle” or “carbocyclic ring” is intended to include any stable monocyclic, bicyclic or tricyclic ring having the specified number of carbons, any of which may be saturated, unsaturated, or aromatic. Carbocycle includes cycloalkyl and aryl. For example, a C3-C14 carbocycle is intended to include a monocyclic, bicyclic or tricyclic ring having 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 carbon atoms. Examples of carbocycles include, but are not limited to, cyclopropyl, cyclobutyl, cyclobutenyl, cyclopentyl, cyclopentenyl, cyclohexyl, cycloheptenyl, cycloheptyl, cycloheptenyl, adamantyl, cyclooctyl, cyclooctenyl, cyclooctadienyl, fluorenyl, phenyl, naphthyl, indanyl, adamantyl and tetrahydronaphthyl. Bridged rings are also included in the definition of carbocycle, including, for example, [3.3.0]bicyclooctane, [4.3.0]bicyclononane, and [4.4.0]bicyclodecane and [2.2.2]bicyclooctane. A bridged ring occurs when one or more carbon atoms link two non-adjacent carbon atoms. In one embodiment, bridge rings are one or two carbon atoms. It is noted that a bridge always converts a monocyclic ring into a tricyclic ring. When a ring is bridged, the substituents recited for the ring may also be present on the bridge. Fused (e.g., naphthyl, tetrahydronaphthyl) and spiro rings are also included.
As used herein, “heterocycle” or “heterocyclic group” includes any ring structure (saturated, unsaturated, or aromatic) which contains at least one ring heteroatom (e.g., N, O or S). Heterocycle includes heterocycloalkyl and heteroaryl. Examples of heterocycles include, but are not limited to, morpholine, pyrrolidine, tetrahydrothiophene, piperidine, piperazine, oxetane, pyran, tetrahydropyran, azetidine, and tetrahydrofuran.
Examples of heterocyclic groups include, but are not limited to, acridinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl, benzothiophenyl, benzoxazolyl, benzoxazolinyl, benzthiazolyl, benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl, benzimidazolinyl, carbazolyl, 4aH-carbazolyl, carbolinyl, chromanyl, chromenyl, cinnolinyl, decahydroquinolinyl, 2H,6H-1,5,2-dithiazinyl, dihydrofuro[2,3-b]tetrahydrofuran, furanyl, furazanyl, imidazolidinyl, imidazolinyl, imidazolyl, 1H-indazolyl, indolenyl, indolinyl, indolizinyl, indolyl, 3H-indolyl, isatinoyl, isobenzofuranyl, isochromanyl, isoindazolyl, isoindolinyl, isoindolyl, isoquinolinyl, isothiazolyl, isoxazolyl, methylenedioxyphenyl (e.g., benzo[d][1,3]dioxole-5-yl), morpholinyl, naphthyridinyl, octahydroisoquinolinyl, oxadiazolyl, 1,2,3-oxadiazolyl, 1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl, 1,2,4-oxadiazol5(4H)-one, oxazolidinyl, oxazolyl, oxindolyl, pyrimidinyl, phenanthridinyl, phenanthrolinyl, phenazinyl, phenothiazinyl, phenoxathinyl, phenoxazinyl, phthalazinyl, piperazinyl, piperidinyl, piperidonyl, 4-piperidonyl, piperonyl, pteridinyl, purinyl, pyranyl, pyrazinyl, pyrazolidinyl, pyrazolinyl, pyrazolyl, pyridazinyl, pyridooxazole, pyridoimidazole, pyridothiazole, pyridinyl, pyridyl, pyrimidinyl, pyrrolidinyl, pyrrolinyl, 2H-pyrrolyl, pyrrolyl, quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, quinuclidinyl, tetrahydrofuranyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl, tetrazolyl, 6H-1,2,5-thiadiazinyl, 1,2,3-thiadiazolyl, 1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl, thianthrenyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl, thienoimidazolyl, thiophenyl, triazinyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,2,5-triazolyl, 1,3,4-triazolyl and xanthenyl.
The term “azole,” as used herein, refers to a class of five-membered nitrogen heterocyclic ring compounds containing at least another non-carbon atom of nitrogen, sulfur, or oxygen.
The term “substituted,” as used herein, means that any one or more hydrogen atoms on the designated atom is replaced with a selection from the indicated groups, provided that the designated atom's normal valency is not exceeded, and that the substitution results in a stable compound. When a substituent is oxo or keto (i.e., ═O), then 2 hydrogen atoms on the atom are replaced. Keto substituents are not present on aromatic moieties. Ring double bonds, as used herein, are double bonds that are formed between two adjacent ring atoms (e.g., C═C, C═N or N═N). “Stable compound” and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
When a bond to a substituent is shown to cross a bond connecting two atoms in a ring, then such substituent may be bonded to any atom in the ring. When a substituent is listed without indicating the atom via which such substituent is bonded to the rest of the compound of a given formula, then such substituent may be bonded via any atom in such formula. Combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds.
When any variable (e.g., R) occurs more than one time in any constituent or formula for a compound, its definition at each occurrence is independent of its definition at every other occurrence. Thus, for example, if a group is shown to be substituted with 0-2 R moieties, then the group may optionally be substituted with up to two R moieties and R at each occurrence is selected independently from the definition of R. Also, combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds.
The term “hydroxy” or “hydroxyl” includes groups with an —OH or —O−.
As used herein, “halo” or “halogen” refers to fluoro, chloro, bromo and iodo. The term “perhalogenated” generally refers to a moiety wherein all hydrogen atoms are replaced by halogen atoms. The term “haloalkyl” or “haloalkoxyl” refers to an alkyl or alkoxyl substituted with one or more halogen atoms.
The term “carbonyl” includes compounds and moieties which contain a carbon connected with a double bond to an oxygen atom. Examples of moieties containing a carbonyl include, but are not limited to, aldehydes, ketones, carboxylic acids, amides, esters, anhydrides, etc.
The term “carboxyl” refers to —COOH or its C1-C6 alkyl ester.
“Acyl” includes moieties that contain the acyl radical (R—C(O)—) or a carbonyl group. “Substituted acyl” includes acyl groups where one or more of the hydrogen atoms are replaced by, for example, alkyl groups, alkynyl groups, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
“Aroyl” includes moieties with an aryl or heteroaromatic moiety bound to a carbonyl group. Examples of aroyl groups include phenylcarboxy, naphthyl carboxy, etc.
“Alkoxyalkyl,” “alkylaminoalkyl,” and “thioalkoxyalkyl” include alkyl groups, as described above, wherein oxygen, nitrogen, or sulfur atoms replace one or more hydrocarbon backbone carbon atoms.
The term “alkoxy” or “alkoxyl” includes substituted and unsubstituted alkyl, alkenyl and alkynyl groups covalently linked to an oxygen atom. Examples of alkoxy groups or alkoxyl radicals include, but are not limited to, methoxy, ethoxy, isopropyloxy, propoxy, butoxy and pentoxy groups. Examples of substituted alkoxy groups include halogenated alkoxy groups. The alkoxy groups can be substituted with groups such as alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino (including alkylamino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moieties. Examples of halogen substituted alkoxy groups include, but are not limited to, fluoromethoxy, difluoromethoxy, trifluoromethoxy, chloromethoxy, dichloromethoxy and trichloromethoxy.
The term “ether” or “alkoxy” includes compounds or moieties which contain an oxygen bonded to two carbon atoms or heteroatoms. For example, the term includes “alkoxyalkyl,” which refers to an alkyl, alkenyl, or alkynyl group covalently bonded to an oxygen atom which is covalently bonded to an alkyl group.
The term “ester” includes compounds or moieties which contain a carbon or a heteroatom bound to an oxygen atom which is bonded to the carbon of a carbonyl group. The term “ester” includes alkoxycarboxy groups such as methoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl, pentoxycarbonyl, etc.
The term “thioalkyl” includes compounds or moieties which contain an alkyl group connected with a sulfur atom. The thioalkyl groups can be substituted with groups such as alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, carboxyacid, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, amino (including alkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moieties.
The term “thiocarbonyl” or “thiocarboxy” includes compounds and moieties which contain a carbon connected with a double bond to a sulfur atom.
The term “thioether” includes moieties which contain a sulfur atom bonded to two carbon atoms or heteroatoms. Examples of thioethers include, but are not limited to alkthioalkyls, alkthioalkenyls, and alkthioalkynyls. The term “alkthioalkyls” include moieties with an alkyl, alkenyl, or alkynyl group bonded to a sulfur atom which is bonded to an alkyl group. Similarly, the term “alkthioalkenyls” refers to moieties wherein an alkyl, alkenyl or alkynyl group is bonded to a sulfur atom which is covalently bonded to an alkenyl group; and alkthioalkynyls” refers to moieties wherein an alkyl, alkenyl or alkynyl group is bonded to a sulfur atom which is covalently bonded to an alkynyl group.
As used herein, “amine” or “amino” refers to —NH2. “Alkylamino” includes groups of compounds wherein the nitrogen of —NH2 is bound to at least one alkyl group. Examples of alkylamino groups include benzylamino, methylamino, ethylamino, phenethylamino, etc. “Dialkylamino” includes groups wherein the nitrogen of —NH2 is bound to two alkyl groups. Examples of dialkylamino groups include, but are not limited to, dimethylamino and diethylamino. “Arylamino” and “diarylamino” include groups wherein the nitrogen is bound to at least one or two aryl groups, respectively. “Aminoaryl” and “aminoaryloxy” refer to aryl and aryloxy substituted with amino. “Alkylarylamino,” “alkylaminoaryl” or “arylaminoalkyl” refers to an amino group which is bound to at least one alkyl group and at least one aryl group. “Alkaminoalkyl” refers to an alkyl, alkenyl, or alkynyl group bound to a nitrogen atom which is also bound to an alkyl group. “Acylamino” includes groups wherein nitrogen is bound to an acyl group. Examples of acylamino include, but are not limited to, alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido groups.
The term “amide” or “aminocarboxy” includes compounds or moieties that contain a nitrogen atom that is bound to the carbon of a carbonyl or a thiocarbonyl group. The term includes “alkaminocarboxy” groups that include alkyl, alkenyl or alkynyl groups bound to an amino group which is bound to the carbon of a carbonyl or thiocarbonyl group. It also includes “arylaminocarboxy” groups that include aryl or heteroaryl moieties bound to an amino group that is bound to the carbon of a carbonyl or thiocarbonyl group. The terms “alkylaminocarboxy”, “alkenylaminocarboxy”, “alkynylaminocarboxy” and “arylaminocarboxy” include moieties wherein alkyl, alkenyl, alkynyl and aryl moieties, respectively, are bound to a nitrogen atom which is in turn bound to the carbon of a carbonyl group. Amides can be substituted with substituents such as straight chain alkyl, branched alkyl, cycloalkyl, aryl, heteroaryl or heterocycle. Substituents on amide groups may be further substituted.
Compounds of the present invention that contain nitrogens can be converted to N-oxides by treatment with an oxidizing agent (e.g., 3-chloroperoxybenzoic acid (mCPBA) and/or hydrogen peroxides) to afford other compounds of the present invention. Thus, all shown and claimed nitrogen-containing compounds are considered, when allowed by valency and structure, to include both the compound as shown and its N-oxide derivative (which can be designated as N→O or N+—O−). Furthermore, in other instances, the nitrogens in the compounds of the present invention can be converted to N-hydroxy or N-alkoxy compounds. For example, N-hydroxy compounds can be prepared by oxidation of the parent amine by an oxidizing agent such as m-CPBA. All shown and claimed nitrogen-containing compounds are also considered, when allowed by valency and structure, to cover both the compound as shown and its N-hydroxy (i.e., N—OH) and N-alkoxy (i.e., N—OR, wherein R is substituted or unsubstituted C1-C6 alkyl, C1-C6 alkenyl, C1-C6 alkynyl, 3-14-membered carbocycle or 3-14-membered heterocycle) derivatives.
In the present specification, the structural formula of the compound represents a certain isomer for convenience in some cases, but the present invention includes all isomers, such as geometrical isomers, optical isomers based on an asymmetrical carbon, stereoisomers, tautomers, and the like, it being understood that not all isomers may have the same level of activity. In addition, a crystal polymorphism may be present for the compounds represented by the formula. It is noted that any crystal form, crystal form mixture, or anhydride or hydrate thereof is included in the scope of the present invention.
“Isomerism” means compounds that have identical molecular formulae but differ in the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers.” Stereoisomers that are not mirror images of one another are termed “diastereoisomers,” and stereoisomers that are non-superimposable mirror images of each other are termed “enantiomers” or sometimes optical isomers. A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a “racemic mixture.”
A carbon atom bonded to four nonidentical substituents is termed a “chiral center.”
“Chiral isomer” means a compound with at least one chiral center. Compounds with more than one chiral center may exist either as an individual diastereomer or as a mixture of diastereomers, termed “diastereomeric mixture.” When one chiral center is present, a stereoisomer may be characterized by the absolute configuration (R or S) of that chiral center. Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. The substituents attached to the chiral center under consideration are ranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog. (Cahn et al., Angew. Chem. Inter. Edit. 1966, 5, 385; errata 511; Cahn et al., Angew. Chem. 1966, 78, 413; Cahn and Ingold, J. Chem. Soc. 1951 (London), 612; Cahn et al., Experientia 1956, 12, 81; Cahn, J. Chem. Educ. 1964, 41, 116).
“Geometric isomer” means the diastereomers that owe their existence to hindered rotation about double bonds or a cycloalkyl linker (e.g., 1,3-cylcobutyl). These configurations are differentiated in their names by the prefixes cis and trans, or Z and E, which indicate that the groups are on the same or opposite side of the double bond in the molecule according to the Cahn-Ingold-Prelog rules.
It is to be understood that the compounds of the present invention may be depicted as different chiral isomers or geometric isomers. It should also be understood that when compounds have chiral isomeric or geometric isomeric forms, all isomeric forms are intended to be included in the scope of the present invention, and the naming of the compounds does not exclude any isomeric forms, it being understood that not all isomers may have the same level of activity.
Furthermore, the structures and other compounds discussed in this invention include all atropic isomers thereof, it being understood that not all atropic isomers may have the same level of activity. “Atropic isomers” are a type of stereoisomer in which the atoms of two isomers are arranged differently in space. Atropic isomers owe their existence to a restricted rotation caused by hindrance of rotation of large groups about a central bond. Such atropic isomers typically exist as a mixture, however as a result of recent advances in chromatography techniques, it has been possible to separate mixtures of two atropic isomers in select cases.
“Tautomer” is one of two or more structural isomers that exist in equilibrium and is readily converted from one isomeric form to another. This conversion results in the formal migration of a hydrogen atom accompanied by a switch of adjacent conjugated double bonds. Tautomers exist as a mixture of a tautomeric set in solution. In solutions where tautomerization is possible, a chemical equilibrium of the tautomers will be reached. The exact ratio of the tautomers depends on several factors, including temperature, solvent and pH. The concept of tautomers that are interconvertable by tautomerizations is called tautomerism.
Of the various types of tautomerism that are possible, two are commonly observed. In keto-enol tautomerism a simultaneous shift of electrons and a hydrogen atom occurs. Ring-chain tautomerism arises as a result of the aldehyde group (—CHO) in a sugar chain molecule reacting with one of the hydroxy groups (—OH) in the same molecule to give it a cyclic (ring-shaped) form as exhibited by glucose.
Common tautomeric pairs are: ketone-enol, amide-nitrile, lactam-lactim, amide-imidic acid tautomerism in heterocyclic rings (e.g., in nucleobases such as guanine, thymine and cytosine), imine-enamine and enamine-enamine.
It is to be understood that the compounds of the present invention may be depicted as different tautomers. It should also be understood that when compounds have tautomeric forms, all tautomeric forms are intended to be included in the scope of the present invention, and the naming of the compounds does not exclude any tautomer form. It will be understood that certain tautomers may have a higher level of activity than others.
The term “crystal polymorphs”, “polymorphs” or “crystal forms” means crystal structures in which a compound (or a salt or solvate thereof) can crystallize in different crystal packing arrangements, all of which have the same elemental composition. Different crystal forms usually have different X-ray diffraction patterns, infrared spectral, melting points, density hardness, crystal shape, optical and electrical properties, stability and solubility. Recrystallization solvent, rate of crystallization, storage temperature, and other factors may cause one crystal form to dominate. Crystal polymorphs of the compounds can be prepared by crystallization under different conditions.
The compounds of any Formula described herein include the compounds themselves, as well as their salts, and their solvates, if applicable. A salt, for example, can be formed between an anion and a positively charged group (e.g., amino) on an azole compound. Suitable anions include chloride, bromide, iodide, sulfate, bisulfate, sulfamate, nitrate, phosphate, citrate, methanesulfonate, trifluoroacetate, glutamate, glucuronate, glutarate, malate, maleate, succinate, fumarate, tartrate, tosylate, salicylate, lactate, naphthalenesulfonate, and acetate (e.g., trifluoroacetate). The term “pharmaceutically acceptable anion” refers to an anion suitable for forming a pharmaceutically acceptable salt. Likewise, a salt can also be formed between a cation and a negatively charged group (e.g., carboxylate) on an azole compound. Suitable cations include sodium ion, potassium ion, magnesium ion, calcium ion, and an ammonium cation such as tetramethylammonium ion. The azole compounds also include those salts containing quaternary nitrogen atoms.
Additionally, the compounds of the present invention, for example, the salts of the compounds, can exist in either hydrated or unhydrated (the anhydrous) form or as solvates with other solvent molecules. Nonlimiting examples of hydrates include monohydrates, dihydrates, etc. Nonlimiting examples of solvates include ethanol solvates, acetone solvates, etc.
“Solvate” means solvent addition forms that contain either stoichiometric or non stoichiometric amounts of solvent. Some compounds have a tendency to trap a fixed molar ratio of solvent molecules in the crystalline solid state, thus forming a solvate. If the solvent is water the solvate formed is a hydrate; and if the solvent is alcohol, the solvate formed is an alcoholate. Hydrates are formed by the combination of one or more molecules of water with one molecule of the substance in which the water retains its molecular state as H2O.
As used herein, the term “analog” refers to a chemical compound that is structurally similar to another but differs slightly in composition (as in the replacement of one atom by an atom of a different element or in the presence of a particular functional group, or the replacement of one functional group by another functional group). Thus, an analog is a compound that is similar or comparable in function and appearance, but not in structure or origin to the reference compound.
As defined herein, the term “derivative” refers to compounds that have a common core structure, and are substituted with various groups as described herein. For example, all of the compounds represented by Formula (I) are azole compounds, and have Formula (I) as a common core.
The term “bioisostere” refers to a compound resulting from the exchange of an atom or of a group of atoms with another, broadly similar, atom or group of atoms. The objective of a bioisosteric replacement is to create a new compound with similar biological properties to the parent compound. The bioisosteric replacement may be physicochemically or topologically based. Examples of carboxylic acid bioisosteres include, but are not limited to, acyl sulfonimides, tetrazoles, sulfonates and phosphonates. See, e.g., Patani and LaVoie, Chem. Rev. 96, 3147-3176, 1996.
The present invention is intended to include all isotopes of atoms occurring in the present compounds. Isotopes include those atoms having the same atomic number but different mass numbers. By way of general example and without limitation, isotopes of hydrogen include tritium and deuterium, and isotopes of carbon include C-13 and C-14.
The present invention provides methods for the synthesis of the compounds of any of the Formulae described herein. The present invention also provides detailed methods for the synthesis of various disclosed compounds of the present invention according to the following schemes as shown in the Examples.
Throughout the description, where compositions are described as having, including, or comprising specific components, it is contemplated that compositions also consist essentially of, or consist of, the recited components. Similarly, where methods or processes are described as having, including, or comprising specific process steps, the processes also consist essentially of, or consist of, the recited processing steps. Further, it should be understood that the order of steps or order for performing certain actions is immaterial so long as the invention remains operable. Moreover, two or more steps or actions can be conducted simultaneously.
The synthetic processes of the invention can tolerate a wide variety of functional groups, therefore various substituted starting materials can be used. The processes generally provide the desired final compound at or near the end of the overall process, although it may be desirable in certain instances to further convert the compound to a pharmaceutically acceptable salt thereof.
Compounds of the present invention can be prepared in a variety of ways using commercially available starting materials, compounds known in the literature, or from readily prepared intermediates, by employing standard synthetic methods and procedures either known to those skilled in the art, or which will be apparent to the skilled artisan in light of the teachings herein. Standard synthetic methods and procedures for the preparation of organic molecules and functional group transformations and manipulations can be obtained from the relevant scientific literature or from standard textbooks in the field. Although not limited to any one or several sources, classic texts such as Smith, M. B., March, J., March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th edition, John Wiley & Sons: New York, 2001; Greene, T. W., Wuts, P. G. M., Protective Groups in Organic Synthesis, 3rd edition, John Wiley & Sons: New York, 1999; R. Larock, Comprehensive Organic Transformations, VCH Publishers (1989); L. Fieser and M. Fieser, Fieser and Fieser's Reagents for Organic Synthesis, John Wiley and Sons (1994); and L. Paquette, ed., Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons (1995), incorporated by reference herein, are useful and recognized reference textbooks of organic synthesis known to those in the art. The following descriptions of synthetic methods are designed to illustrate, but not to limit, general procedures for the preparation of compounds of the present invention.
Compounds of the present invention can be conveniently prepared by a variety of methods familiar to those skilled in the art or those described in WO 2012/142504, WO 2012/142513 and WO 2012/118812, which are incorporated herein by reference. The compounds of this invention having any of the Formulae described herein may be prepared according to the procedures illustrated in Schemes 1-4 below, from commercially available starting materials or starting materials which can be prepared using literature procedures. The R groups (such as R6, R7, R8, and R11) in Schemes 1-4 are as defined in any Formula described herein, unless otherwise specified.
One of ordinary skill in the art will note that, during the reaction sequences and synthetic schemes described herein, the order of certain steps may be changed, such as the introduction and removal of protecting groups.
One of ordinary skill in the art will recognize that certain groups may require protection from the reaction conditions via the use of protecting groups. Protecting groups may also be used to differentiate similar functional groups in molecules. A list of protecting groups and how to introduce and remove these groups can be found in Greene, T. W., Wuts, P. G. M., Protective Groups in Organic Synthesis, 3rd edition, John Wiley & Sons: New York, 1999.
Preferred protecting groups include, but are not limited to:

    
    
        For a hydroxyl moiety: TBS, benzyl, THP, Ac
        For carboxylic acids: benzyl ester, methyl ester, ethyl ester, allyl ester
        For amines: Cbz, BOC, DMB
        For diols: Ac (×2) TBS (×2), or when taken together acetonides
        For thiols: Ac
        For benzimidazoles: SEM, benzyl, PMB, DMB
        For aldehydes: di-alkyl acetals such as dimethoxy acetal or diethyl acetyl.
    
    


In the reaction schemes described herein, multiple stereoisomers may be produced. When no particular stereoisomer is indicated, it is understood to mean all possible stereoisomers that could be produced from the reaction. A person of ordinary skill in the art will recognize that the reactions can be optimized to give one isomer preferentially, or new schemes may be devised to produce a single isomer. If mixtures are produced, techniques such as preparative thin layer chromatography, preparative HPLC, preparative chiral HPLC, or preparative SFC may be used to separate the isomers.
The following abbreviations are used throughout the specification and are defined below:

    
    
        AA ammonium acetate
        ACN acetonitrile
        Ac acetyl
        AcOH acetic acid
        atm atmosphere
        aq. Aqueous
        BID or b.i.d. bis in die (twice a day)
        tBuOK potassium t-butoxide
        Bn benzyl
        BOC tert-butoxy carbonyl
        BOP (benzotriazol-1-yloxy)tris(dimethylamino)-phosphoniumhexafluorophosphate
        Cbz benzyloxy carbonyl
        CDCl3 deuterated chloroform
        CH2Cl2 dichloromethane
        COMU (1-Cyano-2-ethoxy-2-oxoethylidenaminooxy)dimethyl-amino-morpholino-carbenium hexafluorophosphate
        d days
        DBU 1,8-diazabicyclo[5.4.0]undec-7-ene
        DCE 1,2 dichloroethane
        DCM dichloromethane
        DEAD Diethyl azodicarboxylate
        DIAD Diisopropyl azodicarboxylate
        DiBAL-H diisobutyl aluminium hydride
        DIPEA N,N-diisopropylethylamine (Hunig's base)
        DMA Dimethylacetamide
        DMAP N, N dimethyl-4-aminopyridine
        DMB 2,4 dimethoxy benzyl
        DMF N,N-Dimethylformamide
        DMSO Dimethyl sulfoxide
        DPPA Diphenylphosphonic azide
        EA or EtOAc Ethyl acetate
        EDC or EDCI N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide
        Et2O diethyl ether
        ELS Evaporative Light Scattering
        ESI− Electrospray negative mode
        ESI+ Electrospray positive mode
        Et3N or TEA triethylamine
        EtOH ethanol
        FA formic acid
        FC or FCC Flash chromatography
        h hours
        H2O water
        HATU O-(7-Azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate
        HOAT 1-Hydroxy-7-azabenzotriazole
        HOBt 1-Hydroxybenzotriazole
        HO-Su N-Hydroxysuccinimide
        HCl hydrogen chloride or hydrochloric acid
        HPLC High performance liquid chromatography
        K2CO3 potassium carbonate
        KHMDs Potassium hexamethyldisilazide
        LC/MS or LC-MS Liquid chromatography mass spectrum
        LDA Lithium diisopropylamide
        LiHMDs Lithium hexamethyldisilazide
        LG leaving group
        M Molar
        m/z mass/charge ratio
        m-CPBA meta-chloroperbenzoic acid
        MeCN Acetonitrile
        MeOD d4-methanol
        MeI Methyl iodide
        MS3 Å 3 Å molecular sieves
        MgSO4 Magnesium Sulfate
        min minutes
        Ms Mesyl
        MsCl Mesyl chloride
        MsO Mesylate
        MS Mass Spectrum
        MWI microwave irradiation
        Na2CO3 sodium carbonate
        Na2SO4 sodium sulfate
        NaHCO3 sodium bicarbonate
        NaHMDs Sodium hexamethyldisilazide
        NaOH sodium hydroxide
        NaHCO3 sodium bicarbonate
        Na2SO4 sodium sulfate
        NIS N-iodosuccinimide
        NMR Nuclear Magnetic Resonance
        o/n or O/N overnight
        Pd/C Palladium on carbon
        Pd(dppf)Cl2.DCM [1,1′-Bis(diphenylphosphino)ferrocene]dichloropalladium(II), complex with dichloromethane
        PPAA 1-Propanephosphonic acid cyclic anhydride
        Pd(OH)2 Palladium dihydroxide
        PE Petroleum Ether
        PG protecting group
        PMB para methoxybenzyl
        ppm parts per million
        p.o. per os (oral administration)
        prep HPLC preparative High Performance Liquid Chromatography
        prep TLC preparative thin layer chromatography
        p-TsOH para-toluenesulfonic acid
        PYBOP (Benzotriazol-1-yloxy)tripyrrolidinophosphonium Hexafluorophosphate
        QD or q.d. quaque die (once a day)
        RBF round bottom flask
        RP-HPLC Reverse phase High Performance liquid chromatography
        Rt or RT Room temperature
        SEM (Trimethylsilyl)ethoxymethyl
        SEMCl (Trimethylsilyl)ethoxymethyl chloride
        SFC Super critical chromatography
        SGC silica gel chromatography
        STAB Sodium triacetoxy borohydride
        TBAF tetra-n-butylammonium fluoride
        TBME tert-Butyl methyl ether
        TEA Triethylamine
        TFA trifluoroacetic acid
        TfO triflate
        THF tetrahydrofuran
        THP tetrahydropyran
        TID or t.i.d ter in die (three times a day)
        TLC thin layer chromatography
        TMSCl Trimethylsilyl chloride
        Ts tosyl
        TsOH tosic acid
        UV ultraviolet
    
    






Scheme 1 shows the synthesis of modified azole-amine following a general route that utilizes well-established chemistry. Azole-nitrile (e.g., 2,6-dimethyl-2H-indazole-7-carbonitrile, the synthetic method of which is shown in Scheme 2; also see Example 1), many of which are commercially available or can be made by known methods, is reduced to an amine using an appropriate reducing agent, such as Raney-Nickel in the presence of hydrogen, in a protic solvent, such as methanol containing ammonia, at an appropriate temperature, such as 22° C. The obtained amine compound can be used in the subsequent coupling reaction to make the desired compounds.




Scheme 2 shows the synthesis of modified pyrazolopyridine analogs following a general route that utilizes well-established chemistry. Condensation of 1H-pyrazol-3-amine with sodium (E)-1,4-diethoxy-1,4-dioxobut-2-en-2-olate in a polar solvent such as water using a mild acid catalyst such as acetic acid can provide the hydroxyl-pyrazolopyridine (Step 1). The hydroxyl group can then be converted to a leaving group “X” such as bromide using phosphoryl tribromide at elevated temperatures in an appropriate polar solvent such as acetonitrile to give the bromide (Step 2). Introduction of the R7 can be done using an appropriate R7-LG where LG is a leaving group such as OTs or Br. Subjecting the intermediate to R7-LG in the presence of a mild base such as potassium carbonate in an appropriate polar solvent such as acetonitrile gives the desired substituted pyrazolopyridine (Step 3). A variety of R6 substituents can then be introduced using standard transition metal-based protocols that rely upon a leaving group such as a bromide as a connection point or through direct SNAr displacement of the bromide with a nucleophile. The bromide can be combined with an appropriate boronic ester derivative, in the presence of a mild base and a palladium catalyst in a polar solvent such as dioxane/water, at elevated temperature to give the desired pyrazolopyridine ester (Step 4). Alternatively, the bromide can be combined with a nucleophile such as an amine in the presence of a mild base such as potassium carbonate in a polar solvent such as acetone to give the desired pyrazolopyridine ester. The ester moiety can be converted to an amide using a standard two step protocol. The ester can be hydrolyzed to the corresponding acid using a suitable base such as sodium hydroxide in a polar solvent such as ethanol (Step 5). The acid is then subjected to an amide coupling reaction whereupon the appropriate amine is added along with a suitable amide coupling reagent such as PYBOP in a suitable solvent such as DMSO to give the desired amide (Step 6).




Scheme 3 shows the synthesis of modified indazole analogs following a general route that utilizes well-established chemistry. Introduction of a nitro group to a tolyl compound can be achieved using standard nitration conditions such as nitric acid in sulfuric acid (Step 1). The acid can be esterified by treatment with an alkylating agent such as methyliodide in the presence of a base such as sodium carbonate in an appropriate polar solvent such as DMF (Step 2). Reduction of the nitro group using an appropriate reducing agent such as iron with an acid such as ammonium chloride in a protic solvent such as ethanol can provide an aniline (Step 3). Diazotization with an appropriate reagent such as sodium nitrite in a polar solvent such as acetic acid can lead to cyclization to provide an indazole (Step 4). It will be apparent to one skilled in the art that there are multiple ways to synthesize indazoles (J. Org. Chem. 2006, 71, 8166-8172). Introduction of the R7 to the indazole can be done using an appropriate R7-LG where LG is a leaving group such as OTs or Br. Subjecting the intermediate to R7-LG in the presence of a mild base such as cesium carbonate in an appropriate polar solvent such as DMF can give the desired R7-substituted indazole ester (Step 5). The ester moiety can be converted to an amide using a standard two step protocol. The ester can be hydrolyzed to the corresponding acid using a suitable base such as sodium hydroxide in a polar solvent such as ethanol (Step 6). The acid can then reacted with a standard amide coupling reaction whereupon the appropriate amine can be added along with a suitable amide coupling reagent such as PYBOP in a suitable solvent such as DMSO to give the desired amide (Step 7).




When R6 is an appropriate group such as bromide or triflate, a variety of substituents could then be introduced using standard transition metal-based protocols. For example, the bromide can be combined with an appropriate boronic ester derivative, in the presence of a mild base and a palladium catalyst in a polar solvent such as dioxane/water, at elevated temperature to give the desired indazole (Scheme 4).
A person of ordinary skill in the art will recognize that in the above schemes the order of many of the steps are interchangeable.
Compounds of the present invention inhibit the histone methyltransferase activity of EZH2 or a mutant thereof and, accordingly, in one aspect of the invention, certain compounds disclosed herein are candidates for treating, or preventing certain conditions and diseases, in which EZH2 plays a role. The present invention provides methods for treating conditions and diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, wherein said methylation status is mediated at least in part by the activity of EZH2. Modulation of the methylation status of histones can in turn influence the level of expression of target genes activated by methylation, and/or target genes suppressed by methylation. The method includes administering to a subject in need of such treatment, a therapeutically effective amount of a compound of the present invention, or a pharmaceutically acceptable salt, polymorph, solvate, or stereoisomer or thereof.
Unless otherwise stated, any description of a method of treatment includes use of the compounds to provide such treatment or prophylaxis as is described herein, as well as uses of the compounds to prepare a medicament to treat or prevent such condition. The treatment includes treatment of human or non-human animals including rodents and other disease models.
In still another aspect, this invention relates to a method of modulating the activity of the EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono- through tri-methylation of lysine 27 on histone H3 (H3-K27) in a subject in need thereof. For example, the method comprises the step of administering to a subject having a cancer expressing a mutant EZH2 a therapeutically effective amount of a compound described herein, wherein the compound(s) inhibits histone methyltransferase activity of EZH2, thereby treating the cancer.
For example, the EZH2-mediated cancer is selected from the group consisting of follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) of germinal center B cell-like (GCB) subtype. For example, the cancer is lymphoma, leukemia or melanoma. Preferably, the lymphoma is non-Hodgkin's lymphoma (NHL), follicular lymphoma or diffuse large B-cell lymphoma. Alternatively, the leukemia is chronic myelogenous leukemia (CML), acute myeloid leukemia, acute lymphocytic leukemia or mixed lineage leukemia.
For example, the EZH2-mediated precancerous condition is myelodysplastic syndromes (MDS, formerly known as preleukemia).
For example, the EZH2-mediated cancer is a hematological cancer.
The compound(s) of the present invention inhibit the histone methyltransferase activity of EZH2 or a mutant thereof and, accordingly, the present invention also provides methods for treating conditions and diseases the course of which can be influenced by modulating the methylation status of histones or other proteins, wherein said methylation status is mediated at least in part by the activity of EZH2. In one aspect of the invention, certain compounds disclosed herein are candidates for treating, or preventing certain conditions and diseases. Modulation of the methylation status of histones can in turn influence the level of expression of target genes activated by methylation, and/or target genes suppressed by methylation. The method includes administering to a subject in need of such treatment, a therapeutically effective amount of a compound of the present invention.
As used herein, a “subject” is interchangeable with a “subject in need thereof”, both of which refer to a subject having a disorder in which EZH2-mediated protein methylation plays a part, or a subject having an increased risk of developing such disorder relative to the population at large. A “subject” includes a mammal. The mammal can be e.g., a human or appropriate non-human mammal, such as primate, mouse, rat, dog, cat, cow, horse, goat, camel, sheep or a pig. The subject can also be a bird or fowl. In one embodiment, the mammal is a human. A subject in need thereof can be one who has been previously diagnosed or identified as having cancer or a precancerous condition. A subject in need thereof can also be one who has (e.g., is suffering from) cancer or a precancerous condition. Alternatively, a subject in need thereof can be one who has an increased risk of developing such disorder relative to the population at large (i.e., a subject who is predisposed to developing such disorder relative to the population at large). A subject in need thereof can have a precancerous condition. A subject in need thereof can have refractory or resistant cancer (i.e., cancer that doesn't respond or hasn't yet responded to treatment). The subject may be resistant at start of treatment or may become resistant during treatment. In some embodiments, the subject in need thereof has cancer recurrence following remission on most recent therapy. In some embodiments, the subject in need thereof received and failed all known effective therapies for cancer treatment. In some embodiments, the subject in need thereof received at least one prior therapy. In a preferred embodiment, the subject has cancer or a cancerous condition. For example, the cancer is lymphoma, leukemia, melanoma, or rhabdomyosarcoma. Preferably, the lymphoma is non-Hodgkin's lymphoma, follicular lymphoma or diffuse large B-cell lymphoma. Alternatively, the leukemia is chronic myelogenous leukemia (CML). The precancerous condition is myelodysplastic syndromes (MDS, formerly known as preleukemia).
As used herein, “candidate compound” refers to a compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, that has been or will be tested in one or more in vitro or in vivo biological assays, in order to determine if that compound is likely to elicit a desired biological or medical response in a cell, tissue, system, animal or human that is being sought by a researcher or clinician. A candidate compound is a compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof. The biological or medical response can be the treatment of cancer. The biological or medical response can be treatment or prevention of a cell proliferative disorder. The biological response or effect can also include a change in cell proliferation or growth that occurs in vitro or in an animal model, as well as other biological changes that are observable in vitro. In vitro or in vivo biological assays can include, but are not limited to, enzymatic activity assays, electrophoretic mobility shift assays, reporter gene assays, in vitro cell viability assays, and the assays described herein.
For example, an in vitro biological assay that can be used includes the steps of (1) mixing a histone substrate (e.g., an isolated histone sample, an isolated histone peptide representative of human histone H3 residues 21-44 containing either an unmodified lysine 27 (H3K27me0) or dimethylated lysine 27 (H3K27me2), or an isolated oligonucleosome substrate) with recombinant PRC2 enzymes that include a wild type or mutant EZH2 subunit; (2) adding a compound of the invention to this mixture; (3) adding non-radioactive and 3H-labeled S-Adenosyl methionine (SAM) to start the reaction; (4) adding excessive amount of non-radioactive SAM to stop the reaction; (4) washing off the free non-incorporated 3H-SAM; and (5) detecting the quantity of 3H-labeled histone substrate by any methods known in the art (e.g., by a PerkinElmer TopCount platereader).
For example, an in vivo study that can be used includes the steps of (1) administering a compound of the invention into a mouse model (such as WSU-DLCL2 xenograft tumor bearing mouse model or KARPAS-422 human diffused large B-Cell lymphoma mouse xenograft model) at certain level of dosage for certain periods of time, e.g., 7-28 days; (2) sacrificing the mouse and isolating the tumor tissue; (3) measuring the tumor volume and body weight and (4) extracting histone from the tumor tissue for measuring the histone methylation by ELISA.
As used herein, “treating” or “treat” describes the management and care of a patient for the purpose of combating a disease, condition, or disorder and includes the administration of a compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, to alleviate the symptoms or complications of a disease, condition or disorder, or to eliminate the disease, condition or disorder. The term “treat” can also include treatment of a cell in vitro or an animal model.
A compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, can or may also be used to prevent a relevant disease, condition or disorder, or used to identify suitable candidates for such purposes. As used herein, “preventing,” “prevent,” or “protecting against” describes reducing or eliminating the onset of the symptoms or complications of such disease, condition or disorder.
Point mutations of the EZH2 gene at a single amino acid residue (e.g., Y641, A677, and A687) of EZH2 have been reported to be linked to lymphoma. More examples of EZH2 mutants and methods of treatment are described in U.S. Patent Application Publication 2013-0040906, the entire content of which is incorporated herein by reference in its entirety.
One skilled in the art may refer to general reference texts for detailed descriptions of known techniques discussed herein or equivalent techniques. These texts include Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Inc. (2005); Sambrook et al., Molecular Cloning, A Laboratory Manual (3rd edition), Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2000); Coligan et al., Current Protocols in Immunology, John Wiley & Sons, N.Y.; Enna et al., Current Protocols in Pharmacology, John Wiley & Sons, N.Y.; Fingl et al., The Pharmacological Basis of Therapeutics (1975), Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 18th edition (1990). These texts can, of course, also be referred to in making or using an aspect of the invention.
As used herein, “combination therapy” or “co-therapy” includes the administration of a compound of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, and at least a second agent as part of a specific treatment regimen intended to provide the beneficial effect from the co-action of these therapeutic agents. The beneficial effect of the combination includes, but is not limited to, pharmacokinetic or pharmacodynamic co-action resulting from the combination of therapeutic agents.
The present invention also provides pharmaceutical compositions comprising a compound of any of the Formulae described herein in combination with at least one pharmaceutically acceptable excipient or carrier.
A “pharmaceutical composition” is a formulation containing the compounds of the present invention in a form suitable for administration to a subject. In one embodiment, the pharmaceutical composition is in bulk or in unit dosage form. The unit dosage form is any of a variety of forms, including, for example, a capsule, an IV bag, a tablet, a single pump on an aerosol inhaler or a vial. The quantity of active ingredient (e.g., a formulation of the disclosed compound or salt, hydrate, solvate or isomer thereof) in a unit dose of composition is an effective amount and is varied according to the particular treatment involved. One skilled in the art will appreciate that it is sometimes necessary to make routine variations to the dosage depending on the age and condition of the patient. The dosage will also depend on the route of administration. A variety of routes are contemplated, including oral, pulmonary, rectal, parenteral, transdermal, subcutaneous, intravenous, intramuscular, intraperitoneal, inhalational, buccal, sublingual, intrapleural, intrathecal, intranasal, and the like. Dosage forms for the topical or transdermal administration of a compound of this invention include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. In one embodiment, the active compound is mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that are required.
As used herein, the phrase “pharmaceutically acceptable” refers to those compounds, anions, cations, materials, compositions, carriers, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
“Pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic and neither biologically nor otherwise undesirable, and includes excipient that is acceptable for veterinary use as well as human pharmaceutical use. A “pharmaceutically acceptable excipient” as used in the specification and claims includes both one and more than one such excipient.
A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), and transmucosal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates, and agents for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
A compound or pharmaceutical composition of the invention can be administered to a subject in many of the well-known methods currently used for chemotherapeutic treatment. For example, for treatment of cancers, a compound of the invention may be injected directly into tumors, injected into the blood stream or body cavities or taken orally or applied through the skin with patches. The dose chosen should be sufficient to constitute effective treatment but not so high as to cause unacceptable side effects. The state of the disease condition (e.g., cancer, precancer, and the like) and the health of the patient should preferably be closely monitored during and for a reasonable period after treatment.
The term “therapeutically effective amount”, as used herein, refers to an amount of a pharmaceutical agent to treat, ameliorate, or prevent an identified disease or condition, or to exhibit a detectable therapeutic or inhibitory effect. The effect can be detected by any assay method known in the art. The precise effective amount for a subject will depend upon the subject's body weight, size, and health; the nature and extent of the condition; and the therapeutic or combination of therapeutics selected for administration. Therapeutically effective amounts for a given situation can be determined by routine experimentation that is within the skill and judgment of the clinician. In a preferred aspect, the disease or condition to be treated is cancer. In another aspect, the disease or condition to be treated is a cell proliferative disorder.
For any compound, the therapeutically effective amount can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models, usually rats, mice, rabbits, dogs, or pigs. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. Therapeutic/prophylactic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50. Pharmaceutical compositions that exhibit large therapeutic indices are preferred. The dosage may vary within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
Dosage and administration are adjusted to provide sufficient levels of the active agent(s) or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation.
The pharmaceutical compositions containing active compounds of the present invention may be manufactured in a manner that is generally known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. Pharmaceutical compositions may be formulated in a conventional manner using one or more pharmaceutically acceptable carriers comprising excipients and/or auxiliaries that facilitate processing of the active compounds into preparations that can be used pharmaceutically. Of course, the appropriate formulation is dependent upon the route of administration chosen.
Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringeability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol and sorbitol, and sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Oral compositions generally include an inert diluent or an edible pharmaceutically acceptable carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser, which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
The active compounds can be prepared with pharmaceutically acceptable carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.
It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved.
In therapeutic applications, the dosages of the pharmaceutical compositions used in accordance with the invention vary depending on the agent, the age, weight, and clinical condition of the recipient patient, and the experience and judgment of the clinician or practitioner administering the therapy, among other factors affecting the selected dosage. Generally, the dose should be sufficient to result in slowing, and preferably regressing, the growth of the tumors and also preferably causing complete regression of the cancer. Dosages can range from about 0.01 mg/kg per day to about 5000 mg/kg per day. In preferred aspects, dosages can range from about 1 mg/kg per day to about 1000 mg/kg per day. In an aspect, the dose will be in the range of about 0.1 mg/day to about 50 g/day; about 0.1 mg/day to about 25 g/day; about 0.1 mg/day to about 10 g/day; about 0.1 mg to about 3 g/day; or about 0.1 mg to about 1 g/day, in single, divided, or continuous doses (which dose may be adjusted for the patient's weight in kg, body surface area in m2, and age in years). An effective amount of a pharmaceutical agent is that which provides an objectively identifiable improvement as noted by the clinician or other qualified observer. For example, regression of a tumor in a patient may be measured with reference to the diameter of a tumor. Decrease in the diameter of a tumor indicates regression. Regression is also indicated by failure of tumors to reoccur after treatment has stopped. As used herein, the term “dosage effective manner” refers to amount of an active compound to produce the desired biological effect in a subject or cell.
The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
The compounds of the present invention are capable of further forming salts. All of these forms are also contemplated within the scope of the claimed invention.
As used herein, “pharmaceutically acceptable salts” refer to derivatives of the compounds of the present invention wherein the parent compound is modified by making acid or base salts thereof. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines, alkali or organic salts of acidic residues such as carboxylic acids, and the like. The pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. For example, such conventional non-toxic salts include, but are not limited to, those derived from inorganic and organic acids selected from 2-acetoxybenzoic, 2-hydroxyethane sulfonic, acetic, ascorbic, benzene sulfonic, benzoic, bicarbonic, carbonic, citric, edetic, ethane disulfonic, 1,2-ethane sulfonic, fumaric, glucoheptonic, gluconic, glutamic, glycolic, glycollyarsanilic, hexylresorcinic, hydrabamic, hydrobromic, hydrochloric, hydroiodic, hydroxymaleic, hydroxynaphthoic, isethionic, lactic, lactobionic, lauryl sulfonic, maleic, malic, mandelic, methane sulfonic, napsylic, nitric, oxalic, pamoic, pantothenic, phenylacetic, phosphoric, polygalacturonic, propionic, salicyclic, stearic, subacetic, succinic, sulfamic, sulfanilic, sulfuric, tannic, tartaric, toluene sulfonic, and the commonly occurring amine acids, e.g., glycine, alanine, phenylalanine, arginine, etc.
Other examples of pharmaceutically acceptable salts include hexanoic acid, cyclopentane propionic acid, pyruvic acid, malonic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, 4-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, 4-toluenesulfonic acid, camphorsulfonic acid, 4-methylbicyclo-[2.2.2]-oct-2-ene-1-carboxylic acid, 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, muconic acid, and the like. The present invention also encompasses salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base such as ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. In the salt form, it is understood that the ratio of the compound to the cation or anion of the salt can be 1:1, or any ration other than 1:1, e.g., 3:1, 2:1, 1:2, or 1:3.
It should be understood that all references to pharmaceutically acceptable salts include solvent addition forms (solvates) or crystal forms (polymorphs) as defined herein, of the same salt.
The compounds of the present invention can also be prepared as esters, for example, pharmaceutically acceptable esters. For example, a carboxylic acid function group in a compound can be converted to its corresponding ester, e.g., a methyl, ethyl or other ester. Also, an alcohol group in a compound can be converted to its corresponding ester, e.g., acetate, propionate or other ester.
The compounds, or pharmaceutically acceptable salts thereof, are administered orally, nasally, transdermally, pulmonary, inhalationally, buccally, sublingually, intraperintoneally, subcutaneously, intramuscularly, intravenously, rectally, intrapleurally, intrathecally and parenterally. In one embodiment, the compound is administered orally. One skilled in the art will recognize the advantages of certain routes of administration.
The dosage regimen utilizing the compounds is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal and hepatic function of the patient; and the particular compound or salt thereof employed. An ordinarily skilled physician or veterinarian can readily determine and prescribe the effective amount of the drug required to prevent, counter, or arrest the progress of the condition.
Techniques for formulation and administration of the disclosed compounds of the invention can be found in Remington: the Science and Practice of Pharmacy, 19th edition, Mack Publishing Co., Easton, Pa. (1995). In an embodiment, the compounds described herein, and the pharmaceutically acceptable salts thereof, are used in pharmaceutical preparations in combination with a pharmaceutically acceptable carrier or diluent. Suitable pharmaceutically acceptable carriers include inert solid fillers or diluents and sterile aqueous or organic solutions. The compounds will be present in such pharmaceutical compositions in amounts sufficient to provide the desired dosage amount in the range described herein.
All percentages and ratios used herein, unless otherwise indicated, are by weight. Other features and advantages of the present invention are apparent from the different examples. The provided examples illustrate different components and methodology useful in practicing the present invention. The examples do not limit the claimed invention. Based on the present disclosure the skilled artisan can identify and employ other components and methodology useful for practicing the present invention.
In the synthetic schemes described herein, compounds may be drawn with one particular configuration for simplicity. Such particular configurations are not to be construed as limiting the invention to one or another isomer, tautomer, regioisomer or stereoisomer, nor does it exclude mixtures of isomers, tautomers, regioisomers or stereoisomers; however, it will be understood that a given isomer, tautomer, regioisomer or stereoisomer may have a higher level of activity than another isomer, tautomer, regioisomer or stereoisomer.
Compounds designed, selected and/or optimized by methods described above, once produced, can be characterized using a variety of assays known to those skilled in the art to determine whether the compounds have biological activity. For example, the molecules can be characterized by conventional assays, including but not limited to those assays described below, to determine whether they have a predicted activity, binding activity and/or binding specificity.
Furthermore, high-throughput screening can be used to speed up analysis using such assays. As a result, it can be possible to rapidly screen the molecules described herein for activity, using techniques known in the art. General methodologies for performing high-throughput screening are described, for example, in Devlin (1998) High Throughput Screening, Marcel Dekker; and U.S. Pat. No. 5,763,263. High-throughput assays can use one or more different assay techniques including, but not limited to, those described below.
All publications and patent documents cited herein are incorporated herein by reference as if each such publication or document was specifically and individually indicated to be incorporated herein by reference. Citation of publications and patent documents is not intended as an admission that any is pertinent prior art, nor does it constitute any admission as to the contents or date of the same. The invention having now been described by way of written description, those of skill in the art will recognize that the invention can be practiced in a variety of embodiments and that the foregoing description and examples below are for purposes of illustration and not limitation of the claims that follow.
Preparatory Example 1: General PyBOP Coupling Protocol
The carboxylic acid (1 equiv.) was then dissolved in DMSO and an appropriate methanamine (2 eq.) was added to it. The reaction mixture was stirred at room temperature for 15 min before PYBOP (1.5 equiv.) and triethyl amine (1 equiv.) was added to it and stirring was continued for overnight. After completion of the reaction, reaction mass was poured into ice, extracted with 10% MeOH/DCM. Combined organic layers were dried, concentrated to obtain crude; which then purified by column chromatography/prep. HPLC to afford the target compound.
Example 1: (2,4-dimethyl-2H-indazol-7-yl)methanamine
Step 1: Synthesis of 7-bromo-2,4-dimethyl-2H-indazole
To a solution of 7-bromo-4-methyl-1H-indazole (1 equiv.) in acetonitrile, Cs2CO3 (1.3 equiv.) and MeI (3 equiv.) was added and reaction was heated at 80° C. for 1.5 h. On completion, it was cooled and quenched by addition of water. Extraction was carried out using ethyl acetate. Organic layer was dried over Na2SO4 and crude compound was column purified to afford the title compound. (Polar isomer confirmed as N-2-Methyl and non-polar isomer confirmed as N-1-Methyl by NOE experimentation).
Step 2: Synthesis of 2,4-dimethyl-2H-indazole-7-carbonitrile
To a solution of 7-bromo-2,4-dimethyl-2H-indazole (1 eq.) in NMP, was added CuCN (2 equiv.) and heated at 130° C. for 16 h. On completion, water was added to quench the reaction, solid precipitated was filtered and purified by column chromatography to afford the title compound (40-60% yield)
Step 3: Synthesis of (2,4-dimethyl-2H-indazol-7-yl)methanamine
To a solution of 2,4-dimethyl-2H-indazole-7-carbonitrile (1 equiv.) in methanol and aq. ammonia solution (9:1), catalytic amount of Raney Nickel was added. Reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through celite bed and filtrate was concentrated under reduce pressure to afford the title compound (quant. yield).
Example 2: (5,7-dimethylimidazo[1,2-a]pyridin-8-yl)methanamine
Step 1: Synthesis of 5,7-dimethylimidazo[1,2-a]pyridine-8-carbonitrile
To a stirred solution of compound 2-amino-4,6-dimethylnicotinonitrile (1 equiv.) in water was added chloroacetaldehyde (55% aq. solution) (1.2 equiv.) and reaction was heated at 80° C. for 16 h. On completion, it was quenched by 1N NaOH till pH 8. Solid precipitated was filtered and vacuum dried to afford the title compound (75% yield).
Step 2: Synthesis of (5,7-dimethylimidazo[1,2-a]pyridin-8-yl)methanamine
To a solution of 5,7-dimethylimidazo[1,2-a]pyridine-8-carbonitrile (1 equiv.) in methanol and aq. ammonia solution (9:1), a catalytic amount of Raney Nickel was added. The reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through a celite bed and the filtrate was concentrated under reduce pressure to afford respective amines (quantitative yield).
Example 3: (7-methylimidazo[1,2-a]pyridin-8-yl)methanamine
Step 1: Synthesis of 7-methylimidazo[1,2-a]pyridine-8-carbonitrile
To a stirred solution of compound 2-amino-4-methylnicotinonitrile (1 equiv.) in water was added chloroacetaldehyde (55% aq. solution) (1.2 equiv.) and the reaction was heated at 80° C. for 16 h. On completion, it was quenched by 1N NaOH till pH 8. Solid precipitated was filtered and vacuum dried to afford the title compound (75% yield).
Step 2: Synthesis of (7-methylimidazo[1,2-a]pyridin-8-yl)methanamine
To a solution of 7-methylimidazo[1,2-a]pyridine-8-carbonitrile (1 eq) in methanol and aq. ammonia solution (9:1), catalytic amount of Raney Nickel was added. Reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through celite bed and filtrate was concentrated under reduce pressure to afford respective amines (quantitative yield).
Example 4: Imidazo[1,2-a]pyridin-8-ylmethanamine
To a solution of imidazo[1,2-a]pyridine-8-carbonitrile (1 equiv.) in methanol and aq. ammonia solution (9:1), catalytic amount of Raney Nickel was added. Reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through celite bed and filtrate was concentrated under reduce pressure to afford respective amines (quantitative yield).
Example 5: (2,6-dimethyl-2H-indazol-7-yl)methanamine
Step 1: Synthesis of 7-bromo-2,6-dimethyl-2H-indazole
To a solution of 7-bromo-6-methyl-1H-indazole (1 equiv.) in acetonitrile, Cs2CO3 (1.3 equiv.) and MeI (3 eq.) was added and reaction was heated at 80° C. for 1.5 h. On completion, it was cooled and quenched by addition of water. Extraction was carried out using ethyl acetate. Organic layer was dried over Na2SO4 and crude compound was column purified to afford the title compound. (Polar isomer confirmed as N-2-Methyl and non-polar isomer confirmed as N-1-Methyl by NOE experimentation).
Step 2: Synthesis of 2,6-dimethyl-2H-indazole-7-carbonitrile
To a solution of 7-bromo-2,6-dimethyl-2H-indazole (1 equiv.) in NMP, was added CuCN (2 equiv.) and heated at 130° C. for 16 h. On completion, water was added to quench the reaction, solid precipitated was filtered and purified by column chromatography to afford the title compound (40-60% yield)
Step 3: Synthesis of (2,6-dimethyl-2H-indazol-7-yl)methanamine
To a solution of 2,6-dimethyl-2H-indazole-7-carbonitrile (1 equiv.) in methanol and aq. ammonia solution (9:1), catalytic amount of Raney Nickel was added. Reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through celite bed and filtrate was concentrated under reduce pressure to afford the title compound (quant. yield).
Example 6: (2-methyl-2H-indazol-7-yl)methanamine
Step 1: Synthesis of 2-methyl-2H-indazole-7-carbonitrile
To a solution of 1H-indazole-7-carbonitrile (1 equiv.) in acetonitrile, Cs2CO3 (1.3 equiv.) and MeI (3 equiv.) was added and reaction was heated at 80° C. for 1.5 h. On completion, it was cooled and quenched by addition of water. Extraction was carried out using ethyl acetate. Organic layer was dried over Na2SO4 and crude compound was column purified to afford the title compound. (Polar isomer confirmed as N-2-Methyl and non-polar isomer confirmed as N-1-Methyl by NOE experimentation).
Step 2: Synthesis of (2-methyl-2H-indazol-7-yl)methanamine
To a solution of 2-methyl-2H-indazole-7-carbonitrile (1 equiv.) in methanol and aq. ammonia solution (9:1), catalytic amount of Raney Nickel was added. Reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through celite bed and filtrate was concentrated under reduce pressure to afford the title compound (quant. yield).
Example 7: pyrazolo[1,5-a]pyridin-7-ylmethanamine
To a solution of pyrazolo[1,5-a]pyridine-7-carbonitrile (1 equiv.) in methanol and aq. ammonia solution (9:1), catalytic amount of Raney Nickel was added. Reaction mass was stirred at room temperature under hydrogen pressure (balloon pressure) for 2-5 h. On completion of reaction, it was filtered through celite bed and filtrate was concentrated under reduce pressure to afford the title compound (quant. yield).
Example 8: Bioassay Protocol and General Methods
Protocol for Wild-Type and Mutant PRC2 Enzyme Assays
General Materials.
S-adenosylmethionine (SAM), S-adenosylhomocyteine (SAH), bicine, KCl, Tween20, dimethylsulfoxide (DMSO) and bovine skin gelatin (BSG) can be purchased from Sigma-Aldrich at the highest level of purity possible. Dithiothreitol (DTT) was purchased from EMD. 3H-SAM can be purchased from American Radiolabeled Chemicals with a specific activity of 80 Ci/mmol. 384-well streptavidin Flashplates can be purchased from PerkinElmer.









H3K27me0:



(SEQ ID NO: 1)



ATKAARKSAPATGGVKKPHRYRPGGK(biotin)-amide



 



H3K27me2:



(SEQ ID NO: 2)



ATKAARK(me2)SAPATGGVKKPHRYRPGGK(biotin)-amide






Substrates.
Peptides representative of human histone H3 residues 21-44 containing either an unmodified lysine 27 (H3K27me0) or dimethylated lysine 27 (H3K27me2) were synthesized with a C-terminal G(K-biotin) linker-affinity tag motif and a C-terminal amide cap by 21st Century Biochemicals. The peptides were high-performance liquid chromatography (HPLC) purified to greater than 95% purity and confirmed by liquid chromatography mass spectrometry (LC-MS). The sequences are listed below.
Chicken erythrocyte oligonucleosomes are purified from chicken blood according to established procedures.
Recombinant PRC2 Enzymes.
Human PRC2 enzymes are purified as 4-component enzyme complexes co-expressed in Spodoptera frugiperda (sf9) cells using a baculovirus expression system. The subunits expressed are wild-type EZH2 (NM_004456) or EZH2 Y641F, N, H, S or C mutants generated from the wild-type EZH2 construct, EED (NM_003797), Suz12 (NM_015355) and RbAp48 (NM_005610). The EED subunit contains an N-terminal FLAG tag that is used to purify the entire 4-component complex from sf9 cell lysates. The purity of the complexes meets or exceeds 95% as determined by SDS-PAGE and Agilent Bioanalyzer analysis. Concentrations of enzyme stock concentrations (generally 0.3-1.0 mg/mL) is determined using a Bradford assay against a bovine serum albumin (BSA) standard.
General Procedure for PRC2 Enzyme Assays on Peptide Substrates.
The assays are all performed in a buffer consisting of 20 mM bicine (pH=7.6), 0.5 mM DTT, 0.005% BSG and 0.002% Tween20, prepared on the day of use. Compounds in 100% DMSO (1 μL) are spotted into polypropylene 384-well V-bottom plates (Greiner) using a Platemate 2×3 outfitted with a 384-channel pipet head (Thermo). DMSO (1 μL) is added to columns 11, 12, 23, 24, rows A-H for the maximum signal control, and SAH, a known product and inhibitor of PRC2 (1 μL) is added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 μL) containing the wild-type PRC2 enzyme and H3K27me0 peptide or any of the Y641 mutant enzymes and H3K27me2 peptide is added by Multidrop Combi (Thermo). The compounds are allowed to incubate with PRC2 for 30 min at 25° C., then a cocktail (10 μL) containing a mixture of non-radioactive and 3H-SAM is added to initiate the reaction (final volume=51 μL). In all cases, the final concentrations are as follows: wild-type or mutant PRC2 enzyme was 4 nM, SAH in the minimum signal control wells was 1 mM and the DMSO concentration was 1%. The final concentrations of the rest of the components are indicated in Table 4, below. The assays are stopped by the addition of non-radioactive SAM (10 μL) to a final concentration of 600 μM, which dilutes the 3H-SAM to a level where its incorporation into the peptide substrate is no longer detectable. 50 μL of the reaction in the 384-well polypropylene plate is then transferred to a 384-well Flashplate and the biotinylated peptides are allowed to bind to the streptavidin surface for at least 1 h before being washed three times with 0.1% Tween20 in a Biotek ELx405 plate washer. The plates are then read in a PerkinElmer TopCount platereader to measure the quantity of 3H-labeled peptide bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).







TABLE 4







Final concentrations of components for each assay variation


based upon EZH2 identity (wild-type or Y641 mutant EZH2)










PRC2 Enzyme
Peptide
Non-radioactive SAM
3H-SAM


(denoted by EZH2 identity)
(nM)
(nM)
(nM)













Wild-type
185
1800
150


Y641F
200
850
150


Y641N
200
850
150


Y641H
200
1750
250


Y641S
200
1300
200


Y641C
200
3750
250









General Procedure for Wild-Type PRC2 Enzyme Assay on Oligonucleosome Substrate.
The assays are performed in a buffer consisting of 20 mM bicine (pH=7.6), 0.5 mM DTT, 0.005% BSG, 100 mM KCl and 0.002% Tween20, prepared on the day of use. Compounds in 100% DMSO (1 μL) were spotted into polypropylene 384-well V-bottom plates (Greiner) using a Platemate 2×3 outfitted with a 384-channel pipet head (Thermo). DMSO (1 μL) is added to columns 11, 12, 23, 24, rows A-H for the maximum signal control, and SAH, a known product and inhibitor of PRC2 (1 μL) was added to columns 11, 12, 23, 24, rows I-P for the minimum signal control. A cocktail (40 μL) containing the wild-type PRC2 enzyme and chicken erythrocyte oligonucleosome is added by Multidrop Combi (Thermo). The compounds are allowed to incubate with PRC2 for 30 min at 25° C., then a cocktail (10 μL) containing a mixture of non-radioactive and 3H-SAM is added to initiate the reaction (final volume=51 μL). The final concentrations are as follows: wild-type PRC2 enzyme is 4 nM, non-radioactive SAM is 430 nM, 3H-SAM was 120 nM, chicken erythrocyte olignonucleosome was 120 nM, SAH in the minimum signal control wells is 1 mM and the DMSO concentration was 1%. The assay is stopped by the addition of non-radioactive SAM (10 μL) to a final concentration of 600 μM, which dilutes the 3H-SAM to a level where its incorporation into the chicken erythrocyte olignonucleosome substrate is no longer detectable. 50 μL of the reaction in the 384-well polypropylene plate is then transferred to a 384-well Flashplate and the chicken erythrocyte nucleosomes were immobilized to the surface of the plate, which is then washed three times with 0.1% Tween20 in a Biotek ELx405 plate washer. The plates are then read in a PerkinElmer TopCount platereader to measure the quantity of 3H-labeled chicken erythrocyte oligonucleosome bound to the Flashplate surface, measured as disintegrations per minute (dpm) or alternatively, referred to as counts per minute (cpm).
% Inhibition Calculation




  
    %
    ⁢
    
      
    
    ⁢
    inh
  
  =
  
    100
    -
    
      
        (
        
          
            
              dpm
              cmpd
            
            -
            
              dpm
              min
            
          
          
            
              dpm
              max
            
            -
            
              dpm
              min
            
          
        
        )
      
      ×
      100
    
  




Where dpm=disintegrations per minute, cmpd=signal in assay well, and min and max are the respective minimum and maximum signal controls.
Four-Parameter IC50 Fit




  Y
  =
  
    Bottom
    +
    
      
        (
        
          Top
          -
          Bottom
        
        )
      
      
        1
        +
        
          
            (
            
              X
              
                IC
                50
              
            
            )
          
          
            Hill
            ⁢
            
              
            
            ⁢
            Coefficient
          
        
      
    
  




Where top and bottom are the normally allowed to float, but may be fixed at 100 or 0 respectively in a 3-parameter fit. The Hill Coefficient normally allowed to float but may also be fixed at 1 in a 3-parameter fit. Y is the % inhibition and X is the compound concentration.
WSU-DLCL2 Methylation Assay
WSU-DLCL2 suspension cells are purchased from DSMZ (German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany). RPMI/Glutamax Medium, Penicillin-Streptomycin, Heat Inactivated Fetal Bovine Serum, and D-PBS were purchased from Life Technologies, Grand Island, N.Y., USA. Extraction Buffer and Neutralization Buffer (5×) were purchased from Active Motif, Carlsbad, Calif., USA. Rabbit anti-Histone H3 antibody is purchased from Abcam, Cambridge, Mass., USA. Rabbit anti-H3K27me3 and HRP-conjugated anti-rabbit-IgG are purchased from Cell Signaling Technology, Danvers, Mass., USA. TMB “Super Sensitive” substrate is sourced from BioFX Laboratories, Owings Mills, Md., USA. IgG-free Bovine Serum Albumin is purchased from Jackson ImmunoResearch, West Grove, Pa., USA. PBS with Tween (10×PBST) was purchased from KPL, Gaithersburg, Md., USA. Sulfuric Acid is purchased from Ricca Chemical, Arlington, Tex., USA. Immulon ELISA plates were purchased from Thermo, Rochester, N.Y., USA. V-bottom cell culture plates are purchased from Corning Inc., Corning, N.Y., USA. V-bottom polypropylene plates were purchased from Greiner Bio-One, Monroe, N.C., USA.
WSU-DLCL2 suspension cells are maintained in growth medium (RPMI 1640 supplemented with 10% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) and cultured at 37° C. under 5% CO2. Under assay conditions, cells are incubated in Assay Medium (RPMI 1640 supplemented with 20% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) at 37° C. under 5% CO2 on a plate shaker.
WSU-DLCL2 cells are seeded in assay medium at a concentration of 50,000 cells per mL to a 96-well V-bottom cell culture plate with 200 μL per well. Compound (1 μL) from 96 well source plates is added directly to V-bottom cell plate. Plates are incubated on a titer-plate shaker at 37° C., 5% CO2 for 96 hours. After four days of incubation, plates are spun at 241×g for five minutes and medium was aspirated gently from each well of cell plate without disturbing cell pellet. Pellet is resuspended in 200 μL DPBS and plates are spun again at 241×g for five minutes. The supernatant is aspirated and cold (4° C.) Extraction buffer (100 μL) is added per well. Plates are incubated at 4° C. on orbital shaker for two hours. Plates are spun at 3427×g×10 minutes. Supernatant (80 μL per well) is transferred to its respective well in 96 well V-bottom polypropylene plate. Neutralization Buffer 5× (20 μL per well) is added to V-bottom polypropylene plate containing supernatant. V-bottom polypropylene plates containing crude histone preparation (CHP) are incubated on orbital shaker x five minutes. Crude Histone Preparations are added (2 μL per well) to each respective well into duplicate 96 well ELISA plates containing 100 μL Coating Buffer (1×PBS+BSA 0.05% w/v). Plates are sealed and incubated overnight at 4° C. The following day, plates were washed three times with 300 μL per well 1×PBST. Wells are blocked for two hours with 300 μL per well ELISA Diluent ((PBS (1×) BSA (2% w/v) and Tween20 (0.05% v/v)). Plates are washed three times with 1×PBST. For the Histone H3 detection plate, 100 μL per well are added of anti-Histone-H3 antibody (Abcam, ab1791) diluted 1:10,000 in ELISA Diluent. For H3K27 trimethylation detection plate, 100 μL per well are added of anti-H3K27me3 diluted 1:2000 in ELISA diluent. Plates are incubated for 90 minutes at room temperature. Plates are washed three times with 300 μL 1×PBST per well. For Histone H3 detection, 100 μL of HRP-conjugated anti-rabbit IgG antibody diluted to 1:6000 in ELISA diluent is added per well. For H3K27me3 detection, 100 μL of HRP conjugated anti-rabbit IgG antibody diluted to 1:4000 in ELISA diluent is added per well. Plates are incubated at room temperature for 90 minutes. Plates are washed four times with 1×PBST 300 μL per well. TMB substrate 100 μL is added per well. Histone H3 plates are incubated for five minutes at room temperature. H3K27me3 plates were incubated for 10 minutes at room temperature. The reaction is stopped with sulfuric acid 1N (100 μL per well). Absorbance for each plate was read at 450 nm.
First, the ratio for each well is determined by:




  (
  
    
      H
      ⁢
      
        
      
      ⁢
      3
      ⁢
      
        
      
      ⁢
      K
      ⁢
      
        
      
      ⁢
      27
      ⁢
      
        
      
      ⁢
      me
      ⁢
      
        
      
      ⁢
      3
      ⁢
      
        
      
      ⁢
      OD
      ⁢
      
        
      
      ⁢
      450
      ⁢
      
        
      
      ⁢
      value
    
    
      Histone
      ⁢
      
        
      
      ⁢
      H
      ⁢
      
        
      
      ⁢
      3
      ⁢
      
        
      
      ⁢
      OD
      ⁢
      
        
      
      ⁢
      450
      ⁢
      
        
      
      ⁢
      value
    
  
  )




Each plate includes eight control wells of DMSO only treatment (Minimum Inhibition) as well as eight control wells for maximum inhibition (Background wells).
The average of the ratio values for each control type is calculated and used to determine the percent inhibition for each test well in the plate. Test compound is serially diluted three-fold in DMSO for a total of ten test concentrations, beginning at 25 μM. Percent inhibition is determined and IC50 curves were generated using duplicate wells per concentration of compound.




  
    Percent
    ⁢
    
      
    
    ⁢
    Inhibition
  
  =
  
    100
    -
    
      (
      
        
          (
          
            
              
                (
                
                  Individual
                  ⁢
                  
                    
                  
                  ⁢
                  Test
                  ⁢
                  
                    
                  
                  ⁢
                  Sample
                  ⁢
                  
                    
                  
                  ⁢
                  Ratio
                
                )
              
              -
              
                (
                
                  Background
                  ⁢
                  
                    
                  
                  ⁢
                  Avg
                  ⁢
                  
                    
                  
                  ⁢
                  Ratio
                
                )
              
            
            
              
                (
                
                  Minimum
                  ⁢
                  
                    
                  
                  ⁢
                  Inhibition
                  ⁢
                  
                    
                  
                  ⁢
                  Ratio
                
                )
              
              -
              
                (
                
                  Background
                  ⁢
                  
                    
                  
                  ⁢
                  Average
                  ⁢
                  
                    
                  
                  ⁢
                  Ratio
                
                )
              
            
          
          )
        
        *
        100
      
      )
    
  




Cell Proliferation Analysis

WSU-DLCL2 suspension cells are purchased from DSMZ (German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany). RPMI/Glutamax Medium, Penicillin-Streptomycin, Heat Inactivated Fetal Bovine Serum are purchased from Life Technologies, Grand Island, N.Y., USA. V-bottom polypropylene 384-well plates are purchased from Greiner Bio-One, Monroe, N.C., USA. Cell culture 384-well white opaque plates are purchased from Perkin Elmer, Waltham, Mass., USA. Cell-Titer Glo® is purchased from Promega Corporation, Madison, Wis., USA. SpectraMax M5 plate reader is purchased from Molecular Devices LLC, Sunnyvale, Calif., USA.
WSU-DLCL2 suspension cells are maintained in growth medium (RPMI 1640 supplemented with 10% v/v heat inactivated fetal bovine serum and cultured at 37° C. under 5% CO2. Under assay conditions, cells are incubated in Assay Medium (RPMI 1640 supplemented with 20% v/v heat inactivated fetal bovine serum and 100 units/mL penicillin-streptomycin) at 37° C. under 5% CO2.
For the assessment of the effect of compounds on the proliferation of the WSU-DLCL2 cell line, exponentially growing cells are plated in 384-well white opaque plates at a density of 1250 cell/ml in a final volume of 50 μl of assay medium. A compound source plate is prepared by performing triplicate nine-point 3-fold serial dilutions in DMSO, beginning at 10 mM (final top concentration of compound in the assay was 20 μM and the DMSO was 0.2%). A 100 nL aliquot from the compound stock plate is added to its respective well in the cell plate. The 100% inhibition control consists of cells treated with 200 nM final concentration of staurosporine and the 0% inhibition control consisted of DMSO treated cells. After addition of compounds, assay plates are incubated for 6 days at 37° C., 5% CO2, relative humidity >90% for 6 days. Cell viability is measured by quantization of ATP present in the cell cultures, adding 35 μl of Cell Titer Glo® reagent to the cell plates. Luminescence is read in the SpectraMax M5. The concentration inhibiting cell viability by 50% is determined using a 4-parametric fit of the normalized dose response curves. IC50 values for this assay are calculated.
Example 9: Derivation of the Lowest Cytotoxic Concentration (LCC)
It is well established that cellular proliferation proceeds through cell division that results in a doubling of the number of cells after division, relative to the number of cells prior to division. Under a fixed set of environmental conditions (e.g., pH, ionic strength, temperature, cell density, medium content of proteins and growth factors, and the like) cells will proliferate by consecutive doubling (i.e., division) according to the following equation, provided that sufficient nutrients and other required factors are available.




  
    
      
        
          N
          t
        
        =
        
          
            N
            0
          
          ×
          
            2
            
              t
              
                t
                D
              
            
          
        
      
    
    
      
        (
        
          A
          ⁢
          .1
        
        )
      
    
  




where Nt is the cell number at a time point (t) after initiation of the observation period, N0 is the cell number at the initiation of the observation period, t is the time after initiation of the observation period and tD is the time interval required for cell doubling, also referred to as the doubling time. Equation A.1 can be converted into the more convenient form of an exponential equation in base e, taking advantage of the equality, 0.693=ln(2).





  
    
      
        
          N
          t
        
        =
        
          
            N
            0
          
          ⁢
          
            e
            
              
                0.693
                ⁢
                
                  
                
                ⁢
                t
              
              
                t
                D
              
            
          
        
      
    
    
      
        (
        
          A
          ⁢
          .2
        
        )
      
    
  




The rate constant for cell proliferation (kp) is inversely related to the doubling time as follows.




  
    
      
        
          k
          p
        
        =
        
          0.693
          
            t
            D
          
        
      
    
    
      
        (
        
          A
          ⁢
          .3
        
        )
      
    
  




Combining equation A.2 and A.3 yields,

Nt=N0ekpt  (A.4)

Thus, according to equation A.4 cell number is expected to increase exponentially with time during the early period of cell growth referred to as log-phase growth. Exponential equations like equation A.4 can be linearized by taking the natural logarithm of each side.

ln(Nt)=ln(N0)+kpt  (A.5)

Thus a plot of ln(Nt) as a function of time is expected to yield an ascending straight line with slope equal to kp and y-intercept equal to ln(N0).
Changes in environmental conditions can result in a change in the rate of cellular proliferation that is quantifiable as changes in the proliferation rate constant kp. Among conditions that may result in a change in proliferation rate is the introduction to the system of an antiproliferative compound at the initiation of the observation period (i.e., at t=0). When an antiproliferative compound has an immediate impact on cell proliferation, one expects that plots of ln(Nt) as a function of time will continue to be linear at all compound concentrations, with diminishing values of kp at increasing concentrations of compound.
Depending on the mechanistic basis of antiproliferative action, some compounds may not immediately effect a change in proliferation rate. Instead, there may be a period of latency before the impact of the compound is realized. In such cases a plot of ln(Nt) as a function of time will appear biphasic, and a time point at which the impact of the compound begins can be identified as the breakpoint between phases. Regardless of whether a compound's impact on proliferation is immediate or begins after a latency period, the rate constant for proliferation at each compound concentration is best defined by the slope of the ln(Nt) vs. time curve from the time point at which compound impact begins to the end of the observation period of the experiment.
A compound applied to growing cells may affect the observed proliferation in one of two general ways: by inhibiting further cell division (cytostasis) or by cell killing (cytotoxicity). If a compound is cytostatic, increasing concentration of compound will reduce the value of kp until there is no further cell division. At this point, the rate of cell growth, and therefore the value of kp, will be zero. If, on the other hand, the compound is cytotoxic, then the value of kp will be composed of two rate constants: a rate constant for continued cell growth in the presence of the compound (kg) and a rate constant for cell killing by the compound (kd). The overall rate constant for proliferation at a fixed concentration of compound will thus be the difference between the absolute values of these opposing rate constants.

kp=|kg|−|kp  (A.6)

At compound concentrations for which the rate of cell growth exceeds that of cell killing, the value of kp will have a positive value (i.e., kp>0). At compound concentrations for which the rate of cell growth is less than that for cell killing, the value of kp will have a negative value (i.e., kp<0) and the cell number will decrease with time, indicative of robust cytotoxicity. When kg exactly matches kd then the overall proliferation rate constant, kp, will have a value of zero. We can thus define the lowest cytotoxic concentration (LCC) as that concentration of compound that results in a value of kp equal to zero, because any concentration greater than this will result in clearly observable cytotoxicity. Nota bene: at concentrations below the LCC there is likely to be cell killing occurring, but at a rate that is less than that of residual cell proliferation. The treatment here is not intended to define the biological details of compound action. Rather, the goal here is to merely define a practical parameter with which to objectively quantify the concentration of compound at which the rate of cell killing exceeds new cell growth. Indeed, the LCC represents a breakpoint or critical concentration above which frank cytotoxicity is observed, rather than a cytotoxic concentration per se. In this regard, the LCC can be viewed similar to other physical breakpoint metrics, such as the critical micelle concentration (CMC) used to define the concentration of lipid, detergent or other surfactant species above which all molecules incorporate into micellar structures.
Traditionally, the impact of antiproliferative compounds on cell growth has been most commonly quantified by the IC50 value, which is defined as that concentration of compound that reduces the rate of cell proliferation to one half that observed in the absence of compound (i.e., for the vehicle or solvent control sample). The IC50, however, does not allow the investigator to differentiate between cytostatic and cytotoxic compounds. The LCC, in contrast, readily allows one to make such a differentiation and to further quantify the concentration at which the transition to robust cytotoxic behavior occurs.
If one limits the observation time window to between the start of impact and the end of the experiment, then the data will generally fit well to a linear equation when plotted as ln(Nt) as a function of time (vide supra). From fits of this type, the value of kp can be determined at each concentration of compound tested. A replot of the value of kp as a function of compound concentration ([I]) will have the form of a descending isotherm, with a maximum value at [I]=0 of kmax (defined by the vehicle or solvent control sample) and a minimum value at infinite compound concentration of kmin.




  
    
      
        
          k
          p
        
        =
        
          
            
              (
              
                
                  k
                  max
                
                -
                
                  k
                  min
                
              
              )
            
            
              1
              +
              
                
                  [
                  I
                  ]
                
                
                  I
                  mid
                
              
            
          
          +
          
            k
            min
          
        
      
    
    
      
        (
        
          A
          ⁢
          .7
        
        )
      
    
  




where Imid is the concentration of compound yielding a value of kp that is midway between the values of kmax and kmin (note that the value of Imid is not the same as the IC50, except in the case of a complete and purely cytostatic compound). Thus, fitting the replot data to equation A.7 provides estimates of kmax, kmin and Imid. If a compound is cytostatic (as defined here), the value of kmin cannot be less than zero. For cytotoxic compounds, kmin will be less than zero and the absolute value of kmin will relate directly to the effectiveness of the compound in killing cells.

The fitted values derived from equation A.7 can also be used to determine the value of the LCC. By definition, when [I]=LCC, kp=0. Thus, under these conditions equation A.7 becomes.




  
    
      
        0
        =
        
          
            
              (
              
                
                  k
                  max
                
                -
                
                  k
                  min
                
              
              )
            
            
              1
              +
              
                
                  L
                  ⁢
                  
                    
                  
                  ⁢
                  C
                  ⁢
                  
                    
                  
                  ⁢
                  C
                
                
                  I
                  mid
                
              
            
          
          +
          
            k
            min
          
        
      
    
    
      
        (
        
          A
          ⁢
          .8
        
        )
      
    
  




Algebraic rearrangement of equation A.8 yields an equation for the LCC.




  
    
      
        
          L
          ⁢
          
            
          
          ⁢
          C
          ⁢
          
            
          
          ⁢
          C
        
        =
        
          
            I
            mid
          
          ⁡
          
            [
            
              
                (
                
                  
                    
                      k
                      max
                    
                    -
                    
                      k
                      min
                    
                  
                  
                    -
                    
                      k
                      min
                    
                  
                
                )
              
              -
              1
            
            ]
          
        
      
    
    
      
        (
        
          A
          ⁢
          .9
        
        )
      
    
  




This analysis is simple to implement with nonlinear curve fitting software and may be applied during cellular assays of compound activity throughout the drug discovery and development process. In this manner, the LCC may provide a valuable metric for the assessment of compound SAR (structure-activity relationship).
Example 10: In Vivo Assays
Mice
Female Fox Chase SCID® Mice (CB17/Icr-Prkdcscid/IcrIcoCrl, Charles River Laboratories) or athymic nude mice (Crl:NU(Ncr)-Foxn1nu, Charles River Laboratories) are 8 weeks old and had a body-weight (BW) range of 16.0-21.1 g on D1 of the study. The animals are fed ad libitum water (reverse osmosis 1 ppm Cl) and NIH 31 Modified and Irradiated Lab Diet® consisting of 18.0% crude protein, 5.0% crude fat, and 5.0% crude fiber. The mice are housed on irradiated Enrich-o'CobsTM bedding in static microisolators on a 12-hour light cycle at 20-22° C. (68-72° F.) and 40-60% humidity. All procedures comply with the recommendations of the Guide for Care and Use of Laboratory Animals with respect to restraint, husbandry, surgical procedures, feed and fluid regulation, and veterinary care.
Tumor Cell Culture
Human lymphoma cell lines line are obtained from different sources (ATCC, DSMZ), e.g., WSU-DLCL2 obtained from DSMZ. The cell lines are maintained at Piedmont as suspension cultures in RPMI-1640 medium containing 100 units/mL penicillin G sodium salt, 100 g/mL streptomycin, and 25 g/mL gentamicin. The medium is supplemented with 10% fetal bovine serum and 2 mM glutamine. The cells are cultured in tissue culture flasks in a humidified incubator at 37° C., in an atmosphere of 5% CO2 and 95% air.
In Vivo Tumor Implantation
Human lymphoma cell lines, e.g., WSU-DLCL2 cells, are harvested during mid-log phase growth, and re-suspended in PBS with 50% MatrigelTM (BD Biosciences). Each mouse receives 1×107 cells (0.2 mL cell suspension) subcutaneously in the right flank. Tumors are calipered in two dimensions to monitor growth as the mean volume approached the desired 80-120 mm3 range. Tumor size, in mm3, is calculated from:




  
    Tumor
    ⁢
    
      
    
    ⁢
    volume
  
  =
  
    
      
        w
        2
      
      ×
      l
    
    2
  




where w=width and l=length, in mm, of the tumor. Tumor weight can be estimated with the assumption that 1 mg is equivalent to 1 mm3 of tumor volume. After 10-30 days mice with 108-126 mm3 tumors are sorted into treatment groups with mean tumor volumes of 117-119 mm3.

Test Articles

Test compounds are stored at room temperature and protected from light. On each treatment day, fresh compound formulations are prepared by suspending the powders in 0.5% sodium carboxymethylcellulose (NaCMC) and 0.1% Tween® 80 in deionized water. Compound 141 (free base) is dissolved in sterile saline and the pH is adjusted to 4.5 with HCl fresh every day. The vehicles, 0.5% NaCMC and 0.1% Tween® 80 in deionized water or sterile saline pH 4.5, are used to treat the control groups at the same schedules. Formulations are stored away from light at 4° C. prior to administration. Unless otherwise specified, compounds referred to and tested in this experiment are in their specific salt forms mentioned in this paragraph.
Treatment Plan
Mice are treated at compound doses ranging from 12.5-600 mg/kg and at TID (three time a day every 8 h), BID (2 times a day every 12 h) or QD (once a day) schedules for various amounts of days by oral gavage or injections via the intraperitoneal route. Each dose is delivered in a volume of 0.2 mL/20 g mouse (10 mL/kg), and adjusted for the last recorded weight of individual animals. The maximal treatment length is 28 days.
Median Tumor Volume (MTV) and Tumor Growth Inhibition (TGI) Analysis
Treatment efficacy is determined on the last treatment day. MTV(n), the median tumor volume for the number of animals, n, evaluable on the last day, is determined for each group. Percent tumor growth inhibition (% TGI) can be defined several ways. First, the difference between the MTV(n) of the designated control group and the MTV(n) of the drug-treated group is expressed as a percentage of the MTV(n) of the control group:




  
    %
    ⁢
    
      
    
    ⁢
    T
    ⁢
    
      
    
    ⁢
    G
    ⁢
    
      
    
    ⁢
    I
  
  =
  
    
      (
      
        
          
            M
            ⁢
            
              
            
            ⁢
            T
            ⁢
            
              
            
            ⁢
            
              
                V
                ⁡
                
                  (
                  n
                  )
                
              
              control
            
          
          -
          
            M
            ⁢
            
              
            
            ⁢
            T
            ⁢
            
              
            
            ⁢
            
              
                V
                ⁡
                
                  (
                  n
                  )
                
              
              treated
            
          
        
        
          M
          ⁢
          
            
          
          ⁢
          T
          ⁢
          
            
          
          ⁢
          
            
              V
              ⁡
              
                (
                n
                )
              
            
            control
          
        
      
      )
    
    ×
    100
  




Another way of calculating % TGI is taking the change of the tumor size from day 1 to day n into account with n being the last treatment day.



  
    
      %
      ⁢
      
        
      
      ⁢
      T
      ⁢
      
        
      
      ⁢
      G
      ⁢
      
        
      
      ⁢
      I
    
    =
    
      
        (
        
          
            
              Δ
              ⁢
              
                
              
              ⁢
              M
              ⁢
              
                
              
              ⁢
              T
              ⁢
              
                
              
              ⁢
              
                V
                control
              
            
            -
            
              Δ
              ⁢
              
                
              
              ⁢
              M
              ⁢
              
                
              
              ⁢
              T
              ⁢
              
                
              
              ⁢
              
                V
                treated
              
            
          
          
            Δ
            ⁢
            
              
            
            ⁢
            M
            ⁢
            
              
            
            ⁢
            T
            ⁢
            
              
            
            ⁢
            
              V
              control
            
          
        
        )
      
      ×
      100
    
  




  
    
      Δ
      ⁢
      
        
      
      ⁢
      M
      ⁢
      
        
      
      ⁢
      T
      ⁢
      
        
      
      ⁢
      
        V
        control
      
    
    =
    
      
        M
        ⁢
        
          
        
        ⁢
        T
        ⁢
        
          
        
        ⁢
        
          
            V
            ⁡
            
              (
              n
              )
            
          
          control
        
      
      -
      
        M
        ⁢
        
          
        
        ⁢
        T
        ⁢
        
          
        
        ⁢
        
          
            V
            ⁡
            
              (
              1
              )
            
          
          control
        
      
    
  




  
    
      Δ
      ⁢
      
        
      
      ⁢
      M
      ⁢
      
        
      
      ⁢
      T
      ⁢
      
        
      
      ⁢
      
        V
        treated
      
    
    =
    
      
        M
        ⁢
        
          
        
        ⁢
        T
        ⁢
        
          
        
        ⁢
        
          
            V
            ⁡
            
              (
              n
              )
            
          
          treated
        
      
      -
      
        M
        ⁢
        
          
        
        ⁢
        T
        ⁢
        
          
        
        ⁢
        
          
            V
            ⁡
            
              (
              1
              )
            
          
          treated
        
      
    
  



Toxicity

Animals are weighed daily on Days 1-5, and then twice weekly until the completion of the study. The mice are examined frequently for overt signs of any adverse, treatment related side effects, which are documented. Acceptable toxicity for the maximum tolerated dose (MTD) is defined as a group mean BW loss of less than 20% during the test, and not more than 10% mortality due to TR deaths. A death is to be classified as TR if it is attributable to treatment side effects as evidenced by clinical signs and/or necropsy, or due to unknown causes during the dosing period. A death is to be classified as NTR if there is evidence that the death is unrelated to treatment side effects. NTR deaths during the dosing interval would typically be categorized as NTRa (due to an accident or human error) or NTRm (due to necropsy-confirmed tumor dissemination by invasion and/or metastasis). Orally treated animals that die from unknown causes during the dosing period may be classified as NTRu when group performance does not support a TR classification and necropsy, to rule out a dosing error, is not feasible.
Sampling
On days 7 or 28 during the studies mice are sampled in a pre-specified fashion to assess target inhibition in tumors. Tumors are harvested from specified mice under RNAse free conditions and bisected. Frozen tumor tissue from each animal is snap frozen in liquid N2 and pulverized with a mortar and pestle.
Statistical and Graphical Analyses
All statistical and graphical analyses are performed with Prism 3.03 (GraphPad) for Windows. To test statistical significance between the control and treated groups over the whole treatment time course a repeated measures ANOVA test followed by Dunnets multiple comparison post test or a 2 way ANOVA test are employed. Prism reports results as non-significant (ns) at P>0.05, significant (symbolized by “*”) at 0.01<P<0.05, very significant (“**”) at 0.001<P<0.01 and extremely significant (“***”) at P<0.001.
Histone Extraction
For isolation of histones, 60-90 mg tumor tissue is homogenized in 1.5 ml nuclear extraction buffer (10 mM Tris-HCl, 10 mM MgCl2, 25 mM KCl, 1% Triton X-100, 8.6% Sucrose, plus a Roche protease inhibitor tablet 1836145) and incubated on ice for 5 minutes. Nuclei are collected by centrifugation at 600 g for 5 minutes at 4° C. and washed once in PBS. Supernatant is removed and histones extracted for one hour, with vortexing every 15 minutes, with 0.4 N cold sulfuric acid. Extracts are clarified by centrifugation at 10,000 g for 10 minutes at 4° C. and transferred to a fresh microcentrifuge tube containing 10× volume of ice cold acetone. Histones are precipitated at −20° C. for 2 hours-overnight, pelleted by centrifugation at 10,000 g for 10 minutes, and resuspended in water.
ELISA
Histones are prepared in equivalent concentrations in coating buffer (PBS+0.05% BSA) yielding 0.5 ng/ul of sample, and 100 ul of sample or standard is added in duplicate to 2 96-well ELISA plates (Thermo Labsystems, Immulon 4HBX #3885). The plates are sealed and incubated overnight at 4° C. The following day, plates are washed 3× with 300 ul/well PBST (PBS+0.05% Tween 20; 10×PBST, KPL #51-14-02) on a Bio Tek plate washer. Plates are blocked with 300 ul/well of diluent (PBS+2% BSA+0.05% Tween 20), incubated at RT for 2 hours, and washed 3× with PBST. All antibodies are diluted in diluent. 100 ul/well of anti-H3K27me3 (CST #9733, 50% glycerol stock 1:1,000) or anti-total H3 (Abcam ab1791, 50% glycerol 1:10,000) is added to each plate. Plates are incubated for 90 min at RT and washed 3× with PBST. 100 ul/well of anti-Rb-IgG-HRP (Cell Signaling Technology, 7074) is added 1:2,000 to the H3K27Me3 plate and 1:6,000 to the H3 plate and incubated for 90 min at RT. Plates are washed 4× with PBST. For detection, 100 ul/well of TMB substrate (BioFx Laboratories, #TMBS) is added and plates incubated in the dark at RT for 5 min. Reaction is stopped with 100 ul/well 1N H2SO4. Absorbance at 450 nm is read on SpectaMax M5 Microplate reader.
7 Day PD Study
In order to test whether a compound can modulate the H3K27me3 histone mark in tumors in vivo, WSU-DLCL2 xenograft tumor bearing mice are treated with the compound at either 200 mg/kg BID or 400 mg/kg QD or vehicle (BID schedule) for 7 days. There are 4 animals per group. Animals are euthanized 3 h after the last dose and tumor is preserved in a frozen state as described above. Following histone extraction the samples are applied to ELISA assays using antibodies directed against the trimethylated state of histone H3K27 (H3K27me3) or total histone H3. Based on these data the ratio of globally methylated to total H3K27 is calculated. The mean global methylation ratios for all groups as measured by ELISA indicates target inhibition range compared to vehicle.
28 Day Efficacy Study in WSU-DLCL2 Xenograft Model
In order to test whether a compound could induce a tumor growth inhibition in vivo WSU-DLCL2 xenograft tumor bearing mice are treated with the compound at 12.5, 25 or 50 mg/kg QD for 28 days via intraperitoneal injection. Tumor volume and body weights are determined twice a week. A parallel cohort of mice (n=4 per group) is treated at the same doses for 7 days, and mice are euthanized on day 7, 3 h after the last dose for tumor sampling and assessment of target inhibition. The result of the ELISA measuring global methylation of H3K27me3 normalized to total H3 is determined.
Efficacy Study with Increasing Doses in WSU-DLCL2 Xenograft Model
In order to test whether a compound could induce an anti-tumor effect in vivo, WSU-DLCL2 xenograft tumor bearing mice are treated with a compound at, e.g., 37.5, 75 or 150 mg/kg TID for 28 days. There are 12 mice per group for the efficacy arm of the experiment. A parallel cohort is dosed for 7 days at the same doses and schedules for assessment of target inhibition after 7 days (n=6 per group). The tumor growth over the treatment course of 28 days for vehicle and compound treated groups is measured.
Histones are extracted from tumors collected after 7 days of dosing (parallel PD cohort) and at the end of the study on day 28 for the efficacy cohort (3 h after the last dose for both cohorts). The H3K27me3 methyl mark is assessed for modulation with treatment in a dose dependent matter.
Efficacy Study at Different Dose Schedules
To assess whether a compound would lead to tumor growth inhibition at other dosing schedules but TID a WSU-DLCL2 xenograft efficacy study is performed where TID, BID and QD schedules are compared side by side. There are 12 animals per group, and mice are treated for 28 days. The tumor growth over the treatment course of 28 days for vehicle and compound treated groups is measured.
On day 28 mice are euthanized and tumors were collected 3 h after the last dose for assessment of target inhibition.
Example 11: Anti-Cancer Effect on the KARPAS-422 Human Diffused Large B-Cell Lymphoma Mouse Xenograft Model
A test compound is analyzed for its anti-cancer activity in KARPAS-422 mouse xenograft model, which is a human diffused large B-Cell lymphoma xenograft model. 45 female of CAnN.Cg-Foxn1nu/CrlCrlj mice (Charles River Laboratories Japan) with KARPAS-422 tumors whose mean tumor volume (TV) reached approximately 150 mm3 are selected based on their TVs, and are randomly divided into five groups. The oral administration of compound (e.g., 80.5, 161, 322, and 644 mg/kg) or vehicle is started on day 1. Compound is given once daily on day 1 and day 29 and twice daily everyday from day 2 to day 28. The administration volume (0.1 mL/10 g body weight) is calculated from the body weight before administration. The TV and body weight were measured twice a week. The design for this experiment is shown in Table 5.







TABLE 5







Dosing Scheme











No. of




Group
Animals
Treatment (twice a day)
Route and Schedule





1
9
Vehicle (0.5% Methyl
PO; BID × 28 days




Cellulose, 0.1% Tween-80)


2
9
80.5 mg/kg Compound
PO; BID × 28 days


3
9
161 mg/kg Compound
PO; BID × 28 days


4
9
322 mg/kg Compound
PO; BID × 28 days


5
9
644 mg/kg Compound
PO; bid × 28 days









TV is calculated from caliper measurements by the formula for the volume of a prolate ellipsoid (LxW2)/2 where L and W are the respective orthogonal length and width measurements (mm).
Data are expressed as the mean±standard deviation (SD). The differences in TV between the vehicle-treated and compound-treated groups are analyzed by a repeated measures analysis of variance (ANOVA) followed by the Dunnett-type multiple comparison test. A value of P<0.05 (two sided) is considered statistically significant. Statistical analyses are performed using the Prism 5 software package version 5.04 (GraphPad Software, Inc., CA, USA).
The invention can be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.

## Claims

1. A compound of Formula (I) or a pharmaceutically acceptable salt thereof:




wherein
X1 is NR7 or CR7;
X2 is N, NR8, CR8, O, or S;
X3 is NR8, CR8, O, or S;
X4 is C;
Y1 is CH;
Y2 is CR6;
Y3 is N;
each of R5, R9, and R10, independently, is H or C1-C6 alkyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl;
each R6 independently is H, halo, ORa, —NRaRb, —C(O)Ra, —C(O)ORa, —C(O)NRaRb, —NRbC(O)Ra, —S(O)2Ra, —S(O)2NRaRb, or RS2, in which each of Ra and Rb, independently is H or RS3 and each of RS2 and RS3, independently, is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl; or Ra and Rb, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom; and
each of RS2, RS3, and the 4 to 7-membered heterocycloalkyl ring containing Ra and Rb, is optionally substituted with one or more -Q2-T2, wherein Q2 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T2 is H, halo, cyano, —ORc, —NRcRd, —(NRcRdRd′)+A−, —C(O)Rc, —C(O)ORc, —C(O)NRcRd, —NRdC(O)Rc, —NRdC(O)ORc, —S(O)2Rc, —S(O)2NRcRd, or RS4, in which each of Rc, Rd, and Rd′, independently is H or RS5, A− is a pharmaceutically acceptable anion, each of RS4 and RS5, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, or Rc and Rd, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom, and each of RS4, RS5, and the 4 to 7-membered heterocycloalkyl ring containing Rc and Rd, is optionally substituted with one or more -Q3-T3, wherein Q3 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T3 is selected from the group consisting of H, halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 6-membered heteroaryl, ORe, COORe, —S(O)2Re, —NReRf, and —C(O)NReRf, each of Re and Rf independently being H or C1-C6 alkyl optionally substituted with OH, O—C1-C6 alkyl, or NH—C1-C6 alkyl; or -Q3-T3 is oxo; or -Q2-T2 is oxo; or any two neighboring -Q2-T2, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl; provided that -Q2-T2 is not H;
each R7 independently is -Q4-T4, in which Q4 is a bond, C1-C4 alkyl linker, or C2-C4 alkenyl linker, each linker optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T4 is H, halo, cyano, NRgRh, —ORg, —C(O)Rg, —C(O)ORg, —C(O)NRgRh, —C(O)NRgORh, —NRgC(O)Rh, —S(O)2Rg, or RS6, in which each of Rg and Rh, independently is H or RS7, each of RS6 and RS7, independently is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and each of RS6 and RS7 is optionally substituted with one or more -Q5-T5, wherein Q5 is a bond, C(O), C(O)NRk, NRkC(O), NRk, S(O)2, NRkS(O)2, or C1-C3 alkyl linker, Rk being H or C1-C6 alkyl, and T5 is H, halo, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, hydroxyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl, and T5 is optionally substituted with one or more substituents selected from the group consisting of halo, C1-C6 alkyl, hydroxyl, cyano, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl except when T5 is H, halo, hydroxyl, or cyano; or -Q5-T5 is oxo; provided that -Q4-T4 is not H; and
each R8, independently, is H, halo, hydroxyl, COOH, cyano, RS8, ORS8, or COORS8, in which RS8 is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, and RS8 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, and di-C1-C6 alkylamino;
X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRn, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
n is 0, 1, 2, 3, 4, or 5, and when n is 0 or 1 then X is a bicyclic aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more -Q7-T7;
provided that at most one of X2 and X3 is O or S, and X1, X2, X3, X4, Y1, Y2, and Y3 are assigned such that the





moiety in Formula (I) is a bicyclic heteroaryl system.

2. The compound of claim 1, wherein the compound is of Formula (Ia):




wherein R7 is -Q4-T4, wherein Q4 is a bond or methyl linker, T4 is C1-C6 alkyl optionally substituted with one or more -Q5-T5, C3-C8 cycloalkyl optionally substituted with one or more -Q5-T5, or 4- to 14-membered heterocycloalkyl optionally substituted with one or more -Q5-T5.

3. A compound of Formula (Ia) or a pharmaceutically acceptable salt thereof:




wherein
X2 is N, NR8, CR8, O, or S;
X3 is NR8, CR8, O, or S;
X4 is C;
Y1 is CH;
Y3 is N;
each R6 independently is H, halo, ORa, —NRaRb, —C(O)Ra, —C(O)ORa, —C(O)NRaRb, —NRbC(O)Ra, —S(O)2Ra, —S(O)2NRaRb, or RS2, in which each of Ra and Rb, independently is H or RS3 and each of RS2 and RS3, independently, is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl; or Ra and Rb, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom; and
each of RS2, RS3, and the 4 to 7-membered heterocycloalkyl ring containing Ra and Rb, is optionally substituted with one or more -Q2-T2, wherein Q2 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T2 is H, halo, cyano, —ORc, —NRcRd, —(NRcRdRd′)+A−, —C(O)Rc, —C(O)ORc, —C(O)NRcRd, —NRdC(O)Rc, —NRdC(O)ORc, —S(O)2Rc, —S(O)2NRcRd, or RS4, in which each of Rc, Rd, and Rd′, independently is H or RS5, A− is a pharmaceutically acceptable anion, each of RS4 and RS5, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, or Rc and Rd, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom, and each of RS4, RS5, and the 4 to 7-membered heterocycloalkyl ring containing Rc and Rd, is optionally substituted with one or more -Q3-T3, wherein Q3 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T3 is selected from the group consisting of H, halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 6-membered heteroaryl, ORe, COORe, —S(O)2Re, —NReRf, and —C(O)NReRf, each of Re and Rf independently being H or C1-C6 alkyl optionally substituted with OH, O—C1-C6 alkyl, or NH—C1-C6 alkyl; or -Q3-T3 is oxo; or -Q2-T2 is oxo; or any two neighboring -Q2-T2, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl; provided that -Q2-T2 is not H;
R7 is tetrahydropyranyl, piperidine substituted by 1, 2, or 3 C1-4 alkyl groups, or cyclohexyl substituted by N(C1-4 alkyl)2 wherein one or both of the C1-4 alkyl is optionally substituted with C1-6 alkoxyl;
each R8, independently, is H, halo, hydroxyl, COOH, cyano, RS8, ORS8, or COORS8, in which RS8 is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, and RS8 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, and di-C1-C6 alkylamino;
X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
n is 0, 1, 2, 3, 4, or 5;
provided that at most one of X2 and X3 is O or S, and X2, X3, X4, Y1, and Y3 are assigned such that the





moiety in Formula (Ia) is a bicyclic heteroaryl system.

4. A compound of Formula (I) or a pharmaceutically acceptable salt thereof:




wherein
X1 is NR7 or CR7;
X2 is N, NR8, CR8, O, or S;
X3 is NR8, CR8, O, or S;
X4 is C;
Y1 is CH;
Y2 is CR6;
Y3 is N;
each of R5, R9 and R10 independently, is H or C1-C6 alkyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl;
each R6 independently is H, halo, ORa, —NRaRb, —C(O)Ra, —C(O)ORa, —C(O)NRaRb, —NRbC(O)Ra, —S(O)2Ra, —S(O)2NRaRb, or RS2, in which each of Ra and Rb, independently is H or RS3 and each of RS2 and RS3, independently, is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl; or Ra and Rb, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom; and
each of RS2, RS3, and the 4 to 7-membered heterocycloalkyl ring containing Ra and Rb, is optionally substituted with one or more -Q2-T2, wherein Q2 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T2 is H, halo, cyano, —NRcRd, —(NRcRdRd′)+A−, —C(O)Rc, —C(O)ORc, —C(O)NRcRd, —NRdC(O)Rc, —NRdC(O)ORc, —S(O)2Rc, —S(O)2NRcRd, or RS4, in which each of Rc, Rd, and Rd′, independently is H or RS5, A− is a pharmaceutically acceptable anion, each of RS4 and RS5, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, or Rc and Rd, together with the N atom to which they are attached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1 additional heteroatoms to the N atom, and each of RS4, RS5, and the 4 to 7-membered heterocycloalkyl ring containing Rc and Rd, is optionally substituted with one or more -Q3-T3, wherein Q3 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T3 is selected from the group consisting of H, halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, 5 to 6-membered heteroaryl, ORe, COORe, —S(O)2Re, —NReRf, and —C(O)NReRf, each of Re and Rf independently being H or C1-C6 alkyl optionally substituted with OH, O—C1-C6 alkyl, or NH—C1-C6 alkyl; or -Q3-T3 is oxo; or -Q2-T2 is oxo; or any two neighboring -Q2-T2, together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl; provided that -Q2-T2 is not H;
R7 is sec-butyl, cyclopentyl, or iso-propyl;
each R8, independently, is H, halo, hydroxyl, COOH, cyano, RS8, ORS8, or COORS8, in which RS8 is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, and RS8 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, and di-C1-C6 alkylamino;
X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
n is 0, 1, 2, 3, 4, or 5;
provided that at most one of X2 and X3 is O or S, and X1, X2, X3, X4, Y1, Y2, and Y3 are assigned such that the





moiety in Formula (I) is a bicyclic heteroaryl system.

5. A compound of Formula (I) or a pharmaceutically acceptable salt thereof:




wherein
X1 is NR7 or CR7;
X2 is N, NR8, CR8, O, or S;
X3 is NR8, CR8, O, or S;
X4 is C;
Y1 is CH;
Y2 is CR6;
Y3 is N;
each of R5, R9, and R10, independently, is H or C1-C6 alkyl optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl;
R6 is




each R7 independently is -Q4-T4, in which Q4 is a bond, C1-C4 alkyl linker, or C2-C4 alkenyl linker, each linker optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T4 is H, halo, cyano, NRgRh, —ORg, —C(O)Rg, —C(O)ORg, —C(O)NRgRh, —C(O)NRgORh, —NRgC(O)Rh, —S(O)2Rg, or RS6, in which each of Rg and Rh, independently is H or RS7, each of RS6 and RS7, independently is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, or 5 to 6-membered heteroaryl, and each of RS6 and RS7 is optionally substituted with one or more -Q5-T5, wherein Q5 is a bond, C(O), C(O)NRk, NRkC(O), NRk, S(O)2, NRkS(O)2, or C1-C3 alkyl linker, Rk being H or C1-C6 alkyl, and T5 is H, halo, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, hydroxyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C1-C6 alkylene-C3-C8 cycloalkyl, C6-C10 aryl, C1-C6 alkylene-C6-C10 aryl, 4 to 7-membered heterocycloalkyl, C1-C6 alkylene-4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, or C1-C6 alkylene-5- or 6-membered heteroaryl, and T5 is optionally substituted with one or more substituents selected from the group consisting of halo, C1-C6 alkyl, hydroxyl, cyano, C1-C6 alkoxyl, O—C1-C4 alkylene-C1-C4 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 7-membered heterocycloalkyl, and 5 to 6-membered heteroaryl except when T5 is H, halo, hydroxyl, or cyano; or -Q5-T5 is oxo; provided that -Q4-T4 is not H; and
each R8, independently, is H, halo, hydroxyl, COOH, cyano, RS8, ORS8, or COORS8, in which RS8 is C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, amino, mono-C1-C6 alkylamino, or di-C1-C6 alkylamino, and RS8 is optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, and di-C1-C6 alkylamino;
X is a monocyclic or bicyclic 5 to 10-membered saturated, unsaturated, or aromatic ring containing 2-4 heteroatom ring members and optionally substituted with one or more -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9 in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more wherein -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl; and
n is 0, 1, 2, 3, 4, or 5;
provided that at most one of X2 and X3 is O or S, and X1, X2, X3, X4, Y1, Y2, and Y3 are assigned such that the





moiety in Formula (I) is a bicyclic heteroaryl system.

6. The compound of claim 1, wherein X is




wherein
each of D1, D2, and D3, independently, is CR901 or N, provided that at least one of D1, D2, and D3 is N;
D4 is O, S, or NR902; and
each R901 and R902, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

7. The compound of claim 1, wherein X is




wherein
each of E1, E2, and E4, independently, is CR903 or N, provided that at least one of E1, E2, and E4 is N;
E3 is O, S, or NR904; and
each of R903 and R904, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

8. The compound of claim 1, wherein X is




wherein
G1 is O, S, or NR907;
each of G2, G3, and G4, independently, is N or CR908, provided that at least one of G2, G3, and G4 is N; and
each of R905, R906, R907, and R908, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

9. The compound of claim 1, wherein X is




wherein
each of J1, J2, J3, and J4, independently, is N or CR911, provided that at least one of J1, J2, J3, and J4 is N; and
each of R909, R910, and R911, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

10. The compound of claim 1, wherein X is




wherein
each of K1, K2, K3, and K4, independently, is N or CR914, provided that at least one of K1, K2, K3, and K4 is N; and
each of R912, R913, and R914, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

11. The compound of claim 1, wherein X is




wherein
each of U1, U3, and U4, independently, is N or CR917, provided that at least one of U1, U3, and U4 is N;
U2 is O, S, or NR918; and
each of R915, R916, R917 and R918, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

12. The compound of claim 1, wherein X is




wherein
each of V1 and V2, independently, is N or CR919, provided that at least one of V1 and V2 is N; V3 is O, S, or NR920;
each of V4, V5, and V6 is O, S, or NR921, or CR922R923; and
each of R919, R920, R921, R922, and R923, independently, is -Q7-T7, wherein Q7 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T7 is H, —ORn, —NRnRr, —C(O)Rn, —C(O)ORn, —C(O)NRnRr, —S(O)2Rn, —S(O)2NRnRr, or RS9, in which each of Rn and Rr, independently is H or RS10, each of RS9 and RS10, independently, is C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, or Rn and Rr, together with the N atom to which they are attached, form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom, and each of RS9, RS10, and the 4 to 12-membered heterocycloalkyl ring formed by Rn and Rr, is optionally substituted with one or more -Q8-T8, wherein Q8 is a bond or C1-C3 alkyl linker each optionally substituted with halo, cyano, hydroxyl or C1-C6 alkoxy, and T8 is selected from the group consisting of halo, cyano, C1-C6 alkyl, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl, ORs, COORs, —S(O)2Rs, —NRsRt, and —C(O)NRsRt, each of Rs and Rt independently being H or C1-C6 alkyl, or -Q8-T8 is oxo; or -Q7-T7 is oxo; or any two neighboring -Q7-T7 together with the atoms to which they are attached form a 5- or 6-membered ring optionally containing 1-4 heteroatoms selected from N, O and S and optionally substituted with one or more substituents selected from the group consisting of halo, hydroxyl, COOH, C(O)O—C1-C6 alkyl, cyano, C1-C6 alkoxyl, amino, mono-C1-C6 alkylamino, di-C1-C6 alkylamino, C3-C8 cycloalkyl, C6-C10 aryl, 4 to 12-membered heterocycloalkyl, and 5- or 6-membered heteroaryl.

13. The compound of claim 1, wherein X is imidazol-2-yl, imidazol-4-yl, triazol-3-yl, 3H-imidazo[4,5-c]pyridin-7-yl, 1H-benzo[d]imidazol-4-yl, 1H-indazol-7-yl, isoxazol-3-yl, thiazol-2-yl, 1H-pyrazolo[4,3-c]pyridin-7-yl, imidazo[1,2-c]pyrimidin-8-yl, 1,4,6,7-tetrahydropyrano[4,3-c]pyrazol-7-yl, 1,4,6,7-tetrahydropyrano[3,4-]imidazol-7-yl, 4,5,6,7-tetrahydro-1H-benzo[d]imidazol-4-yl, 7H-pyrrolo[2,3-d]pyrimidine-4-yl, 9H-purine-6-yl, 7-methyl-[1,2,4]triazolo[4,3-a]pyridin-5-ol-6-yl, [1,2,4]triazolo[4,3-a]pyridin-6-yl, 3-fluoro-1,5-dimethyl-1H-pyrazol-4-yl, or 5-fluoro-1,3-dimethyl-1H-pyrazol-4-yl.

14. The compound of claim 1, wherein the compound is of the following formula:



wherein Z is

15. A pharmaceutical composition comprising a compound of claim 1 or a pharmaceutically acceptable salt thereof and a pharmaceutically acceptable carrier.

16. The compound of claim 2, wherein
R7 is sec-butyl, cyclopentyl, isopropyl,




n is 0, 1, or 2; and
R6 is

17. The compound of claim 2, wherein
n is 0, 1, or 2; and
R7 is sec-butyl, cyclopentyl, isopropyl,














wherein R′′′ is T5, —C(O)T5, or S(O)2T5.