COMBINATION THERAPIES OF WDR5 INHIBITORS AND PD-1 INHIBITORS

1 . A method of treating cancer in a subject having a tumor, comprising administering to the subject a combination comprising: (1) an MLL1-WDR5 protein-protein interaction inhibitor compound of Formula I, or a pharmaceutically acceptable salt thereof, (2) a PD-1 inhibitor, or a pharmaceutically acceptable salt thereof, and (3) a dose of radiation therapy, wherein the compound of Formula I has a structure:

wherein:

A is

E is

each bond is independently a single or double bond;

L 1 is —NH—or —NH—C(═O)—;

each of R 3a , R 3b , R 13a , R 13b is independently hydrogen or a substituent;

X 1 is O, NR 1 , or CR 1a R 1b wherein R 1 is H, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 2 is a bond, —CHR 2a —, —CHR 2b CH 2 —, or —CH 2 CHR 2c , wherein each of R 2a , R 2b , and R 2c is H, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 3 is N or CR 3 , or, when the bond attached to X 3 is a single bond, X 3 may also be NR 3 ,

wherein R 3 is H or a substitutent;

X 4 is N or CR 4 , wherein R 4 is H or a substitutent;

X 5 is N or CR 5 , or, when the bond attached to X 5 is a single bond, X 5 may also be NR 5 ,

wherein R 5 is H or a substitutent;

X 6 is N or CR 6 , wherein R 6 is H or a substitutent;

X 7 is N or CR 7 , wherein R 7 is H or a substitutent;

X 8 is N or CR 8 , wherein R 8 is H or a substitutent;

X 9 is N or CR 9 , wherein R 9 is H or a substitutent;

X 10 is N or CR 10 , wherein R 10 is H or a substitutent;

X 11 is N or CR 11 , wherein R 11 is H or a substitutent;

X 12 is N or CR 12 , where R 12 is H or a substitutent;

each of R 13a and R 13b is independently H or a substitutent; and

R 14 is H or a substituent.

2 . A method of increasing one or more anti-tumor T cell types in a subject having a tumor, comprising: administering to the subject a combination therapy comprising: (1) a compound of Formula I, or a pharmaceutically acceptable salt thereof, (2) a PD-1 inhibitor, or a pharmaceutically acceptable salt thereof, and (3) a dose of radiation therapy, wherein the compound of Formula I has the structure:

wherein:

A is

E is

each bond is independently a single or double bond;

L 1 is —NH—or —NH—C(═O)—;

each of R 3a , R 3b , R 13a , R 13b is independently hydrogen or a substituent;

X 1 is O, NR 1 , or CR 1a R 1b wherein R 1 is H, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 2 is a bond, —CHR 2a —, —CHR 2b CH 2 —, or —CH 2 CHR 2c , wherein each of R 2a , R 2b , and R 2c is H, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 3 is N or CR 3 , or, when the bond attached to X 3 is a single bond, X 3 may also be NR 3 ,

wherein R 3 is H or a substitutent;

X 4 is N or CR 4 , wherein R 4 is H or a substitutent;

X 5 is N or CR 5 , or, when the bond attached to X 5 is a single bond, X 5 may also be NR 5 ,

wherein R 5 is H or a substitutent;

X 6 is N or CR 6 , wherein R 6 is H or a substitutent;

X 7 is N or CR 7 , wherein R 7 is H or a substitutent;

X 8 is N or CR 8 , wherein R 8 is H or a substitutent;

X 9 is N or CR 9 , wherein R 9 is H or a substitutent;

X 10 is N or CR 10 , wherein R 10 is H or a substitutent;

X 11 is N or CR 11 , wherein R 11 is H or a substitutent;

X 12 is N or CR 12 , where R 12 is H or a substitutent;

each of R 13a and R 13b is independently H or a substitutent; and

R 14 is H or a substituent.

3 . The method of claim 1 or claim 2 , whereby at least one anti-tumor T cell type is increased in a tumor microenvironment of the tumor in the subject.

4 . A method of inducing at least a two-fold increase in expression of at least one gene associated with anti-tumor T cell infiltration in a tumor in a subject having a tumor, comprising administering to the subject a combination therapy comprising: (1) a compound of Formula I, or a pharmaceutically acceptable salt thereof, (2) a PD-1 inhibitor, or a pharmaceutically acceptable salt thereof, and (3) a dose of radiation therapy, wherein the compound of Formula I has the structure:

wherein:

A is

E is

each bond is independently a single or double bond;

L 1 is —NH—or —NH—C(═O)—;

each of R 3a , R 3b , R 13a , R 13b is independently hydrogen or a substituent;

X 1 is O, NR 1 , or CR 1a R 1b wherein R 1 is H, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 2 is a bond, —CHR 2a —, —CHR 2b CH 2 —, or —CH 2 CHR 2c , wherein each of R 2a , R 2b , and R 2c is H, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 3 is N or CR 3 , or, when the bond attached to X 3 is a single bond, X 3 may also be NR 3 ,

wherein R 3 is H or a substitutent;

X 4 is N or CR 4 , wherein R 4 is H or a substitutent;

X 5 is N or CR 5 , or, when the bond attached to X 5 is a single bond, X 5 may also be NR 5 ,

wherein R 5 is H or a substitutent;

X 6 is N or CR 6 , wherein R 6 is H or a substitutent;

X 7 is N or CR 7 , wherein R 7 is H or a substitutent;

X 8 is N or CR 8 , wherein R 8 is H or a substitutent;

X 9 is N or CR 9 , wherein R 9 is H or a substitutent;

X 10 is N or CR 10 , wherein R 10 is H or a substitutent;

X 11 is N or CR 11 , wherein R 11 is H or a substitutent;

X 12 is N or CR 12 , where R 12 is H or a substitutent;

each of R 13a and R 13b is independently H or a substitutent; and

R 14 is H or a substituent.

5 . The method of claim 4 , wherein the gene associated with an anti tumor T cell is Batf2,

Cd274 (PD-L 1 ), Dnase1L 3 , Gbp2, Infg (Inf-γ), IL18 bp, IL24, Lag3, Pdcd11g2 (PD-L 2 ), Tgtp1,

Tnfsf10, or a combination of any two or more thereof.

6 . The method of any one of claims 1-5 , wherein the PD-1 inhibitor is an anti-PD-1 antibody.

7 . The method of claim 2 or claim 3 , wherein the one or more T cell types comprise one or more of tumor-infiltrating T lymphocytes (TILs) and cytotoxic T lymphocytes (CTLs).

8 . The method of any one of claims 1-7 , wherein a ratio of tumor infiltrating leukocytes (TIL) to regulatory T cells (Tregs) in the tumor is increased.

9 . The method of any one of claims 1-8 , wherein one or more of regulatory macrophages (M2), tumor-associated myeloid cells (TAMCs), myeloid-derived suppressor cells (M-MDSCs) and polymorphonucler myeloid-derived suppressor cells (PMN-MDSCs) are reduced in the tumor.

10 . The method of claim 9 , wherein the decrease in one or more of M2, TAMCs, M-MDSCs,

and PMN-MDSCs is measured relative to a baseline obtained from a biopsy taken at or prior to commencement of treatment with the combination.

11 . The method of any of claims 1-10 , wherein A is:

wherein R 14 is a substituent with the structure:

wherein Y is absent, —O—, —S—, —C(O)—, —CH 2 O —, —(CO)O—, —O(CO)—, —NR 15f —, —C(O)NR 15g —, or —NR 15h C(O)—;

m is 0 to 6;

R 15 is hydrogen, amino, hydroxyl, thiol, carboxyl, cyano, C 1 -C 4 alkyl, substituted C 1 -C 4 alkyl, C 1 -C 6 alkoxy, substituted or unsubstituted phenyl, substituted or unsubstituted C 3 -C 6 cycloalkyl, substituted or unsubstituted nitrogen- or oxygen-containing 3 to 7 membered heterocyclic ring, or substituted or unsubstituted 3 to 7 membered heterocyclic ring containing both nitrogen and oxygen, wherein substituents on the heterocyclic ring can optionally be on the hetero atom;

unsaturated heterocycloalkyl containg nitrogen or oxygen or both, —NR 15a COR 15b , —OR 15c —, C(O)O—R 15c , —O(CO)O—R 15c —C(O)NR 15d R 15e or —NR 15d R 15e , wherein

R 15a is hydrogen, C 1 -C 4 alkyl, C 1 -C 4 haloalkyl, substituted or unsubstituted phenyl,

R 15b is hydrogen, amino, hydroxyl, C 1 -C 4 alkyl, C 1 -C 4 alkoxy, substituted or unsubstituted phenyl, substituted or unsubstituted nitrogen- or oxygen-containing 3 to 7 membered heterocyclic ring, wherein substituents on the heterocyclic ring can be on the hetero atom,

R 15d and R 15e are each independently hydrogen, C 1 -C 4 alkyl, substituted or unsubstituted phenyl, substituted or unsubstituted C 3 -C 7 cycloalkyl, substituted or unsubstituted nitrogen- or oxygen- or both containing 3 to 7 membered heterocyclic ring, wherein the heterocyclic ring may be aryl, partially unsaturated, or fully saturated, wherein substituents on the heterocyclic ring can be on the hetero atom, or

R 15c is C 1 -C 4 alkyl, C 1 -C 4 haloalkyl, substituted or unsubstituted phenyl, substituted or unsubstituted C 3 -C 7 cycloalkyl, substituted or unsubstituted nitrogen- or oxygen- or both containing 3 to 7 membered heterocyclic ring; wherein substituents on the heterocyclic ring can be on the hetero atom;

R 15d and R 15e together form: a nitrogen-, oxygen-, or nitrogen and oxygen, or nitrogen and nitrogen or oxygen and oxygen containing 3 to 7 membered heterocyclic ring, wherein the heterocyclic ring is optionally substituted with one, two or three substituents which are independently halogen, C 1 -C 4 alkyl, C 1 -C 4 alkoxy, amino, hydroxyl, thiol, carboxyl, cyano, trifluoromethyl or imidazolyl; wherein substituents on the heterocyclic ring can be on the hetero atom;

R 15f , R 15g , and R 15h each independently represents hydrogen, C 1 -C 4 alkyl, C 1 -C 4 haloalkyl, or substituted or unsubstituted phenyl, wherein the phenyl is substituted with one, two or three of halogen, amino, cyano, hydroxyl, trifluoro C 1 -C 4 alkyl, C 1 -C 4 alkoxy, carboxyl, or imidazolyl.

12 . The method of any of claims 1-11 , wherein A is:

13 . The method of claim 11 or 12 , wherein Y is absent.

14 . The method of claim 13 , wherein Y is —O—, —S—, —C(O)—, —CH 2 O —, —(CO)O—, —O(CO)—, —NR 15f , —C(O)NR 15g , or NR 15h C(O)—.

15 . The method of claim 13 , wherein Y is —O—, —NR 15f , or —C(O)NR 15g —, wherein R 15f and R 15g are independently hydrogen or C 1 -C 4 alkyl.

16 . The method of any of claims 1-11 , wherein A is:

wherein: each of R 8 , R 9 , R 10 , R 11 , and R 12 , when present, is independently selected from H, C 1 -C 6 alkyl; substituted C 1 -C 6 alkyl (wherein each substituent is a 3-7-membered cycloalkyl, a 3-7-membered heterocyclic ring containing nitrogen or oxygen, or a 3-7-membered heterocyclic ring containing both nitrogen and oxygen); unsubstituted, mono-substituted, di-substituted or tri-substituted 3-7-membered heterocyclic ring containing nitrogen, oxygen or both (wherein the heterocyclic ring is aromatic, partially unsaturated or fully saturated and each substituent is independently C 1 -C 6 alkyl, or NR D R E ); —NHCOR E ; —CONR D R E ; —COR E ; or —OR G ; wherein:

R E is: hydrogen, C 1 -C 6 alkyl, 3-7-membered cycloalkyl, 3-7-membered heterocycloalkyl containing nitrogen, oxygen or both, or substituted C 1 -C 6 alkyl (wherein the substituent is 3-7-membered cycloalkyl, 3-7-membered heterocyclic ring containing nitrogen or oxygen, or 3-7-membered heterocyclic ring containing both nitrogen and oxygen);

R D , R E each independently is: hydrogen, C 1 -C 6 alkyl, phenyl or substituted phenyl, substituted or unsubstituted 3-7-membered heterocyclic ring containing nitrogen, oxygen or both; substituted C 1 -C 6 alkyl (wherein each substituent on R D and R E is independently a 3-7-membered cycloalkyl, a 3-7-membered heterocyclic ring containing nitrogen or oxygen, or a 3-7-membered heterocyclic ring containing both nitrogen and oxygen);

R F is: C 1 -C 6 alkyl, C 1 -C 6 substituted alkyl (wherein the substituent is C 3 -C 6 cycloalkyl), or NR D R E (wherein R D and R E are defined in the immediate foregoing paragraph);

R G is: C 1 -C 6 alkyl, C 1 -C 6 substituted alkyl (wherein the substituent is C 3 -C 6 cycloalkyl).

17 . The method of any of claims 1-11 , wherein A is:

wherein:

X 9 is N,

X 11 is N,

X 8 is CR 8 , wherein R 8 is H or a substitutent,

X 12 is CR 12 , wherein R 12 is H or a substitutent,

X 10 is CR 10 , wherein R 10 is H or a substitutent.

18 . The method of any of claims 1-11 , wherein A is:

wherein R 14 is a substituted 5-6-membered aromatic heterocyclic ring containing oxygen, nitrogen or both, wherein each heterocyclic ring substituent is independently C 1 -C 4 alkyl, substituted C 1 -C 4 alkyl (wherein the alkyl substituent is —NR 14a R 14b , wherein R 14a and R 14b are independently C 1 -C 4 alkyl or 3-7-membered heterocyclic ring containing nitrogen or oxygen or both, or R 14a and R 14b are linked together to form a 3-7-membered heterocyclic ring containing nitrogen, oxygen or both).

19 . The method of any of claims 1 to 18 , wherein E is:

wherein each R 3 , R 4 , R 5 , R 6 , R 7 , when present, is independently hydrogen, halogen, amino, cyano, hydroxy, thiol, nitro, C 1 -C 6 alkyl, C 3 -C 7 cycloalkyl, C 1 -C 6 alkoxy, C 3 -C 7 cycloalkoxy, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfinyl, C 1 -C 6 alkylsulfonyl, hydroxy-(C 1 -C 6 )alkyl, amino-(C 1 -C 6 )alkyl, or —C(O)NR H R I , wherein R H and R I are each independently hydrogen or C 1 -C 6 alkyl.

20 . The method of any of claims 1 to 18 , wherein E is:

wherein each R 3 , R 4 , and R 5 when present, is independently hydrogen, halogen, amino, cyano, hydroxy, thiol, nitro, C 1 -C 6 alkyl, C 3 -C 7 cycloalkyl, C 1 -C 6 alkoxy, C 3 -C 7 cycloalkoxy, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfinyl, C 1 -C 6 alkylsulfonyl, hydroxy-(C 1 -C 6 )alkyl, amino-(C 1 -C 6 )alkyl, or —C(O)NR H R I , wherein R H and R I are each independently hydrogen or C 1 -C 6 alkyl.

21 . The method of any of claims 1 to 20 , wherein L 1 is —NH—C(═O)—.

22 . The method of any of claims 1 to 20 , wherein L 1 is —NH—.

23 . The method of any of claims 1 to 22 , wherein:

R 3a is hydrogen, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

R 3b is hydrogen, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

R 13a is hydrogen, halogen, methyl, methoxy, difluoromethoxy, or trifluoromethoxy;

R 13b is hydrogen, halogen, methyl, methoxy, difluoromethoxy, or trifluoromethoxy;

X 1 is NR 1 , wherein R 1 is hydrogen, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

X 2 is —CHR 2a —, —CHR 2b CH 2 —, or —CH 2 CHR 2c , wherein each of R 2a , R 2b , and R 2c is hydrogen, C 1 -C 6 alkyl, or C 3 -C 6 cycloalkyl;

each of R 4 , R 5 , R 6 , and R 7 is independently hydrogen, halogen, amino, cyano, hydroxy, thiol, nitro, C 1 -C 6 alkyl, C 3 -C 7 cycloalkyl, C 1 -C 6 alkoxy, C 3 -C 7 cycloalkoxy, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfinyl, C 1 -C 6 alkylsulfonyl, hydroxy-(C 1 -C 6 )alkyl, amino-(C 1 -C 6 )alkyl, or —C(O)NR A R B , wherein R A and R B are each independently hydrogen or C 1 -C 6 alkyl.

24 . The method of any of claims 1-23 , wherein:

X 3 is CR 3 , wherein R 3 is H or a substitutent;

X 4 is CR 4 , wherein R 4 is H or a substitutent;

X 5 is CR 5 , wherein R 5 is H or a substitutent.

25 . The method of claim 24 , wherein E is:

X 6 is CR 6 , wherein R 6 is H or a substitutent; and

X 7 is CR 7 , wherein R 7 is H or a substitutent.

26 . The method of claim 24 , wherein E is:

and R 6 is H or a substituent.

27 . The method of any of claims 1-23 , wherein:

X 3 is N;

X 4 is CR 4 , wherein R 4 is H or a substituent; and

X 5 is CR 5 , wherein R 5 is H or a substitutent.

28 . The method of claim 27 , wherein E is:

X 6 is CR 6 , wherein R 6 is H or a substitutent;

X 7 is CR 7 , wherein R 7 is H or a substitutent.

29 . The method of claim 27 , wherein E is:

and R 6 is H or a substituent.

30 . The method of any of claims 1-23 , wherein

X 3 is CR 3 , wherein R 3 is H or a substitutent;

X 4 is N; and

X 5 is CR 5 , wherein R 5 is H or a substitutent.

31 . The method of claim 30 , wherein E is:

X 6 is CR 6 , wherein R 6 is H or a substitutent; and

X 7 is CR 7 , wherein R 7 is H or a substitutent.

32 . The method of claim 30 , wherein E is:

and R 6 is H or a substituent.

33 . The method of any of claims 1-23 , wherein

X 3 is CR 3 , wherein R 3 is H or a substitutent;

X 4 is CR 4 , wherein R 4 is H or a substitutent; and

X 5 is N.

34 . The method of claim 33 , wherein E is:

X 6 is CR 6 , wherein R 6 is H or a substitutent; and

X 7 is CR 7 , wherein R 7 is H or a substitutent.

35 . The method of claim 34 , wherein E is:

and R 6 is H or a substituent.

36 . The method of any of claims 1-23 , wherein

X 3 and X 4 are N; and

X 5 is CR 5 , wherein R 5 is H or a substitutent.

37 . The method of claim 36 , wherein E is:

X 6 is CR 6 , wherein R 6 is H or a substitutent; and

X 7 is CR 7 , wherein R 7 is H or a substitutent.

38 . The method of claim 36 , wherein E is:

and R 6 is H or a substituent.

39 . The method of any of claims 1-23 , wherein E is:

X 3 is CR 3 , wherein R 3 is H or a substitutent;

X 4 is CR 4 , wherein R 4 is H or a substitutent;

X 5 is CR 5 , wherein R 5 is H or a substitutent; and

X 6 and X 7 are N.

40 . The method of any of claims 1-23 , wherein one, two, or three of X 3 , X 4 , and X 5 are N.

41 . The method of one of claims 1-23 , wherein at least one of X 3 , X 4 , and X 5 is N.

42 . The method of claim 41 , wherein only one of X 3 , X 4 , and X 5 is N.

43 . The method of claim 39 , wherein X 6 is CR 6 and X 7 is CR 7 .

44 . The method of claim 41 or claim 42 , wherein X 3 is CR 3 , X 4 is N, and X 5 is CR 5 .

45 . The method of any of claims 1-44 , wherein each of R 3 , R 4 , R 5 , R 6 , and R 7 is hydrogen, halogen, amino, cyano, hydroxy, thiol, nitro, C 1 -C 6 alkyl, C 3 -C 7 cycloalkyl, C 1 -C 6 alkoxy, C 3 -C 7 cycloalkoxy, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfinyl, C 1 -C 6 alkylsulfonyl, hydroxy-(C 1 -C 6 )alkyl, amino-(C 1 -C 6 )alkyl, or —C(O)NR A R B , wherein R A and R B are each independently hydrogen or C 1 -C 6 alkyl.

46 . The method of any of claims 1-44 , wherein each of R 3 , R 5 , R 6 and R 7 is independently hydrogen, halogen, C 1 -C 6 alkyl, C 3 -C 7 cycloalkyl, C 1 -C 6 alkoxy, C 3 -C 7 cycloalkoxy, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfinyl, C 1 -C 6 alkylsulfonyl, nitro or cyano.

47 . The method of any of claims 1-11 , wherein E is:

wherein

each of R 3 , R 4 , R 5 , R 6 , and R 7 is hydrogen, halogen, cyano, nitro, C 1 -C 6 alkyl, C 3 -C 7 cycloalkyl, C 1 -C 6 alkoxy, C 3 -C 7 cycloalkoxy, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, C 1 -C 6 alkylthio, C 1 -C 6 alkylsulfinyl, or C 1 -C 6 alkylsulfonyl.

48 . The method of claim 47 , wherein X 3 is NH,

49 . The method of any of claims 1-48 , wherein the compound of Formula I is selected from:

50 . The method of claim 49 , wherein the compound of Formula I is Formula (Id):

51 . The method of any of claims 1-50 , wherein:

a. the compound of Formula I is formulated in a first pharmaceutical composition comprising the compound of Formula I, or a pharmaceutically acceptable salt, and pharmaceutically acceptable excipient; and

b. the PD-1 inhibitor is formulated in a second pharmaceutical composition comprising the PD-1 inhibitor, or a pharmaceutically acceptable salt thereof, and pharmaceutically acceptable excipient.

52 . The method of any one of claims 1-51 , wherein the subject has received one or more previous treatments for the cancer.

53 . The method of claim 52 , wherein the subject has previously received immunotherapy.

54 . The method of claim 53 , wherein the subject has previously received immunotherapy with one or more checkpoint inhibitors.

55 . The method of claim 54 , wherein at least one of the one or more checkpoint inhibitors is selected from one or more PD-1 inhibitors, one or more PD-L 1 inhibitors, one or more CTLA-4 inhibitors, and combinations of two or more thereof.

56 . The method recited in any one of claims 1-55 , wherein the dose of radiation therapy comprises external beam radiation therapy or internal radiation therapy.

57 . The method recited in claim 56 , wherein the dose of anti-cancer radiation therapy comprises external beam radiation therapy and the external beam radiation therapy comprises stereotactic body radiation therapy (SBRT), three-dimensional conformal radiation therapy (3D-CRT), or intensity modulated radiation therapy (IMRT).

58 . The method recited in claim 56 , wherein the dose of anti-cancer radiation therapy comprises internal radiation therapy comprising brachytherapy or radiactive liquid treatment.

59 . The method recited in any one of claims 1-58 , for use in treatment of cancer in a subject in need of such treatment.

60 . A process of making the combination recited in any of claims 1-59 , wherein the combination is for use in the treatment of cancer in a subject in need of such treatment.