Inhibitors of human EZH2, and methods of use thereof

• US 9,175,331 B2
• Filed: 03/12/2012
• Issued: 11/03/2015
• Est. Priority Date: 09/10/2010
• Status: Active Grant

• Current Assignee: Epizyme, Inc. (Ipsen Sa)
• Original Assignee: Epizyme, Inc. (Ipsen Sa)
• Inventors: Kuntz, Kevin Wayne, Knutson, Sarah Kathleen, Wigle, Timothy James Nelson
• Primary Examiner(s): Leith, Nancy J
• Application Number:
  US13/418,242
• Publication Number:
  US 20130040906A1
• Time in Patent Office: 1,331 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: A61K 31/4412 having oxo groups directly attached to the heterocyclic ring
• CPC Class Codes: A61K 31/4427 containing further heterocyclic ring systems
• CPC Class Codes: A61K 31/4439 containing a five-membered ring with nitrogen as a ring hetero atom, e.g. omeprazole nicotine A61K31/465
• CPC Class Codes: A61K 31/444 containing a six-membered ring with nitrogen as a ring heteroatom, e.g. amrinone
• CPC Class Codes: A61K 31/4545 containing a six-membered ring with nitrogen as a ring hetero atom, e.g. pipamperone, anabasine
• CPC Class Codes: A61K 31/496 Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene or sparfloxacin
• CPC Class Codes: A61K 31/497 containing further heterocyclic rings
• CPC Class Codes: A61K 31/5377 not condensed and containing further heterocyclic rings, e.g. timolol
• CPC Class Codes: A61K 31/551 having two nitrogen atoms, e.g. dilazep
• CPC Class Codes: A61K 31/7076 containing purines, e.g. adenosine, adenylic acid
• CPC Class Codes: A61K 31/711 Natural deoxyribonucleic acids, i.e. containing only 2'-deoxyriboses attached to adenine, guanine, cytosine or thymine and having 3'-5' phosphodiester links
• CPC Class Codes: A61K 38/17 from animals; from humans enzyme inhibitors A61K38/005
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: C07D 405/12 linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 473/34 attached in position 6, e.g. adenine
• CPC Class Codes: C12Q 1/48 involving transferase
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: G01N 2333/91011 Methyltransferases (general) (2.1.1.)
• CPC Class Codes: G01N 2333/91017 with definite EC number (2.1.1.-)
• CPC Class Codes: G01N 2800/52 : Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• CPC Class Codes: G01N 33/5011 : for testing antineoplastic activity
• CPC Class Codes: G01N 33/57426 : leukemia
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]

Abstract

The invention relates to inhibition of wild-type and certain mutant forms of human 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). In one embodiment the inhibition is selective for the mutant form of the EZH2, such that trimethylation of H3-K27, which is associated with certain cancers, is inhibited. The methods can be used to treat cancers including follicular lymphoma and diffuse large B-cell lymphoma (DLBCL). Also provided are methods for identifying small molecule selective inhibitors of the mutant forms of EZH2 and also methods for determining responsiveness to an EZH2 inhibitor in a subject.

Claims

1. A method for treating cancer or myelodysplastic syndromes (MDS) in a subject having a Enhancer of Zeste Homolog 2 (EZH2) mutation in the substrate pocket domain of SEQ ID NO:

6, wherein SEQ ID NO;

6 comprises a mutation at amino acid position Y641 of EZH2 of SEQ ID NO;

1, wherein the mutation at amino acid position Y641 is selected from the group consisting of a substitution of phenylalanine (F) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 F);

a substitution of histidine (H) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 H);

a substitution of asparagine (N) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 N); and

a substitution of serine (S) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 S);

comprising administering to said subject a therapeutically effective amount of an EZH2 inhibitor, wherein the EZH2 inhibitor is

2. The method of claim 1, wherein the EZH2 mutation increases EZH2 trimethylation of Lys27 of histone H3 (H3-K27).

4. The method of claim 1 or 3, wherein the EZH2 inhibitor inhibits the conversion of H3K27 to trimethylated H3-K27.

5. The method of claim 1 or 3, wherein administration of the EZH2 inhibitor treats or alleviates a symptom of the cancer or MDS in the subject.

6. The method of claim 1 or 3, wherein the EZH2 mutation is a EZH2 polypeptide mutation or a nucleic acid sequence mutation encoding a mutant EZH2 polypeptide.

7. The method of claim 1 or 3, wherein the cancer is lymphoma.

8. The method of claim 7, wherein the lymphoma is selected from the group consisting of non-Hodgkin lymphoma, follicular lymphoma, and diffuse large B-cell lymphoma.

3. A method for treating cancer or myelodysplastic syndromes (MDS) in a subject having an increased level of trimethylated H3-K27 as a result of an EZH2 mutation in the substrate pocket domain of SEQ ID NO:

6, wherein SEQ ID NO;

6 comprises a mutation at amino acid position Y641 of EZH2 of SEQ ID NO;

1, wherein the mutation at amino acid position Y641 is selected from the group consisting of a substitution of phenylalanine (F) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 F);

a substitution of histidine (H) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 H);

a substitution of asparagine (N) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 N); and

a substitution of serine (S) for the wild type residue tyrosine (Y) at amino acid position 641 of SEQ ID NO;

1 (Y641 S);

comprising administering to said subject a therapeutically effective amount of an EZH2 inhibitor, wherein the EZH2 inhibitor is