Inhibitors of human EZH2 and methods of use thereof

• US 8,895,245 B2
• Filed: 09/12/2011
• Issued: 11/25/2014
• Est. Priority Date: 09/10/2010
• Status: Active Grant

• Current Assignee: Epizyme, Inc. (Ipsen Sa)
• Original Assignee: Epizyme, Inc. (Ipsen Sa)
• Inventors: Copeland, Robert A., Richon, Victoria M., Scott, Margaret D., Sneeringer, Christopher J., Kuntz, Kevin W., Knutson, Sarah K., Pollock, Roy M.
• Primary Examiner(s): Qian, Celine
• Assistant Examiner(s): Leith, Nancy J
• Application Number:
  US13/230,703
• Publication Number:
  US 20120071418A1
• Time in Patent Office: 1,170 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: A61K 31/7076 containing purines, e.g. adenosine, adenylic acid
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07D 473/34 attached in position 6, e.g. adenine
• CPC Class Codes: C07D 493/04 Ortho-condensed systems
• CPC Class Codes: C12Q 1/48 involving transferase
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: G01N 2333/91011 Methyltransferases (general) (2.1.1.)
• CPC Class Codes: G01N 33/5011 for testing antineoplastic activity
• CPC Class Codes: G01N 33/57426 leukemia

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 a cancer in a subject, comprising:

a) providing a nucleic acid sample from a biological sample from a subject having a cancer;

b) contacting the nucleic acid sample with at least one primer that hybridizes to a nucleic acid encoding Enhancer of Zeste Homolog 2 (EZH2), wherein the nucleic acid sample comprises at least a portion of SEQ ID NO;

7 or the sequence complementary to SEQ ID NO;

7, wherein the nucleic acid comprises at least one mutation including a mutation at the nucleotides encoding position Tyr641 (Y641) of the EZH2 of SEQ. ID. NO;

1 and wherein the mutation increases EZH2 trimethylation of Lys27 of histone H3 (H3-K27);

c) amplifying a portion of the nucleic acid molecule containing nucleotides encoding an amino acid other than tyrosine at position Y641 of EZH2;

d) detecting the amplified nucleic acid molecule, wherein detection of an amplified nucleic acid molecule containing nucleotides encoding an amino acid other than tyrosine at position Y641 of EZH2 indicates that the subject is responsive to an inhibitor of EZH2; and

e) administering a therapeutically effective amount of an EZH2 inhibitor to the subject.

2. The method of claim 1, wherein said subject has a cancer selected from leukemia, melanoma, and lymphoma, or is at risk of developing a cancer selected from leukemia, melanoma, and lymphoma.

3. The method of claim 1, wherein said detecting is performed by targeted resequencing.

4. The method of claim 3, wherein the targeted resequencing comprises amplifying at least a portion of the nucleic acid with at least one polymerase chain reaction (PCR) primer.

5. The method of claim 2, wherein said lymphoma is selected from the group consisting of Non-Hodgkin'"'"'s lymphoma, follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) of germinal center B cell-like (GCB) subtype.

6. The method of claim 1, wherein the mutation at Y641 is selected from the group consisting of Y641F, Y641H, Y641N and Y641S.

7. The method of claim 1, wherein inhibition of EZH2 is selective inhibition.

8. The method claim 1, wherein the inhibitor of EZH2 is a small molecule.