Preclinical studies of non-nucleoside DNMT3A/3B inhibitors

PROJECT SUMMARY/ABSTRACT DNA cytosine methylation yielding 5-methylcytosine (5mC) is a major epigenetic modification involved in the regulation of chromatin structure and gene expression. Mammalian DNA methylation is catalyzed by three DNA methyltransferases (DNMTs), belonging to two structurally and functionally distinct families. DNMT3A and

DNMT3B establish the initial cytosine methylation pattern, whereas DNMT1 maintains that pattern on newly replicated DNA. Cancer cells exhibit aberrant DNA methylation patterns, including global hypomethylation, which is associated with low maintenance efficiency, and regional hypermethylation, which is mainly due to abnormal

de novo methylation and/or deficient demethylation. Although the demethylating agents 5-azacytidine and 5- aza-2'-deoxycytidine (decitabine) have been approved by FDA for treating some hematological malignancies, these nucleoside analogs incorporate into DNA, leading to substantial DNA damage and cellular toxicity, and

are ineffective in treating solid tumors. Recently, GlaxoSmithKline (GSK) reported the discovery of a new class of dicyanopyridine-containing DNMT1-selective inhibitors with therapeutic potential. The long-term goal of this research is to develop a highly potent and selective non-nucleoside DNMT3A/3B inhibitor for cancer treatment.

The objective of this 2-year exploratory project is to identify one or more promising leads for further development. The rationale is that remedying hypermethylation by inhibiting DNMT3A/3B would reactivate abnormally silenced genes, including tumor suppressor genes, and thus provide therapeutic benefits for cancer patients. The

proposal is based on preliminary data, generated in the applicants’ laboratories, showing that some dicyanopyridine-containing derivatives and quinoline-based derivatives can selectively inhibit DNMT3A/3B. The applicants propose to perform biochemical and structural studies to improve the potency and selectivity of

DNMT3A/3B inhibitors (Aim 1); and validate the compounds for their potency and selectivity using wild-type and DNMT-deficient mouse embryonic stem cells (mESCs), determine their anti-cancer effects using cancer cell lines with or without mutations in components of the DNA methylation and demethylation enzymes (DNMT3A, TET2

and IDH1/2), and assess their cytotoxicity using untransformed cell lines (Aim 2). The potential impact of identifying non-nucleoside DNMT3A/3B inhibitors is likely to be very substantial..