Mechanism-Based Inhibitor of DNA Cytosine-5 Methyltransferase by a S_N Ar Reaction with an Oligodeoxyribonucleotide...

In chromatin, 5-methylcytosine (mC), which represents the fifth nucleobase in genomic DNA, plays a role as an inducer of epigenetic changes. Tumor cells exhibit aberrant DNA methylation patterns, and inhibition of human DNA cytosine-5 methyltransferase (DNMT), which is responsible for generating mC in CpG sequences, is an effective strategy to treat various cancers. Here, we describe the design, synthesis, and evaluation of the properties of 2-amino-4-halopyridine-C-nucleosides (d^X P) and oligodeoxyribonucleotides (ODNs) containing d^X P as a novel mechanism-based inhibitor of DNMTs. The designed ODN containing ^X PpG forms a complex with DNMTs by covalent bonding through a nucleophilic aromatic substitution (S_N Ar) reaction, and its cell proliferation activity is investigated. This study suggests that d^X P in a CpG sequence of DNA could serve as a potential nucleic acid drug lead in cancer chemotherapy and a useful chemical probe for studies of epigenetics. Our molecular design using a S_N Ar reaction would be useful for DNMTs and other protein-DNA interactions.