Synthesis and Characterization of Transition-State Analogue Inhibitors against Human DNA Methyltransferase 1

Hypermethylation of CpG regions by
human DNA methyltransferase
1 (DNMT1) silences tumor-suppression genes, and inhibition of DNMT1
can reactivate silenced genes. The 5-azacytidines are approved inhibitors
of DNMT1, but their mutagenic mechanism limits their utility. A synthon
approach from the analogues of S-adenosylhomocysteine,
methionine, and deoxycytidine recapitulated the chemical features
of the DNMT1 transition state in the synthesis of 16 chemically stable
transition-state mimics. Inhibitors causing both full and partial
inhibition of purified DNMT1 were characterized. The inhibitors show
modest selectivity for DNMT1 versus DNMT3b. Active-site docking predicts
inhibitor interactions with S-adenosyl-l-methionine and deoxycytidine regions of the catalytic site, validated
by direct binding analysis. Inhibitor action with purified DNMT1 is
not reflected in cultured cells. A partial inhibitor activated cellular
DNA methylation, and a full inhibitor had no effect on cellular DNA
methylation. These compounds provide chemical access to a new family
of noncovalent DNMT chemical scaffolds for use in DNA methyltransferases.