Irreversible Inhibition of DNMT3A by an N-Mustard Analog of S-Adenosyl-L-methionine

DNA methylation, an important epigenetic modification, is catalyzed by DNA methyltransferases and is essential in the regulation of gene expression. Here, the utility of an N-mustard analog designed to mimic the native methyl donor, S-adenosyl-L-methionine (SAM), was explored with the DNA methyltransferase 3A catalytic domain (DNMT3AC). In lieu of the expected analog transfer to DNA, methyltransferase activity was instead inhibited in a concentration dependent manner. Further investigation into the mechanism of analog inhibition did not reveal a typical competitive mechanism. Instead, mass spectrometry analysis provided direct evidence of two cysteine residues in the SAM binding site covalently modified by the SAM analog and confirmed its’ function as an irreversible inhibitor of DNMT3A.