Computer-aided design of inhibitors of DNA methyl transferases


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DNA methylation is a covalent chemical modification of DNA catalyzed by DNA methyltransferases (DNMTs). DNMT inhibition is a promising strategy for the epigenetic treatment of cancer and other diseases. In synergy with experimental approaches, computational methods are increasingly being applied to systematically identify and optimize the activity of inhibitors of DNMTs as well as to rationalize the mechanism of established inhibitors at the molecular level. For example, docking studies of established DNMT1 inhibitors with the crystal structure of human DNMT1 gave rise to a structure-based pharmacophore model that suggests key interactions of the inhibitors with the catalytic binding site. Herein we discuss the progress in the discovery and optimization of inhibitors of DNMTs using structure- and ligand-based approaches including homology modeling, docking, pharmacophore modeling, and molecular dynamics. Successful virtual screenings to identify inhibitors with novel scaffolds are also presented. Emerging efforts to use chemoinformatic-based approaches to identify novel inhibitors in large screening collections of natural products and synthetic commercial libraries are also presented.

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