Discovery of Novel and Selective DNA Methyltransferase 1 Inhibitors by Pharmacophore and Docking-Based Virtual Screening

Abnormal DNA methylation has key roles in the development and progression of diseases including cancer. Mechanism based DNA methyltransferase (DNMT) inhibitors (DNMTi) which inhibit all DNMTs, like 5-azacytidine and decitabine, are in clinical use for the treatment of acute myeloid leukemia and myelodys-plastic syndrome. However, selective inhibitors for specific DNMTs may improve therapy and would be very useful in basic research. Targeting the binding pocket of DNMT1 for the flipped target base, we employed pharmacophore modeling based on known nucleoside-derived DNMTi followed by virtual screening of 500 compounds and docking studies for selection of potential DNMT1 inhibitors. DNMT inhibition assays with selected compounds led to the discovery of novel small molecule scaffolds with a high DNMT1 inhibitory potency. Compound 4b selectively inhibits DNMT1 with K-i in the low micromolar range while inhibition of DNMT3 enzymes is at least 50-fold weaker. Analysis of the inhibitory mechanism revealed non-competitive inhibition with the DNA and mixed with S-adenosyl-L-methionine in good agreement with the mode of action predicted from virtual screening.