Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1

• Published in: Chemical biology & drug design 2016-07, Vol.88 (1), p.5-16
• Main Authors: Joshi, Manali, Rajpathak, Shriram N., Narwade, Santosh C., Deobagkar, Deepti
• Format: Article
• Language: English
• Subjects: Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Binding Sites; DNA (Cytosine-5-)-Methyltransferase 1; DNA (Cytosine-5-)-Methyltransferases - antagonists & inhibitors; DNA (Cytosine-5-)-Methyltransferases - chemistry; DNA (Cytosine-5-)-Methyltransferases - metabolism; DNA methylation; DNA methyltransferase1; Drug Screening Assays, Antitumor - methods; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; epigenetics; Female; human DNA methyltransferase1; Humans; inhibitors; MCF-7 Cells; Models, Chemical; molecular dynamics; virtual screening
• ISSN: 1747-0277; 1747-0285
• DOI: 10.1111/cbdd.12741

Human DNA methyltransferase1 (hDNMT1) is responsible for preserving DNA methylation patterns that play important regulatory roles in differentiation and development. Misregulation of DNA methylation has thus been linked to many syndromes, life style diseases, and cancers. Developing specific inhibitors of hDNMT1 is an important challenge in the area since the currently targeted cofactor and substrate binding site share structural features with various proteins. In this work, we generated a structural model of the active form of hDNMT1 and identified that the 5‐methylcytosine (5‐mC) binding site of the hDNMT1 is structurally unique to the protein. This site has been previously demonstrated to be critical for methylation activity. We further performed multiple nanosecond time scale atomistic molecular dynamics simulations of the structural model followed by virtual screening of the Asinex database to identify inhibitors targeting the 5‐mC site. Two compounds were discovered that inhibited hDNMT1 in vitro, one of which also showed inhibition in vivo corroborating the screening procedure. This study thus identifies and attempts to validate for the first time a unique site of hDNMT1 that could be harnessed for rationally designing highly selective and potent hypomethylating agents. This work identifies that the 5‐methylcytosine (5‐mC) binding site of human DNMT1 is structurally unique. This site is previously known to be critical for methylation activity of DNMT1. Based on virtual screening of the 5‐mC binding site followed by in vitro and in vivo testing, we provide proof of concept in the form of a few compounds that abrogate methylation. These results provide a framework for the future design of highly potent and specific hypomethylating drugs.