©1996-2019. All Rights Reserved. Online Journal of Bioinformatics . You may not store these pages in any form except for your own personal use. All other usage or distribution is illegal under international copyright treaties. Permission to use any of these pages in any other way besides the before mentioned must be gained in writing from the publisher. This article is exclusively copyrighted in its entirety to OJB publications. This article may be copied once but may not be, reproduced or re-transmitted without the express permission of the editors. This journal satisfies the refereeing requirements (DEST) for the Higher Education Research Data Collection (Australia). Linking:To link to this page or any pages linking to this page you must link directly to this page only here rather than put up your own page.
Online Journal of Bioinformatics ©
Volume 14(2):186-196, 2013
Structure based virtual screening for DNS methyl transferase-1 inhibitors.
Madhu Sudhana Saddala, P. Jyothi and A. Usha Rani
Dept. of Zoology, DBT-Bioinformatics center, Sri Venkateswara University, Tirupati.
Saddala MS, Jyothi P, Usha Rani A., Structure based virtual screening for DNS methyl transferase-1 inhibitors. Onl J Bioinform., 14(2):186-196, 2013. DNA methylation alteration is an epigenetic event that can be induced by cadmium. Virtual inhibitors for DNA methyltransferase (DNMT-1) are described. DNMT-1 was energy minimized and subjected to molecular dynamic simulations with NAMD 2.9 software and CHARMM27 force field in water. The receptor structure was minimized with 25,000 steps for 500 ps and simulated 100,000 steps for 2ns. 5000 compounds were screened from the ZINC database through structure based Virtual screening using Zebularine as the reference natural drug. The screened compounds were docked into the active site of the protein using Autodock Vina in PyRx . ZINC00638152, ZINC08426899, ZINC11582506, ZINC15636661, ZINC22055993 and ZINC25694354 had high binding affinities. Lead hit compounds were tested for toxicity and bioavailability using Osiris and Molinspiration online servers. Active sites of Lys 162, Asp701, Pro 955, Leu986, Gly1150, Ala1173, Cys1191, Pro1224, Leu1146, Thy1494, His1502, and Val1586 appeared to have a role in binding and catalytic activity.
KEYWORDS: DNMT1, dynamics, docking, methylation inhibition, Zinc database, Autodock Vina