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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