OnLine Journal of Biological Sciences

Molecular Dynamics Simulation of DENV RNA-Dependent RNA-Polymerase with Potential Inhibitor of Disulfide Cyclic Peptide

Usman Sumo Friend Tambunan, Raima Syahidah Noors, Arli Aditya Parikesit, Elyana and Wahyu Ronggo

DOI : 10.3844/ojbsci.2011.48.62

OnLine Journal of Biological Sciences

Volume 11, Issue 2

Pages 48-62

Abstract

Problem statement: Our researches have proposed two ligands of disulfide cyclic polypeptide, which are CDEEC and CDGSC as potential inhibitor of DENV RNA-dependent RNApolymerase by molecular docking. Approach: Methodological approach was conducted to determine the best ligand to act as inhibitor. Molecular docking simulation was conducted without a solvent in which enzyme was made rigid and ligand was left free to find the most suitable conformation. In actual cellular system there is a solvent which makes the enzyme to have a dynamic movement. Results: Therefore in this study, Molecular Dynamic (MD) simulation was performed to estimate more reliable condition of enzyme-ligand complex. In this study, molecular dynamics simulation was performed during 5 ns with two different temperatures, 300 and 312 K. At the end of MD simulation at 300 K, CDEEC bound to two RdRp important residues, Arg-729 and Arg-737 while CDGSC didn’t bind to any important residues. Conclusion: Simulation at 312 K also showed almost similar result. CDEEC was bound to two RdRP important residues, Arg-737 and Ser-710, whereas CDGSC didn’t bind to any important residues. Based on the result of these two simulations, CDEEC is proposed as a better inhibitor of RdRp dengue virus and feasible to be developed as anti-dengue drug.

Copyright

© 2011 Usman Sumo Friend Tambunan, Raima Syahidah Noors, Arli Aditya Parikesit, Elyana and Wahyu Ronggo. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.