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Online Journal of Bioinformatics

Volume 13(1):130-143, 2012

Pharmacophore model of Dengue virus RNA dependent RNA polymerase


Tanima Shree2(M.Sc), J. Asnet Mary1(M.Sc., ADBI), Ravi Kumar3(PhD), T. Madhan Mohan4(PhD), and R. Shenbagarathai1*(PhD)


1PG and Reseach Department of Zoology and Biotechnology, Lady Doak College, Narimedu, Madurai, Tamilnadu, 2Institute of Computational Biology, Bangalore, 3Schrödinger, Bangalore and 4Department of Biotechnology, New Delhi, India.




Shree T, Asnet JM, Kumar R, Mohan T, Shenbagarathai R., Pharmacophore model of Dengue virus RNA dependent RNA polymerase, Online J Bioinform., 13(1):130-143, 2012., The development of a safe and effective therapy for Dengue Fever is a public health priority at a global level. Novel inhibitors for the viral RNA dependent RNA polymerase (RdRp), were identified through Pharmacophore modeling. Using three known inhibitors for RdRp, ribavirin -5'- triphosphate, cytidine-5'-triphosphate and triaryl pyrazoline, a three point pharmacophore model was generated using Phase. In order to screen efficient binders of RdRp from a commercial database (Asinex platinum collection) containing 150,000 compounds, initial screening was performed using pharmacophore search and the obtained hits were further screened using docking protocol. Finally after screening with ADME filters, five compounds with Asinex Id: 71241, 25341, 14859, 5199, 33289 survived. On comparison of free energies of binding of the obtained hits with the known actives, the novel compounds showed appreciable free energies of binding (0.095989, 0.095989, 0.095989, 0.820135, -0.01717 kcal/mol respectively). Hence, these compounds were reported as potential leads to be optimized into potential drugs after being subjected to in vitro screening.

Keywords: DENV, Molecular docking, prime/MM-GBSA, virtual screening, pharmacophore.