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Exploring the polymerase activity of chikungunya viral non structural protein 4 (nsP4) using molecular modeling, epharmacophore and docking studies

S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, Yogesh T. Jasrai and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies.International Journal of Pharmacy and Life Sciences 3(6): 1752-1765.


Abstract



Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non structural protein 4
(nsp4), an important protein target towards the development of antiviral compounds. The present study deals about the development of homology model of nsP4 followed by molecular docking with known RdRp inhibitors
experimented in Hepatitis C virus (HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric binding sites were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands were selected based upon the interaction profiles and a common pharmacophore was developed. Further, RNA templateprimer complex was docked within the template tunnel of modeled nsP4 to study the mode of polymerase activity.


Key-Words: Chikungunya, nsP4, RdRp, Docking, Pharmacophore, Polymerase activity



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Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies

This study will appear in International Journal of Pharmacy and Life Sciences in June Edition.


Exploring the Polymerase Activity of Chikungunya Viral non structural
Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking
Studies


S. Prasanth Kumar, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya
Department of Bioinformatics, ABC, Gujarat University, Ahmedabad- 380009.

Graphical Abstract

S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, Yogesh T. Jasrai* and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies. International Journal of Pharmacy and Life Sciences 3(6): pp. 1752-1765.

Chikungunya viral RNA-dependent RNA polymerase (RdRp) activity is conferred by non

structural protein 4 (nsp4), an important protein target towards the development of antiviral

compounds. The present study deals about the development of homology model of nsP4

followed by molecular docking with known RdRp inhibitors experimented in Hepatitis C virus

(HCV), HIV-1, Paramyxovirus, etc. The predicted catalytic site and two allosteric binding sites

were docked with nucleosidic and non-nucleosidic inhibitors. The best top five scoring ligands

were selected based upon the interaction profiles and a common pharmacophore was developed.

Copyrighted Material. Write a concern to the corresponding author for getting the
coordinates.Contact: prasanthbioinformatics@gmail.com

Grant of 100% Clean Award to Protein Stability Program

Thanks to the Softpedia Database and its Editorial Team for considering the Protein Stability Program to be available as a freeware, added to the database and granted "100% Clean Award"

Grant ward can be viewed here:
http://www.softpedia.com/progClean/Protein-Stability-Clean-210115.html 

Full text article is available here:
http://iioablett.pitt.edu/ojs/index.php/iioablett/article/view/12 

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