Computational epitope prediction and docking studies of glycoprotein- G in Nipah virus Yadav Pramod Kumar1,*, Mishra Mudit2 1Deptartment of Computational Biology & Bioinformatics, JSBB, SHIATS University, Allahabad-211007 (U.P.), India 2School of Bio Sciences and Technology, VIT University, Vellore-632014 (TN), India *Corresponding Author: Pramod Kumar Yadav, Email: pramod.yadav@shiats.edu.in
Online published on 25 April, 2013. Abstract Nipah viruses are highly pathogenic paramyxoviruses that have recently emerged from flying foxes or bats and horses to cause serious disease outbreaks in humans and livestock in many parts of the world. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses and they are designated as Biosafety level 4 pathogens. Many of the viruses are becoming resistant to some antiviral drugs e.g. Admantanes. Therefore, it is necessary to look for an alternative approach to combat the antiviral resistance. Nipah virus contains two membrane glycoproteins: the G glycoprotein, which is required for cell attachment, and the F glycoprotein, which is required for the fusion of the viral and host -cell membranes. The glycoprotein G plays an important role in the immunogenecity in the host cell. In the present work, in silico epitope prediction for glycoprotein-G in Nipah virus was carried out using variety of online tools. For B-cell epitope prediction, BCPREDS server and for the T-cell (MHC-I & MHC-II), IEDB analysis tool was used. In order to perform the docking study, top ranked predicted epitopes for the MHC class-I and MHC class-II were modeled using the Hhpred server. Subsequently, the predicted epitopes for the MHC-I and MHC-II were docked with their respective receptor using the PatchDock server. The lower energy score reveals higher binding affinity of predicted epitopes toward the receptor. It was found that the epitopes ‘QTEGVSNLV’ and ‘LMMTRLAV’ were showing highest binding affinity for the MHC-I and the epitopes ‘SRPGQSQCPRFNTCP’ and ‘GQSQCPRFNTCPEIC’ were showing highest binding affinity for the MHC-II. For the B-cell, epitope ‘TNVWTPPNPNTVYHCSAVYN’ was highest ranked epitope. These predicted epitopes might be promising vaccine candidates for Nipah virus. Top Keywords Epitope prediction, Glycoprotein-G, Modeling, Docking. Top |