IN SILICO EPITOPE PREDICTION AND HOMOLOGY MODELING OF ENVELOPE SURFACE GLYCOPROTEIN GP160, PRECURSOR REGION FROM HUMAN IMMUNO DEFICIENCY VIRUS -1Abstract
The development of a highly effective AIDS vaccine will depend on the success of designing immunogens that will elicit immune response against broadly neutralizing antibodies to naturally circulating strains of HIV- can be done by reverse vaccinology. Reverse vaccinology is a good approach for provoking the broadly neutralizing antibody response by identifying the specific epitopes i.e. surface proteins. The 3D structure of a protein is a prerequisite for structure based drug design as well as for identifying the conformational epitopes that are essential for the designing vaccines. The objective of this study is to identify peptides that can be used as potential vaccines against HIV using bioinformatics approach. B-cell epitopes which are present in the structural, regulatory and accessory proteins encoded by Clade-B HIV-1 genome were predicted using epitope prediction servers (RANKPEP) available in the public domains. Homology modeling approach was used to determine the 3D structures of these predicted epitopes. In addition to these studies, modes of binding of these epitopes to broadly neutralizing antibodies 2G12, B12, 4E10 and PG9 were also investigated by docking studies.
Amol M. Kanampalliwar*, Amandeep Girdhar, Rakesh Arya, Rupali Saxena and Archana Tiwari
School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya, Bhopal , MP, India
27 January, 2014
05 April, 2014
07 June, 2014
01 July, 2014