Immunoinformatics approach for the study of CD4+ epitopes of HIV-1 Gag protein restricted to HLA-DRB1*07 Allele

Jemmy Christy H.1* and Alex An

Abstract

Clade specific vaccine construction strategy would be ideal solution for currently available HIV/AIDS therapy related problems. Immunoinformatics approach based on Stabilized Matrix Method and Neural Network algorithms were adopted to identify Gag epitope based vaccine candidates namely P1-P6(GLNKIVRMYSPTSIL, LGLNKIVRMYSPTSI, LNKIVRMYSPTSILD, NKIVRMYSPTSILDI, IVRMYSPTSILDIKQ,KIVRMYSPTSILDI) restricted to HLA-DRB1*07, a commonly distributed allele among the south Indian population allele would aid significant CD4+ T cell immune response against HIV infection. Three dimensional structure of epitopes P1-P6 modeled using de nova based I Tasser server, and Epitopes binding affinity on HLA-DRB1*07 allele’s binding groove were analyzed using ClusPro based docking strategy. Finally HLA and Epitope interactions, binding energy potential calculated for resulting docked complexes and molecular interactions like conventional hydrogen bonding, non classical carbon hydrogen bonding ,salt bridges were analyzed using DS visualize 4.0. This systematic Insilico study would be helpful in designing Gag epitope based vaccine candidate for HIV infection, further in vitro and in vivo experiments needed for validating these vaccine candidates