Insilico Epitopes design against Chikungunya Virus

Abstract

Chikungunya virus has been one of the most serious concerns in recent decades due to its rapid global expansion. Symptoms include a high fever, maculopapular rashes, intense joint and muscular pain, severe headaches, nausea, and fatigue. As it is a viral infection, a vaccination could be considered a promising treatment. In this study, peptide epitopes were created to target the structural polyprotein of CHIKV virus. The various domains of the structural polyprotein were examined for B-cell and T-cell epitopes. A total of 43 B-cell epitopes were identified, among which ‘MCMCARR’ had the highest score and antigenicity. T-cell epitopes, including MHC class I ‘VQDISATAMSWVQK’ and MHC class II ‘VVLCVSFSR’, are highly antigenic, non-allergenic, conserved, and can bind with multiple HLA alleles. In total, ten T-cell epitopes (5 MHC-I and 5 MHC-II) were chosen for three-dimensional structural modelling and molecular docking with HLA alleles and the TLR 3 receptor to assess their physicochemical characteristics. The HDOCK server was utilized for molecular docking, and the Chimaera and Pymol molecular graphics systems were used to visualize three-dimensional models and the docking process of the predicted epitopes with TLR 3 and T-cell epitopes in the HLA binding pocket.