Peptide vaccine against chikungunya virus: immuno-informatics combined with molecular docking approach

Abstract

Background: Chikungunya virus (CHIKV), causes massive outbreaks of chikungunya infection in several regions of Asia, Africa and Central/South America. Being positive sense RNA virus, CHIKV replication within the host resulting in its genome mutation and led to difficulties in creation of vaccine, drugs and treatment strategies. Vector control strategy has been a gold standard to combat spreading of CHIKV infection, but to eradicate a species from the face of earth is not an easy task. Therefore, alongside vector control, there is a dire need to prevent the infection through vaccine as well as through antiviral strategies.

Methods: This study was designed to find out conserved B cell and T cell epitopes of CHIKV structural proteins through immuno-informatics and computational approaches, which may play an important role in evoking the immune responses against CHIKV.

Results: Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for CHIKV structural polyprotein and their antigenicity was calculated. Among B-cell epitopes "PPFGAGRPGQFGDI" showed a high antigenicity score and it may be highly immunogenic. In case of T cell epitopes, MHC class I peptides 'TAECKDKNL' and MHC class II peptides 'VRYKCNCGG' were found extremely antigenic.

Conclusion: The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of CHIKV disease.

Keywords: B cell and T cell epitopes; Chikungunya virus (CHIKV); Computational approaches; Vaccine.

Fig. 1

a Prediction of antigenic determinants using Kolaskar and Tongaonkar antigenicity scale, b hydrophilicity prediction using Parker hydrophilicity, c surface accessibility analyses using Emini surface accessibility scale, d beta turns analyses in structural polyprotein using Chou and Fasman beta turn prediction, e flexibility analyses using Karplus and Schulz flexibility scale

Fig. 2

Site of predicted epitopes on chains of the crystal structure of CHIKV structural polyprotein highlighted through cartoon representation

Fig. 3

Phylogenetic tree illustrating the evolutionary conserveness of CHIKV strains form 23 countries

Fig. 4

a Graphical representation of human HLA-B7 allele (shown in cyan and purple) with bound peptide 1 “VMHKKEVVL” (yellow). Multiple residues of the receptor protein (green) interact (dotted lines) with the peptide residues (red). b LigX interaction diagram illustrating the chain A and chains B residues interacting via hydrogen bond (green), two water mediated interaction (yellow), vanderval interaction (blue) to the peptide 1

Fig. 5

a Graphical representation of human HLA-B7 allele (shown in cyan and purple) with bound peptide 2 “GTLKIQVSL” (blue). Multiple residues of the receptor protein (green) interact (dotted lines) with the peptide residues (red). b LigX interaction diagram illustrating the chain A residues interacting via hydrogen bond (green), one water mediated interaction (yellow), vanderval interaction (blue) to the peptide 2

Fig. 6

a Graphical representation of human HLA-B7 allele (shown in cyan and purple) with bound peptide 3 (yellow). Multiple residues of the receptor protein (green) interact (dotted lines) with the peptide residues (red). b LigX interaction diagram illustrating the chain A residues interacting via hydrogen bond (green) and vanderval interaction (blue) to the peptide 3

Fig. 7

a Graphical representation of human HLA-B7 allele (shown in cyan and purple) with bound peptide 4 (black). Multiple residues of the receptor protein (green) interact (dotted lines) with the peptide residues (red). b LigX interaction diagram illustrating the chain A residues interacting via hydrogen bond (green) and vanderval interaction (blue) to the peptide 4