Chikungunya Virus Vaccine Development: Through Computational Proteome Exploration for Finding of HLA and cTAP Binding Novel Epitopes as Vaccine Candidates

Abstract

Chikungunya virus is a major arbovirus of great public health concern in the whole world, but no vaccine is yet available, still advance therapeutic treatment and effective vaccines are in progress. The present multistep screening and structural binding analysis with CHIKV proteome exploration can be crucial in the development phase of CHIKV epitope based vaccine. The approach employed in two phases (i) Sequence based screening of peptides through propred and IEDB Server (ii) Structure based study through autodocking and NAMD VMD simulation analysis. Among all 29 extracted peptides, only two peptides 2 LLANTTFPC 10 of protein E3 and 98 VNSVAIPLL 106 of protein nsP3 were observed most prominent over all consider parameters such as peptide conserve nature, supertype population coverage, TAP binding, docking and simulation study. During docking interaction study, the best peptide and allele docked complexes such as 2 LLANTTFPC 10 –B*0702 allele and 98 VNSVAIPLL 106 –A*0301 allele exhibited best binding energy of − 3.13 kcal/mol and − 3.19 kcal/mol, respectively, with stable bonding patterns and their motion during NAMD simulation which confirm conserve peptide and allele stable interaction. The current study also exhibited the good docking interaction of both peptides 2 LLANTTFPC 10 and 98 VNSVAIPLL 106 with c TAP1 protein (1jj7 -PDB ID) cavity which confirm as a channel passageway to peptide transport through the cytoplasm to lumen of ER during antigen processing and presentation. Overall, this multistep screening and crosscheck structural binding analysis with an exploration of the complete proteome of CHIKV can be a novel step in the development of CHIKV epitope based vaccine as well as diagnostic development with aspect of time, cost and side effects.

T-cell epitope-based vaccine prediction against Aspergillus fumigatus: a harmful causative agent of aspergillosis

“…Also, docked complex was analysed for simulation analysis, and it was found that they show stable interaction pattern as per the RMSD and RMSF plots. Many previous studies show the importance of immunoinformatic study to support our analysis on fungal epitope determination likewise for Candida auris, Tropheryma whipplei [21,22], dengue [23], human cytomegalovirus [24], and chikungunya [25]. Modern chemi-informatic and immunoinformatics study not only supports rapid vaccine prediction but also provides efficient economic resource management [26][27][28], although immunoinformatic requires wet-lab support as future perspectives for epitope synthesis and animal cell line-dependent validations.…”

Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

“…This examination not just give experiences about characteristic and mutational determination pressures acting at genomic levels of T. whipplei yet besides offer a superior cognizance of transformative improvements in this host-versatile bacterium. This computational examination uncovered the data concerning profoundly translated proteins and enzymes of this bacterium, and the conceivable amino acids that can be considered in epitope-based prophylaxis plan to get the inhibitory effect on bacterial action on its host or to create a better conceivable treatment like in immunoinformatics-based recent studies [ 14 , 15 ]. Ribosomal RNA (16S and 23S) codon usage patterns were analyzed here to determine the changes associated with evolutionary or phylogenetic patterns of the bacterium.…”

An Overview of Indian Biomedical Research on the Chikungunya Virus with Particular Reference to Its Vaccine, an Unmet Medical Need

“…Recently Rahatgi’s group from IITR provided a discernment of CHIKV E2-FL protein immunogenic epitopes, which can be used for the development of novel multiepitope-based anti-CHIKV vaccine strategies [ 211 ]. Kumar’s team conducted an in silico study for the development of a CHIKV epitope-based vaccine as well as diagnostic development [ 212 ]. Sreekumar and colleagues reported through another recent study the probable application of an attenuated CHIKV strain RGCB355/KL08-p75 as a probable candidate for vaccine development [ 213 ].…”