Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses

Abstract

Being a Positive sense RNA virus the recent reemergence of Chikungunya and Mayaro virus has taken the concern of the leading scientific communities of the world. Though the outbreak of Mayaro virus is limited to Neotropical region only, Chikungunya is already identified in over 60 countries around the world. Besides, the lack of a strong protective treatment, misdiagnosis issue and co-circulation of both the viruses calls for a new strategy which could potentially prevent these infections from spreading. In this study, we therefore, identified the peptide based vaccine candidates e.g. epitopes for B cell and T cell from Chikungunya virus which also showed to be homologous to the Mayaro virus through immuno-informatics and computational approaches. Final epitopes identified from the most antigenic structural polyprotein of both the viruses were 5 for CD8+ T cell Epitopes ( 209 KPGDSGRPI 217 , 219 TGTMGHFIL 227 , 239 ALSVVTWNK 247 , 98 KPGRRERMC 106 and 100 GRRERMCMK 108 ), 2 epitopes for CD4+ T cell ( 105 MCMKIENDCIFEVKH 119 and 502 DRTLLSQQSGNVKIT 516 ) and a single epitope for B cell ( 504 GGRFTIPTGAGKPGDSGRPI 518 ). Analysis of our predicted epitopes for population coverage showed prominent population coverage (92.43%) around the world. Finally, molecular docking simulation of the foreseen T cell epitopes with respondent HLA alleles secured good HLA-epitope interaction. This study was directed towards the discovery of potential antigenic epitopes which can open up a new skyline to design novel vaccines for combating both of the diseases at the same time.

Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

“…Molecular docking analysis was conducted to further emphasize the supposition as to which mutants have more negative impact on the protein. Molecular docking is a popular In silico method which is particularly used in drug designing and vaccine designing approaches to resolve the binding status between a drug/vaccine with its corresponding macromolecules [ 63 , 64 ]. Ribociclib is such kind of drug (act as CDK4/6 inhibitor) used for treatment of HR+, HER2– advanced or metastatic breast cancer.…”

“…silico method which is particularly used in drug designing and vaccine designing approaches to resolve the binding status between a drug/vaccine with its corresponding macromolecules [63,64]. Ribociclib is such kind of drug (act as CDK4/6 inhibitor) used for treatment of HR+, HER2-advanced or metastatic breast cancer.…”

Mayaro Virus Non-Structural Protein 2 Circumvents the Induction of Interferon in Part by Depleting Host Transcription Initiation Factor IIE Subunit 2

“…Given that this emerging alphavirus has the potential to cause large multicontinental outbreaks similar to CHIKV [ 8 , 10 , 62 ], it is critical to understand how it manipulates host pathways during infection. Indeed, there is considerable interest in developing therapeutic and prophylactic therapies against MAYV [ 14 , 15 , 16 , 17 , 18 ]. The findings from the present study may be of use for development and application of therapeutics against MAYV and other alphaviruses.…”

“…Imported cases of MAYV infection have already been reported in Europe and North America and are expected to increase in the future [ 11 , 12 , 13 ]. While therapeutics and vaccine candidates against MAYV are being investigated [ 14 , 15 , 16 , 17 , 18 ], currently there are no specific antiviral measures that could be used in the case of a MAYV outbreak. As such, further understanding of how this virus affects vital host cell pathways may facilitate development of effective antivirals.…”

Immunoinformatics and molecular dynamics approaches: Next generation vaccine design against West Nile virus

“…The growing advances in the field of bioinformatics open a new era to design next generation vaccines through the knowledge of immunoinformatics; the detailed protocol and immune responses have been widely reviewed in published literatures [28][29][30][31]. In recent years, reverse vaccinology approach has been utilized to design epitope based multi-subunit vaccines against different pathogens and cancers [32][33][34][35][36][37][38][39][40][41]. Sufficient cellular and humoral immune responses triggered by multi-epitope based vaccine against various pathogens including Epstein-Barr virus, Crimean-Congo Hemorrhagic Fever Virus and Chlamydia trachomatis [42][43][44][45].…”