journal of applied pharmaceutical science | 2021
Immunoinformatics approach in designing SARS-CoV-2 vaccine from experimentally determined SARS-CoV T-cell epitopes
Abstract
The rapid transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in the coronavirus disease 2019 pandemic This has caused a global health emergency that warrants accelerated vaccine development Herein, immunoinformatics was utilized in evaluating experimentally validated SARS-CoV CD4+ and CD8+ epitopes retrieved from the database as a potential vaccine against SARS-CoV-2 The protein sequences of SARS-CoV-2 were retrieved Then, multiple sequence alignments and protein variability analysis of retrieved were conducted to obtain highly conserved sequences SARS-CoV epitopes having a 100% overlap with the highly conserved protein sequence of SARS-CoV-2 were further analyzed to identify major histocompatibility complex (MHC) allele binders Epitopes with significant matches to known human protein sequences were excluded to avoid cross-reactivity Population coverage (PC) for an optimized set of CD4+ and CD8+ epitopes was also estimated SARS-CoV-2 epitopes were docked with structures of identified MHC alleles Binding energy and dissociation constant were calculated to analyze the stability of the epitope-MHC complex To further evaluate the stability of interaction, the root mean square deviation plot was obtained using molecular dynamics simulation This work identified a highly conserved potential SARS-CoV-2 vaccine comprising three CD4+ epitopes GAALQIPFAMQMAYRF, MAYRFNGIGVTQNVLY, and QALNTLVKQLSSNFGAI with worldwide PC of 81 81% and seven CD8+ epitopes RLNEVAKNL, VLNDILSRL, GMSRIGMEV, LLLDRLNQL, MEVTPSGTWL, RRPQGLPNNTASWFT, and LQLPQGTTL with global PC of 89 49% © 2020 Leana Rich De Mesa Herrera This is an open access article distributed under the terms of the Creative Commons Attribution 4 0 International License (https://creativecommons org/licenses/by/4 0/)