Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach

Abstract

The recurrent and recent global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has turned into a global concern which has infected more than 42 million people all over the globe, and this number is increasing in hours. Unfortunately, no vaccine or specific treatment is available, which makes it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides [including thymus cells (T-cells) and bone marrow or bursa-derived cells] in the surface glycoprotein (SG) of SARS-CoV-2 which is nontoxic and nonallergenic in nature, nonallergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that cluster of differentiation 4 (CD4 + ) T-cell peptides showed higher cumulative population coverage over cluster of differentiation 8 (CD8 + ) peptides in the 16 different geographical regions of the world. We identified 12 peptides ((LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$80\hbox{--} 90\%$\end{document} identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that the identified peptides are tightly bound in the groove of human leukocyte antigen molecules which can induce the T-cell response. Overall, this study allows us to determine potent peptide antigen targets in the SG on intuitive grounds, which opens up a new horizon in the coronavirus disease (COVID-19) research. However, this study needs experimental validation by in vitro and in vivo .

A common allele of HLA mediates asymptomatic SARS-CoV-2 infection

“…Although our data do not point to a direct mechanism, compelling evidence indicates that B*15:01 is predicted to bind a specific SARS-CoV-2 epitope, WTAGAAAYY, with high affinity. [33][34][35][36][37][38] This epitope has been considered a natural candidate for SARS-Cov-2 vaccine studies 39,40 as it is considered to be highly immunogenic and predicted to elicit a strong CD8+ T cell responses. [41][42][43][44] The dominant recognition and consequent eliciting of immune responses by only a relatively small number of epitopes-immunodominance -is determined by multiple factors, including the binding affinity of the peptide for the HLA molecule.…”

In Silico and In Vivo Evaluation of SARS-CoV-2 Predicted Epitopes-Based Candidate Vaccine

“…A lot of in silico peptide-based prediction studies were implemented to establish a candidate vaccines based on binding with B and T cells with another programs and databases [9,[21][22][23] which lack in vitro or in vivo verification studies.…”

Pharmacophore screening to identify natural origin compounds to target RNA-dependent RNA polymerase (RdRp) of SARS-CoV2

“…Currently, many countries have started vaccination to control this pandemic, but recent mutation reported in SARS-CoV2 can modulate its viral transmission, replication efficiency, and virulence. Identifying peptide-based vaccine [ 59 ] and therapeutic molecule against SARS-CoV2 [ 60 ] can complement the overall control measures. HCQ has been withdrawn as a potential treatment molecule for COVID, but it showed inhibition to SARS-CoV2 in cell-based assays.…”