Computer-Based Immunoinformatic Analysis to Predict Candidate T-Cell Epitopes for SARS-CoV-2 Vaccine Design

Abstract

Since the first outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, its high infectivity led to its prevalence around the world in an exceptionally short time. Efforts have been made to control the ongoing outbreak, and among them, vaccine developments are going on high priority. New clinical trials add to growing evidence that vaccines from many countries were highly effective at preventing SARS-CoV-2 virus infection. One of them is B cell-based vaccines, which were common during a pandemic. However, neutralizing antibody therapy becomes less effective when viruses mutate. In order to tackle the problem, we focused on T-cell immune mechanism. In this study, the mutated strains of the virus were selected globally from India (B.1.617.1 and B.1.617.2), United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1), and the overlapping peptides were collected based on mutation sites of S-protein. After that, residue scanning was used to predict the affinity between overlapping peptide and HLA-A*11:01, the most frequent human leukocyte antigen (HLA) allele among the Chinese population. Then, the binding free energy was evaluated with molecular docking to further verify the affinity changes after the mutations happen in the virus genomes. The affinity test results of three epitopes on spike protein from experimental validation were consistent with our predicted results, thereby supporting the inclusion of the epitope 374FSTFKCYGL382 in future vaccine design and providing a useful reference route to improve vaccine development.

In Silico Screening of Prospective MHC Class I and II Restricted T-Cell Based Epitopes of the Spike Protein of SARS-CoV-2 for Designing of a Peptide Vaccine for COVID-19

“…Here, it is worth mentioning that different mutations in positions such as N501, K444, G446, S477 and N439 are reported to enhance the affinity of these residues towards the binding of human ACE2 receptor [26,40]. In accordance with our study, a few recently published articles also documented the promising role of spike protein and T-cell-based epitopes in vaccine design for COVID-19 infection [41,42]. A recently published article by Zannella et al, 2022, showed that synthesized peptides from the selected nucleotide sequences of the genome of coronaviruses were not found to be toxic to the cultured cells and also had resistant properties against serum proteases.…”