Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage

• Published in: Briefings in bioinformatics 2022-01, Vol.23 (1)
• Main Authors: Shukla, Priyank, Pandey, Preeti, Prasad, Bodhayan, Robinson, Tony, Purohit, Rituraj, D’Cruz, Leon G, Tambuwala, Murtaza M, Mutreja, Ankur, Harkin, Jim, Rai, Taranjit Singh, Murray, Elaine K, Gibson, David S, Bjourson, Anthony J
• Format: Article
• Language: English
• Subjects: Antibodies; Autoimmunity; Binding; Bioinformatics; Case Study; Clinical trials; Coronaviruses; COVID-19 Vaccines - chemistry; COVID-19 Vaccines - immunology; Epitopes; Epitopes, B-Lymphocyte - chemistry; Epitopes, B-Lymphocyte - immunology; Epitopes, T-Lymphocyte - chemistry; Epitopes, T-Lymphocyte - immunology; Free energy; Glycoproteins; Histocompatibility antigen HLA; Humans; Immune response (cell-mediated); Informatics; Lymphocytes; Lymphocytes B; Lymphocytes T; Major histocompatibility complex; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Pandemics; Peptides; Population genetics; SARS-CoV-2 - chemistry; SARS-CoV-2 - immunology; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spike glycoprotein; Vaccines; Vaccines, Subunit - chemistry; Vaccines, Subunit - immunology; Viral diseases; Viruses
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbab496

Abstract The current global pandemic due to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has taken a substantial number of lives across the world. Although few vaccines have been rolled-out, a number of vaccine candidates are still under clinical trials at various pharmaceutical companies and laboratories around the world. Considering the intrinsic nature of viruses in mutating and evolving over time, persistent efforts are needed to develop better vaccine candidates. In this study, various immuno-informatics tools and bioinformatics databases were deployed to derive consensus B-cell and T-cell epitope sequences of SARS-CoV-2 spike glycoprotein. This approach has identified four potential epitopes which have the capability to initiate both antibody and cell-mediated immune responses, are non-allergenic and do not trigger autoimmunity. These peptide sequences were also evaluated to show 99.82% of global population coverage based on the genotypic frequencies of HLA binding alleles for both MHC class-I and class-II and are unique for SARS-CoV-2 isolated from human as a host species. Epitope number 2 alone had a global population coverage of 98.2%. Therefore, we further validated binding and interaction of its constituent T-cell epitopes with their corresponding HLA proteins using molecular docking and molecular dynamics simulation experiments, followed by binding free energy calculations with molecular mechanics Poisson–Boltzmann surface area, essential dynamics analysis and free energy landscape analysis. The immuno-informatics pipeline described and the candidate epitopes discovered herein could have significant impact upon efforts to develop globally effective SARS-CoV-2 vaccines.