In silico prediction of SARS-CoV-2 epitopes for vaccine development

Kitz Paul D Marco; Julia Patricia B Llagas; Maria Teresa A Barzaga; Francisco M Heralde Iii

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In silico prediction of SARS-CoV-2 epitopes for vaccine development

Author: Kitz Paul D. Marco ¹ ; Julia Patricia B. Llagas ¹ ; Maria Teresa A. Barzaga ² ; Francisco M. Heralde III ^{1
,

2}
Author Information

1. Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila City
2. Molecular Diagnostics and Cellular Therapeutics Laboratory, Lung Center of the Philippines, Quezon City
Publication Type:Journal Article
MeSH: COVID-19; SARS-CoV-2; Vaccines; Molecular Docking Simulation
From: Philippine Journal of Health Research and Development 2020;24(4):1-19
CountryPhilippines
Language:English
Abstract: The ongoing coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing major damages in health and economies worldwide. The development of safe and effective vaccines for COVID-19 is of utmost importance yet none have been licensed to date. One of the strategies for vaccine development utilizes dendritic cells which express class I and class II human leukocyte antigen (HLA) molecules. These HLA molecules present the antigenic peptides to T cells which mediate the immune response. Thus, the study aimed to identify SARS-CoV-2 peptides with potential binding to HLA class I and class II molecules using different bioinformatics tools. SYFPEITHI and IEDB were used to predict epitopes for the most common HLA class I and II alleles among Filipinos. The top predicted epitopes were subjected to de novo and template-based molecular docking. Then, binding energies of the generated peptide-HLA complexes to putative T cell receptors were predicted using a homology modeling approach. Several predicted epitopes showed promising MHC and TCR binding, although results varied considerably between the prediction methods used. In particular, the results of de novo and template-based docking methods did not coincide, the latter of which generated complexes that more closely resemble typical peptide-HLA complexes. The results of this study will be validated by the next stage of the vaccine development project which is the in vitro assessment of the T cell responses elicited by dendritic cells pulsed with the candidate peptides.
Full text:pjhrd 36.pdf