Developing a Subunit Vaccine against SARS-CoV-2 Using Bioinformatics Insights on Cytotoxic T-Lymphocytes (CTLs) Epitopes

Abstract

Background: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates urgent solutions. Despite extensive clinical investigations and trials, no approved treatment has been found. To address this critical need, we designed a study to create and validate a subunit vaccine against SARS-CoV-2 based on cytotoxic T-lymphocyte (CTL) epitopes, using various immunoinformatics tools to gain essential insights into the associated immune responses. Methods: We focused on the spike region of SARS-CoV-2, vital for its survival and virulence, to identify potential antigenic CTL epitopes. Our predictions suggested that these epitopes could significantly stimulate cell-mediated immunity. We selected a sequence comprising three antigenic and nontoxic CTL epitopes to enhance the safety and immunogenicity of the final vaccine. We predicted the three-dimensional (3D) structure of the vaccine and conducted docking studies with human major histocompatibility complex 1 (MHC-1) and toll-like receptor-3 (TLR-3) receptors. Molecular dynamics (MD) simulations were performed to confirm the stability of the vaccine binding with these receptors. Additionally, in-silico Polymerase Chain Reaction (PCR) and cloning were conducted to evaluate the amplification and protein expression of the final vaccine. Results: Molecular docking studies showed strong binding between the vaccine construct and the human leukocyte antigen (HLA)-A heavy alpha chain of MHC-1 and the C-terminal domain of TLR-3 receptors. MD simulations in an explicit system further confirmed the robust and stable binding of CTL epitopes with MHC-1 and TLR-3 receptors. Using computational cloning based on SnapGene, excellent protein expression was achieved in the pET-28b(+) plasmid. Conclusions: The findings of this study strongly support the manufacturing and in vitro and in vivo investigations of this vaccine to evaluate its effectiveness as a therapy for COVID-19.