Multiple epitope-based vaccine prediction against SARS-CoV-2 spike glycoprotein

The global emergence of novel coronavirus disease and its rapid global expansion over a short span of time require effective countermeasures to combat it. Development of a specific vaccine can induce an optimal antibody response, thus providing immunity against it. Our study proposes a detailed and comprehensive immunoinformatic approach that can be applied to the currently available coronavirus protein data in the online server for vaccine candidate development. We have identified the receptor binding domain (RBD) of structural spike protein (S1) as a potential target for immunity against COVID- 19 infection. Epitope prediction illustrated cytotoxic T-cell epitopes, helper T-cell epitopes, and B-cell epitopes associated with the target protein. These were joined through specific linkers along with adjuvant beta-defensin located at the N-terminal to create a multi epitope subunit vaccine (MESV). The specificity in the binding of the devised vaccine candidate to the TLR-3 immune cell receptor was evaluated via molecular docking interaction studies. Good docking score combined with robust interactions in the binding cavity certified the stringency of the engineered vaccine. Molecular dynamics simulation data showed minimal variation of the root-mean square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) which confirmed the interaction stability. These results obtained from various in-silico experiments indicate the potency of this vaccine candidate as a probable therapeutic agent against COVID-19. Vaccination strategies targeting conserved epitope-based immune response would be beneficial in providing cross protection across beta-coronaviruses, and such vaccines would be resistant to the ever-evolving viruses.Communicated by Ramaswamy H. Sarma.