In silico design of multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein

Abstract

SARS-CoV-2 has been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia, and economic recession, the virus has brought together countries to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from being particularly effective, a slew of measures and possibilities concerning the design of vaccines are being worked upon. We attempted a structure-based approach utilizing a combination of epitope prediction servers and Molecular dynamic (MD) simulations to develop a multi-epitope-based subunit vaccine that involves the two subunits of the spike glycoprotein of SARS-CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs. The designed constructs were evaluated based on their docking with Toll-Like Receptor (TLR) 4. Our findings provide an epitope-based peptide fragment that can be a potential candidate for the development of a vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-CoV-2
• vaccine design
• spike protein
• docking
• MD simulations
• adjuvant

Acknowledgements

AJ acknowledges the Department of Biotechnology, Govt. of India for the Ramalingamswami Re-entry Fellowship-2019.

Authors' contributions

SS and DM conceived the idea of this study and designed the experiments together. DM performed the experiments. AJ, SS, DM and JP analyzed the data. DM, SS, AJ and JP contributed to drafting the manuscript.

Disclosure statement

Authors declare no conflict of interest.