Denovo Structural Modeling and B cell and T cell Epitope Prediction against SARS-COV-2 PLpro to Cure COVID-19: Vaccinomics Based Approach

Author(s): Carlos Eliel Maya Ramirez, Sajida Ashraf, Faiza Irshad, Tabish Rehman, Moayad Shahwan, Muhammad Sufyan.

Background: In December 2019, SARS COV-2 spread very rapidly and its outbreaks led to cause pneumonia and severe illness. For the first time, the virus was spotted in the city of China (Wuhan). Little is known about this virus, so the vaccine is needed to prevent COVID-19. Papain like protease (PLpro) is conserved among coronaviruses and have multifunctional activities like protease, deubiquitinase, deISGylating and interferon antagonism. Therefore, PLpro is a promising target for drug and vaccine development.

Methods: T cells (MHCI & MHCII) and B cell (Discontinuous & Linear) epitopes of SARS COV-2 PLpro were forecasted via computational and immunoinformatics approaches that show a crucial part in promoting immune responses against COVID-19. Online tools were used to analyze the allergenicity, physiochemical properties, antigenicity and structural details of PLpro.

Results: Fifty-three Linear B-cell epitopes were identified, of which ‘KPLEFGATSAALQP’ and ‘EDDYQGKPLEFGAT’ had higher score and antigenicity. Antigenic, non-allergenic and conserved (T cell) epitopes whichwere bounded to multiple alleles were selected. In total, twelve epitopes were taken (6 MHC I and 6 MHC II).From MHC class I ‘YHTTDPSFLGRY’ and MHC class II ‘PFVMMSAPPAQYELK’ had more antigenicity among T cell epitopes. Furthermore, the protection and stability of peptides were tested through digestion analysis.

Conclusion: Predicted epitopes could be served as vaccine candidate to eliminate COVID-19. Even so, the presented epitopes required to be validated experimentally to check its safety and immunogenic profile