Immunogenomics guided design of immunomodulatory multi-epitope subunit vaccine against the SARS-CoV-2 new variants, and its validation through in silico cloning and immune simulation

Abbas Khan; Shahzeb Khan; Shoaib Saleem; N Nizam-Uddin; Anwar Mohammad; Taimoor Khan; Sajjad Ahmad; Muhammad Arshad; Syed Shujait Ali; Muhammad Suleman; Dong-Qing Wei

doi:10.1016/j.compbiomed.2021.104420

Immunogenomics guided design of immunomodulatory multi-epitope subunit vaccine against the SARS-CoV-2 new variants, and its validation through in silico cloning and immune simulation

Comput Biol Med. 2021 Jun:133:104420. doi: 10.1016/j.compbiomed.2021.104420. Epub 2021 Apr 24.

Authors

Affiliations

¹ Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
² Center for Biotechnology and Microbiology, University of Swat, Swat, KP, Pakistan.
³ National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
⁴ Biomedical Engineering Department, HITEC University, Taxila, Pakistan.
⁵ Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait.
⁶ Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan.
⁷ Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
⁸ Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China. Electronic address: [email protected].

Abstract

Reports of the novel and more contagious strains of SARS-CoV-2 originating in different countries have further aggravated the pandemic situation. The recent substitutions in spike protein may be critical for the virus to evade the host's immune system and therapeutics that have already been developed. Thus, this study has employed an immunoinformatics pipeline to target the spike protein of this novel strain to construct an immunogenic epitope (CTL, HTL, and B cell) vaccine against the new variant. Our investigation revealed that 12 different epitopes imparted a critical role in immune response induction. This was validated by an exploration of physiochemical properties and experimental feasibility. In silico and host immune simulation confirmed the expression and induction of both primary and secondary immune factors such as IL, cytokines, and antibodies. The current study warrants further lab experiments to demonstrate its efficacy and safety.

Keywords: Immune simulation; In silico cloning; New variant; SARS-CoV-2; Vaccine designing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Cloning, Molecular
Computer Simulation
Epitopes, B-Lymphocyte
Epitopes, T-Lymphocyte
Humans
Immunity
Molecular Docking Simulation
SARS-CoV-2
Spike Glycoprotein, Coronavirus / genetics
Vaccines, Subunit
Viral Vaccines*

Substances

Epitopes, B-Lymphocyte
Epitopes, T-Lymphocyte
Spike Glycoprotein, Coronavirus
Vaccines, Subunit
Viral Vaccines