Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein

Abstract

The emergence of the new SARS-CoV-2 variants has led to major concern regarding the efficacy of approved vaccines. Nucleocapsid is a conserved structural protein essential for replication of the virus. This study focuses on identifying conserved epitopes on the nucleocapsid (N) protein of SARS-CoV-2. Using 510 unique amino acid sequences of SARS-CoV-2 N protein, two peptides (193 and 215 aa) with 90% conservancy were selected for T cell epitope prediction. Three immunogenic peptides containing multiple T cell epitopes were identified which were devoid of autoimmune and allergic immune response. These peptides were also conserved (100%) in recent Omicron variants reported in Jan-August 2023. HLA analysis reveals that these peptides are predicted as binding to large number of HLA alleles and 71–90% population coverage in six continents. Identified peptides displayed good binding score with both HLA class I and HLA class II molecules in the docking study. Also, a vaccine construct docked with TLR-4 receptor displays strong interaction with 20 hydrogen bonds and molecular simulation analysis reveals that docked complex are stable. Additionally, the immunogenicity of these N protein peptides was confirmed using SARS-CoV-2 convalescent serum samples. We conclude that the identified N protein peptides contain highly conserved and antigenic epitopes which could be used as a target for the future vaccine development against SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

Keywords:

• Nucleocapsid
• TLR-4
• SARS-CoV-2
• vaccine construct
• omicron

Acknowledgments

I would like to acknowledge Professor Andrew M. Lynn from School of Computational & Integrative Sciences, Jawaharlal Nehru University for this suggestion in molecular docking and simulation study.

Author contributions

JV: Original draft, data curation, formal analysis. NK, MM, VS, EM, SH: Data curation, formal analysis, review and editing. NS, RL, AR, SF, MB: Conceptualization, review and editing and supervision.

Disclosure statement

No potential conflict of interest was reported by the authors.

Institutional review board statement

This study was conducted in accordance with the Declaration of Helsinki and approved by the Local Ethics Committee (66/2012/U/Oss).

Ethics statement

The ethics committee of the Kazan State Medical Academy approved this study, and signed informed consent was obtained from each COVID-19 patient and controls according to the guidelines adopted under this protocol (protocol 4/09 of the meeting of the ethics committee of the KSMA dated September 26, 2019).

Informed consent statement

Informed consent was obtained from all the subjects involved in the study.

Additional information

Funding

This work was supported by the Kazan federal University program of Competitive Growth and Strategic Academic Leadership Program (PRIORITY-2030).