Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants

Abstract

The genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel epitopes were identified as immunogenic triggering immune responses and no toxic after investigation with in silico tools. Furthermore, we found these peptide vaccine candidates showed a significant binding affinity for MHC I and MHC II alleles in molecular docking investigations. We consider them to be promising targets for developing peptide-based vaccines against SARS-CoV-2. Subsequently, we designed two efficient multi-epitopes vaccines against the SARS-CoV-2, the first one based on potent MHC class I and class II T-cell epitopes of S (FPNITNLCPF–NYNYLYRLFR–MFVFLVLLPLVSSQC), M (MWLSYFIASF–GLMWLSYFIASFRLF), E (LTALRLCAY–LLFLAFVVFLLVTLA), and N (SPRWYFYYL–AQFAPSASAFFGMSR). The second candidate is the result of the tailoring of the first designed vaccine according to three classes of SARS-CoV-2 variants. Molecular docking showed that the protein-protein binding interactions between the vaccines construct and TLR2–TLR4 immune receptors are stable complexes. These findings confirmed that the final multi-epitope vaccine could be easily adapted to new viral variants. Our study offers a shortlist of promising epitopes that can accelerate the development of an effective and safe vaccine against the virus and its adaptation to new variants.

Communicated by Ramaswamy H. Sarma

Keywords:

• COVID-19
• molecular docking
• multi-epitopes vaccines
• MM-PBSA/MM-GBSA analysis
• SARS-CoV-2 variants

Acknowledgements

We are particularly grateful to Mr. Henry Smith for pertinent English revision of the manuscript. We acknowledge Mrs. Bouchra Rahim from the Centre National pour la Recherche Scientifique et Technique (CNRST) for the support. We are grateful for the technical support of CNRST/HPC-MARWAN.

Disclosure statement

The authors declare no competing interests.

Additional information

Funding

This work was supported by Institut Pasteur du Maroc.