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

  • Ezzemani, Wahiba1, 2
  • Kettani, Anass2
  • Sappati, Subrahmanyam3, 4
  • Kondaka, Kavya3
  • El Ossmani, Hicham5
  • Tsukiyama-Kohara, Kyoko6
  • Altawalah, Haya7, 8
  • Saile, Rachid2
  • Kohara, Michinori9
  • Benjelloun, Soumaya1
  • Ezzikouri, Sayeh1
  • 1 Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco. , (Morocco)
  • 2 Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco. , (Morocco)
  • 3 Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland. , (Poland)
  • 4 BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland. , (Poland)
  • 5 Institut de Criminalistique de la Gendarmerie Royale, AMSSNuR, Rabat, Morocco. , (Morocco)
  • 6 Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan. , (Japan)
  • 7 Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait. , (Kuwait)
  • 8 Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait. , (Kuwait)
  • 9 Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan. , (Japan)
Published Article
Journal of biomolecular structure & dynamics
Publication Date
May 13, 2022
DOI: 10.1080/07391102.2022.2075468
PMID: 35549819


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.

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