Novel epitope based peptides for vaccine against SARS-CoV-2 virus: immunoinformatics with docking approach

Jesvin Bency B., Mary Helen P. A.


Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative viral strain for the contagious pandemic respiratory illness in humans which is a public health emergency of international concern. There is a desperate need for vaccines and antiviral strategies to combat the rapid spread of SARS-CoV-2 infection.

Methods: The present study based on computational methods has identified novel conserved cytotoxic T-lymphocyte epitopes as well as linear and discontinuous B-cell epitopes on the SARS-CoV-2 spike (S) protein. The predicted MHC class I and class II binding peptides were further checked for their antigenic scores, allergenicity, toxicity, digesting enzymes and mutation.

Results: A total of fourteen linear B-cell epitopes where GQSKRVDFC displayed the highest antigenicity-score and sixteen highly antigenic 100% conserved T-cell epitopes including the most potential vaccine candidates MHC class-I peptide KIADYNYKL and MHC class-II peptide VVFLHVTYV were identified. Furthermore, the potential peptide QGFSALEPL with high antigenicity score attached to larger number of human leukocyte antigen alleles. Docking analyses of the allele HLA-B*5201 predicted to be immunogenic to several of the selected epitopes revealed that the peptides engaged in strong binding with the HLA-B*5201 allele.

Conclusions: Collectively, this research provides novel candidates for epitope-based peptide vaccine design against SARS-CoV-2 infection.


Epitope‐based peptides, S protein, SARS-CoV-2 virus, Vaccine

Full Text:



Khot W, Nadkar M. The 2019 Novel Coronavirus Outbreak - A Global Threat. J Assoc Physicians India. 2020;68:67-71.

Zheng J. SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat. Int J Biol Sci. 2020;16(10):1678-85.

Sah R, Rodriguez-Morales A, Jha R, Chu D, Gu H, Peiris M, et al. Microbiol Resour Announc. 2020;9(11):e00169-20.

He Y, Zhou Y, Siddiqui P, Jiang S. Inactivated SARS-CoV vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry. Biochem Biophys Res Commun. 2004;325(2):445-52.

Cann A. Genomes. In: Principles of Molecular Virology. 5th ed. UK: Academic Press; 2012.

Qamar T, Saleem M, Ashfaq S. Epitope‐based peptide vaccine design and target site depiction against Middle East Respiratory Syndrome Coronavirus: an immune-informatics study. J Transl Med. 2019;17:362.

Dimitrov I, Flower D, Doytchinova I. AllerTOP-a server for in silico prediction of allergens. BMC bioinformatics. Bio Med Central. 2013;14(6):S4.

Buchan D, Minneci F, Nugent T, Bryson K, Jones D. Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res. 2013;41:W349-57.

Yang H, Kim D. Peptide and Protein Vaccines. Curr Opin Immunol. 2003;4:461-70.

Tung T, Zacharias A, Arun K, Raúl G, Stig T, Melanie S, et al. The COVID-19 vaccine development landscape. Nat Rev Drug Discov. 2020.

Hajissa K, Zakaria R, Suppian R, Mohamed Z. Epitope-based vaccine as a universal vaccination strategy against Toxoplasma gondii infection: A mini-review. JAVAR. 2019;6(2):174-82.

Patronov A, Doytchinova I. T-cell epitope vaccine design by immunoinformatics. Open Biol. 2013;3(1):1201-39.

Sette A, Fikes J. Epitope-based vaccines: an update on epitope identification, vaccine design and delivery. Curr Opin Immunol. 2003;15(4):461-70.

Galvani AP, Ndeffo-Mbah ML, Wenzel N, Childs JE. Ebola vaccination: if not now, when?. Ann Int Med. 2014;161(10):749-50.

Naz R, Dabir P. Peptide vaccines against cancer, infectious diseases, and conception. Front Biosci J Virtual Lib. 2006;12:1833-44.

Ma C, Li Y, Wang L. Intranasal vaccination with recombinant receptor-binding domain of MERS-CoV spike protein induces much stronger local mucosal immune responses than subcutaneous immunization: Implication for designing novel mucosal MERS vaccines. Vaccine. 2014;32(18):2100-8.

Yang Z, Kong W, Huang Y. A DNA vaccine induces SARS coronavirus neutralization and protective immunity in mice. Nature. 2004; 428(6982):561-4.

Agnihothram S, Gopal R, Yount B. Platform strategies for rapid response against emerging coronaviruses: MERS-CoV serologic and antigenic relationships in vaccine design. J Infect Dis. 2013;209(7):995-1006.

Zhao B, Sakharkar K, Lim C, Kangueane P, Sakharkar M. MHC-Peptide binding prediction for epitope based vaccine design. IJIB Design. 2007;1(2):127.

Pamer E, Cresswell P. Mechanisms of MHC class I--restricted antigen processing Annu Rev Immunol. 1998;16:323-58.

Varshney A, Wang X, Cook E, Dutta K, Scharff M, Goger M. Generation, characterization, and epitope mapping of neutralizing and protective monoclonal antibodies against staphylococcal enterotoxin B-induced lethal shock. J Biol Chem. 2011;286(11):9737-47.

Ansari H, Raghava G. Identification of conformational B-cell epitopes in an antigen from its primary sequence. Immunome Res. 2010;6:1-9.

Bhattacharya M, Sharma A, Patra P, Ghosh P, Sharma G, Bidhan C, et al. Development of epitope‐based peptide vaccine against novel coronavirus 2019 (SARS‐COV‐2): Immunoinformatics Approach J Med Virol. 2020;2020.

Bui H, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinform. 2007;8:361.

Rognan D, Scapozza L, Folkers G, Daser. A Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes. Biochem. 1994;33:11476-85.

Altuvia Y, Sette A, Sidney J, Southwood S, Margalit H. A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets, Hum. Immunol. 1997;58:1-11.

Brusic V, Bajic V, Petrovsky N. Computational methods for prediction of T-cell epitopes-a framework for modelling, testing, and applications. Methods. 2004;34:436-43.

Schueler-Furman O, Altuvia Y, Sette A, Margalit H. Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Protein Sci. 2000;9:1838-46.