Design of Epitope-Based Vaccine Against SARS-CoV-2: An Immuno-Informatics Study
Epitope-Based Vaccine Against SARS-CoV-2
DOI:
https://doi.org/10.11594/jtls.14.03.07Keywords:
Epitope, Immuno-informatic, SARS-CoV-2, VaccineAbstract
This study aimed to develop an epitope-based vaccine of SARS-CoV-2 S protein through an immuno-informatics study. The whole genome of SARS-CoV-2 sequences was obtained from the GISAID database and then trimmed to obtain the S protein sequences. The alignment was done by Clustal-W of MEGA software. Epitope prediction and modeling were performed by Discotope BepiPred and the PepFold3 web server. The allergic responses and physicochemical characteristics of predicted epitopes were analyzed using the AlgPred and ProtParam from ExPASy. Molecular docking and dynamic stimulation were performed using AutoDock Vina and YASARA. Biovia Discovery Studio 2019 was used to visualize the molecular docking results. The study predicted 3 potential epitopes, including ‘GDEVRQIAPGQTGKIADYNYKLP’ (epitope 1), ‘YTMSLGAENSVAYSNN’ (epitope 2), and ‘VNNSYECDIPI’ (epitope 3) located in the spike head specifically RBD region. The epitopes did not show an allergen reaction based on IgE epitope mapping. The suitable overexpression for the host of epitopes was mammalian cells. Only epitopes 1 and 2 were stable (instability index above 40). Epitopes 1, 2, and 3 interacted with BCR with binding affinity values -6.6, -7.8, and -7.5 kcal/mol. Epitope 2 wasere stable when interacting with the BCR. Therefore, three epitopes were predicted to have high potency as the SARS-CoV-2 epitope-based vaccine.
References
Zhou P, Yang X Lou, Wang XG et al. (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579 (7798): 270–273. doi: 10.1038/s41586-020-2012-7.
Satarker S, Nampoothiri M (2020) Structural Proteins in Severe Acute Respiratory Syndrome Coronavirus-2. Archives of Medical Research 51 (6): 482–491. doi: 10.1016/j.arcmed.2020.05.012.
Xu X, Han M, Li T et al. (2020) Effective treatment of severe COVID-19 patients with tocilizumab. Proceedings of the National Academy of Sciences of the United States of America 117 (20): 10970–10975. doi: 10.1073/pnas.2005615117.
Yang J, Petitjean SJL, Koehler M et al. (2020) Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor. Nat Commun. doi: 10.1038/s41467-020-18319-6
Ali A, Vijayan R (2020) Dynamics of the ACE2–SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms. Sci Rep. doi: 10.1038/s41598-020-71188-3
Di Natale C, La Manna S, De Benedictis I et al. (2020) Perspectives in Peptide-Based Vaccination Strategies for Syndrome Coronavirus 2 Pandemic. Front Pharmacol. doi: 10.3389/fphar.2020.578382
Chukwudozie OS, Gray CM, Fagbayi TA et al. (2021) Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein. PLoS One. doi: 10.1371/journal.pone.0248061
Lamiable A, Thevenet P, Rey J et al. (2016) PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex. Nucleic Acids Research 44 (1): W449–W454. doi: 10.1093/nar/gkw329.
Widodo, Veronica Margarecaesha Anyndita N, Dluha N et al. (2018) Designing and overproducing a tandem epitope of gp350/220 that shows a potential to become an EBV vaccine. Heliyon 4 (3): e00564. doi: 10.1016/j.heliyon.2018.e00564.
Wilkins MR, Gasteiger E, Bairoch A et al. (1999) Protein identification and analysis tools in the ExPASy server. Methods in molecular biology (Clifton, NJ) 112 531–552. doi: 10.1385/1-59259-584-7:531.
Dallakyan S, Olson AJ (2015) Small-molecule library screening by docking with PyRx. Methods in Molecular Biology 1263 243–250. doi: 10.1007/978-1-4939-2269-7_19.
BIOVIA DS (2019) Discovery Studio 2019.
Trott O, Olson AJ (2009) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry 31 (2): NA-NA. doi: 10.1002/jcc.21334.
Krieger E, Vriend G (2014) YASARA View - molecular graphics for all devices - from smartphones to workstations. Bioinformatics (Oxford, England) 30 (20): 2981–2982. doi: 10.1093/bioinformatics/btu426.
Peters B, Sidney J, Bourne P et al. (2005) The immune epitope database and analysis resource: From vision to blueprint. In: PLoS Biol. pp 0379–0381.
Lan J, Ge J, Yu J et al. (2020) Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581 (7807): 215–220. doi: 10.1038/s41586-020-2180-5.
Lin L, Ting S, Yufei H et al. (2020) Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2. Virus Res. doi: 10.1016/j.virusres.2020.198082
Noorimotlagh Z, Karami C, Mirzaee SA et al. (2020) Immune and bioinformatics identification of T cell and B cell epitopes in the protein structure of SARS-CoV-2: A systematic review. Int Immunopharmacol. doi: 10.1016/j.intimp.2020.106738
Sharma N, Patiyal S, Dhall A et al. (2021) AlgPred 2.0: An improved method for predicting allergenic proteins and mapping of IgE epitopes. Brief Bioinform. doi: 10.1093/bib/bbaa294
Kounis NG, Koniari I, de Gregorio C et al. (2021) Allergic reactions to current available covid-19 vaccinations: Pathophysiology, causality, and therapeutic considerations. Vaccines 9 (3): 1–19. doi: 10.3390/vaccines9030221.
Kim R, Skolnick J (2008) Assessment of programs for ligand binding affinity prediction. Journal of Computational Chemistry 29 (8): 1316–1331. doi: 10.1002/jcc.20893.
Majewski M, Ruiz-Carmona S, Barril X (2019) An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Commun Chem. doi: 10.1038/s42004-019-0205-5
Ghosh R, Chakraborty A, Biswas A, Chowdhuri S (2021) Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches. Journal of Biomolecular Structure and Dynamics 39 (17): 6747–6760. doi: 10.1080/07391102.2020.1802347.
SYAHPUTRA WIBOWO, SRI WIDYARTI, AKHMAD SABARUDIN et al. (2019) The THE ROLE OF ASTAXANTHIN COMPARED WITH METFORMIN IN PREVENTING GLYCATED HUMAN SERUM ALBUMIN FROM POSSIBLE UNFOLDING: A MOLECULAR DYNAMIC STUDY. Asian Journal of Pharmaceutical and Clinical Research 276–282. doi: 10.22159/ajpcr.2019.v12i9.34617.
Downloads
Published
Issue
Section
License
Copyright (c) 2024 Journal of Tropical Life Science
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
The work has not been published before (except in the form of an abstract or part of a published lecture or thesis) and it is not under consideration for publication elsewhere. When the manuscript is accepted for publication in this journal, the authors agree to automatic transfer of the copyright to the publisher.
Journal of Tropical Life Science is licensed under Creative Commons Attribution-NonCommercial 4.0 International License
