Volume 8, Issue 3 (2022)
IEM 2022, 8(3): 259-276 |
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BASU A. Strategies for Vaccine Design for Corona Virus for All Variants of Concern Using Immunoinformatics Techniques. IEM 2022; 8 (3) :259-276
URL: http://iem.modares.ac.ir/article-4-57055-en.html
URL: http://iem.modares.ac.ir/article-4-57055-en.html
Lecturer, Girudas College, Calcutta University , anamika.biochem@gurudas.education
Abstract: (1198 Views)
Backgrounds: A short sequence of viral protein or peptide, can be used as a potential vaccine for the treatment of that virus. Considering all variants of concern (VOC), vaccine design with peptide for Severe Acute Respiratory Syndrome coronavirus 2 (SARS CoV2) is a challenging job for scientists.
Materials & Methods: In this current study, an epitope containing peptide vaccine for nonstructural protein 4 (nsp 4) of SARS CoV2 coronavirus has been predicted. With the help of a modified method for both B and T call epitope prediction, verified by molecular docking studies, linear B cell and T cell epitopes for nsp4 protein, are predicted here. Predicted epitopes are analyzed further with population coverage calculation and epitope conservancy analysis.
Findings: A short peptide sequence 74QRGGSYTNDKA84 has been selected as B cell epitope considering the scores for surface accessibility, hydrophilicity, beta turn prediction for each amino acid residues.
Similarly, the peptide sequences 359 FLAHIQWMV367 and 359 FLAHIQWVMFTPLV373 are predicted as T cell epitopes for MHC-I and MHC-II molecules. These two potential epitopes can interest with HLA-A*02:01 and HLA-DRB*01:01, MHC allelic proteins respectively with lowest IC50 values.
Furthermore, no amino acid mutations are observed in GISAD Global initiate on sharing all influenza data) database for alpha, beta, gamma and delta variance of concerns (VOC). Among seven amino acid point mutation of nsp 4 protein in Omicron variant, none of them is present in the peptide sequences of predicted epitope-based vaccines.
Conclusion: The short peptide sequences can be predicted as vaccines to prevent coronavirus infections for all variants of concerns.
Materials & Methods: In this current study, an epitope containing peptide vaccine for nonstructural protein 4 (nsp 4) of SARS CoV2 coronavirus has been predicted. With the help of a modified method for both B and T call epitope prediction, verified by molecular docking studies, linear B cell and T cell epitopes for nsp4 protein, are predicted here. Predicted epitopes are analyzed further with population coverage calculation and epitope conservancy analysis.
Findings: A short peptide sequence 74QRGGSYTNDKA84 has been selected as B cell epitope considering the scores for surface accessibility, hydrophilicity, beta turn prediction for each amino acid residues.
Similarly, the peptide sequences 359 FLAHIQWMV367 and 359 FLAHIQWVMFTPLV373 are predicted as T cell epitopes for MHC-I and MHC-II molecules. These two potential epitopes can interest with HLA-A*02:01 and HLA-DRB*01:01, MHC allelic proteins respectively with lowest IC50 values.
Furthermore, no amino acid mutations are observed in GISAD Global initiate on sharing all influenza data) database for alpha, beta, gamma and delta variance of concerns (VOC). Among seven amino acid point mutation of nsp 4 protein in Omicron variant, none of them is present in the peptide sequences of predicted epitope-based vaccines.
Conclusion: The short peptide sequences can be predicted as vaccines to prevent coronavirus infections for all variants of concerns.
Keywords: Peptide type vaccine design, COVID-19, B and T cell epitopes, MHC allelic protein, molecular docking study
Article Type: Original Research |
Subject:
Virology
Received: 2021/11/10 | Accepted: 2022/07/20 | Published: 2022/09/19
Received: 2021/11/10 | Accepted: 2022/07/20 | Published: 2022/09/19
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