Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach
A new virus termed SARS-COV-2 (causing COVID-19 disease) can exhibit a progressive, fatal impact on individuals. The World Health Organization (WHO) has declared the spread of the virus to be a global pandemic. Currently, there are over 1 million cases and over 100,000 confirmed deaths due to the vi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-01-01
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| Series: | Informatics in Medicine Unlocked |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352914820301581 |
| _version_ | 1818516994256797696 |
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| author | Amit Joshi Bhuwan Chandra Joshi M. Amin-ul Mannan Vikas Kaushik |
| author_facet | Amit Joshi Bhuwan Chandra Joshi M. Amin-ul Mannan Vikas Kaushik |
| author_sort | Amit Joshi |
| collection | DOAJ |
| description | A new virus termed SARS-COV-2 (causing COVID-19 disease) can exhibit a progressive, fatal impact on individuals. The World Health Organization (WHO) has declared the spread of the virus to be a global pandemic. Currently, there are over 1 million cases and over 100,000 confirmed deaths due to the virus. Hence, prophylactic and therapeutic strategies are promptly needed. In this study we report an epitope, ITLCFTLKR, which is biochemically fit to HLA allelic proteins. We propose that this could be used as a potential vaccine candidate against SARS-COV-2. A selected putative epitope and HLA-allelic complexes show not only better binding scores, but also RMSD values in the range of 0–1 Å. This epitope was found to have a 99.8% structural favorability as per Ramachandran-plot analysis. Similarly, a suitable range of IC50 values and population coverage was obtained to represent greater validation of T-cell epitope analysis. Stability analysis using MDWeb and half-life analysis using the ProtParam tool has confirmed that this epitope is well-selected. This new methodology of epitope-based vaccine prediction is fundamental and fast in application, ad can be economically beneficial and viable. |
| first_indexed | 2024-12-11T00:50:00Z |
| format | Article |
| id | doaj.art-5923fc8af3f64f50aca13be0771087fb |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-12-11T00:50:00Z |
| publishDate | 2020-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-5923fc8af3f64f50aca13be0771087fb2022-12-22T01:26:39ZengElsevierInformatics in Medicine Unlocked2352-91482020-01-0119100338Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approachAmit Joshi0Bhuwan Chandra Joshi1M. Amin-ul Mannan2Vikas Kaushik3Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, IndiaDepartment of Biological Sciences and Biotechnology, Surajmal Agarwal Private Girls PG Degree College Kiccha, Kumaun University, Nainital, Uttarakhand, IndiaDomain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, IndiaDomain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India; Corresponding author.A new virus termed SARS-COV-2 (causing COVID-19 disease) can exhibit a progressive, fatal impact on individuals. The World Health Organization (WHO) has declared the spread of the virus to be a global pandemic. Currently, there are over 1 million cases and over 100,000 confirmed deaths due to the virus. Hence, prophylactic and therapeutic strategies are promptly needed. In this study we report an epitope, ITLCFTLKR, which is biochemically fit to HLA allelic proteins. We propose that this could be used as a potential vaccine candidate against SARS-COV-2. A selected putative epitope and HLA-allelic complexes show not only better binding scores, but also RMSD values in the range of 0–1 Å. This epitope was found to have a 99.8% structural favorability as per Ramachandran-plot analysis. Similarly, a suitable range of IC50 values and population coverage was obtained to represent greater validation of T-cell epitope analysis. Stability analysis using MDWeb and half-life analysis using the ProtParam tool has confirmed that this epitope is well-selected. This new methodology of epitope-based vaccine prediction is fundamental and fast in application, ad can be economically beneficial and viable.http://www.sciencedirect.com/science/article/pii/S2352914820301581EpitopeImmuno-informaticsVaccineHLA-AllelesSimulationSARS-COV-2 |
| spellingShingle | Amit Joshi Bhuwan Chandra Joshi M. Amin-ul Mannan Vikas Kaushik Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach Informatics in Medicine Unlocked Epitope Immuno-informatics Vaccine HLA-Alleles Simulation SARS-COV-2 |
| title | Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach |
| title_full | Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach |
| title_fullStr | Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach |
| title_full_unstemmed | Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach |
| title_short | Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach |
| title_sort | epitope based vaccine prediction for sars cov 2 by deploying immuno informatics approach |
| topic | Epitope Immuno-informatics Vaccine HLA-Alleles Simulation SARS-COV-2 |
| url | http://www.sciencedirect.com/science/article/pii/S2352914820301581 |
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