Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design
Hepatitis C virus (HCV) causes chronic and acute hepatitis infections. As there is extreme variability in the HCV genome, no approved HCV vaccine has been available so far. An effective polypeptide vaccine based on the functionally conserved epitopes will be greatly helpful in curing disease. For th...
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MDPI AG
2021-03-01
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| Serija: | Vaccines |
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| Online pristup: | https://www.mdpi.com/2076-393X/9/3/293 |
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| author | Sajjad Ahmad Farah Shahid Muhammad Tahir ul Qamar Habib ur Rehman Sumra Wajid Abbasi Wasim Sajjad Saba Ismail Faris Alrumaihi Khaled S. Allemailem Ahmad Almatroudi Hafiz Fahad Ullah Saeed |
| author_facet | Sajjad Ahmad Farah Shahid Muhammad Tahir ul Qamar Habib ur Rehman Sumra Wajid Abbasi Wasim Sajjad Saba Ismail Faris Alrumaihi Khaled S. Allemailem Ahmad Almatroudi Hafiz Fahad Ullah Saeed |
| author_sort | Sajjad Ahmad |
| collection | DOAJ |
| description | Hepatitis C virus (HCV) causes chronic and acute hepatitis infections. As there is extreme variability in the HCV genome, no approved HCV vaccine has been available so far. An effective polypeptide vaccine based on the functionally conserved epitopes will be greatly helpful in curing disease. For this purpose, an immuno-informatics study is performed based on the published HCV subtype-3a from Pakistan. First, the virus genome was translated to a polyprotein followed by a subsequent prediction of T-cell epitopes. Non-allergenic, IFN-γ producer, and antigenic epitopes were shortlisted, including 5 HTL epitopes and 4 CTL, which were linked to the final vaccine by GPGPG and AAY linkers, respectively. Beta defensin was included as an adjuvant through the EAAAK linker to improve the immunogenicity of the polypeptide. To ensure its safety and immunogenicity profile, antigenicity, allergenicity, and various physiochemical attributes of the polypeptide were evaluated. Molecular docking was conducted between TLR4 and vaccine to evaluate the binding affinity and molecular interactions. For stability assessment and binding of the vaccine-TLR4 docked complex, molecular dynamics (MD) simulation and MMGBSA binding free-energy analyses were conducted. Finally, the candidate vaccine was cloned in silico to ensure its effectiveness. The current vaccine requires future experimental confirmation to validate its effectiveness. The vaccine construct produced might be useful in providing immune protection against HCV-related infections. |
| first_indexed | 2024-03-10T13:01:57Z |
| format | Article |
| id | doaj.art-2fae4dbd274e402d93320effd5ff7251 |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-10T13:01:57Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-2fae4dbd274e402d93320effd5ff72512023-11-21T11:25:55ZengMDPI AGVaccines2076-393X2021-03-019329310.3390/vaccines9030293Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine DesignSajjad Ahmad0Farah Shahid1Muhammad Tahir ul Qamar2Habib ur Rehman3Sumra Wajid Abbasi4Wasim Sajjad5Saba Ismail6Faris Alrumaihi7Khaled S. Allemailem8Ahmad Almatroudi9Hafiz Fahad Ullah Saeed10Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, PakistanDepartment of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, PakistanCollege of Life Science and Technology, Guangxi University, Nanning 530004, ChinaDepartment of Medical, DHQ Hospital, Faisalabad Medical University, Faisalabad 38000, PakistanNUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, PakistanNUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, PakistanNUMS Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, PakistanDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaKing Edward Medical University, Lahore 54000, PakistanHepatitis C virus (HCV) causes chronic and acute hepatitis infections. As there is extreme variability in the HCV genome, no approved HCV vaccine has been available so far. An effective polypeptide vaccine based on the functionally conserved epitopes will be greatly helpful in curing disease. For this purpose, an immuno-informatics study is performed based on the published HCV subtype-3a from Pakistan. First, the virus genome was translated to a polyprotein followed by a subsequent prediction of T-cell epitopes. Non-allergenic, IFN-γ producer, and antigenic epitopes were shortlisted, including 5 HTL epitopes and 4 CTL, which were linked to the final vaccine by GPGPG and AAY linkers, respectively. Beta defensin was included as an adjuvant through the EAAAK linker to improve the immunogenicity of the polypeptide. To ensure its safety and immunogenicity profile, antigenicity, allergenicity, and various physiochemical attributes of the polypeptide were evaluated. Molecular docking was conducted between TLR4 and vaccine to evaluate the binding affinity and molecular interactions. For stability assessment and binding of the vaccine-TLR4 docked complex, molecular dynamics (MD) simulation and MMGBSA binding free-energy analyses were conducted. Finally, the candidate vaccine was cloned in silico to ensure its effectiveness. The current vaccine requires future experimental confirmation to validate its effectiveness. The vaccine construct produced might be useful in providing immune protection against HCV-related infections.https://www.mdpi.com/2076-393X/9/3/293hepatitis C virusimmuno-informaticsdockingmolecular dynamics simulation |
| spellingShingle | Sajjad Ahmad Farah Shahid Muhammad Tahir ul Qamar Habib ur Rehman Sumra Wajid Abbasi Wasim Sajjad Saba Ismail Faris Alrumaihi Khaled S. Allemailem Ahmad Almatroudi Hafiz Fahad Ullah Saeed Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design Vaccines hepatitis C virus immuno-informatics docking molecular dynamics simulation |
| title | Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design |
| title_full | Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design |
| title_fullStr | Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design |
| title_full_unstemmed | Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design |
| title_short | Immuno-Informatics Analysis of Pakistan-Based HCV Subtype-3a for Chimeric Polypeptide Vaccine Design |
| title_sort | immuno informatics analysis of pakistan based hcv subtype 3a for chimeric polypeptide vaccine design |
| topic | hepatitis C virus immuno-informatics docking molecular dynamics simulation |
| url | https://www.mdpi.com/2076-393X/9/3/293 |
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