Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2
The coronavirus that causes serious acute respiratory syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still a major problem in public health and biomedicine. Even if there is no cure for it, the infection is still progressing naturally, and the only time that optimal treatm...
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Elsevier
2024-12-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1687157X24001422 |
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| author | Syed Luqman Ali Awais Ali Waseef Ullah Abdulaziz Alamri Elham Mohammed Khatrawi Gulzira Sagimova Aigul Almabayeva Farida Rakhimzhanova Gulsum Askarova Fatima Suleimenova Nabras Al-Mahrami Prasanta Kumar Parida |
| author_facet | Syed Luqman Ali Awais Ali Waseef Ullah Abdulaziz Alamri Elham Mohammed Khatrawi Gulzira Sagimova Aigul Almabayeva Farida Rakhimzhanova Gulsum Askarova Fatima Suleimenova Nabras Al-Mahrami Prasanta Kumar Parida |
| author_sort | Syed Luqman Ali |
| collection | DOAJ |
| description | The coronavirus that causes serious acute respiratory syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still a major problem in public health and biomedicine. Even if there is no cure for it, the infection is still progressing naturally, and the only time that optimal treatment choices, such as doxycycline, work is at the beginning of the infection. Our project is structured into two critical parts: the first focuses on the identification of potential drug targets, and the second on vaccine design, both aimed at exploring new ways to treat the disease. Initially, cytoplasmic proteins identified through subtractive analysis underwent comprehensive evaluation for potential drug targeting, focusing on metabolic pathways, homology prediction, drugability assessment, essentiality, and protein–protein interactions. Subsequently, surface proteins underwent rigorous assessment for allergenicity, antigenicity, physiochemical attributes, conserved regions, protein interactions, and identification of B and T cell epitopes. Molecular docking and immunological simulation analyses were then employed to develop and characterize a multi-epitope vaccine, integrating findings from the aforementioned evaluations. Findings from the study point to six proteins as potential critical therapeutic targets for SARS-CoV-2, each of which is involved in a distinct metabolic process. The reverse vaccinology analysis suggested that the following proteins could be used as vaccine candidates: sp|P05106, sp|O00187, sp|Q9NYK1, sp|P05556, sp|P09958, and sp|Q9HC29. Four multi-epitope vaccine named as SARS-COV-2-, C1, C2, C3, and C4 was designed by utilizing different adjuvants and eighteen B cell overlapped epitopes which were predicted from top ranked protiens. Based on immune simulation study, the vaccine exhibited adequate immune-reactivity and favorable encounters with toll-type receptors (TLR4, TLR8, HLA, etc ACE), Among them the SARS-COV-2-C2 showed best binding affinity of which all receptors. Findings from this study could be a game-changer in the quest to develop a vaccine and medication that effectively combat SARS-CoV-2. It is necessary to do additional experimental analyses, nevertheless. |
| format | Article |
| id | doaj-art-8df15db546ef4346837f461d0f9092e7 |
| institution | DOAJ |
| issn | 1687-157X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj-art-8df15db546ef4346837f461d0f9092e72025-08-20T02:49:49ZengElsevierJournal of Genetic Engineering and Biotechnology1687-157X2024-12-0122410043910.1016/j.jgeb.2024.100439Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2Syed Luqman Ali0Awais Ali1Waseef Ullah2Abdulaziz Alamri3Elham Mohammed Khatrawi4Gulzira Sagimova5Aigul Almabayeva6Farida Rakhimzhanova7Gulsum Askarova8Fatima Suleimenova9Nabras Al-Mahrami10Prasanta Kumar Parida11Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Paksitan; Corresponding authors.Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Paksitan; Corresponding authors.Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, PaksitanDepartment of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; Corresponding authors.Department of Medical Microbiology and Immunology, Taibah University, College of Medicine, Madinah 42353, Saudi ArabiaDepartment of Human Anatomy, Astana Medical University, Astana 010000, KazakhstanDepartment of Human Anatomy, Astana Medical University, Astana 010000, KazakhstanDepartment of Microbiology, Semey Medical University, Semey, KazakhstanDepartment of Clinical Disciplines, Al Farabi Kazakh National University, Almaty 050000, KazakhstanDepartment of Human Anatomy, Astana Medical University, Astana 010000, KazakhstanBioinformatician, National Genetic Center, Royal Hospital, Ministry of Health, Muscat, OmanDepartment of KIIT School of Rural Management, KIIT University, Bhubaneswar 751024, IndiaThe coronavirus that causes serious acute respiratory syndrome. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still a major problem in public health and biomedicine. Even if there is no cure for it, the infection is still progressing naturally, and the only time that optimal treatment choices, such as doxycycline, work is at the beginning of the infection. Our project is structured into two critical parts: the first focuses on the identification of potential drug targets, and the second on vaccine design, both aimed at exploring new ways to treat the disease. Initially, cytoplasmic proteins identified through subtractive analysis underwent comprehensive evaluation for potential drug targeting, focusing on metabolic pathways, homology prediction, drugability assessment, essentiality, and protein–protein interactions. Subsequently, surface proteins underwent rigorous assessment for allergenicity, antigenicity, physiochemical attributes, conserved regions, protein interactions, and identification of B and T cell epitopes. Molecular docking and immunological simulation analyses were then employed to develop and characterize a multi-epitope vaccine, integrating findings from the aforementioned evaluations. Findings from the study point to six proteins as potential critical therapeutic targets for SARS-CoV-2, each of which is involved in a distinct metabolic process. The reverse vaccinology analysis suggested that the following proteins could be used as vaccine candidates: sp|P05106, sp|O00187, sp|Q9NYK1, sp|P05556, sp|P09958, and sp|Q9HC29. Four multi-epitope vaccine named as SARS-COV-2-, C1, C2, C3, and C4 was designed by utilizing different adjuvants and eighteen B cell overlapped epitopes which were predicted from top ranked protiens. Based on immune simulation study, the vaccine exhibited adequate immune-reactivity and favorable encounters with toll-type receptors (TLR4, TLR8, HLA, etc ACE), Among them the SARS-COV-2-C2 showed best binding affinity of which all receptors. Findings from this study could be a game-changer in the quest to develop a vaccine and medication that effectively combat SARS-CoV-2. It is necessary to do additional experimental analyses, nevertheless.http://www.sciencedirect.com/science/article/pii/S1687157X24001422SARS-CoV-2Drug designmRNA vaccineMolecular dockingsImmune simulation |
| spellingShingle | Syed Luqman Ali Awais Ali Waseef Ullah Abdulaziz Alamri Elham Mohammed Khatrawi Gulzira Sagimova Aigul Almabayeva Farida Rakhimzhanova Gulsum Askarova Fatima Suleimenova Nabras Al-Mahrami Prasanta Kumar Parida Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 Journal of Genetic Engineering and Biotechnology SARS-CoV-2 Drug design mRNA vaccine Molecular dockings Immune simulation |
| title | Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 |
| title_full | Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 |
| title_fullStr | Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 |
| title_full_unstemmed | Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 |
| title_short | Exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against SARS-CoV-2 |
| title_sort | exploring advanced genomic and immunoinformatics techniques for identifying drug and vaccine targets against sars cov 2 |
| topic | SARS-CoV-2 Drug design mRNA vaccine Molecular dockings Immune simulation |
| url | http://www.sciencedirect.com/science/article/pii/S1687157X24001422 |
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