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Arwansyah A, Arif AR, Kade A, Taiyeb M, Ramli I, Santoso T, Ningsih P, Natsir H, Tahril T, Uday Kumar K. Molecular modelling on multiepitope-based vaccine against SARS-CoV-2 using immunoinformatics, molecular docking, and molecular dynamics simulation. SAR QSAR Environ Res 2022; 33:649-675. [PMID: 36083166 DOI: 10.1080/1062936x.2022.2117846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The pandemic of COVID-19 caused by SARS-CoV-2 has made a worldwide health emergency. Despite the fact that current vaccines are readily available, several SARSCoV-2 variants affecting the existing vaccine are to be less effective due to the mutations in the structural proteins. Furthermore, the appearance of the new variants cannot be easily predicted in the future. Therefore, the attempts to construct new vaccines or to modify the current vaccines are still pivotal works for preventing the spread of the virus. In the present investigation, the computational analysis through immunoinformatics, molecular docking, and molecular dynamics (MD) simulation is employed to construct an effective vaccine against SARS-CoV2. The structural proteins of SARS-CoV2 are utilized to create a multiepitope-based vaccine (MEV). According to our findings presented by systematic procedures in the current investigation, the MEV construct may be able to trigger a strong immunological response against the virus. Therefore, the designed MEV could be a potential vaccine candidate against SARS-CoV-2, and also it is expected to be effective for other variants.
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Affiliation(s)
- A Arwansyah
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - A R Arif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - A Kade
- Department of Physics Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - M Taiyeb
- Department of Biology, Faculty of Mathematics and Natural Sciences, Makassar State University, Makassar, Indonesia
| | - I Ramli
- Department of Physics, Faculty of Science, Universitas Cokroaminoto Palopo, Palopo, Indonesia
| | - T Santoso
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - P Ningsih
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - H Natsir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - T Tahril
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - K Uday Kumar
- Department of Radiology, Toxicology and Population Protection, Faculty of Health and Social Studies, University of South Bohemia Cesk´e Budˇejovice, Czech Republic
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Arwansyah A, Arif AR, Ramli I, Kurniawan I, Sukarti S, Nur Alam M, Illing I, Farid Lewa A, Manguntungi B. Molecular modelling on SARS-CoV-2 papain-like protease: an integrated study with homology modelling, molecular docking, and molecular dynamics simulations. SAR QSAR Environ Res 2021; 32:699-718. [PMID: 34392751 DOI: 10.1080/1062936x.2021.1960601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
SARS-CoV-2 PLpro was investigated as a therapeutic target for potent antiviral drugs due to its essential role in not only viral replication but also in regulating the inborn immune response. Several computational approaches, including homology modelling, molecular docking, and molecular dynamics (MD) studies, were employed to search for promising drugs in treating SARS-CoV-2. Eighty-one compounds, sub-structurally similar to the antiviral drug, were used as potential inhibitors of PLpro. From our results, three complexes containing the ligands with Pubchem IDs: 153012995, 12149203, and 123608715 showed lower binding energies than the control (Ritonavir), indicating that they may become promising inhibitors for PLpro. MD was performed in a water solvent to validate the stability of the three complexes. All complexes achieved stable structure during the simulation as no significant fluctuations were observed in the validation parameters. Moreover, the binding energy for each complex was estimated using the MM-GBSA method. Complex 1 was the most stable structure based on the lowest binding energy score and its structure remained in a similar cavity with the docket snapshot. Based on our studies, three ligands were assumed to be potential inhibitors. The ligand of complex 1 may become the most promising antiviral drug against SARS-CoV-2 targeting PLpro.
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Affiliation(s)
- A Arwansyah
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - A R Arif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - I Ramli
- Department of Physics, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - I Kurniawan
- School of Computing, Telkom University, Bandung, Indonesia
- Research Center of Human Centric Engineering, Telkom University, Bandung, Indonesia
| | - S Sukarti
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - M Nur Alam
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - I Illing
- Department of Chemistry, Faculty of Science, Cokroaminoto University of Palopo, Palopo, Indonesia
| | - A Farid Lewa
- Department of Nutrition, Poltekkes Kemenkes Palu, Palu, Indonesia
| | - B Manguntungi
- Department of Biotechnology, Faculty of Biotechnology, Sumbawa University of Technology, Sumbawa, Indonesia
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Karim A, Wahab AW, Raya I, Natsir H, Arif AR. Utilization of Diamine Oxidase Enzyme from Mung Bean Sprouts (Vigna radiataL) for Histamine biosensors. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1742-6596/979/1/012014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Natsir H, Wahab AW, Laga A, Arif AR. Inhibitory activities ofMoringa oleiferaleaf extract against α-glucosidase enzyme in vitro. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1742-6596/979/1/012019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wahab NA, Ramasamy U, George J, Madhavan M, Arif AR, Abdullah J. Intra-cranial metastatic lacrimal gland tumour. Med J Malaysia 2006; 61:641-3. [PMID: 17623971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report a case of an adult who presented with progressive swelling in the right eye with suggestive of intracranial lesion on imaging. Histopathological revealed a lacrimal gland malignant mixed tumour.
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Affiliation(s)
- N A Wahab
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan
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Arif AR. Diet, fluorine, tea and fish. Pak Dent Rev 1967; 17:6-12. [PMID: 5230769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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