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Bhat BA, Algaissi A, Khamjan NA, Dar TUH, Dar SA, Varadharajan V, Qasir NA, Lohani M. Exploration of comprehensive marine natural products database against dengue viral non-structural protein 1 using high-throughput computational studies. J Biomol Struct Dyn 2024:1-10. [PMID: 38165485 DOI: 10.1080/07391102.2023.2297006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential marine natural compounds against the NS1 of DENV. The structure of the NS1 protein was retrieved from Protein Data Bank with (PDB ID: 4O6B). Missing residues were added using modeler software. Molecular operating environment (MOE) programme was used to prepare the protein before docking. Virtual screening was performed on PyRx software to identify natural compounds retrieved from Comprehensive Marine Natural Products Database (CMNPD) against the NS1 protein, and best-docked compounds were examined by molecular docking and molecular dynamic (MD) simulation. Out of 31,561 marine compounds, the top 10 compounds showed docking scores lesser than -8.0 kcal/mol. One of the best hit compounds, CMNPD6802, was further analyzed using MD simulation study at 100 nanoseconds and Molecular Mechanics with Generalized Born and Surface Area Solvation (MM/GBSA). Based on its total binding energy, determined using the MM/GBSA approach, CMNPD6802 was ranked first. Its pharmacokinetic properties concerning the target protein NS1 were also evaluated. The results of the MD simulation showed that CMNPD6802 remained in close contact with the protein throughout the activation period, mapped using principal component analysis. These findings suggest that CMNPD6802 could serve as an NS1 inhibitor and may be a potential candidate for treating DENV infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Basharat Ahmad Bhat
- Department of BioResources, Amar Singh College Campus, Cluster University Srinagar, India
| | - Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Emerging and Epidemic Infectious Diseases Research Unit, Medical Research Centre, Jazan University, Jazan, Saudi Arabia
| | - Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan, Saudi Arabia
| | | | - Naif A Qasir
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohtashim Lohani
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
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