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Alobaida A, Abouzied AS, Younes KM, Alzhrani RM, Alsaab HO, Huwaimel B. Analyzing energetics and dynamics of hepatitis C virus polymerase interactions with marine bacterial compounds: a computational study. Mol Divers 2024:10.1007/s11030-024-10904-x. [PMID: 38856834 DOI: 10.1007/s11030-024-10904-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
Hepatitis C Virus (HCV) is a significant health concern affecting a large portion of the global population and is a major cause of acute liver diseases, including cirrhosis. The variability in the HCV genome mainly results from the rapid replication facilitated by the NS5B polymerase, making it a prime target for anti-HCV drug development. This study explores potential compounds from marine bacteria that could inhibit the HCV NS5B polymerase by virtual screening, analyzing the energetics, and dynamic behavior of target-compound complexes. Virtual screening with the Lipinski filter was employed to select compounds from the marine bacteria database that demonstrated strong binding affinity to NS5B. The top four (CMNPD27216, CMNPD21066, CMNPD21065, and CMNPD27283) compounds, ranked by their re-docking scores, underwent additional evaluation. Molecular dynamics simulations for 200 ns were conducted to assess the dynamic stability of these complexes in a solvent environment. Furthermore, methods such as MM-GBSA, PCA, and free energy landscape analysis were used to analyze the system's energetics and identify stable conformations by locating transition states. The findings suggest that these compounds exhibit promising binding capabilities to HCV polymerase and could be considered for future experimental validation.
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Affiliation(s)
- Ahmed Alobaida
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, 81442, Ha'il, Saudi Arabia
| | - Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia.
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12311, Egypt.
| | - Kareem M Younes
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Analytical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Rami M Alzhrani
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Ha'il, 55473, Hail, Saudi Arabia
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