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El-Araby ME, Omar AM, Soror SH, Arold ST, Khayat MT, Asfour HZ, Bamane F, Elfaky MA. Synthetic bulky NS4A peptide variants bind to and inhibit HCV NS3 protease. J Adv Res 2020; 24:251-259. [PMID: 32373358 PMCID: PMC7195562 DOI: 10.1016/j.jare.2020.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/03/2019] [Accepted: 01/02/2020] [Indexed: 01/21/2023] Open
Abstract
NS4A is a non-structural multi-tasking small peptide that is essential for HCV maturation and replication. The central odd-numbered hydrophobic residues of NS4A (Val-23‘ to Leu-31‘)i are essential for activating NS3 upon NS3/4A protease complex formation. This study aims to design new specific allosteric NS3/4A protease inhibitors by mutating Val-23‘, Ile-25‘, and Ile-29‘ into bulkier amino acids. Pep-15, a synthetic peptide, showed higher binding affinity towards HCV-NS3 subtype-4 than native NS4A. The Kd of Pep-15 (80.0 ± 8.0 nM) was twice as high as that of native NS4A (169 ± 37 nM). The mutant Pep-15 inhibited the catalytic activity of HCV-NS3 by forming an inactive complex. Molecular dynamics simulations suggested that a cascade of conformational changes occurred, especially in the catalytic triad arrangements, thereby inactivating NS3. A large shift in the position of Ser-139 was observed, leading to loss of critical hydrogen bonding with His-57. Even though this study is not a classic drug discovery study—nor do we propose Pep-15 as a drug candidate—it serves as a stepping stone towards developing a potent inhibitor of hitherto untargeted HCV subtypes.
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Affiliation(s)
- Moustafa E El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Abdelsattar M Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Sameh H Soror
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt.,Center for Scientific Excellence Helwan Structural Biology Research (HSBR), Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Maan T Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Hani Z Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Faida Bamane
- Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mahmoud A Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
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