Synthetic bulky NS4A peptide variants bind to and inhibit HCV NS3 protease

Moustafa E El-Araby; Abdelsattar M Omar; Sameh H Soror; Stefan T Arold; Maan T Khayat; Hani Z Asfour; Faida Bamane; Mahmoud A Elfaky

doi:10.1016/j.jare.2020.01.003

Synthetic bulky NS4A peptide variants bind to and inhibit HCV NS3 protease

J Adv Res. 2020 Jan 3:24:251-259. doi: 10.1016/j.jare.2020.01.003. eCollection 2020 Jul.

Authors

Moustafa E El-Araby¹, Abdelsattar M Omar^{1

2}, Sameh H Soror^{3

4}, Stefan T Arold⁵, Maan T Khayat¹, Hani Z Asfour⁶, Faida Bamane⁷, Mahmoud A Elfaky⁸

Affiliations

¹ Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia.
² Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt.
³ Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt.
⁴ Center for Scientific Excellence Helwan Structural Biology Research (HSBR), Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt.
⁵ King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia.
⁶ Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
⁷ Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
⁸ Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia.

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') 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 K _d 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.

Keywords: Allosteric inhibitor; DSLS; Fluorescence anisotropy; HCV; NS3/4A; Peptide mutants.