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

• Main Authors: Moustafa E. El-Araby, Abdelsattar M. Omar, Sameh H. Soror, Stefan T. Arold, Maan T. Khayat, Hani Z. Asfour, Faida Bamane, Mahmoud A. Elfaky
• Format: Article
• Language: English
• Published: Elsevier 2020-07-01
• Series: Journal of Advanced Research
• Subjects: DSLS; Fluorescence anisotropy; Allosteric inhibitor; HCV; NS3/4A; Peptide mutants
• Online Access: http://www.sciencedirect.com/science/article/pii/S2090123220300035

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‘)ii The prime symbol (`) is used to distinguish between NS4A residues and NS3 residues of (no prime). 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.