Identification of a novel class of cyclic penta-peptides against hepatitis C virus as p7 channel blockers

Shukun Wei; Chaolun Liu; Lingyu Du; Bin Wu; Jin Zhong; Yimin Tong; Shuqing Wang; Bo OuYang

doi:10.1016/j.csbj.2022.10.035

Identification of a novel class of cyclic penta-peptides against hepatitis C virus as p7 channel blockers

Comput Struct Biotechnol J. 2022 Oct 28:20:5902-5910. doi: 10.1016/j.csbj.2022.10.035. eCollection 2022.

Authors

Shukun Wei^{1

2}, Chaolun Liu^{3

4}, Lingyu Du¹, Bin Wu⁵, Jin Zhong^{2

3

4}, Yimin Tong^{2

3}, Shuqing Wang⁶, Bo OuYang^{1

2}

Affiliations

¹ State Key Laboratory of Molecular Biology, Centre for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
² University of Chinese Academy of Sciences, Beijing 100049, China.
³ CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
⁴ ShanghaiTech University, Shanghai 201210, China.
⁵ National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, China.
⁶ School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.

Abstract

The hepatitis C virus (HCV) p7 viroporin protein is essential for viral assembly and release, suggesting its unrealised potential as a target for HCV interventions. Several classes of small molecules that can inhibit p7 through allosteric mechanisms have shown low efficacy. Here, we used a high throughput virtual screen to design a panel of eight novel cyclic penta-peptides (CPs) that target the p7 channel with high binding affinity. Further examination of the effects of these CPs in viral production assays indicated that CP7 exhibits the highest potency against HCV among them. Moreover, the IC₅₀ efficacy of CP7 in tests of strain Jc1-S282T suggested that this cyclopeptide could also effectively inhibit a drug-resistant HCV strain. A combination of nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations revealed that CP7 blocking activity relies on direct binding to the p7 channel lumen at the N-terminal bottleneck region. These findings thus present a promising anti-HCV cyclic penta-peptide targeting p7 viroporin, while also describing an alternative strategy for designing a new class of p7 channel blockers for strains resistant to direct-acting antiviral agents (DAA).

Keywords: Channel blocker; Cyclic penta-peptide; Drug design; HCV; Molecular dynamics simulations; NMR; P7.