In silico identification of natural compounds against SARS-CoV-2 main protease from Chinese herbal medicines

Yi Kuang; Wenjing Shen; Xiaodong Ma; Ziwei Wang; Rui Xu; Qingqing Rao; Shengxiang Yang

doi:10.2144/fsoa-2023-0055

In silico identification of natural compounds against SARS-CoV-2 main protease from Chinese herbal medicines

Future Sci OA. 2023 Jun 14;9(7):FSO873. doi: 10.2144/fsoa-2023-0055. eCollection 2023 Aug.

Authors

Yi Kuang¹, Wenjing Shen¹, Xiaodong Ma¹, Ziwei Wang¹, Rui Xu¹, Qingqing Rao¹, Shengxiang Yang¹

Affiliation

¹ College of Chemical & Materials Engineering, Zhejiang A&F University, Lin'an, 311300, Zhejiang, China.

Abstract

Aims: To determine natural compounds with inhibitory effects toward SARS-CoV-2 Mpro from Chinese herbal medicines.

Materials & methods: ∼1200 natural compounds from 19 Chinese herbal medicines were collected. Computational methods including molecular docking, drug-likeness assessment, molecular dynamics simulation and molecular mechanics Poisson-Boltzmann surface area analysis were combined to obtain potent inhibitors against SARS-CoV-2 Mpro.

Results: Top 20 compounds mainly originated from Ranunculus ternatus and Picrasma quassioides exhibited low binding free energies which below -9.0 kcal/mol. Compounds Japonicone G and Picrasidine T were obtained with favorable drug-likeness. Moreover, the complex of Japonicone G and Mpro had prominent stability.

Conclusion: Natural compound Japonicone G is highly promising as a potent inhibitor against SARS-CoV-2 for further study.

Keywords: Chinese herbal medicine; Japonicone G; SARS-CoV-2 Mpro; molecular docking; molecular dynamics simulation.