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

To determine natural compounds with inhibitory effects toward SARS-CoV-2 Mpro from Chinese herbal medicines. ∼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. Top 20 compounds mainly originated from and 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. Natural compound Japonicone G is highly promising as a potent inhibitor against SARS-CoV-2 for further study.