In Silico Screening of Potential Chinese Herbal Medicine Against COVID-19 by Targeting SARS-CoV-2 3CLpro and Angiotensin Converting Enzyme II Using Molecular Docking

Chin J Integr Med. 2020 Jul;26(7):527-532. doi: 10.1007/s11655-020-3476-x. Epub 2020 Jul 6.


Objective: To seek potential Chinese herbal medicine (CHM) for the treatment of coronavirus disease 2019 (COVID-19) through the molecular docking of the medicine with SARS-CoV-2 3CL hydrolytic enzyme and the angiotensin converting enzyme II(ACE2) as receptors, using computer virtual screening technique, so as to provide a basis for combination forecasting.

Methods: The molecular docking of CHM with the SARS-Cov-2 3CL hydrolase and the ACE2 converting enzyme, which were taken as the targets, was achieved by the Autodock Vina software. The CHM monomers acting on 3CLpro and ACE2 receptors were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, the active ingredients were selected, and the key CHMs and compounds were speculated. Based on the perspective of network pharmacology, the chemical-target network was constructed, and the functional enrichment analysis of gene ontology and the pathway enrichment analysis of Kyoto encyclopedia of genes and genomes were carried out by DAVID to speculate about the mechanism of action of the core drug pairs.

Results: There are 6 small molecule compounds that have the optimal binding energy with the two target proteins. Among 238 potential anti-COVID-19 herbs screened in total, 16 kinds of CHM containing the most active ingredients, and 5 candidate anti-COVID-19 herbs that had been used in high frequency, as well as a core drug pair, namely, Forsythiae Fructus-Lonicerae Japonicae Flos were selected.

Conclusion: The core drug pair of Forsythiae Fructus-Lonicerae Japonicae Flos containing multiple components and targets is easy to combine with 3CLpro and ACE2, and exerts an anti-COVID-19 pneumonia effect through multi-component and multi-target, and plays the role of anti-COVID-19 pneumonia in multi-pathway.

Keywords: COVID-19; Chinese medicine; SARS-CoV-2 3CL hydrolytic enzyme; angiotensin converting enzyme II; molecular docking.

MeSH terms

  • Angiotensin-Converting Enzyme 2
  • Betacoronavirus / metabolism*
  • COVID-19
  • COVID-19 Drug Treatment
  • Computer Simulation*
  • Coronavirus Infections / drug therapy*
  • Drugs, Chinese Herbal / therapeutic use*
  • Gene Ontology
  • Humans
  • Molecular Docking Simulation*
  • Pandemics
  • Peptidyl-Dipeptidase A / metabolism*
  • Pneumonia, Viral / drug therapy*
  • SARS-CoV-2
  • Thermodynamics


  • Drugs, Chinese Herbal
  • Peptidyl-Dipeptidase A
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2