Molecular docking prediction of three active components of Paris polyphylla against SARS-CoV-2

ABSTRACT

To explore the active compounds of Chinese herbal medicine Paris polyphylla in the treatment of SARS-CoV-2. SARS-CoV-2 mainly binds to the angiotensin-converting enzyme 2 (ACE2) receptor on the surface of human cells through its S protein.In this study, the molecular docking simulation method was used to predict the binding affinity of ACE2 and three kinds of polyphyllin (I, VI, VII) rich in Paris polyphylla. The results show that the three polyphyllin can bind well with ACE2, and the binding free energy is lower than -8 kcal/mol. The amino acid residues combined by the three compounds include Pro-346, Thr-347, Ala-348, Asp-350, Asn-394, His-401, Glu-402. The core structure shared by the three drugs plays a key role in binding the above sites.In addition, the energy required for the binding of polyphyllin I to ACE2 is the lowest, while the number of key amino acids and the number of hydrogen bonds formed by the interaction of polyphyllin VI with the target protein are the largest. Therefore, structural design based on these three active ingredients is expected to obtain highly effective SARS-CoV-2 inhibitors, in order to provide a research basis for the discovery of COVID-19 therapeutic drugs.