Unravelling the mechanism of action of Huashibaidu formula volatile metabolome for the treatment of COVID-19 and its mutants from the perspectives of network pharmacology and molecular docking

Abstract

Background: Huashibaidu (HSBD) formula, as one of the "3 medicines and 3 prescriptions," has made a great contribution to the fight against COVID-19. As an RNA virus, SARS-CoV-2 is still mutating, and people are still suffering from the disease.

Methods: In the study, gas chromatography-mass spectrometry was utilized to identify the volatile compounds in the volatile oil of the HSBD formula. Through network pharmacology screening of the volatile oil compounds of HSBD formula and SARS-CoV-2, the possible pathways and protein-protein interactions of HSBD formula treated COVID-19 were obtained, and the molecular mechanism of HSBD formula treated COVID-19 was preliminarily explained. Molecular docking was utilized to further screen the small molecules with high potential to interact with COVID-19 after network pharmacology screening, and the results were visualized.

Results: At least 66 small molecular compounds were found in the volatile oil of the HSBD formula. The results showed that β-Eudesmol, was found to bind nicely to the receptor binding domain of the Spike protein with a binding energy of -6.31 kcal/mol to 7yh6 (ο) and β-Eudesmol can form 9 van der Waals bonds and 2 hydrogen bonds with 8SPI protein (XBB1.5 strain).

Conclusions: This study revealed that the HSBD formula not only had a therapeutic effect on the initial SARS-CoV-2, but also had a restraining effect on the virus subtypes. This article gives a basic theory for the treatment of COVID-19 with the HSBD formula, and lays the foundation for further experimental verification of the active ingredients of the HSBD formula. As a traditional Chinese medicine formula, the HSBD formula has the advantage of being able to add, subside, and change the ingredients according to the different symptoms of the patients, which reflects the flexibility and long-term effectiveness of traditional Chinese medicine in the treatment of COVID-19.

Keywords: COVID-19; GC-MS; Huashibaidu formula; SARS-CoV-2; molecular docking; network pharmacology.