Potential Material Basis of Yupingfeng Powder for the Prevention and Treatment of 2019 Novel Coronavirus Pneumonia: A Study Involving Molecular Docking and Molecular Dynamic Simulation Technology

Abstract

Objective. In this study, we investigated the potential material basis of Yupingfeng powder in the prevention and treatment of 2019 novel coronavirus pneumonia (NCP) by applying molecular docking and molecular dynamic simulation technology. Design. The active ingredients and predictive targets of Yupingfeng powder were sourced using the TCMSP, ETCM, and TCMIP traditional Chinese medicine databases. NCP-related targets were then acquired from the DisGeNET and GeneCards databases, and common disease-drug targets were imported into the STRING database, and Cytoscape software was used to generate a protein-protein interaction network following the use of a network topology algorithm to identify key target genes. Gene Ontology (GO) and KEGG pathway enrichment analysis was then performed using the target genes and GOEAST and DAVID online tools. The mechanism of Yupingfeng powder in the prevention and treatment of NCP was analyzed with reference to the relevant literature. AutoDock software was used for molecular docking, the preliminary analysis of binding status, and to identify the best conformation. Desmond software was used to perform molecular dynamic simulations for protein and compound complexes, perform free energy calculations and hydrogen bond analysis, and to further verify the binding mode. Results. Overall, 38 main active components and 218 predictive targets of Yupingfeng powder were identified and 298 disease targets related to NCP were retrieved from disease databases. Yupingfeng powder was found to act predominantly on the TNF, Toll-like receptor, HIF-1, NOD-like receptor, cytokine-receptor interaction, MAPK, T cell receptor, and VEGF signaling pathways. Molecular docking of the three selected key active components with the 3CL-like protease (3CL-Pro) of SARS-CoV-2 showed that they each had a strong binding force and good affinity. Conclusions. Yupingfeng powder primarily acts on multiple active ingredients and potential targets through multiple action channels and signal pathways. Molecular docking and molecular dynamic simulation technology were used to effectively predict and analyze the potential mechanism by which this Chinese medicine can combat NCP. These results provide a reference for developing new modern Chinese medicine preparations against NCP in the future.

An updated meta-analysis of Chinese herbal medicine for the prevention of COVID-19 based on Western-Eastern medicine

“…Several studies shed light on the primary therapeutic effect of Yupingfeng Powder and its effectiveness in improving the barrier function of the airway mucosa. This is accomplished by restoring and safeguarding the airway mucosa’s natural outcomes and controlling the body’s immunological function ( Gao et al, 2009 ; Wang et al, 2022 ; Yu et al, 2022 ). Contemporary pharmacology has demonstrated that Forsythia suspensa (Thunb.)…”

Simultaneous quantitation of 15 bioactive components in Yupingfeng granules by LC–MS/MS

“…3 Recently, YPFG has been used in treating and preventing COVID-19. [4][5][6] The biological activities of flavonoids and saponins from A. membranaceus (Fisch.) Bunge and chromones from S. divaricata (Turcz.)…”

“…It is commonly used to prevent infectious diseases such as colds, pneumonia, 2 and rhinitis 3 . Recently, YPFG has been used in treating and preventing COVID‐19 4–6 . The biological activities of flavonoids and saponins from A. membranaceus (Fisch.)…”