ABSTRACT
Objective: To investigate the possible mechanism of Platycodonis Radix-Licorice drug pair in the intervention of COVID-19 by using network pharmacology and molecular docking technique. Methods The database TCMSP was retrieved for the chemical constituents and targets of Platycodonis Radix-Licorice drug pair. Coronavirus disease targets were screened by the Gene Cards, OMIM,TTD, PharmGkb and DrugBank database. Cytoscape 3.7.2 software was used to construct the drug-component-target network. The PPI(protein-protein interaction) network was obtained by drug-disease intersection targets, and the core genes were found through CytoNCA plug-in. Meanwhile, GO(gene ontology) analysis and KEGG(Kyoto encyclopedia of genes and genomes) pathway analysis were performed by using Bioconductor database to predict the mechanism. AutoDock Tools 1.5.6 software was used to simulate the molecular docking of the main active ingredients with the novel coronavirus key binding site protein [SARS-CoV-2 main protease(severe acute respiratory syndrome coronavirus 2 main protease, Mpro) and ACE2(angiotensin converting enzyme 2)]. Results A total of 7 active ingredients of Platycodonis Radix,92 active ingredients of Licorice,2766 drug targets, and 674 disease targets were obtained, and 67 drug-disease common targets were excavated. The key targets involved RELA,STAT1,MAPK3,TP53,MAPK1,MAPK8,STAT3,MAPK14,IL1 B and TNF by the database STRING and CytoNCA plug-in.Go enrichment analysis showed that the main functions of Platycodonis Radix-Licorice drug pair on the intervention of COVID-19 were antioxidant reaction, cell respond to chemical stress, regulation of apoptotic signaling pathways, reaction to lipopolysaccharides and reaction to bacteria-derived molecules, etc.. KEGG pathways involved Coronavirus disease-COVID-19 pathway, IL-17 signaling pathway and so on, were mainly associated with immune response, inflammation-related pathways, inhibition of viral infection, and other inhibition of cancer. The molecular docking results showed that glepidotin A,quercetin, licochalcone a and luteolin had good binding ability with Mpro and ACE2. Conclusion Platycodonis Radix-Licorice drug pair act on SARS-CoV-2 through multiple components, multiple targets, and multiple channel combination. And the main active ingredients have a fine binding ability with Mpro and ACE2. The method can provide theoretical support for the possibility of traditional Chinese medicine(TCM) against COVID-19.
ABSTRACT
Platycodon grandiflorus (Jacq.) A. DC. (Campanulaceae) is commonly known as a balloon flower whose rhizomes have been widely utilized in traditional Chinese medicine (TCM) and in various Japanese prescriptions for the treatment of respiratory diseases, diabetes, and inflammatory disorders. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) global pandemic requires priming of the virus's spike (S) protein by cleavage of the S proteins by a multi-domain type II transmembrane serine protease, transmembrane protease serine 2 (TMPRSS2) to gain entry into the host cell. The current research aims at the screening of active phytocompounds of P. grandiflorus as potential inhibitors of cellular TMPRSS2 using molecular docking and molecular dynamics simulations approach. In silico toxicity analyses show that out of a total of 34 phytocompounds selected for the study, 12 compounds obey Lipinski's rule of five and have favourable pharmacokinetic properties. The top three lead molecules identified here were Apigenin, Luteolin and Ferulic acid which exhibited binding energies of -7.47 kcal/mol, -6.8 kcal/mol and -6.62 kcal/mol respectively with corresponding inhibition constants of 3.33 µM, 10.39 µM and 13.95 µM. The complexes between the lead molecules and the receptor were held by hydrogen bond interactions with key residues such as Gly383, Gly385, Glu389, Lys390, Asp435, Ser436, Ser441, Cys465 and Lys467, and hydrophobic interactions with surrounding residues. The stability of the protein-ligand complexes was evaluated during 100 ns molecular dynamics (MD) simulation by analysing key geometric properties such as RMSD, RMSF, radius of gyration, total solvent accessible surface area and the number of hydrogen bonds. The binding free energies analysis using MD simulations revealed that the compounds and TMPRSS2 have favourable thermodynamic interactions, which are primarily driven by van der Waals forces. As a result, the selected bioactive phytochemicals from P. grandiflorus that target the cellular TMPRSS2 could offer an alternative treatment option against SARS-CoV-2 infections.