Current Computer-Aided Drug DesignCurrent Computer-Aided Drug DesignCurrent Computer-Aided Drug Design1573-40991875-6697Bentham Science64455710.2174/0115734099272592231004170422ChemistryResearch ArticleExploring the Molecular Mechanism of Niuxi-Mugua Formula in Treating Coronavirus Disease 2019 via Network Pharmacology, Computational Biology, and Surface Plasmon Resonance VerificationWangWeiinfo@benthamscience.netCaoXuinfo@benthamscience.netCaoYi-naninfo@benthamscience.netLiuLian-lianinfo@benthamscience.netZhangShu-linginfo@benthamscience.netQiWen-yinginfo@benthamscience.netZhangJia-xininfo@benthamscience.netYangXian-zhaoinfo@benthamscience.netLiXiao-keinfo@benthamscience.netZaoXiao-bininfo@benthamscience.netYeYong-aninfo@benthamscience.netGastroenterology Department, Dongzhimen Hospital Affiliated to Beijing University of Chinese MedicineSun Simiao Hospital, Beijing University of Chinese MedicineThird School of Clinical Medicine, Beijing University of Chinese MedicineChinese pharmacy, Sun Simiao Hospital, Beijing University of Chinese Medicine, Tongchuan 727031, ChinaDongzhimen Hospital,, Beijing University of Chinese Medicine010720242071113112907012025Copyright ©; 2024, Bentham Science Publishers2024Bentham Science Publishershttps://rjeid.com/1573-4099/article/view/644557

Background:In China, Niuxi-Mugua formula (NMF) has been widely used to prevent and treat coronavirus disease 2019 (COVID-19). However, the mechanism of NMF for treating COVID-19 is not yet fully understood.

Objective:This study aimed to explore the potential mechanism of NMF for treating COVID- 19 by network pharmacology, computational biology, and surface plasmon resonance (SPR) verification.

Materials and Methods:The NMF-compound-target network was constructed to screen the key compounds, and the Molecular Complex Detection (MCODE) tool was used to screen the preliminary key genes. The overlapped genes (OGEs) and the preliminary key genes were further analyzed by enrichment analysis. Then, the correlation analysis of immune signatures and the preliminary key genes was performed. Molecular docking and molecular dynamic (MD) simulation assays were applied to clarify the interactions between key compounds and key genes. Moreover, the SPR interaction experiment was used for further affinity kinetic verification.

Results:Lipid and atherosclerosis, TNF, IL-17, and NF-kappa B signaling pathways were the main pathways of NMF in the treatment of COVID-19. There was a positive correlation between almost the majority of immune signatures and all preliminary key genes. The key compounds and the key genes were screened out, and they were involved in the main pathways of NMF for treating COVID-19. Moreover, the binding affinities of most key compounds binding to key genes were good, and IL1B-Quercetin had the best binding stability. SPR analysis further demonstrated that IL1B-Quercetin showed good binding affinity.

Conclusion:Our findings provided theoretical grounds for NMF in the treatment of COVID- 19.

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