S. aureus is one of the common pathogenic bacteria that causes numerous infectious diseases, such as mastitis, chronic osteomyelitis, pneumonia, etc. [12–14]. The results of previous research have shown that the treatment of S. aureus is accompanied by several drawbacks. Although the antibiotic treatment may be significant for bacterial infections to a certain extent, the abuse of antibiotics not only leads to the emergence of drug-resistant strains-MRSA, but also causes antibiotic residues, seriously threatening food safety . Thus, there is a main challenge to find out an appropriate substitute for antibiotic treatment of S. aureus infection.
With the increased clinical application of TCM and its extracts in prevention and treatment of S. aureus infection, its therapeutic effects have been extensively confirmed. Lan et al. demonstrated that flavonoids from Artemisia rupestris L., a traditional Chinese herb, had antibacterial effects against S. aureus .The antibacterial activity of Sophora flavescens extract, Angelica sinensis extract, S. flavescens extract and herb pair A. sinensis was investigated, and it was found that S. flavescens extract showed a strong antibacterial effect on Chalmers, Escherichia coli, Shigella castellani, and Staphylococcus aureus . In TCM, Scutellaria baicalensis is widely used to treat infections with a symptom of fever. As an active compound of Scutellaria baicalensis, baicalin can effectively reduce the virulence of S. aureus, and cooperate with penicillin G in anti-infection treatment with an improved efficacy of 75% . WWXDY is a kind of TCM, which is often used to treat bacterial infection. It is composed of Lonicera japonica, Dandelion, Semiaquilegiae Radix, Chrysanthemum, and Viola philippica. In our previous study, we attempted to assess the clinical efficacy of the combination of TCM and Western medicine on the traumatic chronic tibial osteomyelitis (CO). We found that combination of the TCM and Western medicine could mitigate the local lesion of traumatic CO and ameliorate the general status . However, the active compounds of WWXDY and its potential molecular mechanisms for the treatment of S. aureus have still remained elusive.
In the current study, 92 active compounds of WWXDY, such as mandenol, ethyllinolenate, eriodyctiol, secologanic dibutylacetal_qt, etc. were identified. In addition, 785 target genes of WWXDY and 683 S. aureus-related genes were predicated using the mentioned databases. Importantly, 122 overlapped genes between WWXDY and S. aureus-related genes mainly belonged to apoptosis-related genes (CASP3, CASP8, CASP1, and SYK), chemokines (MMP2, MMP9), and metabolic genes (Nox4, GLO1). S. aureus infection has been proved to affect cell proliferation, apoptosis, metabolism, as well as secretion of chemokines [20–22]. Therefore, WWXDY has a great potential in the treatment of S. aureus infection.
Based on the constructed PPI network, we found that secologanic dibutylacetal_qt, desacetylmatricarin, chryseriol, luteolin, quercetin, and acacetin were the main active compounds for the treatment of S. aureus infection. These ingredients, e.g. chryseriol, luteolin, quercetin, and acacetin, have been proved to improve the treatment of S. aureus infection [16, 23–25].
The promising applications of PPI networks to disease datasets are mainly 4 areas: (i) identification of disease-related subnetworks, (ii) network-based disease classification, (iii) the identification of genes and proteins associated with diseases, and (iv) the study of network properties and their relation to disease status. By constructing PPI network, it was found that IL-6, TNF-α, VEGFA, AKT1, CXCL8, MAPK3, TLR4, IL-1β, MMP9 and EGFR were the top 10 hub genes, and they were mainly enriched in inflammation-related signaling pathways. It is significant to deepen the understanding of the functional relationship between proteins. In macrophages and epithelial cells, S. aureus could enhance the expression levels of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α [26, 27], which were highly correlated with therapeutic targets of WWXDY. Wu et al.  demonstrated that Chryseriol, which is a main active compound of WWXDY, could significantly inhibit IL-6, TNF-α, and IL-1β in inflammatory diseases.
To explore the roles of the active targets in gene function and signaling pathways, KEGG pathway enrichment and GO functional analyses of the 122 target genes in the PPI network were performed. The effects of WWXDY in the treatment of S. aureus infection are mainly attributed to the regulation of endopeptidase activity, binding receptors to cytokines, and serine-type peptidase activity. Besides,KEGG pathway enrichment analyses indicated that identified genes were mainly enriched in COVID-19, CKR signaling pathway, AGE-RAGE signaling pathway, Pertussis, and Chagas disease. The advantages of TCM in the treatment of COVID-19 include effective relief of symptoms, improvement of cure rate, reduction of mortality, and promotion of rehabilitation . COVID-19 patients have a high probability of co-infection with S. aureus . Our data suggest that WWXDY may provide a new therapeutic option for the treatment of COVID-19. The AGE-RAGE signaling pathway was firstly recognized to be involved in S. aureus infection. The complications of atherosclerosis and nephropathy in type 2 diabetes (T2DM) might be treated with TCM mainly through the AGE-RAGE signaling pathway . We found that WWXDY could treat S. aureus infection, which was correlated with the regulation of AGE-RAGE signaling pathway.