1. The main active ingredients and potential targets of QGD.
38 active ingredients were selected from TCMSP database. Mol ID, molecule names, OB, DL, HL were displayed in Table 1. After summarizing the active component targets of TCMPS and the predicted targets of PharmMapper, 526 potential targets were obtained by running Perl, eliminating duplicate values and converting symbols.
2. The Common Potential Targets Of Qgd And Osteosarcoma
A total of 526 potential targets of osteosarcoma were collected, including 3 from OMIM, 97 from PharmGKB and 439 from DisGeNET (Fig. 2A). Finally, a total of 89 intersecting genes were screened as candidate targets to further research (Fig. 2B).
3. Drug-ingredients-targets network and PPI
The drug-ingredients-targets network was visualized using Cytoscape software. Figure 1C shows Hedyotis diffusa in red, Fritillaria thunbergia in rose red, Coicis semen in green, Astragalus membranaceus in light blue, Platycodon grandiflorum in dark blue. According to supplement Table 1, quercetin was associated with 77 potential targets, luteolin with 56 potential targets, β-sitosterol and kaempferol with 51 potential targets, which may be the main active ingredient of QGD for the treatment of osteosarcoma. In Fig. 1C, the components were represented by the circle in Fig. 1C, and the candidate targets were represented by the square. The greater the size of the shape, the more the components associated with it. KDR, SRC, MAPK14, HPGDS, GSK3B, MET, MMP3, HSP90AA1, GSTP1, FGFR1, ESR1, EGFR, DHFR, CHEK1, CASP3 are found to be the most frequently associated with active ingredients.
89 candidate genes were introduced into String. According to the screening conditions, the "stringinteractions. tsv" were imported into Cytoscape to establish the PPI network. The network was consisted of 82 nodes and 400 edges. The genes with BC, CC, EC, DC and LAC greater than the median were screened to construct the sub-network, which included 28 nodes and 175 edges. According to the final values of BC, CC, EC, DC and LAC (Table 2), 11 targets were obtained to become the core network, and TP53, SRC and ESR1 were considered as the key genes(Fig. 3).
4. Go Enrichment Analysis
Go enrichment includes biological process (BP), cellular component (CC) and molecular function (MF). 89 potential targets of QGD in the treatment of osteosarcoma were analyzed by R-package. As shown in the Fig. 4A, BP mainly included: response to steroid hormones (go: 0048545), response to metal ions (go: 0010038), cell response to oxidative stress (go: 0034599), response to radiation (go: 0009314), response to peptides (go: 1901652), response to oxidative stress (go: 0006979), regulation of apoptosis signal pathway (go: 2001233), Response to toxic substances (go: 0009636), cell response to abiotic stimuli (go: 0071214), cell response to environmental stimuli (go: 0104004); In terms of CC, it mainly included chromatin (go: 0000785), transcription factor complex (go: 0005667), membrane raft (go: 0045121), membrane micro region (go: 0098857), membrane region (go: 0098589), RNA polymerase II transcription factor complex (go: 0090575), nuclear transcription factor complex (go: 0044798), cyclin dependent protein kinase holoenzyme complex (go: 0000307), Serine /threonine protein kinase complex(go: 1902554), protein kinase complex (go: 1902911); MF mainly included: ubiquitin like protein ligase binding (go: 0044389), proximal promoter sequence specific DNA binding (go: 0000987), protein heterodimerization activity (go: 0046982), ubiquitin protein ligase binding (go: 0031625), DNA binding transcription activator activity, RNA polymerase II specificity (go: 0001228), protein tyrosine kinase activity (go: 0004713), nuclear receptor activity (go: 0004879) Transcription factor activity, direct ligand regulated sequence specific DNA binding (go: 0098531), steroid hormone receptor activity (go: 0003707), transmembrane receptor protein tyrosine kinase activity (go: 0004714). Based on this, QGD in the treatment of osteosarcoma might be the result of multiple mechanisms.
5. Kegg Pathway Enrichment Analysis
In order to further explore the possible mechanism of QGD in the treatment of osteosarcoma, we performed KEGG pathway enrichment analysis on 89 target targets. As shown in Fig. 4B. The main related pathways included PI3K Akt signal pathway, proteoglycan in cancer, MAPK signal pathway, chemical carcinogenesis receptor activation pathway, cell aging, IL-17 signal pathway, EGFR tyrosine kinase inhibitor resistance, etc.
6. Molecular Docking Results
Essential genes were selected for molecular docking with compounds that might regulate these targets (Supplement Table 2). The results showed that the docking binding energy of the key targets and the active ingredients were basically lower than − 5 Kcal/mol. Taking the lowest binding energy for example, the results could be seen in Table 3 and the structural diagrams were shown in Fig. 5.