3.1 Preliminary bioinformatics data of targets
After tests by online tools, the number of 245 BPA-related OS disease-genes were detected, and analytical 138 anti-disease genes of calycosin were determined. As shown in Venn graph, a total of 20 mutual genes of calycosin and BPA-related OS were identified before being highlighted in a interaction network of calycosin to treat BPA-related OS (Fig. 1A).
3.2 Findings of all core targets
The mutual genes were further assayed by Cytoscape software, and then the topological data showed that the median degree of freedom of the target was 3.667, and the maximum degree of freedom was 10. Therefore, the core target screening criteria range was set to 4–10. As a result, we identified total 9 core targets of calycosin to treat BPA-related OS, having EGFR, ESR1, HSP90AA1, MAPK14, ESR2, AR, BRCA1, PTGS2, CYP19A1. The findings illustrated in an interaction network (Fig. 1B) and Supplemental Table 1.
3.3 Enrichment analysis findings of core targets
All 9 core targets were used to determine the gene ontology enrichment and KEGG pathway enrichment analyses through R language-related packages. As results, the histogram and Circos circle chart of the biological process of the gene ontology were presented in Figure. 3A-B; and then the histogram and Circos circle chart of KEGG pathways were showed in Figure. 3C-D. The results suggested that the biological process of the gene ontology mainly involved in ossification, positive regulation of bone resorption, positive regulation of bone remodeling, regulation of inflammatory response, neuroinflammatory response, positive regulation of inflammatory response, interleukin-12 secretion, chronic inflammatory response, positive regulation of acute inflammatory response, positive regulation of interleukin-12 production, regulation of neuroinflammatory response, regulation of cytokine production involved in inflammatory response, cytokine production involved in inflammatory response, regulation of interleukin-12 production, regulation of macrophage chemotaxis, macrophage chemotaxis, regulation of macrophage migration, macrophage migration, negative regulation of macrophage migration, positive regulation of macrophage chemotaxis, regulation of cytokine secretion involved in immune response, cytokine secretion involved in immune response, positive regulation of macrophage migration, neutrophil activation involved in immune response, neutrophil mediated immunity, negative regulation of leukocyte migration, negative regulation of I-kappaB kinase/NF-kappaB signaling, positive regulation of cytokine production involved in immune response, response to tumor necrosis factor, response to antineoplastic agent, regulation of signal transduction by p53 class mediator, signal transduction by p53 class mediator, cellular response to tumor necrosis factor, response to steroid hormone, intracellular estrogen receptor signaling pathway, cellular response to steroid hormone stimulus, intracellular steroid hormone receptor signaling pathway, regulation of intracellular estrogen receptor signaling pathway, steroid hormone mediated signaling pathway, hormone-mediated signaling pathway (Supplemental Table 2). The 26 KEGG pathways of the core targets (P < 0.05) were identified with involvement of IL-17 signaling pathway, Th17 cell differentiation, Endocrine resistance, Estrogen signaling pathway, Prolactin signaling pathway, Ovarian steroidogenesis, Progesterone-mediated oocyte maturation, Breast cancer, Prostate cancer, Proteoglycans in cancer, MicroRNAs in cancer, PD-L1 expression and PD-1 checkpoint pathway in cancer, VEGF signaling pathway, GnRH signaling pathway, C-type lectin receptor signaling pathway, PI3K-Akt signaling pathway, TNF signaling pathway, Relaxin signaling pathway, FoxO signaling pathway, Oxytocin signaling pathway (Supplemental Table 3).
3.4 Interaction network findings
The network visualization of calycosin-target-BP-KEGG-BPA/OS was determined and highlighted through Cytoscape software, as revealed in Figure. 4. The core targets enriched in the KEGG pathway were identified in red by R-language software, as detailed in Fig. 5.
3.5 Molecular docking findings
As shown in binding energy data (Fig. 6A), In EGFR (PDB ID: 5UGC), the RMSD of the original ligand 8BS was 3.889 Å, and the hydrogen bond with the 5UGC protein acted on the amino acid residue MET-793 (2.9 Å), and calycosin and the amino acid residue MET-793 (3.0 Å) ) hydrogen bond formation (Fig. 6B). In ESR1 (PDB ID:1UOM), the RMSD of the original ligand PTI was 3.645 Å, which hydrogen bonded with 1UOM protein to the amino acid residues ASP-351(3.5 Å), GLU-353(2.7 Å), ARG-394(3.0 Å), calycosin formed a hydrogen bond with amino acid residues GLU-353(1.8 Å) (Fig. 6C). In HSP90AA1 (PDB ID: 4BQG), the RMSD of the original ligand 50Q was 3.105 Å, and the hydrogen bonded with the 4BQG protein to the amino acid residue ASP-93 (2.7 Å), and Calycosin and the amino acid residue SER-52 (3.5 Å) ), TYR-139 (3.1 Å) formed a hydrogen bond (Fig. 6D). In MAPK14 (PDB ID: 3ZSG), the RMSD of the original ligand T75 was 3.789 Å, and its hydrogen bonded with the 3ZSG protein acts on the amino acid residues LYS-53 (3.2 Å), MET-109 (2.7 Å), calycosin and amino acids Residue MET-109 (3.4 Å) formed a hydrogen bond (Fig. 6E). In AR (PDB ID: 1T7F), the RMSD of the original ligand DHT was 0.0004796 Å, which hydrogen bonded with the 1T7F protein to the amino acid residues ASN-705 (2.7 Å), ARG-752 (3.0 Å), THR-877 (2.8 Å), calycosin formed a hydrogen bond with amino acid residue ARG-752 (2.1 Å) (Fig. 6F). In ESR2 (PDB ID: 2GIU), the RMSD of the original ligand FBR was 2.322 Å, which hydrogen bonded with the 2GIU protein to the amino acid residues GLU-305 (2.5 Å), LEU-339 (3.6 Å), calycosin formed a hydrogen bond with amino acid residue ILE-373 (2.6 Å) (Fig. 6G). In PTGS2 (PDB ID: 5IKR), the RMSD of the original ligand ID8 was 2.874 Å, and the hydrogen bond with the 5IKR protein acted on amino acid residues TYR-385 (2.0 Å), SER-530 (2.0 Å), calycosin formed a hydrogen bond with amino acid residue SER-530 (2.9 Å) (Fig. 6H). In CYP19A1 (PDB ID: 3S79), the RMSD of the original ligand ASD was 0.0004888 Å, which hydrogen bonded with the 3S79 protein to the amino acid residues ARG-115 (3.3 Å), MET-374 (2.8 Å), calycosin formed a hydrogen bond with the amino acid residue ARG-115 (3.1 Å) (Fig. 6I).