Biochemical Targets and Molecular Mechanism of Ginsenoside Compound K in Treating Osteoporosis Based on Network Pharmacology
Abstract
:1. Introduction
2. Results
2.1. Molecular Targets of GCK and Osteoporosis
2.2. PPI Network Analysis of Co-Targets of GCK and Osteoporosis
2.3. GO and KEGG Analysis of Co-Targets of GCK and Osteoporosis
2.4. Molecular Docking of GCK- c-Fms Interaction
3. Discussion
4. Materials and Methods
4.1. Targets of GCK
4.2. Targets of Osteoporosis
4.3. Putative Targets of GCK-Treated Osteoporosis
4.4. Protein–Protein Interactions (PPIs), Network Construction and Analysis
4.5. Enrichment Analysis
4.6. Molecular Docking of Compound–Target Interaction
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Cluster | Nodes | Edges | Score | Genes |
---|---|---|---|---|
1 | 11 | 36 | 7.200 | SYK; STAT3; PLCG1; PIK3CD; PIK3CB; MAP2K1; JAK1; IL2; HSP90AA1; HCK; GRB2 |
2 | 15 | 40 | 5.714 | S1PR1; PSENEN; PSEN2; PSEN1; PIK3R1; PIK3CA; NCSTN; KDR; JAK2; FGF2; FGF1; FES; EPHB4; APH1B; APH1A; |
3 | 5 | 10 | 5.000 | RXRG; RXRB; RARB; HDAC3; HDAC1 |
4 | 11 | 20 | 4.000 | VEGFB; VEGFA; THBS1; SRC; SERPING1; PTPN1; MAPK8; KIT; IGF1R; CFD; AR |
5 | 3 | 3 | 3.000 | MMP9; MMP3; MMP1 |
Methods | Betweenness | BottleNeck | Degree | Closeness | MCC | EcCentricity | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | Score | Gene | Score | Gene | Score | Gene | Score | Gene | Score | Gene | Score | |
1 | STAT3 | 1858.83 | PIK3R1 | 32.00 | PIK3R1 | 35.00 | PIK3R1 | 60.00 | PIK3R1 | 33,711.00 | PIK3CA | 0.32 |
2 | PIK3R1 | 1514.88 | STAT3 | 17.00 | PIK3CA | 34.00 | PIK3CA | 59.33 | PIK3CA | 33,710.00 | PIK3R1 | 0.32 |
3 | PIK3CA | 1166.88 | MMP9 | 12.00 | STAT3 | 30.00 | STAT3 | 57.08 | GRB2 | 23,136.00 | MMP9 | 0.24 |
4 | EPHB4 | 1159.36 | GRB2 | 9.00 | SRC | 23.00 | SRC | 52.00 | PIK3CB | 22,560.00 | HCK | 0.24 |
5 | VEGFA | 568.08 | EPHB4 | 8.00 | GRB2 | 22.00 | GRB2 | 51.75 | PLCG1 | 21,770.00 | SYK | 0.24 |
6 | MTOR | 477.35 | VEGFA | 7.00 | PLCG1 | 21.00 | VEGFA | 50.17 | JAK1 | 20,934.00 | PTPN6 | 0.24 |
7 | PLCG1 | 449.22 | MAPK14 | 6.00 | VEGFA | 20.00 | JAK2 | 49.67 | SYK | 17,220.00 | IGF1R | 0.24 |
8 | CCND1 | 400.60 | MTOR | 4.00 | JAK2 | 19.00 | PLCG1 | 49.08 | HCK | 16,812.00 | PIK3C2B | 0.24 |
9 | MAPK14 | 384.62 | KIT | 4.00 | JAK1 | 19.00 | JAK1 | 49.08 | SRC | 11,096.00 | MAP2K1 | 0.24 |
10 | JAK2 | 377.93 | S1PR1 | 4.00 | IL2 | 17.00 | IL2 | 48.42 | JAK2 | 10,906.00 | STAT3 | 0.24 |
11 | MMP2 | 328.71 | PTPN6 | 3.00 | PIK3CB | 17.00 | HSP90AA1 | 46.42 | IL2 | 8767.00 | MTOR | 0.24 |
12 | KIT | 317.35 | MAP2K1 | 3.00 | SYK | 15.00 | PIK3CB | 46.00 | STAT3 | 7819.00 | JAK2 | 0.24 |
13 | IL2 | 299.91 | JAK2 | 3.00 | KDR | 15.00 | KDR | 46.00 | PIK3CD | 7440.00 | MMP1 | 0.24 |
14 | SRC | 296.80 | PPARG | 3.00 | PTPN6 | 14.00 | PTPN6 | 45.42 | MAP2K1 | 5929.00 | PIK3CD | 0.24 |
15 | MMP9 | 262.75 | RARB | 3.00 | MAPK14 | 14.00 | HCK | 45.33 | KDR | 2580.00 | MMP3 | 0.24 |
16 | HDAC3 | 260.66 | CHEK1 | 3.00 | HCK | 13.00 | KIT | 45.00 | VEGFA | 2392.00 | VEGFA | 0.24 |
17 | S1PR1 | 237.33 | MMP2 | 3.00 | HSP90AA1 | 13.00 | SYK | 44.92 | S1PR1 | 1538.00 | KIT | 0.24 |
18 | GRB2 | 225.02 | F10 | 3.00 | MAP2K1 | 12.00 | MAPK14 | 44.87 | FGF2 | 1344.00 | PTPN1 | 0.24 |
19 | PTPN6 | 212.20 | KDR | 3.00 | S1PR1 | 12.00 | MAP2K1 | 44.75 | HSP90AA1 | 1130.00 | ANXA1 | 0.24 |
20 | MAP2K1 | 205.76 | HDAC3 | 3.00 | MMP9 | 11.00 | FGF2 | 44.75 | EPHB4 | 724.00 | GNRHR | 0.24 |
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Zhang, S.; Shen, S.; Ma, P.; Fan, D. Biochemical Targets and Molecular Mechanism of Ginsenoside Compound K in Treating Osteoporosis Based on Network Pharmacology. Int. J. Mol. Sci. 2022, 23, 13921. https://doi.org/10.3390/ijms232213921
Zhang S, Shen S, Ma P, Fan D. Biochemical Targets and Molecular Mechanism of Ginsenoside Compound K in Treating Osteoporosis Based on Network Pharmacology. International Journal of Molecular Sciences. 2022; 23(22):13921. https://doi.org/10.3390/ijms232213921
Chicago/Turabian StyleZhang, Sen, Shihong Shen, Pei Ma, and Daidi Fan. 2022. "Biochemical Targets and Molecular Mechanism of Ginsenoside Compound K in Treating Osteoporosis Based on Network Pharmacology" International Journal of Molecular Sciences 23, no. 22: 13921. https://doi.org/10.3390/ijms232213921