| Literature DB >> 35497916 |
Wanqing Sun1, Yuan Chen2, Miao Li3,4.
Abstract
Background: ZhiKe GanCao Decoction (ZKGCD) is a commonly used traditional Chinese medicine in the clinical treatment of intervertebral disc degeneration (IDD). However, its active ingredients and mechanism of action remain unclear. This study aims to propose the systematic mechanism of ZKGCD action on IDD based on network pharmacology, molecular docking, and enrichment analysis.Entities:
Year: 2022 PMID: 35497916 PMCID: PMC9054440 DOI: 10.1155/2022/8786052
Source DB: PubMed Journal: Evid Based Complement Alternat Med ISSN: 1741-427X Impact factor: 2.650
Scientific names for all herbs in ZhiKe GanCao Decoction.
| Pin Yin | Latin name |
|---|---|
| ZhiKe (ZK) | Aurantii Fructus |
| GanCao (GC) | Licorice |
| DangGui (DG) | Angelicae Sinensis Radix |
| DanShen (DS) | Radix Salvia |
| SanLeng (SL) | Sparganii Rhizome |
| Ezhu(EZ) | Curcumae Rhizome |
| QianNiuZi (QNZ) | Semen Pharbitidis |
Figure 1Flow chart of the study. OB: oral bioavailability. DL: drug-likeness.
Figure 2Venn diagrams of intersecting genes between IDD and active ingredients in ZKGCD. IDD: intervertebral disc degeneration. ZKGCD : ZhiKe GanCao Decoction.
Figure 3Intersecting genes-active components network. The pink circles represent intersecting genes between IDD and active ingredients in ZKGCD; the blue circles represent active ingredients related to the common genes; the lines between the two circles represent the interaction.
Basic information of 11 active components in ZKGCD.
| Molecule ID | Molecule name | PubChem CID | OB (%) | DL | Source (herb name) | Targeted key genes |
|---|---|---|---|---|---|---|
| MOL000098 | Quercetin | 5280343 | 46.43 | 0.28 | GanCao | AKT1, MMP9, TNF, JUN, IL6, CASP3, TP53, IL1B |
| MOL000006 | Luteolin | 5280445 | 36.16 | 0.25 | DanShen | AKT1, MMP9, TNF, JUN, IL6, CASP3, TP53 |
| MOL000422 | Kaempferol | 5280863 | 41.88 | 0.24 | GanCao | AKT1, TNF, JUN, CASP3 |
| MOL004328 | Naringenin | 932 | 59.29 | 0.21 | ZhiKe, GanCao | AKT1, MAPK3, CASP3 |
| MOL000392 | Formononetin | 5280378 | 69.67 | 0.21 | GanCao, SanLeng | JUN |
| MOL005828 | Nobiletin | 72344 | 61.67 | 0.52 | ZhiKe | MMP9, JUN, TP53 |
| MOL007154 | Tanshinone IIA | 164676 | 49.89 | 0.40 | DanShen | MMP9, JUN, CASP3, TP53 |
| MOL000497 | Licochalcone A | 5318998 | 40.79 | 0.29 | GanCao | STAT3 |
| MOL000354 | Isorhamnetin | 5281654 | 49.60 | 0.31 | GanCao | / |
| MOL004373 | Anhydroicaritin | 44259058 | 45.41 | 0.44 | QianNiuZi | / |
Figure 4Protein-protein interaction (PPI) network and key gene network.
Figure 5Three clusters of common genes by MCODE plugin in Cytoscape.
Cluster information of the protein-protein interaction (PPI) network for common genes.
| Cluster | Score | Nodes | Edges | Gene names |
|---|---|---|---|---|
| 1 | 50.156 | 65 | 1605 | MMP2, TGFB1, SERPINE1, MPO, CCL2, CDK4, MYC, IL2, MDM2, IFNG, IL4, NR3C1, CRP, CDK2, MAPK3 |
| 2 | 7 | 19 | 63 | NCF1, HSPB1, RAF1, AR, F3, PLAU, CCNB1, BIRC5, MAPK1, GSK3B, CAV1, CDK1, KDR, PRKCA, RB1, RUNX2, CCNA2, CASP7, HSPA5 |
| 3 | 3 | 3 | 3 | F2, THBD, PLAT |
∗Core genes are highlighted in red.
Figure 6“IDD-key genes-active ingredients-herbs” network. Red pentagons represent diseases, dark blue triangles represent key genes, purple inverted triangles represent active ingredients associated with core genes, and light blue rectangles represent herbs. The size of each node represents the number of degrees.
Figure 7GO enrichment analysis of common genes. (a) Top 10 significantly enriched terms in biological processes (BPs). (b) Subnetwork showing the top five BP terms and related genes. (c) Top 10 significantly enriched terms in cellular components (CCs). (d) Subnetwork shows the top five CC terms and related genes. (e) Top 10 significantly enriched terms in molecular functions (MFs). (f) Subnetwork shows the top five MF terms and related genes.
The main related pathways for IDD are in the top 30.
| ID | Description | p. adjust | Count |
|---|---|---|---|
| hsa04933 | AGE-RAGE signaling pathway in diabetic complications | 3.36E-34 | 30 |
| hsa04668 | TNF signaling pathway | 1.53E-26 | 29 |
| hsa04657 | IL-17 signaling pathway | 4.17E-26 | 27 |
| hsa04218 | Cellular senescence | 5.35E-19 | 26 |
| Hsa04210 | Apoptosis | 3.71E-18 | 24 |
| Hsa04151 | PI3K-Akt signaling pathway | 2.00E-16 | 33 |
Figure 8KEGG pathway enrichment analysis of common genes. (a) The 30 pathways with the lowest adjusted p values. The darker the color, the smaller the adjusted p value. The larger the circle, the greater the number of target genes in the term. (b) Subnetwork shows the top five KEGG pathways and related genes.
Figure 9Heat map of binding energy between 10 core genes and top three active ingredients by molecular docking.
Figure 10Four examples of conformations for some core compounds and key genes.