| Literature DB >> 34873575 |
Dan He1, Qiang Li2, Guangli Du1, Jijia Sun2, Guofeng Meng3, Shaoli Chen1.
Abstract
OBJECTIVE: Nephrotic syndrome (NS) is a common glomerular disease caused by a variety of causes and is the second most common kidney disease. Guizhi is the key drug of Wulingsan in the treatment of NS. However, the action mechanism remains unclear. In this study, network pharmacology and molecular docking were used to explore the underlying molecular mechanism of Guizhi in treating NS.Entities:
Mesh:
Substances:
Year: 2021 PMID: 34873575 PMCID: PMC8643239 DOI: 10.1155/2021/8141075
Source DB: PubMed Journal: Biomed Res Int Impact factor: 3.411
Figure 1A flow diagram based on a cohesive integration strategy of network pharmacology and molecular docking.
The main active compounds of Guizhi.
| Mol ID | Molecule name | OB (%) | DL | Caco-2 |
|---|---|---|---|---|
| MOL000073 | Ent-Epicatechin | 48.96 | 0.24 | 0.02 |
| MOL000358 | Beta-sitosterol | 36.91 | 0.75 | 1.32 |
| MOL000359 | Sitosterol | 36.91 | 0.75 | 1.32 |
| MOL000492 | (+)-catechin | 54.83 | 0.24 | -0.03 |
| MOL000991 | Cinnamaldehyde | 31.99 | 0.02 | 1.35 |
| MOL001736 | (-)-taxifolin | 60.51 | 0.27 | -0.24 |
| MOL004576 | Taxifolin | 57.84 | 0.27 | -0.23 |
| MOL011169 | Peroxyergosterol | 44.39 | 0.82 | 0.86 |
Figure 2The Venny plot of 93 potential targets.
93 potential targets and UniProt information.
| No. | Gene names | Protein names | UniProt ID |
|---|---|---|---|
| 1 | ABCB1 | ATP-dependent translocase ABCB1 | P08183 |
| 2 | ABCC2 | ATP-binding cassette subfamily C member 2 | Q92887 |
| 3 | ABCG2 | Broad substrate specificity ATP-binding cassette transporter ABCG2 | Q9UNQ0 |
| 4 | ACE | Angiotensin-converting enzyme | P12821 |
| 5 | ACHE | Acetylcholinesterase | P22303 |
| 6 | ACP1 | Low molecular weight phosphotyrosine protein phosphatase | P24666 |
| 7 | AKR1B1 | Aldo-keto reductase family 1 member B1 | P15121 |
| 8 | AKR1B10 | Aldo-keto reductase family 1 member B10 | O60218 |
| 9 | ALK | ALK tyrosine kinase receptor | Q9UM73 |
| 10 | APP | Amyloid-beta precursor protein | P05067 |
| 11 | AR | Androgen receptor | P10275 |
| 12 | AVPR1A | Vasopressin V1a receptor | P37288 |
| 13 | CASR | Extracellular calcium-sensing receptor | P41180 |
| 14 | CCR1 | C-C chemokine receptor type 1 | P32246 |
| 15 | CD4 | T-cell surface glycoprotein CD4 | P01730 |
| 16 | CDK4 | Cyclin-dependent kinase 4 | P11802 |
| 17 | CTSB | Cathepsin B | P07858 |
| 18 | CTSL | Procathepsin L | P07711 |
| 19 | CYP11B2 | Cytochrome P450 11B2 | P19099 |
| 20 | CYP19A1 | Cytochrome P450 19A1 | P11511 |
| 21 | CYP1A1 | Cytochrome P450 1A1 | P04798 |
| 22 | CYP1B1 | Cytochrome P450 1B1 | Q16678 |
| 23 | CYP2A6 | Cytochrome P450 2A6 | P11509 |
| 24 | CYP2C19 | Cytochrome P450 2C19 | P33261 |
| 25 | CYP3A4 | Cytochrome P450 3A4 | P08684 |
| 26 | DNMT1 | DNA (cytosine-5)-methyltransferase 1 | P26358 |
| 27 | DUSP1 | Dual specificity protein phosphatase 1 | P28562 |
| 28 | ELANE | Neutrophil elastase | P08246 |
| 29 | ELAVL1 | ELAV-like protein 1 | Q15717 |
| 30 | ESR1 | Estrogen receptor | P03372 |
| 31 | ESR2 | Estrogen receptor beta | Q92731 |
| 32 | F10 | Coagulation factor X | P00742 |
| 33 | F2 | Coagulation factor II | P00734 |
| 34 | F2R | Coagulation factor II receptor | P25116 |
| 35 | F3 | Coagulation factor III | P13726 |
| 36 | FABP1 | Fatty acid-binding protein 1 | P07148 |
| 37 | G6PD | Glucose-6-phosphate 1-dehydrogenase | P11413 |
| 38 | GC | Group-specific component | P02774 |
| 39 | GLO1 | Glyoxalase I | Q04760 |
| 40 | HDAC2 | Histone deacetylase 2 | Q92769 |
| 41 | HIF1A | Hypoxia-inducible factor 1-alpha | Q16665 |
| 42 | HMGCR | 3-Hydroxy-3-methylglutaryl-coenzyme A reductase | P04035 |
| 43 | HSD11B1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | P28845 |
| 44 | HSD11B2 | Corticosteroid 11-beta-dehydrogenase isozyme 2 | P80365 |
| 45 | HTR2B | 5-Hydroxytryptamine receptor 2B | P41595 |
| 46 | ICAM1 | Intercellular adhesion molecule 1 | P05362 |
| 47 | IGF1R | Insulin-like growth factor 1 receptor | P08069 |
| 48 | ITGAL | Integrin alpha-L | P20701 |
| 49 | ITGB2 | Integrin beta-2 | P05107 |
| 50 | KAT2B | Histone acetyltransferase KAT2B | Q92831 |
| 51 | KCNH2 | Potassium voltage-gated channel subfamily H member 2 | Q12809 |
| 52 | KDR | Kinase insert domain receptor | P35968 |
| 53 | MAP2K1 | Dual specificity mitogen-activated protein kinase kinase 1 | Q02750 |
| 54 | MAPK14 | Mitogen-activated protein kinase 14 | Q16539 |
| 55 | MAPK3 | Mitogen-activated protein kinase 3 | P27361 |
| 56 | MAPK8 | Mitogen-activated protein kinase 8 | P45983 |
| 57 | MAPT | Microtubule-associated protein tau | P10636 |
| 58 | MCL1 | Induced myeloid leukemia cell differentiation protein Mcl-1 | Q07820 |
| 59 | MDM2 | E3 ubiquitin-protein ligase Mdm2 | Q00987 |
| 60 | MET | Hepatocyte growth factor receptor | P08581 |
| 61 | MMP12 | Matrix metalloproteinase-12 | P39900 |
| 62 | MPO | Myeloperoxidase | P05164 |
| 63 | NFE2L2 | Nuclear factor erythroid 2-related factor 2 | Q16236 |
| 64 | NOS1 | Peptidyl-cysteine S-nitrosylase NOS1 | P29475 |
| 65 | NOS2 | Peptidyl-cysteine S-nitrosylase NOS2 | P35228 |
| 66 | NOS3 | NOS type III | P29474 |
| 67 | NR1I2 | Nuclear receptor subfamily 1 group I member 2 | O75469 |
| 68 | NR3C1 | Nuclear receptor subfamily 3 group C member 1 | P04150 |
| 69 | PARP1 | Poly [ADP-ribose] polymerase 1 | P09874 |
| 70 | PLA2G1B | Phosphatidylcholine 2-acylhydrolase 1B | P04054 |
| 71 | PLA2G7 | Platelet-activating factor acetylhydrolase | Q13093 |
| 72 | PPARA | Peroxisome proliferator-activated receptor alpha | Q07869 |
| 73 | PRKCB | Protein kinase C beta type | P05771 |
| 74 | PRKCD | Protein kinase C delta type | Q05655 |
| 75 | PSEN1 | Presenilin-1 | P49768 |
| 76 | PTGS2 | Prostaglandin G/H synthase 2 | P35354 |
| 77 | PTK2B | Protein-tyrosine kinase 2-beta | Q14289 |
| 78 | PTPN11 | Tyrosine-protein phosphatase nonreceptor type 11 | Q06124 |
| 79 | PTPN2 | Tyrosine-protein phosphatase nonreceptor type 2 | P17706 |
| 80 | PTPRC | Receptor-type tyrosine-protein phosphatase C | P08575 |
| 81 | RELA | Transcription factor p65 | Q04206 |
| 82 | SLC6A2 | Sodium-dependent noradrenaline transporter | P23975 |
| 83 | SNCA | Alpha-synuclein | P37840 |
| 84 | SRC | Protooncogene tyrosine-protein kinase Src | P12931 |
| 85 | TGM2 | Protein-glutamine gamma-glutamyltransferase 2 | P21980 |
| 86 | TLR4 | Toll-like receptor 4 | O00206 |
| 87 | TOP1 | DNA topoisomerase 1 | P11387 |
| 88 | TRPA1 | Transient receptor potential cation channel subfamily A member 1 | O75762 |
| 89 | TYMP | Thymidine phosphorylase | P19971 |
| 90 | TYMS | Thymidylate synthase | P04818 |
| 91 | VDR | Vitamin D3 receptor | P11473 |
| 92 | VEGFA | Vascular endothelial growth factor A | P15692 |
| 93 | XDH | Xanthine dehydrogenase/oxidase | P47989 |
Figure 3The active component-target network. The network formed with 101 nodes and 169 edges. The dark purple circles represented active compounds; the light purple inverted triangles represented intersecting targets. The edges represented the connection between active component and targets.
Degree value of 8 main active components of Guizhi.
| Mol ID | Molecule name | Degree |
|---|---|---|
| MOL000358 | Beta-sitosterol | 37 |
| MOL000359 | Sitosterol | 37 |
| MOL000991 | Cinnamaldehyde | 36 |
| MOL011169 | Peroxyergosterol | 29 |
| MOL001736 | (-)-taxifolin | 12 |
| MOL004576 | Taxifolin | 12 |
| MOL000492 | (+)-catechin | 3 |
| MOL000073 | Ent-Epicatechin | 3 |
Figure 4The PPI network diagram (a) and the bar graph of the top 10 intersecting targets with degree values in PPI network (b). In PPI network, nodes represented intersecting targets, and edges represented interactions between targets, and the size reflected the value of degree. In the bar graph, the top 10 targets were selected according to the degree value.
Figure 5Go (a) and KEGG enrichment analysis (b). The top 10 items of BP, CC, and MF and the top 30 KEGG signal pathways were selected according to the P value to draw the GO and KEGG bubble diagram. The color of the bubbles changes from purple to red indicating that the P value decreases from large to small. Gene ratio is the number of targets that located in the pathway. The higher the gene ratio is, the more targets were enriched.
Figure 6The overall network of the top 30 significant KEGG signaling pathways with their corresponding targets. The yellow represents Guizhi, pink represents active compounds, purple represents core targets, green represents signaling pathways, and dark green represents NS.
The top 5 targets in PPI network.
| No. | Target name | PDB ID | Degree |
|---|---|---|---|
| 1 | VEGFA | 6BFT | 58 |
| 2 | MAPK3 | 2ZOQ | 52 |
| 3 | SRC | 6HTY | 49 |
| 4 | PTGS2 | 5IKV | 43 |
| 5 | MAPK8 | 4L7F | 42 |
Molecular docking results of targets and active components.
| Target name | PDB ID | Molecule name | Affinity (kcal/Mol) |
|---|---|---|---|
| VEGFA | 6BFT | Peroxyergosterol | -6.8 |
| Beta-sitosterol | -6.4 | ||
| Sitosterol | -6.3 | ||
| Ent-Epicatechin | -5.9 | ||
| (-)-taxifolin | -5.7 | ||
| Taxifolin | -5.6 | ||
| (+)-catechin | -5.4 | ||
| Cinnamaldehyde | -4.9 | ||
|
| |||
| MAPK3 | 2ZOQ | (-)-taxifolin | -9.0 |
| Beta-sitosterol | -8.7 | ||
| Taxifolin | -8.5 | ||
| (+)-catechin | -8.4 | ||
| Peroxyergosterol | -8.1 | ||
| Ent-Epicatechin | -7.9 | ||
| Sitosterol | -7.3 | ||
| Cinnamaldehyde | -5.4 | ||
|
| |||
| SRC | 6HTY | Peroxyergosterol | -8.7 |
| Beta-sitosterol | -8.5 | ||
| Sitosterol | -8.4 | ||
| (+)-catechin | -8.1 | ||
| Taxifolin | -8.1 | ||
| (-)-taxifolin | -7.9 | ||
| Ent-Epicatechin | -7.8 | ||
| Cinnamaldehyde | -6.6 | ||
|
| |||
| PTGS2 | 5IKV | (+)-catechin | -7.6 |
| Ent-Epicatechin | -7.5 | ||
| (-)-taxifolin | -7.3 | ||
| Taxifolin | -6.8 | ||
| Cinnamaldehyde | -6.1 | ||
| Peroxyergosterol | -3.8 | ||
| Beta-sitosterol | -3.7 | ||
| Sitosterol | -3.7 | ||
|
| |||
| MAPK8 | 4L7F | Beta-sitosterol | -9.8 |
| Sitosterol | -9.8 | ||
| (-)-taxifolin | -9.3 | ||
| (+)-catechin | -9.1 | ||
| Taxifolin | -8.7 | ||
| Ent-Epicatechin | -8.5 | ||
| Peroxyergosterol | -8.5 | ||
| Cinnamaldehyde | -6.0 | ||
Figure 7The binding energy of the main active components of Guizhi and core targets.
Figure 8The molecular docking of active compounds and core targets: (a) cinnamaldehyde-PTGS2, (b) (-)-taxifolin-PTGS2, (c) (+)-catechin-PTGS2, (d) (-)-taxifolin-VEGFA, (e) (+)-catechin-SRC, (f) (+)-catechin-VEGFA, (g) ent-Epicatechin-PTGS2, (h) ent-Epicatechin-SRC, (i) peroxyergosterol-PTGS2, (j) taxifolin-PTGS2, (k) taxifolin-VEGFA, and (l) taxifolin-SRC.