| Literature DB >> 36042622 |
Lili Hu1, Jue Wang1, Xiaoge Zhao2, Donghui Cai1.
Abstract
Many classic decoctions of Chinese medicine including Radix Bupleuri are used to treat major depressive disorder (MDD). Saikosaponin D is a representative bioactive ingredient discovered in Radix Bupleuri. The mechanism of saikogenin G (SGG) as a metabolite in MDD remains unclear to date. This study aims to elucidate the mechanism of SGG in treating MDD with network pharmacology. We evaluated the drug likeness of SGG with SwissADME web tool and predicted its targets using the SwissTargetPrediction and PharmMapper. MDD-related targets were identified from the following databases: DisGeNET, DrugBank, Online Mendelian Inheritance in Man, and GeneCards. The common targets of SGG and MDD were imported to the STRING11.0 database, and then a protein-protein interaction network was constructed. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment were analyzed with DAVID 6.8 database. The molecular weight of SGG was 472.7 g/mol, the topological polar surface area was 69.92 A2 <140 A2, the octanol/water partition coefficient (Consensus LogP0/W) was 4.80, the rotatable bond was 1, the hydrogen bond donors was 3, and the hydrogen bond acceptors was 4. A total of 322 targets of SGG were obtained and there were 1724 MDD-related targets. A total of 78 overlapping genes were selected as targets of MDD treatment including albumin, insulin-like growth factor I, mitogen-activated protein kinase 1, proto-oncogene tyrosine-protein kinase Src, and epidermal growth factor receptor. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that proteoglycans in cancer, pathways in cancer, prostate cancer, hypoxia-inducible factor-1, central carbon metabolism in cancer, estrogen, PI3K-Akt, ErbB, Rap1, and prolactin signaling pathways played an important role(P < .0001). This study showed that SGG exhibits good drug-like properties and elucidated the potential mechanisms of SGG in treating MDD with regulating inflammation, energy metabolism, monoamine neurotransmitters, neuroplasticity, phosphocreatine-creatine kinase circuits, and so on.Entities:
Mesh:
Substances:
Year: 2022 PMID: 36042622 PMCID: PMC9410695 DOI: 10.1097/MD.0000000000030193
Source DB: PubMed Journal: Medicine (Baltimore) ISSN: 0025-7974 Impact factor: 1.817
Figure 1.Prediction of the SGG target genes. (A) Chemical structure of SGG. (B) Classification of SGG target genes for top 15 according to its biochemical criteria. (C) Classification of SGG target genes for all according to its biochemical criteria. SGG = saikogenin G.
Pharmacological and molecular properties of saikogenin G.
| Property | Value |
|---|---|
| Molecular weight | 472.7 g/mol |
| TPSA | 69.92 A2 |
| Consensus LogP0/W | 4.80 |
| Rotatable bonds | 1 |
| H-bond donor | 3 |
| H-bond acceptor | 4 |
| Molar refractivity | 136.21 |
| Log Kp (skin permeation) | −5.09 cm/s |
| Bioavailability score | 0.55 |
TPSA = topological polar surface area.
Figure 2.Targets of SGG against MDD. (A) Seventy-eight overlapping target genes between SGG and MDD. (B) Network of SGG, MDD, and all overlapping target genes. Yellow nodes represent the target genes. MDD = major depressive disorder, SGG = saikogenin G.
Figure 3.Interaction network of common targets. (A) Construction of a PPI network expressed by 76 common targets. Node size and color from orange (high) to wathet (low) represent the degree. The outer ring nodes represent the 22 big hub nodes. (B) Bar plot of the number of 22 hub node links. PPI = protein–protein interaction.
Information of 84 KEGG pathways.
| No. | Term ID | Pathway name | Count | Fold enrichment | |
|---|---|---|---|---|---|
| 1 | hsa05205 | Proteoglycans in cancer | 6.28E–14 | 20 | 9.5542 |
| 2 | hsa05200 | Pathways in cancer | 2.85E–12 | 24 | 5.8346 |
| 3 | hsa05215 | Prostate cancer | 3.14E–12 | 14 | 15.1998 |
| 4 | hsa04066 | HIF-1 signaling pathway | 1.76E–10 | 13 | 12.9379 |
| 5 | hsa05230 | Central carbon metabolism in cancer | 6.94E–10 | 11 | 16.4212 |
| 6 | hsa04915 | Estrogen signaling pathway | 3.91E–09 | 12 | 11.5808 |
| 7 | hsa04151 | PI3K-Akt signaling pathway | 7.05E–09 | 19 | 5.2617 |
| 8 | hsa04012 | ErbB signaling pathway | 1.52E–08 | 11 | 12.0800 |
| 9 | hsa04015 | Rap1 signaling pathway | 2.05E–08 | 15 | 6.8244 |
| 10 | hsa04917 | Prolactin signaling pathway | 3.54E–08 | 10 | 13.4566 |
| 11 | hsa04014 | Ras signaling pathway | 5.21E–08 | 15 | 6.3413 |
| 12 | hsa05219 | Bladder cancer | 1.57E–07 | 8 | 18.6423 |
| 13 | hsa04919 | Thyroid hormone signaling pathway | 2.26E–07 | 11 | 9.1388 |
| 14 | hsa05214 | Glioma | 2.72E–07 | 9 | 13.2289 |
| 15 | hsa05218 | Melanoma | 5.46E–07 | 9 | 12.1109 |
| 16 | hsa04550 | Signaling pathways regulating pluripotency of stem cells | 1.42E–06 | 11 | 7.5068 |
| 17 | hsa04370 | VEGF signaling pathway | 2.59E–06 | 8 | 12.5301 |
| 18 | hsa04068 | FoxO signaling pathway | 8.27E–06 | 10 | 7.1300 |
| 19 | hsa05213 | Endometrial cancer | 1.37E–05 | 7 | 12.8614 |
| 20 | hsa05161 | Hepatitis B | 1.57E–05 | 10 | 6.5891 |
| 21 | hsa04726 | Serotonergic synapse | 1.63E–05 | 9 | 7.7466 |
| 22 | hsa05223 | Nonsmall cell lung cancer | 2.11E–05 | 7 | 11.9427 |
| 23 | hsa05221 | Acute myeloid leukemia | 2.11E–05 | 7 | 11.9427 |
| 24 | hsa04510 | Focal adhesion | 4.37E–05 | 11 | 5.1017 |
| 25 | hsa04960 | Aldosterone-regulated sodium reabsorption | 4.45E–05 | 6 | 14.6987 |
| 26 | hsa05211 | Renal cell carcinoma | 5.44E–05 | 7 | 10.1332 |
| 27 | hsa05231 | Choline metabolism in cancer | 7.35E–05 | 8 | 7.5677 |
| 28 | hsa05220 | Chronic myeloid leukemia | 8.91E–05 | 7 | 9.2888 |
| 29 | hsa04931 | Insulin resistance | 1.13E–04 | 8 | 7.0772 |
| 30 | hsa00330 | Arginine and proline metabolism | 1.50E–04 | 6 | 11.465 |
| 31 | hsa04722 | Neurotrophin signaling pathway | 2.18E–04 | 8 | 6.3694 |
| 32 | hsa04152 | AMPK signaling pathway | 2.54E–04 | 8 | 6.2141 |
| 33 | hsa04914 | Progesterone-mediated oocyte maturation | 2.55E–04 | 7 | 7.6873 |
| 34 | hsa04810 | Regulation of actin cytoskeleton | 2.79E–04 | 10 | 4.5496 |
| 35 | hsa05160 | Hepatitis C | 4.10E–04 | 8 | 5.7469 |
| 36 | hsa05210 | Colorectal cancer | 4.16E–04 | 6 | 9.2460 |
| 37 | hsa04910 | Insulin signaling pathway | 5.12E–04 | 8 | 5.5386 |
| 38 | hsa05212 | Pancreatic cancer | 5.19E–04 | 6 | 8.8192 |
| 39 | hsa04660 | T-cell receptor signaling pathway | 5.42E–04 | 7 | 6.6879 |
| 40 | hsa04062 | Chemokine signaling pathway | 6.09E–04 | 9 | 4.6230 |
| 41 | hsa00982 | Drug metabolism – cytochrome P450 | 6.39E–04 | 6 | 8.4301 |
| 42 | hsa04662 | B-cell receptor signaling pathway | 6.84E–04 | 6 | 8.3080 |
| 43 | hsa04668 | TNF signaling pathway | 7.76E–04 | 7 | 6.2504 |
| 44 | hsa04520 | Adherens junction | 7.80E–04 | 6 | 8.0739 |
| 45 | hsa04930 | Type II diabetes mellitus | 1.44E–03 | 5 | 9.9523 |
| 46 | hsa04650 | Natural killer cell–mediated cytotoxicity | 1.54E–03 | 7 | 5.4819 |
| 47 | hsa05152 | Tuberculosis | 2.20E–03 | 8 | 4.3183 |
| 48 | hsa04912 | GnRH signaling pathway | 2.38E–03 | 6 | 6.2995 |
| 49 | hsa04150 | mTOR signaling pathway | 2.91E–03 | 5 | 8.2364 |
| 50 | hsa05216 | Thyroid cancer | 3.18E–03 | 4 | 13.1782 |
| 51 | hsa04730 | Long-term depression | 3.29E–03 | 5 | 7.9618 |
| 52 | hsa04664 | Fc epsilon RI signaling pathway | 5.16E–03 | 5 | 7.0251 |
| 53 | hsa04610 | Complement and coagulation cascades | 5.44E–03 | 5 | 6.9233 |
| 54 | hsa04725 | Cholinergic synapse | 5.59E–03 | 6 | 5.1644 |
| 55 | hsa04071 | Sphingolipid signaling pathway | 7.74E–03 | 6 | 4.7771 |
| 56 | hsa00380 | Tryptophan metabolism | 7.92E–03 | 4 | 9.5542 |
| 57 | hsa05164 | Influenza A | 8.84E–03 | 7 | 3.8436 |
| 58 | hsa05206 | MicroRNAs in cancer | 8.85E–03 | 9 | 3.0066 |
| 59 | hsa04380 | Osteoclast differentiation | 1.11E–02 | 6 | 4.3760 |
| 60 | hsa05222 | Small cell lung cancer | 1.13E–02 | 5 | 5.6201 |
| 61 | hsa05162 | Measles | 1.18E–02 | 6 | 4.31015 |
| 62 | hsa04540 | Gap junction | 1.27E–02 | 5 | 5.428504 |
| 63 | hsa00360 | Phenylalanine metabolism | 1.29E–02 | 3 | 16.86029 |
| 64 | hsa04913 | Ovarian steroidogenesis | 1.38E–02 | 4 | 7.79932 |
| 65 | hsa04630 | Jak-STAT signaling pathway | 1.66E–02 | 6 | 3.953448 |
| 66 | hsa00220 | Arginine biosynthesis | 1.77E–02 | 3 | 14.33125 |
| 67 | hsa04921 | Oxytocin signaling pathway | 1.90E–02 | 6 | 3.821667 |
| 68 | hsa04916 | Melanogenesis | 1.94E–02 | 5 | 4.777083 |
| 69 | hsa04932 | Nonalcoholic fatty liver disease | .0195 | 6 | 3.796358 |
| 70 | hsa00340 | Histidine metabolism | .0212 | 3 | 13.02841 |
| 71 | hsa05142 | Chagas disease (American trypanosomiasis) | .0221 | 5 | 4.593349 |
| 72 | hsa04620 | Toll-like receptor signaling pathway | .0235 | 5 | 4.506682 |
| 73 | hsa04210 | Apoptosis | .0258 | 4 | 6.163978 |
| 74 | hsa05145 | Toxoplasmosis | .0265 | 5 | 4.342803 |
| 75 | hsa04114 | Oocyte meiosis | .0273 | 5 | 4.303679 |
| 76 | hsa05202 | Transcriptional misregulation in cancer | .0286 | 6 | 3.432635 |
| 77 | hsa04670 | Leukocyte transendothelial migration | .0306 | 5 | 4.153986 |
| 78 | hsa04320 | Dorsoventral axis formation | .0312 | 3 | 10.61574 |
| 79 | hsa05120 | Epithelial cell signaling in | .0315 | 4 | 5.70398 |
| 80 | hsa05034 | Alcoholism | .0355 | 6 | 3.238701 |
| 81 | hsa05140 | Leishmaniasis | .0366 | 4 | 5.382629 |
| 82 | hsa04611 | Platelet activation | .0448 | 5 | 3.674679 |
| 83 | hsa04010 | MAPK signaling pathway | .0457 | 7 | 2.643445 |
| 84 | hsa05204 | Chemical carcinogenesis | .0493 | 4 | 4.777083 |
AMPK = adenosine 5‘-monophosphate (AMP)-activated protein kinase, FoxO = forkhead box O, GnRH = gonadotropin-releasing hormone, KEGG = Kyoto Encyclopedia of Genes and Genomes, MAPK = mitogen-activated protein kinase, mTOR = mammalian target of rapamycin, VEGF = vascular endothelial growth factor.
Figure 4.GO and KEGG enrichment analysis of the targets. (A) Top 10 significantly enriched terms in the GO biological processes, cell component, and molecular function. (B) Bubble chart of the top 20 significantly enriched terms in KEGG pathways. GO = gene ontology, KEGG = Kyoto Encyclopedia of Genes and Genomes.
Figure 5.Schematic diagram of crucial pathways and primary targets of SGG in the treatment of MDD. MDD = major depressive disorder, SGG = saikogenin G.