YANG Jing, ZHAO Yao-wei, NIU Jie, WANG Rui
Heilongjiang University of Chinese Medicine,Harbin 150040, China
Keywords:Internet pharmacology Molecular docking Jianwei Gexia Zhuyu Decoction Non-alcoholic fatty liver disease Target of action Pathway
ABSTRACT Objective: To analyse the key compounds, targets and pathways of the treatment of non-alcoholic fatty liver disease (NAFLD) by Jianwei Gexia Zhuyu Decoction based on network pharmacology, in order to explore the molecular mechanism of its therapeutic effects. Methods: The differential genes between sick and normal conditions were screened by GEO-Datasets, and the heat map and volcano map were drawn. The active compounds in Jianwei Gexia Zhuyu Decoction were searched by TCMSP platform and Drugbank database.OB≥30% and DL≥0.18 were set as thresholds to screen potential active compounds and action targets. The molecular target maps of Jianwei Gexia Zhuyu Decoction and NAFLD differential genes were constructed, and the PPI network and network topology parameters were obtained by STRING database. The PPI network and network topology parameters were visually analyzed by Cytoscape, and the core regulatory genes were screened. At the same time, the SwissDock platform was used to dock the main active components with the target. The main pathways were determined by GO biological function enrichment analysis and KEGG metabolic pathway enrichment analysis by DAVID. Results: After screening,377 differential genes (127 up-regulated genes and 250 down-regulated genes), 225 active compounds of Jianwei Gexia Zhuyu Decoction, 308 corresponding targets were obtained;14 key targets were screened, corresponding to 168 compounds, and the key targets involved MYC, FOSL2, FOS, etc. The results of GO functional enrichment analysis showed that Jianwei Gexia Zhuyu Decoction mainly regulated the activity expression of DNA binding transcriptional activator and the specific transcription of RNA polymeraseⅡ; The results of molecular docking showed that the main active components quercetin and baicalein had good binding activity with VCAM1, HSPB1, MYC, JUN and so on; The results of KEGG enrichment analysis showed that it was mainly involved in IL-17 signal pathway, Wnt receptor signal pathway, NF-κB signal pathway, TNF signal pathway and AGE-RAGE signal pathway in diabetic complications.Conclusion: Through the interaction of multi-components and multi-targets, Jianwei Gexia Zhuyu Decoction has achieved the goal of overall treatment of NAFLD from many ways. The application of network pharmacology provides a new research approach and scientific basis for further study on the mechanism of Jianwei Gexia Zhuyu Decoction in the treatment of NAFLD.
Nonalcoholic fatty liver disease (NAFLD) refers to a clinical syndrome with a large amount of fat deposition in liver cells as the main pathological change, which is caused by alcoholism and other clear causes of liver injury, and is closely related to the occurrence of obesity, diabetes and other metabolic diseases. With changes in dietary habits, NAFLD has become one of the most common chronic liver diseases. According to the global epidemiological survey, the global incidence of NAFLD is 10%-30%, and the average in Asian countries is 11%-16%, among which the prevalence rate in China is about 15%. Moreover, according to the current trend,the age of onset of NAFLD will be lower and lower[1-2].At present,the clinical treatment of NAFLD is still to increase the amount of exercise, improve dietary habits, weight control, there is no ideal drug [3].
Experimental studies have shown that Gexia Zhuyu Decoction can reduce the levels of lipid and liver lipid in NAFLD model rats,indicating that Gexia Zhuyu Decoction can not only inhibit lipid absorption, but also promote lipid degradation and metabolism in the liver[4], In order to relieve the burden of lipid accumulation on the liver.Yang [5] according to the findings of other studies, blood viscosity is positively correlated with the incidence of fatty liver.Therefore, the application of Gexia Zhuyu Decoction in the treatment of fatty liver has rich theoretical basis and practical significance.
In the clinical application, it is necessary to discriminate the syndrome accurately and make treatment according to the patient's condition, so as to obtain better clinical effect. The clinical observation showed that after accurate syndrome differentiation,the effective rate of treating blood stasis and phlegm-blocked fatty liver by adding or subtracting Gexia Zhuyu Decoction could reach 92.16%. In addition, the current treatment of NAFLD is mainly based on lipid-lowering and insulin resistance reducing drugs, which has a certain gap compared with the multi-component and multichannel prescriptions of traditional Chinese medicine. Most lipidlowering drugs have the effect of promoting lipids in the blood to enter the liver for metabolism and excretion, which can easily lead to liver damage and aggravation of hepatic fat deposition. Therefore,drug selection should be more prudent, and traditional Chinese medicine has certain advantages in this respect[6].
Chinese medicine believes that NAFLD belongs to the category of"accumulation". Phlegm, dampness, blood stasis and Qi stagnation are the key factors of NAFLD. The disease is located in the liver and spleen[7].The pathogenesis of NAFLD is relatively long, and the dysfunction of liver and spleen organs runs through the whole process. Therefore, attention should be paid to protecting the liver and spleen when selecting prescription drugs. By cutting the classic prescription of promoting blood circulation and removing blood stasis - Gexia Zhuyu Decoction, removing WuLingzhi and Chuanxiong in the original prescription, and reusing Fructus aurantii to return to the liver and spleen meridian, the original prescription has a strong ability to promote blood circulation, remove blood stasis, break the node and eliminate the deposition. According to the characteristics of multi-yin blood deficiency in modern patients, the strategy of care for liver and spleen and syndrome differentiation is adopted for treatment. Good clinical effect was obtained. Clinically, common patients are prickling pain and discomfort in the ribs, abdominal distension, purple tongue dark or with petechia, sublingual veins blue and astringent. Color ultrasound of the abdomen shows fatty liver (mild). After 2 weeks of treatment,the prickling pain was slightly lighter and abdominal distension was relieved. He was instructed to continue taking the medicine for 2 weeks, and the above symptoms disappeared obviously.Reexamination showed no obvious abnormality in abdominal color ultrasound. Therefore, the use of TCM theory for accurate syndrome differentiation and addition or subtraction according to the patient's condition can often achieve a better effect, which has the value of clinical promotion. After reducing the flavor, the whole recipe is "zhiqiao, chishao,danggui, honghua, mudanpi, taoren, wuyao,xiangfu, yanhusuo, gancao".
In this study, network pharmacological methods were used to study the potential active ingredients and action targets of Jianwei Gexia Zhuyu Decoction in the treatment of NAFLD, and the network relationship of "components-target-pathway" was established, in order to provide a basis for the study of the mechanism of action of Jianwei Gexia Zhuyu Decoction.
GEO(Gene Expression Omnibus)is an international public repository of high-throughput experimental data, login NBCI(https://www.ncbi.nlm.nih.gov/)with "Nonalcoholic fatty liver diseases" or"NAFLD" as a search term in GEO-DataSets retrieved, The species was selected as "Homo sapiens (Human)", and the GSE151158 chip data were obtained through analysis and screening. Use R software to obtain the difference between genes, and set the P value<0.005 and |log2( fold change)|>1,draw heat maps and figure, the difference of the disease genes imported into Excel spreadsheet, get the full difference genetic data[8].
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform[9](TCMSP)can capture the relationships between drugs, targets, and diseases. Various drugs in the prescription of Jianwei Gexia Zhuyu Decoction were submitted to the database for screening, and the screening conditions were set as OB≥30% and DL≥0.18, where OB refers to the location of drug components through circulation and the degree and speed of absorption. DL means that a drug contains some specific functional groups or has the same or similar physical characteristics with most drugs,and these two indexes are the key parameters to screen the active ingredients of the drug[10].The screening results were imported into the Drug Bank(https://go.drugbank.com/)to obtain the corresponding targets of the active compounds.
The intersection between the results of different genes and the corresponding targets of active compounds was obtained through processing. Finally, the relationship network diagram between active compounds and gene targets was obtained by using Cytoscape plot,so as to further determine the main active compounds and potential targets of the therapeutic effect of Jianwei Gexia Zhuyu Decoction.
The study of the interaction network between proteins is helpful to mine the core regulatory genes. DC > 5 and BC > 600 were set, the screening results of 1.3 were input into the STRING database, and the species was set as "Homo sapiens". Then, the processed data was imported into Cytoscape for visual processing, and finally the PPI network diagram was obtained.
GO is a database established by Gene Ontology Consortium that is used to define and describe the function of genes and proteins in different species[11],the enrichment analysis of NAFLD genes was carried out by Jianwei Gexia Zhuyu Decoction in the treatment of NAFLD genes, and a histogram was drawn according to the enrichment number and significance.
KEGG analysis can understand the advanced function and utility of biological system from genomic and molecular level information,and enrich and analyze the NAFLD gene of Jianwei Gexia Zhuyu Decoction for visual analysis.
The above KEGG pathway analysis results were imported into Cytoscape. After Degree processing, the corresponding relationship between pathway and gene was shown and the network map was drawn.
VCAM1, HSPB1 and MYC were selected as the target proteins for molecular docking, and the 3D structure of the protein was obtained with the help of PDB database(https://www.rcsb.org/).Using TCMSP (https://tcmspw.com/tcmsp.php) download the 3D structure of the active ingredient is saved as a mol2 format, as a molecular docking ligands. The above results were imported into Swissdock platform(http://www.swissdock.ch/)for docking.
After processing the GSE151158 chip data retrieved from the Geo-DataSets database, a total of 63 samples were screened and obtained.The R software was used to obtain the differential genes, and 377 differential genes were obtained. Set the P value<0.005 and |log2(fold change)|>1[8],Visual analysis was performed to obtain the corresponding heat map and volcanic map. In the graph, the abscissa is the number of cases, and the ordinate is the gene or related name.Red indicates significantly increased expression of this gene or related gene, green indicates decreased expression of this gene or related gene, and black indicates no difference in expression under this screening condition. See Figure 1 ~ Figure 2.
Figure 1 Heat map of differential genes between normal and NAFLD
Figure 2 volcano map of difference gene between normal and NAFLD
According to OB≥30% and DL≥0.18, the active compounds were screened as follows: 14 active compounds of chishao, 2 active compounds of danggui, 88 active compounds of gancao, 17 active compounds of honghua, 6 active compounds of mudanpi,19 active compounds of taoren, 9 active compounds of wuyao, 16 active compounds of xiangfu, 49 active compounds of yanhusuo, and 5 active compounds of zhiqiao. A total of 308 corresponding targets were obtained after deleting the duplicates.
The corresponding target of active compounds in the jianwei Gexia Zhuyu Decoction was processed with NAFLD differential genes.Cytoscape mapping was applied to obtain the network relationship diagram between active compounds and genes. The different colors of the outer circle in Figure 3 represented that the components came from different drugs, while the inner circle represented the related genes between drug action targets and diseases. Lines in the network indicate a link between a compound and a gene, and the more lines there are, the more central the factor is. Molecule Mol000098 corresponds to the most targets; PTGS2 was the main target. As shown in Figure 3.
Topological analysis was conducted on the results of differential gene intersection between the corresponding targets of active ingredients of Jianwei Gexia Zhuyu Decoction and NAFLD, in order to simplify the PPI protein interaction network through different screening conditions. There were two main screening conditions, one was DC (Degree Centrality) > 5, the other was BC (Betweenness Centrality) > 600, and the topological network of Jianwei Gexia Zhuyu Decoction for the treatment of NAFLD was constructed through screening. The final pink rectangles in the topology represent the major core genes, namely VCAM1, HSPB1 and MYC(Figure 4).
Figure 3 Jianwei Gexia zhuyu Decoction in the treatment of NAFLD molecular gene network diagram and active compounds colors and corresponding drugs
Figure 4 Topological network of Jianwei Gexia Zhuyu Decoction for the treatment of NAFLD
The genes of the active components in the Jianwei Gexia Zhuyu Decoction were enriched and analyzed. According to the number and significance of gene enrichment, 20 GO biological processes were selected to draw a bar chart. The results showed that the reactions to lipopolysaccharide, bacteriogenic molecules and organophosphorus were mainly involved in biological processes (BP). Molecular function (MF) shows that it mainly has the activity of DNA binding transcriptional activator, the specificity of RNA polymerase I1,activation transcription factor binding, binding protease and other functions. It is suggested that the treatment of NAFLD by Jianwei Gexia Zhuyu Decoction mainly involves lipid lipopolysaccharide,organophosphorus metabolism, protein binding and transcription,etc. See Figure 5 for details.
KEGG enrichment analysis was performed on the genes of the active ingredients in Gexia Zhuyu Decoction, and the results showed that there were a total of 60 pathways. The bubble diagram was drawn according to the enrichment number and significance degree(Figure 6), and the top 20 pathways were screened and the table was drawn (Table 1). The results showed that the top 20 pathways mainly included: IL-17 signaling pathway, Wnt receptor signaling pathway in diabetes complications, NF-kappa B signaling pathway Pathway),TNF signaling pathway (TNF signaling pathway), and AGERAGE signaling pathway in diabetic vision Drops), C-type lectin receptor signaling pathway, and C-type lectin receptor signaling pathway, Toll-like receptor signaling Pathway), etc. Therefore, the effective components of Jianwei Gexia Zhuyu Decoction may play a therapeutic role through the above channels.
Figure 5 Biological process(BP)and Molecular function(MF)of Jianwei Gexia Zhuyu Decoction for the treatment of NAFLD
Figure 6 KEGG of Jianwei Gexia Zhuyu Decoction Gexia Zhuyu Decoction for the treatment of NAFLD
The above KEGG pathway was imported into Cytoscape.According to the Degree value, the enrichment Degree of pathway and gene was shown and the network diagram was drawn (Figure 7).The network can reflect the relationship between gene and pathway,the line indicates that the gene belongs to the pathway, the size of the graph reflects the number of connection points, the more the connection points, the bigger the graph. hsa04657 is the pathway with the largest number of corresponding genes, and JUN is the main acting gene. The specific pathway is shown in Table 1.
Swissdock platform was used to conduct separate docking between the receptor and the ligand. The docking results (Table 2) showed that the lowest binding energy between the molecule and the target protein was all less than 0, and the negative binding energy of molecular docking indicated that the ligand and the receptor could spontaneously bind. It was proved that the active ingredients in Jianwei Gexia Zhuyu Decoction could spontaneously combine with NAFLD core genes. The butt binding energies of quercetin with VCAM1, HSPB1, MYC and JUN were -20.071 2, -27.302 5,-33.264 6 and -31.213 2 (kJ·mol-1), respectively. The butt binding energies of baicalein were -37.609 5, -30.042 0, -40.846 8 and-33.432 2 (kJ·mol-1), respectively. The docking results were visualized by Swissdock, as shown in Figure 8. A, B and C are the docking pattern diagrams of quercetin with VCAM1, HSPB1 and MYC. D, E and F are the docking pattern diagrams of baicalein with VCAM1, HSPB1 and MYC.
Figure 7 Pathway and gene network diagram of Jianwei Gexia Zhuyu Decoction for the treatment of NAFLD
Table 1 Pathway of Jianwei Gexia Zhuyu Decoction for the treatment of NAFLD
Figure 8 Molecular docking pattern
Table 2 Molecular docking binding energy of quercetin and baicalein with disease core targets (kJ·mol-1)
According to traditional Chinese medicine, NAFLD is formed by the interaction of turbidities, blood stasis, dampness-heat and qi stagnation. Dampness and blood stasis are not only the main pathological inducement for the formation of NAFLD, but also the key to the treatment of the disease[12].Clinical studies have found that qi stagnation and blood stasis and qi deficiency and blood stasis are the main syndrome types of liver fibrosis, accounting for 27% and 23% of the cases respectively[13]. Therefore, in clinical treatment, the treatment is mainly to promote blood circulation to remove blood stasis and clearing damp to dissolve phlegm.
The original formula of Gexia Zhuyu Decoction has the functions of promoting blood circulation, removing blood stasis, promoting qi and relieving pain. The experiment showed that the NAFLD model rats induced by high fat diet had abnormal liver function in the early stage, such as the elevation of ALT and AST in serum and liver plasma, and the intervention of Gexia Zhuyu Decoction could significantly improve the liver function state[14], In addition, it can also significantly inhibit platelet aggregation induced by ADP[15].The formula for activating blood circulation and removing blood stasis can improve the liver blood flow and inhibit platelet aggregation in early fatty liver of rats, and the effect of inhibition is more significant with the extension of medication time[16]. In addition, after the intervention of Gexia Zhuyu Decoction, the number of round lipid droplets of different sizes in the pericytoplasm decreased, the dilatation degree of rough endoplasmic reticulum, the swelling and dilatation degree of mitochondria and the fuzzy degree of ridge were all reduced under electron microscope[17]. Although taste under the diaphragm reduction by stasis soup achieved good clinical effect,but its specific composition, targets and pathways is not yet clear,the existing research materials are lack, so this study to analyze it through the network pharmacology, screening effective active ingredients in compound, further determine its give play to the role of therapeutic targets and pathways. Finally, it provides the basis for the clinical study and application of Jianwei Gexia Zhuyu Decoction in the treatment of NAFLD.
A total of 225 active compounds were obtained by screening the Jianwei Gexia Zhuyu Decoction, and the molecular target network was obtained after the intersection of these compounds with the differential NAFLD genes (Figure.3). The figure shows 168 effective compounds with 14 corresponding targets. Multiple compounds correspond to a single target, such as most compounds acting on PTGS2; There is also a compound corresponding to multiple targets, such as Mol000098-quercetin and Mol002714-baicalein,which also proves the characteristics of multiple targets of Chinese herbal compounds from the side. PTGS2 is one of the isomerases of endogenous prostaglandin peroxidase (PTGS). PTGS and its products are involved in various physiological and pathological processes such as inflammatory response and blood coagulation balance[18].The expression of immediate early gene PTGS2 plays an important role in inhibiting the development of excessive fibrosis and inflammatory response. When cells are stimulated, the expression of PTGS2 is rapidly up-regulated, and then arachidonic acid is catalysed to produce a variety of prostagnins (PGs), resulting in pain,inflammatory response, anti-fibrosis and other effects[19,20],therefore,PTGS2 may be the main target for the treatment of NAFLD.
Quercetin, a natural flavonoid compound widely found in plants, has anti-inflammatory, antioxidant, anti-cancer and other pharmacological effects[21].Quercetin can treat NAFLD by inhibiting the production of liver inflammatory factors, alleviating oxidative stress of liver cells, improving insulin resistance,regulating liver lipid metabolism and other ways[22]; Baicalein is the main active component of baicalein, which has antibacterial,antiviral, antioxidant, anti-inflammatory, free radical scavenging,cardio-cerebrovascular protection and other effects, as well as liver protection, antioxidant and anti-aging effects. In addition,experimental studies have shown that baicalein can significantly improve liver damage in rapidly aging mouse models[23]. Quercetin and baicalin can regulate most targets, have anti-inflammatory effects, regulate liver lipid disorders, improve blood coagulation and liver injury, etc. Therefore, they may be the main compounds of Qiawei Gexia Zhuyu Decoction in the treatment of liver injury.
To further determine the potential targets of Jianwei Gexia Zhuyu Decoction for the treatment of NAFLD, topological analysis was performed on the 14 targets screened in Figure 3 to make PPI plot(Figure 4). The screening criteria were DC > 5 and BC > 600,respectively, and three potential genes, VCAM1, HSPB1 and MYC,were obtained. Figure 7 shows that JUN is the gene with the highest enrichment number. VCAM-1, namely Vascular Cell Adhesion Molecule-1, is an important cell adhesion molecule involved in the adhesion and migration of immune cells and the growth and development of hematopoietic cells. In addition, VCAM-1 can not only be expressed under the induction of IL-1, TNF-α, IFN-γ and other inflammatory cytokines, but also induce the production of cytokines and chemokines[24];H HSPB1 is an important member of the small molecular heat shock protein subfamily, which is involved in the regulation of signal transduction of proliferation,differentiation and apoptosis of a variety of cells, and is generally expressed in a variety of tissues and cells[25]; MYC genes include c-myc, n-myc and l-myc, and the MYC family and its products have the functions of promoting cell proliferation, dedifferentiation and transformation[26]. Jun gene belongs to a gene family, including c-jun、junB and junD. c-jun can prevent the excessive activation of endoplasmic reticulum stress response of liver cells, and then reduce the damage and apoptosis of liver cells[27]. Therefore, the above 4 genes may be the main targets of the active compounds in the Jianwei Gexia Zhuyu Decoction for the therapeutic effect.
Molecular docking verification results showed (Tab 2) that both quercetin and baicalein, as the main active ingredients, could achieve good docking results with VCAM1, HSPB1, MYC and JUN. It was proved that the active substances of the Jianwei Gexia Zhuyu Decoction may combine with these proteins to play a therapeutic role. In this paper, NAFLD genes were enriched and analyzed in the treatment of Jianwei Gexia Zhuyu Decoction, and the histogram and bubble diagram were drawn (Figure 5 and 6). According to the pathway and gene network diagram (Figure 7), DNA-binding transcription activator activity,RNA polymeraseⅡ-specific (BP),Response to lipopolysaccharide (MF) and IL-17 signaling pathway.
DNA-binding transcription activator activity,RNA polymeraseⅡ-specific refers to the active expression of DNA-binding transcription activator and the non-specific transcription of RNA polymerase.In eukaryotes, RNA polymerase Ⅱ is responsible for transcribing a diverse array of tens of thousands of protein-coding genes. The control of this process is mainly mediated by a network of thousands of specific DNA-binding transcription factors that can interpret genetic regulatory information, such as information in transcription enhtioners and promoters, and deliver appropriate responses to the RNA polymerase II transcription mechanism[28]. For example,the family of liver nuclear factors, mainly including HNF1, HNF3,HNF4, HNF6 and CCAAT/ enhancer binding proteins, are mainly enriched and expressed in the liver and mutually regulate to form a complex transcriptional regulatory network, which is involved in liver differentiation, development and maintenance of normal function of mature liver cells[29], Involved in liver development,metabolism, and functional maintenance.
Lipopolysaccharide (LPS) was significantly correlated with the occurrence and development of NAFLD by animal experiments and population studies. LPS entered into the body mainly detoxifies in the liver, and LPS also has toxic effects on the liver, mainly manifested as causing a large number of reactive oxygen species and inflammatory factors in the liver tissue, and then leading to liver injury and inflammatory response[30], which is closely related to the occurrence of NAFLD.
In summary, the main active components of Jianwei Gexia Zhuyu Decoction, quercetin and baicalin, interact with potential targets such as VCAM1, HSPB1, MYC, and Jun, and involve IL-17 signaling pathway and LPS signal transduction pathway, suggesting that Jianwei Gexia Zhuyu Decoction can reduce inflammatory response, regulate lipid metabolism disorders, and improve blood coagulation. Intervention in the process of NAFLD reflects its multitarget and multi-channel therapeutic characteristics. In this paper,the molecular mechanism of the treatment of NAFLD by the use of network pharmacology was explored in order to provide theoretical basis and scientific basis for the further study of the mechanism of action of the treatment of NAFLD by the treatment of the treatment of NAFLD by the Tang.
Author's contribution: The design ideas of this paper are provided by Professors Yang Jing and Wang Rui. Zhao Yaowei is responsible for target screening, pathway enrichment, protein interaction network construction, molecular docking; Niu Jie is responsible for data visualization and data processing.
Journal of Hainan Medical College2022年16期