Study about target-network of anti-cerebral infarction neuropathy based on theory of neurovascular unit and network pharmacology

Background. Huangqi Sijunzi decoction (HQSJZD) is a commonly used conventional Chinese herbal medicine prescription for invigorating Qi, tonifying Yang, and removing dampness. Modern pharmacology and clinical applications of HQSJZD have shown that it has a certain curative effect on Alzheimer’s disease (AD). Methods. The active components and targets of HQSJZD were searched in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The genes corresponding to the targets were retrieved using UniProt and GeneCard database. The herb-compound-target network and protein-protein interaction (PPI) network were constructed by Cytoscape. The core targets of HQSJZD were analysed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The main active compounds of HQSJZD were docked with acetylcholinesterase (AChE). In vitro experiments were conducted to detect the inhibitory and neuroprotective effects of AChE. Results. Compound-target network mainly contained 132 compounds and 255 corresponding targets. The main compounds contained quercetin, kaempferol, formononetin, isorhamnetin, hederagenin, and calycosin. Key targets contained AChE, PTGS2, PPARG, IL-1B, GSK3B, etc. There were 1708 GO items in GO enrichment analysis and 310 signalling pathways in KEGG, mainly including the cAMP signalling pathway, the vascular endothelial growth factor (VEGF) signalling pathway, serotonergic synapses, the calcium signalling pathway, type II diabetes mellitus, arginine and proline metabolism, and the longevity regulating pathway. Molecular docking showed that hederagenin and formononetin were the top 2 compounds of HQSJZD, which had a high affinity with AChE. And formononetin has a good neuroprotective effect, which can improve the oxidative damage of nerve cells. Conclusion. HQSJZD was found to have the potential to treat AD by targeting multiple AD-related targets. Formononetin and hederagenin in HQSJZD may regulate multiple signalling pathways through AChE, which might play a therapeutic role in AD.

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Shenshuaikang Enema, a Chinese Herbal Remedy, Inhibited Hypoxia and Reoxygenation-Induced Apoptosis in Renal Tubular Epithelial Cells by Inhibiting Oxidative Damage-Dependent JNK/Caspase-3 Signaling Pathways Using Network Pharmacology

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/9457101 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Hongmei Lu ◽

Xinyi Luo ◽

Yuhua He ◽

Bo Qu ◽

Liangbin Zhao ◽

...

Keyword(s):

Oxidative Damage ◽

Caspase 3 ◽

Cell Counting ◽

Network Pharmacology ◽

In Vitro Experiments ◽

Chinese Herbal ◽

Cell Vitality ◽

Target Network ◽

Renal Tubular

Background. Acute kidney injury (AKI) is a common clinically critical illness with serious consequences for the patients. Shenshuaikang enema (SE) is a Chinese herbal compound that is used to treat AKI in clinical practice. However, its mechanism of action remains unclear. Aim. The aim of this study was to investigate the therapeutic effect of SE and explore the molecular mechanisms using network pharmacology and in vitro experiments. Materials and Methods. The herb-component-target network was constructed based on network pharmacology. The predicted targets and pathways were validated using in vitro experiments. A renal tubular epithelial cell line (HK-2 cells) was exposed to hypoxia and reoxygenation (H/R) using air-tight conditions for five hours and treated with different concentrations of SE (25%, 50%, and 75%) to assess cell viability and apoptosis and determine the optimal experimental dose. Subsequently, H/R-injured HK-2 cells were pretreated with the optimal SE dose and then randomly divided into three groups, the SE, SE-SP600125 (inhibitor of JNK), and SE-NAC (antioxidant) groups. The cell vitality, apoptosis, and death were evaluated using the cell counting kit 8 (CCK8) and carboxyfluorescein succinimidyl ester/propidium iodide (CFSF/PI) staining. The apoptosis-related protein JNK and Caspase-3 were assessed by Western blot. Expression of JNK and Caspase-3 genes was analyzed using real-time quantitative polymerase chain reaction (RT-qPCR). Results. 123 active components and 226 targets were identified from four herbs that composed the herb-compound-target network based on transcriptomics and network pharmacology analyses. The KEGG pathway analyses revealed that the mitochondrial apoptosis pathway was involved in the therapeutic AKI effects of SE. Cell vitality of H/R-induced HK-2 cells was obviously increased when treating them with SE, and the apoptosis was significantly inhibited, especially in the SE (50%) group at 4 and 12 h after modeling. Pretreatment with antioxidant NAC obviously prevented cell death compared to the SE (50%) group, while no obvious reduction of apoptosis was observed in the SP600125 group. JNK expression level was significantly increased in the SE (50%) group compared to the SP600125 ( P < 0.01 ) and the NAC group ( P < 0.05 ). Caspase-3 was downregulated in the SE (50%) group compared to the SP600125 ( P < 0.01 ) and NAC group ( P < 0.05 ). Caspase-3 activation in the SP600125 group was higher than that in the NAC group ( P < 0.05 ). Moreover, the oxidative damage-dependent JNK/Caspase-3 pathway was identified in the H/R-injured HK-2 cells by inhibiting the JNK activation and oxidative damage. Conclusions. Our findings suggested that the H/R-triggered apoptosis in HK-2 cells was abrogated by SE by upregulating the oxidative damage-dependent JNK to trigger suppression of Caspase-3.

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Mechanisms of Compound Kushen Injection for the Treatment of Lung Cancer Based on Network Pharmacology

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2019/4637839 ◽

2019 ◽

Vol 2019 ◽

pp. 1-15 ◽

Cited By ~ 7

Author(s):

Ziqi Meng ◽

Xinkui Liu ◽

Jiarui Wu ◽

Wei Zhou ◽

Kaihuan Wang ◽

...

Keyword(s):

Lung Cancer ◽

Molecular Docking ◽

Small Cell Lung Cancer ◽

Docking Simulation ◽

Small Cell ◽

Network Pharmacology ◽

Small Cell Lung ◽

Molecular Docking Simulation ◽

Target Network ◽

Compound Kushen Injection

Background. Compound Kushen Injection (CKI) is a Chinese patent drug that shows good efficacy in treating lung cancer (LC). However, its underlying mechanisms need to be further clarified.Methods. In this study, we adopted a network pharmacology method to gather compounds, predict targets, construct networks, and analyze biological functions and pathways. Moreover, molecular docking simulation was employed to assess the binding potential of selected target-compound pairs.Results. Four networks were established, including the compound-putative target network, protein-protein interaction (PPI) network of LC targets, compound-LC target network, and herb-compound-target-pathway network. Network analysis showed that 8 targets (CHRNA3, DRD2, PRKCA, CDK1, CDK2, CHRNA5, MMP1, and MMP9) may be the therapeutic targets of CKI in LC. In addition, molecular docking simulation indicated that CHRNA3, DRD2, PRKCA, CDK1, CDK2, MMP1, and MMP9 had good binding activity with the corresponding compounds. Furthermore, enrichment analysis indicated that CKI might exert a therapeutic role in LC by regulating some important pathways, namely, pathways in cancer, proteoglycans in cancer, PI3K-Akt signaling pathway, non-small-cell lung cancer, and small cell lung cancer.Conclusions. This study validated and predicted the mechanism of CKI in treating LC. Additionally, this study provides a good foundation for further experimental studies and promotes the reasonable application of CKI in the clinical treatment of LC.

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Mechanism of Action of Bu-Fei-Yi-Shen Formula in Treating Chronic Obstructive Pulmonary Disease Based on Network Pharmacology Analysis and Molecular Docking Validation

BioMed Research International ◽

10.1155/2020/9105972 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12

Author(s):

Longchuan Wu ◽

Yu Chen ◽

Jiao Yi ◽

Yi Zhuang ◽

Lei Cui ◽

...

Keyword(s):

Molecular Docking ◽

Mechanism Of Action ◽

Enrichment Analysis ◽

Network Pharmacology ◽

Chronic Obstructive ◽

Biological Functions ◽

Active Ingredients ◽

Obstructive Pulmonary Disease ◽

The Core ◽

Target Network

Objective. To explore the mechanism of action of Bu-Fei-Yi-Shen formula (BFYSF) in treating chronic obstructive pulmonary disease (COPD) based on network pharmacology analysis and molecular docking validation. Methods. First of all, the pharmacologically active ingredients and corresponding targets in BFYSF were mined by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, the analysis platform, and literature review. Subsequently, the COPD-related targets (including the pathogenic targets and known therapeutic targets) were identified through the TTD, CTD, DisGeNet, and GeneCards databases. Thereafter, Cytoscape was employed to construct the candidate component-target network of BFYSF in the treatment of COPD. Moreover, the cytoHubba plug-in was utilized to calculate the topological parameters of nodes in the network; then, the core components and core targets of BFYSF in the treatment of COPD were extracted according to the degree value (greater than or equal to the median degree values for all nodes in the network) to construct the core network. Further, the Autodock vina software was adopted for molecular docking study on the core active ingredients and core targets, so as to verify the above-mentioned network pharmacology analysis results. Finally, the Omicshare database was applied in enrichment analysis of the biological functions of core targets and the involved signaling pathways. Results. In the core component-target network of BFYSF in treating COPD, there were 30 active ingredients and 37 core targets. Enrichment analysis suggested that these 37 core targets were mainly involved in the regulation of biological functions, such as response to biological and chemical stimuli, multiple cellular life processes, immunity, and metabolism. Besides, multiple pathways, including IL-17, Toll-like receptor (TLR), TNF, and HIF-1, played certain roles in the effect of BFYSF on treating COPD. Conclusion. BFYSF can treat COPD through the multicomponent, multitarget, and multipathway synergistic network, which provides basic data for intensively exploring the mechanism of action of BFYSF in treating COPD.

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Network Pharmacology-Based Antioxidant Effect Study of Zhi-Zi-Da-Huang Decoction for Alcoholic Liver Disease

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2015/492470 ◽

2015 ◽

Vol 2015 ◽

pp. 1-6 ◽

Cited By ~ 11

Author(s):

Li An ◽

Fang Feng

Keyword(s):

Liver Disease ◽

Xanthine Oxidase ◽

Alcoholic Liver Disease ◽

Effect Study ◽

Network Pharmacology ◽

Target Network ◽

Bioactive Ingredients ◽

Stress Damage ◽

Oxide Synthase ◽

Inducible Nitric Oxide

Zhi-Zi-Da-Huang decoction (ZZDHD), a classic traditional Chinese medicine (TCM) formula, has been used for centuries to treat alcoholic liver disease. Reliable therapeutics of ZZDHD has also been validated in clinical practice. In this study, molecular docking and network analysis were carried out to explore the antioxidative mechanism of ZZDHD as an effective therapeutic approach to treat alcoholic liver disease. Multiple active compounds of ZZDHD were screened based on four key original enzymes (cytochrome P450 2E1, xanthine oxidase, inducible nitric oxide synthase, and cyclooxygenase-2) involved in ethanol-induced oxidative stress damage. A drug-target network was constructed through network pharmacology analysis, which predicted the relationships of active ingredients to the targets. Some results had been verified by the previous experimental pharmacological studies; meanwhile, it was first reported that xanthine oxidase and eriocitrin, neoeriocitrin, isorhoifolin, and poncirin had interactions. The network pharmacology strategy used provided a forceful tool for searching the mechanism of action of TCM formula and novel bioactive ingredients.

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Network Pharmacology Identifies the Mechanisms of Action of Tongxie Anchang Decoction in the Treatment of Irritable Bowel Syndrome with Diarrhea Predominant

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/2723705 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Xiang Tan ◽

Wenjing Pei ◽

Chune Xie ◽

Zhibin Wang ◽

Tangyou Mao ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Target Genes ◽

Alternative Therapy ◽

Enrichment Analysis ◽

Network Pharmacology ◽

Active Compounds ◽

Complementary And Alternative Therapy ◽

Pharmacological Mechanism ◽

Target Network ◽

Irritable Bowel

Aim. This study aims to uncover the pharmacological mechanism of Tongxie Anchang Decoction (TXACD), a new and effective traditional Chinese medicine (TCM) prescription, for treating irritable bowel syndrome with diarrhea predominant (IBS-D) using network pharmacology. Methods. The active compounds and putative targets of TXACD were retrieved from TCMSP database and published literature; related target genes of IBS-D were retrieved from GeneCards; PPI network of the common target hub gene was constructed by STRING. Furthermore, these hub genes were analyzed using gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Results. A total of 54 active compounds and 639 targets were identified through a database search. The compound-target network was constructed, and the key compounds were screened out according to the degree. By using the PPI and GO and KEGG enrichment analyses, the pharmacological mechanism network of TXACD in the treatment of IBS-D was constructed. Conclusions. This study revealed the possible mechanisms by which TXACD treatment alleviated IBS-D involvement in the modulation of multiple targets and multiple pathways, including the immune regulation, inflammatory response, and oxidative stress. These findings provide novel insights into the regulatory role of TXACD in the prevention and treatment of IBS-D and hold promise for herb-based complementary and alternative therapy.

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Network Pharmacology-Based Investigation into the Mechanisms of Quyushengxin Formula for the Treatment of Ulcerative Colitis

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2019/7870424 ◽

2019 ◽

Vol 2019 ◽

pp. 1-22

Author(s):

Haojie Yang ◽

Ying Li ◽

Sichen Shen ◽

Dan Gan ◽

Changpeng Han ◽

...

Keyword(s):

Ulcerative Colitis ◽

Bioactive Compounds ◽

Functional Enrichment ◽

Network Pharmacology ◽

Disease Network ◽

Pathway Network ◽

Similarity Algorithm ◽

Target Network ◽

Target Disease ◽

Compound Target

Objective. Ulcerative colitis (UC) is a chronic idiopathic inflammatory bowel disease whose treatment strategies remain unsatisfactory. This study aims to investigate the mechanisms of Quyushengxin formula acting on UC based on network pharmacology. Methods. Ingredients of the main herbs in Quyushengxin formula were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Absorption, distribution, metabolism, and excretion properties of all ingredients were evaluated for screening out candidate bioactive compounds in Quyushengxin formula. Weighted ensemble similarity algorithm was applied for predicting direct targets of bioactive ingredients. Functional enrichment analyses were performed for the targets. In addition, compound-target network, target-disease network, and target-pathway network were established via Cytoscape 3.6.0 software. Results. A total of 41 bioactive compounds in Quyushengxin formula were selected out from the TCMSP database. These bioactive compounds were predicted to target 94 potential proteins by weighted ensemble similarity algorithm. Functional analysis suggested these targets were closely related with inflammatory- and immune-related biological progresses. Furthermore, the results of compound-target network, target-disease network, and target-pathway network indicated that the therapeutic effects of Quyushengxin on UC may be achieved through the synergistic and additive effects. Conclusion. Quyushengxin may act on immune and inflammation-related targets to suppress UC progression in a synergistic and additive manner.

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Network Pharmacology-Based Study on the Mechanism of Aloe Vera for Treating Cancer

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/6077698 ◽

2021 ◽

Vol 2021 ◽

pp. 1-8

Author(s):

Jing Xie ◽

Jun Wu ◽

Sihui Yang ◽

Huaijun Zhou

Keyword(s):

Molecular Docking ◽

Drug Targets ◽

Aloe Vera ◽

Beta Carotene ◽

Network Pharmacology ◽

Potential Mechanism ◽

Active Ingredients ◽

Protein Protein Interaction ◽

Target Network ◽

Molecule Docking

Background. Aloe vera has long been considered an anticancer herb in different parts of the world. Objective. To explore the potential mechanism of aloe vera in the treatment of cancer using network pharmacology and molecule docking approaches. Methods. The active ingredients and corresponding protein targets of aloe vera were identified from the TCMSP database. Targets related to cancer were obtained from GeneCards and OMIM databases. The anticancer targets of aloe vera were obtained by intersecting the drug targets with the disease targets, and the process was presented in the form of a Venn plot. These targets were uploaded to the String database for protein-protein interaction (PPI) analysis, and the result was visualized by Cytoscape software. Go and KEGG enrichment were used to analyze the biological process of the target proteins. Molecular docking was used to verify the relationship between the active ingredients of aloe vera and predicted targets. Results. By screening and analyzing, 8 active ingredients and 174 anticancer targets of aloe vera were obtained. The active ingredient-anticancer target network constructed by Cytoscape software indicated that quercetin, arachidonic acid, aloe-emodin, and beta-carotene, which have more than 4 gene targets, may play crucial roles. In the PPI network, AKT1, TP53, and VEGFA have the top 3 highest values. The anticancer targets of aloe vera were mainly involved in pathways in cancer, prostate cancer, bladder cancer, pancreatic cancer, and non-small-cell lung cancer and the TNF signaling pathway. The results of molecular docking suggested that the binding ability between TP53 and quercetin was the strongest. Conclusion. This study revealed the active ingredients of aloe vera and the potential mechanism underlying its anticancer effect based on network pharmacology and provided ideas for further research.

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Network pharmacology and molecular docking reveal the effective substances and active mechanisms of Dalbergia Odoriferain protecting against ischemic stroke

PLoS ONE ◽

10.1371/journal.pone.0255736 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0255736

Author(s):

Kedi Liu ◽

Xingru Tao ◽

Jing Su ◽

Fei Li ◽

Fei Mu ◽

...

Keyword(s):

Ischemic Stroke ◽

Molecular Docking ◽

Cerebral Infarction ◽

Binding Sites ◽

Network Pharmacology ◽

Dependent Manner ◽

Bioactive Components ◽

Neurological Score ◽

Infarction Volume

Dalbergia Odorifera (DO) has been widely used for the treatment of cardiovascular and cerebrovascular diseasesinclinical. However, the effective substances and possible mechanisms of DO are still unclear. In this study, network pharmacology and molecular docking were used toelucidate the effective substances and active mechanisms of DO in treating ischemic stroke (IS). 544 DO-related targets from 29 bioactive components and 344 IS-related targets were collected, among them, 71 overlapping common targets were got. Enrichment analysis showed that 12 components were the possible bioactive components in DO, which regulating 9 important signaling pathways in 3 biological processes including ‘oxidative stress’ (KEGG:04151, KEGG:04068, KEGG:04915), ‘inflammatory response’(KEGG:04668, KEGG:04064) and ‘vascular endothelial function regulation’(KEGG:04066, KEGG:04370). Among these, 5 bioactive components with degree≥20 among the 12 potential bioactive components were selected to be docked with the top5 core targets using AutodockVina software. According to the results of molecular docking, the binding sites of core target protein AKT1 and MOL002974, MOL002975, and MOL002914 were 9, 8, and 6, respectively, and they contained 2, 1, and 0 threonine residues, respectively. And some binding sites were consistent, which may be the reason for the similarities and differences between the docking results of the 3 core bioactive components. The results of in vitro experiments showed that OGD/R could inhibit cell survival and AKT phosphorylation which were reversed by the 3 core bioactive components. Among them, MOL002974 (butein) had a slightly better effect. Therefore, the protective effect of MOL002974 (butein) against cerebral ischemia was further evaluated in a rat model of middle cerebral artery occlusion (MCAO) by detecting neurological score, cerebral infarction volume and lactate dehydrogenase (LDH) level. The results indicated that MOL002974 (butein) could significantly improve the neurological score of rats, decrease cerebral infarction volume, and inhibit the level of LDH in the cerebral tissue and serum in a dose-dependent manner. In conclusion, network pharmacology and molecular docking predicate the possible effective substances and mechanisms of DO in treating IS. And the results are verified by the in vitro and in vivo experiments. This research reveals the possible effective substances from DO and its active mechanisms for treating IS and provides a new direction for the secondary development of DO for treating IS.

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Using Network Pharmacology to Explore the Mechanism of Peach Kernel-Safflower in the Treatment of Diabetic Nephropathy

BioMed Research International ◽

10.1155/2021/6642584 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Jingxue Han ◽

Xinwei Wang ◽

Jingyi Hou ◽

Yu Liu ◽

Peng Liu ◽

...

Keyword(s):

Diabetic Nephropathy ◽

Fluid Shear Stress ◽

Interaction Network ◽

Network Pharmacology ◽

Screening Process ◽

Protein Protein Interaction ◽

Target Network ◽

The Common ◽

Relationship Of ◽

Protein Protein Interaction Network

Objective. The mechanism of peach kernel-safflower in treating diabetic nephropathy (DN) was investigated using network pharmacology. Methods. Network pharmacology methodology was applied to screen the effective compounds of peach kernel-safflower in the SymMap and TCMSP databases. Potential targets were then screened in the ETCM, SEA, and SymMap databases to construct a compound-target network. This was followed by screening of DN targets in OMIM, Gene, and GeneCards databases. The common targets of drugs and diseases were selected for analysis in the STRING database, and the results were imported into Cytoscape 3.8.0 to construct a protein-protein interaction network. Next, GO and KEGG enrichment analyses were performed. Finally, Schrödinger molecular docking verified the reliability of the results. Results. A total of 23 effective compounds and 794 potential targets resulted from our screening process. Quercetin and luteolin were identified as the main effective ingredients in peach kernel-safflower. Furthermore, five key targets (VEGFA, IL6, TNF, AKT1, and TP53), AGE-RAGE, fluid shear stress and atherosclerosis, IL-17, and HIF-1 signaling pathways may be involved in the treatment of DN using peach kernel-safflower. Conclusions. This study embodies the complex network relationship of multicomponents, multitargets, and multipathways of peach kernel-safflower to treat DN and provides a basis for further research on its mechanism.

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