Exploring the Effects of Changping Decoction on Irritable Bowel Syndrome by Pathway and Pharmacology Network Bioinformatics Analysis

Abstract Background An increasing body of research has confirmed the effectiveness of Traditional Chinese Medicine (TCM) for the treatment of irritable bowel syndrome (IBS).Methods We explored the potential mechanism of Changping decoction (CPD) in the treatment of IBS through pathway analysis based on a network pharmacology approach. Public databases, including the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, Gene Expression Omnibus, and STRING, were used to screen the active ingredients and targets of CPD. Enrichment analysis was performed using the R-3.6.0 software to expound the biological functions and related pathways of CPD targets. The Cytoscape software was used to construct a “disease-CPD-target” network and identify hub genes of CPD relevant for the treatment of IBS. Employing rat models, pathological observation and abdominal withdrawal reflex tests were used to verify the effectiveness of CPD in the treatment of IBS. Immunohistochemistry was used to confirm the relationship between the CPD treatment and hub genes.Results Network pharmacological analysis of CPD for the treatment of IBS identified 159 active ingredients. A total of 118 key targets were identified, including MAPK8, VEGFA, PTGS2, and others. A series of signaling pathways, such as MAPK, Kaposi sarcoma-associated herpesvirus infection, and IL-17 signaling pathway were found to play an important role in the therapeutic mechanism of CPD in the treatment of IBS. Pathological observation and abdominal withdrawal reflex tests confirmed that the symptoms of IBS in rats were relieved by CPD. Moreover, immunohistochemistry confirmed that CPD could inhibit the expression of inflammation-associated factors, such as VEGFA, MAPK8, and PTGS2.Conclusions Based on network pharmacology analysis, the present study provides insights into the potential mechanism of CPD in the treatment of IBS after successfully screening for associated key target genes and signaling pathways. These findings establish a theoretical basis for the development of CPD-derived therapeutics.

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Network pharmacology and molecular docking study on the mechanism of colorectal cancer treatment using Xiao-Chai-Hu-Tang

PLoS ONE ◽

10.1371/journal.pone.0252508 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0252508

Author(s):

Jingyun Jin ◽

Bin Chen ◽

Xiangyang Zhan ◽

Zhiyi Zhou ◽

Hui Liu ◽

...

Keyword(s):

Colorectal Cancer ◽

Molecular Docking ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Signaling Pathways ◽

Target Genes ◽

Network Pharmacology ◽

Signal Pathways ◽

Active Ingredients ◽

Molecular Docking Study

Background and objective We aimed to predict the targets and signal pathways of Xiao-Chai-Hu-Tang (XCHT) in the treatment of colorectal cancer (CRC) based on network pharmacology, just as well as to further analyze its anti-CRC material basis and mechanism of action. Methods We adopted Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and Traditional Chinese Medicine Integrated Database (TCMID) databases to screen the active ingredients and potential targets of XCHT. CRC-related targets were retrieved by analyzing published microarray data (accession number GSE110224) from the Gene Expression Omnibus (GEO) database. The common targets were used to construct the “herb-active ingredient-target” network using the Cytoscape 3.8.0 software. Next, we constructed and analyzed protein-to-protein interaction (PPI) using BisoGenet and CytoNCA plug-in in Cytoscape. We then performed Gene Ontology (GO) functional and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses of target genes using the R package of clusterProfiler. Furthermore, we used the AutoDock Tools software to conduct molecular docking studies on the active ingredients and key targets to verify the network pharmacological analysis results. Results We identified a total of 71 active XCHT ingredients and 20 potential anti-CRC targets. The network analysis revealed quercetin, stigmasterol, kaempferol, baicalein, and acacetin as potential key compounds, and PTGS2, NR3C2, CA2, and MMP1 as potential key targets. The active ingredients of XCHT interacted with most CRC disease targets. We showed that XCHT’s therapeutic effect was attributed to its synergistic action (multi-compound, multi-target, and multi-pathway). Our GO enrichment analysis showed 46 GO entries, including 20 biological processes, 6 cellular components, and 20 molecular functions. We identified 11 KEGG signaling pathways, including the IL-17, TNF, Toll-like receptor, and NF-kappa B signaling pathways. Our results showed that XCHT could play a role in CRC treatment by regulating different signaling pathways. The molecular docking experiment confirmed the correlation between five core compounds (quercetin, stigmasterol, kaempferol, baicalein, and acacetin) just as well as PTGS2, NR3C2, CA2, and MMP1. Conclusion In this study, we described the potential active ingredients, possible targets, and key biological pathways responsible for the efficacy of XCHT in CRC treatment, providing a theoretical basis for further research.

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A Network Pharmacology-Based Study on Irritable Bowel Syndrome Prevention and Treatment Utilizing Shenling Baizhu Powder

BioMed Research International ◽

10.1155/2021/4579850 ◽

2021 ◽

Vol 2021 ◽

pp. 1-14

Author(s):

Meng Meng ◽

Chen Bai ◽

Bo Wan ◽

Luqing Zhao ◽

Zhe Li ◽

...

Keyword(s):

Signal Transduction ◽

Irritable Bowel Syndrome ◽

Molecular Docking ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Signaling Pathway ◽

Target Gene ◽

Network Pharmacology ◽

The Core ◽

Irritable Bowel

Background and Objective. Irritable bowel syndrome (IBS) is a prevalent disorder of the gastrointestinal system with complex pathogenesis. Shenling Baizhu powder (SLBZP) is a Chinese herbal compound with multicomponent and multitarget characteristics. Increasing volumes of evidence demonstrate that it has a notable therapeutic impact on IBS. This study therefore is aimed at exploring the potential effective components of SLBZP and their mechanisms in IBS treatment utilizing network pharmacology. Methods. Metabolomics was used to detect the secondary metabolites in SLBZP; the target protein was acquired by target fishing according to the compound’s structure. The SymMap database was used to search herbal medicines for the target protein. The target gene of IBS gave rise to the common gene protein which is the potential target of SLBZP in IBS therapy. The interactions between target proteins were analyzed in a STRING database, the protein relationship network was analyzed using Cytoscape software, and the Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the core target gene group was carried out in a DAVID database in order to construct the “compound-traditional Chinese medicine/molecule-target-pathway” network. Molecular docking was used to verify the core protein and its related small molecular compounds. Result. There were 129 types of secondary metabolites in SLBZP. 80 target proteins of these metabolites were potential core targets for IBS treatment including acetylcholinesterase (AChE), arachidonate-5-lipoxygenase (ALOX5), B-cell lymphoma-2 (BCL2), recombinant cyclin D1 (CCND1), and catenin-β1 (CTNNB1), among others. Results from these targets indicated that the most enriched pathway was the tumor necrosis factor (TNF) signaling pathway ( p < 0.001 ) and that the most abundant pathway was signal transduction. In the network nodes of the TNF signaling pathway, the Chinese medicines with the highest aggregation were Lablab semen album and Glycyrrhizae radix et rhizoma ( degree = 11 ). The small molecules with the highest aggregation were oxypeucedanin and 3,5,6,7,8,3 ′ ,4 ′ -heptamethoxyflavone ( degree = 4 ). Molecular docking results confirmed that daidzein 7-O-glucoside (daidzin) had the highest degree of binding to TNF proteins in the TNF signaling pathway. Conclusion. This study shows that SLBZP can treat IBS by influencing multiple targets and pathways, of which the TNF signaling pathway may be the most significant. This typifies the pharmacological characteristics of traditional Chinese medicine, i.e., multiple targets, numerous pathways, and specific therapeutic effects on diseases. SLBZP can therefore be used as a candidate drug for clinical IBS by intervening in human signal transduction.

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Exploration of the Molecular Targets and Mechanisms of Suxiao Xintong Dropping Pills for Myocardial Infarction by Network Pharmacology Method

Bioscience Reports ◽

10.1042/bsr20204211 ◽

2021 ◽

Author(s):

Daqiu Chen ◽

Yanqing Wu ◽

Yixing Chen ◽

Qiaoxing Chen ◽

Xianhua Ye ◽

...

Keyword(s):

Myocardial Infarction ◽

Molecular Docking ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Signaling Pathway ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

Overlapping Genes ◽

Active Ingredients ◽

Hub Genes

Background: Suxiao Xintong dropping pills (SXXTDP), a traditional Chinese medicine, is widely applied for treating myocardial infarction (MI). However, its therapy mechanisms are still unclear. Therefore, this research is designed to explore the molecular mechanisms of SXXTDP in treating MI. Methods: The active ingredients of SXXTDP and their corresponding genes of the active ingredients were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. MI-related genes were identified via analyzing the expression profiling data (accession number: GSE97320). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to study the shared genes of drug and disease. Through protein-protein interaction (PPI) network and the Cytoscape plugin cytoHubba, the hub genes were screened out. The compounds and hub targets binding were simulated through molecular docking method. Results: We obtained 21 active compounds and 253 corresponding target genes from TCMSP database. 1833 MI-related genes were identified according to P＜0.05 and |log2FC| ≥ 0.5. 27 overlapping genes between drug and disease were acquired. GO analysis indicated that overlapping genes were mainly enriched in MAP kinase activity and antioxidant activity. KEGG analysis indicated that overlapping genes were mainly enriched in IL-17 signaling pathway and TNF signaling pathway. We obtained 10 hub genes via cytoHubba plugin. Six of the 10 hub genes, including PTGS2, MAPK14, MMP9, MAPK1, NFKBIA, and CASP8, were acted on molecular docking verification with their corresponding compounds of SXXTDP. Conclusion: SXXTDP may exert cardioprotection effect through regulating multiple targets and multiple pathways in MI.

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Stress Reactivity in Traditional Chinese Medicine–Based Subgroups of Patients with Irritable Bowel Syndrome

The Journal of Alternative and Complementary Medicine ◽

10.1089/acm.2013.0197 ◽

2014 ◽

Vol 20 (4) ◽

pp. 276-283 ◽

Cited By ~ 3

Author(s):

Megan C. Chang ◽

David Shapiro ◽

Aditi Joshi ◽

Leila Shahabi ◽

Steven Tan ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Stress Reactivity ◽

Irritable Bowel

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Efficacy and Safety of Acupoint Catgut Embedding for Diarrhea-Predominant Irritable Bowel Syndrome and Constipation-Predominant Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/5812320 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Jing Wu ◽

Qinwei Fu ◽

Shasha Yang ◽

Hui Wang ◽

Yaofeng Li

Keyword(s):

Systematic Review ◽

Irritable Bowel Syndrome ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Recurrence Rate ◽

Western Medicine ◽

Effective Rate ◽

Efficacy And Safety ◽

Irritable Bowel ◽

Meta Analyses

In this study, we aim to evaluate the efficacy and safety of acupoint catgut embedding for the treatment of diarrhea-predominant irritable bowel syndrome and constipation-predominant irritable bowel syndrome. We searched seven online databases to collect studies published up to Feb 29th, 2020. Study quality of each included article was evaluated by the Cochrane Collaboration Risk of Bias Tool. Systematic reviews and meta-analyses were conducted based on the Cochrane systematic review method by using RevMan 5.3 software. Among the included trials, acupoint catgut embedding alone or plus oral western medicine or plus other acupoint-based therapies, or plus oral traditional Chinese medicine were the main therapies in the experimental groups. Interventions in control groups mainly include oral western medicine alone, other acupoint-based therapies alone, or other acupoint-based therapies alone. Primary outcomes in this study include recovery rate, accumulative marked effective rate, accumulative effective rate, and recurrence rate. Finally, 30 trials involving 1889 participants were included. The results of systematic reviews and meta-analyses show that acupoint catgut embedding alone or plus oral western medicine or plus other acupoint-based therapy or plus oral traditional Chinese medicine was significantly better compared with using oral western medicine alone in terms of efficacy for IBS-C and IBS-D. In addition, acupoint catgut embedding alone or plus oral western medicine or plus other acupoint-based therapy or plus oral traditional Chinese medicine could improve the effective rate and decrease the recurrence rate for IBS-D compared with using oral western medicine, other acupoint-based therapies, or oral traditional Chinese medicine alone. Adverse events of acupoint catgut embedding include local induration, redness, swelling, and itchiness, but they were all mild and disappeared swiftly with ordinary local interventions. There is an urgent need for RCTs of high quality and large sample size and with longer treatment duration and follow-up periods of acupoint catgut embedding for IBS.

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A Network Pharmacology-Based Study on the Anti-Lung Cancer Effect of Dipsaci Radix

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/7424061 ◽

2020 ◽

Vol 2020 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Jiayan Wu ◽

Shengkun Hong ◽

Xiankuan Xie ◽

Wangmi Liu

Keyword(s):

Lung Cancer ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Molecular Mechanisms ◽

Target Genes ◽

Interaction Network ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

Hub Genes ◽

Active Compounds

Objective. Dipsaci Radix (DR) has been used to treat fracture and osteoporosis. Recent reports have shown that myeloid cells from bone marrow can promote the proliferation of lung cancer. However, the action and mechanism of DR has not been well defined in lung cancer. The aim of the present study was to define molecular mechanisms of DR as a potential therapeutic approach to treat lung cancer. Methods. Active compounds of DR with oral bioavailability ≥30% and drug-likeness index ≥0.18 were obtained from the traditional Chinese medicine systems pharmacology database and analysis platform. The potential target genes of the active compounds and bone were identified by PharmMapper and GeneCards, respectively. The compound-target network and protein-protein interaction network were built by Cytoscape software and Search Tool for the Retrieval of Interacting Genes webserver, respectively. GO analysis and pathway enrichment analysis were performed using R software. Results. Our study demonstrated that DR had 6 active compounds, including gentisin, sitosterol, Sylvestroside III, 3,5-Di-O-caffeoylquinic acid, cauloside A, and japonine. There were 254 target genes related to these active compounds as well as to bone. SRC, AKT1, and GRB2 were the top 3 hub genes. Metabolisms and signaling pathways associated with these hub genes were significantly enriched. Conclusions. This study indicated that DR could exhibit the anti-lung cancer effect by affecting multiple targets and multiple pathways. It reflects the traditional Chinese medicine characterized by multicomponents and multitargets. DR could be considered as a candidate for clinical anticancer therapy by regulating bone physiological functions.

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A Network Pharmacology-Based Study on Active Ingredients of Corydalis Rhizoma on Coronary Heart Disease

10.21203/rs.3.rs-90765/v1 ◽

2020 ◽

Author(s):

Ying Li ◽

Guhang Wei ◽

Zhenkun Zhuang ◽

Mingtai Chen ◽

Changjian Yuan ◽

...

Keyword(s):

Coronary Heart Disease ◽

Heart Disease ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Signaling Pathway ◽

Network Pharmacology ◽

Active Ingredients ◽

Active Components

Abstract BackgroundCorydalis Rhizoma(CR) showed a high efficacy for coronary heart disease (CHD). However, the interaction between the active ingredients of CR and the targets of CHD has not been unequivocally explained in previous researches. To study the active components and potential targets of Corydalis Rhizoma and to determine the mechanism underlying the exact effect of Corydalis Rhizoma on coronary heart disease, a method of network pharmacology was used.Materials and MethodsThe active components of CR and targets corresponding to each component were scanned out from Traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP), and target genes of CHD were searched on GeneCards database and Online Mendelian Inheritance in Man(OMIM) database. The active components and common targets of CR and CHD were used to build the “CR-CHD” network through Cytoscape (version 3.2.1) software as well as protein-protein interaction(PPI) network on String database. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis was executed by clusterProfiler(version 3.8) and DOSE(version 3.6) package on R platform.Results49 active ingredients and 394 relevant targets of CR and the 7173 CHD-related genes were retrieved. 40 common genes were selected for subsequent analysis. Crucial biological processes and pathways were obtained and analyzed, including DNA-binding transcription activator activity, RNA polymerase II-specific, RNA polymerase II transcription factor binding, kinase regulator activity, ubiquitin-like protein ligase binding, fluid shear stress and atherosclerosis, TNF signaling pathway, apoptosis, MAPK signaling pathway and PI3K-Akt signaling pathway.ConclusionsOverall, CR could alleviate CHD through the mechanisms predicted by network pharmacology, laying the foundation for future development of new drugs from traditional Chinese medicine on CHD.

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Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Coptis chinensis Franchin Polycystic Ovary Syndrome

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/6651307 ◽

2021 ◽

Vol 2021 ◽

pp. 1-15

Author(s):

Jian Xiong Ma ◽

Miaoyong Ye ◽

Ke Ma ◽

Kang Zhou ◽

Yingying Zhang ◽

...

Keyword(s):

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Polycystic Ovary Syndrome ◽

Signaling Pathways ◽

Polycystic Ovary ◽

Interaction Network ◽

Network Pharmacology ◽

Bioactive Components ◽

Coptis Chinensis ◽

Ovary Syndrome

Background. Polycystic ovary syndrome (PCOS) causes low fertility in females. Coptis chinensis (C. chinensis) is used to clear heat and dampness, purify fire, and detoxify in traditional Chinese medicine (TCM). Although C. chinensis has demonstrated efficacy against PCOS in clinical practice, there are no available data regarding the bioactive components of C. chinensis, their targets, and molecular mechanisms underlying their effects. Methods and Results. Network pharmacology was used to analyze the bioactive components of C. chinensis, their targets, and signaling pathways underlying their effects. The TCM systems pharmacology database and analysis platform (TCMSP) was used to screen 14 effective active ingredients and 218 targets of C. chinensis. The GeneCards, OMIM, and PharmGkb databases were used to screen 3517 disease targets for PCOS, and 102 common targets of drugs and diseases were screened using R Cytoscape that was utilized to build a drug-active ingredient-disease target interaction network, and the STRING platform was utilized to construct a common target protein-protein interaction network, including 102 nodes and 221 edges. Key targets of C. chinensis for the treatment of PCOS included JUN, MAPK, IL6, CXCL8, FOS, and IL1B. A total of 123 gene ontology (GO) terms and 129 pathways were acquired by GO and KEGG enrichment analyses. The AGEs/RAGE, TNF, IL-17, MAPK, and HIF-1 signaling pathways were closely related to PCOS and may be the core pathways involved in PCOS. Schrodinger software was used to evaluate the interaction between active components and their targets and explore binding modes. Furthermore, based on the prediction of network pharmacology study, a mouse model of PCOS was established to evaluate the curative role and underlying mechanisms of C. chinensis. The results showed that C. chinensis treatment reversed histopathological damage of the ovary and also ameliorated the mRNA and protein expression levels of the predicted hub targets (MAPK1, CXCL8, IL-6, and IL-1β). These results indicated that WZYZP has a protective effect on spermatogenesis disorder, suggesting that it could be an alternative choice for male infertility therapy. Conclusions. This preliminary study verified the basic pharmacological effects and mechanisms of C. chinensis, a TCM, in the treatment of PCOS. These results indicate that the therapeutic effects of C. chinensis on PCOS may be achieved by regulating the expression of inflammatory factors. This study provides new insights for the systematic exploration of the mechanism of traditional Chinese medicine.

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Traditional chinese medicine for irritable bowel syndrome: a protocol for meta-analysis

10.37766/inplasy2020.10.0052 ◽

2020 ◽

Author(s):

Chengjiao Yao ◽

Yilin Li ◽

Mengjun Pu ◽

Fengjiao Xie ◽

Qin Xiong ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Meta Analysis ◽

Irritable Bowel

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Network Pharmacology-Based Strategy for Predicting Active Ingredients and Potential Targets of Gegen Qinlian Decoction for Rotavirus Enteritis

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/2957567 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12 ◽

Cited By ~ 1

Author(s):

Peicheng Zhong ◽

Lijun Song ◽

Mengyue Gao ◽

Xiaotong Wang ◽

Wenpan Tan ◽

...

Keyword(s):

Nervous System ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Ion Concentration ◽

Network Pharmacology ◽

Receptor Interaction ◽

Basic Rule ◽

Gastrointestinal Hormone ◽

Active Ingredients ◽

Therapeutic Mechanism

Ethnopharmacological Relevance. Gegen Qinlian decoction (GGQLD) is an effective formula treatment for rotavirus enteritis (RVE), which has been applied for 1900 years. It consists of 4 herbal medicines corresponding to the four roles “monarch, minister, assistant, and guide,” which is the basic rule of prescription composition in traditional Chinese medicine (TCM). However, its active ingredients and therapeutic mechanism on RVE have not been fully investigated. Materials and Methods. In this study, a network pharmacology-based strategy was used to elucidate the mechanism of GGQLD for the treatment of RVE. Oral bioavailability and drug-likeness were taken as the judgment criteria to search the active ingredients of GGQLD in traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP). The affinity between protein and ingredients was further determined using the similarity ensemble approach to find the corresponding targets. According to the genes related to enteritis in GeneCards database, the key targets were screened by intersections between drug and disease targets. And the therapeutic mechanism was predicted using the protein-protein interactions (PPIs), the Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, which was verified by detecting calcium ion concentration with the fluorescent probe. Result. 130 active ingredients were screened from GGQLD, including (R)-canadine, moupinamide, formononetin, and other flavonoids. They act on a total of 366 targets, which is mainly distributed in the biological process of hormone binding or signaling pathways of neuroactive ligand receptor interaction, serotonergic synapse, and calcium signaling pathway. Furthermore, serotonin receptors, adrenergic receptors, cholinergic receptors, and dopamine receptors in the enteric nervous system may be the key targets of RVE treatment by GGQLD. Conclusion. This study demonstrated that the potential mechanism that GGQLD can effectively improve the symptoms of RVE may depend on the regulation of calcium ions, serotonin, and gastrointestinal hormone ion that could mutually affect the intestinal nervous system.

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