scholarly journals Data Mining, Network Pharmacology, and Molecular Docking Explore the Effects of Core Traditional Chinese Medicine Prescriptions in Patients with Rectal Cancer and Qi and Blood Deficiency Syndrome

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Shiyu Ma ◽  
Lin Zheng ◽  
Lan Zheng ◽  
Xiaolan Bian
Keyword(s):  
Data Mining ◽  
Rectal Cancer ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Deficiency Syndrome ◽  
Network Pharmacology ◽  
Hub Genes ◽  
The Core ◽  
High Degree

Background. “Zheng” (syndrome) is the basic unit and the basis of traditional Chinese medicine (TCM) treatment. In clinical practice, we have been able to improve the survival time and quality of life for patients with rectal cancer through the treatment of “FuZhengXiaoJi” (strengthening the Qi and reducing accumulation). Purpose. In this study, we elucidated the core prescriptions for patients with rectal cancer and Qi and blood deficiency syndrome, and we explored the potential mechanisms of the prescriptions using an integrated strategy that coupled data mining with network pharmacology. Methods. A Bron–Kerbosch (BK) algorithm was applied to find the core prescriptions. The active ingredients, targets, activated signaling pathways, and biological functions of core prescriptions were analyzed using network pharmacology and directly associated proteins were docked using molecular docking technology to elucidate the multicomponent, multitarget, and inter-related components associated with TCM systematically. Results. Data mining identified 3 core prescriptions, and most of the herbs consisted of “FuZhengXiaoJi” Fang. Network pharmacology identified 15 high-degree active ingredients among the 3 core prescriptions and 16 high-degree hub genes linked with both rectal cancer and the 3 core prescriptions. Additional Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of these 16 targets showed that the most significant pathways were MAPK, interleukin-17, tumor necrosis factor (TNF), and vascular endothelial growth factor (VEGF) pathways. From the 16 genes, TGFB1, IL1B, IL10, IL6, PTGS2, and PPARG closely interacted with the tumor microenvironment, and PPARG, MYC, and ERBB2 were closely linked to survival. In molecular docking, quercetin, kaempferol, and lauric acid showed good binding energy to each target. Conclusion. Data mining, network pharmacology, and molecular docking may help identify core prescriptions, high-degree ingredients, and high-degree hub genes to apply to diseases and treatments. Furthermore, these studies may help discover hub genes that affect the tumor microenvironment and survival. The combination of these tools may help elucidate the relationship between herbs acting on “Zheng” (syndrome) and diseases, thus expanding the understanding of TCM mechanisms.

scholarly journals The Analysis of The Application and Mechanism of Traditional Chinese Medicine in Osteoarthritis Based on Data Mining and Network Pharmacology

2020 ◽  
Author(s):  
Jie YANG ◽  
Dijin JIAO ◽  
Guoguang Zhang ◽  
Juntong LIU ◽  
Chao QU ◽  
...  
Keyword(s):  
Data Mining ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Cell Metabolism ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
String Database ◽  
The Core ◽  
Drug Molecules

Abstract Background: Using Data Mining to retrieve the core drug of osteoarthritis in clinic, predicting the drug molecular action target through the Network Pharmacology, combining with the related targets of osteoarthritis to identify the key nodes of the interaction, exploring the pharmacological mechanism of Traditional Chinese Medicine against osteoarthritis and other possible mechanisms of actions. Methods: Pubmed, CNKI, VIP, CBM and WanFang Database was used to retrieve the commonly used therapeutic formulations for osteoarthritis patients in clinical, and screen out the core drugs through the Ancient and Modern Medical Case Cloud Platform and software Gephi, filtered out the core drug molecules and targets combined with TCMSP database and the targets of osteoarthritis in Genecard, OMIM database, impoting those datas into R project and Cytoscape to construct the intersection model of Drug molecule-osteoarthritis, carrying out PPI network and GO and KEGG enrichment analysis with String database. Vina molecular docking was implemented to draw molecular docking diagram, and the results were analyzed after comprehensive analysis. Results: The core drug pairs were identified as "Eucommiae Cortex - Achyranthis Bidentatae Radix" through correlation analysis, complex network analysis basing on the coefficient. "Eucommiae Cortex - Achyranthis Bidentatae Radix" can intervene cell behaviors through multiple pathways and regulate cell metabolism, cytokine synthesis, oxidative , cellular immunity as a consequence of topology analysis in String Database. Conclusions: "Eucommia bark - achyranthes" drug molecules can be combined with the target to produce hydrogen bond, hydrophobic function and Pi-Pi directly or indirectly affecting the corresponding targets, to participate in the regulation of osteogenesis and osteoclast proliferation, protect the extracellular matrix, inhibition of cell apoptosis and anti-inflammatory for resistance to osteoarthritis, also, providing the basis for interpretation of its action mechanism.

scholarly journals Integrating Data Mining, Network Pharmacology, and Molecular Docking Verification to Investigate the Molecular Mechanism of Traditional Chinese Medicine Prescriptions for Treating Male Infertility

2021 ◽  
Author(s):  
Xue Bai ◽  
Yibo Tang ◽  
Qiang Li ◽  
Guimin Liu ◽  
Dan Liu ◽  
...  
Keyword(s):  
Data Mining ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Male Infertility ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Oxidant Stress ◽  
Estrogen Signaling ◽  
Network Pharmacology

Abstract Background: Male infertility (MI) affects almost 5% adult men worldwide, and 75% of these cases are unexplained idiopathic. There are limitations in the current treatment due to the unclear mechanism of MI, which highlight the urgent need for a more effective strategy or drug. Traditional Chinese Medicine (TCM) prescriptions have been used to treat MI for thousands of years, but their molecular mechanism is not well defined. Methods: Aiming at revealing the molecular mechanism of TCM prescriptions on MI, a comprehensive strategy integrating data mining, network pharmacology, and molecular docking verification was performed. Firstly, we collected 289 TCM prescriptions for treating MI from National Institute of TCM Constitution and Preventive Medicine for 6 years. Then, Core Chinese Materia Medica (CCMM), the crucial combination of TCM prescriptions, was obtained by the TCM Inheritance Support System from China Academy of Chinese Medical Sciences. Next, the components and targets of CCMM in TCM prescriptions and MI-related targets were collected and analyzed through network pharmacology approach.Results: The results showed that the molecular mechanism of TCM prescriptions for treating MI are regulating hormone, inhibiting apoptosis, oxidant stress and inflammatory. Estrogen signaling pathway, PI3K-Akt signaling pathway, HIF-1 signaling pathway, and TNF signaling pathway are the most important signaling pathways. Molecular docking experiments were used to further validate network pharmacology results. Conclusions: This study not only discovers CCMM and the molecular mechanism of TCM prescriptions for treating MI, but may be helpful for the popularization and application of TCM treatment.

scholarly journals Investigation of the Mechanism of Traditional Chinese Medicines in Angiogenesis Through Network Pharmacology and Data Mining

2020 ◽  
Author(s):  
WingYan Yun ◽  
Wenchao Dan ◽  
Jinlei Liu ◽  
Xinyuan Guo ◽  
Min Li ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Network Pharmacology ◽  
Root Bark ◽  
Target Compound ◽  
Potential Core ◽  
Chinese Medicines ◽  
The Core ◽  
Essential Components

Abstract BackgroundAlthough traditional Chinese medicine is safe for the clinical treatment of angiogenesis, the in vivo intervention mechanism is diverse, complex, and largely unknown. Therefore, we aimed to explore the active ingredients of traditional Chinese medicine and their mechanisms for the treatment of angiogenesis.MethodsData on angiogenesis-related targets were collected from the GeneCards, Therapeutic Target Database, Online Mendelian Inheritance in Man, DrugBank, and DisGeNET databases. These were matched to related molecular compounds and ingredients in the traditional Chinese medicine system pharmacology platform. The data were integrated; based on the condition of Degree >1 and relevant literature, a target-compound network as well as compound-medicine and target-compound-medicine networks were constructed using Cytoscape. Molecular docking was used to predict the predominant binding combination of core targets and components.ResultsWe obtained a total of 79 targets for angiogenesis, and 41 targets were matched to 3839 compounds. Then, 110 compounds were selected owing to their high correlation with angiogenesis. Fifty-five combinations in the network were obtained by molecular docking, among which PTGS2-Astragalin (-9.18 kcal/mol), KDR-Astragalin (-7.94 kcal/mol), PTGS2-quercetin (-7.41 kcal/mol), and PTGS2-myricetin (-7.21 kcal/mol) were the top combinations. These results indicated that the selected potential core compounds may have good binding activity with the core targets. Eighty new combinations were obtained from the network, and the top combinations based on affinity were KDR-beta-carotene (-10.13 kcal/mol), MMP9-beta-Sitosterol (-8.04 kcal/mol), MMP9-Astragalin (-7.82 kcal/mol), and MMP9-Diosgenin (-7.51 kcal/mol). The core targets included PTGS2, KDR, VEGFA, and MMP9. The essential components identified were astragalin, kaempferol, myricetin, quercetin, and β-sitosterol. The crucial Chinese medicines identified included Polygoni Cuspidati Rhizoma et Radix, Morus alba Root Bark, and Forsythia Fructus.ConclusionsBy systematically analysing the essential ingredients of traditional Chinese medicine and their targets, it is possible to determine their potential mechanism of action in the treatment of pathological angiogenesis. Our study provides a basis for further research and development of new therapeutics for angiogenesis.

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

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.

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

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.

scholarly journals Exploring the mechanism of aidi injection for lung cancer by network pharmacology approach and molecular docking validation

2021 ◽  
Vol 41 (2) ◽  
Author(s):  
Zhenjie Zhuang ◽  
Tong Lin ◽  
Lixia Luo ◽  
Weixin Zhou ◽  
Junmao Wen ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Target Genes ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Hub Genes ◽  
Aidi Injection

Abstract Background. Aidi injection (ADI) is an effective Traditional Chinese medicine preparation widely used for lung cancer. However, the pharmacological mechanisms of ADI on lung cancer remain to be elucidated. Methods. A network pharmacology (NP)-based approach and the molecular docking validation were conducted to explore underlying mechanisms of ADI on lung cancer. The compounds and target genes were screened by Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (Batman-TCM) database. The STRING database was utilized for protein interaction network construction. The R package clusterProfiler was used for bioinformatics annotation of hub target genes. The gene expression analysis and survival analysis were performed based on The Cancer Genome Atlas (TCGA) database. The Autodock Vina was used for molecular docking validation. Results. A total of five key compounds with 324 putative target genes were screened out, and 14 hub target genes were identified for treating lung cancer. Six hub genes could influence the survival of non-small cell lung cancer (NSCLC) patients. Of these hub genes, the expression pattern of EGFR, MYC, PIK3CA, and SMAD3 were significantly higher in the LUSC, while PIK3CA and RELA expressed lower in the LUAD group and LUSC group, respectively. These six hub genes had good docking affinity with the key compounds of ADI. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that ADI may exert therapeutic effects on lung cancer by regulating critical pathways including the thyroid hormone signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway. Conclusions. The present study explored the potential pharmacological mechanisms of ADI on lung cancer, promoting the clinical application of ADI in treating lung cancer, and providing references for advanced researches.

scholarly journals The Use of Traditional Chinese Medicine in Relieving EGFR-TKI-Associated Diarrhea Based on Network Pharmacology and Data Mining

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Shuaihang Hu ◽  
Wenchao Dan ◽  
Jinlei Liu ◽  
Peng Ha ◽  
Tong Zhou ◽  
...  
Keyword(s):  
Data Mining ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Drug Targets ◽  
Kinase Inhibitor ◽  
Molecular Structures ◽  
Network Pharmacology ◽  
Lipinski’S Rule ◽  
The Core ◽  
Egfr Tki

In this study, the role of traditional Chinese medicine (TCM) in relieving epidermal growth factor receptor-tyrosine kinase inhibitor- (EGFR-TKI-) associated diarrhea was discussed by network pharmacology and data mining. Prediction of drug targets by introducing the EGFR-TKI molecular structures into the SwissTargetPrediction platform and diarrhea-related targets in the DrugBank, GeneCards, DisGeNET, and OMIM databases were obtained. Compounds in the drug-disease target intersection were screened by absorption, distribution, metabolism, and excretion parameters and Lipinski’s rule in Traditional Chinese Medicine Systems Pharmacology. TCM-containing compounds were selected, and information on the property, taste, and meridian tropism of these TCMs was summarized and analyzed. A target-compound-TCM network diagram was constructed, and core targets, compounds, and TCMs were selected. The core targets and components were docked by AutoDock Vina (Version 1.1.2) to explore the target combinations of related compounds and evaluate the docking activity of related targets and compounds. Twenty-three potential therapeutic TCM targets for the treatment of EGFR-TKI-related diarrhea were obtained. There were 339 compounds acting on potential therapeutic targets, involving a total of 402 TCMs. The results of molecular docking showed good binding between the core targets and compounds, and the binding between the core targets and compounds was similar to that of the core target and the recommended drug loperamide. TCMs have multitarget characteristics and are present in a variety of compounds used for relieving EGFR-TKI-associated diarrhea. Antitumor activity and the efficacy of alleviating diarrhea are the pharmacological basis of combining TCMs with EGFR-TKI in the treatment of non-small-cell lung cancer. The core targets, compounds, and TCMs can provide data to support experimental and clinical studies on the relief of EGFR-TKI-associated diarrhea in the future.

scholarly journals Study on the Mechanism of Compound Kidney-Invigorating Granule for Osteoporosis based on Network Pharmacology and Experimental Verification

2022 ◽  
Vol 2022 ◽  
pp. 1-20
Author(s):  
Hao Lv ◽  
Jiuxiang Wang ◽  
Yujun Zhu ◽  
Ting Jiang
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Bioactive Compounds ◽  
Venn Diagram ◽  
Network Pharmacology ◽  
Ppi Network ◽  
Hub Genes ◽  
In Cells

Background. This study used a combination of network pharmacology and experimental confirmation to clarify the mechanism of the compound kidney-invigorating granule (CKG) in treating osteoporosis (OP). Methods. The main bioactive compounds and corresponding targets of CKG were collected and screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), Yet another Traditional Chinese Medicine (YaTCM), and UniProt databases. Disease targets of OP were summarized in GeneCards and the Comparative Toxicogenomics Database (CTD). Targets of CKG for OP were obtained by Venn diagram. The protein-protein interaction (PPI) network was constructed by the STRING database and then screened for hub genes through Cytoscape 3.7.2 software. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed and visualized by R software. Then, CB-Dock was used for molecular docking verification. Finally, we confirmed the antiosteoporosis effect of CKG through animal and cell experiments. Results. A total of 250 putative targets were obtained from 65 bioactive compounds in CKG. Among them, 140 targets were related to OP. Topological analysis of the PPI network yielded 23 hub genes. Enrichment analysis showed the targets of CKG in treating OP might concentrate on the MAPK signaling pathway, the TNF signaling pathway, the PI3K-Akt signaling pathway, etc. The results of molecular docking showed the bioactive components in CKG had good binding ability with the key targets. The experimental results showed that CKG-medicated serum had a promoting effect on proliferating hBMSCs, increasing the expression of AKT, PI3K, ERK1, and IkB in cells and decreasing the expression of IKK in cells. Conclusion. CKG has a complex of multicomponent, multitarget, and multipathway. This study lays the theoretical foundation for further in vitro and in vivo experimental studies and further expands the clinical applications of CKG.

Network Pharmacology-based Study of Simiao Yongan Decoction for Treatment of Herpes Zoster Infection

2020 ◽  
Author(s):  
Liu Hongtao ◽  
Chen Guanyan ◽  
Wu Zhenhai ◽  
Tang Qiuqin
Keyword(s):  
Molecular Docking ◽  
Herpes Zoster ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Network Pharmacology ◽  
Bioactive Components ◽  
Hub Genes ◽  
Topological Parameters ◽  
Lectin Receptor ◽  
Target Network

Abstract Background: Herpes zoster (HZ) is a virus that causes infectious diseases that impact the quality of life of patients. Herein, we applied network pharmacological methods to predict the target of bioactive components in Simiao Yongan Decoction (SYD) that could treat HZ. Methods: We developed a Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMP) and GenneCards databases for screening of bioactive components of SYD, their targets, and HZ related targets. A bioactive component-target network of SYD was constructed using Cytoscape. We also constructed a protein-protein interaction (PPI) network using the Search Tool for the Retrieval of Interacting Genes Database (STRING) to identify potential SYD targets for the treatment of HZ. "ClusterProfiler" in R-project was used for Gene Ontology (GO) and KEGG pathway enrichment analyses. We screened SYD hub genes based on component-target network topological parameters and confirmed the findings by molecular docking. We selected 126 bioactive components and 235 targets. Results: By assessing the topological parameters of the degree network, we identified that CDK2, CASP3, JUN, AKT1, and MAPK1 were hub genes related to SYD-based therapy against HZ. The findings showed that treatment of HZ with SYD mainly involved toll-like receptor, C-type lectin receptor, MAPK, PI3K-Akt, and other signaling pathways. The molecular docking results revealed good binding energy between the SYD bioactive compounds and hub targets. Conclusion: We showed that SYD could effectively treat HZ via multiple targets and pathways. Our results provide theoretical support for treatment of HZ with SYD and a new direction for such treatment using traditional Chinese medicine.

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