Interaction between piperine and genes associated with sciatica and its mechanism based on molecular docking technology and network pharmacology

Yu, Jiuwang; Hu, Yuan; Si, Lengge

doi:10.1007/s11030-020-10055-9

Cited by 24 publications

(8 citation statements)

References 54 publications

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“…Te composition of traditional Chinese medicine is complex, and the study of its mechanism is also complicated. Network pharmacology is a new methodology for investigating traditional Chinese medicine components and mechanisms [24][25][26]. In this study, the genes of ESCC were screened by bioinformatics, RR was screened by network pharmacology to target the hub genes of ESCC, and the inhibitory efect of RR on ESCC was studied in vitro.…”

Section: Discussionmentioning

confidence: 99%

Inhibitory Effects of Rabdosia rubescens in Esophageal Squamous Cell Carcinoma: Network Pharmacology and Experimental Validation

Lin

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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Esophageal squamous cell carcinoma (ESCC) is one of the most frequently occurring diseases in the world. Rabdosia rubescens (RR) has been demonstrated to be effective against ESCC; however, the mechanism is unknown. The primary gene modules related to the clinical characteristics of ESCC were initially investigated in this research using weighted gene co-expression network analysis (WCGNA) and differential expression gene (DEG) analysis. We employed network pharmacology to study the hub genes linked with RR therapy on ESCC. A molecular docking simulation was achieved to identify the binding activity of central genes to RR compounds. Lastly, a chain of experimentations was used to verify the inhibitory effect of RR water extract on the ESCC cell line in vitro. The outcomes revealed that CCNA2, TOP2A, AURKA, CCNB2, CDK2, CHEK1, and other potential central targets were therapeutic targets for RR treatment of ESCC. In addition, these targets are over-represented in several cancer-related pathways, including the cell cycle signaling pathway and the p53 signaling pathway. The predicted targets displayed good bonding activity with the RR bioactive chemical according to a molecular docking simulation. In vitro experiments revealed that RR water extracts could inhibit ESCC cells, induce cell cycle arrest, inhibit cell proliferation, increase P53 expression, and decrease CCNA2, TOP2A, AURKA, CCNB2, CDK2, and CHEK1. In conclusion, our study reveals the molecular mechanism of RR therapy for ESCC, providing great potential for identifying effective compounds and biomarkers for ESCC therapy.

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Section: Discussionmentioning

confidence: 99%

Inhibitory Effects of Rabdosia rubescens in Esophageal Squamous Cell Carcinoma: Network Pharmacology and Experimental Validation

Lin

et al. 2022

Evidence-Based Complementary and Alternative Medicine

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“…PyMOL was used to visualize the results, and the hydrogen bonds and their binding sites were examined. The docking energy value was computed using the consistency score function of the ligand-receptor affinity ( 32 ). The affinity between the active compound and the related target was assessed by measuring the active compound's binding free energy to the target.…”

Section: Methodsmentioning

confidence: 99%

Ferula sinkiangensis against gastric cancer: a network pharmacology, molecular docking and cell experiment study

Wang¹,

Sun²,

Liu³

et al. 2023

Transl Cancer Res

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Background Ferula sinkiangensis ( F. sinkiangensis ) is a traditional Chinese medicine that has been used for thousands of years to treat stomach ailments. To identify the main active compounds and explore the mechanisms underlying the therapeutic effect of F. sinkiangensis against gastric cancer (GC) by network pharmacology, molecular docking analysis and cell experiment. Methods Based on a review of the literature and previous experiments conducted by our research group, the active compounds of F. sinkiangensis were obtained. Active compounds and their target genes were screened from SwissADME, Pubchem, and Pharmmapper databases. GC-related target genes were obtained from GeneCards. The drug-compound-target-disease (D-C-T-D) network and protein-protein interaction (PPI) network were constructed by Cytoscape 3.7.2 and STRING database, and the core target genes and core active compounds were identified. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted using the R package clusterProfiler. The core genes with high expression in GC were screened, which correlated with a poor prognosis using the GEPIA, UALCAN, HPA, and KMplotter databases. KEGG signaling pathway analysis was further conducted to predict the mechanism of F. sinkiangensis during the process of GC inhibition. The AutoDock vina 1.1.2 program was used to verify the molecular docking of the core active compounds and core target genes. MTT, Transwell, and Wound healing assay were used to detect the effects of ethyl acetate extract of F. sinkiangensis on the proliferation, invasion, and apoptosis of GC cells. Results Final results indicated that the active compounds include Farnesiferol C, Assafoetidin, Lehmannolone, Badrakemone, etc. The identified core target genes were GPI , TKT , GLYCTK , ERBB2 , GAPDH , etc. The Glycolysis/Gluconeogenesis pathway and the Pentose Phosphate pathway might play important roles in the treatment of GC with F. sinkiangensis . The data from the study showed that F. sinkiangensis was able to inhibit the proliferation of GC cells. Meanwhile, F. sinkiangensis remarkedly repressed the invasion and migration of GC cells in in vitro experiment. Conclusions This study revealed that F. sinkiangensis has an antitumor effect in in vitro experiment, and that the mechanism of F. sinkiangensis in GC treatment shows characteristics of multi-components, multi-targets, and multi-pathways, which provides a theoretical basis for its...

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“…We searched online databases commonly used for TCM ingredients, The Encyclopedia of Traditional Chinese Medicine (http://www.tcmip.cn/ETCM), Traditional Chinese Medicine Systems Pharmacology database and Analysis Platform (http:// lsp.nwu.edu.cn/tcmsp.php), and the TCM database Taiwan (http://tcm.cmu.edu.tw) to produce a more comprehensive compound list (Yu et al, 2020;Zhu and Hou, 2020). We collected a total of 65 compounds from these databases as candidates for CRP studies (Supplementary Table S2).…”

Section: Compounds Collected From Databasesmentioning

confidence: 99%

Systems Pharmacology Study of the Anti-Liver Injury Mechanism of Citri Reticulatae Pericarpium

Yang

et al. 2021

Front. Pharmacol.

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Liver diseases are mostly triggered by oxidative stress and inflammation, leading to extracellular matrix overproduction and prone to develop into liver fibrosis, cirrhosis and hepatocellular carcinoma. Liver injury (LI) refers to various pathogenic factors leading to the destruction of stem cells that then affect the liver’s normal function, causing a series of symptoms and abnormal liver function indicators. Citri Reticulatae Pericarpium (CRP) is one of the most commonly used traditional Chinese medicines; it contains flavonoids including hesperidin, nobiletin, and tangeretin. CRP has antibacterial, antioxidant, and antitumor effects that reduce cholesterol, prevent atherosclerosis and decrease LI. Here we analyzed the components of CRP and their targets of action in LI treatment and assessed the relationships between them using a systems pharmacology approach. Twenty-five active ingredients against LI were selected based on ultra-performance liquid chromatography-quadrupole/time-of-flight mass spectrometry results and databases. The drug targets and disease-related targets were predicted. The 117 common targets were used to construct a protein-protein interaction network. We identified 1719 gene ontology items in LI treatment, including 1,525 biological processes, 55 cellular components, and 139 molecular functions. These correlated with 49 Kyoto Encyclopedia of Genes and Genomes pathways. These findings suggest that CRP may counteract LI by affecting apoptotic, inflammatory, and energy metabolism modules. In vitro experiments suggested that the mechanism may involve hesperidin and naringenin acting on CASP3, BAX, and BCL2 to affect the apoptosis pathway, attenuating liver fibrosis. Naringenin significantly inhibited AKT1 phosphorylation, which in turn mediated activation of the phosphoinositide 3-kinase-Akt signaling pathways against LI. This study provides a reference for systematically exploring the mechanism of CRP’s anti-LI action and is also expands of the application of systems pharmacology in the study of traditional Chinese medicine.

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Interaction between piperine and genes associated with sciatica and its mechanism based on molecular docking technology and network pharmacology

Cited by 24 publications

References 54 publications

Inhibitory Effects of Rabdosia rubescens in Esophageal Squamous Cell Carcinoma: Network Pharmacology and Experimental Validation

Inhibitory Effects of Rabdosia rubescens in Esophageal Squamous Cell Carcinoma: Network Pharmacology and Experimental Validation

Ferula sinkiangensis against gastric cancer: a network pharmacology, molecular docking and cell experiment study

Systems Pharmacology Study of the Anti-Liver Injury Mechanism of Citri Reticulatae Pericarpium

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