Study of the mechanism underlying therapeutic effect of Compound Longmaining on myocardial infarction using a network pharmacology-based approach

Bu, Diaodiao; Su, Zhuo; Zou, Junbo; Meng, Mei; Wang, Changli

doi:10.1016/j.biopha.2019.109234

Cited by 18 publications

(8 citation statements)

References 34 publications

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“…The degree centrality (DC) is a key network topology parameter that refers to the number of connections of one specific node with others. Nodes with higher DC are considered to be more central [ 23 ]. Therefore, we selected nodes with a DC that was equal or greater than twice the median to form a core PPI network.…”

Section: Methodsmentioning

confidence: 99%

Network Pharmacology to Identify the Pharmacological Mechanisms of a Traditional Chinese Medicine Derived from Trachelospermum jasminoides in Patients with Rheumatoid Arthritis

et al. 2020

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Section: Methodsmentioning

confidence: 99%

Network Pharmacology to Identify the Pharmacological Mechanisms of a Traditional Chinese Medicine Derived from Trachelospermum jasminoides in Patients with Rheumatoid Arthritis

et al. 2020

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“…The degree of a node referred to the number of edges between nodes in a network. The greater a node's degree is, the more nodes are connected 7 BioMed Research International to it and the more important it is in the network [47,48]. We used the value of the degree to analyze the node's importance in the network and screening the top 30 genes, which is more than twice the median of the target genes at least [49].…”

Section: Target Network Analysismentioning

confidence: 99%

A Network Pharmacology and Molecular Docking Strategy to Explore Potential Targets and Mechanisms Underlying the Effect of Curcumin on Osteonecrosis of the Femoral Head in Systemic Lupus Erythematosus

Kang

Zhong

et al. 2021

BioMed Research International

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Background. Systemic lupus erythematosus (SLE) is a refractory immune disease, which is often complicated with osteonecrosis of the femoral head (ONFH). Curcumin, the most active ingredient of Curcuma longa with a variety of biological activities, has wide effects on the body system. The study is aimed at exploring the potential therapeutic targets underlying the effect of curcumin on SLE-ONFH by utilizing a network pharmacology approach and molecular docking strategy. Methods. Curcumin and its drug targets were identified using network analysis. First, the Swiss target prediction, GeneCards, and OMIM databases were mined for information relevant to the prediction of curcumin targets and SLE-ONFH-related targets. Second, the curcumin target gene, SLE-ONFH shared gene, and curcumin-SLE-ONFH target gene networks were created in Cytoscape software followed by collecting the candidate targets of each component by R software. Third, the targets and enriched pathways were examined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Eventually, a gene-pathway network was constructed and visualized by Cytoscape software; key potential central targets were verified and checked by molecular docking and literature review. Results. 201 potential targets of curcumin and 170 related targets involved in SLE-ONFH were subjected to network analysis, and the 36 intersection targets indicated the potential targets of curcumin for the treatment of SLE-ONFH. Additionally, for getting more comprehensive and accurate candidate genes, the 36 potential targets were determined to be analyzed by network topology and 285 candidate genes were obtained finally. The top 20 biological processes, cellular components, and molecular functions were identified, when corrected by a P value ≤ 0.05. 20 related signaling pathways were identified by KEGG analysis, when corrected according to a Bonferroni P value ≤ 0.05. Molecular docking showed that the top three genes (TP53, IL6, VEGFA) have good binding force with curcumin; combined with literature review, some other genes such as TNF, CCND1, CASP3, and MMP9 were also identified. Conclusion. The present study explored the potential targets and signaling pathways of curcumin against SLE-ONFH, which could provide a better understanding of its effects in terms of regulating cell cycle, angiogenesis, immunosuppression, inflammation, and bone destruction.

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“…DAVID, a high-throughput and integrated datamining environment, analyses gene lists derived from high-throughput genomic experiments. P-value < 0.01 and FDR < 0.05 were considered as the criteria for difference screening [31,32].…”

Section: Gene Ontology (Go) and Kyoto Encyclopedia Of Genes And Genommentioning

confidence: 99%

Dissecting the mechanism of Yuzhi Zhixue granule on ovulatory dysfunctional uterine bleeding by network pharmacology and molecular docking

Luo

Liu

et al. 2020

Chin Med

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Background Yuzhi Zhixue Granule (YZG) is a traditional Chinese patent medicine for treating excessive menstrual flow caused by ovulatory dysfunctional uterine bleeding (ODUB) accompanied by heat syndrome. However, the underlying molecular mechanisms, potential targets, and active ingredients of this prescription are still unknown. Therefore, it is imperative to explore the molecular mechanism of YZG. Methods The active compounds in YZG were screened by the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The putative targets of YZG were collected via TCMSP and Search Tool for Interacting Chemicals (STITCH) databases. The Therapeutic Target Database (TTD) and Pharmacogenomics Knowledgebase (PharmGKB) databases were used to identify the therapeutic targets of ODUB. A protein–protein interaction (PPI) network containing both the putative targets of YZG and known therapeutic targets of ODUB was built. Furthermore, bioinformatics resources from the database for annotation, visualization and integrated discovery (DAVID) were utilized for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, molecular docking was performed to verify the binding effect between the YZG screened compounds and potential therapeutic target molecules. Results The study employed a network pharmacology method, mainly containing target prediction, network construction, functional enrichment analysis, and molecular docking to systematically research the mechanisms of YZG in treating ODUB. The putative targets of YZG that treat ODUB mainly involved PTGS1, PTGS2, ALOX5, CASP3, LTA4H, F7 and F10. The functional enrichment analysis suggested that the produced therapeutic effect of YZG against ODUB is mediated by synergistical regulation of several biological pathways, including apoptosis arachidonic acid (AA) metabolism, serotonergic synapse, complement and coagulation cascades and C-type lectin receptor signaling pathways. Molecular docking simulation revealed good binding affinity of the seven putative targets with the corresponding compounds. Conclusion This novel and scientific network pharmacology-based study holistically elucidated the basic pharmacological effects and the underlying mechanisms of YZG in the treatment of ODUB.

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Study of the mechanism underlying therapeutic effect of Compound Longmaining on myocardial infarction using a network pharmacology-based approach

Cited by 18 publications

References 34 publications

Network Pharmacology to Identify the Pharmacological Mechanisms of a Traditional Chinese Medicine Derived from Trachelospermum jasminoides in Patients with Rheumatoid Arthritis

Network Pharmacology to Identify the Pharmacological Mechanisms of a Traditional Chinese Medicine Derived from Trachelospermum jasminoides in Patients with Rheumatoid Arthritis

A Network Pharmacology and Molecular Docking Strategy to Explore Potential Targets and Mechanisms Underlying the Effect of Curcumin on Osteonecrosis of the Femoral Head in Systemic Lupus Erythematosus

Dissecting the mechanism of Yuzhi Zhixue granule on ovulatory dysfunctional uterine bleeding by network pharmacology and molecular docking

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