Bioactive constituents and the molecular mechanism of Curcumae Rhizoma in the treatment of primary dysmenorrhea based on network pharmacology and molecular docking

Phytomedicine ◽  
2021 ◽  
pp. 153558
Author(s):  
Huangjin Tong ◽  
Mengting Yu ◽  
Chenghao Fei ◽  
De JI ◽  
Jiajia Dong ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Molecular Mechanism ◽  
Network Pharmacology ◽  
Primary Dysmenorrhea ◽  
Bioactive Constituents

scholarly journals Molecular mechanism underlying the hypolipidemic effect of Shanmei Capsule based on network pharmacology and molecular docking

2021 ◽  
Vol 29 ◽  
pp. 239-256
Author(s):  
Qian Wang ◽  
Lijing Du ◽  
Jiana Hong ◽  
Zhenlin Chen ◽  
Huijian Liu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Kegg Pathway ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Signal Pathways ◽  
Hypolipidemic Effect ◽  
Active Ingredients ◽  
Pathway Enrichment

BACKGROUND: Shanmei Capsule is a famous preparation in China. However, the related mechanism of Shanmei Capsule against hyperlipidemia has yet to be revealed. OBJECTIVE: To elucidate underlying mechanism of Shanmei Capsule against hyperlipidemia through network pharmacology approach and molecular docking. METHODS: Active ingredients, targets of Shanmei Capsule as well as targets for hyperlipidemia were screened based on database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed via Database for Annotation, Visualization, and Integrated Discovery (DAVID) 6.8 database. Ingredient-target-disease-pathway network was visualized utilizing Cytoscape software and molecular docking was performed by Autodock Vina. RESULTS: Seventeen active ingredients in Shanmei Capsule were screened out with a closely connection with 34 hyperlipidemia-related targets. GO analysis revealed 40 biological processes, 5 cellular components and 29 molecular functions. A total of 15 signal pathways were enriched by KEGG pathway enrichment analysis. The docking results indicated that the binding activities of key ingredients for PPAR-α are equivalent to that of the positive drug lifibrate. CONCLUSIONS: The possible molecular mechanism mainly involved PPAR signaling pathway, Bile secretion and TNF signaling pathway via acting on MAPK8, PPARγ, MMP9, PPARα, FABP4 and NOS2 targets.

Molecular Mechanism of The Effect of Huanglian Jiedu Decoction On Ulcerative Colitis Based On Network Pharmacology And Molecular Docking

2021 ◽  
Author(s):  
Jing Yang ◽  
Chao-Tao Tang ◽  
Ruiri Jin ◽  
Bixia Liu ◽  
Peng Wang ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Molecular Docking ◽  
Molecular Mechanism ◽  
Target Genes ◽  
Signal Pathway ◽  
Intestinal Barrier Function ◽  
Network Pharmacology ◽  
Bioactive Components ◽  
Ppi Network ◽  
Active Components

Abstract Huanglian jiedu decoction (HLJDD) is a heat-clearing and detoxifying agent composed of four kinds of Chinese herbal medicine. Previous studies have shown that HLJDD can improve the inflammatory response of ulcerative colitis (UC) and maintain intestinal barrier function. However, its molecular mechanism is not completely clear. In this study, we verified the bioactive components (BCI) and potential targets of HLJDD in the treatment of UC by means of network pharmacology and molecular docking, and constructed the pharmacological network and PPI network. Then the core genes were enriched by GO and KEGG. Finally, the bioactive components were docked with the key targets to verify the binding ability between them. A total of 54 active components related to UC were identified. Ten genes are considered to be very important to PPI network. Functional analysis showed that these target genes were mainly involved in the regulation of cell response to different stimuli, IL-17 signal pathway and TNF signal pathway. The results of molecular docking showed that the active components of HLJDD had good affinity with Hub gene. This study systematically elucidates the "multi-component, multi-target, multi-pathway" mechanism of anti-UC with HLJDD for the first time, suggesting that HLJDD or its active components may be candidate drugs for the treatment of ulcerative colitis.

scholarly journals Mechanism of Salviae Miltiorrhizae Radix et Rhizoma in the treatment of knee osteoarthritis based on network pharmacology

2020 ◽  
Author(s):  
Xiaoqing Shi ◽  
Haosheng Zhang ◽  
Yue Hu ◽  
Xiaochen Li ◽  
Songjiang Yin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Knee Osteoarthritis ◽  
Molecular Mechanism ◽  
Tanshinone Iia ◽  
Inflammatory Factors ◽  
Venn Diagram ◽  
Network Pharmacology ◽  
Bioinformatics Analyses ◽  
Salviae Miltiorrhizae ◽  
Salviae Miltiorrhizae Radix

Abstract Objective: The molecular mechanism of Salviae Miltiorrhizae Radix et Rhizoma (SMRR) in the treatment of knee osteoarthritis (KOA) was analyzed based on network pharmacology.Methods: Active components and potential targets of SMRR were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). KOA targets were obtained from the OMIM, DisGeNET, DrugBank, PharmGKB and GeneCards Databases. The potential targets of SMRR in the treatment of KOA were identified by Venn diagram. A protein-protein interaction network was generated with the STRING database. Visualization of the interactions in a potential pharmacodynamic component-target network was accomplished with Cytoscape software. The DAVID database and R software were used for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation analyses of common targets. Molecular docking of the potential leading components, as determined by efficacy with the core target molecules, was performed with Discovery Studio.Results: Fifty-seven potential pharmacodynamic components and 58 potential targets of SMRR in the treatment of KOA were found. Bioinformatics analyses showed that the IL-17, HIF-1 and TNF signaling pathways, as well as the AGE-RAGE signaling pathway in cases of diabetic complications, are related to the molecular mechanism of SMRR in the treatment of KOA. Molecular docking results showed that luteolin, Tanshinone IIA, Cryptotanshinone and other components of SMRR had strong affinity for MYC, STAT3, CASP3, JUN, CCND1, PTGS2, EGFR, MAPK1, AKT1, VEGFA and other targets.Conclusion: SMRR indirectly regulates IL-17, HIF-1, TNF and other signal transduction pathways by regulating the expression of proteins including PTGS2, MAPK1, EGFR and CASP3, thus playing a role in promoting chondrocyte proliferation, improving microcirculation, eliminating free radicals, and inhibiting inflammatory factors.

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 Investigating the Mechanism of Guizhi Fuling Formula in the Treatment of Primary Dysmenorrhea based on Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Lu Sun ◽  
Zining Wang ◽  
Jian Li ◽  
Li Xu ◽  
Xiaoou Xue
Keyword(s):  
Molecular Docking ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Primary Dysmenorrhea ◽  
Potential Mechanism ◽  
Protein Protein Interaction ◽  
Long Time ◽  
Hormone Biosynthesis ◽  
Relationship Of

Abstract Background: Primary dysmenorrhea(PD)is the most common gynecologic disorder.Despite the prevalence is high, it is often underdiagnosed,undertreated and normalized even by patients themselves. Guizhi Fuling Formula (GFF) is experientially used for the treatment of PD in a long time. Therefore, the efficiency and potential mechanism are waiting to identify.Methods: We adopted network pharmacology integrated molecular docking strategy in this study.Based on published literatures, the relative compounds of GFF were selected preliminarily. Secondly, the putative targets of PD were obtained by wide-searching DisGeNET, OMIM, Drugbank and GeneCards databases.With protein-protein interaction(PPI) analysis, GO and KEGG pathway enrichment analysis and molecular docking ,we systematically evaluated the relationship of herb ingredients and disease targets.Results: The results showed that 30 ingredients of GFF and 43 hub targets made a difference.Under the further analysis,8 targets(EGFR,AKT1,PTGS2,TNF,ESR1,AHR,CTNNB1,CXCL8) were recognized as key therapeutic targets with excellent binding. The enrichment analyses indicated that the GFF had the potential to influence varieties of biological pathways, especially the pathways in cancer and steroid hormone biosynthesis, which play an important part in the pathogenesis of primary dysmenorrhea.Conclusion: GFF influenced primary dysmenorrhea through the synergistic effect of multiple components, multiple targets, and multiple pathways.This study predictedthe potential mechanism, hope that could made contribution for clinical application and scientific research.

scholarly journals Study on the Mechanism of Baimai Ointment in the Treatment of Osteoarthritis Based on Network Pharmacology and Molecular Docking with Experimental Verification

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingyin Zhu ◽  
Wanling Zhong ◽  
Jing Peng ◽  
Huichao Wu ◽  
Shouying Du
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Animal Experiments ◽  
Tibetan Medicine ◽  
Blue Staining ◽  
Network Pharmacology ◽  
Enzyme Linked Immunosorbent Assay

Purpose: The external preparation of the Tibetan medicine formula, Baimai ointment (BMO), has great therapeutic effects on osteoarthritis (OA). However, its molecular mechanism remains almost elusive. Here, a comprehensive strategy combining network pharmacology and molecular docking with pharmacological experiments was adopted to reveal the molecular mechanism of BMO against OA.Methods: The traditional Chinese medicine for systems pharmacology (TCMSP) database and analysis platform, traditional Chinese medicine integrated database (TCMID), GeneCards database, and DisGeNET database were used to screen the active components and targets of BMO in treating OA. A component–target (C-T) network was built with the help of Cytoscape, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment through STRING. Autodock Tools which was used to dock the key components and key target proteins was analyzed. Animal experiments were performed to verify the key targets of BMO. Hematoxylin–eosin and toluidine blue staining were used to observe the pathology of joints. Protein expression was determined using enzyme-linked immunosorbent assay.Results: Bioactive compounds and targets of BMO and OA were screened. The network analysis revealed that 17-β-estradiol, curcumin, licochalone A, quercetin, and glycyrrhizic acid were the candidate key components, and IL6, tumor necrosis factor (TNF), MAPK1, VEGFA, CXCL8, and IL1B were the candidate key targets in treating OA. The KEGG indicated that the TNF signaling pathway, NF-κB signaling pathway, and HIF-1 signaling pathway were the potential pathways. Molecular docking implied a strong combination between key components and key targets. The pathology and animal experiments showed BMO had great effects on OA via regulating IL6, TNF, MAPK1, VEGFA, CXCL8, and IL1B targets. These findings were consistent with the results obtained from the network pharmacology approach.Conclusion: This study preliminarily illustrated the candidate key components, key targets, and potential pathways of BMO against OA. It also provided a promising method to study the Tibetan medicine formula or external preparations.

scholarly journals Uncovering the Mechanism of the Effects of Pien-Tze-Huang on Liver Cancer Using Network Pharmacology and Molecular Docking

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Shanghui Liu ◽  
Run Wang ◽  
Yan Lou ◽  
Jia Liu
Keyword(s):  
Molecular Docking ◽  
Liver Cancer ◽  
Molecular Mechanism ◽  
Mechanism Of Action ◽  
Network Pharmacology ◽  
Active Ingredients ◽  
The Core ◽  
Molecular Mechanism Of Action ◽  
Pien Tze Huang ◽  
Core Genes

Pien-Tze-Huang (PTH) has a long history in the treatment of liver cancer. However, its molecular mechanism of action remains unclear. TCMSP and TCM were used to collect the active ingredients. Bioactive compounds targets were predicted by reverse pharmacophore models. The antiliver cancer targets of PTH were selected by gene comparison of liver cancer in the GEO database. Molecular docking was used to verify the binding activity of the targets and the active ingredients. The DAVID was used to analyze the gene function and signal pathway. A model was built with Cytoscape. The core genes were obtained by PPI network. We screened the 4 main medicinal ingredients of PTH to obtain 16 active ingredient, 190 potential targets, and 6 core genes. We found that active small molecules exert anticancer effects by multiple pathways. The core genes were involved in multiple biological processes. We also found that eight chemical components play a greater role in inhibiting liver cancer. PTH achieves the effect of inhibiting liver cancer through the synergistic effect of multiple components, multiple targets, and multiple pathways. This study provides a potential scientific basis for further elucidating the molecular mechanism of action of PTH against liver cancer.

scholarly journals Molecular Mechanism of Jinchan Oral Liquid in the Treatment of Children with Respiratory Syncytial Virus Pneumonia Based on Network Pharmacology and Molecular Docking Technology

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Li Shen ◽  
Yiguo Jiang ◽  
Jinmiao Lu ◽  
Guangfei Wang ◽  
Xiaolan Zhang ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Respiratory Syncytial Virus ◽  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Network Pharmacology ◽  
Online Database ◽  
The Core ◽  
Oral Liquid ◽  
Syncytial Virus ◽  
Core Genes

Objective. Exploration of the underlying molecular mechanism of Jinchan Oral Liquid (JOL) in treating children with the respiratory syncytial virus (RSV) pneumonia to provide new evidence for the clinical application. Methods. The active components and target genes of JOL were screened by the TCMSP database. The targets of RSV pneumonia were obtained from the GeneCards, OMIM, DrugBank, and PharmGKB database. Then, we constructed the active component-target network and screened the core genes. The overlaps were screened for PPI network analysis, GO analysis, and KEGG analysis. Finally, result validation was performed by molecular docking. Results. According to the screening criteria of the ADME, 74 active compounds of JOL were obtained; after removing redundant targets, we selected 180 potential targets. By screening the online database, 893 RSV pneumonia-related targets were obtained. A total of 82 overlapping genes were chosen by looking for the intersection. The STRING online database was used to acquire PPI relationships, and 16 core genes were obtained. GO and KEGG analyses showed that the main pathways of JOL in treating RSV pneumonia include TNF signaling pathway and IL17 signaling pathway. The molecular docking results showed that the active compounds of JOL had a good affinity with the core genes. Conclusion. In this study, we preliminarily discussed the main active ingredients, related targets, and pathways of JOL and predicted the pharmacodynamic basis and the potential therapeutic mechanisms of RSV pneumonia. In summary, the network pharmacology strategy may be helpful for the discovery of multitarget drugs against complex diseases.

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