scholarly journals Network Pharmacology and Molecular Docking Verify the Mechanism of Qinshi Simiao San in Treating Chronic Prostatitis in the Rat Model

2022 ◽  
Vol 2022 ◽  
pp. 1-13
Author(s):  
Chenxi Li ◽  
Lei Xu ◽  
Xuyao Lin ◽  
Qingrui Li ◽  
Shaoming Liu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Molecular Docking ◽  
Molecular Mechanism ◽  
Rat Model ◽  
Chronic Prostatitis ◽  
Target Genes ◽  
Reduction Process ◽  
Inflammatory Factors ◽  
Network Pharmacology ◽  
Network Graph

Background. Using network pharmacology and molecular docking, this study aimed to explore the active pharmaceutical ingredients (APIs) and molecular mechanism of Qinshi Simiao San (QSSMS) in the treatment of chronic prostatitis (CP) and verify our findings in the rat model. Methods. The APIs of QSSMS and the common targets of QSSMS and CP were screened from the TCMSP database. The STRING database and Cytoscape software were used to construct the network graph. The enriched GO and KEGG pathways were displayed by David software and R software. Molecular docking was performed to visualize key components and target genes. In addition, the rats model of CP was established to verify the molecular mechanism of QSSMS. Results. Network pharmacology showed that the APIs of QSSMS mainly included quercetin, kaempferol, formononetin, isorhamnetin, and calycosin. QSSMS alleviated CP mainly through the negative regulation of the apoptotic process, oxidation-reduction process, inflammatory response, and immune response. Molecular docking showed that the APIs could bind to the corresponding targets. QSSMS repaired the pathological damage of prostate tissue, upregulated the expression of oxidative stress scavenging enzymes CAT and SOD, and downregulated the peroxidative product MDA, inflammatory factors IL-1β, IL-6, TNF-α, COX-2, PGE2, and NGF, and immune factors IgG and SIgA. Conclusion. The APIs in QSSMS may inhibit inflammation in the rat CP model by regulating immune and oxidative stress.

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 Molecular Mechanism of the Effect of Huanglian Jiedu Decoction on Type 2 Diabetes Mellitus Based on Network Pharmacology and Molecular Docking

2020 ◽  
Vol 2020 ◽  
pp. 1-24
Author(s):  
Bei Yin ◽  
Yi-Ming Bi ◽  
Guan-Jie Fan ◽  
Ya-Qing Xia
Keyword(s):  
Molecular Docking ◽  
Molecular Mechanism ◽  
Target Genes ◽  
Binding Capacity ◽  
Topological Analysis ◽  
Herbal Medicines ◽  
Differentially Expressed ◽  
Network Pharmacology ◽  
Active Components ◽  
Ppi Networks

Background. Huanglian Jiedu Decoction (HLJDD) is a Traditional Chinese Medicine (TCM) formula comprising four herbal medicines. This decoction has long been used in China for clinically treating T2DM. However, the molecular mechanism of HLJDD treat for T2DM is still not fully known. Hence, this study was designed to reveal the synergistic mechanism of HLJDD formula in the treatment of T2DM by using network pharmacology method and molecular docking. Methods. Retrieving and screening of active components of different herbs in HLJDD and corresponding T2DM-related target genes across multiple databases. Subsequently, STRING and Cytoscape were applied to analysis and construct PPI network. In addition, cluster and topological analysis were employed for the analysis of PPI networks. Then, the GO and KEGG enrichment analysis were performed by using ClueGO tool. Finally, the differentially expressed analysis was used to verify whether the expression of key target genes in T2DM and non-T2DM samples was statistically significant, and the binding capacity between active components and key targets was validated by molecular docking using AutoDock. Results. There are 65 active components involved in 197 T2DM-related targets that are identified in HLJDD formula. What is more, 39 key targets (AKT1, IL-6, FOS, VEGFA, CASP3, etc.) and 3 clusters were obtained after topological and cluster analysis. Further, GO and KEGG analysis showed that HLJDD may play an important role in treating T2DM and its complications by synergistically regulating many biological processes and pathways which participated in signaling transduction, inflammatory response, apoptotic process, and vascular processes. Differentially expressed analysis showed that AKT1, IL-6, and FOS were upregulated in T2DM samples and a significant between sample differential expression. These results were validated by molecular docking, which identified 5 high-affinity active components in HLJDD, including quercetin, wogonin, baicalein, kaempferol, and oroxylin A. Conclusion. Our research firstly revealed the basic pharmacological effects and relevant mechanisms of the HLJDD in the treatment of T2DM and its complications. The prediction results might facilitate the development of HLJDD or its active compounds as alternative therapy for T2DM. However, more pharmacological experiments should be performed for verification.

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.

scholarly journals Network Pharmacology and Molecular Docking Suggest the Mechanism for Biological Activity of Rosmarinic Acid

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Minglong Guan ◽  
Lan Guo ◽  
Hengli Ma ◽  
Huimei Wu ◽  
Xiaoyun Fan
Keyword(s):  
Biological Activity ◽  
Molecular Docking ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Rosmarinic Acid ◽  
Target Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis

Rosmarinic acid (RosA) is a natural phenolic acid compound, which is mainly extracted from Labiatae and Arnebia. At present, there is no systematic analysis of its mechanism. Therefore, we used the method of network pharmacology to analyze the mechanism of RosA. In our study, PubChem database was used to search for the chemical formula and the Chemical Abstracts Service (CAS) number of RosA. Then, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was used to evaluate the pharmacodynamics of RosA, and the Comparative Toxicogenomics Database (CTD) was used to identify the potential target genes of RosA. In addition, the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of target genes were carried out by using the web-based gene set analysis toolkit (WebGestalt). At the same time, we uploaded the targets to the STRING database to obtain the protein interaction network. Then, we carried out a molecular docking about targets and RosA. Finally, we used Cytoscape to establish a visual protein-protein interaction network and drug-target-pathway network and analyze these networks. Our data showed that RosA has good biological activity and drug utilization. There are 55 target genes that have been identified. Then, the bioinformatics analysis and network analysis found that these target genes are closely related to inflammatory response, tumor occurrence and development, and other biological processes. These results demonstrated that RosA can act on a variety of proteins and pathways to form a systematic pharmacological network, which has good value in drug development and utilization.

scholarly journals Up-regulated microRNA-185-3p inhibits the development of hyperlipidemia in rats

2021 ◽  
Author(s):  
Hua Zhao ◽  
yanbing Li
Keyword(s):  
Oxidative Stress ◽  
Rat Model ◽  
Lipid Accumulation ◽  
Adenoviral Vectors ◽  
Cellular Morphology ◽  
Inflammatory Factors ◽  
Multiple Cancers ◽  
Biochemical Indices ◽  
Novel Therapeutic ◽  
Liver Tissues

Abstract Objective MicroRNA (miR)-185-3p roles have been probed in multiple cancers, while the underlying function of miR-185-3p in hyperlipidemia remained obscure. This research was conducted to unravel miR-185-3p function in hyperlipidemia development via modulating mastermind-like 1 (MAML1). Methods The hyperlipidemia rat model was constructed. MiR-185-3p and MAML1 levels in hyperlipidemia rats were detected. Adenoviral vectors altering miR-185-3p and MAML1 levels were injected into hyperlipidemia rats to examine the levels of biochemical indices, inflammatory factors, oxidative stress, lipid accumulation and cellular morphology in liver tissues of hyperlipidemia rats. The targeting relation between miR-185-3p and MAML1 was manifested. Results MiR-185-3p levels were depleted while MAML1 expression was elevated in HH rats. MiR-185-3p overexpression or MAML1 silencing reduced levels of inflammatory factors in serum, mitigated oxidative stress and biochemical response, relieved lipid accumulation and cellular morphology in liver tissues; while up-regulated MAML1 reversed the effects of augmented MAML1 in hyperlipidemia rats. MiR-185-3p targeted MAML1. Conclusion Up-regulated miR-185-3p represses hyperlipidemia development via modulating MAML1. This research provides novel therapeutic candidates for the treatment of hyperlipidemia.

Discussing the Mechanism of Dahuang Huanglian Xiexin Decoction in the Treatment of Type 2 Diabetes Mellitus via Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Xi Cen ◽  
Yan Wang ◽  
LeiLei Zhang ◽  
XiaoXiao Xue ◽  
Yan Wang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Molecular Docking ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Overlapping Genes ◽  
Potential Mechanism ◽  
Active Components ◽  
The Core ◽  
Core Genes

Abstract BackgroundType 2 diabetes mellitus (T2DM) is regarded as Pi Dan disease in traditional Chinese medicine (TCM). Dahuang Huanglian Xiexin Decoction (DHXD), a classical TCM formula, has been used for treating Pi Dan disease in clinic, its pharmacological mechanism has not been elucidated. MethodsThis study used network pharmacological analysis and molecular docking approach to explore the mechanism of DHXD on T2DM. Firstly, the compounds in DHXD were obtained from TCMSP and TCMID databases, the potential targets were determined based on TCMSP and UniProt databases. Next, Genecards, Digenet and UniProt databases were used to identify the targets of T2DM. Then, the protein-protein interaction (PPI) network was established with overlapping genes of T2DM and compounds, and the core targets in the network were identified and analyzed. Then, the David database was used for GO and KEGG enrichment analysis. Finally, the target genes were selected and the molecular docking was completed by Autodock software to observe the binding level of active components with target genes.ResultsA total of 397 related components and 128 overlapping genes were identified. After enrichment analysis, it was found that HIF-1, TNF, IL-17 and other signaling pathways, as well as DNA transcription, gene expression, apoptosis and other cellular biological processes had the strongest correlation with the treatment of T2DM by DHXD, and most of them occurred in the extracellular space, plasma membrane and other places, which were related to enzyme binding and protein binding. In addition, 42 core genes of DHXD, such as VEGFA, TP53 and MAPK1, were considered as potential therapeutic targets, indicating the potential mechanism of DHXD on T2DM. Finally, the results of molecular docking showed that HIF-1 pathway had strong correlation with the target genes INSR and GLUT4, quercetin and berberine had the strongest binding power with them respectively.ConclusionThis study summarized the main components of DHXD in the treatment of T2DM, identified the core genes and pathways, and systematically analyzed the interaction of related targets, trying to lay the foundation for clarifying the potential mechanism of DHXD on T2DM, so as to carry out further research in the future.

scholarly journals Identifying Active Compounds and Targets of Fritillariae thunbergii against Influenza-Associated Inflammation by Network Pharmacology Analysis and Molecular Docking

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3853 ◽  
Author(s):  
Minjee Kim ◽  
Ki Hoon Park ◽  
Young Bong Kim
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Target Genes ◽  
Inflammatory Diseases ◽  
Network Pharmacology ◽  
Pharmacokinetic Parameters ◽  
Active Compounds ◽  
Biological Targets ◽  
Underlying Mechanisms ◽  
Cox 1

Complications due to influenza are often associated with inflammation with excessive release of cytokines. The bulbs of Fritillariae thunbergii (FT) have been traditionally used to control airway inflammatory diseases, such as bronchitis and pneumonia. To elucidate active compounds, the targets, and underlying mechanisms of FT for the treatment of influenza-induced inflammation, systems biology was employed. Active compounds of FT were identified through the TCMSP database according to oral bioavailability (OB) and drug-likeness (DL) criteria. Other pharmacokinetic parameters, Caco-2 permeability (Caco-2), and drug half-life (HL) were also identified. Biological targets of FT were retrieved from DrugBank and STITCH databases, and target genes associated with influenza, lung, and spleen inflammation were collected from DisGeNET and NCBI databases. Compound-disease-target (C-D-T) networks were constructed and merged using Cytoscape. Target genes retrieved from the C-D-T network were further analyzed with GO enrichment and KEGG pathway analysis. In our network, GO and KEGG results yielded two compounds (beta-sitosterol (BS) and pelargonidin (PG)), targets (PTGS1 (COX-1) and PTGS2 (COX-2)), and pathways (nitric oxide, TNF) were involved in the inhibitory effects of FT on influenza-associated inflammation. We retrieved the binding affinity of each ligand-target, and found that PG and COX-1 showed the strongest binding affinity among four binding results using a molecular docking method. We identified the potential compounds and targets of FT against influenza and suggest that FT is an immunomodulatory therapy for influenza-associated inflammation.

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