Comparative transcriptomics and network pharmacology analysis to identify the potential mechanism of celastrol against osteoarthritis

2021 ◽  
Author(s):  
Siming Dai ◽  
Hui Wang ◽  
Meng Wang ◽  
Yue Zhang ◽  
Zhiyi Zhang ◽  
...  
Keyword(s):  
Comparative Transcriptomics ◽  
Network Pharmacology ◽  
Potential Mechanism

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 Yixin-Shu facilitated cardiac-like differentiation of mesenchymal stem cells in vitro

RSC Advances ◽  
2018 ◽  
Vol 8 (18) ◽  
pp. 10032-10039 ◽  
Author(s):  
Jingjing Zhang ◽  
Feifei Guo ◽  
Hongwei Wu ◽  
Junying Wei ◽  
Minghua Xian ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Cell Differentiation ◽  
Intestinal Absorption ◽  
Network Pharmacology ◽  
Potential Mechanism

A network pharmacology analysis indicated intestinal absorption liquid of Yixin-Shu capsules had an effect on cell differentiation, which was verified by its effect on cardiac-like differentiation of mesenchymal stem cells and the potential mechanism was also predicted.

scholarly journals Integrating Network Pharmacology with Molecular Docking to Unravel the Active Compounds and Potential Mechanism of Simiao Pill Treating Rheumatoid Arthritis

2020 ◽  
Vol 2020 ◽  
pp. 1-16
Author(s):  
Mengshi Tang ◽  
Xi Xie ◽  
Pengji Yi ◽  
Jin Kang ◽  
Jiafen Liao ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Molecular Docking ◽  
Signaling Pathway ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Binding Activity ◽  
New Combination ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Potential Mechanism

Objective. To explore the main components and unravel the potential mechanism of simiao pill (SM) on rheumatoid arthritis (RA) based on network pharmacological analysis and molecular docking. Methods. Related compounds were obtained from TCMSP and BATMAN-TCM database. Oral bioavailability and drug-likeness were then screened by using absorption, distribution, metabolism, and excretion (ADME) criteria. Additionally, target genes related to RA were acquired from GeneCards and OMIM database. Correlations about SM-RA, compounds-targets, and pathways-targets-compounds were visualized through Cytoscape 3.7.1. The protein-protein interaction (PPI) network was constructed by STRING. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed via R packages. Molecular docking analysis was constructed by the Molecular Operating Environment (MOE). Results. A total of 72 potential compounds and 77 associated targets of SM were identified. The compounds-targets network analysis indicated that the 6 compounds, including quercetin, kaempferol, baicalein, wogonin, beta-sitosterol, and eugenol, were linked to ≥10 target genes, and the 10 target genes (PTGS1, ESR1, AR, PGR, CHRM3, PPARG, CHRM2, BCL2, CASP3, and RELA) were core target genes in the network. Enrichment analysis indicated that PI3K-Akt, TNF, and IL-17 signaling pathway may be a critical signaling pathway in the network pharmacology. Molecular docking showed that quercetin, kaempferol, baicalein, and wogonin have good binding activity with IL6, VEGFA, EGFR, and NFKBIA targets. Conclusion. The integrative investigation based on bioinformatics/network topology strategy may elaborate on the multicomponent synergy mechanisms of SM against RA and provide the way out to develop new combination medicines for RA.

scholarly journals Research on the potential mechanism of Chuanxiong Rhizoma on treating Diabetic Nephropathy based on network pharmacology

2020 ◽  
Vol 17 (15) ◽  
pp. 2240-2247
Author(s):  
Shanshan Hu ◽  
Siteng Chen ◽  
Zhilei Li ◽  
Yuhang Wang ◽  
Yong Wang
Keyword(s):  
Diabetic Nephropathy ◽  
Network Pharmacology ◽  
Potential Mechanism

scholarly journals Mechanism of 1,25(OH)2D3 in the Treatment of Acute Lung Injury Based on UHPLC/Q-TOF MS-Based Metabolomics and Network Pharmacology

2020 ◽  
Author(s):  
Xuan Shi ◽  
Yuanli Chen ◽  
Yiguo Zhang ◽  
Xiaohong Jin ◽  
Huanping Zhou ◽  
...  
Keyword(s):  
Acute Lung Injury ◽  
Lung Injury ◽  
Signaling Pathway ◽  
Network Pharmacology ◽  
Regulation Mechanism ◽  
High Morbidity ◽  
Potential Mechanism ◽  
Serum Samples ◽  
Inflammatory Infiltration ◽  
Tof Ms

Abstract Background: Sepsis-induced acute lung injury (ALI), a high morbidity and mortality disease, still has no effective therapies. 1,25(OH)2D3 is one of the indispensable nutrients in our body. The regulation mechanism of 1,25(OH)2D3 in inflammation has been recognized gradually. Network pharmacology was used wildly to broaden the understanding of diseases and advance drug discovery. In this study, we used network pharmacology and metabolomics to generate the potential mechanism of 1,25(OH)2D3 on acute lung injury.Methods: We used metabolomics and network pharmacology to elucidate the therapeutic mechanism of 1,25(OH)2D3 on acute lung injury. Serum samples, collected from mice with LPS-induced acute lung injury, were detected by UHPLC/Q-TOF MS to evaluate the differential metabolites from multiple metabolic pathways. Meanwhile, the H＆E staining, ELISA and QPCR were used to estimate the efficacy of 1,25(OH)2D3 on acute lung injury. Results: The results of animal experiments showed that 1,25(OH)2D3 could mitigate severe pulmonary edema and inflammatory infiltration caused by LPS, and the treatment of 1,25(OH)2D3 reduced the levels of inflammatory cytokines, interacted 25 related proteins and TNF signaling pathway, Toll-like receptor signaling pathway, PI3K-Akt signaling pathway.Conclusions: The integrated methods coupled with UHPLC/Q-TOF MS and network pharmacology provided a new way to study the potential mechanism of 1,25(OH)2D3 on acute lung injury, which may provide a possible solution for patients with clinical acute lung injury.

scholarly journals Network Pharmacology-Based Study on the Mechanism of Aloe Vera for Treating Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Jing Xie ◽  
Jun Wu ◽  
Sihui Yang ◽  
Huaijun Zhou
Keyword(s):  
Molecular Docking ◽  
Drug Targets ◽  
Aloe Vera ◽  
Beta Carotene ◽  
Network Pharmacology ◽  
Potential Mechanism ◽  
Active Ingredients ◽  
Protein Protein Interaction ◽  
Target Network ◽  
Molecule Docking

Background. Aloe vera has long been considered an anticancer herb in different parts of the world. Objective. To explore the potential mechanism of aloe vera in the treatment of cancer using network pharmacology and molecule docking approaches. Methods. The active ingredients and corresponding protein targets of aloe vera were identified from the TCMSP database. Targets related to cancer were obtained from GeneCards and OMIM databases. The anticancer targets of aloe vera were obtained by intersecting the drug targets with the disease targets, and the process was presented in the form of a Venn plot. These targets were uploaded to the String database for protein-protein interaction (PPI) analysis, and the result was visualized by Cytoscape software. Go and KEGG enrichment were used to analyze the biological process of the target proteins. Molecular docking was used to verify the relationship between the active ingredients of aloe vera and predicted targets. Results. By screening and analyzing, 8 active ingredients and 174 anticancer targets of aloe vera were obtained. The active ingredient-anticancer target network constructed by Cytoscape software indicated that quercetin, arachidonic acid, aloe-emodin, and beta-carotene, which have more than 4 gene targets, may play crucial roles. In the PPI network, AKT1, TP53, and VEGFA have the top 3 highest values. The anticancer targets of aloe vera were mainly involved in pathways in cancer, prostate cancer, bladder cancer, pancreatic cancer, and non-small-cell lung cancer and the TNF signaling pathway. The results of molecular docking suggested that the binding ability between TP53 and quercetin was the strongest. Conclusion. This study revealed the active ingredients of aloe vera and the potential mechanism underlying its anticancer effect based on network pharmacology and provided ideas for further research.

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