scholarly journals Pharmacological Mechanism of Danggui-Sini Formula for Intervertebral Disc Degeneration: A Network Pharmacology Study

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Longjie Wang ◽  
Jialiang Lin ◽  
Weishi Li
Keyword(s):  
Molecular Docking ◽  
Intervertebral Disc ◽  
Signaling Pathway ◽  
Disc Degeneration ◽  
Intervertebral Disc Degeneration ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Biological Mechanism ◽  
Core Genes

Background. Intervertebral disc degeneration (IVDD) is the most significant cause of low back pain, the sixth-largest disease burden globally, and the leading cause of disability. This study is aimed at investigating the molecular biological mechanism of Danggui-Sini formula (DSF) mediated IVDD treatment. Methods. A potential gene set for DSF treatment of IVDD was identified through TCMSP, UniProt, and five disease gene databases. A protein interaction network of common targets between DSF and IVDD was established by using the STRING database. GO and KEGG enrichment analyses were performed using the R platform to discover the potential mechanism. Moreover, AutoDock Vina was used to verify molecular docking and calculate the binding energy. Results. A total of 119 active ingredients and 136 common genes were identified, including 10 core genes (AKT1, IL6, ALB, TNF, VEGFA, TP53, MAPK3, CASP3, JUN, and EGF). Enrichment analysis results showed that the therapeutic targets of DSF for diseases mainly focused on the AGE-RAGE signaling pathway involved in diabetic complications, IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, apoptosis, cellular senescence, PI3K-Akt signaling pathway, and FoxO signaling pathway. These biological processes are induced mainly in response to oxidative stress and reactive oxygen species and the regulation of apoptotic signaling pathways. Molecular docking showed that there was a stable affinity between the core genes and the key components. Conclusions. The combination of network pharmacology and molecular docking provides a practical way to analyze the molecular biological mechanism of DSF-mediated IVDD treatment, which confirms the “multicomponent, multitarget and multipathway” characteristics of DSF and provides an essential theoretical basis for clinical practice.

scholarly journals Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Simiao Powder on Knee Osteoarthritis

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Zhengquan Huang ◽  
Xiaoqing Shi ◽  
Xiaochen Li ◽  
Li Zhang ◽  
Peng Wu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Knee Osteoarthritis ◽  
Signaling Pathway ◽  
Protein Interaction ◽  
Cell Metabolism ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Active Components ◽  
Discovery Studio

Objective. To explore the molecular mechanism of Simiao powder in the treatment of knee osteoarthritis. Methods. Based on oral bioavailability and drug-likeness, the main active components of Simiao powder were screened using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). GeneCard, OMIM, DisGeNET, DrugBank, PharmGkb, and the Therapeutic Target Database were used to establish target databases for knee osteoarthritis. Cytoscape software was used to construct a visual interactive network diagram of “active ingredient - action target – disease.” The STRING database was used to construct a protein interaction network and analyze related protein interaction relationships. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) biological process enrichment analysis were performed on the core targets. Additionally, Discovery Studio software was used for molecular docking verification of active pharmaceutical ingredients and disease targets. Results. Thirty-seven active components of Simiao powder were screened, including 106 common targets. The results of network analysis showed that the targets were mainly involved in regulating biological processes such as cell metabolism and apoptosis. Simiao powder components were predicted to exert their therapeutic effect on the AGE-RAGE signaling pathway in diabetic complications, IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and HIF-1 signaling pathway. The molecular docking results showed that the active components of Simiao powder had a good match with the targets of IL1B, MMP9, CXCL8, MAPK8, JUN, IL6, MAPK1, EGF, VEGFA, AKT1, and PTGS2. Conclusion. Simiao powder has multisystem, multicomponent, and multitarget characteristics in treating knee osteoarthritis. Its possible mechanism of action includes inhibiting the inflammatory response, regulating immune function, and resisting oxidative stress to control the occurrence and development of the disease. Quercetin, wogonin, kaempferol, beta-sitosterol, and other active ingredients may be the material basis for the treatment of knee osteoarthritis.

scholarly journals Network Pharmacology Integrated Molecular Docking Reveals the Mechanism of Zhongfeng Xingnao Formula against Intracerebral Hemorrhage

2020 ◽  
Author(s):  
Can Wan ◽  
Ziyi Zhou ◽  
Yun Lu ◽  
Guangyao Zhang ◽  
Yefeng Cai ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Intracerebral Hemorrhage ◽  
Signaling Pathway ◽  
Fluid Shear Stress ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Network Pharmacology ◽  
Pathway Network ◽  
Drug Compound

Abstract Background: Previous studies have shown that Zhongfeng Xingnao Formula (ZXF) can effectively reduce the mortality of intracerebral hemorrhage (ICH), but the underlying mechanism of the treatment remained still unexplored. This study aimed to expound the potential mechanism of ZXF in the treatment of ICH through network pharmacology and molecular docking.Methods: The putative targets of ZXF were obtained from the TCMSP and Uniprot database, while the potential targets of ICH received from Drugbank, Genecards and OMIM database. Then through the Venn 2.1, the overlapping targets of disease and drug were gotten for the further study. The GO and KEGG enrichment analyses were performed by R version 4.0.2 software so that the signaling pathway was acquired to the subsequent analysis. Cytoscape was used to construct the drug-compound-target-pathway network and String was utilized for the protein-protein interaction network. What’s more, the interaction between compound and target was verified by the AutoDockTools and Autodock Vina. Results: There were a total of 166 ZXF-related targets and 1258 ICH-related targets obtained from the public databases. And 87 potential targets were both related to drug and disease. The GO enrichment analysis mainly involved receptor ligand activity, signaling receptor activator activity, and cytokine receptor binding, while the signaling pathway, such as Fluid shear stress and atherosclerosis, AGE-RAGE signaling pathway in diabetic complications, PI3K-Akt signaling pathway, were significantly enriched in the KEGG enrichment analysis. The molecular docking elucidated that the aloe-emodin, beta-sitosterol, quercetin could bound well to the top five targets sorted by degree value.Conclusions: ZXF treated ICH through multiple compounds, multiple targets, and multiple pathways. The underlying mechanism of the treatment may be promoting angiogenesis, anti-inflammatory, anti-oxidative stress, and reversing atherosclerosis, which is of great significance for the treatment of ICH.

scholarly journals Decoding the Mechanism of Huanglian Jiedu Decoction in Treating Pneumonia Based on Network Pharmacology and Molecular Docking

2021 ◽  
Vol 9 ◽  
Author(s):  
Xianhai Li ◽  
Hua Tang ◽  
Qiang Tang ◽  
Wei Chen
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Clinical Symptoms ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Interleukin 17 ◽  
Active Ingredients ◽  
Hub Genes

Huang-Lian-Jie-Du decoction (HLJDD) has been used to treat pneumonia for thousands of years in China. However, our understanding of its mechanisms on treating pneumonia is still unclear. In the present work, network pharmacology was used to analyze the potential active ingredients and molecular mechanisms of HLJDD on treating pneumonia. A total of 102 active ingredients were identified from HLJDD, among which 54 were hit by the 69 targets associated with pneumonia. By performing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we obtained the main pathways associated with pneumonia and those associated with the mechanism of HLJDD in the treatment of pneumonia. By constructing the protein–protein interaction network of common targets, 10 hub genes were identified, which were mainly involved in the tumor necrosis factor (TNF) signaling pathway, interleukin 17 (IL-17) signaling pathway, and nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway. Moreover, the results of molecular docking showed that the active ingredients of HLJDD had a good affinity with the hub genes. The final results indicate that HLJDD has a greater effect on bacterial pneumonia than on viral pneumonia. The therapeutic effect is mainly achieved by regulating the host immune inflammatory response and oxidative stress reaction, antibacterial microorganisms, alleviating the clinical symptoms of pneumonia, repairing damaged cells, and inhibiting cell migration.

scholarly journals An Investigation Into the Mechanism of Li Chong Pill for Treating Endometriosis Based on Network Pharmacology and Molecular Docking Verification

2021 ◽  
Author(s):  
Shao-Xuan Liu ◽  
Feng-Juan Han ◽  
Chun-Lan Zhang ◽  
Ying Shen ◽  
Jia Li ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Hormone Secretion ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Binding Activity ◽  
Estrogen Signaling ◽  
Network Pharmacology ◽  
Binding Property ◽  
Core Network

Abstract Background and objective: Li Chong Wan (Li Chong pill, LCP) origin from Yi Xue Zhong Zhong Can Xi Lu, (Records of Chinese Medicine with Reference to Western Medicine), widely used in the treatment of endometriosis (EM) in China. The purpose of this study is to investigate the intrinsic mechanisms of LCP against EM and to provide new evidence for its clinical application.Methods: Chemical compounds of LCP were screened and evaluated via retrieving public databases and literature. We also acquired their putative targets and obtained EM-related targets. The above-mentioned data were visualized as a component-target network. In addition, we use Cytoscape3.8.0 to build a protein-protein interaction network and identified hub genes and key active ingredients. Furthermore, through GO and KEGG pathway analyses, which were actualized by R3.6.1 (based on clusterProfiler, org.Hs.eg.Db, and pathview package), we obtained effective signaling pathways and biological functions. Molecular docking was used to verify binding activity between compounds and the key targets at last.Results: Finally, a total of 122 possible active targets and 47 components were screened. Identify the core network and screen out 10 main targets; GO and KEGG enrichment analysis revealed that LCP may have functions of anti-inflammatory, anti-angiogenesis, inhibition of cell proliferation, regulation of hormone secretion, etc. The effect of LCP on EM might be achieved by PI3K/Akt signaling pathway, HIF-1 signaling pathway, estrogen signaling pathway, and VEGF signaling pathway, etc. Finally, molecular docking results demonstrated that 14 components were exhibited good binding property to the key targets of EM.Conclusion: This research ocularly demonstrated the multi-component, multi-target, and multi-channel pharmacological effects for LCP in the treatments of EM and provides evidence for further clinical research and verification of the mechanism.

scholarly journals Studies on the Mechanism of Gegen Qinlian Decoction in Treating Diabetes Mellitus Based on Network Pharmacology

2021 ◽  
Vol 16 (1) ◽  
pp. 1934578X2098213
Author(s):  
Xiaodong Deng ◽  
Yuhua Liang ◽  
Jianmei Hu ◽  
Yuhui Yang
Keyword(s):  
Diabetes Mellitus ◽  
Molecular Docking ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Network Pharmacology ◽  
Hub Genes ◽  
Topological Parameters

Diabetes mellitus (DM) is a chronic disease that is very common and seriously threatens patient health. Gegen Qinlian decoction (GQD) has long been applied clinically, but its mechanism in pharmacology has not been extensively and systematically studied. A GQD protein interaction network and diabetes protein interaction network were constructed based on the methods of system biology. Functional module analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, and Gene Ontology (GO) enrichment analysis were carried out on the 2 networks. The hub nodes were filtered by comparative analysis. The topological parameters, interactions, and biological functions of the 2 networks were analyzed in multiple ways. By applying GEO-based external datasets to verify the results of our analysis that the Gene Set Enrichment Analysis (GSEA) displayed metabolic pathways in which hub genes played roles in regulating different expression states. Molecular docking is used to verify the effective components that can be combined with hub nodes. By comparing the 2 networks, 24 hub targets were filtered. There were 7 complex relationships between the networks. The results showed 4 topological parameters of the 24 selected hub targets that were much higher than the median values, suggesting that these hub targets show specific involvement in the network. The hub genes were verified in the GEO database, and these genes were closely related to the biological processes involved in glucose metabolism. Molecular docking results showed that 5,7,2', 6'-tetrahydroxyflavone, magnograndiolide, gancaonin I, isoglycyrol, gancaonin A, worenine, and glyzaglabrin produced the strongest binding effect with 10 hub nodes. This compound–target mode of interaction may be the main mechanism of action of GQD. This study reflected the synergistic characteristics of multiple targets and multiple pathways of traditional Chinese medicine and discussed the mechanism of GQD in the treatment of DM at the molecular pharmacological level.

scholarly journals Elucidating the Mechanisms of Action of Lianhua Qingwen decoction for the Treatment of COVID-19 via Systems Pharmacology Approaches

2021 ◽  
Author(s):  
Xiting Wang ◽  
Tao Lu
Keyword(s):  
Molecular Docking ◽  
Blood Circulation ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Detection Algorithm ◽  
Network Pharmacology ◽  
Systems Pharmacology ◽  
Protein Protein Interaction ◽  
Further Development ◽  
Protein Protein Interaction Network

Abstract Due to the severity of the COVID-19 epidemic, to identify a proper treatment for COVID-19 is of great significance. Traditional Chinese Medicine (TCM) has shown its great potential in the prevention and treatment of COVID-19. One of TCM decoction, Lianhua Qingwen decoction displayed promising treating efficacy. Nevertheless, the underlying molecular mechanism has not been explored for further development and treatment. Through systems pharmacology and network pharmacology approaches, we explored the potential mechanisms of Lianhua Qingwen treating COVID-19 and acting ingredients of Lianhua Qingwen decoction for COVID-19 treatment. Through this way, we generated an ingredients-targets database. We also used molecular docking to screen possible active ingredients. Also, we applied the protein-protein interaction network and detection algorithm to identify relevant protein groupings of Lianhua Qingwen. Totally, 605 ingredients and 1,089 targets were obtained. Molecular Docking analyses revealed that 35 components may be the promising acting ingredients, 7 of which were underlined according to the comprehensive analysis. Our enrichment analysis of the 7 highlighted ingredients showed relevant significant pathways that could be highly related to their potential mechanisms, e.g. oxidative stress response, inflammation, and blood circulation. In summary, this study suggests the promising mechanism of the Lianhua Qingwen decoction for COVID-19 treatment. Further experimental and clinical verifications are still needed.

scholarly journals The mechanism of Bushen Huoxue decoction in treating intervertebral disc degeneration based on network pharmacology

2021 ◽  
Vol 10 (3) ◽  
pp. 49-49
Author(s):  
Shuai-Hua Feng ◽  
Fang Xie ◽  
Hong-Yan Yao ◽  
Guan-Bao Wu ◽  
Xiang-Yun Sun ◽  
...  
Keyword(s):  
Intervertebral Disc ◽  
Disc Degeneration ◽  
Intervertebral Disc Degeneration ◽  
Network Pharmacology ◽  
Bushen Huoxue Decoction

scholarly journals The Underlying Mechanism of Chinese Herb of Regulating Marrow in the Treatment of  Osteonecrosis of the Femoral Head Based on Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Xiaojian Wang ◽  
Rui Wang ◽  
Ting Xu ◽  
Hongting Jin ◽  
Peijian Tong ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Chinese Medicine ◽  
Signaling Pathway ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Chinese Herbs ◽  
Network Pharmacology ◽  
Active Components ◽  
Pathway Enrichment

Abstract Background The lesion of marrow is a crucial factor in orthopedic diseases, which is recognized by orthopedics-traumatology expert from "Zhe-School of Chinese Medicine". The Chinese herbs of regulating marrow has been widely used to treat osteonecrosis of the femoral head (ONFH) in China, while the interaction mechanisms were still elucidated. Thus, we conducted this study to explore the underlying mechanism of the five highest-frequency Chinese herbs of regulating marrow(HF-CHRM) in the treatment of ONFH with the aid of network pharmacology(NP) and molecular docking(MD). Methods The active components and potential targets of HF-CHRM were obtained through several online databases, such as Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), UniProt database. The gene targets related to ONFH were collected with the help of the OMIM and GeneCards disease-related databases. The "drug- component-target-disease" network and protein-protein interaction(PPI) network of the drug and disease intersecting targets were constructed by using Cytoscape software and the STRING database. R software was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The MD of critical components and targets was carried out using Autodock Vina and Pymol to validate the binding affinity. Results A total of 54 active components, 1074 drug targets and 195 gene targets were obtained. There were 1219 ONFH related targets. 39 drug and disease intersection targets(representative genes: IL6, TP53, VEGFA, ESR1, IL1B) were obtained and considered potential therapeutic targets. 1619 items were obtained by the GO enrichment analysis, including 1517 biological processes, 10 cellular components and 92 molecular functions, which is mainly related to angiogenesis, bone and lipid metabolism and inflammatory reaction. The KEGG pathway enrichment analysis revealed 119 pathways, including AGE-RAGE signaling pathway, PI3K-Akt signaling pathway and IL-17 signaling pathway. MD results showed that quercetin, wogonin, and kaempferol active components had good affinity with IL6, TP53, and VEGFA core proteins. Conclusion The HF-CHRM can treat ONFH by multi-component, multi-target, and multi-pathway comprehensive action.

Sign in / Sign up

Export Citation Format

Share Document