scholarly journals Network pharmacology and molecular docking study on the active ingredients of qidengmingmu capsule for the treatment of diabetic retinopathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mingxu Zhang ◽  
Jiawei Yang ◽  
Xiulan Zhao ◽  
Ying Zhao ◽  
Siquan Zhu
Keyword(s):  
Diabetic Retinopathy ◽  
Molecular Docking ◽  
Molecular Mechanisms ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
Docking Study ◽  
Network Pharmacology ◽  
Biological Processes ◽  
Active Ingredients ◽  
Molecular Docking Study

AbstractDiabetic retinopathy (DR) is a leading cause of irreversible blindness globally. Qidengmingmu Capsule (QC) is a Chinese patent medicine used to treat DR, but the molecular mechanism of the treatment remains unknown. In this study, we identified and validated potential molecular mechanisms involved in the treatment of DR with QC via network pharmacology and molecular docking methods. The results of Ingredient-DR Target Network showed that 134 common targets and 20 active ingredients of QC were involved. According to the results of enrichment analysis, 2307 biological processes and 40 pathways were related to the treatment effects. Most of these processes and pathways were important for cell survival and were associated with many key factors in DR, such as vascular endothelial growth factor-A (VEGFA), hypoxia-inducible factor-1A (HIF-1Α), and tumor necrosis factor-α (TNFα). Based on the results of the PPI network and KEGG enrichment analyses, we selected AKT1, HIF-1α, VEGFA, TNFα and their corresponding active ingredients for molecular docking. According to the molecular docking results, several key targets of DR (including AKT1, HIF-1α, VEGFA, and TNFα) can form stable bonds with the corresponding active ingredients of QC. In conclusion, through network pharmacology methods, we found that potential biological mechanisms involved in the alleviation of DR by QC are related to multiple biological processes and signaling pathways. The molecular docking results also provide us with sound directions for further experiments.

scholarly journals Mechanism of Fei-Xian Formula in the Treatment of Pulmonary Fibrosis on the Basis of Network Pharmacology Analysis Combined with Molecular Docking Validation

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Xiao-Li Chen ◽  
Cheng Tang ◽  
Qing-Ling Xiao ◽  
Zhong-Hua Pang ◽  
Dan-Dan Zhou ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virus Infection ◽  
Pulmonary Fibrosis ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Core Network ◽  
Active Ingredients ◽  
Molecular Docking Study ◽  
The Core ◽  
Target Network

Objective. This study aimed to clarify the mechanism of Fei-Xian formula (FXF) in the treatment of pulmonary fibrosis based on network pharmacology analysis combined with molecular docking validation. Methods. Firstly, ingredients in FXF with pharmacological activities, together with specific targets, were identified based on the BATMA-TCM and TCMSP databases. Then, targets associated with pulmonary fibrosis, which included pathogenic targets as well as those known therapeutic targets, were screened against the CTD, TTD, GeneCards, and DisGeNet databases. Later, Cytoscape was employed to construct a candidate component-target network of FXF for treating pulmonary fibrosis. In addition, for nodes within the as-constructed network, topological parameters were calculated using CytoHubba plug-in, and the degree value (twice as high as the median degree value for all the nodes) was adopted to select core components as well as core targets of FXF for treating pulmonary fibrosis, which were subsequently utilized for constructing the core network. Furthermore, molecular docking study was carried out on those core active ingredients together with the core targets using AutoDock Vina for verifying results of network pharmacology analysis. At last, OmicShare was employed for enrichment analysis of the core targets. Results. Altogether 12 active ingredients along with 13 core targets were identified from our constructed core component-target network of FXF for the treatment of pulmonary fibrosis. As revealed by enrichment analysis, the 13 core targets mostly concentrated in regulating biological functions, like response to external stimulus (from oxidative stress, radiation, UV, chemical substances, and virus infection), apoptosis, cell cycle, aging, immune process, and protein metabolism. In addition, several pathways, like IL-17, AGE-RAGE, TNF, HIF-1, PI3K-AKT, NOD-like receptor, T/B cell receptor, and virus infection-related pathways, exerted vital parts in FXF in the treatment of pulmonary fibrosis. Conclusions. FXF can treat pulmonary fibrosis through a “multicomponent, multitarget, and multipathway” mean. Findings in this work lay foundation for further exploration of the FXF mechanism in the treatment of pulmonary fibrosis.

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 Study on the Mechanism of Ginkgo Seeds in Treating Bronchitis by Network Pharmacology

2021 ◽  
Vol 50 (5) ◽  
pp. 1433-1444
Author(s):  
Tingting Wu ◽  
Lihu Zhang ◽  
Dongdong Li ◽  
Tao Wu ◽  
Yan Jiang ◽  
...  
Keyword(s):  
Metabolic Pathway ◽  
Fluid Shear Stress ◽  
Molecular Networks ◽  
Network Pharmacology ◽  
Interleukin 17 ◽  
Biological Processes ◽  
Active Ingredients ◽  
Molecular Docking Study ◽  
Protein Targets ◽  
Proteins Interactions

In recent years, with the global environmental deterioration and air pollution, the incidence of bronchitis has increased year by year, and the sales of anti-bronchitis drugs are growing rapidly, mainly due to the long treatment cycle and the difficulty of curing. Developing available traditional Chinese medicines with significant curative effect against bronchitis would be a promising strategy; for instance, Ginkgo seeds, as the fruit of natural plant ginkgo, has been used in ancient times to cure coughs. However, the detailed mechanism of curing cough has not been shown yet. Investigate the mechanism of Ginkgo Semen in the treatment of bronchitis by establishing a series of molecular networks including active ingredients-targets, proteins interactions, biological functions, pathway, and biological processes of targets. In this study, the main active ingredients of Ginkgo seeds and the potential targets related to bronchitis could be obtained by retrieving corresponding database. The molecular docking study between active molecules and protein targets was performed by Glide 6.6. Subsequently, a total of forty potential targets were manually selected. Based on this, the ingredients-target network was constructed using Cytoscape software, as well as proteins interactions network combing with the String database. Finally, the molecular biological function, metabolic pathway, and biological processes of these forty targets were analyzed by Clue GO plug-in. The results indicated that these protein targets were closely related to lipid transport, positive regulation of DNA replication, cAMP metabolic pathway, and other processes, which played a vital role in the treatment of bronchitis by mediating interleukin 17, fluid shear stress and atherosclerosis, asthma, renin secretion, p53, and other signaling pathways. Among these targets, the two protein ALB (Albumin) and DHRS2 (Dehydrogenase 2) can interact with compounds more frequently, and the top three compounds ranked by the docking scores were amentoflavone, (+)-catechin-5-O-glucoside, and liquiritin, implying that these compounds might be used for the treatment of bronchitis. It is obvious that the pharmacological effect of Ginkgo seeds on bronchitis displayed a characteristic of multi-components, multi-targets, and multi-pathways. Nevertheless, the two protein targets and three compounds derived from Ginkgo seeds could be further used for the explanation for Ginkgo seeds in curing bronchitis. This research can provide a scientific basis for studying on the anti-bronchitis mechanism of Ginkgo seeds.

scholarly journals Mechanism of Action of Bu-Fei-Yi-Shen Formula in Treating Chronic Obstructive Pulmonary Disease Based on Network Pharmacology Analysis and Molecular Docking Validation

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Longchuan Wu ◽  
Yu Chen ◽  
Jiao Yi ◽  
Yi Zhuang ◽  
Lei Cui ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Mechanism Of Action ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Chronic Obstructive ◽  
Biological Functions ◽  
Active Ingredients ◽  
Obstructive Pulmonary Disease ◽  
The Core ◽  
Target Network

Objective. To explore the mechanism of action of Bu-Fei-Yi-Shen formula (BFYSF) in treating chronic obstructive pulmonary disease (COPD) based on network pharmacology analysis and molecular docking validation. Methods. First of all, the pharmacologically active ingredients and corresponding targets in BFYSF were mined by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, the analysis platform, and literature review. Subsequently, the COPD-related targets (including the pathogenic targets and known therapeutic targets) were identified through the TTD, CTD, DisGeNet, and GeneCards databases. Thereafter, Cytoscape was employed to construct the candidate component-target network of BFYSF in the treatment of COPD. Moreover, the cytoHubba plug-in was utilized to calculate the topological parameters of nodes in the network; then, the core components and core targets of BFYSF in the treatment of COPD were extracted according to the degree value (greater than or equal to the median degree values for all nodes in the network) to construct the core network. Further, the Autodock vina software was adopted for molecular docking study on the core active ingredients and core targets, so as to verify the above-mentioned network pharmacology analysis results. Finally, the Omicshare database was applied in enrichment analysis of the biological functions of core targets and the involved signaling pathways. Results. In the core component-target network of BFYSF in treating COPD, there were 30 active ingredients and 37 core targets. Enrichment analysis suggested that these 37 core targets were mainly involved in the regulation of biological functions, such as response to biological and chemical stimuli, multiple cellular life processes, immunity, and metabolism. Besides, multiple pathways, including IL-17, Toll-like receptor (TLR), TNF, and HIF-1, played certain roles in the effect of BFYSF on treating COPD. Conclusion. BFYSF can treat COPD through the multicomponent, multitarget, and multipathway synergistic network, which provides basic data for intensively exploring the mechanism of action of BFYSF in treating COPD.

scholarly journals Molecular Analysis of AFP and HSA Interactions with PTEN Protein

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Mingyue Zhu ◽  
Bo Lin ◽  
Peng Zhou ◽  
Mengsen Li
Keyword(s):  
Molecular Docking ◽  
Molecular Mechanisms ◽  
Docking Study ◽  
Phosphatidylinositol 3 Kinase ◽  
Molecular Docking Study ◽  
Pten Protein ◽  
Phosphatase And Tensin Homolog ◽  
Tensin Homolog ◽  
Significant Homology ◽  
Modeling Data

Human cytoplasmic alpha-fetoprotein (AFP) has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA), but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway, but HSA plays a key role as a transport protein. To probe their molecular mechanisms, we have applied colocalization, coimmunoprecipitation (co-IP), and molecular docking approaches to analyze the differences between AFP and HSA. The data from colocalization and co-IP displayed a strong interaction between AFP and PTEN (phosphatase and tensin homolog), demonstrating that AFP did bind to PTEN, but HSA did not. The molecular docking study further showed that the AFP domains I and III could contact with PTEN.In siliconsubstitutions of AFP binding site residues at position 490M/K and 105L/R corresponding to residues K490 and R105 in HSA resulted in steric clashes with PTEN residues R150 and K46, respectively. These steric clashes may explain the reason why HSA cannot bind to PTEN. Ultimately, the experimental results and the molecular modeling data from the interactions of AFP and HSA with PTEN will help us to identify targets for designing drugs and vaccines against human hepatocellular carcinoma.

scholarly journals Exploration of the mechanism of Ziyin Tongluo Formula on preventing and treating postmenopausal osteoporosis based on the network pharmacology and molecular docking

2020 ◽  
Author(s):  
Rong-Bin Chen ◽  
Ying-Dong Yang ◽  
Kai Sun ◽  
Shan Liu ◽  
Wei Guo ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Postmenopausal Osteoporosis ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Active Ingredients ◽  
Active Compounds ◽  
Core Proteins ◽  
Key Genes

Abstract Background: Postmenopausal osteoporosis (PMOP) is a global chronic and metabolic bone disease, which poses huge challenges to individuals and society. Ziyin Tongluo Formula (ZYTLF) has been proved effective in the treatment of PMOP. However, the material basis and mechanism of ZYLTF against PMOP have not been thoroughly elucidated.Methods: Online databases were used to identify the active ingredients of ZYTLF and corresponding putative targets. Genes associated with PMOP were mined, and then mapped with the putative targets to obtain overlapping genes. Multiple networks were constructed and analyzed, from which the key genes were selected. The key genes were imported to the DAVID database to performs GO and KEGG pathway enrichment analysis. Finally, AutoDock Tools and other software were used for molecular docking of core compounds and key proteins. Results: Ninety-two active compounds of ZYTLF corresponded to 243 targets, with 129 target genes interacting with PMOP, and 50 key genes were selected. Network analysis showed the top 5 active ingredients including quercetin, kaempferol, luteolin, scutellarein, and formononetin., and the top 50 key genes such as VEGFA, MAPK8, AKT1, TNF, ESR1. Enrichment analysis uncovered two significant types of KEGG pathways in PMOP, hormone-related signaling pathways (estrogen , prolactin, and thyroid hormone signaling pathway) and inflammation-related pathways (TNF, PI3K-Akt, and MAPK signaling pathway). Moreover, molecular docking analysis verified that the main active compounds were tightly bound to the core proteins, further confirming the anti-PMOP effects. Conclusions: Based on network pharmacology and molecular docking technology, this study initially revealed the mechanisms of ZYTLF on PMOP, which involves multiple targets and multiple pathways.

scholarly journals Dissecting the Mechanism of Yuzhi Zhixue Granule on Ovulatory Dysfunctional Uterine Bleeding by Network Pharmacology and Molecular Docking

2020 ◽  
Author(s):  
Jialin Li ◽  
Hua Luo ◽  
Xinkui Liu ◽  
Jingyuan Zhang ◽  
Wei Zhou ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Therapeutic Target ◽  
Molecular Mechanisms ◽  
Therapeutic Targets ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Uterine Bleeding ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Dysfunctional Uterine Bleeding

Abstract 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.

scholarly journals A Network Pharmacology Approach to Determine the Mechanisms of Action of Shuangshen Granules in Suppressing Pancreatic Cancer Precursor Lesions

2020 ◽  
Author(s):  
Juling Jiang ◽  
Zhenhua Zhang ◽  
Yixin Yuan ◽  
Runzhi Qi ◽  
Shuntai Chen ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Molecular Docking ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Mechanisms Of Action ◽  
Network Pharmacology ◽  
Precursor Lesions ◽  
Active Components ◽  
Docking Simulations ◽  
Improve Patient Survival

Abstract Background and purpose: Pancreatic cancer is an insidious and highly lethal disease. Recognition and treatment of pancreatic cancer precursor lesions (PCPL) are important measures and can improve patient survival rate. Shuangshen Granules (SSG) have been prescribed for use in clinical practice for more than seven years and are widely used to treat the precursor lesions of various tumours. In this study, we used network pharmacology to explore the pharmacological mechanisms through which SSG suppress PCPL. We aimed to provide a basis for further research and the development of small, molecular, natural chemical drugs.Methods: We first searched databases and screened the bioactive components of SSG and the related targets acting on PCPL to construct a component-target network. Then, network topology analysis was used to analyse the hub target of SSG acting on PCPL. Enrichment analyses of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were also performed to determine the potential pathways. Finally, molecular docking simulations were carried out to investigate the interactions between PCPL-target proteins and the active components of SSG.Results: Seven of the main components of SSG affected PCPL, with 100 key targets including 16 hub targets. In addition, GO and KEGG enrichment analysis revealed that SSG regulated 111 molecular functions, 46 cellular components, 2334 biological processes, and 144 related signalling pathways, of which 26 were closely related to PCPL. Results of molecular docking analysis showed that the PCPL-related targets had strong binding properties with the active components of SSG, quercetin, and ginsenoside rh2, mainly TNF, IL-6, AKT1, TP53, and EGFR.Conclusion: This study has revealed the pharmacological and molecular mechanisms through which SSG acts on PCPL. It also provides powerful evidence to support the exploration of the pharmacological mechanisms of action and clinical applications of traditional Chinese medicine.

scholarly journals Network Pharmacology-based Investigation of the Underlying Mechanism of Panax notoginseng Treatment of Diabetic Retinopathy

2020 ◽  
Vol 23 (4) ◽  
pp. 334-344
Author(s):  
Chunli Piao ◽  
Zheyu Sun ◽  
De Jin ◽  
Han Wang ◽  
Xuemin Wu ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Molecular Mechanisms ◽  
Topological Analysis ◽  
Enrichment Analysis ◽  
Panax Notoginseng ◽  
Diabetic Microangiopathy ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Annotation Database ◽  
Cox 2

Background: Panax notoginseng, a Chinese herbal medicine, has been widely used to treat vascular diseases. Diabetic retinopathy (DR) is one of the complications of diabetic microangiopathy. According to recent studies, the application of Panax notoginseng extract and related Chinese patent medicine preparations can significantly improve DR. However, the pharmacological mechanisms remain unclear. Therefore, the purpose of this study was to decipher the potential mechanism of Panax notoginseng treatment of DR using network pharmacology. Methods: We evaluated and screened the active compounds of Panax notoginseng using the Traditional Chinese Medicine Systems Pharmacology database and collected potential targets of the compounds by target fishing. A multi-source database was also used to organize targets of DR. The potential targets as the treatment of DR with Panax notoginseng were then obtained by matching the compound targets with the DR targets. Using protein-protein interaction networks and topological analysis, interactions between potential targets were identified. In addition, we also performed gene ontology-biological process and pathway enrichment analysis for the potential targets by using the Biological Information Annotation Database. Results: Eight active ingredients of Panax notoginseng and 31 potential targets for the treatment of DR were identified. The screening and enrichment analysis revealed that the treatment of DR using Panax notoginseng primarily involved 28 biological processes and 10 related pathways. Further analyses indicated that angiogenesis, inflammatory reactions, and apoptosis may be the main processes involved in the treatment of DR with Panax notoginseng. In addition, we determined that the mechanism of intervention of Panax notoginseng in treating DR may involve five core targets, VEGFA, MMP-9, MMP-2, FGF2, and COX-2. Conclusion: Panax notoginseng may treat diabetic retinopathy through the mechanism of network pharmacological analysis. The underlying molecular mechanisms were closely related to the intervention of angiogenesis, inflammation, and apoptosis with VEGFA, MMP-9, MMP-2, FGF2, and COX-2 being possible targets.

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