Potential active compounds and mechanisms of Shen-Qi-Yi-Chang granule for the treatment of colorectal cancer: an analysis of network pharmacology and molecular docking

2021 ◽  
Vol 3 (3) ◽  
pp. 13
Author(s):  
JiaLin Gu ◽  
JiaLin Yu ◽  
ZiWei Song ◽  
GuoLi Wei ◽  
Yi Ji ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Docking ◽  
Network Pharmacology ◽  
Active Compounds

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.

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 Exploring the Mechanisms Underlying the Therapeutic Effect of Xixin Decoction on Alzheimer's Disease Based on Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
Zhuo Zhang ◽  
Jiang-lin Xu ◽  
Ming-qing Wei ◽  
Ting Li ◽  
Jing Shi
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Docking ◽  
Signaling Pathway ◽  
Therapeutic Effect ◽  
Mapk Signaling ◽  
Network Pharmacology ◽  
Receptor Interaction ◽  
Ppi Network ◽  
Active Compounds

Abstract Background and objective: Alzheimer’s disease (AD) has been a worldwide problem, not only the treatment but also the prevention. As a commonly used Chinese Herbal Formula, Xixin Decoction (XXD) has significant therapeutic effect on AD but without clear mechanism. This study was aimed to predict the main active compounds and targets of XXD in the treatment of AD and to explore the potential mechanism by using network pharmacology and molecular docking. Methods: The compounds of XXD were searched in the TCMSP and the TCMID database, and the active compounds were screened based on the ADME model and SwissADME platform. SwissTargetPrediction platform was used to search for the primary candidate targets of XXD. The common targets related to AD obtained by two databases (GeneCards and DisGeNET) were determined as candidate proteins involved in AD. To acquire the related targets of XXD in the treatment of AD, the target proteins related to AD were intersected with the predicted targets of XXD. Then these overlapping targets were imported into the STRING database to build PPI network including hub targets; Cytoscape 3.7.2 software was used to construct the topology analysis for the herb-compound-target network diagram while one of it’s plug-in called CytoNCA was used to calculate degree value to screen the main active compounds of XXD. GO and KEGG pathway enrichment analyses were conducted to explore the core mechanism of action and biological pathways associated with the decoction via Metascape platform. We used AutoDock Vina and PyMOL 2.4.0 softwares for molecular docking of hub targets and main compounds.Results: We determined 114 active compounds which meet the conditions of ADME screening, 973 drug targets, and 973 disease targets. However, intersection analysis screened out 208 shared targets. PPI network identified 9 hub targets, including TP53, PIK3CA, MAPK1, MAPK3, STAT3, AKT1, etc. The 10 main active compounds play a major role in treatment of AD by XXD. Hub targets were found to be enriched in 10 KEGG pathways, involving the Pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, Alzheimer's disease, Neuroactive ligand-receptor interaction, Dopaminergic synapse, Serotonergic synapse and MAPK signaling pathway. The docking results indicated that the 8 hub targets exhibit good binding activity with the 9 main active compounds of XXD.Conclusions: We found the advantages of multi-compounds-multi-targets-multi-pathways regulation to reveal the mechanism of XXD for treating AD based on network pharmacology and molecular docking. Our study provided a theorical basis for further clinical application and experimental research of XXD for anti-AD in the future.

scholarly journals Network pharmacology based research into the effect and mechanism of Yinchenhao Decoction against Cholangiocarcinoma

2021 ◽  
Author(s):  
Zhiqiang Chen ◽  
Tong Lin ◽  
Xiaozhong Liao ◽  
Zeyun Li ◽  
Ruiting Lin ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Experimental Results ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Active Components ◽  
Active Compounds ◽  
Apoptosis Rate

Abstract Background: Cholangiocarcinoma refers to an epithelial cell malignancy with poor prognosis. Yinchenhao decoction (YCHD) showed positive effects on cancers, and associations between YCHD and cholangiocarcinoma remain unclear. This study aimed to screen out the effective active components of Yinchenhao decoction (YCHD) using network pharmacology, estimate their potential targets, screen out the pathways, as well as delve into the potential mechanisms on treating cholangiocarcinoma. Methods: By the traditional Chinese medicine system pharmacology database and analysis platform (TCMSP) as well as literature review, the major active components and their corresponding targets were estimated and screened out. Using the software Cytoscape 3.6.0, a visual network was established using the active components of YCHD and the targets of cholangiocarcinoma. Based on STRING online database, the protein interaction network of vital targets was built and analyzed. With the Database for Annotation, Visualization, and Integrated Discovery (DAVID) server, the gene ontology (GO) biological processes and the Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways of the targets enrichment were performed. The AutoDock Vina was used to perform molecular docking and calculate the binding affinity. The PyMOL software was utilized to visualize the docking results of active compounds and protein targets. In vivo experiment, the IC50 values and apoptosis rate in PI-A cells were detected using CCK-8 kit and Cell Cycle Detection Kit. The predicted targets were verified by the real-time PCR and western blot methods. Results: 32 effective active components with anti-tumor effects of YCHD were sifted in total, covering 209 targets, 96 of which were associated with cancer. Quercetin, kaempferol, beta-sitosterol, isorhamnetin, and stigmasterol were identified as the vital active compounds, and AKT1, IL6, MAPK1, TP53 as well as VEGFA were considered as the major targets. The molecular docking revealed that these active compounds and targets showed good binding interactions. These 96 putative targets exerted therapeutic effects on cancer by regulating signaling pathways (e.g., hepatitis B, the MAPK signaling pathway, the PI3K-Akt signaling pathway, and MicroRNAs in cancer). Our in vivo experimental results confirmed that YCHD showed therapeutic effects on cholangiocarcinoma by decreasing IC50 values, down-regulating apoptosis rate of cholangiocarcinoma cells, and lowering protein expressions. Conclusion:As predicted by network pharmacology strategy and validated by the experimental results, YCHD exerts anti-tumor effectsthrough multiple components, targets, and pathways, thereby providing novel ideas and clues for the development of preparations and the treatment of cholangiocarcinoma.

scholarly journals Study on the Multitarget Mechanism of Sanmiao Pill on Gouty Arthritis Based on Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-11 ◽  
Author(s):  
Huiqin Qian ◽  
Qianqian Jin ◽  
Yichen Liu ◽  
Ning Wang ◽  
Yuru Chu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Gouty Arthritis ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Receptor Signaling ◽  
Active Compounds ◽  
Receptor Signaling Pathway ◽  
Compound Target

Sanmiao pill (SMP), a Chinese traditional formula, had been used to treat gouty arthritis (GA). However, the active compounds and underlying mechanism remained unclear. Hence, network pharmacology and molecular docking were utilized to explore bioactive compounds and potential mechanism of action of SMP in treating GA. In the study, the compounds of SMP, corresponding targets, and GA-related targets were mined from various pharmacological databases. Then, herb-compound-target, compound-target, PPI, and target-pathway networks were constructed. Ultimately, molecular docking was carried out to verify the predicted results. The results indicated that 47 active compounds, 338 targets, and 144 disease targets were collected. Network analysis implied that Phellodendron chinense Schneid. played a vital role in the whole formula. Moreover, 7 compounds (quercetin, kaempferol, wogonin, rutaecarpine, baicalein, beta-sitosterol, and stigmasterol) and 4 targets (NFKB1, RELA, MAPK1, and TNF) might be the kernel compounds and targets of SMP against GA. According to GOBP and KEGG pathway enrichment analysis and target-pathway network, SMP might exert a therapeutic role in GA by regulating numerous biological processes and pathways, including lipopolysaccharide-mediated signaling pathway, positive regulation of transcription, Toll-like receptor signaling pathway, JAK-STAT signaling pathway, NOD-like receptor signaling pathway, and MAPK signaling pathway. The results of molecular docking showcased that 11 pairs of compound with targets had tight binding strength. Thereinto, 4 compounds of MAPK1 and 5 compounds of NFKB1 possessed a better combination, suggesting that MAPK1 and NFKB1 might be considered as therapeutic targets in treatment of GA. This study verified that SMP had synergistic effect on GA by multicomponents, multitargets, and multipathways.

Exploring the mechanisms of Drynariae Rhizoma on treating memory impairment through network pharmacology

2021 ◽  
Author(s):  
Wangmi Liu ◽  
Jiayan Wu
Keyword(s):  
Molecular Docking ◽  
Nerve Growth Factor ◽  
Chinese Medicine ◽  
Growth Factor ◽  
Traditional Chinese Medicine ◽  
Memory Impairment ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Major Health Problem ◽  
Nerve Growth

Abstract Background Memory impairment continues to be a major health problem and increases with age, especially in the elderly population worldwide. However, a causal mechanism has not been clearly identified. Currently, an interaction between bone and brain, the so-called “bone-brain crosstalk,” has emerged. We used a network pharmacology approach to explore the potential mechanisms of Drynariae Rhizoma (DR), a traditional Chinese medicine for fracture treatment, for therapeutic intervention of human conditions associated with memory impairment. Methods The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform was used to screen out the active compounds of DR, and the targets of the active compounds were predicted using PharmMapper. Targets related to memory impairment were downloaded from the DisGeNET database. The compound-target network and protein-protein interaction network were built by NetworkAnalyst and Cytoscape software. Gene ontology analysis and Reactome pathway enrichment analysis were performed using NetworkAnalyst. SYBYL-X software was used to perform molecular docking simulation. Results Our study demonstrated that DR had 7 active compounds. There were 60 target genes related to these active compounds as well as to memory impairment. Signalling by nerve growth factor was among the top 3 enriched Reactome terms. Akt1 was an important signalling hub gene belonging to signalling by nerve growth factor pathway. Molecular docking results showed that the one of the active compounds, xanthogalenol, exhibited acceptable affinities to Akt1. Conclusion This study demonstrated the molecular mechanism that DR may alleviate memory impairment via regulation of Akt1 and signalling by nerve growth factor pathway. These results offer new ideas in searching for novel strategies for the treatment of memory impairment.

scholarly journals Exploring the Active Compounds of Traditional Mongolian Medicine Baolier Capsule (BLEC) in Patients with CAD Based on Network Pharmacology Analysis and Molecular Docking Method

2021 ◽  
Author(s):  
Mengqiu Wei ◽  
Jun Liu ◽  
Jun Lai ◽  
Meifang Leng ◽  
Zebing Ye ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Topological Analysis ◽  
Network Pharmacology ◽  
Pharmacological Effects ◽  
Ppi Network ◽  
Active Ingredients ◽  
Active Compounds ◽  
Docking Method ◽  
Traditional Mongolian Medicine ◽  
Molecular Docking Method

Abstract Baolier Capsule (BLEC) is a Traditional Mongolian Medicine comprising of fifteen herbs. In China, this medicine has been used to treat CAD for many years. However, the molecular mechanism of BLEC in the treatment of CAD is not yet fully understood. Hence, this study aims to illustrate the synergistic mechanism of BLEC in the treatment of CAD by using network pharmacology method and molecular docking. Searching and screening the active ingredients of different herbs in BLEC and target genes related to CAD in multiple databases. Subsequently, STRING and Cytoscape were used to analyze and construct the PPI network. In addition, clustering and topological analysis are used to analyze the PPI network. Then, using R project for GO and KEGG enrichment analysis. Finally, AutoDock was used to verify the binding ability between the active ingredient and the key target through molecular docking. There are 144 active components and 80 CAD-related targets that are identified in BLEC in the treatment of CAD. What is more, 8 core genes (AKT1, EGFR, FOS, etc.) were obtained by clustering and topological analysis. Further, GO and KEGG analysis showed that fluid shear stress and atherosclerosis is the key pathways for RWW to treat CAD. These results were validated by molecular docking method. Our research firstly revealed the basic pharmacological effects and relevant mechanisms of the BLEC in the treatment of CAD. The prediction results might facilitate the development of BLEC or its active compounds as alternative therapy for CAD. Our research first revealed the basic pharmacological effects and related mechanisms of BLEC in the treatment of CAD. The predicted results provide some theoretical support for BLEC or its important active ingredients to treat CAD.

scholarly journals Network Pharmacology and Molecular Docking-Based Analysis on Bioactive Anticoronary Heart Disease Compounds in Trichosanthes kirilowii Maxim and Bulbus allii Macrostemi

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Yi-Ding Yu ◽  
Wang-Jun Hou ◽  
Juan Zhang ◽  
Yi-Tao Xue ◽  
Yan Li
Keyword(s):  
Insulin Resistance ◽  
Heart Disease ◽  
Molecular Docking ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
Ethyl Linoleate ◽  
Arachidonic Acid Metabolism ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Trichosanthes Kirilowii

Trichosanthes kirilowii Maxim. and Bulbus allii Macrostemi are the components of Gualou Xiebai decoction (GLXB), a commonly used herbal combination for the treatment of coronary heart disease (CHD) in traditional Chinese medicine. Although GLXB is associated with a good clinical effect, its active compounds and mechanism of action remain unclear, which limits its clinical application and the development of novel drugs. In this study, we explored key compounds, targets, and mechanisms of action for GLXB in the treatment of CHD using the network pharmacology approach. We identified 18 compounds and 21 action targets via database screening. Enrichment analysis indicated that the effects of GLXB in patients with CHD are primarily associated with the regulation of signalling pathways for tumour necrosis factor, nuclear factor-kappa B, hypoxia-inducible factor-1, arachidonic acid metabolism, and insulin resistance. GLXB thus exerts anti-inflammatory, antihypoxic, and antiagglutinating effects; regulates lipid metabolism; and combats insulin resistance in CHD via these pathways, respectively. After reverse targeting, we observed that the main active compounds of GLXB in the treatment of CHD were quercetin, naringenin, β-sitosterol, ethyl linolenate, ethyl linoleate, and prostaglandin B1. To explore the potential of these compounds in the treatment of CHD, we verified the affinity of the compounds and targets via molecular docking analysis. Our study provides a bridge for the transformation of natural herbs and molecular compounds into novel drug therapies for CHD.

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