scholarly journals In silico screening of potentially bioactive-anti-functional dyspepsia constituents of Magnoliae officinalis Cortex based on molecular docking and network pharmacology

2020 ◽  
Vol 19 (8) ◽  
pp. 1723-1730
Author(s):  
Jun He ◽  
Longjing Wang ◽  
Guanghua Lv ◽  
Yingfang Wei ◽  
Meng Yang ◽  
...  

Purpose: To screen for bioactive anti-functional dyspepsia compounds from Magnoliae officinalis Cortex (Hou Po) and to identify the mechanism(s) of action involved.Methods: The compounds of Hou Po were collected from the literature. The related target proteins were identified from DrugBank. Through  “Libdock” module of Discovery Studio 3.5, the compounds were matched with related target proteins. Taking the Libdock score of the original ligand with target protein as standard, components with higher scores than this standard were considered as potential bioactive compounds. Based on Cytoscape software, the interaction networks of the bioactive compound-target protein complexes were mapped. On the other hand, the online DAVID database was used to analyze the GO enrichment and KEGG pathway of each target.Results: A total of 199 chemical constituents and 13 correlated target proteins were obtained. One hundred and thirty-nine (139) potential bioactive constituents were acquired based on molecular docking. Thirty-one (31) bioactive compounds were selected based on degree values in networkanalysis. “Palmitone” and “magnolignan G” which had the highest degree values were considered promising and leading compounds. The result of gene enrichment analysis showed that the bioactive compounds exerted their effects mainly via “neuroactive ligand-receptor interaction” pathway and “Cholinergic synapse” pathways.Conclusion: Based on molecular docking and network pharmacology technique, the material basis for the use of Hou Po in the treatment of FD has been revealed. This finding provides a useful guide in the development of Hou Po-based anti-FD drugs. Keywords: Magnolia officinalis, Hou Po, Molecular docking, Functional dyspepsia, Network pharmacology

2021 ◽  
Vol 12 ◽  
Author(s):  
Jia Chen ◽  
Lin-Fu Li ◽  
Xiao-Ru Hu ◽  
Feng Wei ◽  
Shuangcheng Ma

Licorice (Glycyrrhiza spp.) is used widely in traditional Chinese medicine (TCM) due to its numerous pharmacologic effects. However, the mechanisms of action of the chemical constituents of licorice and their structure–function relationships are not fully understood. To address these points, we analyzed the chemical compounds in licorice listed in the TCM Systems Pharmacology database and TCM Integrated database. Target proteins of the compounds were predicted using Integrative Pharmacology-based Research Platform of TCM v2.0. Information on the pharmacologic effects of licorice was obtained from the 2020 Chinese Pharmacopoeia, and disease-related genes that have been linked to these effects were identified from the Encyclopedia of TCM database. Pathway analyses using the Kyoto Encyclopedia of Genes and Genomes database were carried out for target proteins, and pharmacologic networks were constructed based on drug target–disease-related gene and protein–protein interactions. A total of 451 compounds were analyzed, of which 211 were from the medicinal parts of the licorice plant. The 241 putative targets of 106 bioactive compounds in licorice comprised 52 flavonoids, 47 triterpenoids, and seven coumarins. Four distinct pharmacologic effects of licorice were defined: 61 major hubs were the putative targets of 23 compounds in heat-clearing and detoxifying effects; 68 were targets of six compounds in spleen-invigorating and qi-replenishing effects; 28 were targets of six compounds in phlegm-expulsion and cough-suppressant effects; 25 compounds were targets of six compounds in spasm-relieving and analgesic effects. The major bioactive compounds of licorice were identified by ultra-high-performance liquid chromatography–quadrupole time-of-flight–tandem mass spectrometry. The anti-inflammatory properties of liquiritin apioside, liquiritigenin, glycyrrhizic acid and isoliquiritin apioside were demonstrated by enzyme-linked immunosorbent assay (ELISA) and Western blot analysis. Liquiritin apioside, liquiritigenin, isoliquiritin, isoliquiritin apioside, kaempferol, and kumatakenin were the main active flavonoids, and 18α- and 18β-glycyrrhetinic acid were the main active triterpenoids of licorice. The former were associated with heat-clearing and detoxifying effects, whereas the latter were implicated in the other three pharmacologic effects. Thus, the compounds in licorice have distinct pharmacologic effects according to their chemical structure. These results provide a reference for investigating the potential of licorice in treatment of various diseases.


2020 ◽  
Vol 23 (5) ◽  
pp. 419-432
Author(s):  
Yao Wang ◽  
Junbo Zou ◽  
Yanzhuo Jia ◽  
Yulin Liang ◽  
Xiaofei Zhang ◽  
...  

Aim and Objective: The common disease of insomnia has complex and diverse clinical manifestations. Lavender represents an effective treatment of insomnia, but the molecular mechanism underlying the effectiveness of this treatment is not clear. The purpose of this study is to investigate the active components, target proteins and molecular pathways of lavender in the treatment of insomnia, thus explaining its possible mechanism. Materials and Methods: Firstly, 54 active components of lavender were identified by gas chromatography-mass spectrometry (GC-MS). The target protein of lavender was predicted by the Traditional Chinese Medicine System Pharmacological Database and Analysis Platform and the SwissTargetPredicating tool, and the target protein of insomnia was predicted by the DisGeNET and DrugBank databases. Then, the "component-target-disease" network diagram was constructed using the Cytoscape 3.7.1 software. KEGG and GO enrichments were analyzed using the R statistical language. Finally, the key target proteins were verified by collecting and verifying the target protein GEO data using the Discovery Studio 3.5 molecular docking verification software. Results: 906 target proteins of lavender were predicted by the Traditional Chinese Medicine System Pharmacological Database and Analysis Platform and the SwissTargetPredicating tool, and 182 insomnia target proteins were predicted by the DisGeNET and DrugBank databases. The results of GO enrichment analysis showed that it included the reaction process of ammonium ion, the regulation of the membrane potential and the secretion of catecholamine, while the results of KEGG enrichment included the calcium signaling pathway, serotonin synapse, morphine addiction and many more. Finally, using the Discovery Studio3.5 molecular docking verification software, it was verified that the key target proteins are ADRB1 and HLA-DRB1. Conclusion: The components in the lavender essential oil include the Ethyl 2-(5-methyl-5-vinyltetrahydrofuran- 2-yl)propan-2-ylcarbonate (0.774); 5-Oxatricyclo[8.2.0.04,6]dodecane, 4,12,12-trimethyl- 9-methylene-, (1R,4R,6R,10S)-(0.147); P-Cymen-7-ol (0.063); .alpha-Humulenem (0.317); Acetic acid, hexyl ester (1.374); etc. The role lavender plays in the treatment of insomnia might be accomplished through the regulation of the key targets ADRB1 and HLA-DRB1.


2021 ◽  
Vol 18 (10) ◽  
pp. 2125-2131
Author(s):  
Qing Zhang ◽  
Ruolan Li ◽  
Jia Liu ◽  
Wei Peng ◽  
Yongxiang Gao ◽  
...  

Purpose: To investigate by in silico screening the anti-inflammatory constituents of Cinnamomum cassia twigs. Methods: Information on the constituents of C. cassia twigs was retrieved from the online Traditional Chinese Medicines (TCM) database and literature. Inflammation-related target proteins were identified from DrugBank, Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), Genetic Association Database (GAD), and PharmGKB. The identified compounds were filtered by Lipinski’s rules with Discovery Studio software. The “Libdock” module was used to perform molecular docking; LibdockScores and default cutoff values for hydrogen bonds and van der Waals interactions were recorded. LibdockScores between the prototype ligand and target protein were set as the threshold; compounds with higher LibdockScores than threshold were regarded as active compounds. Cytoscape software was used to construct active constituent-target protein interaction networks. Results: Sixty-nine potential inflammatory constituents with good drug-like properties in C. cassia twigs were screened in silico based on molecular docking and network pharmacology analysis. JAK2, mPEGS-1, COX-2, IL-1β, and PPARγ were considered the five most important target proteins. Compounds such as methyl dihydromelilotoside, hierochin B, dihydromelilotoside, dehydrodiconiferyl alcohol, balanophonin, phenethyl (E)-3-[4-methoxyphenyl]-2-propenoate, quercetin, and luteolin each interacted with more than six of the selected target proteins. Conclusion: C. cassia twigs possess active compounds with good drug-like properties that can potentially be developed to treat inflammation with multi-components on multi-targets.


2020 ◽  
Vol 22 (9) ◽  
pp. 584-598 ◽  
Author(s):  
Qing Zhang ◽  
Ruolan Li ◽  
Wei Peng ◽  
Mengmeng Zhang ◽  
Jia Liu ◽  
...  

Aim and Objective: This study was designed to explore the active compounds and significant pathways of Guizhi-Shaoyao-Zhimu decoction (GSZD) for treating diabetes mellitus using molecular docking combined with network pharmacology. Materials and Methods: Chemical constituents of GSZD and diabetes-related target proteins were collected from various databases. Then, compounds were filtered by Lipinski’s and Veber’s rules with Discovery studio software. The “Libdock” module was used to carry out molecular docking, and LibDockScores, default cutoff values for hydrogen bonds, and van der Waals interactions were recorded. LibDockScore of the target protein and its prototype ligand was considered as the threshold, and compounds with higher LibDockScores than the threshold were regarded as the active constituents of GSZD. Cytoscape software was used to construct the herb-active molecule-target interaction network of GSZD. ClueGO and CluePedia were applied to enrich the analysis of the biological functions and pathways of GSZD. Results: A total of 275 potential active compounds with 57 possible pathways in GSZD were identified by molecular docking combined with network pharmacology. TEN, INSR, PRKAA2, and GSK3B are the four most important target proteins. Gancaonin E, 3'-(γ,γ-dimethylallyl)-kievitone, aurantiamide, curcumin and 14-O-cinnamoylneoline, could interact with more than 14 of the selected target proteins. Besides, 57 potential pathways of GSZD were identified, such as insulin signaling pathway, metabolites and energy regulation, glucose metabolic process regulation, and positive regulation of carbohydrate metabolic process, etc. Conclusion: These results showed that molecular docking combined with network pharmacology is a feasible strategy for exploring bioactive compounds and mechanisms of Chinese medicines, and GSZD can be used to effectively treat diabetes through multi-components and multi-targets & pathways.


2021 ◽  
Author(s):  
yanni yang ◽  
yirixiati aihaiti ◽  
peng xu ◽  
haishi zheng

Abstract Purpose:To explore the potential target proteins underlying the effect of Angelicae Pubescentis Radix(APR) on rheumatoid arthritis (RA) using a network pharmacology and molecular docking approach .Methods:First, the active components and target proteins of APR and RA related disease targets were obtained from the TCMSP, Gene Card,OMIM,DisGeNET and STRING databases. Then the active ingredient target in the RA network diagram was drawn using Cytoscape 3.7.1 software. Protein-protein interaction analysis, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analyses were carried out using the STRING and David databases. The crystal structures of RA related targets were retrieved from the RCSB PDB database. Finally, the potential active compounds and their related targets were validated using molecular docking technology.Results: Five active components of Angelicae Pubescentis Radix(APR) were screened out, including ammidin, isoimperatorin, beta-sitosterol, O-acetylcolumbianetin and angelicone and 80 key targets including MAPK8,EGFR,PTGS2,CASPASE3,MTOR,SRC,KDR,MAPK1,NOS3 and MAPK14, etc were obtained. GO enrichment analysis showed that 222 biological processes, 34 cell components and 72 molecular functions were identified; KEGG analysis showed that the targets of APR in the treatment of RA were significantly enriched in pathways in cancer, the PI3K−Akt signaling pathway, Proteoglycans in cancer, osteoclast differentiation, neuroactive ligand−receptor interaction, tuberculosis,TNF signaling pathway, serotonergic synapse, Rap1 signaling pathway,cAMP signaling pathway. The results of molecular docking showed that ammidin, isoimperatorin, beta-sitosterol, O-acetylcolumbianetin and angelicone had strong affinity for PTGS2, EGFR and MAPK8.Conclusion: APR treats RA through the characteristics of multi-component, multi-target and multi-pathway regulation.


Author(s):  
Feng Xu ◽  
Xiangpei Wang ◽  
Xiujuan Wei ◽  
Teng Chen ◽  
Hongmei Wu

Background: Musa basjoo pseudostem juice (MBSJ) is a well-known Chinese medicine, and Miao people use MBSJ to treat diabetes. In this work, the active ingredients and molecular mechanism of MBSJ against diabetes were explored. Methods: Anti-diabetic activity of MBSJ was evaluated using diabetic rats, and then the ingredients in the small-polar parts of MBSJ were analyzed by gas chromatography-mass spectrometer (GC-MS). Targets were obtained from several databases to develop the "ingredient-target-disease" network by Cytoscape. A collaborative analysis was carried out using the tools in Cytoscape and R packages, and molecular docking was also performed. Results: MBSJ improved the oral glucose tolerance and insulin tolerance, and reduced fasting blood glucose, glycosylated hemoglobin, total cholesterol, triglyceride, and low-density lipoprotein levels in the serum of diabetic rats. 13 potential compounds were identified by GC-MS for subsequent analysis, including Dibutyl phthalate, Oleamide, Stigmasterol, Stigmast-4-en-3-one, etc. The anti-diabetic effect of MBSJ was related to multiple signaling pathways, including Neuroactive ligand-receptor interaction, Phospholipase D signaling pathway, Endocrine resistance, Rap1 signaling pathway, EGFR tyrosine kinase inhibitor resistance, etc. Molecular docking at least partially verified the screening results of network pharmacology. Conclusion: MBSJ had good anti-diabetic activity. The small-polar parts of MBSJ were rich in anti-diabetic active ingredients. Furthermore, the analysis results showed that the anti-diabetic effect of the small-polar parts of MBSJ may be the result of multiple components, multiple targets, and multiple pathways. The current research results can provide important support for studying the active ingredients and exploring the underlying mechanism of MBSJ against diabetes.


2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Yangyun Wang ◽  
Wandong Yu ◽  
Chaoliang Shi ◽  
Wei Jiao ◽  
Junhong Li ◽  
...  

Purpose. We aimed to find the possible key targets of Yougui pill and Buzhong Yiqi decoction for the treatment of sexual dysfunction. Materials and Methods. The composition of Yougui pill combined with Buzhong Yiqi decoction was obtained, and its effective components of medicine were screened using ADME; the component target proteins were predicted and screened based on the TCMSP and BATMAN databases. Target proteins were cross-validated using the CTD database. We performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for target proteins using the Cytoscape plugin ClueGO + CluePedia and the R package clusterProfiler, respectively. Subsequently, protein-protein interaction (PPI) analyses were conducted using the STRING database. Finally, a pharmacological network was constructed. Results. The pharmacological network contained 89 nodes and 176 relation pairs. Among these nodes, there were 12 for herbal medicines (orange peel, licorice, Eucommia, Aconite, Astragalus, Chinese wolfberry, yam, dodder seed, ginseng, Cornus officinalis, Rehmannia, and Angelica), 9 for chemical components (18-beta-glycyrrhetinic acid, carvacrol, glycyrrhetinic acid, higenamine, nobilin, quercetin, stigmasterol, synephrine, and thymol), 62 for target proteins (e.g., NR3C1, ESR1, PTGS2, CAT, TNF, INS, and TP53), and 6 for pathways (MAPK signaling pathway, proteoglycans in cancer, dopaminergic synapse, thyroid hormone signaling pathway, cAMP signaling pathway, and neuroactive ligand-receptor interaction). Conclusion. NR3C1, ESR1, PTGS2, CAT, TNF, INS, and TP53 may be important targets for the key active elements in the decoction combining Yougui pill and Buzhong Yiqi. Furthermore, these target proteins are relevant to the treatment of sexual dysfunction, probably via pathways associated with cancer and signal transduction.


2021 ◽  
Author(s):  
Zhuo Zhang ◽  
Jiang-lin Xu ◽  
Ming-qing Wei ◽  
Ting Li ◽  
Jing Shi

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.


2020 ◽  
Vol 19 (7) ◽  
pp. 1449-1457
Author(s):  
Chuan Liu ◽  
Fang-Fang Fan ◽  
Xuan-Hao Li ◽  
Wen-Xiang Wang ◽  
Ya Tu ◽  
...  

Purpose: To study the mechanism involved in the anti-cholecystitis effect the Tibetan medicine “Dida”, using network pharmacology-integrated molecular docking simulationsMethods: In this investigation, the bioactive compounds of Dida were collected, network pharmacology methods to predict their targets, and networks were constructed through GO and KEGG pathway analyses. The potential binding between the bioactive compounds and the targets were demonstrated using molecular docking simulations.Results: A total of 12 bioactive compounds and 50 key targets of Dida were identified. Two networks, namely, protein–protein interaction (PPI) network of cholecystitis targets, and compound–target– pathway network, were established. Network analysis showed that 10 targets (GAPDH, AKT1, CASP3, EGFR, TNF, MAPK3, MAPK1, HSP90AA1, STAT3, and BCL2L1) may be the therapeutic targets of Dida in cholecystitis. Analysis of the KEGG pathway indicated that the anti-cholecystitis effect of Dida may its regulation of a few crucial pathways, such as apoptosis, as well as toll-like  receptor, T cell receptor, NOD-like receptor, and MAPK signaling pathways. Furthermore, molecular docking simulation revealed that CASP3, CAPDH, HSP90AA1, MAPK3, MAPK1, and STAT3 had well-characterized interactions with the corresponding compounds.Conclusion: The mechanism underlying the anti-cholecystitis effect of Dida has been successfully predicted and verified using a combination of network pharmacology and molecular docking simulation. This provides a firm basis for the experimental verification of the use of Dida in the treatment of cholecystitis, and enhances its rational application in clinical practice. Keywords: Tibetan medicine, Dida, Cholecystitis, Mechanism, Network pharmacology, Molecular docking simulation


Sign in / Sign up

Export Citation Format

Share Document