scholarly journals Anti-inflammatory Properties of Fangji Huangqi Tang: Discovery Based on Network Pharmacology, Molecular Docking and Arrowsmith Tools

Author(s):  
Qingtao Jiang ◽  
Lei Han ◽  
Xin Liu ◽  
Feng Zhang

Abstract Fangji Huangqi Tang (FHT) is a classical formula widely used in Chinese clinical practice. In this study, a creative application of FHT for inflammation has been identified by network pharmacology-based framework. Specifically, a total of 17 bioactive compounds including 42 potential targets of FHT, and 205 related targets involved in inflammation were retrieved from mainstream databases and subjected to network analysis. 13 intersection targets indicated the principal elements linked to inflammation therapy. Top terms of Gene Ontology (GO) analysis were identified, while 7 related signaling pathways were revealed by Kyoto Encyclopedia of Genes and Genomes (KEGG) results. Subsequently, Calycosin-PTGS2 with tight binding affinity (BA) was manifested by molecular docking as the critical compound-target couple. Meaningful links between Calycosin and inflammation were implied through Arrowsmith, which overlapped with the findings in enrichment analysis, such as MAPK, NF-κB that could be regulators of PTGS2. In summary, the present study explored the potential targets and signaling pathways of FHT against inflammation, which may help to illustrate the mechanisms responsible for the action of FHT and provide a better understanding of its anti-inflammatory effects.

2021 ◽  
Author(s):  
jianjun wu ◽  
Ping-an Zhang ◽  
Ming-zhe Chen ◽  
Yi-xuan Li ◽  
Ying-xue Zhang ◽  
...  

Abstract PurposeJinwei decoction can enhance the anti-inflammatory effect of glucocorticoid (GC) on chronic obstructive pulmonary disease (COPD) by restoring the activity of HDAC2. But the upstream mechanism of Jinwei decoction on HDAC2 expression is not clear. ObjectiveTo explore whether Jinwei decoction can enhance the anti-inflammatory effect of GC on COPD through microRNA21 (miR-21) by network pharmacology. MethodsThe TCMSP database was used to screen active ingredients and target genes of Jinwei decoction, and miRWalk2.0 was used to predict downstream target genes of miR-21. COPD-related genes were identified by searching GeneCards and OMIM databases; Venny 2.1 was used to screen intersection genes; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of intersection genes were analyzed by R software. Protein-protein interactions (PPIs) were analyzed by Cytoscape 3.7.2 software to identify core genes. Finally, interactions between main compounds and potential targets were verified by molecular docking. ResultsTwo hundred ninety-two active ingredients, 316 Jinwei drug targets, 10170 miR-21 target genes, 6617 COPD target genes, and 184 intersection gene were identified. Eleven core proteins of PPI networks may be involved. GO enrichment analysis showed that oxidative stress, regulation of inflammatory response, hormone transport, and histone modification were involved; KEGG pathway enrichment analysis concentrated in the PI3K-Akt, mitogen-activated protein kinase (MAPK), HIF-1, neutrophil extracellular bactericidal network, and other signaling pathways. ConclusionJinwei decoction can regulate histone deacetylase-2 activity and enhance the anti-inflammatory effect of GC on COPD by modulating miR-21. Its mechanism of action may be related to its effect on the PI3K Akt, MAPK, and TNF signaling pathways and neutrophil extracellular trap formation through miR-21.


2020 ◽  
Author(s):  
Huiqin Qian ◽  
Bai-Ling Wang ◽  
Ling-Yun Zhang ◽  
Jia-Xiang Li ◽  
Xiu-Xiu Huang

Abstract Background Inula japonica Thunb. (IJT) is an extensively applied herbal medicine for treating non-small cell lung cancer (NSCLC) due to its anti-asthma, antitussive, and expectorant properties. However, the mechanism of IJT against NSCLC remains to be elucidated. Methods Network pharmacology analysis was applied to determine the function mechanism of IJT against NSCLC. Databases were used to collect compounds and their related and known therapeutic targets. The compound–target (C–T) and target–target networks were then constructed to screen the kernel compounds and NSCLC-related targets of IJT. Moreover, the NSCLC-related targets of IJT were input in the DAVID Bioinformatics Resources (version 6.8) for Gene Ontology Biological Processes (GOBP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Finally, the binding affinity of major compounds with the NSCLC-relevant targets of IJT was further verified by molecular docking. Results Two active compounds (quercetin and luteolin) and six putative targets (RAC-alpha serine/threonine-protein kinase, G1/S-specific cyclin-D1, cyclin-dependent kinase inhibitor 2A, epidermal growth factor receptor, receptor tyrosine-protein kinase erbB-2, and cellular tumor antigen p53) were screened as the effective compounds and NSCLC-related targets of IJT. GOBP and KEGG enrichment analysis indicated that NSCLC was the major pathway of IJT in the treatment of NSCLC and the mediation of apoptosis, cell cycle, tumor progression, and proliferation of biological processes, including the Ras, ERBB, MAPK, PI3K–Akt, calcium, and p53 signaling pathways. The results of molecular docking validated that 10 of the 12 pairs of compound-target had effective binding. Conclusions The mechanisms of IJT against NSCLC through multi-compounds, multi-targets, and multi-pathways were elucidated.


2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Xiang Yu ◽  
Peng Zhang ◽  
Kai Tang ◽  
Gengyang Shen ◽  
Honglin Chen ◽  
...  

Naringin (NG), as the most abundant component of Drynariae Rhizoma (Chinese name: Gusuibu), has been proved to be an antioxidant flavonoid on promoting osteoporotic fracture (OF) healing, but relevant research is scanty on the underlying mechanisms. We adopted target prediction, protein-protein interaction (PPI) analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and molecular docking to establish a system pharmacology database of NG against OF. Totally 105 targets of naringin were obtained, including 26 common targets with OF. A total of 415 entries were obtained through GO Biological Process enrichment analysis ( P < 0.05 ), and 37 entries were obtained through KEGG pathway enrichment analysis with seven signaling pathways included ( P < 0.05 ), which were primarily concerned with p53, IL-17, TNF, estrogen, and PPAR signaling pathways. According to the results of molecular docking, naringin is all bound in the active pockets of the core targets with 3–9 hydrogen bonds through some connections such as hydrophobic interactions, Pi-Pi stacked interactions, and salt bridge, demonstrating that naringin binds tightly to the core targets. In general, naringin may treat OF through multiple targets and multiple pathways via regulating oxidative stress, etc. Notably, it is first reported that NG may regulate osteoclast differentiation and oxidative stress through the expression of the core targets so as to treat OF.


2020 ◽  
Author(s):  
Xiao Song ◽  
Fei Guo ◽  
Xiao-Chen Sun ◽  
Shu-Yue Wang ◽  
Yao-Hui Yuan ◽  
...  

Abstract Background: Leukemia was listed by the World Health Organization as one of the five most intractable diseases in the world. The multi-drug resistance (MDR) of leukemia cells limits the efficacy of anti-tumor drugs and is the major reason for the chemotherapy failure and recurrence of leukemia chemotherapy. Some studies have shown that Euphorbiae semen (ES) possesses the characteristics of new therapeutic drugs for MDR. However, the molecular mechanisms and active compounds have not yet been fully clarified. Therefore, there is a need for explore its active compounds and demonstrate its mechanisms through network pharmacology and molecular docking technology.Method: First, the TCMSP database was searched and screened the active compounds of the ES, supplemented with compounds verified by literature, so as to further identify the core compounds in the active ingredient. Simultaneously, the TCMSP and Swiss database were searched to the targets of active compounds, and the targets of reverses leukemia multidrug resistance (RL-MDR) were screened in the relevant databases, such as GeneCards and DrugBank. Then, the targets of active compounds were intersected with RL-MDR targets to obtain potential targets of ES acting on MDR. The compound–target network was constructed by Cytoscape. The target protein–protein interaction network was built using STRING and Cytoscape database. Second, the R language and DAVID database were used to analyse Gene Ontology (GO) biological functions analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathways enrichment. Finally, molecular docking method was utilized to investigate the binding activity between the core targets and the active compounds of ES.Results: Compound–target network mainly contained 22 compounds and 81 corresponding targets. Finally, seven components in ES were selected and 10 core targets were identified; Key targets contained JUN, CASP3, MAOA, AR, PPARG, DRD2, ADRA2A, CHRM2, PTGS2 and MAPK14. GO enrichment analysis indicated the main biological functions of potential genes of ES in the treatment of MDR. KEGG pathway enrichment analysis showed the main pathways, mainly including apoptosis, pathways in cancer, p53 signaling pathway, VEGF signaling pathway, TNF signaling pathway and PI3K–Akt signaling pathway. Finally, we chose the top 10 common targets for molecular docking with the 7 active compounds of ES. The results of molecular docking indicated that the compounds of ES, which had good affinity with targets. Conclusion: The molecular mechanism of ES in the treatment of MDR showed the synergistic reaction of multi-compound, multi-target, and multi-pathway of traditional Chinese medicine, which provided ideas for further clinical research.


Author(s):  
Rong Zhao ◽  
Meng-Meng Zhang ◽  
Dan Wang ◽  
Wei Peng ◽  
Qing Zhang ◽  
...  

Background: Zanthoxylum bungeanum Maxim., a traditional Chinese herbal medicine, has been reported to possess therapeutic effects on diseases induced by oxidative stress (DOS), such as atherosclerosis and diabetes complication. However, the active components and its related mechanisms are still not systematically reported. Objective: The current study was aimed to explore the main active ingredients and its molecular mechanisms of Z. bungeanum for treating DOS using network pharmacology combined with molecular docking simulation. Methods: The active components of Z. bungeanum pericarps, in addition to the interacting targets, were identified from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. These components were filtered using the parameters of oral bioavailability and drug-likeness, and the targets related to DOS were obtained from the Genecards and OMIM database. Furthermore, the overlapping genes were obtained, and a protein-protein interaction was visualized using the STRING database. Next, the Cytoscape software was employed to build a disease/drug/component/target network, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using R software. Finally, the potential active compounds and their related targets were validated using molecular docking technology. Results: A total of 61 active compounds, 280 intersection genes, and 105 signaling pathways were obtained. Functional enrichment analysis suggested that DOS occurs possibly through the regulation of many biological pathways, such as AGERAGE and HIF-1 signaling pathways. Thirty of the identical target genes showed obvious compact relationships with others in the STRING analysis. Three active compounds, quercetin, diosmetin, and beta-sitosterol, interacting with the four key targets, exhibited strong affinities. Conclusion: The findings of this study not only indicate the main mechanisms involving in the oxidative stress-induced diseases, but also provide the basis for further research on the active components of Z. bungeanum for treating DOS.


2021 ◽  
Vol 12 ◽  
Author(s):  
Qian Zhang ◽  
Xue Li ◽  
Jun Li ◽  
Yuxia Hu ◽  
Jing Liu ◽  
...  

Background and Aim: QingXiaoWuWei Decoction (QXWWD) is a traditional Chinese medicine that is commonly used in clinical settings to treat inflammatory and bacterial diseases. However, there is still a lot to learn about its molecular mechanism. A network pharmacology approach was applied to investigate the pharmacological mechanisms of QXWWD in inflammation treatment.Methods: The basic mechanisms involved in the anti-inflammatory and antibacterial potentials of QXWWD were identified using network pharmacology and molecular docking. The principal components of QXWWD were identified by the HPLC-Q-Exactive-MS method. The antibacterial bioactivity of QXWWD was further investigated using the Kirby-Bauer disc diffusion method and the determination of the minimum inhibitory concentration. The anti-inflammatory activity of QXWWD was evaluated using mice ear swelling test, RAW264.7 cell culture, and pro-inflammatory cytokines measurement. Skin irritation and HE staining were employed to evaluate the safety of QXWWD topical use and to depict the drug’s potential therapeutic function. The hub genes and signaling pathways associated with inflammatory and bacterial diseases were validated by western blot in addition to biochemical and pathological markers.Results: Our findings revealed that the ethanolic extract of QXWWD had a strong inhibitory effect against Staphylococcus aureus, Enterococcus faecalis, and Streptococcus pneumoniae. Meanwhile, QXWWD was potentially effective in suppressing ear swelling, elevated white blood cell counts, and the TNF-α, IL-1, and IL-6 levels. According to skin irritation, QXWWD was found to be safe when tested for topical application. The results of HE staining showed that the possible therapeutic role of QXWWD was related to the change in skin microstructure. Also, the network pharmacology, molecular docking as well as Q-Exactive-MS and HPLC analysis suggested that the synergistic effect of quercetin, luteolin and other ingredients could serve as main contributor of QXWWD for its anti-inflammatory and antibacterial activities. Moreover, the JUN, MAPK1, RELA, NFKBIA, MYC, and AKT1 were the potential identified key targets, and MAPK/PI3K/Akt was among the possibly involved signaling pathways in the anti-inflammatory and antibacterial activities of QXWWD.Conclusions: From a therapeutic standpoint, QXWWD may be a promising antibacterial and anti-inflammatory agent for the treatment of bacterial, acute, and chronic dermatitis.


2021 ◽  
Author(s):  
Jingyun Jin ◽  
Bin Chen ◽  
Xiangyang Zhan ◽  
Zhiyi Zhou ◽  
Hui Liu ◽  
...  

Abstract Background and objective: To predict the targets and signal pathways of Xiao-Chai-Hu-Tang (XCHT) in the treatment of colorectal cancer (CRC) based on network pharmacology, to further analyze its anti-CRC material basis and mechanism of action.Methods: TCMSP and TCMID databases were adopted to screen the active ingredients and potential targets of XCHT. CRC-related targets were retrieved by analyzing published microarray data (accession number GSE110224) from the Gene Expression Omnibus (GEO) database. The above common targets were used to construct the “herb-active ingredients-target” network by Cytoscape 3.8.0 software. And then, the protein-to-protein interaction(PPI)was constructed and analyzed with BisoGenet and CytoNCA plug-in in Cytoscape. Gene Ontology (GO) functional and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis for target genes were then performed using the R package of cluster Profiler. Further, AutoDock Vina software was used to conduct molecular docking studies on the active ingredients and key targets to verify the network pharmacological analysis results.Results: A total of 71 active ingredients of XCHT and 20 potential targets for anti-CRC were identified. The network analysis revealed that quercetin, stigmasterol, kaempferol, baicalein, acacetin may be the key compounds. And PTGS2, NR3C2, CA2, MMP1 may be the key targets. The active ingredients of XCHT interacted with most disease targets of CRC. It fully showed that XCHT exerted its therapeutic effect through the synergistic action of the multi-compound, multi-target, and multi-pathway. Gene ontology enrichment analysis showed 46 GO entries, including 20 biological processes, 6 cellular components, and 20 molecular functions. 11 KEGG signaling pathways had been identified, including IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and NF-kappa B signaling pathway. It showed that XCHT played a role in the treatment of CRC by regulating different signal pathways. Molecular docking confirmed the correlation between five core compounds (including quercetin, stigmasterol, kaempferol, baicalein, and acacetin) and PTGS2.Conclusion: The potential active ingredients, possible targets, and key biological pathways for the efficacy of XCHT in the treatment of CRC were preliminarily described, which provided a theoretical basis for further experimental verification research.


2021 ◽  
Vol 16 (2) ◽  
pp. 1934578X2199767
Author(s):  
Tian-jiao Zhou ◽  
Jun-feng Liu ◽  
Ping Wang ◽  
An-na Hu ◽  
Lin-lin Chen ◽  
...  

Yiqi Sanjie formula (YQSJF) is mainly applied clinically for the treatment of lung neoplasms. The purpose of this study was to explore the pharmacodynamics of the active components of YQSJF and the mechanism of therapeutic effects in the treatment of lung neoplasm diseases based on network pharmacology. The network of component-target, target-pathway, and pathway-disease of YQSJF was constructed by using Cytoscape software. According to the screening result, 37 key components, 57 important targets, and 866 candidate pathways were obtained. The enrichment analysis results indicated that YQSJF might play a therapeutic role in lung cancer by regulating several signaling pathways, such as the PI3K-AKT, non-small cell lung cancer, small cell lung cancer, and apoptosis pathways. There were 53 intersection genes between YQSJF and the lung cancer gene, 52 common genes, and 11 key targets, including CASP8, CASP9, AR, ESR1, PTGS2, NOS3, PGR, TGFB1, PPARG, RELA, and NOS2, screened by using Protein-Protein Interaction (PPI) analysis. These could be the potential therapeutic targets of YQSJF against lung cancer. Enrichment analysis of the intersection gene pathways revealed 10 major functional pathways, including the VEGF, apoptosis, and IL-17 signaling pathways. The molecular docking results showed the potential regulating activity of kaempferol against AR, pelargonidin against PGR, and baicalein against both PTGS2 and AR. In conclusion, combinational network pharmacology analysis results indicated that YQSJF might present its efficacy of alleviating lung neoplasm symptoms through multiple targets in a synergetic way.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yankai Dong ◽  
Bo Tao ◽  
Xing Xue ◽  
Caixia Feng ◽  
Yating Ren ◽  
...  

Abstract Background Increasing attention has been paid to the effect of Epimedium on the nervous system, particularly anti-depression function. In the present study, we applied network pharmacology to introduce a testable hypothesis on the multi-target mechanisms of Epicedium against depression. Methods By reconstructing the network of protein–protein interaction and drug–component–target, we predicted the key protein targets of Epicedium for the treatment of depression. Then, through molecular docking, the interaction of the main active components of Epicedium and predicted candidate targets were verified. Results Nineteen active compounds were selected from Epicedium. There were 200 targets associated with Epicedium and 537 targets related to depression. The key targets of Epicedium for treating depression were IL6, VEGFA, AKT1, and EGF. According to gene ontology functional enrichment analysis, 22 items of biological process (BP), 13 items of cell composition (CC) and 9 items of molecular function (MF) were obtained. A total of 56 signaling pathways (P < 0.05) were identified by Kyoto Encyclopedia of Genes and Genomes analysis, mainly involving depression-related pathways such as dopaminergic synapse, TNF signaling pathway, and prolactin signaling pathway. The results of molecular docking showed that the most important activity components, including luteoklin, quercetin and kaempferol, were well combined with the key targets. Conclusions Luteoklin, quercetin, kaempferol and other active compounds in Epicedium can regulate multiple signaling pathways and targets such as IL6, AKT1, and EGF, therefore playing therapeutic roles in depression.


2021 ◽  
Author(s):  
Xinyue Han ◽  
Yimin Xu ◽  
Xiaoqiang Liu ◽  
Yuan Li ◽  
Cui Guo ◽  
...  

Abstract Background: Curcumin is a potential drug for the treatment of colorectal cancer (CRC). Its mechanism of action has not been elucidated.Aim: To investigate the mechanism of action of curcumin in the treatment of CRC via network pharmacology, molecular docking and experimental verification.Methods: The targets of curcumin and CRC were obtained from the public databases. The component-targets network of curcumin in the treatment of CRC was constructed by Cytoscape v3.7.2. Through protein-protein interaction (PPI), the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), important targets and signaling pathways related to CRC treatment were identified. Finally, the results were verified by molecular docking and in vitro experiments.Results: A total of 30 potential targets of curcumin for CRC treatment were collectedThe core targets included AKT1, EGFR and STAT3 were identified. GO function enrichment analysis showed 140 items, and KEGG pathway enrichment analysis showed 61 signaling pathways, that were related to the regulation of protein kinase activity, negative regulation of apoptosis process, cancer signaling pathway and PI3K-Akt signali-ng pathway. In vitro experimental verification showed that curcumin could promote the apoptosis of CRC cells, and the key proteins of these signaling pathways were differentially expressed.Conclusion: This study explored the targets and pathways of curcumin in the treatment of colorectal cancer. In vitro experiments showed that curcumin has a therapeutic effect against CRC by inhibiting PI3K-Akt signaling pathway. Our results will lay a foundation for subsequent clinical research and drug development.


Sign in / Sign up

Export Citation Format

Share Document