scholarly journals Uncovering the Pharmacology of Xiaochaihu Decoction in the Treatment of Acute Pancreatitis Based on the Network Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Lianghui Zhan ◽  
Jinbao Pu ◽  
Yijuan Hu ◽  
Pan Xu ◽  
Weiqing Liang ◽  
...  

Background. Xiaochaihu decoction (XD) has demonstrated the pharmacodynamics on acute pancreatitis. This study was aimed at investigating the material and molecular basis of Xiaochaihu decoction. Methods. Firstly, compounds of seven herbs containing XD were collected from the TCMSP, ETCM, and BATMAN-TCM databases, and the putative targets of pancreatitis were obtained from the OMIM, TTD, and GeneCards databases. Then, the PPI network was constructed according to the matching results between XD potential targets and pancreatic neoplasm targets. Furthermore, enrichment analysis on GO and KEGG by DAVID utilized bioinformatics resources. Finally, molecular docking was performed to simulate the interaction between the active compound of XD and putative targets. In an in vitro experiment, AR42J cells were induced by LPS and then treated with Quercetin (25, 50, and 100 μM) or XCHD. The IL-6, TNF-α, and IL-1β levels were detected by ELISA kit, MAPK3 and TP53 mRNA expressions were measured by qRT-PCR, and the proteins of MAPK3 and TP53 expressions were measured by WB. Results. A total of 196 active ingredients and 91 putative targets were selected. The PPI network analysis demonstrated that Quercetin was the candidate agent and MAPK3, IL-6, and TP53 were the potential targets for the XD treatment of acute pancreatitis. The KEGG analysis revealed that pathways in cancers, TNF signaling way, and MAPK signaling way might play an important role in pancreatitis therapy. And molecular docking results showed that Quercetin combined well with MAPK3, IL-6, and TP53. An in vitro experiment indicated that XCHD and Quercetin inhibited the IL-6, TNF-α, and IL-1β levels and MAPK3 and TP53. Conclusion. This study illustrated that XCHD and Quercetin contained in XD played an important role in the treatment of acute pancreatitis by acting on the key genes of MPAK3, IL-6, and TP53 which were associated with inflammation and apoptosis.

2020 ◽  
Author(s):  
Lianghui Zhan ◽  
Jinbao Pu ◽  
Yijuan Hu ◽  
Pan Xu ◽  
Weiqing Liang ◽  
...  

Abstract BackgroundXiaochaihu Decoction (XD) has been demonstrated the pharmacodynamic on pancreatitis. This study was aimed to investigate the material and molecular basis of Xiaochaihu Decoction.MethodsFirstly, compounds of seven herbs containing XD were collected from TCMSP Database and the putative targets of Pancreatitis were obtained from OMIM, TTD, Genecards Database. Then PPI network was constructed according to the matching results between XD potential targets and pancreatic neoplasms targets. Furthermore, enrichment analysis on GO and KEGG by DAVID utilized bioinformatics resources. Finally, Molecular Docking was performed to simulate the interaction between the active compound of XD and putative targets. In vitro experiment, AR42J cells were induced by LPS and then treated with Quercetin (25, 50, 100 μM). The IL-6, TNF-α, IL-1β levels were detected by Elisa kit and MAPK3, TP53 mRNA expressions were measured by RT-PCR.ResultsA total of 196 active ingredients and 91 putative targets were selected out. The PPI interaction network analysis demonstrated that Quercetin was the candidate agents and MAPK3, IL-6 and TP53 were the potential targets for the XD treatment of pancreatitis. The KEGG analysis revealed that pathways in cancers, TNF signaling way, MAPK signaling way might play an important role in pancreatitis therapy. And Molecular Docking results showed that Quercetin combined well with MAPK3, IL-6 and TP53. In vitro experiment indicated that, Quercetin inhibited the IL-6, TNF-α, IL-1β levels and MAPK3, TP53 mRNA. ConclusionThis study illustrated that Quercetin containing in XD might played an important role in pancreatitis therapy by acting the key genes of MPAK3, IL-6 and TP53 which were associating with inflammation and apoptosis.


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.


Author(s):  
Zhen Zhang ◽  
Puhua Zeng ◽  
Wenhui Gao ◽  
Ruoxia Wu ◽  
Tianhao Deng ◽  
...  

Aim and Objective: Calculus Bovis (CB) has been employed to treat diseases for a long time. It has been identified to play significant anti-inflammatory and anti-tumor roles. However, the mechanism of treating primary liver cancer (PLC) remains to be revealed. This study aims to clarify the molecules and mechanisms of CB in treating PLC. Materials and Methods: After oral bioavailability (OB) and drug-likeness (DL) screening, 15 small molecules were identified as the potential ingredients against PLC. Following this, related targets network constructions and pathways were applied to clarify the mechanism of CB in treating PLC. An in vitro experiment was carried out to identify the function of CB in treating PLC. Results: Eleven compounds of CB were identified that play an anti-PLC role, including oleanolic acid, ergosterol, ursolic acid, etc. The potential targets which were observed include: IL6, MAPK-8, VEGFA, Caspase-3, etc. Further analysis showed that the mechanism of CB in the treatment of PLC involved apoptosis-related pathways and immune- related pathways. Conclusion: In summary, the current study combines network pharmacology and in vitro experiments to reveal the mechanism of CB against PLC. We concluded that 11 ingredients of CB have an anti-PLC effect. Furthermore, CB plays a key role in treating PLC mainly by apoptosis-related pathways and immune-related pathways. Our experiment verifies that CB promotes the apoptosis of SMMC-7721.


2021 ◽  
Vol 70 (7) ◽  
Author(s):  
Li Wang ◽  
Yuhe Wang ◽  
Wei Yang ◽  
Xue He ◽  
Shilin Xu ◽  
...  

Introduction. Coronavirus disease 2019 (COVID-19) is a highly contagious disease and ravages the world. Hypothesis/Gap Statement. We proposed that R. crenulata might have potential value in the treatment of COVID-19 patients by regulating the immune response and inhibiting cytokine storm. Aim. We aimed to explore the potential molecular mechanism for Rhodiola crenulata (R. crenulata), against the immune regulation of COVID-19, and to provide a referenced candidate Tibetan herb (R. crenulata) to overcome COVID-19. Methodology. Components and targets of R. crenulata were retrieved from the TCMSP database. GO analysis and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment were built by R bioconductor package to explore the potential biological effects for targets of R. crenulata. The R. crenulata-compound-target network, target pathway network and protein–protein interaction (PPI) network were constructed using Cytoscape 3.3.0. Autodock 4.2 and Discovery Studio software were applied for molecular docking. Result. Four bioactive components (quercetin, kaempferol, kaempferol-3-O-α-l-rhamnoside and tamarixetin) and 159 potential targets of R. crenulata were identified from the TCMSP database. The result of GO annotation and KEGG-pathway-enrichment analyses showed that target genes of R. crenulata were associated with inflammatory response and immune-related signalling pathways, especially IL-17 signalling pathway, and TNF signalling pathway. Targets-pathway network and PPI network showed that IL-6, IL-1B and TNF-α were considered to be hub genes. Molecular docking showed that core compound (quercetin) had a certain affinity with IL-1β, IL-6 and TNF-α. Conclusion. R. crenulata might play an anti-inflammatory and immunoregulatory role in the cytokine storm of COVID-19.


2020 ◽  
Author(s):  
Lianghui Zhan ◽  
Jinbao Pu ◽  
Yijuan Hu ◽  
Pan Xu ◽  
Weiqing Liang ◽  
...  

Abstract BackgroundXiaochaihu Decoction (XD) was a traditional prescription, has been demonstrated the pharmacodynamic on pancreatitis. But the underline mechanism remained to be explored. Therefore, this study was aimed to combined network pharmacology method and molecular docking technology to demonstrate the potential mechanism of XD treated with pancreatitis.MethodsFirstly, compounds of seven herbs containing XD were collected from TCMSP Database and the putative targets of Pancreatitis were obtained from OMIM, TTD, Genecards Database. Then PPI network was constructed according to the matching results between XD potential targets and pancreatic neoplasms targets. Furthermore, enrichment analysis on GO and KEGG by DAVID utilized bioinformatics resources. Finally, Molecular Docking was performed to simulate the interaction between the active compound of XD and putative targets.ResultsA total of 196 active ingredients and 91 putative targets were selected out. The PPI interaction network analysis demonstrated that Quercetin was the candidate agents and MAPK3, IL-6 and TP53 were the potential targets for the XD treatment of pancreatitis. The KEGG analysis revealed that pathways in cancers, TNF signaling way, MAPK signaling way might play an important role in pancreatitis therapy. And Molecular Docking results showed that Quercetin combined well with MAPK3, IL-6 and TP53.ConclusionThis study illustrated that Quercetin containing in XD might played an important role in pancreatitis therapy by acting the key genes of MPAK3, IL-6 and TP53. And it also provided a strategy to elucidate the mechanisms of Traditional Chinese Medicine (TCM) at the level of network pharmacology.


2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Guang-yao Chen ◽  
Xiao-yu Liu ◽  
Jia-qi Chen ◽  
Xin-bo Yu ◽  
Jing Luo ◽  
...  

Rhizoma Drynariae has been widely used for the treatment of osteoarthritis (OA), but its potential targets and molecular mechanisms remain to be further explored. Targets of Rhizoma Drynariae and OA were predicted by relevant databases, and a protein-protein interaction (PPI) network was constructed to identify key targets. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed to obtain related pathways and then select significant pathways associated with OA. The OA chondrocyte model was established by inflammatory factor-induced SW1353 chondrocytes, and molecular docking was conducted to verify the above theoretical prediction. The results showed that a total of 86 Rhizoma Drynariae-OA interaction targets were identified, among which IL-6 and AKT1 were the key targets in the PPI network. Luteolin was the most critical component of Rhizoma Drynariae. KEGG results indicated that the effects of Rhizoma Drynariae on OA are associated with the PI3K/AKT, TNF, IL-17, apoptosis, and HIF-1 signaling pathway. The PI3K/AKT pathway can activate the downstream NF-κB pathway and further regulate the transcription and expression of downstream IL-6, IL-17, HIF-1α, Bax, and TNF, suggesting that the PI3K/AKT/NF-κB pathway is the critical pathway in the treatment of OA with Rhizoma Drynariae. Active components of Rhizoma Drynariae and key proteins of the PI3K/AKT/NF-κB signaling pathway were subjected to molecular docking, whose results showed that luteolin and IKK-α played a critical role. In vitro experiments indicated that both aqueous extracts of Rhizoma Drynariae (AERD) and luteolin inhibited the expression of IL-6 and HIF-1α and suppressed the activation of PI3K/AKT/NF-κB, IL-17, and TNF pathways. The measurement of mitochondrial membrane potential (Δψm) indicated that AERD and luteolin can decrease the LPS-induced early apoptotic cells. Luteolin had a more prominent inhibitory effect than AERD in the abovementioned in vitro experiments. In conclusion, the therapeutic mechanism of Rhizoma Drynariae against OA may be closely related to the inhibition of the PI3K/AKT/NF-κB pathway and downstream pathways, and luteolin plays a vital role in the treatment.


2021 ◽  
Author(s):  
lu wang ◽  
Wenxiang Zhu ◽  
Rui Sun ◽  
Jing Liu ◽  
Qihong Ma ◽  
...  

Abstract Background Pulmonary fibrosis (PF) is a devastating lung disease. The two drugs approved by the FDA, pirfenidone and nintedanib, can only delay the progression of the disease but cannot cure the disease. These drugs also present adverse effects. Wen-yu-jin (WYJ) obtained from steamed roots of Curcuma wenyujin showed a variety of pharmacological activities. In this study we investigated whether WYJ present anti-lung fibrosis effects. Methods Ultra-high pressure liquid chromatography combined with linear ion trap-orbital tandem mass spectrometry (UHPLC-LTQ-orbital trap) was used to identify chemical composition of WYJ. PF-related and WYJ-related targets were obtained from public databases. Network pharmacological was performed to acquire potential targets and major signaling pathways. The binding activity of composition with core targets was predicted by molecular docking. Based on the predicted results, the anti-lung fibrosis effect of WYJ was verified in vivo and in vitro experiments. Results 23 major compositions of WYJ were identified based on UHPLC-LTQ-Orbitrap. According to the results of network pharmacology, MAPK signaling pathway might play an important role in WYJ against lung fibrosis and STAT3 also could be the potential therapeutic targets. Molecular docking results indicated that most of the compositions have good binding activities with core targets. In vivo and in vitro experiments showed that WYJ alleviated process of fibrosis by inhibiting MAPK signaling pathway and the levels of phosphorylated STAT3 (p-STAT3). Conclusion According to the results of network pharmacology and molecular docking, in vivo and in vitro experiments further verified potential targets and molecular mechanism of WYJ against lung fibrosis. Our study provided a novel approach to explain the pharmacological basis of other herbs.


2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Dong Zhang ◽  
Lang Guo ◽  
Xiaoting Wu ◽  
Meng Luo ◽  
Xinyi Liang ◽  
...  

The Chinese medicine Qigesan can be used to treat esophageal adenocarcinoma in the Chinese mainland widely, but its mechanism is unclear. In order to investigate the mechanism of Qigesan in the treatment of esophageal adenocarcinoma, the concept of network pharmacology was used in this study. The database named TCMSP was used to identify the active therapeutic components as well as targets of Qigesan. The TTD, OMIM, CTD, DrugBank, and GeneCards database were used to identify genes related to esophageal adenocarcinoma. In STRING database, the potential targets were imported to obtain a PPI network, and then Cytoscape software has been used to analyse the results. Subsequently, important components and targets were simulated by molecular docking. Finally, experiments on the cell have been done to verify well docking targets. A total of 124 effective compounds and 646 corresponding targets were filtered. 1478 genes were found to be related to esophageal adenocarcinoma. 68 genes were identified as potential targets for esophageal adenocarcinoma. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the 68 potential targets indicated that the genes were mainly involved in cell transcription, translation, and apoptosis and mostly expressed in cancer-related pathways. The molecular docking analysis of the hub targets with their corresponding compounds indicated that the well docking targets were AR, ERBB2, and VEGFA. The cell experiments showed that Qigesan can reduce the expression of AR, ERBB2, and VEGFA at transcription and translation level. This network pharmacology study described that the possible targets of Qigesan in treatment of esophageal adenocarcinoma were AR, ERBB2, and VEGFA.


2019 ◽  
Vol 22 (1) ◽  
pp. 4-12 ◽  
Author(s):  
Chaohui Duan ◽  
Yang Li ◽  
Xiaorui Dong ◽  
Weibin Xu ◽  
Yingli Ma

Aim and Objective: Avicularin has been found to inhibit the proliferation of HepG-2 cells in vitro in the screening of our laboratory. We intended to explain the molecular mechanism of this effect. Therefore, the combined methods of reverse molecular docking and network pharmacology were used in order to illuminate the molecular mechanisms for Avicularin against cancer. Materials and Methods: Potential targets associated with anti-tumor effects of Avicularin were screened by reverse molecular docking, then a protein database was established through constructing the drugprotein network from literature mining data, and the protein-protein network was built through an in-depth exploration of the relationships between the proteins, and then the network topology analysis was performed. Additionally, gene function and signaling pathways were analyzed by Go bio-enrichment and KEGG Pathway. Results: The result showed that Avicularin was closely related to 16 targets associated with cancer, and it may significantly influence the pro-survival signals in MAPK signaling pathway that can activate and regulate a series of cellular activities and participate in the regulation of cell proliferation, differentiation, transformation and apoptosis. Conclusion: The network pharmacology strategy used herein provided a powerful means for the mechanisms of action for bioactive ingredients.


2019 ◽  
Vol 16 (4) ◽  
pp. 307-313 ◽  
Author(s):  
Nasrin Zarkar ◽  
Mohammad Ali Nasiri Khalili ◽  
Fathollah Ahmadpour ◽  
Sirus Khodadadi ◽  
Mehdi Zeinoddini

Background: DAB389IL-2 (Denileukin diftitox) as an immunotoxin is a targeted pharmaceutical protein and is the first immunotoxin approved by FDA. It is used for the treatment of various kinds of cancer such as CTCL lymphoma, melanoma, and Leukemia but among all of these, treatment of CTCL has special importance. DAB389IL-2 consists of two distinct parts; the catalytic domain of Diphtheria Toxin (DT) that genetically fused to the whole IL-2. Deamidation is the most important reaction for chemical instability of proteins occurs during manufacture and storage. Deamidation of asparagine residues occurs at a higher rate than glutamine residues. The structure of proteins, temperature and pH are the most important factors that influence the rate of deamidation. Methods: Since there is not any information about deamidation of DAB389IL-2, we studied in silico deamidation by Molecular Dynamic (MD) simulations using GROMACS software. The 3D model of fusion protein DAB389IL-2 was used as a template for deamidation. Then, the stability of deamidated and native form of the drug was calculated. Results: The results of MD simulations were showed that the deamidated form of DAB389IL-2 is more unstable than the normal form. Also, deamidation was carried by incubating DAB389IL-2, 0.3 mg/ml in ammonium hydrogen carbonate for 24 h at 37o C in order to in vitro experiment. Conclusion: The results of in vitro experiment were confirmed outcomes of in silico study. In silico and in vitro experiments were demonstrated that DAB389IL-2 is unstable in deamidated form.


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