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Article ; Online: Involvement of gut microbiota recovery and autophagy induction in Youhua Kuijie Formula's protection against experimental ulcerative colitis.

Sheng, Tianjiao / Wang, Lei / Yan, Simeng / Wei, Qiuyu / Geng, Xiao / Lan, Weiru / Chen, Yan / Liu, Yuedong / Li, Na

2024

Abstract: ... mucosal barrier and disrupted gut microbiota. Youhua Kuijie formula is a classic empirical prescription ... of Youhua Kuijie Formula on DSS-induced UC in mice and uncover the related mechanism. Youhua Kuijie Formula ... The protective effect of Youhua Kuijie Formula was evidenced by reduced pathological symptoms accompanied by palliative ...

Abstract	Ulcerative colitis (UC) is characterized by overactive inflammatory response, impaired intestinal mucosal barrier and disrupted gut microbiota. Youhua Kuijie formula is a classic empirical prescription based on the pathogenesis of UC. The present study was designed to verify the protective effect of Youhua Kuijie Formula on DSS-induced UC in mice and uncover the related mechanism. Youhua Kuijie Formula were orally administrated to UC mice induced by DSS dissolved in drinking water for ten days. The protective effect of Youhua Kuijie Formula was evidenced by reduced pathological symptoms accompanied by palliative inflammatory response and relatively intact intestinal barrier. The data from 16S rRNA gene sequencing and GC-MS untargeted metabolomics indicated that the supplement of Youhua Kuijie Formula restructured gut microbiota community structure, and thereby modulated the metabolic profiles in UC mice. The analysis of pathway enrichment analysis suggested the major alterations in metabolic pathway were related to protein digestion and absorption. Besides, the results of the following experiments suggested that Youhua Kuijie Formula treatment increased adenosine monophosphate-activated protein kinase (AMPK) activation, decreased mechanistic target of rapamycin (mTOR) phosphorylation, and thereby reversing autophagy deficiency in the intestinal tract of UC mice. Collectively, our results demonstrated that the regulation of AMPK/mTOR was involved in Youhua Kuijie Formula administration mediated protective effect on UC.
Language	English
Publishing date	2024-04-09
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2088228-2
ISSN	1881-7122 ; 1341-1357 ; 0007-5124
ISSN (online)	1881-7122
ISSN	1341-1357 ; 0007-5124
DOI	10.1538/expanim.23-0166
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Article: Effect of Kuijie Granule on the Expression of TGF-β/Smads Signaling Pathway in Patients with Ulcerative Colitis.

Xu, Xinjie / Xu, Chunhua / Saud, Shakir M / Lu, Xiaoming / Liu, Lei / Fang, Li / Zhang, Xiaowei / Hu, Jiangong / Li, Weidong

Evidence-based complementary and alternative medicine : eCAM

2016 Volume 2016, Page(s) 2601830

Abstract: ... to the development of ulcerative colitis (UC) and the manifestation of clinical symptoms. Kuijie Granule is ... whether the clinical benefit of Kuijie Granule is associated with TGF-β/Smads signaling, we measured the expression ... in the intestinal mucosa of 72 patients with UC treated with Kuijie Granule for 60 days. Colonic tissues were obtained ...

Abstract	The dysregulation of TGF-β/Smads signaling pathway has been postulated to contribute to the development of ulcerative colitis (UC) and the manifestation of clinical symptoms. Kuijie Granule is a prescription medicine used clinically in China to alleviate the symptoms associated with UC. To evaluate whether the clinical benefit of Kuijie Granule is associated with TGF-β/Smads signaling, we measured the expression levels of TGF-β/Smads signaling proteins (TGF-β1, TGF-βRII, Smad2, Smad4, Smad6, and Smad7) in the intestinal mucosa of 72 patients with UC treated with Kuijie Granule for 60 days. Colonic tissues were obtained by a virtual colonoscopy guided biopsy before and after Kuijie Granule treatment followed by pathological analysis and quantitative analysis of TGF-β/Smads using immunohistochemistry. Kuijie Granule treatment significantly improved symptoms associated with UC, which include diarrhea, mucus production, pus and blood in stool, abdominal pain and distention, and tenesmus. The clinical benefit of Kuijie Granule treatment correlated with decreased expression of TGF-β1 and Smad7 and increased expression of TGF-βRII and Smad4. These clinical results indicate that Kuijie Granule can alleviate the symptoms associated with UC and modulate TGF-β/Smads signaling.
Language	English
Publishing date	2016-02-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2171158-6
ISSN	1741-4288 ; 1741-427X
ISSN (online)	1741-4288
ISSN	1741-427X
DOI	10.1155/2016/2601830
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Article ; Online: A Systems Pharmacology Approach to Determine Active Compounds and Action Mechanisms of Xipayi KuiJie’an enema for Treatment of Ulcerative colitis

Wei Yu / Zhihong Li / Fei Long / Wen Chen / Yurong Geng / Zhiyong Xie / Meicun Yao / Bo Han / Teigang Liu

Scientific Reports, Vol 7, Iss 1, Pp 1-

2017 Volume 16

Abstract: Abstract Xipayi Kui Jie’an (KJA), a type of traditional Uygur medicine (TUM), has shown promising therapeutic effects in Ulcerative colitis (UC). Owing to the complexity of TUM, the pharmacological mechanism of KJA remains vague. Therefore, the ... ...

Abstract	Abstract Xipayi Kui Jie’an (KJA), a type of traditional Uygur medicine (TUM), has shown promising therapeutic effects in Ulcerative colitis (UC). Owing to the complexity of TUM, the pharmacological mechanism of KJA remains vague. Therefore, the identification of complex molecular mechanisms is a major challenge and a new method is urgently needed to address this problem. In this study, we established a feasible pharmacological model based on systems pharmacology to identify potential compounds and targets. We also applied compound-target and target-diseases network analysis to evaluate the action mechanisms. According to the predicted results, 12 active compounds were selected and these compounds were also identified by HPLC-ESI-MS/MS analysis. The main components were tannins, this result is consistent with the prediction. The active compounds interacted with 22 targets. Two targets including PTGS2 and PPARG were demonstrated to be the main targets associated with UC. Systematic analysis of the constructed networks revealed that these targets were mainly involved in NF-κB signaling pathway. Furthermore, KJA could also regulate the CD4 + CD25 + Foxp3 + Treg cells. In conclusion, this systems pharmacology-based approach not only explained that KJA could alleviate the UC by regulating its candidate targets, but also gave new insights into the potential novel therapeutic strategies for UC.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2017-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effect of Kuijie Granule on the Expression of TGF-β/Smads Signaling Pathway in Patients with Ulcerative Colitis

Xinjie Xu / Chunhua Xu / Shakir M. Saud / Xiaoming Lu / Lei Liu / Li Fang / Xiaowei Zhang / Jiangong Hu / Weidong Li

Evidence-Based Complementary and Alternative Medicine, Vol

2016 Volume 2016

Abstract	The dysregulation of TGF-β/Smads signaling pathway has been postulated to contribute to the development of ulcerative colitis (UC) and the manifestation of clinical symptoms. Kuijie Granule is a prescription medicine used clinically in China to alleviate the symptoms associated with UC. To evaluate whether the clinical benefit of Kuijie Granule is associated with TGF-β/Smads signaling, we measured the expression levels of TGF-β/Smads signaling proteins (TGF-β1, TGF-βRII, Smad2, Smad4, Smad6, and Smad7) in the intestinal mucosa of 72 patients with UC treated with Kuijie Granule for 60 days. Colonic tissues were obtained by a virtual colonoscopy guided biopsy before and after Kuijie Granule treatment followed by pathological analysis and quantitative analysis of TGF-β/Smads using immunohistochemistry. Kuijie Granule treatment significantly improved symptoms associated with UC, which include diarrhea, mucus production, pus and blood in stool, abdominal pain and distention, and tenesmus. The clinical benefit of Kuijie Granule treatment correlated with decreased expression of TGF-β1 and Smad7 and increased expression of TGF-βRII and Smad4. These clinical results indicate that Kuijie Granule can alleviate the symptoms associated with UC and modulate TGF-β/Smads signaling.
Keywords	Other systems of medicine ; RZ201-999
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mechanism underlying the effect of Pulsatilla decoction in hepatocellular carcinoma treatment

Kuijie Liu / Zhenyu Cao / Siqi Huang / Fanhua Kong

BMC Complementary Medicine and Therapies, Vol 23, Iss 1, Pp 1-

a network pharmacology and in vitro analysis

2023 Volume 17

Abstract: Abstract Background Currently, hepatocellular carcinoma (HCC) is associated with a poor prognosis. Moreover, there exist limited strategies for treating HCC. Pulsatilla decoction (PD), a traditional Chinese medicine formula, has been used to treat ... ...

Abstract	Abstract Background Currently, hepatocellular carcinoma (HCC) is associated with a poor prognosis. Moreover, there exist limited strategies for treating HCC. Pulsatilla decoction (PD), a traditional Chinese medicine formula, has been used to treat inflammatory bowel disease and several cancer types. Accordingly, we explored the mechanism of PD in HCC treatment via network pharmacology and in vitro experiments. Methods Online databases were searched for gene data, active components, and potential target genes associated with HCC development. Subsequently, bioinformatics analysis was performed using protein–protein interaction and Network Construction and Kyoto Encyclopedia of Genes and Genomes (KEGG) to screen for potential anticancer components and therapeutic targets of PD. Finally, the effect of PD on HCC was further verified by in vitro experiments. Results Network pharmacological analysis revealed that 65 compounds and 180 possible target genes were associated with the effect of PD on HCC. These included PI3K, AKT, NF-κB, FOS, and NFKBIA. KEGG analysis demonstrated that PD exerted its effect on HCC mainly via the PI3K-AKT, IL-17, and TNF signaling pathways. Cell viability and cell cycle experiments revealed that PD could significantly inhibit cancer cell proliferation and kill HCC cells by inducing apoptosis. Furthermore, western blotting confirmed that apoptosis was mediated primarily via the PI3K-AKT, IL-17, and TNF signaling pathways. Conclusion To the best of our knowledge, this is the first study to elucidate the molecular mechanism and potential targets of PD in the treatment of HCC using network pharmacology.
Keywords	Hepatocellular carcinoma ; Pulsatilla decoction ; Network pharmacology ; Traditional Chinese medicine ; Proliferation ; Apoptosis ; Other systems of medicine ; RZ201-999
Subject code	610
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mechanism underlying the effect of Pulsatilla decoction in hepatocellular carcinoma treatment: a network pharmacology and in vitro analysis.

Liu, Kuijie / Cao, Zhenyu / Huang, Siqi / Kong, Fanhua

BMC complementary medicine and therapies

2023 Volume 23, Issue 1, Page(s) 405

Abstract: Background: Currently, hepatocellular carcinoma (HCC) is associated with a poor prognosis. Moreover, there exist limited strategies for treating HCC. Pulsatilla decoction (PD), a traditional Chinese medicine formula, has been used to treat inflammatory ... ...

Abstract	Background: Currently, hepatocellular carcinoma (HCC) is associated with a poor prognosis. Moreover, there exist limited strategies for treating HCC. Pulsatilla decoction (PD), a traditional Chinese medicine formula, has been used to treat inflammatory bowel disease and several cancer types. Accordingly, we explored the mechanism of PD in HCC treatment via network pharmacology and in vitro experiments. Methods: Online databases were searched for gene data, active components, and potential target genes associated with HCC development. Subsequently, bioinformatics analysis was performed using protein-protein interaction and Network Construction and Kyoto Encyclopedia of Genes and Genomes (KEGG) to screen for potential anticancer components and therapeutic targets of PD. Finally, the effect of PD on HCC was further verified by in vitro experiments. Results: Network pharmacological analysis revealed that 65 compounds and 180 possible target genes were associated with the effect of PD on HCC. These included PI3K, AKT, NF-κB, FOS, and NFKBIA. KEGG analysis demonstrated that PD exerted its effect on HCC mainly via the PI3K-AKT, IL-17, and TNF signaling pathways. Cell viability and cell cycle experiments revealed that PD could significantly inhibit cancer cell proliferation and kill HCC cells by inducing apoptosis. Furthermore, western blotting confirmed that apoptosis was mediated primarily via the PI3K-AKT, IL-17, and TNF signaling pathways. Conclusion: To the best of our knowledge, this is the first study to elucidate the molecular mechanism and potential targets of PD in the treatment of HCC using network pharmacology.
MeSH term(s)	Carcinoma, Hepatocellular/drug therapy ; Interleukin-17 ; Network Pharmacology ; Pulsatilla ; Phosphatidylinositol 3-Kinases ; Proto-Oncogene Proteins c-akt ; Liver Neoplasms/drug therapy ; Biological Products
Chemical Substances	Interleukin-17 ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Biological Products
Language	English
Publishing date	2023-11-10
Publishing country	England
Document type	Journal Article
ISSN	2662-7671
ISSN (online)	2662-7671
DOI	10.1186/s12906-023-04244-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CHL-DTI: A Novel High-Low Order Information Convergence Framework for Effective Drug-Target Interaction Prediction.

Wang, Shudong / Liu, Yingye / Zhang, Yuanyuan / Zhang, Kuijie / Song, Xuanmo / Zhang, Yu / Pang, Shanchen

Interdisciplinary sciences, computational life sciences

2024

Abstract: Recognizing drug-target interactions (DTI) stands as a pivotal element in the expansive field of drug discovery. Traditional biological wet experiments, although valuable, are time-consuming and costly as methods. Recently, computational methods grounded ...

Abstract	Recognizing drug-target interactions (DTI) stands as a pivotal element in the expansive field of drug discovery. Traditional biological wet experiments, although valuable, are time-consuming and costly as methods. Recently, computational methods grounded in network learning have demonstrated great advantages by effective topological feature extraction and attracted extensive research attention. However, most existing network-based learning methods only consider the low-order binary correlation between individual drug and target, neglecting the potential higher-order correlation information derived from multiple drugs and targets. High-order information, as an essential component, exhibits complementarity with low-order information. Hence, the incorporation of higher-order associations between drugs and targets, while adequately integrating them with the existing lower-order information, could potentially yield substantial breakthroughs in predicting drug-target interactions. We propose a novel dual channels network-based learning model CHL-DTI that converges high-order information from hypergraphs and low-order information from ordinary graph for drug-target interaction prediction. The convergence of high-low order information in CHL-DTI is manifested in two key aspects. First, during the feature extraction stage, the model integrates both high-level semantic information and low-level topological information by combining hypergraphs and ordinary graph. Second, CHL-DTI fully fuse the innovative introduced drug-protein pairs (DPP) hypergraph network structure with ordinary topological network structure information. Extensive experimentation conducted on three public datasets showcases the superior performance of CHL-DTI in DTI prediction tasks when compared to SOTA methods. The source code of CHL-DTI is available at https://github.com/UPCLyy/CHL-DTI .
Language	English
Publishing date	2024-03-14
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2493085-4
ISSN	1867-1462 ; 1913-2751
ISSN (online)	1867-1462
ISSN	1913-2751
DOI	10.1007/s12539-024-00608-z
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Article: A systematic analysis of

Jiang, Yuhong / Wang, Xiaobo / Li, Lun / He, Jun / Jin, Qianqian / Long, Dongju / Liu, Chao / Zhou, Weihan / Liu, Kuijie

Frontiers in genetics

2022 Volume 13, Page(s) 926943

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2022-08-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.926943
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Article ; Online: Chronic exposure to BDE-47 aggravates acute pancreatitis and chronic pancreatitis by promoting acinar cell apoptosis and inflammation.

Qi, Xiaoyan / Liu, Qiong / Wei, Zuxing / Hou, Xuyang / Jiang, Yuhong / Sun, Yin / Xu, Shu / Yang, Leping / He, Jun / Liu, Kuijie

Toxicological sciences : an official journal of the Society of Toxicology

2024 Volume 199, Issue 1, Page(s) 120–131

Abstract: The effect of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), a persistent environmental pollutant commonly used as a flame retardant in various consumer products, on pancreatitis has not been clearly elucidated, although it has been reported to be toxic to ...

Abstract	The effect of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), a persistent environmental pollutant commonly used as a flame retardant in various consumer products, on pancreatitis has not been clearly elucidated, although it has been reported to be toxic to the liver, nervous system, and reproductive system. Acute pancreatitis (AP) and chronic pancreatitis (CP) models were induced in this study by intraperitoneal injection of caerulein. The aim was to investigate the impact of BDE-47 on pancreatitis by exposing the animals to acute (1 week) or chronic (8 weeks) doses of BDE-47 (30 mg/kg in the low-concentration group and 100 mg/kg in the high-concentration group). Additionally, BDE-47 was utilized to stimulate mouse bone marrow-derived macrophages, pancreatic primary stellate cells, and acinar cells in order to investigate the impact of BDE-47 on pancreatitis. In vivo experiments conducted on mice revealed that chronic exposure to BDE-47, rather than acute exposure, exacerbated the histopathological damage of AP and CP, leading to elevated fibrosis in pancreatic tissue and increased infiltration of inflammatory cells in the pancreas. In vitro experiments showed that BDE-47 can promote the expression of the inflammatory cytokines Tnf-α and Il-6 in M1 macrophages, as well as promote acinar cell apoptosis through the activation of the PERK and JNK pathways via endoplasmic reticulum stress. The findings of this study imply chronic exposure to BDE-47 may exacerbate the progression of both AP and CP by inducing acinar cell apoptosis and dysregulating inflammatory responses.
MeSH term(s)	Animals ; Halogenated Diphenyl Ethers/toxicity ; Apoptosis/drug effects ; Pancreatitis, Chronic/chemically induced ; Pancreatitis, Chronic/pathology ; Acinar Cells/drug effects ; Acinar Cells/pathology ; Acinar Cells/metabolism ; Male ; Pancreatitis/chemically induced ; Pancreatitis/pathology ; Macrophages/drug effects ; Mice, Inbred C57BL ; Mice ; Ceruletide/toxicity ; Pancreas/drug effects ; Pancreas/pathology ; Inflammation/chemically induced ; Inflammation/pathology ; Pancreatic Stellate Cells/drug effects ; Pancreatic Stellate Cells/pathology ; Pancreatic Stellate Cells/metabolism ; Endoplasmic Reticulum Stress/drug effects ; Flame Retardants/toxicity ; Cells, Cultured
Chemical Substances	2,2',4,4'-tetrabromodiphenyl ether (0N97R5X10X) ; Halogenated Diphenyl Ethers ; Ceruletide (888Y08971B) ; Flame Retardants
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1420885-4
ISSN	1096-0929 ; 1096-6080
ISSN (online)	1096-0929
ISSN	1096-6080
DOI	10.1093/toxsci/kfae024
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Article ; Online: MSGNN-DTA

Shudong Wang / Xuanmo Song / Yuanyuan Zhang / Kuijie Zhang / Yingye Liu / Chuanru Ren / Shanchen Pang

International Journal of Molecular Sciences, Vol 24, Iss 8326, p

Multi-Scale Topological Feature Fusion Based on Graph Neural Networks for Drug–Target Binding Affinity Prediction

2023 Volume 8326

Abstract: The accurate prediction of drug–target binding affinity (DTA) is an essential step in drug discovery and drug repositioning. Although deep learning methods have been widely adopted for DTA prediction, the complexity of extracting drug and target protein ... ...

Abstract	The accurate prediction of drug–target binding affinity (DTA) is an essential step in drug discovery and drug repositioning. Although deep learning methods have been widely adopted for DTA prediction, the complexity of extracting drug and target protein features hampers the accuracy of these predictions. In this study, we propose a novel model for DTA prediction named MSGNN-DTA, which leverages a fused multi-scale topological feature approach based on graph neural networks (GNNs). To address the challenge of accurately extracting drug and target protein features, we introduce a gated skip-connection mechanism during the feature learning process to fuse multi-scale topological features, resulting in information-rich representations of drugs and proteins. Our approach constructs drug atom graphs, motif graphs, and weighted protein graphs to fully extract topological information and provide a comprehensive understanding of underlying molecular interactions from multiple perspectives. Experimental results on two benchmark datasets demonstrate that MSGNN-DTA outperforms the state-of-the-art models in all evaluation metrics, showcasing the effectiveness of the proposed approach. Moreover, the study conducts a case study based on already FDA-approved drugs in the DrugBank dataset to highlight the potential of the MSGNN-DTA framework in identifying drug candidates for specific targets, which could accelerate the process of virtual screening and drug repositioning.
Keywords	drug–target binding affinity prediction ; graph neural networks ; feature representation learning ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	006
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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