Integrated network pharmacology and bioinformatics to identify therapeutic targets and molecular mechanisms of Huangkui Lianchang Decoction for ulcerative colitis treatment

Background Gegen Qinlian (GGQL) decoction is a common Chinese herbal compound for the treatment of ulcerative colitis (UC). In this study, we aimed to identify its molecular target and the mechanism involved in UC treatment by network pharmacology and molecular docking. Material and Methods. The active ingredients of Puerariae, Scutellariae, Coptis, and Glycyrrhiza were screened using the TCMSP platform with drug‐like properties (DL) ≥ 0.18 and oral availability (OB) ≥ 30%. To find the intersection genes and construct the TCM compound-disease regulatory network, the molecular targets were determined in the UniProt database and then compared with the UC disease differential genes with P value < 0.005 and ∣log2 (fold change) | >1 obtained in the GEO database. The intersection genes were subjected to protein-protein interaction (PPI) construction and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. After screening the key active ingredients and target genes, the AutoDock software was used for molecular docking, and the best binding target was selected for molecular docking to verify the binding activity. Results A total of 146 active compounds were screened, and quercetin, kaempferol, wogonin, and stigmasterol were identified as the active ingredients with the highest associated targets, and NOS2, PPARG, and MMP1 were the targets associated with the maximum number of active ingredients. Through topological analysis, 32 strongly associated proteins were found, of which EGFR, PPARG, ESR1, HSP90AA1, MYC, HSPA5, AR, AKT1, and RELA were predicted targets of the traditional Chinese medicine, and PPARG was also an intersection gene. It was speculated that these targets were the key to the use of GGQL in UC treatment. GO enrichment results showed significant enrichment of biological processes, such as oxygen levels, leukocyte migration, collagen metabolic processes, and nutritional coping. KEGG enrichment showed that genes were particularly enriched in the IL-17 signaling pathway, AGE-RAGE signaling pathway, toll-like receptor signaling pathway, tumor necrosis factor signaling pathway, transcriptional deregulation in cancer, and other pathways. Molecular docking results showed that key components in GGQL had good potential to bind to the target genes MMP3, IL1B, NOS2, HMOX1, PPARG, and PLAU. Conclusion GGQL may play a role in the treatment of ulcerative colitis by anti-inflammation, antioxidation, and inhibition of cancer gene transcription.

To evaluate the therapeutic effects of Xiahuo Pingwei San (, XHPWS) on ulcerative colitis (UC) in mice and to explore the underlying mechanisms through a network pharmacology approach. Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was utilized to identify the chemical composition and authenticate the active constituents of XHPWS, ensuring rigorous quality control across batches. A dextran sulfate sodium (DSS)-induced UC model was established in C57BL/6 mice, which were treated with XHPWS in vivo. The efficacy against UC was assessed by measuring parameters such as body weight, disease activity index (DAI) scores, and colon length. Levels of inflammatory cytokines, including interleukin-6 (IL-6), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α), in colonic tissue were evaluated using enzyme-linked immunosorbent assay (ELISA). Histological analysis of colon sections was conducted using hematoxylin and eosin staining. A network pharmacology approach was employed to explore the mechanisms of XHPWS and to predict its potential targets in UC treatment. Predicted protein expressions in colonic tissue were validated using immune-ohistochemistry (IHC) and Western blotting techniques. XHPWS effectively alle viated DSS-induced UC symptoms in mice, as evidenced by restored body weight, reduced colon shortening, and decreased DAI scores. Histopathological examination revealed that XHPWS significantly reduced intestinal inflammatory infiltration, restored intestinal epithelial permeability, and increased goblet cell count. Network pharmacology analysis identified 63 active compounds in XHPWS and suggested that it might target 35 potential proteins associated with UC treatment. Functional enrichment analysis indicated that the protective mechanism of XHPWS could be related to the advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathway. Notably, quercetin, kaempferol, wogonin, and nobiletin, the main components of XHPWS, showed strong correlations with the core targets. Additionally, experimental validation demonstrated that XHPWS significantly decreased levels of inflammatory cytokines interleukin 6 (IL-6), interleukin 1 beta (IL-1β), and tumor necrosis factor alpha (TNF-α) in UC mice, while downregulating the expression of proteins related to the AGE-RAGE pathway. Our study demonstrated that XHPWS effectively alle viates colitis symptoms and inflammation in UC mice, potentially through the regulation of the AGE-RAGE pathway. These findings provide strong evidence for the therapeutic potential of XHPWS in UC treatment, thereby broadening its clinical applications.

Gegen Qinlian Decoction(GQD) is commonly used for the clinical treatment of ulcerative colitis(UC) and other diseases, but its compatibility mechanism has not been elucidated systematically. In this study, the compatibility mechanism of GQD against UC was revealed based on the blood components in the mouse model of UC by network pharmacology. The targets of blood components of GQD were collected to construct a protein-protein interaction(PPI) network. The key targets were screened out according to the topological parameters of the network, and 16 core components were identified, such as puerarin, chrysin, berberine, and liquiritigenin, based on the key targets in the blood components. Functional enrichment analysis was performed on the key targets, and the regulatory network of the prescription was constructed, which elucidated the compatibility mechanism of the Chinese herbal drugs in the prescription at both target and pathway levels. The results showed that all the Chinese herbal drugs in GQD had heat-clearing and toxin-removing effects, and the four Chinese herbal drugs synergistically exerted their effects by co-regulating protooncogenes, such as FOS and JUN, and characteristically regulating signal transducer and activator of transcription 3(STAT3) and interleukin-6(IL-6). The pathway analysis revealed that GQD exerted heat-clearing and toxin-removing effects mainly by regulating the inflammatory response-related signaling pathways, such as Toll-like receptor, tumor necrosis factor(TNF), and mitogen-activated protein kinase(MAPK). Furthermore, the study revealed the synergistic effects of Chinese herbal drugs in GQD based on the TNF signaling pathway. The results showed that the sovereign drug Puerariae Lobatae Radix played a primary role in the regulation of targets in the TNF signaling pathway, the minister drugs Scutellariae Radix and Coptidis Rhizoma showed the synergistic effects with Puerariae Lobatae Radix, and the assistant and guiding drug Glycyrrhizae Radix et Rhizoma supported Puerariae Lobatae Radix in the key target NF-κB and the process of cell adhesion. The drugs in GQD showed good characteristics of compatibility in the TNF signaling pathway. This study is expected to provide the basis for the further exploration of the compatibility mechanism of GQD.

Objective: Using network pharmacology and molecular docking technology, our aim was to clarify the biological activity, key targets, and potential pharmacological mechanisms of modified Pulsatilla decoction (MPD) in the treatment of ulcerative colitis (UC). Materials and Methods: The main active ingredients of MPD were screened using the traditional Chinese medicine systems pharmacology platform. UC targets were obtained from the GeneCard, OMIM, DisGeNET, PharmGkb, and DrugBank databases. The common genes of MPD in the treatment of UC were identified by Venn diagram. The visual interactive network diagram of “active ingredient-target-disease” was constructed using the software Cytoscape. We used the STRING database to construct a protein–protein interaction network and analyze the correlation in protein interaction. We conducted gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis for common genes using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database and R software. Subsequently, the molecular docking verification of ingredients and targets was conducted through Discovery Studio. Last, in vivo experiments were conducted to further verify the findings. Results: A total of 51 active ingredients were screened, involving 141 common genes. The top 5 ingredients in MPD were quercetin, β-sitosterol, luteolin, kaempferol, and stigmasterol. Pathways involved in the treatment of UC include the advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathway, the interleukin-17 (IL-17) signaling pathway, the tumor necrosis factor (TNF) signaling pathway, viral infection-related signaling pathways, and some cancer pathways. Molecular docking showed that the important ingredients of MPD were well docked with mitogen-activated protein kinase 1 (MAPK1), mitogen-activated protein kinase 8 (MAPK8), RAC-alpha serine (AKT1), vascular endothelial growth factor-A (VEGFA), transcription factor AP-1 (JUN), and interleukin-6 (IL-6). Animal experiments showed that MPD could ameliorate the injury and colitis in dextran sulfate sodium (DSS)-induced colitic rats. MPD inhibited the expression of p-p38A and p-MLC in UC rats. Conclusions: MPD has the characteristics of a multisystem, multi-ingredient, and multitarget in the treatment of UC. The possible mechanisms include inhibition of inflammation, apoptosis, oxidation, and tumor gene transcription. MPD may have a protective effect in the treatment of UC.

Integrated network pharmacology and metabolomics analysis to reveal the potential mechanism of Ershen Wan in ameliorating ulcerative colitis.

Network pharmacology and transcriptomics to determine Danggui Yifei Decoction mechanism of action for the treatment of chronic lung injury

Ulcerative colitis (UC), a chronic inflammatory bowel disease with increasing global incidence and limited therapeutic options, underscores the urgent need for novel multi-target agents. Swertiamarin (STM), a secoiridoid glycoside derived from traditional medicine, exhibits anti-inflammatory properties, but its pharmacological mechanisms in UC remain unclear. In this study, we integrated network pharmacology and experimental validation to systematically decipher STM's therapeutic effects. Network analysis identified 67 overlapping targets between STM and UC, which were significantly enriched in key pathways such as Toll-like receptor 4/Nuclear factor-kappa B (TLR4/NF-κB), Interleukin-17 (IL-17), and apoptosis. Molecular docking and protein-protein interaction (PPI) networks prioritized core targets such as TLR4, Caspase-3 (CASP3), and Prostaglandin-endoperoxide synthase (PTGS2). In a dextran sulfate sodium (DSS)-induced murine UC model, STM treatment significantly alleviated colitis severity, evidenced by reduced disease activity index (DAI), attenuated colon shortening (56.5% improvement vs. DSS group,p < 0.01), and restored histological integrity. Mechanistically, STM suppressed TLR4/NF-κB signaling, decreasing phosphorylated Inhibitor of NF-κB alpha (p-IκBα) (1.84 ± 0.33 vs. DSS 2.32 ± 0.28) and NF-κB (1.62 ± 0.39 vs. DSS 2.33 ± 0.38), while downregulating pro-inflammatory mediators (TNF-α, Interleukin-1β) and elevating anti-inflammatory Interleukin10 (IL-10) (98.33 ± 4.13 vs. DSS 61.70 ± 6.70,p < 0.01). Furthermore, STM reduced intestinal epithelial apoptosis (20 ± 2 vs. DSS 55 ± 3,p < 0.01) and modulated systemic immune responses by normalizing lymphocyte/neutrophil ratios. These findings reveal STM's multi-target efficacy in UC, bridging traditional medicine with modern mechanistic insights, and position it as a promising candidate for further clinical development.

Monocytes have emerged as critical driving force of acute inflammation. Here, we show that inhibition of Toll-like receptor 2(TLR2) dimerization by a TLR2 transmembrane peptide (TLR2-p) ameliorated DSS-induced colitis by interfering specifically with the activation of Ly6C(+) monocytes without affecting their recruitment to the colon. We report that TLR2-p directly interacts with TLR2 within the membrane, leading to inhibition of TLR2-TLR6/1 assembly induced by natural ligands. This was associated with decreased levels of extracellular signal-regulated kinases (ERK) signaling and reduced secretion of pro-inflammatory cytokines, such as interleukin (IL)-6, IL-23, IL-12, and IL-1β. Altogether, our study provides insights into the essential role of TLR2 dimerization in the activation of pathogenic pro-inflammatory Ly6C(hi) monocytes and suggests that inhibition of this aggregation by TLR2-p might have therapeutic potential in the treatment of acute gut inflammation.

Baiyu Decoction (BYD), a clinical prescription of traditional Chinese medicine, has been proven to be valuable for treating ulcerative colitis (UC) by enema. However, the mechanism of BYD against UC remains unclear. A combination of bioinformatics methods including network pharmacology and molecular docking and animal experiments were utilized to investigate the potential mechanism of BYD in the treatment of UC. Firstly, the representative compounds of each herb in BYD were detected by liquid chromatography-mass spectrometry. Subsequently, we predicted the core targets and potential pathways of BYD for treating UC through network pharmacology. And rat colitis model was established with dextran sodium sulfate. UC rats were subjected to BYD enema administration, during which we recorded body weight changes, disease activity index, and colon length to assess the effectiveness of BYD. Besides, quantitative real-time PCR, western blotting, ELISA and immunofluorescence were used to detect intestinal inflammatory factors, intestinal barrier biomarkers and TOLL-like receptor pathway in rats. Finally, the core components and targets of BYD were subjected to molecular docking so as to further validate the results of network pharmacology. A total of 41 active compositions and 203 targets related to BYD-UC were subjected to screening. The results of bioinformatics analysis showed that quercetin and kaempferol may be the main compounds. Additionally, AKT1, IL-6, TP53, TNF and IL-1β were regarded as potential therapeutic targets. KEGG results explained that TOLL-like receptor pathway might play a pivotal role in BYD protecting against UC. In addition, animal experiments and molecular docking validated the network pharmacology results. BYD enema treatment can reduce body weight loss, lower disease activity index score, reverse colon shortening, relieve intestinal inflammation, protect intestinal barrier, and inhibit TOLL-like receptor pathway in UC rats. Besides, molecular docking suggested that quercetin and kaempferol docked well with TLR4, AKT1, IL-6, TP53. Utilizing network pharmacology, animal studies, and molecular docking, enema therapy with BYD was confirmed to have anti-UC efficacy by alleviating intestinal inflammation, protecting the intestinal barrier, and inhibiting the TOLL-like receptor pathway. Researchers should focus not only on oral medications but also on the rectal administration of medications in furtherance of the cure of ulcerative colitis.

Integrating network pharmacology and experimental verification to explore the mucosal protective effect of Chimonanthus nitens Oliv. Leaf Granule on ulcerative colitis

Ulcerative colitis (UC) is a chronic inflammatory gastrointestinal disease mainly associated with immune dysfunction and microbiota disturbance. Cinnamaldehyde (CIN) is an active ingredient of Cinnamomum cassia with immunomodulatory and anti-inflammatory properties. However, the therapeutic effect and detailed mechanism of CIN on UC remains unclear, and warrant further dissection. In this study, network pharmacology and molecular docking analyses were introduced to predict the potential targets and mechanism of CIN against UC. The therapeutic effect and the predicted targets of CIN on UC were further validated by in vivo and in vitro experiments. Seven intersection targets shared by CIN and UC were obtained, and four hub targets, i.e., toll-like receptor 4 (TLR4), transcription factor p65 (NF-κB), NF-kappa-B inhibitor alpha (IκBα), prostaglandin G/H synthase 2 (COX2) were acquired, which were mainly involved in NF-κB, tumour necrosis factor (TNF), Toll-like receptor and NOD-like receptor signaling pathways. CIN alleviated the symptoms of dextran sulfate sodium (DSS)-induced colitis by decreasing the disease active index (DAI), restoring colon length, and relieving colonic pathology. CIN attenuated systemic inflammation by reducing serum myeloperoxidase (MPO), TNF-α, interleukin-6 (IL-6), and interleukin-1β (IL-1β), down-regulating TLR4, phosphorylated-NF-κB (p-NF-κB), phosphorylated-IκBα (p-IκBα), and COX2 expression in colonic tissues, and decreasing NOD-like receptor protein 3 (NLRP3), Caspase-1, and IL-1β protein expression in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. These results indicate that CIN alleviates DSS-induced colitis inflammattion by modulating TLR4/NF-κB signaling pathway and NLRP3 inflammasome activation.

Integrated network pharmacology, transcriptomics, and metabolomics analysis to reveal the mechanism of salt Eucommiae cortex in the treatment of chronic kidney disease mineral bone disorders via the PPARG/AMPK signaling pathway

The aim of this study was to identify the potential compounds, core targets and possible mechanism of Huanglian Jiedu decoction in treating ulcerative colitis based on network pharmacology and molecular docking. At first, potential compounds of Huanglian Jiedu decoction were retrieved from traditional Chinese medicine systems pharmacology. And then, the targets related to compounds and ulcerative colitis was obtained from traditional Chinese medicine systems pharmacology, Online Mendelian Inheritance in Man, GeneCards and DisGeNET. Next, Cytoscape was used to visualize drug-compound-common target-disease network and protein-protein interaction network. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes enrichment analysis was performed by database for annotation, visualization and integrated discovery to investigate possible mechanism of Huanglian Jiedu decoction against ulcerative colitis. At last, molecular docking verified the reliability of the prediction results. 55 compounds and 84 targets of Huanglian Jiedu decoction were screened out as potential players on ulcerative colitis. After network analyses, 10 core compounds (quercetin, kaempferol, wogonin, baicalein, acacetin, 5-hydroxy-7-methoxy-2-(3,4,5- trimethoxyphenyl) chromone, beta-sitosterol, moslosooflavone, 5,7,4'-trihydroxy-8-methoxyflavone, oroxylin A) and 10 core targets (interleukin-6, interleukin-1 beta, tumor necrosis factor-alpha, threonine-protein kinases, tumor antigen p53, prostaglandin-endoperoxide synthase 2, JUN, CXCL8, C-C motif chemokine 2, matrix metalloproteinase-9) were identified. Furthermore, the inflammatory response, tumor necrosis factoralpha signaling pathway, pathways in cancer, T cell receptor signaling pathway, toll-like receptor signaling pathway and nuclear factor kappa B signaling pathway may be involved in the treatment of ulcerative colitis using Huanglian Jiedu decoction. This study reveals that Huanglian Jiedu decoction contains multiple ingredients, multiple targets and multiple pathways in treating ulcerative colitis, which provides a basis for further research.

The aim of this study was to investigate the effect and molecular mechanism of Xuebijing Injection in the treatment of sepsis-associated acute respiratory distress syndrome(ARDS) based on network pharmacology and in vitro experiment. The active components of Xuebijing Injection were screened and the targets were predicted by the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). The targets of sepsis-associated ARDS were searched against GeneCards, DisGeNet, OMIM, and TTD. Weishengxin platform was used to map the targets of the main active components in Xuebijing Injection and the targets of sepsis-associated ARDS, and Venn diagram was established to identify the common targets. Cytoscape 3.9.1 was used to build the &quot;drug-active components-common targets-disease&quot; network. The common targets were imported into STRING for the building of the protein-protein interaction(PPI) network, which was then imported into Cytoscape 3.9.1 for visualization. DAVID 6.8 was used for Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment of the common targets, and then Weishe-ngxin platform was used for visualization of the enrichment results. The top 20 KEGG signaling pathways were selected and imported into Cytoscape 3.9.1 to establish the KEGG network. Finally, molecular docking and in vitro cell experiment were performed to verify the prediction results. A total of 115 active components and 217 targets of Xuebijing Injection and 360 targets of sepsis-associated ARDS were obtained, among which 63 common targets were shared by Xuebijing Injection and the disease. The core targets included interleukin-1 beta(IL-1β), IL-6, albumin(ALB), serine/threonine-protein kinase(AKT1), and vascular endothelial growth factor A(VEGFA). A total of 453 GO terms were annotated, including 361 terms of biological processes(BP), 33 terms of cellular components(CC), and 59 terms of molecular functions(MF). The terms mainly involved cellular response to lipopolysaccharide, negative regulation of apoptotic process, lipopolysaccharide-mediated signaling pathway, positive regulation of transcription from RNA polyme-rase Ⅱ promoter, response to hypoxia, and inflammatory response. The KEGG enrichment revealed 85 pathways. After diseases and generalized pathways were eliminated, hypoxia-inducible factor-1(HIF-1), tumor necrosis factor(TNF), nuclear factor-kappa B(NF-κB), Toll-like receptor, and NOD-like receptor signaling pathways were screened out. Molecular docking showed that the main active components of Xuebijing Injection had good binding activity with the core targets. The in vitro experiment confirmed that Xuebijing Injection suppressed the HIF-1, TNF, NF-κB, Toll-like receptor, and NOD-like receptor signaling pathways, inhibited cell apoptosis and reactive oxygen species generation, and down-regulated the expression of TNF-α, IL-1β, and IL-6 in cells. In conclusion, Xuebijing Injection can regulate apoptosis and response to inflammation and oxidative stress by acting on HIF-1, TNF, NF-κB, Toll-like receptor, and NOD-like receptor signaling pathways to treat sepsis-associated ARDS.

Type 2 diabetes mellitus (T2DM) is a notable health care load that imposes a serious impact on the quality of life of patients. The small amount of reported data and multiple spectra of pathophysiological mechanisms of T2DM make it a challenging task and serious economic burden in health care management. Abrus precatorius L. is a slender, perennial, deciduous, and woody twining plant used in various regions of Asia to treat a variety of ailments, including diabetes mellitus. Various in vitro studies revealed the therapeutic significance of A. precatorius against diabetes. However, the exact molecular mechanism remains unclarified. In the present study, a network pharmacology technique was employed to uncover the active ingredients, their potential targets, and signaling pathways in A. precatorius for the treatment of T2DM. In the framework of this study, we explored the active ingredient–target–pathway network and figured out that abrectorin, abrusin, abrisapogenol J, sophoradiol, cholanoic acid, precatorine, and cycloartenol decisively contributed to the development of T2DM by affecting AKT1, MAPK3, TNFalpha, and MAPK1 genes. Later, molecular docking was employed to validate the successful activity of the active compounds against potential targets. Lastly, we conclude that four highly active constituents, namely, abrusin, abrisapogenol J, precatorine, and cycloartenol, help in improving the body’s sensitivity to insulin and regulate the expression of AKT1, MAPK3, TNFalpha, and MAPK1, which may act as potential therapeutic targets of T2DM. Integrated network pharmacology and docking analysis revealed that A. precatorius exerted a promising preventive effect on T2DM by acting on diabetes-associated signaling pathways. This provides a basis to understand the mechanism of the anti-diabetes activity of A. precatorius.