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PubMed2025

Based on network pharmacology, molecular docking, and validation experiments to investigate the active components and mechanisms of action of Tibetan Medog County Citrus medica L.: In antioxidant activity.

BACKGROUND: The antioxidant potential of citrus plants is closely related to their geographical origin, making it crucial to evaluate the natural antioxidant properties of Citrus medica L. (C. medica) from Medog County, Tibet. METHODS: This study systematically investigates the antioxidant mechanisms of C. medica using network pharmacology, molecular docking, and experimental assays. RESULTS: The antioxidant activity experiments showed that C. medica exhibits good bioactivity, and the fruit has better antioxidant activity than the leaves. Network pharmacology revealed 11 active components of C. medica with 1547 antioxidant-related targets. Key targets include TP53, IL6, AKT1, STAT3, and TNF. Gene ontology (GO) analysis identified 1419 biological process entries, 147 cellular component entries, and 306 molecular function entries. Kyoto Encyclopedia of Genes and Genomes analysis identified 212 antioxidant-related signaling pathways. The GO and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the targets are involved in cancer pathways, protein binding, enzyme binding, lipid metabolism, and atherosclerosis. Molecular docking demonstrated that the 11 active components of Medog C. medica exhibit binding energies with core targets TP53, IL6, AKT1, STAT3, and TNF generally less than -5 kcal·mol-1, indicating good affinity. CONCLUSION: This study identifies the excellent antioxidant activity of C. medica from multiple aspects and elucidates its potential antioxidant mechanisms, providing a theoretical basis for the development and application of C. medica as an antioxidant functional additive.

Molecular Docking Simulation↗
PubMed2026

Active components and potential mechanisms of Wuzhuyu decoction in the treatment of ethanol-induced acute gastric mucosal injury: a network pharmacology and experimental verification.

OBJECTIVE: To investigate the underlying mechanisms and active components of Wuzhuyu decoction (, WD) in alleviating ethanol-induced acute gastric mucosal injury (GMI) using an integrated approach of network pharmacology and experimental verification. METHODS: Sprague-Dawley rats were randomly divided into six groups: control (Con), model (Mod), bismuth potassium citrate (BPC), WD at low (WD-L), medium (WD-M), and high (WD-H) doses. Following seven days of continuous intragastric administration of the respective treatments, an ethanol-induced gastric mucosal injury model was established in all groups except the control group by oral gavage of anhydrous ethanol. The gastric mucosal injury index was evaluated, and pathological changes were assessed viahematoxylin and eosin (HE) staining. Levels of tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) were measured by enzyme-linked immunosorbent assay (ELISA). The chemical composition was identified by ultra-performance liquid chromatography-tandem mass spectrometry. Active compounds were screened using the Swiss-absorption, distribution, metabolism, and excretion database, and their potential targets were predicted using the Swiss Target Prediction database and bioinformatics annotation database for molecular mechanism. Simultaneously, disease targets related to GMI were retrieved from the online mendelian inheritance in man and GeneCards databases. A protein-protein interaction (PPI) network was constructed, and functional enrichment analyses of gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed using the Metascape database. Key predictions from the network pharmacology analysis were subsequently verified through animal experiments. Protein expression levels of B-cell lymphoma-2 (Bcl-2), Bcl-2-associated X protein (Bax), Cleaved Caspase-3, and Cleaved Caspase-9 were analyzed by Western blot. Finally, molecular docking was performed using AutoDock Vina to investigate the interactions between the active components and core targets. RESULTS: WD treatment significantly reduced the gastric mucosal injury index and the levels of TNF-α, IL-1β, MDA, while it increased the activities of SOD and GSH-Px. Histopathological examination revealed marked improvement in gastric tissue morphology. A total of 145 compounds were identified in WD. Network pharmacology analysis identified 440 overlapping targets between WD and GMI. GO and KEGG enrichment analyses highlighted the apoptosis signaling pathway as a key mechanism for WD's protective effect against ethanol-induced GMI. Experimental validation demonstrated that WD treatment reduced the apoptosis of gastric mucosal epithelial cells, promoted the expression of Bcl-2, and inhibited the expression of Bax, Cleaved Caspase-3 and Cleaved Caspase-9. Molecular docking results indicated that dehydroevodiamine, rutaecarpine, evodiamine, hexahydrocurcumin, and isorhamnetin are potential active components in WD that contribute to the inhibition of apoptosis. CONCLUSIONS: WD alleviates ethanol-induced acute GMI, at least in part, by inhibiting the apoptosis. The primary active components responsible for this effect are dehydroevodiamine, rutaecarpine, evodiamine, hexahydrocurcumin, and isorhamnetin.

Drugs, Chinese Herbal↗
PubMed2025

Investigating the molecular mechanism of Yangxin decoction in treating major depressive disorder using network pharmacology and molecular docking technology approaches.

Yangxin decoction has been used to treat major depressive disorder (MDD). This study aims to identify the active components and potential mechanisms of Yangxin decoction in treating MDD using network pharmacology and molecular docking technology. The active components and targets of Yangxin decoction were screened, and MDD-related targets were predicted. Networks of "herbal medicine-active components-potential targets" and protein-protein interaction were constructed. Core components and core targets were identified through network topology analysis. Gene ontology functional and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on candidate genes. Molecular docking was conducted using AutoDock software (Olson Laboratory of the Scripps Research Institute, San Diego) to explore the interactions between core targets and active components, and the results were visualized using PyMOL (DeLano Scientific LLC, South San Francisco). A total of 433 active components and 392 targets of Yangxin decoction were identified, along with 11,796 MDD-related targets. There were 680 overlapping targets between Yangxin decoction and MDD, associated with 104 active components. Core targets identified through network topology analysis and molecular docking included serine/threonine kinase 1 (AKT1), tumor necrosis factor, interleukin-6, tumor protein P53, and proto-oncogene tyrosine-protein kinase Src. Gene ontology enrichment analysis revealed 1606 biological processes, 191 cellular components, and 373 molecular functions. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified 212 signaling pathways, with significant enrichment in caffeine metabolism, bladder cancer, advanced glycation end products-receptor for advanced glycation end products signaling pathway in diabetic complications, and vascular endothelial growth factor signaling pathway. Molecular docking results showed strong binding energy between core active components and core targets. Yangxin decoction exhibits multi-component, multi-pathway, and multi-target therapeutic characteristics. It primarily regulates targets such as AKT1, tumor necrosis factor, interleukin-6, tumor protein P53, and proto-oncogene tyrosine-protein kinase Src through advanced glycation end products-receptor for advanced glycation end products, vascular endothelial growth factor, and ErbB signaling pathways, exerting anti-inflammatory, immune-regulating, and oxidative stress-inhibiting effects to alleviate MDD.

Molecular Docking Simulation↗
PubMed2026

Elucidating the Mechanism of Xiaoqinglong Decoction in Chronic Urticaria Treatment: An Integrated Approach of Network Pharmacology, Bioinformatics Analysis, Molecular Docking, and Molecular Dynamics Simulations.

INTRODUCTION: Xiaoqinglong Decoction (XQLD) is a traditional Chinese medicinal formula commonly used to treat chronic urticaria (CU). However, its underlying therapeutic mechanisms remain incompletely characterized. This study employed an integrated approach combining network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulations to identify the active components, potential targets, and related signaling pathways involved in XQLD's therapeutic action against CU, thereby providing a mechanistic foundation for its clinical application. METHODS: The active components of XQLD and their corresponding targets were identified using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. CU-related targets were retrieved from the OMIM and GeneCards databases. Subsequently, core components and targets were determined via protein-protein interaction (PPI) network analysis and component-target-pathway network construction. Topological analyses were performed using Cytoscape software to prioritize core nodes within these networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database to identify enriched biological processes and signaling pathways. Molecular docking was performed to evaluate binding interactions between key components and core targets, while molecular dynamics (MD) simulations were employed to assess the stability of the component-target complexes with the lowest binding energy. Finally, CU-related targets of XQLD were validated using datasets from the Gene Expression Omnibus (GEO) database. RESULTS: A total of 135 active components and 249 potential targets of XQLD were identified, alongside 1,711 CU-related targets. Core components, such as quercetin, kaempferol, beta-sitosterol, naringenin, stigmasterol, and luteolin, exhibited high degree values in the constructed networks. The core targets identified included AKT1, TNF, IL6, TP53, PTGS2, CASP3, BCL2, ESR1, PPARG, and MAPK3. GO and KEGG pathway enrichment analyses revealed the PI3K-Akt signaling pathway as a central regulatory mechanism. Molecular docking studies demonstrated strong binding affinities between active components and core targets, with the stigmasterol-AKT1 complex exhibiting the lowest binding energy (-11.4 kcal/mol) and high stability in MD simulations. Validation using GEO datasets identified 12 core genes shared between CU-related targets and XQLD-associated targets, including PTGS2 and IL6, which were also prioritized as core targets in the network pharmacology analyses. DISCUSSION: This study comprehensively integrates multidisciplinary approaches to clarify the potential molecular mechanisms of XQLD in treating CU, highlighting its multitarget and multipathway synergistic effects. Molecular docking and dynamics simulations confirm the stable interaction between stigmasterol and the core target AKT1. Additionally, GEO dataset analysis verifies the pathogenic relevance of targets such as PTGS2 and IL6, significantly enhancing the credibility of our findings. These results provide a modern scientific basis for the traditional therapeutic effects of XQLD on CU and have important implications for developing multitarget treatments for this condition. However, this study mainly relies on database mining and computational simulations. Further in vitro and in vivo experimental validations are needed to confirm the predicted component-target-pathway interactions. CONCLUSION: This study identifies the active components, potential targets, and pathways through which XQLD exerts therapeutic effects on CU. These findings provide a theoretical foundation for further mechanistic studies and support their clinical application in the treatment of CU.

Molecular Docking Simulation↗
PubMed2026

Effects and mechanisms of Stauntonia brachyanthera Hand.-Mazz against Alzheimer's disease through network pharmacology and experimental validation.

Stauntonia brachyanthera Hand.-Mazz. (SB), a traditional medicinal plant of the Dong ethnic group with nutraceutical applications, exhibits broad-spectrum pharmacological activity. However, the therapeutic effects and mechanisms of SB on Alzheimer's disease (AD) remain unclear. This study aims to investigate the neuroprotective potential and underlying mechanisms of SB against AD. We utilized network pharmacology and molecular docking to predict the active components, targets, and pathways of SB associated with AD treatment. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were further used to identify potential therapeutic targets and underlying mechanisms of SB in relation to AD. Then, the neuroprotective effects, neuronal differentiation-promoting activity and potential mechanism of key active components of SB on the main therapeutic targets were verified by in vitro experiments. The network pharmacological prediction results showed that the treatment of AD with SB was closely related to MAPK and PI3K/Akt pathways. Further experiments showed that the SB active component kaempferol (KMF) alleviated Aβ1-42-induced injury and promoted neuronal differentiation. Additionally, we found that KMF-mediated promotion of neuronal differentiation in N2a cells was dependent on the PI3K/Akt and MAPK pathways. In this study, we employed a combined computational-experimental approach to elucidate the neuroprotective mechanisms of SB against Alzheimer's disease. We further validated KMF as a key active component of SB that alleviates Aβ1-42-induced injury and promotes neuronal differentiation through the PI3K/Akt and MAPK pathways.

Alzheimer's disease↗
PubMed2026

Integrative computational analysis combining network pharmacology, regulatory network modeling, and molecular dynamics reveals the mechanisms of Quanshen compound in ITP.

UNLABELLED: Immune thrombocytopenia (ITP) is a hemorrhagic disorder caused by immune dysfunction. Quanshen Compound (QSC) is an in-house preparation developed by the Uyghur Hospital in Hotan Prefecture. This study primarily investigates and validates the potential pharmacological basis and mechanism of action of QSC in modulating immune thrombopoiesis. Based on the multi-database screening of the QSC and the related targets of ITP, the intersection was obtained to construct a protein-protein interaction (PPI) network and screen the core targets; the intersection targets were analyzed for gene ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis using R packages; a component-target-pathway network was constructed to screen the key active components and their mechanisms of action. At the same time, the TF-mRNA-miRNA regulatory network of the core targets was constructed, and chromosome localization and subcellular localization analysis were performed; further, the binding stability of key components and core targets was verified through molecular docking and molecular dynamics simulation. A total of 227 potential target sites were screened out, among which TNF, IL6, AKT1, TP53 and IL1B were the core targets. The enrichment results indicated that these intersecting target sites mainly participated in inflammatory responses, immune regulation and hemostasis-related biological processes, and were significantly enriched in the PI3K-Akt signaling pathway, Toll-like receptor signaling pathway, Th17 cell differentiation and PD-1/PD-L1 signaling pathway. The core target TF-mRNA-miRNA regulatory network contained 184 nodes and 200 edges, suggesting that the core targets were subject to multi-level regulation. Molecular docking results showed that the main active components had good binding activity with the core targets, and molecular dynamics simulation further verified the stability of the complex. QSC may improve ITP through a multi-component, multi-target, and multi-pathway synergistic mechanism involving key targets such as TNF, IL6, AKT1, TP53, and IL1B, as well as the PI3K-Akt signaling pathway. These findings provide new insights into the potential therapeutic mechanisms of QSC against ITP and warrant further experimental validation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s40203-026-00718-0.

Immune thrombocytopenia↗
PubMed2026

[Effects and mechanisms of Jiawei Yigong San on the Th17/Treg balance in food allergy].

Objective To explore the effects and mechanisms of Jiawei Yigong San (JWYGS) on the T helper type 17 (Th17)/regulatory T (Treg) cell balance in food allergy (FA). Methods Active components, action targets of JWYGS, and FA-related targets, were screened via network pharmacology. Overlapping targets between JWYGS and FA were used to construct a protein-protein interaction (PPI) network. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed to predict key signaling pathways. Molecular docking was conducted to validate the binding affinity between the main active components and the predicted targets. Mice were randomly divided into control group, model group, JWYGS low-dose, medium-dose, and high-dose groups, and dexamethasone (DXM) group. An ovalbumin (OVA)-induced FA model was established. During the OVA challenge period, mice received daily intragastric administration, after which allergy and diarrhea scores were assessed. Small intestinal pathology was evaluated by HE staining. Serum ovalbumin-specific immunoglobulin E (OVA-sIgE), interleukin 6 (IL-6), IL-17, IL-2, and IL-10 were measured by ELISA. Small intestinal IL-6, IL-17, and IL-10 protein expression was detected by immunohistochemistry. Splenic Th17 and Treg cells were quantified by flow cytometry, and the Th17/Treg ratio was calculated. The mRNA expression of IL-6, retinoic acid receptor-related orphan receptor γt (RORγt), and forkhead box protein P3 (FOXP3) in the small intestine was detected by qPCR. Results Network pharmacology identified 235 active components of JWYGS and 136 common targets. GO and KEGG enrichment analyses highlighted cytokine response and Th17 differentiation. Molecular docking confirmed stable binding between core components and targets. Compared with the control group, the model group exhibited aggravated allergy and diarrhea scores, marked small intestinal inflammation and mucosal damage, elevated serum levels of OVA-sIgE, IL-6, IL-17 and IL-2, along with increased splenic Th17 cell frequency and Th17/Treg ratio. Intestinal IL-6 and IL-17 protein levels as well as IL-6 and RORγt mRNA expression were upregulated, whereas serum IL-10 levels were decreased, and intestinal expression of IL-10 protein and FOXP3 mRNA was downregulated. After JWYGS treatment, allergy and diarrhea scores were significantly reduced. Small intestinal inflammation and mucosal damage were alleviated. Serum levels of OVA-sIgE, IL-17, IL-6 and IL-2, Th17 cell frequency and the Th17/Treg ratio, intestinal IL-6 and IL-17 protein levels were decreased. IL-6 and RORγt mRNA expression was downregulated. Serum IL-10 levels were increased and intestinal expression of IL-10 protein and FOXP3 mRNA was upregulated. Moreover, the JWYGS high-dose group demonstrated comparable efficacy to the DXM group. Conclusion JWYGS can ameliorate symptoms and reverse the Th17/Treg imbalance in FA mice, potentially by inhibiting IL-6 transcription and regulating RORγt/FOXP3 expression.

Animals↗
PubMed2026

[Effects and mechanisms of ethanol extract of Salvia miltiorrhiza on liver fibrosis in mice].

To identify clinically advantageous TCMs for anti-hepatic fibrosis and to elucidate the effects and molecular mechanisms of Salvia miltiorrhiza ethanol extract in the intervention of liver fibrosis, this study screened high-frequency anti-hepatic fibrosis TCMs through a review of clinical literature. The S. miltiorrhiza active components, potential targets, and liver fibrosis-related disease targets were obtained using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), the GeneCards database, and other databases. Gene Ontology(GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analyses were performed on the shared targets between drugs and diseases. Molecular docking was conducted to evaluate the binding affinities between key components and core targets. In animal experiments, male Kunming mice were used to establish a liver fibrosis model induced by carbon tetrachloride(CCl_4). The mice were administered low, medium, and high doses of S. miltiorrhiza ethanol extract by gavage. The liver index, as well as serum aspartate aminotransferase(AST) and alanine aminotransferase(ALT) levels, were measured. Histopathological changes in liver tissue were observed using hematoxylin-eosin(HE) staining and Masson's trichrome staining. Western blot analysis was used to detect the protein expression levels of α-smooth muscle actin(α-SMA), Collagen Ⅰ, and heat shock protein 90 alpha family class A member 1(HSP90AA1) in liver tissue. The results showed that S. miltiorrhiza was the most frequently used TCM in clinical anti-hepatic fibrosis. A total of 65 active components and 135 potential targets were identified, and 109 common targets were obtained by intersecting these with liver fibrosis-related targets. The core targets included tumor protein p53(TP53), serine/threonine protein kinase AKT1(AKT1), Jun proto-oncogene(JUN), signal transducer and activator of transcription 3(STAT3), and HSP90AA1, which were mainly enriched in pathways related to cancer, hepatitis B, and the PI3K-AKT signaling pathway. Molecular docking indicated that the main active components of S. miltiorrhiza bound stably to the core targets, with the strongest binding affinity observed for HSP90AA1. Animal experiments demonstrated that the liver index, serum ALT and AST levels, and the expression of α-SMA, Collagen Ⅰ, and HSP90AA1 in liver tissue were significantly increased in the model group, accompanied by obvious pathological manifestations of fibrosis. Compared with the model group, different dose groups of S. miltiorrhiza ethanol extract reduced the liver index and serum ALT and AST levels to varying degrees, alleviated pathological damage and collagen deposition in liver tissue, and downregulated the protein expression of α-SMA, Collagen Ⅰ, and HSP90AA1. In conclusion, S. miltiorrhiza ethanol extract exerts a significant protective effect on CCl_4-induced liver fibrosis in mice, and its mechanisms may be related to the inhibition of HSP90AA1 expression and the regulation of liver fibrosis-related signaling pathways.

Animals↗
PubMed2026

Biocontrol effect of a solid-state fermentation-derived extract mixture of Trichoderma asperellum on sunflower Sclerotinia rot and associated host defense responses.

Sclerotinia disease is a destructive fungal disease of sunflowers, soybeans, and other economically important crops, causing substantial yield loss and quality deterioration. Long-term reliance on dose-dependent broad-spectrum fungicides is constrained by resistance risks and potential environmental burdens, creating tension with the sustainability goal of "reducing pesticide use while improving efficacy." Here, we explore a Trichoderma spp.-based microbial disease management strategy. Whole-genome sequencing of Trichoderma asperellum TCS007 isolated from Antarctic marine sediments, coupled with genome mining, predicted diverse biosynthetic gene clusters putatively associated with siderophores, polyketides, nonribosomal peptides, and terpenoids; the corresponding metabolites are not chemically confirmed and require further validation. Using a solid-state fermentation workflow, we prepared a fermentation-derived extract mixture (TCS007-SSF-Ex). In vitro assays showed dose-dependent inhibition of Sclerotinia sclerotiorum by TCS007-SSF-Ex (EC50 = 1.252 mg/L), and microscopy revealed cellular damage-consistent changes, including organelle disruption and plasmolysis. Pathogen transcriptomic and metabolism-related analyses indicated broad perturbations in organelle biogenesis and metabolic processes, with significant alterations in pathways associated with succinate, D-glucose, and phenylacetate; these results are consistent with growth inhibition and reduced pathogenicity, but specific molecular targets and causal links remain to be validated. In vivo, under certain application conditions, triple applications increased APX activity (+492.5%) and β-1,3-glucanase activity (+419.6%). Collectively, this work supports a "pathogen suppression-host defense induction" framework and facilitates subsequent identification of active components and mechanistic validation.IMPORTANCESclerotinia diseases cause recurrent and economically important losses in oilseed crops, while long-term fungicide use is constrained by resistance risks and environmental burdens. Trichoderma-based biocontrol is a promising complementary strategy, yet evidence supporting metabolite-containing Trichoderma-derived preparations as immune elicitors remains less consolidated than that for living inoculants, and scalable production routes are still needed. Here, we examine an Antarctic marine sediment-derived strain, Trichoderma asperellum TCS007, and a solid-state fermentation (SSF)-derived extract mixture (TCS007-SSF-Ex) produced via solid-state fermentation. We combine in vitro antifungal assays, pathogen ultrastructural observations, and correlative omics analyses with in vivo measurements of sunflower defense enzymes (APX and β-1,3-glucanase) to evaluate a "pathogen suppression-host defense induction" framework. Our findings support the potential of SSF-derived Trichoderma metabolite mixtures for greener management of Sclerotinia disease and provide a foundation for future chemical identification of active components and mechanistic validation.

Ascomycota↗
PubMed2024

DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression.

Super-enhancers are a class of DNA cis-regulatory elements that can regulate cell identity, cell fate, stem cell pluripotency, and even tumorigenesis. Increasing evidence shows that epigenetic modifications play an important role in the pathogenesis of various types of cancer. However, the current research is far from enough to reveal the complex mechanism behind it. This study found a super-enhancer enriched with abnormally active histone modifications in pancreatic ductal adenocarcinoma (PDAC), called DKK1-super-enhancer (DKK1-SE). The major active component of DKK1-SE is component enhancer e1. Mechanistically, AP1 induces chromatin remodeling in component enhancer e1 and activates the transcriptional activity of DKK1. Moreover, DKK1 was closely related to the malignant clinical features of PDAC. Deletion or knockdown of DKK1-SE significantly inhibited the proliferation, colony formation, motility, migration, and invasion of PDAC cells in vitro, and these phenomena were partly mitigated upon rescuing DKK1 expression. In vivo, DKK1-SE deficiency not only inhibited tumor proliferation but also reduced the complexity of the tumor microenvironment. This study identifies that DKK1-SE drives DKK1 expression by recruiting AP1 transcription factors, exerting oncogenic effects in PDAC, and enhancing the complexity of the tumor microenvironment.

Humans↗
PubMed2026

[Study on mechanism of Wendan Decoction in intervening in nonalcoholic fatty liver disease based on proteomics and network pharmacology].

This study systematically explored the molecular mechanism of Wendan Decoction(WDD) in treating nonalcoholic fatty liver disease(NAFLD) by integrating network pharmacology, proteomics, and experimental validation. A mouse NAFLD model was established using a high-fat diet, and the mice were randomly divided into a blank control group, a model group, a positive drug group(simvastatin, 3.03 mg·kg~(-1)), and low-(3.035 g·kg~(-1)), medium-(6.07 g·kg~(-1)), and high-dose(12.14 g·kg~(-1)) WDD groups, with intervention lasting for 6 weeks. After the intervention, the serum levels of alanine aminotransferase(ALT), aspartate aminotransferase(AST), triglycerides(TG), total cholesterol(TC), low-density lipoprotein cholesterol(LDL-C), and high-density lipoprotein cholesterol(HDL-C) were measured using an automatic biochemical analyzer. The serum levels of interleukin-1β(IL-1β), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α) were detected by ELISA. Liver histopathology was observed via hematoxylin-eosin(HE) staining and oil red O staining. Network pharmacology was used to predict potential targets and pathways, and proteomics was applied to identify differentially expressed proteins and related pathways. RT-qPCR and Western blot were performed to detect mRNA and protein expression of relevant genes. Animal experiments demonstrated that WDD dose-dependently ameliorated hepatic steatosis, inflammation, and lipid deposition, significantly reducing serum levels of ALT, AST, TG, TC, LDL-C, and pro-inflammatory cytokines(IL-1β, IL-6, and TNF-α), while significantly increasing serum HDL-C levels. Network pharmacology screening identified naringenin, baicalein, and other key active components, which were involved in pathways such as the peroxisome proliferator-activated receptor(PPAR), lipid, and atherosclerosis pathways. Proteomics further revealed differentially expressed pathways including the PPAR and advanced glycation end product-receptor(AGE-RAGE) signaling pathways. Integrated analysis highlighted the PPAR signaling pathway as the core mechanism. Molecular biology validation showed that WDD significantly regulated the mRNA expression of sterol regulatory element-binding protein-1c(SREBP-1c), fatty acid synthase(FASN), carnitine palmitoyl transferase 1A(CPT1A), acyl-CoA oxidase 1(ACOX1), and PPARα, as well as protein expression of PPARα, CPT1A, and PPARγ in mouse liver tissue. These results suggested that WDD might exert a multi-component, multi-target, and multi-pathway synergistic effect to improve lipid metabolism disorders and inflammatory responses with the PPAR signaling pathway as the central hub, thereby alleviating NAFLD progression.

Animals↗
PubMed2026

Multi-omics reveals that burdock seed aglycone alleviates renal fibrosis by restoring mitochondrial oxidative phosphorylation function.

Renal fibrosis (RF), a common pathological process driving chronic kidney disease (CKD) progression to end-stage renal failure, is closely associated with oxidative phosphorylation (OXPHOS). Arctigenin (ATG), the main active component of burdock seed, exhibits anti-inflammatory and anti-fibrotic activities, but its mechanisms in RF treatment remain unclear. Here, we performed integrated transcriptomic and proteomic analyses to identify key targets and pathways of ATG in a unilateral ureteral obstruction-induced rat RF model. Multi-omics enrichment analysis revealed that NDUFS8 and NDUFS2 were the core targets of ATG, with the OXPHOS pathway as the central intersecting pathway. Our results suggest that ATG exerts anti-renal fibrosis effects by targeting the OXPHOS pathway to inhibit excessive reactive oxygen species production and oxidative stress. SIGNIFICANCE: Chronic kidney disease (CKD) continues to impose an escalating global health and socioeconomic burden, while renal fibrosis (RF), as the convergent pathological endpoint of virtually all progressive nephropathies, remains the principal determinant of irreversible renal failure and adverse clinical outcomes. Despite extensive efforts to develop antifibrotic therapies, effective clinical interventions remain elusive, largely due to the complex and multifactorial nature of RF pathogenesis. In this study, we employed an integrated multi-omics framework encompassing transcriptomics, proteomics, and metabolomics to systematically decipher the antifibrotic mechanism of arctigenin (ATG), a bioactive natural compound derived from traditional Chinese medicine. Our findings identify mitochondrial oxidative phosphorylation as the pivotal regulatory axis underlying the renoprotective effects of ATG and further establish key catalytic subunits of mitochondrial complex I as its direct molecular targets. Mechanistically, ATG not only restores complex I activity and reprograms mitochondrial energy metabolism but also preserves the intracellular stability and localization of these subunits, thereby preventing their aberrant release-mediated inflammatory activation and disrupting the self-perpetuating cycle linking metabolic dysfunction, inflammation, and fibrosis progression. Beyond revealing a previously unrecognized dual mechanism integrating metabolic and inflammatory regulation, this study provides compelling evidence that mitochondrial dysfunction is not merely a secondary consequence of tissue injury but a fundamental driver of fibrotic remodeling. Importantly, our work highlights the translational potential of natural product-based mitochondrial interventions for CKD treatment and supports a broader conceptual shift toward metabolism-centered therapeutic strategies for chronic fibrotic diseases. Given the central role of mitochondrial dysfunction across multiple organs, these findings may also have far-reaching implications for the treatment of systemic fibrosis-related disorders beyond the kidney.

Animals↗
PubMed2026

Intraductal Papillary Squamous Neoplasm (IPSN) of the Pancreas: Histological and Molecular Characterization of a Novel and Distinct Intraductal Cancer Precursor.

We report 6 intraductal papillary squamous neoplasms (IPSNs) of the pancreas, a rare but distinctive tumor whose biological features remain largely unknown. Five cases were investigated using an integrated approach combining histomorphological evaluation, immunohistochemistry, and multiregional molecular profiling through whole-exome DNA sequencing and whole-transcriptome RNA sequencing. Only targeted DNA sequencing was available on a sixth recently diagnosed case. Histologically, the intraductal lesions were characterized by large, confluent papillae with fibrovascular cores lined by multilayered epithelial cells with diffuse squamous differentiation. All cases harbored a concomitant invasive carcinoma. The associated invasive carcinomas consistently included a pancreatic tubular/ductal adenocarcinoma; in 5 cases, a poorly differentiated squamous cell carcinoma was also present, the proportion/features of which met the diagnostic criteria of adenosquamous carcinoma in 2 of them. Genomic analyses revealed that IPSNs and their matched invasive carcinomas shared the majority of somatic alterations, supporting a shared clonal origin for the 2 components. Activating KRAS mutations and biallelic inactivation of CDKN2A were detected in all cases. Recurrent mutations involved members of the SWI/SNF chromatin-remodeling complex and KMT2D. Additionally, FGFR1 and MYC amplifications were identified in 2 distinct cases (1 case each). Molecular alterations restricted to the invasive component involved mediators of the transforming growth factor-β signaling pathway. Transcriptomic profiling demonstrated a basal-like expression pattern in all IPSNs and squamous cell carcinomas, although in 2 cases, the matched pancreatic tubular/ductal adenocarcinoma shifted toward a classical transcriptomic subtype. In conclusion, through integrated histological assessment and multiregional molecular sequencing, we demonstrate that IPSN represents a bona fide precursor of invasive pancreatic cancer, a new addition to the intraductal neoplasms category. This study challenges the current paradigm that pancreatic squamous epithelium plays no role in the initiation of pancreatic carcinogenesis, providing the first evidence of its involvement in early tumorigenic processes and yielding immediate implications for pancreatic tumor classification and biological understanding.

Humans↗
PubMed2026

A Network Pharmacology and Molecular Docking Study of TongBi Formula for Osteoarthritis.

This study applied network pharmacology combined with molecular docking to predict the potential therapeutic targets and molecular mechanisms of TongBi Formula (TBF) in osteoarthritis (OA). Active components and corresponding targets of TBF were retrieved from the traditional Chinese medicine Systems Pharmacology Database and Analysis Platform, while OA-related targets were collected from Online Mendelian Inheritance in Man, GeneCards, DrugBank, and Therapeutic Target Database. A network visualization and analysis software was used to construct compound-target and protein-protein interaction (PPI) networks. Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery platform. Molecular docking analysis was conducted using a molecular docking software to evaluate the predicted binding affinity between key active compounds and core target proteins. A total of 47 overlapping targets between TBF and OA were identified. PPI network analysis highlighted JUN, RELA, IL6, MAPK1, and IL10 as potential hub targets. Enrichment analysis suggested that TBF may regulate inflammation, lipid metabolism, and multiple intracellular signaling pathways associated with OA progression. Molecular docking results demonstrated favorable predicted binding affinities between core active compounds and key OA-related protein targets. These findings provide a computational framework for understanding the potential mechanisms of TBF against OA and support further experimental validation.

Molecular Docking Simulation↗
PubMed2026

Intratumoral Mycobacterium abscessus promotes cytidine deaminase mutagenesis in non-small cell lung cancer.

The intratumoral microbiota is increasingly recognized as an active component of the tumor microenvironment, yet whether it directly drives tumor mutagenesis remains unclear. Here, integrated multi-omics analysis of human non-small cell lung cancer (NSCLC) identifies Mycobacterium abscessus as a microbial determinant of APOBEC3A-associated mutagenesis. Mechanistically, the bacterial effector nucleoside diphosphate kinase (NDK) directly targets the host transcription factor IRF3 and installs a non-canonical 1-phosphohistidine modification at H263, thereby amplifying type I interferon signaling and sustaining APOBEC3A expression. This inter-kingdom phosphotransfer event links intratumoral microbial colonization to an endogenous mutational process that promotes genomic diversification. Genetic inactivation of NDK, or pharmacologic elimination using an engineered NDK-PROTAC, suppresses APOBEC3A activation and attenuates microbe driven mutagenesis. Together, these findings establish a direct microbial effector mechanism that promotes APOBEC3A-associated mutagenesis and provide a therapeutic framework to intercept microbiome driven mutagenesis in NSCLC.

Humans↗
PubMed2026

Dictamnine alleviates oxidative stress in rheumatoid arthritis via modulation of the NR1D1-Keap1/Nrf2/ARE axis.

Rheumatoid arthritis (RA) is a persistent systemic disorder of autoimmune origin, with its core pathological manifestation being inflammation of the synovial tissue. The excessive growth of fibroblast-like synoviocytes (FLS) represents a critical pathological mechanism in RA, actively driving the advancement of the condition. Dictamnus dasycarpus Turcz. (D. dasycarpus) exhibits prominent anti-inflammatory effects and shows favorable therapeutic efficacy against RA. Dictamnine (Dic) is a major active component of D. dasycarpus, however, its therapeutic effectiveness and underlying mechanisms in RA have yet to be fully elucidated. This study investigated the effect of Dic on synovial hyperplasia in RA and elucidated the underlying mechanisms. Using a TNF-α-induced human fibroblast-like synoviocyte (HFLS-RA) model and a collagen-induced arthritis (CIA) mouse model, Dic was found to effectively inhibit synovial cell proliferation and pathological hyperplasia. Proteomics analysis was employed to clarify its potential mechanism in ameliorating the disease, and the findings were further validated through hematoxylin and eosin (H&E) staining, immunofluorescence (IF), ROS detection, JC-1 staining, cellular thermal shift assay (CETSA), drug affinity responsive target stability (DARTS) analysis, quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting (WB). The results suggested that the anti-RA activity of Dic is associated with its interaction with the nuclear receptor NR1D1. Moreover, the NR1D1 antagonist SR8278 reversed Dic's effects on Nrf2 and cytoprotection, confirming that Dic functions through NR1D1. This activation consequently influences the Keap1/Nrf2/ARE cascade, leading to decreased intracellular reactive oxygen species (ROS) accumulation and an improvement in compromised mitochondrial membrane potential. siRNA knockdown experiments further confirmed that NR1D1 is a target of Dic and regulates the downstream Keap1/Nrf2/HO-1 signaling pathway, through which Dic ameliorates RA both in vitro and in vivo by upregulating NR1D1 expression to activate the Keap1/Nrf2/ARE antioxidant pathway, thereby mitigating oxidative stress, inhibiting synovial cell proliferation, and ultimately alleviating pathological synovial hyperplasia.

Arthritis, Rheumatoid↗
PubMed2026

Littoral and wetland vegetation decrease carbon emissions from dry inland waters.

Lakes are recognized as active components of the inland water carbon (C) cycle, as organic matter is processed by microbial respiration, inducing large carbon dioxide (CO2) and methane (CH4) emissions. In the context of long-lasting drought periods, large uncertainties remain about: (1) the influence of wet-dry cycle on CO2 and CH4 fluxes in littoral zones and lacustrine wetlands; and (2) the contribution of emergent vegetation to C fluxes in dry inland waters. At the water-land interface of two shallow lakes, this study focuses on CO2 and CH4 fluxes from vegetated and bare dry inland waters in relation to hydrological fluctuations. Three seasonal campaigns were conducted to measure daytime CO2 and CH4 fluxes in pelagic, littoral and wetland surface waters, as well as in temporarily air-exposed sediments, using floating and static chambers, respectively. Our results reveal that wet-dry cycle in the littoral zone and wetlands strongly influence gaseous C fluxes through contrasting patterns, especially in late summer, when the biological processes are most active (primary production and respiration). In air-exposed littoral zones, organic-poor sandy sediments presented the lowest CO2 and CH4 emissions, whereas in air-exposed lacustrine wetlands, water-saturated sediments accumulated high amounts of plant-derived organic matter, promoting intense microbial activity and the highest C emissions. However, amphiphytes and helophytes vegetation in exposed littoral zones and wetlands reversed the direction of C fluxes, inducing the highest CO2 uptake due to high photosynthesis rates. This study underlines the relevance of considering vegetation in dry inland waters, particularly in lacustrine littoral zones and wetlands, to obtain comprehensive lake C budgets, especially under climate change scenarios.

Wetlands↗
PubMed2026

Exploring the mechanism of Shengmai San in treating lung adenocarcinoma based on bioinformatics and molecular dynamics simulation.

To investigate the mechanism of Shengmai San (SMS) in the treatment of lung adenocarcinoma (LUAD) based on an integrated strategy combining "network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulation," aiming to provide a precise combination therapy strategy and identify potential bioactive compounds. Differentially expressed genes in LUAD were identified from the Gene Expression Omnibus database using R (originally developed at Bell Laboratories and currently managed by Lucent Technologies). SMS components (ginseng, Ophiopogon japonicus, and Schisandra chinensis) were retrieved from encyclopaedia of traditional Chinese medicine, with Lipinski-compliant compounds selected. Compound targets were predicted via SwissTargetPrediction and Similarity Ensemble Approach. Intersecting targets between differentially expressed genes and compound targets were identified for "herbs-compounds-targets-disease" network construction. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed. Hub targets were identified by analyzing the protein-protein interaction network. High-prognostic relevance targets were screened from The Cancer Genome Atlas. Compounds targeting these were identified through the herbs-compounds-targets-disease network, and absorption, distribution, metabolism, excretion, and toxicity-compliant compounds were selected using SwissADME (a web-based tool provided by the Molecular Modeling Group of the Swiss Institute of Bioinformatics). Core regulatory targets were identified through molecular docking, with complex stability assessed by molecular dynamics simulations. The key bioactive compounds of SMS for treating LUAD were identified as 7-hydroxy-2,5-dimethyl-4H-1-benzopyran-4-one, N-trans-feruloyltyramine, paprazine, and (E)-N-[(2S)-2-hydroxy-2-(4-hydroxyphenyl)ethyl]-3-(4-hydroxyphenyl)prop-2-enamide. Hub targets included AURKA, CCNA2, CCNB1, CDK1, CHEK1, KIF11, NEK2, PLK1, TTK, and TYMS. Among these, CDK1, CHEK1, and PLK1 demonstrated both high-prognostic relevance and strong binding affinity with SMS, emerging as core regulatory targets for SMS in LUAD treatment. Mechanistically, SMS exerts its anticancer effects primarily by modulating the tumor necrosis factor, interleukin-17, cell cycle, and Lipid and atherosclerosis signaling pathways. The active components of SMS, such as paprazine, may exert antitumor effects partly through downregulating CDK1, CHEK1, and PLK1 expression. Although the present study did not examine drug-resistance models or combination regimens, our findings raise the possibility that, in patients with high expression of these genes, combining SMS with standard chemotherapy or targeted therapy could potentially enhance chemosensitivity and mitigate the development of resistance. This hypothesis, however, requires formal testing in appropriate preclinical models and functional validation studies.

Molecular Dynamics Simulation↗