Combinatorial Chemistry & High Throughput Screening - Online First

Cartilage defects (CDs) are orthopedic conditions with limited regenerative potential. This study aimed to identify endoplasmic reticulum (ER) stress-related biomarkers and construct a diagnostic model to enhance the early detection of CD.

This study analyzed the transcriptomic dataset GSE129147 to identify ER stress-related differentially expressed genes (ERSRDEGs) between CD and control tissues using the limma package (version 3.58.1). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were employed for functional enrichment. Immune infiltration was assessed using cell-type identification, which involved estimating the relative subsets of RNA transcripts and single-sample gene set enrichment analysis. Diagnostic models were constructed using logistic regression, support vector machine, and least absolute shrinkage and selection operator regression.

Twenty ERSRDEGs were identified, with CYBB, ATP6V1A, and TNFRSF12A significantly upregulated in CD samples. GO and KEGG analyses highlighted oxidative stress response and extracellular matrix remodeling as key mechanisms in CD pathogenesis. Immune analysis revealed an increase in regulatory T cells and a reduction in CD8⁺ T cells. TNFRSF12A showed strong immune associations and, together with TWIST1 and ATP6V1A, formed the final preliminary diagnostic model. The preliminary LASSO model achieved satisfactory predictive accuracy (AUC: 0.7–0.9).

These findings suggest that ER stress and immune imbalance jointly contribute to cartilage degeneration. The identified genes, particularly TNFRSF12A, TWIST1, and ATP6V1A, not only serve as potential biomarkers but also provide preliminary evidence for new mechanistic insights into stress–immune crosstalk in CD.

This study reveals the key roles of ER stress and immune dysregulation in CDs. Moreover, the ERSRDEG-based diagnostic model provides preliminary bioinformatics evidence and potential molecular indicators for targeted diagnostics and therapies.

Topological indices serve as mathematical descriptors for chemical structures, playing a crucial role in elucidating the physicochemical characteristics of compounds. Ambient-stable electroactive graphene nanoribbons are air-stable, electronically tunable and easily fabricated nanostructures, formed by the elongation of nanographene ribbon segments. This study aimed to develop precise topological formulations for three types of ambient-stable electroactive graphene nanoribbons (AEGNR) using graph-theoretical structural measures, and to evaluate their energetic properties along with their ¹³C NMR spectral characteristics.

The study employs the cut method, which is based on the Djoković-Winkler relation, to calculate topological indices.

In this article, we evaluated selected spectral and energetic properties of AEGNR variants.

The computed topological indices based on distance and vertex degree could provide important chemical insights into the properties of AEGNR(l).

We developed exact mathematical expressions for bond-additive molecular descriptors corresponding to three types of ambient-stable electroactive graphene nanoribbons (AEGNRs). An evaluation of HOMO-LUMO energy gaps was also performed for the AEGNR(l) chains.

Sleep disorders (SD) affect approximately 25% of the global population. Traditional Chinese Medicine (TCM) formulas have been shown to alleviate SD by modulating endogenous melatonin. This study used data mining, network pharmacology, and meta-analysis to identify key herbal pairs from TCM formulas and the mechanism of action.

Literature was retrieved from PubMed, Web of Science, Embase, Cochrane Library, CNKI, Wanfang Data Information Site, China Science and Technology Journal Database, and SinoMed. R was used for frequency and association rule analysis, SPSS for clustering, and Cytoscape, STRING, Gene Ontology, and KEGG enrichment analyses were utilized to explore targets, protein-protein interactions, and pathways. A meta-analysis using the Metan command was performed to assess the optimal herbal pairs for SD treatment.

Data mining identified 77 commonly used herbs, revealing four advantageous herbal pairs: PAEONIAE RADIX ALBA (PRA)-BUPLEURI RADIX (BR), COPTIDIS RHIZOMA (CR)-CINNAMOMI CORTEX (CC), PORIA (PA)-BUPLEURI RADIX (BR), and ZIZIPHI SPINOSAE SEMEN (ZSS)-MARGARITIFERA CONCHA (MC). Network pharmacology showed that (PRA-BR)-SD, (PA-BR)-SD, (CR-CC)-SD, and (ZSS-MC)-SD targeted CACNA1D, GRIN2A, AGT, and ATP1A1 via prion diseases, nicotine addiction, neuroactive ligand-receptor interaction, and cardiac muscle contraction pathways, respectively.

Research shows that CACNA1D could regulate Ca²⁺ inward flow, avoid mitochondrial dysfunction in prion diseases, and reduce ROS generation, thus indirectly maintaining MT levels and sleep. GRIN2A as an amygdala hub gene closely related to daily smoking, combining brain transcriptome analysis and tobacco consumption GWAS data. The sleep regulation mechanism of MT relies on the neuroactive ligand-receptor pathway. As a neuroactive ligand, MT triggers sleep-promoting physiological responses by activating the G-protein-coupled receptors MT1 and MT2 and transmitting “night” signals to the relevant neural networks. Insufficient MT secretion or circadian rhythm disruption might lead to abnormal blood pressure rhythms accompanied by sympathetic overactivation, increasing the risk of insomnia and cardiovascular disease. ATP1A1 is a key molecule in the maintenance of electrochemical gradients in cardiac myocytes through the modulation of the Na⁺/K⁺ homeostasis affects myocardial excitability, calcium kinetics, and contractile function.

Meta-analysis and network pharmacology suggest that the PA-BR pair might offer superior efficacy by modulating membrane potential and nicotine addiction pathways, targeting GRIN2A, GRIN1, GRIN3A, and GRIN2B to regulate melatonin levels.

Observational studies have linked diabetes with cataracts, but they cannot fully elucidate the underlying causes and mechanisms. This investigation aims to evaluate the causal relationship between genetically predicted diabetes and cataract risk utilizing Mendelian randomisation (MR) techniques.

We identified single nucleotide polymorphisms (SNPs) with a significant threshold of P < 5×10^-8 as instrumental variables from genome-wide association study datasets pertaining to Type 1 (finn-b-E4_DM1, n=189,113), Type 2 diabetes (finn-b-E4_DM2, n=215,654), and cataract (ukb-b-8329, controls=136,388, cataract=14,254). Various Mendelian randomisation methods were employed, including inverse-variance weighted (IVW), MR-Egger, weighted median, simple mode (SM), and weighted mode analyses. Additionally, sensitivity analyses were conducted to assess the robustness of the findings, encompassing tests for heterogeneity, pleiotropy, and leave-one-out assessments. A multivariable (MVMR) approach was used to account for potential confounders, such as obesity (IEUA-92, controls = 47468, obesity = 2896), smoking (ukb-a-16, n = 337030), and alcohol consumption (IEUA-1283, n = 112,117).

The analysis included 12 SNPs, which were derived from loci specifically associated with Type 1 diabetes and known to govern immune-inflammatory and metabolic pathways. The genetically-predicted Type 1 diabetes was found to elevate cataract risk significantly (OR=1.003, 95% CI: 1.001–1.005, P=0.001). The results of the sensitivity analyses corroborated the robustness of these findings, showing no significant heterogeneity (Cochran Q, P value = 0.73) or pleiotropy (MR-Egger intercept, P value = 0.38). Furthermore, multivariable MR demonstrated that the impact of diabetes on cataract risk remained significant after adjustment for multiple lifestyle factors.

We provide novel MR evidence that Type 1 diabetes causally increases the risk of cataract through the synergistic activity of immune dysregulation, chronic inflammation, and metabolic disturbance, with immune-metabolic crosstalk as the primary driver.

T1D causally increases the risk of cataract through the disruption of immune-inflammatory and metabolic pathways. Targeting immune-metabolic interactions may offer novel therapeutic strategies for preventing diabetic cataracts.

This study investigated the anti-ovarian cancer (OC) effects of Shuangzi Powder (SZP) and its regulatory impact on the tumor microenvironment.

This study employed systems biology approaches, integrating molecular docking and experimental validation, to explore the pharmacological mechanisms of SZP in OC treatment. To identify potential bioactive compounds and target genes of SZP, network pharmacology, protein–protein interaction network analysis, Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were conducted.

Among the 11 bioactive ingredients identified in SZP, 1,767 potential therapeutic targets were predicted, while 2,637 differentially expressed genes were found to be associated with OC. KEGG pathway analysis revealed significant enrichment in pathways related to cancer, apoptosis, the PI3K-Akt signaling pathway, and the PD-L1/PD-1 checkpoint pathway. Treatment of A2780 cells with β,β-Dimethylacrylshikonin (DMAS) inhibited cell viability, migration, and invasion. Moreover, DMAS downregulated the expression of cell cycle- and apoptosis-related genes (CCNB1, CHEK1, CCNE1, and PARP1) and upregulated the immune checkpoint gene PD-L1.

These findings indicate that multiple components, targets, and pathways are involved in OC treatment by SZP.

DMAS, one of the bioactive ingredients of SZP, was predicted and preliminarily validated to exert inhibitory effects on OC cells, mainly through the regulation of the cell cycle, apoptosis, and immune response, as demonstrated by molecular docking and experimental analyses.

Y-box binding protein 1 (YBX1), an RNA-binding protein capable of recognizing the 5-methylcytosine (m5C), plays a role in the development and progression of various cancers. In this study, we aim to investigate the functional mechanism of YBX1-mediated m5C modification in Bladder Cancer (BCa).

The impact of YBX1 on glycolysis and biological functions in BCa cells was evaluated through a set of in vitro experiments. The underlying mechanisms involving YBX1, Transmembrane 4 L six family 1 (TM4SF1), and β-catenin/C-myc in BCa and their relationship were investigated using RNA immunoprecipitation (RIP), m⁵C-RIP, Actinomycin D, and luciferase reporter gene assays.

BCa cells exhibited elevated expression levels of YBX1 compared to human transitional bladder epithelial cells. YBX1 knockdown inhibited BCa cell proliferation, migration, and invasion while also attenuating glycolytic activity, as evidenced by reduced glucose uptake, lactic acid production, and ATP synthesis. Mechanically, we found that YBX1-dependent m⁵C modification promoted the stability of TM4SF1 mRNA, thereby upregulating TM4SF1 expression and subsequently activating the β-catenin/C-myc signaling. Furthermore, we discovered that overexpression of β-catenin could reverse the inhibitory effects of TM4SF1 silencing on proliferation and glycolysis in BCa cells.

This study has refined the mechanism of BCa progression, but the clinical significance and in vivo functions of the YBX1/TM4SF1 axis still require further verification.

YBX1 stabilizes TM4SF1 mRNA via m⁵C modification in BCa, activating β-catenin/c-Myc signaling to drive tumor growth and glycolysis. This reveals a novel therapeutic target for BCa.

Barberry Root (Sankezhen, SKZ), a traditional Uyghur herb from Xinjiang, China, has been shown to alleviate diarrhea-predominant irritable bowel syndrome (IBS-D); however, its molecular mechanisms remain unclear. This study aimed to systematically predict SKZ’s therapeutic targets and pathways for IBS-D using computational and experimental integration.

Active SKZ compounds and targets were sourced from TCM-Suite, BATMAN-TCM, and related databases. IBS-D targets were identified via DisGeNET and GeneCards, etc. Protein-Protein Interaction (PPI) networks, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Molecular docking and 100-ns Molecular Dynamics (MD) simulations validated compound-target stability. In vitro (LPS-induced RAW264.7 macrophages) and in vivo (IBS-D model rats, isolated intestinal segments) experiments verified SKZ’s effects.

Fifteen bioactive compounds and 85 overlapping targets were identified, with four key compounds [(R)-Reticuline, Ferulic acid 4-O-glucoside, Magnoflorine, SW 7] and 15 hub targets (e.g., ESR1, EGF, ALB) prioritized. Enrichment analyses linked targets to inflammation and intestinal motility pathways. Docking showed strong binding affinities (<-8.0 kcal/mol), and MD simulations confirmed stability. SKZ suppressed inflammatory mediators, downregulated CHAT/C-FOS/5-HT3R/5-HT4R mRNA, and antagonized acetylcholine/barium chloride-induced intestinal contractions.

The findings highlight SKZ’s synergistic role in ameliorating IBS-D via multi-pathway regulation, consistent with existing research on inflammation and neurotransmission, though limitations include the need for further validation of individual compounds.

SKZ exerts synergistic therapeutic effects on IBS-D by ameliorating inflammation and regulating neurotransmission and intestinal motility, potentially via NF-κB/MAPK, COX-2/PGE2, cholinergic/5-HT, and calcium/potassium channel pathways, forming a multidimensional network.

Sarcopenia (Sar) is an age-related loss of muscle mass and function. Propolis, a natural product with anti-inflammatory properties, may help prevent Sar, but its active components and mechanisms remain unclear.

Network pharmacology identified intersecting targets of propolis ethanol extract (PEE) and Sar. PPI and CTP networks highlighted key compounds and targets, verified by molecular docking. In vitro, apigenin (Ap), the predicted main compound, was tested on D-galactose-induced senescent C2C12 myoblasts via cell viability and Western blotting.

Twelve overlapping targets were identified between PEE and Sar, with TNFα and IL6 highlighted as hub targets. Network analysis determined Ap as the main active compound. Molecular docking revealed strong binding affinities of Ap with TNFα and IL6. In vitro experiments demonstrated that Ap significantly enhanced the viability and differentiation of senescent C2C12 cells, downregulated TNFα and IL6 expression, and inhibited JAK2 and STAT3 phosphorylation, indicating suppression of the JAK-STAT signaling pathway.

The findings suggest that PEE, primarily through Ap, alleviates Sar by targeting inflammatory pathways and suppressing JAK-STAT signaling, thereby promoting muscle regeneration. The integration of network pharmacology, molecular docking, and in vitro validation provides mechanistic insights supporting the therapeutic potential of PEE in Sar. Limitations include the absence of in vivo confirmation, which warrants further animal and clinical studies to validate these effects and explore translational applications.

This study identifies Ap as the key active compound in PEE that alleviates Sar by downregulating TNFα and IL6 and inhibiting the JAK-STAT pathway. The results provide a molecular basis for the use of propolis as a natural intervention for Sar and support its development as a functional food or therapeutic agent targeting age-related muscle degeneration.

Hua-Zhuo-Ning-Fu decoction (HZD) is a traditional Chinese medicine prescription that has been clinically used by Chinese medical master Wang Xinlu for treating psoriasis. However, the specific molecular mechanisms remain unclear.

To identify the effective compounds of HZD and psoriasis-related genes, we conducted comprehensive searches in public databases, including TCMSP, SwissTargetPrediction, Gene Cards, and OMIM. Based on the degree values, core genes of HZD against psoriasis were determined. Furthermore, the affinity energy between the active compounds of HZD and their core targets was validated via molecular docking. Finally, the anti-psoriasis effects and potential mechanisms of HZD were examined in M5-stimulated HaCaT cells in vitro and IMQ-induced psoriasis mice in vivo.

Network pharmacological analysis of HZD for psoriasis treatment identified 43 active components and 243 targets. Topological and molecular docking analyses identified interleukin (IL)-6 and tumor necrosis factor-α (TNF-α) as core targets for its anti-psoriasis effects. Specifically, the docking energy of isovitexin with IL-6 was lower (-7.30 kcal/mol), and that of baicalin with TNF-α was lower (-6.70 kcal/mol). KEGG analysis revealed that the main pathway was the PI3K/AKT pathway. HZD inhibited cell viability, inflammation, and oxidative stress in M5-induced HaCaT cells. Animal experiments demonstrated that HZD alleviated psoriatic dermatitis, histopathological features, and inflammation in IMQ-induced mice with psoriatic plaques. Notably, HZD inhibited the expression of TNF-α and IL-6 and the activation of the PI3K/AKT pathway both in vivo and in vitro.

Specific upstream/downstream regulators of the PI3K/AKT axis regulated by HZD still need to be explored. Further investigation is essential to clarify the functional relationship between the predicted targets and active components.

In summary, HZD potentially mitigated inflammatory responses by targeting the TNF-α and IL-6 proteins, interfered with the PI3K/AKT pathway, and consequently drove the anti-psoriatic effect in IMQ-induced mice. Our findings provide a theoretical basis for HZD’s clinical use in psoriasis treatment.

The comorbidity of myocardial ischemia reperfusion injury (MIRI) and depression (DEP) may worsen the prognosis of coronary heart disease surgery. Currently, research on medications and therapeutic mechanisms for MIRI combined with DEP is still insufficient. This study aims to explore the relationship between DEP and MIRI, and the therapeutic effects and mechanisms of Baihe Dihuang Danshen decoction (BDDSD) on DEP combined with MIRI.

SD rats were assigned to a final experimental framework of six groups (Sham, MIRI, DEP+MIRI, BDDSD, DEP drug control, MIRI drug control). DEP was induced via 6-week chronic unpredictable mild stress (CUMS), with BDDSD administered during the final 2 weeks. MIRI was then induced by 30-minute coronary artery ligation and 2-hour reperfusion. DEP severity was assessed using behavioral tests (open field, elevated plus maze, sucrose preference, forced swimming). MIRI outcomes were evaluated via infarct size, histopathology, serum markers (LDH, IL-6, IL-1β), myocardial oxidative stress (MDA, GSH, SOD, Fe²⁺), and NADPH/FSP1/CoQ10 pathway proteins (FSP1, CoQ10, FTL, NOX2, NOX4, COX2).

Compared with the MIRI group, DEP significantly exacerbated MIRI, manifested by increased serum IL-6 and IL-1β levels, enlarged infarction area, and aggravated oxidative damage (elevated MDA/Fe²⁺, decreased SOD/GSH). Compared with the DEP+MIRI group, BDDSD intervention relieved DEP of rats, and subsequently reduced infarction area; decreased serum LDH, IL-6, and IL-1β; lowered myocardial MDA and Fe²⁺ while increasing SOD and GSH; upregulated FSP1/CoQ10/FTL; and downregulated NOX2/NOX4/COX2 expression.

DEP can aggravate inflammation and oxidative stress, promoting cardiac ferroptosis, thereby exacerbating MIRI. Our results demonstrate that BDDSD alleviates MIRI-DEP comorbidity through a dual mechanism, mitigating depressive symptoms and inhibiting myocardial ferroptosis via modulation of the NADPH/FSP1/CoQ10 pathway. Although the efficacy of BDDSD is encouraging, its dose-effect relationship and long-term safety require further study.

BDDSD effectively treats DEP-MIRI comorbidity through its dual mechanism, mitigating DEP and protecting against myocardial ferroptosis. Our study not only offers a novel therapeutic strategy for patients with DEP requiring coronary heart disease surgery but also provides new targets for developing drugs to treat MIRI combined with DEP.

Chronic atrophic gastritis (CAG) is an important stage in the occurrence and development of gastric cancer, and the morbidity of CAG is increasing year by year. Qilianshupi Decoction (QLSP) is a Chinese herbal compound which has been proved to reverse CAG, but its mechanism remains unknown. We wanted to identify the main components of QLSP by mass spectrometry and liquid phase analysis, and investigate their potential pathways for CAG treatment in combination with network pharmacology.

The main active components of QLSP were identified by liquid chromatography and mass spectrometry. Combined with network pharmacology, the targets where the drugs may act were identified and verified by animal experiments. Rats were randomly divided into control group, model group, QLSP low-dose group, QLSP medium-dose group, QLSP high-dose group and Weifuchun group. Rat CAG model was prepared by “N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) + ethanol intragastric + ranitidine feed”. After the test, gastric tissues were taken for pathological staining and immunohistochemistry.

We identified 51 prototype components of QLSP and found that QLSP treatment of CAG was closely related to p53. In animal experiments, CAG results in the decrease of E-cadherin and the increase of N-cadherin, Vimentin, p53, SMAD2 and TGF-β (p<0.05). Both QLSP and Weifuchun can increase E-cadherin and decrease N-cadherin, Vimentin, p53, SMAD2 and TGF-β (p<0.05).

QLSP, a traditional Chinese medicine formula with multi-component and multi-target characteristics, has been shown in our study to effectively regulate key EMT (epithelial-mesenchymal transition) markers and their upstream/downstream regulators. In animal experiments, QLSP successfully reversed the EMT process in CAG model rats. This finding provides new therapeutic targets for CAG treatment, though several challenges remain in clinical translation: First, rat CAG models differ from human CAG in pathological features and disease progression, and species-specific physiological and metabolic variations may limit the extrapolation of these findings. Second, network pharmacology analysis identified IL-6, alongside TP53, as another critical target of QLSP in CAG intervention. Therefore, future studies should further clarify the molecular mechanisms by which QLSP modulates EMT via IL-6-related pathways and validate its efficacy through well-designed clinical trials, ultimately providing a comprehensive understanding of QLSP's therapeutic potential in CAG.

QLSP inhibits epithelial-mesenchymal transition (EMT) in gastric mucosal epithelial cells and prevents CAG, possibly by regulating p53/TGF-β signaling pathway.

Metabolic syndrome (MetS) is a metabolic disorder characterized by the accumulation of various risk factors, including obesity, dyslipidemia, hypertension and so on. Songyang Duanwu Tea (SYT) has a high value in nutrition and health care, and it is widely used in traditional Chinese medicine for weight loss. Nevertheless, the mechanisms of SYT improving MetS remain to be elucidated. The objective of this study was to investigate the molecular targets and potential mechanisms by which SYT may improve MetS based on animal experiments and bioinformatics.

MetS model mice were established by a high-fat, high-sugar, high-salt diet (HFSSD). Obesity, dyslipidemia, hypertension, hyperuricemia and non-alcoholic fatty liver disease (NAFLD) of MetS model mice were evaluated to assess the effect of SYT on the treatment effects of MetS. The bioactive components in SYT were identified by bioinformatics and verified by HPLC-QTOF-MS. The possible molecular targets and mechanisms of action were predicted and verified using bioinformatics.

SYT (1.2 g/kg) ameliorated obesity, dyslipidemia, hypertension, hyperuricemia and NAFLD in HFSSD-induced mice. Bioinformatics results suggested that the major bioactive components in SYT include the flavonoid components apigenin, kaempferol, luteolin and quercetin, and the polyphenolic component eugenol. HPLC-QTOF-MS further validated the presence of apigenin, kaempferol, luteolin and quercetin. These 4 bioactive components are involved in the regulation of SYT to improve MetS by regulating metabolism and attenuating inflammation, and the key targets include peroxisome proliferator-activated receptor gamma (PPARG), tumor necrosis factor alpha (TNFα), interleukin 1beta (IL1B) and interleukin 6 (IL6).

SYT effectively improved the MetS model mice induced by HFSSD. The potential mechanism may regulate PPARG and attenuate inflammatory targets: TNFα, IL1B and IL6 through 4 flavonoid components: apigenin, kaempferol, luteolin and quercetin.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a global health concern, even among lean individuals. The Gan-Jiang-Ling-Zhu decoction (GZD), a traditional Chinese medicine formula, shows therapeutic potential against MASLD. This study investigated the efficacy of GZD in lean MASLD and explored its mechanisms of action.

A lean MASLD mouse model was established using C57BL/6 mice fed with a cholesterol-rich Paigen’s diet (PD). Following successful modeling, mice were administered GZD (1.8, 3.6, or 7.2 g/kg) or vehicle control. Body weight, food intake, and liver weight were monitored. Hepatic steatosis and lipid accumulation were assessed via H&E and Oil Red O staining, while serum enzymes were quantified biochemically. Gut microbiota composition was analyzed by 16S rRNA gene sequencing, and bile acid (BA) profiles in feces and serum were measured using UPLC-TQMS.

Twelve weeks of PD feeding induced a lean MASLD phenotype characterized by reduced body weight alongside hepatic steatosis and dyslipidemia. The GZD treatment dose-dependently ameliorated liver steatosis and lipid accumulation, with the highest dose (7.2 g/kg) showing superior efficacy. GZD restored gut microbiota balance by reducing pathogenic bacteria and enriching taxa involved in BA metabolism, leading to increased fecal excretion of secondary BAs. Conversely, serum levels of secondary BAs were significantly reduced after GZD treatment.

Our study highlights the promising role of GZD in lean MASLD, the involvement of gut microbiota and related BA metabolism that aligns with emerging evidence that gut dysbiosis and disrupted BA homeostasis are central to MASLD pathogenesis, even in lean individuals. However, the mechanistic links between specific microbial changes, BA pool composition, and hepatic outcomes remain to be elucidated.

GZD ameliorates hepatic steatosis in lean MASLD mice, an effect associated with modulation of gut microbiota composition and increased fecal excretion of secondary BAs. These findings suggest the potential of GZD as a therapeutic option for lean MASLD through gut-liver axis regulation.

Bladder cancer (BLCA) is a highly aggressive malignancy with poor prognosis. DNA replication stress-related genes (DRSGs) hold prognostic significance in multiple cancers, and their expression patterns in BLCA may reveal novel biomarkers and therapeutic targets.

This study was designed using a public database and the Cancer Genome Atlas (TCGA). Genes associated with DNA replication stress in BLCA were discovered by analyzing data from the TCGA and GEO databases using bioinformatics tools. The prognostic gene expression profiles in BLCA cell lines were analyzed using Western blotting (WB). The motility capacity of BLCA cells was evaluated using the wound healing and Transwell migration assays, while cell growth was ascertained with the CCK-8 assay.

Five DRSGs with prognostic significance were identified, and a risk score model was constructed using univariate Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm. Kaplan-Meier (KM) analysis showed worse Overall Survival (OS) in the high-risk group (P < 0.05). Gene Set Enrichment Analysis (GSEA) indicated involvement in tumor-related pathways. The nomogram effectively predicted OS in both training and validation cohorts. WB and functional assays confirmed gene expression and effects on BLCA cell proliferation and migration.

This study first validates DRSGs’ prognostic value in bladder cancer, highlighting potential biomarkers and targets. Limitations include reliance on public data and in vitro tests. Future research should use multicenter cohorts and animal models to confirm clinical relevance.

This study aims to validate the hypothesis that Modified Qianzheng Powder (MQZP) exerts a protective effect on atherosclerosis (AS) by targeting macrophage-associated inflammatory pathways through a multi-target approach.

The active compounds and targets of MQZP were identified through TCMSP, HERB, and published literature. AS-related targets were extracted from disease databases. Using Venny 2.1.0, intersection targets were obtained, followed by PPI network construction and topological analysis to identify core therapeutic targets of MQZP for AS. Metascape facilitated GO and KEGG enrichment analyses. Molecular docking validated core target-compound interactions, with experimental verification of network pharmacology results.

We identified 124 active compounds and 417 potential therapeutic targets for atherosclerosis. Key bioactive constituents included cyclo(D)-Pro-(D)-Phe, aurantiamide, and beauverilide A, with TP53, SRC, STAT3, and AKT1 as core targets. GO and KEGG enrichment analyses revealed 3,417 biological processes and 238 signaling pathways. Molecular docking confirmed stable binding between core targets and compounds. In vitro, MQZP exhibited no significant cytotoxicity, effectively reducing ox-LDL-induced macrophage lipid accumulation and downregulating the levels of IL-1β, TNF-α, and MCP-1.

In summary, we found a variety of active ingredients of MOZP, which interfere with multiple targets of AS through multiple pathways. In vitro experiments verified that MOZP can reduce lipid accumulation in macrophages, reduce inflammation levels, and inhibit the IL-6/STAT3 signaling pathway, thereby exerting its anti-atherosclerosis effect.

In this paper, the molecular mechanism of MOZP against AS has been preliminarily explored; nonetheless, the therapeutic mechanism needs to be further investigated.

Chronic atrophic gastritis (CAG) is the initial phase in the carcinogenesis of gastric cancer (GC). Therefore, effective treatment for CAG is important in reducing the risk of GC progression. As an isoflavone compound, formononetin (FMN) has been identified as a potential therapeutic agent for acute gastric ulcers and GC. However, no study has reported the protective effect of FMN against CAG and its underlying mechanism. This study aimed to explore the therapeutic effects of FMN on CAG and its underlying mechanisms in vitro.

Network pharmacology was applied to predict the core targets of FMN therapy in CAG. The CAG cell model was developed using N-methyl-N-nitro-N-nitrosoguanidine (MNNG)-triggered human gastric epithelial cells (GES-1). The CCK-8 assay was applied to estimate cellular viability. The expression of inflammatory cytokines in cell supernatant was detected by ELISA. The protein levels and localization of nuclear receptor coactivator 1 (NCOA1), c-Jun, and c-Fos were evaluated using western blotting and immunofluorescence staining. Cell apoptosis was measured using flow cytometry.

Network pharmacology analysis identified c-Jun as the core target of FMN in the treatment of CAG, with biological processes primarily involving the regulation of apoptosis and inflammation. In vitro, MNNG exposure reduced GES-1 cell viability as well as increased inflammation and cellular apoptosis, and these effects were reversed by FMN treatment. In detail, FMN decreased the protein levels of NCOA1, c-Jun, and c-Fos in MNNG-triggered GES-1 cells. The activator protein-1 (AP-1) inhibitor T-5224 enhanced the effects of FMN treatment on cell viability, inflammatory response, and apoptosis in MNNG-triggered GES-1 cells.

This study employed network pharmacology analysis to identify FMN's therapeutic targets for CAG and validated the underlying mechanisms in vitro. While these results are promising, in vivo validation is required to confirm the efficacy of FMN. A comparative pharmacological evaluation against existing therapeutic agents and bioactive compounds would further elucidate FMN's therapeutic potential for CAG treatment.

FMN ameliorated the cell damage that MNNG triggered in GES-1 cells. The mechanism involved the anti-inflammatory and anti-apoptotic effects of FMN via modulation of the NCOA1/AP-1 signaling axis. The present preliminary study found FMN to exhibit a potential therapeutic effect against CAG.

With a large number of species' genomes assembled, sequence comparison has become an effective method for further studying biological classification and evolution. Traditional sequence alignment relies on predefined scoring functions, but it is computationally intensive and lacks molecular justification for scoring the differences between sequences. Therefore, we have developed a graphical representation method for DNA sequences to facilitate better sequence comparison and evolutionary analysis.

In this article, we introduce a novel method for representing DNA sequences using three-dimensional (3D) graphics. This method possesses two significant properties: (1) the graphical representation is acyclic; (2) each DNA sequence maintains a bijective relationship with its graphical representation.

Leveraging this proposed visualization method, we computed the corresponding ALE index for any DNA sequence by converting it into an L/L matrix and constructed a 12-dimensional feature vector. The feasibility of our proposed method has been validated through the construction of phylogenetic trees in four test sets: terrestrial vertebrates, hantavirus, fish and Japanese encephalitis virus.

This method enables both quantitative analysis and visual comparison of DNA sequences, providing a versatile tool for evolutionary studies.

Individual constitutions are classified into nine types in traditional Chinese medicine (TCM), and qi stagnation constitution (QSC) manifests as disrupted Qi circulation and increased susceptibility to emotional disorders and cancers. However, as a pre-disease state mainly affecting women, the biological basis of QSC and its susceptible mechanism to related diseases are still unclear. Exosomal microRNAs (miRNAs) are the stable regulators of gene expression and intercellular communication, and analysis of miRNAs enables us to understand the QSC better. This study profiles plasma exosomal miRNAs in QSC and balanced constitution (BC) females via high-throughput sequencing, aiming to identify the potential biomarkers of QSC and reveal its biological basis and the mechanism of its susceptible disease.

In this cross-sectional observation, female college students were recruited according to the criterion of QSC and BC in Classification and Determination of Constitution in TCM. Exosomal miRNAs were isolated from peripheral blood plasma and then profiled using high-throughput sequencing. Differentially expressed miRNAs (DEMs) were identified with fold change > 2 and P < 0.05, and screened as biomarkers to construct the receiver operating characteristic (ROC) curve. The diagnostic values of these biomarkers in different types of cancers were also validated based on the published data. Functional analysis were explored based on the predicted target genes.

Subjects with QSC showed significantly higher concentrations of albumin (ALB) and alkaline phosphatase (ALP) compared to those with BC, while there was no significant difference in baseline information and other clinical indicators between groups. A total of 54 DEMs were identified, including 30 up-regulated and 24 down-regulated miRNAs in the QSC group. The area under the ROC curve (AUC) for 7 specific up-regulated DEMs was 1.0, as well as the AUCs for therein 6 DEMs in various cancers were all above 0.9. The enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways included “signal transduction,” “infectious disease,” and “cancers”, and the most associating systems included immune, endocrine, and nervous systems, while the GO (Gene Ontology) function was mainly enriched in “protein binding,” “nucleus” and “transcription, DNA-templated”.

These 7 potential biomarkers of QSC have been confirmed to regulate oncogenic processes through epithelial-mesenchymal transition modulation and metabolic reprogramming, as well as therein 1 can also improve depression by lowering the expression of 5-hydroxytryptamine 1A receptor. The results of this study deepen the understanding of the constitutions in TCM. However, the small single-sex sample limits the application of the conclusion, and a large-scale clinical cohort including both sexes is still needed in future.

The expression of exosomal miRNAs in QSC showed unique features that have the potential to serve as biomarkers, and the related functional changes might be the biological basis for the susceptible diseases of QSC.

Depression is a common comorbidity in epilepsy, significantly impacting patients' quality of life. The hippocampus, linked to depression and neurodegeneration, is vulnerable in epilepsy. Epileptogenesis involves inflammation, oxidative stress, and neuronal damage, with the PI3K/AKT pathway playing a key role. Apigenin (API), a flavonoid in fruits and vegetables, shows neuroprotective, anti-inflammatory, and anti-apoptotic effects. This study investigates API's mechanisms in a LiCl-pilocarpine epileptic rat model, focusing on hippocampal neurogenesis and PI3K/AKT signaling as potential therapeutic targets.

We studied the effects of API and valproate (VPA) on depressive behavior and astrocytes in Lithium chloride (LiCl)-pilocarpine-induced epileptic rats. Additionally, we predicted the potential molecular targets of API for treating epilepsy using network pharmacology. Finally, we conducted in vivo experiments to validate the predicted mechanism.

In the API and VPA groups, there was a reduction in seizure frequency and seizure severity compared with the control group. The model group showed more depressive behavior than the control (CON) group, and these behaviors improved significantly after VPA and API treatment. HE staining showed that both API and VPA treatment improved LiCl-pilocarpine-induced nuclear contraction and cell swelling. Nissl staining demonstrated that Nissl vesicles in the CA3 region of the hippocampus were decreased in the model group, but the neurons were larger, more abundant, and more neatly arranged after API and VPA treatment. In the model group, the p-PI3K/PI3K and p-AKT/AKT protein ratios and PI3K, AKT mRNA expression were reduced, while brain-derived neurotrophic factor (BDNF) and glial fibrillary acidic protein (GFAP) were markedly increased. API and VPA treatment effectively reversed these changes.

API reduces seizures and depressive behaviors in LiCl-pilocarpine-induced epileptic rats, comparable to VPA API mitigates hippocampal neuronal damage, preserves Nissl bodies, and suppresses astrocyte activation via the PI3K/AKT pathway, suggesting neuroprotective and anti-inflammatory effects. While API shows promise as an antiepileptic and antidepressant agent, further studies are needed to confirm its direct modulation of PI3K/AKT and efficacy in other epilepsy models.

Our study suggests that API improves depression in rats and has anti-epilepsy activity, which may be involved in activating the PI3K/AKT pathway to protect astrocytes.

Obesity is a global health issue linked to metabolic disorders and cardiovascular diseases. Guang hawthorn (Malus doumeri) leaves have been traditionally used for medicinal purposes, but their bioactive compounds and anti-obesity potential remain underexplored.

This study extracted compounds from M. doumeri leaves using 70% ethanol and ethyl acetate. The extracts were administered to high-fat diet-induced obese rats. Serum levels of total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) were measured. The chemical composition of the extracts (HML) was analyzed using chromatography, NMR, and mass spectrometry. Network pharmacology and enrichment analyses were conducted using R and Cytoscape to identify compound-target interactions.

Rats treated with high-dose extracts showed significantly reduced TC, TG, and LDL-C levels and increased HDL-C (all p < 0.05). Three major compounds-phlorizin, sieboldin, and kumatakenin β-7-O-glucoside-were identified. A total of 272 overlapping targets and 32 core targets were found between compound-related and obesity-related gene sets. Functional analysis linked these targets to phosphorylation, apoptosis, cell proliferation, and kinase regulation.

The anti-obesity effects of M. doumeri may be mediated by modulation of the PI3K-Akt and FoxO signaling pathways, as well as proteoglycan biosynthesis. These pathways are associated with metabolic regulation and obesity-related changes.

M. doumeri leaf extracts demonstrate anti-obesity potential through multi-target and multi-pathway mechanisms, particularly via sieboldin and kumatakenin β-7-O-glucoside. These findings support their potential as natural therapeutic agents for obesity management.

Soaps are vital for preserving our health and personal hygiene since they not only eliminate germs but also rid the body of pollutants.

The current study aims to determine the physicochemical and antibacterial properties of Eucalyptus camaldulensis leaves using the agar disc diffusion technique and assess the effectiveness of different branded liquid soaps (25 mg/ml, 50 mg/ml, 75 mg/ml, and 100 mg/ml) with the Eucalyptus leaf extract against skin-infecting human pathogenic bacteria.

The combined antimicrobial susceptibility of E. camaldulensis and five liquid soaps showed an inhibition zone of 17.67±0.58, 13.33±0.58, 12.67±0.58, and 15.67±0.58 against Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa, and Escherichia coli. The antibacterial properties of Av soap by itself did not work against S. pyogenes. Nevertheless, the extract and DI together showed a detrimental effect against S. aureus and P. aeruginosa, with no halo forming.

The absence of inhibition zones for the extract combined with DI against S. aureus and P. aeruginosa may indicate antagonistic interactions or reduced efficacy in that formulation. Overall, the data highlight the potential of E. camaldulensis to improve the antimicrobial properties of commercial soaps, though the effectiveness varies with microbial strain and formulation.

Antimicrobial activity was observed to increase with higher concentrations of the soap-extract combinations. Although liquid soap (seve) was effective against bacterial isolates, a combination of eucalyptus and aqua vera was shown to be more effective.

Obstructive sleep apnea syndrome [OSAS] is a common sleep breathing disorder accompanied by multiple organ intermittent hypoxemia. Our previous study has suggested that the expression of a lncRNA termed ENST00000592016 [lnc2016 for short] derived from plasma exosomes is remarkably elevated in OSA patients compared to the normal population, and lnc2016 can improve the diagnostic efficiency of OSA.

To unmask the role of the lnc2016 in vascular endothelial cells, targeted hypoxia is the goal of the current research.

Primary human ADSCs and HUVEC cells were cultured. CCK-8, cytometric assay, transwell, and tubular formation assay were used to determine cell viability, cell apoptosis, cell cycle, cell migration, as well as tubular formation ability.

Adipose-derived stem cells [ADSCs]-derived exosomes contained robust lnc2016. After co-culture with human umbilical vein endothelial cells [HUVECs], exosomal lnc2016 could enhance cell proliferation, DNA synthesis, migration, and tubular formation, whereas suppress cell apoptosis of HUVECs against hypoxic conditions.

Under hypoxic conditions, ADSCs secrete various reparative factors and transmit them via exosomes; among them, lnc2016 may participate in the regulation of hypoxia-induced injury through the ceRNA network, which requires further investigation.

Ln2016 can promote the cell growth, migration, DNA synthesis, and tubular formation as well as suppress the cell apoptosis of vascular endothelial cells against hypoxia in vitro.

Transcriptome-level insights into electroacupuncture (EA)’s mechanisms for alleviating intestinal mucosal barrier damage in diarrhea-predominant irritable bowel syndrome (IBS-D) are limited. This study aimed to construct ceRNA networks and elucidate EA's role in restoring barrier integrity via lncRNA-miRNA-mRNA regulation in IBS-D rats.

The IBS-D model was established by neonatal maternal separation (NMS), 4% acetic acid enema and restrain stress (RS). Rats were randomized into control, model, and EA groups. After 2-week EA treatment, colonic morphology was assessed by HE staining and TEM; intestinal barrier biomarkers were analyzed via ELISA and WB. RNA-seq identified differentially expressed RNAs (DE RNAs) to construct ceRNA networks. GO and KEGG analyzed EA-modulated DE mRNAs. RT-qPCR validated RNA-seq; WB and IF confirmed mast cell (MC) involvement in EA-regulated pathways.

RNA-seq identified 426 up-regulated and 429 down-regulated DE mRNAs, 342 up-regulated and 362 down-regulated DE lncRNAs, and 10 up-regulated and 48 down-regulated DE miRNAs following EA. Constructed ceRNA networks included 7 DE lncRNAs-miR-139-3p-Bid and -miR-378b-Slc4a5. GO analysis linked EA to defense response, hormone regulation, and cytokine function pathways. KEGG implicated antigen processing/presentation, neuroactive ligand-receptor interaction, PPAR signaling, and glutathione metabolism. RT-qPCR validated RNA-seq results.

This RNA-seq study reveals EA mitigates IBS-D intestinal mucosal barrier damage by regulating genes and ceRNA networks, providing novel transcriptomic insights into its therapeutic mechanisms.