Combinatorial chemistry & high throughput screening最新文献

Background: Prostaglandin D2 (PGD2) can inhibit the development of gastric cancer (GC); however, its role in the autophagic death of GC stem cells (GCSCs) remains elusive. Therefore, this study aims to evaluate the mechanisms by which PGD2 regulates the stemness in GCSCs.

Methods: In this study, HGC27-derived GCSCs were employed to knock down PGD2 receptor 2 (PTGDR2). Subsequently, cell stemness and autophagic activity in these GCSCs were assessed via sphere-forming capacity, transmission electron microscopy, and western blot analyses.

Results: The results revealed that PGD2 suppressed the stemness of GCSCs and induced GCSCs autophagy, whereas the downregulation of PTGDR2 had the opposite effect. Furthermore, PGD2 was also found to inhibit the expression of stemness-associated proteins CD44 and OCT4, which were blocked by 3-MA and enhanced by RAPA. Moreover, the shPTGDR2 + PGD2 group indicated higher stemness than the PGD2 group, with 3-MA enhancing this effect and RAPA reducing this change.

Conclusion: In summary, this study indicated that PGD2/PTGDR2 signaling affects stemness and autophagy in GCSCs. The results suggest that PGD2/PTGDR2 signaling may affect the stemness of GCSCs by regulating autophagy.

Introduction: Gynostemma pentaphyllum is commonly used in southern China to treat hyperlipidemia and tumors, primarily due to its active saponin compounds. This study aimed to analyze the inhibitory effect of gypenoside LI (Gyp LI) on clear cell renal cell carcinoma (ccRCC), which is mediated through DUSP1-related lipid metabolism.

Materials and methods: The concentration of Gyp LI required to inhibit the ccRCC cell lines 769-P and ACHN was determined using a CCK8 assay, and DUSP1 upregulation was confirmed by transcriptomic sequencing, RT-qPCR, and Western blot analysis. The roles of DUSP1 and Gyp LI in regulating cell proliferation were further validated using CCK-8, colony formation, and flow cytometry assays. . Additionally, we established a nude mouse xenograft tumor model using ACHN cells that overexpress DUSP1. We assessed the effects of Gyp LI and DUSP1 on tumor growth through histopathological examinations. We employed untargeted tissue metabolomics to identify metabolic pathways influenced by Gyp LI via upregulation of DUSP1.

Results: CCK-8 experiments showed that Gyp LI inhibited the proliferation of ccRCC cells. Additionally, transcriptome sequencing revealed that DUSP1 expression increased following Gyp LI intervention. We transfected cells with siDUSP1 and ovDUSP1 and assessed cell proliferation using CCK8, colony formation, flow cytometry, and WB analyses of apoptosis-related proteins, confirming that both ovDUSP1 and Gyp LI inhibited ccRCC cell proliferation. Animal studies revealed that both ovDUSP1 and Gyp LI inhibited tumor growth. Non-targeted metabolomics analysis revealed that Gyp LI affected seven metabolites associated with ccRCC treatment by upregulating DUSP1.

Conclusion: Gyp LI upregulates DUSP1 to suppress the metabolism of choline, linoleic acid, and alpha-linolenic acid, ultimately suppressing the incidence and progression of ccRCC.

Introduction: Polygonatum sibiricum (P. sibiricum) possesses antioxidant and antiinflammatory activities. We explored the multi-target mechanisms of P. sibiricum against hepatocellular carcinoma (HCC), aiming to improve its poor prognosis.

Materials and methods: Active compounds and disease targets of P. sibiricum were retrieved from the TCMSP and CTD databases. A PROTEIN-PROTEIN INTERACTION (PPI) network was constructed using the STRING database, and functional enrichment was performed with the clusterProfiler package. A compound-target-pathway network was developed in Cytoscape. Immune infiltration was assessed via CIBERSORT and ESTIMATE algorithms, while ligand-target binding was evaluated by molecular docking and 100-ns molecular dynamics (MD) simulations. In vitro experiments were performed to explore the expression and functions of the key genes.

Results: We screened 9 active components, 87 putative targets, and 240 HCC-related genes. Twenty overlapping targets were used to construct a PPI network. Network analysis identified baicalein and five core targets (FOS, MMP9, AKT1, TP53, and PTGS2). Molecular docking and 100-ns MD simulations confirmed stable ligand-protein binding. Immune profiling showed that higher expression of the core targets was related to higher StromalScore, ImmuneScore, and lower tumor purity. Enrichment analysis revealed that these genes were involved in critical pathways, including angiogenesis, EMT, and inflammation response. Functionally, MMP9 knockdown suppressed HCC cell proliferation, migration, and invasion.

Discussion: P. sibiricum, particularly through baicalein targeting FOS/MMP9/AKT1/ TP53/PTGS2, inhibited HCC development by modulating EMT/angiogenesis pathways and immune milieu. However, these findings required further verification.

Conclusion: Baicalein was identified as an active compound targeting five crucial genes to suppress HCC progression, uncovering a new anti-HCC mechanism of P. sibiricum.

Introduction: Longlutong Decoction (LLTD) is a Chinese traditional prescription used for coronary heart disease (CHD). The present study aimed to illuminate the mechanisms of LLTD treatment on CHD.

Methods: The therapeutic effect of LLTD on CHD was investigated using a CHD rat model. The chemical components of LLTD were identified, following which network pharmacology approaches were utilized to identify active components and disease-related targets. GO and KEGG analyses were conducted to explore potential molecular mechanisms. Finally, the molecular mechanism of LLTD treatment of CHD was verified.

Results: Histopathological assessment revealed markedly attenuated myocardial injury severity in the medicated groups when compared to the model group. Moreover, 81 potential active ingredients were identified in LLTD, with 645 overlapping targets between component targets and disease targets. Network analysis identified Pinocembrin, Magnoflorine, Jatrorrhizine as key active ingredients, and AKT1, TNF, IL-6, STAT3, and Bcl-2 as primary core targets. A total of 1792 biological processes were affected according to GO analysis, and 187 pathways were identified through KEGG analysis. Finally, molecular docking and experimental results validated that LLTD could alleviate cardiomyocyte injury in CHD by regulating the primary core targets.

Discussion: This study indicates that LLTD may achieve systematic modulating of the signaling network through a "network pharmacology" model, which provides valuable insights for the development of multi-target therapies targeting the complex pathological mechanism underlying CHD.

Conclusion: LLTD may exert cardioprotective effects by regulating inflammatory responses, apoptosis, and oxidative stress.

Introduction: Hyperglycemia-induced renal inflammation and the subsequent activation of inflammatory cytokines play critical roles in Diabetic Kidney Disease (DKD) progression. However, the underlying molecular mechanisms, particularly those involving microRNAs, remain poorly understood.

Methods: Serum samples from DKD patients (n = 10) and healthy controls (n = 10) were subjected to microRNA transcriptome profiling. An in vitro DKD model was established by treating Human Renal Tubular Epithelial Cells (RTECs and HK-2) with High Glucose (HG). The levels of pro-inflammatory cytokines, Interleukin (IL)-1β, IL-6, and Tumor Necrosis Factor (TNF)-α, were assessed using quantitative reverse transcription-PCR and enzyme-linked immunosorbent assay. Dual-luciferase reporter assays evaluated the relationship between miR-509-3p and Yesassociated protein 1 (YAP1). In situ hybridization and immunohistochemistry were performed to validate the expressions of miR-509-3p and YAP1 in kidney tissues from DKD patients (n = 38) and controls (n = 38).

Results: MiR-509-3p was identified as one of the most significantly dysregulated microRNAs in the serum of DKD patients. Its expression was significantly downregulated in a dose-dependent manner in HG-induced RTECs and HK-2 cells (p <0.01). Overexpression of miR-509-3p significantly suppressed HG-induced pro-inflammatory cytokine expression (p <0.01). Suppression of miR-509-3p further enhanced HG-induced IL-1β, TNF-α, and IL-6 expression, whereas this effect was reversed by silencing YAP1 (p <0.01). Mechanistically, miR-509-3p directly targeted the 3'-UTR of YAP1 mRNA. Consistently, DKD renal tissues exhibited reduced miR-509-3p and elevated YAP1 expression, with a significant negative correlation (p = 0.002). Furthermore, miR-509-3p and YAP1 were significantly correlated with estimated glomerular filtration rate and urine albumin-creatinine ratio (p <0.001).

Conclusion: The study preliminarily suggests that miR-509-3p/YAP1 axis may act as a crucial regulator of hyperglycemia-induced tubular inflammation, offering a potential therapeutic target for DKD.

Introduction: 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.

Methods: This study analyzed the transcriptomic dataset GSE129147 to identify ER stressrelated 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.

Results: 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).

Discussion: 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.

Conclusion: 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.

Introduction: All-trans retinoic acid (ATRA), a therapeutic mainstay for acute promyelocytic leukemia, is associated with off-target effects on skeletal development, including premature growth plate closure. However, the molecular mechanisms underlying ATRA-induced growth plate senescence remain poorly understood.

Methods: Using Sprague-Dawley rats, ADTC5 chondrocyte cell lines, and integrated multiomics approaches (transcriptome sequencing, weighted gene co-expression network analysis, molecular docking, and functional assays), we investigated how ATRA modulates growth plate development. Animal models were treated with graded ATRA doses, while in vitro studies included cell viability assays, RNA interference, and Western blot analysis to validate interactions in the signaling pathway.

Results: ATRA induced dose-dependent growth plate thinning (high-dose: 59.79 μm vs. control: 511.35 μm) and skeletal growth retardation in rats. Transcriptomic analysis identified ITGB2 as a pivotal gene, with molecular docking revealing a strong binding interaction (-240.25 kcal/mol) between ITGB2 and YAP mediated by hydrogen bonds/salt bridges. Functional experiments revealed that ATRA upregulated ITGB2, which activated YAP, a Hippo pathway effector, thereby suppressing Wnt/β-catenin signaling by inhibiting β-catenin. This led to downregulation of osteogenic markers (Runx2/SOX9) and enhanced growth plate closure. YAP knockdown reversed these effects, restoring β-catenin and downstream target gene expression (c-myc, cyclin D).

Conclusion: ATRA accelerates growth plate closure through the ITGB2-YAP axis, disrupting Wnt/β-catenin signaling. These findings establish a mechanistic framework for developing therapeutic strategies targeting ITGB2 or YAP to delay premature growth plate senescence in pediatric disorders.

Introduction: This study aimed to investigate the therapeutic mechanism of Duzhong Bushen Formula (DBF) in ameliorating lumbar Intervertebral Disc Degeneration (IDD) via regulation of the MAPK/AP-1 pathway.

Methods: Based on a circular puncture-induced rat model of IDD, network pharmacology and molecular docking analysis were employed to identify key therapeutic targets and pathways for DBF in treating IDD. In vivo validation of these targets was conducted via MRI, histopathology, ELISA, Western blot, and qPCR, with therapeutic efficacy further evaluated.

Results: DBF administration significantly reduced inflammatory markers (CRP, IL-6, TNF-α), increased serum levels of Albumin (ALB) and Estrogen (E2), and downregulated key components of the MAPK/AP-1 pathway (p-p38, c-FOS, c-JUN). High-dose DBF demonstrated the most pronounced therapeutic effects.

Discussion: The results suggest that DBF attenuates IDD by suppressing inflammatory responses and oxidative stress through modulation of the MAPK/AP-1 signaling axis.

Conclusion: DBF may be a promising multi-target therapeutic agent for the treatment of IDD, particularly in cases involving kidney deficiency and blood stasis.

Introduction: Ölmei-7, a traditional Mongolian medicine used for edema since the 16th century, and has remained clinically relevant. . Its mechanisms for treating cirrhotic ascites are underexplored. . This study integrates metabolomics and network pharmacology to elucidate these mechanisms and validates its taste properties using electronic tongue analysis.

Methods: Taste was analyzed using an electronic tongue. Bioactive components were identified via HILIC UHPLC-Q-TOF MS and databases (TCMSP, GeneCards). PPI networks were built with Cytoscape and STRING, followed by GO/KEGG analyses using OmicBeans. Molecular docking was performed with OpenBabel.

Results: Electronic tongue analysis confirmed Ölmei-7's bitter and umami tastes, aligning with Mongolian medical theory. Metabolomics identified 997 targets, 130 overlapping with cirrhotic ascites genes. GO analysis showed enrichment in 6200 biological processes, 513 cellular components, and 784 molecular functions. KEGG analysis identified 255 pathways, including TNF and IL-17 signaling. Molecular docking of five proteins (TNF, EGFR, MMP9, JUN, BCL2) with five compounds showed stable binding, with Rutin-MMP9 at -9.1 kcal•mol-¹.

Discussion: Ölmei-7's active components (e.g., quercetin, luteolin) likely reduce ascites by inhibiting TNF-α-mediated inflammation and vascular permeability, protecting liver function via BCL2, improving fibrosis via MMP9/EGFR, and reducing oxidative stress via JUN. These findings support its traditional use and elucidate its mechanisms.

Conclusion: Ölmei-7 alleviates cirrhotic ascites through anti-inflammatory, antifibrotic, , and antioxidative pathways, as revealed by metabolomics and network pharmacology. This study enhances understanding of its pharmacological basis and supports clinical applications.

Introduction: One of the most dangerous illnesses in the world today is hepatitis B virus (HBV) infection, which mainly affects the liver and can cause cirrhosis, hepatocellular carcinoma (HCC), and chronic infection. The primary goal of this study was to determine whether genotype polymorphisms at particular locations of the IL-18 promoter region may affect the host susceptibility to HBV infection in the North Indian population.

Methods: Genetic polymorphism of the IL-18 gene in the promoter region at positions -607 and - 137 was performed in the North Indian population (100 controls and 100 HBV patients) using the PCR-RFLP method. Genotypic, allelic, and haplotype frequencies were compared using SHEsis software.

Results: There were no significant differences in individual genotype or allele frequencies at positions -607 and -137 between HBV patients and controls. However, there were statistically significant differences with high frequencies of the -607A/-137C haplotype in HBV patients (p=0.010), whereas the -607C/-137C haplotype was more prevalent in controls (p=0.001), indicating a protective effect.

Discussion: The individual SNPs did not show significant association, but specific haplotypes of the IL-18 promoter region may influence the risk of HBV infection. These results align partially with previous studies and suggest that haplotype-based analysis provides improved insight into genetic susceptibility.

Conclusion: The present study indicates that a double mutation (polymorphism) -607A/-137C in the IL-18 gene promoter region may contribute to the onset of HBV infection, while a single nucleotide polymorphism (-607C/-137C) may provide less susceptibility to HBV and may have a protective impact.