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.