Search Results (5,668)

Hepatocellular carcinoma (HCC) is sustained by coordinated interactions among malignant hepatocytes, immune cells, and stromal populations that collectively drive tumor growth, immune evasion, and vascular remodeling. Using integrative single-cell transcriptomics on 93,032 cells from tumor and healthy human liver, we characterized cell-type-specific transcriptional programs underlying immunometabolic reprogramming and reconstructed the intercellular communication circuits that maintain the tumor microenvironment. Malignant hepatocytes displayed upregulation of genes encoding both glycolytic and oxidative phosphorylation (OXPHOS) metabolic enzymes, consistent with metabolic plasticity, while concurrently suppressing genes involved in antigen presentation—a transcriptional pattern indicative of coordinated metabolic and immune-evasive reprogramming. Tumor-associated macrophages acquired TREM2-enriched, lipid-handling phenotypes consistent with immunosuppressive polarization, and tumor endothelial cells upregulated angiocrine and extracellular matrix programs while silencing innate immune outputs. Ligand–receptor inference revealed a qualitative rewiring of intercellular communication: the antigen-presentation-centered network of the healthy liver was replaced by a tumor-driven architecture dominated by pro-angiogenic, ECM–integrin, inflammatory chemokine, and lipid-associated signaling circuits, with malignant hepatocytes, TAMs, and TECs collectively assuming the dominant signaling burden. These findings establish that HCC progression is an emergent property of a stabilized multicellular network, rather than the autonomous behavior of malignant cells, and define cooperative immunometabolic modules that constitute tractable targets for combinatorial therapeutic intervention. Full article

The rate of fatty acid (FA) uptake by cells depends on the presence of the CD36 receptor on the cell surface. However, unesterified FAs cannot circulate freely in plasma; they are bound to serum albumin. The molecular mechanisms of FA transfer from albumin to CD36 remain poorly understood. This study used macromolecular docking and molecular dynamics methods to investigate the interaction of the CD36 receptor with human serum albumin (HSA) loaded with oleic acid at the FA1-7 fatty acid-binding sites, with the aim of identifying potential mechanisms of FA transfer from HSA to CD36. The data obtained indicate that the interaction of HSA with CD36 does not result in direct FA transfer, but rather causes a local weakening of the affinity of individual FA sites on HSA. A comparative analysis was performed between the interaction interfaces predicted by macromolecular docking and those generated by AlphaFold 3. To further evaluate the influence of ligand nature, an additional molecular docking of HSA loaded with saturated (palmitic, PALM) and polyunsaturated (arachidonic, ARA) acids to the CD36 receptor was performed. This revealed a marked sensitivity of the protein–protein interface architecture to the type of lipid ligand, with the effect of ARA being more pronounced than PALM. Conversely, an alternative structure prediction using the AlphaFold3 algorithm demonstrated the opposite trend, indicating high geometric invariance and reproducibility of the complex. Ultimately, the proposed dynamic mechanism expands our understanding of the multi-stage processes governing FA transport across the endothelium. Full article

Dipeptidyl peptidase-4 (DPP-4) is an established therapeutic target in the treatment of type 2 diabetes mellitus (T2DM), primarily due to its role in regulating incretin activity and glucose homeostasis. Although clinically approved DPP-4 inhibitors are widely used, their moderate efficacy has driven the search for novel compounds with improved properties. In this context, natural products have attracted considerable attention as a source of structurally diverse and biologically active molecules. At the same time, molecular docking has emerged as a key computational tool for the identification and evaluation of potential DPP-4 inhibitors. This review summarizes and critically analyzes current molecular docking studies of natural compounds targeting DPP-4. Over 150 studies were evaluated with respect to docking methodologies, selection of protein structures, and validation strategies. The results reveal substantial variability in computational protocols. Frequently used protein structures include ligand-bound DPP-4 models such as 1X70 and 6B1E. Among the investigated compounds, flavonoids represent the most extensively studied class, followed by alkaloids, phenolics, terpenoids, and peptides. Despite numerous reports of favorable binding interactions within the DPP-4 active site, many studies rely solely on docking results without further validation. The limited use of molecular dynamics simulations and experimental assays highlights a significant gap in the current literature. Overall, while molecular docking provides valuable preliminary insights, improved standardization and integration with complementary approaches are essential to enhance the reliability and translational relevance of in silico findings. Full article

Objectives: This study aimed to identify core genes associated with mitochondria-related transcriptomic signatures and evaluate their potential as computational biomarkers, immune characteristics, regulatory mechanisms, and potential therapeutic relevance. Methods: Obesity-related transcriptome datasets were obtained from the GEO database. Differentially expressed genes (DEGs) were intersected with mitochondria-related genes (MRGs) to identify obesity-related MRGs. Functional enrichment, protein–protein interaction (PPI) analysis, CytoHubba, LASSO and random forest algorithms were used to screen core genes. External validation, ROC analysis, immune infiltration analysis, regulatory network construction, candidate drug prediction, and molecular docking were further performed. Results: A total of 527 DEGs and 15 differentially expressed MRGs were identified. Enrichment analysis suggested that these mitochondria-related genes were mainly associated with disrupted mitochondrial energy metabolism, lipid metabolic remodeling, and altered substrate utilization. ECHDC2, FASN, NAT8L, and AASS were identified as core MRGs; these genes are respectively associated with mitochondrial metabolic regulation, de novo fatty acid synthesis, N-acetylaspartate-related mitochondrial metabolism, and lysine degradation. These genes were significantly downregulated in obesity and showed good diagnostic performance. Immune infiltration analysis revealed alterations in the immune microenvironment, and the core genes were negatively correlated with multiple immune cell types. Molecular docking showed that Genistein had the lowest predicted binding free energy with NAT8L (−8.89 kcal/mol), suggesting relatively favorable binding among the tested ligand–target pairs. Conclusions: ECHDC2, FASN, NAT8L, and AASS may serve as candidate computational biomarkers, among which FASN represents a known lipid metabolism-related gene, supporting the biological plausibility of the workflow. Full article

A pyranochromene-based ligand, 2-amino-4-(4-chlorophenyl)-5-oxo-4H,5H-pyrano[3,2-c]chromene-3-carbonitrile (ACLPh-PC-3-CN), was employed as a chelating modifier for the electrochemical determination of Cd(II) in water samples. ACLPh-PC-3-CN was co-immobilized with Nafion on a glassy carbon electrode to form a stable ACLPh-PC-3-CN/Nafion film that combines ligand-based coordination with cation-exchange-assisted preconcentration of Cd²⁺ at the electrode surface. The Cd(II) response at the modified electrode was characterized by cyclic voltammetry and differential pulse anodic stripping voltammetry, and the data support a predominantly 1:1 Cd(II)–ligand interaction at the interface under the selected conditions. At an optimized pH of 6.0, the sensor provided a linear calibration range from 16.21 to 56.72 μM, with a detection limit of 0.60 μM and a quantification limit of 2.0 μM, and showed good precision (repeatability 2.3% RSD, reproducibility 3.1% RSD) and short-term stability (94% of the initial response after 14 days). The ACLPh-PC-3-CN/Nafion-modified electrode tolerated common inorganic ions and surfactant species (≤5% signal change) and was successfully applied to the determination of Cd(II) in tap water and Red Sea water, affording recoveries between 98.7% and 101%. While the current detection limit is higher than typical guideline values for Cd in drinking water, the proposed sensor compares favorably with several reported electrochemical Cd(II) sensors in terms of simplicity, precision, and matrix tolerance, and represents a useful platform for coordination-based electrochemical sensing of cadmium in environmental water samples. Full article

Diabetic neuropathy is typically diagnosed with distal sensory and nerve conduction abnormalities. These symptoms may reflect earlier disturbances of axonal maintenance. This review examines axonal transport and cytoskeletal failure as convergent cellular mechanisms of diabetic axonopathy. Long peripheral axons are particularly vulnerable to damage because their integrity depends on continuous communication between the neuronal soma and distal terminals. This process involves the continuous renewal of cytoskeletal and functional proteins and the involvement of organelles such as mitochondria. Diabetes in experimental models disrupts this system at several levels. It slows cargo transport. The supply of neurofilaments, tubulin and retrograde signaling is reduced, and regenerative growth after injury is weakened. Carbonyl stress and AGEs cause modifications of neural proteins, the extracellular matrix, vascular barriers, and the excitability of sensory neurons. RAGE ligands, including AGEs and the proteins HMGB1 and S100, link the diabetic tissue environment to redox and inflammatory signaling. This occurs in neural and glial compartments, as well as in vascular tissue and the immune system. RAGE interacts with DIAPH1 to activate GTPase signaling and remodel the cytoskeleton. The RAGE–DIAPH1 interaction provides a plausible route from diabetic ligand accumulation to cytoskeletal remodeling. These observations provide a mechanistic context for axonal transport, although not all represent direct measurements of cargo movement. Direct evidence for transport impairment comes mainly from experimental studies showing altered slow cytoskeletal transport, impaired retrograde signaling, and weakened regenerative responses. This work highlights the possibility of developing therapies that go beyond symptomatic relief. Verifying the effectiveness of interventions in protecting axonal transport and nerve fiber integrity in diabetic neuropathy may be therapeutically beneficial. Full article

The selective detection of small, highly hydrophilic metabolites differing only in stereochemistry represents a major challenge in biosensor development. Here, we present a computational investigation to elucidate the molecular basis of the experimentally observed selectivity of a protein-based electrochemical biosensor toward myo-inositol over D-chiro-inositol. Although the two stereoisomers differ only in the orientation of a single hydroxyl group, they induce distinct dynamic effects on the protein recognition element. Molecular docking revealed comparable binding regions and similar affinity scores, indicating that selectivity does not arise from differences in binding site or docking energy. To investigate dynamic contributions, all-atom molecular dynamics simulations were performed in triplicate (3 × 100 ns) using the AMBER99SB force field and explicit TIP3P water. Trajectory analyses showed that myo-inositol forms a more persistent hydrogen bond network, resulting in reduced residue-level flexibility, more stable ligand–protein interactions, and enhanced local structural stabilization. Overall, these findings support a dynamic model of stereoselective recognition in which ligand-induced modulation of protein conformational ensembles, rather than static affinity, governs biosensor performance. This work highlights the value of molecular dynamics simulations in the rational design of biosensors targeting structurally similar analytes. Full article

Identification of ligands targeting essential enzymes in Mycobacterium species remains an important strategy for anti-tuberculosis drug discovery. Here, a native mass spectrometry approach was employed using pooled 100-compound mixtures, enabling the direct detection of intact HPPK–ligand complexes in solution. Dual-mode MS acquisitions (low collision energy for complex detection and high collision energy for ligand confirmation), combined with an automated data analysis workflow, ensured robust identification of binding events from these complex samples. This strategy led to the identification of several HPPK-binding small molecules, all belonging to the dammarane triterpene glycoside (ginsenoside) class. Subsequent analysis of the hits revealed clear structure–affinity relationships, highlighting how specific aglycone modifications and glycosylation patterns influence binding to HPPK. Our findings expand the known chemical space of HPPK ligands and demonstrate the utility of native MS-based screening coupled with automated data analysis to uncover new ligand scaffolds for challenging enzyme targets. Full article

This study aimed to compare the chemical composition and antimicrobial activity of essential oils obtained from the rhizomes and leaves of Conamomum pierreanum (Zingiberaceae), and to evaluate interactions of selected constituents with microbial targets using molecular docking and molecular dynamics simulations. Gas chromatography–mass spectrometry (GC-MS) identified 21 compounds in the rhizome essential oil (EO) and 10 in the leaf EO of C. pierreanum, with 1,8-cineole (54.44% and 75.73%, respectively) as the predominant constituent. Notably, the rhizome EO was uniquely characterized by epi-γ-eudesmol (3.47%) and isobornyl acetate (3.39%), which were absent in the leaf oil. In vitro assays revealed that the rhizome EO possessed stronger antibacterial and antifungal activities (MIC = MBC = MFC = 0.4%) compared to the leaf EO (0.8%) against Staphylococcus aureus and Candida albicans. Molecular docking identified epi-γ-eudesmol as the most potential ligand, exhibiting remarkably high binding affinities for S. aureus DHFR (−8.1 kcal/mol) and C. albicans CYP51 (−8.5 kcal/mol), significantly outperforming the major constituents. A total of 100 ns molecular dynamics simulations and MM-PBSA analysis further confirmed the structural stability and energetically favorable binding of these complexes, with epi-γ-eudesmol maintaining a low average RMSD (<1.2 Å) throughout the simulation. The enhanced efficacy of the rhizome oil is attributed to the synergistic contribution of these high-affinity minor constituents. These findings suggest that C. pierreanum rhizome EO may serve as a potential source of bioactive compounds for antimicrobial applications, warranting further investigation. Full article

Carbonyl stress, chronic inflammation, and progressive tissue injury accompany type 2 diabetes mellitus (T2DM) and obesity. Yet, the molecular systems that connect these processes with cardiac, vascular and neuronal complications are incompletely defined. This review examines the AGE–RAGE–DIAPH1 axis as a mechanistic link between metabolic dysfunction and diabetic myocardial and neuronal injury, with emphasis on vascular and myocardial remodeling and emerging implications for autonomic neuronal vulnerability. We summarize current evidence on the formation and accumulation of advanced glycation end-products and other RAGE ligands in metabolic disease, DIAPH1’s structural and signaling role as an intracellular effector of RAGE, and the cellular consequences of pathway activation in vascular, neural, and cardiac tissues. Across experimental models, this signaling axis promotes oxidative stress and inflammatory activation, leading to endothelial dysfunction and barrier failure. Subsequent fibrotic remodeling provides a biologically plausible route through which metabolic stress may be translated into persistent organ injury. In the heart, these mechanisms are linked to coronary microvascular dysfunction, altered cardiomyocyte phenotype, calcium handling abnormalities, and myocardial fibrosis. In the autonomic nervous system, limited but emerging data connect RAGE activation to oxidative injury and mitochondrial dysfunction, abnormal neuronal excitability, and structural vulnerability. Direct evidence linking DIAPH1 to autonomic neurons is lacking. We also review biomarker candidates related to this pathway, including circulating AGEs and soluble RAGE isoforms, skin AGE measurements, imaging markers of myocardial remodeling, and autonomic functional measures. Finally, we discuss pharmacological and natural compounds that target AGE formation, ligand accumulation, RAGE signaling, or intracellular protein interactions linked to this axis. Overall, the available evidence supports the AGE–RAGE–DIAPH1 axis as a credible mechanistic concept and a potentially informative translational hypothesis in T2DM. However, the AGE–RAGE component is supported more strongly than DIAPH1-specific involvement in human diabetic myocardial disorder or cardiovascular autonomic neuropathy. The value of DIAPH1 as a biomarker or therapeutic target in these neurocardiac complications remains to be established. Full article

Alzheimer’s disease (AD) and type 2 diabetes mellitus (T2DM) are major global health burdens that share interconnected pathological mechanisms involving impaired insulin signaling, metabolic stress, and chronic neuroinflammation. This study applied an integrative systems biology and atomistic simulation framework to investigate bioactive compounds from Caesalpinia sappan L. targeting shared molecular regulators linking AD and T2DM. Network topology analysis identified four central hub genes, STAT3, SRC, HSP90AA1, and TP53, representing key regulatory nodes involved in inflammatory signaling, kinase regulation, proteostasis, and cellular stress responses. Compound-specific interaction analysis revealed distinct target preferences among phytochemical subclasses. Protosappanin B showed strong binding toward both STAT3 and HSP90α, whereas flavonols including quercetin and rhamnetin exhibited high affinity for SRC, and the chalcone derivative sappanchalcone preferentially interacted with TP53. Atomistic molecular dynamics simulations and MM-PBSA calculations supported stable protein ligand interactions and favorable binding energetics, while density functional theory analysis indicated electronic properties consistent with sustained intermolecular interactions. Collectively, these findings suggest that structurally distinct subclasses of C. sappan phytochemicals converge on complementary regulatory hubs within the shared AD and T2DM molecular network, supporting coordinated multi-target modulation of interconnected inflammatory, kinase signaling, proteostasis, and cellular stress pathways underlying AD–T2DM comorbidity. Full article

Osteoarthritis (OA) is a highly prevalent joint disorder traditionally considered a consequence of mechanical cartilage wear; however, it is now recognized as a complex, multifactorial disease driven by interconnected molecular and cellular mechanisms. This narrative review synthesizes current knowledge on key pathogenic pathways underlying OA progression, with a focus on inflammatory signaling, subchondral bone remodeling, and dysregulation of mineral metabolism. Chronic low-grade inflammation promotes catabolic responses in chondrocytes and contributes to cartilage degradation. In addition, obesity influences OA pathogenesis through both biomechanical loading and adipokine-mediated inflammatory mechanisms. Alterations in the receptor activator of nuclear factor kappa-B/receptor activator of nuclear factor kappa-B ligand/osteoprotegerin (RANK/RANKL/OPG) axis disrupt bone homeostasis and promote pathological subchondral remodeling, while imbalances in inorganic phosphate metabolism contribute to crystal deposition and further joint damage. These processes interact synergistically, driving disease progression. Current therapeutic strategies remain largely symptomatic and do not adequately target underlying molecular drivers. A deeper understanding of these mechanisms may facilitate the development of disease-modifying therapies. Full article

Mono- and bis-guanyl hydrazone-functionalized tricyclic compounds were here designed and investigated as putative G-quadruplex ligands in the context of anticancer drug development. The G-quadruplex on Controlled Pore Glass (G4-CPG) assay, a fast and easy screening method based on affinity chromatography for identifying potential G-quadruplex binders, together with biophysical techniques such as circular dichroism and fluorescence spectroscopy, demonstrated a higher selectivity of mono- with respect to disubstituted derivatives in recognizing G-quadruplexes from telomeric and oncogenic DNA regions vs. duplexes. Among the mono-substituted compounds, higher G-quadruplex selectivity was found for those containing the pyrido[3,4-b]indole and dibenzofuran scaffolds compared to the 9H-fluorene, 9H-carbazole, and dibenzothiophene ones. Molecular docking studies suggested that the investigated ligands bound the hybrid telomeric G-quadruplex model by adopting a coplanar arrangement of the core and guanyl hydrazone moieties, both stacked on the 5′-G-quartet, while in the interaction with the parallel oncogenic G-quadruplex model the guanyl hydrazone moieties pointed towards the grooves/loops. Finally, biological assays highlighted the higher potential of mono-guanyl hydrazone-derivatized tricyclic compounds as selective anticancer agents, showing higher anticancer activity and selectivity of action than the bis-guanyl hydrazone derivatives. Full article

Epithelial ovarian cancer (EOC) remains one of the most aggressive gynecological malignancies, largely due to late-stage diagnosis, therapeutic resistance, and molecular heterogeneity. This study aimed to identify biologically relevant hub genes and evaluate potential dual-target compounds against Cyclin-Dependent Kinase 1 (CDK1) and DNA Topoisomerase II Alpha (TOP2A) through an integrated computational framework. Transcriptomic datasets from GSE28799, GSE54388, and GSE14407 were analyzed to identify overlapping differentially expressed genes, followed by protein–protein interaction analysis, functional enrichment, survival assessment, molecular docking, ADMET profiling, and molecular dynamics simulations. Mechanistically, CDK1 and TOP2A participate in coordinated cell-cycle regulation associated with G2/M progression and chromosomal dynamics in ovarian cancer. Among the identified hub genes, CDK1 and TOP2A demonstrated marked overexpression and central topological importance within the interaction network. Functional enrichment analyses highlighted significant associations with mitotic cell-cycle regulation, DNA replication, and proliferative signaling pathways. Molecular docking analyses identified Naringin as a potential dual-target candidate with favorable binding affinity toward both CDK1 and TOP2A. ADMET profiling suggested acceptable pharmacokinetic and toxicity characteristics, while molecular dynamics simulations supported stable protein–ligand interactions under dynamic conditions. Although survival analyses did not demonstrate statistically significant independent prognostic associations, the findings support the biological relevance of CDK1 and TOP2A in EOC progression. Collectively, this study provides an integrated computational perspective on CDK1/TOP2A-associated oncogenic signaling and prioritizes Naringin as a preliminary candidate for future experimental investigation in epithelial ovarian cancer. Full article

CXCL8, a pro-inflammatory chemokine, which can be induced by TNF-α or IL-1, is responsible for the recruitment and activation of neutrophils. Chemokines interact with glycosaminoglycans on endothelial cells and are thus protected from degradation and sequestration, holding them in an optimal position for recruiting immune cells. Inhibiting the interaction of chemokines with their glycosaminoglycan co-receptors represents an attractive approach for the treatment of chemokine-mediated diseases. Two polyketide-pyrone compounds, PA501 and PA502 were synthesized, which bind to CXCL8 with affinities higher than the natural glycosaminoglycan ligand heparan sulfate, and in a similar range as heparin. Significant structural changes were induced in the chemokine by interacting with the two compounds, as expressed in fluorescence and far-UV CD experiments. In filter binding assays, both compounds were found to displace heparan sulfate efficiently from CXCL8, with PA501 displaying the highest competition efficacy. Using a C-terminally truncated form of the chemokine, CXCL81-58, which lacks the main glycosaminoglycan-binding α-helical domain, the two compounds are suggested to use—to a varying degree—different binding sites on the protein, which have also been proposed for the natural heparan sulfate ligand. In a transmigration assay, PA501 and PA502 exhibited dose-dependent modulation of CXCL8-induced neutrophil mobilization and migration. The compounds PA501 and PA502 may thus be regarded as early novel lead compounds in the quest for anti-inflammatory, chemokine-targeting drugs. Full article