Search Results (4,525)

Background/Objectives: Muscle aging is a complex, dynamic process that impairs overall metabolism and physiological function. The molecular mechanisms underlying declines in muscle performance and metabolic efficiency remain poorly understood, largely due to the time and resource demands of traditional model organisms. The hawk moth Manduca sexta offers a promising alternative, with a short adult lifespan (~10 days) and notable similarities to vertebrate muscle systems, making it well-suited for time-course molecular dissection of muscle aging. Methods: In this study, we performed high-resolution temporal analysis of muscle tissues from aging M. sexta, spanning the physiomuscular aging process from middle age to advanced age. Results: We observed decreased expression of genes involved in fatty acid β-oxidation, ATP synthase subunits, superoxide dismutase, glutathione S-transferases, and heat shock proteins. In contrast, genes associated with proteolysis, catabolic processes, insulin signaling, akirin, titin, high-affinity choline transporters, and vesicular acetylcholine transporters were increased in expression. Conclusions: These changes suggest a shift toward increased proteolysis and protein catabolism with age. Our findings support the use of M. sexta as a complementary model for muscle aging research. However, it remains unclear whether the observed gene expression changes are driven by intrinsic, sex-specific age-related muscle aging or confounded by potential starvation effects in older males. Full article

This study aimed to elucidate the vasorelaxant mechanism of action for apigenin 7-glucoside (A7G) by integrating computational and ex vivo pharmacological approaches. Molecular docking simulations were conducted to predict the binding affinities and interactions of A7G with key vascular proteins, specifically human endothelial nitric oxide synthase (eNOS-PDB ID: 1M9M), and human intermediate (IKCa-PDB ID: 9ED1) and small-conductance (SKCa-PDB ID: 6CNN) Ca2+-activated K+ channels. The vasodilatory properties of A7G were subsequently evaluated in isolated mesenteric vascular beds (MVBs) from normotensive Wistar Kyoto (WKY) and spontaneously hypertensive rats (SHR). The in silico analysis indicated that A7G possesses favorable binding affinities for the 1M9M, 9ED1, and 6CNN protein targets. Pharmacological assessments demonstrated that A7G induced a dose- and endothelium-dependent reduction in perfusion pressure in MVBs from WKY and SHR rats. The vasodilatory response to A7G was completely abrogated by perfusion with a high-potassium solution or a non-selective K+ channelblocker. Furthermore, co-administration of apamin and TRAM-34, selective inhibitors of SKCa and IKCa, respectively, also abolished the vasorelaxant effects of A7G. Collectively, these findings suggest that the vascular effects of A7G in both WKY and SHR rats involve an endothelium-dependent mechanism, likely initiated by the activation of the NO/cGMP pathway, which culminates in the opening of IKCa and SKCa channels. Full article

This study integrates network toxicology with molecular docking technology to systematically elucidate the key molecular mechanisms and signaling pathways by which bisphenol A (BPA) induces obesity. By cross-referencing multiple databases—including the Comparative Toxicogenomics Database (CTD), SwissTarget prediction platform, and PharmMapper—potential BPA target genes were identified, yielding a total of 1326 candidate targets. Obesity-related genes were collected from GeneCards and OMIM databases, yielding 4570 disease-associated targets. Among these, 653 overlapping genes were identified as potential mediators linking BPA exposure to obesity. Protein interaction networks were constructed using STRING and Cytoscape, and the MCC algorithm identified five core hub genes: STAT3, MYC, TP53, IL6, and mTOR. Validation using random datasets demonstrated significant upregulation of these genes in the obesity group (p < 0.05), highlighting their potential central role in BPA-induced obesity effects. Functional enrichment analysis via GO and KEGG pathways indicated that BPA may promote obesity by interfering with endocrine signaling, activating lipid metabolism, and stimulating atherosclerosis pathways. Molecular docking analysis using CB-Dock2 confirmed strong binding affinity between BPA and core targets, providing structural evidence for their potential interactions. This study elucidates the potential biological mechanism by which BPA exacerbates obesity through endocrine disruption and metabolic reprogramming, employing a multidimensional approach encompassing cross-target analysis, pathway enrichment, and molecular interactions. It provides an innovative systems toxicology framework and empirical basis for assessing metabolic health risks induced by environmental pollutants. Full article

Acne Vulgaris is a chronic inflammatory skin disorder driven by a combination of microbial colonization, immune dysregulation, and disruption of the epidermal barrier. Although isotretinoin remains the most effective treatment, the molecular mechanisms underlying its anti-inflammatory effects are incompletely understood. This study integrates transcriptomic meta-analysis and computational drug screening to identify novel therapeutic targets and candidate compounds for acne management. Three publicly available GEO datasets (GSE6475, GSE10433, GSE11792) were analyzed to identify differentially expressed genes (DEGs) associated with isotretinoin response. Among these, Spectrin beta, non-erythrocytic 1 (SPTBN1) and Signal-induced proliferation-associated 1-like protein 1 (SIPA1L1) emerged as consistently regulated genes with known roles in cytoskeletal organization and immune signaling, respectively. To assess the druggability of these targets, molecular docking was conducted using gentamicin and natural compounds derived from Cymbopogon winterianus, including citronellol, citral, citronellal, and geraniol. Gentamicin demonstrated the strongest binding affinity to SIPA1L1 (−8.6 kcal/mol) and SPTBN1 (−5.9 kcal/mol), forming multiple hydrogen bonds and hydrophobic contacts. Subsequent 100 ns molecular dynamics (MD) simulations confirmed the stability of the gentamicin–protein complexes, as evidenced by favorable RMSD, RMSF, and energy profiles. Interaction energy decomposition revealed strong contributions from electrostatic and van der Waals forces. These findings highlight the potential of gentamicin, and possibly structurally related natural compounds, as modulators of host inflammatory pathways implicated in acne. The study further underscores the utility of integrating transcriptomics, molecular docking, and MD simulation for early-phase therapeutic discovery targeting inflammation and barrier dysfunction in dermatological diseases. Full article

Background: Heart failure (HF) is a leading cause of mortality and represents the final stage of various cardiovascular disorders. Although traditional Chinese herbs have been extensively applied in HF treatment and their clinical efficacy has been investigated, the underlying molecular mechanisms remain insufficiently understood. To address this gap, systematic approaches are required to elucidate the therapeutic basis of herbal interventions. Methods: In this study, we systematically analyzed the bioactive compounds from seven traditional Chinese herbs, Baiguo (Ginkgo biloba), Chishao (Radix Paeoniae Rubra), Biba (Piper longum), Aidicha (Ilex latifolia), Bajiaolian (Dysosma spp.), Beiwuweizi (Schisandra chinensis), and Baiqucai (Sedum sarmentosum) and explored their potential mechanisms in HF by integrating network pharmacology, molecular docking, and molecular dynamics simulations. Result: We identified key targets and pathways implicated in HF pathogenesis and herbal interventions. A total of 63 active compounds were found to regulate 1947 genes. Through integrative analysis of the GSE57338 heart failure dataset from the GEO database, we further identified 265 intersecting targets shared between herb-associated genes and HF-related genes, highlighting their potential involvement in HF progression. Network analysis prioritized three hub proteins, STAT3, SRC, and TP53, which were subsequently subjected to molecular docking with the top bioactive compounds (quercetin, kaempferol, and epigallocatechin-3-gallate). Docking studies revealed strong binding affinities, and molecular dynamics (MD) simulations further validated the stability of these protein compound interactions. Conclusions: This study elucidates key bioactive components and targets involved in HF treatment, with kaempferol and epigallocatechin-3-gallate emerging as promising therapeutic candidates. These results provide a foundation for future experimental validation and the development of targeted HF therapies derived from traditional Chinese medicine. Full article

Cystic echinococcosis (CE) is an endemic zoonotic disease caused by Echinococcus granulosus, which forms cysts in ungulates’ intermediate hosts. Humans are accidental hosts, and CE affects more than one million people worldwide. Imaging remains the diagnostic gold standard, outperforming serological methods. This study presents an in silico analysis of two glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isoenzymes from E. granulosus (EgGAPDH), isolated from a parasite cell line (EGPE). EgGAPDHs were recognized by sera from CE patients, identified through LC-MS/MS and PCR of metacestodes from cattle liver. One isoenzyme is intracellular (IC) (UniProt: W6UJ19), and the other is extracellular (EC) (UniProt: W6V1T8). GAPDH is involved in host–parasite interactions and metabolic processes. We characterized the physicochemical properties; linear epitopes (LEPs); and amino acid domains of EgGAPDH, its hosts, and other parasites. W6UJ19 emerged as the most promising isoenzyme as a marker of infection. Molecular dynamics simulations of isoenzymes, performed in the presence or absence of two bisphosphonates (BPs), revealed how drug binding alters conformational epitopes (CEPs) and suggested that W6UJ19 is more responsive to BP modulation. Binding affinity analysis using the MMPBSA method revealed that etidronate (EHDP) binds EgGAPDH with greater affinity than phosphate (Pi) and alendronate (AL), in the following order: EHDP > Pi > AL. Full article

In order to conveniently and efficiently determine the Permissible Exposure Limits (PELs) of organic chemicals in the workplace, this study employed Quantitative Structure–Activity Relationship (QSAR) modeling to predict properties related to occupational health and safety. The predictive study was conducted by correlating the PELs of 75 hydrocarbons and their oxygen-containing derivatives with the molecular structures of the organic compounds. Meanwhile, this study conducted a comprehensive and in-depth comparative analysis of the four developed predictive models. The sample set was partitioned using the Affinity Propagation (AP) clustering algorithm. Four characteristic molecular descriptors were selected by integrating the Genetic Algorithm (GA) with the variance inflation factor (VIF) value. Subsequently, the Multiple Linear Regression (MLR) model and two nonlinear models, namely the Support Vector Machine (SVM) and the Extreme Gradient Boosting (XGBoost), were developed and used for predictive comparison. Furthermore, the performance of the models was evaluated through both internal and external validation methods, and the Williams plots were constructed to define the model’s applicability domain. The results indicated that the XGBoost model achieved high performance, with a coefficient of determination (R²) of 0.9962 on the training set and 0.8892 on the testing set. The corresponding root mean square errors (RMSE) were 0.1012 and 0.6623 for the training and testing sets, respectively. The internal validation coefficient (Q²loo) was 0.8975, while the external validation coefficient (Q²ext) was 0.832. Moreover, the majority of the sample data (approximately 96%) fell within the application domain defined by ±3 times the standard residue-to-critical arm ratio, where h* = 0.2. This demonstrates that the XGBoost model exhibits excellent fitting capability, stability, and predictive power, thereby uncovering a significant nonlinear relationship between the molecular structure of compounds and the PELs. As outlined above, the utilization of the QSAR method for predicting the PELs of hydrocarbons and their oxygen-containing derivatives constitutes a highly effective approach. Full article

Nanoplastics are pervasive contaminants that adversely affect male reproductive function, yet the molecular basis of polystyrene nanoplastic (PS-NP) toxicity in immature testes and effective preventive strategies remain unclear. Here, male mice (postnatal days 22–35, PND 22–35) and TM3 Leydig cells were exposed to graded PS-NPs, followed by transcriptomic profiling to identify differentially expressed genes (DEGs). Candidate therapeutics were prioritized using Connectivity Map (CMap) analysis and molecular docking, and protein interactions were examined by co-immunoprecipitation (Co-IP). PS-NPs accumulated in immature testes, eliciting excessive reactive oxygen species (ROS) and activation of NF-κB. These events coincided with the downregulation of steroidogenic enzymes (CYP11A1 and StAR) and disruption of testicular microarchitecture. In TM3 cells, PS-NPs suppressed testosterone synthesis in a concentration-dependent manner; this effect was fully reversed by pretreatment with N-acetylcysteine (NAC) or Bay 11-7082. Co-IP demonstrated p65–steroidogenic factor-1 (SF-1) binding consistent with formation of a transcriptional repressor complex targeting steroidogenic genes. CMap and docking analyses nominated parthenolide (PTL) as a candidate inhibitor of NF-κB nuclear translocation (predicted binding affinity, −6.585 kcal/mol), and PTL mitigated PS-NP-induced impairment of testosterone synthesis in vitro. Collectively, these data indicate that PS-NPs disrupt testosterone biosynthesis in immature testes through the ROS/NF-κB/p65–SF-1 axis, while PTL emerges as a candidate small molecule to counter nanoplastic-associated reproductive toxicity. These findings underscore translational relevance and support future evaluation under chronic low-dose exposure conditions, including in vivo validation of PTL efficacy, pharmacokinetics, and safety. Full article

This study successfully established a novel discriminative model that distinguishes between Thai and foreign hemp seed extracts based on gas chromatography/mass spectrometry (GC/MS) metabolic profiling combined with machine learning algorithms such as hierarchy clustering analysis (HCA), principal component analysis (PCA), and partial least square-discriminant analysis (PLS-DA). The findings highlighted significant metabolic features, such as vitamin E, clionasterol, and linoleic acid, related with anti-aging properties via elastase inhibition. Our biological validation experiment revealed that the individual compound at 2 mg/mL exhibited a moderate elastase inhibitory activity, 40.97 ± 1.80% inhibition (n = 3). However, a binary combination among these metabolites at 1 mg/mL of each compound demonstrated a synergistic effect against elastase activities up to 89.76 ± 1.20% inhibition (n = 3), showing 119% improvement. Molecular docking experiments aligned with biological results, showing strong binding affinities and enhanced inhibitory effects in all combinations. This integrated approach provided insights into the bioactive compounds responsible for anti-aging effects and established a dependable framework for quality control and standardization of hemp seed-based skincare products. Additionally, the developed models enable effective discrimination between Thai and foreign strains, which is valuable for sourcing and product consistency. Overall, this research advances our understanding of hemp seed phytochemicals and their functional potential, paving the way for optimized natural anti-aging formulations and targeted functional foods. Full article

Radionuclide molecular imaging of epidermal growth factor receptor (EGFR) expression might permit the selection of patients for EGFR-targeting therapies. Designed ankyrin repeat protein (DARPin) E01 with a high affinity to the ectodomain III of the EGFR is a possible EGFR imaging probe. The goal of this study was to evaluate the potential of radiolabeled DARPin E01 for in vivo imaging of EGFR. DARPin E01 containing the (HE)₃-tag was site-specifically labeled with a residualizing ^99mTc (using ^99mTc]Tc(CO)₃). Two methods providing non-residualizing ¹²³I labels, direct electrophilic radioiodination and indirect radioiodination using [¹²³I]I-para-iodobenzoate (PIB), were tested. [^99mTc]Tc-(HE)₃-E01 and [¹²³I]I-(HE)₃-E01-PIB preserved specific binding to EGFR-expressing cells and affinity in the single-digit nanomolar range. Direct labeling with ¹²³I resulted in a substantial loss of binding. In vitro cellular processing studies showed that both [^99mTc]Tc-(HE)₃-E01 and [¹²³I]I-(HE)₃-E01-PIB had rapid binding and relatively slow internalization. Evaluation of [^99mTc]Tc-(HE)₃-E01 biodistribution in normal CD1 mice showed that its hepatic uptake was non-saturable, suggesting that this tracer does not bind to murine EGFR. A side-by-side comparison of biodistribution and tumor targeting of [^99mTc]Tc-(HE)₃-E01 and [¹²³I]I-(HE)₃-E01-PIB was performed in Nu/j mice bearing EGFR-positive A-431 and EGFR-negative Ramos human cancer xenografts. Both radiolabeled DARPins demonstrated EGFR-specific tumor uptake. However, [¹²³I]I-(HE)₃-E01-PIB had appreciably lower uptake in normal organs compared to [^99mTc]Tc-(HE)₃-E01, which provided significantly (p < 0.05) higher tumor-to-organ ratios. Gamma-camera imaging confirmed that [¹²³I]I-(HE)₃-E01-PIB demonstrated a higher imaging contrast in preclinical models than [^99mTc]Tc-(HE)₃-E01. In conclusion, DARPin (HE)₃-E01 labeled using a non-residualizing [¹²³I]I-para-iodobenzoate (PIB) label is the preferred radiotracer for in vivo imaging of EGFR expression in cancer. Full article

Background: Infectious pneumonia remains a major global health challenge with high morbidity and mortality, especially among vulnerable groups. Current diagnostic approaches lack sufficient specificity and accuracy. This study aimed to identify core diagnostic genes, explore their biological functions, and predict potential natural compounds targeting these genes to improve diagnostic and therapeutic strategies. Methods: Gene expression profiles from the GEO database (GSE103119) were analyzed to identify differentially expressed genes (DEGs). Hub genes were selected by integrating protein–protein interaction (PPI) networks and multiple machine learning algorithms. Expression patterns of the identified hub gene were validated in a murine pneumonia model. Reverse network pharmacology was applied to screen natural compounds, followed by molecular docking and molecular dynamics simulations to evaluate binding affinity and complex stability. Results: A total of 2550 DEGs were identified. FCER1A was consistently determined as a hub gene through PPI and machine learning analyses, showing significant downregulation in infectious pneumonia patients. Animal experiments confirmed pronounced reduction of Fcer1a transcription in both lung tissue and whole blood of pneumonia model mice. Two natural compounds, pyrogallol and tectorigenin, were identified as potential ligands for FCER1A. Molecular simulations confirmed stable binding with the target protein, with tectorigenin exhibiting superior binding affinity. Conclusions: This study proposes FCER1A as a promising diagnostic biomarker for infectious pneumonia and suggests tectorigenin as a candidate compound for further therapeutic development. Full article

Dengue virus remains a major global health threat due to the lack of a safe and broadly effective vaccine. Traditional antibody-based vaccines often show limited protection and can exacerbate disease severity in individuals without prior exposure. A new generation of T-cell epitope-based vaccines offers a promising and safer approach by activating the cellular arm of the immune system to complement antibody responses. Instead of targeting only surface structural proteins, these vaccines focus on highly conserved peptide regions within non-structural proteins, particularly NS3 and NS5, that are shared across all four dengue virus serotypes. Peptides such as DTTPFGQQR, KPGTSGSPI, and MYFHRRDLRL have been identified as potent immunogenic targets capable of inducing strong cytotoxic and helper T-cell responses, promoting viral clearance and long-term immune memory. Advanced immunoinformatic enables precise prediction and selection of epitopes with high binding affinity to human leukocyte antigens and broad cross-serotype conservation. These peptides can be integrated into next-generation vaccine delivery systems, including messenger RNA and nanoparticle platforms, which enhance antigen presentation, improve molecular stability, and reduce the risk of antibody-dependent disease enhancement. Together, this integrative design represents a rational path toward a safer, cross-protective, and durable dengue vaccine that closely mimics the balanced cellular and humoral immunity observed after natural infection, offering renewed hope for effective global dengue prevention. Full article

Galectin-3 (Gal-3) is a histologic marker of pancreatic cancer and a potential therapeutic target. This study aimed to characterize a novel sulfated agarose-derived oligosaccharide (DP9) from marine algae, Gracilaria lemaneiformis, evaluate its Gal-3 inhibitory activity, and investigate its anti-pancreatic cancer mechanisms. Through controlled acid hydrolysis, a series of odd-numbered oligosaccharides (DP3-11) were obtained, in which DP9 showed the strongest Gal-3 inhibition in hemagglutination assays. Structural analysis confirmed DP9’s unique composition including an alternating β (1→4)-D-galactose and α (1→3)-3,6-anhydro-L-galactose backbone, featuring partial 6-O-methylation on β-D-galactose and 6-O-sulfation on 3,6-anhydro-α-L-galactose residues. Molecular docking revealed DP9’s binding to Gal-3’s carbohydrate recognition domain through key hydrogen bonds (His158, Arg162, Lys176, Asn179 and Arg186) and hydrophobic interactions (Pro117, Asn119, Trp181 and Gly235), with the sulfate group enhancing binding affinity. In vitro studies demonstrated DP9’s selective anti-pancreatic cancer activity against BxPC-3 cells, including inhibition of cell proliferation; S-phase cell cycle arrest; induction of apoptosis; and suppression of migration and invasion. Mechanistically, DP9 attenuated the Gal-3/EGFR/AKT/FOXO3 signaling pathway while showing minimal cytotoxicity to normal cells. This study first demonstrated that agarose-derived odd-numbered oligosaccharides (DP9) can serve as effective Gal-3 inhibitors, which proved its potential as a marine oligosaccharide-based therapeutic agent for pancreatic cancer. Full article

Distant hybridization is key to trait innovation and speciation, with Cyprinidae hybrid phylogeny helping to clarify diversification mechanisms. Yet, a major gap persists in Cyprinidae studies: the stabilization mechanisms of interspecific distant hybrid lineages. To address this, we systematically analyzed the molecular phylogeny of seven Cyprinidae distant hybrid lineages and their parental species, using an integrative genetic framework encompassing four mitochondrial genes (Cytb, COI, 16S rRNA, D-loop) and five nuclear genes (EGR2b, IRBP2, RAG1, RAG2, RH2). Homologous sequences of 41 representative Cyprinidae species (85 samples) were retrieved from GenBank to supplement the dataset. Phylogenies were reconstructed from concatenated sequences, complemented by haplotype networks. Intra-/interspecific divergence was quantified using two mitochondrial genes (COI, Cytb) and two nuclear (RAG1, RH2). The results showed that these hybrid lineages exhibited variation patterns analogous to other Cyprinidae species. Both ML and BI trees reconstructed exhibited congruent topologies with high support (bootstrap/BPP > 80%), resolving genus/species-level relationships. While most hybrids clustered intermediately between their parental species, they typically displayed maternal affinity. A notable exception was the 2nNCRC (a homodiploid hybrid from Cyprinus carpio ♀ × Megalobrama amblycephala ♂), which displayed convergent evolution toward Carassius auratus. COI-based K2P genetic distance analysis revealed 2nNCRC had a much closer relationship with C. auratus (0.0119) than with its parents (0.1249 to C. carpio, 0.1552 to M. amblycephala). These nine genes elucidate the genetic relationships between Cyprinid hybrid lineages and progenitors, serving as pivotal molecular markers for parentage tracing and genetic dissection of distant hybridization mechanisms. The integrated mitochondrial–nuclear marker system in this study advances understanding of cytonuclear coadaptation and the stabilization of interspecific distant hybrid lineages in Cyprinidae. Specifically, it provides a precise tool for parentage tracing, Cyprinid germplasm conservation, and targeted regulation of hybrid breeding—laying a foundation for exploring hybrid speciation and developing elite aquaculture germplasms. Full article

Nucleic acid aptamers leverage defined tertiary structures for precise molecular recognition, positioning them as transformative biomedical tools. We engineered AP1-F, a G-quadruplex (G4)-structured aptamer that selectively binds membrane-anchored nucleolin (NCL) non-permeabilizing, overcoming a key limitation of conventional probes. Microscale thermophoresis confirmed nanomolar affinity to NCL. By means of rigorous optimization, AP1-F attained a greater than ten-fold fluorescence signal ratio between malignant and normal cells in co-cultures, exceeding the extensively researched AS1411. Dual-channel flow cytometry demonstrated over 98.78% specificity at single-cell resolution within heterogeneous cell populations, owing to AP1-F’s unique membrane localization—unlike AS1411’s intracellular uptake, which elicited erroneous signals from cytoplasmic NCL. Competitive binding experiments and Laser Confocal Imaging confirmed that AP1-F specifically identifies cancer cells by binding to the NCL recognition site on the membrane. In pathological sections, AP1-F exhibited a 40.5-fold fluorescence intensity ratio between tumor and normal tissue, facilitating accurate tissue-level differentiation. Significantly, it delineated molecular subtypes by associating membrane NCL patterns with morphometric analysis: luminal-like MCF-7 displayed consistent staining in cohesive clusters, whereas basal-like MDA-MB-468 revealed sporadic NCL with irregular outlines—characteristics imperceptible to intracellular-targeted antibodies, thus offering subtype-specific diagnostic insights. This combination biochemical–morphological approach accomplished subtype differentiation with a single-step, non-permeabilized process that maintained lower cytotoxicity and tissue integrity. AP1-F enhances diagnostic accuracy by utilizing spatial confinement to eradicate intracellular interference, connecting molecular specificity to intraoperative margin evaluation or biopsy categorization. Full article