Search Results (2,109)

Usutu virus is an emerging mosquito-borne flavivirus with an expanding geographic distribution and increasing public health relevance, yet no licensed vaccine is currently available. This study used an integrated reverse vaccinology strategy to identify conserved immunogenic regions from the Envelope protein and NS5 protein, and construct a multi-epitope vaccine. Following sequential computational screening, the retained T-cell and B-cell epitopes satisfied the predefined selection criteria, while selected T-cell epitopes achieved an estimated 96.41% global population coverage. The final vaccine consisted of 240 amino acids and incorporated an adjuvant together with peptide linkers. Computational characterization indicated favorable physicochemical features and a refined three-dimensional model with improved stereochemical characteristics. Receptor-binding analyses predicted favorable interactions with TLR2 and TLR4, producing weighted docking scores of −1326.1 and −1230.2, respectively. Molecular dynamics simulation further characterized the temporal behavior of the vaccine–TLR2 complex, while MM-GBSA analysis yielded an estimated binding energy of −74.78 kcal/mol. C-ImmSim predicted enhanced humoral and cellular immune-response patterns following repeated antigen administration, including increased simulated antibody levels and changes in immune-cell populations. All findings in this study are based on in silico analyses and represent computational predictions rather than experimentally confirmed results. Further experimental validation is required to verify the predicted properties, immunogenicity, and protective potential of the proposed vaccine candidate. Full article

In this study, ternary composite active packaging films composed of chitosan (CH), deep eutectic solvent (DES), and chestnut shell extract (CSE) were prepared. The physicochemical properties, structural characteristics, and application in strawberry preservation were studied. The results show that the DES hydrogen-bond network may promote interactions between CSE and CH, enhancing compatibility and stability. At 5% CSE addition, the maximum values were observed for antioxidant activity (DPPH: 80.49%, ABTS: 86.69%) and antibacterial activity (Antibacterial Zone Diameter (AZD): 27.61 mm for Escherichia coli E. coli and 27.15 mm for Staphylococcus aureus). FTIR analysis indicated the hydrogen bonding between CSE and the polymer matrix. XRD results indicated that CSE addition enhanced the crystallinity of the film matrices, while SEM revealed that it promoted the formation of a dense structure. Molecular docking results provide computational evidence suggesting that DES may serve as an interfacial bridge connecting CH and CSE. Satisfactorily, after treatment with the CH–DES–CSE-5% film, the shelf life of strawberries was significantly extended. After 8 days of storage, the decay rate (36.67%) was significantly lower than that of the control group (96.67%). The original quality indicators were well maintained. This study provides a theoretical basis for both the valorization of chestnut shell waste and the development of CSE-based active food packaging materials. Full article

Background/Objectives: The programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) immune checkpoint is a key therapeutic target in cancer immunotherapy, but small-molecule inhibition remains challenging due to its shallow and dynamic interaction interface. This study aimed to develop an artificial intelligence (AI)-guided workflow to identify novel small-molecule inhibitors targeting the PD-L1 dimer interface. Methods: A combined computational and experimental approach was established. A support vector regression-genetic algorithm (SVR-GA) model was trained on a dataset of 1385 known PD-L1 inhibitors to predict activity and guide molecular generation. From 470 AI-generated candidates, docking and molecular dynamics (MD) simulations were used for virtual screening. Selected compounds were synthesized and evaluated for PD-1/PD-L1 binding disruption using homogeneous time-resolved fluorescence (HTRF) assays. Cytotoxicity was tested in MDA-MB-231 and 4T1 cell monocultures, and in vivo efficacy was assessed in an immunocompetent 4T1 tumor model. Results: Two hits, PD-L1-Ser and PD-L1-Ser-OEt, were identified. Both disrupted PD-1/PD-L1 binding in HTRF assays, with PD-L1-Ser-OEt showing higher potency (IC₅₀ = 0.2068 μM). Both compounds exhibited limited direct cytotoxicity in cancer cell monocultures, suggesting an immune-mediated mechanism. In the 4T1 syngeneic mouse model, both inhibitors suppressed tumor growth without causing body weight loss. PD-L1-Ser-OEt demonstrated superior antitumor efficacy and elevated serum levels of IFN-γ and IL-4. Conclusions: This AI-guided workflow combining machine-learning-based molecular generation with structure validation is feasible for discovering PD-L1 dimer-interface inhibitors. PD-L1-Ser-OEt represents a promising lead compound for further development as an immune checkpoint inhibitor. Full article

Background: Euryale ferox Salisb. seed (Euryales Semen) is a traditional Chinese medicine whose therapeutic application is modulated by wheat bran stir-frying, a process that enhances its effects on tonifying the spleen and kidney. The molecular mechanisms and alterations in bioactive components underlying this processing-enhanced efficacy remain to be fully elucidated. This study aimed to systematically investigate the impact of wheat bran stir-frying on the metabolite profile of Euryales Semen and to reveal its potential pharmacological mechanisms. Methods: An integrated strategy combining UPLC-MS/MS-based metabolomics, network pharmacology, and molecular docking was employed. First, differential metabolites between raw and processed Euryales Semen were identified and quantified. Second, a “metabolite-target-disease” network was constructed to predict core targets and pathways. The docking protocol was validated by re-docking of co-crystallized ligands, with all RMSD values below 2.0 Å. Finally, molecular docking was used to predict the binding interactions between key metabolites and potential protein targets. Results: A total of 1597 metabolites were identified, and 244 were defined as differentially expressed (VIP > 1, |log2(FC)| ≥ 1). Processing significantly upregulated 19 of the 22 key metabolites identified, with Urolithin B showing the most dramatic increase (168-fold), which was identified with Level 1 confidence using an authentic standard. Network pharmacology analysis identified 10 core targets (e.g., MMP2, MMP9, AKR1B1) primarily associated with tumors, diabetes, and other chronic diseases. Molecular docking predicted strong binding affinities (<−9.0 kcal·mol⁻¹) between these core targets and key upregulated metabolites, including Urolithin B, Tangeretin, and Syringetin. Conclusions: This study suggests that wheat bran stir-frying fundamentally reshapes the metabolic profile of Euryales Semen, leading to the enrichment of bioactive metabolites (e.g., Urolithin B) and suggesting a potential for enhanced tonifying, anti-tumor, and anti-diabetic activities that warrants further experimental investigation. The dramatic increase in the content of Urolithin B, a metabolite not commonly found in plants, raises the hypothesis of a processing-induced chemical transformation, which warrants further experimental validation, and highlights its potential as a critical component for the herb’s efficacy. The findings offer a preliminary computational basis for understanding traditional processing practices, linking traditional knowledge with modern scientific evidence. Full article

This narrative review summarizes current data on the role of desialylation of low-density lipoproteins (LDL) as a key initiating mechanism of atherogenesis that precedes oxidative modification. The structural and functional significance of sialic acid in apolipoprotein B-100 is considered, and the enzymes of the sialidase (neuraminidase) family responsible for its cleavage are characterized. The pathogenic role of increased sialidase activity in atherosclerosis, type 2 diabetes mellitus, and other diseases is discussed. The advantages of using dietary supplements based on natural sialidase inhibitors for long-term prevention compared with synthetic drugs are shown. Examples of already existing dietary supplements with antiatherosclerotic effects are described. A separate section is devoted to computer methods (molecular docking) for searching for new sialidase inhibitors among flavonoids; according to virtual screening data, gallated catechins were identified as the most promising candidates. The feasibility of further experimental and clinical studies to create effective and safe nutraceuticals that affect the early stages of atherogenesis is substantiated. Full article

Objectives: Herpetrione (HPE) is a bioactive lignan recognized for its hepatoprotective properties; however, it exhibits limited oral bioavailability. This study aimed to classify HPE within the framework of the biopharmaceutics classification system (BCS) and to develop a nanoparticle formulation. Methods: To this end, a comprehensive investigation was conducted, encompassing computer prediction analysis, equilibrium solubility measurements across the gastrointestinal pH range, Caco-2 bidirectional transportation, in situ single-pass intestinal perfusion (SPIP), and molecular docking with P-glycoprotein (P-gp). Results: In silico analyses suggested that HPE possesses low solubility and low permeability characteristics. Experimental assays revealed pH-dependent solubility and inherently low aqueous dissolution. Unlike the computer prediction results, Caco-2 studies revealed moderate permeability but a high efflux ratio, suggestive of possible P-gp substrate activity for HPE, a finding further supported by molecular docking simulations. Conversely, SPIP studies demonstrated that the effective permeability (P_eff) of jejunal intestinal segments exceeded the high-permeability threshold, thereby classifying HPE as a high-permeability drug. Based on these findings, HPE was classified as a BCS class II compound. To overcome its solubility-limited absorption, a nanoparticle was developed, resulting in a marked enhancement of both solubility and dissolution rates. Conclusions: These findings underscore the importance of integrating experimental biopharmaceutical evaluations with computational tools when designing delivery systems for natural products. Full article

The triterpenoid and polysaccharide constituents of Ganoderma lucidum (GL) are believed to influence key pathogenic pathways in Alzheimer’s disease (AD). This study first examined the molecular rationale for GL’s neuroprotective properties by subjecting its principal triterpenoids, Ganoderic Acid A&B, to computational profiling. Molecular docking was performed against human acetylcholinesterase (AChE), TNF-α, COX-2, IL-6, caspase-3, Bcl-2, and the Keap1–Nrf2 complex using CB-Dock2, alongside SwissADME-based physicochemical and ProTox-3.0-based toxicological screening. These targeted pathways were then biologically validated in an in vitro AD model induced by Aβ_1–42 toxicity in SH-SY5Y cells, assessing AChE activity, apoptosis, ROS levels, mitochondrial membrane potential (MMP), and cytokine expression (COX-2, TGF-β1, IL-6, TNF-α, IL-10). Docking revealed high binding affinities of both triterpenoids toward all seven targets (Vina scores: −7.3 to −10.4 kcal/mol), predicting strong modulation of cholinergic, inflammatory, apoptotic, and antioxidant pathways. Consistent with these predictions, GL extract significantly reduced TNF-α, COX-2, and IL-6 mRNA and protein levels, attenuated ROS accumulation, preserved MMP except at 500 µg/mL, and exerted a concentration-dependent antiapoptotic effect. IL-10 and TGF-β1 showed complex, dose-dependent patterns, reflecting indirect regulatory responses. Together, these findings support GL’s neuroprotective potential against Aβ-induced toxicity through direct engagement of cholinergic, inflammatory, apoptotic, and antioxidant regulatory proteins. Full article

Nipah virus (NiV) is a zoonotic virus that causes severe encephalitis and respiratory disease with a mortality rate often exceeding 70%. Currently, there are no licensed vaccines or therapeutics for NiV disease. This study aimed to identify and experimentally evaluate small-molecule inhibitors targeting the NiV-G (attachment) glycoprotein using integrated in silico and in vitro approaches. A high-throughput virtual screening of >215,000 compounds was conducted against the NiV-G glycoprotein, using docking and molecular dynamics (MD) simulations. The next potential candidates were evaluated using an established, BSL-2-compatible recombinant Cedar virus (rCedV)-based green fluorescent protein (GFP) reporter virus expressing the NiV-F (fusion) and G glycoproteins (rCedV-NiV-B-GFP). During MD simulations, quercetin demonstrated the most stable binding, maintaining a consistent RMSD (3.25 ± 0.3 Å). In vitro testing showed dose-dependent inhibition of rCedV-NiV-B-GFP infection. Although quercetin alone was less potent (IC₅₀ = 24 µM; 95% CI: 7.6–93.6 µM) than a reference NiV-neutralizing monoclonal antibody mAb-7B7 (IC₅₀ = 0.027 μg/mL; approximately 0.00018 μM; 95% CI: 0.0108 to 0.0735), combination with ascorbic acid enhanced neutralization (IC₅₀ = 4.4 µM; 95% CI: 2.9–6.8 µM). Quercetin demonstrated a high Selectivity Index of >20.8. The study identifies quercetin as a promising small-molecule inhibitor of NiV cellular infection, potentially through a stable interaction with NiV-G at the ephrin-B2/B3 binding interface identified computationally. These findings highlight the importance of combining computational screening with BSL-2 cell-based bioassays to accelerate NiV countermeasure discovery. Full article

Background/Objectives: Polyendocrine metabolic ovarian syndrome (PMOS) is characterized by hyperandrogenism, particularly excessive testosterone, as a core clinical feature and a key pathogenic metabolite, yet its molecular mechanisms remain incompletely understood. Methods: This study integrated multi-omics data from Gene Expression Omnibus (GEO) databases with network toxicology, weighted gene co-expression network analysis (WGCNA), and machine learning to identify testosterone-associated core genes in PMOS. Results: Differential expression analysis and WGCNA yielded 42 candidate genes, from which five core genes, including GK5, CYP3A5, EGLN3, VCAM1, and AGTR1, were prioritized as top predictive features through ensemble modeling (RF + XGBoost). Molecular docking predicted favorable testosterone binding conformations. Regulatory network and drug enrichment analysis additionally predicted several upstream transcription factors, hub miRNAs, and potential repurposable drugs. Conclusions: These findings proposed a computational framework for a multi-target molecular landscape linking testosterone to PMOS. The identified genes, regulatory networks, and candidate drugs provided prioritized hypotheses for mechanistic exploration and future evaluation of potential diagnostic and therapeutic applications in hyperandrogenism-related PMOS. Full article

Background/Objectives: Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease, and ginger contains phenolic constituents with anti-inflammatory potential. This study evaluated the antiarthritic efficacy of ginger ethanolic extract (GE) and explored its potential mechanisms through integrated pharmacological and computational approaches. Methods: GE was prepared by 70% ethanol reflux extraction and administered to adjuvant-induced arthritis (AIA) rats, with methotrexate as a positive control. Body weight; paw swelling; arthritis index; spleen index; and serum interleukin-6 (IL-6), interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and prostaglandin E2 (PGE2) were measured. Chemical profiling was performed by ultra-performance liquid chromatography–quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS), followed by network pharmacology, molecular docking, and molecular dynamics (MD) simulation. Results: GE attenuated paw edema, arthritis index elevation, splenic enlargement, and elevated serum inflammatory mediators in AIA rats. UPLC-Q-TOF-MS/MS annotated 38 constituents, mainly gingerols, shogaols, gingerdiones, gingerdiols, and related phenolic derivatives. Network analysis identified 217 overlapping ginger- and RA-associated targets, with TNF, IL6, and matrix metalloproteinase 9 (MMP9) prioritized among inflammatory and matrix-remodeling nodes. Docking and MD simulations supported stable predicted interactions for 8-gingerol-TNF and 6-gingerol-MMP9. Conclusions: GE showed antiarthritic activity in AIA rats. The integrated chemical, in vivo, and computational data suggest that ginger phenolics may modulate inflammatory mediators and candidate RA-related pathways; however, these mechanisms remain exploratory and require histological, tissue-level, and molecular validation. Full article

Background/Objectives: Stereochemistry can substantially influence the biological activity and pharmaceutical properties of small molecules. This study investigated the stereochemistry-dependent biological activity and chiral recognition of novel naphthylethyl thiourea enantiomers using an integrated biological, chromatographic, and computational approach. Methods: Ten pairs of naphthylethyl thiourea enantiomers were synthesized from enantiomerically pure precursors and characterized. Antiproliferative and antibacterial activity, chiral HPLC behavior on polysaccharide- and protein-based stationary phases, molecular docking, and multivariate relationships were evaluated. Results: Target-dependent enantioselectivity and substituent-dependent activity patterns were observed. All enantiomeric pairs were chromatographically distinguished under at least one condition, and selected compounds showed selector- and mobile-phase-dependent changes in elution order. AGP-based chromatography showed stereoselective recognition for a subset of compounds, while computational analyses provided complementary support for the experimental trends. Conclusions: Stereochemistry and substitution jointly influence biological and chromatographic behavior in this thiourea series. Integrated biological, chromatographic, and computational profiling provides a useful framework for early enantiomer-resolved developability assessment. Full article

Catechol 2,3-dioxygenase (C23O) is the rate-limiting enzyme in the meta-cleavage pathway of aromatic compound degradation, yet its functional annotation within the structurally conserved VOC superfamily remains challenging due to high sequence homology. Here, we isolated a catechol-degrading strain from bovine feces and identified it as Bacillus thuringiensis HHY919 via whole-genome sequencing. Genome annotation revealed four VOC genes sharing the same COG annotation (“catechol 2,3-dioxygenase”) but divergent KO annotations (two as glyoxalases and two as C23O), suggesting functional divergence. Using homology modeling and molecular docking, we compared their binding affinities toward catechol and 11 derivatives. All four proteins showed typical meta-cleavage binding energies (−4.9 to −5.4 kcal/mol), with slightly more favorable binding than an ortho-cleavage control. Notably, gene4224 exhibited the broadest and strongest predicted affinities in virtual screening against 212 compounds, particularly for trichlorophenol (−6.0 kcal/mol) and complex natural products (qvina_score ≤ −7.6 kcal/mol). Phylogenetic analysis and docking results jointly identified gene3355 and gene4224 as computationally prioritized C23O candidates, with gene4224 recommended as the top candidate for future enzyme engineering and bioremediation studies. This study provides a computational workflow for resolving functional ambiguity in VOC family enzymes and generating testable hypotheses for experimental validation. Full article

The argan tree (Argania spinosa) is an endemic Moroccan species known for its primary product, argan oil, which possesses exceptional nutritional and medicinal properties. The current study aimed to evaluate and compare the antidiabetic and antioxidant activities of argan oil obtained from the introduced and native argan tree in eastern Morocco, to analyze its chemical composition using HPLC-DAD and GC-MS, and to investigate the molecular mechanisms behind the obtained pharmacological activities through an in silico pharmacological networking and molecular docking study. The results revealed that argan oil from all three regions of Morocco (Oujda, Agadir, and Chouihya) is rich in oleic and linoleic acids as major constituents, along with the presence of significant tocopherols. Regarding the antioxidant assays, including DPPH radical scavenging and iron-reducing power tests, argan oil from Oujda exhibited the highest activity, with the lowest IC₅₀ values of 15.25 ± 0.022 mg/mL and 28.5 ± 1.7 mg/mL, respectively. Concerning the antidiabetic activity, we found that oil from Chaouihya showed the strongest α-amylase inhibition, while Oujda oil had the highest antiglycation activity, indicating that even introduced argan trees retain potent bioactivity. The results of the in silico investigation suggested that tocopherols may contribute to the antioxidant and antidiabetic potential of argan oil, showing predicted antioxidant activity (Pa = 0.843–0.967) and favorable binding affinities toward iNOS (ΔG = −9.3 kcal mol⁻¹) and α-glucosidase (ΔG = −8.2 kcal mol⁻¹). The identified fatty acids also showed predicted insulin-promoting activity (Pa = 0.59–0.75) and moderate enzyme-binding potential. Pharmacological network analysis identified 51 shared genes associated with antioxidant, antidiabetic, and argan-related targets, with enrichment of the AGE–RAGE signaling pathway. These computational findings provide possible molecular associations that may help explain the observed biological activities, although they remain predictive and require experimental validation. Overall, the in silico analysis suggests that tocopherols could be among the contributors to the multi-target profile of Argania spinosa oil, while fatty acids may provide complementary effects related to glycemic regulation. Full article

Prinsepia utilis Royle seeds are traditionally used in Northwestern Yunnan to relieve skin inflammation and irritation. However, its active constituents and potential molecular mechanisms remain unclear. To investigate the bioactive constituents and anti-inflammatory and skin-soothing effects of P. utilis seed-derived extracts, we characterized their chemical profiles and investigated the potential molecular mechanisms through phytochemical, computational, and complementary biological approaches, as well as in vitro and in vivo tests in this study. The results of this study show that the 75% ethanol eluate (QC04) of P. utilis seeds exhibited the strongest inhibitory effect on lipopolysaccharide-induced nitric oxide production in RAW 264.7 macrophages, with an IC₅₀ value of 239.21 ± 6.70 μg/mL. Subsequently, untargeted metabolomics identified 1039 metabolites, and 20 representative compounds were selected for downstream analysis. Furthermore, network pharmacology analysis identified AKT1, MAPK1, MAPK8, and MAPK14 as core targets, which are mainly involved in the TNF and MAPK signaling pathways. Molecular docking confirmed favorable binding interactions between representative metabolites and these core proteins; meanwhile, a 100 ns molecular dynamics simulation verified the conformational stability of the euscaphic acid–AKT1 complex. Moreover, in the UVB-induced 3D epidermal model (EpiKutis^®), QC04 treatment reduced IL-6 and PGE₂ secretion and downregulated TNF-α and NF-κB p65 expression. In vivo zebrafish assays further demonstrated that QC04 inhibited copper sulfate-induced neutrophil recruitment and histamine-induced vasodilation. Overall, these findings link the metabolites identified in the activity-enriched QC04 fraction with predicted molecular targets and anti-inflammatory and skin-soothing effects, providing experimental evidence for the biological potential of P. utilis seed-derived preparations and supporting further investigation of QC04 as a potential skin-soothing active fraction. Full article

Occupant-centric building operation requires timely information on occupant states and local indoor conditions, but fixed sensors provide limited spatial coverage, and wearables depend on user participation. This study develops a Robot Operating System 2 (ROS 2)-based wheeled mobile sensing platform for buildings. The main contribution is the integration of autonomous mapping and navigation, target approach, multisensor occupant-data acquisition, lightweight edge-based human detection, and return-to-dock operation on a Raspberry Pi 5. During operation, the robot patrols indoor locations, detects and approaches occupants, collects human and environmental data, uploads the data to a server, and returns to the charging dock. To support concurrent perception and navigation, YOLOv5n was compressed using structured channel pruning and multi-scale feature distillation. The compressed model reduced parameters and computation by approximately 53% and 61%, increased inference throughput from 7.5 to 16.5 frames per second, and enabled the robot to complete all 60 controlled trials across five locations and three postures. This study does not quantify HVAC energy savings or carbon-emission reductions. Instead, it validates a mobile sensing and edge-perception layer for future server-side thermal comfort inference, demand-responsive HVAC control, and evaluation of building energy and carbon performance. Full article