Search Results (8,404)

In this work, molecular dynamics (MD) simulations are applied to investigate the dependence of the Wenzel–Cassie transition on water droplet size. During the Wenzel–Cassie transition, the critical water droplet and corresponding critical roughness may be expected, which are respectively described as the critical radius (R_Droplet,c) and wetting parameter (W_Roughness,c). From the work, R_Droplet,c may be termed as the smallest droplet size at which the Cassie state is expected for the corresponding W_Roughness,c. In combination with the structural study of water, it is due to the structural competition between interfacial and bulk water. Additionally, R_Droplet,c may be dependent on the W_Roughness,c. It is found that the R_Droplet,c is influenced by the distribution and geometric characteristics of surface roughness. A denser distribution of roughness is expected to result in a lower R_Droplet,c. Consequently, superhydrophobicity may be influenced by the characteristics of surface roughness and the size of the water droplet. The Cassie state is achieved when the wetting parameter of roughness is less than the W_Roughness,c and the water droplet is larger than the R_Droplet,c. Full article

Lupus nephritis (LN) is a severe complication of systemic lupus erythematosus (SLE), characterized by immune system disorders and multiple organ damage. Current clinical treatment of LN requires a complex multi-drug combination, which is often associated with severe side effects and low patient compliance. The aim of this study was to design a self-nanoemulsifying drug delivery system (SNEDDS) co-loading total glucosides of Paeonia (TGP) and dihydroartemisinin (DHA) to increase the solubility of the drug as well as achieve synergistic anti-inflammatory and immunomodulatory effects for LN therapy. Network pharmacology, molecular docking and molecular dynamics simulations were employed to predict the core therapeutic targets and related signaling pathways. The SNEDDS co-loaded with TGP and DHA was optimized via central composite design response surface methodology (CCD-RSM). Its physicochemical properties, particle size and the polydispersity index (PDI) of the optimized formulation were characterized. In vivo therapeutic efficacy was evaluated in MRL/lpr mice by measuring disease-related indicators (urinary protein, serum ANA, and anti-ds-DNA) and inflammatory cytokines (TNF-α, IL-6, and IL-1β). Renal tissue pathology was also examined. All data were analyzed by one-way analysis of variance (ANOVA) with p < 0.05 considered statistically significant. The core therapeutic targets predicted with high relevance were AKT1, MAPK1, MAPK3, and RELA. The optimized SNEDDS achieved a high loading capacity of 16.11 ± 0.43 mg/g for TGP and 12.79 ± 1.33 mg/g for DHA, with a particle size of (25.84 ± 0.30) nm and PDI of (0.07 ± 0.02). In MRL/lpr mice, SNEDDS treatment significantly reduced urinary protein levels (p < 0.01), serum ANA (p < 0.01) and anti-ds-DNA titers (p < 0.01) compared with the model group. Additionally, the levels of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β) were markedly decreased (p < 0.05), and renal tissue damage was alleviated. Conclusions: The SNEDDS co-loaded TGP and DHA is a promising oral nanotherapeutic strategy for LN, offering synergistic anti-inflammatory and immunomodulatory effects. Full article

Medicarpin, a natural pterocarpan phytoalexin, contributes to tree defense against microbial decay, particularly from the aggressive white-rot fungus Trametes versicolor, an ASTM standard for wood durability testing. To improve upon the inhibitory effect of medicarpin against this fungus (150 mg/L), eleven derivatives were synthesized and evaluated. The acetylated analog demonstrated superior activity, achieving complete growth inhibition at 100 mg/L. To establish a structure–activity relationship, molecular docking was performed on the copper cluster on fungal laccase, the primary oxidative enzyme of T. versicolor. The acetylated derivative bound the T1 copper site with a more favorable free energy (−8.5 kcal/mol) than the parent compound, exhibiting enhanced stabilizing interactions and a binding pose anchored closer to the trinuclear copper cluster (TNC). These results were corroborated by 80 ns molecular dynamics simulations, confirming complex stability and the persistence of key interactions. This study demonstrates that targeted chemical modification of natural phytoalexins can significantly improve their antifungal potency. The superior performance of the acetylated medicarpin derivative, linked to optimized binding at the laccase active site, establishes a clear structure–activity relationship and highlights the potential of such engineered compounds as leads for next-generation, bio-inspired wood preservatives. Full article

Cytokine storm is a central pathogenic mechanism underlying sepsis-induced acute lung injury (SALI) and severe coronavirus disease 2019 (COVID-19), yet effective therapeutic strategies remain limited. Eupatorium lindleyanum DC. (EL), a traditional Chinese medicinal herb, has been reported to possess anti-inflammatory, antioxidant, and antiviral-related activities; however, its protective mechanisms in SALI and virus-associated inflammatory lung injury remain incompletely understood. In this study, an integrated strategy combining computational prediction and experimental validation was employed to investigate the therapeutic potential and underlying mechanisms of EL. The chemical constituents of EL were characterized by UPLC–Q–TOF/MS, followed by network pharmacology, molecular docking, and molecular dynamics analyses to predict key targets and signaling pathways. A cecal ligation and puncture (CLP)-induced SALI rat model was used to evaluate lung histopathology, pulmonary edema, cytokine production, and inflammatory signaling activation. In parallel, LPS-stimulated RAW264.7 macrophages were used to assess cytokine secretion and pathway regulation in vitro. In addition, a SARS-CoV-2 pseudovirus-induced mouse model was employed to further evaluate the in vivo relevance of the representative bioactive compound hyperoside in pseudovirus-associated lung injury. A total of 32 active compounds and 697 putative targets were identified, among which 116 were associated with sepsis and COVID-19. In vivo, EL markedly alleviated lung injury, reduced the lung coefficient and wet/dry ratio, and suppressed excessive production of proinflammatory cytokines and activation of key signaling proteins. In vitro, EL dose-dependently inhibited TNF-α and IL-6 secretion and regulated the PI3K–Akt and NF-κB signaling pathways. Notably, hyperoside showed favorable predicted interactions with PI3K–Akt pathway-related targets (EGFR, PI3K, and Akt), while molecular dynamics simulations supported stable interactions with several COVID-19-related targets, including ACE2, Mpro, and RdRp. Furthermore, hyperoside significantly alleviated SARS-CoV-2 pseudovirus-associated lung injury, reduced ACE2 protein expression, and downregulated EGFR, PI3K, and Akt mRNA levels in vivo. Collectively, these findings indicate that EL exerts protective effects through multi-component, multi-target, and multi-pathway mechanisms, and support its potential value for further investigation in SALI and virus-associated inflammatory lung injury. Full article

Eringen’s integral constitutive relation is more general than its differential counterpart for modeling small-scale effects in micro- and nanostructures; however, it leads to integro-differential governing equations that are difficult to solve, which has limited the practical use of integral formulations. To directly address this gap, this paper introduces a novel symplectic-based numerical method that efficiently and accurately analyzes the free vibration of small-scale Kirchhoff plates governed by Eringen’s integral nonlocal model. The method discretizes the nonlocal integral operator by introducing inter-belt elements for long-range interactions and adopting a truncated influence domain, while balancing computational efficiency and accuracy. The effects of the nonlocal parameter, two-phase mixture parameter, mode numbers, kernel types, and geometric parameters on the natural frequencies are systematically investigated. The results indicate stiffness softening. For a simply supported square nanoplate with side length a = 10 nm, the first-order frequency parameter decreases by approximately 25% as the nonlocal parameter increases from 0 to 4 nm, and higher-order modes exhibit substantially greater sensitivity to nonlocal effects. Convergence and accuracy are validated against published continuum-level solutions and molecular dynamics simulations; relative deviations are below 2% in most cases, and the local limit (l_a = 0) yields errors on the order of 10⁻³. Full article

Dihydroquercetin (DHQ) is a promising object for the development of a treatment for patients with obesity and prediabetes requiring a moderate therapeutic effect. This paper reports a clinical case of DHQ application in a 30-year-old Caucasian male and proposes a molecular mechanism of its anti-obesity effect. DHQ was administrated as a dietary supplement at a dose of 100–200 mg/day during 3 months with treatment interruption for 1 month. The data collected one month before the treatment were used as a control. The molecular aspects were studied via molecular docking with β₃-adrenoceptor (ADRB3, PDB ID: 9IJE) and peroxisome proliferator-activated receptor γ (PPARG, PDB ID: 2ZNO) and molecular dynamic simulation under conditions mimicking a human cellular environment. A pronounced weight decrease up to 0.73 kg/week was observed during DHQ administration. The highest affinity to ADRB3 was observed for the non-ionized H2aH3e-conformation of 2S,3R-DHQ (–8.846 kcal/mol). Molecules with 2S-configuration demonstrate 0.332 kcal/mol higher affinity to PPARG compared to 2R-stereoisomers. The intermolecular complex with cis-DHQ demonstrated higher stability in molecular dynamics simulation. The insights gained from this study may contribute to our understanding of flavonoids not merely as antioxidants but also as active ingredients that selectively interact with receptors. If future investigations confirm these results, they may serve as a foundation for developing a new class of anti-obesity remedies that act via ADRB3. Full article

The enzymatic production of low-molecular-weight chitosan and chitooligosaccharides (COS), with broad application potential in agriculture, food, medicine, and cosmetics, has emerged as an attractive alternative to chemical chitosan depolymerization owing to its substrate specificity and environmentally benign catalytic action. However, the functional properties of available chitosanases need to be enhanced to meet the demands of industrial COS manufacturing under high temperature and substrate concentrations. In this work, we performed directed evolution on a recombinant Bacillus subtilis chitosanase to increase chitosan hydrolysis performance and thermal resistance. Three rounds of directed evolution screening (~9000 clones) yielded variants MT1, MT2, and MT3 with higher specific activity, achieved through Vmax improvement and increased T_1/2 at 60 °C. HPLC, DLS, and MALDI-TOF results indicate differences in the hydrolysis kinetics and size distribution of COS products over reaction time, suggesting a narrower distribution and a lower average molecular weight. Molecular dynamics simulations and docking studies revealed potential modulation of chitosanase activity via changes in the opening and closing dynamics of the active-site cleft. These results suggest that future efforts targeting the cleft interface could significantly advance both the catalytic performance and the mechanistic understanding of GH46 family chitosanases. Full article

The rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need for antivirals that are resilient to resistance. Current Food and Drug Administration (FDA)-approved therapies primarily target single viral mechanisms, leaving gaps in efficacy. Here, we developed a Deep Learning-based Activity Screening Model (DLASM), which integrates graph convolutional network with machine learning to identify SARS-CoV-2 inhibitors, using experimental 3-chymotrypsin-like (3CL) main protease assay data. The optimized DLASMs virtually screened ~170,000 compounds from diverse in-house collections and yielded novel hits, several of which not only inhibited the 3CL protease but also blocked viral entry by interfering with heparan sulfate-mediated host interactions. These activities were validated through multiple assays, including 3CL enzymatic inhibition, SARS-CoV-2 pseudotyped particle entry, α-synuclein fibril uptake as a proxy for endocytosis, live virus cytopathic effect, heparan sulfate-dependent entry assay, and a 3D human lung mucociliary tissue model. Molecular docking studies elucidated binding modes at the 3CL protease active site, while molecular dynamics simulations provided insights into compound–heparan sulfate interactions. The identified compounds represent early-stage hits with moderate potency that demonstrate dual-mechanism antiviral activity. Together, these findings establish dual-target inhibition as a promising antiviral strategy, offering not only enhanced potency but also reduced risk of resistance. Moreover, our DLASM framework provides a generalizable pipeline for identifying chemically diverse scaffolds and for broader applications beyond SARS-CoV-2. Full article

Polyethylene terephthalate (PET) is a synthetic polymer that is widely used in the production of textiles, packaging materials, and beverage bottles. However, its high durability and resistance to abiotic degradation result in serious environmental and health problems. PETase is an enzyme that can depolymerize PET into value-added products, thereby providing an environmentally friendly strategy for PET recycling. PETaseSM14 from a marine sponge, Streptomyces sp. SM14, has a high salt tolerance and thermal stability, thus suggesting its potential for PET degradation applications. However, the substrate recognition mechanism of PETase remains unclear because the catalytic residue is buried within residues that form the substrate-binding cleft. To elucidate the molecular mechanism of PETaseSM14, all-atom molecular dynamics simulations were performed at 300, 320, and 340 K. The results revealed that the overall α/β fold remained stable at all temperatures, whereas temperature-dependent local fluctuations and conformational changes were observed in the substrate-binding cleft and N-terminal region. At 300 and 320 K, positional shifts and conformational changes in Tyr88 exposed the catalytic Ser156 to the solvent, thereby forming a potential substrate-binding cleft. In contrast, at 340 K, which is higher than the melting temperature of PETaseSM14, disruption of the charge-relay system of the catalytic triad occurs through conformational changes in His234. Substantial temperature-dependent conformational and positional changes in the N-terminal region of PETaseSM14 were observed at 320 and 340 K. These results provide mechanistic insight into the temperature-dependent active-site rearrangements and offer rational engineering strategies to enhance the efficiency of PETase for PET biodegradation. Full article

The progression of prostate cancer to castration-resistant disease (CRPC) remains a clinical challenge in which oxidative stress intersects with the PI3K/AKT–androgen receptor (AR) axis. Quercetin (QRC) is a redox-active dietary flavonol, yet its mechanistic impact on CRPC is incompletely defined. Here, we tested whether QRC suppresses AR output by directly modulating AKT. C4-2B and 22Rv1 CRPC cell lines were treated with increasing QRC concentrations, with or without enzalutamide (Enz). Proliferation and viability were monitored by IncuCyte imaging and SYTOX Green incorporation. AKT phosphorylation (S473), AR phosphorylation (S210/213), AR abundance and localization, and prostate-specific antigen (PSA) secretion were assessed by immunoblotting, immunofluorescence, and dot blot, respectively. Docking and molecular dynamic simulations were performed to identify and evaluate a putative QRC-binding site on AKT. QRC produced a dose-dependent cytostatic effect (IC₅₀ 24.37 μM in C4-2B; 21.54 μM in 22Rv1) without marked cell death, reduced pAKT(S473) by up to 80%, decreased pAR(S210/213), and diminished nuclear AR and PSA secretion. Simulations suggested a putative druggable allosteric pocket in the AKT1 N-lobe, with G159 emerging as a potential anchor residue. Enz cotreatment with QRC did not produce additive effects, consistent with a model in which QRC acts upstream of ligand-driven AR activation and thereby limits the incremental benefit of AR antagonism under these conditions. These data support QRC as an AKT–AR axis modulator in CRPC and provide a target engagement framework beyond simple ROS scavenging. Full article

Chlorogenic acid (CGA), which is ubiquitous in diverse botanical sources, demonstrates considerable anticancer potential through modulation of multiple targets or signaling pathways, thereby posing substantial challenges for mechanistic elucidation and target identification. Based on the proteolysis targeting chimera (PROTAC) technology’s ability to induce targeted protein degradation via ubiquitin-proteasome pathway recruitment, we synthesized a panel of CGA-PROTACs. These compounds incorporated the natural product CGA as the target-binding ligand, conjugated to pomalidomide (an E3 ligase-recruiting moiety) via various synthetic linkers. The findings indicated that compound A7, linked with an alkane linker, exhibited a notable anti-proliferative effect on 4T1 and A375 cells in vitro. The IC₅₀ value of A7 on A375 cells reached 69.70 μM, which is 2.2 times better than the effect of the precursor compound CGA (IC₅₀ = 148.80 μM). Mouse double minute 4 (MDM4) was confirmed as a potential target of compound A7 through a combination of proteomics, Western blot analysis and molecular dynamics simulation. CGA-PROTAC A7 treatment led to a dose-dependent reduction in MDM4 protein levels while significantly upregulating p53 and p21 protein expression, and thus inhibited proliferation, induced G2/M phase cell cycle arrest, and markedly enhanced apoptosis in melanoma A375 cells. This study successfully applied an effective strategy for target identification and medication discovery of natural compounds. In addition, CGA-PROTAC A7 was synthesized in one step with an overall yield of 45.96%, providing a feasible route for synthesis and establishing a basis for the combination of natural product polyphenols with PROTAC technology. Full article

In the pathological cascade of cerebral ischemia, the pyroptosis axis mediated by the NLRP3 inflammasome in activated microglia is a core link driving neuroinflammation and secondary brain injury. Quercetin has been proven to possess multi-target neuroprotective activity, and its anti-inflammatory effect has attracted particular attention. However, direct molecular evidence is lacking regarding how quercetin precisely regulates the NLRP3/Caspase-1/GSDMD core pyroptosis axis in microglia in cerebral ischemia models and whether it can directly target NLRP3 to inhibit this axis, thereby alleviating cerebral ischemic injury. This study aimed to investigate the molecular mechanism by which quercetin alleviates cerebral ischemic injury through inhibiting the pyroptosis axis, combining cellular and animal models with molecular docking and molecular dynamics simulations. The oxygen-glucose deprivation (OGD) model of BV2 microglia and the photothrombotic (PT) model of focal cortical ischemia in male C57BL/6 mice were used to detect the ameliorative effect of quercetin on cerebral ischemia-related injury through cellular and animal experiments. AutoDock Vina 1.5.7 and GROMACS 2025.3 software were employed for molecular docking and molecular dynamics simulations, respectively, to analyze the binding mode and complex stability between quercetin and the NLRP3 protein. The results showed that quercetin could significantly ameliorate OGD-induced injury in BV2 cells and downregulate the expression of pyroptosis and inflammation-related proteins and factors. Meanwhile, it relieved motor dysfunction in PT mice, attenuated cortical neuronal injury, and inhibited the activation of the cerebral pyroptosis axis. At the molecular level, molecular simulation predictions indicated that quercetin might specifically bind to the NACHT domain of the NLRP3 protein, forming a complex with a stable conformation, and van der Waals interactions served as the main driving force for binding. This study confirmed that quercetin can directly bind to the NLRP3 protein and alleviate cerebral ischemia-induced inflammatory injury by inhibiting the activation of the NLRP3/Caspase-1/GSDMD pyroptosis axis and the release of downstream inflammatory factors. Combined with the molecular simulation results, a predictive hypothesis is proposed: direct binding of quercetin to the NLRP3 protein is one of its core mechanisms of action. These findings provide direct experimental evidence for the development of NLRP3-based drugs against ischemic brain injury. Full article

Backgrounds: Premature ovarian insufficiency (POI) is a clinical syndrome characterized by premature ovarian dysfunction, amenorrhea, and infertility. Ferulic acid (FA) is a prominent bioactive phenolic compound derived from traditional Chinese herbs Angelica sinensis (Oliv.) Diels and Ligusticum chuanxiong Hort. These herbs are commonly used to treat gynecological disorders including menstrual irregularities and infertility, and are known to modulate endoplasmic reticulum (ER) stress. However, the therapeutic potential and molecular mechanisms of FA in the context of POI remain largely unexplored. This study aimed to investigate the protective effects of FA against POI and to elucidate the underlying pharmacological mechanisms. Methods: In vivo, a mouse model of POI was established via a single intraperitoneal injection of cyclophosphamide (CTX; 120 mg/kg), and using FA for 28 days of continuous gavage to observe its therapeutic effect. Ovarian function and pathological changes were assessed by hormone levels, follicle development and oxidative stress (OS) level. In vitro, the effects of FA were examined using 4-hydroperoxy cyclophosphamide (4-OHCP)-treated KGN granulosa cells. Transcriptome sequencing, molecular docking, and molecular dynamics simulations were employed to identify potential targets of FA. Results: Our findings demonstrated that FA administration helped preserve regular estrous cycles, promoted follicle development and hormone secretion, and attenuated OS in both ovarian tissue and granulosa cells (GCs). Transcriptomic profiling combined with molecular docking and molecular dynamics simulations suggested that FA potentially targets key ER stress proteins, specifically Grp78 and Perk. Further in vivo and in vitro experiments confirmed that FA alleviates ER stress by inhibiting the overactivation of the Perk/eIF2α/ATF4/CHOP signaling pathway. Notably, the protective effects of FA were comparable to those of the ER stress inhibitor 4-Phenylbutyric acid (4-PBA) and were reversed by the ER stress activator tunicamycin (TM). Additionally, FA downregulates ERO1α expression, further blocking secondary oxidative damage triggered by ER stress. In KGN cells, FA significantly inhibits 4-OHCP-induced apoptosis and upregulates the anti-apoptotic proteins BCL-2 and BCL-xL, exhibiting efficacy similar to 4-PBA. Conclusions: FA improves ovarian function in CTX-induced POI by coordinately regulating OS and ER stress, inhibiting the Perk/eIF2α/ATF4/CHOP pathway, and suppressing GC apoptosis. These findings provide experimental evidence supporting FA as a potential therapeutic candidate for POI. Full article

Marine mesozooplankton (0.2–20 mm), as a critical trophic link between primary producers and higher trophic levels, are pivotal drivers of trophic cascades regulating pelagic ecosystem structure and function. This review synthesizes recent advances in understanding mesozooplankton-mediated trophic cascades (MMTC), with a focus on selective feeding mechanisms, and presents an original, integrated quantitative framework that fills gaps in quantification and prediction of MMTC. This framework includes the following: a dual-pathway conceptual model distinguishing density-mediated and trait-mediated cascades; a three-level grazing rate correction model addressing long-standing underestimations of mesozooplankton direct grazing rate on phytoplankton; a comprehensive Cascade Strength Index for quantifying cascade intensity; an extended numerical model—NPMZ model (Nutrient–Phytoplankton–Microzooplankton–Mesozooplankton) for simulating MMTC dynamics and their biogeochemical impacts. The review further elucidates the spatiotemporal heterogeneity of MMTC and its implications for plankton community size structure and biological carbon pump efficiency. It also systematically assess the combined impacts of global change drivers (ocean warming, acidification, eutrophication) on MMTC and their ecological consequences. This review advances the theoretical framework of marine trophic cascade research by establishing a unified quantitative paradigm for MMTC and provides mechanistic insights and predictive tools for understanding how climate change modulates pelagic food web dynamics and marine ecosystem services. Moreover, the proposed integrated research paradigm combining molecular tools, multi-factor experiments, and high-resolution numerical modeling offers a critical roadmap for future MMTC research in the Anthropocene. This provides a scientific basis for the conservation and adaptive management of marine ecosystems under global change. Full article

Background/Objectives: Alzheimer’s disease (AD) involves amyloid and tau pathology with neuroimmune dysregulation, and Yixin Yangshen Granules (YXYS) shows neuroprotective promise, though mechanisms remain unclear. This study aimed to elucidate the multi-target mechanisms of YXYS in AD. Methods: The study began by analyzing a public human AD hippocampal snRNA-seq dataset to identify cell-type-specific pathological pathways and profiled YXYS constituents by UPLC-QTOF-MS. In vitro, YXYS cytoprotection against mitochondrial dysfunction and oxidative stress was tested in Aβ_25–35-challenged HT22 cells; in vivo efficacy was assessed in Aβ_1–42-induced mice via behavioral and histopathological analyses. Integrated transcriptomic and proteomic profiling of brain tissue, with ELISA, qRT-PCR, and Western blot validation, confirmed pathway targets. Using the intersection of transcriptomic and proteomic targets as biological input, the DTIAM deep learning framework was employed to prioritize active YXYS constituents. Finally, molecular docking and 100-ns dynamics simulations demonstrated direct binding of Ganosporelactone A to HIF−1α. Results: AD snRNA-seq analysis highlighted HIF−1 and AGE-RAGE signaling as prominent pathways in the AD hippocampus, particularly enriched in brain microvascular endothelial cells, implicating neurovascular hypoxic and inflammatory stress. In Aβ-induced mice, YXYS improved cognition, reduced Aβ pathology, suppressed neuroinflammation, and promoted neuronal survival, consistent with in vitro evidence of restored mitochondrial function. Multi-omics confirmed convergence on HIF−1 and AGE-RAGE pathways, with YXYS rebalancing the neuroimmune microenvironment by reducing pro-inflammatory M0 macrophages. Screening against these consensus signaling hubs, deep learning analysis prioritized Ganosporelactone A as the top-ranked modulator, and molecular further demonstrated the stable binding of Ganosporelactone A to HIF−1α, linking YXYS to mitigation of hypoxic stress. Conclusions: Guided by multi-omics and deep learning, our findings suggest that YXYS may alleviate AD-related phenotypes through multi-target modulation of the HIF−1 and AGE-RAGE pathways, with associated improvements in neuro-immune homeostasis and reductions in oxidative stress, neuroinflammation, and hypoxia. Full article