Search Results (4,779)

Background: Due to chronic venous insufficiency, venous leg ulcers (VLUs) develop as chronic wounds characterized by impaired healing, persistent inflammation, and endothelial dysfunction. Nitrosative stress, mitochondrial damage, and tissue apoptosis caused by excess nitric oxide (NO) produced by iNOS in macrophages and fibroblasts are contributing factors in the chronic wound environment; therefore, pharmacological modulation of iNOS presents an attractive mechanistic target in chronic wound pathophysiology. Methods: Herein, we present the use of a structure-based computational strategy to assess the inhibition of tavaborole, a boron-based antifungal agent, against iNOS using human iNOS crystal structure (PDB ID: iNOS) by molecular docking using AutoDock 4.2, 500 ns simulation of molecular dynamics (MD), with equilibration within ~50 ns and analyses over full trajectory and binding free energy calculations through the MM-PBSA approach. Results: Docking studies showed favorable binding of tavaborole (–6.1 kcal/mol) in the catalytic domain, which stabilizes contacts with several key residues (CYS200, PRO350, PHE369, GLY371, TRP372, TYR373, and GLU377). MD trajectories for 1 ns showed stable structural configurations with negligible deviations (RMSD ≈ 0.44 ± 0.10 nm) and hydrogen bonding, and MM-PBSA analysis confirmed energetically favorable complex formation (ΔG_binding ≈ 18.38 ± 63.24 kJ/mol) similar to the control systems (L-arginine and 1400W). Conclusions: Taken together, these computational findings indicate that tavaborole can stably occupy the iNOS active site and interact with key catalytic residues, providing a mechanistic basis for further in vitro and ex vivo validation of its potential as an iNOS inhibitor to reduce nitrosative stress and restore endothelial homeostasis in venous leg ulcers, rather than direct therapeutic proof. Full article

Electrochemical CO₂ reduction (CO₂RR) is a promising route to transform a major greenhouse gas into value-added fuels and chemicals. However, its deployment is still hindered by the sluggish activation of CO₂, poor selectivity toward multielectron products, and competition with the hydrogen evolution reaction (HER). Single-atom catalysts (SACs) have emerged as powerful materials to address these challenges because they combine maximal metal utilization with well-defined coordination environments whose electronic structure can be precisely tuned through metal–support interactions. This minireview summarizes current understanding of how structural, electronic, and chemical features of SAC supports (e.g., porosity, heteroatom doping, vacancies, and surface functionalization) govern the adsorption and conversion of key CO₂RR intermediates and thus control product distributions from CO to CH₄, CH₃OH and C₂⁺ species. Particular emphasis is placed on selectivity descriptors (e.g., coordination number, d-band position, binding energies of *COOH and *OCHO) and on rational design strategies that exploit curvature, microenvironment engineering, and electronic metal–support interactions to direct the reaction along desired pathways. Representative SAC systems based primarily on N-doped carbons, complemented by selected examples on oxides and MXenes are discussed in terms of Faradaic efficiency (FE), current density and operational stability under practically relevant conditions. Finally, the review highlights remaining bottlenecks and outlines future directions, including operando spectroscopy and data-driven analysis of dynamic single-site ensembles, machine-learning-assisted DFT screening, scalable mechanochemical synthesis, and integration of SACs into industrially viable electrolyzers for carbon-neutral chemical production. Full article

Human carboxylesterases (CES) are enzymes that play a central role in the metabolism and biotransformation of diverse endogenous substances and xenobiotics. The two most relevant isoforms, CES1 and CES2, are crucial in clinical pharmacotherapy as they catalyze the hydrolysis of numerous approved drugs and prodrugs. Elucidating the structural basis of CES isoform substrate specificity is essential not only for understanding and anticipating the biological fate of administered drugs, but also for designing prodrugs with optimized site-specific bioactivation. Additionally, this knowledge is also important for the design of biomedically useful molecules such as subtype-targeted CES inhibitors and fluorescent probes. In this context, both experimental and computational methodologies have been used to explore the mechanistic and thermodynamic properties of CES-mediated catalysis. Experimental designs commonly employ recombinant CES or human tissue microsomes as enzyme sources, utilizing quantification methods such as spectrophotometry (UV and fluorescence) and mass spectrometry. Computational approaches fall into two categories: (1) modeling substrate: CES recognition and affinity (molecular docking, molecular dynamics simulation, and free-energy binding calculations), and (2) modeling substrate: CES reaction coordinates (hybrid QM/MM simulations). While experimental and theoretical approaches are highly synergistic in studying the catalytic properties of CES subtypes, they represent distinct technical and scientific fields. This review aims to provide an integrated discussion of the key concepts and the interplay between the most commonly used wet-lab and dry-lab strategies for investigating CES catalytic activity. We hope this report will serve as a concise resource for researchers exploring CES isoform specificity, enabling them to effectively utilize both experimental and computational methods. Full article

Chemokines play a central role in orchestrating neutrophil recruitment from the bloodstream and determining their effector functions at sites of infection. Chemokine activity is determined by three key properties: reversible monomer–dimer equilibrium, binding to glycosaminoglycans (GAGs), and signaling through the GPCR class of receptors CXCR1 and CXCR2. In this study, we investigated the structural basis of CXCL8 monomer and dimer binding to GAG chondroitin sulfate (CS) using nuclear magnetic resonance (NMR) spectroscopy, docking, and molecular dynamics (MD) measurements. Our studies reveal that both the monomer and dimer use essentially the same set of basic residues for binding, that the interface is extensive, that the dimer is the high-affinity CS ligand, and that the CS-binding residues form a contiguous surface within a monomer. Several of these residues also participate in receptor interactions, suggesting that CS-bound CXCL8 is likely impaired in its ability to bind receptors. Notably, we observe that the same basic residues are involved in binding CS and heparin/heparan sulfate, even though these GAGs differ in backbone structures and sulfation patterns. We conclude that the strategic distribution and topology of basic residues on the CXCL8 scaffold enable engagement with diverse GAG structures, which likely allows fine-tuning receptor signaling to regulate neutrophil trafficking and effector functions. Full article

This manuscript reports the preparation, surface characterization, and modeling of chars and activated carbons obtained from avocado biomass for hydrogen storage. Activated carbons were prepared from avocado biomass via the following stages: (a) pyrolysis of avocado biomass, (b) impregnation of the avocado-based char using an aqueous lithium solution, and (c) thermal activation of lithium-loaded avocado char. The synthesis conditions of char and activated carbon samples were tailored to maximize their hydrogen adsorption properties at 77 K, where the impact of both pyrolysis and activation conditions was assessed. The hydrogen storage mechanism was discussed based on computational chemistry calculations and multilayer adsorption simulation. The modelling focuses on the analysis of the saturation of activated carbon active sites via the adsorption of multiple hydrogen molecules. The results showed that the activated carbon samples displayed adsorption capacities higher than their char counterparts by 71–91% because of the proposed activation protocol. The best activated carbon obtained from avocado residues showed a maximum hydrogen adsorption capacity of 142 cm³/g, and its storage performance can compete with other carbonaceous adsorbents reported in the literature. The hydrogen adsorption mechanism implied the formation of 2–4 layers on activated carbon surface, where physical interactions via oxygenated functionalities played a relevant role in the binding of hydrogen dimers and trimers. The results of this study contribute to the application of low-cost activated carbons from residual biomass as a storage medium in the green hydrogen supply chain. Full article

Per- and polyfluoroalkyl substances (PFASs), as a class of “permanent chemicals” with high environmental persistence and bioaccumulation, have attracted much attention. In this study, we focused on the molecular mechanism of the interaction between perfluoroalkyl acids (PFAAs) and peroxisome proliferator-activated receptor δ (PPARδ). Using molecular docking, binding free energy calculation, and structural analysis, we systematically investigated the binding modes, key amino acid residues, and binding energies of 20 structurally diverse PFAAs with PPARδ. The results showed that the binding energies of PFAAs with PPARδ were significantly affected by the molecular weight, the number of hydrogen bond donors, and the melting point of PFAAs. PFAAs with smaller molecular weights and fewer hydrogen bond donors showed stronger binding affinity. The binding sites were concentrated in high-frequency amino acid residues such as TRP-256, ASN-269, and GLY-270, and the interaction forces were dominated by hydrogen and halogen bonds. PFAAs with branched structure of larger molecular weight (e.g., 3m-PFOA, binding energy of −2.92 kcal·mol⁻¹; 3,3m₂-PFOA, binding energy of −2.45 kcal·mol⁻¹) had weaker binding energies than their straight-chain counterparts due to spatial site-blocking effect. In addition, validation group experiments further confirmed the regulation law of binding strength by physicochemical properties. In order to verify the binding stability of the key complexes predicted by molecular docking, and to investigate the dynamic behavior under the conditions of solvation and protein flexibility, molecular dynamics simulations were conducted on PFBA, PFOA, 3,3m₂-PFOA, and PFHxA. The results confirmed the dynamic stability of the binding of the high-affinity ligands selected through docking to PPARδ. Moreover, the influence of molecular weight and branched structure on the binding strength was quantitatively verified from the perspectives of energy and RMSD trajectories. The present study revealed the molecular mechanism of PFAAs interfering with metabolic homeostasis through the PPARδ pathway, providing a theoretical basis for assessing its ecological and health risks. Full article

Schiff bases are bioactive compounds that have been synthesized by many researchers in recent years. They may also exhibit strong antimicrobial activities against various pathogenic microorganisms in both medicine and veterinary applications. The synthesis of new Schiff base-derived compounds remains of interest due to the increasing problem of antibiotic-resistance in clinical practice. Seven new Schiff base derivatives were synthesized, and their chemical structures were characterized using FT-IR, ¹H/¹³C NMR, and LCMS-MS analyses. The antimicrobial activities of thesyntesized compounds against various pathogenic bacteria, yeasts, and fungi were evaluated using the disk-diffusion method, and their MIC values were also determined. In addition, one representative microorganisms from each class were selected for molecular docking studies. IFD analyses were performed for the 4f and 4g ligands using the dihydrofolate reductase enzyme. Spectroscopic analyses confirmed the structures of the synthesized compounds, revealing the presence of characteristic imine functionalities and validating the integrity of the molecular frameworks. Antimicrobial assays demonstrated that several derivatives exhibited measurable activity, with compounds 4f and 4g showing the most potent effects, displaying MIC values of 32 µg/mL against B. cereus and E. faecalis, respectively. Molecular docking studies further indicated that both 4f and 4g bind efficiently to the DHFR active site. These findings indicate that among the synthesized Schiff base derivatives, compounds 4f and 4g exhibit particularly promising antimicrobial activity, warranting further pharmacological evaluation and medicinal chemistry optimization. Full article

Flexible biosensors offer rapid and low-cost diagnostics but are often limited by the mechanical and electrochemical instability of polymer-based designs in biological media. Here, we introduce a metallic flexible microcrack transducer that exploits the intrinsic deformability of superelastic nickel–titanium (NiTi) for label-free impedimetric detection. Mechanical bending of NiTi wires spontaneously generates martensitic-phase microcracks whose metal–gap–metal geometry forms the active transduction sites, where functional interfacial layers and captured analytes modulate the local dielectric environment and govern the impedance response. Our approach imparts a novel dielectric character to the alloy, enabling its unexplored application in the megahertz (MHz) frequency domain (0.01–10 MHz) where native NiTi is merely conductive. Functionalization with Escherichia coli (E. coli)-specific antibodies renders these microdomains biologically active. This effectively transforms the mechanically induced microcracks into tunable impedance elements driven by analyte binding. The γ-bent NiTi sensors achieved stable and quantitative detection of E. coli ATCC 25922 in sterile human urine, with a detection limit of 64 colony forming units (CFU) mL⁻¹ within 45 min, without redox mediators, external labels, or amplification steps. This work pioneers the use of martensitic microcrack networks, mimicking self-healing behavior in a superelastic alloy as functional transduction elements, defining a new class of metallic flexible biosensors that integrate mechanical robustness, analytical reliability, and scalability for point-of-care biosensing. Full article

Slugs are significant agricultural pests and act as vectors for zoonotic parasites. However, current molluscicide options are limited and associated with substantial environmental risks. This study investigates the role of aldehyde dehydrogenase (ALDH) in the biosynthesis of farnesoic acid (FA), a key intermediate in the sesquiterpenoid hormone pathway, in two slug species: Philomycus bilineatus and Laevicaulis alte. Transcriptomic analysis revealed that both species possess conserved sesquiterpenoid biosynthetic pathways, yet they exhibit distinct levels of ALDH gene expression and differences in FA content. RNA interference (RNAi)-mediated gene silencing was employed to validate the potential of these candidate genes as targets for molluscicide development. Structural modeling of ALDH proteins using AlphaFold2 demonstrated notable divergence in the architecture of their active sites, suggesting species-specific enzymatic properties. Citral, a known inhibitor of ALDH, significantly reduced FA production in vivo and exhibited contact toxicity against both slug species. The lethal concentration 50 (LC₅₀) values were determined to be 378.2 g/L for P. bilineatus and 85.2 g/L for L. alte, respectively. Molecular docking analyses indicated that citral binds within the conserved substrate-binding tunnel of ALDH, potentially inhibiting the oxidation of farnesal. These findings establish ALDH as a critical enzymatic target for disrupting endogenous hormone biosynthesis in slugs and support the development of novel, eco-friendly molluscicides targeting the sesquiterpenoid pathway. Full article

Background/Objectives: Caffeic acid is a hydroxycinnamic acid that has a wide range of applications in the medical field. The synthesis of caffeic acid using microbial fermentation technology is an environmentally friendly method. Methods: By engaging various enzymes, specifically 4-hydroxyphenylacetate 3-monooxygenase (HpaB), sourced from diverse bacterial strains, we successfully engineered a functional version of this enzyme within Escherichia coli, enabling the production of caffeic acid. In addition to the two common tyrosine ammonia lyases (TAL) and HpaC, different combinations of HpaB demonstrated varying abilities in converting the substrate L-tyrosine into the desired product, caffeic acid. Results: Under shake-flask culture conditions, the highest yield of caffeic acid was achieved with an enzyme mixture containing HpaB from Escherichia coli, reaching 75.88 mg/L. Enhancing the activity of the rate-limiting enzyme through engineering could potentially increase caffeic acid titer. This study aims to conduct a semi-rational design of HpaB through structure-based approaches to screen for mutants that can enhance the production of caffeic acid. Initially, the predicted three-dimensional structure of HpaB was generated using AlphaFold2, and subsequent analysis was conducted to pinpoint the critical mutation sites within the substrate-binding pocket. Five key amino acid residues (R113, Y117, H155, S210 and Y461) located in the vicinity of the flavin adenine dinucleotide binding domain in HpaB from Escherichia coli could be instrumental in modulating enzyme activity. Subsequently, the mutant S210G/Y117A was obtained by iterative saturation mutagenesis, which increased the titer of caffeic acid by 1.68-fold. The caffeic acid titer was further improved to 2335.48 mg/L in a 5 L fermenter. The findings show that the yield of caffeic acid was significantly enhanced through the integration of semi-rational design and fermentation process optimization. Full article

Hydrogen is frequently incorporated in alkaline-earth oxides during crystal growth or post-deposition annealing. For MgO, several studies in the past showed that interstitial monatomic hydrogen can also favourably bind with oxygen vacancies to form stable substitutional defect complexes (substitutional hydrogen or U-defect centers). The present study reports first-principles density-functional calculations of the formation energies of both interstitial and substitutional forms of the hydrogen impurity in MgO. Determination of the site-resolved densities of electronic states allowed for a detailed identification of the nature of the impurity-induced levels, both in the valence-energy region and inside the band gap of the host. The stability and diffusion mechanisms of both hydrogen defects was also studied with the aid of nudged elastic-band (NEB) calculations. Interstitial hydrogen was found to be an amphoteric defect with the lower formation energy for any realistic environment conditions (temperature and oxygen partial pressure). The NEB calculations showed that it is a fast-diffusing species when it is thermodynamically stable as a positively-charged state (bare proton). In contrast, the hydrogen-vacancy complex is a shallow donor, extremely stable against dissociation and virtually immobile as an isolated defect. Its formation is found to be favoured for a range of mid-gap Fermi-level positions where positively-charged interstitial hydrogen and neutral oxygen vacancies (F centers) are both thermodynamically stable low-energy defects. The present findings are consistent with the established consensus on the electrical activity of hydrogen in MgO as well as with experimental observations reporting the remarkable thermal stability of substitutional hydrogen defects and their ability to act as electron traps. Full article

S. suis is a prominent zoonotic pathogen responsible for diseases such as arthritis in piglets, swine septicemia, and meningitis. The emergence of multi-drug resistance (MDR) underscores the urgent need for the development of novel antibacterial strategies. In this context, a systematic evaluation of the antibacterial potential of the bacteriophage lytic enzyme Ply900 was conducted in this study, along with an analysis of its domain functions and an in vivo study of its therapeutic dynamics. Ply900 exhibits potent in vitro lytic activity against multiple bacteria, including Streptococcus suis, Streptococcus agalactiae, and Staphylococcus aureus. Notably, it possesses broad biochemical stability, with tolerance to diverse environmental conditions. In a mouse model of S. suis serotype 2 SC19 infection, both the direct Ply900 treatment group and the triple therapy group achieved effective eradication of S. suis, with markedly improved survival rates. The remaining bacteria remained susceptible to Ply900, with no evidence of induced resistance development. Mechanistic analysis revealed that the SH3B domain of Ply900 enhances targeted cleavage efficiency by binding synergistically to peptidoglycan with the CHAP domain, with CYS-34, HIS-59, and ASP-28 serving as key amino acid sites for Ply900’s cleavage activity. Collectively, these findings lay the foundation for the potential dual applications of the lysin Ply900, both in the clinical treatment of S. suis infections and in the prevention and control of these pathogenic bacteria in livestock farming. Full article

The interplay between chromatin structure and phase-separating proteins is an emerging topic in cell biology with implications for understanding disease states. Here, we investigate the functional relationship between bromodomain protein 4 (BRD4) and chromatin architecture. By combining molecular dynamics simulations with live-cell imaging, we demonstrate that BRD4, when mutated at specific N-terminus sites, significantly impacts the organization and dynamics of chromatin nanodomains, known as nucleosome clutches. Our findings reveal that a constitutively phosphorylated mutant of BRD4 condenses nucleosome clutches, while treatment with (+)-JQ1 increases the diffusion dynamics of single nucleosomes and decondenses nucleosome clutches. Simultaneously, we demonstrate that BRD4 mutations can alter localization of BRD4 to chromatin as well as modify single nucleosome dynamics. These results suggest that both chromatin binding and phase separation of BRD4 could co-regulate the nanoscale chromatin architecture and the chromatin microenvironment. Our observations shed light on the nuanced regulation of chromatin structure by BRD4, offering insights into its role in maintaining the nuclear architecture and transcriptional activity. Full article

A promising direction for the creation of new biologically active derivatives of the alkaloid lupinine is the synthesis of “hybrid molecules” that combine a fragment of the alkaloid and the pharmacophore of 1,2,3-triazole in their structure. From a biological perspective, this work presents the first X-ray diffraction study of a single crystal of (1S,9aR)-1-({4-[4-(Benzyloxy)-3-methoxyphenyl]-1H-1,2,3-triazol-1-yl}methyl)octahydro-2H-quinolizine, a new, recently synthesized 1,2,3-triazole derivative of lupinine. A comparison of theoretically predicted and experimentally observed structural parameters was carried out. The FTIR spectroscopy study and vibrational properties calculations allowed us to interpret the FTIR absorption spectrum and localize specific vibrational modes in quinolizidine, 1,2,3-triazole, and benzene rings. Such information can be fruitful for further characterization of the synthesis process and products. The molecular docking of the compound was performed. It was shown that the studied molecules are capable of interacting with the Mpro binding site via non-covalent and hydrophobic interactions with subsites S3 (Met165, Glu166, Leu167, Pro168) and S5 (Gln189, Thr190, Gln192), which ensure the stabilization of the Mpro substrate. Blocking of the active site of the enzyme in the region of the oxyanion hole does not occur, but stable stacking interactions with the π-system of one of the catalytic amino acids, His41, are observed. Full article

Background: Aggregatibacter actinomycetemcomitans is a Gram-negative, facultative anaerobic, immobile oral bacterium responsible for the secretion of virulence factors, namely leukotoxin (LtxA), a large exotoxin of the RTX family that enables the bacterium to evade the immune system by destroying leukocytes, resulting in aggressive periodontitis (AP) leading to tooth loss. Methods: This study aimed to screen 106 molecules derived from Moroccan propolis in order to identify potential inhibitors of the active sites of LtxA based on molecular docking, ADMET property evaluation, and molecular dynamics (MD) simulation. Results: Epigallocatechin gallate (EGCg), used as a reference compound, showed binding energies of −6.9 kcal/mol, −6.1 kcal/mol, −6.5 kcal/mol, and −5.9 kcal/mol with the four active sites P1, P2, P3, and P4, respectively. By establishing conventional hydrogen bonds, pi-alkyl bonds, and non-covalent pi–pi bonds. Chrysin and luteolin showed favorable binding affinities with the four active sites, named as follows: P1–P4 (P1–chrysin = −7.5 kcal/mol; P2–chrysin = −7.9 kcal/mol; P3–chrysin = −8.1 kcal/mol; P4–chrysin = −6.9 kcal/mol; P1–luteolin = −7.3 kcal/mol; P2–luteolin = −7.6 kcal/mol; P3–luteolin = −8.1 kcal/mol; P4–luteolin = −7.3 kcal/mol). The binding affinity of these two propolis derivatives was stabilized by pi−sigma bonds, pi−alkyl bonds, conventional hydrogen bonds, pi-cation interactions, non-covalent pi–pi bonds, and carbon–hydrogen bonds. According to free energy calculations performed with Prime MM-GBSA, the complexes formed by chrysin demonstrated the most stable interactions due to Van der Waals and lipophilic forces. Luteolin formed significant interactions, but slightly weaker than those of chrysin. These results reveal the inhibitory potential of chrysin and luteolin with protein active sites. MD simulations corroborated the excellent stability of complexes formed by chrysin, as indicated by low RMSD values, suggesting favorable dynamic behavior. Conclusions: These results highlight the potential of chrysin as a versatile inhibitor capable of interacting with the four active sites. These findings are a strong foundation for further experimental confirmations. Full article