Search Results (236)

Per- and polyfluoroalkyl substances (PFASs) are persistent environmental contaminants whose mobility in soil and groundwater is strongly controlled by adsorption and desorption processes. In saturated clay-rich soils, these processes are complex because PFASs interact with hydrated mineral surfaces, organic matter, metal oxides, exchangeable cations, and pore-water constituents. This review synthesizes the current literature on PFAS adsorption and desorption in saturated soils, with an emphasis on clay mineralogy, mineral–water interfaces, pore-water chemistry, and electrochemical double layer (EDL) effects. PFAS retention is influenced by molecular properties such as chain length, functional head group, and charge state, as well as soil properties such as organic carbon content, clay mineral type, surface charge, cation exchange capacity, and Fe/Al oxide content. Longer-chain PFASs and sulfonate-based compounds generally show stronger retention, while shorter-chain PFASs tend to remain more mobile. This review focuses particularly on how an EDL affects PFAS behavior in saturated clay systems. Unlike dry clay surfaces, saturated clay surfaces are covered by structured water, exchangeable ions, and diffuse counterion layers. These hydrated interfacial conditions influence how closely anionic PFASs can approach negatively charged clay surfaces, how dissolved cations reduce electrostatic repulsion or promote cation-mediated binding, and how effectively short-range interactions such as hydrophobic association, van der Waals forces, hydrogen bonding, and surface association contribute to adsorption. Desorption is also emphasized because adsorption does not necessarily represent permanent immobilization. Changes in pH, ionic strength, cation composition, dissolved organic matter, or competing solutes can weaken retention and promote PFAS release. Overall, PFAS mobility in saturated clay-rich soils should be interpreted as a coupled interfacial process rather than simple partitioning to soil solids. Future work should better connect molecular-scale mechanisms, EDL behavior, adsorption–desorption experiments, and saturated transport studies to improve predictions of PFAS retention and long-term groundwater release. Full article

4-Methyl- (1) and 4-ethyl-8-hydroxyquinoline (2) crystallize from a mixture of diethyl ether and chloroform in the triclinic space group P$\overline{1}$. X-ray analysis reveals that both compounds form discrete molecular dimers stabilized by intermolecular O-H∙∙∙N and C-H∙∙∙O hydrogen bonds, resulting in $R_2^2\left(5\right)$ cyclic synthons. This pattern of hydrogen bonds is further stabilized by intramolecular O-H∙∙∙N bonds so that the quinoline nitrogen atom acts as a bifurcated binding site. The dimers exhibit a planar geometry and arrange into layer-like structures held together by π∙∙∙π stacking and van der Waals forces. While the fundamental bonding motifs are similar, the increased steric demand of the ethyl group in compound 2 induces a shift in the crystallographic orientation of the layers and alters the degree of π-overlap compared to the methyl-substituted analogue 1. Full article

Recognized for its dual nutritional and therapeutic value, the fungus Hericium erinaceus is increasingly acknowledged as a rich resource of naturally derived α-glucosidase inhibitors. In this study, eight compounds were isolated from H. erinaceus, including three novel compounds designated as erinacerins X−Z (1, 2, and 6). Their absolute configurations were definitively elucidated using a combination of NMR, HR-MS, and ECD calculations. Furthermore, an integrated screening strategy combining molecular docking, molecular dynamics (MD) simulations, and surface plasmon resonance (SPR) analysis identified two isoindolin-1-ones (2 and 3) as potent naturally derived α-glucosidase inhibitors. Notably, in vitro testing established compounds 2 and 3 as robust α-glucosidase inhibitors, affording IC₅₀ values of 17.80 ± 1.03 μM and 19.50 ± 1.33 μM, respectively. MD simulations revealed that electrostatic interactions and van der Waals forces are the primary drivers of this intermolecular association. These findings were further corroborated by SPR analysis, which quantified their high-affinity binding kinetics to the enzyme. Overall, this combined approach establishes a solid foundation for the discovery and development of natural α-glucosidase inhibitors from H. erinaceus. Full article

Alzheimer’s disease (AD) is a common neurodegenerative disorder linked to cholinergic dysfunction, with butyrylcholinesterase (BChE) being a key therapeutic target for moderate–severe AD. Cortex Mori Radicis, a traditional Chinese medicinal herb, is rich in Diels–Alder adducts with potential neuroprotective effects; here, eighteen Diels–Alder adducts (four new: morusalbanol B–E, 1–4) were isolated and identified from its 80% ethanol extract. Their cholinesterase inhibitory activities were assessed via Ellman’s method, with enzyme kinetics and molecular docking performed for active compounds. Most compounds showed selective BChE inhibition, with kuwanon X (14) being the most potent (IC₅₀ = 2.3 μM). morusalbanol B (1), cathayanon A (8), and kuwanon G (12) acted as noncompetitive inhibitors, while Morusalbanol C (2) and kuwanon X (14) were mixed competitive inhibitors. Molecular docking suggested that potent inhibitors occupied the BChE active pocket via hydrogen bonds, π-π stacking, and hydrophobic interactions with Trp82, His438, and Phe329. MD simulations and MM-GBSA binding free energy analysis further verified that all three representative complexes (1, 8, and 14) achieved favorable thermodynamic and structural stability, with binding driven primarily by van der Waals forces. Residue decomposition revealed that Trp82 and Phe329 served as core binding hotspots for all tested inhibitors. Structure–activity analysis indicated that a cis-trans methylcyclohexene configuration, shorter aliphatic ester chains, and more prenyl groups enhanced BChE inhibition. This study provides new lead compounds and a systematic molecular mechanism basis for developing novel anti-AD BChE inhibitors from natural products. Full article

Background/Objectives: Immune evasion remains a critical barrier to effective hepatocellular carcinoma (HCC) therapy. Lactate dehydrogenase A (LDHA) drives lactate accumulation and histone lysine lactylation (Kla), reshaping the immunosuppressive microenvironment, while bromodomain-containing protein 4 (BRD4) sustains B7-H3 transcription via super-enhancer occupancy. Despite their synergistic roles in the lactate–Kla–B7-H3 immunosuppressive axis, no dual-target inhibitor simultaneously engaging both proteins has been reported. This study aimed to discover dual LDHA/BRD4 inhibitors from natural product libraries using an integrated AI-driven computational pipeline. Methods: We established a multi-tier virtual screening cascade comprising Lipinski/QED drug-likeness filtration, DiffDock-based AI docking, QuickVina binding energy validation, PLIP interaction profiling, 200 ns all-atom molecular dynamics simulations, MM-GBSA binding free energy calculations, and density functional theory analysis. Natural product libraries from COCONUT and CMNPD databases (84,730 compounds post-filtration) were screened against both targets. Results: High-throughput DiffDock screening identified 11 dual-target hits, from which CNP0038114.1 and CMNPD16582 emerged as prioritized lead candidates. All four protein–ligand complexes maintained structural stability throughout MD simulations, with MM-GBSA binding free energies ranging from −27.24 to −32.45 kcal/mol, predominantly driven by van der Waals interactions. DFT calculations revealed distinct electronic profiles: CNP0038114.1 exhibited a narrow HOMO–LUMO gap (2.718 eV) favoring charge-transfer reactivity, whereas CMNPD16582 displayed a larger gap (4.822 eV), suggesting superior chemical stability. Conclusions: This computational study furnishes two novel natural product leads for targeting the lactate–Kla–B7-H3 immunosuppressive axis in HCC, establishing a generalizable AI-driven workflow for dual-target inhibitor discovery. Full article

This study focused on the inhibitory effects of wheat bran feruloyl oligosaccharides (FOs) on the formation of AGEs in three bovine serum albumin (BSA)-based non-enzymatic glycation models, namely BSA-fructose, BSA-methylglyoxal (MGO), and BSA-glyoxal (GO). In the BSA-fructose model, FOs at 0.25 mg/mL achieved a 62% inhibition rate of fructosamine, equivalent to approximately 78% of the activity of the positive control aminoguanidine (AG), and reduced fluorescent AGEs by over 50% on day 12. Additionally, FOs suppressed the accumulation of α-dicarbonyl compounds, key intermediates in the glycation pathway. In the BSA-MGO and BSA-GO system, the decreased fluorescence intensity of tryptophan residues indicated that FOs bound to BSA, inducing conformational changes in the protein microenvironment; this binding also inhibited protein carbonyl formation and the loss of thiol groups, thereby modulating the protein glycation process. Compared with their precursors (ferulic acid, FA; xylooligosaccharides, XOS), FOs exhibited comparable or even superior inhibitory activity against specific AGE subtypes, suggesting a synergistic effect between the feruloyl and oligosaccharide moieties. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed that FOs reduced the band intensity of 90 kDa AGEs in the glycation system, indicating the inhibition of protein-fructose cross-linking. Fluorescence spectroscopy confirmed that FOs dynamically quenched BSA with a single binding site, and thermodynamic calculations demonstrated that the binding was spontaneous (ΔG < 0), primarily driven by hydrogen bonds and van der Waals forces (ΔH < 0, ΔS < 0). This study systematically investigated the anti-glycation activities of FOs and their precursors. The findings demonstrate that FOs are promising natural glycation inhibitors and provide important theoretical and experimental support for related research. Furthermore, this study establish a basis for the green and high-value utilization of agricultural by-products like wheat bran. Full article

The efficient capture of chlorinated volatile organic compounds (Cl-VOCs) represents a significant challenge in environmental protection and sustainable chemical engineering. In this study, a functional deep eutectic solvent (DES) composed of tetrabutylphosphonium bromide ([P₄₄₄₄][Br]) and levulinic acid (LEV) at a 1:2 molar ratio was prepared, and its absorption performance toward two typical Cl-VOCs, namely dichloromethane (DCM) and chloroform (TCM), was evaluated using this DES as a recyclable absorbent. Based on COSMO-SAC model predictions and experimental validation, the [P₄₄₄₄][Br]-LEV (1:2) system was identified as the preferred candidate. Under mild conditions (10 °C, N₂ flow rate of 100 mL/min), the saturated absorption capacities of this DES reached 1521.71 mg/g and 1620.30 mg/g for DCM and TCM, respectively. The absorbent exhibited favorable regeneration stability over five consecutive absorption–desorption cycles, retaining over 90% of its initial absorption efficiency. Mechanistic studies, including proton nuclear magnetic resonance (¹H NMR), Fourier-transform infrared spectroscopy (FT-IR), DSC (Differential Scanning Calorimetry), TGA (Thermogravimetric Analysis) and quantum chemical calculations, including electrostatic potential (ESP), independent gradient model (IGM), and reduced density gradient (RDG), demonstrated that the absorption process was dominated by physical interactions such as hydrogen bonding and van der Waals forces, with no chemical reactions involved. At the laboratory scale, this DES system showed excellent Cl-VOCs absorption performance, providing a useful reference for the rational design of high-efficiency VOC absorbents. Full article

A zinc complex of chelidonic acid (4-oxo-4H-pyran-2,6-dicarboxylic acid) was obtained by reaction with zinc oxide under isothermal conditions. Its composition was confirmed by elemental and thermogravimetric analyses, and its molecular structure was characterized using NMR and IR spectroscopy. Single-crystal X-ray diffraction revealed that the complex crystallizes as a one-dimensional coordination polymer, [ZnChel(H₂O)₄]_n, in the triclinic space group P-1, featuring a distorted octahedral Zn(II) center coordinated by two chelidonate ligands and four water molecules. This six-coordinate arrangement contrasts with previously described tetra-coordinated Zn–chelidonate complexes. Quantum-chemical calculations and molecular dynamics simulations indicated that, in aqueous solution, Zn(II) preferentially forms a monodentate ZnChel(H₂O)₅ species, consistent with the solid-state coordination environment. The interaction of the complex with bovine serum albumin (BSA) was examined by fluorescence, UV–Vis absorption, and circular dichroism spectroscopy, revealing a mixed static–dynamic quenching mechanism, moderate binding affinity, and hydrogen-bonding/van der Waals contributions accompanied by alterations in BSA secondary structure. These results expand the structural chemistry of chelidonic acid and provide biophysical insight into the protein-binding behavior of zinc chelidonate, supporting its potential relevance as a zinc-based bioactive compound. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells when the spike receptor-binding domain (RBD) engages angiotensin-converting enzyme 2 (ACE2). Cannabinoid scaffolds have recently been reported to bind S1/RBD, block spike-mediated membrane fusion, and modulate host inflammatory pathways, making them attractive candidates for entry inhibition. Here, we applied an integrated computational pipeline to prioritize cannabis-derived compounds as interfacial blockers of the RBD–ACE2 complex across variants. Eleven phytocannabinoids were docked into the wild-type (WT) RBD–ACE2 interface, identifying three cavities, with ligands preferentially occupying pocket 1. Complexes were subjected to triplicate 200 ns all-atom molecular dynamics (MD) simulations for WT, Delta, and Omicron BA.1 RBD–ACE2. Binding energetics were quantified using molecular mechanics/generalized Born surface area (MM/GBSA) and solvated interaction energy (SIE), and per-residue contributions were analyzed together with solvent-accessible surface area (SASA) and residue interaction networks. Among all compounds, cannabidiol (CBD) and cannabinol (CBN) were the only ligands that remained stably bound in pocket 1 for all variants. CBN showed the most favorable ligand–complex binding in WT, whereas CBD preserved favorable binding in Omicron BA.1 despite reduced interface burial, indicating that van der Waals/electrostatic complementarity and solvation, rather than surface coverage alone, govern affinity. Both ligands weakened modeled RBD–ACE2 binding by perturbing hot-spot residues centered on Y505 or N501Y in RBD and E37, A387, and R393 in ACE2. Overall, our results highlight CBD and CBN as tractable, variant-spanning interface disruptors and illustrate how MD-based free-energy calculations can support computational drug discovery against evolving viral protein–protein interfaces. Full article

Understanding the adsorption of organic pollutants onto microplastics in aqueous environments is crucial for assessing their environmental behavior and ecological risks. Herein, we used density functional theory (DFT) computations to simulate the aqueous adsorption of 54 organic compounds onto three representative microplastics, namely polyethylene (PE), polyoxymethylene (POM), and polyvinyl alcohol (PVA). Afterwards, based on theoretical molecular structural descriptors, we developed six quantitative structure activity relationship (QSAR) models based on datasets of 43 and 54 organic compounds, respectively. The results demonstrated that the oxygen-containing POM and PVA microplastics exhibited weaker adsorption in the aqueous phase compared to that in the gas phase. Furthermore, it revealed that the electron-rich atoms, van der Waals volumes and molecular polarizability exert substantial effects on the adsorption process on microplastics in water. These robust QSAR models can enable the prediction of adsorption energies for various organic pollutants on microplastics, which can offer a rapid approach for generating adsorption data. Moreover, the insights into adsorption mechanisms can provide a theoretical basis for designing modified or alternative plastics with lower environmental risks. Full article

CD38 is a multifunctional enzyme that plays a pivotal role in NAD⁺ metabolism and calcium signaling, and its abnormal activity is closely associated with multiple myeloma, age-related metabolic decline, neurodegenerative diseases, and other disorders. Although monoclonal antibodies such as daratumumab have been approved for clinical application, their inherent limitations necessitate the development of novel small-molecule CD38 inhibitors. In this study, we employed DNA-encoded library (DEL) technology for the high-throughput screening of CD38 inhibitors, using a DEL library containing more than 100,000 unique compounds to screen against recombinant human CD38. A total of 1043 enriched compounds were initially identified, and after rigorous validation and screening to exclude non-specific binding and previously reported active compounds, eight hit compounds with diverse chemical scaffolds were obtained, among which Fenbendazole—a clinically approved antiparasitic drug—was included. Surface plasmon resonance (SPR) assays confirmed the direct binding of these hit compounds to CD38, with dissociation constants (KD) ranging from 7.74 × 10⁻⁵ M to 2.15 × 10⁻⁴ M. Fluorescence-based enzymatic activity assays demonstrated that these compounds exert dose-dependent inhibitory effects on both the hydrolase (with ε-NAD as substrate) and cyclase (with NGD as substrate) activities of CD38. Further structure–activity relationship (SAR) analysis of Fenbendazole analogues revealed the critical structural features that regulate CD38 inhibitory potency, and Flubendazole was found to exhibit excellent inhibitory activity, with an IC₅₀ of 14.78 ± 4.21 μM against CD38 hydrolase and 26.31 ± 3.40 μM against cyclase. Molecular docking and 100 ns molecular dynamics (MD) simulations further elucidated the molecular mechanism of CD38 inhibition by lead compounds, confirming that van der Waals interactions are the main driving force for the binding of small-molecule ligands to CD38, with conserved aromatic residues in the active site mediating ligand recognition. This study validates DEL technology as an efficient and reliable platform for the discovery of CD38 inhibitors, and the identified lead compounds—especially Fenbendazole and its analog Flubendazole—provide valuable molecular scaffolds for the further structural optimization of CD38 inhibitors. These findings lay a solid foundation for the development of novel therapeutic agents for the treatment of CD38-associated diseases. Full article

Recent findings demonstrate that concentrated sulfuric acid supports rich organic chemistry, including the stability of the canonical DNA bases adenine, thymine, guanine and cytosine. Yet, due to full protonation in concentrated sulfuric acid, these bases may not pair as effectively as they do in water. We are therefore motivated to study nucleic acid bases that pair via hydrophobic and van der Waals interactions instead of canonical hydrogen bonding. Here, we investigate the stability of 14 selected, commercially available alternative nucleobases in concentrated sulfuric acid to evaluate their potential for forming DNA-like polymers in this solvent. The reactivity of compounds 1–14 have not been previously investigated in concentrated sulfuric acid. We incubate the selected compounds in 98% and 81% w/w sulfuric acid and monitor their stability using ¹H and ¹³C NMR spectroscopy over 3 weeks at room temperature. In 98% w/w sulfuric acid, six bases—benzo[c][1,2,5]thiadiazole (1), 2,2′-bipyridine (2), 1,1′-biphenyl (3), 1-methoxy-3-methylbenzene (MMO2) (7) and 1-chloro-3-methoxybenzene (ClMO) (13), and 2,4-difluorotoluene (14)—remain soluble and stable with no detectable degradation. A few compounds show non-destructive reactivity, like sulfonation (compound 3) or H/D exchange (compounds 7, 13, 14). The other compounds react rapidly or are insoluble in 98% w/w sulfuric acid. In 81% w/w sulfuric acid, only compounds 1 and 2 remain stable and soluble, while other selected compounds are insoluble or unstable. Our findings identify a subset of alternative bases stable in concentrated sulfuric acid, advancing efforts towards the design of an example genetic-like polymer in this unusual solvent. Our work further highlights sulfuric acid’s potential for supporting complex organic chemistry, with implications for astrobiology, planetary science of Venus and synthetic biology. Full article

Background: Numerous plant-derived products have shown notable potential in preclinical studies and traditional use for the management of periodontitis, although clinical studies validating their efficacy remain scarce. The present study investigated the efficacy of a polyherbal phytopreparation as an adjunctive therapy to scaling and root planing (SRP) in patients with periodontitis, and further examined its underlying mechanisms of action, pharmacokinetic behavior, and toxicological profile using in silico approaches. Methods: Eighty patients with moderate periodontitis (stage II, grade A) were randomly assigned to two groups: a control group (n = 40) treated with SRP alone, and an experimental group (n = 40) receiving SRP followed by topical phytotherapeutic treatment with the polyherbal Tinctura paradentoica^®. Efficacy was evaluated using the gingival index, periodontal pocket depth, and cytomorphometric analysis of gingival cells before treatment and one month after. The in silico analysis, guided by HPLC profiling, included MolDock-based docking to assess interactions of bioactive compounds with cyclooxygenase isoforms COX-1 and COX-2 as anti-inflammatory targets, and evaluation of their pharmacokinetic and toxicity properties (ADME/Tox) using SwissADME, ProTox-3.0, and pkCSM. Results: Compared with SRP treatment, the experimental treatment significantly reduced the gingival index and periodontal pocket depth (p < 0.05), as well as the assessed cytomorphometric parameters (nuclear area, perimeter, and Feret’s diameter values) (p < 0.001). Rerank analysis revealed van der Waals-driven isoform selectivity: compact phenolic acids and aglycones favored COX-1, whereas bulky glycosides (e.g., rutin, narcissoside) were optimized for COX-2, with luteolin-7-O-glucoside showing near-balanced engagement. The ADME/Tox analysis indicated generally favorable pharmacokinetic and safety characteristics of phenolic compounds from the phytopreparation, including low systemic absorption and no predicted mutagenicity or skin sensitization potential. Conclusions: The topical application of the polyherbal phytopreparation demonstrated significant potential to enhance the efficacy of conventional SRP therapy by promoting the regression of gingival inflammation in patients with moderate periodontitis, further supported by in silico findings. Full article

Cyclooxygenase-2 (COX-2) is a key enzyme in inflammatory pathways and serves as a therapeutic target in the treatment of inflammation-related diseases. Curcumin, a bioactive polyphenol from turmeric, has gained scientific attention due to its potent anti-inflammatory properties, largely mediated through COX-2 inhibition. However, the poor solubility and limited bioavailability of Curcumin limit its potential as a therapeutic agent targeting inflammatory diseases. We used an in silico approach to identify Curcumin-like scaffolds as novel COX-2 inhibitors with improved drug-like properties and therapeutic potential. A pharmacophore model derived from the key binding moieties of Curcumin was used to virtually screen the ZINC-22 database, identifying 237 candidate compounds for further evaluation. Molecular docking further prioritized these compounds to 10 candidates with the highest binding affinities. Most hits obeyed Lipinski’s rules, except for ZINC32605424 and ZINC47133707, which exhibited high LogP and molecular weight, respectively. Toxicity screening indicated that ZINC47133693 and ZINC09499196 exhibited high safety profiles, with ZINC15942488 being highly toxic. Furthermore, certain hits such as ZINC32605424 and ZINC15942488 were predicted to be P-glycoprotein substrates and potential inhibitors of cytochrome P450. Molecular dynamics simulations confirmed the stability of COX-2–ligand complexes, with critical interactions observed at conserved residues Tyr323 and Leu320. Binding energy calculations identified ZINC32605424 as the strongest COX-2 binder, mainly stabilized by Van der Waals forces. Overall, compounds such as ZINC32605424, ZINC08644750, ZINC47133693, and ZINC09499196 demonstrated potent COX-2 inhibition. These candidates show strong potential for further preclinical validation in studies investigating inflammation-related metabolic complications. Full article

The pressing need for sustainable, plant-based alternatives is highlighted by the growing resistance of agricultural pests to synthetic pesticides. This study examined the pesticidal potential of phytocompounds from C. tora discovered by GC–MS analysis against important tomato insect (T. absoluta) and fungal pathogen (A. solani). The binding stability and interaction dynamics of specific metabolites with fungal virulence (polygalacturonase, MAP kinase HOG1, and effector AsCEP50) and insect neuromuscular (ryanodine receptor and sodium channel protein) targets were assessed using molecular docking and 100 ns molecular dynamics simulations. Among the screened compounds, squalene and 4,7,10,13,16,19-docosahexaenoic acid, methyl ester (DHAME) exhibited the strongest binding affinities and conformational stability, with MM-GBSA binding free energies of −38.09 kcal·mol⁻¹ and −52.81 kcal·mol⁻¹ for squalene complexes in T. absoluta and A. solani, respectively. Persistent hydrophobic and mixed hydrophobic–polar contacts that stabilised active-site residues and limited protein flexibility were found by ProLIF analysis. These lively and dynamic profiles imply that DHAME and squalene may interfere with calcium signalling and stress-response pathways, which are essential for the survival and pathogenicity of pests. Hydrophobic interactions were further confirmed as the primary stabilising force by the preponderance of van der Waals and nonpolar solvation energies. The findings show that C. tora metabolites, especially squalene and DHAME, are promising environmentally friendly biopesticide candidates that have both insecticidal and antifungal properties. Their development as sustainable substitutes in integrated pest management systems are supported by their stability, binding efficacy and predicted biosafety. Full article