Search Results (118)

Background: Non-small cell lung carcinoma (NSCLC) is the most prevalent form of lung cancer, and its progression is closely associated with constitutive activation of signal transducer and activator of transcription 3 (STAT3). This study used surface plasmon resonance (SPR) technology to develop a STAT3-targeting recognition system and identify natural STAT3-targeting compounds from the traditional Chinese medicine Psoralea corylifolia and to evaluate their anti-NSCLC activities, with particular attention to reactive oxygen species (ROS) regulation. Methods: The SPR biosensor immobilized with STAT3 was used to screen and enrich STAT3-binding constituents of Psoralea corylifolia, and to determine ligand-STAT3 affinities. Molecular docking was performed to characterize interactions within the STAT3 SH2 domain. Functional effects were assessed in A549 cells using proliferation and scratch migration assays. Antioxidant capacity was evaluated via hydroxyl radical and superoxide anion scavenging assays, and intracellular ROS levels were measured in hydrogen peroxide (H₂O₂)-induced oxidative stress models in human umbilical vein endothelial cells (HUVECs) and A549 cells. Results: SPR analysis showed that psoralen and isopsoralen bind to STAT3, with equilibrium dissociation constants (KD) of 80.92 µM and 28.11 µM, respectively. Molecular docking further confirmed their interaction with the STAT3 SH2 domain. Both compounds inhibited A549 proliferation and reduced migration. Beyond direct STAT3 inhibition, both compounds demonstrated notable free radical scavenging activity. In a H₂O₂-induced oxidative stress model, pretreatment with psoralen or isopsoralen significantly reduced ROS levels in HUVECs, while increasing ROS accumulation in A549 lung cancer cells. Conclusions: This work identifies psoralen and isopsoralen as novel dual-function STAT3 inhibitors that exert anti-NSCLC effects through combined STAT3 suppression and context-dependent ROS modulation, and demonstrates the utility of SPR for screening bioactive natural products. 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

Neonicotinoids are synthetic nicotine-like compounds extensively used globally as insecticides for agricultural and urban purposes. Neonicotinoid-contaminated produce is a major public health concern worldwide. Limited epidemiological studies have shown an association of neonicotinoid exposure with abnormal semen analysis. This study aimed to elucidate the potential disruption of the androgen receptor (AR) by eight common neonicotinoids, including imidacloprid (IMI), acetamiprid, clothianidin, thiamethoxam, dinotefuran, thiacloprid (THI), nitenpyram, and nithiazine using docking and molecular dynamics (MD) simulation. The results showed good binding strength of all compounds (except THI) with AR, as indicated by high binding energy, high binding affinity, and number of bonding interactions. The results of MD simulation supported the conformational stability and structural dynamic behavior of the AR-IMI (receptor-neonicotinoid) complex upon binding. This was indicated by root mean square deviation showing stability of the complex; the root mean square fluctuation showing minimized residual fluctuations upon binding; the radius of gyration showing greater compactness of the protein structure; the solvent-accessible surface area showing no changes upon binding; and the Gibbs funnel energy of the landscape showing a stable conformation state with minimum energy and slight change in size and position of the sampled energy basin of the AR, with a stable equilibrium. Taken together, the structural dynamics results showed that neonicotinoids are bound stably in the same ligand-binding domain of the AR as the native ligand testosterone. This may perturb the natural binding of testosterone with the AR and potentially disrupt downstream signaling and biological pathways, leading to male reproductive dysfunction. Full article

Nanoparticles interact dynamically with proteins, often leading to adsorption-induced conformational changes that alter protein function and contribute to corona formation. Here we investigated the adsorption and unfolding of a model protein GB1 on latex nanoparticle surfaces using a combination of mutational analysis, equilibrium binding assays, stopped-flow kinetics and Φ-value interpretation. Seven site-directed variants of GB1 were studied to dissect residue-specific contributions to adsorption energetics. Fluorescence binding isotherms revealed that D46A and T53A mutations weakened surface affinity, while kinetic analysis demonstrated that D46A reduced adsorption rate by ~6-fold and produced a dramatic unfolding/refolding shift, identifying Asp46 as a key docking site. Φ-value analysis further highlighted Asp46 and Thr53 as central residues in the adsorption transition state, whereas mutations in the hydrophobic core or distal loops had negligible effects. These results support a dock–loosen–unfold mechanism in which electrostatic recognition initiates binding, followed by hydrophobic exposure and hairpin stabilization. This residue-level sampling of key sites advances mechanistic understanding of protein–nanoparticle interactions and suggests strategies for tuning surface charge to control corona formation. Our approach provides a generalizable method to map adsorption transition states, with implications for designing safer nanomaterials, predicting protein corona composition, and harnessing protein unfolding in biosensing applications. Full article

Transmembrane facilitation of substrates by channels and secondary active transporters results in a defined steady-state concentration ratio across the membrane. Evidence is accumulating that asymmetry in the structural build of the transporters, or interaction with asymmetric partner proteins, can shift the position of the transmembrane equilibrium by biased transport directionality. For instance, the bacterial lactose transporter, LacY, and two amino acid transporters, i.e., the human excitatory amino acid carrier, EAAC1, and the yeast lysine permease, Lyp1, were reported to exhibit distinct transport kinetics in the inward and outward direction by protein-intrinsic properties. A recent example is transport modulation of human monocarboxylate transporters, MCT, by shedding of the extracellular domain of an ancillary protein, basigin. Loss of the domain selectively increases export of lactate from lung cancer cells by a factor of four, contributing to the Warburg effect and malignancy. Further, intrinsic properties of monocarboxylate transporters involving asymmetric affinities of substrate binding, or biased open probabilities were shown to generate preference for one transport direction. Here, we discuss molecular mechanisms and physiological contexts of asymmetric secondary active transmembrane transport. Focus is laid on experimentally established cases, and examples are given in which putative bias in transport directionality may have been overlooked. Full article

Fluorescence Anisotropy (FA) is a sensitive and efficient technique for quantifying biomolecular interactions, offering advantages such as minimal sample requirements and elimination of separation of bound from unbound species. Thus, it is well suited for aptamer–protein binding affinity studies. However, accurately determining equilibrium dissociation constants (K_D) in FA requires low concentrations of fluorescently labeled aptamers to prevent ligand depletion. A significant challenge arises at low aptamer concentrations due to an unexpected and physically nonmeaningful increase in apparent anisotropy, which impairs accurate data fitting. This anomalous increase in apparent anisotropy may arise from non-specific adsorption of aptamers to surfaces. In this study, we investigated the use of non-ionic surfactants to mitigate these effects and stabilize the anisotropy signal at low aptamer concentrations using the thrombin aptamer as a model system. We evaluated the impact of varying concentrations of two surfactants (Tween 20 and Triton X-100) on plots of anisotropy as a function of aptamer concentration and determined aptamer–protein binding affinities. Addition of 0.1% Tween 20 corrects the anomalous increase in anisotropy at low aptamer concentrations, enabling the use of aptamer concentrations as low as 5 nM in binding assays. Triton X-100 was less effective. By incorporating optimized concentrations of Tween 20, we demonstrated improved assay reproducibility and accuracy in K_D determination, expanding the dynamic range of usable aptamer concentrations in FA-based binding affinity studies. Similar benefits were observed with the clinically relevant aptamer s10yh2 and human serum albumin. These findings provide a practical strategy for enhancing the robustness of FA measurements and may be applicable to other aptamer–target systems and high-throughput assay formats. Full article

Despite the prevalence and toxicity of heavy metals in the environment, arsenic and cobalt are of particular concern due to their high mobility and bioaccumulation potential, particularly in contaminated groundwater. Herein, we studied the adsorption behavior of commercially available sorbents, including Fluorosorb-100 (FS-100), Fluorosorb-200 (FS-200), and Filtrasorb-400 (F-400), for the removal of arsenite (As(III)) and cobalt (Co(II)), aiming at the selection of filter media in terms of future groundwater remediation. Kinetic analysis revealed that As(III) adsorption followed a pseudo-second-order model, while Co(II) showed mixed first- and second-order behavior, reflecting sorbent-dependent mechanisms. Equilibrium isotherm modeling revealed strong correlations with both Langmuir and Freundlich models, confirming heterogeneous adsorption sites and multilayer interactions. FS-100 demonstrated the highest affinity for As(III) (qₘ = 0.46 mg/g) and F-400 exhibited the greatest adsorption capacity for Co(II) (qₘ = 1.00 mg/g), while FS-200 consistently showed relatively weaker adsorption for both metals. Desorption studies indicated predominantly irreversible binding, with minimal release of As(III) from F-400 and Co(II) from FS-200 and F-400, even at high concentrations. Overall, these findings highlight that commercially available sorbents can effectively capture arsenite and cobalt, offering cost-effective and scalable options for heavy-metal removal in groundwater remediation systems under realistic environmental conditions. Full article

This study employed an integrated computational approach to discover novel nucleoprotein (NP) inhibitors for influenza A virus (IAV). Beginning with virtual screening of over 10 million compounds using Schrödinger’s Glide module (HTVS, SP, XP docking), the workflow identified promising candidates with favorable binding energies. Subsequent molecular mechanics/generalized born surface area (MM-GBSA) calculations and 100 ns molecular dynamics (MD) simulations prioritized 16 compounds for experimental validation. Surface plasmon resonance (SPR) assays revealed that compounds 8, 13, and 14 demonstrated superior target engagement, showing equilibrium dissociation constants (K_D) of 7.85 × 10⁻⁵ M, 3.82 × 10⁻⁵ M, and 6.97 × 10⁻⁵ M, respectively. Molecular dynamics, alanine scanning mutagenesis, and quantum mechanics/molecular mechanics (QM/MM) analysis were conducted to analyze the binding modes, providing a reference for the design of subsequent compounds. These findings validate the efficacy of structure-based virtual screening in identifying high-affinity NP inhibitors and provide insights for the development of broad-spectrum anti-influenza therapeutics. Full article

The assessment of a ligand’s activity is typically established by measuring its binding affinity in a biochemical assay, often expressed as K_a or K_d values. Further validation of its biological activity is achieved through cellular assays. There is frequently an inconsistency between the activity values obtained from those assays, which could delay research progress as well as drug development. Factors such as the permeability, solubility, specificity, and stability of active compounds are usually held responsible for this discrepancy. Even when these values are known, inconsistencies in activity measurements remain challenging to explain. This is not surprising since intracellular physicochemical conditions are undoubtedly different from the simplified conditions used in most in vitro biochemical assays. It is therefore reasonable to assume that these differences would be minimized if biochemical measurements were performed under conditions that more accurately mimic the intracellular environment. These physicochemical conditions can alter the K_d values. While the cellular environment has been extensively studied for decades, more recent efforts have focused on obtaining equilibrium and kinetic data directly from in-cell environments. Clarifying molecular crowding, salt composition, and lipophilic parameters inside the cell and thus their effect on molecular equilibrium is a crucial step toward replicating the intracellular environment. Full article

Adhesion of cell membranes is relevant to many biological processes and arises from the specific binding of membrane-anchored receptor proteins to their ligands present in the apposing membrane. Here, we employ a statistical–mechanical model and perform Monte Carlo simulations to study a system of adhered membranes in which the receptor and ligand proteins exhibit affinity for association with so-called lipid rafts, which are fluctuating nanoscale molecular clusters enriched in sphingolipid and cholesterol. We focus on equilibrium properties of the adhered membranes in the mixed phase, where both the membrane-anchored proteins and lipid rafts are distributed more-or-less uniformly within the membranes. Our simulation results show that lateral attraction between lipid rafts enhances the receptor–ligand binding, affecting the adhesion of the membranes. On the other hand, the receptor–ligand binding causes lipid rafts to be distributed less uniformly within the membranes and, simultaneously, leads to an increased co-localization of the membrane-anchored proteins with lipid rafts. We quantify and discuss all these effects, providing a detailed picture of the complex interplay between the adhesion of the membranes and the lateral distribution of the membrane-anchored proteins and lipid rafts. Our results broaden the understanding of the physical mechanisms that determine the supra-molecular organization of lipid rafts and membrane receptors in cell membranes. This understanding may help to elucidate how lipid rafts function in biological processes such as cell signaling and immune responses. Full article

Background: When an antigen molecule is exposed to serum, many different kinds of antibodies bind to it. The complexity of these binding events is only poorly characterized by assays that generate a single variable, generally reflecting the fractional saturation of the antigen, as the readout. Methods: We have previously devised an assay that delivers the essential biochemical variables to determine fractional saturation as the output: an equilibrium dissociation constant for affinity, the ratio of antibody concentration to the equilibrium constant and the concentration of bound antibodies under reference conditions. Here we propose a visualization method for the practical and informative display of these variables. Results: Using total antigen concentration and free and bound antibody concentration as coordinates in a three-dimensional space, a surface plot can depict the behavior of serum antibodies in the measurement range and identify the values of the key variables of binding activity. This surface display (antibody binding in 3-concentration display, Ab3cD) was used for the characterization of antibody binding to the SARS-CoV-2 spike protein in seronegative and seropositive sera. We demonstrate that this visualization scheme is suitable for presenting both individual and group differences and that epitope density changes, not commonly measured by immunoassays, are also revealed by the method. Conclusions: We recommend the use of 3D visualization whenever detailed, informative and characteristic differences in serum antibody reactivity are studied. Full article

Receptors capable of binding both positive and negative ions are an important domain of supramolecular chemistry with valuable application potential. A Complete thermodynamic description of the equilibria related to ion pair recognition is beneficial in developing the optimized receptor systems, although it represents a difficult task that is rarely resolved due to various coupled processes. Here, we present a comprehensive study of ion pair (NaCl, NaHSO₄, and NaH₂PO₄) binding by a ureido–amide calix[4]arene host in acetonitrile using a series of experimental techniques and molecular dynamics simulations. We devoted particular attention to characterizing the side processes (ion association and salt precipitation) and included them in the models describing ion pair complex formation. For this purpose, a multimethod approach (potentiometry, conductometry, ITC, flame AES) was employed, generating reliable data which provided insight into the thermodynamic effect of each included equilibrium. Positive cooperativity was observed in the context of NaCl and NaHSO₄ binding by the studied calixarene. Computational results related to the NaCl complex in acetonitrile revealed that favorable Coulombic interactions, changes in affinity for solvent molecule inclusion, and intramolecular hydrogen bonding contributed to cation-induced cooperativity. Full article

The effects of magnesium and sodium on the interactions between aptamer, its specific ligand, and short complementary oligonucleotides (cDNAs) differing in affinity of their binding with the aptamer were studied. Aflatoxin B1 (AFB1) and AFB1-binding aptamer were used in the study. Dependencies for the aptamer binding with the fluorophore-labeled AFB1 under varied concentrations of the cations were obtained using fluorescence anisotropy measurements. The increase of the aptamer affinity to AFB1 in the presence of cations was demonstrated using fluorescence anisotropy and isothermal calorimetry. The collected data indicate that 300 mM Mg²⁺ (significantly more than the range commonly used in aptamer sensors) provides the best affinity (16.5 ± 2.2 nM) of the aptamer–AFB1 complexation. Sodium decreases the Mg²⁺-modulated affinity at some Na⁺/Mg²⁺ ratios. The aptamer affinity with cDNAs increases with concentration of cations, but not in the same way as for AFB1. Based on the characterized conditions for bimolecular interactions, the ligand-induced displacement of cDNAs was studied with the registration of the Forster fluorescence energy transfer (FRET). The most sensitive revealing of AFB1 (IC10% 3.2 ± 0.3 nM) in this three-compound FRET system was demonstrated for cDNA having an equilibrium constant of the aptamer binding close to the constant of the aptamer–AFB1 reaction. Full article

Industrial hemp (Cannabis sativa L.) was investigated as a sustainable biosorbent for removing Congo Red (CR) and Remazol Brilliant Blue R (RBBR) from wastewater. The unmodified hemp biosorbent exhibited moderate but practically relevant sorption capacities (4.47 mg/g for CR; 2.44 mg/g for RBBR), outperforming several agricultural waste materials. Kinetic studies revealed rapid uptake, with CR following pseudo-first-order kinetics (t₁/₂ < 15 min) and RBBR fitting the Elovich model, indicating heterogeneous surface interactions. Equilibrium data showed CR adsorption was best described by the Temkin isotherm (R² = 0.983), while RBBR followed the Langmuir model (R² = 0.998), reflecting their distinct binding mechanisms. Thermodynamic analysis confirmed spontaneous (ΔG° < 0), exothermic (ΔH° ≈ −2 kJ/mol), and entropy-driven processes for both dyes. Molecular docking elucidated the structural basis for performance differences: CR’s stronger binding (−7.5 kcal/mol) involved weak noncovalent interaction arising from partial overlap between the π-electron cloud of an aromatic ring and σ-bonds C-C or C-H (π-σ stacking) and hydrogen bonds with cellulose, whereas RBBR’s weaker affinity (−5.4 kcal/mol) relied on weak intermolecular interaction between a hydrogen atom (from a C-H bond) and the π-electron system of an aromatic ring (C-H∙∙∙π interactions). This work establishes industrial hemp as an eco-friendly alternative for dye removal, combining renewable sourcing with multi-mechanism adsorption capabilities suitable for small-scale water treatment applications. Full article

Clinical data as well as animal and cell studies indicate that certain antidiabetic drugs, including glucagon-like peptide 1 receptor agonists (GLP-1RAs), exert therapeutic effects in Alzheimer’s disease (AD) by modulating amyloid-β peptide (Aβ) metabolism. Meanwhile, the direct interactions between GLP-1RAs and Aβ and their functional consequences remain unexplored. In this study, the interactions between monomeric Aβ40/Aβ42 of GLP-1(7-37) and its several analogs (semaglutide (Sema), liraglutide (Lira), exenatide (Exen)) were studied using biolayer interferometry and surface plasmon resonance spectroscopy. The quaternary structure of GLP-1RAs was investigated using dynamic light scattering. The effects of GLP-1RAs on Aβ fibrillation were assessed using the thioflavin T assay and electron microscopy. The impact of GLP-1RAs on Aβ cytotoxicity was evaluated via the MTT assay. Monomeric Aβ40 and Aβ42 directly bind to GLP-1(7-37), Sema, Lira, and Exen, with the highest affinity for Lira (the lowest estimates of equilibrium dissociation constants were 42–60 nM). GLP-1RAs are prone to oligomerization, which may affect their binding to Aβ. GLP-1(7-37) and Exen inhibit Aβ40 fibrillation, whereas Sema promotes it. GLP-1 analogs decrease Aβ cytotoxicity toward SH-SY5Y cells, while GLP-1(7-37) enhances Aβ40 cytotoxicity without affecting the cytotoxic effect of Aβ42. Overall, GLP-1RAs interact with Aβ and differentially modulate its fibrillation and cytotoxicity, suggesting the need for further studies of our observed effects in vivo. Full article