Fluorescence quenching and ligand binding: A critical discussion of a popular methodology

Engineered collaborative grown model regulation and LSPR-tunable of Pd@Au core-shell nanoparticles for highly sensitive fluorescence quenching lateral flow immunoassay

Lateral flow immunoassay (LFIA) based on fluorescence quenching is a novel approach to improve the detection sensitivity in recent years. However, inefficient fluorescence quenchers and unclear fluorescence quenching mechanisms have limited the development of fluorescence quenching lateral flow immunoassay (FQ-LFIA). Herein, we synthesized Pd@Au core-shell nanostar (Pd@Au NSs) and Pd@Au core-shell icosahedra nanoparticles (Pd@Au IHNPs) with excellent fluorescence-quenching ability and localized surface plasmon resonance (LSPR) tunable performance by adjusting the injection rate of Au(III) precursors. The absorption peaks of Pd@Au NSs and Pd@Au IHNPs were highly coincident with the emission peaks of the red and green quantum dot nanobeads (QBs), respectively. The fluorescence of green QBs and red QBs was absorbed by the Pd@Au NSs and Pd@Au IHNPs in the inner-filter effect (IFE) approach, which achieved efficient fluorescence quenching (kn(Pd@Au NSs) = 3.41 and kn(Pd@Au IHNPs) = 3.68). Based on Pd@Au NSs and Pd@Au IHNPs as efficient quenchers, the highly sensitive FQ-LFIA was established. The Limits of detection (LODs) of Pd@Au NSs-FQ-LFIA and Pd@Au IHNPs-FQ-LFIA were 0.051 and 0.012 ng mL-1, respectively. Furthermore, the method demonstrated satisfactory recoveries (89.68-117.20 %) for the detection of ABZ in food samples.

Nanocomplex of selachyl alcohol and sodium caseinate: Preparation, physicochemical properties, and interaction mechanism

Selachyl alcohol (SA), a naturally occurring 1-O-alkylglycerol, has garnered significant attention due to its wide biological activities. To enhance its aqueous solubility, the complexation with sodium caseinate (NaCas) was investigated. Results showed the SA-NaCas complex, optimally formed at a 1:4 mass ratio, yielded a nanoscale dispersion with enhanced surface hydrophobicity, reduced dynamic surface tension, and superior emulsifying indices compared to NaCas alone. Fluorescence spectroscopy elucidated the interaction between SA and NaCas as a spontaneous process, mainly driven by hydrophobic forces. The binding constant and Gibbs free energy change were 1.17 × 103 L/mol and - 18.09 kJ/mol at 308 K. Molecular docking revealed that hydrophobic and hydrogen bonding interactions were the main forces driving the binding of SA to the α- and β-casein components of NaCas. The SA-NaCas nanocomplex not only enhances SA's water solubility, but also can be used as an effective nano-delivery system with better physicochemical properties than NaCas.

High pressure induced in situ orderly encapsulation of apoferritin and its application in protecting non-acylated anthocyanin

Anthocyanins are important natural plant pigments with many physiological activities. However, because of their highly reactive nature, anthocyanins are unstable, a new approach was established in this study to encapsulate cyanidin 3-β-D-glucoside (C3G) into the inner cavity of recombinant H-2 of soybean seed apoferritin (rH-2) using high pressure processing (HPP) to improve its stability. At the optimal conditions (500 MPa/20 min, C3G/rH-2 mass ratio of 1 to 1), 15 C3G molecules could be encapsulated by per protein cage, which is comparable with pH shift method with stirring, and much higher than urea method. Moreover, the antioxidant capacity of C3G was improved by rH-2 and such interaction and encapsulation increased the stability of C3G at different temperatures and against metal ions. Multi-spectroscopy methods and molecular dynamics simulation revealed that HPP induced significant conformational changes in ferritin, disturbing the highly ordered α-helix structure and increasing the overall flexibility, which allowed the diffusion of C3G into the nanocage via emerging gaps. Furthermore, HPP encapsulation was applied in C3G enriched plant-based beverage and pudding, showing high retention of C3G. The findings of this study suggest that HPP encapsulation is a novel and green approach for in situ orderly encapsulation of heat-sensitive bioactive hydrophilic phytochemicals. Moreover, this approach has been successfully used for non-acylated anthocyanins stabilization in the real plant-based foods for the first time.

Enhanced fluorescence emission or singlet oxygen production of cationic porphyrazines and porphyrins through combination with carbon dots

A cationic porphyrin and porphyrazine with the 3-ethylpyridyl substituent (H2P and H2Pz) and their respective zinc complexes (ZnP and ZnPz) were assembled to a carbon dot (CD) synthesized from citric acid and ammonium citrate. A titration was performed using a fluorescence spectrophotometer to determine the stoichiometric ratio at which the maximum interaction between the substances occurs, as well as the Stern-Volmer constant and intrinsic binding constant. The combination between CD and porphyrins or porphyrazines was confirmed using UV-VIS absorption spectroscopy, fluorescence emission, zeta potential, and Diffusion-Ordered NMR Spectroscopy (DOSY). It was observed that after combination, there is a decline in the absorption of porphyrin derivatives, a variation in the emission of porphyrazines, a subtle increase in the zeta potential compared to the isolated CD particles, and a variation in the translational diffusion coefficient. It was also found that upon combination with the CD, changes in the photophysical properties of the macrocycles occur, for example, the fluorescence quantum yield of H2Pz increases from 0.81 ± 0.03% to 1.97 ± 0.05% while the singlet oxygen quantum yield of H2P increases ca. 70%. These results exemplify the capacity of CD to boost some properties of photosensitizers that are key for photodynamic therapy applications.

Macromolecular crowding effect on the β-galactosidase cascade reaction under multivalency and chain overlapping conditions of glycopolymers

Enzymes catalyze cascade reactions in a crowded cellular environment where as much as half of cell volume is occupied by various macromolecules. Nonspecific interaction between enzymes and crowders and excluded volume of the crowders can superimpose on each other and complicate catalytic activity of the enzymes. This study investigates the interaction between a β-galactosidase (β-Gal) and glycosylated acrylamide polymer (P(Glc-β-EAAm)) and unravels the macromolecular crowding effect of the glycopolymer on enzymatic cascade catalysis consisting of β-Gal, glucose oxidase and hydrogen peroxidase. Binding of the glycopolymer induced conformational alterations in β-Gal and gave rise to static fluorescence quenching and stable complex formation with β-Gal via nonspecific interaction. Fluorescence resonance energy transfer assays further demonstrated a compact association between β-Gal and glycopolymer crowders, with binding affinity correlating with the molecular weight of glycopolymer. The reduction of the apparent kinetic constants of the catalysis with the glycopolymer size showed the role of the multivalent effect in enzyme-substrate interactions. The kinetics also depended on the chain overlapping conditions of the crowders. Therefore, the macromolecular crowding effect on the cascade reaction is jointly associated with the crowder's multivalent effect, chain overlapping conditions of the crowders, in addition to the volume exclusion effect of the crowders.

Design and synthesis of azole derivatives of echinocystic acid as α-glucosidase inhibitors with hypoglycemic activity

Diabetes mellitus necessitates strict control of postprandial hyperglycemia via α-glucosidase inhibitors. In this study, novel azole derivatives of Echinocystic acid (EA), a natural pentacyclic triterpenoid, were synthesized through molecular hybridization to enhance hypoglycemic potential. Compound A4 exhibited superior α-glucosidase inhibition (IC50 = 2.72 μM) than that of EA (IC50 = 59.91 μM), and acarbose (IC50 = 342.0 μM). Kinetic analysis revealed mixed-type inhibition (Ki = 15.31 μM, Kis = 10.23 μM), suggesting ternary complex formation. Analysis by spectroscopic studies confirmed A4 altered the enzyme's microenvironment and secondary structure. The combination of molecular docking and molecular dynamics simulations further elucidated the interaction between A4 and α-glucosidase. A4 enhanced binding stability through π-cation and π-π stacking interactions, with low RMSD values indicating structural stability. In vivo studies showed that A4 has an excellent safety profile, with no organ damage observed at a single dose of 0.5 g/kg. In a sucrose loading test in normal mice, A4 demonstrated glucose control comparable to that of acarbose at the same dose. Diabetic mice treated with A4 exhibited reduced fasting blood glucose, improved glucose tolerance, lipid normalization, and antioxidant effects, underscoring its therapeutic promise.

Enhanced Binding Site Identification in Protein-Ligand Complexes with a Combined Blind Docking and Dipolar Electron Paramagnetic Resonance Approach

Understanding protein-drug complex structures is crucial for elucidating therapeutic mechanisms and side effects. Blind docking facilitates site identification but is hindered by computational complexity and imprecise scoring, causing ambiguity. Dipolar electron paramagnetic resonance (EPR) provides spin-spin distances but struggles to determine relative positions within complexes. We present a novel approach combining GPU-accelerated blind docking with EPR distance constraints to enhance binding site detection. Our algorithm uses a single EPR distance distribution to filter and validate docking results. Ligand poses from blind docking are clustered, filtered by expected distances, and refined through focused docking. To illustrate our approach, we investigated human serum albumin binding with porphyrin-based photosensitizers used in photodynamic therapy. Combining docking and EPR, we identified possible binding sites, demonstrating that EPR data significantly reduce possible configurations and provide experimentally validated information. This strategy produces a detailed map of photoligand binding sites, revealing that binding may occur away from standard albumin sites and often involves multiple locations. Furthermore, it overcomes key limitations of fluorescence-based methods, which are prone to misinterpretation in albumin studies due to non one-to-one donor-acceptor relationships. By resolving ambiguities in both blind docking and EPR, our framework provides a versatile platform for investigating EPR-active ligands.

Interaction of normelinonine F and related N-methyl-β-carbolines derivatives with bovine serum albumin. Spectroscopic profiles, multivariate analysis and theoretical calculations

β-carbolines (βCs) represent a large family of bioactive alkaloids, including norharmane and normelinonine F, known for their diverse pharmacological activities. The effects of these alkaloids may depend, among other factors, on their delivery, accumulation in different subcellular compartments, and interactions with biomacromolecules such as serum albumins. In this study, we investigated the pH dependence of the interactions between bovine serum albumin (BSA) and four βCs (norharmane, normelinonine F, and their corresponding N(9)-methyl derivatives) using UV-vis and fluorescence spectroscopy, combined with multivariate analysis and molecular docking. This selected set of N-methyl derivatives provides valuable insights into molecular-level binding interactions, clarifying aspects observed in previous studies. The results reveal a distinct spectroscopic interaction pattern for quaternary βCs compared to derivatives with a free N(2)-pyridinic nitrogen. Specifically, normelinonine F and N(9)-methyl-normelinonine F exhibited weak interactions, likely with external sites (site 3, subdomain IB) and/or the protein surface. In contrast, for N(2)-unsubstituted derivatives such as norharmane and N(9)-methyl-norharmane, stronger interactions and internalization into less polar and/or hydrophobic BSA sites predominate across the investigated pH-range (4 < pH < 9), likely site 2 (subdomain IIIA). However, the interaction of the corresponding cationic species of norharmane and N(9)-methyl-norharmane with BSA remains unclear due to low interaction levels and similar UV-vis absorption and emission spectra between free and BSA-bound species.

Bismuth(III) complexes of Schiff bases derived from aliphatic amines: interaction with biomolecules and antimicrobial activity

Schiff bases bearing a sterically hindered phenolic moiety and their Bi(III) complexes were synthesized and characterized by physicochemical, quantum chemical, and biological methods. The compounds were screened in vitro against bacterial and yeast strains. It was found that Bi(III) complexes demonstrate higher antimicrobial activity compared to the parent ligands as well as to the commonly used drug (De-Nol®). Moreover, the antibacterial activity of investigated compounds did not directly correlate with their hemolytic activity, indicating that the antimicrobial effect of Bi(III) complexes cannot be explained solely by their membranolytic properties. Spectrofluorometric studies of the interaction of the Bi(III) complexes with plasma proteins indicate their moderate to high affinity toward BSA and hemoglobin, which is crucial for the determination of their pharmacological profile as well as toxicity assessment. Additionally, molecular docking was performed to predict the possible interaction modes and binding energies of the tested compounds at the molecular level. The results obtained may provide the basis for the design and development of novel Bi(III)-based antimicrobial agents.

Naphthalimide-Buckybowl Tweezer for Selective Recognition of Fullerene C70

Supramolecular tweezers-like receptors represent a simple and efficient approach for the molecular recognition of fullerenes. Straightforward synthesis and easy fine-tuning of their geometry are the advantages that allow one to achieve strong binding and specific selectivity. However, the use of buckybowls in constructing tweezers and incorporating fluorescent dyes is still underexplored. To achieve this goal, we have designed mono- and di-substituted receptors by attaching indacenopicene to a naphthalimide dye. The tweezers-like receptor shows the highest selectivity for C70 with an affinity of 2150 M-1, which is about 50-fold stronger than the recognition of C60. DFT and NMR data indicate that the preferred binding mode involves the ellipsoidal C70 molecule coordinating with buckybowls at its poles. In this arrangement, the naphthalimide core establishes two CH-π interactions with the fullerene. The results indicate that conjugating buckybowls with naphthalimides in a suitable design presents a promising method for selective binding and fine-tuning photoinduced electron transfer in the host-guest complex.

NAD+ modulation with nicotinamide mononucleotide coated 3D printed microneedle implants

Nicotinamide adenine dinucleotide (NAD+) deficiency has been shown to cause pathogenesis of age-related functional decline and diseases. Investigational studies have demonstrated improvements in age-associated pathophysiology and disease conditions. However, invasive methods such as immunohistochemistry, metabolic assays, and polymerase chain reaction currently used to measure cell metabolism render cells unviable and unrecoverable for longitudinal studies and are incompatible with in vivo dynamic observations. We report a non-invasive optical technique to investigate the upregulation of nicotinamide adenine dinucleotide (NAD+) in keratinocytes (both in vitro and ex vivo) upon administration of nicotinamide mononucleotide (NMN) coated microneedle (μNDs) implants. Our technique exploits intrinsic autofluorescence of cells and tissues using multiphoton microscopy. Additionally, μND coating formulations to date have been evaluated using fluorescence microscopy to determine the coated amount, often an imprecise correlation between fluorescence intensity and the coated amount on the μND surface. We also show that rheomechanical attributes of the coating formulation (containing two different viscosity enhancers: sucrose and carboxy methyl cellulose) affect the flow mechanics of the coating formulation at micron scale, and thus the amount of drug coated on the μND surface. In vitro keratinocyte cells were investigated with four concentrations of NMN (50, 250, 500 and 1000 μg), and evaluated with time-dependent NMN (500 μg) treatment at 0, 5, 10, 30, 60, 360 and 1460 min. We demonstrate that intracellular keratinocyte fluorescence of the endogenous NADH shows a decreasing trend in both the average fluorescence lifetime (τm) and the free unbound NADH (τ1), with increasing dosage of NMN administration. A similar trend in the average fluorescence lifetime (τm) of endogenous NAD(P)H was also seen in mouse ear skin ex vivo skin upon administration of NMN. We show a promising, minimally invasive, alternative delivery system for the NAD+ precursor molecule that can enhance patient compliance and therapeutic outcomes.

Exploring the binding interactions of bicalutamide with bovine serum albumin: spectroscopic techniques and molecular modeling studies

The current study employed a variety of spectroscopic methods and molecular modeling to thoroughly look at, under physiological settings, the interaction between bicalutamide (BIC) and bovine serum albumin (BSA). According to our study, the BSA-BIC system's static quenching procedure is supported by the Stern-Volmer quenching constants. The binding constant dropped with temperature, implying that the BSA-BIC complex was weakened. The BSA absorption spectra shifted to a lower wavelength area (from 278 to 272 nm) upon the addition of BIC. The distance (r) between the acceptor and donor in the complex of BIC-BSA and circular dichroism (CD) spectra show the molecular exchanges between BIC and BSA. This study is essential for understanding the therapeutic approach to cancer management through drug distribution and pharmacological effectiveness.

Enhanced or Inhibited Activity of Lipase in Macromolecular Media: Quantification and Prediction

The activity of lipase was inhibited or promoted by different macromolecular colloids, but the underlined general rules were not clear. In this paper, lipase activity was systematically analyzed in different macromolecular media. The detailed factors that affect the enzyme activity were extracted for quantification. Three functions, including viscosity, the crowding effect, and soft interactions, were established to describe the macromolecular medium effect. The medium parameter based on the Huggins constant and Kramer constant was able to characterize the quality of the macromolecular media. A multivariate nonlinear regression model was proposed for the correlation or prediction between three groups of factors and enzyme activity, and a crowding enzyme factor CCef was proposed. This study pioneered the qualification and prediction of the multiple factors that affect the enzyme activity in complex media. It is also significant for scientifically predicting the efficacy of functional macromolecules related to healthy food and the formulation of dietary fibers.

Rendering Proteins Fluorescent Inconspicuously: Genetically Encoded 4-Cyanotryptophan Conserves Their Structure and Enables the Detection of Ligand Binding Sites

Cyanotryptophans (CN-Trp) are privileged multimodal reporters on protein structure. They are similar in size to the canonical amino acid tryptophan and some of them exhibit bright fluorescence which responds sensitively to changes in the environment. We selected aminoacyl-tRNA synthetases specific for 4-, 5-, 6-, and 7-CN-Trp for high-yield in vivo production of proteins with a single, site-specifically introduced nitrile label. The absorption maximum of 4-CN-Trp is distinct from Trp, allowing the selective excitation of its intense fluorescence. 4-CN-Trp fluoresces in the visible range with an intensity rivalling that of 7-hydroxy-coumarin. Crystal structures of maltose binding protein demonstrate near-complete structural conservation when a native buried Trp residue is replaced by 4-CN-Trp. Besides presenting an inconspicuous tag for live cell microscopy, the intense fluorescence of 4-CN-Trp enables measurements of subnanomolar ligand binding affinities in isotropic solution, as demonstrated by the complex between rapamycin and the peptidyl-prolyl isomerase FKBP12 furnished with a 4-CN-Trp residue in the substrate binding pocket. Furthermore, 4-CN-Trp residues positioned at different locations of a protein containing multiple tryptophan residues permits using fluorescence quenching experiments to detect the proximity of individual Trp residues to the binding site of aromatic ligands.

Challenges and Advances in the Encapsulation of Bioactive Ingredients Using Whey Proteins

Functional foods represent an emerging trend in the food industry. Fortifying foods with bioactive ingredients results in health benefits and reduces the risk of disease. Encapsulation techniques protect sensitive ingredients from degradation due to heat, light, moisture and other factors. Among encapsulating materials, milk whey proteins are particularly attractive due to their availability, GRAS status and remarkable ligand-binding ability. Whey protein was once considered a by-product in the dairy industry but is now seen as a promising resource given its natural role as a nutrient carrier. This work reviews the encapsulation systems that employ whey proteins in the food industry. The structural features of β-lactoglobulin (β-LG), the main protein constituent of milk whey, are presented in the context of its ligand-binding properties. Different types of encapsulation systems using whey proteins are discussed, focusing on the recent advances in stable formulations of bioactives using whey protein, alone or in hybrid systems. Whey proteins are a valuable asset capable of binding sensitive bioactive compounds such as vitamins, polyphenols and antioxidants and forming stable complexes that can be formulated as nanoparticles, nanofibrils, emulsions and other micro- and nanostructures. Developing scalable, solid and stable encapsulation systems is identified as a main challenge in the field.

Metal-free production of natural blue colorants through anthocyanin-protein interactions

INTRODUCTION

The scarcity of naturally available sources for blue colorants has driven reliance on synthetic alternatives. Nevertheless, growing health concerns have prompted the development of naturally derived blue colorants, which remains challenging with limited success thus far. Anthocyanins (ACNs) are known for providing blue colors in plants, and metal complexation with acylated ACNs remains the primary strategy to generate stable blue hues. However, this approach can be costly and raise concerns regarding potential metal consumption risks.

OBJECTIVES

Our study aims to introduce a metal-free approach to achieve blue coloration in commonly distributed non-acylated 3-glucoside ACNs by exploring their interactions with proteins and unveiling the underlying mechanisms.

METHODS

Using human serum albumin (HSA) as a model protein, we investigated the structural influences of ACNs on their blue color generation using visible absorption spectroscopy, fluorescence quenching, and molecular simulations. Additionally, we examined the bluing effects of six proteins derived from milk and egg and identified the remarkable roles of bovine serum albumin (BSA) and lysozyme (LYS).

RESULTS

Our findings highlighted the importance of two or more hydroxyl or methoxyl substituents in the B-ring of ACNs for generating blue colors. Cyanidin-, delphinidin- and petunidin-3-glucoside, featuring two neighboring hydroxyl groups in the B-ring, exhibited blue coloration when interacting with HSA or LYS, driven primarily by favorable enthalpy changes. In contrast, malvidin-3-glucoside, with two methoxyl substituents, achieved blue coloration through interactions with HSA or BSA, where entropy change played significant roles.

CONCLUSION

Our work, for the first time, demonstrates the remarkable capability of widely distributed 3-glucoside ACNs to generate diverse blue shades through interactions with certain proteins. This offers a promising and straightforward strategy for the production of ACN-based blue colorants, stimulating further research in this field.

Microplate fluorescence quenching for high throughput screening of affinity constants - Serum albumins and zearalenones case study

Measurements of changes in fluorescence signal is one of the most commonly applied methods for studying protein-ligand affinities. These measurements are generally carried out using cuvettes in spectrofluorometers, which can only measure one sample at a time. This makes screening procedures for multiple ligands and proteins extremely laborious, as each protein must be measured with multiple ligand concentrations, and usually in triplicate. Moreover, multiple equations exist to extract the affinity constants and other information from the data, and their underlying assumptions are often disregarded. In this study, the affinities of human, bovine and rat serum albumins for the mycotoxin zearalenone and five of its common derivatives were measured in 96-well microplates, allowing quick measurements of multiple samples using less reagent amounts. In comparison to measurements using a cuvette in a spectrofluorometer, the microplate method was shown to reproduce the affinity constants accurately. The results were discussed in terms of common pitfalls regarding experimental setup and available equations to analyze protein-ligand binding in fluorescence quenching assays. The commonly used Stern-Volmer equation was discussed in detail and the results used to show how inaccurate it is when a fluorescent protein-ligand complex is formed, and when other underlying approximations are ignored.

Human Serum Albumin and Human Serum Albumin Nanoparticles as Carriers of 10-(2'-Pyrimidyl)-3,6-diazaphenothiazine: In Vitro Spectroscopic Studies

Human serum albumin (HSA) plays a fundamental role in the human body, including the transport of exogenous and endogenous substances. HSA is also a biopolymer with a great medical and pharmaceutical potential. Due to nontoxicity and biocompatibility, this protein can be used as a nanocarrier. 10-(2'-Pyrimidyl)-3,6-diazaphenothiazine (10-Pyr-3,6-DAPT) is a phenothiazine showing high anticancer potential in vitro against glioma, melanoma and breast cancer cells. Additionally, this compound is characterized by selectivity of action towards MCF-7 breast cancer and has low cytotoxicity towards normal cells. Considering the promising pharmacological potential of this compound and using spectroscopic techniques, HSA and human serum albumin nanoparticles (HSA-NP) were tested as carriers of this molecule. Based on the obtained data and the appropriate mathematical models (Stern-Volmer and Klotz models), it can be concluded that 10-Pyr-3,6-DAPT probably forms a weak (Ka = (5.24 ± 0.57) × 104 and Ka = (4.67 ± 0.59) × 104) for excitation wavelengths λex 275 nm and λex 295 nm, respectively) static complex (kq > 1010) with HSA (at Sudlow site II (subdomain IIIA), and the phenomenon of it having both strong therapeutic and toxic effects is possible. High encapsulation efficiency of 10-Pyr-3,6-DAPT into the HSA-NPs was obtained, and the changes in albumin secondary structure due to the presence of 10-Pyr-3,6-DAPT were registered. Based on the data presented, it can be concluded that due to the high toxic effects of 10-Pyr-3,6-DAPT, a better carrier may be HSA-NPs.

In vitro spectroscopic studies of 9-amino-5-alkyl-12(H)-quino[3,4-b][1,4]benzothiazine chloride with main carrier plasma proteins

Current methods of cancer treatment, particularly chemotherapy, are associated with harmful side effects. For this reason, it is significant to study new substances with anticancer potential with the highest possible efficacy and the lowest possible side effects. The aim of the study was the spectroscopic analysis of the interaction between 9-amino-5-alkyl-12(H)-quino[3,4-b][1,4]benzothiazine chloride (Salt3) and main carrier proteins, such as human serum albumin (HSA), α1 acid glycoprotein (AGP), human γ globulin (HGG) and controlled normal serum (CNS). The association constants (Ka [mol·L-1]) and the number of binding site classes (n) for the binding of Salt3 with studied carrier proteins and controlled normal serum were calculated using the Klotz equation. To study HSA and AGP high affinity binding sites, the fluorescent markers were used. Spectral parameter A and the second derivative of differential absorption spectra were used to assess environmental changes around aromatic amino acids residues. The changes in HSA and AGP secondary structure in the complexes with Salt3 were evaluated using the analysis using circular dichroism. Salt3 slightly binds to HSA, AGP, HGG molecules and CNS. In addition, Salt3 affects the tertiary structure of the studied proteins, while it does not damage the secondary structure of the main carrier proteins responsible for Salt3 distribution in the bloodstream. Because Salt3 binds weakly to model carrier proteins and normal control serum, it can lead to both strong therapeutic and toxic effects. Considering these preliminary spectroscopic studies, additional tests as well as expanding research to include other techniques seem justified.

Is Silver a Precious Metal for G-Quadruplex Stabilization Mediated by Porphyrins?

Cancer is a leading cause of death, so continuous efforts into cancer therapy are imperative. In tumor cells, telomerase and oncogene activity are key points for uncontrolled cell growth. Targeting these processes with ligands that inhibit telomerase and/or reduce oncogene expression has been identified as a promising cancer therapy. This study evaluated the selectivity and affinity of the silverII complex of 5,10,15,20-tetrakis(N-methyl-4-pyridinium)porphyrin (AgTMPyP) to stabilize DNA sequences capable of forming G4 structures mimicking the telomeric and oncogene regions, using spectroscopic, biochemical methods and in vitro assays. The tetracationic silver complex was compared with the free base, H2TMPyP, and the zincII complex, ZnTMPyP. The results obtained from UV-Vis and fluorescence methods pointed to a great affinity and good selectivity of AgTMPyP to G4 structures, especially for the oncogene MYC. In general, an increase in the ability of the studied ligands for 1O2 generation when interacting with oncogenic and telomeric G4 sequences was found. The results of the PCR stop assays proved that AgTMPyP has the ability to inhibit Taq polymerase. Additionally, in vitro assays demonstrated that the silverII complex exhibits low cytotoxicity against HaCaT- an immortalized, non-tumorigenic, skin keratinocytes cell line-and, although nonexclusive, AgTMPyP shows nuclear co-localization.

Alternate recognition by dengue protease: Proteolytic and binding assays provide functional evidence beyond an induced-fit

Proteases are key enzymes in viral replication, and interfering with these targets is the basis for therapeutic interventions. We previously introduced a hypothesis about conformational selection in the protease of dengue virus and related flaviviruses, based on conformational plasticity noted in X-ray structures. The present work presents the first functional evidence for alternate recognition by the dengue protease, in a mechanism based primarily on conformational selection rather than induced-fit. Recognition of distinct substrates and inhibitors in proteolytic and binding assays varies to a different extent, depending on factors reported to influence the protease structure. The pH, salinity, buffer type, and temperature cause a change in binding, proteolysis, or inhibition behavior. Using representative inhibitors with distinct structural scaffolds, we identify two contrasting binding profiles to dengue protease. Noticeable effects are observed in the binding assay upon inclusion of a non-ionic detergent in comparison to the proteolytic assay. The findings highlight the impact of the selection of testing conditions on the observed ligand affinity or inhibitory potency. From a broader scope, the dengue protease presents an example, where the induced-fit paradigm appears insufficient to explain binding events with the biological target. Furthermore, this protein reveals the complexity of comparing or combining biochemical assay data obtained under different conditions. This can be particularly critical for artificial intelligence (AI) approaches in drug discovery that rely on large datasets of compounds activity, compiled from different sources using non-identical testing procedures. In such cases, mismatched results will compromise the model quality and its predictive power.

Cytotoxic potential of novel selenolato-bridged manganese(I)-based CORM and its molecular interaction with human serum albumin and DNA through spectroscopic and in silico docking studies

The prevalence of cancer is increasing steadily over the past few decades due to social and environmental factors. Several drugs and medications have also been reported, but with inevitable side effects. Herein comes the urgent need for the development of precision medicine, which increases the efficiency of the drug on the target tissue and minimizes systemic toxicity and non-specificity. One of the several approaches developed includes the formulation of smart or trigger-specific drugs for spatiotemporal delivery. In this view, an arena of carbon monoxide-releasing molecules (CORMs) that could be rendered trigger-specific using labile ligands has been developed. In the present investigation, one such novel, manganese based CORM (Mn-CORM) was synthesized and analysed for its selective cytotoxic potential. The Mn-CORM exerted a broad-spectrum cytotoxicity against cancer cells such as PAN C1 (pancreatic cancer), PC 3 (prostate cancer) and HT 29 (colon cancer). Present study further investigated the binding potential of Mn-CORM for human serum albumin (HSA), the major transporter of anticancer drugs and DNA using a multi-spectroscopic (UV-VIS absorption, quenching analysis, time resolved fluorescence spectroscopy, circular dichroism spectroscopy) and molecular docking techniques. The analysis of thermodynamic parameters ΔS0and ΔH0 showed that the binding of Mn-CORM to HSA was spontaneous and dominated by Van der Waals forces and hydrogen bonding. The binding potential of Mn-CORM for CT DNA was also investigated using spectroscopic studies, dye displacement assay, circular dichroism spectroscopy, thermal denaturation and DNA cleavage studies. Results demonstrated a good binding potential of Mn-CORM for CT DNA. The probable mode of binding of Mn-CORM and CT DNA was concluded to be a partial intercalation. All these experimental and computational results confirmed that the novel Mn-CORM used in the present study can be a promising anticancer agent.

Wheat gliadin/xanthan gum intermolecular complexes: Interaction mechanism and structural characterization

In this study, the interactions between wheat gliadin (GL) and xanthan gum (XG) were investigated to design new systems with potential applications as a gluten-free substitute product. Combining spectral with morphological and molecular docking methods allowed the establishment of the complexation mechanism between globular hydrophobic GL and the hydrophilic XG with an extended and partially disordered backbone. GL maintains intact its hydrophobic core even at high GL/XG ratios and organizes into small aggregate-type assemblies. The stable and uniform complexes have a low GL content, based on intermolecular hydrogen bonds and hydrophobic interactions. The GL/XG combining ratio influences the size, structure and interaction mechanism of the microparticles. The preferred sites of interaction and the binding affinities were determined by molecular docking on GL libraries and XG models. This research may provide significant knowledge for the development of low-GL wheat food products using a dietary fiber polysaccharide as a functional compound.

Probing G-quadruplex-ligand binding using DNA intrinsic fluorescence

G-quadruplexes (G4s) are helical four-stranded nucleic acid structures that can form in guanine-rich sequences, which are mostly found in functional cellular regions, such as telomeres, promoters, and DNA replication origins. Great efforts are being made to target these structures towards the development of specific small molecule G4 binders for novel anti-cancer, neurological, and viral therapies. Here, we introduce an optical assay based on quenching of the intrinsic fluorescence of DNA G-quadruplexes for assessing and comparing the G4 binding affinity of various small molecule ligands in solutions. We show that the approach allows direct quantification of ligand binding to distinctive G4 topologies. We believe that this method will facilitate quick and reliable evaluation of small molecule G4 ligands and support their development.

Ligand binding to proteins - When flawed fluorescence quenching methodology and interpretation become the new norm

Intrinsic protein fluorescence quenching measurements have become a widespread methodology to determine ligand-binding properties of in particular serum albumin. Particularly common is the use of double log equations to extract parameters like binding constant and stoichiometry and/or number of binding sites. In this article we discuss that the methodology has several significant and often unrecognized pitfalls, and the double log equations are improperly derived for their purported use. Using simulations, it is shown that the binding stoichiometry and binding constants obtained using these equations may differ substantially from their true values. In addition, it is illustrated how this methodology, via the use of site markers, is unsuited to determine the binding site of ligands on serum albumin. We thus call for a reassessment of the literature in which this methodology plays a central role in characterizing ligand binding to proteins.

The Role of Medium Polarity in the Efficiency of Albumin Binding with Hydrophobic Ligands: Experimental Studies and a Molecular Dynamics Investigation

This study evaluates how the polarity of the medium affects the binding efficiency of hydrophobic ligands with human serum albumin (HSA). The polarity of the aqueous medium was changed by adding 1,4-dioxane in concentrations of 0%, 10%, and 20% w/w, resulting in solvent mixtures with decreasing dielectric constants (ε = 80, 72, and 63). The addition of 1,4-dioxane did not affect the integrity of the protein, as confirmed by Far-UV-CD, Rayleigh scattering, and time-resolved fluorescence experiments. The impact of medium polarity on the binding constants was evaluated using 1,6-diphenyl-1,3,5-hexatriene (DPH), octyl gallate (OG), quercetin, and rutin as ligands. The association constants of DPH decreased as the medium hydrophobicity increased: at 0%, Ka = 19.8 × 105 M-1; at 10%, Ka = 5.3 × 105 M-1; and at 20%, Ka = 1.7 × 105 M-1. The decrease was still higher using OG: at 0%, Ka = 5.2 × 106 M-1; and at 20%, Ka = 2.2 × 105 M-1. The results in the same direction were obtained using quercetin and rutin as ligands. Molecular dynamics simulations illustrated the hydrophobic effect at the molecular level. The energy barrier for DPH to detach from the protein's hydrophobic site and to move into the bulk solution was higher at 0% (9 kcal/mol) than at 20% 1,4-dioxane (7 kcal/mol). The difference was higher for OG, with 14 and 6 kcal/mol, respectively. Based on these findings, it was shown that the difference in hydrophobicity between the protein's microenvironment and the surrounding solvent is an essential component for the effectiveness of the interaction. These results shed light on albumin-ligand complexation, a molecular interaction that has been extensively studied.

Novel Discrete and Imprinted Fluoride-Selective Sensors: Bridging the Gap from DMSO to Aqueous Samples

Fluoride in drinking water has beneficial or harmful health effects depending on its concentration. This highlights the need for new low-cost and portable sensors capable of in situ monitoring of F- ions. Unfortunately, achieving high levels of water compatibility and fluoride specificity remains a challenge. Here, four new urea-based discrete sensors are prepared and characterized. The sensors containing anthracenyl- (5) and 9H-fluorenyl- (7) signaling units exhibit intense luminescent emissions in dimethyl sulfoxide, the former being particularly sensitive and selective to fluoride. In water, 5 displays a superior sensitivity (871 M-1) and a detection limit (8 µm) below international guidelines, albeit with cross-sensitivity to H2PO4‾. To enhance the performance, 5 and 7 are embedded into a fluoride-imprinted polymeric matrix to give solid-state sensors (5P and 7P, respectively). 5P shows good sensitivity (360 M-1) and specificity in water. Besides, it has a low detection limit (35 µm) and a response linear range (118-6300 µm) encompassing the limit established by the Environmental Protection Agency (211 µm). Furthermore, 5P also displays good reusability and adequate recovery values in real-sample testing (102 ± 2%), constituting the first example of a low-cost anion-imprinted polymeric probe tailored for the selective sensing of fluoride in aqueous samples.

Synthesis and anti-ureolitic activity of Biginelli adducts derived from formylphenyl boronic acids

Urease is a metalloenzyme that contains two Ni(II) ions in its active site and catalyzes the hydrolysis of urea into ammonia and carbon dioxide. The development of effective urease inhibitors is crucial not only for mitigating nitrogen losses in agriculture but also for offering an alternative treatment against infections caused by resistant pathogens that utilize urease as a virulence factor. This study focuses on synthesizing and investigating the urease inhibition potential of Biginelli Adducts bearing a boric acid group. An unsubstituted or hydroxy-substituted boronic group in the Biginelli adducts structure enhances the urease inhibitory activity. Biophysical and kinetics studies revealed that the best Biginelli adduct (4e; IC50 = 132 ± 12 µmol/L) is a mixed inhibitor with higher affinity to the urease active site over an allosteric one. Docking studies confirm the interactions of 4e with residues essential for urease activity and demonstrate its potential to coordinate with the nickel atoms through the oxygen atoms of carbonyl or boronic acid groups. Overall, the Biginelli adduct 4e shows great potential as an additive for developing enhanced efficiency fertilizers and/or for medical applications.

The investigation of the interaction determination between carbendazim and elastase, using both in vitro and in silico methods

Pesticides, including fungicides, are one of the important groups of environmental toxins that affect human and animal health. Studies have shown that these compounds are considered chemical pollutants. Carbendazim is a systemic fungicide. Unfortunately, excessive use of carbendazim has caused environmental pollution all over the world. In this study, the effect of carbendazim on the enzyme elastase (secreted from the endocrine gland of the pancreas) has been investigated. In a study, the performance and reaction of carbendazim with elastase were investigated using spectroscopic techniques. The stability and structure of elastase enzymes were studied under the influence of carbendazim. The results of fluorescence emission and UV-visible absorption spectrum showed that in the presence of carbendazim, there is an increase in UV-Vis absorption and a decrease in the intensity of the intrinsic fluorescence emission in the protein spectrum. Additionally, a decrease in the thermal stability of elastase was observed in the presence of carbendazim. The stability and structure of elastase enzyme were investigated in the presence of carbendazim. The results revealed that the UV-Vis absorption increased due to the presence of carbendazim, as indicated by the hyperchromic spectrum at 220 and 280 nm peaks. Additionally, the intrinsic fluorescence emission in the protein spectrum decreased with increasing carbendazim concentration at three different temperatures (298, 303, and 313 K). Moreover, the study demonstrated that the TM decreased from 2.59 to 4.58 with the increase of carbendazim, suggesting a decrease in the stability of the elastase structure in response to the elevated carbendazim concentration. According to the results of the research, the interaction between elastase and carbendazim has occurred, and changes have been made in the enzyme under the influence of carbendazim. The formation of the complex between elastase and carbendazim was consistent with the results obtained from molecular simulation and confirmed the thermodynamic data.

Interaction of myricetin, ampelopsin (dihydromyricetin), and their sulfate metabolites with serum albumin, cytochrome P450 (CYP2C9, 2C19, and 3A4) enzymes, and organic anion-transporting polypeptides (OATP1B1 and OATP2B1)

Myricetin (MYR) and ampelopsin (AMP, or dihydromyricetin) are flavonoid aglycones found in certain plants and dietary supplements. During the presystemic biotransformation of flavonoids, mainly sulfate and glucuronide derivatives are produced, which are the dominant metabolites in the circulation. In this study, we tested the interactions of MYR, myricetin-3'-O-sulfate (M3'S), AMP, and ampelopsin-4'-O-sulfate (A4'S) with human serum albumin (HSA), cytochrome P450 enzymes (CYPs), and organic anion-transporting polypeptides (OATPs) using in vitro models, including the recently developed method for measuring flavonoid levels in living cells. M3'S and MYR bound to albumin with high affinity, and they showed moderate displacing effects versus the Site I marker warfarin. MYR, M3'S, AMP, and A4'S exerted no or only minor inhibitory effects on CYP2C9, CYP2C19, and CYP3A4 enzymes. M3'S and MYR caused considerable inhibitory actions on OATP1B1 at low micromolar concentrations (IC50 = 1.7 and 6.4 μM, respectively), while even their nanomolar levels resulted in strong inhibitory effects on OATP2B1 (IC50 = 0.3 and 0.4 μM, respectively). In addition, M3'S proved to be a substrate of OATP1B1 and OATP2B1. These results suggest that MYR-containing dietary supplements may affect the OATP-mediated transport of certain drugs, and OATPs are involved in the tissue uptake of M3'S.

Maximizing the Accuracy of Equilibrium Dissociation Constants for Affinity Complexes: From Theory to Practical Recommendations

The equilibrium dissociation constant (Kd) is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of Kd obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of Kd determination to large systematic errors, even when random errors are small. It is imperative to both minimize and quantitatively assess the systematic errors inherent in Kd determination. Traditionally, Kd values are determined through nonlinear regression of binding isotherms. This analysis utilizes three variables: concentrations of two reactants and a fraction R of unbound limiting reactant. The systematic errors in Kd arise directly from systematic errors in these variables. Therefore, to maximize the accuracy of Kd, this study thoroughly analyzes the sources of systematic errors within the three variables, including (i) non-additive signals to calculate R, (ii) mis-calibrated experimental instruments, (iii) inaccurate calibration parameters, (iv) insufficient incubation time, (v) unsaturated binding isotherm, (vi) impurities in the reactants, and (vii) solute adsorption onto surfaces. Through this analysis, we illustrate how each source contributes to inaccuracies in the determination of Kd and propose strategies to minimize these contributions. Additionally, we introduce a method for quantitatively assessing the confidence intervals of systematic errors in concentrations, a crucial step toward quantitatively evaluating the accuracy of Kd. While presenting original findings, this paper also reiterates the fundamentals of Kd determination, hence guiding researchers across all proficiency levels. By shedding light on the sources of systematic errors and offering strategies for their mitigation, our work will help researchers enhance the accuracy of Kd determination, thereby making binding studies more reliable and the conclusions drawn from such studies more robust.

Complexes of soybean protein fibrils and chlorogenic acid: Interaction mechanism and antibacterial activity

This study explored the mechanism of interaction between chlorogenic acid (CA) and protein fibrils (PF) as well as the effects of varying the CA/PF concentration ratio on antibacterial activity. Analysis of various parameters, such as ζ-potential, thioflavin T fluorescence intensity, surface hydrophobicity, and free sulfhydryl groups, revealed that the interaction between PF and CA altered the structure of PF. Fluorescence analysis revealed that hydrogen bonding and hydrophobic interactions were the primary interaction forces causing conformational rearrangement, resulting in a shorter, more flexible, and thicker fibril structure, as observed through transmission electron microscopy. Fourier-transform infrared spectroscopy, small-angle X-ray scattering, and X-ray diffraction analyses revealed that the characteristic fibril structure was destroyed when the CA/PF ratio exceeded 0.05. Notably, the CA-PF complexes inhibited the growth of Escherichia coli and Staphylococcus aureus and also exhibited antioxidant activity. Overall, this study expands the application prospects of CA and PF in the food industry.

A Bis(Acridino)-Crown Ether for Recognizing Oligoamines in Spermine Biosynthesis

Oligoamines in cellular metabolism carry extremely diverse biological functions (i.e., regulating Ca2+-influx, neuronal nitric oxide synthase, membrane potential, Na+, K+-ATPase activity in synaptosomes, etc.). Furthermore, they also act as longevity agents and have a determinative role in autophagy, cell growth, proliferation, and death, while oligoamines dysregulation is a key in a variety of cancers. However, many of their mechanisms of actions have just begun to be understood. In addition to the numerous biosensing methods, only a very few simple small molecule-based tests are available for their selective but reversible tracking or fluorescent labeling. Motivated by this, we present herein a new fluorescent bis(acridino)-crown ether as a sensor molecule for biogenic oligoamines. The sensor molecule can selectively distinguish oligoamines from aliphatic mono- and diamino-analogues, while showing a reversible 1:2 (host:guest) complexation with a stepwise binding process accompanied by a turn-on fluorescence response. Both computational simulations on molecular docking and regression methods on titration experiments were carried out to reveal the oligoamine-recognition properties of the sensor molecule. The new fluorescent chemosensor molecule has a high potential for molecular-level functional studies on the oligoamine systems in cell processes (cellular uptake, transport, progression in cancers, etc.).

Exploring high hydrostatic pressure effects on anthocyanin binding to serum albumin and food-derived transferrins

This study investigated the effects of high hydrostatic pressure (HHP) on the binding interactions of cyanindin-3-O-glucoside (C3G) to bovine serum albumin, human serum albumin (HSA), bovine lactoferrin, and ovotransferrin. Fluorescence quenching revealed that HHP reduced C3G-binding affinity to HSA, while having a largely unaffected role for the other proteins. Notably, pretreating HSA at 500 MPa significantly increased its dissociation constant with C3G from 24.7 to 34.3 μM. Spectroscopic techniques suggested that HSA underwent relatively pronounced tertiary structural alterations after HHP treatments. The C3G-HSA binding mechanisms under pressure were further analyzed through molecular dynamics simulation. The localized structural changes in HSA under pressure might weaken its interaction with C3G, particularly polar interactions such as hydrogen bonds and electrostatic forces, consequently leading to a decreased binding affinity. Overall, the importance of pressure-induced structural alterations in proteins influencing their binding with anthocyanins was highlighted, contributing to optimizing HHP processing for anthocyanin-based products.

In Vitro Evaluation of Antipseudomonal Activity and Safety Profile of Peptidomimetic Furin Inhibitors

Inhibitors of the serine protease furin have been widely studied as antimicrobial agents due to their ability to block the cleavage and activation of certain viral surface proteins and bacterial toxins. In this study, the antipseudomonal effects and safety profiles of the furin inhibitors MI-1851 and MI-2415 were assessed. Fluorescence quenching studies suggested no relevant binding of the compounds to human serum albumin and α1-acid glycoprotein. Both inhibitors demonstrated significant antipseudomonal activity in Madin-Darby canine kidney cells, especially compound MI-1851 at very low concentrations (0.5 µM). Using non-tumorigenic porcine IPEC-J2 cells, neither of the two furin inhibitors induced cytotoxicity (CCK-8 assay) or altered significantly the intracellular (Amplex Red assay) or extracellular (DCFH-DA assay) redox status even at a concentration of 100 µM. The same assays with MI-2415 conducted on primary human hepatocytes also resulted in no changes in cell viability and oxidative stress at up to 100 µM. Microsomal and hepatocyte-based CYP3A4 activity assays showed that both inhibitors exhibited a concentration-dependent inhibition of the isoenzyme at high concentrations. In conclusion, this study indicates a good safety profile of the furin inhibitors MI-1851 and MI-2415, suggesting their applicability as antimicrobials for further in vivo investigations, despite some inhibitory effects on CYP3A4.

Buckybowl Molecular Tweezers for Recognition of Fullerenes

Buckybowl tweezers are a relatively young research area closely associated with the development of non-planar polycyclic aromatic systems and supramolecular chemistry. Since the appearance of the first prototypes in the early 2000s, the tweezers have undergone evolutionary changes. Nowadays they are able to effectively interact with fullerenes and the results opened up prospects for development in the field of sensing, nonlinear optics, and molecular switchers. In the present study, examples of corannulene-based and other buckybowl tweezers for the recognition of C60 and C70 fullerenes were summarized and analyzed. The main structural components of the tweezers were also reviewed in detail and their role in the formation of complexes with fullerenes was evaluated. The revealed structural patterns should trigger the development of novel recognition systems and materials with a wide range of applications.

Fluorescence Spectroscopic Studies to Evaluate Binding Interaction between Hoechst 33258 and Bilirubin

A detailed spectroscopic study (fluorescence, absorption, and lifetime) was conducted to gain insight into the nature of the binding interaction between fluorophore Hoechst33258 (H258) and jaundice marker Bilirubin (Br). The fluorescence emission of the H258 (Ex/Em = 340-502nm) showed a conc. dependent quenching in the presence of Br (1.25 μ M to 10 μ M). The Stern-Volmer constant demonstrated an upward curve depicting the occurrence of both static and dynamic quenching with an acquired value of KSV = 3.1x 103 M- 1 and biomolecular quenching rate constant Kq = 8.6 x 1011 M- 1 S- 1 . The static quenching was evaluated using the sphere of action model and a sphere radius of 0.3nm indicated the presence of a static component in the quenching. The FRET analysis with overlap integral (J) = 1.4x1014 M- 1 cm- 1 nm4 and Foster Radius(R0 ) = 26.82 Å with 59% efficiency suggested occurrence of dynamic quenching. Further studies with the time-resolved fluorescence also indicated the presence of dynamic quenching. The lifetime values of H258 reduced from 3.9ns to 0.5ns. Molecular docking studies further support both static and dynamic components in quenching. A non-covalent interaction of H258 with Br in the presence of HSA is predominantly characterized by H-bonding with residues Lys, Asn, Glu, Gln, and Br. The H258 and Br interaction was within the distance of 3.04 Å, which is in coherence with the sphere of action model (0.3nm) and Van-der-Waals along with hydrophobic interactions, which suggested both static and dynamic quenching. Thus, H258 can serve as an efficient fluorophore to monitor binding interactions and can be further exploited as a suitable probe for investigating conformational changes and detection of Br in subsequent studies.

Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies

Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.

Multiresponsive luminescent metal-organic framework for cooking oil adulteration detection and gallium(III) sensing

A new 3D metal-organic framework {[Cd16(tr2btd)10(dcdps)16(H2O)3(EtOH)]∙15DMF}n (MOF 1, tr2btd = 4,7-di(1,2,4-triazol-1-yl)benzo-2,1,3-thiadiazole, H2dcdps = 4,4'-sulfonyldibenzoic acid) was obtained and its luminescent properties were studied. MOF 1 exhibited bright blue-green luminescence with a high quantum yield of 74 % and luminescence quenching response to a toxic natural polyphenol gossypol and luminescence enhancement response to some trivalent metal cations (Fe3+, Cr3+, Al3+ and Ga3+). The limit of gossypol detection was 0.20 µM and the determination was not interfered by the components of the cottonseed oil. The limit of detection of gallium(III) was 1.1 µM. It was demonstrated that MOF 1 may be used for distinguishing between the genuine sunflower oil and oil adulterated by crude cottonseed oil through qualitative luminescent and quantitative visual gossypol determination.

pH-induced interaction mechanism of zearalenone with zein: Binding characteristics, conformational structure and intermolecular forces

Zein-bound zearalenone (ZEN) complexes are naturally existed in maize by their spontaneous interaction, which significantly impacts the risk assessment of ZEN. Additionally, the pH levels in processing could affect the binding or release of zein-bound ZEN. In this study, pH-induced interaction mechanism of ZEN with zein were studied. Results showed that the acid conditions increased the binding constant (Ka) from 3.46 to 10.0 × 104 L/mol, binding energy from -17.38 to -43.49 kJ mol-1. By increasing hydrophobic interaction and hydrogen bond of ZEN with zein, the binding of ZEN with zein was promoted, forming zein-bound ZEN. Whereas, alkaline conditions decreased the Ka to 1.45 × 104 L/mol and binding energy to 148.48 kJ mol-1, weakened ZEN-zein interaction and stretched zein molecules, resulting the release of ZEN from zein. This study could provide important theoretical basis for perfecting risk assessment and controlling zein-bound ZEN during processing.

In vitro studies of hemoglobin's affinity for the Vitamin B9 and control of its stability character

Vitamin B9, known as folic acid, and hemoglobin play an important biological role in the human body. This study was designed to investigate the nature of the complex through multispectroscopic methods at physiological conditions due to the lack of research on the binding interactions between folic acid and hemoglobin. Structural analysis showed that the interactions between the molecules are mainly hydrophobic with binding constant of 0.73 × 104 L/mol at 37 °C. The secondary structure of the protein was stable after the addition of folic acid with a 20-fold excess of ligand per mol protein. The stability effect of folic acid on hemoglobin was examined as a function of release of iron ions and determination of the level of phenanthroline-Fe2+ complex. The protective function of folic acid was observed at a concentration of 6.12 nmol/L, and the release of iron ions was lower than in the control probe.

Hydroxyl group-induced enhancement of antioxidant activity of resveratrol over pterostilbene by binding to lactoferrin

The reduced antioxidant capacity of trans-resveratrol (Res) than the second generation of Res, namely pterostilbene (Pte), severely prohibits its in-depth intriguing radical-scavenging applications in food formulations. Herein, a unique chemical structure-dependent strategy was proposed to specifically enhance the radical scavenging activity of Res over Pte, relying on the two more hydroxyl groups on the A-benzene ring of Res, thus facilitating its binding with lactoferrin (LF) to form stable complexes through more hydrogen bonds. We prepared LF-Res and LF-Pte complexes, revealed their binding mechanisms by multispectral analysis and molecular docking/dynamics simulations, further evaluated their antioxidant properties via ABTS and DPPH assays and a model of inhibiting apple browning, eventually elucidated their structure-binding-property relationships. This contribution offers a new approach to restore the antioxidant capability of Res, also paves the way to precisely regulate the fascinating bioactivities of hydrophobic compounds by protein-binding in a chemical structure-, especially hydroxyl group-dependent manner.

Revealing the Improved Binding Interaction of Plant Alkaloid Harmaline with Human Hemoglobin in Molecular Crowding Condition

Harmaline and harmine are two structurally similar β-carboline alkaloids with several therapeutic activities, such as anti-inflammatory, antioxidant, neuroprotective, nephroprotective, antidiabetic, and antitumor activities. It has been previously reported that the interaction between harmaline and hemoglobin (Hb) is weak in buffer media compared to harmine. Crowding agents induce a molecular crowding environment in the ex vivo condition, which is almost similar to the intracellular environment. In this present study, we have investigated the nature of the interactions of harmaline and harmine with Hb by increasing the percentage of the crowding agent in buffer solution. The results of the UV-vis and fluorescence spectroscopy analysis have showed that with an increasing proportion of crowding agents, the interaction between harmaline and Hb is steadily improving in comparison to harmine. It has been found that the binding constant of Hb-harmaline reaches 6.82 × 105 M-1 in the 40% polyethylene glycol 200-mediated crowding condition, indicating high affinity compared to very low interaction in buffer media. Steady-state fluorescence anisotropy along with fluorescence lifetime measurements further revealed that the rotational movement of harmaline is maximally restricted by Hb in high crowding environments. Stoichiometry results represent that Hb and harmaline interacts in a 1:1 ratio in different percentages of the crowding agent. The circular dichroism spectroscopic results predict stronger interaction of harmaline with Hb (secondary structure alterations) in a higher crowding environment. From the melting study, it was found that the reactions between Hb and harmaline in crowding environments are endothermic (ΔH > 0) and disordering (ΔS > 0) in nature, indicating that hydrogen bonding and van der Waals interactions are the main interacting forces between Hb and harmaline. Harmaline molecules are more reactive in molecular crowding conditions than in normal buffer condition. This study represents that the interaction between harmaline and Hb is stronger compared to the structurally similar harmine in a molecular crowding environment, which may enlighten the drug discovery process in cell-mimicking conditions.

Synergizing structure and function: Cinnamoyl hydroxamic acids as potent urease inhibitors

The current investigation encompasses the structural planning, synthesis, and evaluation of the urease inhibitory activity of a series of molecular hybrids of hydroxamic acids and Michael acceptors, delineated from the structure of cinnamic acids. The synthesized compounds exhibited potent urease inhibitory effects, with IC50 values ranging from 3.8 to 12.8 µM. Kinetic experiments unveiled that the majority of the synthesized hybrids display characteristics of mixed inhibitors. Generally, derivatives containing electron-withdrawing groups on the aromatic ring demonstrate heightened activity, indicating that the increased electrophilicity of the beta carbon in the Michael Acceptor moiety positively influences the antiureolytic properties of this compounds class. Biophysical and theoretical investigations further corroborated the findings obtained from kinetic assays. These studies suggest that the hydroxamic acid core interacts with the urease active site, while the Michael acceptor moiety binds to one or more allosteric sites adjacent to the active site.

Understanding synchronous regulating effects of starch-protein interactions on starch digestion and retrogradation under thermal shear processing

Although starch-protein interactions have been widely used to regulate starch digestibility and retrogradation during food processings, their synchronous regulating effects on both properties still remain largely unexplored. The effects of interactions with pea protein (PP) under thermal shear processing on the digestion and retrogradation properties of modified chestnut starch were investigated. Results show that thermal shear processing broke starch multi-scale structure, leading to the reduction in molar mass, short-range ordered structure, crystallinity, and starch compactness, in turn increasing starch digestibility and accelerating starch retrogradation. However, PP molecules would interact with chestnut starch through hydrogen bonding to form the starch-protein complexes during thermal shear processing, which caused an increased resistant starch. These starch-protein interactions also inhibited the formation of short-range, long-range ordered structure, aggregate structure during storage, causing a reduced degree of retrogradation. The results provided new insights into the synchronously regulating effects of starch-protein interactions under thermal shear processing on starch digestion and retrogradation, which would facilitate the development of starch-based foods with high nutrition and quality.

Exploring the promising potential of noscapine for cancer and neurodegenerative disease therapy through inhibition of integrin-linked kinase-1

Integrin-linked kinase (ILK), a β1-integrin cytoplasmic domain interacting protein, supports multi-protein complex formation. ILK-1 is involved in neurodegenerative diseases by promoting neuro-inflammation. On the other hand, its overexpression induces epithelial-mesenchymal transition (EMT), which is a major hallmark of cancer and activates various factors associated with a tumorigenic phenotype. Thus, ILK-1 is considered as an attractive therapeutic target. We investigated the binding affinity and ILK-1 inhibitory potential of noscapine (NP) using spectroscopic and docking approaches followed by enzyme inhibition activity. A strong binding affinity of NP was measured for the ILK-1 with estimated Ksv (M-1) values of 1.9 × 105, 3.6 × 105, and 4.0 × 105 and ∆G0 values (kcal/mol) -6.19554, -7.8557 and -8.51976 at 298 K, 303 K, and 305 K, respectively. NP binds to ILK-1 with a docking score of -6.6 kcal/mol and forms strong interactions with active-site pocket residues (Lys220, Arg323, and Asp339). The binding constant for the interaction of NP to ILK-1 was 1.04 × 105 M-1, suggesting strong affinity and excellent ILK-1 inhibitory potential (IC50 of ∼5.23μM). Conformational dynamics of ILK-1 were also studied in the presence of NP. We propose that NP presumably inhibits ILK-1-mediated phosphorylation of various downstream signalling pathways that are involved in cancer cell survival and neuroinflammation.

Detection of Arsenic(V) by Fluorescence Sensing Based on Chlorin e6-Copper Ion

The high toxicity of arsenic (As) can cause irreversible harm to the environment and human health. In this study, the chlorin e6 (Ce6), which emits fluorescence in the infrared region, was introduced as the luminescence center, and the addition of copper ion (Cu2+) and As(V) provoked a regular change in fluorescence at 652 nm, whereas that of As(III) was 665 nm, which was used to optionally detect Cu2+, arsenic (As(III), and As(V)). The limit of detection (LOD) values were 0.212 μM, 0.089 ppm, and 1.375 ppb for Cu2+, As(III), and As(V), respectively. The developed method can be used to determine Cu2+ and arsenic in water and soil with good sensitivity and selectivity. The 1:1 stoichiometry of Ce6 with Cu2+ was obtained from the Job plot that was developed from UV-visible spectra. The binding constants for Cu2+ and As(V) were established to be 1.248 × 105 M-1 and 2.35 × 1012 M-2, respectively, using B-H (Benesi-Hildebrand) plots. Fluorescence lifetimes, B-H plots, FT-IR, and 1H-NMR were used to postulate the mechanism of Cu2+ fluorescence quenching and As(V) fluorescence restoration and the interactions of the two ions with the Ce6 molecule.

Understanding protein-nanoparticle interactions leading to protein corona formation: In vitro - in vivo correlation study

Nanoparticles (NPs) in contact with biological fluids form a biomolecular corona through interactions with proteins, lipids, and sugars, acquiring new physicochemical properties. This work explores the interaction between selected proteins (hemoglobin and fetuin-A) that may alter NP circulation time and NPs of different surface charges (neutral, positive, and negative). The interaction with key proteins albumin and transferrin, the two of the most abundant proteins in plasma was also studied. Binding affinity was investigated using quartz crystal microbalance and fluorescence quenching, while circular dichroism assessed potential conformational changes. The data obtained from in vitro experiments were compared to in vivo protein corona data. The results indicate that electrostatic interactions primarily drive protein-NP interactions, and higher binding affinity does not necessarily translate into more significant structural changes. In vitro and single protein-NP studies provide valuable insights that can be correlated with in vivo observations, opening exciting possibilities for future protein corona studies.

Elucidating binding mechanisms of naringenin by alpha-chymotrypsin: Insights into non-binding interactions and complex formation

As an inevitable parameter in the description of enzyme properties, the investigation of enzyme-ligand interactions has attracted a lot of attention. Alpha-Chymotrypsin (α-Chy) is essential for protein digestion and plays an important role in human health. Naringenin (NAG) as a potent antioxidant has recently been applied in the pharmaceutical industry. Using multispectral methods and computational simulation techniques, the binding strength of NAG to α-Chy was investigated in this research. UV-vis and fluorescence quenching data showed significant spectral changes upon binding of NAG to α-Chy. As demonstrated by fluorescence techniques, NAG could employ a static quenching process to decrease the intrinsic fluorescence of α-Chy. Both circular dichroism (CD) and FTIR spectroscopic analyses revealed that binding of NAG to α-Chy caused more flexible conformation. The slight increases in RMSD (0.06 nm) were observed for the NAG-(α-Chy) compound was supported by the results of thermal stability data. Docking computation confirmed that hydrogen and Van der Waals interactions are the important forces, which is in exact agreement with thermodynamics studies. Kinetic analysis of the enzyme showed an increase in activity, which was consistent, with the MD simulation results. The findings from the in-silico studies were in complete agreement with the experimental results.

Structural changes and anti-hepatocellular carcinoma activity of interferon-γ after interaction with sinensetin

Exploring the interaction of small molecules with therapeutic proteins can provide useful information about development of ligand-protein complexes as synergistically therapeutic platforms. In this study, the interaction of sinensetin with human interferon gamma (IFNγ) was evaluated experimentally and theoretically. Also, the synergistic effects of IFNγ- sinensetin complex on the inhibition of hepatocellular carcinoma HepG2 cell proliferation were assessed by cell viability and quantitative real time PCR assays. It was realized that sinensetin interacts with IFNγ through a static quenching mechanism and hydrophobic forces mediated by presence of Lys55 and Lys58 amino acid residues in the binding site were the main contributing forces in the spontaneous formation of IFNγ-sinensetin complex. Also, the interaction of sinensetin with IFNγ did not induce a significant change in the secondary and tertiary structure of the protein. Cellular assays revealed a synergistic effect of sinensetin on IFNγ -triggered anticancer action in HepG2 cells through overexpression of caspase-3 mRNA and protein. In conclusion, this study may hold great promise for the development of potential ligand- protein complexes for therapeutic purposes.