Characterization of binding interactions between selected phenylpropanoid glycosides and trypsin

Comparison of ovalbumin glycation induced by high-temperature steaming and high-temperature baking: A study combining conventional spectroscopy with high-resolution mass spectrometry

High-temperature steaming (HTS) and high-temperature baking (HTB)-induced ovalbumin (OVA)-glucose glycation (140 °C, 1-3 min) were compared, and the different mechanisms were evaluated by changes in protein conformation, glycation sites and average degree of substitution per peptide molecule (DSP) values as well as the antioxidant activity of glycated OVA. Conventional spectroscopic results suggested that in comparison with HTB, HTS promoted protein expansion, increased β-sheet content and made OVA structure more orderly. Liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis showed that 10 glycation sites were found under HTB, while 4 new glycation sites R111, R200, R219 and K323 appeared under HTS, and 2 of them (R219 and K323) were located in internal β-sheet chains. The antioxidant activities of glycated OVA increased with increasing treatment time, and HTS showed stronger enhancement effect than HTB. Furthermore, the DSP values were generally higher under HTS than HTB. Compared with HTB, HTS with high penetrability could enhance the change of OVA primary structure and spatial conformation, making the protein structure more unfolded and stable, leading to more protein-sugar collisions occurred in inner OVA molecular and significantly promoted glycation. In conclusion, HTS is a promising method for high-temperature short-time glycation reaction, with drastically increasing the protein antioxidant activities.

Effects of combined binding of chlorogenic acid/caffeic acid and gallic acid to trypsin on their synergistic antioxidant activity, enzyme activity and stability

The combined application of multiple natural polyphenols in functional foods may provide better health benefits. The binding of polyphenols with different structures to proteins will affect their respective functions. Spectroscopy and molecular docking were used to investigate the competitive binding of chlorogenic acid (CGA)/caffeic acid (CA) and gallic acid (GA) to trypsin. The effects of different molecular structures and the order of adding the three phenolic acids on the binding were assessed. The stability of trypsin and its docked complexes with CGA/CA/GA was evaluated by molecular dynamics simulation. The effects of the binding process on the activity and thermal stability of trypsin, as well as on the antioxidant activity and stability of CGA/CA/GA were explored. The competitive binding of CGA/CA and GA to trypsin affected their synergistic antioxidant effects. The results may provide a reference for the combined application of CGA/CA and GA in food and pharmaceutical fields.

Application of Molecular Simulation Methods in Food Science: Status and Prospects

Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.

Investigation on conformational variation and enzymatic activity of trypsin affected by Ti3C2 QDs via spectroscopic technique and molecular modeling

In this paper, Ti₃C₂ quantum dots (Ti₃C₂ QDs) were synthesized by simply treating Ti₃C₂ MXene powder with acid and base via hydrothermal method. Ti₃C₂ QDs exhibited superior fluorescence property and were used for the fluorescent imaging of living HeLa cells successfully. In order to evaluate the influence of Ti₃C₂ QDs on protease with specific biological functions, binding interaction of Ti₃C₂ QDs with trypsin was studied comprehensively and deeply through spectroscopic strategies and molecular modeling technique. The intrinsic fluorescence of trypsin was spontaneously quenched by Ti₃C₂ QDs through static quenching mode under van der Waals interaction force, and Ti₃C₂ QDs bound with the inactive residue domain of trypsin firmly with stoichiometric ratio of 1:1. Ti₃C₂ QDs induced the microenvironmental variation of the amino acid residues in trypsin, reducing the thermal stability of trypsin significantly. Gel electrophoresis experiments and microscopic imaging experiments demonstrated that Ti₃C₂ QDs inhibited the enzymatic activity of trypsin on the digestion of human serum albumin and HeLa cells obviously. These results revealed not only the deep interaction mechanism between Ti₃C₂ QDs and protease but also the influence of Ti₃C₂ QDs on the enzymatic activity of trypsin, paving the way for the safe biological application of Ti₃C₂ QDs in the diagnosis and the therapy of protease-related diseases.

Validation of Deep Learning-Based DFCNN in Extremely Large-Scale Virtual Screening and Application in Trypsin I Protease Inhibitor Discovery

Computational methods with affordable computational resources are highly desirable for identifying active drug leads from millions of compounds. This requires a model that is both highly efficient and relatively accurate, which cannot be achieved by most of the current methods. In real virtual screening (VS) application scenarios, the desired method should perform much better in selecting active compounds by prediction than by random chance. Here, we systematically evaluate the performance of our previously developed DFCNN model in large-scale virtual screening, and the results show our method has approximately 22 times the success rate compared to the random chance on average with a score cutoff of 0.99. Of the 102 test cases, 10 cases have more than 98 times the success rate of a random guess. Interestingly, in three cases, the prediction success rate is 99 times that of a random guess by a score cutoff of 0.99. This indicates that in most situations after our extremely large-scale VS, the dataset can be reduced 20 to 100 times for the next step of virtual screening based on docking or MD simulation. Furthermore, we have employed an experimental method to verify our computational method by finding several activity inhibitors for Trypsin I Protease. In addition, we also show its proof-of-concept application in de novo drug screening. The results indicate the massive potential of this method in the first step of the real drug development workflow. Moreover, DFCNN only takes about 0.0000225s for one protein–compound prediction on average with 80 Intel CPU cores (2.00 GHz) and 60 GB RAM, which is at least tens of thousands of times faster than AutoDock Vina or Schrödinger high-throughput virtual screening. Additionally, an online webserver based on DFCNN for large-scale screening is available at http://cbblab.siat.ac.cn/DFCNN/index.php for the convenience of the users.

Interactions between puerarin/daidzein and micellar casein

Puerarin (PUE) and daidzein (DAI) are polyphenols with extensive biological activities. In the present study, the interactions between PUE/DAI and micellar casein (MC) were investigated, and the physicochemical properties of their complexes were analyzed. The results of fluorescence spectrum analysis and molecular docking revealed that the main interactions between DAI and MC were hydrophobic forces, while that between PUE and MC was hydrogen bonding. The FTIR and XRD analyses confirmed the formation of complexes between MC and PUE/DAI. After binding to PUE/DAI, the size of MC increased. The weight loss rate of MC decreased after complexing with PUE/DAI, but its morphology was not extensively modified. The DPPH radical scavenging capacities of PUE-MC and DAI-MC complexes were higher than those of free PUE/DAI in both water and ethanol. In vitro release experiments showed that the release rate of PUE/DAI was inhibited by MC under simulated intestinal conditions. PRACTICAL APPLICATIONS: The low water solubility and poor bioavailability of PUE and DAI limit their application. Micellar casein has high affinity for PUE and DAI. After encapsulated by micellar casein, the release rates of PUE and DAI were prolonged during simulated intestinal digestion. The results would provide useful information for improving the solubility and bioavailability of PUE and DAI, and broadening the use of them in the food and pharmaceutical industry.

A review on the structure and pharmacological activity of phenylethanoid glycosides

Phenylethanoid glycosides (PhGs) are compounds made of phenylethyl alcohol, caffeic acid and glycosyl moieties. The first published references about phenylethanoid glycosides concerned the isolation of echinacoside from Echinaceu ungustifolia (Asteraceae) in 1950 and verbascoside from Verbascum sinuatum (Scrophulariaceae) in 1963. Over the past 60 years, many compounds with these structural characteristics have been isolated from natural sources, and most of these compounds possess significant bioactivities, including antibacterial, antitumor, antiviral, anti-inflammatory, neuro-protective, antioxidant, hepatoprotective, and immunomodulatory activities, among others. In this review, we will summarize the phenylethanoid glycosides described in recent papers and list all the compounds that have been isolated over the past few decades. We will also attempt to present and assess recent studies about the separation, extraction, determination, and pharmacological activity of the excellent natural components, phenylethanoid glycosides.

Evaluation inhibitory activity of catechins on trypsin by capillary electrophoresis-based immobilized enzyme microreactor with chromogenic substrate

In this study, a capillary electrophoresis-based online immobilized enzyme microreactor was developed for evaluating the inhibitory activity of green tea catechins and tea polyphenol extracts on trypsin. The immobilized trypsin activity and other kinetic parameters were evaluated by measuring the peak area of the hydrolyzate of chromogenic substrate S-2765. The results indicated that the activity of the immobilized trypsin remained approximately 90.0% of the initial immobilized enzyme activity after 30 runs. The value of Michaelis-Menten constant (K_m ) was (0.47 ± 0.08) mM, and the half-maximal inhibitory concentration (IC₅₀ ) and inhibition constant (K_i ) of benzamidine were measured as 3.34 and 3.00 mM, respectively. Then, the inhibitory activity of four main catechins (epicatechin, epigallocatechin, epicatechin gallate, and epigallocatechin gallate) and three tea polyphenol extracts (green tea, white tea, and black tea) on trypsin were investigated. The results showed that four catechins and three tea polyphenol extracts had potential trypsin inhibitory activity. In addition, molecular docking results illustrated that epigallocatechin gallate, epicatechin gallate, epicatechin, and epigallocatechin were all located not only in the catalytic cavity, but also in the substrate-binding pocket of trypsin. These results indicated that the developed method is an effective tool for evaluating inhibitory activity of catechins on trypsin.

FTIR Spectroscopy Study of the Secondary Structure Changes in Human Serum Albumin and Trypsin under Neutral Salts

The effect of neutral salts on protein conformation was first analyzed by Hofmeister in 1888, however, even today this phenomenon is not completely understood. To clarify this effect, we studied changes in the secondary structure of two proteins: human serum albumin with predominantly α-helical structure and porcine pancreas β-trypsin with the typical β-structural arrangement in aqueous solutions of neutral salts (KSCN, KCl, (NH₄)₂SO₄). The changes in the secondary structure were studied at 23 °C and 80 °C by using the second derivative deconvolution method of the IR spectra. Our results demonstrated that the ability of the salts to stabilize/destabilize these two proteins correlates with the Hofmeister series of ions. At the same time, some exceptions were also observed. The destabilization of the native structures of both α-helical albumin and β-structural trypsin upon interaction with neutral salts leads to the formation of intermolecular β-sheets typical for amyloid fibrils or amorphous aggregates. Thus, our quantitative FTIR-spectroscopy analysis allowed us to further clarify the mechanisms and complexity of the neutral salt actions on protein structures which may lead to strategies preventing unwelcome misfolding of proteins.

Effect of ultrasound on binding interaction between emodin and micellar casein and its microencapsulation at various temperatures

Emodin is a bioactive compound with strong anti-inflammatory and antioxidant properties. Micellar casein is casein concentrates close to the native state of casein micelles. The interaction of emodin and micellar casein under heat treatment in the absence and presence of ultrasound was investigated, and the properties of microencapsulated emodin in micellar casein were compared. Fluorescence experiments proved that the major interaction between emodin and micellar casein was through hydrophobic forces under heat treatment in the absence and presence of ultrasound. However, ΔH, ΔS and ΔG of emodin-casein complexation without sonication were higher than those with sonication, in contradiction to binding constants. The particle sizes of emodin-casein complexes in the presence of ultrasound were smaller than those without sonication, while the specific surface area showed an opposite trend. As to encapsulation, emodin-casein capsules under heat-sonication treatment showed higher antioxidant properties than those of heat treatment alone under similar experimental conditions. Interestingly, micellar casein-emodin encapsulation in the presence of ultrasound showed a lower release rate of emodin in gastrointestinal conditions than that without ultrasound at the emdoin concentration of 10 μmol per gram casein. Ultrasound has been shown to be a potential processing technology for customizing the release kinetics of bioactive compounds.

On-line immobilized trypsin microreactor for evaluating inhibitory activity of phenolic acids by capillary electrophoresis and molecular docking

Phenolic acids, which are important aromatic secondary metabolites, are widely distributed in plant foods. In this study, a simple, economical and fast on-line immobilized trypsin microreactor was developed for evaluating the inhibitory activity of phenolic acids by capillary electrophoresis. The Michaelis-Menten constant (K_m) of immobilized trypsin was determined as 0.99 mM, and the half-maximal inhibitory concentration (IC₅₀) and inhibition constant (K_i) of benzamidine were measured as 3.39 and 1.68 mM, respectively. Then, the developed strategy was applied to investigate the inhibitory activity of six phenolic acids on trypsin. The results showed that gallic acid, caffeic acid and ferulic acid had high inhibitory activity at concentration of 150 μM. Molecular docking results illustrated that gallic acid, caffeic acid and ferulic acid can interact indirectly with the catalytic and substrate-binding sites of trypsin. The developed strategy is an effective tool for evaluating inhibitory activity of phenolic acids on trypsin.

Effect of Covalent Interaction with Chlorogenic Acid on the Allergenic Capacity of Ovalbumin

Ovalbumin (OVA) is a major allergen in avian egg white. Here, we investigated the conjugation of OVA and chlorogenic acid (CHA) to reduce the allergenic capacity of OVA. OVA-CHA conjugate was characterized by SDS-PAGE, MALDI-TOF-MS, differential scanning calorimetry, and multispectroscopic methods. Sites of the OVA-CHA conjugate were identified by LC-MS/MS. CHA possibly conjugated with Lys20 and Lys17 in OVA, which resulted in the unfolding of OVA. ELISA and Western blot assay indicated that the OVA-CHA conjugate reduced the IgE binding capacity of OVA. The results also indicated that the ability of the OVA-CHA conjugate to activate histamine release was reduced. The decreased allergenic capacity of OVA was attributed to changes in the protein structure. Moreover, the CHA binding site in OVA might directly shield the linear IgE epitope, thereby reducing the IgE binding ability. Also, the OVA-CHA conjugate showed high antioxidant activity. OVA conjugated with CHA may be a promising method of OVA hyposensitization.

Trypsin inhibition by Ligupurpuroside B as studied using spectroscopic, CD, and molecular docking techniques

It is well known that Ligupurpuroside B is a water-soluble polyphenolic compound and used to brew bitter tea with antioxidant activities. It acted as a stimulant to the central nervous system and a diuretic (increase the excretion of urine), was used to treat painful throat and high blood pressure, and also exerted weight-loss function. In this regard, a detailed investigation on the mechanism of interaction between Ligupurpuroside B and trypsin could be of great interest to know the pharmacokinetic behavior of Ligupurpuroside B and for the design of new analogues with effective pharmacological properties. Ligupurpuroside B successfully quenched the intrinsic fluorescence of trypsin via static quenching mechanism. The binding constants (K_a) at three temperatures (288, 298, and 308 K) were 1.7841 × 10⁴, 1.6251 × 10⁴ and 1.5483 × 10⁴ L mol^-1, respectively. Binding constants revealed the stronger binding interaction between Ligupurpuroside B and trypsin. The number of binding sites approximated to one, indicating a single class of binding for Ligupurpuroside B in trypsin. The enzyme activity result suggested that Ligupurpuroside B can inhibit trypsin activity. Thermodynamic results revealed that both hydrogen bonds and hydrophobic interactions play main roles in stabilization of Ligupurpuroside B-trypsin complex. Circular dichroism (CD) results showed that the conformation of trypsin changed after bound to ligupurpuroside B. Molecular docking indicated that Ligupurpuroside B can enter the hydrophobic cavity of trypsin and was located near Trp215 and Tyr228 of trypsin. Communicated by Ramaswamy H. Sarma.

Studies of the binding properties of the food preservative thiabendazole to DNA by computer simulations and NMR relaxation

Thiabendazole (TBZ) is a commonly used food preservative and has a wide range of anthelmintic properties. In this study, computer simulations and experiments were conducted to investigate the interaction mechanism of TBZ and herring sperm DNA (hsDNA) at the molecular level. Molecular docking showed that TBZ interacted with DNA in groove mode and bound in A-T and C-G base pair regions. Molecular dynamics (MD) was used to evaluate the stability of the TBZ-DNA complex and found that the three phases in MD and the hydrogen bonds helped maintain the combination. NMR relaxation indicated that TBZ had a certain affinity to hsDNA with a binding constant of 462.43 L mol-1, and the thiazole ring was the main group bound with DNA. Results obtained from fluorescence experiments showed that the binding of TBZ and hsDNA was predominantly driven by enthalpy through a static quenching mechanism. Circular dichroism and viscosity measurements proved the groove binding mode. The FTIR results clarified the conformational changes of DNA, that the DNA helix became shorter and compact, and the DNA structure transformed from B-form to A-form.