Exploring the interactions of naringenin and naringin with trypsin and pepsin: Experimental and computational modeling approaches

Investigating the impact of common migration substances found in milk packaging on proteases: A multispectral and molecular docking approach

The effects of common migration substances in milk packaging on digestive protease were studied. We choose the common migrants found in eight types of multi-layer composite milk packaging. Enzyme activity experiments revealed that pepsin activity decreased by approximately 18 % at 500 μg/mL of stearic acid and stearamide treatment, while trypsin activity decreased by approximately 18 % only by stearic acid treatment (500 μg/mL). Subsequently, fluorescence spectroscopy, circular dichroism spectroscopy, and molecular docking technology were employed to investigate the inhibition mechanism of protease activity by migrating substances in three systems: stearic acid-trypsin, stearic acid-pepsin, and stearamide-pepsin. Results showed that the inhibitory effect of stearic acid on trypsin is a reversible mixed inhibition, whereas the inhibitory effects of stearic acid and stearamide on pepsin are non-competitive. In all three systems, ΔH < 0, ΔS < 0, and ΔG < 0, indicating the binding process between the migrant and the protease is a spontaneous exothermic process primarily driven by hydrogen bonding and van der Waals forces. In addition, their binding constants are all around 104 L/moL, indicating that there are moderate binding affinities exist between migrants and proteases. The binding process results in the quenching of the protease's endogenous fluorescence and induces alterations in the enzyme's secondary structure. Synchronized fluorescence spectroscopy showed that stearic acid enhanced the hydrophobicity near the Tyr residue of trypsin. The molecular docking results indicated that the binding affinity of stearic acid-trypsin, stearic acid-pepsin, and stearamide-pepsin was -22.51 kJ/mol, -12.35 kJ/mol, -19.28 kJ/mol respectively, which consistent with the trend in the enzyme activity results. This study can provide references for the selection of milk packaging materials and the use of processing additives, ensuring food health and safety.

Interaction of major saffron constituent safranal with trypsin: An experimental and computational investigation

Trypsin is a serine protease, an important digestive enzyme that digests the proteins in the small intestine. In the present study, we have investigated the interaction of safranal, a major saffron metabolite, with trypsin using spectroscopic and molecular docking analyses. Fluorescence emission spectra of trypsin were largely affected by the inner filter effect from safranal; that's why these were corrected using the standard procedure. The corrected fluorescence spectra have shown that the safranal quenched the intrinsic fluorescence of trypsin with a blue shift in the wavelength of emission maximum, which revealed that the microenvironment of the fluorophore became more hydrophobic. There was approximately 1: 1 fair binding between them, which increased with a rise in temperature. The interaction was favored, principally, by hydrophobic forces, and there was an efficient energy transfer from the fluorophore to the safranal. Synchronous fluorescence spectra suggested that the tryptophan residues were the major ones taking part in the fluorescence quenching of trypsin. Safranal also influenced the secondary structure of trypsin and caused partial unfolding. Molecular Docking and the Molecular Dynamics simulation of the free and complexed trypsin was also carried out. Safranal formed a stable, non-covalent complex within the S2'-S5' subsite. Moreover, two nearby tyrosine residues (Tyr39 and Tyr151) stabilized safranal through π-π interactions. Additionally, the presence of safranal led to changes in the protein flexibility and compactness, which could indicate changes in the surrounding of tryptophan residues, impacting their fluorescence. Furthermore, a loss in compactness is in line with the partial unfolding observed experimentally. Thus, both experimental and computational studies were in good agreement with each other.

Self-Assembled Aggregated Structures of Natural Products for Oral Drug Delivery

The self-assembling aggregated structures of natural products have gained significant interest due to their simple synthesis, lack of carrier-related toxicity, and excellent biological efficacy. However, the mechanisms of their assembly and their ability to traverse the gastrointestinal (GI) barrier remain unclear. This review summarizes various intermolecular non-covalent interactions and aggregated structures, drawing on research indexed in Web of Science from 2010 to 2024. Cheminformatics analysis of the self-assembly behaviors of natural small molecules and their supramolecular aggregates reveals assembly-favorable conditions, aiding drug formulation. Additionally, the review explores the self-assembly properties of macromolecules like polysaccharides, proteins, and exosomes, highlighting their role in drug delivery. Strategies to overcome gastrointestinal barriers and enhance drug bioavailability are also discussed. This work underscores the potential of natural products in oral drug delivery and offers insights for designing more effective drug delivery systems.

The essential role of aggregation for the emulsifying ability of a fungal CYS-rich protein

Biosurfactants are in demand by the global market as natural commodities suitable for incorporation into commercial products or utilization in environmental applications. Fungi are promising producers of these molecules and have garnered interest also for their metabolic capabilities in efficiently utilizing recalcitrant and complex substrates, like hydrocarbons, plastic, etc. Within this framework, biosurfactants produced by two Fusarium solani fungal strains, isolated from plastic waste-contaminated landfill soils, were analyzed. Mycelia of these fungi were grown in the presence of 5% olive oil to drive biosurfactant production. The characterization of the emulsifying and surfactant capacity of these extracts highlighted that two different components are involved. A protein was purified and identified as a CFEM (common in fungal extracellular membrane) containing domain, revealing a good propensity to stabilize emulsions only in its aggregate form. On the other hand, an unidentified cationic smaller molecule exhibits the ability to reduce surface tension. Based on the 3D structural model of the protein, a plausible mechanism for the formation of very stable aggregates, endowed with the emulsifying ability, is proposed. KEY POINTS: • Two Fusarium solani strains are analyzed for their surfactant production. • A cationic surfactant is produced, exhibiting the ability to remarkably reduce surface tension. • An identified protein reveals a good propensity to stabilize emulsions only in its aggregate form.

Probing the toxic effect of chlorpyrifos as an environmental pollutant on the structure and biological activity of lysozyme under physiological conditions

The pervasive use of pesticides like chlorpyrifos (CPY) has been associated with deleterious effects on biomolecules, posing significant risks to environmental integrity, public health, and overall ecosystem equilibrium. Accordingly, in this study, we investigated the potential binding interaction between the well-conserved enzyme, lysozyme (LSZ), and CPY through various spectroscopic techniques and molecular modeling. The UV-vis absorption and fluorescence experiments confirmed the complex formation and static quenching of the intrinsic fluorescence intensity. LSZ revealed a singular binding site for CPY, with binding constants around 105 M-1 across different temperature ranges. Analysis of thermodynamic parameters showed the spontaneous nature of the complexation process, while also revealing the pivotal role of hydrophobic interactions in stabilizing the LSZ-CPY system. According to circular dichroism and Fourier transform infrared studies, CPY binding changed the secondary structure of LSZ by boosting α-helix presence and reducing the levels of β-sheet and β-turn content. Further, CPY decreased the stability and activity of LSZ. Computational docking delineated the specific and highly preferred binding site of CPY within the structure of LSZ. Molecular dynamic simulation indicated the enduring stability of the LSZ/CPY complex and revealed structural modifications in the LSZ after binding with CPY. This research provides a detailed understanding of the intermolecular dynamics between CPY and LSZ, concurrently elucidating the molecular-level implications for the potential hazards of pesticides in the natural environment.

S. Marinho V, H. Holanda F, M. Ferreira I, Oliveira da Silva E. Polymeric nanoparticles containing kojic acid induce structural alterations and apoptosis-like death in Leishmania (Leishmania) amazonensis

Leishmaniasis encompasses a cluster of neglected tropical diseases triggered by kinetoplastid phatogens belonging to the genus Leishmania. Current therapeutic approaches are toxic, expensive, and require long-term treatment. Nanoparticles are emerging as a new alternative for the treatment of neglected tropical diseases. Silk Fibroin is a biocompatible and amphiphilic protein that can be used for formulating nanoemulsions, while kojic acid is a secondary metabolite with antileishmanial actions. Thus, this study evaluated the efficacy of a nanoemulsion, formulated with silk fibroin as the surfactant and containing kojic acid (NanoFKA), against promastigote and amastigote forms of Leishmania (Leishmania) amazonensis. The NanoFKA had an average particle size of 176 nm, Polydispersity Index (PDI) of 0.370, and a Zeta Potential of -32.3 mV. It presented inhibitory concentration (IC50) values of >56 μg/mL and >7 μg/mL for the promastigote and amastigote forms, respectively. Ultrastructural analysis, cell cycle distribution and phosphatidylserine exposure showed that NanoFKA treatment induces apoptosis-like cell death and cell cycle arrest in L. (L.) amazonensis. In addition, NanoFKA exhibited no cytotoxicity against macrophages. Given these results, NanoFKA present leishmanicidal activity against L. (L.) amazonensis.

Spectroscopic and molecular docking study of three kinds of cinnamic acid interaction with pepsin

In this work, under simulated physiological conditions (pH = 2.2, glycine hydrochloric acid buffer solution), the interactions of cinnamic acid (CA), m-hydroxycinnamic acid (m-CA) and p-hydroxycinnamic acid (p-CA) with pepsin were studied by fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy, circular dichroism (CD) spectroscopy, Fourier transform infrared spectroscopy (FTIR), molecular docking and molecular dynamic simulation (MD). The spectrogram results showed that these three kinds of CA had a strong ability to quench the intrinsic fluorescence of pepsin, and the quenching effects were obvious with the increase of concentration of these three kinds of molecules. The quenching mechanism of CA, m-CA and p-CA on the fluorescence of pepsin was static quenching. In addition, a stable complex was formed between three kinds of CA with pepsin. Thermodynamic data and docking information suggested that three kinds of CA combine with pepsin were mainly driven by electrostatic force and hydrogen bond. The binding constant and the number of binding sites were determined. The interaction of CA, m-CA and p-CA with pepsin was spontaneous, and accompanied by non-radiative energy transfer. The results from CD, FTIR, UV-Vis and synchronous fluorescence spectra measurements manifested that the secondary structure of pepsin was changed by the binding of three kinds of CA. The β-sheet of pepsin increased after the interaction with three kinds of CA. The assay results of pepsin activity showed that three kinds of CA led to a decrease in pepsin activity within the investigated concentrations. Molecular docking investigation revealed the formation of polar hydrogen bonds as well as hydrophobic interactions between three kinds of CA with pepsin, and the ligand within the binding pocket of pepsin. MD results implied the formation of a stable complex between three kinds of CA and pepsin. The research suggested that cinnamic acid and its derivatives could be a potential effect on the structure and properties of digestive enzyme.

New insights on the binding of butyl-paraben to trypsin: experimental and computational approaches

Butyl-paraben (BP) is one of the most widely used preservatives in numerous foodstuffs, skin care products, and a variety of drugs, and trypsin is the main digestive enzyme, the research on the binding between the two is essential for human health. In the present paper, the effect of BP on trypsin has been explored using experimental and computational techniques to evaluate BP toxicity at the protein level. The obtained results from molecular docking and kinetic assay revealed BP was embedded in the hydrophobic cavity-S1 binding pocket of the enzyme to inhibit its activity by a competitive model. Intrinsic fluorescence of trypsin after interaction with BP revealed the static mode of quenching. FRET indicated that the distance of the enzyme to BP is 1.89 nm with high energy efficiency. Thermodynamic results proved that BP spontaneously bound to trypsin in an enthalpy-driven manner, the van der Waals interactions and H-bonds serving as the predominant forces in binding processes. CD spectroscopy and molecular dynamics (MD) simulation revealed that the trypsin structure transformed from the β-Sheet structure to the unordered Coil structure upon interacting with BP. Resonance light scattering (RLS), synchronous fluorescence, and three-dimensional (3 D) spectroscopies further supported the alteration in the conformation of trypsin. Differential scanning calorimetry (DSC) showed that trypsin was somewhat destabilized in the presence of BP. Accordingly, all of the experimental data were confirmed by MD simulation.Communicated by Ramaswamy H. Sarma.

Evaluation of the Binding Properties of A New Phenylurea Appended Carbazole Compound to Pepsin/Trypsin by Computational and Multi-Spectral Analysis

A novel carbazole compound, named 1-(9-ethyl-9H-carbazol-3-yl)-3-phenylurea (Cpu) was synthesized and its binding properties with protease enzymes (pepsin and trypsin) has been examined by steady-state fluorescence measurements, UV/vis absorption, infrared (FT-IR) and circular dicroism (CD) spectroscopies and also computational methods. The fluorescence experimental results indicated that the quenching mechanism of enzyme by Cpu is static process. The thermodynamic parameters (both negative ΔH/ΔS) and molecular docking results suggested that the binding of Cpu to pepsin/trypsin were driven by hydrogen bonds and van der Waals forces. Based on Förster's theory, the binding distance (r) between pepsin/trypsin and Cpu was calculated to be 3.072/2.784 nm, which implies that non-radiative energy transfer occurs from enzyme to Cpu. Furthermore, absorption, CD, and FT-IR spectral analysis provided an evidence that the presence of Cpu induced notable changes in the secondary structures and microenvironmental of both pepsin and trypsin, supporting its significant influence on these enzymes.

Development of nanostructured formulation from naringenin and silk fibroin and application for inhibition of lipoxygenase (LOX)

A simple low-energy method was used to obtain polymeric nanoparticles containing silk fibroin (SF), fatty butyl esters (oily phase) and the flavonoid naringenin. Experimental planning (Box-Behnken) was applied to investigate the optimal conditions for three factors (variation of the concentrations of SF, naringenin and fatty butyl ester) at three levels, with evaluation of particle size, polydispersity index (PDI) and zeta potential (ZP) as responses. The results showed that the polymeric particle was formed with sizes of 179.6 to 633.9 nm, PDI of 0.33 to 0.77 and ZP of -60.4 to -38.8 mV. The best responses under the optimized conditions (Nari-SF 9 and 15) were characterized through transmission electron microscopy (TEM), Fourier-transform infrared (FT-IR), visible ultraviolet (UV-vis) and fluorescence, which confirmed that coated nanoparticles had been obtained. It was shown that the nanoformulation had excellent stability, the bioavailability of naringenin had been improved through use of the biopolymer and high inhibition of the enzyme lipoxygenase had been achieved in vitro.

Digital Database of Absorption Spectra of Diverse Flavonoids Enables Structural Comparisons and Quantitative Evaluations

Flavonoids play diverse roles in plants, comprise a non-negligible fraction of net primary photosynthetic production, and impart beneficial effects in human health from a plant-based diet. Absorption spectroscopy is an essential tool for quantitation of flavonoids isolated from complex plant extracts. The absorption spectra of flavonoids typically consist of two major bands, band I (300-380 nm) and band II (240-295 nm), where the former engenders a yellow color; in some flavonoids the absorption tails to 400-450 nm. The absorption spectra of 177 flavonoids and analogues of natural or synthetic origin have been assembled, including molar absorption coefficients (109 from the literature, 68 measured here). The spectral data are in digital form and can be viewed and accessed at http://www.photochemcad.com. The database enables comparison of the absorption spectral features of 12 distinct types of flavonoids including flavan-3-ols (e.g., catechin, epigallocatechin), flavanones (e.g., hesperidin, naringin), 3-hydroxyflavanones (e.g., taxifolin, silybin), isoflavones (e.g., daidzein, genistein), flavones (e.g., diosmin, luteolin), and flavonols (e.g., fisetin, myricetin). The structural features that give rise to shifts in wavelength and intensity are delineated. The availability of digital absorption spectra for diverse flavonoids facilitates analysis and quantitation of these valuable plant secondary metabolites. Four examples are provided of calculations─multicomponent analysis, solar ultraviolet photoprotection, sun protection factor (SPF), and Förster resonance energy transfer (FRET)─for which the spectra and accompanying molar absorption coefficients are sine qua non.

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.

Effects of Naringin on Postharvest Storage Quality of Bean Sprouts

This study investigated the effects of naringin on soybean and mung bean sprouts postharvest quality. It was found that naringin could maintain the appearance and quality of soybean sprouts and mung bean sprouts during a 6-day storage period as well as delay the occurrence of browning in mung bean sprouts and soybean sprouts. The optimal application rate of naringin was 50–100 μg/mL, which could effectively inhibit the activity of polyphenol oxidase (PPO) and peroxidase (POD) in bean sprouts and increase the ascorbic acid content, where this inhibition response to the browning of mung bean sprouts and soybean sprouts was significantly reduced. Naringin treatment increased gallic acid and p-coumaric acid content in mung bean sprouts as well as the daidzin and rutin content in soybean sprouts, which was also reflected in the improvement of antioxidant activity. The binding of naringin with PPO and POD was analyzed with molecular docking, naringin, and PPO had a lower binding energy (−1.09 Kcal/mol). In conclusion, naringin application in postharvest preservation of mung bean sprouts and soybean sprouts can maintain favorable consumer quality.

Multispectroscopic and synergistic antioxidant study on the combined binding of caffeic acid and (-)-epicatechin gallate to lysozyme

The binding of caffeic acid (CA) and/or (-)-epicatechin gallate (ECG) to lysozyme was investigated by multispectroscopic methods and molecular docking. The effects of the single and combined binding on the structure, activity and stability of lysozyme and the synergistic antioxidant activity of CA and ECG were also studied. Fluorescence quenching spectra, time-resolved fluorescence spectra, and UV-vis absorption difference spectra all ascertained the static quenching mechanism of lysozyme by CA/ECG. Thermodynamic parameters indicated that CA and ECG competitively bound to lysozyme, and CA had a stronger binding affinity, which was consistent with the results of molecular docking. Hydrogen bonding, van der Waals' force and electrostatic interaction were the main driving forces for the binding process. Synchronous fluorescence spectra displayed that the interaction of CA/ECG exposed the tryptophan residues of lysozyme to a more hydrophilic environment. Circular dichroism spectroscopy, Fourier transform infrared spectroscopy and dynamic light scattering indicated that the binding of CA and/or ECG to lysozyme resulted in the change of the secondary structure and increased the particle size of lysozyme. The binding of CA and/or ECG to lysozyme inhibited the enzyme activity and enhanced the thermal stability of lysozyme. The combined application of CA and ECG showed antioxidant synergy which was influenced by the encapsulation of lysozyme and cellular uptake. In summary, this work provides theoretical guidance for lysozyme as a carrier for the combined application of CA and ECG.

Purification and characterization of a novel thermostable anticoagulant protein from medicinal leech Whitmania pigra Whitman

ETHNOPHARMACOLOGICAL RELEVANCE

The prevalence of cardiovascular disease (CVD) is increasing worldwide. Despite significant improvements in novel targeted treatment agents, natural products purified from medicinal animals with minimal side effects have attracted much attention. Several native proteins explored from suck-blood leeches, such as non-thermostable hirudin and its variants, revealed potent anticoagulant activity. Traditional Chinese medicine clinics have proved that non-suck-blood leech Whitmania pigra Whitman (W. pigra) also played notable roles in CVD treatments even after decoction. However, only a few natural proteins and peptides have been identified from the fresh material of this medicinal species.

AIM OF THE STUDY

We aimed to purify and characterize thermostable anticoagulant proteins from W. pigra for further development of a therapeutic agent for thrombosis.

MATERIALS AND METHODS

W. pigra crude extract was prepared by decoction in water. Anticoagulant proteins were purified by DEAE cellulose DE-52, Sephadex G-75, and reversed-phase liquid chromatography sequentially and analyzed by SDS-PAGE and LC-MS/MS for structural information. In addition, we conducted in vitro anticoagulant experiments, including plasma recalcification time (PRT) assay, fibrinolytic assay, activated partial thromboplastin time (APTT), prothrombin time (PT), thrombin time (TT), fibrinogen (Fib) assay, and cell viability assays. Furthermore, a carrageenan-induced chronic thromboembolism model was employed in ICR mice, and four coagulation factors (APTT, PT, TT, and Fib) activities were determined after intragastric administration.

RESULTS

The anticoagulant protein WP-77 has a relative molecular weight of ca. 20.8 kDa. It was effective over a broad temperature range from 20 °C to 100 °C and a pH 2-8 condition. The anticoagulant activity of WP-77 was retained after incubation with pepsin but was greatly inhibited by trypsin (P < 0.01). It significantly prolonged APTT and TT (P < 0.05) but had little effect on PT and Fib in vitro. Furthermore, WP-77 of a low concentration resulted in the recovery of injured EA.hy926 by thrombin. The protein also significantly prolonged APTT and TT (P < 0.01) and inhibited thrombus formation in carrageenan-induced thrombosis mice, demonstrating its antithrombotic effect in vivo.

CONCLUSION

Our results suggest that WP-77 from W. pigra plays a distinct role in treating thrombotic diseases, and it is an essential substance of anticoagulant activity of non-suck-blood medicinal leeches. This thermostable anticoagulant protein could be a promising candidate for the development of clinical antithrombosis medicines.