Interaction of phenolic acids with trypsin: Experimental and molecular modeling studies

The synergistic effects of rice bran rancidity and dephenolization on digestive properties of rice bran protein

Both rice bran (RB) rancidity and dephenolization could affect the structural characteristics and phenolics composition of rice bran protein (RBP), thereby affecting RBP digestibility. The synergistic effects of RB rancidity and dephenolization on RBP digestibility were investigated. Excessive RB rancidity (RB stored for 10 d) and non-dephenolization reduced RBP digestibility, while moderate RB rancidity (RB stored for 1 d) combined with dephenolization improved RBP digestibility to a maximum of 74.19%. Dephenolization reduced the antioxidant capacities of RBP digestive products. The digestibility of non-dephenolized RBP (NDRBP) was significantly (P < 0.05) related with its carbonyl content, surface hydrophobicity, and ζ-potential. The digestibility of dephenolized RBP (DRBP) was significantly related with its β-sheet structure content, surface hydrophobicity, ζ-potential, and average particle size. Overall, moderate RB rancidity combined with dephenolization enhanced RBP digestibility by reducing the non-competitive inhibition of endogenous phenolics on protease and regulating the spatial structural characteristics of RBP.

Complexation of bovine lactoferrin with selected phenolic acids via noncovalent interactions: Binding mechanism and altered functionality

Noncovalent interactions of 4 selected phenolic acids, including gallic acid (GA), caffeic acid (CA), chlorogenic acid (CGA), and rosmarinic acid (RA) with lactoferrin (LF) were investigated. Compound combined with LF in the binding constant of CA > GA > RA > CGA, driven by van der Waals and hydrogen bonding for GA, and hydrophobic forces for others. Conformation of LF was affected at secondary and ternary structure levels. Molecular docking indicated that GA and CA located in the same site near the iron of the C-lobe, whereas RA and CGA bound to the C2 and N-lobe, respectively. Significantly enhanced antioxidant activity of complexes was found compared with pure LF, as demonstrated by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azinobis(2-ethylbenzothiazoline-6-sulfonate) (ABTS), and ferric reducing antioxidant power (FRAP) models. Caffeic acid, CGA, and RA significantly decreased the emulsifying stability index and improved foam ability of LF, and the effect of CA and RA was the most remarkable, respectively.

In vitro protein digestibility of RuBisCO-enriched wheat dough: a comparative study with pea and gluten proteins

Growing demand for sustainable, plant-based protein sources has stimulated interest in new ingredients for food enrichment. This study investigates the nutritional and digestive implications of enriching wheat dough with RuBisCO, in comparison to pea protein-enriched and gluten-enriched doughs. The protein quality and digestibility of these enriched doughs were analysed through dough characterization, in vitro digestion experiments and biochemical analysis of digesta. Our findings indicate that an enrichment at 10% of RuBisCO or pea proteins improves the chemical score and the in vitro PDCAAS (IV-PDCAAS) score of wheat dough as compared to the control dough. Digestibility assays suggest that RuBisCO introduction modifies the protein hydrolysis kinetics: the nitrogen release is lower during gastric digestion but larger during intestinal digestion than other samples. The analysis of the protein composition of the soluble and insoluble parts of digesta, using size-exclusion chromatography, reveals that the protein network in RuBisCO-enriched dough is more resistant to gastric hydrolysis than the ones of other doughs. Indeed, non-covalently bound peptides and disulfide-bound protein aggregates partly composed of RuBisCO subunits remain insoluble at the end of the gastric phase. The digestion of these protein structures is then mostly performed during the intestinal phase. These results are also discussed in relation to the digestive enzymatic cleavage sites, the presence of potential enzyme inhibitors, the protein aggregation state and the secondary structures of the protein network in each dough type.

Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation

Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and β-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.

Chymotrypsin and Trypsin Inhibitory Activity of Some Medicinal Plants Collected from Rize (Türkiye)

In this research, the evaluation of in vitro chymotrypsin and trypsin inhibitory activities of ten plant species collected from Rize were aimed, and fractions that showed strong activity were analyzed through HPLC. Daphne pontica L. and Mentha longifolia (L.) L. were found to have the highest chymotrypsin inhibitory activities (87.75 and 84.24 % inhibition). Similarly, the highest trypsin inhibitory activity was observed in D. pontica (%99.93 inhibition), followed by Sambucus ebulus L. flowers (87.47 % inhibition). Extracts showing strong enzyme inhibition were fractioned and subjected to activity tests. The highest chymotrypsin inhibitory activity was observed in the n-hexane fraction of D. pontica (%80.70 inhibition), while the highest trypsin inhibitory activity was found in the n-butanol fraction of S. ebulus (%86.81 inhibition). HPLC studies determined that the 80 % ethanol extract of D. pontica and its dichloromethane and ethyl acetate fractions contained umbelliferone. It was found that chlorogenic acid was present in the 80 % ethanol extracts of S. ebulus flowers. M. longifolia was found to contain chlorogenic acid, caffeic acid, luteolin-7-glucoside, and rosmarinic acid. M. longifolia has been identified as the plant exhibiting the highest antioxidant activity in ABTS and CUPRAC tests, consistent with its high phenolic and flavonoid content.

Study of an inhibitory effect of plant polyphenolic compounds against digestive enzymes using bench-working experimental evidence predicted by molecular docking and dynamics

The substantial nutritional content and diversified biological activity of plant-based nutraceuticals are due to polyphenolic chemicals. These chemicals are important and well-studied plant secondary metabolites. Their protein interactions are extensively studied. This relationship is crucial for the logical development of functional food and for enhancing the availability and usefulness of polyphenols. This study highlights the influence of protein types and polyphenols on the interaction, where the chemical bindings predominantly consist of hydrophobic interactions and hydrogen bonds. The interaction between polyphenolic compounds (PCs) and digestive enzymes concerning their inhibitory activity has not been fully studied. Therefore, we have examined the interaction of four digestive enzymes (α-amylase, pepsin, trypsin, and α-chymotrypsin) with four PCs (curcumin, diosmin, morin, and 2',3',4'-trihydroxychalcone) through in silico and in vitro approaches. In vitro plate assays, enzyme kinetics, spectroscopic assays, molecular docking, and simulations were performed. We observed all these PCs have significant docking scores and preferable interaction with the active site of the digestive enzymes, resulting in the reduction of enzyme activity. The enzyme-substrate binding mechanism was determined using the Lineweaver Burk plot, indicating that the inhibition occurred competitively. Among four PCs diosmin and morin has the highest interaction energy over digestive enzymes with IC50 value of 1.13 ± 0.0047 and 1.086 ± 0.0131 μM. Kinetic studies show that selected PCs inhibited pepsin, trypsin, and chymotrypsin competitively and inhibited amylase in a non-competitive manner, especially by 2',3',4'-trihydroxychalcone. This study offers insights into the mechanisms by which the selected PCs inhibit the enzymes and has the potential to enhance the application of curcumin, diosmin, morin, and 2',3',4'-trihydroxychalcone as natural inhibitors of digestive enzymes.

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.

A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods

The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.

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 of the binding behavior of bioactive 7-methoxyflavone to human serum albumin by coupling multi-spectroscopic with computational approaches

The natural flavonoids with bioactivity as secondary plant metabolites are mostly found in fruits, vegetables, tea and herbs, the distribution and bioavailability of which in vivo depends on the interaction and successive binding with carrier proteins in the systemic circulation. In this paper, the binding behavior of bioactive 7-methoxyflavone (7-MF) with human serum albumin (HSA) was studied with the aid of the combination of multi-spectroscopic methods, molecular docking and molecular dynamic simulation. The results of multi-spectroscopic experiments revealed that 7-MF interacted with HSA predominantly via fluorescence static quenching and the microenvironment around the fluorophore Trp residues in HSA became more hydrophilicity with the binding of 7-MF. Thermodynamic analysis demonstrated that hydrogen bonds and van der Waals forces played a dominant role in stabilizing the HSA-7-MF complex. Moreover, the docking experiment and molecular dynamic simulation further confirmed that 7-MF could enter the active cavity of HSA and caused more stable conformation and change of secondary structure of HSA through forming hydrogen bond. The exploration of the mechanism of 7-MF binding to HSA lights a new avenue to understand the stability, transport and distribution of 7-MF and 7-MF may hold great potential to be extended as a promising alternative of dietary supplements or pharmaceutical agents.

Binding parameters and molecular dynamics of Trypsin-Acid Yellow 17 complexation as a function of concentration

Acid Yellow 17 is a kind of azo dye used in food, textile, and cosmetics. Several studies explain the toxicity of azo dye for our body, but one could not find further information about the effects of these dyes on human macromolecules. In the current study, the interaction of AY17 with trypsin is investigated using several techniques. The UV analysis displayed that the absorption of trypsin could be decreased in the presence of this color. The fluorescence investigation indicated that a static form of quenching happens, and a 50% decrease in the fluorescence intensity, also showed the Vander Waals and hydrogen bond are the main forces in the interaction of this color and trypsin. Furthermore, we can observe that the T_m point of trypsin decreases from 46.5 to 42. On the other hand, the CD results were indicated that the interaction of this color with trypsin could decrease the percent of turn, coil and α-helix in trypsin structure. The computational study was undertaken to obtain more information about the interaction between trypsin and AY17. The results were in agreement with the experimental investigation and indicated that the interaction between this color and trypsin leads to less compactness in the trypsin structure.

Proteomic and computational characterisation of 11S globulins from grape seed flour by-product and its interaction with malvidin 3-glucoside by molecular docking

Grape seed flour by-product (GSBP) is an economic and renewable source of proteins, increasingly being explored due to interesting technological application such as colour protection in rich-anthocyanins beverages. Globulin-like proteins from GSBP were characterised by proteomic and computational studies. MALDI TOF/TOF analysis revealed the presence of two 11S globulins (acid and basic), whose 3D structures have been elucidated for the first time in Vitis vinifera L. grape seeds by using homology models and molecular dynamics. The secondary structure showed 11 α-helices and 25 β-sheets for acid and 12 α-helices and 24 β-sheets for basic 11S globulins. Molecular docking results indicate that both grape seed 11S globulins could establish different types of non-covalent interactions (π-π) with malvidin 3-O-glucoside (wine anthocyanin), which suggest a possible colour protection similar to that occurring in copigmentation phenomenon. These findings provide valuable information of globulin family proteins that could be relevant in food industry applications.

Synthesis and in vitro evaluation of chlorogenic acid amides as potential hypoglycemic agents and their synergistic effect with acarbose

Type 2 Diabetes mellitus is a chronic disease considered one of the most severe global health emergencies. Chlorogenic acid (1) has been shown to delay intestinal glucose absorption by inhibiting the activity of α-glucosidase (α-Glu) and α-amylase (α-Amy). In the present work, eleven chlorogenic acid amides have been synthesized and evaluated for their antioxidant properties (as DPPH and ORAC) and inhibition activity towards the two enzymes and, with the aim to obtain dual-action antidiabetic agents. The two most promising hypoglycemic compounds, bearing a tertiary amine function on an alkyl chain (8) and a benzothiazole scaffold (11), showed IC₅₀ values lower than that of (1) (45.5 µM α-Glu; 105.2 µM α-Amy). Amides 8 and 11 were by far more potent α-Glu inhibitors than the antidiabetic drug acarbose (IC₅₀ = 268.4 µM) and about twice less active toward α-Amy than acarbose (IC₅₀ = 34.4 µM). Kinetics experiments on amides 8 and 11 indicated these compounds as mixed-type inhibitors of α-Glu with K'_i values of 13.3 and 6.3 µM, respectively. The amylase inhibition occurred with a competitive mechanism in the presence of 8 (K_i = 79.7 µM) and with a mixed-type mechanism with 11 (K_i = 19.1 µM; K'_i = 93.6 µM). Molecular docking analyses supported these results, highlighting the presence of additional binding sites in both enzymes. Fluorescence experiments confirmed the grater affinity of amides 8 and 11 towards the two enzymes respect to (1). Moreover, a significant enhancement in acarbose efficacy was observed when inhibition assays were performed adding acarbose and amide 11. The above outcomes pinpointed the benzothiazole-based amide 11 as a promising candidate for further studies on type 2 diabetes treatment, both alone or combined with acarbose.

Unravelling the effects of procyanidin on gliadin digestion and immunogenicity

The effect of procyanidin dimer B3, a common food tannin, on the digestion of gliadin proteins was investigated by monitoring the changes in the immunogenic peptides produced during in vitro digestion and immunoreactivity. Interaction studies between procyanidin dimer B3, gluten proteins and/or digestive enzymes were performed by SDS-PAGE. The effect of procyanidin B3 on the enzymatic activity of trypsin, chymotrypsin and pancreatin was evaluated. The differences in the number and nature of immunogenic peptides released during digestion were identified by mass spectrometry. Briefly, the enzymatic activity of gastrointestinal enzymes was only slightly affected but a significant decrease in the immunological properties of the peptides produced during digestion was observed. Overall, although further studies are needed, the interaction between polyphenols and gluten proteins clearly influences gluten protein digestion and immunogenicity, thus suggesting that the consumption of dietary polyphenols can significantly affect the degree of celiac disease downstream immune reactions.

Interaction mechanism of aloe-emodin with trypsin: molecular structure-affinity relationship and effect on biological activities

The molecular mechanism of interaction between aloe-emodin (AE) and trypsin was investigated, exhibiting remarkable outcomes. To detect the interaction mechanism, the binding of AE with trypsin was examined by a multi-spectroscopy and molecular docking method. Results showed that the binding of AE and trypsin would lead to static quenching and their binding forces were van der Waals forces and hydrogen bonding. The results of simultaneous and three-dimensional fluorescence spectroscopy showed that the combination of AE and trypsin caused changes in the microenvironment around the trypsin fluorophore, which might change the spatial structure of trypsin. FT-IR spectroscopy showed that the contents of α-helix and β-turn in trypsin were decreased and the contents of β-sheet, random coil and antiparallel β-sheet were increased. Moreover, all these experimental results were verified and reasonably explained by molecular docking results. We also investigated the enzyme activity of trypsin and the antioxidant activity of AE. The results showed that both the enzyme activity of trypsin and the antioxidant activity of AE were decreased after interaction between AE and trypsin. The findings outlined in this study should elucidate the molecular mechanisms of interaction between AE and trypsin and contribute to making full use of AE in the food industry.

Novel Angiotensin-Converting Enzyme-Inhibitory Peptides From Fermented Bovine Milk Started by Lactobacillus helveticus KLDS.31 and Lactobacillus casei KLDS.105: Purification, Identification, and Interaction Mechanisms

Fermented milks with strong angiotensin I-converting enzyme (ACE)-inhibitory activity were obtained through a culture with Lactobacillus helveticus KLDS.31 and Lactobacillus casei KLDS.105 with a fermentation and storage temperature of 37 °C. Ultrafiltration fractions with a molecular weight less than 3 kDa in fermented milk whey exhibited the strongest inhibitory activity. Correspondingly, a gastrointestinal digestion experiment showed retention of the bioactivity of these fractions with pepsin and trypsin treatment. Four ACE-inhibitory peptides from fermented milk were isolated, purified by two-step reverse chromatography, and sequenced. Furthermore, the interaction mechanisms between ACE and four isolated peptides were investigated by a molecular docking method and the Independent Gradient Model. Experimental determination of IC50 was done to verify theoretical results. The inhibitory peptide interacted with ACE as follows: Lys-Pro-Ala-Gly-Asp-Phe > Lys-Ala-Ala-Leu-Ser-Gly-Met > Lys-Lys-Ala-Ala-Met-Ala-Met > Leu-Asp-His-Val-Pro-Gly-Gly-Ala-Arg.

Modulation of Formation, Physicochemical Properties, and Digestion of Ovotransferrin Nanofibrils with Covalent or Non-Covalent Bound Gallic Acid

The impact of covalent or non-covalent bound gallic acid (GA) on the formation, physicochemical properties, and digestion of ovotransferrin (OTF) nanofibrils was comprehensively studied. Thioflavin T fluorescence results revealed that bound GA could inhibit OTF nanofibrillation and that the fibril-inhibitory activity of bound GA was dose dependent. Covalent bound GA exerted stronger inhibition on OTF nanofibrillation than an equal amount of non-covalent bound GA. Atomic force microscopy revealed that covalent bound GA shortened OTF nanofibrils significantly, while non-covalent bound GA did not change the contour length of OTF fibrils remarkably. Bound GA altered diameter of OTF nanofibrils. Both covalent and non-covalent bound GA could alter the zeta potential, surface hydrophobicity, and rheological properties of OTF nanofibrils. Bound GA endowed OTF nanofibrils with a strong antioxidant activity. In vitro gastrointestinal digestion results showed that covalent bound GA elevated the fibril digestion rate better than non-covalent bound GA. Polyphenol binding provided a new approach to modulating the physicochemical properties of protein nanofibrils.

Interaction of chromium(III) or chromium(VI) with catalase and its effect on the structure and function of catalase: An in vitro study

Heavy metal chromium (Cr) poses a severe health risk to humans via food chain contamination. In this study, the interactions of either trivalent chromium (Cr(III)) or hexavalent chromium (Cr(VI)) with catalase (CAT) were investigated via multi-spectroscopic studies and computational simulations. The fluorescence analysis showed that Cr(III) and Cr(VI) quenched the fluorescence of CAT through a dynamic and a static quenching mechanism, respectively. The binding constant of Cr(VI) with CAT was 3.44×10⁴lmol^-1 at 298K. Other detailed binding characterizations of the Cr(VI)-CAT complex were also obtained using spectra analysis and molecular docking. Synchronous fluorescence, UV-vis and circular dichroism (CD) spectral studies showed that either Cr(III) or Cr(VI) induced conformational changes of CAT, but the degree of influence was different. The response of CAT activity to Cr(III) or Cr(VI) was found to be variable depending on their valence states and concentrations.