Elucidation of the 3D structure of grape seed 7S globulin and its interaction with malvidin 3-glucoside: A molecular modeling approach

Obtention and Characterisation of Antioxidant-Rich Peptides from Defatted Grape Seed Meal Using Different Enzymes

Defatted grape seed meal (DGSM) is a residue obtained from grape pomace and is an important source of protein. The aim of this study was to select peptides with optimal antioxidant and colour properties, obtained using enzymes of different origins and proteolytic character, for application in winemaking. For this purpose, the assay was performed using novo-ProD (NP), alcalase (AL), novozym (NZ), pepsin (PE), flavourzyme (FZ), and papain (PA) enzymes. The peptide percentage, peptide yield, molecular size of the peptide fractions, total amino acid, peptide content, antioxidant activity, and CIELAB colour coordinates of the hydrolysates were determined. The peptide hydrolysates obtained using PE showed the significantly (p < 0.05) highest percentages of peptides (93%), amino acid content (188 mg aa/g hydrolysate), and lightness (L*, 70.3). On the other hand, NP peptide hydrolysates displayed the significantly (p < 0.05) highest antioxidant activity (154 µmol TE/g hydrolysate) and peptide yield (39%). Regarding molecular weight (MW), PE led to hydrolysates with a lower proportion of low-MW peptides (MW < 1 kDa). In conclusion, the peptide hydrolysates obtained by NP and PE exhibited the greatest chemical characteristics for further application, both separately and combined in targeted hydrolysis, as colour stabilisers and antioxidant capacity enhancers in warm climate winemaking.

New approaches for screening grape seed peptides as colourimetric modulators by malvidin-3-O-glucoside stabilisation

The colour of red wine is due to the presence of anthocyanins and their derived pigments, with malvidin-3-O-glucoside being the most predominant. Due to their chemical conformation, anthocyanins are susceptible to several conditions and have limited stability. Through copigmentation processes, anthocyanins can interact non-covalently with other molecules to enhance their stability. As a natural source of proteins and peptides, grape seeds are of particular interest because they may be of significant techno-functional value in the modulation of wine quality characteristics, such as acting as copigments to enhance colour stability. The proposed methodology allowed predicting in-depth insights into the molecular-level nature of interaction between the identified peptides when complexed with malvidin 3-O-glucoside and their colour stabilising properties. Thereby, allowing a prior screening in silico to facilitate their future application in experimental assays, such as obtaining the tested peptides with the characteristics already studied by means of grape seed meal directed hydrolysis.

Investigating the interaction mechanisms between arachin and resveratrol: Utilizing multi-spectroscopy and computational chemistry

Arachin (ARA) and resveratrol (RES) are the primary protein and bioactive compound in peanuts and their processed products. However, the mechanism of interaction between these two substances remained unclear. To investigate protein structural changes, conformational variations, and molecular mechanisms in the interaction between them, multispectral analysis and computational chemistry methods were employed. Experimental results confirmed that RES quenched ARA's intrinsic fluorescence through static quenching, indicating their interaction. Thermodynamic analysis revealed the interaction between them was endothermic, spontaneous, and primarily hydrophobic. Molecular dynamics (MD) simulations highlighted strong affinity between RES and ARA, with key amino acids (His425, Val426, Phe405, and Phe464) facilitating their interaction. RES binding increased stability without significant protein conformational changes. The independent gradient model based on Hirshfeld partition (IGMH) validated their interaction, emphasizing van der Waals (VDW) interactions and hydrogen bonds (H-bonds) as crucial for stable binding. This research lays a theoretical foundation for potential applications of ARA-RES complex products in the food industry.

Research Progress on the Extraction and Purification of Anthocyanins and Their Interactions with Proteins

Anthocyanins, as the most critical water-soluble pigments in nature, are widely present in roots, stems, leaves, flowers, fruits, and fruit peels. Many studies have indicated that anthocyanins exhibit various biological activities including antioxidant, anti-inflammatory, anti-tumor, hypoglycemic, vision protection, and anti-aging. Hence, anthocyanins are widely used in food, medicine, and cosmetics. The green and efficient extraction and purification of anthocyanins are an important prerequisite for their further development and utilization. However, the poor stability and low bioavailability of anthocyanins limit their application. Protein, one of the three essential nutrients for the human body, has good biocompatibility and biodegradability. Proteins are commonly used in food processing, but their functional properties need to be improved. Notably, anthocyanins can interact with proteins through covalent and non-covalent means during food processing, which can effectively improve the stability of anthocyanins and enhance their bioavailability. Moreover, the interactions between proteins and anthocyanins can also improve the functional characteristics and enhance the nutritional quality of proteins. Hence, this article systematically reviews the extraction and purification methods for anthocyanins. Moreover, this review also systematically summarizes the effect of the interactions between anthocyanins and proteins on the bioavailability of anthocyanins and their impact on protein properties. Furthermore, we also introduce the application of the interaction between anthocyanins and proteins. The findings can provide a theoretical reference for the application of anthocyanins and proteins in food deep processing.

Targeted drug delivery to the thrombus by fusing streptokinase with a fibrin-binding peptide (CREKA): an in silico study

Aim: Streptokinase has poor selectivity and provokes the immune response. In this study, we used in silico studies to design a fusion protein to achieve targeted delivery to the thrombus. Materials & methods: Streptokinase was analyzed computationally for mapping. The fusion protein modeling and quality assessment were carried out on several servers. The enzymatic activity and the stability of the fusion protein and its complex with plasminogen were assessed through molecular docking analysis and molecular dynamics simulation respectively. Results: Physicochemical properties analysis, protein quality assessments, protein-protein docking and molecular dynamics simulations predicted that the designed fusion protein is functionally active. Conclusion: Our results showed that this fusion protein might be a prospective candidate as a novel thrombolytic agent with better selectivity.

Deciphering the interaction mechanism and binding mode between chickpea protein isolate and flavonoids based on experimental studies and molecular simulation

Chickpea protein isolate (CPI) is a promising novel plant protein, and protein-flavonoid system has also been applied in various food products. However, the interaction mechanism between CPI and flavonoids remains to be elucidated. In this paper, the affinity behavior between flavonoids and CPI was explained by constructing the three-dimensional quantitative structure-activity relationship (R2 = 0.988, Q2 = 0.777). Subsequently, four representative flavonoids were selected for further study. Multi-spectroscopy analysis showed that the sequence of affinity for CPI was puerarin > apigenin > naringenin > epigallocatechin gallate. Meanwhile, flavonoids altered the secondary structure and spatial conformation of CPI, leading to the static quenching of CPI. Additionally, thermodynamic analysis indicated that hydrogen bonding and van der Waals forces were the main driving forces for complex binding. Molecular docking and molecular dynamics simulations further explored the binding sites and conformations of complexes. This study provides theoretical guidance for in-depth research on the interaction patterns between biomacromolecules and small molecules in food matrices.

Computational insight into stability-enhanced systems of anthocyanin with protein/peptide

Anthocyanins, which belong to the flavonoid group, are commonly found in the organs of plants native to South and Central America. However, these pigments are unstable under conditions of varying pH, heat, etc., which limits their potential applications. One method for preserving the stability of anthocyanins is through encapsulation using proteins or peptides. Nevertheless, the complex and diverse structure of these molecules, as well as the limitation of experimental technologies, have hindered a comprehensive understanding of the encapsulation processes and the mechanisms by which stability is enhanced. To address these challenges, computational methods, such as molecular docking and molecular dynamics simulation have been used to study the binding affinity and dynamics of interactions between proteins/peptides and anthocyanins. This review summarizes the mechanisms of interaction between these systems, based on computational approaches, and highlights the role of proteins and peptides in the stability enhancement of anthocyanins. It also discusses the current limitations of these methods and suggests possible solutions.

First insights into the binding mechanism and colour effect of the interaction of grape seed 11S globulin with malvidin 3-O-glucoside by fluorescence spectroscopy, differential colorimetry and molecular modelling

Recently, the search for alternative proteins endogenous to grapes to be used as wine colour protecting agents became an important research trend. In this study, the molecular interaction between the grape seed 11S globulin from winemaking by-product and malvidin-3-O-glucoside was investigated by fluorescence, differential colorimetry and molecular modelling. Fluorescence studies revealed the formation of grape seed protein- pigment complex whose KS was 8.5 × 104 M-1 and binding sites, n = 1.3. Malvidin-3-O-glucoside showed darker and more vivid bluish colour of in the presence of 11S globulin, suggesting the flavylium cation protection in a hydrophobic region of the protein. Docking analysis and molecular dynamics simulation indicated that malvidin-3-O-glucoside interacts mainly with the acidic subunit (40 kDa) of the 11S globulin monomer (60 kDa). An average of two hydrogen bonds and Van der Wall forces were the main interaction forces found for the protein-pigment complex, whose stability was confirmed by root-means-square deviation.

Development of high internal phase emulsions with noncovalent crosslink of soy protein isolate and tannic acid: Mechanism and application for 3D printing

In this study, we propose a design strategy using soy protein isolate (SPI)-tannic acid (TA) complexes crosslinked through noncovalent interactions to develop high internal phase emulsions (HIPEs) for 3D printing materials. The results of Fourier transform infrared spectroscopy, intrinsic fluorescence, and molecular docking analyses indicated that the dominant interactions occurring between the SPI and TA were mediated by hydrogen bonds and hydrophobic interactions. The secondary structure, particle size, ζ-potential, hydrophobicity and wettability of SPI was significantly altered by the addition of TA. The microstructure of HIPEs stabilized by SPI-TA complexes exhibited more regular and even polygonal shapes, thereby allowing the protein to form a dense self-supporting network structure. When the concentration of TA exceeded 50 μmol/g protein, the formed HIPEs remained stable after 45 days of storage. Rheological tests revealed that the HIPEs exhibited a typical gel-like (G' > G'') and shear-thinning behavior, which contributed to preferable 3D printing behavior.

Molecular dynamics simulations on interactions of five antibiotics with luciferase of Vibrio Qinghaiensis sp.-Q67

A large number of antibiotics have been used in the medical industry, agriculture, and animal husbandry industry in recent years. It may cause pollution to the aquatic environment and ultimately threaten to human health due to their prolonged exposure to the environment. We aim to study the toxicity mechanism of enrofloxacin (ENR), chlortetracycline hydrochloride (CTC), trimethoprim (TMP), chloramphenicol (CMP), and erythromycin (ETM) to luciferase of Vibrio Qinghaiensis sp.-Q67 (Q67) by using toxicity testing combined with molecular docking, molecular dynamics, and binding free energy analysis. The curve categories for ENR were different from the other four antibiotics, with ENR being J-type and the rest being S-type, and the toxicity of these five antibiotics (pEC50) followed the order of ENR (7.281) > ETM (6.814) > CMP (6.672) > CTC (6.400) > TMP (6.123), the order of toxicity value is consistent with the the magnitude of the binding free energy (ENR (-47.759 kcal/mol), ETM (-46.821 kcal/mol), CMP (-42.905 kcal/mol), CTC (-40.946 kcal/mol), TMP (-28.251 kcal/mol)). The van der Waals force provided the most important contribution to the binding free energy of the five antibiotics in the binding system with Q67 luciferase. Therefore, the dominant factor for the binding of antibiotics to luciferase was shape compensation. The face-to-face π-π stacking interaction between the diazohexane structure outside the active pocket region and the indoles structure of Phe194 and Phe250 in the molecular structure was the main reason for the highest toxicity value of antibiotic ENR. The hormesis effect of ENR has a competitive binding relationship with the α and β subunits of luciferase. Homology modeling, molecular docking, molecular dynamics simulations and binding free energy calculations were used to derive the toxicity magnitude of different antibiotics against Q67, and insights at the molecular level. The conclusion of toxicological experiments verified the correctness of the simulation results. This study contributes to the understanding of toxicity mechanisms of five antibiotics and facilitates risk assessment of antibiotic contaminants in the aquatic environment.

In Vitro and In Silico Protocols for the Assessment of Anti-Tick Compounds from Pinus roxburghii against Rhipicephalus (Boophilus) microplus Ticks

Pinus roxburghii, also known by the name "Himalayan chir pine," belongs to the Pinaceae family. Rhipicephalus (Boophilus) microplus tick is one of the most significant bovine ectoparasites, making it a major vector of economically important tick-borne diseases. The researchers conducted adult immersion tests (AIT) and larval packet tests (LPT) to investigate the acaricidal effect of P. roxburghii plant extract on R. (B.) microplus and its potential modulatory function when used with cypermethrin. Eggs were also assessed for their weight, egg-laying index (IE), hatchability rate, and control rate. After exposure to essential extract concentrations ranging from 2.5 to 40 mg/mL for 48 h, adult female ticks' oviposition inhibition and unfed R. (B.) microplus larvae's mortality rates were analyzed. Engorged females exposed to P. roxburghii at 40 mg/mL had reduced biological activity (oviposition, IE) compared to positive and negative controls. A concentration of 40 mg/mL of P. roxburghii caused 90% mortality in R. (B.) microplus larvae, whereas cypermethrin (the positive control) caused 98.3% mortality in LPT. In AIT, cypermethrin inhibited 81% of oviposition, compared to the 40 mg/mL concentration of P. roxburghii, which inhibited 40% of the ticks' oviposition. Moreover, this study assessed the binding capacity of selected phytocompounds with the targeted protein. Three servers (SWISS-MODEL, RoseTTAFold, and TrRosetta) recreated the target protein RmGABACl's 3D structure. The modeled 3D structure was validated using the online servers PROCHECK, ERRAT, and Prosa. Molecular docking using Auto Dock VINA predicted the binding mechanisms of 20 drug-like compounds against the target protein. Catechin and myricetin showed significant interactions with active site residues of the target protein, with docking scores of -7.7 kcal/mol and -7.6 kcal/mol, respectively. In conclusion, this study demonstrated the acaricidal activity of P. roxburghii extract, suggesting its potential as an alternative natural acaricide for controlling R. (B.) microplus.

Natural carriers: Recent advances in their use to improve the stability and bioaccessibility of food active compounds

In the last decades, the incorporation of bioactive compounds in food supplements aroused the attention of scientists. However, these ingredients often exhibit both low solubility and stability and their poor bioaccessibility within the gastrointestinal tract limits their effectiveness. To overcome these drawbacks, many carriers have been investigated for encapsulating nutraceuticals and enhancing their bioavailability. It is note that several different vegetable wall materials have been applied to build delivery systems. Considering their encapsulation mechanism, lipid and protein-based carriers display specific interaction patterns with bioactives, whereas polysaccharidic-based carriers can entrap them by creating porous highly stable networks. To maximize the encapsulation efficiency, mixed systems are very promising. Following the current goal of using natural and sustainable ingredients, only a limited number of studies about the isolation of new ingredients from agro-food waste are available. In this review, a comprehensive overview of the state of art in the development of innovative natural lipid-, protein- and polysaccharide-based plant carriers is presented, focusing on their application as food active compounds. Different aspects to be considered in the design of delivery systems are discussed, including the carrier structure and chemical features, the interaction between the encapsulating and the core material, and the parameters affecting bioactives entrapment.

An updated review on the stability of anthocyanins regarding the interaction with food proteins and polysaccharides

The health benefits of anthocyanins are compromised by their chemical instability and susceptibility to external stress. Researchers found that the interaction between anthocyanins and macromolecular components such as proteins and polysaccharides substantially determines the stability of anthocyanins during food processing and storage. The topic thus has attracted much attention in recent years. This review underlines the new insights gained in our current study of physical and chemical properties and functional properties in complex food systems. It examines the interaction between anthocyanins and food proteins or polysaccharides by focusing on the "structure-stability" relationship. Furthermore, multispectral and molecular computing simulations are used as the chief instruments to explore the interaction's mechanism. During processing and storage, the stability of anthocyanins is generally influenced by the adverse characteristics of food and beverage, including temperature, light, oxygen, enzymes, pH. While the action modes and types between protein/polysaccharide and anthocyanins mainly depend on their structures, the noncovalent interaction between them is the key intermolecular force that increases the stability of anthocyanins. Our goal is to provide the latest understanding of the stability of anthocyanins under food processing conditions and further improve their utilization in food industries. Practical Application: This review provides support for the steady-state protection of active substances.

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.

Structure-based in silico design and in vitro acaricidal activity assessment of Acacia nilotica and Psidium guajava extracts against Sarcoptes scabiei var. cuniculi

Infestation by Sarcoptes scabiei var. cuniculi mite causes scabies in humans and mange in animals. Alternative methods for developing environmentally friendly and effective plant-based acaricides are now a priority. The purpose of this research was the in silico design and in vitro evaluation of the efficacy of ethanol extracts of Acacia nilotica and Psidium guajava plant leaves against S. scabiei. Chem-Draw ultra-software (v. 12.0.2.1076.2010) was used to draw 36 distinct compounds from these plants that were employed as ligands in docking tests against S. scabiei Aspartic protease (SsAP). With docking scores of - 6.50993 and - 6.16359, respectively, clionasterol (PubChem CID 457801) and mangiferin (PubChem CID 5281647) from A. nilotica inhibited the targeted protein SsAP, while only beta-sitosterol (PubChem CID 222284) from P. guajava interacted with the SsAP active site with a docking score of - 6.20532. Mortality in contact bioassay at concentrations of 0.25, 0.5, 1.0, and 2.0 g/ml was determined to calculate median lethal time (LT₅₀) and median lethal concentration (LC₅₀) values. Acacia nilotica extract had an LC₅₀ value of 0.218 g/ml compared to P. guajava extract, which had an LC₅₀ value of 0.829 g/ml at 6 h. These results suggest that A. nilotica extract is more effective in killing mites, and these plants may have novel acaricidal properties against S. scabiei. Further research should focus on A. nilotica as a potential substitute for clinically available acaricides against resistant mites.

Ultrahigh Pressure Facilitates the Acylation of Malvidin and Chlorogenic Acid to Increase the Stability and Protective Effect of Malvidin Derivatives on H2O2-Induced ARPE-19 Cells

We explored the effects of ultrahigh-pressure technology and chlorogenic acid on the color stability and structure-activity relationship of malvidin (MV). Experimental conditions were optimized through single-factor experiments and response surface analysis at a pressure of 300 MPa, mass ratio of MV to chlorogenic acid of 1:3.64 (w/w), and time of 5 min. Compared with MV, MV derivatives showed higher stability and in vitro antioxidant activity. X-ray diffraction analysis, UV-vis spectroscopy, Fourier transform infrared spectroscopy, high-performance liquid chromatography, and mass spectrometry were conducted to determine the structures of MV derivatives for the first time. Ultrahigh pressure facilitated acylation of chlorogenic acid and MV and produced four new MV derivatives. Analysis of the effect of malvidin-3-O-6-(acrylic acid-(2-hydroxy, 4-carboxy-cyclohexanol) ester)-guaiacol (Mv3ACEC) on ARPE-19 cells exposed to H₂O₂ by RNA transcriptome sequencing showed that Mv3ACEC simultaneously inhibited various inflammatory and apoptotic signal transduction pathways, exerted a synergistic effect, and partly inhibited cell apoptosis through the MAPK signaling pathway. Therefore, the results show that ultrahigh pressure will cause acylation of chlorogenic acid and MV to produce four new MV derivatives, and MV derivatives protect ARPE-19 cells from H₂O₂-induced oxidative stress.

Hypericin Inhibit Alpha-Coronavirus Replication by Targeting 3CL Protease

The porcine epidemic diarrhea virus (PEDV) is an Alphacoronavirus (α-CoV) that causes high mortality in infected piglets, resulting in serious economic losses in the farming industry. Hypericin is a dianthrone compound that has been shown as an antiviral activity on several viruses. Here, we first evaluated the antiviral effect of hypericin in PEDV and found the viral replication and egression were significantly reduced with hypericin post-treatment. As hypericin has been shown in SARS-CoV-2 that it is bound to viral 3CLpro, we thus established a molecular docking between hypericin and PEDV 3CLpro using different software and found hypericin bound to 3CLpro through two pockets. These binding pockets were further verified by another docking between hypericin and PEDV 3CLpro pocket mutants, and the fluorescence resonance energy transfer (FRET) assay confirmed that hypericin inhibits the PEDV 3CLpro activity. Moreover, the alignments of α-CoV 3CLpro sequences or crystal structure revealed that the pockets mediating hypericin and PEDV 3CLpro binding were highly conserved, especially in transmissible gastroenteritis virus (TGEV). We then validated the anti-TGEV effect of hypericin through viral replication and egression. Overall, our results push forward that hypericin was for the first time shown to have an inhibitory effect on PEDV and TGEV by targeting 3CLpro, and it deserves further attention as not only a pan-anti-α-CoV compound but potentially also as a compound of other coronaviral infections.

Prediction and evaluation of the 3D structure of Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and its interaction with palmitoleic acid or oleic acid: An integrated computational approach

This study investigated the physicochemical properties and 3D structure of Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and its interaction with palmitoleic acid (POA) or oleic acid (OA) in macadamia oil. The 3D structure of MiAMP2 was constructed for the first time by ab initio modelling using the TrRosetta server. The results showed that MiAMP2 was highly hydrophilic and had seven disulfide bonds and higher α-helix and β-sheet/turn contents. Molecular simulation showed that the hydrophobic pocket of MiAMP2 created a favourable environment for the binding of POA and OA. Free energy landscape and independent gradient model (IGM) analyses revealed that hydrogen bonds and van der Waals forces were the major driving forces stabilizing complexes formed by MiAMP2 and POA or OA. The present study provides a theoretical basis and new insight for the future development and utilization of macadamia nut protein in the food industry.

Chiral separation and molecular simulation study of six antihistamine agents on a coated cellulose tri-(3,5-dimethylphenycarbamate) column (Chiralcel OD-RH) and its recognition mechanisms

Enantiomeric separation of six antihistamine agents was first systematically investigated on a cellulose-based chiral stationary phase (CSP), that is, cellulose tris-(3,5-dimethyl phenyl carbamate) (Chiralcel OD-RH), under the reversed-phase mode. Orphenadrine, meclizine, terfenadine, dioxopromethazine, and carbinoxamine enantiomers were completely separated under the optimized mobile phase conditions with resolutions of 5.02, 1.93, 1.68, 1.67, and 1.54, respectively. Mequitazine was partially separated with a resolution of 0.77. The influences of type and concentration of buffer salt, the pH of buffer solution, and the type and ratio of organic modifier on the chiral separation were evaluated and optimized. For a better insight into the enantiorecognition mechanisms, molecular docking was carried out via the Autodock software. The lowest binding energy and the optimal conformations of the analytes/CSP complexes were supplied, and the mechanisms of chiral recognition were determined. According to the results, the key interactions for the chiral recognition of these six analytes on CDMPC were π-π interactions, hydrophobic interactions, hydrogen bond interactions, and some special interactions.