A molecular docking and molecular dynamics simulation study on the interaction between cyanidin-3-O-glucoside and major proteins in cow's milk

Elucidating the interaction mechanism of rutin with β-casein and β-lactoglobulin: A comprehensive analysis using multi-spectroscopy, molecular docking, and molecular dynamic simulations

Polyphenol-protein interactions are crucial for food processing, nutrition, and functional properties. This study investigates the interaction between rutin and β-casein (β-CAS) or β-lactoglobulin (β-LG) using multispectral analysis, molecular docking, and molecular dynamics (MD) simulations. Fluorescence spectroscopy reveals that rutin binds spontaneously (ΔG < 0) to β-CAS and β-LG, forming complexes with binding constants (Ka) at 298 K of 42.500 × 103 and 2.101 × 103 L·mol-1, respectively, and at 308 K of 5.814 × 103 and 4.350 × 103 L·mol-1. Multispectral analysis and microscopy reveal complex formation and changes in the proteins' secondary, crystalline, and microstructures. Molecular docking and MD simulations verify complex stability, showing heightened binding affinity between rutin and β-CAS. These results validate hydrophobic interactions and hydrogen bonding as the main forces between rutin and the two proteins. These findings offer insights for using milk proteins as rutin carriers and support potential food industry application.

In silico identification and experimental validation of two types of angiotensin-converting enzyme (ACE) and xanthine oxidase (XO) milk inhibitory peptides

Bioactive peptides have received significant attention due to their natural origin, low toxicity, and targeting specificity in the past decade. This study identified highly active ACE/XO inhibitors using molecular simulation and online databases and validated their in vitro antioxidant activity and the mechanisms of molecular interactions. According to computer predictions, Asp-Gly-Gly (DGG) and Asp-Gly-Met (DGGM) were identified as potential hydrolysates of common gastrointestinal peptidases with well water-soluble, non-toxic, and non-allergenic. Fourier transform infrared spectroscopy showed that the two peptides altered the enzyme's secondary structure, decreasing α-helix content by about 13 %, along with increasing β-sheet, randam coli, and β-turns content. Molecular docking and molecular dynamics simulations showed that hydrogen bonding and electrostatic interactions caused DGG and DGGM to form stable and dense complexes with the two enzymes. This study provides a new way for economical and efficient screening of new ACE and XO inhibitory peptides from natural proteins.

Green synthesis of N-succinyl-L-tyrosine: Decoding its taste-enhancing effects and mechanisms via sensory evaluation and molecular simulation

Amid escalating global public health concerns linked to dietary habits, the reduction of salt, monosodium glutamate, and sugar is increasingly recognized as a prevailing trend. This study explored the green synthesis of a novel taste enhancer, N-succinyl-L-tyrosine (N-Suc-Tyr), alongside its mechanisms of taste enhancement. N-Suc-Tyr was synthesized through an enzymatic process utilizing food-grade enzymes within an aqueous environment. Sensory evaluations revealed that the addition of N-Suc-Tyr at a concentration of 2 mg/L markedly enhanced the intensities and durations of umami, saltiness, sweetness, and kokumi tastes. Sigmoid curve analysis further confirmed the synergistic effects of N-Suc-Tyr on enhancing these taste sensations. Through molecular docking and dynamic simulations, it was demonstrated that N-Suc-Tyr bound tightly and stably to various taste receptors, thus enhancing the sensations of umami, sweetness, saltiness, and kokumi. These results provided a comprehensive understanding of the potential and mechanisms through which enzymatically synthesized N-Suc-Tyr could enhance tastes, thereby contributing to the advancement of the high-grade condiment industry.

Exploring the potential of Halalkalibacterium halodurans laccase for endosulfan and chlorophacinone degradation: insights from molecular docking and molecular dynamics simulations

Pesticides are widely used in agriculture but at the same time, a majority of them are known to cause serious harm to health and the environment. In the recent past, laccases have been reported as key enzymes having the ability to degrade pollutants by converting them into less toxic forms. In this investigation, laccase from polyextremophilic bacterium Halalkalibacterium halodurans C-125 was analyzed for its structural, physicochemical, and functional characterization using in silico approaches. The 3D model of the said enzyme is unknown; therefore, the model was generated by template-independent modeling using ROBETTA, I-TASSER, and Alphafold server. The best-generated model from Alphafold with a confidence of 0.95 was validated from ERRAT and Verify 3D scores of 89.95 and 91.80%, respectively. The Ramachandran plot generated using the PROCHECK server further predicted the accuracy of the model with 93.7% and 5.9% of residues present in most favored and additional allowed regions of the plot respectively. The active sites, ion binding sites, and subcellular localization of laccase were also predicted. The generated model was docked with 121 pollutants (pesticides, insecticides, herbicides, fungicides, and rodenticides) for its degradation potential towards these pollutants. Two ligands chlorophacinone (based on the highest binding energy) and endosulfan (based on agricultural uses) were selected for molecular dynamic simulation studies. Endosulfan as a pesticide is banned but in some countries governments allow its use for special purposes which need serious consideration on developing bioremediation approaches for endosulfan degradation. MD simulation studies revealed that both chlorophacinone and endosulfan form hydrogen bonds and hydrophobic bonds with the active site of laccase and chlorophacinone-laccase complex were more stable in comparison to endosulfan. The present investigation provides insight into the structural features of laccase and its potential for the degradation of pesticides which can be further validated by experimental data.Communicated by Ramaswamy H. Sarma.

Exploration of rutin derivatives as potential inhibitors of prostate cancer signaling pathways: A comprehensive in-silico study

Prostate cancer is a widespread health issue that affects men worldwide. It is one of the most common forms of cancer, and its development is influenced by a combination of hereditary, epigenetic, environmental, age, and lifestyle factors. Given that it is the second most common cause of cancer-related deaths in men, it is crucial to comprehend its complex facets. Present research especially targets the 3-kinase/protein kinase B, Epidermal Growth Factor Receptor, and extracellular signal-related kinase pathways, which are known to be significantly involved in prostate cancer progression. Here, Rutin derivatives were screened against selected prostate cancer targets. Molecular docking was performed to identify favorable interactions and the most promising compound. Further, Density functional theory, pharmacokinetics, Molecular dynamics simulation, principal component analysis, free energy landscape analysis, and Molecular Mechanics Poisson-Boltzmann Surface Area provided additional insights into selecting the best drug candidate. Among all the selected rutin derivatives, RU4b1 has potent inhibitory action. We also performed predictive analysis to identify the distinct metabolic sites within the structure of RU4b1. RU4b1 also exhibits drug-like properties and potent antioxidant activity. The findings were also compared with standard drugs and reference molecules of the respective proteins, and it is noteworthy that RU4b1 exhibited superior action compared to the standard drugs and reference molecules. This study aims to contribute valuable insights into developing targeted therapies for prostate cancer, emphasizing the potential of rutin derivatives as effective anti-cancer agents.

Elucidating the potential of bioactive of Trichoderma sp.. in combating pathogenesis by Fusarium sp.. by targeting pectin lyases: a bioinformatics approach

Pectin lyase is an industrially important enzyme, predominately used in fruit juice clarification and retting of fibers. It also promotes pathogenesis via the degradation of the pectin. The phytopathogen, Fusarium infects various crops and causes several diseases. Trichoderma sp. is a promising biocontrol agent that is vital in maintaining plant health and disease prevention. In the current study, a computational approach utilizing structure prediction, molecular docking, molecular dynamics, and MM-PBSA analysis was used to analyze the potential role of bioactive compounds secreted by Trichoderma sp. in inhibiting the pectin lyase enzyme from Fusarium proliferatum, F. fujikuroi, F. graminearum, F. oxysporum and F. verticillioides. Molecular docking with secondary metabolites revealed that Viridiofungin A secreted by Trichoderma harzianum and Virone secreted by T. virens are bioactive compounds with immense potential to inhibit PNLs of Fusarium species. Further, the rigidity of the structure and stability of the docked complex were confirmed via Molecular dynamic simulations assessed through multiple parameters from the simulation trajectory data. Dual culture assay of T. harzianum and T. virens with F. proliferatum, F. fujikuroi, F. graminearum, F. oxysporum, and F. verticillioides showed variable mycelial inhibition. The research provides insight into the potential of the bioactive compounds secreted by Trichoderma species as an effective agent for the inhibition of pectin lyases produced by phytopathogens, especially Fusarium species. The proposed research can be used to develop bioformulations that function as biopesticides, offering a sustainable replacement for chemical products.

A new parameter for quantitatively characterizing antibiotic hormesis: QSAR construction and joint toxic action judgment

Antibiotics usually induce the hormetic effects on bacteria, featured by low-dose stimulation and high-dose inhibition, which challenges the central belief in toxicity assessment and environmental risk assessment of antibiotics. However, there are currently no ideal parameters to quantitatively characterize hormesis. In this study, an effective area in hormesis (AH) was developed to quantify the biphasic dose-responses of single antibiotics (sulfonamides (SAs), sulfonamides potentiators (SAPs), and tetracyclines (TCs)) and binary mixtures (SAs-SAPs, SAs-TCs, and SAs-SAs) to the bioluminescence of Aliivibrio fischeri. Using Ebind (the lowest interaction energy between antibiotic and target protein) and Kow (octanol-water partition coefficient) as the structural descriptors, the reliable quantitative structure-activity relationship (QSAR) models were constructed for the AH values of test antibiotics and mixtures. Furthermore, a novel method based on AH was established to judge the joint toxic actions of binary antibiotics, which mainly exhibited synergism. The results also indicated that SAPs (or TCs) contributed more than SAs in the hormetic effects of antibiotic mixtures. This study proposes a new quantitative parameter for characterizing and predicting antibiotic hormesis, and considers hormesis as an integrated whole to reveal the combined effects of antibiotics, which will promote the development of risk evaluation for antibiotics and their mixtures.

Dairy and nondairy proteins as nano-architecture structures for delivering phenolic compounds: Unraveling their molecular interactions to maximize health benefits

Phenolic compounds are recognized for their benefits against degenerative diseases. Clinical and nutritional applications are limited by their low solubility, stability, and bioavailability, compromising their efficacy. Natural macromolecules, such as lipids, polysaccharides, and proteins, employed as delivery systems can efficiently overcome these limitations. In this sense, proteins are attractive due to their biocompatibility and dynamic structure properties, functional adaptability and self-assembly capabilities, offering stability, efficient encapsulation, and controlled release. This review explores the potential use of dairy proteins, caseins, and whey proteins, and, alternatively, nondairy proteins, gelatin, human serum albumin, maize zein, and soybean proteins, in building wall materials for the delivery of phenolic compounds. To optimize performance, aspects, such as protein-phenolic affinity and complex stability/activity, should be considered when designing particle nano-architecture. Molecular interactions between protein-phenolic compound complexes are, thus, further discussed, as well as the effects of temperature and pH and strategies to stabilize and preserve nano-architecture and retain phenolic compound activity. All proteins harbor one or more putative binding sites, shared or not, depending on the phenolic compound. Preservation techniques are still a case-to-case study, as no behavior patterns among different complexes are noted. Safety aspects necessary for the marketing of nanoproducts, such as characterization, toxicity assessments, and post-market monitoring as defined by the European Food Safety Authority and the Food and Drug Administration, are discussed, evidencing the need for a unified regulation. This review broadens our understanding and opens new opportunities for the development of novel protein-based nanocarriers to obtain more effective and stable products, enhancing phenolic compound delivery and health benefits.

Integrated characterization of arabica coffee husk tea using flavoromics, targeted screening, and in silico approaches

This study aimed to identify the key volatile compounds in two types of processed arabica coffee husk tea, elucidate their olfactory characteristics, and investigate their antioxidant and anti-inflammatory activities. Sensory evaluation indicated differences between the two groups. A total of 64 and 99 compounds were identified in the C and FC groups, respectively, with 5 identified as key aroma compounds (ROAV≥1). Molecular simulations indicated that four common key aroma compounds were successfully docked with OR1A1 and OR5M3 receptors, forming stable complexes. Furthermore, 14 volatile compounds interacted with 140 targets associated with oxidation and inflammation, linking to 919 gene ontology (GO) terms and 135 kyoto encyclopedia of genes and genomes (KEGG) pathways. Molecular simulations revealed that these volatile components showed antioxidant and anti-inflammatory effects by interacting with core receptors through several forces, including van der Waals, Pi-alkyl, and Pi-cation interactions and hydrogen bonds.

Review of Bio-Based Biodegradable Polymers: Smart Solutions for Sustainable Food Packaging

Conventional passive packaging plays a crucial role in food manufacturing by protecting foods from various external influences. Most packaging materials are polymer-based plastics derived from fossil carbon sources, which are favored for their versatility, aesthetic appeal, and cost-effectiveness. However, the extensive use of these materials poses significant environmental challenges due to their fossil-based origins and persistence in the environment. Global plastic consumption for packaging is expected to nearly triple by 2060, exacerbating the ecological crisis. Moreover, globalization has increased access to a diverse range of foods from around the world, heightening the importance of packaging in providing healthier and safer foods with extended shelf life. In response to these challenges, there is a growing shift to eco-friendly active packaging that not only protects but also preserves the authentic qualities of food, surpassing the roles of conventional passive packaging. This article provides a comprehensive review on the viability, benefits, and challenges of implementing bio-based biodegradable polymers in active food packaging, with the dual goals of environmental sustainability and extending food shelf life.

Application of the molecular dynamics simulation GROMACS in food science

Food comprises proteins, lipids, sugars and various other molecules that constitute a multicomponent biological system. It is challenging to investigate microscopic changes in food systems solely by performing conventional experiments. Molecular dynamics (MD) simulation serves as a crucial bridge in addressing this research gap. The Groningen Machine for Chemical Simulations (GROMACS) is an open-source, high-performing molecular dynamics simulation software that plays a significant role in food science research owing to its high flexibility and powerful functionality; it has been used to explore the molecular conformations and the mechanisms of interaction between food molecules at the microcosmic level and to analyze their properties and functions. This review presents the workflow of the GROMACS software and emphasizes the recent developments and achievements in its applications in food science research, thus providing important theoretical guidance and technical support for obtaining an in-depth understanding of the properties and functions of food.

Identification, screening and molecular mechanisms of natural stable angiotensin-converting enzyme (ACE) inhibitory peptides from foxtail millet protein hydrolysates: a combined in silico and in vitro study

The stability of bioactive peptides under various food processing conditions is the basis for their use in industrial manufacturing. This study aimed to identify natural ACE inhibitors with excellent stability and investigate their physicochemical properties and putative molecular mechanisms. Five novel ACE inhibitory peptides (QDPLFPL, FPGVSPF, SPAQLLPF, LVPYRP, and WYWPQ) were isolated and identified using RP-HPLC and Nano LC-MS/MS with foxtail millet protein hydrolysates as the raw material. These peptides are non-toxic and exhibit strong ACE inhibitory activity in vitro (IC50 values between 0.13 mg mL-1 and 0.56 mg mL-1). In addition to QDPLFPL, FPGVSPF, SPAQLLPF, LVPYRP, and WYWPQ have excellent human intestinal absorption. Compared to FPGVSPF and SPAQLLPF, the stable helical structure of LVPYRP and WYWPQ allows them to maintain high stability under conditions that mimic gastrointestinal digestion and various food processing (temperatures, pH, sucrose, NaCl, citric acid, sodium benzoate, Cu2+, Zn2+, K+, Mg2+, Ca2+). The results of molecular docking and molecular dynamics simulation suggest that LVPYRP has greater stability and binding capacity to ACE than WYWPQ. LVPYRP might attach to the active pockets (S1, S2, and S1') of ACE via hydrogen bonds and hydrophobic interactions, then compete with Zn2+ in ACE to demonstrate its ACE inhibitory activity. The binding of LVPYRP to ACE enhances the rearrangement of ACE's active structural domains, with electrostatic and polar solvation energy contributing the most energy to the binding. Our findings suggested that LVPYRP derived from foxtail millet protein hydrolysates has the potential to be incorporated into functional foods to provide antihypertensive benefits.

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.

Investigation of collagen reconstruction mechanism in skin wound through dual-beam laser welding: Insights from multi-spectroscopy, molecular dynamics simulation, and finite element multiphysics simulation

Since the mechanism underlying real-time acquisition of mechanical strength during laser-induced skin wound fusion remains unclear, and collagen is the primary constituent of skin tissue, this study investigates the structural and mechanical alterations in collagen at temperatures ranging from 40 °C to 60 °C using various spectroscopic techniques and molecular dynamics calculations. The COMSOL Multiphysics coupling is employed to simulate the three-dimensional temperature field, stress-strain relationship, and light intensity distribution in the laser thermal affected zone of skin wounds during dual-beam laser welding process. Raman spectroscopy, synchronous fluorescence spectroscopy and circular dichroism measurement results confirm that laser energy activates biological activity in residues, leading to a transformation in the originally fractured structure of collagen protein for enhanced mechanical strength. Molecular dynamics simulations reveal that stable hydrogen bonds form at amino acid residues within the central region of collagen protein when the overall temperature peak around the wound reaches 60 °C, thereby providing stability to previously fractured skin incisions and imparting instantaneous strength. However, under a 55 °C system, Type I collagen ensures macrostructural stability while activating biological properties at amino acid bases to promote wound healing function; this finding aligns with experimental analysis results. The COMSOL simulation outcomes also correspond well with macroscopic morphology after laser welding samples, confirming that by maintaining temperatures between 55 °C-60 °C during laser welding of skin incisions not only can certain instantaneous mechanical strength be achieved but irreversible thermal damage can also be effectively controlled. It is anticipated that these findings will provide valuable insights into understanding the healing mechanism for laser-welded skin wounds.

Acute toxicity of binary mixtures for quorum sensing inhibitors and sulfonamides against Aliivibrio fischeri: QSAR investigations and joint toxic actions

Quorum sensing inhibitors (QSIs), as a kind of ideal antibiotic substitutes, have been recommended to be used in combination with traditional antibiotics in medical and aquaculture fields. Due to the co-existence of QSIs and antibiotics in environmental media, it is necessary to evaluate their joint risk. However, there is little information about the acute toxicity of mixtures for QSIs and antibiotics. In this study, 10 QSIs and 3 sulfonamides (SAs, as the representatives for traditional antibiotics) were selected as the test chemicals, and their acute toxic effects were determined using the bioluminescence of Aliivibrio fischeri (A. fischeri) as the endpoint. The results indicated that SAs and QSIs all induced S-shaped dose-responses in A. fischeri bioluminescence. Furthermore, SAs possessed greater acute toxicity than QSIs, and luciferase (Luc) might be the target protein of test chemicals. Based on the median effective concentration (EC50) for each test chemical, QSI-SA mixtures were designed according to equitoxic (EC50(QSI):EC50(SA) = 1:1) and non-equitoxic ratios (EC50(QSI):EC50(SA) = 1:10, 1:5, 1:0.2, and 1:0.1). It could be observed that with the increase of QSI proportion, the acute toxicity of QSI-SA mixtures enhanced while the corresponding TU values decreased. Furthermore, QSIs contributed more to the acute toxicity of test binary mixtures. The joint toxic actions of QSIs and SAs were synergism for 23 mixtures, antagonism for 12 mixtures, and addition for 1 mixture. Quantitative structure-activity relationship (QSAR) models for the acute toxicity QSIs, SAs, and their binary mixtures were then constructed based on the lowest CDOCKER interaction energy (Ebind-Luc) between Luc and each chemical and the component proportion in the mixture. These models exhibited good robustness and predictive ability in evaluating the toxicity data and joint toxic actions of QSIs and SAs. This study provides reference data and applicable QSAR models for the environmental risk assessment of QSIs, and gives a new perspective for exploring the joint effects of QSI-antibiotic mixtures.

Deciphering the interaction mechanism between soy protein isolate and fat-soluble anthocyanin on experiments and molecular simulations

In this work, the acylated anthocyanin (Ca-An) was prepared by enzymatic modification of black rice anthocyanin with caffeic acid, and the binding mechanism of Ca-An to soybean protein isolate (SPI) was investigated by experiments and computer simulation to expand the potential application of anthocyanin in food industry. Multi-spectroscopic studies revealed that the stable binding of Ca-An to SPI induced the folding of protein polypeptide chain, which transformed the secondary structure of SPI trended to be flexible. The microenvironment of protein was transformed from hydrophobic to hydrophilic, while tyrosine played dominant role in quenching process. The binding sites and forces of the complexes were determined by computer simulation for further explored. The protein conformation of the 7S and 11S binding regions to Ca-An changed, and the amino acid microenvironment shifted to hydrophilic after binding. The results showed that more non-polar amino acids existed in the binding sites, while in binding process van der Waals forces and hydrogen bonding played a major role hydrophobicity played a minor role. Based on MM-PBSA analysis, the binding constants of 7S-Ca-An and 11S-Ca-An were 0.518 × 106 mol-1 and 5.437 × 10-3 mol-1, respectively. This information provides theoretical guidance for further studying the interaction between modified anthocyanins and biomacromolecules.

Analysis of SIKVAV's receptor affinity, pharmacokinetics, and pharmacological characteristics: a matrikine with potent biological function

Matrikines are biologically active peptides generated from fragments fragmentation of extracellular matrix components (ECM) that are functionally distinct from the original full-length molecule. The active matricryptic sites can be unmasked by ECM components enzymatic degradation or multimerization, heterotypic binding, adsorption to other molecules, cell-mediated mechanical forces, exposure to reactive oxygen species, ECM denaturation, and others. Laminin α1-derived peptide (SIKVAV) is a bioactive peptide derived from laminin-111 that participates in tumor development, cell proliferation, angiogenesis in various cell types. SIKVAV has also a potential pharmaceutical activity that may be used for tissue regeneration and bioengineering in Alzheimer's disease and muscular dystrophies. In this work, we made computational analyzes of SIKVAV regarding the ADMET panel, that stands for Administration, Distribution, Metabolism, Excretion, and Toxicity. Docking analyzes using the α3β1 and α6β1 integrin receptors were performed to fill in the gaps in the SIKVAV's signaling pathway and coupling tests showed that SIKVAV can interact with both receptors. Moreover, there is no indication of cytotoxicity, mutagenic or carcinogenic activity, skin or oral sensitivity. Our analysis suggests that SIKVAV has a high probability of interacting with peroxisome proliferator-activated receptor-gamma (NR-PPAR-γ), which has anti-inflammatory activity. The results of bioinformatics can help understand the participation of SIKVAV in homeostasis and influence the understanding of how this peptide can act as a biological asset in the control of dystrophies, neurodegenerative diseases, and tissue engineering.

Combining molecular docking and molecular dynamics simulation to discover four novel umami peptides from tuna skeletal myosin with sensory evaluation validation

Umami peptides are an important component of food flavoring agents and have high nutritional value. This work aimed to identify umami peptides from tuna skeletal myosin using a new model method of computer simulation, explore their umami mechanism, and further validate the umami tastes with sensory evaluation. Umami peptides LADW, MEIDD, VAEQE, and EEAEGT were discovered, and all of them bound to taste type 1 receptor 1 and receptor 3 via hydrogen bonds and van der Waals forces to form stable complexes. LADW exhibited the best affinity energy and binding capability. Sensory evaluation and electronic tongue confirmed that all peptides possessed an umami taste, and LADW exhibited the strongest umami intensity. This study not only explored four novel umami peptides to improve the value of tuna skeletal myosin but also provided a new method for the rapid discovery of umami peptides.

Exploring the Blood Glucose-Lowering Potential of the Umami Peptides LADW and EEAEGT Derived from Tuna Skeletal Myosin: Perspectives from α-Glucosidase Inhibition and Starch Interaction

This study aimed to explore the potential of umami peptides for lowering blood glucose. Molecular docking results showed that the peptides LADW and EEAEGT bound to the active amino acid residues of α-glucosidase via hydrogen bonds and Van der Waals forces, a finding supported by an independent gradient model (IGM). Molecular dynamics (MD) simulations demonstrated that the peptides LADW and EEAEGT can decelerate the outward expansion of α-glucosidase and reduce amino acid fluctuations at the active site. In vitro findings indicated that the peptides LADW and EEAEGT showed potent inhibitory activity against α-glucosidase, with IC50 values of 4.40 ± 0.04 and 6.46 ± 0.22 mM, respectively. Furthermore, MD simulation and morphological observation results also revealed that LADW and EEAEGT alter starch structure and form weak interactions with starch through intermolecular hydrogen bonding, leading to the inhibition of starch hydrolysis. Peptides inhibit the ability of starch to produce reducing sugars after simulated gastrointestinal digestion, providing additional evidence of the inhibition of starch hydrolysis by the added peptides. Taken together, these findings suggest that consuming the umami peptides LADW and EEAEGT may alleviate postprandial blood glucose elevations via inhibiting α-glucosidase and starch hydrolysis.

Investigation on the interaction mechanisms for stability of preheated whey protein isolate with anthocyanins from blueberry

Proteins and anthocyanins coexist in complex food systems. This research mainly studied the steady-state protective design and mechanism of the preheated protein against anthocyanins. Multispectral and molecular dynamics are utilized to illustrate the interaction mechanism between preheated whey protein isolate (pre-WPI) and anthocyanins. The pre-WPI could effectively protect the stability of anthocyanins, and the effect was better than that of the natural whey protein isolate (NW). Among them, NW after preheating treatment at 55 °C showed better protection against anthocyanin stability. Fluorescence studies indicated that pre-WPI there existed a solid binding affinity and static quenching for malvidin-3-galactoside (M3G). Multispectral data showed a significant variation in the secondary structure of pre-WPI. Furthermore, molecular dynamics simulation selects AMBER18 as the protein force field, and the results showed that hydrogen bonding participated as an applied force. Compared with NW, pre-WPI could better wrap anthocyanins and avoid damage to the external environment due to tightening of the pockets. Protein protects anthocyanins from degradation, and this protective effect is influenced by the preheating temperature of protein and the structure of protein. On the basis of the above results, it is possible to pinpoint the interaction mechanism between preheated proteins and anthocyanins.

Bioactive Dairy-Fermented Products and Phenolic Compounds: Together or Apart

Fermented dairy products (e.g., yogurt, kefir, and buttermilk) are significant in the dairy industry. They are less immunoreactive than the raw materials from which they are derived. The attractiveness of these products is based on their bioactivity and properties that induce immune or anti-inflammatory processes. In the search for new solutions, plant raw materials with beneficial effects have been combined to multiply their effects or obtain new properties. Polyphenols (e.g., flavonoids, phenolic acids, lignans, and stilbenes) are present in fruit and vegetables, but also in coffee, tea, or wine. They reduce the risk of chronic diseases, such as cancer, diabetes, or inflammation. Hence, it is becoming valuable to combine dairy proteins with polyphenols, of which epigallocatechin-3-gallate (EGCG) and chlorogenic acid (CGA) show a particular predisposition to bind to milk proteins (e.g., α-lactalbumin β-lactoglobulin, αs1-casein, and κ-casein). Reducing the allergenicity of milk proteins by combining them with polyphenols is an essential issue. As potential 'metabolic prebiotics', they also contribute to stimulating the growth of beneficial bacteria and inhibiting pathogenic bacteria in the human gastrointestinal tract. In silico methods, mainly docking, assess the new structures of conjugates and the consequences of the interactions that are formed between proteins and polyphenols, as well as to predict their action in the body.

Identification of Novel Umami Peptides in Termitornyces albuminosus (Berk) Heim Soup by In Silico Analyses Combined with Sensory Evaluation: Discovering Potential Mechanism of Umami Taste Formation with Molecular Perspective

In this study, 24 peptides were identified in Termitornyces albuminosus (Berk) Heim soup, 12 of which were predicted to possess an umami taste based on the BIOPEP-UWM or Umami-MRNN databases. Among these 12 peptides, four peptides (i.e., QNDF, QGGDF, EPVTLT, and EVNYDFGGK) exhibited the lowest affinity energy with the umami receptor type 1 member 1 (T1R1) subunit. Molecular docking and molecular dynamics simulation further confirmed the strong binding of these four umami peptides to the umami receptor T1R1/T1R3, with the EVNYDFGGK forming the most stable complex. After synthesizing the four peptides, their umami taste was validated through sensory and electronic tongue analyses with recognition thresholds ranging from 0.0938 to 0.3750 mmol/L. Notably, the EVNYDFGGK peptide displayed the strongest umami taste (recognition threshold, 0.0938 mmol/L). This study may contribute to the industrial development of T. albuminosus by providing a new understanding of the mechanism of its umami formation.

Construction of a QSAR Model Based on Flavonoids and Screening of Natural Pancreatic Lipase Inhibitors

Pancreatic lipase (PL) is a key hydrolase in lipid metabolism. Inhibition of PL activity can intervene in obesity, a global sub-health disease. The natural product is considered a good alternative to chemically synthesized drugs due to its advantages, such as low side effects. However, traditional experimental screening methods are labor-intensive and cost-consuming, and there is an urgent need to develop high-throughput screening methods for the discovery of anti-PL natural products. In this study, a high-throughput virtual screening process for anti-PL natural products is provided. Firstly, a predictable anti-PL natural product QSAR model (R2train = 0.9444, R2test = 0.8962) were developed using the artificial intelligence drug design software MolAIcal based on genetic algorithms and their conformational relationships. 1068 highly similar (FS > 0.8) natural products were rapidly enriched based on the structure-activity similarity principle, combined with the QSAR model and the ADMET model, for rapid prediction of a total of five potentially efficient anti-PL natural products (IC50pre < 2 μM). Subsequently, molecular docking, molecular dynamics simulation, and MMGBSA free energy calculation were performed to not only reveal the interaction of candidate novel natural products with the amino acid residues of PL but also to validate the stability of these novel natural compounds bound to PL. In conclusion, this study greatly simplifies the screening and discovery of anti-PL natural products and accelerates the development of novel anti-obesity functional foods.

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.

Gelation behavior and mechanism of Nicandra physalodes (Linn.) Gaertn. seeds pectin induced by Glucono-delta-lactone

In this study, the physicochemical properties of pectin from Nicandra physalodes (Linn.) Gaertn. seeds (NPGSP) were analysed firstly, and the rheological behavior, microstructure and gelation mechanism of NPGSP gels induced by Glucono-delta-lactone (GDL) were investigated. The hardness of NPGSP gels was increased from 26.27 g to 226.77 g when increasing GDL concentration from 0 % (pH = 4.0) to 1.35 % (pH = 3.0), and the thermal stability was improved. The peak around 1617 cm^-1 was decreased as the adsorption peak of the free carboxyl groups was attenuated with addition of GDL. GDL increased the crystalline degree of NPGSP gels, and its microstructure exhibited more smaller spores. Molecular dynamics was performed on systems of pectin and gluconic acid (GDL hydrolysis product), indicating that inter-molecular hydrogen bonds and van der Waals forces were the main interactions to promote gels formation. Overall, NPGSP has the potential commercial value for developing as a thickener in food processing.

Exploring the Promotive Effects and Mechanisms of Different Polyphenolic Extracts from Prinsepia utilis Royle Seed Shell on Tyrosinase

Prinsepia utilis Royle (P. utilis) is commonly used as a food ingredient and herbal medicine according to folk records, yet little research has been done on the seed shell, a processing waste. The aim of this study was to investigate the distribution of polyphenolic components and the tyrosinase activation activity of different extracts from the seed shell by UHPLC-ESI-HRMS/MS, in vitro tyrosinase activity assay, molecular docking and molecular dynamics. A total of 16 phytochemicals were identified, of which (+)-catechin and (-)-epicatechin were the major polyphenolic compounds. Both the esterified and insoluble bound polyphenols exhibited tyrosinase activation activity, and the esterified polyphenols showed better tyrosinase activation activity. (+)-Catechin and (-)-epicatechin might be the main activators of tyrosinase, both of which may act as substrate to affect tyrosinase activity. By molecular docking and molecular dynamics simulation studies, (+)-catechin and (-)-epicatechin can be efficiently and stably bound to the tyrosinase active site through hydrogen bonds, van der Waals forces and π-bonds. The results of this study may not only provide a scientific basis for exploring P. utilis seed shell as a potential activator of tyrosinase, but also contribute to the high value utilization of P. utilis processing by-products.

Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science

Having played important roles in human growth and development, livestock animals are regarded as integral parts of society. However, industrialization has depleted natural resources and exacerbated climate change worldwide, spurring the emergence of various diseases that reduce livestock productivity. Meanwhile, a growing human population demands sufficient food to meet their needs, necessitating innovations in veterinary sciences that increase productivity both quantitatively and qualitatively. We have been able to address various challenges facing veterinary and farm systems with new scientific and technological advances, which might open new opportunities for research. Recent breakthroughs in multi-omics platforms have produced a wealth of genetic and genomic data for livestock that must be converted into knowledge for breeding, disease prevention and management, productivity, and sustainability. Vetinformatics is regarded as a new bioinformatics research concept or approach that is revolutionizing the field of veterinary science. It employs an interdisciplinary approach to understand the complex molecular mechanisms of animal systems in order to expedite veterinary research, ensuring food and nutritional security. This review article highlights the background, recent advances, challenges, opportunities, and application of vetinformatics for quality veterinary services.

The effects of β-lactoglobulin on cyanidin-3-O-glucoside antioxidant activity and bioaccessibility after heat treatment

The impact of heat treatment at different temperatures on the interaction of β-lactoglobulin (β-Lg) and anthocyanin-3-O-glucoside (C3G) was studied. Heat treatment and the addition of C3G changed the secondary structure of β-Lg with decreasing β-sheets and increasing random coils. Interactions between C3G and β-Lg were mainly via hydrogen bonds and van der Waals forces at 25 °C. The elevated temperature promoted hydrophobic interactions between C3G and β-Lg due to an increase in the hydrophobic groups and amino groups on the surface of β-Lg molecules. The addition of β-Lg to the C3G eliminated heat-induced thermal degradation of C3G. The β-Lg-C3G interactions accompanied with increased particle size and constant zeta potential could increase the antioxidant capacity of C3G approximately by 4% to 10% and protect the colour of C3G from degradation under heat treatment. The C3G bioaccessibility with β-Lg addition increased by 26.08%, 33.45%, 83.09%, 72.27%, and 354.62% compared with C-25, C-60, C-85, C-100, and C-121, respectively. The protective effect of the non-covalent interactions on C3G at high temperatures (85 °C to 121 °C) was significantly stronger than at 25 °C and 60 °C. The application of β-Lg in foodstuffs could enhance the antioxidant activity and bioaccessibility of C3G.

Advances in dietary proteins binding with co-existed anthocyanins in foods: Driving forces, structure-affinity relationship, and functional and nutritional properties

Anthocyanins, which are the labile flavonoid pigments widely distributed in many fruits, vegetables, cereal grains, and flowers, are receiving intensive interest for their potential health benefits. Proteins are important food components from abundant sources and present high binding affinity for small dietary compounds, e.g., anthocyanins. Protein-anthocyanin interactions might occur during food processing, ingestion, digestion, and bioutilization, leading to significant changes in the structure and properties of proteins and anthocyanins. Current knowledge of protein-anthocyanin interactions and their contributions to functions and bioactivities of anthocyanin-containing foods were reviewed. Binding characterization of dietary protein-anthocyanins complexes is outlined. Advances in understanding the structure-affinity relationship of dietary protein-anthocyanin interaction are critically discussed. The associated properties of protein-anthocyanin complexes are considered in an evaluation of functional and nutritional values.

Preparation, characterization and antioxidant activity of sinapic acid grafted chitosan and its application with casein as a nanoscale delivery system for black rice anthocyanins

Anthocyanins (ACNs) have attracted considerable research attention because of their excellent health benefits, but their low stability and bioavailability limit their applications. In this study, sinapic acid-grafted-chitosan (SA-g-CS) conjugate was synthesized by grafting SA onto CS via a free radical mediated method. Nanoparticles were prepared using casein (CA) together with SA-g-CS to improve the performance and sustained release of black rice anthocyanins (BRA). The results of UV-Vis, FTIR and ¹H NMR spectra for SA-g-CS conjugates demonstrated the successful grafting of SA onto CS. The results of DPPH, ABTS and ferric ion reducing antioxidant power assays showed that the SA-g-CS conjugates had strong antioxidant capacities, and the higher the pH of the grafting reaction system, the stronger the antioxidant capacity of the conjugates. X-ray diffraction and scanning electron microscopy analyses showed that the crystallographic property and microstructure of CS were improved by the grafting of SA. Compared with BRA loaded nanoparticles prepared with CA alone or the combination of CS and CA, the BRA loaded nanoparticles constructed by SA-g-CS and CA have smaller particle size, better dispersion, encapsulation efficiency and sustained-release property. These results provided great potential for the application of phenolic acid grafted CS in stabilizing ACNs.

Interfering effects on the bioactivities of several key proteins of COVID-19/variants in diabetes by compounds from Lianqiao leaves: In silico and in vitro analyses

Diabetes is considered to be one of the diseases most associated with COVID-19. In this study, interfering effects and potential mechanisms of several compounds from Lianqiao (Forsythia suspensa (Thunb.) Vahl) leaves on the bioactivities of some key proteins of COVID-19 and its variants, as well as diabetic endothelial dysfunctions were illuminated through in vitro and in silico analyses. Results showed that, among the main ingredients in the leaves, forsythoside A showed the strongest docking affinities with the proteins SARS-CoV-2-RBD-hACE2 of COVID-19 and its variants (Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617)), as well as neuropilin-1 (NRP1), and SARS-CoV-2 main protease (MPro) to interfere coronavirus entering into the human body. Moreover, forsythoside A was the most stable in binding to receptors in Delta (B.1.617) system. It also has good antiviral activities and drug properties and has the strongest binding force to the RBD domain of COVID-19. In addition, forsythoside A reduced ROS production in AGEs-induced EA.hy926 cells, maintained endothelial integrity, and bound closely to protein profilin-1 (PFN1) receptor. This work may provide useful knowledge for further understanding the interfering effects and potential mechanisms of compounds, especially forsythoside A, from Lianqiao leaves on the bioactivities of key proteins of COVID-19/variants in diabetes.

Novel angiotensin-converting enzyme (ACE) inhibitory mechanism of peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2)

This work aimed to identify novel angiotensin-converting-enzyme (ACE) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2). The MiAMP2 protein was hydrolyzed through in silico digestion, and the generated peptides were screened for ACE inhibitory activity. The in silico enzyme digestion results revealed that 18 unreported peptides were obtained using AHTPDB and BIOPEP-UWM, and none were thought to be toxic based on absorption, distribution, metabolism, and excretion (ADMET) prediction. PGPR, RPLY, MNPQR, and AAPR were predicted to exhibit good biological activity. The molecular docking results revealed that the four peptides tightly bound to the active pocket of ACE via hydrogen bonds and hydrophobic interactions, among which RPLY and MNPQR bound to ACE more strongly. The in vitro assay results confirmed that RPLY and MNPQR peptides inhibited ACE via competitive manner. These results provide theoretical guidance for the development of novel foodborne antihypertensive peptides from Macadamia nut proteins. PRACTICAL APPLICATIONS: This study provides new insight on the inhibitory potential of Macadamia nut peptides against ACE, which may be further applied to the development of antihypertensive peptides in the medical industry.

The interactions between anthocyanin and whey protein: A review

Anthocyanins (ACN) are natural pigments that produce bright red, blue, and purple colors in plants and can be used to color food products. However, ACN sensitivity to different factors limits their applications in the food industry. Whey protein (WP), a functional nutritional additive, has been shown to interact with ACN and improve the color, stability, antioxidant capacity, bioavailability, and other functional properties of the ACN-WP complex. The WP's secondary structure is expected to unfold due to heat treatment, which may increase its binding affinity with ACN. Different ACN structures will also have different binding affinity with WP and their interaction mechanism may also be different. Circular dichroism (CD) spectroscopy and Fourier transform infrared (FTIR) spectroscopy show that the WP secondary structure changes after binding with ACN. Fluorescence spectroscopy shows that the WP maximum fluorescence emission wavelength shifts, and the fluorescence intensity decreases after interaction with ACN. Moreover, thermodynamic analysis suggests that the ACN-WP binding forces are mainly hydrophobic interactions, although there is also evidence of electrostatic interactions and hydrogen bonding between ACN and WP. In this review, we summarize the information available on ACN-WP interactions under different conditions and discuss the impact of different ACN chemical structures and of WP conformation changes on the affinity between ACN and WP. This summary helps improve our understanding of WP protection of ACN against color degradation, thus providing new tools to improve ACN color stability and expanding the applications of ACN and WP in the food and pharmacy industries.

Inactivation kinetics and cell envelope damages of foodborne pathogens Listeria monocytogenes and Salmonella Enteritidis treated with cold plasma

In recent years, more attention has been paid to the application of cold plasma (CP) in eliminating foodborne pathogenic bacteria. This work investigated CP effects on inactivation kinetics and cell envelopes of Listeria monocytogenes (L. monocytogenes) and Salmonella Enteritidis (S. Enteritidis). Bacterial suspensions were treated with dielectric barrier discharge atmospheric CP at 75 kV for different treatment time. Three regression models were tested for estimating inactivation kinetics. Reactive species generated in plasma, the appearance and integrity of bacterial cells, the activity and secondary structure of enzymes in the cell envelope, and molecular docking, were measured for evaluating the envelope damages. Results indicated that Log-linear model was suitable for L. monocytogenes and the Weibull model was suitable for S. Enteritidis. S. Enteritidis was more sensitive to short-lived reactive species (such as OH radicals) in plasma than L. monocytogenes, and the cell envelope of S. Enteritidis was more severely damaged (the increased membrane permeability and leakage of intracellular substances) after plasma treatment. Interestingly, compared with S. Enteritidis, the decrease in the activity of enzymes existing in the cell envelope of L. monocytogenes did not contribute significantly to the death of bacteria. Molecular docking further suggested that the decrease in the enzyme activity might be due to the modification of the enzyme, by the interaction between reactive species in plasma (H₂O₂) and amino acid residues of the enzyme through the hydrogen bond.

In silico analysis of novel dipeptidyl peptidase-IV inhibitory peptides released from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and the possible pathways involved in diabetes protection

The aim of the present study was to screen novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2) and evaluate the potential antidiabetic targets and involved signaling pathways using in silico approaches. In silico digestion of MiAMP2 with pepsin, trypsin and chymotrypsin was performed with ExPASy PeptideCutter and the generated peptides were subjected to BIOPEP-UWM, iDrug, INNOVAGEN and Autodock Vina for further analyses. Six novel peptides EQVR, EQVK, AESE, EEDNK, EECK, and EVEE were predicted to possess good DPP-IV inhibitory potentials, water solubility, and absorption, distribution, metabolism, excretion, and toxicity properties. Molecular dynamic simulation and molecular docking displayed that AESE was the most potent DPP-IV inhibitory peptide and can bind with the active sites of DPP-IV through hydrogen bonding and van der Waals forces. The potential antidiabetic targets of AESE were retrieved from SwissTargetPrediction and GeneCards databases. Protein-protein interaction analysis identified BIRC2, CASP3, MMP7 and BIRC3 to be the hub targets. Moreover, the KEGG pathway enrichment analysis showed that AESE prevented diabetes through the apoptosis and TNF signaling pathways. These results will provide new insights into utilization of MiAMP2 as functional food ingredients for the prevention and treatment of diabetes.

Molecular Simulation Study on the Interaction between Tyrosinase and Flavonoids from Sea Buckthorn

Isorhamnetin, kaempferol, myricetin, and quercetin are four kinds of secondary metabolites in sea buckthorn, which have a wide range of biological activities. Investigating their interactions with tyrosinase at the atomic level can improve the bioavailability of sea buckthorn. Both molecular docking and molecular dynamics simulation methods were employed to study the interactions of these ligands with tyrosinase. The results of molecular docking indicated that these four small molecules such as isorhamnetin, kaempferol, myricetin, and quercetin can all dock into the active center of tyrosinase, and by occupying the active site, they can prevent substrate binding, thereby reducing the catalytic activity of tyrosinase. Molecular dynamics simulation trajectory analysis showed that all tyrosinase-ligand complexes reach an equilibrium within 100 ns. In addition, quercetin has the lowest binding energy among these four ligands, and the complex with tyrosinase is the most stable. This study not only provides valuable information for improving the bioavailability of sea buckthorn but also contributes to the discovery of effective natural inhibitors of tyrosinase.

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.