Structure-function relationship of small peptides generated during the ripening of Spanish dry-cured ham: Peptidome, molecular stability and computational modelling

Dual function antioxidant and anti-inflammatory fish maw peptides: Isolation and structure-activity analysis via tandem molecular docking and quantum chemical calculation

The structure-function relationship of gastrointestinal tract digestion-derived fish maw peptides remains largely unknown. This study aims to elucidate the active sites and cellular bioactivities of these peptides through molecular docking (MD), density functional theory (DFT) computations, in silico bioinformatic analysis, and in cellulo Caco-2 cell studies. In silico screening identified 29 non-toxic, non-allergenic, and water-soluble peptides. Seven peptides exhibited favorable binding to the Keap1-Kelch (2FLU) and TNF-α (2AZ5) proteins. Specifically, peptides WIDPNQG, GFPGER, and FLLFRQ demonstrated the highest electron affinities and smallest HOMO-LUMO energy gaps, suggesting strong free-radical scavenging potential. Both DFT and ex situ MD confirmed the active sites of the seven peptides. The guanidinium group was the dominant active site on six peptides. The isolated peptides improved cellular redox balance, reduced malonaldehyde, and suppressed inflammatory cytokines. This study confirmed DFT computations as a novel tool for elucidating the structure-function relationship of food-derived peptides.

Sacha Inchi (Plukenetia volubilis L.) Protein Hydrolysate as a New Ingredient of Functional Foods

Sacha inchi (Plukenetia volubilis L.) is an under-exploited crop with great potential due to its nutritional and medicinal characteristics. A Sacha inchi protein isolate (SII), obtained from defatted Sacha inchi flour (SIF), was hydrolyzed by Bioprotease LA 660 under specific conditions. The hydrolysates were characterized chemically, and their digestibility and antioxidant capacity were evaluated by in vitro cell-free experiments to select the hydrolysate with major antioxidant activity. Sacha inchi protein hydrolysate at 20 min (SIH20B) was selected, and the anti-inflammatory capacity was evaluated by RT-qPCR and ELISA techniques, using two different doses in monocytes THP-1 stimulated with lipopolysaccharide (LPS). The results obtained showed that the in vitro administration of SIH20B down-regulated the TNF-α gene and reduced the release of this cytokine, whereas the anti-inflammatory cytokines IL-10 and IL-4 were up-regulated in LPS-stimulated monocytes and co-administrated with SIH20B. The peptides contained in SIH20B were identified, and the 20 more relatively abundant peptides with a mass by 1 kDa were subjected to in silico analysis to hypothesize those that could be responsible for the bioactivity reported in the hydrolysate. From the identified peptides, the peptides AAGALKKFL and LGVKFKGGL, among others, are proposed as the most biologically actives. In conclusion, SIH20B is a novel, natural source of high-value-added biopeptides that could be used as an ingredient in formulations of food or nutraceutical compounds.

Unlocking the potential of chicken liver byproducts: Identification of antioxidant peptides through in silico approaches and anti-aging effects of a selected peptide in Caenorhabditis elegans

Chicken meat processing generates a substantial number of byproducts, which are either underutilized or improperly disposed. In this study, we employed in silico approaches to identify antioxidant peptides in chicken liver byproducts. Notably, the peptide WYR exhibited remarkable 2,2-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) radical scavenging activity with an IC50 of 0.13 ± 0.01 mg/mL and demonstrated stability under various conditions, including thermal, pH, NaCl, and simulated gastrointestinal digestion. Molecular docking analysis revealed significant hydrogen bonding interactions, while molecular dynamics showed differential stability with ABTS and 2,2-Diphenyl-1-picrylhydrazyl (DPPH). WYR exhibited improved stress resistance, decreased levels of reactive oxygen species (ROS), elevated the activities of superoxide dismutase (SOD) and catalase (CAT), and modulated the expression of crucial genes through the insulin/insulin-like growth factor (IIS) signaling pathway, mitogen-activated protein kinase (MAPK), and heat shock transcription factor-1 (HSF-1) pathways. These effects collectively contributed to the extension of Caenorhabditis elegans' lifespan. This study not only provides an effective method for antioxidant peptide analysis but also highlights the potential for enhancing the utilization of poultry byproducts.

Identification and Free Radical Scavenging Activity of Oligopeptides from Mixed-Distillate Fermented Baijiu Grains and Soy Sauce Residue

This study aimed to explore the potential antioxidant activity and mechanism of oligopeptides from sauce-aroma Baijiu. The oligopeptides of Val-Leu-Pro-Phe (VLPF), Pro-Leu-Phe (PLF), Val-Gly-Phe-Cys (VGFC), Leu-Tyr-Pro (LYP), Leu-Pro-Phe (LPF), and Phe-Thr-Phe (FTF) were identified by liquid chromatography-mass spectrometry (LC-MS) from the mixed-distillate of Baijiu fermented grains and soy sauce residue (MDFS). The antioxidant mechanism of these oligopeptides on scavenging DPPH•, ABTS•+, and hydroxide radicals was investigated, respectively. Among them, VGFC had the strongest potential antioxidant activity, which was responsible for its hydrogen bonds with these radicals with high affinity. The binding energies between VGFC and these radicals were -1.26 kcal/mol, -1.33 kcal/mol, and -1.93 kcal/mol, respectively. Additionally, free radicals prefer to bind the oligopeptide composed of hydrophobic amino acid residues such as Leu, Val, Phe, and Pro, thus being scavenged for exerting antioxidant activity. It provided a new idea for the development and utilization of bioactive oligopeptides in sauce-aroma Baijiu.

Novel antioxidant peptides identified from coix seed by molecular docking, quantum chemical calculations and invitro study in HepG2 cells

The aim of the study was to identify potent antioxidant peptides sourced from coix seed, analyze the structure-activity relationship through molecular docking and quantum chemical calculation. Molecular docking results showed that among thirteen peptides selected in silico, eight had favourable binding interaction with the Keap1-Kelch domain (2FLU). Promising peptides with significant binding scores were further evaluated using quantum calculation. It was shown that peptide FFDR exhibited exceptional stability, with a high energy gap of 5.24 eV and low Highest Occupied Molecular Orbitals (HOMO) and Lowest Unoccupied Molecular Orbitals (LUMO) values. Furthermore, FFDR displayed the capacity to enhance the expression of Nrf2-Keap1 antioxidant genes (CAT, SOD, GSH-Px) and improved cellular redox balance by increasing reduced glutathione (GSH) while reducing oxidized glutathione (GSSG) and malonaldehyde (MDA) levels. These findings highlight the potential of coix seed peptides in developing novel, effective and stable antioxidant-based functional foods.

Identification of the Bioavailable Peptidome of Chia Protein Hydrolysate and the In Silico Evaluation of Its Antioxidant and ACE Inhibitory Potential

The incorporation of novel, functional, and sustainable foods in human diets is increasing because of their beneficial effects and environmental-friendly nature. Chia (Salvia hispanica L.) has proved to be a suitable source of bioactive peptides via enzymatic hydrolysis. These peptides could be responsible for modulating several physiological processes if able to reach the target organ. The bioavailable peptides contained in a hydrolysate obtained with Alcalase, as functional foods, were identified using a transwell system with Caco-2 cell culture as the absorption model. Furthermore, 20 unique peptides with a molecular weight lower than 1000 Da and the higher statistical significance of the peptide-precursor spectrum match (-10 log P) were assessed by in silico tools to suggest which peptides could be those exerting the demonstrated bioactivity. From the characterized peptides, considering the molecular features and the results obtained, the peptides AGDAHWTY, VDAHPIKAM, PNYHPNPR, and ALPPGAVHW are anticipated to be contributing to the antioxidant and/or ACE inhibitor activity of the chia protein hydrolysates.

Goat milk-derived short chain peptides: Peptide LPYV as species-specific characteristic and their versatility bioactivities by MOF@Fe3O4@GO mesoporous magnetic-based peptidomics

Goat milk as an ideal substitute for human milk has not been sufficiently explored. An in-situ synthesized MOF@Fe₃O₄@GO was demonstrated as a magnetic mesoporous adsorbent for efficiently enriching short chain peptides (SCPs) in milk compared with the routine solid phase extraction approach with graphite carbon black or C₁₈ as the packing material in terms of the number of enriched SCPs and data stability. A total of 61 and 126 SCPs were identified and quantified in bovine milk (0.09-89.34 μg L^-1) and goat milk (10.5-1267.06 μg L^-1), respectively, and peptide LPYV can be used as a potential marker for adulteration of goat milk. Relative high expression of chymotrypsin and pepsin by EnzymePredictor analysis could partially elaborate the reason of the abundance of SCPs in goat milk. Compared with bovine milk, further bioinformatics analysis indicated that goat milk could own higher nutritional value because of relative higher concentrations (>1 mg/L) of SCPs (LLV, FL, LVYP) with confirmed bioactivities including angiotensin-converting enzyme (ACE) inhibitor, antioxidant, dipeptidylpeptidase (DPP) III and DPP IV inhibitor, etc. Overall, this study opened a novel avenue for understanding versatility benefit of dairy products from a perspective of SCPs by using a developed MOF@Fe₃O₄@GO mesoporous magnetic-based peptidomics.

Bioactive and Sensory Di- and Tripeptides Generated during Dry-Curing of Pork Meat

Dry-cured pork products, such as dry-cured ham, undergo an extensive proteolysis during manufacturing process which determines the organoleptic properties of the final product. As a result of endogenous pork muscle endo- and exopeptidases, many medium- and short-chain peptides are released from muscle proteins. Many of them have been isolated, identified, and characterized, and some peptides have been reported to exert relevant bioactivity with potential benefit for human health. However, little attention has been given to di- and tripeptides, which are far less known, although they have received increasing attention in recent years due to their high potential relevance in terms of bioactivity and role in taste development. This review gathers the current knowledge about di- and tripeptides, regarding their bioactivity and sensory properties and focusing on their generation during long-term processing such as dry-cured pork meats.

Identification of Antioxidant Peptides Derived from Tilapia (Oreochromis niloticus) Skin and Their Mechanism of Action by Molecular Docking

Antioxidants, which can activate the body’s antioxidant defence system and reduce oxidative stress damage, are important for maintaining free radical homeostasis between oxidative damage and antioxidant defence. Six antioxidant peptides (P1–P6) were isolated and identified from the enzymatic hydrolysate of tilapia skin by ultrafiltration, reversed-phase high-performance liquid chromatography (RP-HPLC) and liquid chromatography–tandem mass spectrometry (LC–MS/MS). Moreover, the scavenging mechanism of the identified peptides against DPPH (2,2-Diphenyl-1-picrylhydrazyl) and ABTS (2-azido-bis (3-ethylbenzothiazoline-6-sulfonic acid) was studied by molecular docking. It was found that Pro, Ala and Tyr were the characteristic amino acids for scavenging free radicals, and hydrogen bonding and hydrophobic interactions were the main interactions between the free radicals and antioxidant peptides. Among them, the peptide KAPDPGPGPM exhibited the highest DPPH free radical scavenging activity (IC₅₀ = 2.56 ± 0.15 mg/mL), in which the hydrogen bond between the free radical DDPH and Thr-6 was identified as the main interaction, and the hydrophobic interactions between the free radical DDPH and Ala, Gly and Pro were also identified. The peptide GGYDEY presented the highest scavenging activity against ABTS (IC₅₀ = 9.14 ± 0.08 mg/mL). The key structures for the interaction of this peptide with the free radical ABTS were identified as Gly-1 and Glu-5 (hydrogen bond sites), and the amino acids Tyr and Asp provided hydrophobic interactions. Furthermore, it was determined that the screened peptides are suitable for applications as antioxidants in the food industry, exhibit good water solubility and stability, are likely nonallergenic and are nontoxic. In summary, the results of this study provide a theoretical structural basis for examining the mechanism of action of antioxidant peptides and the application of enzymatic hydrolysates from tilapia skin.

Effects of Short-Chain Peptides on the Flavor Profile of Baijiu by the Density Functional Theory: Peptidomics, Sensomics, Flavor Reconstitution, and Sensory Evaluation

The effect of peptides on the flavor profile of Baijiu is unclear as a result of their trace concentrations in the complex matrix, and therefore, the study involving the interaction mechanism between peptides and flavor compounds is limited. In this study, short-chain peptides (amino acid number between 2 and 4, SCPs) associated with the Feng-flavor Baijiu (FFB) were comprehensively analyzed by a dedicated workflow using ultra-high-performance liquid chromatography Q Orbitrap high-resolution mass spectrometry, flavor reconstitution experiments, sensory analysis, and density functional theory (DFT) analysis. The concentrations of 96 SCPs intimately related with six different grades of honey aroma intensity in FFB were quantified (0.12-155.01 μg L^-1) after multivariable analysis, Spearman's correlation analysis (ρ ≥ 0.7), and confirmation with synthetic standards, and 32 dominant odorants with an odor activity value of ≥1 in FFB with the highest intensity of honey aroma were quantified by gas chromatography-mass spectrometry and gas chromatography-flame ionization detection analyses. The results of flavor reconstitution experiments and sensory analysis indicated that the SCPs can obviously influence the honey aroma with amplifying the fruity, sweet, and flora flavor odor characters (p < 0.05) while significantly reducing the acidic character (p < 0.001), which could be attributed to the most stable complex structure between SCPs and odor-active compounds calculated by DFT being butanoic acid, followed by β-damascenone, 3-methylbutanal, and ethyl hexanoate, and the multiple sites as a hydrogen bond donor or acceptor in SCPs can form a stable ternary structure with water and ethanol inside the peptide chain or carboxyl terminal of SCPs, consequently improving the stability of the Baijiu system. The results highlighted the important role of SCPs on the volatiles in Baijiu and laid the foundation for further facilitating the sensory quality of Baijiu products.

BIOPEP-UWM Virtual—A Novel Database of Food-Derived Peptides with In Silico-Predicted Biological Activity

The novel BIOPEP-UWM Virtual database is designed as a repository of peptide sequences whose bioactivity or taste information was the result of in silico predictions. It is a tool complementary to the existing BIOPEP-UWM database summarizing the results of experimental data on bioactive peptides. The layout and organization of the new database are identical to those of the existing BIOPEP-UWM database of bioactive peptides. The peptide data record includes the following information: name; sequence and function information (understood as information about the predicted target biomacromolecule); bibliographic data with the reference paper describing the peptide; additional information, including the peptide structure, annotated using chemical codes as well as the specification of the method used for bioactivity prediction; information about other activities discovered experimentally or predicted using computational methods; peptide taste (if available); and a database reference tab providing information about compound annotations in other databases (if available).