Active sites of peptides Asp-Asp-Asp-Tyr and Asp-Tyr-Asp-Asp protect against cellular oxidative stress

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.

Novel and efficient techniques in the discovery of antioxidant peptides

As a research hotspot in food science and nutrition, antioxidant peptides can function by scavenging free radicals, inhibiting peroxides, and chelating metal ions. Therefore, how to efficiently discover and screen antioxidant peptides has become a key issue in research and production. Traditional discovery methods are time-consuming and costly, but also challenging to resolve the quantitative structure-activity relationship of antioxidant peptides. Several novel techniques, including artificial intelligence, molecular docking, bioinformatics, quantum chemistry, phage display, switchSENSE, surface plasmon resonance, and fluorescence polarization, are emerging rapidly as solutions. These techniques possess efficient capability for the discovery of antioxidant peptides, even with the potential for high-throughput screening. In addition, the quantitative structure-activity relationship can be resolved. Notably, combining these novel techniques can overcome the drawbacks of a single one, thus improving efficiency and expanding the discovery horizon. This review has summarized eight novel and efficient techniques for discovering antioxidant peptides and the combination of techniques. This review aims to provide scientific evidence and perspectives for antioxidant peptide research.

Cyperus peptide SFRWQ inhibits oxidation and inflammation in RAW264.7 cell model

Oxidative stress can induce many diseases. Antioxidant peptides from food sources have the advantages of good safety, high activity, and good absorbability. In this study, a pentapeptide (SFRWQ; SER-PHE-ARG-TRP-GLN) was identified in a protein hydrolysate of Cyperus (Cyperus esculentus L.). Enzyme-linked immunosorbent assay (ELISA), real-time quantitative (qPCR), immunofluorescence and other techniques were used to evaluate the anti-inflammatory and antioxidant effects of SFRWQ. SFRWQ was found to have 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical-scavenging ability, help increase superoxide dismutase (SOD) and catalase (CAT) levels in RAW264.7 cells, reduce reactive oxygen species (ROS) levels, and decrease tumor necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) gene expression and secretion. The binding score of SFRWQ to recombinant Kelch-like ECH-associated protein 1 (Keap1) was greater than that of TX6. These findings suggest that SFRWQ activates the Keap1-Nrf2 cellular antioxidant signaling pathway. According to metabolomics studies, SFRWQ increased glutathione (GSH), glutathione disulfide (GSSG), and γ-glutamylcysteine levels and decreased the levels of Prostaglandin D2 (PGD2), Prostaglandin E2 (PGE2), and Prostaglandin H2 (PGH2), which are involved in arachidonic acid metabolism, to protect cells from LPS-induced damage. By elucidating the mechanism of action of SFRWQ, we provide a reference for the development of dietary antioxidant peptides.

De novo antioxidant peptide design via machine learning and DFT studies

Antioxidant peptides (AOPs) are highly valued in food and pharmaceutical industries due to their significant role in human function. This study introduces a novel approach to identifying robust AOPs using a deep generative model based on sequence representation. Through filtration with a deep-learning classification model and subsequent clustering via the Butina cluster algorithm, twelve peptides (GP1-GP12) with potential antioxidant capacity were predicted. Density functional theory (DFT) calculations guided the selection of six peptides for synthesis and biological experiments. Molecular orbital representations revealed that the HOMO for these peptides is primarily localized on the indole segment, underscoring its pivotal role in antioxidant activity. All six synthesized peptides exhibited antioxidant activity in the DPPH assay, while the hydroxyl radical test showed suboptimal results. A hemolysis assay confirmed the non-hemolytic nature of the generated peptides. Additionally, an in silico investigation explored the potential inhibitory interaction between the peptides and the Keap1 protein. Analysis revealed that ligands GP3, GP4, and GP12 induced significant structural changes in proteins, affecting their stability and flexibility. These findings highlight the capability of machine learning approaches in generating novel antioxidant peptides.

Isolation, identification of antioxidant peptides from earthworm proteins and analysis of the structure-activity relationship of the peptides based on quantum chemical calculations

Earthworms are emerging sources of edible animal proteins. Earthworm extracts exhibit good in vivo antioxidant activity after oral administration. To better understand the antioxidant activity of earthworms, antioxidant peptides derived from earthworm proteins after gastrointestinal digestion were isolated and identified, and their structure-activity relationships were analysed in this research. Results showed that earthworm protein gastrointestinal digestion products exhibited good antioxidant activity, and 6030 peptide sequences were identified after separation using ion-exchange and gel-chromatography columns. Eleven peptides were screened using computer simulation activity scores, among which AFWYGLPCKL, WPWQMSLY, and GCFRYACGAFY showed the best antioxidant activities. Highest Occupied Molecular Orbital (HOMO) analysis indicated that N29-H10, O122-H38, and the peptide bond binding sites of serine and leucine were active sites of peptides AFWYGLPCKL, GCFRYACGAFY, and WPWQMSLY, respectively. This study provides a new understanding of substance basis of antioxidant activity in earthworms and contributes to application of earthworm proteins as antioxidants in health-foods.

Novel Antioxidant Peptides Derived from Feather Keratin Alleviate H2O2-Induced Oxidative Damage in HepG2 Cells via Keap1/Nrf2 Pathway

Reactive oxygen species (ROS) are crucial for signal transduction and the maintenance of cellular homeostasis. However, superfluous ROS may engender chronic pathologies. Feather keratin is a promising new source of antioxidant peptides that can eliminate excess ROS and potentially treat oxidative stress-related diseases, but the underlying mechanisms have remained elusive. This study investigated the antioxidant effects and mechanisms against H2O2-induced oxidative damage in HepG2 cells of the two latest discovered antioxidant peptides, CRPCGPTP (CP-8) and ANSCNEPCVR (AR-10), first decrypted from feather keratin. The results revealed that CP-8 and AR-10 did not exhibit cytotoxicity to HepG2 cells while reducing intracellular ROS accumulation. Simultaneously, they enhanced the activities of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px), thus alleviating H2O2-induced cell apoptosis. Molecular docking analysis demonstrated that CP-8, AR-10 interacted well with the key amino acids in the Kelch domain of Keap1, thereby directly disrupting the Keap1-Nrf2 interaction. The peptides' biosafety and antioxidant activity via Keap1/Nrf2 signaling lay the groundwork for further animal studies and applications as functional food additives.

Protein Hydrolysates from Fishery Processing By-Products: Production, Characteristics, Food Applications, and Challenges

Fish processing by-products such as frames, trimmings, and viscera of commercial fish species are rich in proteins. Thus, they could potentially be an economical source of proteins that may be used to obtain bioactive peptides and functional protein hydrolysates for the food and nutraceutical industries. The structure, composition, and biological activities of peptides and hydrolysates depend on the freshness and the actual composition of the material. Peptides isolated from fishery by-products showed antioxidant activity. Changes in hydrolysis parameters changed the sequence and properties of the peptides and determined their physiological functions. The optimization of the value of such peptides and the production costs must be considered for each particular source of marine by-products and for their specific food applications. This review will discuss the functional properties of fishery by-products prepared using hydrolysis and their potential food applications. It also reviews the structure-activity relationships of the antioxidant activity of peptides as well as challenges to the use of fishery by-products for protein hydrolysate production.

Oyster-derived dipeptides RI, IR, and VR promote testosterone synthesis by reducing oxidative stress in TM3 cells

Short peptides have gained widespread utilization as functional constituents in the development of functional foods due to their remarkable biological activity. Previous investigations have established the positive influence of oysters on testosterone biosynthesis, although the underlying mechanism remains elusive. This study aims to assess the impact of three dipeptides derived from oysters on the oxidative stress state of TM3 cells induced by AAPH while concurrently examining alterations in cellular testosterone biosynthesis capacity. The investigation encompasses an analysis of reactive oxygen species (ROS) content, antioxidant enzyme activity, apoptotic status, and expression levels of crucial enzymes involved in the testosterone synthesis pathway within TM3 cells, thus evaluating the physiological activity of the three dipeptides. Additionally, molecular docking was employed to investigate the inhibitory activity of the three dipeptides against ACE. The outcomes of this study imply that the oxidative stress state of cells impedes the synthesis of testosterone by inhibiting the expression of essential proteins in the testosterone synthesis pathway. These three dipeptides derived from oysters ameliorate cellular oxidative stress by directly scavenging excess ROS or reducing ROS production rather than enhancing cellular antioxidant capacity through modulation of antioxidant enzyme activity. These findings introduce a novel avenue for developing and utilizing antioxidant peptides derived from food sources.

More simple, efficient and accurate food research promoted by intermolecular interaction approaches: A review

The investigation of intermolecular interactions has become increasingly important in many studies, mainly by combining different analytical approaches to reveal the molecular mechanisms behind specific experimental phenomena. From spectroscopic analysis to sophisticated molecular simulation techniques like molecular docking, molecular dynamics (MD) simulation, and quantum chemical calculations (QCC), the mechanisms of intermolecular interactions are gradually being characterized more clearly and accurately, leading to revolutionary advances. This article aims to review the progression in the main techniques involving intermolecular interactions in food research and the corresponding experimental results. Finally, we discuss the significant impact that cutting-edge molecular simulation technologies may have on the future of conducting deeper exploration. Applications of molecular simulation technology may revolutionize the food research, making it possible to design new future foods with precise nutrition and desired properties.

Adaptive Responses of a Peroxidase-like Polyoxometalate-Based Tri-Assembly to Bacterial Microenvironment (BME) Significantly Improved the Anti-Bacterial Effects

The present study presents the tertiary assembly of a POM, peptide, and biogenic amine, which is a concept to construct new hybrid bio-inorganic materials for antibacterial applications and will help to promote the development of antivirus agents in the future. To achieve this, a Eu-containing polyoxometalate (EuW₁₀) was first co-assembled with a biogenic amine of spermine (Spm), which improved both the luminescence and antibacterial effect of EuW₁₀. Further introduction of a basic peptide from HPV E6, GL-22, induced more extensive enhancements, both of them being attributed to the cooperation and synergistic effects between the constituents, particularly the adaptive responses of assembly to the bacterial microenvironment (BME). Further intrinsic mechanism investigations revealed in detail that the encapsulation of EuW₁₀ in Spm and further GL-22 enhanced the uptake abilities of EuW₁₀ in bacteria, which further improved the ROS generation in BME via the abundant H₂O₂ involved there and significantly promoted the antibacterial effects.

Protective Effect of Peptides from Pinctada Martensii Meat on the H2O2-Induced Oxidative Injured HepG2 Cells

Pinctada martensii is a major marine pearl cultured species in southern China, and its meat is rich in protein, which is an excellent material for the preparation of bioactive peptides. In this study, the peptides from Pinctada martensii meat were prepared by simulated gastrointestinal hydrolysis, and after multistep purification, the structures of the peptides were identified, followed by the solid-phase synthesis of the potential antioxidant peptides. Finally, the antioxidant activities of the peptides were verified using HepG2 cells, whose oxidative stress was induced by hydrogen peroxide (H₂O₂). It was shown that the antioxidant peptide (S4) obtained from Pinctada martensii meat could significantly increase the cell viability of HepG2 cells. S4 could also scavenge reactive oxygen species (ROS) and reduce the lactate dehydrogenase (LDH) level. In addition, it could enhance the production of glutathione (GSH) and catalase (CAT) in HepG2 cells, as well as the expression of key genes in the Nrf2 signaling pathway. Three novel antioxidant peptides, arginine-leucine (RL), arginine-glycine-leucine (RGL), and proline-arginine (PR), were also identified. In conclusion, peptides from Pinctada martensii meat and three synthetic peptides (RGL, RL, PR) showed antioxidant activity and could have the potential to be used as antioxidant candidates in functional foods.

Abalone visceral peptides containing Cys and Tyr exhibit strong in vitro antioxidant activity and cytoprotective effects against oxidative damage

The in vitro antioxidation and cytoprotection of abalone visceral peptides against oxidative damage were investigated. Results show that the DPPH· scavenging activities of the 16 chemically synthesized peptides were significantly and positively correlated with their reducing power. Their scavenging activities against ABTS·⁺ were positively correlated with their ability to inhibit linoleic acid oxidation. Only Cys containing peptides exhibited good DPPH· scavenging activity, while only Tyr containing peptides showed significant ABTS·⁺ scavenging activity. In the cytoprotection assay, all four representative peptides significantly increased the viability of H₂O₂-damaged LO2 cells and the activities of GSH-Px, CAT, and SOD, and all decreased MDA levels and LDH leakage, in which the Cys-containing peptides were more effective at increasing the activities of antioxidant enzymes, while the Tyr-containing peptides were more effective at decreasing MDA levels and LDH leakage. Abalone visceral peptides containing both Cys and Tyr exhibit strong in vitro and cellular antioxidation.

Comparative in silico and in vitro study of the stability and biological activity of an octapeptide from microalgae Isochrysis zhanjiangensis and its truncated short peptide

In this study, the structural characteristics and active sites of the octapeptide (IIAVEAGC), the pentapeptide (IIAVE) and tripeptide (AGC) were studied in silica and in vitro.

Food Protein-Derived Antioxidant Peptides: Molecular Mechanism, Stability and Bioavailability

The antioxidant activity of protein-derived peptides was one of the first to be revealed among the more than 50 known peptide bioactivities to date. The exploitation value associated with food-derived antioxidant peptides is mainly attributed to their natural properties and effectiveness as food preservatives and in disease prevention, management, and treatment. An increasing number of antioxidant active peptides have been identified from a variety of renewable sources, including terrestrial and aquatic organisms and their processing by-products. This has important implications for alleviating population pressure, avoiding environmental problems, and promoting a sustainable shift in consumption. To identify such opportunities, we conducted a systematic literature review of recent research advances in food-derived antioxidant peptides, with particular reference to their biological effects, mechanisms, digestive stability, and bioaccessibility. In this review, 515 potentially relevant papers were identified from a preliminary search of the academic databases PubMed, Google Scholar, and Scopus. After removing non-thematic articles, articles without full text, and other quality-related factors, 52 review articles and 122 full research papers remained for analysis and reference. The findings highlighted chemical and biological evidence for a wide range of edible species as a source of precursor proteins for antioxidant-active peptides. Food-derived antioxidant peptides reduce the production of reactive oxygen species, besides activating endogenous antioxidant defense systems in cellular and animal models. The intestinal absorption and metabolism of such peptides were elucidated by using cellular models. Protein hydrolysates (peptides) are promising ingredients with enhanced nutritional, functional, and organoleptic properties of foods, not only as a natural alternative to synthetic antioxidants.

Dual antioxidant activity and the related mechanisms of a novel pentapeptide GLP4 from the fermented mycelia of Ganoderma lingzhi

Oxidative stress causes chronic inflammation, and mediates various diseases. The discovery of antioxidants from natural sources is important to research. Here we identified a novel antioxidant peptide (GLP4) from Ganoderma lingzhi mycelium and investigated its antioxidant type and potential protective mechanisms. Through free radical scavenging assay, active site shielding validation, superoxide dismutase (SOD) activity assay, and lipid peroxidation assay, we demonstrated that GLP4 was a novel protective agent with both direct and indirect antioxidant activities. GLP4 could directly enter human umbilical vein endothelial cells (HUVECs) as an exogenous substance. Meanwhile, GLP4 promoted the nuclear translocation of nuclear factor erythroid-2-related factor 2 (Nrf2) and activated the Nrf2/antioxidant response element (ARE) signaling pathway, exhibiting antioxidant and anti-apoptotic cytoprotective effects on hydrogen peroxide (H₂O₂)-induced HUVECs. Pull-down experiments of GLP4 target proteins, bioinformatics analysis and molecular docking further revealed that GLP4 mediated Nrf2 activation through binding to phosphoglycerate mutase 5 (PGAM5). The results suggested that GLP4 is a novel peptide with dual antioxidant activity and has promising potential as a protective agent in preventing oxidative stress-related diseases.

Isolation, Identification, and Immunomodulatory Mechanism of Peptides from Lepidium meyenii (Maca) Protein Hydrolysate

Maca is a protein-enriched edible plant with immunomodulatory activity. However, the role of proteins in the immunomodulatory activity of maca is unclear. In this study, peptide products of maca proteins obtained through in vitro gastrointestinal digestion were isolated and purified, and the immunomodulatory activities of these peptides were assessed in macrophages (RAW 264.7 cells). The results show that the maca protein hydrolysate enhanced the phagocytic capacity and NO, TNF-α, and IL-6 secretion of RAW 264.7 cells. Forty-five peptides from known proteins of maca or the cruciferous family were identified by ultraperformance liquid chromatography-tandem mass spectrometry in the hydrolysate, and the peptide RNPFLP exhibited the strongest immunomodulatory activity. Antibody blocking, siRNA, pathway inhibitors, and western blot assays showed that RNPFLP-activated RAW 264.7 cells through the NF-κB and MAPK signaling pathways mediated by TLR2 and TLR4 receptors. An analysis of the structure-activity relationship showed that the N₉-H₆₀ active site in arginine plays an important role in the immunomodulatory activity of RNPFLP. This study provides a new understanding of the immunomodulatory activity of maca.