In silico analysis and in vivo tests of the tuna dark muscle hydrolysate anti-oxidation effect

Identification and molecular docking of novel antioxidant peptides from Candida utilis

The current trend is the promotion of antioxidants that are beneficial for both health and the environment. Candida utilis have garnered considerable attention due to their commendable attributes such as non-toxicity and the ability to thrive in waste. Therefore, Candida utilis was used as raw material to isolate and identify new antioxidant peptides by employing methods such as ultrafiltration, DEAE Sepharose Fast Flow, and liquid chromatography-tandem mass spectrometry. The antioxidant mechanism of peptides was investigated by molecular docking. The properties of antioxidant peptides were evaluated using a variety of computational tools. This study resulted in the identification of two novel antioxidant peptides. According to the molecular docking results, the antioxidant mechanism of Candida utilis peptides operates by obstructing the entry to the myeloperoxidase activity cavity. The (-) CDOCKER energy of antioxidant peptides was 6.2 and 6.1 kcal/mol, respectively. Additionally, computer predictions indicated that antioxidant peptides exhibited non-toxicity and poor solubility.

Functional attributes of bioactive peptides of bovine milk origin and application of in silico approaches for peptide prediction and functional annotations

Bovine milk peptides are the protein fragments with diverse bioactive properties having antioxidant, anticarcinogenic, other therapeutic and nutraceutical potentials. These peptides are formed in milk by enzymatic hydrolysis, gastrointestinal digestion and fermentation processes. They have significant health impact with high potency and low toxicity making them a suitable natural alternative for preventing and managing diseases. Antibiotic resistance has increased the quest for better peptide candidates with antimicrobial effects. This article presents a comprehensive review on well documented antimicrobial, immunological, opioid, and anti-hypertensive activities of bovine milk peptides. It also covers the usage of computational biology tools and databases for prediction and analysis of the food-derived bioactive peptides. In silico analysis of amino acid sequences of Bos taurus milk proteins have been predicted to generate peptides with dipeptidyl peptidase IV inhibitory and ACE inhibitory properties, making them favorable candidates for developing blood sugar lowering drugs and anti-hypertensives. In addition to the prediction of new bioactive peptides, application of bioinformatics tools to predict novel functions of already known peptides is also discussed. Overall, this review focuses on the reported as well as predicted biologically active peptide of casein and whey proteins of bovine milk that can be utilized to develop therapeutic agents.

Tuna Dark Muscle Feeding Improved the Meat Quality of Holland Mini-Piglets and Modulated the Gut Microbiota

Pork is one of the most widely produced and consumed meats in the world, and it is also an important source of animal protein. The continuous rise in feed prices has forced the pig industry to consider adding cost-effective alternative feed to pig diets. In this study, we aimed to explore the beneficial effects of tuna dark muscle as a nutritional supplement on the growth performance, serum lipids and antioxidant levels of Holland mini-piglets, as well as on the odor and volatile substances of pork and the gut microbiota. Two-month-old male mini-piglets (n = 24) were fed a control diet or supplemented with either 2% (LD) or 4% (HD) tuna dark muscle for 8 weeks. The use of tuna dark muscle at low and high dosages significantly increased the average daily weight gain, but it showed no significant effect on organ indices or blood lipids. In addition, dark muscle treatment significantly increased the antioxidant capacity, characterized by increased SOD and GSH-Px activities, and it decreased the content of MDA in serum. Moreover, tuna dark muscle feeding shifted the odor of rib muscle and tendon meat away from that of the control group, while similar odor patterns were observed in the longissimus dorsi muscle. Among these volatile substances, hexanal, nonanal, and heptanal increased in response to dietary tuna dark muscle and were regarded as indispensable contributors to the feeding. Furthermore, dietary tuna dark muscle modulated the gut microbiota of the piglets, increasing the abundance of beneficial bacteria such as butyric acid-producing bacteria, and reduced the abundance of harmful bacteria. The feeding strategy reported in this study not only reduces the production costs of pork but also utilizes tuna processing by-products in an environmentally friendly way.

A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques

Peptides acquire target affinity based on the combination of residues in their sequences and the conformation formed by their flexible folding, an ability that makes them very attractive biomaterials in therapeutic, diagnostic, and assay fields. With the development of computer technology, computer-aided design and screening of affinity peptides has become a more efficient and faster method. This review summarizes successful cases of computer-aided design and screening of affinity peptide ligands in recent years and lists the computer programs and online servers used in the process. In particular, the characteristics of different design and screening methods are summarized and categorized to help researchers choose between different methods. In addition, experimentally validated sequences are listed, and their applications are described, providing directions for the future development and application of computational peptide screening and design.

In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms

Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.

Analyzing the mechanism by which oyster peptides target IL-2 in melanoma cell apoptosis based on RNA-seq and m6A-seq

Melanoma is a kind of skin cancer with high malignancy and strong proliferation and invasion abilities. Chemotherapy drugs in the clinic have the disadvantages of high price and high toxicity. Peptides are natural active ingredients that have many functions and are safe and effective. Previous studies have shown that oysters are rich in protein and have antitumor effects. In this study, a high-throughput strategy combined with MALDI TOF/TOF-MS and molecular docking was developed to screen peptides with antitumor functions from oyster hydrolysate. Three dominant peptides were predicted to have similar functions to IL-2 via molecular docking. Then, the activity of the peptides was confirmed in B16 cells, and we found that the three peptides increased the apoptosis of B16 cells. Furthermore, via RNA-seq and m6A-seq of B16 cells treated with the peptides, we found that ILADSAPR downregulates the expression of Pcna, Tlr4, and Ncbp2 and upregulates the expression of Bax, Bad, Pak4, Rasa2, Cct6, and Gbp2. ILADSAPR inhibited B16 cell proliferation and promoted cell apoptosis by regulating the expression of these genes. In addition, the result of metabolic pathway analysis also proved this point. This study provides a preliminary reference for antitumor research on oyster peptides.

Emerging ROS-Modulating Technologies for Augmentation of the Wound Healing Process

Reactive oxygen species (ROS) is considered a double-edged sword. The slightly elevated level of ROS helps in wound healing by inhibiting microbial infection. In contrast, excessive ROS levels in the wound site show deleterious effects on wound healing by extending the inflammation phase. Understanding the ROS-mediated molecular and biomolecular mechanisms and their effect on cellular homeostasis and inflammation thus substantially improves the possibility of exogenously augmenting and manipulating wound healing with the emerging antioxidant therapeutics. This review comprehensively delves into the relationship between ROS and critical phases of wound healing and the processes underpinning antioxidant therapies. The manuscript also discusses cutting-edge antioxidant therapeutics that act via ROS scavenging to enhance chronic wound healing.

Preparation, purification, and identification of novel antioxidant peptides derived from Gracilariopsis lemaneiformis protein hydrolysates

Gracilariopsis lemaneiformis (G. lemaneiformis) protein was hydrolyzed with alkaline protease to obtain antioxidant peptides. The enzymatic hydrolysis conditions were optimized through single-factor and orthogonal experiments. The results showed that the optimal process parameters were using 2% of alkaline protease, and substrate concentration of 1 g/100 mL and hydrolyzed 2 h at pH 8.0. Gel filtration chromatography and RP-HPLC were adopted for isolating and purifying the antioxidant peptides from the G. lemaneiformis protein hydrolysate (GLPH). Three novel antioxidant peptides were identified as LSPGEL (614.68 Da), VYFDR (698.76 Da), and PGPTY (533.57 Da) by nano-HPLC-MS/MS. The results of ABTS free radical scavenging rate demonstrated PGPTY exhibited the best antioxidant activity (IC₅₀ = 0.24 mg/mL). Moreover, LSPGEL, VYFDR, and PGPTY were docked with Keap1, respectively. The molecular docking results suggested PGPTY had smaller docking energy and inhibition constants than the other two peptides. Finally, the cell viability assay evidenced the protective effect exerted by the antioxidant peptide on H₂O₂-induced oxidative damage. Above findings showed the potential of using antioxidant peptides from GLPH as antioxidants.

Bioinformatics and Computer Simulation approaches to the discovery and analysis of Bioactive Peptides

The traditional process of separating and purifying bioactive peptides is laborious and time-consuming. Using a traditional process to identify is difficult, and there is a lack of fast and accurate activity evaluation methods. How to extract bioactive peptides quickly and efficiently is still the focus of bioactive peptides research. In order to improve the present situation of the research, bioinformatics techniques and peptidome methods are widely used in this field. At the same time, bioactive peptides have their own specific pharmacokinetic characteristics, so computer simulation methods have incomparable advantages in studying the pharmacokinetics and pharmacokinetic-pharmacodynamic correlation models of bioactive peptides. The purpose of this review is to summarize the combined applications of bioinformatics and computer simulation methods in the study of bioactive peptides, with focuses on the role of bioinformatics in simulating the selection of enzymatic hydrolysis and precursor proteins, activity prediction, molecular docking, physicochemical properties, and molecular dynamics. Our review shows that new bioactive peptide molecular sequences with high activity can be obtained by computer-aided design. The significance of the pharmacokinetic-pharmacodynamic correlation model in the study of bioactive peptides is emphasized. Finally, some problems and future development potential of bioactive peptides binding new technologies are prospected.

The gut microbiota mediates the protective effects of anserine supplementation on hyperuricaemia and associated renal inflammation

Hyperuricaemia is a disease associated with elevated serum uric acid content, which has emerged rapidly in recent decades. The drugs used to treat clinical hyperuricaemia have side effects, and their safety is poor. However, anserine is a natural carnosine derivative that shows an anti-hyperuricaemic effect. A previous study demonstrated that anserine inhibits uric acid synthesis and promotes uric acid excretion, but there is no evidence regarding the effect of anserine from the perspective of the gut microbiota. In this study, the anti-hyperuricaemic and anti-inflammatory effects of anserine were explored in a diet-induced hyperuricaemic mouse model. Anserine alleviated hyperuricaemia and renal inflammation phenotypes, inhibited uric acid biosynthesis, promoted uric acid excretion, and inhibited NLRP3 inflammasome and TLR4/MyD88/NF-κB signalling pathway activation. The results showed that the anti-hyperuricaemic effect of anserine was dependent on the gut microbiota in the germ-free mice experiment. Furthermore, anserine treatment reversed gut microbiota dysbiosis, repaired the intestinal epithelial barrier and increased short-chain fatty acid production. Moreover, the anti-hyperuricaemic effect of anserine was transmissible by transplanting the faecal microbiota from anserine-treated mice, indicating that the protective effects were at least partially mediated by the gut microbiota. Thus, we identified a new and safe prebiotic material to alleviate hyperuricaemia and provided ideas for the development of oligopeptides.

FermFooDb: A database of bioactive peptides derived from fermented foods

Globally fermented foods are in demands due to their functional and nutritional benefits. These foods are sources of probiotic organisms and bioactive peptides, various amino acids, enzymes etc. that provides numerous health benefits. FermFooDb (https://webs.iiitd.edu.in/raghava/fermfoodb/) is a manually curated database of bioactive peptides derived from wide range of foods that maintain comprehensive information about peptides and process of fermentation. This database comprises of 2205 entries with following major fields, peptide sequence, Mass and IC50, food source, functional activity, fermentation conditions, starter culture, testing conditions of sequences in vitro or in vivo, type of model and method of analysis. The bioactive peptides in our database have wide range of therapeutic potentials that includes antihypertensive, ACE-inhibitory, antioxidant, antimicrobial, immunomodulatory and cholesterol lowering peptides. These bioactive peptides were derived from different types of fermented foods that include milk, cheese, yogurt, wheat and rice. Numerous, web-based tools have been integrated to retrieve data, peptide mapping of proteins, similarity search and multiple-sequence alignment. This database will be useful for the food industry and researchers to explore full therapeutic potential of fermented foods from specific cultures.

Identification of novel antioxidant peptides from snakehead (Channa argus) soup generated during gastrointestinal digestion and insights into the anti-oxidation mechanisms

Antioxidant peptides obtained from snakehead (Channa argus) soup (SHS) after simulated gastrointestinal (GI) digestion were separated, identified and characterized. Results showed that the fraction with MW < 3 kDa had the highest antioxidant capacity. Four novel antioxidant peptides were identified after RP-HPLC and UPLC-MS/MS. PGMLGGSPPGLLGGSPP and SDGSNIHFPN had the highest DPPH radical scavenging activity (IC₅₀ = 1.39 mM) and Fe²⁺ chelating ability (IC₅₀ = 4.60 mM), respectively. Structures in silico for IVLPDEGK, PGMLGGSPPGLLGGSPP and SDGSNIHFPN suggest at least one β-turn and/or α-helix, which are associated with antioxidant activity. Moreover, our results showed that these three peptides docked with a recombinant Kelch-like ECH-associated protein 1 (Keap1) with a binding score greater than TX6, a good ligand of Keap1. The cell viability assay also showed significant cytoprotective effects against H₂O₂-induced cellular oxidative damage. This information implies that antioxidant mechanisms of novel SHS peptides occurred via activation of cellular anti-oxidation Keap1-Nrf2 signaling pathway.

The novel peptides ICRD and LCGEC screened from tuna roe show antioxidative activity via Keap1/Nrf2-ARE pathway regulation and gut microbiota modulation

In this study, a high-throughput strategy combined with MALDI TOF/TOF-MS and Discovery Studio 2017 was developed to screen peptides with certain functions from hydrolysate. Two dominant peptides, Ile-Cys-Arg-Asp (ICRD) and Leu-Cys-Gly-Glu-Cys (LCGEC), were predicted to have antioxidant activity by Discovery Studio 2017. Then the activity in vitro of peptides had been confirmed via DPPH assay. Both two peptides decreased apoptosis induced by UVB treatment in HaCaT cells and altered Keap1/Nrf2-ARE pathway transcription. Furthermore, the antioxidant activity of LCGEC was achieved after 6-week treatment in mice via regulating the Keap1/Nrf2-ARE pathway, inhibiting the release of proinflammatory cytokines, increasing the abundance of 3-indolepropionic acid and short-chain fatty acids production in feces and modulating gut microbiota composition. This study provided two tuna roe peptides with in vitro and in vivo antioxidant activity.

Protective effects of tuna meat oligopeptides (TMOP) supplementation on hyperuricemia and associated renal inflammation mediated by gut microbiota

Recently, interest in using whole food-derived mixtures to alleviate chronic metabolic syndrome through potential synergistic interactions among different components is increasing. In this study, the effects and mechanisms of tuna meat oligopeptides (TMOP) on hyperuricemia and associated renal inflammation were investigated in mice. Dietary administration of TMOP alleviated hyperuricemia and renal inflammation phenotypes, reprogramed uric acid metabolism pathways, inhibited the activation of NLRP3 inflammasome and TLR4/MyD88/NF-κB signaling pathways, and suppressed the phosphorylation of p65-NF-κB. In addition, TMOP treatments repaired the intestinal epithelial barrier, reversed the gut microbiota dysbiosis and increased the production of short-chain fatty acids. Moreover, the antihyperuricemia effects of TMOP were transmissible by transplanting the fecal microbiota from TMOP-treated mice, indicating that the protective effects were at least partially mediated by the gut microbiota. Thus, for the first time, we clarify the potential effects of TMOP as a whole food derived ingredient on alleviating hyperuricemia and renal inflammation in mice, and additional efforts are needed to confirm the beneficial effects of TMOP on humans.

Furcellaran-Coated Microcapsules as Carriers of Cyprinus carpio Skin-Derived Antioxidant Hydrolysate: An In Vitro and In Vivo Study

Carp skin gelatine hydrolysate (CSGH) may be a possible bioactive peptide source, as promising antioxidant properties have been noted during in vivo testing. Hence, the present study focused on improving the bioavailability of the antioxidant peptides from CSGH and on the use of furcellaran (FUR), which can protect the biopeptides during digestion in the gastrointestinal tract. Therefore, in this study, microcapsules coated with furcellaran and containing CSGH cores were prepared. The structural properties of the sample were determined using FT-IR and SEM analysis. The antioxidant properties of hydrolysate, uncoated, and encapsulated samples were investigated. In vivo analysis included determination of its safety in an animal organism and evaluation of the lipid profile, antioxidant blood status, and mRNA expression of some genes involved in antioxidant status in Wistar rats. The results showed no adverse effects of microencapsulated protein hydrolysates in laboratory animals. Nonetheless, there was a statistically significant rise in the level of total antioxidant status blood serum among animals consuming CSGH and not inducing oxidative stress. This can be viewed as a promising indication of the positive effects of antioxidant properties tested in vivo. The process of CSGH microencapsulation in FUR cause a decrease in antioxidant hydrolysate activity, both in vitro, as well as in healthy Wistar rats. When considering the results of the presented diverse therapeutic potential, further research on CSGH being a potential bioactive peptide source used as a functional food or nutraceutical, but with a different microencapsulation coating, is encouraged.

FeptideDB: A web application for new bioactive peptides from food protein

BACKGROUND

Bioactive peptides derived from food are important sources for alternative medicine and possess therapeutic activity. Several biochemical methods have been achieved to isolate bioactive peptides from food, which are tedious and time consuming. In silico methods are an alternative process to reduce cost and time with respect to bioactive peptide production. In this paper, FeptideDB was used to collect bioactive peptide (BP) data from both published research articles and available bioactive peptide databases. FeptideDB was developed to assist in forecasting bioactive peptides from food by combining peptide cleavage tools and database matching. Furthermore, this application was able to predict the potential of cleaved peptides from 'enzyme digestion module' to identify new ACE (angiotensin converting enzyme) inhibitors using an automatic molecular docking approach.

RESULTS

The FeptideDB web application contains tools for generating all possible peptides cleaved from input protein by various available enzymes. This database was also used for analysis and visualization to assist in bioactive peptide discovery. One module of FeptideDB has the ability to create 3-dimensional peptide structures to further predict inhibitors for the target protein, ACE (angiotensin converting enzyme).

CONCLUSIONS

FeptideDB is freely available to researchers who are interested in exploring bioactive peptides. The FeptideDB interface is easy to use, allowing users to rapidly retrieve data based on desired search criteria. FeptideDB is freely available at http://www4g.biotec.or.th/FeptideDB/. Ultimately, FeptideDB is a computational aid for assessing peptide bioactivities.