Bioinformatics: Current perspectives and future directions for food and nutritional research facilitated by a Food-Wiki database

Bioactive peptides in dry-cured ham: A comprehensive review of preparation methods, metabolic stability, safety, health benefits, and regulatory frameworks

Dry-cured hams contain abundant bioactive peptides with significant potential for the development of functional foods. However, the limited bioavailability of food-derived bioactive peptides has hindered their utilization in health food development. Moreover, there is insufficient regulatory information regarding bioactive peptides and related products globally. This review summarizes diverse bioactive peptides derived from dry-cured ham and by-products originating from various countries and regions. The bioactivity, preparation techniques, bioavailability, and metabolic stability of these bioactive peptides are described, as well as the legal and regulatory frameworks in various countries. The primary objectives of this review are to dig deeper into the functionality of dry-cured ham and provide theoretical support for the commercialization of bioactive peptides from food sources, especially the dry-cured ham.

Discovery of potential anti- Staphylococcus aureus natural products and their mechanistic studies using machine learning and molecular dynamic simulations

The structure-activity analysis (SAR) and machine learning were used to investigate potential anti-S. aureus agents in a faster method. In this study, 24 oxygenated benzene ring components with S. aureus inhibition capacity were confirmed by literature exploring and in-house experiments, and the SAR analysis suggested that the hydroxyl group position may affect the anti-S. aureus activity. The 2D-MLR-QSAR model with 9 descriptors was further evaluated as the best model among the 21 models. After that, hesperetic acid and 2-HTPA were further explored and evaluated as the potential anti-S. aureus agents screening in the natural product clustering library through the best QSAR model calculation. The antibacterial capacities of hesperetic acid and 2-HTPA had been investigated and proved the similar predictive pMIC value resulting from the QSAR model. Besides, the two novel components were able to inhibit the growth of S. aureus by disrupting the cell membrane through the molecular dynamics simulation (MD), which further evidenced by scanning electron microscopy (SEM) test and PI dye results. Overall, these results are highly suggested that QSAR can be used to predict the antibacterial agents targeting S. aureus, which provides a new paradigm to research the molecular structure-antibacterial capacity relationship.

Impact of Lactiplantibacillus plantarum and casein fortification on angiotensin converting enzyme inhibitory peptides in yogurt: identification and in silico analysis

In this study, the effects of Lactiplantibacillus plantarum M11 (Lb. plantarum M11) in conjunction with sodium caseinate on the characteristics and angiotensin converting enzyme (ACE) inhibitory activity of yogurt were investigated. ACE inhibitory peptides (ACEIPs) in yogurt were identified by nano-LC-MS/MS and potential ACEIPs were predicted by in silico and molecular docking methods. The results showed that the ACE-inhibitory activity of yogurt was significantly enhanced (p < 0.05), while maintaining the quality characteristics of the yogurt. Thirteen ACEIPs in the improved yogurt (883 + M11-CS group) were identified, which were more abundant than the other yogurt groups (control 883 group, 883 + M11 group and 883-CS group). Two novel peptides with potential ACE inhibitory activity, YPFPGPIH and NILRFF, were screened. The two peptides showed PeptideRanker scores above 0.8, small molecular weight and strong hydrophobicity, and were non-toxic after prediction. Molecular docking results showed that binding energies with ACE were -9.4 kcal mol-1 and -10.7 kcal mol-1, respectively, and could bind to the active site of ACE. These results indicated that yogurt with Lb. plantarum M11 and sodium caseinate has the potential to be utilized as a functional food with antihypertensive properties. The combination of ACEIP-producing strains and casein fortification could be an effective method to promote the release of ACEIPs from yogurt.

Bioinformatics and bioactive peptides from foods: Do they work together?

We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.

An innovative insecticidal approach based on plant protease inhibitor and Bt protoxins inhibits trypsin-like activity in zebrafish

The Leucaena leucocephala trypsin inhibitor (LTI) + Bacillus thuringiensis (Bt) protoxins mix has been proposed as a novel larvicide agent in order to control the vector mosquito of dengue virus, Aedes aegypti, in their aquatic breeding sites. However, use of this insecticide formulation has raised concerns about its impacts on aquatic biota. In this context, this work aimed to assess the effects of LTI and Bt protoxins, separately or in combination, in zebrafish, in regard to the evaluation of toxicity at early life stages and to the presence of LTI inhibitory effects on intestinal proteases of this fish. Results showed that LTI and Bt concentrations (250 mg/L, and 0.13 mg/L, respectively), and LTI + Bt mix (250 mg/L + 0.13 mg/L) - 10 times superior to those with insecticidal action - did not cause death nor did it induce morphological changes during embryonic and larval development (3 to 144 h post-fertilization) of zebrafish. Molecular docking analyses highlighted a possible interaction between LTI and zebrafish trypsin, especially through hydrophobic interactions. In concentrations near to those with larvicidal action, LTI (0.1 mg/mL) was able to inhibit in vitro intestinal extracts of trypsin in female and male fish by 83 % and 85 %, respectively, while LTI + Bt mix promoted trypsin inhibition of 69 % in female and 65 % in male ones. These data show that the larvicidal mix can potentially promote deleterious effects to nutrition and survival in non-target aquatic organisms, especially those with trypsin-like dependent protein digestion.

Antioxidant and Antimicrobial Peptides Derived from Food Proteins

Recently, the demand for food proteins in the market has increased due to a rise in degenerative illnesses that are associated with the excessive production of free radicals and the unwanted side effects of various drugs, for which researchers have suggested diets rich in bioactive compounds. Some of the functional compounds present in foods are antioxidant and antimicrobial peptides, which are used to produce foods that promote health and to reduce the consumption of antibiotics. These peptides have been obtained from various sources of proteins, such as foods and agri-food by-products, via enzymatic hydrolysis and microbial fermentation. Peptides with antioxidant properties exert effective metal ion (Fe2+/Cu2+) chelating activity and lipid peroxidation inhibition, which may lead to notably beneficial effects in promoting human health and food processing. Antimicrobial peptides are small oligo-peptides generally containing from 10 to 100 amino acids, with a net positive charge and an amphipathic structure; they are the most important components of the antibacterial defense of organisms at almost all levels of life-bacteria, fungi, plants, amphibians, insects, birds and mammals-and have been suggested as natural compounds that neutralize the toxicity of reactive oxygen species generated by antibiotics and the stress generated by various exogenous sources. This review discusses what antioxidant and antimicrobial peptides are, their source, production, some bioinformatics tools used for their obtainment, emerging technologies, and health benefits.

Peptides derived from the gastrointestinal digestion of amaranth 11S globulin: Structure and antioxidant functionality

The relationship between structural and physicochemical properties and antioxidant activity of peptides from amaranth 11S-globulin was studied. Peptides AWEEREQGSR, TEVWDSNEQ, IYIEQGNGITGM and YLAGKPQQEH had the greatest in vitro activity (ORAC, HORAC). GDRFQDQHQ, HVIKPPSRA and KFNRPETT were the most active ones against Cu⁺²/H₂O₂-induced-LDL oxidation. In a cellular system (H₂O₂-induced-Caco2-TC7), TEVWDSNEQ, IYIEQGNGITGM, GDRFQDQHQ, LAGKPQQEHSGEHQ and KFNRPETT were the most effective in decreasing ROS, while the effects on SOD, GPx, and GSH were variable. To understand the structure-antioxidant activity relationships, the content of aromatic and acidic amino acids, the degree of hydrophobicity and the charge distribution on the accessible surface of peptides structures obtained by molecular dynamics were analysed. The low correlation between in vitro, ex vivo and cellular activities could be explained by the influence of physicochemical and structural properties on the interaction with complex systems (LDL/cells), peptide modifications and/or mechanisms other than direct ROS inhibition in the cells.

Production of the Antihypertensive Peptide Tyr-Pro from Milk Using the White-Rot Fungus Peniophora sp. in Submerged Fermentation and a Jar Fermentor

In order to evaluate the blood pressure-lowering peptide Tyr-Pro (YP) derived from casein, we wanted to develop an efficient fermentation method. Therefore, we chose to use a jar fermentor for this purpose. Strains with an excellent antihypertensive peptide-releasing ability from casein were selected from basidiomycete fungi that grow well in milk under shaking conditions accompanied by physical stimulation. Among them, the white-rot fungus Peniophora sp., which is suited for growth only in cow’s milk or low-fat milk under vigorous shaking conditions, was found to release peptides and amino acids from milk. When comparing the growth in cow’s milk and low-fat milk, there was no particular difference in the growth of mycelia between the two, but this fungus tended to preferentially consume lactose under low-fat conditions. The fermented milk exhibited good production of the target peptide YP. The expression of many genes encoding proteolytic enzymes, such as aminopeptidases and carboxypeptidases, was observed during the milk fermentation. Furthermore, this fungus showed good growth in a jar fermentor culture using only cow’s milk or low-fat milk, which enabled the efficient production of YP and ACE-inhibitory activity. At this time, it was more effective to use cow’s milk than low-fat milk. These results suggest that Peniophora sp. could be potentially useful in the production of the functional YP peptide from milk.

In silico-screened cationic dipeptides from scallop with synergistic gelation effect on ι-carrageenan

In this paper, some cationic dipeptides from scallop (Patinopecten yessoensis) male gonads (SMGs), which can synergistically gel with ι-carrageenan (ι-C), were screened by the in silico approach. Fourteen protein sequences of SMGs were obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and nano liquid chromatography-mass spectrometry/mass spectrometry (nanoLC-MS/MS) analysis and were then hydrolyzed via in silico simulation. A total of 414 sequences were obtained with 56 duplicates, half of which were positively charged at pH 7. Among the cation sequences, 171 had good water solubility, including two amino acids (Lys and Arg). The molecular weight analysis of the cationic water-soluble sequences showed that 0.2-0.3 kDa accounted for the highest proportion. Based on the obvious synergistic effect of Lys and ι-C, 11 Lys-containing dipeptides, including Ser-Lys (SK), Thr-Lys (TK), Trp-Lys (WK), Ala-Lys (AK), Leu-Lys (LK), Gly-Lys (GK), Val-Lys (VK), Cys-Lys (CK), Asn-Lys (NK), Phe-Lys (FK), and Met-Lys (MK), were finally screened out to study gelation with ι-C. It was found that the dipeptides/ι-C formed firm gels except WK/ι-C. The values of the storage modulus (G') of 11 dipeptides/ι-C were investigated by a rheometer. The G' of 8 dipeptides/ι-C was higher than 1000 Pa. These results indicated that the in silico-screened dipeptides from SMGs can form composite gels with ι-C, which can be used for the design and development of functional hydrogels.

Characterising the efficacy and bioavailability of bioactive peptides identified for attenuating muscle atrophy within a Vicia faba-derived functional ingredient

Characterising key components within functional ingredients as well as assessing efficacy and bioavailability is an important step in validating nutritional interventions. Machine learning can assess large and complex data sets, such as proteomic data from plants sources, and so offers a prime opportunity to predict key bioactive components within a larger matrix. Using machine learning, we identified two potentially bioactive peptides within a Vicia faba derived hydrolysate, NPN_1, an ingredient which was previously identified for preventing muscle loss in a murine disuse model. We investigated the predicted efficacy of these peptides in vitro and observed that HLPSYSPSPQ and TIKIPAGT were capable of increasing protein synthesis and reducing TNF-α secretion, respectively. Following confirmation of efficacy, we assessed bioavailability and stability of these predicted peptides and found that as part of NPN_1, both HLPSYSPSPQ and TIKIPAGT survived upper gut digestion, were transported across the intestinal barrier and exhibited notable stability in human plasma. This work is a first step in utilising machine learning to untangle the complex nature of functional ingredients to predict active components, followed by subsequent assessment of their efficacy, bioavailability and human plasma stability in an effort to assist in the characterisation of nutritional interventions.

Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products

This review presents the primary applications of various proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Aquaculture is a quickly growing sector that represents 47% of total fish production. Food quality, dietary management, fish welfare, the stress response, food safety, and antibiotic resistance, which are covered by this review, are among the primary topics in which proteomic techniques and strategies are being successfully applied. The review concludes by outlining future directions and potential perspectives.

An enumeration of natural products from microbial, marine and terrestrial sources

The discovery of a new drug is a multidisciplinary and very costly task. One of the major steps is the identification of a lead compound, i.e. a compound with a certain degree of potency and that can be chemically modified to improve its activity, metabolic properties, and pharmacokinetics profiles. Terrestrial sources (plants and fungi), microbes and marine organisms are abundant resources for the discovery of new structurally diverse and biologically active compounds. In this chapter, an attempt has been made to quantify the numbers of known published chemical structures (available in chemical databases) from natural sources. Emphasis has been laid on the number of unique compounds, the most abundant compound classes and the distribution of compounds in terrestrial and marine habitats. It was observed, from the recent investigations, that ~500,000 known natural products (NPs) exist in the literature. About 70 % of all NPs come from plants, terpenoids being the most represented compound class (except in bacteria, where amino acids, peptides, and polyketides are the most abundant compound classes). About 2,000 NPs have been co-crystallized in PDB structures.

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

Artificial intelligence identified peptides modulate inflammation in healthy adults

Dietary bioactive peptides have been, among many functionalities, associated with immune modulation and thereby may improve resolution of inflammation. The goals of this research were to assess (1) whether specific peptides with immune-modulating activity consumed as part of a rice protein hydrolysate could be absorbed into blood and (2) whether they modulate inflammation markers. Artificial intelligence algorithms were applied to target, predict and unlock inflammation-modulating peptides from rice protein. A food application was developed containing four bioactive peptides. Protein docking simulation studies revealed high binding energies of these peptides with inflammation markers. In a small kinetic study 10 healthy subjects consumed the peptides with a single bolus of 20 g protein hydrolysate. Although absorption of the four predicted peptides at plasma concentrations deemed biologically relevant could not be confirmed (quantitative LC-MS/MS), several cytokines responded (ELISA kits). The 24-hour kinetic study revealed a slight suppression of pro-inflammatory TNF-α, IP-10 and NOx, whereas IL-6 increased temporarily (timepoints 2-12 hours). These markers returned to the baseline after 24 hours whereas others were not affected significantly (IL-10, hs-CRP, IL-8, and MCP-1). Consumption of a single dose protein hydrolysate containing immune modulatory peptides induced a mild temporary response most likely through intestinal signaling. Forthcoming studies will examine dietary supplementation in situations of stress.

Free Accessible Databases as a Source of Information about Food Components and Other Compounds with Anticancer Activity⁻Brief Review

Diet is considered to be a significant factor in cancer prevention and therapy. Many food components reveal anticancer activity. The increasing number of experiments concerning the anticancer potential of chemical compounds, including food components, is a challenge for data searching. Specialized databases provide an opportunity to overcome this problem. Data concerning the anticancer activity of chemical compounds may be found in general databases of chemical compounds and databases of drugs, including specialized resources concerning anticancer compounds, databases of food components, and databases of individual groups of compounds, such as polyphenols or peptides. This brief review summarizes the state of knowledge of chemical databases containing information concerning natural anticancer compounds (e.g., from food). Additionally, the information about text- and structure-based search options and links between particular internet resources is provided in this paper. Examples of the application of databases in food and nutrition sciences are also presented with special attention to compounds that are interesting from the point of view of dietary cancer prevention. Simple examples of potential database search possibilities are also discussed.

Food-Derived Bioactive Peptides in Human Health: Challenges and Opportunities

Recent scientific evidence suggests that food proteins not only serve as nutrients, but can also modulate the body's physiological functions. These physiological functions are primarily regulated by some peptides that are encrypted in the native protein sequences. These bioactive peptides can exert health beneficial properties and thus are considered as a lead compound for the development of nutraceuticals or functional foods. In the past few decades, a wide range of food-derived bioactive peptide sequences have been identified, with multiple health beneficial activities. However, the commercial application of these bioactive peptides has been delayed because of the absence of appropriate and scalable production methods, proper exploration of the mechanisms of action, high gastro-intestinal digestibility, variable absorption rate, and the lack of well-designed clinical trials to provide the substantial evidence for potential health claims. This review article discusses the current techniques, challenges of the current bioactive peptide production techniques, the oral use and gastrointestinal bioavailability of these food-derived bioactive peptides, and the overall regulatory environment.

Peptide selection and antibody generation for the prospective immunorecognition of Cry1Ab16 protein of transgenic maize

The introduction of genes isolated from different Bacillus thuringiensis strains to express Cry-type toxins in transgenic crops is a common strategy to confer insect resistance traits. This work intended to extensively in silico analyse Cry1A(b)16 protein for the identification of peptide markers for the biorecognition of transgenic crops. By combining two different strategies based on several bioinformatic tools for linear epitope prediction, a set of seven peptides was successfully selected as potential Cry1A(b)16 immunogens. For the prediction of conformational epitopes, Cry1A(b)16 models were built on the basis of three independent templates of homologue proteins of Cry1A(a) and Cry1A(c) using an integrated approach. PcH_736-746 and PcH_876-886 peptides were selected as the best candidates, being synthesised and used for the production of polyclonal antibodies. To the best of our knowledge, this is the first attempt of selecting and defining linear peptides as immunogenic markers of Cry1A(b)-type toxins in transgenic maize.

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software. Data mining options may be enhanced by navigating through a network of links and cross-links between databases. Exemplary databases reviewed in this article belong to two classes: tools concerning small molecules (including general and specialized databases annotating food components) and tools annotating enzymes and metabolism. Some problems associated with database application are also discussed. Data summarized in computer databases may be used for calculation of daily intake of bioactive compounds, prediction of metabolism of food components, and their biological activity as well as for prediction of interactions between food component and drugs.

Recent trends in the analysis of bioactive peptides in milk and dairy products

Food-derived constituents represent important sources of several classes of bioactive compounds. Among them peptides have gained great attention in the last two decades thanks to the scientific evidence of their beneficial effects on health in addition to their established nutritional value. Several functionalities for bioactive peptides have been described, including antioxidative, antihypertensive, anti-inflammatory, immunomodulatory, and antimicrobial activity. They are now considered as novel and potential dietary ingredients to promote human health, though in some cases they may also have detrimental effects on health. Bioactive peptides can be naturally occurring, produced in vitro by enzymatic hydrolysis, and formed in vivo during gastrointestinal digestion of proteins. Thus, the need to gain a better understanding of the positive health effects of food peptides has prompted the development of analytical strategies for their isolation, separation, and identification in complex food matrices. Dairy products and milk are potential sources of bioactive peptides: several of them possess extra-nutritional physiological functions that qualify them to be classified under the functional food label. In this trends article we briefly describe the state-of-the-art of peptidomics methods for the identification and discovery of bioactive peptides, also considering recent progress in their analysis and highlighting the difficulty in the analysis of short amino acid sequences and endogenous peptides.

Inactivation and sublethal injury kinetics of Staphylococcus aureus in broth at low temperature storage

Low temperatures are widely used to ensure food quality and safety. However, sublethally injured Staphylococcus aureus is an important microbiological safety concern in low temperature food. The objective of this study was to develop predictive inactivation kinetic models for the inactivation and sublethal injury of S. aureus in broth at different temperatures (4 to -18°C) and time points. S. aureus was diluted in tryptic soy broth plus 0.6% (wt/vol) yeast extract (TSBYE) to obtain approximately 10(8) CFU/ml and was stored separately at 4, -3, -11, and -18°C. After specific time points within 96 days, survival of S. aureus was determined on TSBYE and TSBYE agar plus 10% NaCl for enumeration of the total viable and noninjured cell numbers, respectively. Linear, Weibull, and modified Gompertz models were applied to determine survival curve regression. The combination of low temperature and time resulted in S. aureus inactivation, although the cells were able to survive in this sublethal state. Storage temperature was the critical parameter in survival of S. aureus. The modified Weibull model successfully described a second model of noninjured S. aureus cell survival at different low temperatures, whereas only the linear model was able to fit the total viable cells. The predictive model may be used to estimate the level of S. aureus contamination in food at low storage temperatures and times, and it provides new insight into the sublethally injured survival state of S. aureus in low temperature food.

Dipeptide Phe-Cys derived from in silico thermolysin-hydrolysed RuBisCO large subunit suppresses oxidative stress in cultured human hepatocytes

A dipeptide (Phe-Cys) was predicted to be bioactive following bioinformatics analysis of the large subunit of plant and microalgae ribulose-1,5-bisphosphate carboxylase (RuBisCO), which was hydrolysed in silico with thermolysin. The peptide was synthesised and found to possess in vitro reducing potential and inhibitory activity against lipid peroxidation, comparable to the activity of glutathione. In cultured Chang human hepatocytes, 2.5-10 μM Phe-Cys was found to induce the suppression of reactive oxygen species formation and membrane lipid peroxidation in oxidative stressed cells. Intracellular glutathione levels were found to increase in the peptide-treated cells under normal condition, which can potentially contribute in protecting the cells from oxidative damage. Furthermore, Western blot analysis showed that the levels of antioxidant enzymes, catalase and superoxide dismutase-1, increased in the hepatic cells when treated with Phe-Cys in the presence of the oxidant. The results show that this peptide has great potential to be used against oxidative stress-induced health conditions.