Elucidation of the role of in silico methodologies in approaches to studying bioactive peptides derived from foods

Bioinformatics tools for the study of bioactive peptides from vegetal sources: evolution and future perspectives

Bioactive peptides from vegetal sources have been shown to have functional properties as anti-inflammatory, antioxidant, antihypertensive or antidiabetic capacity. For this reason, they have been proposed as an interesting and promising alternative to improve human health. In recent years, the numerous advances in the bioinformatics field for in silico prediction have speeded up the discovery of bioactive peptides, also reducing the associated costs when using an integrated approach between the classical and bioinformatics discovery. This review aims to provide an overview of the evolution, limitations and latest advances in the field of bioinformatics and computational tools, and specifically make a critical and comprehensive insight into computational techniques used to study the mechanism of interaction that allows the explanation of plant bioactive peptide functionality. In particular, molecular docking is considered key to explain the different functionalities that have been previously identified. The assumptions to simplify such a high complex environment implies a degree of uncertainty that can only be guaranteed and validated by in vitro or in vivo studies, however, the combination of databases, software and bioinformatics applications with the classical approach has become a promising procedure for the study of bioactive peptides.

Peptide recovery from chicken feather keratin and their anti-biofilm properties against methicillin-resistant Staphylococcus aureus (MRSA)

Bacteria have the potential to adhere to abiotic surfaces, which has an undesirable effect in the food industry because they can survive for sustained periods through biofilm formation. In this study, an antibacterial peptide (ABP), with a molecular mass of 3861 Da, was purified from hydrolyzed chicken feathers using a locally isolated keratinolytic bacterium, namely Rhodococcus erythropolis, and its antibacterial and antibiofilm potential were investigated against planktonic and biofilm cells of Methicillin-Resistant Staphylococcus Aureus (MRSA). The results demonstrated that purified ABP showed the growth inhibition of MRSA cells with the minimum inhibitory concentration (MIC) of 45 µg/ml and disrupted MRSA biofilm formation at a concentration of 200 ug/ml, which results were confirmed by scanning electron micrograph (SEM). Moreover, the secondary structures of the peptide were assessed as part of the FTIR analysis to evaluate its mode of action. ExPASy tools were used to predict the ABP sequence, EPCVQUQDSRVVIQPSPVVVVTLPGPILSSFPQNTA, from a chicken feather keratin sequence database following in silico digestion by trypsin. Also, ABP had 54.29% hydrophobic amino acids, potentially contributing to its antimicrobial activity. The findings of toxicity prediction of the peptide by the ToxinPred tool revealed that ABP had non-toxic effects. Thus, these results support the potential of this peptide to be used as an antimicrobial agent for the treatment or prevention of MRSA biofilm formation in feed, food, or pharmaceutical applications.

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.

Targeted Affinity Purification and Mechanism of Action of Angiotensin-Converting Enzyme (ACE) Inhibitory Peptides from Sea Cucumber Gonads

Protein hydrolysates from sea cucumber (Apostichopus japonicus) gonads are rich in active materials with remarkable angiotensin-converting enzyme (ACE) inhibitory activity. Alcalase was used to hydrolyze sea cucumber gonads, and the hydrolysate was separated by the ultrafiltration membrane to produce a low-molecular-weight peptide component (less than 3 kDa) with good ACE inhibitory activity. The peptide component (less than 3 kDa) was isolated and purified using a combination method of ACE gel affinity chromatography and reverse high-performance liquid chromatography. The purified fractions were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the resulting products were filtered using structure-based virtual screening (SBVS) to obtain 20 peptides. Of those, three noncompetitive inhibitory peptides (DDQIHIF with an IC50 value of 333.5 μmol·L-1, HDWWKER with an IC50 value of 583.6 μmol·L-1, and THDWWKER with an IC50 value of 1291.8 μmol·L-1) were further investigated based on their favorable pharmacochemical properties and ACE inhibitory activity. Molecular docking studies indicated that the three peptides were entirely enclosed within the ACE protein cavity, improving the overall stability of the complex through interaction forces with the ACE active site. The total free binding energies (ΔGtotal) for DDQIHIF, HDWWKER, and THDWWKER were -21.9 Kcal·mol-1, -71.6 Kcal·mol-1, and -69.1 Kcal·mol-1, respectively. Furthermore, a short-term assay of antihypertensive activity in spontaneously hypertensive rats (SHRs) revealed that HDWWKER could significantly decrease the systolic blood pressure (SBP) of SHRs after intravenous administration. The results showed that based on the better antihypertensive activity of the peptide in SHRs, the feasibility of targeted affinity purification and computer-aided drug discovery (CADD) for the efficient screening and preparation of ACE inhibitory peptide was verified, which provided a new idea of modern drug development method for clinical use.

Antihypertensive peptide resources map of ribulose-1,5-bisphosphate carboxylase/oxygenases (RuBisCO) in angiosperms: Revealed by an integrated in silico and in vitro approach

As the most abundant protein on earth, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) has been considered a promising resource of functional foods. This study aimed to explore the full potential of plant RuBisCO proteins as precursors of antihypertensive peptides on a large scale. In total, 12,766 RuBisCO large subunit and 1,020 RuBisCO small subunit sequences of angiosperms were collected for simulated proteolysis and evaluation of antihypertensive potential, revealing a vast reservoir of antihypertensive peptides. Moreover, RuBisCO-derived novel antihypertensive peptides TTVW, TMW, and VPCL were identified with in vitro IC50 of 12.89 ± 0.82, 23.97 ± 1.02, and 339.12 ± 21.64 μM, respectively. Notably, TTVW and TMW are noncompetitive inhibitors predicted to bound adjacent to the catalytic region of ACE, while VPCL is a competitive inhibitor predicted to bound to the central active site inside ACE. Overall, this work provides a powerful theoretical guidance in developing antihypertensive functional foods utilizing plant RuBisCO.

Identification of novel α-glucosidase and ACE inhibitory peptides from Douchi using peptidomics approach and molecular docking

In this study, the effect of Douchi extract (DWE) on α-glucosidase and angiotensin-converting enzymes (ACE) were investigated, and several novel peptides with inhibitory activity against α-glucosidase and ACE were identified using peptidomics approach based on UPLC-MS/MS. The average inhibition rates of DWE on α-glucosidase and ACE were 73.75-78.10% and 4.56-27.07%, respectively. In the DWE, a total of 710 peptides were detected. Two novel peptides with potential inhibitory activity against α-glucosidase were identified using the correlation analysis, database alignment and molecular docking methods. They were DVFRAIPSEVL and DRPSINGLAGAN, with the IC50 values of 0.121 and 0.128 mg/mL, respectively. Also, four novel peptides with potential inhibitory activity against ACE were identified: PSSPFTDLWD, EEQDERQFPF, PVPVPVQQAFPF and PSSPFTDL, with IC50 values of 1.388, 0.041, 0.761 and 0.097 mg/mL, respectively. These results indicated that combining peptidomics and molecular docking is an effective alternative strategy for rapidly screening numbers of novel bioactive peptides from foods.

Current state of insect proteins: extraction technologies, bioactive peptides and allergenicity of edible insect proteins

This review aims to provide an updated overview of edible insect proteins and the bioactivity of insect-derived peptides. The essential amino acid content of edible insects is compared with well-known protein sources to demonstrate that edible insects have the potential to cover the protein quality requirements for different groups of the population. Then the current methodologies for insect protein extraction are summarized including a comparison of the protein extraction yield and the final protein content of the resulting products for each method. Furthermore, in order to improve our understanding of insect proteins, their functional properties (such as solubility, foaming capacity, emulsifying, gelation, water holding capacity and oil holding capacity) are discussed. Bioactive peptides can be released according to various enzymatic hydrolysis protocols. In this context, the bioactive properties of insect peptides (antihypertensive, antidiabetic, antioxidant and anti-inflammatory properties) have been discussed. However, the allergens present in insect proteins are still a major concern and an unsolved issue for insect-based product consumption; thus, an analysis of cross reactivity and the different methods available to reduce allergenicity are proposed. Diverse studies of insect protein hydrolysates/peptides have been ultimately promoting the utilization of insect proteins for future perspectives and the emerging processing technologies to enhance the wider utilization of insect proteins for different purposes.

Processing Enhances Coix Seed Prolamins Structure and Releases Functional Peptides after Digestion: In Silico and In Vitro Studies

Dipeptidyl peptidase-IV (DPP-IV) is a key target for the treatment of type 2 diabetes mellitus. It is possible that peptides that precisely regulate DPP-IV could be released from coix seed prolamins (CSP), but whether this happens has not yet been investigated. We performed the in silico digestion of CSP and predicted the bioactivity, absorption, transport, toxicity, and allergenicity of the resulting peptides. The simulation predicted that 47 non-toxic bioactive peptides would be released. After screening these, we found that 64.58% of them could possess DPP-IV inhibitory activity. The effect of thermal processing on the amino acid composition and structural properties of CSP was determined, and the DPP-IV inhibitory activity of its digestion-derived peptides was also assessed. The results showed that processing could change the flavour of coix seed and the supply of amino acids. After processing, the spatial conformation of CSP changed from ordered to disordered, and the peptide content and the DPP-IV inhibitory activity of its digestion products significantly increased by 19.89-30.91% and 36.84-42.02%, respectively. These results support the hypothesis that processing can change the protein structure and increase the probability that bioactive peptides will be released. They also have important implications for the development of bioactive peptides and the intensive processing of coix seeds.

A Comprehensive Review on Nutraceuticals: Therapy Support and Formulation Challenges

Nutraceuticals are the nourishing components (hybrid of nutrition and pharmaceuticals) that are biologically active and possess capability for maintaining optimal health and benefits. These products play a significant role in human health care and its endurance, most importantly for the future therapeutic development. Nutraceuticals have received recognition due to their nutritional benefits along with therapeutic effects and safety profile. Nutraceuticals are globally growing in the field of services such as health care promotion, disease reduction, etc. Various drug nutraceutical interactions have also been elaborated with various examples in this review. Several patents on nutraceuticals in agricultural applications and in various diseases have been stated in the last section of review, which confirms the exponential growth of nutraceuticals' market value. Nutraceuticals have been used not only for nutrition but also as a support therapy for the prevention and treatment of various diseases, such as to reduce side effects of cancer chemotherapy and radiotherapy. Diverse novel nanoformulation approaches tend to overcome challenges involved in formulation development of nutraceuticals. Prior information on various interactions with drugs may help in preventing any deleterious effects of nutraceuticals products. Nanotechnology also leads to the generation of micronized dietary products and other nutraceutical supplements with improved health benefits. In this review article, the latest key findings (clinical studies) on nutraceuticals that show the therapeutic action of nutraceutical's bioactive molecules on various diseases have also been discussed.

Advances in the stability challenges of bioactive peptides and improvement strategies

Bioactive peptides are widely used in functional foods due to their remarkable efficacy, selectivity, and low toxicity. However, commercially produced bioactive peptides lack quality stability between batches. Furthermore, the efficacies of bioactive peptides cannot be guaranteed in vivo due to gastrointestinal digestion and rapid plasma, liver, and kidney metabolism. The problem of poor stability has restricted the development of peptides. Bioactive peptide stability assessments use different stability assays, so the results of different studies are not always comparable. This review summarizes the quality stability challenges in the enzymatic hydrolysis production of bioactive peptides and the metabolism stability challenges after oral administration. Future directions on the strategies for improving their stability are provided. It was proposed that we use fingerprinting as a quality control measure using qualitative and quantitative characteristic functional peptide sequences. The chemical modification and encapsulation of bioactive peptides in microcapsules and liposomes are widely used to improve the digestive and metabolic stability of bioactive peptides. Additionally, the establishment of a universal stability test and a unified index would greatly improve uniformity and comparability in research into bioactive peptides. In summary, the reliable evaluation of stability is an essential component of peptide characterization, and these ideas may facilitate further development and utilization of bioactive peptides.

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Stability challenges encountered by bioactive peptides were summarized.

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Strategies to improve the stability of bioactive peptides were provided.

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A universal stability test and unified index would improve uniformity and comparability in research into bioactive peptides.

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It was proposed that we use a method of traditional Chinese medicine fingerprinting as a quality control measure.

Arginine-Containing Peptides Derived from Walnut Protein Against Cognitive and Memory Impairment in Scopolamine-Induced Zebrafish: Design, Release, and Neuroprotection

The purpose of this study was to investigate the neuroprotective effect of Arg-containing peptides from walnut storage protein sequences in scopolamine-induced zebrafish and further to validate the potential neuroprotection of Arg-containing peptide enriched walnut hydrolysates prepared by in silico hydrolysis and controlled enzymatic release. Results showed that walnut derived Arg-containing peptides with high abundance and great bioactivity predicted by bioinformatics displayed potent neuroprotection in scopolamine-induced zebrafish, and regulation of neurotransmitter level and antioxidant enzyme activity might be the main target for Arg-containing peptides to exert neuroprotection. Notably, Arg-containing peptides (not free arginine) contributed greater neuroprotection, and the positive charge and cell-penetrating properties also affected their neuroprotection. Subsequently, Arg-containing peptides could be released efficiently from walnut protein following hydrolysis by trypsin, pepsin, papain, and thermolysin (bound arginine content: ranging from 110.43 ± 1.58 to 121.82 ± 1.02 mg/g). Among them, trypsin had excellent potential for releasing Arg-containing peptides in silico hydrolysis, and its hydrolysate was confirmed to have neuroprotective capacity, indicating that the combination of in silico hydrolysis and controlled enzymatic release might be an effective approach to obtain Arg-containing neuroprotective peptides.

Food-derived dipeptidyl peptidase IV inhibitory peptides: Production, identification, structure-activity relationship, and their potential role in glycemic regulation

Dipeptidyl Peptidase IV (DPP-IV) inhibitory peptides are attracting increasing attention, owing to their potential role in glycemic regulation by preventing the inactivation of incretins. However, few reviews have summarized the current understanding of DPP-IV inhibitory peptides and their knowledge gaps. This paper reviews the production, identification and structure-activity relationships (SAR) of DPP-IV inhibitory peptides. Importantly, their bioavailability and hypoglycemic effects are critically discussed. Unlike the traditional method to identifying peptides after separation step by step, the bioinformatics approach identifies peptides via virtual screening that is more convenient and efficient. In addition, the bioinformatics approach was also used to investigate the SAR of peptides. Peptides with proline (Pro) or alanine (Ala) residue at the second position of N-terminal are exhibit strong DPP-IV inhibitory activity. Besides, the bioavailability of DPP-IV inhibitory peptides is related to their gastrointestinal stability and cellular permeability, and in vivo studies showed that the glucose homeostasis has been improved by these peptides. Especially, the intestinal transport of DPP-IV inhibitory peptides and cell biological assays used to evaluate their potential role in glycemic regulation are innovatively summarized. For further successful development of DPP-IV inhibitory peptides in glycemic regulation, future study should elucidate their SAR and in vivo hypoglycemic effects .

An integrated approach to the analysis of antioxidative peptides derived from Gouda cheese with a modified β-casein content

This study is the first to present an integrated approach involving in silico and in vitro protocols that was pursued to analyse an antioxidative potency of Gouda cheese with modified content of β-casein. Firstly, the predictions of the presence of antioxidant peptides in the casein sequences were computed using the BIOPEP-UWM database. Then, the antioxidative bioactivity of six variants of Gouda cheese (with reduced, normative, and increased content of β-casein at the initial and final stage of ripening) was assessed. Finally, the RP-HPLC–MS/MS was applied to identify antioxidative peptides in Gouda-derived water-soluble extracts (WSEs). Analyses were supported with the heatmaps and the computation of parameters describing the efficiency of proteolysis of caseins in the modified Gouda cheeses, i.e., the frequency and the relative frequency of the release of antioxidative fragments during cheese ripening (A_Eexp and W_exp., respectively). All Gouda cheese variants exhibited the antioxidative potential which differed depending on the assay employed. The highest antioxidative activity (ABTS^·+ radical scavenging effect, FRAP, and Fe-chelating) was observed for WSEs derived from Gouda cheese with increased content of β-casein after the 60th day of ripening. The results obtained suggest the potential of Gouda cheese as the antioxidant-promoting food.

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).

Identification of antidiabetic peptides derived from in silico hydrolysis of three ancient grains: Amaranth, Quinoa and Chia

The antidiabetic potential of bioactive peptides derived from simulated gastrointestinal digestion (SGID) of proteins present in amaranth quinoa and chia was evaluated using their bioactivity profile and theoretical interaction with DPP-IV and α-glucosidases. In silico SGID generated 52 different fragments with in vitro antidiabetic activity where fragments PW, PF, PPG, PM, SW, IW, SF, PP, PPL, PG, PY, VW and PL scored highly in bioactivity probability, with molecular weights ranging from 172.2 to 325.44 Da; positive bulkiness index and hydrophobicity (except PP and PY) and no toxic properties. Fragments IW and PW presented the lowest free energy values for enzymes DPP-IV, maltase-glucoamylase, pancreatic α-amylase and sucrase-isomaltase (-8.2, -7.5, -7.7 and -7.5 kcal/mol; and -7.8, -7.4, -8.2, -7.4 kcal/mol respectively) We can conclude that proteins from amaranth, quinoa and chia may be a good source of antidiabetic BP and may exert antidiabetic activity through the release of BP after digestion.

Insight of the Functional and Biological Activities of Coconut (Cocos nucifera L.) Protein by Proteomics Analysis and Protein-Based Bioinformatics

Coconut (Cocos nucifera L.) is one of the most critical economic crops in the tropics and sub-tropics. Although coconut protein has attracted more and more attention due to its nutritional potential, the lack of proteomic information has limited its practical application. The present study aimed to investigate the coconut meat proteome by shotgun proteomics and protein-based bioinformatic analysis. A grand total of 1686 proteins were identified by searching the National Center for Biotechnology Information (NCBI) protein database and self-constructed C. nucifera transcriptome repository. Among them, 17 and 9 proteins were identified as antioxidant proteins and globulins, respectively. Network analysis of the globulins referred to the sub-works of Cupin and Oleosin, and the antioxidant proteins were related to the sub-networks of glutathione metabolism and peroxisome. The bioactive peptides acquired by in-silico digestion of the targeted proteins have the potential to be applied as antioxidants and emulsifiers for both healthcare and food stabilization.

Conventional and in silico approaches to select promising food-derived bioactive peptides: A review

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Seaweed and edible insects are considered new sources of bioactive peptides.

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Conventional approaches are necessary to validate the bioactivity of peptides.

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Bioinformatics tools accelerate the obtaining of bioactive peptides.

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The integrated approach is a promising strategy to obtain bioactive peptides.

The interest for food-derived bioactive peptides, either from common or unconventional sources, has increased due to their potential therapeutic effect against a wide range of diseases. The study of such bioactive peptides using conventional methods is a long journey, expensive and time-consuming. Hence, bioinformatic approaches, which can not only help to predict the formation of bioactive peptides from any known protein source, but also to analyze the protein structure/function relationship, have gained a new meaning in this scientific field. Therefore, this review aims to provides an overview of conventional characterization methods and the most recent advances in the field of in silico approaches for predicting and screening promising food-derived bioactive peptides.

Exploration of bioactive peptides from various origin as promising nutraceutical treasures: In vitro, in silico and in vivo studies

The current health scenarios describe growing public health problems, such as diabetes, hypertension and cancer. Therefore, researchers focused on studying these health issues are interested in exploring bioactive compounds from different food sources. Among them, bioactive peptides have garnered huge scientific interest because of their multifunctional biological activities such as antioxidative, antimicrobial, antihypertensive, anticancer, antidiabetic, immunomodulatory effect. They can be used as food and pharmaceutical ingredients with a great potential against disease targets. This review covers methods of production in general for several peptides obtained from various food sources including seed, milk and meat, and described their biological activities. Particular focus was given to bioinformatic tools to advance quantification, detection and characterize each peptide sequence obtained from different protein sources with predicted biological activity. Besides, various in vivo studies have been discussed to provide a better understanding of their physiological functions, which altogether could provide valuable information for their commercialization in future foods.

Prediction of Bioactive Peptides From Chicken Feather and Pig Hair Keratins Using In Silico Analysis Based on Fragmentomic Approach

BACKGROUND

Keratin is among the most abundant structural proteins of animal origin, however it remains broadly underutilized. <P> Objective: Bioinformatic investigation was performed to evaluate selected keratins originating from mass-produced waste products, i.e., chicken feathers and pig hair, as potential sources of bioactive peptides. <P> Methods: Pepsin, trypsin, chymotrypsin, papain, and subtilisin were used for in silico keratinolysis with the use of "Enzyme(s) action" and fragmentomic analysis of theoretical products was performed using "Profiles of potential biological activity" in BIOPEP-UWM database of bioactive peptides. Bioactivity probability calculation and toxicity prediction of the peptides obtained were estimated using PeptideRanker and ToxinPred tools, respectively. <P> Results: Our results showed that the keratins are a potential source of a variety of biopeptides, including dipeptidyl peptidase IV, angiotensin converting enzyme, prolyl endopeptidase inhibitory and antioxidative. Papain and subtilisin were found to be the most appropriate enzymes for keratin hydrolysis. This study presents possible structures of keratin-derived bioactive peptides that have not been previously described. <P> Conclusion: Our data suggest additional in vitro and in vivo studies to verify theoretical predictions and further investigate the possibility of using keratin-rich waste as a source of peptide nutraceuticals.

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.

Properties of peptides released from salmon and carp via simulated human-like gastrointestinal digestion described applying quantitative parameters

Apart from the classical (experimental) methods, biologically active peptides can be studied via bioinformatics approach, also known as in silico analysis. This study aimed to verify the following research hypothesis: ACE inhibitors and antioxidant peptides can be released from salmon and carp proteins during simulated in silico human-like gastrointestinal digestion. The potential to release biopeptides was evaluated using the BIOPEP-UWM quantitative criteria including the profile of biological activity, frequency of the occurrence (A)/release (AE) of fragments with an ACE inhibitory or antioxidant activity by selected enzymes, and relative frequency of release of bioactive fragments with a given activity by selected enzymes (W). Salmon collagen and myofibrillar proteins of carp turned out to be the best potential source of the searched peptides-ACE inhibitors and antioxidant peptides. Nonetheless, after digestion, the highest numbers of ACE inhibitors and antioxidant peptides were potentially released from the myofibrillar proteins of salmon and carp. Peptide Ranker Score, Pepsite2, and ADMETlab platform were applied to evaluate peptides' bioactivity potential, their safety and drug-like properties. Among the 63 sequences obtained after the simulated digestion of salmon and carp proteins, 30 were considered potential biopeptides. The amino acid sequences of ACE-inhibiting and antioxidant peptides were predominated by P, G, F, W, R, and L. The predicted high probability of absorption of most analyzed peptides and their low toxicity should be considered as their advantage.

Emerging Emulsifiers: Conceptual Basis for the Identification and Rational Design of Peptides with Surface Activity

Emulsifiers are gradually evolving from synthetic molecules of petrochemical origin to biomolecules mainly due to health and environmental concerns. Peptides represent a type of biomolecules whose molecular structure is composed of a sequence of amino acids that can be easily tailored to have specific properties. However, the lack of knowledge about emulsifier behavior, structure-performance relationships, and the implementation of different design routes have limited the application of these peptides. Some computational and experimental approaches have tried to close this knowledge gap, but restrictions in understanding the fundamental phenomena and the limited property data availability have made the performance prediction for emulsifier peptides an area of intensive research. This study provides the concepts necessary to understand the emulsifying behavior of peptides. Additionally, a straightforward description is given of how the molecular structure and conditions of the system directly impact the peptides' ability to stabilize emulsion droplets. Moreover, the routes to design and discover novel peptides with interfacial and emulsifying activity are also discussed, along with the strategies to address some of their major pitfalls and challenges. Finally, this contribution reviews methodologies to build and use data sets containing standard properties of emulsifying peptides by looking at successful applications in different fields.

Gouda Cheese with Modified Content of β-Casein as a Source of Peptides with ACE- and DPP-IV-Inhibiting Bioactivity: A Study Based on In Silico and In Vitro Protocol

In silico and in vitro methods were used to analyze ACE- and DPP-IV-inhibiting potential of Gouda cheese with a modified content of β-casein. Firstly, the BIOPEP-UWM database was used to predict the presence of ACE and DPP-IV inhibitors in casein sequences. Then, the following Gouda cheeses were produced: with decreased, increased, and normative content of β-casein after 1 and 60 days of ripening each (six variants in total). Finally, determination of the ACE/DPP-IV-inhibitory activity and the identification of peptides in respective Gouda-derived water-soluble extracts were carried out. The identification analyses were supported with in silico calculations, i.e., heatmaps and quantitative parameters. All Gouda variants exhibited comparable ACE inhibition, whereas DPP-IV inhibition was more diversified among the samples. The samples derived from Gouda with the increased content of β-casein (both stages of ripening) had the highest DPP-IV-inhibiting potency compared to the same samples measured for ACE inhibition. Regardless of the results concerning ACE and DPP-IV inhibition among the cheese samples, the heatmap showed that the latter bioactivity was predominant in all Gouda variants, presumably because it was based on the qualitative approach (i.e., peptide presence in the sample). Our heatmap did not include the bioactivity of a single peptide as well as its quantity in the sample. In turn, the quantitative parameters showed that the best sources of ACE/DPP-IV inhibitors were all Gouda-derived extracts obtained after 60 days of the ripening. Although our protocol was efficient in showing some regularities among Gouda cheese variants, in vivo studies are recommended for more extensive investigations of this subject.

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes

Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to describe a simple code for the annotation of phosphopeptide sequences. The proposed code describes the location of phosphate residues in amino acid side chains (including new rules of atom numbering in amino acids) and the diversity of phosphate residues (e.g., di- and triphosphate residues and phosphate amidation). This article also includes translating the proposed biological code into SMILES, being the most commonly used chemical code. Finally, it discusses possible errors associated with applying the proposed code and in the resulting SMILES representations of phosphopeptides. The proposed code can be extended to describe other modifications in the future.

Prospects of cereal protein-derived bioactive peptides: Sources, bioactivities diversity, and production

Cereals account for a large proportion of the human diet and are an important source of protein. The preparation of cereal protein peptides is a good way to utilize these proteins. Cereal protein peptides have good application potential as antioxidant, antibacterial, anti-inflammatory and anticancer compounds, in lowering blood pressure, controlling blood sugar, and inhibiting thrombosis. This article reviews the literature on the functional properties, mechanisms of action, and applications of cereal protein peptides in the food industry with two perspectives, and summarizes the methods for their preparation and identification. The biologically active peptides derived from different grain proteins have varied main functional properties, which may be related to the differences in the amino acid composition and protein types of different grains. On this basis, the structure-activity relationship of cereal protein peptides was discussed. The advancement of identification technology makes the integration of bioinformatics and bioactive peptide research closer. Bioinformatics by combination of online database, computer simulation and experimental verification is helpful to in-deep study the structure-activity relationship of biologically active peptides, and improve efficiency in the process of obtaining target peptides with less cost. In addition, the application of cereal protein peptides in the food industry is also discussed.

Recent Progress in Enzymatic Release of Peptides in Foods of Animal Origin and Assessment of Bioactivity

There is a wide variety of peptides released from food proteins that are able to exert a relevant benefit for human health, such as angiotensin-converting enzyme inhibition, antioxidant, anti-inflammatory, hypoglucemic, or antithrombotic activity, among others. This manuscript is reviewing the recent advances on enzymatic mechanisms for the hydrolysis of proteins from foods of animal origin, including the types of enzymes and mechanisms of action involved, the strategies followed for the isolation and identification of bioactive peptides through advanced proteomic tools, and the assessment of bioactivity and its beneficial effects. Specific applications in fermented and/or ripened foods where a significant number of bioactive peptides have been reported with relevant in vivo physiological effects on laboratory rats and humans as well as the hydrolysis of animal food proteins for the production of bioactive peptides are also reviewed.

Advances on Food-Derived Peptidic Antioxidants-A Review

The oxidation process is considered to be the main reason behind human aging, human degenerative diseases and food quality degradation. Food-derived peptidic antioxidants (PAs) have wide sources and great activity, and have broad application prospects in removing excess reactive oxygen species in the body, anti-aging and preventing and treating diseases related to oxidative stress. On the other hand, PAs are expected to inhibit the lipid peroxidation of foods and increase the stability of the food system in the food industry. However, the production pathways and action mechanism of food-derived PAs are diverse, which makes it is difficult to evaluate the performance of PAs which is why the commercial application of PAs is still in its infancy. This article focuses on reviewing the preparation, purification, and characterization methods of food-derived PAs, and expounds the latest progress in performance evaluation and potential applications, in order to provide an effective reference for subsequent related research of PAs.

In Vitro Pepsin Digestion Characteristics of Silver Carp (Hypophthalmichthys molitrix) Surimi Gels with Different Degrees of Cross-Linking Induced by Setting Time and Microbial Transglutaminase

Surimi gels are favored for their abundant proteins and unique taste. In this study, the pepsin digestion behaviors of surimi gels with different degrees of cross-linking induced by microbial transglutaminase (MTGase) and different setting times were investigated. For gels without (CK group) and with (TG group) MTGase, the slowest digestion rate (t_M/2 = 20.13 and 79.19 min for CK and TG group, respectively), the least amino acid concentration (5.32 and 3.73 μmol/mL for CK and TG group, respectively), and the peptide amounts (1355 and 1788 for CK and TG group, respectively) were obtained at a moderate setting time (1-4 h) with the finest microstructure. However, the excessive setting time (8-12 h) formed an inhomogenous network, which accelerated the hydrolysis of gel proteins (t_M/2 = 9.40 and 52.33 min for CK and TG group, respectively) and produced more amino acids (6.63 and 5.15 μmol/mL for CK and TG group, respectively) and peptide amounts (1644 and 2143 for CK and TG group, respectively). The above results also demonstrated that the presence of MTGase strengthened the compactness of gels as well as slowed down the digestion process with the release of less amino acids but more peptides. A large proportion of unique peptides were from the tail domain of myosin heavy chain. The discrepancy in bioactive peptides between different gels might be reduced in the subsequent intestinal digestion according to the in silico methods, demonstrating the diminished difference in the gastrointestinal digestion process in the aspect of releasing functional peptides. This study provides the theoretical basis and guideline in the field of gelation food digestion and surimi food industry to produce healthier surimi-based food.

Characteristics of Biopeptides Released In Silico from Collagens Using Quantitative Parameters

The potential of collagens to release biopeptides was evaluated using the BIOPEP-UWM-implemented quantitative criteria including the frequency of the release of fragments with a given activity by selected enzyme(s) (AE), relative frequency of release of fragments with a given activity by selected enzyme(s) (W), and the theoretical degree of hydrolysis (DHt). Cow, pig, sheep, chicken, duck, horse, salmon, rainbow trout, goat, rabbit, and turkey collagens were theoretically hydrolyzed using: stem bromelain, ficin, papain, pepsin, trypsin, chymotrypsin, pepsin+trypsin, and pepsin+trypsin+chymotrypsin. Peptides released from the collagens having comparable AE and W were estimated for their likelihood to be bioactive using PeptideRanker Score. The collagens tested were the best sources of angiotensin I-converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV) inhibitors. AE and W values revealed that pepsin and/or trypsin were effective producers of such peptides from the majority of the collagens examined. Then, the SwissTargetPrediction program was used to estimate the possible interactions of such peptides with enzymes and proteins, whereas ADMETlab was applied to evaluate their safety and drug-likeness properties. Target prediction revealed that the collagen-derived peptides might interact with several human proteins, especially proteinases, but with relatively low probability. In turn, their bioactivity may be limited by their short half-life in the body.

Metabolic Syndrome-Preventive Peptides Derived from Milk Proteins and Their Presence in Cheeses: A Review

The metabolic syndrome (MetS) is defined as the occurrence of diet-related diseases such as abdominal obesity, atherogenic dyslipidemia, hyperglycemia (insulin resistance) and hypertension. Milk-derived peptides are well-known agents acting against high blood pressure, blood glucose level, and lipoprotein disproportion. The aim of this review are metabolic syndrome-preventive peptides derived from milk proteins which were identified in cheeses. Special attention was paid to the sequences acting as angiotensin converting enzyme (ACE), dipeptidyl peptidase IV (DDP4), and α-glucosidase inhibitors, as well as antioxidative, hypocholesterolemic, antiobesity, and anti-inflammatory agents. Some results of meta-analyses concerning the consumption of cheese and the risk of MetS diseases were also presented.

Soybean (Glycine max) Protein Hydrolysates as Sources of Peptide Bitter-Tasting Indicators: An Analysis Based on Hybrid and Fragmentomic Approaches

The aim of this study was to analyze soybean proteins as sources of peptides likely to be bitter using fragmentomic and hybrid approaches involving in silico and in vitro studies. The bitterness of peptides (called parent peptides) was theoretically estimated based on the presence of bitter-tasting motifs, particularly those defined as bitter-tasting indicators. They were selected based on previously published multilinear stepwise regression results. Bioinformatic-assisted analyses covered the hydrolysis of five major soybean-originating protein sequences using bromelain, ficin, papain, and proteinase K. Verification of the results in experimental conditions included soy protein concentrate (SPC) hydrolysis, RP-HPLC (for monitoring the proteolysis), and identification of peptides using RP-HPLC-MS/MS. Discrepancies between in silico and in vitro results were observed when identifying parent peptide SPC hydrolysate samples. However, both analyses revealed that conglycinins were the most abundant sources of parent peptides likely to taste bitter. The compatibility percentage of the in silico and in vitro results was 3%. Nine parent peptides with the following sequences were identified in SPC hydrolysates: LSVISPK, DVLVIPLG, LIVILNG, NPFLFG, ISSTIV, PQMIIV, PFPSIL, DDFFL, and FFEITPEK (indicators are in bold). The fragmentomic idea of research might provide a supportive method for predicting the bitterness of hydrolysates. However, this statement needs to be confirmed experimentally.

Enzymatic release of dipeptidyl peptidase-4 inhibitors (gliptins) from pigeon pea (Cajanus cajan) nutrient reservoir proteins: In silico and in vitro assessments

In silico and in vitro parameters were used to assess the potential of pigeon pea (Cajanus cajan) nutrient reservoir proteins as sources of dipeptidyl peptidase (DPP)-4 inhibitors. In silico, 40 pigeon pea proteins evaluated had 46% of amino acids associated with DPP-4 inhibition. After virtual hydrolysis, pepsin had the highest frequency of release and bioactivity of released DPP-4 inhibiting peptides, compared to papain and thermolysin. In vitro, thermolysin released the most active DPP-4 inhibitors. The protein hydrolysates contained similar amino acids but different particle sizes. Thus, the bioactivity patterns are attributable to the different nature and behavior of proteins/peptides under actual and virtual conditions. Using eight physicochemical variables, a random forest model with moderate prediction accuracy was developed for predicting DPP-4 inhibitory activity of papain hydrolysates. The findings demonstrate that proteins from pigeon pea are precursors of DPP-4 inhibitors, with potential use in formulating functional food for managing type 2 diabetes. PRACTICAL APPLICATIONS: The emerging use of in silico simulations to predict bioactivity of peptides can provide a framework to direct further wet lab assessments. This pattern can enhance focusing on factors relevant to the bioactive properties of interest. However, there is still limited evidence to confirm the reliability and accuracy of this tool. This study therefore provides insight into the practical use of in silico simulations to predict bioactivity of food peptides by assessing the factors relevant to the enzymatic release of dipeptidyl peptidase-4 inhibitors from pigeon pea seed storage proteins and validating the findings with wet lab assessment. This work also provides important information that can enhance the utilization of pigeon pea, which is an orphan crop, in developing functional food products for managing type 2 diabetes mellitus in developing countries.

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.