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.

Multi-Bioactivity of Protein Digests and Peptides from Oat (Avena sativa L.) Kernels in the Prevention of the Cardiometabolic Syndrome.

The aim of this study was to characterize the digests and peptides derived from oat kernel proteins in terms of their major enzyme inhibitory activities related to the prevention of cardiometabolic syndrome. It also entailed the characteristics of antioxidant bioactivity of the analyzed material. The study was carried out using coupled in silico and in vitro methods. The additional goal was to investigate whether identified peptides can pervade Caco-2 cells. Based on the results of bioinformatic analysis, it was found that the selected oat proteins may be a potential source of 107 peptides with DPP-IV and/or ACE inhibitory and/or antioxidant activity. The duodenal digest of oat kernels revealed multiple activities. It inhibited the activities of the following enzymes: DPP-IV (IC50 = 0.51 vs. 10.82 mg/mL of the intact protein), α-glucosidase (IC50 = 1.55 vs. 25.20 mg/mL), and ACE (IC50 = 0.82 vs. 34.52 mg/mL). The DPPH• scavenging activity was 35.7% vs. 7.93% that of the intact protein. After in silico digestion of oat proteins, 24 peptides were selected for identification using LC-Q-TOF-MS/MS. Among them, 13 sequences were successfully identified. One of them, i.e., VW peptide, exhibited triple activities, i.e., DPP-IV and ACE inhibitory and DPPH• scavenging activity. The multifunctional peptides: PW, TF, VF, and VW, were identified in the basolateral samples after transport experiments. Both in silico and in vitro analyses demonstrated that oat kernel proteins were the abundant sources of bioactive digests and peptides to be used in a diet for patients suffering from cardiometabolic syndrome.

An integrated approach to the analysis of antioxidative peptides derived from Gouda cheese with a modified ß-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 ß-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 ß-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 (AEexp and Wexp., 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 ß-casein after the 60th day of ripening. The results obtained suggest the potential of Gouda cheese as the antioxidant-promoting food.

Gouda Cheese with Modified Content of ß-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 ß-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 ß-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 ß-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.

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.

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.

Understanding the nature of bitter-taste di- and tripeptides derived from food proteins based on chemometric analysis.

Multiple linear regression (MLR) models were constructed to explain the bitter taste of di- and tripeptides based on their chemical nature (structure). Sequences (51 di- and 51 tripeptides) were derived from the BIOPEP-UWM database of sensory peptides and amino acids. The measure of their bitterness was Rcaf. , that is, bitterness relative to that of 1 mM caffeine solution (Rcaf. = 1.0). The variables were the indices describing properties of a single residue forming a peptide structure taken from ProtScale and Biological Magnetic Resonance Data Bank. MLR was made for two separate data sets by use of Statistica 13.1. We found that the presence of branched side residues or ring in a di- or tripeptide sequence (as in L, I, V, Y, F) affected its bitterness. Another variable affecting the bitter taste of di- and tripeptides was the hydrophobicity of amino acids. Using the commonly available statistical tools as well as chemical information reflecting the nature of peptides may be helpful in understanding the structure-taste relationship in food peptides. PRACTICAL APPLICATIONS: Our approach takes account of bioinformatic and cheminformatic techniques of data mining to analyze structure-bitterness of di- and tripeptides derived from food protein sources. Data on bitter peptides available in databases of biological and chemical information can be useful in creating models which help understanding the relationship between the role of structural properties of a molecule (e.g., peptide) and its function (e.g., taste). The bitterness of a peptide resulting from the presence of specific residues in its sequence, which represent different physicochemical properties may contribute to extending the knowledge about their taste-forming role in food systems. Such knowledge may be useful in designing food products with improved properties like taste which can be either enhanced or masked (considered as unwanted when thinking about the sensory value of foods). Our research strategy is universal and can also be applied to study structure-function relationships of peptides with other activities.

Structure⁻Activity Prediction of ACE Inhibitory/Bitter Dipeptides-A Chemometric Approach Based on Stepwise Regression.

Forward and backward stepwise regression (FR and BR, respectively) was applied for the structure⁻bioactivity prediction of angiotensin converting enzyme (ACE)-inhibitory/bitter-tasting dipeptides. The datasets used in this study consisted of 28 sequences and numerical variables reflecting dipeptides' physicochemical nature. The data were acquired from the BIOPEP-UWM, Biological Magnetic Resonance Databank, ProtScale, and AAindex databases. The calculations were computed using STATISTICA®13.1. FR/BR models differed in R² (0.91/0.76, respectively). The impact of C-atC(-) and N-Molw(+) on the dual function of dipeptides was observed. Positive (+) and negative (-) correlations with log IC50 are presented in parens. Moreover, C-Bur(+), N-atH(+), and N-Pol(-) were also found to be important in the FR model. The additional statistical significance of N-bul(-), N-Bur(-), and N-Hdr(+) was reported in the BR model. These attributes reflected the composition of the dipeptides. We report that the "ideal" bitter ACE inhibitor should be composed of P, Y, F (C-end) and G, V, I, L (N-end). Functions: log Rcaf. = f (observed log IC50) and log Rcaf. = f (predicted log IC50) revealed no direct relationships between ACE inhibition and the bitterness of the dipeptides. It probably resulted from some structural discrepancies between the ACE inhibitory/bitter peptides and/or the measure of activity describing one of the two bioactivities. Our protocol can be applicable for the structure⁻bioactivity prediction of other bioactivities peptides.

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.

Peptides Derived from Foods as Supportive Diet Components in the Prevention of Metabolic Syndrome.

Metabolic syndrome (MSyn) includes physiological, biochemical, clinical, and metabolic abnormalities, leading to an increase in health problems like obesity, dyslipidemia, cardiovascular diseases, and diabetes, which contribute to an increase in mortality rate. One of the main factors having a key impact on our health is the food we consume. Thus, scientists work towards the discovery of novel bioactive compounds with therapeutic potential to address MSyn. According to scientific reports, peptides derived from food proteins exhibit bioactivities important for the prevention of MSyn diseases; that is, they regulate blood pressure and glycemia; reduce cholesterol level and body mass; and scavenge free radicals. The aim of this review is to study the potential role of peptides in the prevention of MSyn. Particularly peptides which exhibit the following activities: antihypertensive [angiotensin-converting enzyme (ACE) inhibition (EC 3.4.15.1)], antidiabetic [dipeptidyl peptidase IV (DPP-IV) (EC 3.4.14.5)/α-glucosidase (EC 3.2.1.20)/α-amylase (EC 3.2.1.1) inhibition)], cholesterol level reduction, antioxidative, and obesity prevention, were studied. If possible, special attention is paid in the review to the bioactivities of peptides that were measured in vivo. Some examples of peptides showing dual or multiple action against MSyn targets are presented. Moreover, using the database of bioactive peptide sequences (BIOPEP) we made a list of peptides serving simultaneous functions in counteracting MSyn dysfunctions. Such an approach may simplify the discovery of MSyn preventive peptides, as well as highlight some of them as potent bioactive ingredients that may be incorporated into foods. Moreover, the research strategy involving the in silico and in vitro/in vivo methodologies may be useful in the production of food protein hydrolysates supporting the treatment of MSyn dysfunctions.

Annotation of Peptide Structures Using SMILES and Other Chemical Codes-Practical Solutions.

Contemporary peptide science exploits methods and tools of bioinformatics, and cheminformatics. These approaches use different languages to describe peptide structures-amino acid sequences and chemical codes (especially SMILES), respectively. The latter may be applied, e.g., in comparative studies involving structures and properties of peptides and peptidomimetics. Progress in peptide science "in silico" may be achieved via better communication between biologists and chemists, involving the translation of peptide representation from amino acid sequence into SMILES code. Recent recommendations concerning good practice in chemical information include careful verification of data and their annotation. This publication discusses the generation of SMILES representations of peptides using existing software. Construction of peptide structures containing unnatural and modified amino acids (with special attention paid on glycosylated peptides) is also included. Special attention is paid to the detection and correction of typical errors occurring in SMILES representations of peptides and their correction using molecular editors. Brief recommendations for training of staff working on peptide annotations, are discussed as well.

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.

Food protein-originating peptides as tastants - Physiological, technological, sensory, and bioinformatic approaches.

Taste is one of the factors based on which the organism makes the selection of what to ingest. It also protects humans from ingesting toxic compounds and is one of the main attributes when thinking about food quality. Five basic taste sensations are recognized by humans: bitter, salty, sour, sweet, and umami. The taste of foods is affected by some molecules of some specific chemical nature. One of them are peptides derived from food proteins. Although they are not the major natural compounds originating from food sources that are responsible for the taste, they are in the area of scientific research due to the specific composition of amino acids which are well-known for their sensory properties. Literature data implicate that sweet, bitter, and umami are the tastes attributable to peptides. Moreover, the bitter peptide tastants are the dominant among the other tastes. Additionally, other biological activities like, e.g., inhibiting enzymes that regulate the body functions and acting as preventive food agents of civilization diseases, are also associated with the taste of peptides. The advance in information technologies has contributed to the elaboration of internet archives (databases) as well as in silico tools for the analysis of biological compounds. It also concerns peptides - namely taste carriers originating from foods. Thus, our paper provides a summary of knowledge about peptides as tastants with special attention paid to the following aspects: a) basis of taste perception, b) taste peptides detected in food protein sequences with special emphasis put on the role of bitter peptides, c) peptides that may enhance/suppress the taste of foods, d) databases as well as bioinformatic approaches suitable to study the taste of peptides, e) taste-taste interactions, f) basis of sensory analysis in the evaluation of the taste of molecules, including peptides, and g) the methodology applied to reduce/eliminate the undesired taste of peptides. The list of taste peptides serving some biological functions is presented in the Supplement file. The information provided includes database resources, whereas peptide sequences are given with InChiKeys, which is aimed at facilitating the Google® search. Our collection of data regarding taste peptides may be supportive for the scientists working with the set of peptide data in the context of structure-function activity of peptides.

BIOPEP database of sensory peptides and amino acids.

Peptides and amino acids belong to compounds that influence the taste of foods. The aim of this study was to develop a database of sensory peptides and amino acids. Information about the taste of the analyzed compounds was obtained from sensory studies described in the literature. The database of sensory peptides and amino acids has identical structure to the BIOPEP database of biologically active peptides. The information about sensory peptides and amino acids was inserted into the database using standard BIOPEP layouts for bioactive peptides. Information about the biological activity of sensory peptides was obtained from BIOPEP and other databases. The information annotated in the BIOPEP database of sensory peptides and amino acids includes: sequence written in a one-letter code, information about taste, reference, structure written with the use of chemical codes (SMILES, InChI and InChIKey), bioactivity data (mainly inhibition of proteolytic enzymes), if applicable, and ID numbers from other biological and chemical databases. The database contains tools for determining the location of peptides in protein sequences (profiles of potential sensory activity), comparing protein sequences as precursors of sensory peptides based on the frequency of sensory fragments as a quantitative descriptor, simulating proteolysis and calculating novel parameters for quantitative description of simulated proteolysis. The BIOPEP database of sensory peptides and amino acids is available at http://www.uwm.edu.pl/biochemia/index.php/pl/biopep. It is an open access resource that does not require user registration.

Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science.

A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. An individual bioactive fragment, in particular the shortest fragment containing two or three amino acid residues, may occur in many protein sequences. An individual linear epitope may also be present in multiple sequences of precursor proteins. Although recent recommendations for prediction of allergenicity and cross-reactivity include not only sequence identity, but also similarities in secondary and tertiary structures surrounding the common fragment, local sequence identity may be used to screen protein sequence databases for potential allergens in silico. The main weakness of the screening process is that it overlooks allergens and cross-reactivity cases without identical fragments corresponding to linear epitopes. A single peptide may also serve as a marker of a group of allergens that belong to the same family and, possibly, reveal cross-reactivity. This review article discusses the benefits for food scientists that follow from the common subsequences concept.

[Biologically active peptides derived from food proteins as the food components with cardioprotective properties]. / Biologicznie aktywne peptydy pochodzqce z bialek zywnosci jako skladniki diety o wlasciwosciach kardioprotekcyjnych.

Food proteins are the source of peptides with many biological activities. One of them is their impact on blood circulatory system. This group of peptides includes the ones with the ability to reduce the blood pressure (inhibitors of angiotensin converting enzyme--ACE), antithrombotic, and to lower the cholesterol level. Among the above-mentioned peptides' bioactivities, the most of them act as the ACE inhibitors. Some of them are the functional food components and nutraceuticals and possess the status of food with special use. The main known source of antithrombotic and cholesterol lowering peptides are milk and soy proteins, respectively. However, the scientists make the efforts to find new alternative sources of peptides with the above-mentioned activities. It should be noted, that although the bioactive peptides are considered as the safe food components and thus be supportive in the cardiovascular diseases therapy, they cannot substitute the drugs. This review shows the characteristics of selected peptides with: blood pressure reducing, antithrombotic, and cholesterol level reducing activities. We focused on the sequences that were identified in food proteins as well as were tested on humans or animals.

Angiotensin I-converting enzyme (ACE) inhibitory activity and ACE inhibitory peptides of salmon (Salmo salar) protein hydrolysates obtained by human and porcine gastrointestinal enzymes.

The objectives of the present study were two-fold: first, to detect whether salmon protein fractions possess angiotensin I-converting enzyme (ACE) inhibitory properties and whether salmon proteins can release ACE inhibitory peptides during a sequential in vitro hydrolysis (with commercial porcine enzymes) and ex vivo digestion (with human gastrointestinal enzymes). Secondly, to evaluate the ACE inhibitory activity of generated hydrolysates. A two-step ex vivo and in vitro model digestion was performed to simulate the human digestion process. Salmon proteins were degraded more efficiently by porcine enzymes than by human gastrointestinal juices and sarcoplasmic proteins were digested/hydrolyzed more easily than myofibrillar proteins. The ex vivo digested myofibrillar and sarcoplasmic duodenal samples showed IC50 values (concentration required to decrease the ACE activity by 50%) of 1.06 and 2.16 mg/mL, respectively. The in vitro hydrolyzed myofibrillar and sarcoplasmic samples showed IC50 values of 0.91 and 1.04 mg/mL, respectively. Based on the results of in silico studies, it was possible to identify 9 peptides of the ex vivo hydrolysates and 7 peptides of the in vitro hydrolysates of salmon proteins of 11 selected peptides. In both types of salmon hydrolysates, ACE-inhibitory peptides IW, IY, TVY and VW were identified. In the in vitro salmon protein hydrolysates an ACE-inhibitory peptides VPW and VY were also detected, while ACE-inhibitory peptides ALPHA, IVY and IWHHT were identified in the hydrolysates generated with ex vivo digestion. In our studies, we documented ACE inhibitory in vitro effects of salmon protein hydrolysates obtained by human and as well as porcine gastrointestinal enzymes.

Food-Originating ACE Inhibitors, Including Antihypertensive Peptides, as Preventive Food Components in Blood Pressure Reduction.

This work is a literature overview on angiotensin-converting enzyme (ACE) inhibitory/antihypertensive peptides in food protein sources. The following aspects related to peptides with the above-mentioned bioactivity are discussed: (i) mechanism of action of ACE, (ii) the structural character of ACE inhibitors/antihypertensive peptide sequences determined by different methods, including quantitative structure-activity relationship studies, (iii) their food sources, (iv) absorption of peptides, (v) in vitro and in vivo approaches involved in the production and potential release of peptide ACE inhibitors as well as in silico methods applied in research concerning peptides.

BIOPEP database and other programs for processing bioactive peptide sequences.

This review presents the potential for application of computational tools in peptide science based on a sample BIOPEP database and program as well as other programs and databases available via the World Wide Web. The BIOPEP application contains a database of biologically active peptide sequences and a program enabling construction of profiles of the potential biological activity of protein fragments, calculation of quantitative descriptors as measures of the value of proteins as potential precursors of bioactive peptides, and prediction of bonds susceptible to hydrolysis by endopeptidases in a protein chain. Other bioactive and allergenic peptide sequence databases are also presented. Programs enabling the construction of binary and multiple alignments between peptide sequences, the construction of sequence motifs attributed to a given type of bioactivity, searching for potential precursors of bioactive peptides, and the prediction of sites susceptible to proteolytic cleavage in protein chains are available via the Internet as are other approaches concerning secondary structure prediction and calculation of physicochemical features based on amino acid sequence. Programs for prediction of allergenic and toxic properties have also been developed. This review explores the possibilities of cooperation between various programs.