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In Silico
In Silico
A R T I C LE I N FO A B S T R A C T
Keywords: The purpose of this study is to estimate the concentration of digestion-resistant and bioactive peptides in dairy
Food proteins products using an in silico method. The major contributors of milk protein sequences including αs1-casein, αs2-
Bioactive peptides casein, β-casein, k-casein, β-lactoglobulin, and α-lactalbumin were obtained from UniProt Knowledgebase
In silico (UniProtKB). In silico digestion and bioactive fragment, findings were analyzed using the BIOPEP tool. Bioactive
Functional food
peptide content of the dairy products was estimated based on molecular weight, percent of major proteins
Dairy products
existing in the food items, and the number of peptides obtained after in silico digestion from each protein. The
results showed that 100 g milk contains 6700.241 μmol digestion-resistant peptides; in which 1880.434 μmol out
of total peptides have anti-diabetic properties. Of all digestion-resistant peptides, 1978.24, 1955.024, 1700.907,
and 1066.07 μmol belong to very low, low, medium, and high bioactivity sub-groups, respectively. Using the
data introduced here, risk assessment could be done for dairy originated bioactive peptides and chronic disease.
1. Introduction Lucarini, & Santini, 2020; Santini, Novellino, Armini, & Ritieni, 2013).
The molecules with amino acids as their building blocks such as food-
In the last few decades, natural ingredients in specific raw and derived bioactive peptides (BPs) are one of the major components of
processed foods have been of great interest to the different fields of foods that affect the functional and biological activity of food products.
science and industry (Li-Chan, 2015). These compounds have diverse BPs usually consist of short chains of 2–20 amino acids and become
biological activities and are widely employed in the food and phar- biologically active following the enzymatic or microbial hydrolysis of
maceutical industry (Betoret, Betoret, Vidal, & Fito, 2011; Vieira da their parent proteins where they are encrypted (Mohanty, Mohapatra,
Silva, Barreira, & Oliveira, 2016). Functional foods and nutraceuticals Misra, & Sahu, 2016). The function of proteolytic enzymes is very im-
are produced by components derived from plant or animal sources and portant in the synthesis of BPs during gastrointestinal digestion or food
have attracted the attention of scientists in recent decades (Nazhand processing such as ripening and fermentation by breaking proteins into
et al., 2020). Nutraceuticals can play a role in preventing many diseases shorter fragments (Toldrá, Reig, Aristoy, & Mora, 2018).
including heart disease, stroke, and type 2 diabetes if their mechanism Several food products have been analyzed for their potential BP
of action is fully established and their safety is confirmed (Durazzo, content, but, milk and dairy products are one of the richest sources of
∗
Corresponding author.
∗∗
Corresponding author.
E-mail addresses: hdavoodi@sbmu.ac.ir, hdavoodi1345@gmail.com (S.H. Davoodi), mousavi@unicamp.br (A. Mousavi Khaneghah).
https://doi.org/10.1016/j.lwt.2020.109616
Received 7 April 2020; Received in revised form 8 May 2020; Accepted 15 May 2020
Available online 04 June 2020
0023-6438/ © 2020 Elsevier Ltd. All rights reserved.
M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
BPs and many studies have been published about the functional prop- protein derived from cow's milk was used in this study. The major
erties of dairy product-derived BPs (Basilicata et al., 2018; Georgalaki contributors of milk protein sequences are αs1-casein (UniProtKB -
et al., 2017). These BPs possess very essential biological activities and P02662), αs2-casein (UniProtKB - P02663), β-casein (UniProtKB -
functionalities including antimicrobial, antihypertensive, antioxidative, P02666), k-casein (UniProtKB - P02668), β-lactoglobulin (UniProtKB -
anticytotoxic, immunomodulatory, opioid, and mineral-carrying activ- P02754) and α-lactalbumin (UniProtKB - P00711) obtained from
ities (Korhonen & Pihlanto–Leppälä, 2016; Lopez-Exposito & Recio, UniProt Knowledgebase (UniProtKB) (https://www.uniprot.org) and
2008; Mada, Ugwu, & Abarshi, 2019). Numerous studies have shown re-checked in The National Center for Biotechnology Information
that α-, β-, and κ-casein (Bessette et al., 2016) and whey proteins such (NCBI) database (https://www.ncbi.nlm.nih.gov). The mass of the
as α-lactalbumin, β-lactoglobulin, and glycomacropeptide (GMP) mature proteins was obtained by subtracting the signal peptides from
(Arrutia, Rubio, & Riera, 2016) are prominent parent proteins which the total mass of the pre-proteins. The signal peptide mass was calcu-
are major sources for releasing a number of BPs. Despite their pro- lated by the Expasy peptide mass calculator (https://web.expasy.org/
mising benefits, unfortunately, scale-up production of BPs is mainly peptide_mass/). Pre-protein mass and variables related to post-transla-
hindered by bioprocess challenges related to purification and quanti- tional modifications such as numbers of disulfide bonds, phosphory-
fication (Agyei, Ongkudon, Wei, Chan, & Danquah, 2016). lated residues, glycosylated residues were extracted from UniProtKB.
An efficient quantification of the beneficial effects of BPs is highly
required to better understand their role in our health. Although in vitro 2.2. Food item selection
(Kwon et al., 2011), in vivo (Carrizzo et al., 2019) and meta-analysis of
randomized control trial (Fekete, Givens, & Lovegrove, 2015) studies This study was performed within the framework of the Tehran Lipid
have been done to explore the short-term beneficial effects of BPs and Glucose Study (TLGS). For estimation of dietary intake of BPs
(especially dairy originated ones) on human health, investigations on originated from dairy products, all of the dairy-related food items from
the long-term beneficial effects of these BPs are still at unsatisfactory the FFQ list of TLGS including fat-free milk, low-fat milk, high-fat milk,
levels. This is mostly due to the general lack of consistent methods to cacao milk, strained yogurt, low-fat yogurt, high-fat yogurt, doogh,
better understand their synthesis from different food products cheese, ice cream (traditional), ice cream (industrial), butter, cream
(Chakrabarti, Guha, & Majumder, 2018). Cohort and case-control stu- and kashk were included (Mirmiran, Esfahani, Mehrabi, Hedayati, &
dies are commonly used to assess the long-term effects of food-in- Azizi, 2010). The characteristics of the food items in terms of protein
gredients (Song & Chung, 2010). To the best of our knowledge, due to composition were abstracted in Table 1.
the lack of quantitative measurement of BPs in food items, no case-
control or cohort studies have been done to reveal the association of 2.3. In silico digestion and function prediction
BPs intake and reduction in chronic diseases. The major reason why BPs
content of food items have not been measured so far is the high cost of The extracted protein sequences (without signal peptide) of bovine
BPs measurement and characterization. Therefore, if we successfully milk protein were separately used for in silico digestion. Theoretical
measure the BP content of food items included in food frequency prediction of released peptide sequences in the result of the application
questionnaires (FFQ) used in cohort or case-control studies, the asso- of proteolytic enzymes was performed using the BIOPEP tool
ciation between BPs intake and their effect on chronic diseases such as (Minkiewicz, Dziuba, Iwaniak, Dziuba, & Darewicz, 2008). The pepsin
cancer, cardiovascular disease, and other diseases can be effectively (pH: 1.3), chymotrypsin A and trypsin were used for the in silico pro-
assessed. teolysis. Furthermore, theoretically released peptides derived from
The rapid promotion of bioinformatics leads to the establishment of bovine milk proteins using the proteases were submitted to the BIOPEP
integrated biological knowledge databases such as PepBank, BioPD, tool for search of active fragments option. The in silico digestion was
BIOPEP, EROP-Moscow, and SwePep. Among all, BIOPEP focuses separately done for each milk proteins and the number of (1) total
mainly on peptides of food origins (Iwaniak, Minkiewicz, Darewicz, peptides, (2) peptides with biological function, (3) di, tri, tetra, penta,
Sieniawski, & Starowicz, 2016; Kęska, Stadnik, Kononiuk, Libera, & hexa, heptapeptide, and peptides with more residues, (4) anti-diabetic
Wójciak, 2018). In the food sciences, computer simulation (in silico) can peptides, (5) anti-hypertensive peptides, and (6) antioxidant peptides
be used as a rapid and low-cost primary screening tool for sequencing were calculated.
bioactive peptides analysis and their biological effects in various foods
(Sayd et al., 2018). In silico studies allow the creation of profiles for 2.4. Peptide ranking
potential biological activities of proteins, as well as all activities which
may be found in a protein sequence (Carrasco-Castilla, Hernández- PeptideRanker tool (http://bioware.ucd.ie/compass/biowareweb/)
Álvarez, Jiménez-Martínez, Gutiérrez-López, & Dávila-Ortiz, 2012). was used for the prediction of the potential of peptides derived from the
Also, in silico proteolysis can help us to select the appropriate enzyme bovine dairy proteins (Mooney, Haslam, Pollastri, & Shields, 2012).
for hydrolysis in the simulation of gastrointestinal digestion and is PeptideRanker is a server for the prediction of bioactive peptides and
useful for identifying the relationship between peptide structure and its gives a score in the range of 0–1 for each peptide. The maximum score
function (Lin et al., 2018). represents the most potent active peptides and the minimum score
Research on BPs has shown that they have great potential to im- denotes the peptides with the lowest bioactivity. In the current study,
prove human health and prevent chronic diseases by exerting positive the obtained peptides were divided into multiple subgroups based on
effects on the body's digestive, cardiovascular, immune, and nervous their bioactivity scores. The peptides classified as number (1) had < 0.1
systems, but the beneficial effects of them should also be proved in long scores, (2) 0.1 ≤ X < 0.3 scores, (3) 0.3 ≤ X < 0.7 scores, and (4)
term studies. In vitro and/or in vivo measurement and characterization had 0.7≤ scores and above made the mentioned sub-groups.
of dairy originated BPs are time-consuming and expensive. Therefore,
the objective of the present study is to estimate the amount of BPs in 2.5. Toxicity and physicochemical assessment
dairy products using an in silico method.
The toxicity and physicochemical properties of the obtained pep-
2. Methods tides were assessed using the ToxinPred online tool (Gupta et al., 2013).
(https://webs.iiitd.edu.in/raghava/toxinpred/multi_submit.php). The
2.1. Bovine milk proteins sequences support vector machine (SVM)-based prediction method with a
threshold value of 0.0 was chosen for the toxicity prediction. Several
According to the literature, the initial sequence of six types of food parameters including peptide charge, hydrophobicity, and
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M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Table 1
The protein composition (per 100 g) of the included food items.
Proteins
Food Item Total αs1-casein αs2-casein k-casein β-casein α-lactalbumin β-lactoglobulin Ref.
protein
Fat free Milk 3.4 1.08 0.27 0.32 1.22 0.08 0.39 (Kukovics & Németh, 2013)
Low fat milk 3.4 1.08 0.27 0.32 1.22 0.08 0.39 (Kukovics & Németh, 2013)
Full fat milk 3.4 1.08 0.27 0.32 1.22 0.08 0.39 (Kukovics & Németh, 2013)
Cacao milk 3.4 1.08 0.27 0.32 1.22 0.08 0.39 (Kukovics & Németh, 2013)
Strained yogurt 9 2.88 0.72 0.86 3.24 0.23 1.04 (Ozer, Stenning, Grandison, & Robinson, 1999; Trachoo,
2002)
Low fat yogurt 4.5 1.44 0.36 0.43 1.62 0.52 0.11 (Puvanenthiran, Williams, & Augustin, 2002)
High fat yogurt 3.9 1.24 0.31 0.37 1.40 0.1 0.45 (Jahanbakhsh Oskouie, Hesari, Azadmard Damirchi, Rafat,
& Rezaei Kouchemeshki, 2016)
Doogh 1.9 0.61 0.15 0.20 0.68 0.04 0.22 (Kiani, Mousavi, & Emam-Djomeh, 2008)
Cheese 25 6 1.50 2.75 6.25 0.97 3 (Wedholm, Larsen, Lindmark-Månsson, Karlsson, &
Andrén, 2006)
Cream cheese 8 3.2 0.8 0.96 3.6 0 0 (Jeon, Lee, Ganesan, & Kwak, 2012)
Ice cream (traditional) 3 0.96 0.24 0.29 1.08 0.07 0.34 (Kukovics & Németh, 2013)
Ice cream (industrial) 4 1.28 0.32 0.38 1.44 0.10 0.46 (Kukovics & Németh, 2013)
Butter 1.16 0.37 0.09 0.11 0.41 0.03 0.13 (Holzmüller & Kulozik, 2016)
Cream 2.67 0.85 0.21 0.25 0.95 0.06 0.30 (Holzmüller & Kulozik, 2016)
Kashk 8 2.56 0.64 0.76 2.88 0.20 0.92 (Mashak, Sodagari, Mashak, & Niknafs, 2014)
100
food items
For estimation of digestion resistant-peptides, first, the molar con- 2.7. The validation
centration of each dairy protein is calculated by dividing the amount (g)
of each protein (per 100 g food item) by its molecular weight multiplied The validation was performed according to the results reported by
by 106 (first calculation) and then the number of digestion resistant- Barbé et al. (2014). They reported about 16000 digestion-resistant
peptides obtained from each protein was multiplied with the value peptides in an experimental model for the digestion of dairy products.
obtained in the first calculation (second calculation). The result of the From the identified peptides, 3297 of them were related to the digestion
sum of the second calculations for each dairy protein is the digestion- of raw milk. After ignoring duplicates, 867 peptides were enrolled for
resistant content of each food item per 100 g. Digestion-resistant and the validity assessment of our study. All of the enrolled peptides have
bioactive peptide content of the food items were estimated using the more than 5 residues. From the peptides obtained from our in silico
following equation: study, only peptides with more than 5 residues were enrolled. There-
fore, the similarity of the in silico identified peptides with the peptides
Digestion − resistant peptide content reported by Barbé et al. (867 peptides) was assessed using bioinfor-
matics. The similarity assessment was done using The Basic Local
(μmol/g)
Alignment Search Tool (BLAST) for proteins in NCBI (https://blast.ncbi.
(( A
A1 ) ) ((
× 106 × a +
B
B1 ) ) ((
× 106 × b +
C
C1 ) )
× 106 × c + nlm.nih.gov/Blast.cgi#Query_47856). Each of the in silico identified
peptides was individually aligned to all of the experimentally char-
=
(( D
D1
× 10 ) × d ) + ( (
6 E
E1
× 10 ) × e ) + ( (
6 F
F1
× 10 ) × f )
6
acterized peptides and the number of similar structures for each of our
100 peptides was recorded. The similarity criterion in this study was E-
value < 0.05 and 100% identity. The similarity was also checked
Where A is αs1-casein content per 100 g food item, B is αs2-casein within the in silico derived peptides.
content per 100 g food item, C is β-casein content per 100 g food item,
D is κ-casein content per 100 g food item, E is β-lactoglobulin content 3. Results
per 100 g food item, F is α-lactalbumin content per 100 g food item, A1
is αs1-casein molecular weight (MW), B1 is αs2-casein MW, C1 is β- In the present study, six different proteins derived from dairy pro-
casein MW; D1 is κ-casein MW, E1 is β-lactoglobulin MW, F1 is α-lac- ducts were included for in situ analysis. The mass of the pre-proteins,
talbumin MW, a is the number of peptides obtained after in-silico di- signal peptides, and mature proteins are reported in Table 2. Among the
gestion of αs1-casein, b is the number of peptides obtained after in silico proteins, αs2-casein (Mass: 24,331.07 Da) and α-lactalbumin (Mass:
digestion of αs2-casein, c is the number of peptides obtained after in- 14,168.88 Da) have the highest and lowest masses, respectively. As
silico digestion of β-casein, d is the number of peptides obtained after in reported in Table 3, after in silico digestion of each molecule of αs1-
silico digestion of κ-casein, e is the number of peptides obtained after in casein, αs2-casein, β-casein, k-casein, α-Lactalbumin, and β-lactoglo-
silico digestion of β-lactoglobulin, and f is the number of peptides ob- bulin, the number of obtained peptides were 44, 46, 49, 35, 32 and 38,
tained after in silico digestion of α-lactalbumin. For instance, the esti- respectively. Therefore, β-casein, compared to other proteins, produces
mation of milk-derived di-peptides could be calculated by the following more fragments per molecule. Among the obtained fragments, 77 of all
equation: identified peptides were known for their biological functions. The
3
M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Table 2 casein made four QK, three TK, two AL, two PQY, and two PW frag-
Dairy proteins mass after subtracting the mass of signal peptides. ments; however, no similar fragments were obtained from αs1-casein
Protein name Pre-protein Mass Signal peptide Mass Mature Protein Mass digestion. On the other hand, some peptides were found to have several
origins; for instance, in this study, EL was obtained after digestion of
αs1-casein 24529 1571.962 22956.46 αs1-casein, β-casein, and β-lactoglobulin.
αs2-casein 26019 1687.931 24331.07
The final part of the current study was the estimation of BPs origi-
β-casein 25107 1541.952 23565.05
k-casein 21269 2312.316 18956.68
nated from dairy products. In supplementary Tables (S2, S3, S4, S5, S6,
α- lactalbumin 19883 1619.868 14168.88 S7, S8, S9, S10, S11, S12, and S13), the amount of different BPs in terms
β-lactoglobulin 16247 2087.117 18263.13 of molecular weight (MW), charge, bioactivity, hydrophobicity, and
function are summarized. One of the most important food items in this
Data are presented as Dalton.
study was milk. The results showed that 100 g milk contains
6700.241 μmol digestion-resistant peptides; in which, 1880.434 μmol
number of anti-diabetic molecules originated from αs1-casein, αs2- out of total peptides have anti-diabetic properties. Of 6700.241 μmol
casein, β-casein, κ-casein, α-Lactalbumin, and β-lactoglobulin were 10, digestion-resistant peptides obtained from 100 g milk, 1978.24,
14, 14, 11, 8, and 14, respectively. The results showed that κ-casein is 1955.024, 1700.907, and 1066.07 μmol belong to very low, low,
very diverse in terms of post-translational modifications compared to medium, and high bioactivity sub-groups, respectively (Table S2). For
other proteins due to the presence of three disulfide bonds, eight gly- each protein, it was observed that the amount of peptide (μmol) was
cosylated residues, four phosphorylated residues, and one pyrrolidone strongly associated with its bioactivity. The smaller peptides were
carboxylic acid-modified residue, which are highly active molecules in found to show more bioactivity than bigger ones. This finding was
protein modification (Lodish et al., 2000). Proteolysis of each molecule previously demonstrated for different bioactive peptides (Ajibola,
of α-Lactalbumin produces 3, 13, 8, and 5 peptides with very low, low, Fashakin, Fagbemi, & Aluko, 2011; Cheung, Cheung, Tan, & Li-Chan,
medium, and high bioactivity, respectively. 2012). Estimation of digestion-resistant peptides and BPs were also
In Table S1, the physicochemical and functional properties of the performed for strained yogurt (Table S3), low-fat yogurt (Table S4),
obtained peptides after in silico proteolysis are reported. The highest high-fat yogurt (Table S5), Doogh (Table S6), cheese (Table S7), cream
peptide in terms of bioactivity for αs1-casein (Fig. 1), αs2-casein (Fig. 2), cheese (Table S8), ice cream (industrial) (Table S9), ice cream (tradi-
β-casein (Fig. 3), κ-casein (Fig. 4), α-Lactalbumin (Fig. 5), and β-lac- tional) (Table S10), butter (Table S11), cream (Table S12) and kashk
toglobulin (Fig. 6) was GF, PW, PF, SF, IW, and CM, respectively. (Table S13). Among all analyzed food items, the cheese was found to
EAESISSSEEIVPN is the heaviest fragment obtained from αs1-casein. contain the highest BP content (40842.02 μmol), while the butter has
SIGSSSEESAEVATEEVK, QSEEQQQTEDEL, TIASGEPTSTPTTEAVESTV- the lowest BP content (2273.194 μmol).
ATL, DTQAIVQN, and TPEVDDEAL are the heaviest fragments obtained Among 226 types of peptide obtained during the in silico digestion,
from αs2-casein, β-casein, κ-casein, α-Lactalbumin, and β-lactoglobulin, 76 peptides with known biological properties could be identified.
respectively. The in silico digestion did not make necessarily different Among the peptides with known biological activity, 12 and 33 peptides
peptides in terms of amino-acid residues. For instance, digestion of αs2- possess only anti-hypertensive and anti-diabetic properties,
Table 3
Number of peptides obtained from in silico digestion of dairy proteins with respect to physico-chemical and functional properties.
Variables The dairy proteins
Total Peptides 44 46 49 35 32 38
di-peptides 14 22 17 14 12 20
Tri-peptides 11 8 11 8 8 1
Tetra-peptides 8 8 6 2 6 5
Penta-peptides 6 1 7 4 5 5
Hexa-peptides 2 4 4 2 0 2
Hepta-peptides 1 0 0 1 0 3
Peptides with more than 7 residues 2 3 4 4 1 2
Antidiabetic peptide 10 14 14 11 8 14
Hypotensive peptide 7 7 6 8 6 9
Antioxidant peptide 4 2 2 0 2 2
DPP-III inhibitor 1 0 0 0 0 1
Vasoactive peptide 1 0 0 0 0 0
Disulfide bond 0 0 0 3 0 3
Glycosylated residue 0 0 0 8 0 0
Phosphorylated residue 9 13 5 4 9 0
PCA modified residue 0 0 0 1 0 0
Immunomodulatory peptide 0 0 1 0 0 0
CaMPDE inhibitor peptide 0 0 0 0 0 1
Peptide bioactivity Very Low 15 22 11 10 3 12
Low 12 10 15 9 13 13
Medium 12 9 13 10 8 7
High 5 5 10 6 5 6
Peptide charge Zero 19 20 26 20 16 21
Negative 19 12 13 5 11 13
Positive 6 14 10 10 5 4
hydrophobicity Low 33 34 26 26 17 19
High 11 12 23 9 15 19
hydrophilicity Low 20 19 28 19 15 19
High 24 27 21 16 17 19
PCA: Pyrrolidone carboxylic acid; CaMPDE: Calmodulin-dependent cyclic nucleotide phosphodiesterase.
4
M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
5
M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Fig. 3. Sequences and functional properties of peptides derived from in-silico digestion of β-casein. ACE-I: Angiotensin converting enzyme inhibitor; DPP: dipeptidyl
peptidase; R: Arginine; N: Asparagine; D: Aspartic acid; C: Cysteine; E: Glutamic acid; Q: Glutamine; G: Glycine; H: Histidine; I: Isoleucine; L: Leucine; K: Lysine; M:
Methionine; F: Phenylalanine; P: Proline; S: Serine; T: Threonine; Y: Tyrosine; V: Valine.
respectively, while 26 peptides have both anti-hypertensive and anti- fat yogurt, high-fat yogurt, Doogh, cheese, cream cheese, ice cream
diabetic properties. The β-casein-originated peptide PGPIPN is the only (industrial), ice cream (traditional), butter, cream and kashk (kashk as a
immunomodulatory peptide that was characterized in all of the dairy fermented dairy product is produced either in dry or liquid form) were
proteins analyzed in the current in silico study. The peptides with pre- estimated based on MW, percent of major proteins existing in the food
viously reported biological activity were summarized in Table 4. items and a number of peptides obtained after in silico digestion from
The data reported by Barbé et al. study (Barbé et al., 2014) were each protein. The selection of proteolytic enzymes is also essential for a
used for the validation of our results. From the in-silico identified more efficient quantification. In this study, we used pepsin (pH: 1.3),
peptides only 36 peptides have more than 5 residues. The validation chymotrypsin A and trypsin. These proteolytic enzymes are excellent
results were reported in Table 5. In model 1 of the validation, in which models as they facilitate the cleavage of numerous peptide bonds via
peptides with E-value less than 0.05 were considered as similar pep- hydrolysis in the digestive systems (S. Wang, Li, Zhang, Wang, &
tides, the structure of 44.5 percent of the experimental results was Copeland, 2017).
predicted. While in the second model, 79.46 percent of the experi- As previously stated, the quantitative measurement of BP content of
mentally characterized peptides were estimated. In model 2, the simi- food items is of extreme importance to understand their potential
larity was considered for E-value < 0.05 or 100% identity. No sig- benefits on our health. Recent immunological studies have shown that
nificant similarity was seen between the in silico characterized peptides. BPs exert potent immunomodulatory effects by induction of oral tol-
Among the assessed peptides, the maximum similarity percentage be- erance elements (Moronta, Smaldini, Fossati, Añon, & Docena, 2016;
longed to QSEEQQQTEDEL. QSEEQQQTEDEL predict 5.99 and 6.68 Nishikimi et al., 2018; Thota, Ponnusamy, Philip, Lu, & Mundkur,
percent of the experimentally identified peptides in model 1 and 2, 2017). Although the elements of oral tolerance have a positive role in
respectively. Also, TEEEK predicts 4.15 percent of the results in both cardiovascular disease (CVD) and allergy treatment, it was shown to
models as reported by Barbé et al. increase the risk of cancer (Barth et al., 2015). In fact, the lack of BPs
content of food items has limited cohort and retrospective studies to
evaluate the long-term effects of digestion-resistant and bioactive
4. Discussion peptides.
In the present in-silico study, 226 types of peptide were
The digestion-resistant and bioactive peptide content of yogurt, low-
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M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
characterized. Almost all of the obtained peptides (the intact or similar activity (n = 76) and (2) peptides with un-known biological activity
structure) were previously reported by in vitro or in vivo studies. As (n = 150); in other words, %33.6 percent of the in-silico analyzed
shown in Tables 4 and 6, the peptides obtained in the current in silico peptides were previously characterized either in-vitro or in-vivo and
study were divided into two groups: (1) peptides with known biological submitted to BIOPEP-UWM database as functional peptides. Among the
Fig. 5. Sequences and functional properties of peptides derived from in-silico digestion of α-Lactalbumin. ACE-I: Angiotensin converting enzyme inhibitor; DPP:
dipeptidyl peptidase; A: Alanine; G: Glycine; H: Histidine; I: Isoleucine; L: Leucine; K: Lysine; P: Proline; T: Threonine; W: Tryptophan; Y: Tyrosine.
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M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Table 4
Peptides with known biologically function obtained after the in-silico digestion.
Protein Hypotensive BPs Anti-diabetic BPs hypotensive and anti-diabetic BPs Antioxidant BPs Immunomodulatory BPs
αs1-casein GK, GTQY PK, QL, SK, VN, VPL QF, PL, GY, AY, EK EL, PEL, AY, GTQY –
αs2-casein QK, TVY AL, SK, TK, TM, QH, EH, QY, PW QF, VR PW –
β-casein PQR, DM SL, TL, PK, IN, VL, PF, IH VY, VK, PL EL, VY PGPIPN
k-casein PSY, IAK, AR IPIQY, QW, PY, IN, VL QF, SF, GL, PH – –
α-Lactalbumin – AL, TK IL, GL, GY, PH, IW, AH EL, AH –
β-lactoglobulin IIAEK, VAGTW, QK VL, AL, SL, PM, TK, IPAVF SF, GL, VR, EK, IR, VY IR, VY –
Biological activity of digestion resistance peptides were retrieved from BIOPEP database (Minkiewicz et al., 2008; Søren Drud Nielsen, Robert L. Beverly, Yunyao Qu,
& David C. Dal as, 2017l).
A: Alanine; R: Arginine; N: Asparagine; D: Aspartic acid; C: Cysteine; E: Glutamic acid; Q: Glutamine; G: Glycine; H: Histidine; I: Isoleucine; L: Leucine; K: Lysine; M:
Methionine; F: Phenylalanine; P: Proline; S: Serine; T: Threonine; W: Tryptophan; Y: Tyrosine; V: Valine.
obtained peptides in the current study, only PGPIPN has im- summarized in Table 6. Among the peptides with unknown function,
munomodulatory effects. The immunomodulatory effects of PGPIPN neither exact nor similar structures for EEEY, EVVR, and CVK were
were examined in many different in vivo and in vitro studies (Qi et al., reported by the in vitro or in vivo studies.
2017). Although the BIOPEP-UWM database introduces PGPIPN as an Table 6 shows that the results of in silico studies are slightly different
anti-inflammatory peptide, recent studies showed anti-tumor effects of from in vitro and in vivo due to the different conditions of in vitro and in
PGPIPN (W. Wang et al., 2013; Zhao et al., 2016). vivo environments. Thus, in silico studies will help us to identify these
Based on the results of this study, 150 of the characterized peptides differences and move the conditions toward the production of the de-
sequences have an unknown biological function. To the best of our sired BPs, which will be crucial to predicting biotechnological treat-
knowledge, only 4 in vivo studies have been done to characterize milk- ments to develop functional foods with specific health effects.
derived digestion resistant peptides (Barbé et al., 2014; Bouzerzour Among the assessed peptides, the maximum similarity percentage
et al., 2012; Tu et al., 2019; Wada, Phinney, Weber, & Lonnerdal, belonged to QSEEQQQTEDEL. QSEEQQQTEDEL predicts 5.99 and 6.68
2017). In most of the experimental studies, after dairy consumption, percent of the experimentally identified peptides in models 1 and 2,
small intestine content was aspirated and dairy digestion-resistant respectively. Also, TEEEK predicts 4.15 percent of the results obtained
peptides were characterized. Bouzerzour et al. (2012) and Barbé et al. by Barbé et al., 2014. The most abundant residues in both peptides are
(2014) used piglet and mini-pig models, respectively (Barbé et al., glutamine (Q) and glutamate (E) and it seems these residues have a
2014; Bouzerzour et al., 2012). On the other hand, the suckling rat pup critical role in digestion resistance.
and mice models have been used by Wada et al. (2017) and Tu et al. To the best of our knowledge, there was no study trying to quantify
(2019), respectively (Tu et al., 2019; Wada et al., 2017). Peptides with digestion resistance and bioactive peptides in foodstuffs. For the first
unknown physiological function obtained in the current study and si- time in the current in-silico study, the concentration of dairy items'
milar structures reported by the mentioned in vivo studies were peptides was estimated; however, this method has also its limitations.
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M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Table 5
The validation of in-silico obtained results using data reported by Barbé et al. study (Barbé et al., 2014).
In-silico obtained peptides Number and percent of similar peptides reported by Barbé et al. study.
Model 1 Model 2
Model 1: peptides with E-value less than 0.05 were considered as similar peptides.
Model 2: peptides with E-value less than 0.05 or 100% identity were considered as similar.
* Percent was calculated as (number of similar peptides/867) × 100.
The lack of validation experiments was the main limitation of the Disclosure statement
present study. Although lack of validation experiments may call our
results into question, using current in silico study, for the first time, we No potential conflict of interest was reported by the authors.
tried to reveal that determination of digestion resistance and bioactive
peptide content of foodstuffs is a very important matter. Without ret-
Author contributions
rospective and/or prospective studies we could not consider food-de-
rived peptides as bioactive. In other words, although in vitro, in vivo,
Conceptualization, M.B; Data collection and analysis, M.B, F.J, M.J;
and RCTs showed that most food-derived peptides are bioactive, but
writing—original draft preparation, A.M.Y, FF, F.J, M.B.; Software,
beneficial or detrimental effects of these peptides on health and disease
M.B, H.F; review and editing, A.M.K and I.E, S.H.D. All authors have
should be confirmed in long-term studies. Determination of food-de-
read and agreed to the published version of the manuscript.
rived peptides can help researchers to perform long-term studies.
9
M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Table 6
The obtained peptides with un-known biological function and similar structures which have been reported by in-vivo studies.
αs1-casein
In-silico peptide Similar peptides characterized in-vivo In-silico peptide Similar peptides characterized in-vivo
Sequence Sequence
PSGAW QLDAYPSGA (Wada et al., 2017) IGVN IGVNQE (Wada et al., 2017), QQKEPMIGVN (Barbé et al., 2014)
EN EGIH EGIHAQQKEPMIG (Wada et al., 2017), HSMKEGIHA (Barbé et al.,
2014)
SEK PIGSEN PNPIGSENSEK (Barbé et al., 2014)
SVEQK SVEQKHIQKEDVPSER (Barbé et al., 2014) PQEVL HQGLPQEVL (Barbé et al., 2014)
EDIK AMEDIK (Bouzerzour et al., 2012), DAY QLDAYPSGA (Wada et al., 2017)
DQAMEDIKQ (Wada et al., 2017), EDIKQMEAE
(Barbé et al., 2014)
EQL YLGYLEQLLR (Barbé et al., 2014) VPQL KYKVPQL (Wada et al., 2017), KYKVPQL (Barbé et al., 2014)
SAEER EIVPNSAEER (Barbé et al., 2014) PIK HPIKH (Wada et al., 2017), HPIKHQGLPQEV (Barbé et al., 2014)
QEL QQKEPMIGVNQEL (Barbé et al., 2014) SDIPN FSDIPNG (Bouzerzour et al., 2012), FSDIPNPI (Wada et al., 2017),
SDIPNPIGSENSEK (Barbé et al., 2014), SDIPNPI (Tu et al., 2019)
IQK IQKEDVPSER (Barbé et al., 2014), HIQKE PEVF APFPEVFG (Wada et al., 2017), PFPEVFGK (Barbé et al., 2014)
(Wada et al., 2017)
AQQK GIHAQQKEPMIG (Barbé et al., 2014), TDAPSF TDAPSFS (Wada et al., 2017), TDAPSFSDIPNPIGSENSEKT (Barbé
IHAQQKEPMIG (Wada et al., 2017) et al., 2014)
EDVPSER EDVPSERY (Barbé et al., 2014) EPM GIHAQQKEPMIG (Barbé et al., 2014), IHAQQKEPMIG (Wada et al.,
2017)
EAESISSSEEIVPN SSEEIVPN, SEEIVPN, ISSSEEI (Bouzerzour QGL HQGLPQEVL (Barbé et al., 2014), HPIKHQGLPQEV (Barbé et al.,
et al., 2012), ISSSEEIVPNS (Wada et al., 2017) 2014)
EIVPN SEEIVPNS (Wada et al., 2017), EIVPNSAEER QM EDIKQMEAE (Barbé et al., 2014)
(Barbé et al., 2014)
DIGSESTEDQAM TEDQAMEDIK (Bouzerzour et al., 2012), SM HSMKEGIHA (Barbé et al., 2014)
DIGSESTEDQAMEDIK (Barbé et al., 2014)
TTM VAPF FVAPFPE (Tu et al., 2019), FFVAPFPE (Wada et al., 2017),
FVAPFPEVFGK (Barbé et al., 2014)
αs2-casein
CSTF NLCSTFC (Wada et al., 2017) TVDM KTVDMESTEVFTKKT (Barbé et al., 2014)
AM ESTEVF TVDMESTEVFTK
QGPIVL YQGPIVLNPWDQVK (Barbé et al., 2014) SIGSSSEESAEVATEEVK SIGSSSEESAE (Wada et al., 2017), TEEVKITVDDKHYQ (Barbé et al.,
2014)
PQY FALPQYLKT (Wada et al., 2017) VSSSEESIISQETY KNTMEHVSSSEESIISQETYKQE (Barbé et al., 2014)
CK EQL
AVPITPTL VPITPTL (Bouzerzour et al., 2012), EIN ALNEINQFYQKFPQ (Barbé et al., 2014)
NAVPITPTLN (Barbé et al., 2014)
VIPY TKVIPYVRY (Barbé et al., 2014) DQVK NPWDQVKR (Barbé et al., 2014)
IQPK KPWIQPK (Tu et al., 2019), AMKPWIQPK ITVDDK ITVDDKHYQ (Barbé et al., 2014)
(Barbé et al., 2014)
PSK NPSKENLCSTFC (Barbé et al., 2014), STSEEN NREQLSTSEENSKK (Barbé et al., 2014)
NPSKENLC (Wada et al., 2017),
AIN AINPSKENLCSTFCKE (Barbé et al., 2014) EN
ISQR LKKISQRYQK (Barbé et al., 2014) QEK KNTMEHVSSSEESIISQETYKQEK (Barbé et al., 2014)
AN EEEY –
EVVR – TEEEK LTEEEKNRL (Barbé et al., 2014)
Beta-casein
GPF GPFPIIV (Tu et al., 2019), PVRGPFPII (Barbé EM
et al., 2014), RGPFP (Wada et al., 2017)
IPPL NIPPLT (Bouzerzour et al., 2012), QEPVL LLYQEPVLGPVRGPF (Barbé et al., 2014), QEPVLGPV (Wada et al.,
SLPQNIPPLTQ (Barbé et al., 2014), IPPL 2017)
(Nongonierma et al., 2017), PQNIPPLTQT
(Barbé et al., 2014)
PIQAF DMPIQAF (Nongonierma et al., 2017), EAM VKEAMAPK (Barbé et al., 2014)
SQSKVLPVPQKAVPYPQRDMPIQAF (Barbé
et al., 2014)
QSW QSWMHQPHQPLPPTV (Barbé et al., 2014), SSSEESITR GEIVESLSSSEESITRINKKIEKFQSEKQQQTEDELQDKIHPF (Barbé
LQSWMHQPH (Nongonierma et al., 2017) et al., 2014)
QPL HQPLPPT (Tu et al., 2019), QPLPPT VPGEIVESL NVPGEIV (Bouzerzour et al., 2012), LNVPGEIVESL (Barbé et al.,
(Nongonierma et al., 2017), HQPLPP (Wada 2014)
et al., 2017), MHQPHQPLPPT (Barbé et al.,
2014)
PVEPF PKYPVEPF (Tu et al., 2019), YPVEPF AQTQSL IHPFAQTQSL (Barbé et al., 2014)
(Nongonierma et al., 2017), PVEPFT (Wada
et al., 2017), PVEPFTERQ (Barbé et al., 2014)
PPTVM LPPTVMFPPQ (Tu et al., 2019), PLPPTVMFPP SQSK QSKVL (Bouzerzour et al., 2012), SQSKVLPVPQK (Barbé et al.,
(Wada et al., 2017), HQPHQPLPPTVM (Barbé 2014)
et al., 2014)
GPVR LLYQEPVLGPVRGPF (Barbé et al., 2014), GVSK SLPQNIPPLTQTPVVVPPFLQPEVMGVSKVKEA (Wada et al., 2017),
GPVRGPFP (Wada et al., 2017) MGVSKVKE (Barbé et al., 2014)
PPQSVL HQPHQPLPPTVMFPPQSVLS (Wada et al., QDK DELQDKIHP (Wada et al., 2017), LQDKIHP (Barbé et al., 2014)
2017), MHQPHQPLPPTVMFPPQSVL (Barbé
et al., 2014)
(continued on next page)
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M. Barati, et al. LWT - Food Science and Technology 130 (2020) 109616
Table 6 (continued)
QPH QPHQPLPPT (Wada et al., 2017), TESQSL PVEPFTESQSLT (Barbé et al., 2014)
HQPHQPLPPT (Barbé et al., 2014),
QPHQPLPPT (Nongonierma et al., 2017)
AVPY AVPYPQR (Tu et al., 2019), KAVPYPQR (Barbé QSEEQQQTEDEL FQSEEQQQTEDEL (Barbé et al., 2014)
et al., 2014)
APK VKEAMAPK (Barbé et al., 2014) IEK
PQN LPQNIPP (Nongonierma et al., 2017), EEL
SLPQNIPPLT (Wada et al., 2017), PQNIPPLTQT
(Barbé et al., 2014)
QPEVM QPEVM (Bouzerzour et al., 2012), TDVEN TDVENLHLPLP (Barbé et al., 2014)
TQTPVVVPPFLQPEVMGV (Wada et al., 2017),
PVVVPPFLQPEVM (Barbé et al., 2014)
PIIV GPFPIIV (Tu et al., 2019) TQTPVVVPPF TQTPVVVPPFL (Bouzerzour et al., 2012), VVVPPFLQP (Barbé et al.,
2014)
PVPQK SKVLPVPQK (Barbé et al., 2014)
k-casein
SPAQIL VRSPAQIL (Barbé et al., 2014), SPAQILQWQ PAAVR YAKPAAVR (Barbé et al., 2014)
(Tu et al., 2019)
AIPPK MAIPPK (Wada et al., 2017), MAIPPKKNQDK EDSPEVIESPPEIN EDSPEVIESPPEINT (Barbé et al., 2014), EDSPEVIESPPEINT (Wada
(Barbé et al., 2014) et al., 2017)
SCQAQPTTM SNTVPAKSCQAQPT (Wada et al., 2017) CEK EQPIRCEKDE (Wada et al., 2017)
QEQPIR EQNQEQPI (Wada et al., 2017), SN SNTVPAKSC (Wada et al., 2017)
SR QVL SPAQILQWQVL (Wada et al., 2017)
PVAL YQQKPVAL (Barbé et al., 2014) AK
TEIPTIN TEIPTINT (Wada et al., 2017), DKTEIPTINT TVPAK SNTVPAKSC (Wada et al., 2017)
(Barbé et al., 2014)
DER – SDK FFSDKIAK (Tu et al., 2019), FSDKIAK (Barbé et al., 2014)
QQK YQQKPVAL (Barbé et al., 2014) QDK NQDKTEIP (Barbé et al., 2014), MAIPPKKNQDK (Barbé et al., 2014)
QEQN QEQNQEQPI (Wada et al., 2017) TVQVTSTAV TVQVTSTAV (Skrzypczak et al., 2017)
TIASGEPTSTPTTEAVESTVATL PTTEAVES (Bouzerzour et al., 2012),
TIASGEPTSTPTTEAVEST (Wada et al., 2017)
α-Lactalbumin
PEW LPEWV (Wada et al., 2017) CEVF EQLTKCEVFR (Wada et al., 2017), TKCEVFRE (Nongonierma et al.,
2017)
DQW DQWLCE (Wada et al., 2017) CK
ICN SSNICNI (Wada et al., 2017) VCTTF CTTFHTSGYDTQA (Wada et al., 2017)
DL GGVSL GYGGVSLP (Wada et al., 2017)
DDDL FLDDDLTDD (Wada et al., 2017) ISCDK NISCDK (Wada et al., 2017)
TSGY TTFHTSGYDT TDDIM DLTDDIMC (Wada et al., 2017)
CVK – CEK
VGIN ILDKVGINY (Nongonierma et al., 2017) CSEK CSEKLDQ (Wada et al., 2017), LCSEKLDQ (Nongonierma et al.,
2017)
QIN GLFQINNKIWCKDDQNPHSSNIC (Wada et al., SSN SSNICNI (Wada et al., 2017)
2017)
DDQN DDQNPH (Barbé et al., 2014) DK NISCDK (Wada et al., 2017)
DSTEY IVQNNDSTEYGLF (Nongonierma et al., 2017) DTQAIVQN TTFHTSGYDTQA (Wada et al., 2017)
EQL EQLTKCEVFR (Wada et al., 2017)
β-lactoglobulin
CM CMENSAEP (Wada et al., 2017) PTQL NPTQLE (Wada et al., 2017), LSFNPTQLEEQCHI (Barbé et al., 2014)
ACQCL MENSAEPEQSLACQC (Wada et al., 2017) SAEPEQSL NSAEPEQSL (Wada et al., 2017), MENSAEPEQSL (Barbé et al.,
2014)
AM GECAQK WENGECAQ (Wada et al., 2017)
DAQSAPL DAQSAPLR (Wada et al., 2017), LDAQSAPLR DTDY VLDTDY (Nongonierma et al., 2017), VLDTDYKK (Wada et al.,
(Barbé et al., 2014) 2017)
PTPEGDL ELKPTPEGD (Bouzerzour et al., 2012), EIL LKPTPEGDLEIL (Nongonierma et al., 2017), VEELKPTPEGDLEIL
LKPTPEGDL (Barbé et al., 2014) (Barbé et al., 2014) VEELKPTPEGDLEILLQKWEN (Wada et al.,
KPTPEGDLE (Wada et al., 2017) 2017)
IDAL KIDALNE (Barbé et al., 2014) EEQCH EEQCHI (Wada et al., 2017), LSFNPTQLEEQCH (Barbé et al., 2014)
AASDISL SDISLLDAQSAPLR (Wada et al., 2017), TPEVDDEAL TPEVDDEALEK ( Nongonierma et al., 2017), VRTPEVDDEAL (Barbé
SDISLLDAQSAPL (Barbé et al., 2014) et al., 2014)
DIQK LIVTQTMKGLDIQKVAGT (Wada et al., 2017), EN
LDIQKVAGTW (Barbé et al., 2014)
IVTQTM IVTQTMKGLDIQ (Wada et al., 2017), VEEL RVYVEEL (Bouzerzour et al., 2012), YVEELKPT (Wada et al., 2017),
IVTQTMK (Barbé et al., 2014) VEELKPTPEGD (Barbé et al., 2014)
DK ALEKFDK (Barbé et al., 2014)
Declaration of competing interest Committee, Shahid Beheshti University of Medical Sciences, Tehran,
Iran. We also appreciate the “Student Research Committee” and
The authors declare that they have no conflict of interest. “Research & Technology Chancellor” at Shahid Beheshti University of
Medical Sciences for their financial support of this study.
This study is related to the project NO 20803 with a code of ethics Supplementary data to this article can be found online at https://
“IR.SBMU.RETECH.REC.1398.774” from the Student Research doi.org/10.1016/j.lwt.2020.109616.
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