An in silico model to predict and estimate digestion-resistant and bioactive peptide content of dairy products: A primarily study of a time-saving and affordable method for practical research purposes

Discovery of potential antidiabetic peptides using deep learning

Antidiabetic peptides (ADPs), peptides with potential antidiabetic activity, hold significant importance in the treatment and control of diabetes. Despite their therapeutic potential, the discovery and prediction of ADPs remain challenging due to limited data, the complex nature of peptide functions, and the expensive and time-consuming nature of traditional wet lab experiments. This study aims to address these challenges by exploring methods for the discovery and prediction of ADPs using advanced deep learning techniques. Specifically, we developed two models: a single-channel CNN and a three-channel neural network (CNN + RNN + Bi-LSTM). ADPs were primarily gathered from the BioDADPep database, alongside thousands of non-ADPs sourced from anticancer, antibacterial, and antiviral peptide datasets. Subsequently, data preprocessing was performed with the evolutionary scale model (ESM-2), followed by model training and evaluation through 10-fold cross-validation. Furthermore, this work collected a series of newly published ADPs as an independent test set through literature review, and found that the CNN model achieved the highest accuracy (90.48 %) in predicting the independent test set, surpassing existing ADP prediction tools. Finally, the application of the model was considered. SeqGAN was used to generate new candidate ADPs, followed by screening with the constructed CNN model. Selected peptides were then evaluated using physicochemical property prediction and structural forecasts for pharmaceutical potential. In summary, this study not only established robust ADP prediction models but also employed these models to screen a batch of potential ADPs, addressing a critical need in the field of peptide-based antidiabetic research.

Estimation of bioactive peptide content of milk from different species using an in silico method

This study assessed the bioactive peptides content of milk from different species, including humans, camel, bovine, buffalo, donkey, sheep, goat, and horse. The highest and lowest concentrations of total digestion-resistant peptides were estimated in sheep and human milk. Donkey milk casein contains a higher angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase III (DPP-III) inhibitory, DPP-IV inhibitory, and antioxidant peptides. On the other hand, camel whey protein contains the highest ACE-inhibitory peptides. To discover BPs with immunomodulatory and cholesterol-lowering functions, goat milk casein and sheep milk whey protein can be considered, respectively.

Preparation, identification, and inhibitory mechanism of dipeptidyl peptidase IV inhibitory peptides from goat milk whey protein

This study explores potential hypoglycemic mechanisms by preparing and identifying novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from goat milk (GM) whey protein. Papain was used to hydrolyze the GM whey protein. After purification by ultrafiltration, the Sephadex column, and preparative RP-HPLC, the peptide inhibited DPP-IV, α-glucosidase, and α-amylase with IC50 of 0.34, 0.37, and 0.72 mg/mL, respectively. To further explore the inhibitory mechanism of peptides on DPP-IV, SPPEFLR, LDADGSY, YPVEPFT, and FNPTY were identified and synthesized for the first time, with IC50 values of 56.22, 52.16, 175.7, and 62.32 µM, respectively. Molecular docking and dynamics results show that SPPEFLR, LDADGSY, and FNPTY bind more tightly to the active pocket of DPP-IV, which was consistent with the in vitro activity. Furthermore, the first three N-terminals of SPPEFLR and FNPTY peptides exhibit proline characteristics and competitively inhibit DPP-IV. Notably, the first N-terminal leucine of LDADGSY may play a key role in inhibiting DPP-IV.

An in silico approach to unveil peptides from Acheta domesticus with potential bioactivity against hypertension, diabetes, cardiac and pulmonary fibrosis

Entomophagy is a sustainable alternative source of proteins for human nutrition. Acheta domesticus is one of the three insect species that complies with the European Union Regulation on novel foods, but to date, there are no reports on their potential bioactive peptides. In this study, an in silico approach was applied to simulate the gastrointestinal (GI) digestion of six A. domesticus proteins and identify new peptides with potential anti-hypertensive and/or anti-diabetic properties, resulting from their capability to inhibit the somatic Angiotensin-I converting enzyme (sACE) and/or dipeptidyl peptidase 4 (DPP-4), respectively. A molecular docking protocol was applied to evaluate the binding interactions between the 43 peptides ranked with high probability of being bioactive and three drug targets: DPP-4 and two catalytic domains (N- and C-) of sACE. Five peptides (AVQPCF, CAIAW, IIIGW, DATW and QIVW) showed high docking scores for both enzymes, suggesting their potential to inhibit the DPP-4 and both catalytic domains of sACE, thus possessing multifunctional bioactive properties. Two peptides (PIVCF and DVW) showed higher docking scores for the N-domain of sACE, indicating a potential action as selective inhibitors and consequently with anti-cardiac and pulmonary fibrosis bioactivities. This is the first study identifying peptides originated from the simulated GI digestion of A. domesticus with potential activities against hypertension, diabetes, cardiac and pulmonary fibrosis.

Bioactive Peptides and Protein Hydrolysates as Lipoxygenase Inhibitors

Lipoxygenases are non-heme iron-containing enzymes that catalyze the oxidation of polyunsaturated fatty acids, resulting in the production of lipid hydroperoxides, which are precursors of inflammatory lipid mediators. These enzymes are widely distributed in humans, other eukaryotes, and cyanobacteria. Lipoxygenases hold promise as therapeutic targets for several human diseases, including cancer and inflammation-related disorders. Inhibitors of lipoxygenase have potential applications in pharmaceuticals, cosmetics, and food. Bioactive peptides are short amino acid sequences embedded within parent proteins, which can be released by enzymatic hydrolysis, microbial fermentation, and gastrointestinal digestion. A wide variety of bioactivities have been documented for protein hydrolysates and peptides derived from different biological sources. Recent findings indicate that protein hydrolysates and peptides derived from both edible and non-edible bioresources can act as lipoxygenase inhibitors. This review aims to provide an overview of the current knowledge regarding the production of anti-lipoxygenase protein hydrolysates and peptides from millet grains, chia seeds, insects, milk proteins, fish feed, velvet antler blood, fish scales, and feather keratins. The anti-lipoxygenase activities and modes of action of these protein hydrolysates and peptides are discussed. The strengths and shortcomings of previous research in this area are emphasized. Additionally, potential research directions and areas for improvement are suggested to accelerate the discovery of anti-lipoxygenase peptides in the near future.

Calcium bioaccessibility increased during gastrointestinal digestion of α-lactalbumin and β-lactoglobulin

Calcium bioaccessibility depends on the amount of soluble calcium under intestinal digestion. The changes in calcium during in vitro static digestion of α-lactalbumin and β-lactoglobulin in presence of calcium chloride (0 mM, 20 mM and 50 mM) were followed by combining electrochemical determination of free calcium with the determination of soluble calcium by inductively coupled plasma optical emission spectroscopy. α-Lactalbumin and, more evident, β-lactoglobulin were found to increase calcium bioaccessibility with increasing intestinal digestion time by around 5% and 10%, respectively, due to the complex binding of calcium to peptides formed from protein hydrolysis by gastrointestinal enzymes. In vitro digested samples of β-lactoglobulin in presence of CaCl₂ had nearly twice as much complex bound calcium as α-lactalbumin samples. The calcium bioaccessibility decreased significantly with the increasing concentration of added calcium chloride, although the amount of calcium chloride had little effect on the extension of digestion of α-lactalbumin and β-lactoglobulin. Simulated digestion fluids were found to have a negative effect on calcium bioaccessibility, especially the presence of hydrogen phosphate, and the amount of precipitated calcium increased significantly with increasing amount of added calcium chloride. Based on analysis and visualization by sequences of the peptides formed during digestion of α-lactalbumin and β-lactoglobulin, it was observed that peptides containing aspartic acid and glutamic acid acting as calcium chelators, may prevent precipitation of calcium in the intestines and increase calcium bioaccessibility. These results provide knowledge for the design of new dairy based functional foods to prevent calcium deficiency.

Novel angiotensin I-converting enzyme (ACE) inhibitory peptides from walnut protein isolate: Separation, identification and molecular docking study

Walnut protein isolate was hydrolyzed using alcalase® to obtain angiotensin-I-converting enzyme (ACE) inhibitory (ACEI) peptides. The components with high ACEI activity were successfully purified from walnut protein isolate hydrolysates (WPIH) by ultrafiltration and G-25 gel chromatography. The 1520 peptides were identified by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Then the screening model of ACEI peptides was established by in silico approach. It was found that four ACEI active peptides (PPKP, YPQY, YLPP, and PKPP) were obtained with IC₅₀ values ranging from 506 to 89 μmol/L, among which PPKP had the highest ACEI activity (IC₅₀  = 89 ± 1 μmol/L). The four peptides mentioned above were novel, non-toxic, and resistant to gastrointestinal digestion. The molecular docking studies showed that the ACEI effect of ACEI peptide was mainly due to the interaction with residues of Gln281 and His353 in the ACE active pockets. In vivo availability of ACEI peptides showed that the probability of PPKP binding to ACE was 37.9% in the human body. Our studies suggest that the ACEI peptides derived from the WPIH can be considered functional foods that can prevent hypertension. PRACTICAL APPLICATIONS: Hypertension is a significant risk factor for cardiovascular and cerebrovascular disease, the leading cause of death worldwide. This study used a cost-effective method to isolate and identify potential ACEI peptides from the walnut meal. Since the walnut meal is often discarded in the processing of walnut products and thus pollutes the environment, the preparation of walnut meal into ACEI peptides can reduce the impact of hypertension on people and reduce environmental pollution. The experimental results show that walnut ACEI peptides are a safe and healthy nutritional product.

In Silico Approach of Glycinin and Conglycinin Chains of Soybean By-Product (Okara) Using Papain and Bromelain

This study explores utilization of a sustainable soybean by-product (okara) based on in silico approach. In silico approaches, as well as the BIOPEP database, PeptideRanker database, Peptide Calculator database (Pepcalc), ToxinPred database, and AllerTop database, were employed to evaluate the potential of glycinin and conglycinin derived peptides as a potential source of bioactive peptides. These major protein precursors have been found as protein in okara as a soybean by-product. Furthermore, primary structure, biological potential, and physicochemical, sensory, and allergenic characteristics of the theoretically released antioxidant peptides were predicted in this research. Glycinin and α subunits of β-conglycinin were selected as potential precursors of bioactive peptides based on in silico analysis. The most notable among these are antioxidant peptides. First, the potential of protein precursors for releasing bioactive peptides was evaluated by determining the frequency of occurrence of fragments with a given activity. Through the BIOPEP database analysis, there are several antioxidant bioactive peptides in glycinin and β and α subunits of β-conglycinin sequences. Then, an in silico proteolysis using selected enzymes (papain, bromelain) to obtain antioxidant peptides was investigated and then analyzed using PeptideRanker and Pepcalc. Allergenic analysis using the AllerTop revealed that all in silico proteolysis-derived antioxidant peptides are probably nonallergenic peptides. We also performed molecular docking against MPO (myeloperoxidases) for this peptide. Overall, the present study highlights that glycinin and β and α subunits of β-conglycinin could be promising precursors of bioactive peptides that have an antioxidant peptide for developing several applications.

The anti-anxiety/depression effect of a combined complex of casein hydrolysate and γ-aminobutyric acid on C57BL/6 mice

In view of a series of adverse side effects of drugs for anxiety/depression on the market at present, it is imminent to extract and develop novel anti-anxiety and depression drugs from plants and proteins (like casein hydrolysate) as adjuncts or substitutes for existing anti-anxiety and depression drugs. Consequently, this study investigated the improvement of the anxiety/depression function by the compound of casein hydrolysate and γ-aminobutyric acid (GABA) (casein hydrolysate: GABA = 4:1; CCHAA) on mice induced by chronic restraint stress-corticosterone injection. Animal experiments revealed that oral gavage administration of CCHAA significantly reversed the anxiety/depression-like behaviors. Compared to the model control group, body weights were increased after treatment with CCHAA groups [1.5, 0.75 mg/(g⋅d)]. As a diagnostic index of anxiety and depression, we assessed GABA and 5-HT levels in response to CCHAA ingestion. The GABA and 5-HT levels were increasingly enhanced by the CCHAA diet. In addition, histopathological changes in the hippocampus CA3 region of the anxious/depressed mice were also alleviated after the treatment with the CCHAA. Thus, the casein hydrolysate and GABA formula diets may induce beneficial effects on the mice with anxiety/depression.

Peptide profile of Parmigiano Reggiano cheese after simulated gastrointestinal digestion: From quality drivers to functional compounds

Time of ripening has a strong impact on shaping the valuable and recognizable characteristics of long-ripened types of cheese such as Parmigiano Reggiano (PR) due to the interrelationship between microbiota and proteolysis that occurs during ripening. The derived peptide profile is linked to cheese quality and represents the canvas for enzymes upon digestion, which could be responsible for the release of potentially bioactive peptides (BPs). In this study, we aimed at investigating the presence of BP in 72 PR cheese samples of different ripening times, from curd to 24 months of ripening, produced in six different dairies, and following their fate after simulated gastrointestinal digestion. A small number of peptide sequences sharing 100% similarity with known antimicrobial, antioxidant, and ACE-inhibitor sequences were found in PR cheeses, while a higher number of potential BPs were found after their simulated gastrointestinal digestion, in different amounts according to ripening time. Taking advantage of the complex organization of the sampling plan, we were able to follow the fate of peptides considered quality drivers during cheese ripening to their release as functional compounds upon digestion.

The significance and potential of functional food ingredients for control appetite and food intake

Dramatically rising global levels of obesity have raised consumers’ commercial and public health interest in foods that may help control appetite and weight. The satiety cascade consists of sensory, cognitive, physical, and hormonal events following food intake, preventing overeating, and the desire to eat for a long time. Functional foods can be one of the most influential factors in reducing appetite as long as effective ingredients, such as fiber and protein, are used to design these products. Also, functional foods should be designed to reduce appetite at different levels of oral processing, stomach, small intestine, and large intestine by various mechanisms. Therefore, the satiety power of functional foods depends on the type of ingredients and their amount. Because each compound has a different mechanism of action, it is recommended to use different compounds to influence satiety in functional foods.

The Association between Consumption of Dairy-Originated Digestion Resistant and Bioactive Peptides and Breast Cancer Risk: A Case-Control Study

Bioactive peptides (BPs) content of dairy products is suggested to be a significant ingredient for reducing breast cancer (BC) risk. There is no observational study regarding the correlation between BPs and the risk of chronic disease because BPs' content of food items has not been evaluated in any study. The goal of the current study was to assess the association of dairy-originated BPs with BC risk. One hundred thirty-four women with BC and 267 cancer-free controls were selected from referral hospitals in Tehran, Iran. The development of an in-silico model for estimation of the bioactive and digestion-resistant peptides content of dairy products was done in our previous research. The risk assessment for BPs and BC association was performed across the tertiles of the peptide's intake. Odds ratios (OR) were calculated by logistic regression. The negative association of all bioactive and digestion-resistant peptides except for peptides with high hydrophilicity and low bioactivity was seen in all models. In PR-negative subjects only the association of total dairy intake (OR: 0.61; 95% CI: 0.26-1.45; P _{for trend}: 0.276), peptides with low bioactivity (OR: 0.40; 95% CI: 0.16-1.02; P _{for trend}: 0.0.052), antidiabetic peptides (OR: 0.42; 95% CI: 0.17-1.05; P _{for trend}: 0.0.062) and di-peptides (OR: 0.42; 95% CI: 0.17-1.05; P _{for trend}: 0.0.062) were not significant in the final model. Also, no significant association between ER-negative subjects and total dairy intake (OR: 0.41; 95% CI: 0.16-1.07; P _{for trend}: 0.0.068) was noted. Our findings deduced that milk-derived BPs negatively associate with the risk of ER/PR/HER2 negative BC among Iranian women.Supplemental data for this article is available online at https://doi.org/10.1080/01635581.2021.2009884.

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.

Dairy-originated digestion-resistant and bioactive peptides increase the risk of hypertension: Tehran Lipid and Glucose Study

Milk-protein-derived bioactive peptides (BPs) have been proposed as modulators of different regulatory processes involved in blood pressure regulation. Studies on the long-term effects of BPs on blood pressure have not yet been conducted. We aimed to investigate the association of dairy-originated BPs with the risk of hypertension (HTN) in the Tehran Lipid and Glucose Cohort Study (TLGS). In this cohort study, 4378 subjects with a mean follow-up period of 3.1 years were included in the final analysis. Dietary intake, physical activity, demographic, and anthropometric data and blood pressure measurements were obtained for all participants. Various types of dairy-originated BPs were determined by an in silico method. High intake of total digestion-resistant and bioactive peptides (OR: 1.31, CI 95%: 1.01-1.70), dipeptides (OR: 1.33, CI 95%: 1.03-1.73), peptides with more than seven residues (OR: 1.32, CI 95%: 1.01-1.71), glycosylated residues (OR: 1.39, CI 95%: 1.07-1.80), highly hydrophilic peptides (OR: 1.32, CI 95%: 1.01-1.71), and low hydrophobic peptides (OR: 1.32, CI 95%: 1.01-1.71) was associated with an increased risk of HTN in the adjusted model. In addition, subjects in the higher tertile of anti-HTN peptide (OR: 1.33, CI 95%: 1.02-1.72) and antidiabetic peptide (OR: 1.35, CI 95%: 1.04-1.76) intake had a higher risk of HTN than those in the lower tertile. No significant association emerged between calcium intake from dairy and incident risk of HTN. Our results showed that the intake of some forms of digestion-resistant and BPs, such as anti-HTN peptides, dipeptides, and peptides with more than seven residues, can increase the risk of HTN in the TLGS population.