A heuristic, computer-driven and top-down approach to identify novel bioactive peptides: A proof-of-principle on angiotensin I converting enzyme inhibitory peptides

Structures, antioxidant, and angiotensin I-converting enzyme (ACE)-inhibitory activities of peptides derived from protein hydrolysates of three phenolics-rich legume genera

Lentil, black soybean, and black turtle bean are rich in phenolic antioxidants but belong to different scientific genera with different protein structures. This study's objective was to compare the characteristics of peptides derived from the protein hydrolysates of these legumes. Proteins were isolated, cooked, and subjected to in vitro digestion with pepsin, trypsin, and chymotrypsin. Hydrolyzed peptides were fractionated by ultrafiltration (UF), anion-exchange chromatography, and gel-permeation chromatography (GPC). GPC-eluted peptides of <3 kDa with high angiotensin I-converting enzyme (ACE)-inhibitory activities were sequenced. Antioxidant profiles of peptides from the three legumes analyzed by five methods did not follow the same activity patterns associated with the decreases in peptide's molecular size. Among the UF fractions, the <3 kDa fraction had the highest ACE-inhibition with approximately 45%, 42%, and 39% at 100 µg/mL. Stepwise purifications of the hydrolysates enhanced the ACE-inhibitory capacity (IC50) by two to nine folds after GPC to approximately 85, 64, and 93 µg/mL for lentil, black soybean, and black turtle bean, respectively. The 210 peptides sequenced in the <3 kDa fractions had chain-lengths, ranging from 6 to 18 amino acids with lentil having the shortest average length of 7.7 per peptide. Overall, based on chemical analyses, peptides contributed higher antioxidant capacity and ACE-inhibition than phenolics in legumes. Black turtle bean may need to be heated more prior to consumption to achieve the same digestibility as lentil and soy proteins. Results provided a foundation for making bioactive peptides from the three legumes. PRACTICAL APPLICATION: Three antioxidant-rich legume genera, lentil, black soybean, and black turtle bean, produced different peptides with different angiotensin I-converting enzyme (ACE) potencies and different peptide lengths. The results provided a scientific basis for producing peptides from the selected genera for the development of functional foods or dietary supplement with high antioxidant, ACE inhibitory activities, and digestibility.

Predicting variable-length ACE inhibitory peptides based on graph convolutional network

Traditional molecular descriptors have contributed to the prediction of angiotensin I-converting enzyme (ACE) inhibitory peptides, but they often fall short in capturing the complex structure of the molecule. To address these limitations, this study introduces molecular graphs as an advanced method for peptide characterization. Peptides containing 2-10 amino acids were represented using molecular graphs, and a graph convolutional network (GCN) model was constructed to predict variable-length peptides. This model was compared with machine learning (ML) models based on molecular descriptors, including Random Forest (RF), Support Vector Machine (SVM), and k-Nearest Neighbor (kNN), under the same benchmark. Notably, the GCN model outperformed the other models with an accuracy of 0.78, effectively identifying ACE inhibitory potential. Furthermore, the GCN model also demonstrated superior performance, exceeding existing methods with an accuracy rate of over 98 % on an independent test set. To validate our predictions, we synthesized peptides VAPE and AQQKEP with high predicted probabilities, and their IC50 values of 2.25 ± 0.11 and 3.75 ± 0.17 μM, respectively, indicating potent ACE inhibitory activity. The developed GCN model presents a powerful tool for the rapid screening and identification of ACE inhibitory peptides, offering promising opportunities for developing antihypertensive components in functional foods.

Free fatty acid receptors beyond fatty acids: A computational journey to explore peptides as possible binders of GPR120

Free fatty acids receptors, with members among G protein-coupled receptors (GPCRs), are crucial for biological signaling, including the perception of the so called "fatty taste". In recent years, GPR120, a protein belonging to the GPCR family, drew attention as an interesting pharmacological target to cope with obesity, satiety and diabetes. Apart from long chain fatty acids, which are GPR120 natural agonists, other synthetic molecules were identified as agonists expanding the chemical space of GPR120's ligands. In this scenario, we unveiled peptides as possible GPR120 binders toward a better understanding of this multifaceted and relevant target. This study analyzed a virtual library collecting 531 441 low-polar hexapeptides, providing mechanistic insights on the GPR120 activation and further extending the possible chemical space of GPR120 agonists. The computational pipeline started with a narrow filtering of hexapeptides based on their chemical similarity with known GPR120 agonists. The best hits were tested through docking studies, molecular dynamics and umbrella sampling simulations, which pointed to G[I,L]FGGG as a promising GPR120 agonist sequence. The presence of both peptides in food-related proteins was thoroughly assessed, revealing they may occur in mushrooms, food-grade bacteria and rice. Simulations on the counterparts with D-amino acids were also performed. Umbrella sampling simulations described that GdIFGGG may have a better interaction compared to its all-L counterpart (-13 kCal/mol ΔG and -6 kCal/mol ΔG, respectively). Overall, we obtained a predictive model to better understand the underpinning mechanism of GPR120-hexapeptides interaction, hierarchizing novel potential agonist peptides for further analysis and describing promising food sources worth of further dedicated investigations.

Evaluation of the multifunctional dipeptidyl-peptidase IV and angiotensin converting enzyme inhibitory properties of a casein hydrolysate using cell-free and cell-based assays

The objective of the study was the evaluation of the potential pleiotropic effect of a commercial casein hydrolysate (CH). After an analysis of the composition, the BIOPEP-UWM database suggested that these peptides contained numerous sequences with potential inhibitory activities on angiotensin converting enzyme (ACE) and dipeptidyl-peptidase IV (DPP-IV). The anti-diabetic and anti-hypertensive effects of these peptides were thus assessed using either cell-free or cell-based assays. In the cell-free system, CH displayed inhibitory properties against DPP-IV (IC₅₀ value equal to 0.38 ± 0.01 mg/mL) and ACE (IC₅₀ value equal to 0.39 ± 0.01 mg/mL). Further, CH reduced the DPP-IV and ACE activities expressed by human intestinal Caco-2 cells by 61.10 ± 1.70% and 76.90 ± 4.47%, respectively, versus untreated cells, after 6 h of treatment at the concentration of 5 mg/mL. This first demonstration of the multifunctional behavior of this material suggests that it may become an anti-diabetic and/or anti-hypertensive ingredient to be included in the formulation of different functional food or nutraceutics.

Rainbow Trout (Oncorhynchus mykiss) as Source of Multifunctional Peptides with Antioxidant, ACE and DPP-IV Inhibitory Activities

The present study aimed at characterizing the possible biological activities of the multifunctional low molecular weight fractions (<3 kDa) peptides isolated from rainbow trout (Oncorhynchus mykiss) obtained by enzymatic hydrolysis. The fish protein hydrolysate (FPH) was tested for its antioxidant property along with its angiotensin converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV) inhibitory activities. In particular, the 2,2-diphenyl-1-picrylhydrazyl (DPPH), the ferric reducing antioxidant power (FRAP), the oxygen radical absorbance capacity (ORAC) assay and the 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) assays were carried out for the evaluation of the in vitro antioxidant activity. The cell-free ACE and DPP-IV inhibitory activity assays were also estimated, showing a dose-dependent inhibition. These biological properties were additionally quantified at the cellular level using human intestinal Caco-2 cells. Namely, the antioxidant activity was determined by evaluating the capability of the hydrolysate to reduce the H2O2-induced reactive oxygen species (ROS) and lipid peroxidation levels, and the DPP-IV activity assays show a reduction of enzyme activity of up to 27.57 ± 3.7% at 5 mg/mL. The results indicate that Oncorhynchus mykiss-derived peptides may have potential employment as health-promoting ingredients.

An In Silico Framework to Mine Bioactive Peptides from Annotated Proteomes: A Case Study on Pancreatic Alpha Amylase Inhibitory Peptides from Algae and Cyanobacteria

Bioactive peptides may exert beneficial activities in living organisms such as the regulation of glucose metabolism through the inhibition of alpha amylases. Algae and cyanobacteria are gaining a growing interest for their health-promoting properties, and possible effects on glucose metabolism have been described, although the underlying mechanisms need clarification. This study proposes a computer-driven workflow for a proteome-wide mining of alpha amylase inhibitory peptides from the proteome of Chlorella vulgaris, Auxenochlorella protothecoides and Aphanizomenon flos-aquae. Overall, this work presents an innovative and versatile approach to support the identification of bioactive peptides in annotated proteomes. The study: (i) highlighted the presence of alpha amylase inhibitory peptides within the proteomes under investigation (including ELS, which is among the most potent inhibitory tripeptides identified so far); (ii) mechanistically investigated the possible mechanisms of action; and (iii) prioritized further dedicated investigation on the proteome of C. vulgaris and A. flos-aquae, and on CSSL and PGG sequences.

Mechanistic Insights into Angiotensin I-Converting Enzyme Inhibitory Tripeptides to Decipher the Chemical Basis of Their Activity

Food proteins are an important source of bioactive peptides, and the angiotensin I-converting enzyme (ACE) inhibitors are worthy of attention for their possible beneficial effects in subjects with mild hypertension. However, the chemical basis underpinning their activity is not well-understood, hampering the discovery of novel inhibitory sequences from the plethora of peptides encrypted in food proteins. This work combined computational and in vitro investigations to describe precisely the chemical basis of potent inhibitory tripeptides. A substantial set of previously uncharacterized tripeptides have been investigated in silico and in vitro, and LCP was described for the first time as a potent ACE inhibitory peptide with IC₅₀ values of 8.25 and 6.95 μM in cell-free and cell-based assays, respectively. The outcomes presented could serve to better understand the chemical basis of already characterized potent inhibitory tripeptides or as a blueprint to design novel and potent inhibitory peptides and peptide-like molecules.

Integrated Evaluation of the Multifunctional DPP-IV and ACE Inhibitory Effect of Soybean and Pea Protein Hydrolysates

Nowadays, notwithstanding their nutritional and technological properties, food bioactive peptides from plant sources garner increasing attention for their ability to impart more than one beneficial effect on human health. Legumes, which stand out thanks to their high protein content, represent valuable sources of bioactive peptides. In this context, this study focused on the characterization of the potential pleotropic activity of two commercially available soybean (SH) and pea (PH) protein hydrolysates, respectively. Since the biological activity of a specific protein hydrolysate is strictly correlated with its chemical composition, the first aim of the study was to identify the compositions of the SH and PH peptides. Peptidomic analysis revealed that most of the identified peptides within both mixtures belong to storage proteins. Interestingly, according to the BIOPEP-UWM database, all the peptides contain more than one active motive with known inhibitory angiotensin converting enzyme (ACE) and dipeptidyl-dipeptidases (DPP)-IV sequences. Indeed, the results indicated that both SH and PH inhibit DPP-IV and ACE activity with a dose-response trend and IC50 values equal to 1.15 ± 0.004 and 1.33 ± 0.004 mg/mL, and 0.33 ± 0.01 and 0.61 ± 0.05 mg/mL, respectively. In addition, both hydrolysates reduced the activity of DPP-IV and ACE enzymes which are expressed on the surface of human intestinal Caco-2 cells. These findings clearly support that notion that SH and PH may represent new ingredients with anti-diabetic and hypotensive effects for the development of innovative multifunctional foods and/or nutraceuticals for the prevention of metabolic syndrome.