In Silico Approaches Applied to the Study of Peptide Analogs of Ile-Pro-Ile in Relation to Their Dipeptidyl Peptidase IV Inhibitory Properties

DPP-IV and FAS inhibitory peptides: therapeutic alternative against diabesity

Diabesity is a modern epidemic that indicates a strong association between obesity and diabetes. Key enzymes have been identified in the development and progression of both diseases, DPP-IV in glucose uptake and FAS in fatty acid synthesis. In both cases, the molecular mechanisms of how each one acts separately have been described, and which are the key inhibitory drugs and molecules for each one. However, although it is known that there is an association between both clinically and molecularly, the mechanism has not been elucidated; therefore, this review focuses on proposing a mechanism of convergence of DPP-IV and FAS in diabesity, and the possible mode of action in which bioactive peptides obtained from plant and animal sources can inhibit these two enzymes in a similar way as drugs do.

Exploring the DPP IV inhibitory potential: molecular docking and dynamic simulations of pyridine-3-carboxylic acid and pyrrolidine-2-carboxylic acid analogs

Diabetes mellitus remains a global challenge, with Type 2 Diabetes Mellitus (T2DM) prevalence increasing from 4% to 6.4% in the past 30 years. Presently oral hypoglycaemic agents like GLP-1 agonists, biguanides, sulphonylureas, glinides, and thiazolidinediones are employed in clinical practice. Very recently, novel targets including Dipeptidyl peptidase IV (DPP IV), PPAR, GIP, FFA1, and melatonin have been in the limelight for the development of novel treatment strategies. The present study focuses on the development of DPP IV inhibitors through computational approaches. DPP IV, also referred to as CD26 (cluster of differentiation 26) or adenosine deaminase complexing protein 2, is a protein that is encoded by the DPP IV gene in humans. This enzyme is involved in the metabolism of incretin hormones such as glucagon-like peptides (GLP-1). DPP IV inhibitors prevent the degradation of GLP-1, glucose-dependent insulinotropic peptide (GIP), thereby controlling the concentration of glucose in the blood. Considering the safety and efficacy of DPP IV inhibitors newer molecules were designed with better binding affinity with the protein as compared to existing Sitagliptin, and Vildagliptin-like drugs. Derivatives of nicotinic acid and proline were designed and studied using molecular docking and dynamic simulations. Docking results demonstrated that the NA-13 molecule possesses potent binding affinity with target protein 6B1E (-38.1498 kcal/mol) as compared to standard Sitagliptin (-33.3187 kcal/mol). MD simulation studies showcased that there are fewer variations of RMSD and RMSF for 6B1E-NA-13, 6B1E-P1, and 6B1E-P7 complexes, suggesting the potential of the designed DPP IV inhibitors in the management of T2DM.

In Silico Hydrolysis of Lupin (Lupinus angustifolius L.) Conglutins with Plant Proteases Releases Antihypertensive and Antidiabetic Peptides That Are Bioavailable, Non-Toxic, and Gastrointestinal Digestion Stable

Lupin (Lupinus angustifolius L.) proteins are potential sources of bioactive peptides (LBPs) that can inhibit dipeptidyl peptidase IV (DPP-IV) and angiotensin I-converting enzyme (ACE-I) activity. However, the capacity of different enzymes to release LBPs, the pharmacokinetic and bioactivities of the peptides released, and their binding affinities with the active sites of DPP-IV and ECA-I are topics scarcely addressed. Therefore, we used in silico hydrolysis (BIOPEP-UWM platform) with various enzymes to predict the release of LBPs. Among the bioactive peptides identified in lupin proteins (n = 4813), 2062 and 1558 had DPP-IV and ACE-I inhibitory activity, respectively. Ficin, bromelain, and papain released the highest proportion of ACE-I (n = 433, 411, and 379, respectively) and DPP-IV (n = 556, 544, and 596, respectively) inhibitory peptides. LBPs with favorable pharmacokinetics and gastrointestinal stability tightly interacted with the active sites of ACE-I (-5.6 to -8.9 kcal/mol) and DPP-IV (-5.4 to -7.6 kcal/mol). Papain generated the most bioavailable LBPs (n = 459) with ACE-I (n = 223) and DPP-IV (n = 412) inhibitory activity. These peptides were non-toxic and gastrointestinal digestion stable. Notably, papain-based hydrolysis released some LBPs (n = 270) that inhibited both ACE-I and DPP-IV. Plant protease-based hydrolysis is a promising approach for producing lupin hydrolysates with ACE-I and DPP-IV inhibitory activities.

Precooked Jack Bean [Canavalia ensiformis (L.) DC] Sprout: Generation of Dipeptidyl Peptidase-IV Inhibitory Peptides during Simulated Digestion

Bioactive peptides generated from jack bean sprouts are reported to function as dipeptidyl peptidase IV (DPP-IV) inhibitors. However, no studies have investigated the effect of precooking followed by simulated digestion using pepsin-pancreatin to increase DPP-IV inhibitory peptide generation in jack bean sprouts. Therefore, the present study aimed to explore the generation of DPP-IV inhibitory peptides from precooked jack bean [Canavalia ensiformis (L.) DC] sprouts during simulated digestion with pepsin-pancreatin. The results showed that peptide fractions of the sample hydrolysate with molecular weight <1 kDa exhibited the strongest DPP-IV inhibitory activity (84.77%±0.49%) after simulated digestion. This activity was slightly greater than that (74.12%±0.85%) observed prior to simulated digestion. These findings demonstrate that the DPP-IV inhibitory activity of precooked jack bean sprouts can be retained following simulated digestion. Moreover, our investigation revealed the sequences of two novel peptides following simulated digestion with critical amino acids. The presence of alanine and glycine at the penultimate N-terminus of AAGPKP and LGDLLK confirmed the presence of DPP-IV inhibitors. Both peptide sequences are nontoxic and interact with the catalytic sites of enzymes through hydrogen bonds.

Functional attributes of bioactive peptides of bovine milk origin and application of in silico approaches for peptide prediction and functional annotations

Bovine milk peptides are the protein fragments with diverse bioactive properties having antioxidant, anticarcinogenic, other therapeutic and nutraceutical potentials. These peptides are formed in milk by enzymatic hydrolysis, gastrointestinal digestion and fermentation processes. They have significant health impact with high potency and low toxicity making them a suitable natural alternative for preventing and managing diseases. Antibiotic resistance has increased the quest for better peptide candidates with antimicrobial effects. This article presents a comprehensive review on well documented antimicrobial, immunological, opioid, and anti-hypertensive activities of bovine milk peptides. It also covers the usage of computational biology tools and databases for prediction and analysis of the food-derived bioactive peptides. In silico analysis of amino acid sequences of Bos taurus milk proteins have been predicted to generate peptides with dipeptidyl peptidase IV inhibitory and ACE inhibitory properties, making them favorable candidates for developing blood sugar lowering drugs and anti-hypertensives. In addition to the prediction of new bioactive peptides, application of bioinformatics tools to predict novel functions of already known peptides is also discussed. Overall, this review focuses on the reported as well as predicted biologically active peptide of casein and whey proteins of bovine milk that can be utilized to develop therapeutic agents.

Discarded CHO cells as a valuable source of bioactive peptides for sustainable biotechnological applications

Repurposing discarded cells stands as a groundbreaking paradigm shift in sustainable biotechnology, with profound implications across diverse industrial sectors. Our study proposes a transformative concept by harnessing histone proteins from discarded CHO cells to produce bioactive peptides. We systematically isolated and hydrolyzed histones using Trypsin and Neutrase enzymes, optimizing reaction conditions. Ultrafiltration yielded distinct peptide fractions (<3 kDa and 3-10 kDa), which we analyzed for DPP-IV inhibition, antioxidant potential, and other activities. Furthermore, LC-Q-TOF-MS analysis and in silico tools unveiled the structural composition of bioactive peptides within these fractions. Three peptide sequences with high bioactivity potential were identified: KLPFQR, VNRFLR, and LSSCAPVFL. Our findings demonstrated exceptional DPP-IV inhibition, potent antioxidant effects, and effective anti-lipid peroxidation activities, surpassing reference compounds. Hemolytic activity assessment indicated promising biocompatibility, enhancing therapeutic application prospects. Pioneering the strategic repurposing of discarded cells, this research addresses cost-efficiency in cell-based studies and promotes sustainable use of biological resources across sectors. This novel approach offers an efficient, eco-friendly method for bioactive molecule procurement and resource management, revolutionizing cell culture studies and biotechnological applications.

Enrichment and Quantitation of Dipeptidyl Peptidase IV Inhibitory Peptides in Quinoa upon Systematic Malting

Food-derived peptides with an inhibitory effect on dipeptidyl peptidase IV (DPP-IV) can be used as an additive treatment for type 2 diabetes. The inhibitory potential of food depends on technological protein hydrolysis and gastrointestinal digestion, as the peptides only act after intestinal resorption. The effect of malting as a hydrolytic step on the availability of these peptides in grains has yet to be investigated. In this study, quinoa was malted under systematic temperature, moisture, and time variations. In the resulting malts, the DPP-IV inhibition reached a maximum of 45.02 (±10.28) %, whereas the highest overall concentration of literature-known inhibitory peptides was 4.07 μmol/L, depending on the malting parameters. After in vitro gastrointestinal digest, the inhibition of most malts, as well as the overall concentration of inhibitory peptides, could be increased significantly. Additionally, the digested malts showed higher values in both the inhibition and the peptide concentration than the unmalted quinoa. Concerning the malting parameters, germination time had the highest impact on the inhibition and the peptide concentration after digest. An analysis of the protein sizes before and after malting gave first hints toward the origin of these peptides, or their precursors, in quinoa.

Molecular Mechanistic Insights into Dipeptidyl Peptidase-IV Inhibitory Peptides to Decipher the Structural Basis of Activity

Dipeptidyl peptidase-IV (DPP-IV) inhibiting peptides have attracted increased attention because of their possible beneficial effects on glycemic homeostasis. However, the structural basis underpinning their activities has not been well understood. This study combined computational and in vitro investigations to explore the structural basis of DPP-IV inhibitory peptides. We first superimposed the Xaa-Pro-type peptide-like structures from several crystal structures of DPP-IV ligand-protein complexes to analyze the recognition interactions of DPP-IV to peptides. Thereafter, a small set of Xaa-Pro-type peptides was designed to explore the effect of key interactions on inhibitory activity. The intramolecular interaction of Xaa-Pro-type peptides at the first and third positions from the N-terminus was pivotal to their inhibitory activities. Residue interactions between DPP-IV and residues of the peptides at the fourth and fifth positions of the N-terminus contributed significantly to the inhibitory effect of Xaa-Pro-type tetrapeptides and pentapeptides. Based on the interaction descriptors, quantitative structure-activity relationship (QSAR) studies with the DPP-IV inhibitory peptides resulted in valid models with high R2 values (0.90 for tripeptides; 0.91 for tetrapeptides and pentapeptides) and Q2 values (0.33 for tripeptides; 0.68 for tetrapeptides and pentapeptides). Taken together, the structural information on DPP-IV and peptides in this study facilitated the development of novel DPP-IV inhibitory peptides.

Encapsulation of Tenebrio molitor Hydrolysate with DPP-IV Inhibitory Activity by Electrospraying and Spray-Drying

This study investigates the encapsulation of Tenebrio molitor hydrolysate exhibiting DPP-IV inhibitory activity by spray-drying and electrospraying techniques. First, we optimized the feed formulation and processing conditions required to obtain nano-microcapsules by electrospraying when using Arabic gum as an encapsulating agent and pullulan and Tween 20 as additives. The optimum formulation was also dried by spray-drying, where the removal of the additives was also assayed. Morphology analysis reveals that electrosprayed capsules have a smaller size (1.2 ± 0.5 µm vs. 12.4 ± 8.7 µm) and greater uniformity compared to those obtained by spray-drying. Regarding the surface nitrogen content and DPP-IV inhibitory activity, our results show no significant difference between the electrosprayed capsules and spray-dried capsules containing additives (IC50 of ~1.5 mg protein/mL). Therefore, it was concluded that adding additives during spray-drying allows for a similar encapsulation efficiency and reduced degradation during processing, as achieved by electrospraying technique but providing higher productivity. On the other hand, spray-dried capsules without additives displayed a higher surface nitrogen content percentage, which was mainly due to the absence of Tween 20 in the feed formulation. Consequently, these capsules presented a higher IC50 value (IC50 of 1.99 ± 0.03 mg protein/mL) due to the potential degradation of surface-exposed peptides.

Computational Modeling of the Interactions between DPP IV and Hemorphins

Type 2 diabetes is a chronic metabolic disorder characterized by high blood glucose levels due to either insufficient insulin production or ineffective utilization of insulin by the body. The enzyme dipeptidyl peptidase IV (DPP IV) plays a crucial role in degrading incretins that stimulate insulin secretion. Therefore, the inhibition of DPP IV is an established approach for the treatment of diabetes. Hemorphins are a class of short endogenous bioactive peptides produced by the enzymatic degradation of hemoglobin chains. Numerous in vitro and in vivo physiological effects of hemorphins, including DPP IV inhibiting activity, have been documented in different systems and tissues. However, the underlying molecular binding behavior of these peptides with DPP IV remains unknown. Here, computational approaches such as protein-peptide molecular docking and extensive molecular dynamics (MD) simulations were employed to identify the binding pose and stability of peptides in the active site of DPP IV. Findings indicate that hemorphins lacking the hydrophobic residues LVV and VV at the N terminal region strongly bind to the conserved residues in the active site of DPP IV. Furthermore, interactions with these critical residues were sustained throughout the duration of multiple 500 ns MD simulations. Notably, hemorphin 7 showed higher binding affinity and sustained interactions by binding to S1 and S2 pockets of DPP IV.

Screening of novel DPP-IV inhibitory peptides derived from bovine milk proteins using a peptide array platform

Dipeptidyl peptidase IV (DPP-IV) has become an important target in the prevention and treatment of diabetes. Although many DPP-IV inhibitory peptides have been identified by a general approach involving the repeated fractionation of food protein hydrolysates, the obtained results have been dependent on the content of each peptide and fractionation conditions. In the present study, a peptide array that provides comprehensive assays of peptide sequences was used to identify novel DPP-IV inhibitory peptides derived from bovine milk proteins; these peptides were then compared with those identified using the general approach. While the general approach identified only known peptides that were abundant in the hydrolysate, the peptide array-based approach identified 10 novel DPP-IV inhibitory peptides, all of which had proline at the second residue from the N-terminus. The proper or combined use of these two approaches, which have different advantages, will enable the efficient development of novel bioactive foods and drugs.

Evaluating the In Situ Insulinotropic Effects of Pea Protein Hydrolysates Mediated by Active GLP-1 via a 2D and Dual-Layered Coculture Cell Model

The aim of this study was to evaluate the in situ insulinotropic effects of pea protein hydrolysates (PPHs) mediated by active glucagon-like peptide-17-36 (active GLP-1) using a 2D and dual-layered coculture cell model. Following this model, a mixed Caco-2 and NCI-H716 cell monolayer was differentiated on the apical side to study the effects of PPHs on active GLP-1 levels; meanwhile, the beta-TC-6 cells were seeded on the basolateral side to investigate the insulin responses induced by active GLP-1. The in situ DPP-4 half-maximal inhibitory concentration (IC50) of PPHs, PPHs-120G, and PPHs-120I was 2.94, 3.43, and 2.26 mg/mL, respectively. They directly stimulated active GLP-1 secretion in NCI-H716 cells by 3.03 ± 0.21, 1.99 ± 0.03, and 2.24 ± 0.02 times, respectively. Insulin release in beta-TC-6 cells was directly stimulated by PPHs but not by PPHs-120G and PPHs-120I. Interestingly, PPHs-120G and PPHs-120I indirectly stimulated insulin release in this coculture cell model by enhancing active GLP-1 concentrations. More importantly, PPHs, PPHs-120G, and PPHs-120I increase active GLP-1 levels by their dual function of stimulating active GLP-1 secretion and DPP-4 inhibition. This study suggests that the 2D and dual-layered coculture cell model supports a more comprehensive assessment of in situ insulinotropic effects of protein hydrolysates mediated by active GLP-1.

Chemical and biological characterization of the DPP-IV inhibitory activity exerted by lupin (Lupinus angustifolius) peptides: From the bench to the bedside investigation

Dipeptidyl peptidase IV (DPP-IV) is considered a key target for the diabetes treatment, since it is involved in glucose metabolism. Although lupin protein consumption shown hypoglycemic activity, there is no evidence of its effect on DPP-IV activity. This study demonstrates that a lupin protein hydrolysate (LPH), obtained by hydrolysis with Alcalase, exerts anti-diabetic activity by modulating DPP-IV activity. In fact, LPH decreased DPP-IV activity in a cell-free and cell-based system. Contextually, Caco-2 cells were employed to identify LPH peptides that can be intestinally trans-epithelial transported. Notably, 141 different intestinally transported LPH sequences were identified using nano- and ultra-chromatography coupled to mass spectrometry. Hence, it was demonstrated that LPH modulated the glycemic response and the glucose concentration in mice, by inhibiting the DPP-IV. Finally, a beverage containing 1 g of LPH decreased DPP-IV activity and glucose levels in humans.

Isolation and identification of dipeptidyl peptidase-IV inhibitory peptides from Sacha inchi meal

BACKGROUND

Sacha inchi meal (SIM) is a by-product of oil processing. Our previous studies showed that SIM hydrolysates exhibited dipeptidyl peptidase-IV (DPP-IV) inhibition activity. The objective of the present work was to identify and characterize the bioactive peptides from protein hydrolysates of SIM; enzyme kinetics and peptide-enzyme interaction were also investigated.

RESULTS

From SIM hydrolysates, ten peptides responsible for the activity were identified: GPSRGF (GF-6), FPILSPDPA (FA-9), APYRRGGKI (AI-9), WPYH (WH-4), DPATWLALPT (DT-10), NPEDEFRQQ (NQ-9), APESKPVGV (AV-9), LEWRDR (LR-6), APVYWVQ (AQ-7) and LLMWPY (LY-6). The IC₅₀ values of five peptides (GF-6, WH-4, AQ-7, AV-9 and LY-6) with better inhibitory activity on DPP-IV were within the range of 23.43-128.40 μmol L^-1 . AQ-7 had the best activity, with an IC₅₀ value of 23.43 μmol L^-1 . Enzyme kinetics indicated the presence of various inhibition types (mixed, non-competitive and competitive). Isothermal titration microcalorimetry showed that the main forces of the binding sites between peptide (GF-6 or AQ-7) and DPP-IV were hydrogen bond, hydrophobic interaction and van der Waals force. The key residues involved in peptide-enzyme interaction were determined by molecular docking. Furthermore, at a concentration of 800 μmol L^-1 , GF-6 was found to significantly increase the glucose consumption in insulin-resistant HepG2 cells (P < 0.05) compared with the model group.

CONCLUSION

Sacha inchi meal-derived peptides displayed potent DPP-IV inhibition activity and could be used in the health food industry and as lead compounds for diabetes therapy. © 2023 Society of Chemical Industry.

In Vitro Assessment Methods for Antidiabetic Peptides from Legumes: A Review

Almost 65% of the human protein supply in the world originates from plants, with legumes being one of the highest contributors, comprising between 20 and 40% of the protein supply. Bioactive peptides from various food sources including legumes have been reported to show efficacy in modulating starch digestion and glucose absorption. This paper will provide a comprehensive review on recent in vitro studies that have been performed on leguminous antidiabetic peptides, focusing on the α-amylase inhibitor, α-glucosidase inhibitor, and dipeptidyl peptidase-IV (DPP-IV) inhibitor. Variations in legume cultivars and methods affect the release of peptides. Different methods have been used, such as in sample preparation, including fermentation (t, T), germination (t), and pre-cooking; in protein extraction, alkaline extraction, isoelectric precipitation, phosphate buffer extraction, and water extraction; in protein hydrolysis enzyme types and combination, enzyme substrate ratio, pH, and time; and in enzyme inhibitory assays, positive control type and concentration, inhibitor or peptide concentration, and the unit of inhibitory activity. The categorization of the relative scale of inhibitory activities among legume samples becomes difficult because of these method differences. Peptide sequences in samples were identified by means of HPLC/MS. Software and online tools were used in bioactivity prediction and computational modelling. The identification of the types and locations of chemical interactions between the inhibitor peptides and enzymes and the type of enzyme inhibition were achieved through computational modelling and enzyme kinetic studies.

Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds

The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.

In silico study to predict potential precursors of human dipeptidyl peptidase-IV inhibitors from hazelnut

Chinese hazelnut was chosen to become a probable precursor of biological active peptides via computer simulations in this article. There were a large number of bioactive peptides in Chinese hazelnut sequences according to analytical results from the BIOPEP database. The most prominent of these was the inhibitory peptide for dipeptidyl peptidase-IV (DPP-IV; EC 3.4.14.5), which can be used to treat type 2 diabetes, so the theoretical method to obtain DPP-IV inhibitory peptides by hydrolysis with a single or combination of enzymes was studied. Cytotoxicity analysis performed by ToxinPred showed that all of the DPP-IV inhibitory peptides generated from protein hydrolysis were not cytotoxic. Structural interaction fingerprint analysis revealed that Asp663 and Phe357 may be important residues for ligand binding. In order to further understand the inhibitory mechanism of peptide, VR with lowest half maximum inhibitory concentration (IC50) and IPI (inhibitors have been reported) were selected as ligand of DPP-IV to perform steered molecular dynamics simulations and PMF calculations. The results showed that P1 is the preferred (un)binding tunnel for the inhibitors obtained. Our findings help in the development of new DPP-IV inhibitors which were derived from common food.Communicated by Ramaswamy H. Sarma.

DPP-IV Inhibitory Peptides GPF, IGL, and GGGW Obtained from Chicken Blood Hydrolysates

Blood is a meat by-product rich in proteins with properties that can be improved after hydrolysis, making it a sustainable alternative for use in the generation of bioactive peptides. The objective of this study was to identify dipeptidyl peptidase IV (DPP-IV) inhibitory peptides obtained from different chicken blood hydrolysates prepared using combinations of four different enzymes. Best results were observed for AP (2% Alcalase + 5% Protana Prime) and APP (2% Alcalase + 5% Protana Prime + 3% Protana UBoost) hydrolysates obtaining inhibition values of 60.55 and 53.61%, respectively, assayed at a concentration of 10 mg/mL. Free amino acids were determined to establish the impact of exopeptidase activity in the samples. A total of 79 and 12 sequences of peptides were identified by liquid chromatography and mass spectrometry in tandem (LC-MS/MS) in AP and APP samples, respectively. Nine of the identified peptides were established as potential DPP-IV inhibitory using in silico approaches and later synthesized for confirmation. Thus, peptides GPF, IGL, and GGGW showed good DPP-IV inhibitory activity with IC₅₀ values of 0.94, 2.22, and 2.73 mM, respectively. This study confirmed the potential of peptides obtained from chicken blood hydrolysates to be used as DPP-IV inhibitors and, therefore, in the control or modulation of type 2 diabetes.

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.

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

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

Rapid Screening of Novel Dipeptidyl Peptidase-4 Inhibitory Peptides from Pea (Pisum sativum L.) Protein Using Peptidomics and Molecular Docking

Pea protein hydrolysates (PPHs) possess good hypoglycemic effects; however, their dipeptidyl peptidase-4 (DPP-4) inhibitory activity is poorly understood, and none of the DPP-4 inhibitory peptides have been identified from PPHs. This paper aims to rapidly screen these peptides from PPHs by combining peptidomics and molecular docking. In this study, 543 peptides were identified by peptidomics, and four peptides (IPYWTY, IPYWT, LPNYN, and LAFPGSS) with DPP-4 half-maximal inhibitory concentration (IC50) values <100 μM were screened for the first time. Significantly, peptide IPYWTY exhibited the most potent DPP-4 inhibitory activity (IC50 = 11.04 μM) mainly because it formed hydrophobic interactions with the S1 pocket in DPP-4. These results indicated that combining peptidomics and molecular docking is an effective strategy for rapidly screening DPP-4 inhibitory peptides.

Bioactive Peptides: An Understanding from Current Screening Methodology

Bioactive peptides with high potency against numerous human disorders have been regarded as a promising therapy in disease control. These peptides could be released from various dietary protein sources through hydrolysis processing using physical conditions, chemical agents, microbial fermentation, or enzymatic digestions. Considering the diversity of the original proteins and the complexity of the multiple structural peptides that existed in the hydrolysis mixture, the screening of bioactive peptides will be a challenge task. Well-organized and well-designed methods are necessarily required to enhance the efficiency of studying the potential peptides. This article, hence, provides an overview of bioactive peptides with an emphasis on the current strategy used for screening and characterization methods. Moreover, the understanding of the biological activities of peptides, mechanism inhibitions, and the interaction of the complex of peptide–enzyme is commonly evaluated using specific in vitro assays and molecular docking analysis.

Transport, Stability, and In Vivo Hypoglycemic Effect of a Broccoli-Derived DPP-IV Inhibitory Peptide VPLVM

Diabetes is a major metabolic disease that requires long-term pharmacotherapy. Bioactive peptides have unique advantages such as higher potency, selectivity, and safety over small molecules and have achieved great success in the treatment of diabetes. We previously isolated a dipeptidyl peptidase-IV (DPP-IV) inhibitory peptide VPLVM with IC₅₀ = 99.68 μM from the protein hydrolysates of broccoli stems and leaves. Here, we evaluated the interaction with DPP-IV, transport, stability, and in vivo hypoglycemic effects of VPLVM. VPLVM interacted closely and steadily with DPP-IV at S1 and S2 pockets. VPLVM had a good gastrointestinal enzyme resistance and was transported through the Caco-2 cell monolayer via paracellular diffusion and by the PepT1 with a P_app of 6.96 × 10^-7 cm/s. VPLVM has a t_1/2 of 12.56 ± 0.41 min in vitro plasma stability. In the oral glucose tolerance test, VPLVM showed an excellent hypoglycemic effect at 30 min after administration. VPLVM has potential as a candidate for the treatment of hyperglycemia.

Characteristics of Food Protein-Derived Antidiabetic Bioactive Peptides: A Literature Update

Diabetes, a glucose metabolic disorder, is considered one of the biggest challenges associated with a complex complication of health crises in the modern lifestyle. Inhibition or reduction of the dipeptidyl peptidase IV (DPP-IV), alpha-glucosidase, and protein-tyrosine phosphatase 1B (PTP-1B) enzyme activities or expressions are notably considered as the promising therapeutic strategies for the management of type 2 diabetes (T2D). Various food protein-derived antidiabetic bioactive peptides have been isolated and verified. This review provides an overview of the DPP-IV, PTP-1B, and α-glucosidase inhibitors, and updates on the methods for the discovery of DPP-IV inhibitory peptides released from food-protein hydrolysate. The finding of novel bioactive peptides involves studies about the strategy of separation fractionation, the identification of peptide sequences, and the evaluation of peptide characteristics in vitro, in silico, in situ, and in vivo. The potential of bioactive peptides suggests useful applications in the prevention and management of diabetes. Furthermore, evidence of clinical studies is necessary for the validation of these peptides’ efficiencies before commercial applications.

Identification of dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from vegetable protein sources

Vegetable proteins are appearing as a sustainable source for human consumption. Food-derived peptides are an important field of research in terms of bioactive molecules. In this study, seven vegetable proteins were enzymatically hydrolysed following an optimised treatment (sequential hydrolysis with subtilisin-trypsin-flavourzyme) to obtain dipeptidyl peptidase IV (DPP-IV) inhibitory peptides. Hydrolysates were fractionated by size exclusion chromatography and, from the most bioactive fractions (corresponding to Glycine max, Chenopodium quinoa and Lupinus albus proteins); peptides responsible for this bioactivity were identified by mass spectrometry. Peptides with adequate molecular features and based on in silico analysis were proposed as DPP-IV inhibitors from soy (EPAAV) lupine (NPLL), and quinoa (APFTVV). These vegetable protein sources are adequate to obtain protein hydrolysates for functional food.

An in vitro study on the transport and phase II metabolism of the mycotoxin alternariol in combination with the structurally related gut microbial metabolite urolithin C

Alternariol is a mycotoxin produced by Alternaria spp. relevant to the food safety area due to its abundance in certain foods. The shortage of data on its toxicology, also as a part of chemical mixtures, prevents setting regulation to limit its abundance in food. To extend knowledge on the possible mechanisms underpinning alternariol toxicology in chemical mixtures, this work assessed the effects of urolithin C, a structurally related gut ellagitannin-derived metabolite, on its absorption and phase II metabolism in a monolayer of Caco-2 cells. A computational study was also used to provide a mechanistic explanation for the results obtained. Urolithin C influenced transport and phase II metabolism of alternariol with a late reduction of transport to the basolateral compartment. Moreover, it caused an early effect in terms of accumulation of alternariol glucuronides in the basolateral compartment, followed by a late reduction of glucuronides in both compartments. Concerning alternariol sulfates, the data collected pointed to a possible competition of urolithin C for the sulfotransferases resulting in a reduced production of alternariol sulfates. Our results provide a compelling line-of-evidence pointing to the need to systematically tackle the evaluation of mycotoxin toxicity in the context of chemical mixture.

Assessment of the Multifunctional Behavior of Lupin Peptide P7 and Its Metabolite Using an Integrated Strategy

LTFPGSAED (P7) is a multifunctional hypocholesterolemic and hypoglycemic lupin peptide. While assessing its angiotensin-converting enzyme (ACE) inhibitory activity, it was more effective in intestinal Caco-2 cells (IC₅₀ of 13.7 μM) than in renal HK-2 cells (IC₅₀ of 79.6 μM). This discrepancy was explained by the metabolic transformation mediated by intestinal peptidases, which produced two main detected peptides, TFPGSAED and LTFPG. Indeed LTFPG, dynamically generated by intestinal dipeptidyl peptidase IV as well as its parent peptide P7 were linearly absorbed by mature Caco-2 cells. An in silico study demonstrated that the metabolite was a better ligand of the ACE enzyme than P7. These results are in agreement with an in vivo study, previously performed by Aluko et al., which has shown that LTFPG is an effective hypotensive peptide. Our work highlights the dynamic nature of bioactive food peptides that may be modulated by the metabolic activity of intestinal cells.

Exploration of dipeptidyl-peptidase IV (DPP IV) inhibitors in a low-molecular mass extract of the earthworm Eisenia fetida and identification of the inhibitors as amino acids like methionine, leucine, histidine, and isoleucine

We have reported previously that the water extract of the earthworm Eisenia fetida has inhibitory effect on human dipeptidyl-peptidase IV (DPP IV) in vitro. Here we studied to identify DPP IV inhibitors in a low-molecular mass extract (designated U3EE) under 3 kDa prepared from the water extract. U3EE showed 50 % inhibition (IC₅₀) at the concentration of 5.3 ± 0.3 mg/mL. An inhibitory active fraction obtained by solid-phase extraction of U3EE was separated into three parts by reversed-phase HPLC. These parts were shown by GC/MS to be composed of ten (Ala, Gly, Thr, Ser, Asn, Asp, Lys, His, Orn, and cystine), two (Leu and Ile), and one (Met) amino acids, respectively. Among them, Met, Leu, and His showed strong inhibition with IC₅₀ values of 3.4 ± 0.3, 6.1 ± 0.3 and 14.7 ± 1.2 mM, respectively; Ala, Lys, Orn, and Ile showed rather weaker inhibition than those, while the others showed no inhibition. Met, Leu, and Ile were competitive inhibitors and His was a mixed-type one. DPP IV inhibition by U3EE might be due to additive and/or synergistic effects of the inhibitory amino acids, suggesting that it could be useful as pharmaceutical and supplement for diabetes prevention.

"Bottom-Up" Strategy for the Identification of Novel Soybean Peptides with Angiotensin-Converting Enzyme Inhibitory Activity

IAVPTGVA (Soy1) and LPYP are two soybean peptides, which display a multifunctional behavior, showing in vitro hypocholesterolemic and hypoglycemic activities. A preliminary screening of their structures using BIOPEP suggested that they might be potential angiotensin-converting enzyme (ACE) inhibitors. Therefore, a bottom-up-aided approach was developed in order to clarify the in vitro hypotensive activity. Soy1 and LPYP dropped the intestinal and renal ACE enzyme activity with IC50 values equal to 14.7 ± 0.28 and 5.0 ± 0.28 μM (Caco-2 cells), and 6.0 ± 0.35 and 6.8 ± 0.20 μM (HK-2 cells), respectively. In parallel, a molecular modeling study suggested their capability to act as competitive inhibitors of this enzyme. Finally, in order to increase both their stability and hypotensive properties, a suitable strategy for the harmless control of their release from a nanomaterial was developed through their encapsulation into the RADA16-assembling peptide.

Identification and characterisation of peptides from a boarfish (Capros aper) protein hydrolysate displaying in vitro dipeptidyl peptidase-IV (DPP-IV) inhibitory and insulinotropic activity

Twenty-two novel dipeptidyl peptidase-IV (DPP-IV) inhibitory peptides (with IC₅₀ values <200 µM) and fifteen novel insulinotropic peptides were identified in a boarfish protein hydrolysate generated at semi-pilot scale using Alcalase 2.4L and Flavourzyme 500L. This was achieved by bioassay-driven semi-preparative reverse phase-high performance liquid chromatography fractionation, liquid chromatography-mass spectrometry and confirmatory studies with synthetic peptides. The most potent DPP-IV inhibitory peptide (IPVDM) had a DPP-IV half maximal inhibitory concentration (IC₅₀) value of 21.72 ± 1.08 µM in a conventional in vitro and 44.26 ± 0.65 µM in an in situ cell-based (Caco-2) DPP-IV inhibition assay. Furthermore, this peptide stimulated potent insulin secretory activity (1.6-fold increase compared to control) from pancreatic BRIN-BD11 cells grown in culture. The tripeptide IPV exhibited potent DPP-IV inhibitory activity (IC₅₀: 5.61 ± 0.20 µM) comparable to that reported for the known DPP-IV inhibitor IPI (IC₅₀: 3.20 µM). Boarfish proteins contain peptide sequences with potential to play a role in glycaemic management in vivo.

Structure-activity relationships study on biological activity of peptides as dipeptidyl peptidase IV inhibitors by chemometric modeling

The aim of this study is to identify the potential descriptors affecting the inhibitory activity of the peptides inhibiting dipeptidyl peptidase IV (DPP-IV). This study provides important information for assessing the biological activity of the new peptide sequences of food origin or making structural modifications to the current inhibitors to improve their performance. For this purpose, the chemometric method describing the relationship between the structure of food peptides and their biological activity (structure-activity relationship [SAR]) was used to theoretically predict the potential of bioactivity of peptides. Data on the physicochemical properties of amino acids in the dipeptides acting as inhibitors of DPP-IV were collected and analyzed for using these properties as descriptors in further analysis. A total of 252 dipeptide sequences with confirmed DPP-IV inhibitory activity available in the BIOPEP-UWM database were included in the analysis, and 16 descriptors defining individual amino acids (such as molecular weight, polarity, hydropathicity, bulkiness, buried residue, and acceptable and normalized frequency of alpha-helix and beta-sheet) were identified. Based on this information, a data matrix was constructed and used in the chemometric analysis (principal component analysis and multiple linear regression). From the SAR model created, a multiple regression equation was derived to predict the biological activity of the dipeptide DPP-IV inhibitors.

In Vitro Metabolic Stability of a Casein-Derived Dipeptidyl Peptidase-IV (DPP-IV) Inhibitory Peptide VPYPQ and Its Controlled Release from Casein by Enzymatic Hydrolysis

The aim of this study was to investigate the dipeptidyl peptidase-IV (DPP-IV) inhibition and metabolic stability of a casein-derived peptide Val-Pro-Tyr-Pro-Gln (VPYPQ) and its fragments as well as their release from casein following hydrolysis. Results showed that VPYPQ was the most potent DPP-IV inhibitory peptide among them with an IC₅₀ value of 41.45 μM. This might be due to its two internal Pro residues at positions 2 and 4. Moreover, VPYPQ was resistant to hydrolysis by gastrointestinal enzymes and was relatively more stable to hydrolysis by DPP-IV and peptidases in plasma compared with its fragments. Additionally, oral administration of VPYPQ at a dose of 90 μmol/kg body weight could reduce the postprandial blood glucose levels in mice. More importantly, VPYPQ could be released efficiently from casein following hydrolysis by a combination of papain and in vitro digestion, reaching up to 3211.15 μg/g. Therefore, VPYPQ was a promising casein-derived DPP-IV inhibitor.

FeptideDB: A web application for new bioactive peptides from food protein

BACKGROUND

Bioactive peptides derived from food are important sources for alternative medicine and possess therapeutic activity. Several biochemical methods have been achieved to isolate bioactive peptides from food, which are tedious and time consuming. In silico methods are an alternative process to reduce cost and time with respect to bioactive peptide production. In this paper, FeptideDB was used to collect bioactive peptide (BP) data from both published research articles and available bioactive peptide databases. FeptideDB was developed to assist in forecasting bioactive peptides from food by combining peptide cleavage tools and database matching. Furthermore, this application was able to predict the potential of cleaved peptides from 'enzyme digestion module' to identify new ACE (angiotensin converting enzyme) inhibitors using an automatic molecular docking approach.

RESULTS

The FeptideDB web application contains tools for generating all possible peptides cleaved from input protein by various available enzymes. This database was also used for analysis and visualization to assist in bioactive peptide discovery. One module of FeptideDB has the ability to create 3-dimensional peptide structures to further predict inhibitors for the target protein, ACE (angiotensin converting enzyme).

CONCLUSIONS

FeptideDB is freely available to researchers who are interested in exploring bioactive peptides. The FeptideDB interface is easy to use, allowing users to rapidly retrieve data based on desired search criteria. FeptideDB is freely available at http://www4g.biotec.or.th/FeptideDB/. Ultimately, FeptideDB is a computational aid for assessing peptide bioactivities.

Discovery of Food-Derived Dipeptidyl Peptidase IV Inhibitory Peptides: A Review

Diabetes is a chronic metabolic disorder which leads to high blood sugar levels over a prolonged period. Type 2 diabetes mellitus (T2DM) is the most common form of diabetes and results from the body's ineffective use of insulin. Over ten dipeptidyl peptidase IV (DPP-IV) inhibitory drugs have been developed and marketed around the world in the past decade. However, owing to the reported adverse effects of the synthetic DPP-IV inhibitors, attempts have been made to find DPP-IV inhibitors from natural sources. Food-derived components, such as protein hydrolysates (peptides), have been suggested as potential DPP-IV inhibitors which can help manage blood glucose levels. This review focuses on the methods of discovery of food-derived DPP-IV inhibitory peptides, including fractionation and purification approaches, in silico analysis methods, in vivo studies, and the bioavailability of these food-derived peptides. Moreover, food-derived DPP-IV inhibitory peptides discovered during this decade are listed and distributed in a 3D scatter plot graph based on their IC50, molecular weight, and grand average of hydropathicity values, which can help us to understand the relationship between the features of the peptides and their activities.

On the Mechanism of Action of Anti-Inflammatory Activity of Hypericin: An In Silico Study Pointing to the Relevance of Janus Kinases Inhibition

St. John's Wort (Hypericum perforatum L.) flowers are commonly used in ethnomedical preparations with promising outcomes to treat inflammation both per os and by topical application. However, the underlying molecular mechanisms need to be described toward a rational, evidence-based, and reproducible use. For this purpose, the aptitude of the prominent Hypericum metabolite hypericin was assessed, along with that of its main congeners, to behave as an inhibitor of janus kinase 1, a relevant enzyme in inflammatory response. It was used a molecular modeling approach relying on docking simulations, pharmacophoric modeling, and molecular dynamics to estimate the capability of molecules to interact and persist within the enzyme pocket. Our results highlighted the capability of hypericin, and some of its analogues and metabolites, to behave as ATP-competitive inhibitor providing: (i) a likely mechanistic elucidation of anti-inflammatory activity of H. perforatum extracts containing hypericin and related compounds; and (ii) a rational-based prioritization of H. perforatum components to further characterize their actual effectiveness as anti-inflammatory agents.

Multiple antidiabetic effects of three α-glucosidase inhibitory peptides, PFP, YPL and YPG: Dipeptidyl peptidase-IV inhibition, suppression of lipid accumulation in differentiated 3T3-L1 adipocytes and scavenging activity on methylglyoxal

Antidiabetic agents with multiple targets have the greatest pharmaceutical potential. In this study, three α-glucosidase inhibitory peptides, PFP, YPL and YPG, were investigated for additional antidiabetic targets viz.; dipeptidyl peptidase-IV inhibition (DPP-IV), lipid accumulation and the differentiation of 3T3-L1 adipocytes, and scavenging of methylglyoxal (MGO), reactive oxygen species (ROS) and nitric oxide (NO). The peptides were subjected to molecular docking on human DPP-IV where the binding free energies were PFP < YPG < YPL < diprotin A while hydrogen bond interactions were critical in the binding of YPL and YPG. Moreover, YPG demonstrated significantly higher (p < 0.05) in vitro DPP-IV inhibition than PFP and YPL. Kinetic analysis revealed that all three peptides are uncompetitive inhibitors of DPP-IV while YPG had the lowest inhibition binding constant. PFP and YPG prevented lipid accumulation in 3T3-L1 differentiated adipocytes but may be due to cytotoxicity for PFP. The peptides scavenged MGO, ROS and NO but only the ROS and NO scavenging activities of YPG were comparable to glutathione. In conclusion, PFP, YPL and YPG exhibited DPP-IV inhibitory activity, reduced adipocyte differentiation and lipid accumulation as well as scavenged MGO, ROS and NO. However, YPG had the best potential as a possible multifunctional antidiabetic agent.

Bioactive Peptides from Germinated Soybean with Anti-Diabetic Potential by Inhibition of Dipeptidyl Peptidase-IV, α-Amylase, and α-Glucosidase Enzymes

Functional foods containing peptides offer the possibility to modulate the absorption of sugars and insulin levels to prevent diabetes. This study investigates the potential of germinated soybean peptides to modulate postprandial glycaemic response through inhibition of dipeptidyl peptidase IV (DPP-IV), salivary α-amylase, and intestinal α-glucosidases. A protein isolate from soybean sprouts was digested by pepsin and pancreatin. Protein digest and peptide fractions obtained by ultrafiltration (<5, 5⁻10 and >10 kDa) and subsequent semipreparative reverse phase liquid chromatography (F1, F2, F3, and F4) were screened for in vitro inhibition of DPP-IV, α-amylase, maltase, and sucrase activities. Protein digest inhibited DPP-IV (IC50 = 1.49 mg/mL), α-amylase (IC50 = 1.70 mg/mL), maltase, and sucrase activities of α-glucosidases (IC50 = 3.73 and 2.90 mg/mL, respectively). Peptides of 5⁻10 and >10 kDa were more effective at inhibiting DPP-IV (IC50 = 0.91 and 1.18 mg/mL, respectively), while peptides of 5⁻10 and <5 kDa showed a higher potency to inhibit α-amylase and α-glucosidases. Peptides in F1, F2, and F3 were mainly fragments from β-conglycinin, glycinin, and P34 thiol protease. The analysis of structural features of peptides in F1⁻F3 allowed the tentative identification of potential antidiabetic peptides. Germinated soybean protein showed a promising potential to be used as a nutraceutical or functional ingredient for diabetes prevention.