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.

Transplanting network pharmacology technology into food science research: A comprehensive review on uncovering food-sourced functional factors and their health benefits

Network pharmacology is an emerging interdisciplinary research method. The application of network pharmacology to reveal the nutritional effects and mechanisms of active ingredients in food is of great significance in promoting the development of functional food, facilitating personalized nutrition, and exploring the mechanisms of food health effects. This article systematically reviews the application of network pharmacology in the field of food science using a literature review method. The application progress of network pharmacology in food science is discussed, and the mechanisms of functional factors in food on the basis of network pharmacology are explored. Additionally, the limitations and challenges of network pharmacology are discussed, and future directions and application prospects are proposed. Network pharmacology serves as an important tool to reveal the mechanisms of action and health benefits of functional factors in food. It helps to conduct in-depth research on the biological activities of individual ingredients, composite foods, and compounds in food, and assessment of the potential health effects of food components. Moreover, it can help to control and enhance their functionality through relevant information during the production and processing of samples to guarantee food safety. The application of network pharmacology in exploring the mechanisms of functional factors in food is further analyzed and summarized. Combining machine learning, artificial intelligence, clinical experiments, and in vitro validation, the achievement transformation of functional factor in food driven by network pharmacology is of great significance for the future development of network pharmacology research.

Multiple roles of food-derived bioactive peptides in the management of T2DM and commercial solutions: A review

Type 2 diabetes mellitus (T2DM), a disease that threatens public health worldwide and can cause a series of irreversible complications, has been a major concern. Although the treatment based on hypoglycemic drugs is effective, its side effects should not be ignored, which has led to an urgent need for developing new hypoglycemic drugs. Bioactive peptides with antidiabetic effects obtained from food proteins have become a research hotspot as they are safer and with higher specificity than traditional hypoglycemic drugs. Here, we reviewed antidiabetic peptides that have the ability to inhibit key enzymes (α-glucosidase, α-amylase, and DPP-IV) in T2DM, the hypoglycemic mechanisms and structure-activity relationships were summarized, some antidiabetic peptides that improve insulin resistance and reverse gut microbiota and their metabolites were overviewed, the bitterness of antidiabetic peptides was predicted in silico, proposed solutions to the current challenges encountered in the development of antidiabetic peptide drugs, and provided an outlook on the future focus of commercial production. It provides a reference for the application of food-derived antidiabetic peptides.

The screening of α-glucosidase inhibitory peptides from β-conglycinin and hypoglycemic mechanism in HepG2 cells and zebrafish larvae

Inhibition of carbohydrate digestive enzymes is a key focus across diverse fields, given the prominence of α-glucosidase inhibitors as preferred oral hypoglycaemic drugs for diabetes treatment. β-conglycinin is the most abundant functional protein in soy; however, it is unclear whether the peptides produced after its gastrointestinal digestion exhibit α-glucosidase inhibitory properties. Therefore, we examined the α-glucosidase inhibitory potential of soy peptides. Specifically, β-conglycinin was subjected to simulated gastrointestinal digestion by enzymatically cleaving it into 95 peptides with gastric, pancreatic and chymotrypsin enzymes. Eight soybean peptides were selected based on their predicted activity; absorption, distribution, metabolism, excretion and toxicity score; and molecular docking analysis. The results indicated that hydrogen bonding and electrostatic interactions play important roles in inhibiting α-glucosidase, with the tripeptide SGR exhibiting the greatest inhibitory effect (IC50 = 10.57 μg/mL). In vitro studies revealed that SGR markedly improved glucose metabolism disorders in insulin-resistant HepG2 cells without affecting cell viability. Animal experiments revealed that SGR significantly improved blood glucose and decreased maltase activity in type 2 diabetic zebrafish larvae, but it did not result in the death of zebrafish larvae. Transcriptomic analysis revealed that SGR exerts its anti-diabetic and hypoglycaemic effects by attenuating the expression of several genes, including Slc2a1, Hsp70, Cpt2, Serpinf1, Sfrp2 and Ggt1a. These results suggest that SGR is a potential food-borne bioactive peptide for managing diabetes.

Novel strategy to the characterization and enhance the glycemic control properties of walnut-derived peptides via zinc chelation

This study aimed to utilize zinc coordination to promote the hypoglycemic and antioxidant properties of walnut-derived peptides, such as walnut protein hydrolysate (WPH) and Leu-Pro-Leu-Leu-Arg (LPLLR, LP5), of which LP5 was previously identified from WPH. The optimal conditions for the chelation were a peptide-to-zinc ratio of 6:1, pH of 9, duration of 50 min, and temperature of 50 °C. The WPH-Zn and LP5-Zn complexes increased the α-glucosidase inhibition, α-amylase inhibition, and antioxidant activity more than WPH and LP5 (p < 0.05). In particular, the antioxidant activity of WPH-Zn was superior to LP5-Zn. This is attributable to the WPH containing more aromatic amino acids, carboxylate groups and the imidazole groups, which implies its capacity to potentially coordinate with Zn2+ to form the WPH-Zn complex. Moreover, particle size, zeta potential, and scanning electron microscope indicated that the chelation of Zn2+ by peptides led to intramolecular and intermolecular folding and aggregation.

Identification, structural characterization, and molecular dynamic simulation of ACE inhibitory peptides in whey hydrolysates from Chinese Rushan cheese by-product

To realize the high-value utilization of Rushan cheese by-product, Rushan cheese whey was used as a raw material to prepare angiotensin-Ⅰ-converting enzyme inhibitory peptides (ACEIPs). After enzymatic hydrolysisn and ultrafiltration, the sequences of peptides were identified by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Two novel ACE inhibitory peptides Phe-Asp-Arg-Pro-Phe-Leu (FDRPFL) and Lys-Trp-Glu-Lys-Pro-Phe (KWEKPF) were identified. Additionally, both of the peptides exhibited good water-solubility and no toxicity according to in-silico prediction. Fourier transform infrared spectroscopy results show that both FDRPFL and KWEKPF were enriched in β-turn and β-sheet structures. Lineweaver-Burk plots revealed that FDRPFL and KWEKPF exhibited non-competitive and mixed inhibition patterns, respectively. Molecular docking and MD simulation showed that hydrogen bonds and ionic bonds forces allowed FDRPFL and KWEKPF to form stable and compact complexes with ACE. In conclusion, enzymatic hydrolysis of Rushan cheese by-products yields bioactive peptides, increases the added value of whey and reduces environmental pollution.

Exploration of hypoglycemic peptides from porcine collagen based on network pharmacology and molecular docking

In recent years, the extraction of hypoglycemic peptides from food proteins has gained increasing attention. Neuropeptides, hormone peptides, antimicrobial peptides, immune peptides, antioxidant peptides, hypoglycemic peptides and antihypertensive peptides have become research hotspots. In this study, bioinformatic methods were used to screen and predict the properties of pig collagen-derived hypoglycemic peptides, and their inhibitory effects on α-glucosidase were determined in vitro. Two peptides (RL and NWYR) were found to exhibit good water solubility, adequate ADMET (absorption, distribution, metabolism, elimination, and toxicity) properties, potentially high biological activity, and non-toxic. After synthesizing these peptides, NWYR showed the best inhibitory effect on α-glucosidase with IC50 = 0.200±0.040 mg/mL, and it can regulate a variety of biological processes, play a variety of molecular functions in different cellular components, and play a hypoglycemic role by participating in diabetic cardiomyopathy and IL-17 signaling pathway. Molecular docking results showed that NWYR had the best binding effect with the core target DPP4 (4n8d), with binding energy of -8.8 kcal/mol. NWYR mainly bonded with the target protein through hydrogen bonding, and bound with various amino acid residues such as Asp-729, Gln-731, Leu-765, etc., thus affecting the role of the target in each pathway. It is the best core target for adjuvant treatment of T2DM. In short, NWYR has the potential to reduce type 2 diabetes, providing a basis for further research or food applications as well as improved utilization of pig by-products. However, in subsequent studies, it is necessary to further verify the hypoglycemic ability of porcine collagen active peptide (NWYR), and explore the hypoglycemic mechanism of NWYR from multiple perspectives such as key target genes, protein expression levels and differences in metabolites in animal models of hyperglycemia, which will provide further theoretical support for its improvement in the treatment of T2DM.

Exploring the Blood Glucose-Lowering Potential of the Umami Peptides LADW and EEAEGT Derived from Tuna Skeletal Myosin: Perspectives from α-Glucosidase Inhibition and Starch Interaction

This study aimed to explore the potential of umami peptides for lowering blood glucose. Molecular docking results showed that the peptides LADW and EEAEGT bound to the active amino acid residues of α-glucosidase via hydrogen bonds and Van der Waals forces, a finding supported by an independent gradient model (IGM). Molecular dynamics (MD) simulations demonstrated that the peptides LADW and EEAEGT can decelerate the outward expansion of α-glucosidase and reduce amino acid fluctuations at the active site. In vitro findings indicated that the peptides LADW and EEAEGT showed potent inhibitory activity against α-glucosidase, with IC50 values of 4.40 ± 0.04 and 6.46 ± 0.22 mM, respectively. Furthermore, MD simulation and morphological observation results also revealed that LADW and EEAEGT alter starch structure and form weak interactions with starch through intermolecular hydrogen bonding, leading to the inhibition of starch hydrolysis. Peptides inhibit the ability of starch to produce reducing sugars after simulated gastrointestinal digestion, providing additional evidence of the inhibition of starch hydrolysis by the added peptides. Taken together, these findings suggest that consuming the umami peptides LADW and EEAEGT may alleviate postprandial blood glucose elevations via inhibiting α-glucosidase and starch hydrolysis.

Hypoglycemic Effect of Edible Fungi Polysaccharides Depends on Their Metabolites from the Fermentation of Human Fecal Microbiota

Edible fungi polysaccharides are widely sourced and have various physiological activities, including hypoglycemic. Current studies mainly focus on the hypoglycemic activity of polysaccharides themselves, while the strength of the hypoglycemic activity of edible fungi polysaccharides from different sources remained elusive. This study compared the hypoglycemic activity of different edible fungi polysaccharides after in vitro fermentation by fecal bacteria, combined with non-targeted metabolomics and 16S rDNA analysis, to screen out potential key metabolites related to the hypoglycemic activity. The results show that the fermentation supernatants of all four edible fungi polysaccharides significantly increased the glucose consumption and glycogen synthesis of IR-HepG2, also up-regulated the level of hexokinase and down-regulated the level of phosphoenolpyruvate carboxylase. All fermentation supernatants could alleviate the insulin resistance of IR-HepG2 cells by regulating the expression levels of genes related to the IRS-1/PI3K/Akt signaling pathway. Gingerglycolipid A, sphinganine 1-phosphate, matricin, tricarballylic acid, N-carbamoylputrescine, nomega-acetylhistamine, tyramine, and benzamide could be considered as potential key metabolites to evaluate the hypoglycemic effects. Their levels were strongly positively correlated with the abundance of Candidatus_Stoquefichu, Faecalibacterium, Coprococcus, Bacteroides, Eubacterium_ventriosum_group, Anaerostipes, Parabacteroides, and Agathobacter. These metabolites and microorganisms are closely related to the hypoglycemic activity of edible fungi polysaccharides.

Virtual Screening Technology for Two Novel Peptides in Soybean as Inhibitors of α-Amylase and α-Glucosidase

Soybean peptides (SPs) have bioactivities of enzyme inhibition that are beneficial to human health, but their mechanism is not clear. This study aimed to identify peptide fragments in SPs that simultaneously inhibit α-amylase and α-glucosidase and to explore their enzyme inhibition mechanism. Firstly, the inhibitory activity of SPs against the enzymes was determined. And two octapeptides, LDQTPRVF and SRNPIYSN, were identified for the first time by using HPLC-QTOF-MS/MS and virtual screening. Molecular simulation results showed that hydrogen bonds and π-π bonds were the key factors, and the N-terminal (Leu and Ser) and C-terminal (Phe) of peptide were important inhibiting sites. Both octapeptides were synthesized, and their IC50 values were 3.08 and 5.58 mmol/L for α-amylase, and 2.52 and 4.57 mmol/L for α-glucosidase, respectively. This study provided evidence for SPs as a potential inhibitor of α-amylase and α-glucosidase in special dietary foods.

Molecular Targets and Mechanisms of Casein-Derived Tripeptides Ile-Pro-Pro and Val-Pro-Pro on Hepatic Glucose Metabolism

The objective of this study was to explore the molecular targets and mechanism of Ile-Pro-Pro (IPP) and Val-Pro-Pro (VPP) on regulating glucose metabolism in hepatic cells and their in vivo hypoglycemic activities in mice. Results showed that both IPP and VPP (600 μM) significantly enhanced the glucose consumption in HepG2 cells and primary hepatocytes (p < 0.05). They also regulated activities of glucose metabolizing enzymes and increased the protein expression of p-AKT and GLUT2 in HepG2 cells. IPP directly interacted with the insulin receptor (IR) to activate the insulin/AKT signaling pathway. The activity of VPP on glucose consumption was not attributed to IR binding, and 76 potential antidiabetic targets were predicted by similarity ensemble and shape similarity approaches. Among them, the AKT and MAPK signaling pathway, in which two hub genes AKT1 and MAPK4 existed, were evaluated to make major contributions to the activity of VPP on glucose consumption. Moreover, both IPP and VPP (300 μmol/kg) could significantly reduce the blood glucose levels in mice (p < 0.05), with blood glucose area under the curve dropping by approximately 19% ± 0.09 and 21% ± 0.11%, respectively. This study provides a new theoretical support for the development of IPP and VPP as functional foods to regulate glucose metabolic disorders.

Network pharmacology: a bright guiding light on the way to explore the personalized precise medication of traditional Chinese medicine

Network pharmacology can ascertain the therapeutic mechanism of drugs for treating diseases at the level of biological targets and pathways. The effective mechanism study of traditional Chinese medicine (TCM) characterized by multi-component, multi-targeted, and integrative efficacy, perfectly corresponds to the application of network pharmacology. Currently, network pharmacology has been widely utilized to clarify the mechanism of the physiological activity of TCM. In this review, we comprehensively summarize the application of network pharmacology in TCM to reveal its potential of verifying the phenotype and underlying causes of diseases, realizing the personalized and accurate application of TCM. We searched the literature using "TCM network pharmacology" and "network pharmacology" as keywords from Web of Science, PubMed, Google Scholar, as well as Chinese National Knowledge Infrastructure in the last decade. The origins, development, and application of network pharmacology are closely correlated with the study of TCM which has been applied in China for thousands of years. Network pharmacology and TCM have the same core idea and promote each other. A well-defined research strategy for network pharmacology has been utilized in several aspects of TCM research, including the elucidation of the biological basis of diseases and syndromes, the prediction of TCM targets, the screening of TCM active compounds, and the decipherment of mechanisms of TCM in treating diseases. However, several factors limit its application, such as the selection of databases and algorithms, the unstable quality of the research results, and the lack of standardization. This review aims to provide references and ideas for the research of TCM and to encourage the personalized and precise use of Chinese medicine.

Alpha-Glucosidase Inhibitory Peptides: Sources, Preparations, Identifications, and Action Mechanisms

With the change in people's lifestyle, diabetes has emerged as a chronic disease that poses a serious threat to human health, alongside tumor, cardiovascular, and cerebrovascular diseases. α-glucosidase inhibitors, which are oral drugs, have proven effective in preventing and managing this disease. Studies have suggested that bioactive peptides could serve as a potential source of α-glucosidase inhibitors. These peptides possess certain hypoglycemic activity and can effectively regulate postprandial blood glucose levels by inhibiting α-glucosidase activity, thus intervening and regulating diabetes. This paper provides a systematic summary of the sources, isolation, purification, bioavailability, and possible mechanisms of α-glucosidase inhibitory peptides. The sources of the α-glucosidase inhibitory peptides were introduced with emphasis on animals, plants, and microorganisms. This paper also points out the problems in the research process of α-glucosidase inhibitory peptide, with a view to providing certain theoretical support for the further study of this peptide.

Production of Food-Derived Bioactive Peptides with Potential Application in the Management of Diabetes and Obesity: A Review

The prevalence of diabetes mellitus and obesity is increasing worldwide. Bioactive peptides are naturally present in foods or in food-derived proteins. Recent research has shown that these bioactive peptides have an array of possible health benefits in the management of diabetes and obesity. First, this review will summarize the top-down and bottom-up production methods of the bioactive peptides from different protein sources. Second, the digestibility, bioavailability, and metabolic fate of the bioactive peptides are discussed. Last, the present review will discuss and explore the mechanisms by which these bioactive peptides help against obesity and diabetes based on in vitro and in vivo studies. Although several clinical studies have demonstrated that bioactive peptides are beneficial in alleviating diabetes and obesity, more double-blind randomized controlled trials are needed in the future. This review has provided novel insights into the potential of food-derived bioactive peptides as functional foods or nutraceuticals to manage obesity and diabetes.

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.

Amphibian Skin and Skin Secretion: An Exotic Source of Bioactive Peptides and Its Application

Amphibians have been consumed as an alternative protein source all around the world due to their delicacy. The skin of edible amphibians, particularly frogs and giant salamanders, always goes to waste without further utilization. However, these wastes can be utilized to extract protein and bioactive peptides (BPs). Various BPs have been extracted and reported for numerous biological activities such as antioxidant, antimicrobial, anticancer, antidiabetic, etc. The main BPs identified were brevinins, bombesins, dermaseptins, esculentins, magainin, temporins, tigerinins, and salamandrins. This review provides a comprehensive discussion on various BPs isolated and identified from different amphibian skins or skin secretion and their biological activities. The general nutritional composition and production statues of amphibians were described. Additionally, multiple constraints against the utilization of amphibian skin and secretions are reported. Finally, the prospective applications of BPs in food and biomedical industries are presented such as multifunctional food additives and/or supplements as well as drug delivery agents.

Antidiabetic effects of protein hydrolysates from Trachinotus ovatus and identification and screening of peptides with α-amylase and DPP-IV inhibitory activities

In the present study, the antidiabetic properties of Trachinotus ovatus protein hydrolysates (TOH) in streptozotocin-induced diabetic mice were investigated, and peptides with α-amylase (AAM) and dipeptidyl peptidase IV (DPP-IV) inhibitory activities were identified and screened. The results showed that TOH alleviated body weight loss, polyphagia, blood glucose elevation and insulin secretion decline in diabetic mice. After 4 weeks of TOH administration, random blood glucose (RBG) decreased significantly. The TOH groups showed a dose-dependent reduction in fasting blood glucose (FBG), especially in the high-dose TOH group, which reduced FBG by 58% versus the effect of metformin. Moreover, TOH exerted a remarkable protective effect on hepatorenal function, as evidenced by increased superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX) and decreased serum urea levels. Histopathological studies confirmed that TOH can significantly protect the kidney and pancreas from histological changes, which was of great benefit for ensuring the normal secretion of insulin and preventing the occurrence of complications such as diabetic nephropathy. Two fractions with higher inhibitory activity against AAM and DPP-IV, F4 and F6, were obtained from the ultrafiltration of TOH-2 (≤3 kDa). A total of 19 potentially active peptides from F4 and 3 potentially active peptides from F6 were screened by LC‒MS/MS combined with bioinformatic analysis. These peptides are small molecular peptides composed of 2-6 amino acids, rich in characteristic amino acids such as proline, arginine, phenylalanine and asparagine, and contain high proportions of peptides (68% for F4, 67% for F6) with hydrophobicity ≥50%. They offer potent antidiabetic potential and could potentially bind to the active sites in the internal cavities of the target enzymes AAM and DPP-IV. In summary, this study revealed for the first time the antidiabetic effects of protein hydrolysates of Trachinotus ovatus and their derived peptides, which are promising natural ingredients with the potential to be used for the treatment or prevention of diabetes.

Food proteins in the regulation of blood glucose control

Food proteins, depending on their origin, possess unique characteristics that regulate blood glucose via multiple physiological mechanisms, including the insulinotropic effects of amino acids, the activation of incretins, and slowing gastric emptying rate. The strategies aimed at curbing high blood glucose are important in preventing impaired blood glucose control, including insulin resistance, prediabetes and diabetes. The effect of proteins on blood glucose control can be achieved with high-protein foods short-term, and high-protein diets long-term using foods that are naturally high in protein, such as dairy, meat, soy and pulses, or by formulating high-protein functional food products using protein concentrates and isolates, or blended mixtures of proteins from different sources. Commercial sources of protein powders are represented by proteins and hydrolysates of caseins, whey proteins and their fractions, egg whites, soy, yellow pea and hemp which will be reviewed in this chapter. The effective doses of food protein that are capable of reducing postprandial glycemia start from 7 to 10g and higher per serving; however, the origin of protein, and macronutrient composition of a meal will determine the magnitude and duration of their effect on glycemia. The theoretical and methodological framework to evaluate the effect of foods, including food proteins, on postprandial glycemia for substantiation of health claims on food has been proposed in Canada and is discussed in the context of global efforts to harmonize the international food regulation and labeling.