NeuroPpred-SHE: An interpretable neuropeptides prediction model based on selected features from hand-crafted features and embeddings of T5 model

Neuropeptides are the most ubiquitous neurotransmitters in the immune system, regulating various biological processes. Neuropeptides play a significant role for the discovery of new drugs and targets for nervous system disorders. Traditional experimental methods for identifying neuropeptides are time-consuming and costly. Although several computational methods have been developed to predict the neuropeptides, the accuracy is still not satisfactory due to the representability of the extracted features. In this work, we propose an efficient and interpretable model, NeuroPpred-SHE, for predicting neuropeptides by selecting the optimal feature subset from both hand-crafted features and embeddings of a protein language model. Specially, we first employed a pre-trained T5 protein language model to extract embedding features and twelve other encoding methods to extract hand-crafted features from peptide sequences, respectively. Secondly, we fused both embedding features and hand-crafted features to enhance the feature representability. Thirdly, we utilized random forest (RF), Max-Relevance and Min-Redundancy (mRMR) and eXtreme Gradient Boosting (XGBoost) methods to select the optimal feature subset from the fused features. Finally, we employed five machine learning methods (GBDT, XGBoost, SVM, MLP, and LightGBM) to build the models. Our results show that the model based on GBDT achieves the best performance. Furthermore, our final model was compared with other state-of-the-art methods on an independent test set, the results indicate that our model achieves an AUROC of 97.8 % which is higher than all the other state-of-the-art predictors. Our model is available at: https://github.com/wenjean/NeuroPpred-SHE.

Exploring the Potential of Bioactive Peptides: From Natural Sources to Therapeutics

Bioactive peptides, specific protein fragments with positive health effects, are gaining traction in drug development for advantages like enhanced penetration, low toxicity, and rapid clearance. This comprehensive review navigates the intricate landscape of peptide science, covering discovery to functional characterization. Beginning with a peptidomic exploration of natural sources, the review emphasizes the search for novel peptides. Extraction approaches, including enzymatic hydrolysis, microbial fermentation, and specialized methods for disulfide-linked peptides, are extensively covered. Mass spectrometric analysis techniques for data acquisition and identification, such as liquid chromatography, capillary electrophoresis, untargeted peptide analysis, and bioinformatics, are thoroughly outlined. The exploration of peptide bioactivity incorporates various methodologies, from in vitro assays to in silico techniques, including advanced approaches like phage display and cell-based assays. The review also discusses the structure-activity relationship in the context of antimicrobial peptides (AMPs), ACE-inhibitory peptides (ACEs), and antioxidative peptides (AOPs). Concluding with key findings and future research directions, this interdisciplinary review serves as a comprehensive reference, offering a holistic understanding of peptides and their potential therapeutic applications.

A review on bioactive peptides derived from meat and by-products: Extraction methods, biological activities, applications and limitations

Meat and its by-products offer a rich source of bioactive compounds which have potential applications in both the food and pharmaceutical industries. In this review, we present several extraction methods and report the identification and properties of bioactive peptides. We also examine the challenges and limitations associated with their use in food applications. Enzymatic hydrolysis and fermentation using starts cultures are common methods for generating bioactive peptides from meat proteins. Additionally, natural gastrointestinal digestion can also produce bioactive peptides. However, emerging technologies like high hydrostatic pressure, subcritical extraction and pulsed electric fields can improve hydrolysis and increase the yield of bioactive peptides. Online bioinformatics applications have emerged as an established method for identifying potentially bioactive peptides. These tools reduce the cost and time required for traditional methods of research. Finally, incorporating bioactive peptides into diets for specific purposes such as supporting vulnerable populations like children and the elderly ensures safety and efficacy.

Dietary-Nutraceutical Properties of Oat Protein and Peptides

Oats are considered the healthiest grain due to their high content of phytochemicals, dietary fibers, and protein. In recent years, oat protein and peptides have gained popularity as possible therapeutic or nutraceutical candidates. Generally, oat peptides with bioactive properties can be obtained by the enzymatic hydrolysis of proteins and are known to have a variety of regulatory functions. This review article focused on the nutraceutical worth of oat proteins and peptides and also describes the application of oat protein as a functional ingredient. Outcomes of this study indicated that oat protein and peptides present various therapeutical properties, including antidiabetic, antioxidant, antihypoxic, antihypertensive, antithrombotic, antifatigue, immunomodulatory, and hypocholestrolaemic. However, most of the conducted studies are limited to in vitro conditions and less data is available on assessing the effectiveness of the oat peptides in vivo. Future efforts should be directed at performing systematic animal studies; in addition, clinical trials also need to be conducted to fully support the development of functional food products, nutraceutical, and therapeutical applications.

Glucoregulatory and Anti-Inflammatory Activities of Peptide Fractions Separated by Electrodialysis with Ultrafiltration Membranes from Salmon Protein Hydrolysate and Identification of Four Novel Glucoregulatory Peptides

Natural bioactive peptides are suitable candidates for preventing the development of Type 2 diabetes (T2D), by reducing the various risk factors. The aim of this study was to concentrate glucoregulatory and anti-inflammatory peptides, from salmon by-products, by electrodialysis with ultrafiltration membrane (EDUF), and to identify peptides responsible for these bioactivities. Two EDUF configurations (1 and 2) were used to concentrate anionic and cationic peptides, respectively. After EDUF separation, two fractions demonstrated interesting properties: the initial fraction of the EDUF configuration 1 and the final fraction of the EDUF configuration 2 both showed biological activities to (1) increase glucose uptake in L6 muscle cells in insulin condition at 1 ng/mL (by 12% and 21%, respectively), (2) decrease hepatic glucose production in hepatic cells at 1 ng/mL in basal (17% and 16%, respectively), and insulin (25% and 34%, respectively) conditions, and (3) decrease LPS-induced inflammation in macrophages at 1 g/mL (45% and 30%, respectively). More impressive, the initial fraction of the EDUF configuration 1 (45% reduction) showed the same effect as the phenformin at 10 μM (40%), a drug used to treat T2D. Thirteen peptides were identified, chemically synthesized, and tested in-vitro for these three bioactivities. Thus, four new bioactive peptides were identified: IPVE increased glucose uptake by muscle cells, IVDI and IEGTL decreased hepatic glucose production (HGP) of insulin, whereas VAPEEHPTL decreased HGP under both basal condition and in the presence of insulin. To the best of our knowledge, this is the first time that (1) bioactive peptide fractions generated after separation by EDUF were demonstrated to be bioactive on three different criteria; all involved in the T2D, and (2) potential sequences involved in the improvement of glucose uptake and/or in the regulation of HGP were identified from a salmon protein hydrolysate.

Whey Proteins and Its Derivatives: Bioactivity, Functionality, and Current Applications

With the increased consumer demand for nutritional foods, it is important to develop value-added products, which will not only catch the attention of a wider consumer group but also provide greater benefits in terms of enhanced nutrition and functionality. Milk whey proteins are one of the most valued constituents due to their nutritional and techno-functional attributes. Whey proteins are rich in bioactive peptides, possessing bioactive properties such as being antioxidant and antihypertensive as well as having antimicrobial activities, which, when ingested, confers several health benefits. These peptides have the potential to be used as an active food ingredient in the production of functional foods. In addition to their bioactivities, whey proteins are known to possess enhanced functional attributes that allow them to be utilized in broad applications, such as an encapsulating agent or carrier materials to entrap bioactive compounds, emulsification, and in edible and active packaging. Hence, over the recent years, several whey protein-based ingredients have been developed and utilized in making formulations for a wide range of foods to harness their beneficial properties. This review highlights the bioactive properties, functional characteristics, associated processing limitations, and applications of different whey protein fractions and derivatives in the field of food formulations, encapsulation, and packaging.

Identification and Detection of Bioactive Peptides in Milk and Dairy Products: Remarks about Agro-Foods

Food-based components represent major sources of functional bioactive compounds. Milk is a rich source of multiple bioactive peptides that not only help to fulfill consumers 'nutritional requirements but also play a significant role in preventing several health disorders. Understanding the chemical composition of milk and its products is critical for producing consistent and high-quality dairy products and functional dairy ingredients. Over the last two decades, peptides have gained significant attention by scientific evidence for its beneficial health impacts besides their established nutrient value. Increasing awareness of essential milk proteins has facilitated the development of novel milk protein products that are progressively required for nutritional benefits. The need to better understand the beneficial effects of milk-protein derived peptides has, therefore, led to the development of analytical approaches for the isolation, separation and identification of bioactive peptides in complex dairy products. Continuous emphasis is on the biological function and nutritional characteristics of milk constituents using several powerful techniques, namely omics, model cell lines, gut microbiome analysis and imaging techniques. This review briefly describes the state-of-the-art approach of peptidomics and lipidomics profiling approaches for the identification and detection of milk-derived bioactive peptides while taking into account recent progress in their analysis and emphasizing the difficulty of analysis of these functional and endogenous peptides.

Structure-informed detection and quantification of peptides in food and biological fluids

Peptides with biological properties, that is, bioactive peptides, are a class of biomolecules whose health-promoting properties are increasingly being exploited in food and health products. However, research on targeted techniques for the detection and quantification of these peptides is still in its infancy. Such information is needed in order to enhance the biological and chemometric characterization of peptides and their subsequent application in the functional food and pharmaceutical industries. In this review, the role of classic techniques such as electrophoretic, chromatographic, and peptide mass spectrometry in the structure-informed detection and quantitation of bioactive peptides are discussed. Prospects for the use of aptamers in the characterization of bioactive peptides are also discussed. PRACTICAL APPLICATIONS: Although bioactive peptides have huge potential applications in the functional foods and health area, there are limited techniques in enhancing throughput detection, quantification, and characterization of these peptides. This review discusses state-of-the-art techniques relevant in complementing bioactive detection and profiling irrespective of the small number of amino acid units. Insights into challenges, possible remedies and prevailing areas requiring thorough research in the extant literature for food chemists and biotechnologists are also presented.

Fractionation and identification of novel antioxidant peptides from buffalo and bovine casein hydrolysates

Buffalo and bovine caseins were hydrolysed by alcalase and trypsin to produce novel antioxidant peptides. The casein hydrolysates were purified using ultrafiltration (UF) and further characterized by RP-HPLC. The fractions produced higher antioxidant activities were identified for their peptides using LC MS/MS. All UF-VI (MW<1kDa) fractions showed higher antioxidant activity. Hydrolysate produced by alcalase for buffalo casein (UF-VI with 54.84-fold purification) showed higher antioxidant activity than that obtained by trypsin. Trypsin hydrolysate contained high amount of hydrophobic amino acids while alcalase hydrolysate consisted mainly of Ser, Arg, Ala and Leu. The antioxidant peptides identified by LC MS/MS were RELEE, MEDNKQ and TVA, EQL in buffalo casein hydrolysates produced by trypsin and alcalase, respectively. Mechanism and reaction pathways of selected antioxidant peptides with ABTS were proposed. Conclusively, buffalo casein provided antioxidant peptides similar to bovine, suggesting that buffalo casein is a novel source of antioxidant.

Isolation and characterization of peptides with antihypertensive activity in foodstuffs

Hypertension is one of the main causes of cardiovascular diseases. Synthetic drugs inhibiting ACE activity present high effectiveness in the treatment of hypertension but cause undesirable side effects. Unlike these synthetic drugs, antihypertensive peptides do not show any adverse effect. These peptides are naturally present in some foods and since hypertension is closely related to modern diet habits, the interest for this kind of foods is increasing. Different methods for the purification, isolation, and characterization of antihypertensive peptides in foods have been developed. Nevertheless, there is no revision work summarizing and comparing these strategies. In this review, in vivo and in vitro pathways to obtain antihypertensive peptides have been summarized. The ACE mechanism and the methodologies developed to assay the ACE inhibitory activity have also been described. Moreover, a comprehensive overview on the isolation, purification, and identification techniques focusing on the discovery of new antihypertensive peptides with high activity has been included. Finally, it is worthy to highlight that the quantitation of antihypertensive peptides in foods is a new trend since genotype and processing conditions could affect their presence. Analytical methodologies using mass spectrometry constitute an interesting option for this purpose.

Learnings from quantitative structure–activity relationship (QSAR) studies with respect to food protein-derived bioactive peptides: a review

QSAR studies may help to better understand structural requirements for peptide bioactivity and therefore to develop potent BAPs.

Biologically active peptides: Processes for their generation, purification and identification and applications as natural additives in the food and pharmaceutical industries

Recent technological advances have created great interest in the use of biologically active peptides. Bioactive peptides can be defined as specific portions of proteins with 2 to 20 amino acids that have desirable biological activities, including antioxidant, anti-hypertensive, antithrombotic, anti-adipogenic, antimicrobial and anti-inflammatory effects. Specific characteristics, including low toxicity and high specificity, make these molecules of particular interest to the food and pharmaceutical industries. This review focuses on the production of bioactive peptides, with special emphasis on fermentation and enzymatic hydrolysis. The combination of different technologies and the use of auxiliary processes are also addressed. A survey of isolation, purification and peptide characterization methods was conducted to identify the major techniques used to determine the structures of bioactive peptides. Finally, the antioxidant, antimicrobial, anti-hypertensive, anti-adipogenic activities and probiotic-bacterial growth-promoting aspects of various peptides are discussed.

Preventive and therapeutic potential of peptides from cereals against cancer

Epidemiological studies have shown that regular consumption of food based on whole-grain cereals and their products is associated with reduced risks of various types of degenerative chronic diseases. Food proteins are considered an important source of nutraceutical peptides and amino acids that can exert biological functions to promote health and prevent disease, including cancer. There have been several reports on peptides with anti-tumour activity in recent years. Plant-derived peptides, such as rapeseed, amaranth and soybean lunasin have received main attention. In this review, we extend this vision to analyse the evidence of current advances in peptides in cereals such as wheat, maize, rice, barley, rye and pseudocereals compared with soybean. We also show evidence of several mechanisms through which bioactive peptide exerts anti-tumour activity. Finally, we report the current status of major strategies for the fractionation, isolation and characterisation of bioactive peptides in cereals.

BIOLOGICAL SIGNIFICANCE

In recent reports, it has been shown that peptides are an interesting alternative in the search for new treatments for cancer. One of the most studied sources of these peptides is food proteins; however, a review that includes more recent findings for cereals as a potential source of bioactive peptides in the treatment of cancer, the techniques for their isolation and characterisation and the assays used to prove their bioactivity is not available. This review can be used as a tool in the search for new sources of anti-cancer peptides. The authors have no conflicts of interest, financial or otherwise.

Development of a capillary high performance liquid chromatography-ion trap-mass spectrometry method for the determination of VLIVP antihypertensive peptide in soybean crops

Soybean peptide VLIVP presents a very high antihypertensive activity (IC50 value 1.69μM), even higher than extensively studied IPP and VPP peptides from milk. Nevertheless, no much attention has been paid to this peptide and there is no method enabling its determination in soybeans. The aim of this work was the development of an analytical methodology for this purpose. A methodology consisting of the extraction of soybean proteins, their digestion with Protease P enzyme, their chromatographic separation using capillary-HPLC, and IT-MS detection was optimized. Protein extraction was performed by the use of high intensity focused ultrasounds to obtain a reduced extraction time. Optimization of chromatographic and mass spectrometry parameters enabled the separation of VLIVP peptide within just 7min and its sensitive detection. The analytical characteristics of the capillary-HPLC-IT-MS method were evaluated through the study of linearity, LOD, LOQ, study of the presence of matrix interferences, precision, and recovery. The method enabled to detect as low as 3.6ng of peptide and to determine as low as 12ng of peptide in 1g of soybean (as dry basis). Finally, the developed method was applied to the determination of the antihypertensive peptide VLIVP in different soybean varieties. The results showed the highest yield of VLIVP peptide in variety Mazowiecka II from Poland.

Functional significance of bioactive peptides derived from soybean

Biologically active peptides play an important role in metabolic regulation and modulation. Several studies have shown that during gastrointestinal digestion, food processing and microbial proteolysis of various animals and plant proteins, small peptides can be released which possess biofunctional properties. These peptides are to prove potential health-enhancing nutraceutical for food and pharmaceutical applications. The beneficial health effects of bioactive peptides may be several like antihypertensive, antioxidative, antiobesity, immunomodulatory, antidiabetic, hypocholesterolemic and anticancer. Soybeans, one of the most abundant plant sources of dietary protein, contain 36-56% of protein. Recent studies showed that soy milk, an aqueous extract of soybean, and its fermented product have great biological properties and are a good source of bioactive peptides. This review focuses on bioactive peptides derived from soybean; we illustrate their production and biofunctional attributes.

LC-ESI-TOF MS method for the evaluation of the immunostimulating activity of soybeans via the determination of the functional peptide soymetide

Bioactive peptides content in foodstuffs can seriously vary with many factors such as crop variety, food processing, animal breeding, etc. Because of this variability, quantitative methodologies are required to evaluate the content of bioactive peptides in foodstuffs. Progress in liquid chromatography and mass spectrometry technologies offer a great opportunity for the quantitation of bioactive peptides. This study undertook the development of a liquid chromatography-electrospray ionization-time-of-flight mass spectrometry method using a fused-core technology column for the sensitive and unambiguous determination of the immunostimulating peptide soymetide in soybean varieties. Soymetide precursor protein (α' subunit of β-conglycinin) was extracted with a Tris-HCl buffer (pH 8.0) containing urea and digested with trypsin. Soymetide separation conditions by reversed phase liquid chromatography (ion-pairing reagent, organic modifier, separation column, and elution gradient) and detection by MS were optimized, and a study of soymetide stability was also conducted. The method selectivity having been demonstrated, the linearity, accuracy, precision, and limits of detection and quantitation were evaluated. The developed method enabled the detection and quantitation of soymetide concentrations in the ppb range (7.5 ng/mL and 25 ng/mL, respectively), and about 30 times lower than those detected and determined in a previous work by capillary liquid chromatography with UV detection. These values could allow the quantitation of only 17 μg of soymetide per gram of soybean. The developed methodology was applied to the quantitation of soymetide in different soybean varieties from Europe, Japan, and USA observing great differences in soymetide content that ranged from 40 to 600 μg per gram of soybean depending on the soybean variety.

Development of a high-performance liquid chromatography-electrospray ionization-quadrupole-time-of-flight-mass spectrometry methodology for the determination of three highly antihypertensive peptides in maize crops

The simultaneous quantification of three highly antihypertensive peptides (LRP, LSP, and LQP) in six maize crops using novel HPLC-ESI-Q-ToF methodology is presented. The method included the extraction of α-zein proteins from maize, their purification by acetone precipitation, digestion with thermolysin and HPLC separation in a fused-core column. Several MS parameters were optimized to increase sensitivity and reduce spontaneous fragmentation of peptide ions into the ESI source. The ions with m/z 193.1315, 385.2558 (for LRP), 316.1867 (for LSP), and 357.2132 (for LQP) were monitored in the optimization and characterization of the method. In order to improve the repeatability, sensitivity, and the stability of peptides in the sample, the removal of urea was required. The use of two solid-phase extraction methods to remove urea from digested extract was evaluated. For the first time filter-aided sample preparation approach for the study of bioactive peptides in foodstuffs has been proposed. The optimized HPLC-ESI-Q-ToF method was characterized by the evaluation of linearity, LOD, LOQ, precision, and recovery. A study on the existence of matrix interferences was also performed. The developed method was applied to the quantification of LRP, LQP, and LSP peptides in maize lines using the standard addition method. The results showed the highest yield of LSP peptide in EZ11A line and LRP and LQP peptides in A632 line.

Mass spectrometry for nutritional peptidomics: How to analyze food bioactives and their health effects

We describe nutritional peptidomics for discovery and validation of bioactive food peptide and their health effects. Understanding nature and bioactivity of nutritional peptides means comprehending an important level of environmental regulation of the human genome, because diet is the environmental factor with the most profound life-long influence on health. We approach the theme from three angles, namely the analysis, the discovery and the biology perspective. Food peptides derive from parent food proteins via in vitro hydrolysis (processing) or in vivo digestion by various unspecific and specific proteases, as opposed to the tryptic peptides typically generated in biomarker proteomics. A food bioactive peptide may be rare or unique in terms of sequence and modification, and many food genomes are less well annotated than e.g. the human genome. Bioactive peptides can be discovered either empirically or by prediction: we explain both the classical hydrolysis strategy and the bioinformatics-driven reversed genome engineering. In order to exert bioactivity, food peptides must be either ingested and then reach the intestine in their intact form or be liberated in situ from their parent proteins to act locally, that is in the gut, or even systemically, i.e. through the blood stream. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.

Development of a reversed-phase high-performance liquid chromatography analytical methodology for the determination of antihypertensive peptides in maize crops

The aim of this work was to estimate the content of three highly antihypertensive peptides (LQP, LSP, and LRP) in different maize crops. For that purpose, a method consisting of the extraction of the protein containing these peptides (α-zeins), releasing of peptides by thermolysin digestion, and separation and detection of peptides was designed. The rapid and efficient ultrasound assisted extraction of α-zeins proteins from whole maize kernels was achieved using 70% of ethanol followed by precipitation with acetone. A 10 mM Tris-HCl (pH 8.0) buffer containing 8M urea enabled to dissolve the precipitated α-zeins. This buffer was diluted to reach a 6 M urea concentration before digestion to keep active the enzyme. Other digestion parameters that were optimized were: enzyme to substrate ratio (5:100 was selected), digestion temperature (50°C) and digestion time (6 h). The RP-HPLC separation in a fused-core column was also optimized allowing the separation of the three peptides extracted from maize kernels in 6 min. The presence of the three antihypertensive peptides in the digested extract was confirmed using HPLC-Q-TOF-MS analysis and by comparison with peptide standards. Clear differences were observed in the content of the three antihypertensive peptides and, thus, in the antihypertensive activity of the analyzed crops. The content of LRP peptide was very low regardless of the maize variety while the content of LQP and LSP significantly varied among studied maize lines.

Human cancer cell proliferation inhibition by a pentapeptide isolated and characterized from rice bran

Food-derived bioactive peptides promote functional activity against diseases and present as nutraceutical agents. The purpose of our research was to isolate and fully characterize peptide(s) derived from rice bran having anti-cancer properties. Gastrointestinal juices resistant peptide fractions were initially generated from heat stabilized de-fatted rice bran from which <5 kDa fraction was shown to inhibit proliferation of cancer cells. Based on these published findings the <5 kDa peptide fraction was selected for further characterization to obtain single pure peptide(s) with enhanced anti-cancer properties. Purification and characterization from the fraction was done employing chromatography and mass spectrometric techniques. Cancer cell viability was measured using a cell titer assay that uses a tetrazolium dye [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt; (MTS)] and the electron coupling reagent, phenazine methosulfate. Ion-exchange chromatography elutes that showed anti-cancer properties were further purified to liberate pure peptide. The pure peptide at 600-700 microg/mL dose caused 84% inhibition to colon cancer cells (Caco-2, HCT-116) growth, 80% to breast cancer cells (MCF-7, MDA-MB-231) growth and 84% to liver cancer cells (HepG-2) growth. Mass spectrometry analysis and de novo sequencing revealed the sequence of Glu-Gln-Arg-Pro-Arg for the peptide with a molecular mass of 685.378 Da. A novel pentapeptide was isolated from rice bran to possess cancer growth inhibitory properties on colon, breast, lung and liver cancer cells. This peptide could serve as a nutraceutical agent against cancer.