In silico methods to identify meat-derived prolyl endopeptidase inhibitors

Integrating Computational and Experimental Methods to Identify Novel Sweet Peptides from Egg and Soy Proteins

Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners in the food industry. However, the widespread use of sweeteners has sparked health concerns. This underscores the importance of developing and screening natural, health-conscious sweeteners. Our study represents a groundbreaking venture into the discovery of such sweeteners derived from egg and soy proteins. Employing virtual hydrolysis as a novel technique, our research entailed a comprehensive screening process that evaluated biological activity, solubility, and toxicity of the derived compounds. We harnessed cutting-edge machine learning methodologies, specifically the latest graph neural network models, for predicting the sweetness of molecules. Subsequent refinements were made through molecular docking screenings and molecular dynamics simulations. This meticulous research approach culminated in the identification of three promising sweet peptides: DCY(Asp-Cys-Tyr), GGR(Gly-Gly-Arg), and IGR(Ile-Gly-Arg). Their binding affinity with T1R2/T1R3 was lower than -15 kcal/mol. Using an electronic tongue, we verified the taste profiles of these peptides, with IGR emerging as the most favorable in terms of taste with a sweetness value of 19.29 and bitterness value of 1.71. This study not only reveals the potential of these natural peptides as healthier alternatives to traditional sweeteners in food applications but also demonstrates the successful synergy of computational predictions and experimental validations in the realm of flavor science.

Exploring bi-carbazole-linked triazoles as inhibitors of prolyl endo peptidase via integrated in vitro and in silico study

A serine protease called prolyl endopeptidase (PEP) hydrolyses the peptide bonds on the carboxy side of the proline ring. The excessive PEP expression in brain results in neurodegenerative illnesses like dementia, Alzheimer's disease, and Parkinson's disease. Results of the prior studies on antioxidant activity, and the non-cytotoxic effect of bi-carbazole-linked triazoles, encouraged us to extend our studies towards its anti-diabetic potential. Hence, for this purpose all compounds 1-9 were evaluated to reveal their anti-prolyl endo peptidase activity. Fortunately, seven compounds resulted into significant inhibitory capability ranging from 26 to 63 µM. Among them six compounds 4-9 exhibited more potent inhibitory activity with IC50 values 46.10 ± 1.16, 42.30 ± 1.18, 37.14 ± 1.21, 26.29 ± 0.76, 28.31 ± 0.64 and 31.11 ± 0.84 µM respectively, while compound 3 was the least active compound in the series with IC50 value 63.10 ± 1.58 µM comparing with standard PEP inhibitor bacitracin (IC50 = 125 ± 1.50 µM). Moreover, mechanistic study was performed for the most active compounds 7 and 8 with Ki values 24.10 ± 0.0076 and 23.67 ± 0.0084 µM respectively. Further, the in silico studies suggested that the compounds exhibited potential interactions and significant molecular conformations, thereby elucidating the structural basis for their inhibitory effects.

Peptide recovery from chicken feather keratin and their anti-biofilm properties against methicillin-resistant Staphylococcus aureus (MRSA)

Bacteria have the potential to adhere to abiotic surfaces, which has an undesirable effect in the food industry because they can survive for sustained periods through biofilm formation. In this study, an antibacterial peptide (ABP), with a molecular mass of 3861 Da, was purified from hydrolyzed chicken feathers using a locally isolated keratinolytic bacterium, namely Rhodococcus erythropolis, and its antibacterial and antibiofilm potential were investigated against planktonic and biofilm cells of Methicillin-Resistant Staphylococcus Aureus (MRSA). The results demonstrated that purified ABP showed the growth inhibition of MRSA cells with the minimum inhibitory concentration (MIC) of 45 µg/ml and disrupted MRSA biofilm formation at a concentration of 200 ug/ml, which results were confirmed by scanning electron micrograph (SEM). Moreover, the secondary structures of the peptide were assessed as part of the FTIR analysis to evaluate its mode of action. ExPASy tools were used to predict the ABP sequence, EPCVQUQDSRVVIQPSPVVVVTLPGPILSSFPQNTA, from a chicken feather keratin sequence database following in silico digestion by trypsin. Also, ABP had 54.29% hydrophobic amino acids, potentially contributing to its antimicrobial activity. The findings of toxicity prediction of the peptide by the ToxinPred tool revealed that ABP had non-toxic effects. Thus, these results support the potential of this peptide to be used as an antimicrobial agent for the treatment or prevention of MRSA biofilm formation in feed, food, or pharmaceutical applications.

Identification of novel antioxidant collagen peptides for preventing and treating H2 O2 -induced oxidative stress in HepG2 cells through in vitro and in silico approaches

BACKGROUND

Nowadays, the prevalence of oxidative stress-related chronic diseases is increasing. The identification of novel antioxidant collagen peptides to counteract oxidative stress for individuals' health has gained significant attention.

RESULTS

In this study, collagen peptides with antioxidant activities were separated and identified by ion chromatography, reversed-phase high-performance liquid chromatography and liquid chromatography-tandem mass spectrometry. The identified antioxidant collagen peptides were further screened by molecular docking for Keap1-targeted peptide inhibitors and their theoretical interaction mechanisms were investigated. Four novel antioxidant collagen peptides, GPAGPIGPVG, GPAGPpGPIG, ISGPpGPpGPA and IDGRPGPIGPA, with high binding affinity to Keap1 were selected. Molecular docking results demonstrated that the putative antioxidant mechanism of the four antioxidant collagen peptides contributed to their blockage of Keap1-Nrf2 interactions. The results of antioxidant activity of the four antioxidant collagen peptides proved that IDGRPGPIGPA exerted a high scavenging capacity for DPPH and ABTS free radicals, while GPAGPpGPIG improved the resistance of cells to hydrogen peroxide-induced oxidative damage by promoting the activation of intracellular antioxidant enzymes and the production of reduced glutathione in human hepatoma (HepG2) cells.

CONCLUSION

The antioxidant collagen peptides (GPAGPIGPVG, GPAGPpGPIG, ISGPpGPpGPA and IDGRPGPIGPA) will be developed as novel functional food for human health in the near future. © 2023 Society of Chemical Industry.

Identification, in silico selection, and mechanism study of novel antioxidant peptides derived from the rice bran protein hydrolysates

The work aimed to assess the antioxidant ability and obtain a new antioxidant peptide from rice bran protein. Rice bran protein was hydrolyzed by Alcalase, Neutral, Pepsin, Chymotrypsin, and Trypsin, separately. Trypsin hydrolysate (T-RBPH) showed high Fe²⁺ chelating activity (IC₅₀, 2.271 ± 0.007 mg/mL), DPPH and hydroxyl radical scavenging ability (IC₅₀, 0.191 ± 0.006 and 1.038 ± 0.034 mg/mL). Moreover, T-RBPH could alleviate the H₂O₂-induced oxidative damage in Caco-2. The T-RBPH was purified and identified by UF, GF, FPLC, and LC-MS/MS. Finally, 9-amino acid peptide-AFDEGPWPK with low molecular weight (1045.48 Da), high antioxidant activity, good safety, and solubility was screened by in silico method and chemical oxidation determination, and its interaction with Keap1 was also demonstrated. The ORAC and DPPH radical scavenging ability of AFDEGPWPK were 44.16 ± 0.79 and 28.38 ± 0.14 μmol TE/mM. Moreover, the Molecular docking and Western blot (WB) results showed that AFDEGPWPK could enter the binding pocket in the Kelch domain and activate Keap1/Nrf2/HO-1 pathway.

The biological role of prolyl oligopeptidase and the procognitive potential of its peptidic inhibitors from food proteins

Prolyl oligopeptidase (POP) is a conserved serine protease belonging to proline-specific peptidases. It has both enzymatic and non-enzymatic activity and is involved in numerous biological processes in the human body, playing a role in e.g., cellular growth and differentiation, inflammation, as well as the development of some neurodegenerative and neuropsychiatric disorders. This article describes the physiological and pathological aspects of POP activity and the state-of-art of its peptidic inhibitors originating from food proteins, with a particular focus on their potential as cognition-enhancing agents. Although some milk, meat, fish, and plant protein-derived peptides have the potential to be applied as natural, procognitive nutraceuticals, their effectiveness requires further evaluation, especially in clinical trials. We demonstrated that the important features of the most promising POP-inhibiting peptides are very short sequence, high content of hydrophobic amino acids, and usually the presence of proline residue.

Proteomics Characterization of Food-Derived Bioactive Peptides with Anti-Allergic and Anti-Inflammatory Properties

Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial action, mainly by the gastrointestinal microbiota from proteins present in food, originating from either vegetable or animal matter or by the action of different gastrointestinal proteases. Proteomics can play an important role in the identification of bioactive peptides. High-resolution mass spectrometry is the principal technique used to detect and identify different types of analytes present in complex mixtures, even when available at low concentrations. Moreover, proteomics may provide the characterization of epitopes to develop new food allergy vaccines and the use of immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. In addition, food-derived bioactive peptides have been investigated for their anti-inflammatory properties to provide safer alternatives to nonsteroidal anti-inflammatory drugs (NSAIDs). All these bioactive peptides can be a potential source of novel drugs and ingredients in food and pharmaceuticals. The following review is focused on food-derived bioactive peptides with antiallergic and anti-inflammatory properties and summarizes the new insights into the use of proteomics for their identification and quantification.

Novel angiotensin-converting enzyme (ACE) inhibitory mechanism of peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2)

This work aimed to identify novel angiotensin-converting-enzyme (ACE) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2). The MiAMP2 protein was hydrolyzed through in silico digestion, and the generated peptides were screened for ACE inhibitory activity. The in silico enzyme digestion results revealed that 18 unreported peptides were obtained using AHTPDB and BIOPEP-UWM, and none were thought to be toxic based on absorption, distribution, metabolism, and excretion (ADMET) prediction. PGPR, RPLY, MNPQR, and AAPR were predicted to exhibit good biological activity. The molecular docking results revealed that the four peptides tightly bound to the active pocket of ACE via hydrogen bonds and hydrophobic interactions, among which RPLY and MNPQR bound to ACE more strongly. The in vitro assay results confirmed that RPLY and MNPQR peptides inhibited ACE via competitive manner. These results provide theoretical guidance for the development of novel foodborne antihypertensive peptides from Macadamia nut proteins. PRACTICAL APPLICATIONS: This study provides new insight on the inhibitory potential of Macadamia nut peptides against ACE, which may be further applied to the development of antihypertensive peptides in the medical industry.

Identification of Oncorhynchus mykiss nebulin-derived peptides as bitter taste receptor TAS2R14 blockers by in silico screening and molecular docking

Human bitter taste receptor TAS2R14 (T2R14) can widely perceive bitterness, which has always been an issue for people to overcome. This study was aimed at identifying bioactive peptides obtained from Oncorhynchus mykiss nebulin hydrolysates as bitter taste receptor blockers by physicochemical property prediction, molecular docking, and in vitro determination of bitterness intensity using electronic tongue. Exploration of the interaction mechanism of these peptides with T2R14 by molecular docking models indicated that peptides ADM and ADW had high affinities for T2R14 to block the binding of bitter substances into the receptor. Addition of ADM and ADW to quinine caused reduction in bitterness intensity, with IC₅₀ values of 420.32 ± 6.26 μM and 403.29 ± 4.10 μM, respectively. Hydrogen bond interaction and hydrophobic interaction were responsible for manifesting the high affinities of these peptides for the receptor. Residues Thr86, Asp168, and Phe247 may be the key amino acids within the binding site.

Identification of lactoferrin-derived peptides as potential inhibitors against the main protease of SARS-CoV-2

COVID-19 is a global health emergency that causes serious concerns. A global effort is underway to identify drugs for the treatment of COVID-19. One possible solution to the present problem is to develop drugs that can inhibit SARS-CoV-2 main protease (M^pro), a coronavirus protein that been considered as one among many drug targets. In this work, lactoferrin from Bos taurus L. was in silico hydrolyzed. The bioactivity, water solubility, and ADMET properties of the generated peptides were predicted using various online tools. The molecular interactions between M^pro and the peptides were studied using molecular docking and molecular dynamic simulation. The results demonstrated that peptide GSRY was predicted to have better physicochemical properties, and the value of '-C DOCKER interaction energy' between peptide GSRY and M^pro was 80.8505 kcal/mol. The interaction between the peptide GSRY and the native ligand N3 co-crystallized with M^pro had overlapped amino acids, i.e., HIS163, GlY143, GLU166, GLN189 and MET165. Molecular dynamic simulation revealed that M^pro/GSRY complexes were stable. Collectively, the peptide GSRY may be a potential candidate drug against M^pro of SARS-CoV-2.

Prediction of Bioactive Peptides From Chicken Feather and Pig Hair Keratins Using In Silico Analysis Based on Fragmentomic Approach

BACKGROUND

Keratin is among the most abundant structural proteins of animal origin, however it remains broadly underutilized. <P> Objective: Bioinformatic investigation was performed to evaluate selected keratins originating from mass-produced waste products, i.e., chicken feathers and pig hair, as potential sources of bioactive peptides. <P> Methods: Pepsin, trypsin, chymotrypsin, papain, and subtilisin were used for in silico keratinolysis with the use of "Enzyme(s) action" and fragmentomic analysis of theoretical products was performed using "Profiles of potential biological activity" in BIOPEP-UWM database of bioactive peptides. Bioactivity probability calculation and toxicity prediction of the peptides obtained were estimated using PeptideRanker and ToxinPred tools, respectively. <P> Results: Our results showed that the keratins are a potential source of a variety of biopeptides, including dipeptidyl peptidase IV, angiotensin converting enzyme, prolyl endopeptidase inhibitory and antioxidative. Papain and subtilisin were found to be the most appropriate enzymes for keratin hydrolysis. This study presents possible structures of keratin-derived bioactive peptides that have not been previously described. <P> Conclusion: Our data suggest additional in vitro and in vivo studies to verify theoretical predictions and further investigate the possibility of using keratin-rich waste as a source of peptide nutraceuticals.

Discovery and functional mechanism of novel dipeptidyl peptidase Ⅳ inhibitory peptides from Chinese traditional fermented fish (Chouguiyu)

Dipeptidyl peptidase-IV (DPP-IV) inhibitory peptides from fermented foods exhibit great potential to alleviate type 2 diabetes mellitus (T2DM). In this study, the DPP-IV inhibition activity of peptide extract from Chouguiyu was obviously enhanced after 4–8 d fermentation. A total of 125 DPP-IV inhibitory peptides in Chouguiyu were identified by peptidomics and were obtained from 46 precursor proteins, mainly including nebulin, titin, muscle-type creatine kinase, hemoglobin, and actin. After molecular docking with DPP-IV, four novel DPP-IV inhibitory peptides possessing the lowest docking energy were selected, including EPAEAVGDWR (D37), IPHESVDVIK (D22), PDLSKHNNHM (D35), and PFGNTHNNFK (D1). The DPP-IV inhibition activity of D37, D22, D35, and D1 were further verified after synthesis with the IC₅₀ of 0.10 mM, 2.69 mM, 3.88 mM, and 8.51 mM, respectively, in accordance with their docking energies. Energy interaction showed that the structures of EP-, IPH-, -NHM, and PF- in these peptides were easy to connect with DPP-IV enzyme through hydrogen bond, salt bridge, and alkyl. The surface force including the H-bond interaction, hydrophobicity, aromatic interaction, and SAS, played a major role in the interaction between DPP-IV enzyme and peptides. The peptides that possess high hydrophobicity and can form strong hydrogen bond and salt bridge are potential DPP-IV inhibitory peptides using for T2DM remission.

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DPP-Ⅳ inhibition activity of peptide extract in Chouguiyu increased by fermentation.

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The main precursor proteins of DPP-Ⅳ inhibitory peptides were nebulin and titin.

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Inhibition mechanism was explored by energy interaction and surface force.

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Docking energy was an effective index to select DPP-IV inhibitory peptides.

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DPP-IV inhibitory peptides formed hydrogen bond and salt bridge with DPP-IV.

Identification and molecular docking of peptides from Mizuhopecten yessoensis myosin as human bitter taste receptor T2R14 blockers

Bitter taste receptor 14(T2R14) is one of the most widely regulated bitter taste receptors (T2Rs) and plays a vital role in the research of T2R blockers. In this study, potential T2R14 blockers were identified from the myosin of Mizuhopecten yessoensis. Myosin was hydrolyzed in silico by gastrointestinal proteases, and the peptides were obtained. The peptides' biological activity, solubility, and toxicity were predicted, and the potential T2R14 blocking peptides were docked with T2R14. Subsequently, the in vitro T2R14 blocking activity of the selected peptide was verified by an electronic tongue. The results showed that QRPR had T2R14 blocking activity with an IC₅₀ value of 256.69 ± 1.91 μM. Molecular docking analysis suggested the key role of the amino residues Asp168, Leu178, Asn157, and Ile262 in blocking T2R14, and revealed that the amino acid residues of T2R14 bound with the peptide QRPR via electrostatic interaction, hydrophobic interaction, conventional hydrogen bond, and hydrogen bond. The novel T2R14 blocking peptide QRPR is a potential candidate for suppressing bitterness.

Trends in In Silico Approaches to the Prediction of Biologically Active Peptides in Meat and Meat Products as an Important Factor for Preventing Food-Related Chronic Diseases

The increasing awareness of modern consumers regarding the nutritional and health value of food has changed their preferences, as well their requirements, for food products, including meat and meat products. Expanding the knowledge on the impact of food on human health is currently one of the most important research areas for scientists worldwide, and it is also of interest to consumers who want to consciously compose their daily diets. New research methods, such as in silico techniques, offer solutions to these new challenges. These research methods are preferred over food evaluation, e.g., from meat, because of their advantages, such as low costs, shorter analysis times, and general availability (e.g., online databases), and are often used to design in vitro and, subsequently, in vivo tests. This review focuses on the possible use of in silico computerized methods to assess the potential of food as a source of these health-relevant biomolecules by using examples from the literature on meat and meat products. This review also provides information and important suggestions for analyzing peptides in terms of assessing their best sources, and screening those resistant to digestive factors and that show biological activity. The information provided in this review could contribute to the development of new sources of foods as biomolecules important for preventing or treating food-related chronic diseases, such as obesity, hypertension, and diabetes.

Bioactive Peptides in Preventative Healthcare: An Overview of Bioactivities and Suggested Methods to Assess Potential Applications

Food derived bioactive peptides can be generated from various protein sources and usually consist of between 2-30 amino acids with bulky, side-chain aromatic amino acids preferred in the ultimate and penultimate positions at the C-terminal end of the amino acid chain. They are reported to impart a myriad of preventative health beneficial effects to the consumer once ingested and these include heart health benefits through inhibition of enzymes including renin (EC 3.4.23.15) and angiotensin- I-converting enzyme (ACE-1; EC 3.4.15.1) within the renin angiotensin aldosterone system (RAAS) anti-inflammatory (due to inhibition of ACE-I and other enzymes) and anti-cancer benefits, prevention of type-2 diabetes through inhibition of dipeptidyl peptidase IV (DPP-IV), bone and dental strength, antimicrobial and immunomodulatory effects and several others. Peptides have also reported health benefits in the treatment of asthma, neuropathic pain, HIV and wound healing. However, the structure, amino acid composition and length of these peptides, along with the quantity of peptide that can pass through the gastrointestinal tract and often the blood-brain barrier (BBB), intact and reach the target organ, are important for the realisation of these health effects in an in vivo setting. This paper aims to collate recent important research concerning the generation and detection of peptides in the laboratory. It discusses products currently available as preventative healthcare peptide options and relevant legislation barriers to place a food peptide product on the market. The review also highlights useful in silico computer- based methods and analysis that may be used to generate specific peptide sequences from proteins whose amino acid sequences are known and also to determine if the peptides generated are unique and bioactive. The topic of food-derived bioactive peptides for health is of great interest to scientific research and industry due to evolving drivers in food product innovation, including health and wellness for the elderly, infant nutrition and optimum nutrition for sports athletes and the humanisation of pets. This paper provides an overview of what is required to generate bioactive peptide containing hydrolysates, what methods should be used in order to characterise the beneficial health effects of these hydrolysates and the active peptide sequences, potential applications of bioactive peptides and legislative requirements in Europe and the United States. It also highlights success stories and barriers to the development of peptide-containing food products that currently exist.

Xanthine oxidase inhibitory peptides derived from tuna protein: virtual screening, inhibitory activity, and molecular mechanisms

BACKGROUND

There has been growing interest in the use of xanthine oxidase (XO) as a therapeutic agent to prevent gout and hyperuricemia. In the present study, XO inhibitory peptides were identified from tuna protein by virtual screening, and molecular docking was used to elicit the interaction mechanism between XO and peptides.

RESULTS

A novel tetrapeptide, EEAK, exhibited high XO inhibitory activity with an IC₅₀ of 173.00 ± 0.06 μM. Molecular docking analysis revealed that EEAK bound with the pivotal residues of XO's active sites (i.e., Glu802, Arg880, Glu1261) through two conventional hydrogen bond interactions, two attractive charge interactions, and one salt bridge. EEAK could also bind with the residues Phe649, Leu648, Lys771, Ser876, Phe914, and Thr1010 of XO.

CONCLUSION

This study suggested that conventional hydrogen bond interactions and electrostatic interactions play an important role in XO inhibition. The novel XO inhibitory peptide EEAK from tuna protein could be used as potential candidate for controlling gout and hyperuricemia. © 2020 Society of Chemical Industry.

Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry for Simultaneous Determination of Antipsychotic Drugs in Human Plasma and Its Application in Therapeutic Drug Monitoring

PURPOSE

We developed and validated an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for simultaneous therapeutic drug monitoring (TDM) and clinical pharmacokinetic antipsychotic drugs: clozapine (CLP), chlorpromazine (CPZ), risperidone (RPD), paliperidone (PLD), quetiapine (QTP;), aripiprazole (APZ), dehydroaripiprazole (DAP), olanzapine (OZP), ziprasidone (ZRD), and amisulpride (ASP).

METHODS

Analytes and internal standards (ISs) were separated using a Phenomenex phenyl-hexyl column (50.0 × 2.1 mm, 1.7 μm) with water containing 0.1% formic acid and 2 mM ammonium acetate, and methanol containing 0.1% formic acid and 2 mM ammonium acetate as the mobile phase. The antipsychotic drugs and ISs were extracted from 50 μL of plasma using acetonitrile.

RESULTS

The calibration ranges were 25.0-1500.0 ng/mL for CLP, CPZ, DAP, and QTP, 10.0-600.0 ng/mL for CPZ and ZRD, 2.5-150.0 ng/mL for RPD, 5.0-300.0 ng/mL for PLD and OZP, and 20.0-1200.0 ng/mL for ASP. Validation was carried out according to the guidelines for bioanalytical validation, including assessment of calibration curves, specificity, accuracy, precision, recovery, stability, dilution integrity, and matrix effect. All the results satisfied the requirements.

CONCLUSION

The results provided significant information to support future clinical TDM and rational drug use research. The proposed method also provided a simple, reliable, specific, and suitable technique for TDM and pharmacokinetic studies.

Techniques, perspectives, and challenges of bioactive peptide generation: A comprehensive systematic review

Due to the digestible refractory and absorbable structures of bioactive peptides (BPs), they could induce notable biological impacts on the living organism. In this regard, the current study was devoted to providing an overview regarding the available methods for BPs generation by the aid of a systematic review conducted on the published articles up to April 2019. In this context, the PubMed and Scopus databases were screened to retrieve the related publications. According to the results, although the characterization of BPs mainly has been performed using enzymatic and microbial in-vitro methods, they cannot be considered as suitable techniques for further stimulation of digestion in the gastrointestinal tract. Therefore, new approaches for both in-vivo and in-silico methods for BPs identification should be developed to overcome the obstacles that belonged to the current methods. The purpose of this review was to compile the recent analytical methods applied for studying various aspects of food-derived biopeptides, and emphasizing generation at in vitro, in vivo, and in silico.

Identification of tuna protein-derived peptides as potent SARS-CoV-2 inhibitors via molecular docking and molecular dynamic simulation

The present study aimed to identify potential SARS-CoV-2 inhibitory peptides from tuna protein by virtual screening. The molecular docking was performed to elicit the interaction mechanism between targets (M^pro and ACE2) and peptides. As a result, a potential antiviral peptide EEAGGATAAQIEM (E-M) was identified. Molecular docking analysis revealed that E-M could interact with residues Thr190, Thr25, Thr26, Ala191, Leu50, Met165, Gln189, Glu166, His164, His41, Cys145, Gly143, and Asn119 of M^pro via 11 conventional hydrogen bonds, 9 carbon hydrogen bonds, and one alkyl interaction. The formation of hydrogen bonds between peptide E-M and the residues Gly143 and Gln189 of M^pro may play important roles in inhibiting the activity of M^pro. Besides, E-M could bind with the residues His34, Phe28, Thr27, Ala36, Asp355, Glu37, Gln24, Ser19, Tyr83, and Tyr41 of ACE2. Hydrogen bonds and electrostatic interactions may play vital roles in blocking the receptor ACE2 binding with SARS-CoV-2.

A comprehensive review of bioactive peptides obtained from animal byproducts and their applications

Livestock generates high quantities of residues, which has become a major socioeconomic issue for the meat industry. This review focuses on the identification of bioactive peptides (BPs) in animal byproducts and meat wastes. Firstly, the main bioactivities that peptides can have will be described and the methods for their evaluation will be discussed. Secondly, the various origins of these BPs will be studied. Then, the techniques and tools for the generation of BPs will be detailed in order to discuss, in the final part, how peptides could be used and assimilated. BPs possess diverse biological activities and can be strategic candidates for substituting synthetic molecules. In silico potentiality studies are a helpful tool to understand and predict BPs released from proteins and their potential activities. However, in vitro validation is often required. Although BP use is compelled by strict regulations in relation to the field of application, they are also limited by their low bioavailability and bioaccessibility. Therefore, it is important to test peptide stability during gastrointestinal digestion. Protective strategies have been discussed since their use could improve the stability and effectiveness of BPs.

Identification and molecular docking study of fish roe-derived peptides as potent BACE 1, AChE, and BChE inhibitors

Acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and beta-secretase 1 (BACE 1) play vital roles in the development and progression of Alzheimer's disease (AD).

Novel ACE inhibitors derived from soybean proteins using in silico and in vitro studies

The widespread application of soybean-derived peptides is currently limited due to the challenges in the identification of peptides. In the present work, in silico and in vitro analysis were applied to identify ACE inhibitory tri-peptides from soybean protein. The soybean protein was cleaved by PeptideCutter. Then, unknown tri-peptides were selected to solubility estimation and ADME prediction. Subsequently, Discovery Studio was applied to evaluate the interaction mechanism between ACE and tri-peptides. Finally, in vitro activity of theoretical ACE inhibitory tri-peptides was verified by RP-HPLC method. As a result, DMG was selected as a potent ACE inhibitory peptide. Cell experiment showed that DMG had no cytotoxic effects on HEK-293 cells. And molecular docking results indicated that DMG contacted well with ACE's active sites (Gln281, His353, Ala354, Glu384, Lys511, His513, and Tyr520). Furthermore, DMG could exert potent activity against ACE, with IC50 value of 3.95 ± 0.11 mM. PRACTICAL APPLICATIONS: Present research showed soybean is a potential protein resource to obtain ACE inhibitory peptides. Simultaneously, virtual screening method is a feasible way to substitute for classical method in emerging nutritional fields. What's more, present study provides a theoretical basis for industrial research on foodstuff for ACE inhibitory peptides without side effects.

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.

Novel Angiotensin-Converting Enzyme Inhibitory Peptides Derived from Oncorhynchus mykiss Nebulin: Virtual Screening and In Silico Molecular Docking Study

Excessive concentrations of angiotensin-converting enzyme (ACE) can give rise to high blood pressure, and is harmful to the body. ACE inhibitory peptides from food proteins are considered good sources of function food. However, the preparation of ACE inhibitory peptides by classical method faces many challenges. Three novel ACE inhibitory peptides were identified by in silico methods, and showed potent activity against ACE in vitro. The simulation hydrolysis of nebulin was performed with ExPASy PeptideCutter program. Potential activity, solubility, and absorption, distribution, metabolism, excretion, and toxicity properties of generated peptides were predicted using program online. Molecular docking displayed that EGF, HGR, and VDF were docked into the S₁ and S₂ pockets of ACE. Meanwhile, Phe and Arg at the C-terminal enhance ACE affinity. The IC₅₀ values of EGF, HGR, and VDF were 474.65 ± 0.08, 106.21 ± 0.52, and 439.27 ± 0.09 μM, respectively. Three peptides EGF, HGR, and VDF from Oncorhynchus mykiss nebulin were identified, and the molecular mechanism between ACE and peptides was clarified using in silico methods. The results suggested that Oncorhynchus mykiss nebulin would be an attractive raw material of antihypertensive nutraceutical ingredients.

PRACTICAL APPLICATION

This study has shown the potential of Oncorhynchus mykiss nebulin as good sources for producing ACE inhibitory peptides. According to this finding, in silico approach is the feasible way for prediction and identification of food-derived ACE inhibitory peptides in emerging nutraceutical field.

Identification and molecular docking study of novel angiotensin-converting enzyme inhibitory peptides from Salmo salar using in silico methods

BACKGROUND

In order to circumvent some challenges of the classical approach, the in silico method has been applied to the discovery of angiotensin-converting enzyme (ACE) inhibitory peptides from food proteins. In this study, some convenient and efficient in silico tools were utilized to identify novel ACE inhibitory peptides from Salmo salar.

RESULTS

Collagen from Salmo salar was digested in silico into hundreds of peptides. Results revealed that tetrapeptides PGAR and IGPR showed potent ACE inhibitory activity, with IC₅₀ values of 0.598 ± 0.12 and 0.43 ± 0.09 mmol L^-1 , respectively. The molecular docking result showed that PGAR and IGPR interact with ACE mostly via hydrogen bonds and attractive charge. Peptide IGPR interacts with Zn⁺ at the ACE active site, showing high inhibitory activity.

CONCLUSION

Interaction with Zn⁺ in ACE may lead to higher inhibitory activity of peptides, and Pi interactions may promote the effect of peptides on ACE. The in silico method can be an effective method to predict potent ACE inhibitory peptides from food proteins. © 2018 Society of Chemical Industry.

Opportunities and perspectives for utilisation of co-products in the meat industry

Meat co-products are the non-meat components arising from meat processing/fabrication and are generated in large quantities on a daily basis. Co-products are considered as low added-value products, and in general it is difficult for industries to divert efforts into increasing their value. While many of these products can be edible those not used for human consumption or pet food is usually processed to be used as animal feed, fertilizer or fuel. However, to a large extent meat co-products are an excellent source of high nutritive value protein, minerals and vitamins and hence may be better diverted to contribute to alleviate the increasing global demand for protein. In this review the current uses, legislation and potential techniques for meat co-products processing are reviewed with the aim of showing a route to improve meat industry sustainability, profitability and better usage of available resources.

Tryptophan-Containing Dual Neuroprotective Peptides: Prolyl Endopeptidase Inhibition and Caenorhabditis elegans Protection from β-Amyloid Peptide Toxicity

Neuroprotective peptides represent an attractive pharmacological strategy for the prevention or treatment of age-related diseases, for which there are currently few effective therapies. Lactoferrin (LF)-derived peptides (PKHs) and a set of six rationally-designed tryptophan (W)-containing heptapeptides (PACEIs) were characterized as prolyl endopeptidase (PEP) inhibitors, and their effect on β-amyloid peptide (Aβ) toxicity in a Caenorhabditis elegans model of Alzheimer's disease (AD) was evaluated. Two LF-derived sequences, PKH8 and PKH11, sharing a W at the C-terminal end, and the six PACEI heptapeptides (PACEI48L to PACEI53L) exhibited significant in vitro PEP inhibition. The inhibitory peptides PKH11 and PACEI50L also alleviated Aβ-induced paralysis in the in vivo C. elegans model of AD. Partial or total loss of the inhibitory effect on PEP was achieved by the substitution of W residues in PKH11 and PACEI50L and correlated with the loss of protection against Aβ toxicity, pointing out the relevance of W on the neuroprotective activity. Further experiments suggest that C. elegans protection might not be mediated by an antioxidant mechanism but rather by inhibition of Aβ oligomerization and thus, amyloid deposition. In conclusion, novel natural and rationally-designed W-containing peptides are suitable starting leads to design effective neuroprotective agents.

Bioinformatics and peptidomics approaches to the discovery and analysis of food-derived bioactive peptides

There are emerging advancements in the strategies used for the discovery and development of food-derived bioactive peptides because of their multiple food and health applications. Bioinformatics and peptidomics are two computational and analytical techniques that have the potential to speed up the development of bioactive peptides from bench to market. Structure-activity relationships observed in peptides form the basis for bioinformatics and in silico prediction of bioactive sequences encrypted in food proteins. Peptidomics, on the other hand, relies on "hyphenated" (liquid chromatography-mass spectrometry-based) techniques for the detection, profiling, and quantitation of peptides. Together, bioinformatics and peptidomics approaches provide a low-cost and effective means of predicting, profiling, and screening bioactive protein hydrolysates and peptides from food. This article discuses the basis, strengths, and limitations of bioinformatics and peptidomics approaches currently used for the discovery and analysis of food-derived bioactive peptides.

Omics-prediction of bioactive peptides from the edible cyanobacterium Arthrospira platensis proteome

BACKGROUND

Bioinformatics approaches are widely used to evaluate the prospects of novel protein sources in bioactive peptide research. Edible cyanobacteria are considered as potential protein precursors. However, the abundance of unicellular cyanobacterial proteins is largely unknown and highly dynamic according to the cultivation conditions, which need to be considered in this research field. The objective of this work was to evaluate the protein abundance of Arthrospira platensis, as well as to map the bioactive peptide sequences from the high-abundance proteins of the A. platensis proteome.

RESULTS

The high-abundance proteins of the A. platensis proteome were identified with a high-performance liquid chromatography-tandem mass spectrometry-based method. A total of 593 proteins were detected and quantified. The occurrence frequency of the bioactive peptides in A. platensis proteome was calculated according to the amino acid sequences via the bioinformatics approaches. Further in silico digested by trypsin, pepsin and chymotrypsin, these proteins liberated 78, 99, and 96 bioactive peptides, respectively. In each case, angiotensin-converting enzyme inhibitors and dipeptidyl peptidase IV inhibitors were enriched.

CONCLUSION

This work will help rationally design the protocols for cyanobacterial cultivation, protein pre-treatment and peptide separation, and further produce more peptides with specific functions. © 2017 Society of Chemical Industry.

Combined in vivo and in silico approaches for predicting the release of bioactive peptides from meat digestion

We studied the kinetics of peptide release during the gastric digestion of meat proteins in vivo, in view to predicting the release of bioactive peptides further on in the digestive tract. Six mini pigs fitted with gastric cannulas received a meal with cooked beef as protein source. Digesta was collected at regular time intervals up to 5½ h. The peptides generated by the gastric digestion of meat were identified and quantified using label-free LC MS, thereafter subjected to in silico digestion mimicking the action of intestinal enzymes. Three clusters of proteins presenting similar evolutions according to their dynamic hydrolysis were obtained. This study clearly improves the in silico prediction of the intestinal release of bioactive peptides by mapping meat protein degradation in the stomach in an in vivo model. Knowledge of the conformation of the peptides released in the stomach further improves this prediction.

Identification and the molecular mechanism of a novel myosin-derived ACE inhibitory peptide

The objective of this work was to identify a novel ACE inhibitory peptide from myosin using a number of in silico methods.

High-Throughput and Rapid Screening of Novel ACE Inhibitory Peptides from Sericin Source and Inhibition Mechanism by Using in Silico and in Vitro Prescriptions

Several novel peptides with high ACE-I inhibitory activity were successfully screened from sericin hydrolysate (SH) by coupling in silico and in vitro approaches for the first time. Most screening processes for ACE-I inhibitory peptides were achieved through high-throughput in silico simulation followed by in vitro verification. QSAR model based predicted results indicated that the ACE-I inhibitory activity of these SH peptides and six chosen peptides exhibited moderate high ACE-I inhibitory activities (log IC₅₀ values: 1.63-2.34). Moreover, two tripeptides among the chosen six peptides were selected for ACE-I inhibition mechanism analysis which based on Lineweaver-Burk plots indicated that they behave as competitive ACE-I inhibitors. The C-terminal residues of short-chain peptides that contain more H-bond acceptor groups could easily form hydrogen bonds with ACE-I and have higher ACE-I inhibitory activity. Overall, sericin protein as a strong ACE-I inhibition source could be deemed a promising agent for antihypertension applications.

Antihypertensive properties of tilapia (Oreochromis spp.) frame and skin enzymatic protein hydrolysates

Proteins from tilapia frame and skin can potentially be precursors of antihypertensive peptides according to the result of BIOPEP analyses. The aim was to generate peptides with inhibitory effects against angiotensin-converting enzyme (ACE) and renin from tilapia frame and skin protein isolates (FPI and SPI). The most active hydrolysate was then tested for blood pressure-lowering ability in spontaneously hypertensive rats (SHRs). Tilapia frame and skin protein hydrolysates (FPHs and SPHs) were respectively produced from FPI and SPI hydrolysis using pepsin, papain, or bromelain. The ACE-inhibitory activities of tilapia protein hydrolysates with varying degree of hydrolysis (DH) were evaluated. In order to enhance the activity, the hydrolysate was fractionated into four fractions (<1 kDa, 1–3 kDa, 3–5 kDa, and 5–10 kDa) and the one with the greatest ability to inhibit in vitro ACE and renin activities was subjected to oral administration (100 mg/kg body weight) to SHRs. Systolic and diastolic blood pressure (SBP and DBP), mean arterial pressure (MAP), and heart rates (HR) were subsequently measured within 24 h. The pepsin-hydrolyzed FPH (FPHPe) with the highest DH (23%) possessed the strongest ACE-inhibitory activity (IC₅₀: 0.57 mg/mL). Its <1 kDa ultrafiltration fraction (FPHPe1) suppressed both ACE (IC₅₀: 0.41 mg/mL) and renin activities more effectively than larger peptides. In addition, FPHPe1 significantly (p < 0.05) reduced SBP (maximum −33 mmHg), DBP (maximum −24 mmHg), MAP (maximum −28 mmHg), and HR (maximum −58 beats) in SHRs. FPHPe1 showed both in vitro and in vivo antihypertensive effects, which suggest tilapia processing coproducts may be valuable protein raw materials for producing antihypertensive peptides.

Bioactive Peptides in Animal Food Products

Proteins of animal origin represent physiologically active components in the human diet; they exert a direct action or constitute a substrate for enzymatic hydrolysis upon food processing and consumption. Bioactive peptides may descend from the hydrolysis by digestive enzymes, enzymes endogenous to raw food materials, and enzymes from microorganisms added during food processing. Milk proteins have different polymorphisms for each dairy species that influence the amount and the biochemical characteristics (e.g., amino acid chain, phosphorylation, and glycosylation) of the protein. Milk from other species alternative to cow has been exploited for their role in children with cow milk allergy and in some infant pathologies, such as epilepsy, by monitoring the immune status. Different mechanisms concur for bioactive peptides generation from meat and meat products, and their functionality and application as functional ingredients have proven effects on consumer health. Animal food proteins are currently the main source of a range of biologically-active peptides which have gained special interest because they may also influence numerous physiological responses in the organism. The addition of probiotics to animal food products represent a strategy for the increase of molecules with health and functional properties.