Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity

Valorization of Salmo salar Skin Waste for the Synthesis of Angiotensin Converting Enzyme-1 (ACE1) Inhibitory Peptides

One of potential inhibitors which is widely used for the clinical treatment of COVID-19 in comorbid patients is Angiostensin Converting Enzyme-1 (ACE1) inhibitor. A safer peptide-based ACE1 inhibitor derived from salmon skin collagen, that is considered as the by-product of the fish processing industry have been investigated in this study. The inhibitory activity against ACE1 was examined using in vitro and in silico methods. In vitro analysis includes the extraction of acid-soluble collagen, characterization using FTIR, Raman, UV-Vis, XRD, cytotoxicity assay, and determination of inhibition against ACE1. In silico method visualizes binding affinity, molecular interaction, and inhibition type of intact collagen and active peptides derived from collagen against ACE1 using molecular docking. The results of FTIR spectra detected amide functional groups (A, B, I, II, III) and imine proline/hydroxyproline, while the results of Raman displayed peak absorption of amide I, amide III, proline/hydroxyproline ring, phenylalanine, and protein backbone. Furthermore, UV-Vis spectra showed typical collagen absorption at 230 nm and based on XRD data, the chain types in the samples were α-helix. ACE1 inhibition activity was obtained in a concentration-dependent manner where the highest was 82.83% and 85.84% at concentrations of 1000, and 2000 µg/mL, respectively, and showed very low cytotoxicity at the concentration less than 1000 µg/mL. In silico study showed an interaction between ACE1 and collagen outside the active site with the affinity of - 213.89 kcal/mol. Furthermore, the active peptides of collagen displayed greater affinity compared to lisinopril, namely HF (His-Phe), WYT (Trp-Tyr-Thr), and WF (Trp-Phe) of - 11.52; - 10.22; - 9.58 kcal/mol, respectively. The salmon skin-derived collagen demonstrated ACE1 inhibition activity with a non-competitive inhibition mechanism. In contrast, the active peptides were predicted as potent competitive inhibitors against ACE1. This study indicated that valorization of fish by-product can lead to the production of a promising bioactive compound to treat COVID-19 patient with diabetic comorbid.

Graphical Abstract

Electrosprayed Mesenchymal Stromal Cell Extracellular Matrix Nanoparticles Accelerate Cellular Wound Healing and Reduce Gram-Negative Bacterial Growth

Treatments for acute respiratory distress syndrome are still unavailable, and the prevalence of the disease has only increased due to the COVID-19 pandemic. Mechanical ventilation regimens are still utilized to support declining lung function but also contribute to lung damage and increase the risk for bacterial infection. The anti-inflammatory and pro-regenerative abilities of mesenchymal stromal cells (MSCs) have shown to be a promising therapy for ARDS. We propose to utilize the regenerative effects of MSCs and the extracellular matrix (ECM) in a nanoparticle. Our mouse MSC (MMSC) ECM nanoparticles were characterized using size, zeta potential, and mass spectrometry to evaluate their potential as pro-regenerative and antimicrobial treatments. The nanoparticles had an average size of 273.4 nm (±25.6) and possessed a negative zeta potential, allowing them to surpass defenses and reach the distal regions of the lung. It was found that the MMSC ECM nanoparticles are biocompatible with mouse lung epithelial cells and MMSCs, increasing the wound healing rate of human lung fibroblasts while also inhibiting the growth of Pseudomonas aeruginosa, a common lung pathogen. Our MMSC ECM nanoparticles display characteristics of healing injured lungs while preventing bacterial infection, which can increase recovery time.

Identification and molecular interactions of novel ACE inhibitory peptides from rapeseed protein

Plant-derived bioactive peptides have drawn much attention because of their physiological functions. This study aimed to evaluate bioactive peptides in rapeseed protein and identify novel angiotensin Ⅰ-converting enzyme (ACE) inhibitory peptides using bioinformatics methods. A total of 24 kinds of bioactive peptides were encrypted in the 12 selected rapeseed proteins by analysis in BIOPEP-UWM, with higher occurrence frequency of dipeptidyl peptidase Ⅳ (DPP-Ⅳ) inhibitory peptides (0.5727-0.7487) and ACE inhibitory peptides (0.3500-0.5364). Novel ACE inhibitory peptides FQW, FRW and CPF were identified by in silico proteolysis, and they had strong inhibitory effects on ACE in vitro, showing IC₅₀ values of 44.84 ± 1.48 μM, 46.30 ± 1.39 μM and 131.35 ± 3.87 μM, respectively. Molecular docking results displayed that these three peptides were able to interact with ACE active site via hydrogen bonds and hydrophobic interactions, and coordinate with Zn²⁺. It suggested that rapeseed protein could be a good source for the production of ACE inhibitory peptides.

Identifying Natural Bioactive Peptides from the Common Octopus (Octopus vulgaris Cuvier, 1797) Skin Mucus By-Products Using Proteogenomic Analysis

The common octopus is a cephalopod species subject to active fisheries, with great potential in the aquaculture and food industry, and which serves as a model species for biomedical and behavioral studies. The analysis of the skin mucus allows us to study their health in a non-invasive way, by using a hardly exploited discard of octopus in the fishing sector. A shotgun proteomics approach combined with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using an Orbitrap-Elite instrument was used to create a reference dataset from octopus skin mucus. The final proteome compilation was investigated by integrated in-silico studies, including Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, network studies, and prediction and characterization analysis of potential bioactive peptides. This work presents the first proteomic analysis of the common octopus skin mucus proteome. This library was created by merging 5937 identified spectra of 2038 different peptides. A total of 510 non-redundant proteins were identified. Obtained results show proteins closely related to the defense, which highlight the role of skin mucus as the first barrier of defense and the interaction with the environment. Finally, the potential of the bioactive peptides with antimicrobial properties, and their possible application in biomedicine, pharmaceutical, and nutraceutical industry was addressed.

Musculus senhousei as a promising source of bioactive peptides protecting against alcohol-induced liver injury

Alcohol-induced liver injury has become a leading risk for human health, however, effective strategies for the prevention or treatment are still lacking. Hence, the present study explored the potential of Musculus senhousei as a source of hepatoprotective peptides against alcoholic liver injury using in vitro, in vivo and in silico methods. Results indicated that Musculus senhousei peptides (MSP, extracted by simulated gastrointestinal digestion of cooked mussel) exhibited notable antioxidant (ABTS and DPPH assays) and alcohol dehydrogenase (ADH) stabilizing activity in vitro. The ingestion of MSP markedly alleviated alcohol-induced liver injury in mice, as indicated by the decrease of serum transaminases (AST and ALT). In line with in vitro assays, significantly increased hepatic ADH activity and activated antioxidative defense system (GSH, SOD, GSH-Px and CAT) were observed, whereas the oxidative stress (MDA) was decreased. Peptidomic analysis revealed over 6000 peptides with favorable amino acid compositions, and a total of 20 potentially novel peptides with bioactivity and bioavailability were excavated among 746 of the most influential peptides using an in silico strategy. Peptides (i.e. WLPMKL, WLWLPA, RLC and RCL) were further synthesized and validated in vitro to be bioactive. These findings suggest that Musculus senhousei can be an ideal source of bioactive peptides for the prevention of alcoholic liver injury.

Insights into Common Octopus (Octopus vulgaris) Ink Proteome and Bioactive Peptides Using Proteomic Approaches

The common octopus (Octopus vulgaris) is nowadays the most demanded cephalopod species for human consumption. This species was also postulated for aquaculture diversification to supply its increasing demand in the market worldwide, which only relies on continuously declining field captures. In addition, they serve as model species for biomedical and behavioral studies. Body parts of marine species are usually removed before reaching the final consumer as by-products in order to improve preservation, reduce shipping weight, and increase product quality. These by-products have recently attracted increasing attention due to the discovery of several relevant bioactive compounds. Particularly, the common octopus ink has been described as having antimicrobial and antioxidant properties, among others. In this study, the advanced proteomics discipline was applied to generate a common octopus reference proteome to screen potential bioactive peptides from fishing discards and by-products such as ink. A shotgun proteomics approach by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using an Orbitrap Elite instrument was used to create a reference dataset from octopus ink. A total of 1432 different peptides belonging to 361 non-redundant annotated proteins were identified. The final proteome compilation was investigated by integrated in silico studies, including gene ontology (GO) term enrichment, pathways, and network studies. Different immune functioning proteins involved in the innate immune system, such as ferritin, catalase, proteasome, Cu/Zn superoxide dismutase, calreticulin, disulfide isomerase, heat shock protein, etc., were found in ink protein networks. Additionally, the potential of bioactive peptides from octopus ink was addressed. These bioactive peptides can exert beneficial health properties such as antimicrobial, antioxidant, antihypertensive, and antitumoral properties and are therefore considered lead compounds for developing pharmacological, functional foods or nutraceuticals.

Novel Plant-Protein (Quinoa) Derived Bioactive Peptides with Potential Anti-Hypercholesterolemic Activities: Identification, Characterization and Molecular Docking of Bioactive Peptides

Hypercholesterolemia remains a serious global public health concern. Previously, synthetic anti-hypercholesterolemic drugs were used for ameliorating this condition; however, long-term usage presented several side-effects. In this regard, natural products as an adjunct therapy has emerged in recent times. This study aimed to produce novel bioactive peptides with anti-hypercholesterolemic activity (cholesterol esterase (CEase) and pancreatic lipase (PL)) from quinoa protein hydrolysates (QPHs) using three enzymatic hydrolysis methods (chymotrypsin, protease and bromelain) at 2-h hydrolysis intervals (2, 4, and 6 h). Chymotrypsin-generated hydrolysates showed higher CEase (IC₅₀: 0.51 mg/mL at 2 h) and PL (IC₅₀: 0.78 mg/mL at 6 h) inhibitory potential in comparison to other derived hydrolysates and intact quinoa proteins. Peptide profiling by LC-MS QTOF and in silico interaction with target enzymes showed that only four derived bioactive peptides from QPHs could bind in the active site of CEase, whereas twelve peptides could bind in the active site of PL. Peptides QHPHGLGALCAAPPST, HVQGHPALPGVPAHW, and ASNLDNPSPEGTVM were identified to be potential CEase inhibitors, and FSAGGLP, QHPHGLGALCAAPPST, KIVLDSDDPLFGGF, MFVPVPH, and HVQGHPALPGVPAHW were identified as potential PL inhibitors on the basis of the maximum number of reactive residues in these bioactive peptides. In conclusion, QPHs can be considered as an alternative therapy for the treatment of hypercholesterolemia.

In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms

Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.

The Bioaccessibility of Yak Bone Collagen Hydrolysates: Focus on Analyzing the Variation Regular of Peptides and Free Amino Acids

The lack of a bioaccessibility test for yak bone collagen hydrolysates (YBCH) limits their development as functional foods. In this study, simulated gastrointestinal digestion (SD) and absorption (SA) models were utilized to evaluate the bioaccessibility of YBCH for the first time. The variation in peptides and free amino acids was primarily characterized. There was no significant alteration in the concentration of peptides during the SD. The transport rate of peptides through the Caco-2 cell monolayers was 22.14 ± 1.58%. Finally, a total of 440 peptides were identified, more than 75% of them with lengths ranging from 7 to 15. The peptide identification indicated that about 77% of the peptides in the beginning sample still existed after the SD, and about 76% of the peptides in the digested YBCH could be observed after the SA. These results suggested that most peptides in the YBCH resist gastrointestinal digestion and absorption. After the in silico prediction, seven typical bioavailable bioactive peptides were screened out and they exhibited multi-type bioactivities in vitro. This is the first study to characterize the changes in peptides and amino acids in the YBCH during gastrointestinal digestion and absorption, and provides a foundation for analyzing the mechanism of YBCH's bioactivities.

Characterization and Biological Activities of In Vitro Digested Olive Pomace Polyphenols Evaluated on Ex Vivo Human Immune Blood Cells

Olive pomace (OP) represents one of the main by-products of olive oil production, which still contains high quantities of health-promoting bioactive compounds. In the present study, three batches of sun-dried OP were characterized for their profile in phenolic compounds (by HPLC-DAD) and in vitro antioxidant properties (ABTS, FRAP and DPPH assays) before (methanolic extracts) and after (aqueous extracts) their simulated in vitro digestion and dialysis. Phenolic profiles, and, accordingly, the antioxidant activities, showed significant differences among the three OP batches, and most compounds showed good bioaccessibility after simulated digestion. Based on these preliminary screenings, the best OP aqueous extract (OP-W) was further characterized for its peptide composition and subdivided into seven fractions (OP-F). The most promising OP-F (characterized for its metabolome) and OP-W samples were then assessed for their potential anti-inflammatory properties in ex vivo human peripheral mononuclear cells (PBMCs) triggered or not with lipopolysaccharide (LPS). The levels of 16 pro-and anti-inflammatory cytokines were measured in PBMC culture media by multiplex ELISA assay, whereas the gene expressions of interleukin-6 (IL-6), IL-10 and TNF-α were measured by real time RT-qPCR. Interestingly, OP-W and PO-F samples had a similar effect in reducing the expressions of IL-6 and TNF-α, but only OP-W was able to reduce the release of these inflammatory mediators, suggesting that the anti-inflammatory activity of OP-W is different from that of OP-F.

Identification of umami peptides based on virtual screening and molecular docking from Atlantic cod (Gadus morhua)

Umami peptides have currently become the research focus in the food umami science field and the key direction for umami agent development. This is because umami peptides have good processing characteristics, umami and nutritional values. We here used virtual screening (including online enzymolysis through ExPASy PeptideCutter, bioactivity screening using the PeptideRanker, toxicity and physicochemical property prediction using Innovagen and ToxinPred software), molecular docking, and electronic tongue analysis to identify umami peptides generated from Atlantic cod myosin. Twenty-three putative umami peptides were screened from the myosin. Molecular docking results suggested that these 23 peptides could enter the binding pocket in the T1R3 cavity, wherein Glu128 and Asp196 were the main amino acid residues, and that hydrogen bonding and electrostatic interactions were the main binding forces. Twelve synthetic peptides tested on the electronic tongue exhibited umami taste and a synergistic effect with monosodium glutamate (MSG). Among them, GGR, AGCD, and SGDAW had higher umami intensities than the other peptides, while SGDAW and NDDGW exhibited stronger umami-enhancing capabilities in 0.1% MSG solution. This study offers a method for the rapid screening of umami peptides from marine protein resources and places the foundation for their application in the food industry.

Chitosan and HPMCAS double-coating as protective systems for alginate microparticles loaded with Ctx(Ile21)-Ha antimicrobial peptide to prevent intestinal infections

The incorrect use of conventional drugs for both prevention and control of intestinal infections has contributed to a significant spread of bacterial resistance. In this way, studies that promote their replacement are a priority. In the last decade, the use of antimicrobial peptides (AMP), especially Ctx(Ile²¹)-Ha AMP, has gained strength, demonstrating efficient antimicrobial activity (AA) against pathogens, including multidrug-resistant bacteria. However, gastrointestinal degradation does not allow its direct oral application. In this research, double-coating systems using alginate microparticles loaded with Ctx(Ile²¹)-Ha peptide were designed, and in vitro release assays simulating the gastrointestinal tract were evaluated. Also, the AA against Salmonella spp. and Escherichia coli was examined. The results showed the physicochemical stability of Ctx(Ile²¹)-Ha peptide in the system and its potent antimicrobial activity. In addition, the combination of HPMCAS and chitosan as a gastric protection system can be promising for peptide carriers or other low pH-sensitive molecules, adequately released in the intestine. In conclusion, the coated systems employed in this study can improve the formulation of new foods or biopharmaceutical products for specific application against intestinal pathogens in animal production or, possibly, in the near future, in human health.

Identification of Bioactive Peptides from a Laminaria digitata Protein Hydrolysate Using In Silico and In Vitro Methods to Identify Angiotensin-1-Converting Enzyme (ACE-1) Inhibitory Peptides

Bioactive peptides range in size from 2-30 amino acids and may be derived from any protein-containing biomass using hydrolysis, fermentation or high-pressure processing. Pro-peptides or cryptides result in shorter peptide sequences following digestion and may have enhanced bioactivity. Previously, we identified a protein hydrolysate generated from Laminaria digitata that inhibited ACE-1 in vitro and had an ACE-1 IC50 value of 590 µg/mL compared to an ACE-1 IC50 value of 500 µg/mL (~2.3 µM) observed for the anti-hypertensive drug Captopril©. A number of peptide sequences (130 in total) were identified using mass spectrometry from a 3 kDa permeate of this hydrolysate. Predicted bioactivities for these peptides were determined using an in silico strategy previously published by this group utilizing available databases including Expasy peptide cutter, BIOPEP and Peptide Ranker. Peptide sequences YIGNNPAKGGLF and IGNNPAKGGLF had Peptide Ranker scores of 0.81 and 0.80, respectively, and were chemically synthesized. Synthesized peptides were evaluated for ACE-1 inhibitory activity in vitro and were found to inhibit ACE-1 by 80 ± 8% and 91 ± 16%, respectively. The observed ACE-1 IC50 values for IGNNPAKGGLF and YIGNNPAKGGLF were determined as 174.4 µg/mL and 133.1 µg/mL. Both peptides produced sequences following simulated digestion with the potential to inhibit Dipeptidyl peptidase IV (DPP-IV).

In Silico Prospecting for Novel Bioactive Peptides from Seafoods: A Case Study on Pacific Oyster (Crassostrea gigas)

Pacific oyster (Crassostrea gigas), an abundant bivalve consumed across the Pacific, is known to possess a wide range of bioactivities. While there has been some work on its bioactive hydrolysates, the discovery of bioactive peptides (BAPs) remains limited due to the resource-intensive nature of the existing discovery pipeline. To overcome this constraint, in silico-based prospecting is employed to accelerate BAP discovery. Major oyster proteins were digested virtually under a simulated gastrointestinal condition to generate virtual peptide products that were screened against existing databases for peptide bioactivities, toxicity, bitterness, stability in the intestine and in the blood, and novelty. Five peptide candidates were shortlisted showing antidiabetic, anti-inflammatory, antihypertensive, antimicrobial, and anticancer potential. By employing this approach, oyster BAPs were identified at a faster rate, with a wider applicability reach. With the growing market for peptide-based nutraceuticals, this provides an efficient workflow for candidate scouting and end-use investigation for targeted functional product preparation.

Characterisation of a novel crustin isoform from mud crab, Scylla serrata (Forsskål, 1775) and its functional analysis in silico

A 336-base pair (bp) sized mRNA sequence encoding 111 amino acid size crustin isoform (MC-crustin) was obtained from the gill sample of the green mud crab, Scylla serrata. MC-crustin possessed an N-terminal signal peptide region comprising of 21 amino acid residues, followed by a 90 amino acid mature peptide region having a molecular weight of 10.164 kDa, charge + 4.25 and theoretical pI of 8.27. Sequence alignment and phylogenetic tree analyses revealed the peptide to be a Type I crustin, with four conserved cysteine residues forming the cysteine rich region, followed by WAP domain. MC-crustin was cationic with cysteine/proline rich structure and was predicted with antimicrobial, anti-inflammatory, anti-angiogenic and anti-hypertensive property making it a potential molecule for possible therapeutic applications.

Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection

SARS-CoV-2 and its variants cause serious health concerns throughout the world. The alarming increase in the daily number of cases has become a nightmare in many low-income countries; although some vaccines are available, their high cost and low vaccine production make them unreachable to ordinary people in developing countries. Other treatment strategies are required for novel therapeutic options. The peptide-based drug is one of the alternatives with low toxicity, more specificity, and ease of synthesis. Herein, we have applied structure-based virtual screening to identify potential peptides targeting the critical proteins of SARS-CoV-2. Non-toxic natural antiviral peptides were selected from the enormous number of peptides. Comparative modeling was applied to prepare a 3D structure of selected peptides. 3D models of the peptides were docked using the ClusPro docking server to determine their binding affinity and peptide-protein interaction. The high-scoring peptides were docked with other crucial proteins to analyze multiple targeting peptides. The two best peptides were subjected to MD simulations to validate the structure stability and evaluated RMSD, RMSF, Rg, SASA, and H-bonding from the trajectory analysis of 100 ns. The proposed lead peptides can be used as a broad-spectrum drug and potentially develop as a therapeutic to combat SARS-CoV-2, positively impacting the current pandemic.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11224-022-02113-9.

Identification of Bioactive Peptides from Nannochloropsis oculata Using a Combination of Enzymatic Treatment, in Silico Analysis and Chemical Synthesis

In vitro ACE-1 inhibitory peptides were characterised previously from a number of microalgal species including Spirulina platensis (peptide IAPG), Chlorella vulgaris (peptides FDL, AFL, VVPPA), Isochrysis galbana (peptide YMGLDLK), Chlorella sorokiniana (peptides IW and LW) and indeed Nannochloropsis oculata (peptides GMNNLTP and LEQ). The isolation of protein from Nannochloropsis oculata using a combination of ammonium salt precipitation and xylanase treatment of resulting biomass combined with molecular weight cut off filtration to produce a permeate and characterisation of bioactive peptides is described. The Angiotensin-1-converting enzyme (ACE-1) IC₅₀ value for the generated permeate fraction was 370 µg/mL. Ninety-five peptide sequences within the permeate fraction were determined using mass spectrometry and eight peptides were selected for chemical synthesis based on in silico analysis. Synthesized peptides were novel based on a search of the literature and relevant databases. In silico, simulated gastrointestinal digestion identified further peptides with bioactivities including ACE-1 inhibitory peptides and peptides with antithrombotic and calcium/calmodulin-dependent kinase II (CAMKII) inhibition. This work highlights the potential of Nannochloropsis oculata biomass as both a protein and bioactive peptide resource, which could be harnessed for use in the development of functional foods and feeds.

A novel peptide HSP-17 ameliorates oxidative stress injury and apoptosis in H9c2 cardiomyocytes by activating the PI3K/Akt pathway

Background

Oxidative stress and cell apoptosis play pivotal roles in the pathogenesis of doxorubicin (DOX)-induced myocardial injury. Heat shock protein-derived peptide (HSP-17) is a peptide which is low-expressed in DOX treated mouse heart tissue. It has high bioactivity and interspecies sequence consistency, and is predicted to have myocardial protective effect.

Methods

Firstly, we added 1 µM DOX to H9c2 cell culture medium for 24 hours to construct the myocardial cytotoxicity model. Then we detected the effect of HSP-17 on DOX induced H9c2 cardiomyocyte injury by measuring cell viability and lactate dehydrogenase (LDH) level. In addition, reactive oxygen species (ROS) and tetraethylbenzimidazolylcarbocyanine iodide kits are used to evaluate the effect of the HSP-17 peptide on DOX-induced oxidative stress injury to cardiomyocytes, and the detection of apoptosis related proteins and flow cytometry were applied to detect the level of apoptosis. Furthermore, the protein expression levels [phosphorylated Akt (p-Akt) and phosphorylated PI3K (p-PI3K)] of the PI3K/Akt pathway were also detected by western blotting.

Results

We found that the HSP-17 peptide can increase cell viability, protect mitochondrial potential, reduce LDH levels, and reduce ROS and cardiomyocyte apoptosis. In addition, we also observed that HSP-17 upregulated the expression level of p-Akt, and LY294002, a typical inhibitor of PI3K/Akt, was found to eliminate the protective roles of HSP-17.

Conclusions

In conclusion, this study demonstrated that the HSP-17 peptide protected H9c2 cells against oxidative stress and apoptosis via PI3K/Akt pathway activation, which provides a new idea for the treatment of DOX-induced myocardial injury.

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

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

Multi-Bioactivity of Protein Digests and Peptides from Oat (Avena sativa L.) Kernels in the Prevention of the Cardiometabolic Syndrome

The aim of this study was to characterize the digests and peptides derived from oat kernel proteins in terms of their major enzyme inhibitory activities related to the prevention of cardiometabolic syndrome. It also entailed the characteristics of antioxidant bioactivity of the analyzed material. The study was carried out using coupled in silico and in vitro methods. The additional goal was to investigate whether identified peptides can pervade Caco-2 cells. Based on the results of bioinformatic analysis, it was found that the selected oat proteins may be a potential source of 107 peptides with DPP-IV and/or ACE inhibitory and/or antioxidant activity. The duodenal digest of oat kernels revealed multiple activities. It inhibited the activities of the following enzymes: DPP-IV (IC₅₀ = 0.51 vs. 10.82 mg/mL of the intact protein), α-glucosidase (IC₅₀ = 1.55 vs. 25.20 mg/mL), and ACE (IC₅₀ = 0.82 vs. 34.52 mg/mL). The DPPH^• scavenging activity was 35.7% vs. 7.93% that of the intact protein. After in silico digestion of oat proteins, 24 peptides were selected for identification using LC-Q-TOF-MS/MS. Among them, 13 sequences were successfully identified. One of them, i.e., VW peptide, exhibited triple activities, i.e., DPP-IV and ACE inhibitory and DPPH^• scavenging activity. The multifunctional peptides: PW, TF, VF, and VW, were identified in the basolateral samples after transport experiments. Both in silico and in vitro analyses demonstrated that oat kernel proteins were the abundant sources of bioactive digests and peptides to be used in a diet for patients suffering from cardiometabolic syndrome.

Novel insight into the transformation of peptides and potential benefits in brown fermented goat milk by mesoporous magnetic dispersive solid phase extraction-based peptidomics

Brown fermented goat milk as an excellent source of bioactive peptides has only been partially elucidated. Meticulously synthesized MOF@MG as magnetic sorbent for enriching endogenous peptides owned higher reproducibility and uniform distribution of peptides PI compared with ultrafiltration. Combined with UHPLC-Q-Orbitrap, fermentation for 12 h in brown goat milk with the highest overall acceptable degree through sensory evaluation was utilized to explore the transformation of peptides and health benefits, with trypsin or plasmin hydrolyzing proteins and aminopeptidase or carboxypeptidase hydrolyzing peptides to small peptides or amino acids. A total of 1317 peptides were identified by database matching (1259) and de novo sequencing (58), among 18 peptides could originate from gene-independent enzymatic formation and top 25 characteristic peptides were quantified with concentration ranging from 0.12 to 6.40 mg L^-1. Bioinformatic analysis results indicated that brown fermented goat milk possesses higher health benefits because of more than 50 peptides with potential bioactivity.

In Silico Analysis of Bioactive Peptides Produced from Underutilized Sea Cucumber By-Products-A Bioinformatics Approach

Bioinformatic tools are widely used in predicting potent bioactive peptides from food derived materials. This study was focused on utilizing sea cucumber processing by-products for generating antioxidant and ACE inhibitory peptides by application of a range of in silico techniques. Identified peptides using LC-MS/MS were virtually screened by PepRank technique followed by in silico proteolysis simulation with representative digestive enzymes using BIOPEP-UWMTM data base tool. The resultant peptides after simulated digestion were evaluated for their toxicity using ToxinPred software. All digestive resistance peptides were found to be non-toxic and displayed favorable functional properties indicating their potential for use in a wide range of food applications, including hydrophobic and hydrophilic systems. Identified peptides were further assessed for their medicinal characteristics by employing SwissADME web-based application. Our findings provide an insight on potential use of undervalued sea cucumber processing discards for functional food product development and natural pharmaceutical ingredients attributed to the oral drug discovery process.

Antioxidant Potential of the Sweet Whey-Based Beverage Colada after the Digestive Process and Relationships with the Lipid and Protein Fractions

Whey-based beverages could be an effective way of reusing a by-product of th cheese industry, mitigating environmental hazards and, at the same time, profiting a useful food with high nutritional and antioxidant properties. In this study, a traditional Ecuadorian beverage (Colada) was prepared combining sweet whey, Maracuyá and barley. Antioxidant properties before and after an in vitro digestion using the INFOGEST method were determined, and relationships with intestinal transformations of the lipid and protein fractions were analyzed. The digestive process had a positive effect on antioxidant properties based on increased values of ABTS and FRAP located in the bioaccessible fraction (BF), together with strong increments of total polyphenols. Moreover, pretreatment of Caco-2 cells with the BF of Colada significantly reduced ROS generation (p < 0.001) measured by the dichlorofluorescein assay. Substantial changes of the fatty acid profile occurred during digestion, such as a fall of saturated fatty acids and a rise of polyunsaturated. The protein profile, examined by SDS-PAGE and exclusion molecular chromatography in the BF, showed that the major part of the proteins were digested in the intestinal phase. Analysis of NanoLC-MS/MS revealed 18 antioxidant peptides originated from whey proteins, but also 16 peptides from barley with potential antioxidant properties. In conclusion, combining sweet whey with Maracuyá and barley constitutes an excellent nutritional beverage with a strong antioxidant potential.

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

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

A Lupin (Lupinusangustifolius) Protein Hydrolysate Exerts Anxiolytic-Like Effects in Western Diet-Fed ApoE−/− Mice

Anxiety is the most prevalent psychiatric disorder worldwide, causing a substantial economic burden due to the associated healthcare costs. Given that commercial anxiolytic treatments may cause important side effects and have medical restrictions for prescription and high costs, the search for new natural and safer treatments is gaining attention. Since lupin protein hydrolysate (LPH) has been shown to be safe and exert anti-inflammatory and antioxidant effects, key risk factors for the anxiety process and memory impairment, we evaluated in this study the potential effects of LPH on anxiety and spatial memory in a Western diet (WD)-induced anxiety model in ApoE^−/− mice. We showed that 20.86% of the 278 identified LPH peptides have biological activity related to anxiolytic/analgesic effects; the principal motifs found were the following: VPL, PGP, YL, and GQ. Moreover, 14 weeks of intragastrical LPH treatment (100 mg/kg) restored the WD-induced anxiety effects, reestablishing the anxiety levels observed in the standard diet (SD)-fed mice since they spent less time in the anxiety zones of the elevated plus maze (EPM). Furthermore, a significant increase in the number of head dips was recorded in LPH-treated mice, which indicates a greater exploration capacity and less fear due to lower levels of anxiety. Interestingly, the LPH group showed similar thigmotaxis, a well-established indicator of animal anxiety and fear, to the SD group, counteracting the WD effect. This is the first study to show that LPH treatment has anxiolytic effects, pointing to LPH as a potential component of future nutritional therapies in patients with anxiety.

Structural and Biofunctional Insights into the Cyclo(Pro-Pro-Phe-Phe-) Scaffold from Experimental and In Silico Studies: Melanoma and Beyond

Short peptides have great potential as safe and effective anticancer drug leads. Herein, the influence of short cyclic peptides containing the Pro-Pro-Phe-Phe sequence on patient-derived melanoma cells was investigated. Cyclic peptides such as cyclo(Leu-Ile-Ile-Leu-Val-Pro-Pro-Phe-Phe-), called CLA, and cyclo(Pro-homoPro-β3homoPhe-Phe-), called P11, exert the cytotoxic and the cytostatic effects in melanoma cells, respectively. CLA was the most active peptide as it reduced the viability of melanoma cells to 50% of control at about 10 µM, whereas P11 at about 40 µM after 48 h incubation. Interestingly, a linear derivative of P11 did not induce any effect in melanoma cells confirming previous studies showing that cyclic peptides exert better biological activity compared to their linear counterparts. According to in silico predictions, cyclic tetrapeptides show a better pharmacokinetic and toxic profile to humans than CLA. Notably, the spatial structure of those peptides containing synthetic amino acids has not been explored yet. In the Cambridge Structural Database, there is only one such cyclic tetrapeptide, cyclo((R)-β2homoPhe-D-Pro-Lys-Phe-), while in the Protein Data Bank—none. Therefore, we report the first crystal structure of cyclo(Pro-Pro-β3homoPhe-Phe-), denoted as 4B8M, a close analog of P11, which is crucial for drug discovery. Comparative molecular and supramolecular analysis of both structures was performed. The DFT findings revealed that 4B8M is well interpreted in the water solution. The results of complex Hirshfeld surface investigations on the cooperativity of interatomic contacts in terms of electrostatic and energetic features are provided. In short, the enrichment ratio revealed O…H/H…O and C…H/H…C as privileged intercontacts in the crystals in relation to basic and large supramolecular H-bonding synthon patterns. Furthermore, the ability of self-assemble 4B8M leading to a nanotubular structure is also discussed.

Identification of Di/Tripeptide(s) With Osteoblasts Proliferation Stimulation Abilities of Yak Bone Collagen by in silico Screening and Molecular Docking

Endothelial protein C receptor (EPCR), cannabinoid receptor 2 (CBR2), and estrogen receptor α (ERα) play vital roles in osteoblasts proliferation. Also, collagen peptides have osteoblasts proliferation stimulation abilities, and di/tri-peptides could be absorbed by the intestine more easily. This study obtained three di/tripeptides with potential osteoblasts proliferation stimulation abilities of yak bone collagen, namely, MGF, CF, and MF, by in silico screening. Results suggested that these three peptides exhibited good absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. They also had strong affinities with EPCR, CBR2, and ERα, and the total -CDOCKER energy (-CE) values were 150.9469, 113.1835, and 115.3714 kcal/mol, respectively. However, further Cell Counting Kit-8 (CCK-8) assays indicated that only MGF could significantly (P < 0.05) stimulate osteoblasts proliferation at 0.3 mg/ml. At the same time, the proliferating index (PI) of the osteoblasts treated with MGF increased significantly (P < 0.05), and the alkaline phosphatase (ALP) activity decreased highly significantly (P < 0.01). In summary, MGF exhibited the potential to be an effective treatment for osteoporosis.

Identification of antidiabetic peptides derived from in silico hydrolysis of three ancient grains: Amaranth, Quinoa and Chia

The antidiabetic potential of bioactive peptides derived from simulated gastrointestinal digestion (SGID) of proteins present in amaranth quinoa and chia was evaluated using their bioactivity profile and theoretical interaction with DPP-IV and α-glucosidases. In silico SGID generated 52 different fragments with in vitro antidiabetic activity where fragments PW, PF, PPG, PM, SW, IW, SF, PP, PPL, PG, PY, VW and PL scored highly in bioactivity probability, with molecular weights ranging from 172.2 to 325.44 Da; positive bulkiness index and hydrophobicity (except PP and PY) and no toxic properties. Fragments IW and PW presented the lowest free energy values for enzymes DPP-IV, maltase-glucoamylase, pancreatic α-amylase and sucrase-isomaltase (-8.2, -7.5, -7.7 and -7.5 kcal/mol; and -7.8, -7.4, -8.2, -7.4 kcal/mol respectively) We can conclude that proteins from amaranth, quinoa and chia may be a good source of antidiabetic BP and may exert antidiabetic activity through the release of BP after digestion.

Peptidomics as a useful tool in the follow-up of food bioactive peptides

There is an intense research activity on bioactive peptides derived from food proteins in view of their health benefits for consumers. However, their identification is quite challenging as a consequence of their small size and low abundance in complex matrices such as foods or hydrolyzates. Recent advances in peptidomics and bioinformatics are getting improved sensitivity and accuracy and therefore such tools are contributing to the development of sophisticated methodologies for the identification and quantification of peptides. These developments are very useful for the follow-up of peptides released through proteolysis either in the food itself through the action of endogenous peptidases during processing stages like fermentation, drying or ripening, or from food proteins hydrolyzed by commercial peptidases or microorganisms with proteolytic activity. This chapter is presenting the latest advances in peptidomics and its use for the identification and quantification of peptides, and as a useful tool for controlling the proteolysis phenomena in foods and protein hydrolyzates.