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

Novel bioactive peptides from ginger rhizome: Integrating in silico and in vitro analysis with mechanistic insights through molecular docking

Ginger (Zingiber officinale) is widely recognised for its functional benefits, primarily attributed to its diverse phytochemicals. However, its proteome remains largely unexplored. This study hypothesised that isolated peptides may exhibit different bioactivities or more targeted mechanisms of action and could be investigated at a molecular level. Proteins were enzymatically hydrolysed under five conditions, and peptides were identified using LC-MS/MS. In silico screening suggested antioxidant, ACE-inhibitory, and antibacterial properties, further assessed through molecular docking and in vitro validation. 41 potentially bioactive peptides were identified. In vitro assays confirmed these properties for selected peptides, P1 (GSPVWIIPEPT), P2 (FASYPVKK), P3 (GPEKIFYDGPYL), and P4 (IAISPSYPIK). Notably, P4 exhibited potent mixed-type ACE-inhibition and bacteriostatic effects. Molecular docking provided mechanistic insights into these interactions. These findings highlight ginger as a promising source of bioactive peptides while underscoring the need to complement AI tools with in vitro and in vivo validations due to observed discrepancies.

Plant-derived bioactive peptides and protein hydrolysates for managing MAFLD: A systematic review of in vivo effects

Metabolic dysfunction-associated fatty liver disease (MAFLD) represents a growing health concern worldwide. Among the pursuit of therapeutic interventions, interest in natural bioactive compounds has intensified because of their potential hepatoprotective effects. This systematic review aims to evaluate the impact of plant-derived hydrolysates and peptides on MAFLD through the current literatures, encompassing their mechanisms of action. Key outcomes evaluated included changes in liver enzymes, liver lipid content, inflammation markers, and histopathological improvements. Preliminary findings suggest a potential beneficial effect of plant-derived hydrolysates and peptides on the improvement of MAFLD-related parameters, with mechanisms implicating antioxidant, anti-inflammatory, and lipid-lowering properties. This review highlights emerging evidence supporting the potential therapeutic role of plant-derived hydrolysates and peptides in the management of MAFLD. However, more well-designed clinical trials with larger sample sizes and longer durations are warranted to elucidate their efficacy, optimal dose, and long-term safety.

Identification, characterization, and molecular docking of immunomodulatory peptides in Astragalus (Astragalus membranaceus (Fisch.)Bge) seed protein hydrolysates

Developing bioactive peptides from natural plant sources into functional foods and immunomodulators is becoming an attractive approach. In this study, the protein hydrolysates (APH) of Astragalus membranaceus (Fisch.)Bge seed was prepared by alkaline protease digestion method, and components with less than 3KDa were obtained by ultrafiltration (UAPH). The peptide sequence of UAPH was identified by UPLC-MS/MS. silico analysis screened 46 peptides with biological activity. Cell experiments and molecular docking results showed that UAPH can regulate the immune activity of RAW264.7 cells by enhancing cell phagocytic activity and ROS generation, upregulating the expression of TNF -α, IL-6, IL-1β, and TLR4. Peptides DWVSLPG, WVSLPGVP, and FTSIVGNVF are expected to contribute to the immune regulatory activity of UAPH. This study first discovered that the hydrolyzed protein of A. membranaceus seed is a source of immunomodulatory agents, revealing the potential of A. membranaceus seed peptides in developing novel and effective immunomodulatory functional foods.

Screening novel anti-inflammatory peptides inhibiting the NLRP3 inflammasome from UHPLC-MS/MS-characterized peptide profiles of cocoa tea protein hydrolysates

Cocoa tea (Camellia ptilophylla) is a popular beverage enjoyed worldwide, yet its protein-rich residues are often underutilized during processing. In this study, proteins from cocoa tea were extracted and hydrolyzed with alkaline protease to produce cocoa tea protein hydrolysates (CTPH). The results showed that CTPH exhibited promising anti-inflammatory activity. To uncover bioactive peptides, the hydrolysates were analyzed using UHPLC-MS/MS, and potential peptides were screened through molecular docking targeting the NLRP3 inflammasome. In an in vitro model of NLRP3 inflammasome activation, two active peptides, LLR and LIGF, were found to significantly reduce IL-1β production in PMA-differentiated THP-1 macrophages following treatment with nigericin or ATP. These peptides interact with the NACHT domain of NLRP3 via hydrogen bonding and hydrophobic interactions. Their binding to NLRP3 was further confirmed by CETSA assay. These findings suggest that cocoa tea-derived peptides could offer therapeutic potential for managing inflammation.

Using novel approaches to conjugate peptides of Macrotermes bellicosus and Curcuma longa for targeted intervention of irritable bowl diseases caused by tumor necrosis factor superfamily member 15 (TNFSF15)

This study presents an in-silico approach to develop targeted therapies for Irritable Bowel Disease (IBD) by focusing on TNFSF15. Peptides derived from Macrotermes bellicosus and Curcuma longa were selected, conjugated with the 50S ribosomal protein L7/L12 adjuvant, and analyzed for immunogenic potential. Gene expression analysis showed differential TNFSF15 expression in gastrointestinal tissues. Functional enrichment revealed its role in immune regulation and cytokine signaling. Of the 20 peptides identified, 8 showed high antigenicity and 4 were allergenic. Structural modeling and docking predicted stable interactions with TNFSF15 (binding energy: -9.4 kJ/mol), supported by molecular dynamics. Immune simulations indicated robust IgM and IgG responses. These findings suggest that plant and insect derived peptides may offer promising therapeutic candidates for TNFSF15-associated IBD.

In silico prospecting of ADH activating peptides from Pacific oyster (Crassostrea gigas) and protective effect on ethanol-induced damage in HepG2 cells

Alcoholic liver disease (ALD) is becoming a major health threat in the world today. Alcohol dehydrogenase (ADH) plays an important role in alcohol metabolism. Pacific oyster (Crassostrea gigas) has been identified as a food-borne hepatoprotective agent. For the first time, we integrated in silico strategy, including simulated hydrolysis, bioinformatic prediction and molecular docking to screen ADH activating peptides from C. gigas. In vitro ADH activation activity and surface plasmon resonance (SPR) results showed that this strategy could stably screen ADH activating peptides. We selected six of them to further verify their protective effect on EtOH-induced HepG2 cells. Among them, peptide LQPPR (Leu-Gln-Pro-Pro-Arg) pretreatment increased cell viability, can effectively resist EtOH-induced cytotoxicity. And the transaminase (ALT, AST) in the cell supernatant decreased, indicating the cell damage was improved. The results also showed that the antioxidant capacity (SOD, GSH) of LQPPR pretreated cells increased, and the oxidative stress (MDA) decreased.

On the cellular selectivity of targeting peptide-nanoparticle conjugates - a nanoparticle perspective

INTRODUCTION

Peptide-targeted nanoparticles are promising drug carriers that can enhance drug efficacy at low systemic doses. However, clinical applications are compromised by off-target effects. Nanoparticle surface chemistry fine-tuning is key for solving these problems.

AREAS COVERED

The literature related to peptide-based, active targeting is reviewed, and critically discussed, with focus on the influence of surface chemistry influences on targetability. Furthermore, issues related to limited in vitro-in vivo predictivity are discussed.

EXPERT OPINION

The potential of more advanced in vitro methods for an increased in vivo prediction is discussed in combination with advanced computational approaches. Efforts toward enhancing endosomal escape are identified as key future developments, in combination with decreasing off-target effects.

Design, synthesis and evaluation of lysine- and leucine-rich hydrocarbon-stapled peptides as antibacterial agents

To address the challenge of antimicrobial resistance, we investigated new antibacterial peptides based on lysine- and leucine-rich sequences. We stabilised their membrane-active secondary structures by applying hydrocarbon stapling at sequence positions i and i+4. Stapling improved peptide structural stability in both aqueous and lipid environments, regardless of the staple position. It also enhanced antibacterial efficiency against both gram-negative and gram-positive bacteria, including antibiotic-resistant strains, with minimum inhibitory concentrations (MICs) of 2-4 μM (2.5-5.5 μg/mL). The stapled peptides showed increased resistance to enzymatic degradation, particularly with staples incorporated near the N-terminus, and were not haemolytic or cytotoxic at their MICs. Molecular dynamics simulations revealed how stapling aids in (i) stabilising the membrane-active secondary structure of amphipathic peptides and (ii) accelerating their membrane insertion. Our results provide insight into peptide design for antimicrobial use. We show that hydrocarbon stapling of lysine- and leucine-rich short sequences may offer a pathway towards more stable and effective antibacterial agents.

Identification of bioaccessible and neuroprotective peptides from fermented casein hydrolysate

Fermented dairy products are beneficial to cognitive health. Fermentation-released bioactive peptides have the potential to contribute to the neuroprotective effects of fermented dairy products. However, known neuroprotective peptides are mostly prepared by enzymatic hydrolysis, and physicochemical screening of food-derived functional peptides typically overlooks the interference of biotransport after ingestion. Thus, we aimed to identify neuroprotective peptides from casein fermented by Lactobacillus delbrueckii ssp. bulgaricus to provide more evidence supporting the contribution of fermentation-released peptides. We first screened bioaccessible peptides from fermented casein hydrolysate by simulating digestion, absorption, and blood-brain barrier penetration using INFOGEST standardized protocols, human colon Caco-2 cells, and human brain microvascular endothelial hCMEC/D3 cells sequentially. Next, we identified peptides of each stage by nano-liquid chromatography tandem MS. The intersections were considered bioaccessible peptides. We performed molecular docking against Kelch-like ECH-associated protein 1 (Keap1) to predict potential bioactive peptides and validated the predicted effects in BV2 microglial cells induced by LPS. As a result, we identified 1,971, 663, 276, and 208 casein peptides from the simulated products at each stage, and 63 bioaccessible peptides were identified during fermentation, underwent simulated digestion, and were transported via the simulated intestinal epithelial barrier and blood-brain barrier. Among these peptides, 7 nontoxic small peptides had relatively high predicted affinities for Keap1 and were verified in LPS-treated BV2 cells. We found that Phe-Val-Ala-Pro-Phe-Pro-Glu (FE7) decreased nitric oxide, IL-1β, reactive oxygen species, and lipid peroxidation levels by 69.6%, 103.6%, 119.3%, and 75.3%, respectively, in LPS-treated BV2 cells. In conclusion, FE7 could be a promising neuroprotective peptide in fermented casein hydrolysate by reducing neuroinflammation and oxidative stress. Our approach provides a feasible paradigm for identifying bioaccessible and neuroprotective peptides from dairy products.

Identification and exploration of the potential antiaging role of the novel antioxidant peptide DGGY derived from yak milk proteins

Yak milk has substantial nutritional value yet remains underutilized for high-value applications. Because yak milk is a rich source of bioactive peptides due to its elevated protein composition, this study investigated yak milk-derived peptides with antioxidant properties and their potential antiaging mechanisms. First, 8 major yak milk proteins were hydrolyzed in silico via BIOPEP. Compared with other enzymes, proteinase K plus subtilisin could generate more antioxidant peptides. Six potential antioxidant peptides were efficiently screened in silico; DGGY presented the strongest hydroxyl radical scavenging rate, and its antioxidant activity was further verified in Caenorhabditis elegans. Additionally, the results of network pharmacology analysis suggested an antiaging role of DGGY, which was validated in C. elegans; specifically, supplementation with DGGY (50 and 300 μg/mL) significantly extended the life span of C. elegans by regulating the expression of related genes (including sod-3, snk-1, daf-16, daf-2, and hsp-16.2). In summary, a novel yak milk protein-derived antioxidant peptide, DGGY, was efficiently screened and found to exert potential antiaging effects. This study provides a method for the high-value utilization of yak milk and novel information for antiaging research.

Identification and Taste Characteristics of Six Novel Umami Peptides from Mytilus coruscus and Their Interaction with the T1R1/T1R3 Receptor

Mytilus coruscus is a commercially significant shellfish, highly regarded for its umami taste. In this study, umami taste peptides in M. coruscus were isolated and characterized through virtual screening, molecular docking, molecular dynamics simulations, sensory evaluation, and electronic tongue assessment. In silico enzymatic hydrolysis of M. coruscus myosin was performed, enabling the selection of six potential umami peptides (CR, ACR, GAR, PDL, PDPN, and SDADCF) based on predictions of umami taste, biological activity, toxicity, and water solubility. The interaction mechanisms between these peptides and the umami receptor T1R1/T1R3 were analyzed through molecular docking and dynamics simulations, revealing that SDADCF exhibited the most stable binding with T1R1/T1R3. The key residues of Asp, His, Glu, and Ser in T1R1 and T1R3 were identified as crucial active sites for umami peptide binding. Hydrogen bonding and electrostatic interactions were found to be the primary forces driving this binding. Furthermore, the umami taste of these peptides was validated using sensory evaluation, indicating that SDADCF had the most intense umami taste (umami score of 5.8) and a threshold of 0.25-0.99 mmol/L for the six peptides. Electronic tongue analysis further recognized the umami taste of the peptides. The identification of these six umami peptides contributes to a deep molecular basis of the strong umami taste within M. coruscus.

Compositional profiling of protein hydrolysates by high resolution liquid chromatography-mass spectrometry and chemometric analysis

Protein hydrolysates have attracted growing research and commercial attention due to their numerous nutritional, functional, and biological activities. However, only a limited range of proximate properties are determined routinely due to their substantial structural complexity and compositional variability. From both a manufacturing and functional perspective, it is of critical importance to monitor the compositional variations and identify potential similar or disparate features between different protein hydrolysates. In the current study, a single-approached method employing reverse phase ultra-high performance liquid chromatography coupled to high resolution electrospray ionization tandem mass spectrometry (RP-UHPLC-HR-ESI-MS/MS) was developed, optimized, and cross-validated for comprehensive structural and compositional profiling of a range of protein hydrolysates of varying raw materials, including soy, cotton, wheat, rice, and meat. Untargeted chemometric analysis and feature-based molecular network demonstrated potential for large-scale compositional assessment of protein hydrolysates without the need of prior component annotation. Signature features were identified to differentiate soy hydrolysates prepared from different batches of raw material and by different manufacturing processes. A hybrid approach combining de novo sequencing and target-decoy database homology search for peptide annotation is also described. Short peptides of 2 to 5 amino acids represented the most abundant components in soy protein hydrolysates (SPHs). A simple yet reliable integrated workflow for comprehensive structural and compositional profiling of protein hydrolysates was developed to enable an eventual correlation between their structure and function.

Antioxidant bioactivity of sunflower protein hydrolysates in Caco-2 cells and in silico structural properties

Sunflower protein hydrolysate (SPH), with 95 % reduced phenolic content, was studied for its protective effects against oxidative stress in intestinal cells (Caco-2). Produced via alcalase hydrolysis, SPH's molecular weight, amino acid composition, and hydrophobicity were characterized. The antioxidant activity of SPH, tested by ABTS, was maintained in Caco-2 cells under oxidative stress, modulating glutathione and catalase enzymes. LC/MS/MS identified 196 peptides, which were cross-referenced with a bioactive database and found to contain several di- and tripeptides with antioxidant activity. Higher hydrophobicity and molecular weight correlated with predicted antioxidant and anti-inflammatory activity scores, provided by tools that use machine learning methods. The study shows that SPH exhibits antioxidant properties in enterocyte cell models, even with reduced phenolic content, suggesting its potential use in functional foods.

Cold argon plasma-modified pea protein isolate: A strategy to enhance ink performance and digestibility in 3D-printed plant-based meat

Pea protein isolate (PPI) is rich in protein and low in allergenicity, but its poor functionality limits its application in 3D food printing. This study examined the effects of cold argon plasma (CP) pre-treatment of PPI combined with sodium carboxymethyl cellulose on the ink properties of 3D-printed plant-based meat and its digestive characteristics. The results showed that CP treatment significantly increased the apparent viscosity and storage modulus of the PPI-polysaccharide mixture through hydrogen bonding and other molecular interactions, improving the self-supporting ability and printing accuracy of the plant-based meat. X-ray diffraction (XRD) and microstructural analysis revealed that CP treatment altered the secondary structure of PPI, improved its compatibility with polysaccharides, reduced surface roughness and pore size, and resulted in a more compact and regular network structure. Additionally, CP treatment shortened the bound water relaxation time, indicating stronger interactions that promoted gel formation. During gastrointestinal digestion, CP-modified plant-based meat exhibited improved digestibility, with a significant rise in the number and relative abundance of bioactive peptides, thereby enhancing bioavailability. These findings provided a theoretical foundation for the application of CP treatment in plant-based products enriched with PPI and other plant proteins, offering new insights into the development of highly functional plant-protein foods.

ACE- and DPP-IV-Inhibitory Peptides from Bambara Groundnut Hydrolysate: Elucidation Using Computational Tools and Molecular Docking

Hypertension and type 2 diabetes are the major metabolic syndromes, often managed using synthetic ACE and DPP-IV inhibitors that may cause adverse effects on health. This study investigated Bambara groundnut protein hydrolysates as a natural source of dual ACE- and DPP-IV-inhibitory peptides. Protein isolates were hydrolyzed using Flavourzyme, and the resulting peptides were fractionated using membranes with different molecular weight cut-offs. Those fractions were then analyzed for enzyme inhibition. Peptides were identified by LC-MS/MS and screened using PeptideRanker and BIOPEP-UWM, followed by molecular docking against ACE (PDB: 1O8A) and DPP-IV (PDB: 1NU6). The >10 kDa and 5-10 kDa fractions showed the highest ACE- and DPP-IV-inhibitory activities, respectively. Some peptides such as YKDGLYSPHW, LPVSTPGKF, and EPWWPK displayed strong binding affinities (ΔG: -10.2 to -11.3 kcal/mol for ACE, -8.6 to -9.1 kcal/mol for DPP-IV) and interacted with key catalytic residues, including His387 and Glu411 in ACE, and Ser630, Glu205, and Phe357 in DPP-IV. These findings highlight the potential of Bambara groundnut hydrolysates or peptides as a source of natural ACE and DPP-IV inhibitors.

Preparation, identification, and molecular mechanism of novel DPP-IV inhibitory peptides from pumpkin seed: In silico screening and experimental validation

The rising prevalence of Type 2 diabetes mellitus (T2DM) and the limitations of synthetic DPP-IV inhibitors emphasize the need for natural alternatives with fewer side effects. This study explored pumpkin seed protein (PSP) as a source of potential DPP-IV inhibitory peptides. Through in silico screening and experimental validation, seven novel peptides were identified, with LPGFF, LPGF, and MPLPA exhibiting potent inhibitory activities (IC50: 449.68-478.88 μM). Molecular docking and dynamics simulations revealed stable binding to DPP-IV's active site, interacting with key residues (Tyr547, Ser630, Tyr662, Arg125, Glu205). Kinetic analysis indicated competitive inhibition. In vivo studies in C57BL/6 J mice demonstrated significant hypoglycemic effects, reducing blood glucose AUC by 14.98-18.65 % at 100 mg/kg. The peptides also exhibited stability under varying temperatures, pH, and gastrointestinal conditions. These findings position PSP as a promising source of DPP-IV inhibitors and highlight the potential of in silico screening for bioactive peptide discovery in T2DM management.

Characterization of Rugulopteryx okamurae algae: A source of bioactive peptides, omega-3 fatty acids, and volatile compounds

This study provides a detailed characterization of the invasive algae Rugulopteryx okamurae, highlighting its nutritional composition, mineral content, and potential bioactive compounds. This biomass contains 14.18 % protein, 21.29 % lipids (with a high omega-3 content), fibre (31.32 %), and significant amounts of minerals like calcium, sodium, potassium, sulphur, and iron. Phenolic compounds (0.74 %) and volatile compounds, such as retinol, were also identified. Peptidome analysis revealed 626 unique peptides, with 21 low molecular weight peptides showing potential activity against angiotensin converting enzyme and dipeptidyl peptidase IV when assessed using in silico tools and using molecular docking. Additionally, the antioxidant capacity of the alga was demonstrated with a significant free radical inhibition (EC50: 2.09 mg/mL). Overall, this study provides initial evidence on the nutritional potential of R. okamurae, which may have potential for future applications in food and biotechnology fields.

Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide

Peptide hormones, a class of pharmacologically active molecules, have a critical role in regulating energy homeostasis. Prohormone convertase 1/3 (also known as PCSK1/3) represents a key enzymatic mechanism in peptide processing, as exemplified with the therapeutic target glucagon-like peptide 1 (GLP-1)1,2. However, the full spectrum of peptides generated by PCSK1 and their functional roles remain largely unknown. Here we use computational drug discovery to systematically map more than 2,600 previously uncharacterized human proteolytic peptide fragments cleaved by prohormone convertases, enabling the identification of novel bioactive peptides. Using this approach, we identified a 12-mer peptide, BRINP2-related peptide (BRP). When administered pharmacologically, BRP reduces food intake and exhibits anti-obesity effects in mice and pigs without inducing nausea or aversion. Mechanistically, BRP administration triggers central FOS activation and acts independently of leptin, GLP-1 receptor and melanocortin 4 receptor. Together, these data introduce a method to identify new bioactive peptides and establish pharmacologically that BRP may be useful for therapeutic modulation of body weight.

Genomic and Computational Analysis Unveils Bacteriocin Based Therapeutics against Clinical Mastitis Pathogens in Dairy Cows

Clinical mastitis (CM) remains a critical challenge in dairy production, exacerbated by the global rise of antibiotic-resistant pathogens, which threatens herd health and productivity. This study pioneers a dual genomic-computational strategy to develop bacteriocin-based therapeutics-a promising alternative to conventional antibiotics-by targeting conserved virulence mechanisms in CM-causing pathogens. We aimed to (i) identify essential core proteins in CM-causing pathogens of dairy cows using the genomic approach; and (ii) assess the efficacy of bacteriocin peptides (BPs) as novel therapeutic agents targeting the selected core proteins for sustainable management of mastitis. Through pan-genomic analysis of 16 clinically relevant pathogens, including Staphylococcus aureus, S. warneri, Streptococcus agalactiae, S. uberis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, P. putida, and P. asiatica, we identified 65 evolutionarily conserved core proteins. Prioritization based on essentiality, virulence, and resistance potential revealed Rho (transcription termination factor) and HupB (nucleoid-associated protein) as high-value therapeutic targets due to their critical roles in bacterial survival and pathogenicity. A computational screen of 70 BPs identified 14 candidates with high binding affinity for both Rho and HupB proteins. Molecular dynamics simulations demonstrated that BP8, a novel dual-action bacteriocin, competitively inhibits Rho-mediated transcription termination and disrupts HupB-DNA interactions, effectively crippling bacterial replication and virulence. BP8 exhibited superior structural stability and binding efficacy compared to other candidates, positioning it as a potent broad-spectrum agent against diverse CM pathogens, including multidrug-resistant strains. Our study underscores the untapped potential of bacteriocins in veterinary medicine, offering a sustainable solution to mitigate antibiotic overuse and resistance. The computational validation of BP8 provides a foundational framework for developing targeted therapies, with implications for reducing dairy industry losses and improving animal welfare. Further in vitro and in vivo studies are warranted to translate these insights into practical therapeutics.

Hydrolyzing collagen by extracellular protease Hap of Aeromonas salmonicida: Turning chicken by-products into bioactive resources

Collagen-rich meat processing by-products have potential utilization value. Extracellular protease Hap from meat-borne Aeromonas salmonicida has been identified as an ideal protease for hydrolyzing collagen. Here, to explore the possible application of Hap for giving chicken by-products a high added value, the hydrolysis ability and mechanism were investigated. With a Vmax of 31.9 μg/mL/min and a Km of 1.18 mg/mL, Hap demonstrated obvious substrate specificity to pepsin-solubilized collagen (PSC) derived from chicken by-products, and significantly affected the tertiary structure and microstructure of PSC. Hap was found to preferentially cleave the peptide bond between Gly-X by peptide release kinetics, attacking from two ends to the middle region for α1 chain. Sixteen peptides are anticipated to be non-toxic with twenty potential biological activities at the end of hydrolysis. These observations will enrich the collagen hydrolysis mechanism of protease secreted by meat-borne bacteria and provide new insights into the utilization of meat by-products.

Main methods and tools for peptide development based on protein-protein interactions (PPIs)

Protein-protein interactions (PPIs) regulate essential physiological and pathological processes. Due to their large and shallow binding surfaces, PPIs are often considered challenging drug targets for small molecules. Peptides offer a viable alternative, as they can bind these targets, acting as regulators or mimicking interaction partners. This review focuses on competitive peptides, a class of orthosteric modulators that disrupt PPI formation. We provide a concise yet comprehensive overview of recent advancements in in-silico peptide design, highlighting computational strategies that have improved the efficiency and accuracy of PPI-targeting peptides. Additionally, we examine cutting-edge experimental methods for evaluating PPI-based peptides. By exploring the interplay between computational design and experimental validation, this review presents a structured framework for developing effective peptide therapeutics targeting PPIs in various diseases.

Investigation of Anticancer Peptides Derived from Arca Species Using In Silico Analysis

This study employed an integrated in silico approach to identify and characterize anticancer peptides (ACPs) derived from Arca species. Using a comprehensive bioinformatics pipeline (BIOPEP, ToxinPred, ProtParam, ChemDraw, SwissTargetPrediction, and I-TASSER), we screened hydrolyzed bioactive peptides from Arca species, identifying seventeen novel peptide candidates. Subsequent in vitro validation revealed three peptides (KW, WQIWYK, KGKWQIWYKSL) with significant anticancer activity, demonstrating both high biosafety and clinical potential. Our findings highlight Arca species proteins as a valuable source of therapeutic ACPs and establish bioinformatics as an efficient strategy for rapid discovery of bioactive peptides. This approach combines computational prediction with experimental validation, offering a robust framework for developing novel peptide-based therapeutics.

Enhancement of Apostichopus japonicus peptide flavor through bacterial and enzyme co-fermentation (BECF) and the identification of novel antioxidant peptides in the fermented product

In this study, we optimized the BECF process parameters by single-factor experiments and response surface methodology (RSM). Additionally, various analytical techniques were employed to determine the volatile flavor compounds, amino acid composition, and peptide sequences of the fermented product. The antioxidant activities of 10 peptides were evaluated via free radical scavenging assays. The results indicated that the optimal BECF conditions for Apostichopus japonicus body wall (AJBW) were as follows: 2.3 % bacterial inoculum, fermentation for 31 h at 30 °C, 463 U/g enzyme dosage, and enzymatic hydrolysis at 50 °C for 4 h. Gas chromatography-ion mobility spectrometry analysis revealed a significant reduction in aldehydes, which impart a pungent odor, in the co-fermented product (AJM) as compared to the control. While the content of alcohols, ketones, and esters, which contribute to aromatic flavors, was significantly increased. The content of essential amino acids in AJM, as analyzed through an automatic amino acid analyzer, was slightly higher compared to that in AJBW. Liquid chromatography-tandem mass spectrometry identified a total of 808 sea cucumber peptide fragments with high confidence. DPPH, ABTS, and hydroxyl radical scavenging assays revealed that peptides LFW and LFPW exhibited the strongest antioxidant activities. Molecular docking studies showed significant hydrogen-bonding interactions. In conclusion, BECF is an effective strategy for enhancing the flavor of A. japonicus peptide.

In silico toxicology investigation of μ-conotoxin KIIIA on human Na+ channel Nav1.2

Conotoxins(CTXs) can specifically act on multiple ion channels, which are crucial for the development of neurobiology and novel targeted drug development. At present, >10,000 kinds of CTXs have been sequenced, it would be extremely laborious to conduct experiments for each. μ-CTX KIIIA is a type of substance that can selectively recognize voltage-gated sodium ion channels. This article constructs four derivatives of KIIIA and predicts their 3D structures; afterwards, their molecular orbital arrangements and physicochemical properties were calculated using DFT; then, predicted their toxicokinetic parameters such as absorption, distribution, metabolism, excretion (ADME) and toxicity (T) through Machine Learning (ML); finally, molecular docking and molecular dynamics are used to investigate the interaction modes and binding affinity. The results indicate that the toxicity of KIIIA and its derivatives (KIIIA-1 -KIIIA-4) to the human body is mainly concentrated in the liver and respiratory tract. Among four derivatives, KIIIA-2 (5 Ser → Arg) has better toxicokinetics properties and its binding energy to Nav1.2 is -65.32 kcal/mol, which is higher than that of wild type(-32.13 kcal/mol). This study indicate that computational toxicology can facilitate the druggability research of CTXs, and KIIIA-2 can be developed as a potential antiepileptic drug.

Antidiabetic and Immunomodulatory Properties of Peptide Fractions from Sacha Inchi Oil Press-Cake

Sacha inchi (SI) oil press-cake (SIPC), a by-product of the sacha inchi oil extraction process, represents a novel protein source with potential bioactive applications in food. In this study, a sacha inchi protein concentrate (SPC) derived from SIPC was subjected to simulated gastrointestinal digestion (SGID) using the INFOGEST 2.0 protocol. The resulting digests were fractionated by ultrafiltration (<3, 3-10, and >10 kDa), and the bioactive properties of the peptide fractions were evaluated. In vitro α-amylase inhibition was assessed, along with immunomodulatory markers (NO, IL-6, and TNF-α), in an ex vivo RAW 264.7 cell model. Both gastric and intestinal digests exhibited significant α-amylase inhibition (20-45%), with the <3 kDa intestinal fraction showing the highest inhibition (45% at 20 mg/mL). Both gastric and intestinal <3 kDa fractions reduced NO production in RAW 264.7 macrophages subjected to a lipopolysaccharide challenge. HPLC-MS/MS analysis facilitated de novo sequencing of the peptide fractions, identifying 416 peptides resistant to SGID through the find-pep-seq script, which were further assessed in silico for toxicity, allergenicity, and bioavailability, revealing no significant risks and potential drug-likeness development. Molecular docking simulations of three peptides (RHWLPR, RATVSLPR, and QLSNLEQSLSDAEQR) with α-amylase and four peptides (PSPSLVWR, RHWLPR, YNLPMLR, and SDTLFFAR) with the TLR4/MD-2 complex suggesting potential roles in α-amylase inhibition and anti-inflammatory activity, respectively. The findings suggest that SI protein concentrates could be used in functional foods to prevent starch breakdown through α-amylase-inhibiting peptides released during digestion, reduce blood glucose, and mitigate inflammation and oxidative tissue damage.

Investigation of solid-state fermentation of red seaweed (Pyropia spp.) with lactic acid Bacteria: Effects on protein profile and in vitro digestibility

This study aimed to investigate the effects of solid-state fermentation (SSF) on the protein profile and digestibility of red seaweed (Pyropia spp.). The results indicated that compound lactic acid bacteria (LAB) performed better than a single strain in terms of growth and metabolism on the red seaweed substrate. Specifically, the simultaneous inoculation of Lactobacillus reuteri and Lactobacillus paracasei (at a 1:2 ratio) for 3 days significantly increased the soluble protein content in red seaweed than other inoculation schemes. Under these conditions, more free peptides were detected in the SSF samples. Among these, 58 peptide segments were predicted to have biological functions. Furthermore, SSF samples were more easily digested by gastric and intestinal fluids in vitro which led to higher antioxidant activity in the digesta. Overall, this study provides valuable insights into enhancing the nutritional value and functional properties of seaweed, contributing to the development of seaweed-processed products for food applications.

Discovery of PD-L1 Peptide Inhibitors from Ascidian Enzymatic Hydrolysates by Affinity Ultrafiltration Coupled to NanoLC-MS/MS

Anti-PD-1 and anti-PD-L1 antibodies have achieved great clinical success in cancer immunotherapy, and peptide and small molecule inhibitors of PD-1/PD-L1 binding also attract much attention. Ascidians are not only seafood, but are also an important source of bioactive substances, including anti-tumor components. In this study, ascidian enzymatic hydrolysates were found to contain PD-1/PD-L1 inhibitory components. Affinity ultrafiltration (AUF) coupled with the nanoLC-MS/MS method was first applied in screening for PD-L1 peptide inhibitors from ascidian enzymatic hydrolysates. Two anti-PD-L1 ascidian peptides, C5 (LDVVIHTVTYGDR) and S2 (VLRDNIQGITKPAIR), were filtered out from the ascidians Ciona intestinalis and Styela clava, respectively. C5 and S2 showed moderate anti-PD-1/PD-L1 effects with the IC50 values of 33.9 µM (C5) and 112.8 μM (S2), respectively, by homogenous time-resolved fluorescence (HTRF) binding assay, and the KD values of 22.9 µM (C5) and 29.1 µM (S2), respectively, by surface plasmon resonance (SPR) assay. The results of this study suggest that ascidian enzymatic hydrolysates may be a potential source of bioactive peptides with anti-PD-1/PD-L1 activity.

Bioactive peptides as multipotent molecules bespoke and designed for Alzheimer's disease

In an increasingly aging world where neurodegenerative diseases (NDs) are exponentially rising, research into more effective and innovative treatments seems paramount. Bioactive peptides (BPs) emerge as promising compounds with revolutionary potential in the treatment of NDs, particularly in well-known conditions like Alzheimer's disease (AD). The biological potential of these compounds is primarily attributed to their drug development advantages such as enhanced penetration, low toxicity, and rapid clearance, as well as, their antioxidant, and anti-inflammatory properties bio-linked to the neuroprotective effect, able to attenuate the multifactorial pathologies of AD. BPs can be sourced from common dietary origins, like animals, plants, marine, and from emerging sources like edible insects. However, to isolate an active BP with beneficial biological effects it must first be released from its parent protein, followed by a synthesis-flow. While in silico approaches can predict a BP's potential bioactivity and structural characteristics, in vitro, cell-based, and in vivo assays should be conducted to ensure these properties. The blood-brain-barrier (BBB) microenvironment and permeability in health or disease state are key factors to consider since they can limit the ability of circulating therapeutical agents, including BPs, to reach the brain. This review focuses on the bioactivity properties of BPs from different dietary protein sources and explores their beneficial effect and neuroprotective activity in AD, unraveling new paths of treatment.

Identification and Molecular Mechanism of Novel α-Glucosidase Inhibitory Peptides from the Hydrolysate of Hemp Seed Proteins: Peptidomic Analysis, Molecular Docking, and Dynamics Simulation

There is a growing demand for natural and potent α-glucosidase inhibitors due to the rising prevalence of diabetes. In this study, newly identified α-glucosidase inhibitory peptides were identified from the tryptic hydrolysate of hemp seed proteins based on peptidomics and in silico analysis. A total of 424 peptides, primarily derived from four cupin-type-1 domain-containing proteins, were identified, and 13 ultimately were selected for validation based on their higher PeptideRanker scores, solubility, non-toxicity, and favorable ADMET properties. Molecular docking revealed that these 13 peptides primarily interacted with α-glucosidase via hydrogen bonding and hydrophobic interactions. Among them, three novel peptides-NPVSLPGR (-8.7 kcal/mol), LSAERGFLY (-8.5 kcal/mol), and PDDVLANAF (-8.4 kcal/mol)-demonstrated potent α-glucosidase inhibitory activity due to their lower binding energies than acarbose (-8.1 kcal/mol), the first approved α-glucosidase inhibitor for type 2 diabetes treatment. The molecular mechanism analysis revealed that the peptides NPVSLPGR and LSAERGFLY inhibited α-glucosidase by simultaneously blocking substrate entry through occupying the entrance of the active site gorge and preventing catalysis by binding to active sites. In contrast, the peptide PDDVLANAF primarily exerted inhibitory effects by occupying the entrance of the active site gorge. Molecular dynamics simulation validated the stability of the complexes and provided additional insights into the molecular mechanism determined through docking. These findings contribute essential knowledge for the advancement of natural α-glucosidase inhibitors and offer a promising approach to effectively manage diabetes.

TRPA1-Activated Peptides from Saiga Antelope Horn: Screening, Interaction Mechanism, and Bioactivity

Saiga antelope horn (SAH), a rare traditional Chinese medicine, exhibits activities of anti-feverish convulsions and anti-inflammation, whereas its underlying mechanism and specific pharmacological components are still unclear. In the present study, transient receptor potential ankyrin 1 (TRPA1), a major transient receptor potential cation channel was used as a target protein to identified TRPA1 high-affinity peptides (THPs) from SAH digests. Firstly, the SAH was digested under in vitro gastrointestinal conditions. With the method of affinity ultrafiltration and liquid chromatography-mass spectrometry (AUF-LC/MS), about 200 peptides that have a high-affinity interaction with the TRPA1 protein were screened from SAH digests. Subsequently, bioactivity databases and molecular docking were further exploited to identified three THPs, including RCWPDCR, FGFDGDF, and WFCEGSF. Furthermore, RIN-14B cells, characterized by the high expression of TRPA1 on cell surfaces, were used as the cell model to investigate the biological effect of THPs. Immunofluorescence and ELISA were conducted and showed that THPs can increase the intracellular Ca2+ concentration and serotonin (5-HT) secretion in RIN-14B cells by activating TRPA1, which is evidenced by impaired upregulation of intracellular Ca2+ levels and 5-HT secretion after pretreatment with the TRPA1 inhibitor (HC-030031). Moreover, an analysis of Western blots displayed that THPs up-regulated the expression levels of the 5-HT synthesis rate-limiting enzyme (TPH1) and 5-hydroxytryptophan decarboxylase (Ddc), while serotonin reuptake transporter (SERT) levels were down-regulated, suggesting that THPs enhance 5-HT secretion by regulating the 5-HT synthesis pathway. In summary, our findings demonstrate that THPs, which were identified from SAH digest via TRPA1-targeted affinity panning, exhibited the activation of the TRPA1 channel and enhanced 5-HT release in RIN-14B cells.

Angiotensin-Converting Enzyme (ACE)-Inhibitor Activity of Novel Peptides Derived from Porcine Liver and Placenta

Peptides isolated from various biological materials are potential sources for novel angiotensin-converting enzyme (ACE) inhibitors. Here, the ACE-inhibitory activity of peptides derived from papain-digested hydrolysates of porcine liver and placenta were investigated. A high-throughput method was developed to identify potential bioactive peptides from the hydrolysates using in silico enzymatic cleavage, HPLC-MS/MS, and bioinformatics tools. Four peptides (FWG, MFLG, SDPPLVFVG, and FFNDA) were selected based on their predicted bioactivity, then synthesised and tested for ACE inhibition. All samples demonstrated ACE-inhibitory activity, with FWG and MFLG showing greater potency than SDPPLVFVG and FFNDA. The placenta hydrolysate outperformed both the liver hydrolysate and synthetic peptides in ACE inhibition, possibly due to it containing a higher proportion of dipeptides. The synthetic peptides' IC50 values were comparable to those reported for porcine muscle-derived peptides in previous studies. While less potent than the commercial ACE inhibitor captopril, the identified peptides showed promising ACE-inhibitory activity. This research demonstrates the potential of porcine liver and placenta as sources of novel ACE-inhibitory peptides and highlights the effectiveness of the developed high-throughput method for identifying bioactive peptides; this method could subsequently be adapted to other peptide sources, facilitating the development of innovative functional foods or nutraceuticals.

Exploring Tenebrio molitor as a source of low-molecular-weight antimicrobial peptides using a n in silico approach: correlation of molecular features and molecular docking

BACKGROUND

Yellow mealworm (Tenebrio molitor) larvae are increasingly recognized as a potential source of bioactive peptides due to their high protein content. Antimicrobial peptides from sustainable sources are a research topic of interest. This study aims to characterize the peptidome of T. molitor flour and an Alcalase-derived hydrolysate, and to explore the potential presence of antimicrobial peptides using in silico analyses, including prediction tools, molecular docking and parameter correlations.

RESULTS

T. molitor protein was hydrolysed using Alcalase, resulting in a hydrolysate (TMH10A) with a 10% degree of hydrolysis. The peptidome was analysed using LC-TIMS-MS/MS, yielding over 6000 sequences. These sequences were filtered using the PeptideRanker tool, selecting the top 100 sequences with scores >0.8. Bioactivity predictions indicated that specific peptides, particularly WLNSKGGF and GFIPYEPFLKKMMA, showed significant antimicrobial potential, particularly against bacteria, fungi and viruses. Correlations were found between antifungal activity and physicochemical properties such as net charge, hydrophobicity and isoelectric point.

CONCLUSIONS

The study identified specific T. molitor-derived peptides with strong predicted antimicrobial activity through in silico analysis. These peptides, particularly WLNSKGGF and GFIPYEPFLKKMMA, might offer potential applications in food safety and healthcare. Further experimental validation is required to confirm their efficacy. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Targeted discovery of pea protein-derived GLP-1-secreting peptides by CaSR activation-based molecular docking and their digestive stability

Dietary proteins could stimulate Glucagon-like peptide 1 (GLP-1) secretion. However, only a few food-derived GLP-1-secreting peptides have been identified. Herein, three GLP-1-secreting peptides were identified from pea protein hydrolysate (PPH) by calcium-sensing receptor (CaSR) activation-based molecular docking. PPH-triggered GLP-1 secretion was mediated by CaSR activation. A total of 4221 peptides were sequenced from PPH through peptidomic analysis. Subsequently, three GLP-1-secreting peptides, including RFY, FEPF, and FLFK, were screened by CaSR activation-based molecular docking, and peptide-induced GLP-1 secretion were mediated by CaSR activation. More importantly, FEPF and FLFK exhibited good digestive stability. The molecular docking suggested that binding energy between peptides and CaSR was negatively correlated with their ability to stimulate GLP-1 secretion, and some binding sites in CaSR, such as Asn102 and Tyr218, play a crucial role in stimulating GLP-1 secretion. Our findings suggest that the targeted discovery of pea protein-derived GLP-1-secreting peptides through CaSR activation-based molecular docking is an effective strategy.

Plant-based oat peptides as cryoprotectants mitigate freezing damage to Lactobacillus bulgaricus CICC 22163

The freezing process leads to the death of lactic acid bacteria (LAB), making cryoprotection a significant research focus. In this study, plant-derived oat peptides demonstrated effective cryoprotective effects against Lactobacillus bulgaricus. First, the oat peptide extraction process was optimized with cell viability as the indicator: the yield was found to be 59.51 %. After freezing, it was identified that a 40 mg/mL oat peptide solution provided the best protective effect. The oat peptides enhanced fermentation vigor and reduced cell membrane damage. The mechanisms of action were explored. The oat peptides preserved the intact morphology of cells and significantly improved the viability of lactic dehydrogenase and β-galactosidase. Additionally, the peptides lowered the freezing point to -2.1 °C, which mitigated ice crystal edge formation and reduced both ice crystal diameter and area. The oat peptides physically absorbed onto the surface of the bacteria, exerting an antifreeze effect. Finally, based on amino acid evaluation, three peptide fragments (LSCDKYCFME, FDGCFMEN, and QHCWLGGK) were synthesized, and these synthesized peptides effectively increased the survival rate of L. bulgaricus, with QHCWLGGK also exhibiting protective effects. Therefore, plant-based oat peptides can be utilized as cryoprotectants for freezing LAB.

High-Accuracy Identification and Structure-Activity Analysis of Antioxidant Peptides via Deep Learning and Quantum Chemistry

Antioxidant peptides (AOPs) hold great promise for mitigating oxidative-stress-related diseases, but their discovery is hindered by inefficient and time-consuming traditional methods. To address this, we developed an innovative framework combining machine learning and quantum chemistry to accelerate AOP identification and analyze structure-activity relationships. A Bi-LSTM-based model, AOPP, achieved superior performance with accuracies of 0.9043 and 0.9267, precisions of 0.9767 and 0.9848, and Matthews correlation coefficients (MCCs) of 0.818 and 0.859 on two data sets, outperforming existing methods. Compared with XGBoost and LightGBM, AOPP demonstrated a 4.67% improvement in accuracy. Feature fusion significantly enhanced classification, as validated by UMAP visualization. Experimental validation of ten peptides confirmed the antioxidant activity, with LLA exhibiting the highest DPPH and ABTS scavenging rates (0.108 and 0.437 mmol/g, respectively). Quantum chemical calculations identified LLA's lowest HOMO-LUMO gap (ΔE = 0.26 eV) and C3-H26 as the key active site contributing to its superior antioxidant potential. This study highlights the synergy of machine learning and quantum chemistry, offering an efficient framework for AOP discovery with broad applications in therapeutics and functional foods.

Functional and Bioactive Benefits of Selected Microalgal Hydrolysates Assessed In Silico and In Vitro

BIOPEP-UWM, a peptide database, contains 5128 peptides from a myriad of resources. Five listed peptides are Angiotensin-I-converting enzyme (ACE-1; EC3.4.15.1) inhibitory peptides derived from a red alga, while two from Chlorella vulgaris have anti-cancer and antioxidative bioactivities. Herein, we describe a process combining hydrolysis with two enzymes, Alcalase and Viscozyme, and filtration to generate protein-rich, bioactive peptide-containing hydrolysates from mixed species of Chlorella sp. and Scenedesmus sp. The potential of generated algal hydrolysates to act as food ingredients was determined by assessment of their techno-functional (foaming, emulsification, solubility, water holding, and oil holding capacity) properties. Bioactive screening of hydrolysates in vitro combined with mass spectrometry (MS) and in silico predictions identified bioactive and functional hydrolysates and six novel peptides. Peptides derived from Chlorella mix have the sequences YDYIGNNPAKGGLF and YIGNNPAKGGLF with predicted anti-inflammatory (medium confidence) and umami potential. Peptides from Scenedesmus mix have sequences IEWYGPDRPKFL, RSPTGEIIFGGETM, TVQIPGGERVPFLF, and IEWYGPDRPKFLGPF with predicted anti-inflammatory, anti-diabetic, and umami attributes. Such microalgal hydrolysates could provide essential amino acids to consumers as well as tertiary health benefits to improve human global health.

Microalgae-Derived Peptides: Exploring Bioactivities and Functional Food Innovations

A variety of bioactive peptides with unique and diverse structures could be found in microalgae with various bioactivities including antioxidant, antihypertensive, and antibacterial bioactivities. Food products containing microalgae peptides hold significant health and nutrition potential. Peptide liberation through enzymatic and other processes enhanced protein extraction, and some animal studies were conducted to verify their health-promoting effects. Various studies have focused on developing practical methods for their production, purification, and identification of bioactive peptides. The emerging trends of in silico peptide therapies, computational approaches, artificial intelligence, and the prospects of microalgae peptide research are briefly highlighted. Moreover, this article focused on the potential of microalgae-derived peptides as functional food ingredients their role in promoting health, and their future applications in nutraceutical industries. It also discussed the challenges of bioavailability in functional foods.

Structural characterization, HepG2 cell cytoprotective ability, and antioxidant mechanism of novel antioxidant peptides identified from black soldier fly larvae (Hermetia illucens L.)

This study isolated a novel antioxidant peptide from black soldier fly larvae (BSFL) using enzymatic hydrolysis. Firstly, the BSFL enzymatic hydrolysate was fractionated through ultrafiltration, with the <3 kDa fraction exhibiting the strongest DPPH and ABTS radical scavenging activity. Subsequently, this fraction was further fractionated through gel filtration chromatography and RP-HPLC. Totally, 153 peptides were identified through LC-MS/MS analysis, from which a novel peptide EDEGTYKCVLS (Pep6) was screened according to activity prediction and verification. Pep6 exhibited high radical scavenging capacity and cytoprotective effect on HepG2 cells against H2O2 damage, meanwhile significantly increasing the intracellular antioxidant enzymes activity. Molecular docking analysis indicated that Pep6 competitively bound to Keap1, thereby inhibiting the formation of Keap1-Nrf2 complex, ultimately protecting cells from oxidative stress damage. In this study, a novel antioxidant peptide Pep6 was identified from BSFL, and its antioxidant mechanism was elucidated, providing a theoretical basis for its use as a natural antioxidant.

Integrative approach to assessing bioactivity from hempseed protein isolate extracted and dehydrated by different methods: Synergising in silico prediction and in vitro validation

This study demonstrated a comprehensive workflow combining in silico screening and prediction with in vitro validation to investigate the bioactivity of hempseed protein isolate (HPI) extracted and dehydrated using different methods. By adopting an in silico approach, 13 major proteins of HPI were hydrolysed by 20 selected enzymes, leading to the prediction of 20 potential bioactivities. With papain hydrolysis, dipeptidyl peptidase-IV (DPP4) and angiotensin-converting enzyme (ACE) inhibitory activities emerged as having the highest potential. In vitro experiments confirmed these predictions, with DPP4 and ACE inhibitory activities displaying IC50 values of 0.32-0.42 mg/mL and 6.8-9.17 μg/mL, respectively. A strong correlation (r2 = 0.96) was observed between in vitro protein inhibitory results and in silico predicted data. This study demonstrated an effective integrative approach for predicting bioactive peptides in food protein, providing valuable guidance on its processing to create value-added products.

Microalga Nannochloropsis gaditana as a Sustainable Source of Bioactive Peptides: A Proteomic and In Silico Approach

The impact of the world's growing population on food systems and the role of dietary patterns in the management of non-communicable diseases underscore the need to explore sustainable and dietary protein sources. Although microalgae have stood out as alternative sources of proteins and bioactive peptides, some species such as Nannochloropsis gaditana remain unexplored. This study aimed to characterize N. gaditana's proteome and evaluate its potential as a source of bioactive peptides by using an in silico approach. A total of 1955 proteins were identified and classified into functional groups of cellular components, molecular functions, and biological processes. In silico gastrointestinal digestion of identified proteins demonstrated that 202 hydrophobic and low-molecular-size peptides with potential bioactivity were released. Among them, 27 exhibited theorical antioxidant, antihypertensive, antidiabetic, anti-inflammatory, and/or antimicrobial activities. Seven of twenty-seven peptides showed ≥20% intestinal absorption, suggesting potential systemic effects, while the rest could act at local level. Molecular docking demonstrated strong affinities with key enzymes such as MPO, ACE, and DPPIV. Resistance to the digestion, capacity to be absorbed, and multifunctionality were demonstrated for peptide FIPGL. This study highlights N. gaditana's potential as a sustainable source of novel potential bioactive peptides with promising local and systemic biological effects.

De novo Designing of the Antimicrobial Peptide as a Curative Agent for Methicillin-Resistant Staphylococcus aureus through a Computational Approach

BACKGROUND

The emergence of resistance to multiple drugs has posed a multitude of difficulties that demand immediate attention and solutions. Multiple drug resistance arises from the accumulation of numerous genes within a single cell, each conferring resistance to a specific drug, and from the heightened expression of genes responsible for multidrug efflux pumps. These pumps effectively expel a diverse array of drugs from the cell.

OBJECTIVE

The multi-drug-resistant organisms, including methicillin-resistant Staphylococcus aureus, are the hub of numerous diseases, from minute ailments to fatal diseases, like catheter infections. Nowadays, a combination of many antibiotics is given together as a multimodality therapy to cure MRSA infections. However, researchers are exploring novel approaches to find better solutions.

METHODS

De novo designing of the peptide sequences has been done through an in silico tool. The peptides were further screened using different computational methods. Following this, the selection was conducted utilizing physicochemical properties as criteria. Molecular docking of the selected peptide sequence was carried out. Based on the highest docking score, the model complex was chosen for validation purposes by conducting studies through molecular dynamics simulations.

RESULTS

A total of fifty-two novel antimicrobial peptides were designed and evaluated based on various parameters, targeting MRSA-specific proteins PBP2a and PVL toxin. Among these designed peptides, the peptide sequence VILRMFYHWAVKTNGP emerged as the optimal candidate, satisfying all the necessary parameters to be an effective antimicrobial peptide.

CONCLUSION

Molecular docking and MD simulation results showed that the designed peptide sequence could be the possible solution for MRSA treatment.

Proximate composition, peptide characterization and bioactive properties of faba bean blanching water

Faba bean (Vicia faba L.) offers a rich nutritional profile with high protein content and abundant vitamins and minerals. Processing of faba beans for freezing requires blanching, yielding liluva (legume processing water), possibly containing leached macronutrients, with potential for upcycling. Past evidence has shown that legume processing water may be high in protein. Peptides generated from faba bean proteins during processing have been shown to have bioactivity and can, for example, inhibit HMG-CoA reductase. HMG-CoA reductase is rate-limiting in the biosynthesis of cholesterols and high cholesterol increases the risk of cardiovascular diseases. Thus, this study examined the composition of legume blanching water, analysed the peptides resulting from in vitro digestion and assayed HMG-CoA reductase inhibitory activity of liluva from faba beans sourced from two farms in Canterbury, New Zealand. Results showed that the blanching water contained around 1.7 g/100 mL solid content. These solids were approximately 30 % protein, 12 % water-soluble carbohydrates, 4 % dietary fibre, and 0.17 % ash. Mineral analysis showed high levels of potassium in macro minerals and zinc in trace minerals. Free amino acid analysis revealed high levels of arginine, alanine, asparagine, and glutamic acid, and low levels of methionine and tryptophan. Mass spectrometry analysis identified 111 and 72 endogenous peptides in farm 1 and 2 raw samples, respectively. Most of these peptides were derived from tripeptidyl-peptidase II and subtilisin-like protease. To understand potential bioactivity of these peptides, peptides were also analyzed after in vitro digestion. The resulting identified peptides indicated in silico predicted bioactivities such as anti-thrombotic, antioxidative, ACE dipeptidyl peptidase -III and -IV inhibition and HMG-CoA reductase inhibition activities. Further validation of the faba bean blanching water after in vitro digestion demonstrated approximately 67 % inhibition of HMG-CoA reductase activity, suggesting potential hypocholesterolemic properties. These findings suggest that faba bean blanching water may serve as a sustainable and functional ingredient with potential cholesterol-lowering effects in food production.

In Silico Enzymolysis-Guided Mining of Aminopeptidases with Molecular Insights into Their Substrate Specificity Mechanism

The palatability of protein-based food heavily relies on aminopeptidases with the ability for bitter peptides degradation. However, there is a lack of methods for rational mining of aminopeptidases toward different proteins as well as the evolution direction for substrate specificity remaining unclear. In this study, an in silico simulated enzymolysis-based method for aminopeptidases mining was developed with Crassostrea gigas protein as a model. Results indicated that Ala and Ile were the most frequently exposed hydrophobic amino acids, causing a bitter taste in C. gigas hydrolysates. Furthermore, an aminopeptidase APs1 with putative Ala specificity was heterologously expressed and characterized with high enzyme activity toward Ala (4.92 ± 0.136 U/mg) and Arg (3.50 ± 0.178 U/mg). Site-saturation mutation and molecular docking results revealed that changes in steric hindrance and salt bridge formation within the active site contribute to enhanced catalytic efficiency. Among the mutants, APs1(F316M) showed significantly improved activity toward tested hydrophobic amino acids, especially the activity toward Ala was increased to 14.50 ± 0.137 U/mg. This study presents a directional approach to aminopeptidase mining and evolution, contributing to the rapid selection and combination of protein-degrading enzymes for food quality improvement.

Bioactive Peptides in Greek Goat Colostrum: Relevance to Human Metabolism

Colostrum is essential for the survival and development of newborn mammals. This primary source of nourishment during the first days of infant life is rich in functional components conductive to the enhancement of neonate immunity and growth. Compared with mature milk, a higher protein and peptide content is observed in colostrum, whilst it is low in fat and carbohydrates. The functional properties of colostrum are closely linked to the release of bioactive peptides during the gastrointestinal digestion of colostrum proteins. Our study aimed to comprehensively analyze the whey proteome of colostrum from indigenous Greek goats and to examine the influence of bioactive peptides released during digestion on human metabolism. Colostrum and mature milk samples from healthy ewes were subjected to nanoLC-MS/MS analysis, revealing differentially expressed proteins. These proteins were functionally characterized and subjected to in silico digestion. Using machine learning models, we classified the peptide functional groups, while molecular docking assessed the binding affinity of the proposed angiotensin-converting enzyme (ACE)- and dipeptidyl peptidase IV (DPPIV)-inhibitory peptides to their target molecules. A total of 898 proteins were identified in colostrum, 40 of which were overexpressed compared with mature milk. The enzymatic cleavage of upregulated proteins by key gastrointestinal tract proteases and the downstream analysis of peptide sequences identified 117 peptides predicted (with >80% confidence) to impact metabolism, primarily through modulation of the renin-angiotensin system, insulin secretion, and redox pathways. This work advances our understanding of dietary bioactive peptides and their relevance to human metabolism, highlighting the potential health benefits of colostrum consumption.

Effect of ultrasound and enzymatic pre-treatments on the profile of bioactive peptides of beef liver hydrolysates

The use of meat by-products as a potential source of protein hydrolysates rich in bioactive peptides is of growing interest to valorise these products and improve their sustainable use. This study aimed to evaluate the effect of different pre-treatments (hydrolysis with pepsin, ultrasounds, and ultrasounds-assisted pepsin hydrolysis) on the peptide profile and bioactivity of beef liver hydrolysed with flavourzyme. The pre-treatments with pepsin increased the degree of hydrolysis and generation of free amino acids in the liver hydrolysates, whereas the subsequent hydrolysis with flavourzyme influenced the molecular weight distribution of the peptides. Samples pre-treated with pepsin and ultrasounds-assisted pepsin hydrolysates showed the highest values of antioxidant and inhibitory activity of ACE-I, ECE-I, DPP-IV, and neprilysin enzymes, and therefore these hydrolysates were characterised to obtain the bioactive peptide profiles. A total of 995 peptides were identified by tandem mass spectrometry in the most active fractions separated by reversed-phase liquid chromatography, and 20 of them were predicted as potentially responsible for the observed bioactivities and subsequently characterised by in silico tools. These results evidenced the potential of hydrolysis pre-treatments with pepsin and ultrasounds-assisted pepsin to obtain beef liver hydrolysates rich in bioactive peptides that could exert multifunctional bioactivities such as antioxidant, antihypertensive, and antidiabetic, while giving added value to this meat by-product.

Identification of novel antioxidant and anti-inflammatory peptides from bovine hemoglobin by computer simulation of enzymolysis, molecular docking and molecular dynamics

Due to the structural diversity and complex mechanisms of action of bioactive peptides, screening for specific functional peptides is often challenging. To efficiently screen bioactive peptides with antioxidant and anti-inflammatory effects from bovine hemoglobin, we employed bioinformatics methods to perform virtual enzymatic hydrolysis using online tools and predicted the bioactivity, toxicity, and sensitization scores of the resulting peptides. Molecular docking and molecular dynamics simulations with Keap1 and TLR4 were subsequently conducted to screen for antioxidant and anti-inflammatory peptides. Finally, peptides ARRF and ARNF were synthesized using the Fmoc solid-phase method. The oxidative stress and inflammation model in RAW264.7 cells was induced using lipopolysaccharide (LPS), followed by treatment with peptides ARRF and ARNF to verify their antioxidant and anti-inflammatory activities. The results demonstrated that 529 bovine hemoglobin oligopeptides were produced following virtual enzymatic hydrolysis, of which nine were identified as eligible based on predictions of biological activity, toxicity, solubility, and sensitization. Molecular docking results indicated that the oligopeptides ARNF, QADF, and ARRF exhibited favorable interactions with Keap1, while ARNF, RRF, and ARRF showed strong interactions with TLR4. The primary active sites binding to the Keap1 receptor included Val465, Thr560, and Gly464. The main active sites binding to the TLR4 receptor were Asn309, Asn305, and Glu286. Hydrogen bonding, electrostatic interactions, and hydrophobic interactions were identified as the primary modes of interaction between the oligopeptides and the Keap1 and TLR4 receptors. Molecular dynamics simulations further confirmed that the selected bovine hemoglobin peptides could stably bind to Keap1 and TLR4 receptors. Cell experiments demonstrated that ARRF and ARNF effectively ameliorated LPS-induced oxidative stress and inflammation in RAW264.7 cells.

Conclusion

Compared to traditional methods, this study promptly screens bovine hemoglobin antioxidant and anti-inflammatory peptides, offering a novel approach for rapidly identifying food-derived bioactive peptides.

Exploring the Potential of Biomimetic Peptides in Targeting Fibrillar and Filamentous Alpha-Synuclein-An In Silico and Experimental Approach to Parkinson's Disease

Alpha-synuclein (ASyn) is a protein that is known to play a critical role in Parkinson's disease (PD) due to its propensity for misfolding and aggregation. Furthermore, this process leads to oxidative stress and the formation of free radicals that cause neuronal damage. In this study, we have utilized a biomimetic approach to design new peptides derived from marine natural resources. The peptides were designed using a peptide scrambling approach where antioxidant moieties were combined with fibrillary inhibition motifs in order to design peptides that would have a dual targeting effect on ASyn misfolding. Of the 20 designed peptides, 12 were selected for examining binding interactions through molecular docking and molecular dynamics approaches, which revealed that the peptides were binding to the pre-NAC and NAC (non-amyloid component) domain residues such as Tyr39, Asn65, Gly86, and Ala85, among others. Because ASyn filaments derived from Lewy body dementia (LBD) have a different secondary structure compared to pathogenic ASyn fibrils, both forms were tested computationally. Five of those peptides were utilized for laboratory validation based on those results. The binding interactions with fibrils were confirmed using surface plasmon resonance studies, where EQALMPWIWYWKDPNGS, PYYYWKDPNGS, and PYYYWKELAQM showed higher binding. Secondary structural analyses revealed their ability to induce conformational changes in ASyn fibrils. Additionally, PYYYWKDPNGS and PYYYWKELAQM also demonstrated antioxidant properties. This study provides insight into the binding interactions of varying forms of ASyn implicated in PD. The peptides may be further investigated for mitigating fibrillation at the cellular level and may have the potential to target ASyn.

Immunomodulatory properties of hempseed oligopeptides in an LRRK2-associated Parkinson's disease animal model

Parkinson's disease (PD) is the second most common neurodegenerative disease, with genetic factors like mutations in the LRRK2 gene being a key cause of late-onset autosomal dominant parkinsonism. Nutritional strategies, such as using bioactive peptides with anti-inflammatory properties from sources like hemp protein, are gaining interest as an alternative to pharmacological therapies. In this study, we used an LRRK2-associated PD mouse model to test the efficacy of a hempseed protein hydrolysate (HPH60A + 15F) with antioxidant and anti-inflammatory properties. Mice were given HPH60A + 15F (10 mg kg-1 day-1) orally for 7 days. After treatment, brain tissue and macrophages were analyzed to assess neuroinflammation markers. Additionally, the neuroavailable peptidome was characterized using an in vitro model simulating the intestinal and blood-brain barriers. The oral treatment has been shown to reduce protein aggregates of α-syn, CD68, iNOS, and COX2 in the brain. The treatment also significantly lowered TNF-α gene expression in the striatum, with a notable reduction in the gene expression of other pro-inflammatory cytokines in bone marrow-derived macrophages (BMDMs), such as IL-1β or IL-6. The peptide TVTAMNVVYALK was proposed as a potential highly active peptide, able to exert anti-inflammatory effects in the brain. The results have shown that HPH60A + 15F is capable of alleviating neuroinflammation by reducing the expression of pro-inflammatory cytokines, which could have promising effects in PD.

Initial Exploration of the In Vitro Activation of GLP-1 and GIP Receptors and Pancreatic Islet Cell Protection by Salmon-Derived Bioactive Peptides

This study examines the in vitro effects of a soluble protein hydrolysate (SPH) derived from Atlantic salmon (Salmo salar) on incretin receptor activity and pancreatic islet cell protection to explore the mechanisms underlying SPH's observed benefits on weight loss and metabolic health in overweight individuals. SPH demonstrated a dose-dependent enhancement of glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP) receptor activity, with significant increases of 2.4-fold (p < 0.05) and 2.6-fold (p < 0.01) at 10 mg/mL, respectively, compared to the control. Pancreatic islet cell assays showed a substantial proliferation effect, with up to a 57% increase at 50 µL/well, indicating potential protective properties against inflammation-induced cell loss. Notably, the smallest SPH peptide fraction (<1000 Da) exhibited GLP-1 agonist activity comparable to semaglutide, a widely used therapeutic agent, underscoring SPH's potential efficacy in modulating metabolic pathways. These results suggest that SPH not only enhances key incretin signaling but also promotes islet cell health, positioning it as a promising dietary intervention to improve age-related metabolic health, including the weight gain and underlying adverse metabolic changes frequently encountered through the menopause.

Discovery of novel dipeptidyl peptidase-IV inhibitory peptides derived from walnut protein and their bioactivities in vivo and in vitro

The inhibition of dipeptidyl peptidase IV (DPP-IV) has been regarded as a major target for treating type-2 diabetes (T2D). Food-derived peptides are a great source of DPP-IV inhibitory peptides. In this study, we utilized walnut protein as the raw material and hydrolyzed it using four different proteases. The trypsin hydrolysate exhibited the highest DPP-IV inhibitory activity. A DEAE-52 anion exchange column and a Sephadex G-25 gel filtration column were used to sequentially separate and purify the enzymatic hydrolysates. Mass spectrometry identified 117 peptide sequences, of which LPFA, VPFWA, and WGLP were three highly active DPP-IV inhibitory peptides. Molecular docking results revealed that three peptides primarily bind tightly to DPP-IV through hydrogen bonds and van der Waals forces. The inhibitory activity and absorption transport of the peptides were examined using a Caco-2 cell model. LPFA, VPFWA, and WGLP could cross the Caco-2 cell monolayer intact, with in situ IC50s of 267.9 ± 7.2 μM, 325.0 ± 8.4 μM, and 350.9 ± 8.3 μM, respectively. Oral glucose tolerance tests (OGTT) demonstrated that the three inhibitory peptides significantly improved glucose metabolism in normal ICR mice. This study establishes a theoretical basis for the high-value utilization of walnuts and the therapeutic treatment of T2D.