Bioactive Peptides and Its Alternative Processes: A Review

Novel Computational Approaches in the Discovery and Identification of Bioactive Peptides: A Bioinformatics Perspective

Bioactive peptides are protein molecules known for their specific biological functions, offering promising applications across various fields including medicine, food, and cosmetics. Traditional approaches to the investigation of bioactive peptides typically encompass extraction, separation, purification, identification, and experimental evaluation. However, these methodologies are frequently subject to human-related variables, which consequently lead to reduced efficiency and compromised accuracy. Bioinformatics techniques, including computer simulation screening, quantitative structure-activity relationship (QSAR) analysis, and machine learning, have emerged as powerful tools in the field of bioactive peptide research. These advanced methodologies not only enhance the efficiency of bioactive peptide screening but also provide valuable insights into the underlying mechanisms of action of these peptides. This review discusses the identification, analysis, and evaluation of bioactive peptides through innovative bioinformatics technology while also highlighting traditional techniques that have been developed and improved. This review provides robust theoretical support and valuable references for future research and applications involving bioactive peptides.

Deep Learning-Driven Optimization of Antihypertensive Properties from Whey Protein Hydrolysates: A Multienzyme Approach

This study utilized deep learning to optimize antihypertensive peptides from whey protein hydrolysate. Using the Large Language Models (LLMs), we identified an optimal multienzyme combination (MC5) with an ACE inhibition rate of 89.08% at a concentration of 1 mg/mL, significantly higher than single-enzyme hydrolysis. MC5 (1 mg/mL) exhibited excellent biological stability, with the ACE inhibition decreasing by only 6.87% after simulated digestion. In in vivo experiments, MC5 reduced the systolic and diastolic blood pressure of hypertensive rats to 125.00 and 89.00 mmHg, respectively. MC5 significantly lowered inflammatory markers (TNF-α and IL-6) and increased antioxidant enzyme activity (SOD, GSH-Px, GR, and CAT). Compared to the MC group, the MC5 group showed significantly reduced serum renin and ET-1 levels by 1.25-fold and 1.04-fold, respectively, while serum NO content increased by 3.15-fold. Furthermore, molecular docking revealed four potent peptides (LPEW, LKPTPEGDL, LNYW, and LLL) with high ACE binding affinity. This approach demonstrated the potential of combining computational methods with traditional hydrolysis processes to develop effective dietary interventions for hypertension.

The Role and Mechanisms of Antimicrobial Peptides in Overcoming Multidrug-Resistant Bacteria

Multidrug-resistant (MDR) bacteria are becoming more and more common, which presents a serious threat to world health and could eventually render many of the antibiotics we currently use useless. The research and development of innovative antimicrobial tactics that can defeat these hardy infections are imperative in light of this predicament. Antimicrobial peptides (AMPs), which have attracted a lot of attention due to their distinct modes of action and capacity to elude conventional resistance mechanisms, are among the most promising of these tactics. As a promising substitute for conventional antibiotics, AMPs are a varied class of naturally occurring compounds that target bacteria membranes and disrupt cellular activities to demonstrate broad-spectrum antimicrobial activity. The objective of this study is to present a thorough summary of the current knowledge regarding AMP mechanisms against MDR bacteria, including immunological modulation, interactions with microbial membranes, and possible synergy with currently used antimicrobial drugs. In addition, we define the review's scope to include the most recent developments in AMP research, emphasizing the innovations' development, optimization, and therapeutic promise. We hope to emphasize the crucial role that AMPs will play in the future of antimicrobial therapy by bringing together recent research and highlighting current issues. We also hope to advocate for AMPs' continued research and development as part of a comprehensive strategy to counteract the growing threat of antibiotic resistance.

A novel method for exploration and prediction of the bioactive target of rice bran-derived peptide (KF-8) by integrating computational methods and experiments

The investigation into the bioactive peptide's activity and target action poses a significant challenge in the field of food. An active peptide prepared from rice bran, KF-8, was confirmed to possess antioxidant activity in our previous study, but the specific target was unclear. This study used eight target prediction tools based on artificial intelligence and chemoinformatics to preliminarily screen potential antioxidant targets by integrating different computational methods. Then five different types of docking software were comparatively analyzed to further clarify their interaction sites and possible modes of action. The results showed that SIRT1 and CXCR4 are potential antioxidant targets of KF-8. Different docking software suggested that KF-8 interacts with SIRT1 and CXCR4 as major residues. Meanwhile, the results of Immunofluorescence co-localization experiments showed that the co-localization coefficients of KF-8 with SIRT1 and CXCR4 reached 0.5879 and 0.5684. This study provides new alternative means for the discovery of active peptide targets.

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

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

Animal Food Products to Support Human Nutrition and to Boost Human Health: The Potential of Feedstuffs Resources and Their Metabolites as Health-Promoters

Recent attention has been given to animal feeding and its impact on human nutrition. Animal feeding is essential for meeting human dietary needs, making it a subject of significant interest and investigation. This review seeks to outline the current understanding of this disciplinary area, with a focus on key research areas and their potential implications. The initial part of the paper discusses the importance of animal feed resources and recognizes their crucial role in guaranteeing sufficient nutrition for both humans and animals. Furthermore, we analyzed the categorization of animal feeds based on the guidelines established by the National Research Council. This approach offers a valuable structure for comprehending and classifying diverse types of animal feed. Through an examination of this classification, we gain an understanding of the composition and nutritional content of various feedstuffs. We discuss the major categories of metabolites found in animal feed and their impact on animal nutrition, as well as their potential health advantages for humans. Flavonoids, polyphenols, tannins, terpenoids, vitamins, antioxidants, alkaloids, and essential oils are the primary focus of the examination. Moreover, we analyzed their possible transference into animal products, and later we observed their occurrence in foods from animal sources. Finally, we discuss their potential to promote human health. This review offers an understanding of the connections among the major metabolites found in feedstuffs, their occurrence in animal products, and their possible impact on the health of both animals and humans.

Rapid and sensitive detection of domoic acid in shellfish using a magnetic bead-based competitive ELISA with a high-affinity peptide as a molecular binder

Addressing the critical health concerns posed by domoic acid (DA), a neurotoxic compound produced by toxic marine algae and bioaccumulated in shellfish, necessitates the development of a rapid, precise, and robust detection system. Traditional DA detection methods have stability and sensitivity issues, which hinder effective toxin detection. To overcome these limitations, we developed a novel direct competitive enzyme-linked immunosorbent assay (dc-ELISA) platform that utilizes peptide-immobilized magnetic beads (MGBs/peptide). The affinity peptides identified through phage display and chemically synthesized with biotin labels present an innovative alternative to conventional antibodies for ELISA applications. Streptavidin-modified MGBs were used as the bioreceptor carriers to facilitate magnetic separation and simplify sample preparation, making the MGB/peptide-based dc-ELISA platform an ideal tool for comprehensive monitoring efforts. The developed platform exhibits a detection range of 0.5-10 ng mL-1 and a low limit of detection of 0.29 ng mL-1, offering enhanced sensitivity and cost-effectiveness. Moreover, our developed dc-ELISA demonstrated a high recovery rate when validated with DA-spiked CRM-mussel samples. This method overcomes the limitations of traditional detection techniques and offers a scalable and efficient approach to marine toxin surveillance with improved marine environmental monitoring and public health management.

Nanozyme-assisted molecularly imprinted polymer-based indirect competitive ELISA for the detection of marine biotoxin

Saxitoxin (STX), which is produced by certain dinoflagellate species, is a type of paralytic shellfish poisoning toxin that poses a serious threat to human health and the environment. Therefore, developing a technology for the convenient and cost-effective detection of STX is imperative. In this study, we developed an affinity peptide-imprinted polymer-based indirect competitive ELISA (ic-ELISA) without using enzyme-toxin conjugates. AuNP/Co3O4@Mg/Al cLDH was synthesized by calcining AuNP/ZIF-67@Mg/Al LDH, which was obtained by combining AuNPs, ZIF-67, and flower-like Mg/Al LDH. This synthesized nanozyme exhibited high catalytic activity (Km = 0.24 mM for TMB and 132.5 mM for H2O2). The affinity peptide-imprinted polymer (MIP) was imprinted with an STX-specific template peptide (STX MIP) on a multi-well microplate and then reacted with an STX-specific signal peptide (STX SP). The interaction between the STX SP and MIP was detected using a streptavidin-coated nanozyme (SA-AuNP/Co3O4@Mg/Al cLDH). The developed MIP-based ic-ELISA exhibited excellent selectivity and sensitivity, with a limit of detection of 3.17 ng/mL (equivalent: 0.317 μg/g). Furthermore, the system was validated using a commercial ELISA kit and mussel tissue samples, and it demonstrated a high STX recovery with a low coefficient of variation. These results imply that the developed ic-ELISA can be used to detect STX in real samples.

An Integrated Comprehensive Peptidomics and In Silico Analysis of Bioactive Peptide-Rich Milk Fermented by Three Autochthonous Cocci Strains

Bioactive peptides (BPs) are molecules of paramount importance with great potential for the development of functional foods, nutraceuticals or therapeutics for the prevention or treatment of various diseases. A functional BP-rich dairy product was produced by lyophilisation of bovine milk fermented by the autochthonous strains Lactococcus lactis subsp. lactis ZGBP5-51, Enterococcus faecium ZGBP5-52 and Enterococcus faecalis ZGBP5-53 isolated from the same artisanal fresh cheese. The efficiency of the proteolytic system of the implemented strains in the production of BPs was confirmed by a combined high-throughput mass spectrometry (MS)-based peptidome profiling and an in silico approach. First, peptides released by microbial fermentation were identified via a non-targeted peptide analysis (NTA) comprising reversed-phase nano-liquid chromatography (RP nano-LC) coupled with matrix-assisted laser desorption/ionisation-time-of-flight/time-of-flight (MALDI-TOF/TOF) MS, and then quantified by targeted peptide analysis (TA) involving RP ultrahigh-performance LC (RP-UHPLC) coupled with triple-quadrupole MS (QQQ-MS). A combined database and literature search revealed that 10 of the 25 peptides identified in this work have bioactive properties described in the literature. Finally, by combining the output of MS-based peptidome profiling with in silico bioactivity prediction tools, three peptides (75QFLPYPYYAKPA86, 40VAPFPEVFGK49, 117ARHPHPHLSF126), whose bioactive properties have not been previously reported in the literature, were identified as potential BP candidates.

Food Peptides for the Nutricosmetic Industry

In recent years, numerous reports have described bioactive peptides (biopeptides)/hydrolysates produced from various food sources. Biopeptides are considered interesting for industrial application since they show numerous functional properties (e.g., anti-aging, antioxidant, anti-inflammatory, and antimicrobial properties) and technological properties (e.g., solubility, emulsifying, and foaming). Moreover, they have fewer side effects than synthetic drugs. Nevertheless, some challenges must be overcome before their administration via the oral route. The gastric, pancreatic, and small intestinal enzymes and acidic stomach conditions can affect their bioavailability and the levels that can reach the site of action. Some delivery systems have been studied to avoid these problems (e.g., microemulsions, liposomes, solid lipid particles). This paper summarizes the results of studies conducted on biopeptides isolated from plants, marine organisms, animals, and biowaste by-products, discusses their potential application in the nutricosmetic industry, and considers potential delivery systems that could maintain their bioactivity. Our results show that food peptides are environmentally sustainable products that can be used as antioxidant, antimicrobial, anti-aging, and anti-inflammatory agents in nutricosmetic formulations. Biopeptide production from biowaste requires expertise in analytical procedures and good manufacturing practice. It is hoped that new analytical procedures can be developed to simplify large-scale production and that the authorities adopt and regulate use of appropriate testing standards to guarantee the population's safety.

PepQSAR: a comprehensive data source and information platform for peptide quantitative structure-activity relationships

Peptide quantitative structure-activity relationships (pQSARs) have been widely applied to the statistical modeling and empirical prediction of peptide activity, property and feature. In the procedure, the peptide structure is characterized at sequence level using amino acid descriptors (AADs) and then correlated with observations by machine learning methods (MLMs), consequently resulting in a variety of quantitative regression models used to explain the structural factors that govern peptide activities, to generalize peptide properties of unknown from known samples, and to design new peptides with desired features. In this study, we developed a comprehensive platform, termed PepQSAR database, which is a systematic collection and decomposition of various data sources and abundant information regarding the pQSARs, including AADs, MLMs, data sets, peptide sequences, measured activities, model statistics, and literatures. The database also provides a comparison function for the various previously built pQSAR models reported by different groups via distinct approaches. The structured and searchable PepQSAR database is expected to provide a useful resource and powerful tool for the computational peptidology community, which is freely available at http://i.uestc.edu.cn/PQsarDB .