Large-scale mapping of bioactive peptides in structural and sequence space

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

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

Bioactive compounds for human and planetary health

Bioactive compounds found in edible plants and foods are vital for human and planetary health, yet their significance remains underappreciated. These natural bioactives, as part of whole diets, ingredients, or supplements, can modulate multiple aspects of human health and wellness. Recent advancements in omic sciences and computational biology, combined with the development of Precision Nutrition, have contributed to the convergence of nutrition and medicine, as well as more efficient and affordable healthcare solutions that harness the power of food for prevention and therapy. Innovation in this field is crucial to feed a growing global population sustainably and healthily. This requires significant changes in our food system, spanning agriculture, production, distribution and consumption. As we are facing pressing planetary health challenges, investing in bioactive-based solutions is an opportunity to protect biodiversity and the health of our soils, waters, and the atmosphere, while also creating value for consumers, patients, communities, and stakeholders. Such research and innovation targets include alternative proteins, such as cellular agriculture and plant-derived protein; natural extracts that improve shelf-life as natural preservatives; upcycling of agricultural by-products to reduce food waste; and the development of natural alternatives to synthetic fertilizers and pesticides. Translational research and innovation in the field of natural bioactives are currently being developed at two levels, using a systems-oriented approach. First, at the biological level, the interplay between these compounds and the human host and microbiome is being elucidated through omics research, big data and artificial intelligence, to accelerate both discovery and validation. Second, at the ecosystem level, efforts are focused on producing diverse nutrient-rich, flavorful, and resilient, yet high-yield agricultural crops, and educating consumers to make informed choices that benefit both their health and the planet. Adopting a system-oriented perspective helps: unravel the intricate and dynamic relationships between bioactives, nutrition, and sustainability outcomes, harnessing the power of nature to promote human health and wellbeing; foster sustainable agriculture and protect the ecosystem. Interdisciplinary collaboration in this field is needed for a new era of research and development of practical food-based solutions for some of the most pressing challenges humanity and our planet are facing today.

An In Silico Framework to Mine Bioactive Peptides from Annotated Proteomes: A Case Study on Pancreatic Alpha Amylase Inhibitory Peptides from Algae and Cyanobacteria

Bioactive peptides may exert beneficial activities in living organisms such as the regulation of glucose metabolism through the inhibition of alpha amylases. Algae and cyanobacteria are gaining a growing interest for their health-promoting properties, and possible effects on glucose metabolism have been described, although the underlying mechanisms need clarification. This study proposes a computer-driven workflow for a proteome-wide mining of alpha amylase inhibitory peptides from the proteome of Chlorella vulgaris, Auxenochlorella protothecoides and Aphanizomenon flos-aquae. Overall, this work presents an innovative and versatile approach to support the identification of bioactive peptides in annotated proteomes. The study: (i) highlighted the presence of alpha amylase inhibitory peptides within the proteomes under investigation (including ELS, which is among the most potent inhibitory tripeptides identified so far); (ii) mechanistically investigated the possible mechanisms of action; and (iii) prioritized further dedicated investigation on the proteome of C. vulgaris and A. flos-aquae, and on CSSL and PGG sequences.

Quantitative In Silico Evaluation of Allergenic Proteins from Anacardium occidentale, Carya illinoinensis, Juglans regia and Pistacia vera and Their Epitopes as Precursors of Bioactive Peptides

The aim of the study presented here was to determine if there is a correlation between the presence of specific protein domains within tree nut allergens or tree nut allergen epitopes and the frequency of bioactive fragments and the predicted susceptibility to enzymatic digestion in allergenic proteins from tree nuts of cashew (Anacardium occidentale), pecan (Carya illinoinensis), English walnut (Juglans regia) and pistachio (Pistacia vera) plants. These bioactive peptides are distributed along the length of the protein and are not enriched in IgE epitope sequences. Classification of proteins as bioactive peptide precursors based on the presence of specific protein domains may be a promising approach. Proteins possessing a vicilin, N-terminal family domain, or napin domain contain a relatively low occurrence of bioactive fragments. In contrast, proteins possessing the cupin 1 domain without the vicilin N-terminal family domain contain a relatively high total frequency of bioactive fragments and predicted release of bioactive fragments by the joint action of pepsin, trypsin, and chymotrypsin. This approach could be utilized in food science to simplify the selection of protein domains enriched for bioactive peptides.

Selar (Selar crumenophthalmus) Fish Protein Hydrolysate Has Antidiabetic Properties Possibly through GLP-1

Background :

Enzymatic hydrolysis of fish protein using protease or fish protein hydrolysate can form bioactive peptides that have antidiabetic activity. One potential mechanism of fish protein hydrolysate is reducing blood glucose through increased endogenous glucagon like peptide (GLP)-1 production. Tempeh is soy fermented food that has protease which is potential biocatalyst in producing fish protein hydrolysate.

Objective:

To evaluate the antidiabetic properties of Selar (Selar crumenophthalmus) fish protein hydrolysate using tempeh protease as biocatalyst and duodenal gene expression of GLP-1.

Methods:

Selar fish protein isolate was digested for 8 hours at 37°C using crude tempeh protease. Diabetes mellitus was induced in rats by intraperitoneal injection of streptozotosin (65 mg/kg bw) and nicotinamide (230 mg/kg bw). Fish protein isolate and hydrolysate in dose of 300 mg/bw and 500 mg/ bw were orally administered daily for 4 weeks. Blood was drawn for fasting serum glucose and lipid profile analysis. Total RNAs were isolated from duodenum and quantitative real time PCR was performed to quantify mRNA expression of GLP-1. Data were analyzed using one way ANOVA and gene expression analysis were performed using Livak.

Results and Discussion:

There is a significant difference on fasting serum glucose, total cholesterol, triglyceride, LDL-cholesterol, HDL-cholesterol and duodenal GLP-1 mRNA expression level between groups (p<0.05). The duodenal GLP-1 mRNA expression was the highest in rats who received hydrolyzed fish protein 500 mg/ bw.

Conclusion:

Hydrolysis of selar fish protein using tempeh protease has anti-diabetic properties possibly through GLP-1 production.

Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery

Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.

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

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

A Novel Angiotensin Converting Enzyme 2 (ACE2) Activating Peptide: A Reflection of 10 Years of Research on a Small Peptide Ile-Arg-Trp (IRW)

IRW (Ile-Arg-Trp) was identified as an inhibitor of angiotensin converting enzyme (ACE) from egg white protein ovotransferrin through an integrated in silico digestion and quantitative structure and activity relationship prediction in 2011. Oral administration of IRW to spontaneously hypertensive rats (SHRs) can significantly reduce blood pressure, via upregulation of ACE2, but not through the inhibition of ACE. ACE2 converts Ang II into Ang (1-7), thus lowering blood pressure via Mas receptor (MasR); coinfusion of Mas receptor antagonist A779 and IRW in SHRs abolished blood pressure-lowering effect of IRW, supporting a key role of ACE2/Ang (1-7)/MasR axis. Our ongoing study further established new roles of IRW as an antioxidant, an anti-inflammatory agent, an insulin sensitizer, and a bone cell anabolic. Future studies are warranted to understand the unique structure features of this peptide, its mechanisms of action at various targets, its bioavailability and metabolism, and its possible roles toward COVID-19.

A biotechnological approach for the production of branched chain amino acid containing bioactive peptides to improve human health: A review

Improper nutrition provokes many types of chronic diseases and health problems, which consequently are associated with particularly high costs of treatments. Nowadays, consumer's interest in healthy eating is shifting towards specific foods or food ingredients. As a consequence, bioactive peptides as a promising source of health promoting food additives are currently an intensely debated topic in research. Process design is still on its early stages and is significantly influenced by important preliminary decisions. Thus, parameters like peptide bioactivity within the product, selection of the protein source, enzyme selection for hydrolysis, peptide enrichment method, as well as stability of the peptides within the food matrix and bioavailability are sensitive decision points, which have to be purposefully coordinated, as they are directly linked to amino acid content and structure properties of the peptides. Branched chain amino acids (BCAA) are essential components for humans, possessing various important physiologic functions within the body. Incorporated within peptide sequences, they may induce dual functions, when used as nutraceuticals in functional food, thus preserving the foodstuff and prevent several widespread diseases. Furthermore, there is evidence that consuming this peptide-class can be a nutritional support for elderly people or improve human health to prevent diseases caused by incorrect nutrition. Based on the knowledge about the role of BCAA within various peptide functions, discussed in the review, special attention is given to different approaches for systematic selection of the protein source and enzymes used in hydrolysis, as well as suitable peptide enrichment methods, thereby showing current trends in research.

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities

The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introduction of new information about the existing ones (e.g., chemical codes and references to other databases) is in progress. New opportunities include the possibility of annotating peptides containing D-enantiomers of amino acids, batch processing option, converting amino acid sequences into SMILES code, new quantitative parameters characterizing the presence of bioactive fragments in protein sequences, and finding proteinases that release particular peptides.

Nitrogen-Doped Hollow Copolymer Tube via Template-Free Asynchronous Polymerization with Highly Selective Separation of Hydrophilic Dipeptide for Enhancing Inhibitory Activity of Angiotensin Converting Enzyme

A N-doped hollow copolymer tube (NHCT) was fabricated via template-free one-pot asynchronous polymerization strategy. Discrepancies of monomer polymerization speed and their hydrophilic-hydrophobic interaction resulted in the assembly of a hollow tube having inner diameter and double wall thickness of ∼230 and 40 nm, respectively. The formation and growth mechanism of NHCT analyzed via advanced characterization revealed that the unique growth processes tuned a demarcating surface layer between inner (hydrophilic) and outer (hydrophobic) layers. The screening and recognition ability of NHCT were determined for two specific dipeptides (WW and RR) possessing great discrepancies in hydrophilicity and angiotensin converting enzyme inhibitory (ACE-I) activity. NHCT realized high adsorption capacity (1.57 mmol/g) and selectivity (∼1274) for hydrophilic dipeptide RR (low ACE-I activity) from the mixture of RR/WW. As a result, ACE-I activity for residual solution were enhanced about 4.1 times as compared to original solution from natural silkworm pupae protein hydrolysate. Awarding to these results and its facile and discerning ability, NHCT can be envisioned to be of great value for the separation of small functional peptides from a natural edible source.

Amino Acid Imprinted UiO-66s for Highly Recognized Adsorption of Small Angiotensin-Converting-Enzyme-Inhibitory Peptides

Introduction of targeted defects into microporous UiO-66s for manipulating their three-dimensional size and surface properties can endow them with adsorption and separation areas involving angiotensin-converting-enzyme-inhibitory (ACE-inhibitory) peptides. Three hydrophobic amino acids (AAs) (i.e., proline (Pro), phenylalanine (Phe), and tryptophan (Trp)) having different physical/chemical properties were applied to in situ tailor defects in UiO-66 through targeted incoordination of missing linkers or missing nodes. Characterization results revealed a uniform oval shape of the developed defects with lengths ranging from 1.8 to 3.1 nm, which was also highly consistent with our molecular simulation. Among these three defective UiO-66s, Phe and Trp imprinted UiO-66s significantly promoted the adsorption affinity of small ACE-inhibitory peptides (uptake: 1.25 mmol g^-1 for DDFF and 1.37 mmol g^-1 for DDWW) and ultrahigh selectivity for DDFF (249) or DDWW (279) from inactive KKKK solution based on a lock-and-key mechanism. As a result, the imprinted UiO-66 showed an enrichment capacity for ACE-inhibitory peptides about eight times higher than that of pristine UiO-66. Therefore, the amino acid imprinting strategy endorsed by its facile and discerning ability can be envisioned to be of great value for small functional peptide separation and oriented enrichment in biomedicines.