Search Results (115)

Biologically active peptides can be obtained with various research methods, depending on the starting material, biological activity, and intended use. To use the most efficient method, it is worth combining in silico and in vitro experiments. Among the tools that can support an in silico analysis are databases such as the Antimicrobial Peptide Database (AMPD) or BIOPEP-UWM. The aim of this study was to make an in silico hydrolysis of peptides with anticancer properties selected from the AMP database, using pepsin, trypsin, and chymotrypsin. Most peptides obtained had properties inhibiting ACE and dipeptidyl peptidase IV activity. Among the resulting peptides, those with the sequence AR, CF, ER, TF, IY, ER, AW, GF, TW, SK and IM are potentially resistant to peptidase from microbial action. An analysis of the peptides’ characteristics showed that peptides with the sequence AR, EK, ER and SK are well-soluble in water and have high affinity for protein and ligand binding. Peptides with the sequence TF, IL and PF are unstable. Thermostable peptides are PGL, IL, GL, IY, VF, PL, IM and QL. The results of the study may be used to design in vitro experiments. Full article

Background/Objectives: Human milk provides essential nutrients and immune factors with beneficial impact on term, but especially preterm infants’ development. Therefore, this study focuses on the quantification of differences in the peptidome composition of breast milk from mothers of preterm and term infants, keeping in mind that this could reflect different biological needs of these infants or indicate nutritional gaps for healthy development. Methods: In a prospective observational study, breast milk samples were collected from 10 mothers of preterm infants (29–36 weeks gestational age,) and 13 mothers of term infants (37–41 weeks) at day 4 to 6 postnatally. A non-targeted tandem mass spectrometry approach was employed to analyze the milk peptidome. Results: In total, 4570 peptides were quantified. Adjusting the results for maternal age, weight, and height revealed a significant difference for 130 peptides derived from 19 different proteins between preterm and term milk. Proteins comprised high abundant proteins (e.g., α_S1-casein, κ- casein, or ß-casein), but also proteins that are less prominent in milk but of high functional importance (e.g., Hypoxia-inducible factor 1-alpha, Olfactory receptor 4M1). The differentially abundant peptides included peptides derived from ß-casein, which have already been described as being involved in antimicrobial functions as well as proliferation stimulating. For another 32 peptides, bioactivity was predicted. Conclusions: The current study provides a comprehensive overview on the differences in the milk peptidome at different gestational ages independent from common maternal phenotypes and improved the database for future peptide functionality studies. Full article

Background: Peptides are a class of molecules that can be presented as good antimicrobials and with mechanisms that avoid resistance, and the design of peptides with good activity can be complex and laborious. The study of their quantitative structure–activity relationships through machine learning algorithms can shed light on a rational and effective design. Methods: Information on the antimicrobial activity of peptides was collected, and their structures were characterized by molecular descriptors generation to design regression and classification models based on machine learning algorithms. The contribution of each descriptor in the generated models was evaluated by determining its relative importance and, finally, the antimicrobial activity of new peptides was estimated. Results: A structured database of antimicrobial peptides and their descriptors was obtained, with which 56 machine learning models were generated. Random Forest-based models showed better performance, and of these, regression models showed variable performance (R² = 0.339–0.574), while classification models showed good performance (MCC = 0.662–0.755 and ACC = 0.831–0.877). Those models based on bacterial groups showed better performance than those based on the entire dataset. The properties of the new peptides generated are related to important descriptors that encode physicochemical properties such as lower molecular weight, higher charge, propensity to form alpha-helical structures, lower hydrophobicity, and higher frequency of amino acids such as lysine and serine. Conclusions: Machine learning models allowed to establish the structure–activity relationships of antimicrobial peptides. Classification models performed better than regression models. These models allowed us to make predictions and new peptides with high antimicrobial potential were proposed. Full article

Background: Endophytic fungi are prolific sources of bioactive metabolites with potential in pharmaceutical and biotechnological applications. Methods: Here, the endophytic fungus, Alternaria alstroemeriae S6, was isolated from Veronica acinifolia (speedwell), and conducted its anti-microbial activities, whole-genome sequencing and metabolome analysis. Results: The ethyl acetate extract of this fungus exhibited strong anti-bacterial activity and the inhibition zones, induced by the fungal extract at 20 mg/mL, reached 16.25 ± 0.5 mm and 26.5 ± 0.5 mm against Gram-positive and Gram-negative bacteria. To unravel the biosynthetic potential for anti-bacterial compounds, whole-genome sequencing was conducted on A. alstroemeriae S6, resulting in a high-quality assembly of 42.93 Mb encoding 13,885 protein-coding genes. Comprehensive functional genome annotation analyses, including gene ontology (GO) terms, clusters of orthologous groups (COGs), Kyoto encyclopedia of genes and genomes (KEGG), carbohydrate-active enzymes (CAZymes), and antibiotics and secondary metabolites analysis shell (antiSMASH) analyses, were performed. According to the antiSMASH analysis, 58 biosynthetic gene clusters (BGCs), including 16 non-ribosomal peptide synthetases (NRPSs), 21 terpene synthases, 12 polyketide synthetases (PKSs), and 9 hybrids, were identified. In addition, succinic acid was identified as the major metabolite within the fungal extract, while 20 minor bioactive compounds were identified through LC-MS/MS-based molecular networking on a GNPS database. Conclusions: These findings support the biotechnological potential of A. alstroemeriae S6 as an alternative producer of succinic acid, as well as novel anti-bacterial agents. Full article

Background: The overwhelming majority of the antimicrobial peptides (AMPs) studied in mussels (Mytilus spp.) so far are specifically expressed by hemocytes and display compact disulfide-stabilized structures. However, gill-specific myticalins play a role in mucosal immunity and are one of the very few examples of known molluscan AMPs lacking cysteine residues. Methods: We investigate the molecular evolution of myticalins, compiling a collection of sequences obtained by carefully annotating 169 genome assemblies of different Mytilus species. We determine the gene presence/absence patterns and gene expression profiles for the five myticalin subfamilies, including the newly reported myticalin E. Results: All sequences are deposited in MyticalinDB, a novel database that includes a total of 100 unique mature myticalin peptides encoded by 215 protein precursors, greatly enriching the compendium of these molecules from previous reports. Among the five subfamilies, myticalin A and C are the most widespread and highly expressed across all Mytilus species. Interestingly, structural prediction reveals a previously unreported strong amphipathic nature for some myticalins, which may be highly relevant for their biological activity. Conclusions: The results reported in this work support the role of myticalins in gill-associated mucosal immunity and highlight the importance of inter-individual molecular diversity in establishing an efficient response to microbial infections. The newly established MyticalinDB provides a valuable resource for investigating the evolution and extraordinary molecular diversity of this AMP family. Full article

Porcine intestinal mucosa hydrolysates (PIMHs) are by-products of heparin production obtained through a specific enzymatic hydrolysis process, which can theoretically generate bioactive peptides (BAPs). This study aimed to identify, characterize, and quantify BAPs in two Palbio products manufactured by Bioiberica S.A.U. (Palafolls, Spain), which are PIMH protein sources used for animal feed: Palbio^® HP (PHP) and Palbio^® 62 SP^® (P62). Using mass spectrometry (MS)-based peptidomics, we analyzed three samples from each product, fractionated based on molecular weight (<3 kDa, 3 to 10 kDa, and >10 kDa). The <3 kDa fraction was analyzed directly, while the other two fractions were enzymatically digested before MS analysis. The workflow identified 961 peptides in PHP and 1134 in P62. Subsequent bioinformatic analysis using public databases (APD2, StraPep, AHTPDB, and BIOPEP-UWM) led to the identification of six significant BAPs in both PHP and P62, with respective quantified amounts (pg peptide/μg sample): DAVEDLESVGK (0.1626, 0.1939), EGIPPDQQRLIFAGK (0.2637, 0.1852), TITLEVEPSDTIENVK (0.3594, 0.4327), TNVPRASVPDGFLS (1.4596, 0.1898), TNVPRASVPDGFLSEL (8.0500, 0.9224), and VHVVPDQLMAF (0.0310, 0.0054). The first three BAPs are related to antimicrobial activity, while the latter three are associated with cytokine/growth factor-like, antioxidant, and immunomodulatory activities. These bioactivities align with previously reported in vivo benefits observed in animal nutrition using Palbio products. Our findings demonstrate that PHP and P62 are valuable sources of BAPs, supporting their potential role in improving animal health and performance. Full article

Background: Vitamin D is increasingly recognized not only for its role in skeletal development but also for its immunomodulatory and gastrointestinal effects. Maternal and neonatal vitamin D deficiency (VDD) has been associated with alterations in gut microbiota, impaired intestinal barrier integrity, and increased susceptibility to inflammatory conditions in neonates. However, the exact mechanisms linking perinatal vitamin D status to neonatal gastrointestinal morbidity remain incompletely understood. Methods: This review synthesizes current evidence (2015–2024) from clinical studies, animal models, and mechanistic research on the impact of VDD during pregnancy and the neonatal period on gastrointestinal health. Databases such as PubMed, Scopus, and Web of Science were systematically searched using keywords, including “vitamin D”, “neonate”, “gut microbiome”, “intestinal barrier”, and “necrotizing enterocolitis”. Results: Emerging data suggest that VDD in utero and postnatally correlates with dysbiosis, increased intestinal permeability, and elevated inflammatory responses in neonates. Notably, low 25(OH)D levels in mothers and newborns have been linked with a higher incidence of necrotizing enterocolitis (NEC), delayed gut maturation, and altered mucosal immunity. Vitamin D appears to modulate the expression of tight junction proteins, regulate antimicrobial peptides, and maintain microbial diversity through the vitamin D receptor (VDR). Conclusions: Understanding the gastrointestinal implications of early-life VDD opens a potential window for preventive strategies in neonatal care. Timely maternal supplementation and targeted neonatal interventions may mitigate gut-related morbidities and improve early-life health outcomes. Further longitudinal and interventional studies are warranted to clarify causality and optimal intervention timing. Full article

Lacticaseibacillus rhamnosus (L. rhamnosus) is a safe probiotic with no side effects, providing benefits such as gut microbiota regulation and immune enhancement, making it highly valuable with strong potential. However, strains from different sources have unique traits, and whole-genome sequencing (WGS) helps analyse these differences. In this study, we used WGS to examine L. rhamnosus strains from mice with fish oil-treated smoking-induced pneumonia to better understand their biological functions and explore possible anti-inflammatory mechanisms. Methods: We isolated a strain, Lacticaseibacillus rhamnosus CP-1 (L. rhamnosus CP-1), from mice intestines where fish oil alleviated smoking-induced pneumonia. Identification of probiotic-related genes by WGS and characterised the strain’s probiotic properties. Results: L. rhamnosus CP-1 has a single circular chromosome (2,989,570 bp, 46.76% GC content) and no plasmids. COG, GO, and KEGG databases revealed genes linked to carbohydrate metabolism. The CAZy database identified GH25 lysozyme and PL8 polysaccharide lyase genes. KEGG highlighted an antimicrobial peptide ABC transporter permease, while TCDB noted the ABC-type antimicrobial peptide transporter (the main active transport component). KEGG also showed 10 genes for terpenoid skeleton biosynthesis and 5 for keto-glycan unit biosynthesis. Additionally, L. rhamnosus CP-1 carries metabolic regulators and bacteriocin-related genes. Conclusions: Whole-genome sequencing analysis revealed that L. rhamnosus CP-1 has carbohydrate utilisation and potential anti-inflammatory effects at the molecular level. Potential functional genes include carbohydrate transport and hydrolase, antimicrobial peptide ABC transporter and its osmotic enzyme components, bacteriocin immune protein, terpenoid skeleton, and keto-glycan synthesis. Full article

Ferulic acid esterase (FAE) plays an important role in plant fiber degradation by catalyzing the hydrolysis of lignocellulosic structures. FAE-producing lactic acid bacteria (LAB), as potential probiotics, can improve ruminant digestion and gut health. In this study, two LAB strains (Q2 and Q6) with FAE activity were isolated from sheep rumen. Based on 16S rDNA sequencing, they were identified as Lactobacillus mucosae and Streptococcus equinus, respectively. Compared to Q2, Q6 demonstrated higher enzyme production, lactic acid yield, broader carbohydrate utilization, and stronger antimicrobial activity. The whole genome sequencing revealed Q2 and Q6 possess genomes of 2.14 Mbp and 1.95 Mbp, with GC contents of 46.81% and 37.30%, respectively. Q2 and Q6 exhibited the highest average nucleotide identity (ANI) with L. mucosae DSM 13345 (97.30%) and S. equinus ATCC 33317 (97.92%), respectively. The strains harbored 2101 and 1928 predicted genes, including 1984 and 1837 coding sequences (CDSs), respectively. GO enrichment analysis showed the CDSs predominantly associated with membranes (or cells), catalytic activity, and metabolic processes. KEGG analysis revealed both strains enriched in metabolic pathways, with Q6 showing a notably higher number of proteins in the ABC transporters and quorum sensing than Q2. Carbohydrate-active enzymes database (CAZy) profiling identified 75 CAZymes in Q2 and 93 CAZymes in Q6, with each strain containing one novel fae gene. Safety assessment identified 1 and 33 pathogenic genes, along with 2 and 4 putative antimicrobial peptide genes, in Q2 and Q6, respectively. Notably, Q6 carried 12 virulence factor genes. These findings suggest Q2 exhibits a superior safety profile compared to Q6, indicating a higher probability of Q2 being an effective probiotic strain. In conclusion, both LAB strains produce FAE. L. mucosae Q2 demonstrates suitability as a direct-fed probiotic for livestock, while Q6 exhibits potential as a silage inoculant, though comprehensive safety evaluations are required prior to its application. Full article

Background/Objectives: The increasing threat of antibiotic resistance and the declining efficiency of traditional drug discovery pipelines highlight the urgent need for novel drug targets and effective enzyme inhibitors against infectious diseases. Oligopeptidase B (OPB), a serine protease with trypsin-like specificity that processes low-molecular-weight peptides and oligopeptides, is present in bacteria and certain parasites but absent in mammals. This unique distribution makes OPB an attractive and selective target for antimicrobial drug development. Methods: Three-dimensional models of OPB from Serratia marcescens and Stenotrophomonas maltophilia, previously identified by our research group, were constructed via homology modeling using the best available OPB template from the RCSB Protein Data Bank. The S. marcescens OPB model was subjected to high-throughput virtual screening (HTVS) against the Natural Products Atlas (npatlas) database. Top-ranking compounds were further evaluated using Glide standard precision (SP) and extra precision (XP) docking protocols. Binding affinities were refined using molecular mechanics with generalized born and surface area (MM–GBSA) calculations. Molecular dynamics (MD) simulations assessed binding stability, while absorption distribution metabolism excretion and toxicity (ADMET) profiling evaluated drug-likeness and pharmacokinetic properties. Results: Ten natural product compounds demonstrated stronger binding affinities than antipain, a well-known oligopeptide-based protease inhibitor, as indicated by their more favorable MM–GBSA scores of −60.90 kcal/mol (S. marcescens) and −27.07 kcal/mol (S. maltophilia). Among these, dichrysobactin and validamycin E consistently exhibited favorable binding profiles across both OPB models. MD simulations confirmed the stability of their interactions with OPB active sites, maintaining favorable binding conformations throughout the simulation period. ADMET analysis suggested that while both compounds show promise, lead optimization is required to enhance their drug-like characteristics. Conclusions: This study identifies dichrysobactin and validamycin E as promising OPB inhibitors with potential antimicrobial activity. These findings support their further development as selective and potent agents against bacterial pathogens, including resistant strains, and underscore the need for experimental validation to confirm their efficacy and safety. Full article

Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human–pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine. Full article

Despite its ecological and economic importance, many aspects of Varroa destructor’s biology remain poorly understood, particularly its defense mechanisms against pathogens. The limited knowledge of Varroa’s immunity has hindered the development of RNA interference (RNAi)-based strategies targeting immune-related genes. In this study, we investigated the immune gene repertoire of V. destructor by querying its NCBI nr protein database and comparing it to model species of ticks (Ixodes scapularis) and mites (Galendromus occidentalis and Tetranychus urticae). Transcription of candidate immune genes was confirmed by analyzing a de novo assembled transcriptome of V. destructor. Our findings reveal that V. destructor shares key immunological traits with ticks, including lysozymes, chitinases, and thioester-containing proteins (TEPs), but also shares the absence of transmembrane peptidoglycan recognition proteins (PGRPs), Gram-negative binding proteins, and several lectin families involved in pathogen recognition. Additionally, Varroa mites, like ticks, lack homologs of crucial immune signaling components, such as the unpaired ligand (JAK/STAT), Eiger (JNK), and multiple elements of the IMD pathway. They also do not encode canonical antimicrobial peptides (AMPs) like defensins but possess putative homologs of ctenidins, AMPs previously identified in spiders and ticks, which may be adopted as a novel genetic readout for immune response in mites. Our findings lay the groundwork for future functional studies on mite immunity and open new avenues for RNAi-based biocontrol strategies targeting immune pathways to enhance Varroa management. Full article

In light of the growing interest in antimicrobial peptides (AMPs) as potential alternatives to traditional antibiotics, proteomic research has increasingly focused on this area. Addressing this significant scientific need, we undertook an initiative to review and analyze the available databases containing information on AMPs. These databases play a pivotal role as a foundation for most AMP-related studies, enabling not only the identification of new compounds, but also a deeper understanding of their properties and therapeutic potential. As part of this study, we evaluated the quality of information within selected AMP databases, considering their accessibility, content, and research potential. The initial step of the analysis involved a comparison of the per-database and cross-database peptide sequences. A diamond, high-throughput protein alignment program was used to compare the degree of sequence similarity among peptides across the individual databases. The redundancy of the data was also evaluated. Collected information was used for an in silico evaluation of the selected species’ venom proteomes in order to identify putative antimicrobial peptide candidates. An example candidate was further evaluated via a combination of structural analysis based on the computed homology based structural model, the in silico digestion of the source protein, and the antimicrobial potential. Full article

The intensification of aquaculture has escalated disease outbreaks and overuse of antibiotics, driving the global antimicrobial resistance (AMR) crisis. Antimicrobial peptides (AMPs) provide a promising alternative due to their rapid, broad-spectrum activity, low AMR risk, and additional bioactivities, including immunomodulatory, anticancer, and antifouling properties. AMPs derived from aquatic invertebrates, particularly marine-derived, are well-suited for aquaculture, offering enhanced stability in high-salinity environments. This study compiles and analyzes data from AMP databases and over 200 scientific sources, identifying approximately 350 AMPs derived from aquatic invertebrates, mostly cationic and α-helical, across 65 protein families. While in vitro assays highlight their potential, limited in vivo studies hinder practical application. These AMPs could serve as feed additives, therapeutic agents, or in genetic engineering approaches like CRISPR/Cas9-mediated transgenesis to enhance resilience of farmed species. Despite challenges such as stability, ecological impacts, and regulatory hurdles, advancements in peptidomimetics and genetic engineering hold significant promise. Future research should emphasize refining AMP enhancement techniques, expanding their diversity and bioactivity profiles, and prioritizing comprehensive in vivo evaluations. Harnessing the potential of AMPs represents a significant step forward on the path to aquaculture sustainability, reducing antibiotic dependency, and combating AMR, ultimately safeguarding public health and ecosystem resilience. Full article

Marine microalgae are a rich source of natural products, and their amino acid-based antimicrobial agents are usually obtained by enzymatic hydrolysis, which is inefficient and limits the research on antimicrobial peptides (AMPs) from microalgae. In this study, Aureococcus anophagefferens is used as a model to predict antimicrobial peptides through high-throughput methods, and 471 putative peptides are identified based on the de novo transcriptome technique. Among them, three short peptides, P1, P6, and P7 were found to have antimicrobial activity against Escherichia coli, Staphylococcus aureus, Micro1coccus luteus, and yeast Pichia pastoris, and they showed no hemolytic activity even at higher concentrations up to 10 mg/mL. Especially P6, a 12-amino acid peptide with three positive charges, which exhibited the most significant microbicidal effect with the lowest MIC of 31.25 μg/mL against E. coli, and electron microscope observations showed the surface of P6 treated E. coli with granular protrusions and ruptures, suggesting that it likely caused cell death by directly destroying the bacterial cell membrane. This study may enrich the database of microalgal AMPs and demonstrate an efficient process for searching and validating microalgal source AMPs by combining computer analysis with bioactivity experiments. Full article