RESUMEN
BACKGROUND: The antimicrobial peptide LL37 is produced by white blood cells (mainly neutrophils) and various epithelial cells, and has the outstanding advantages of participating in immune regulation, causing chemotaxis of immune cells and promoting wound healing. However, the central domain of LL37 needs to be improved in terms of antimicrobial activity. RESULTS: In this study, the amino acid substitution method was used to improve the antimicrobial activity of the LL37 active center, and a dimeric design with a better selection index was selected. A flexible linker was selected and combined with the 6 × His-SUMO tag and LG was successfully expressed using Pichia pastoris as a host. Recombinant LG displayed strong antimicrobial activity by destroying the cell membrane of bacteria but had low hemolytic activity. In addition, compared with monomeric peptide FR, rLG had improved ability to tolerate salt ions. CONCLUSION: This research provides new ideas for the production of modified AMPs in microbial systems and their application in industrial production.
Asunto(s)
Sustitución de Aminoácidos/genética , Péptidos Catiónicos Antimicrobianos/genética , Expresión Génica , Pichia/genética , Proteínas Recombinantes/genética , Antibacterianos/farmacología , Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/farmacología , Bacterias/efectos de los fármacos , Pared Celular/efectos de los fármacos , Eritrocitos/efectos de los fármacos , Hemólisis , Humanos , Pruebas de Sensibilidad Microbiana , Proteínas Recombinantes/farmacología , CatelicidinasRESUMEN
Host defense peptides (HDPs) are part of the innate immune system and constitute a first line of defense against invading pathogens. They possess antimicrobial activity against a broad spectrum of pathogens. However, pathogens have been known to adapt to hostile environments. Therefore, the bacterial response to treatment with HDPs was investigated. Previous observations suggested that sublethal concentrations of HDPs increase the release of outer membrane vesicles (OMVs) in Escherichia coli. First, the effects of sublethal treatment with HDPs CATH-2, PMAP-36, and LL-37 on OMV release of several Gram-negative bacteria were analyzed. Treatment with PMAP-36 and CATH-2 induced release of OMVs, but treatment with LL-37 did not. The OMVs were further characterized with respect to morphological properties. The HDP-induced OMVs often had disc-like shapes. The beneficial effect of bacterial OMV release was studied by determining the susceptibility of E. coli toward HDPs in the presence of OMVs. The minimal bactericidal concentration was increased in the presence of OMVs. It is concluded that OMV release is a means of bacteria to dispose of HDP-affected membrane. Furthermore, OMVs act as a decoy for HDPs and thereby protect the bacterium. IMPORTANCE Antibiotic resistance is a pressing problem and estimated to be a leading cause of mortality by 2050. Antimicrobial peptides, also known as host defense peptides (HDPs), and HDP-derived antimicrobials have potent antimicrobial activity and high potential as alternatives to antibiotics due to low resistance development. Some resistance mechanisms have developed in bacteria, and complete understanding of bacterial defense against HDPs will aid their use in the clinic. This study provides insight into outer membrane vesicles (OMVs) as potential defense mechanisms against HDPs, which will allow anticipation of unforeseen resistance to HDPs in clinical use and possibly prevention of bacterial resistance by the means of OMVs.
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Antibacterianos/farmacología , Péptidos Catiónicos Antimicrobianos/farmacología , Proteínas de la Membrana Bacteriana Externa/metabolismo , Vesículas Extracelulares/efectos de los fármacos , Bacterias Gramnegativas/efectos de los fármacos , Animales , Péptidos Catiónicos Antimicrobianos/clasificación , Escherichia coli/química , Escherichia coli/efectos de los fármacos , Infecciones por Bacterias Gramnegativas/microbiología , Infecciones por Bacterias Gramnegativas/veterinaria , Humanos , PorcinosRESUMEN
Bombinins are a wide family of antimicrobial peptides from Xenopus skin. By sequence clustering, we highlighted at least three families named A, B, and H, which might exert antibacterial activity by different modes of action. In this work, we study bombinin-like peptide 3 (BLP-3) as a nonhemolytic representative of the quite unexplored class A due to its appealing activity toward WHO-priority-list bacteria such as Neisseria, Pseudomonas aeruginosa, and Staphylococcus aureus. A marked preference for cardiolipin and phosphatidylglycerol head groups, typically found in bacteria, is proven with biomimetic membranes studied by liquid and solid NMR and MD simulations. BLP-3 gets structured upon interaction and penetrates deeply into the bilayer in two steps involving a superficial insertion of key side chains and subsequent internalization. All along the pathway, a fundamental role is played by lysine residues in the conserved region 11-19, which act in synergy with other key residues.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/metabolismo , Materiales Biomiméticos/metabolismo , Membrana Dobles de Lípidos/metabolismo , Secuencia de Aminoácidos , Animales , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/clasificación , Materiales Biomiméticos/química , Membrana Dobles de Lípidos/química , Espectroscopía de Resonancia Magnética , Simulación de Dinámica Molecular , Filogenia , Unión Proteica , Conformación Proteica en Hélice alfa , Piel/metabolismo , Xenopus/metabolismoRESUMEN
Mytimycins are cysteine-rich antimicrobial peptides that show antifungal properties. These peptides are part of the immune network that constitutes the defense system of the Mediterranean mussel (Mytilus galloprovincialis). The immune system of mussels has been increasingly studied in the last decade due to its great efficiency, since these molluscs, particularly resistant to adverse conditions and pathogens, are present all over the world, being considered as an invasive species. The recent sequencing of the mussel genome has greatly simplified the genetic study of some of its immune genes. In the present work, we describe a total of 106 different mytimycin variants in 16 individual mussel genomes. The 13 highly supported mytimycin clusters (A-M) identified with phylogenetic inference were found to be subject to the presence/absence variation, a widespread phenomenon in mussels. We also identified a block of conserved residues evolving under purifying selection, which may indicate the "functional core" of the mature peptide, and a conserved set of 10 invariable plus 6 accessory cysteines which constitute a plastic disulfide array. Finally, we extended the taxonomic range of distribution of mytimycins among Mytilida, identifying novel sequences in M. coruscus, M. californianus, P. viridis, L. fortunei, M. philippinarum, M. modiolus, and P. purpuratus.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/genética , Genoma , Genómica , Mytilus/genética , Secuencia de Aminoácidos , Animales , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/clasificación , Perfilación de la Expresión Génica , Punto Isoeléctrico , Sistemas de Lectura Abierta , Filogenia , Regiones Promotoras Genéticas , Isoformas de Proteínas , TranscriptomaRESUMEN
Supplementing chicken feed with antibiotics can improve survival and prevent disease outbreaks. However, overuse of antibiotics may promote the development of antibiotic-resistant bacteria. Recently, antimicrobial peptides have been proposed as alternatives to antibiotics in animal husbandry. Here, we evaluate the effects of antimicrobial peptide, Epinephelus lanceolatus piscidin (EP), in Gallus gallus domesticus. The gene encoding EP was isolated, sequenced, codon-optimized and cloned into a Pichia pastoris recombinant protein expression system. The expressed recombinant EP (rEP) was then used as a dietary supplement for G. g. domesticus; overall health, growth performance and immunity were assessed. Supernatant from rEP-expressing yeast showed in vitro antimicrobial activity against Gram-positive and Gram-negative bacteria, according to an inhibition-zone diameter (mm) assay. Moreover, the antimicrobial peptide function of rEP was temperature independent. The fermentation broth yielded a spray-dried powder formulation containing 262.9 µg EP/g powder, and LC-MS/MS (tandem MS) analysis confirmed that rEP had a molecular weight of 4279 Da, as expected for the 34-amino acid peptide; the DNA sequence of the expression vector was also validated. We then evaluated rEP as a feed additive for G. g. domesticus. Treatment groups included control, basal diet and rEP at different doses (0.75, 1.5, 3.0, 6.0 and 12%). Compared to control, rEP supplementation increased G. g. domesticus weight gain, feed efficiency, IL-10 and IFN-γ production. Our results suggest that crude rEP could provide an alternative to traditional antibiotic feed additives for G. g. domesticus, serving to enhance growth and health of the animals.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/metabolismo , Pollos/inmunología , Sistema Inmunológico/metabolismo , Perciformes/metabolismo , Secuencia de Aminoácidos , Animales , Antiinfecciosos/análisis , Antiinfecciosos/metabolismo , Antiinfecciosos/farmacología , Péptidos Catiónicos Antimicrobianos/análisis , Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/genética , Pollos/crecimiento & desarrollo , Cromatografía Líquida de Alta Presión , Clonación Molecular , Suplementos Dietéticos , Bacterias Gramnegativas/efectos de los fármacos , Bacterias Grampositivas/efectos de los fármacos , Sistema Inmunológico/efectos de los fármacos , Interferón gamma/metabolismo , Interleucina-10/metabolismo , Filogenia , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/farmacología , Alineación de Secuencia , Espectrometría de Masas en Tándem , TemperaturaRESUMEN
Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that play an essential role in innate immunity across taxa from invertebrates to vertebrates. The evolution system of AMP system has not been well explained in the literature. In this study, we cloned and sequenced AMP transcriptomes of three frog species, namely Rana dybowskii, Rana amurensis, and Pelophylax nigromaculatus, which are partially sympatric in northeast Asia, but show different habitat preferences. We found that each species contained 7 to 14 families of AMPs and the diversity was higher in species with a large geographic range and greater habitat variation. All AMPs are phylogenetically related but not associated with the speciation process. Most AMP genes were under negative selection. We propose that the diversification and addition of novel functions and improvement of antimicrobial efficiency are facilitated by the expansion of family members and numbers. We also documented significant negative correlation of net charges and numbers of amino acid residues between the propiece and mature peptide segments. This supports the Net Charge Balance Hypothesis. We propose the Cut Point Sliding Hypothesis as a novel diversification mechanism to explain the correlation in lengths of the two segments.
Asunto(s)
Antiinfecciosos/clasificación , Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/genética , Anuros/clasificación , Evolución Molecular , Mutación , Secuencia de Aminoácidos , Animales , Antiinfecciosos/química , Antiinfecciosos/metabolismo , Péptidos Catiónicos Antimicrobianos/química , Anuros/genética , Asia , Filogenia , Homología de Secuencia , Simpatría/genética , TranscriptomaRESUMEN
Innate immunity is the primary defense of crustaceans against pathogens. Crustins, as antimicrobial peptides, are important to crustacean innate immunity. In this study, two kinds of Gly-rich crustin genes were cloned from Macrobrachium nipponense and were referred to as Mn-Gly-Cru1 and Mn-Gly-Cru2. These crustins belong to type II crustins with typical type II crustin structures. The full-length cDNA of Mn-Gly-Cru1 is 677 bp and contains a 576 bp open reading frame (ORF) encoding 191 amino acids. The full-length cDNA of Mn-Gly-Cru2 is 727 bp, with 573 bp ORF encoding 190 amino acids. The constructed phylogenetic tree indicated that Mn-Gly-Cru1 and Mn-Gly-Cru2 belong to the type IIa subfamily. RT-PCR analysis showed that Mn-Gly-Cru1 and Mn-Gly-Cru2 are widely distributed in various tissues. qRT-PCR results indicated that Mn-Gly-Cru1 is mainly expressed in the gills, whereas Mn-Gly-Cru2 is expressed at the highest level in hemocytes. The transcripts of Mn-Gly-Cru1 and Mn-Gly-Cru2 respond to bacterial or white spot syndrome virus (WSSV) stimuli. After injection of 48 h dsMnRelish, the expression of MnRelish, Mn-Gly-Cru1, and Mn-Gly-Cru2 were all inhibited. After WSSV, Vibrio parahaemolyticus, or Staphylococcus aureus challenge, MnRelish, Mn-Gly-Cru1, and Mn-Gly-Cru2 were all upregulated. However, the expression levels of MnRelish, Mn-Gly-Cru1, and Mn-Gly-Cru2 at 6 h bacteria or 36 h WSSV challenge were downregulated in Relish-silenced prawns when compared with the control (bacteria or WSSV challenge only, bacteria or WSSV challenge plus dsGFP injection). Results suggest that Mn-Gly-Cru1 and Mn-Gly-Cru2 play essential roles in M. nipponense innate immunity against bacteria or WSSV, and the expression levels of both genes are regulated by Relish transcriptional factor.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/genética , Clonación Molecular , Regulación de la Expresión Génica/fisiología , Palaemonidae/genética , Secuencia de Aminoácidos , Animales , Péptidos Catiónicos Antimicrobianos/clasificación , Secuencia de Bases , Perfilación de la Expresión Génica , Silenciador del Gen , Variación Genética , Filogeografía , Distribución TisularRESUMEN
Lipopolysaccharide-binding proteins (LBPs) and bactericidal permeability-increasing proteins (BPIs) are effectors of the innate immune response which act in a coordinated manner to bind and neutralize the LPS present in Gram negative bacteria. The structural organization that confers the function of LBPs and BPIs is very similar, however, they are antagonistic to each other. In this work, we characterized two LBP/BPIs from the scallop Argopecten purpuratus, namely ApLBP/BPI1 and ApLBP/BPI2. The molecular and phylogenetic analyses of ApLBP/BPIs indicated that both isoforms display classic characteristics of LBP/BPIs from other invertebrates. Additionally, ApLBP/BPIs are constitutively expressed in scallop tissues and their transcript expression is upregulated in hemocytes and gills in response to an immune challenge. However, some structural characteristics of functional importance for the biological activity of these molecules, such as the net charge differ substantially between ApLBP/BPI1 and ApLBP/BPI2. Furthermore, each isoform displays a specific profile of basal expression among different tissues, as well as specific patterns of expression during the activation of the immune response. Results suggest that functional specialization of ApLBP/BPIs might happen, with potential role as LBP or BPI in this species of scallop. Further research on the biological activities of ApLBP/BPIs are necessary to elucidate their participation in the scallop immune response.
Asunto(s)
Proteínas de Fase Aguda/genética , Péptidos Catiónicos Antimicrobianos/genética , Proteínas Sanguíneas/genética , Proteínas Portadoras/genética , Lipopolisacáridos/metabolismo , Glicoproteínas de Membrana/genética , Pectinidae/genética , Filogenia , Proteínas de Fase Aguda/clasificación , Animales , Péptidos Catiónicos Antimicrobianos/clasificación , Acuicultura , Proteínas Sanguíneas/clasificación , Proteínas Portadoras/clasificación , Expresión Génica , Inmunidad Innata , Glicoproteínas de Membrana/clasificación , Pectinidae/inmunología , Isoformas de Proteínas/genética , Alineación de Secuencia , Transducción de SeñalRESUMEN
There is a growing interest in the complex role of host defense peptides (HDPs) in the pathophysiology of several immune-mediated inflammatory diseases. The physicochemical properties and selective interaction of HDPs with various receptors define their immunomodulatory effects. However, it is quite challenging to understand their function because some HDPs play opposing pro-inflammatory and anti-inflammatory roles, depending on their expression level within the site of inflammation. While it is known that HDPs maintain constitutive host protection against invading microorganisms, the inducible nature of HDPs in various cells and tissues is an important aspect of the molecular events of inflammation. This review outlines the biological functions and emerging roles of HDPs in different inflammatory conditions. We further discuss the current data on the clinical relevance of impaired HDPs expression in inflammation and selected diseases.
Asunto(s)
Inmunidad Adaptativa/inmunología , Péptidos Catiónicos Antimicrobianos/inmunología , Bacterias/inmunología , Inmunidad Innata/inmunología , Inflamación/inmunología , Animales , Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/genética , Bacterias/clasificación , Catelicidinas/genética , Catelicidinas/inmunología , Catelicidinas/metabolismo , Defensinas/genética , Defensinas/inmunología , Defensinas/metabolismo , Interacciones Huésped-Patógeno/inmunología , Humanos , Inflamación/genética , Inflamación/microbiologíaRESUMEN
Antimicrobial peptides (AMPs) are part of the innate immune response to pathogens in all of the kingdoms of life. They have received significant attention because of their extraordinary variety of activities, in particular, as candidate drugs against the threat of super-bacteria. A systematic study of the relation between the sequence and the mechanism of action is urgently needed, given the thousands of sequences already in multiple web resources. ADAPTABLE web platform (http://gec.u-picardie.fr/adaptable) introduces the concept of "property alignment" to create families of property and sequence-related peptides (SR families). This feature provides the researcher with a tool to select those AMPs meaningful to their research from among more than 40,000 nonredundant sequences. Selectable properties include the target organism and experimental activity concentration, allowing selection of peptides with multiple simultaneous actions. This is made possible by ADAPTABLE because it not only merges sequences of AMP databases but also merges their data, thereby standardizing values and handling non-proteinogenic amino acids. In this unified platform, SR families allow the creation of peptide scaffolds based on common traits in peptides with similar activity, independently of their source.
Asunto(s)
Antiinfecciosos/química , Péptidos Catiónicos Antimicrobianos/química , Péptidos/farmacología , Secuencia de Aminoácidos , Antiinfecciosos/clasificación , Péptidos Catiónicos Antimicrobianos/clasificación , Bacterias/metabolismo , Bases de Datos Factuales , Bases de Datos de ProteínasRESUMEN
Antimicrobial peptides (AMPs) occur in all kingdoms of life and are integral to host defense. They have diverse structures and target a variety of organisms, both by nonspecific membrane interactions and via specific targets. Here we discuss the structures of AMPs from the four main classes currently recognized - that is, peptides with (i) α-helical, (ii) ß-sheet, (iii) αß, or (iv) non-αß elements - as well as the growing pool of complex topologies including various post-translational modifications (PTMs). We propose to group these latter peptides into a fifth class of AMPs. Such peptides exhibit high stability and amenability to chemical engineering, making them of interest for the development of novel antimicrobial agents. Advances and challenges in the development of these peptides towards therapeutic leads are presented.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/química , Secuencia de Aminoácidos , Animales , Péptidos Catiónicos Antimicrobianos/clasificación , Humanos , Modelos Moleculares , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Relación Estructura-ActividadRESUMEN
Due to increase in antibiotic resistance in recent years, development of efficient and accurate techniques for discovery and design of biologically active peptides such as antimicrobial peptides (AMPs) has become essential. The screening of natural and synthetic AMPs in the wet lab is a challenge due to time and cost involved in such experiments. Bioinformatics methods can be used to speed up discovery and design of antimicrobial peptides by limiting the wet-lab search to promising peptide sequences. However, most such tools are typically limited to the prediction of whether a peptide exhibits antimicrobial activity or not and they do not identify the exact type of the biological activities of these peptides. In this work, we have designed a machine learning based model called AMAP for predicting biological activity of peptides with a specialized focus on antimicrobial activity prediction. AMAP used multi-label classification to predict 14 different types of biological functions of a given peptide sequence with improved accuracy in comparison to existing state of the art techniques. We have performed stringent performance analyses of the proposed method. In addition to cross-validation and performance comparison with existing AMP predictors, AMAP has also been benchmarked on recently published experimentally verified peptides that were not a part of our training set. We have also analyzed features used in this work and our analysis shows that the proposed predictor can generalize well in predicting biological activity of novel peptide sequences. A webserver of the proposed method is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#AMAP.
Asunto(s)
Antiinfecciosos , Péptidos Catiónicos Antimicrobianos , Biología Computacional/métodos , Antiinfecciosos/química , Antiinfecciosos/clasificación , Antiinfecciosos/farmacología , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/farmacología , Bases de Datos de Proteínas , Descubrimiento de Drogas , Escherichia coli/efectos de los fármacos , Fusarium/efectos de los fármacos , Aprendizaje Automático , Programas InformáticosRESUMEN
Ovodefensins (OvoDs) represent a group of cysteine-rich host defense peptides that are abundant in the egg white. Recent studies have found that ovodefensins are specific to birds and reptiles. However, the entire repertoire and evolutionary relationships of this gene family have not been thoroughly elucidated to date. Following our cross-species and genome-wide computational study, a total of 94 ovodefensin genes with multiple novel cysteine sequence motifs were identified from 22 phylogenetically divergent species. Phylogenetic analysis suggests that a large number of OvoDs evolved by gene duplication after species divergence. Furthermore, the OvoD genes in each species trend to be clustered densely in a syntenic region flanked by the XKR6 and MTMR9 genes, indicating that they are of monophyletic origin and appear to have emerged via independent gene duplication events in snakes, turtles, crocodiles, birds and the green lizard. Furthermore, positive selection sites are located primarily in the mature peptide region of the turtle, lizard and snake OvoD genes. Moreover, the duplicate OvoDAs in birds seem to be maintained in almost identical sequences and functions by strong purifying selection. Genome-wide identification and analyses of the OvoD gene family may greatly improve our understanding of the potential evolutionary relationship scenario of the OvoD gene family. Continued sequence mining and functional studies of OvoDs will be helpful in shedding light on the relationships between OvoDs and other defensin-related gene families.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/genética , Resistencia a la Enfermedad/genética , Estudio de Asociación del Genoma Completo , Genoma , Interacciones Huésped-Patógeno/genética , Familia de Multigenes , Secuencia de Aminoácidos , Animales , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/clasificación , Mapeo Cromosómico , Secuencia Conservada , Evolución Molecular , Duplicación de Gen , Filogenia , Selección GenéticaRESUMEN
Antimicrobial peptides (AMPs), critical components of the innate immune system, are widely distributed throughout the animal and plant kingdoms. They can protect against a broad array of infection-causing agents, such as bacteria, fungi, parasites, viruses, and tumor cells, and also exhibit immunomodulatory activity. AMPs exert antimicrobial activities primarily through mechanisms involving membrane disruption, so they have a lower likelihood of inducing drug resistance. Extensive studies on the structure-activity relationship have revealed that net charge, hydrophobicity, and amphipathicity are the most important physicochemical and structural determinants endowing AMPs with antimicrobial potency and cell selectivity. This review summarizes the recent advances in AMPs development with respect to characteristics, structure-activity relationships, functions, antimicrobial mechanisms, expression regulation, and applications in food, medicine, and animals.
Asunto(s)
Antibacterianos/farmacología , Péptidos Catiónicos Antimicrobianos/farmacología , Secuencia de Aminoácidos , Animales , Antibacterianos/química , Antibacterianos/clasificación , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/clasificación , Quimioterapia Combinada , Humanos , Inmunomodulación , Relación Estructura-ActividadRESUMEN
BACKGROUND: Antimicrobial peptides attract considerable interest as novel agents to combat infections. Their long-time potency across bacteria, viruses and fungi as part of diverse innate immune systems offers a solution to overcome the rising concerns from antibiotic resistance. With the rapid increase of antimicrobial peptides reported in the databases, peptide selection becomes a challenge. We propose similarity analyses to describe key properties that distinguish between active and non-active peptide sequences building upon the physicochemical properties of antimicrobial peptides. We used an iterative supervised machine learning approach to classify active peptides from inactive peptides with low false discovery rates in a relatively short computational search time. RESULTS: By generating explicit boundaries, our method defines new categories of active and inactive peptides based on their physicochemical properties. Consequently, it describes physicochemical characteristics of similarity among active peptides and the physicochemical boundaries between active and inactive peptides in a single process. To build the similarity boundaries, we used the rough set theory approach; to our knowledge, this is the first time that this approach has been used to classify peptides. The modified rough set theory method limits the number of values describing a boundary to a user-defined limit. Our method is optimized for specificity over selectivity. Noting that false positives increase activity assays while false negatives only increase computational search time, our method provided a low false discovery rate. Published datasets were used to compare our rough set theory method to other published classification methods and based on this comparison, we achieved high selectivity and comparable sensitivity to currently available methods. CONCLUSIONS: We developed rule sets that define physicochemical boundaries which allow us to directly classify the active sequences from inactive peptides. Existing classification methods are either sequence-order insensitive or length-dependent, whereas our method generates the rule sets that combine order-sensitive descriptors with length-independent descriptors. The method provides comparable or improved performance to currently available methods. Discovering the boundaries of physicochemical properties may lead to a new understanding of peptide similarity.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/clasificación , Fenómenos Químicos , Péptidos Catiónicos Antimicrobianos/metabolismo , Modelos MolecularesRESUMEN
BACKGROUND: Antimicrobial peptides are a promising alternative for combating pathogens resistant to conventional antibiotics. Computer-assisted peptide discovery strategies are necessary to automatically assess a significant amount of data by generating models that efficiently classify what an antimicrobial peptide is, before its evaluation in the wet lab. Model's performance depends on the selection of molecular descriptors for which an efficient and effective approach has recently been proposed. Unfortunately, how to adapt this method to the selection of molecular descriptors for the classification of antimicrobial peptides and the performance it can achieve, have only preliminary been explored. RESULTS: We propose an adaptation of this successful feature selection approach for the weighting of molecular descriptors and assess its performance. The evaluation is conducted on six high-quality benchmark datasets that have previously been used for the empirical evaluation of state-of-art antimicrobial prediction tools in an unbiased manner. The results indicate that our approach substantially reduces the number of required molecular descriptors, improving, at the same time, the performance of classification with respect to using all molecular descriptors. Our models also outperform state-of-art prediction tools for the classification of antimicrobial and antibacterial peptides. CONCLUSIONS: The proposed methodology is an efficient approach for the development of models to classify antimicrobial peptides. Particularly in the generation of models for discrimination against a specific antimicrobial activity, such as antibacterial. One of our future directions is aimed at using the obtained classifier to search for antimicrobial peptides in various transcriptomes.
Asunto(s)
Algoritmos , Antiinfecciosos/clasificación , Péptidos Catiónicos Antimicrobianos/clasificación , Bacterias/efectos de los fármacos , Evolución Molecular , Reconocimiento de Normas Patrones Automatizadas , Antiinfecciosos/química , Antiinfecciosos/farmacología , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/farmacología , Simulación por Computador , Modelos Moleculares , Relación Estructura-Actividad CuantitativaRESUMEN
Antimicrobial peptides (AMPs) are produced by the stimulated humoral immune system. Most mature AMPs contain less than 50 amino acid residues. Some of them are generated from proproteins upon microbial challenges. Here, we report the antimicrobial activities of a proline-rich proprotein, named SlLebocin1 (SlLeb1), from the tobacco cutworm Spodoptera litura. SlLebocin1 cDNA contains a 477-bp open reading frame (ORF). It is mainly expressed in hemocytes and the midgut in naïve larvae. The transcript level was significantly induced in hemocytes but repressed in the midgut and fat body by bacterial challenges. The proprotein contains 158 amino acids with 3 RXXR motifs that are characteristic of some Lepidopteral lebocin proproteins. Four peptides corresponding to the predicted processed fragments were synthesized chemically, and their antimicrobial activities against two Gram-negative and two Gram-positive bacterial strains were analyzed. The peptides showed differential antimicrobial activities. For Escherichia coli and Bacillus subtilis, only the C-terminal fragment (124-158) showed strong inhibitory effects. For Staphylococcus aureus, all peptides showed partial inhibitions. None of them inhibited Serratia marcescens. Bacterial morphologies were examined by the scanning electron microscopy and confocal laser scanning microscopy. The antimicrobial peptides either disrupted cellular membrane or inhibited cell division and caused elongated/enlarged morphologies. The results may provide ideas for designing novel antibiotics.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/genética , Proteínas de Insectos/genética , Dominios Proteicos Ricos en Prolina/genética , Precursores de Proteínas/genética , Spodoptera/genética , Secuencia de Aminoácidos , Animales , Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/farmacología , Secuencia de Bases , Sistema Digestivo/metabolismo , Escherichia coli/efectos de los fármacos , Escherichia coli/ultraestructura , Perfilación de la Expresión Génica , Hemocitos/metabolismo , Proteínas de Insectos/clasificación , Proteínas de Insectos/farmacología , Larva/genética , Microscopía Electrónica de Rastreo , Filogenia , Precursores de Proteínas/clasificación , Precursores de Proteínas/farmacología , Homología de Secuencia de Aminoácido , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/ultraestructuraRESUMEN
Mature proteins can act as potential sources of encrypted bioactive peptides that, once released from their parent proteins, might interact with diverse biomolecular targets. In recent work we introduced a systematic methodology to uncover encrypted intragenic antimicrobial peptides (IAPs) within large protein sequence libraries. Given that such peptides may interact with membranes in different ways, resulting in distinct observable outcomes, it is desirable to develop a predictive methodology to categorize membrane active peptides and establish a link to their physicochemical properties. Building upon previous work, we explored the interaction of a range of IAPs with model membranes probed by differential scanning calorimetry (DSC) and circular dichroism (CD) techniques. The biophysical data were submitted to multivariate statistical methods and resulting peptide clusters were correlated to peptide structure and to their antimicrobial activity. A re-evaluation of the physicochemical properties of the peptides was conducted based on peptide cluster memberships. Our data indicate that membranolytic peptides produce characteristic thermal transition (DSC) profiles in model vesicles and that this can be used to categorize novel molecules with unknown biological activity. Incremental expansion of the model presented here might result in a unified experimental framework for the prediction of novel classes of membrane active peptides.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/clasificación , Péptidos Catiónicos Antimicrobianos/farmacología , Membrana Celular/efectos de los fármacos , Membrana Celular/metabolismo , Secuencia de Aminoácidos , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/genética , Bacterias/metabolismo , Rastreo Diferencial de Calorimetría , Membrana Celular/química , Péptidos de Penetración Celular/química , Péptidos de Penetración Celular/clasificación , Péptidos de Penetración Celular/farmacología , Fenómenos Químicos , Humanos , Lípidos de la Membrana/química , Lípidos de la Membrana/metabolismo , Pruebas de Sensibilidad Microbiana , Conformación Proteica en Hélice alfaRESUMEN
Antibiotic resistance is projected as one of the greatest threats to human health in the future and hence alternatives are being explored to combat resistance. Antimicrobial peptides (AMPs) have shown great promise, because use of AMPs leads bacteria to develop no or low resistance. In this review, we discuss the diversity, history and the various mechanisms of action of AMPs. Although many AMPs have reached clinical trials, to date not many have been approved by the US Food and Drug Administration (FDA) due to issues with toxicity, protease cleavage and short half-life. Some of the recent strategies developed to improve the activity and biocompatibility of AMPs, such as chemical modifications and the use of delivery systems, are also reviewed in this article.
Asunto(s)
Péptidos Catiónicos Antimicrobianos/farmacología , Animales , Péptidos Catiónicos Antimicrobianos/efectos adversos , Péptidos Catiónicos Antimicrobianos/química , Péptidos Catiónicos Antimicrobianos/clasificación , Bacterias , Membrana Celular/efectos de los fármacos , HumanosRESUMEN
OBJECTIVES: hCAP18/LL-37 is an endogenous antibiotic having a role in innate immunity. The aim of the present study was to evaluate serum and gingival crevicular fluid (GCF) hCAP18/LL-37 levels in patients with generalized aggressive periodontitis (G-AgP). MATERIALS AND METHODS: Twenty-six G-AgP patients, 24 gingivitis patients, and 25 healthy subjects were included in this study. Periodontal parameters including probing depth, clinical attachment level, plaque index, and papilla bleeding index were recorded. GCF and serum hCAP18/LL-37 levels were analyzed by enzyme-linked immunosorbent assay. RESULTS: GCF hCAP18/LL-37 level was significantly higher in G-AgP compared to others (p = 0.038, p < 0.001). Gingivitis patients had significantly higher GCF hCAP18/LL-37 levels than controls (p < 0.001). No significant differences were observed in serum hCAP18/LL-37 levels among the study groups (p = 0.524). While there were positive correlations between GCF hCAP18/LL-37 levels and periodontal parameters of sampling sites (p < 0.005), no significant correlation was observed between serum hCAP18/LL-37 levels and whole-mouth periodontal parameters (p > 0.05). CONCLUSION: Increased levels of GCF hCAP18/LL-37 in G-AgP might show that it is abundantly expressed in the presence of periodontal tissue destruction. Serum hCAP18/LL-37 levels do not seem to be related with the presence of G-AgP. CLINICAL RELEVANCE: hCAP18/LL-37 antimicrobial peptide might be associated with periodontal tissue destruction in the presence of aggressive periodontitis.