Mammalian antibiotic peptides

Antimicrobial Peptides with Antibacterial Activity against Vancomycin-Resistant Staphylococcus aureus Strains: Classification, Structures, and Mechanisms of Action

The emergence of bacteria resistant to conventional antibiotics is of great concern in modern medicine because it renders ineffectiveness of the current empirical antibiotic therapies. Infections caused by vancomycin-resistant Staphylococcus aureus (VRSA) and vancomycin-intermediate S. aureus (VISA) strains represent a serious threat to global health due to their considerable morbidity and mortality rates. Therefore, there is an urgent need of research and development of new antimicrobial alternatives against these bacteria. In this context, the use of antimicrobial peptides (AMPs) is considered a promising alternative therapeutic strategy to control resistant strains. Therefore, a wide number of natural, artificial, and synthetic AMPs have been evaluated against VRSA and VISA strains, with great potential for clinical application. In this regard, we aimed to present a comprehensive and systematic review of research findings on AMPs that have shown antibacterial activity against vancomycin-resistant and vancomycin-intermediate resistant strains and clinical isolates of S. aureus, discussing their classification and origin, physicochemical and structural characteristics, and possible action mechanisms. This is the first review that includes all peptides that have shown antibacterial activity against VRSA and VISA strains exclusively.

EMA and EFSA Joint Scientific Opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA)

EFSA and EMA have jointly reviewed measures taken in the EU to reduce the need for and use of antimicrobials in food-producing animals, and the resultant impacts on antimicrobial resistance (AMR). Reduction strategies have been implemented successfully in some Member States. Such strategies include national reduction targets, benchmarking of antimicrobial use, controls on prescribing and restrictions on use of specific critically important antimicrobials, together with improvements to animal husbandry and disease prevention and control measures. Due to the multiplicity of factors contributing to AMR, the impact of any single measure is difficult to quantify, although there is evidence of an association between reduction in antimicrobial use and reduced AMR. To minimise antimicrobial use, a multifaceted integrated approach should be implemented, adapted to local circumstances. Recommended options (non-prioritised) include: development of national strategies; harmonised systems for monitoring antimicrobial use and AMR development; establishing national targets for antimicrobial use reduction; use of on-farm health plans; increasing the responsibility of veterinarians for antimicrobial prescribing; training, education and raising public awareness; increasing the availability of rapid and reliable diagnostics; improving husbandry and management procedures for disease prevention and control; rethinking livestock production systems to reduce inherent disease risk. A limited number of studies provide robust evidence of alternatives to antimicrobials that positively influence health parameters. Possible alternatives include probiotics and prebiotics, competitive exclusion, bacteriophages, immunomodulators, organic acids and teat sealants. Development of a legislative framework that permits the use of specific products as alternatives should be considered. Further research to evaluate the potential of alternative farming systems on reducing AMR is also recommended. Animals suffering from bacterial infections should only be treated with antimicrobials based on veterinary diagnosis and prescription. Options should be reviewed to phase out most preventive use of antimicrobials and to reduce and refine metaphylaxis by applying recognised alternative measures.

QSAR modeling: where have you been? Where are you going to?

Quantitative structure-activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR studies, as well as encourage the use of high quality, validated QSARs for regulatory decision making.

Six defensins from the triangle-shell pearl mussel Hyriopsis cumingii

Antimicrobial peptides (AMPs) are the first line of defense of invertebrates against invading pathogens. Defensins, unique AMPs, have a cysteine-stabilized α-helix and β-sheet (CSαβ) motif. In invertebrates, defensins have been reported in arthropods and mussels. Recently, six defensins were identified from Hyriopsis cumingii for the first time, and were designated as HcDef1, HcDef2, HcDef3, HcDef4, HcDef5, and HcDef6. HcDef1 and HcDef2 encode a protein containing 61 and 60 amino acids, respectively. HcDef3, HcDef4, and HcDef6 have 65 amino acids each. HcDef5 is longer than the other five defensins, comprising 83 amino acids. HcDef3 and HcDef4 have three pairs of disulfide bonds. HcDef1, HcDef5, and HcDef6 are exceptions; each has four pairs of disulfide bonds. Evolutionary analysis revealed that only purifying selection and no positive selection could be detected in defensin genes; purifying selection might be the major evolutionary driving force in the evolution of defensin genes. The present study reveals for the first time that the defensins from H. cumingii are diverse and phylogenetic analysis showed that these 6 defensins from H. cumingii were clustered into one group. Reverse transcriptase polymerase chain reaction (RT-PCR) analysis showed that HcDef1-HcDef4 could be detected in the hepatopancreas and gills whereas HcDef5-HcDef6 could only be detected in gills. In addition, the expression levels of HcDef2, HcDef3, and HcDef5 in H. cumingii with pearls were higher than that in H. cumingii without pearls. Quantitative RT-PCR analysis showed that HcDef1, HcDef2, HcDef3, and HcDef5 were downregulated by Vibrio anguillarum challenge whereas HcDef4 and HcDef6 were upregulated under Vibrio challenge. Our results suggest the roles of defensins in the innate immunity of H. cumingii.

Defensin from disk abalone Haliotis discus discus: molecular cloning, sequence characterization and immune response against bacterial infection

Gene-encoded antimicrobial peptides (AMPs) serve a major role in host defense systems against pathogens. In this study, cDNA of a new mollusk defensin was identified from a normalized cDNA library constructed from whole tissues of disk abalone. Abalone defensin peptide (pro-defensin) has a 198-bp coding sequence comprised of a putative 66 amino acids with a mature defensin consisting of 48 amino acid residues. The presence of an invertebrate defensin family domain, an arrangement of six cysteine residues and their disulfide linkage in C(1)-C(4), C(2)-C(5) and C(3)-C(6) form, an alpha helix in three-dimensional structure and a phylogenetic relationship suggests that abalone defensin could be a new member of the invertebrate defensin family, and related to arthropod defensins. In non-stimulated abalone, defensin transcripts were constitutively expressed in all examined tissues including hemocytes, gills, mantle, muscle, digestive tract and hepatopancreas. It was observed that abalone defensin transcripts were significantly induced in hemocytes, gills and digestive tract at different time intervals after infection by pathogenic bacteria mixture containing Vibrio alginolyticus, Vibrio parahemolyticus and Lysteria monocytogenes. Our overall results suggest that disk abalone defensin could be involved in the immune response reactions as a host defense against pathogenic bacteria.

Identification of novel host defense peptides and the absence of alpha-defensins in the bovine genome

Host defense peptides (historically called antimicrobial peptides, AMPs) are key components in the mammalian innate immune system, and are responsible for both direct killing and immunomodulatory effects in host defense against pathogenic organisms. In order to identify novel host defense peptides by sequence analysis, we constructed the AMPer resource (http://www.cnbi2.com/cgi-bin/amp.pl) that utilizes hidden Markov models to recognize sequences of antimicrobial peptides. In the current work, we utilized the AMPer resource to search bovine expressed sequence tags from the NCBI dbEST project and the bovine genome sequence for novel host defense peptides. Of the 34 known bovine AMPs, 27 were identified with high confidence in the AMPs predicted from ESTs. A further potential 68 AMPs predicted from the EST data were found that appear to be novel giving a total estimate of 102 AMPs present in the genome. Two of these were cathelicidins and selected for experimental verification in RNA derived from bovine tissue. One predicted AMP, most similar to rabbit '15 kDa protein' AMP, was confirmed to be present in infected bovine intestinal tissue using PCR. These findings demonstrated the practical applicability of the developed bioinformatics approach and laid a foundation for future discoveries of gene-coded AMPs. No members of the alpha-defensin family were found in the bovine sequences. Since we could find no technical reasons these would be missed and no references to bovine alpha-defensins in the literature, this suggests that cattle lack this important family of host defense peptides.

AMPer: a database and an automated discovery tool for antimicrobial peptides

MOTIVATION

Increasing antibiotics resistance in human pathogens represents a pressing public health issue worldwide for which novel antibiotic therapies based on antimicrobial peptides (AMPs) may offer one possible solution. In the current study, we utilized publicly available data on AMPs to construct hidden Markov models (HMMs) that enable recognition of individual classes of antimicrobials peptides (such as defensins, cathelicidins, cecropins, etc.) with up to 99% accuracy and can be used for discovering novel AMP candidates.

RESULTS

HMM models for both mature peptides and propeptides were constructed. A total of 146 models for mature peptides and 40 for propeptides have been developed for individual AMP classes. These were created by clustering and analyzing AMP sequences available in the public sources and by consequent iterative scanning of the Swiss-Prot database for previously unknown gene-coded AMPs. As a result, an additional 229 additional AMPs have been identified from Swiss-Prot, and all but 34 could be associated with known antimicrobial activities according to the literature. The final set of 1045 mature peptides and 253 propeptides have been organized into the open-source AMPer database.

AVAILABILITY

The developed HMM-based tools and AMP sequences can be accessed through the AMPer resource at http://www.cnbi2.com/cgi-bin/amp.pl

Effects of picolinic acid on the antimicrobial functions of host macrophages against Mycobacterium avium complex

Picolinic acid (PA) potentiates macrophage (MPhi) antimicrobial activity against intracellular Mycobacterium avium complex (MAC). Here, we studied the mechanisms of this phenomenon using human THP-1 MPhis. First, when PA-treated MAC-infected MPhis were cultured in the presence or absence of reactive oxygen intermediate (ROI) scavengers, nitric oxide synthase (NOS) inhibitors or phospholipase A(2) (PLA(2)) inhibitors, none of these agents blocked the activity of PA in potentiating MPhi anti-MAC activity. Second, when PA was added to the in vitro anti-MAC bactericidal system consisting of either ROIs, reactive nitrogen intermediates (RNIs) or free fatty acid (FFA) molecules, which are the major MPhi antimicrobial effectors, PA inhibited the activity of ROIs and conversely potentiated the activity of RNIs; PA did not affect the activity of FFAs. Third, PA reduced mRNA expression of NADPH oxidase and beta-defensin-1 by MAC-infected MPhis, whilst neither cytosolic PLA(2) nor CAP37 mRNA expression was affected. Notably, inducible NOS and secretory PLA(2) mRNA expression was not detected for MAC-infected MPhis even when given PA treatment. These findings suggest that ROIs, RNIs, FFAs and beta-defensin-1 do not play important roles in the PA-induced potentiation of MPhi anti-MAC activity.

Probiotics manipulate host cytokine response and induce antimicrobial peptides

Probiotics modulate production of both cytokine and antimicrobial peptides. This effect can be regarded as a part of complex interplay between them and the host.

Facilitation of expression and purification of an antimicrobial peptide by fusion with baculoviral polyhedrin in Escherichia coli

Several fusion strategies have been developed for the expression and purification of small antimicrobial peptides (AMPs) in recombinant bacterial expression systems. However, some of these efforts have been limited by product toxicity to host cells, product proteolysis, low expression levels, poor recovery yields, and sometimes an absence of posttranslational modifications required for biological activity. For the present work, we investigated the use of the baculoviral polyhedrin (Polh) protein as a novel fusion partner for the production of a model AMP (halocidin 18-amino-acid subunit; Hal18) in Escherichia coli. The useful solubility properties of Polh as a fusion partner facilitated the expression of the Polh-Hal18 fusion protein ( approximately 33.6 kDa) by forming insoluble inclusion bodies in E. coli which could easily be purified by inclusion body isolation and affinity purification using the fused hexahistidine tag. The recombinant Hal18 AMP ( approximately 2 kDa) could then be cleaved with hydroxylamine from the fusion protein and easily recovered by simple dialysis and centrifugation. This was facilitated by the fact that Polh was soluble during the alkaline cleavage reaction but became insoluble during dialysis at a neutral pH. Reverse-phase high-performance liquid chromatography was used to further purify the separated recombinant Hal18, giving a final yield of 30% with >90% purity. Importantly, recombinant and synthetic Hal18 peptides showed nearly identical antimicrobial activities against E. coli and Staphylococcus aureus, which were used as representative gram-negative and gram-positive bacteria, respectively. These results demonstrate that baculoviral Polh can provide an efficient and facile platform for the production or functional study of target AMPs.

Characterization of a defensin from the oyster Crassostrea gigas. Recombinant production, folding, solution structure, antimicrobial activities, and gene expression

In invertebrates, defensins were found in arthropods and in the mussels. Here, we report for the first time the identification and characterization of a defensin (Cg-Def) from an oyster. Cg-def mRNA was isolated from Crassostrea gigas mantle using an expressed sequence tag approach. To gain insight into potential roles of Cg-Def in oyster immunity, we produced the recombinant peptide in Escherichia coli, characterized its antimicrobial activities, determined its solution structure by NMR spectroscopy, and quantified its gene expression in vivo following bacterial challenge of oysters. Recombinant Cg-Def was active in vitro against Gram-positive bacteria but showed no or limited activities against Gram-negative bacteria and fungi. The activity of Cg-Def was retained in vitro at a salt concentration similar to that of seawater. The Cg-Def structure shares the so-called cystine-stabilized alpha-beta motif (CS-alphabeta) with arthropod defensins but is characterized by the presence of an additional disulfide bond, as previously observed in the mussel defensin (MGD-1). Nevertheless, despite a similar global fold, the Cg-Def and MGD-1 structures mainly differ by the size of their loops and by the presence of two aspartic residues in Cg-Def. Distribution of Cg-def mRNA in various oyster tissues revealed that Cg-def is mainly expressed in mantle edge where it was detected by mass spectrometry analyses. Furthermore, we observed that the Cg-def messenger concentration was unchanged after bacterial challenge. Our results suggest that Cg-def gene is continuously expressed in the mantle and would play a key role in oyster by providing a first line of defense against pathogen colonization.

A cumulative experience examining the effect of natural and synthetic antimicrobial peptides vs. Chlamydia trachomatis

We tested the activity of 48 structurally diverse antimicrobial peptides against Chlamydia trachomatis, serovar L2. The peptides' activity against C. trachomatis, serovar L2 was measured in 48-h McCoy cell shell vial assays. Peptides of 16-20 amino acids were more active than larger peptides, such as defensins. Beta-sheet protegrins, as well as alpha-helical peptides such as novispirin (G-10) were equally active. Enantiomers were as active as native structures. Moderate-sized circular mini-defensins were less effective against C. trachomatis. Moderate-sized cationic peptides may be useful in microbicide preparations designed to prevent chlamydial infection.

Expression of inflammatory markers in pig amnion after intraamniotic infection with nonpathogenic or enteropathogenic Escherichia coli

The pig amnion was in vivo intraamniotically infected with E. coli for 10 h at 80-85 d of gestation either with the nonpathogenic O86 strain or enteropathogenic O55 strain. TNF-alpha, IL-10, IL-1beta and IFN-gamma were determined in amniotic fluids by ELISA, the expression of cytokines and some other inflammatory markers was determined by immunohistochemistry. Intraamniotic infection induced high levels of TNF-alpha in amniotic fluids which correlated with bacterial virulence whereas IL-10 was induced only by O86. The IL-1beta level did not increase significantly and was expressed in all infected membranes. IFN-gamma was negligible or absent. TNF-alpha, IL-12p40, calprotectin, HSP65 and gp91phox were found by immunohistochemistry only in amnion membranes infected with the enteropathogenic strain 055.

Properties and structure–activity studies of cyclic β-hairpin peptidomimetics based on the cationic antimicrobial peptide protegrin I

The properties and structure-activity relationships (SAR) of a macrocyclic analogue of porcine protegrin I (PG-I) have been investigated. The lead compound, having the sequence cyclo-(-Leu-Arg-Leu-Lys-Lys-Arg-Arg-Trp-Lys-Tyr-Arg-Val-d-Pro-Pro-), shows antimicrobial activity against Gram-positive and -negative bacteria, but a much lower haemolytic activity and a much reduced ability to induce dye release from phosphatidylcholine/phosphatidylglycerol liposomes, when compared to PG-I. The enantiomeric form of the lead peptide shows comparable antimicrobial activity, a property shared with other cationic antimicrobial peptides acting on cell membranes. SAR studies involving the synthesis and biological profiling of over 100 single site substituted analogues, showed that the antimicrobial activity was tolerant to a large number of the substitutions tested. Some analogues showed slightly improved antimicrobial activities (2-4-fold lowering of MICs), whereas other substitutions caused large increases in haemolytic activity on human red blood cells.

Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides

On the basis of the inductive QSAR descriptors we have created a neural network-based solution enabling quantification of antibacterial activity in the series of 101 synthetic cationic polypeptides (CAMEL-s). The developed QSAR model allowed 80% correct categorical classification of antibacterial potencies of the CAMEL-s both in the training and the validation sets. The accuracy of the activity predictions demonstrates that a narrow set of 3D sensitive 'inductive' descriptors can adequately describe the aspects of intra- and intermolecular interactions that are relevant for antibacterial activity of the cationic polypeptides. The developed approach can be further expanded for the larger sets of biologically active peptides and can serve as a useful quantitative tool for rational antibiotic design and discovery.

A novel carrier molecule for high-level expression of peptide antibiotics in Escherichia coli

Peptide antibiotics are often hard to express in engineered bacteria at high level. According to the properties of peptide antibiotics, a heterologous protein PaP3.30, encoded by ORF30 of Pseudomonas aeruginosa bacteriophage PaP3, was selected as a carrier molecule. The gene of the carrier molecule was constructed into the plasmid pQE-32 to give rise to the vector pQE-PaP30 for expression of peptide antibiotics in Escherichia coli. A his-tagged fusion protein was genetically constructed with a peptide antibiotic at its carboxy terminus. The novel carrier molecule was used for high-level expression of six peptide antibiotics with different sizes and isoelectric points in E. coli, which are hPAB-beta, MSI-78, Melletin, hBD-1, Cecropin A, and an ovine anion peptide. And further, one of six peptide antibiotics, hPAB-beta (an analog of a human peptide antibiotic), was taken as an example for studies of recovery of interesting products from the fusion partner, purification and antimicrobial activity evaluation. The results indicated that the expressed fusion protein existed as an inclusion body in the cytoplasm and the expression amounts of six peptide antibiotic fusions are all higher than 34% of the total cell protein. The expression products could be easily purified by Ni-NTA chromatography. Cyanogen bromide was used to cut at the methionine linker between the carrier and hPAB-beta peptide. hPAB-beta was recovered from the fusion partner and purified to homogeneity with High S cation-exchange and Bio-gel P6 gel chromatography. The bactericidal activities of the purified recombinant hPAB-beta against P. aeruginosa are 31-64 microg/ml, and against Staphylococcus aureus are > or = 128 microg/ml, being comparable to that of the chemical synthesis peptide. These results show that the carrier molecule can result in high-level expression of peptide antibiotics, and expression products can be easily recovered from their fusion partner and retain their bioactivity.

Nonmammalian vertebrate antibiotic peptides

With the exception of cyclostomes, all vertebrates share the common immune strategy of adaptive, highly specific immunity, based on the products of recombination-activating genes and recombined noninherited receptors for antigens. In addition, they have retained ancient vectors of innate immunity, such as antimicrobial peptides, which are widespread in all eukaryotic organisms and show a high degree of structural homology across most animal taxa. Recently, these substances have become the objects of intensive study for their outstanding bioactive properties with the aim to be applied as very efficient antibiotics, antimicrobials, and even cancerostatics in clinical practice.