Natural Antimicrobial Peptides Research Articles

Massive analysis of 64,628 bacterial genomes to decipher water reservoir and origin of mobile colistin resistance genes: is there another role for these enzymes?

Since 2015, new worrying colistin resistance mechanism, mediated by mcr-1 gene has been reported worldwide along with eight newly described variants but their source(s) and reservoir(s) remain largely unexplored. Here, we conducted a massive bioinformatic analysis of bacterial genomes to investigate the reservoir and origin of mcr variants. We identified 13’658 MCR-1 homologous sequences in 494 bacterial genera. Moreover, analysis of 64’628 bacterial genomes (60 bacterial genera and 1’047 species) allows identifying a total of 6’651 significant positive hits (coverage >90% and similarity >50%) with the nine MCR variants from 39 bacterial genera and more than 1’050 species. A high number of MCR-1 was identified in Escherichia coli (n = 862). Interestingly, while almost all variants were identified in bacteria from different sources (i.e. human, animal, and environment), the last variant, MCR-9, was exclusively detected in bacteria from human. Although these variants could be identified in bacteria from human and animal sources, we found plenty MCR variants in unsuspected bacteria from environmental origin, especially from water sources. The ubiquitous presence of mcr variants in bacteria from water likely suggests another role in the biosphere of these enzymes as an unknown defense system against natural antimicrobial peptides and/or bacteriophage predation.

Carbon quantum dots derived from lysine and arginine simultaneously scavenge bacteria and promote tissue repair

Effectively targeting and killing microbial pathogens is a major challenge in the treatment of infectious diseases. Inspired by the high efficacy of natural antimicrobial peptides (AMPs), in this study we prepared two types of carbon quantum dots (CQDs) by pyrolysis of lysine and arginine, the two major functional moieties of natural AMPs. Both lysine-derived CQDs (Lys-CQDs) and arginine-derived CQDs (Arg-CQDs) exhibited distinctive antibacterial activity against both Gram-negative and Gram-positive bacteria without inducing drug resistance. They also effectively inhibited the formation of bacterial biofilms. Such excellent antibacterial properties might be the result of positive charges derived from the amino acid residues on CQD surface and the generation of rich intracellular reactive oxygen species (ROS). Surprisingly, instead of being cytotoxic, CQDs dramatically promoted the growth of typical mammalian cells. Moreover, no hemolysis of red blood cells (RBCs) happened when CQD concentration was less than 4,000 μg/mL. In vivo, administration of CQDs to infected wounds effectively inhibited bacterium growth and accelerated wound healing. Together, findings from this study indicate that Lys-CQDs and Arg-CQDs can simultaneously kill bacteria and facilitate cell growth, and may therefore be promising candidates for treating bacterial infections and promoting tissue repair.

Optically Pure Metallohelices That Accumulate in Cell Nuclei, Condense/Aggregate DNA, and Inhibit Activities of DNA Processing Enzymes.

The water-compatible optically pure metallohelices made by self-assembly of simple nonpeptidic organic components around Fe(II) ions are now recognized as a distinct subclass of helicates that exhibit similar architecture to some natural cationic antimicrobial peptides. Notably, a new series of metallohelices was recently shown to exhibit biological activity, displaying high, structure-dependent activity against bacteria. It is also important that, thanks to their properties, such metallohelices can exhibit specific interactions with biomacromolecules. Here, following our prior report on the metallohelices that have high, structure-dependent activity against bacteria, we investigated the interactions of the series of iron(II) metallohelices with DNA, which is a potential pharmacological target of this class of coordination compounds. The results obtained with the aid of biophysical and molecular biology methods show that the investigated metallohelices accumulate in eukaryotic cells and that a significant fraction of the metallohelices accumulates in the cell nucleus, allowing them to interact also with nuclear DNA. Additionally, we have demonstrated that some metallohelices have a high affinity to DNA and are able to condense/aggregate DNA molecules more efficiently than conventional DNA-condensing agents, such as polyamines. Moreover, this capability of the metallohelices correlates with their efficiency to inhibit DNA-related enzymatic activities, such as those connected with DNA transcription, catalysis of DNA relaxation by DNA topoisomerase I, and cleavage by restriction enzymes.

Characterization and Identification of Natural Antimicrobial Peptides on Different Organisms.

Because of the rapid development of multidrug resistance, conventional antibiotics cannot kill pathogenic bacteria efficiently. New antibiotic treatments such as antimicrobial peptides (AMPs) can provide a possible solution to the antibiotic-resistance crisis. However, the identification of AMPs using experimental methods is expensive and time-consuming. Meanwhile, few studies use amino acid compositions (AACs) and physicochemical properties with different sequence lengths against different organisms to predict AMPs. Therefore, the major purpose of this study is to identify AMPs on seven categories of organisms, including amphibians, humans, fish, insects, plants, bacteria, and mammals. According to the one-rule attribute evaluation, the selected features were used to construct the predictive models based on the random forest algorithm. Compared to the accuracies of iAMP-2L (a web-server for identifying AMPs and their functional types), ADAM (a database of AMP), and MLAMP (a multi-label AMP classifier), the proposed method yielded higher than 92% in predicting AMPs on each category. Additionally, the sensitivities of the proposed models in the prediction of AMPs of seven organisms were higher than that of all other tools. Furthermore, several physicochemical properties (charge, hydrophobicity, polarity, polarizability, secondary structure, normalized van der Waals volume, and solvent accessibility) of AMPs were investigated according to their sequence lengths. As a result, the proposed method is a practical means to complement the existing tools in the characterization and identification of AMPs in different organisms.

Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

BackgroundLactoferrampin (LFampin), Lactoferricin (LFcin), and LFchimera are three well-known antimicrobial peptides derived from Lactoferrin and proposed as alternatives for antibiotics. Although the intracellular activity of these peptides has been previously demonstrated, their mode of action is not yet fully understood. Here, we performed a molecular dynamics simulation study to understand the molecular interactions between camel Lactoferrin derived peptides, including CLFampin, CLFcin, and CLFchimera, and DNA as an important intracellular target.ResultsOur results indicate that all three peptides bind to DNA, albeit with different propensities, with CLFchimera showing the highest binding affinity. The secondary structures of the peptides, modeled on Lactoferrin, did not undergo significant changes during simulation, supporting their functional relevance. Main residues involved in the peptide-DNA interaction were identified based on binding free energy estimates calculated over 200 ns, which, as expected, confirmed strong electrostatic interactions between DNA phosphate groups and positively charged peptide side chains. Interaction between the different concentrations of CLFchimera and DNA revealed that after binding of four copies of CLFchimera to DNA, hydrogen bonds between the two strands of DNA start to break from one of the termini.ConclusionsImportantly, our results revealed that there is no DNA-sequence preference for peptide binding, in line with a broad antimicrobial activity. Moreover, the results showed that the strength of the interaction between DNA and CLFchimera is concentration dependent. The insight provided by these results can be used for the rational redesign of natural antimicrobial peptides targeting the bacterial DNA.

USING SEQUENCE PATTERNS TO IDENTIFY AND DESIGN NEW ANTIMICROBIAL PEPTIDES

Natural antimicrobial peptides (AMPs) are remarkably diverse, yet they all share some common structural and functional features. In an attempt to find what determines similar activities of non-homologous molecules, we performed a comprehensive analysis of sequence patterns in AMPs. We found that natural AMPs possess characteristic sequence patterns, and these patterns differ for peptides with α-helical and β-sheet structure. We showed that the patterns facilitate computational identification of AMPs in databases. We then used patterns to design new peptides, synthesized them and assayed for antibacterial activity. The most active among synthetic peptides exhibited activity against Gram(+) and Gram(-) pathogens comparable to best natural AMPs.

A Putative Microcin Amplifies Shiga Toxin 2a Production of Escherichia coli O157:H7.

Escherichia coli O157:H7 is a foodborne pathogen implicated in various multistate outbreaks. It encodes Shiga toxin on a prophage, and Shiga toxin production is linked to phage induction. An E. coli strain, designated 0.1229, that amplified Stx2a production when cocultured with E. coli O157:H7 strain PA2 was identified. Growth of PA2 in 0.1229 cell-free supernatants had a similar effect, even when supernatants were heated to 100°C for 10 min, but not after treatment with proteinase K. The secreted molecule was shown to use TolC for export and the TonB system for import. The genes sufficient for production of this molecule were localized to a 5.2-kb region of a 12.8-kb plasmid. This region was annotated, identifying hypothetical proteins, a predicted ABC transporter, and a cupin superfamily protein. These genes were identified and shown to be functional in two other E. coli strains, and bioinformatic analyses identified related gene clusters in similar and distinct bacterial species. These data collectively suggest that E. coli 0.1229 and other E. coli strains produce a microcin that induces the SOS response in target bacteria. Besides adding to the limited number of microcins known to be produced by E. coli, this study provides an additional mechanism by which stx2a expression is increased in response to the gut microflora.IMPORTANCE How the gut microflora influences the progression of bacterial infections is only beginning to be understood. Antibiotics are counterindicated for E. coli O157:H7 infections, limiting treatment options. An increased understanding of how the gut microflora directs O157:H7 virulence gene expression may lead to additional treatment options. This work identified E. coli strains that enhance the production of Shiga toxin by O157:H7 through the secretion of a proposed microcin. Microcins are natural antimicrobial peptides that target specific species, can act as alternatives to antibiotics, and mediate microbial competition. This work demonstrates another mechanism by which non-O157 E. coli strains may increase Shiga toxin production and adds to our understanding of microcins, a group of antimicrobials less well understood than colicins.

Antibiotics: From the Beginning to the Future: Part 2.

We read, write, and discuss the option of adding new agents to the armamentarium of antibiotic therapy very frequently. However, the past and present has taught us that resistance is likely to develop to any and all kinds of antibiotics. Here we start with an overview of potential future antibiotics from novel sources and targets that may circumvent most known resistance mechanisms. The other future options for antibiotic discovery include antibiotic hybridization, harvesting, and modifying natural antimicrobial peptides from eukaryote and prokaryote organisms. Non bacteriostatic and bactericidal agents that have the potential of becoming therapeutic agents include bacterial attachment inhibitors, bacteriophages, and live microbial vectors. In this review, we have incorporated all the possible avenues that might be useful in the future. However, none is more important than relearning the judicious use of antibiotics based on microbiology, pharmacology, and genetics.

Snake Venom Cathelicidins as Natural Antimicrobial Peptides.

Bioactive small molecules isolated from animals, plants, fungi and bacteria, including natural antimicrobial peptides, have shown great therapeutic potential worldwide. Among these peptides, snake venom cathelicidins are being widely exploited, because the variation in the composition of the venom reflects a range of biological activities that may be of biotechnological interest. Cathelicidins are short, cationic, and amphipathic molecules. They play an important role in host defense against microbial infections. We are currently facing a strong limitation on pharmacological interventions for infection control, which has become increasingly complex due to the lack of effective therapeutic options. In this review, we will focus on natural snake venom cathelicidins as promising candidates for the development of new antibacterial agents to fight antibiotic-resistant bacteria. We will highlight their antibacterial and antibiofilm activities, mechanism of action, and modulation of the innate immune response.

Genetically engineered distal airway stem cell transplantation protects mice from pulmonary infection

Severe pulmonary infection is a major threat to human health accompanied by substantial medical costs, prolonged inpatient requirements, and high mortality rates. New antimicrobial therapeutic strategies are urgently required to address the emergence of antibiotic resistance and persistent bacterial infections. In this study, we show that the constitutive expression of a native antimicrobial peptide LL‐37 in transgenic mice aids in clearing Pseudomonas aeruginosa (PAO1), a major pathogen of clinical pulmonary infection. Orthotopic transplantation of adult mouse distal airway stem cells (DASCs), genetically engineered to express LL‐37, into injured mouse lung foci enabled large‐scale incorporation of cells and long‐term release of the host defense peptide, protecting the mice from bacterial pneumonia and hypoxemia. Further, correlates of DASCs in adult humans were isolated, expanded, and genetically engineered to demonstrate successful construction of an anti‐infective artificial lung. Together, our stem cell‐based gene delivery therapeutic platform proposes a new strategy for addressing recurrent pulmonary infections with future translational opportunities.

Characterization, Cytotoxic Analysis and Action Mechanism of Antilisterial Bacteriocin Produced by Lactobacillus plantarum Isolated from Cheddar Cheese

Emergence of food borne pathogens and multidrug resistant organisms has enforced the screening of natural antimicrobial compounds. Bacteriocins are ribosomally synthesized natural antimicrobial peptides produced by numerous bacteria. These antimicrobial peptides are gaining more attention as alternative therapeutics in pharmaceutical industry as next-generation antibiotics targeting the multi-drug resistant pathogens and as a bio preservative in food industry. The current study is aimed to purify and characterize a broad spectrum bacteriocin (Bac-IB45) with the determination of its plausible mode/mechanism of action. In this research, Bac-IB45 from Lactobacillus plantarum KIBGE-IB45 was 41.71-fold purified with the molecular mass of 20.5 kDa estimated using tricine SDS-PAGE. This bacteriocin is highly thermostable and pH stable in nature. It also exhibited stability against various metal ions, surfactants and organic solvents. Purified Bac-IB45 showed broad antimicrobial potential against various multidrug resistant, food borne bacterial and fungal pathogens. However, Bac-IB45 was found to be sensitive to various proteolytic enzymes. The time-kill assay of Bac-IB45 and scanning electron microscopic analysis revealed the bactericidal mode/mechanism of action against Listeria monocytogenes ATCC 7644. This unique Bac-IB45 with broad spectrum of inhibition and bactericidal mode of action could be used as a natural food preservative and as alternative therapeutics to solve the unrestrained problems of industries.

Plantaricin bacteriocins: As safe alternative antimicrobial peptides in food preservation—A review

AbstractMany peptides are excreted by gram‐positive (+) and gram‐negative (−) bacteria, possessing antimicrobial properties, called bacteriocins. Common bacterial species produce bacteriocins are called lactic acid bacteria. Nowadays, plantaricins are natural antimicrobial peptides produced byLactobacillus plantarumstrains have obtained special attention. TheL. plantarumand their bacteriocins have got great importance in different areas as food biopreservatives and/or starters in dairy products, meat products, and fish products also, were used for treating diseases caused by pathogenic bacteria that is, reducing symptoms of irritable bowel syndrome disease (IBS) and decreasing the number of colonies of pathogenic bacteria in the wound‐burning model in mice. Moreover, plantaricins have got a potent protective role against urinary tract infection (UTI). Although there are many studies on the types of bacteriocins and their purification and uses, such as Nisin and Pediocin, there have been no reports in the literature on the characterizations, production, and purification of plantaricins. The present review aims to describe plantaricins and some of their features and applications in general. Also mentioned are the most common methods of isolation and purification.

Rhesus Theta Defensin 1 Promotes Long Term Survival in Systemic Candidiasis by Host Directed Mechanisms

Invasive candidiasis is an increasingly frequent cause of serious and often fatal infections in hospitalized and immunosuppressed patients. Mortality rates associated with these infections have risen sharply due to the emergence of multidrug resistant (MDR) strains of C. albicans and other Candida spp., highlighting the urgent need of new antifungal therapies. Rhesus theta (θ) defensin-1 (RTD-1), a natural macrocyclic antimicrobial peptide, was recently shown to be rapidly fungicidal against clinical isolates of MDR C. albicans in vitro. Here we found that RTD-1 was rapidly fungicidal against blastospores of fluconazole/caspofungin resistant C. albicans strains, and was active against established C. albicans biofilms in vitro. In vivo, systemic administration of RTD-1, initiated at the time of infection or 24 h post-infection, promoted long term survival in candidemic mice whether infected with drug-sensitive or MDR strains of C. albicans. RTD-1 induced an early (4 h post treatment) increase in neutrophils in naive and infected mice. In vivo efficacy was associated with fungal clearance, restoration of dysregulated inflammatory cytokines including TNF-α, IL-1β, IL-6, IL-10, and IL-17, and homeostatic reduction in numbers of circulating neutrophils and monocytes. Because these effects occurred using peptide doses that produced maximal plasma concentrations (Cmax) of less than 1% of RTD-1 levels required for in vitro antifungal activity in 50% mouse serum, while inducing a transient neutrophilia, we suggest that RTD-1 mediates its antifungal effects in vivo by host directed mechanisms rather than direct fungicidal activity. Results of this study suggest that θ-defensins represent a new class of host-directed compounds for treatment of disseminated candidiasis.

Controlling the Formation of Peptide Films: Fully Developed Helical Peptides are Required to Obtain a Homogenous Coating over a Large Area.

The influence of conformational dynamics on the self-assembly process of a conformationally constrained analogue of the natural antimicrobial peptide Trichogin GA IV was analysed by spectroscopic methods, microscopy imaging at nanometre resolution, and molecular dynamics simulations. The formation of peptide films at the air/water interface and their deposition on a graphite or a mica substrate were investigated. A combination of experimental evidence with molecular dynamics simulation was used to demonstrate that only the fully developed helical structure of the analogue promotes formation of ordered aggregates that nucleate the growth of micrometric rods, which give rise to homogenous coating over wide regions of the hydrophilic mica. This work proves the influence of helix flexibility on peptide self-organization and orientation on surfaces, key steps in the design of bioinspired organic/inorganic hybrid materials.

Modulation of the activity of certain genes involved in tumor cell metabolism in the presence of the cytotoxic peptides defensin and cathelicidin LL37.

It is common knowledge that some natural antimicrobial peptides also have a tumoricidal effect. We have shown that the peptides defensin and cathelicidin LL37 have cytostatic effects on human tumor cell lines HT29 (colorectal carcinoma) and A549 (alveolar carcinoma). In order to determine the modulating mechanism of these peptides we assessed the gene expression of the AKT, HIF-1α, XBP, NRF2, PERK, CHOP, BCL2, IRE1α and PI3K molecular targets involved in the survival, growth, proliferation and apoptosis pathways of tumor cells in the presence or absence of the studied peptides. Thus, this research enabled us to determine molecular markers and methods of assessment and monitoring of tumor cell cytotoxicity by high-performance molecular biology techniques. Defensin and cathelicidin LL37 activated tumor cell apoptosis, especially for the HT29, but also for A549 line, by increasing gene expression of CHOP and by lowering BCL2 gene expression. Oxidative stress determined the increase in gene expression of XBP, which directly influenced CHOP. The decrease in NRF2 gene expression highlighted the inhibition of cell proliferation, while the decrease in HIF1α gene expression evidenced the decrease in cell survival.

A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity.

Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.

Harnessing slaughterhouse by-products: From wastes to high-added value natural food preservative

Blood, from slaughterhouses, is an inevitable part of meat production, causing environmental problems due to the large volumes recovered and its low valorization. However, the α137–141 peptide, a natural antimicrobial peptide, can be obtained after hydrolysis of hemoglobin, the main constituent of blood red part. To recover it at a sufficient concentration for antimicrobial applications, a new sustainable technology, called electrodialysis with ultrafiltration membrane (EDUF), was investigated. The α137–141 concentration was increased about 4-fold at a feed peptide concentration of 8% with an enrichment factor above 24-fold. This feed peptide concentration also needed the lowest relative energy consumption. Moreover, this peptide fraction protected meat against microbial growth, as well as rancidity, during 14 days under refrigeration. This peptide fraction was validated as a natural preservative and substitute for synthetic additives against food spoilage. Finally, producing antimicrobial/antioxidant peptide from wastes by EDUF fits perfectly with the concept of circular economy.

The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides.

This article is written for the 2020 tool issue of Protein Science. It briefly introduces the widely used antimicrobial peptide database, initially online in 2003. After a description of the main features of each database version and some recent additions, the focus is on the peptide design parameters for each of the four unified classes of natural antimicrobial peptides (AMPs). The amino acid signature in AMPs varies substantially, leading to a variety of structures for functional and mechanistic diversity. Also, Nature is a master of combinatorial chemistry by deploying different amino acids onto the same structural scaffold to tune peptide functions. In addition, the single-domain AMPs may be posttranslationally modified, self-assembled, or combined with other AMPs for function. Elucidation of the design principles of natural AMPs will facilitate future development of novel molecules for various applications.

Disulfide engineering on temporin-SHf: Stabilizing the bioactive conformation of an ultra-short antimicrobial peptide.

In Silico searching for short antimicrobial peptides has revealed temporin-SHf as the short (8AA), hydrophobic, broad spectrum, and natural antimicrobial peptide. Important drawback associated with temporin-SHf is the susceptibility of its bioactive conformation for denaturation and proteolytic degradation. In the current report, disulfide engineering strategy has been adopted to improve the stability of bioactive conformation of temporin-SHf. The functionally non-critical Leu4 and Ile7 residues at i and i+3 position of helical conformation of temporin-SHf were mutated with cysteine disulfide. Designed [L4C, I7C]temporin-SHf was synthesized, characterized using NMR spectroscopy, and accessed for antimicrobial activity. [L4C, I7C]Temporin-SHf adopts helical conformation from Phe3 to Phe8 in the absence of membrane-mimetic environment and retains broad spectrum antimicrobial activity. The reduction potential of cysteine disulfide of [L4C, I7C]temporin-SHf is -289 mV. Trypsin-induced digestion and serum-induced digestion have confirmed the advantage of cysteine disulfide in imparting proteolytic stability to temporin-SHf. Disulfide-stabilized temporin-SHf may serve as a good model for the rational design of temporin-SHfbased antibiotics for treatment of infectious diseases.

Membrane-Disrupting Nanofibrous Peptide Hydrogels.

Self-assembled peptide nanofibers can form biomimetic hydrogels at physiological pH and ionic strength through noncovalent and reversible interactions. Inspired by natural antimicrobial peptides, we designed a class of cationic amphiphilic self-assembled peptides (CASPs) that self-assemble into thixotropic nanofibrous hydrogels. These constructs employ amphiphilicity and high terminal charge density to disrupt bacterial membranes. Here, we focus on three aspects of the self-assembly of these hydrogels: (a) the material properties of the individual self-assembled nanofibers, (b) emergence of bulk-scale elasticity in the nanofibrous hydrogel, and (c) trade-off between the desirable material properties and antimicrobial efficacy. The design of the supramolecular nanofibers allows for higher-order noncovalent ionic cross-linking of the nanofibers into a viscoelastic network. We determine the stiffness of the self-assembled nanofibers via the peak force quantitative nanomechanical atomic force microscopy and the bulk-scale rheometry. The storage moduli depend on peptide concentration, ionic strength, and concentration of multivalent ionic cross-linker. CASP nanofibers are demonstrated to be effective against Pseudomonas aeruginosa colonies. We use nanomechanical analysis and microsecond-time scale coarse-grained simulation to elucidate the interaction between the peptides and bacterial membranes. We demonstrate that the membranes stiffen, contract, and buckle after binding to peptide nanofibers, allowing disruption of osmotic equilibrium between the intracellular and extracellular matrix. This is further associated with dramatic changes in cell morphology. Our studies suggest that self-assembled peptide nanofibrils can potentially acts as membrane-disrupting antimicrobial agents, which can be formulated as injectable hydrogels with tunable material properties.