Characterization and identification of antimicrobial peptides with different functional activities

2019 ◽  
Vol 21 (3) ◽  
pp. 1098-1114 ◽  
Author(s):  
Chia-Ru Chung ◽  
Ting-Rung Kuo ◽  
Li-Ching Wu ◽  
Tzong-Yi Lee ◽  
Jorng-Tzong Horng
Keyword(s):  
Antimicrobial Peptides ◽  
Hot Spot ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Van Der Waals Volume ◽  
Gram Negative ◽  
Functional Activities ◽  
Wide Range ◽  
Anti Cancer ◽  
Anti Fungal

Abstract In recent years, antimicrobial peptides (AMPs) have become an emerging area of focus when developing therapeutics hot spot residues of proteins are dominant against infections. Importantly, AMPs are produced by virtually all known living organisms and are able to target a wide range of pathogenic microorganisms, including viruses, parasites, bacteria and fungi. Although several studies have proposed different machine learning methods to predict peptides as being AMPs, most do not consider the diversity of AMP activities. On this basis, we specifically investigated the sequence features of AMPs with a range of functional activities, including anti-parasitic, anti-viral, anti-cancer and anti-fungal activities and those that target mammals, Gram-positive and Gram-negative bacteria. A new scheme is proposed to systematically characterize and identify AMPs and their functional activities. The 1st stage of the proposed approach is to identify the AMPs, while the 2nd involves further characterization of their functional activities. Sequential forward selection was employed to extract potentially informative features that are possibly associated with the functional activities of the AMPs. These features include hydrophobicity, the normalized van der Waals volume, polarity, charge and solvent accessibility—all of which are essential attributes in classifying between AMPs and non-AMPs. The results revealed the 1st stage AMP classifier was able to achieve an area under the receiver operating characteristic curve (AUC) value of 0.9894. During the 2nd stage, we found pseudo amino acid composition to be an informative attribute when differentiating between AMPs in terms of their functional activities. The independent testing results demonstrated that the AUCs of the multi-class models were 0.7773, 0.9404, 0.8231, 0.8578, 0.8648, 0.8745 and 0.8672 for anti-parasitic, anti-viral, anti-cancer, anti-fungal AMPs and those that target mammals, Gram-positive and Gram-negative bacteria, respectively. The proposed scheme helps facilitate biological experiments related to the functional analysis of AMPs. Additionally, it was implemented as a user-friendly web server (AMPfun, http://fdblab.csie.ncu.edu.tw/AMPfun/index.html) that allows individuals to explore the antimicrobial functions of peptides of interest.

scholarly journals Cathelicidin Peptides Restrict Bacterial Growth via Membrane Perturbation and Induction of Reactive Oxygen Species

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Dean A. Rowe-Magnus ◽  
Adenine Y. Kao ◽  
Antonio Cembellin Prieto ◽  
Meng Pu ◽  
Cheng Kao
Keyword(s):  
Reactive Oxygen Species ◽  
Antimicrobial Peptides ◽  
Single Cell ◽  
Reactive Oxygen ◽  
Cellular Damage ◽  
Primary Effect ◽  
Gram Negative Bacteria ◽  
Oxygen Species ◽  
Gram Positive ◽  
Gram Negative

ABSTRACT All metazoans produce antimicrobial peptides (AMPs) that have both broad antimicrobial and immunomodulatory activity. Cathelicidins are AMPs that preferentially kill Gram-negative bacteria in vitro, purportedly by assembling into higher-order structures that perforate the membrane. We utilized high-resolution, single-cell fluorescence microscopy to examine their mechanism of action in real time. Engineered cathelicidins rapidly bound to Gram-negative and Gram-positive cells and penetrated the cytoplasmic membrane. Rapid failure of the peptidoglycan superstructure in regions of active turnover caused leakage of cytoplasmic contents and the formation of membrane-bound blebs. A mutation anticipated to destabilize interactions between cathelicidin subunits had no effect on bactericidal activity, suggesting that cathelicidins have activities beyond perforating the membrane. Nanomolar concentrations of cathelicidins, although not bactericidal, reduced the growth rate of Gram-negative and Gram-positive bacteria. The cells exhibited expression changes in multiple essential processes, including protein synthesis, peptidoglycan biosynthesis, respiration, and the detoxification of reactive oxygen species (ROS). Time-lapse imaging revealed that ROS accumulation preceded bleb formation, and treatments that reduced cellular ROS levels overcame these bactericidal effects. We propose that that the primary effect of cathelicidins is to induce the production of ROS that damage bacterial molecules, leading to slowed growth or cell death. Given their low circulating levels in vivo, AMPs may serve to slow bacterial population expansion so that cellular immunity systems can respond to and battle the infection. IMPORTANCE Antimicrobial peptides (AMPs) are an important part of the mammalian innate immune system in the battle against microbial infection. How AMPs function to control bacteria is not clear, as nearly all activity studies use nonphysiological levels of AMPs. We monitored peptide action in live bacterial cells over short time frames with single-cell resolution and found that the primary effect of cathelicidin peptides is to increase the production of oxidative molecules that cause cellular damage in Gram-positive and Gram-negative bacteria.

scholarly journals Antibacterial Peptides

Antibiotics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 142
Author(s):  
Jean-Marc Sabatier
Keyword(s):  
Antimicrobial Peptides ◽  
Host Defense ◽  
Life Forms ◽  
Natural Host ◽  
Gram Negative Bacteria ◽  
Antibacterial Peptides ◽  
Chemotherapeutic Drugs ◽  
Gram Positive ◽  
Defense Compounds ◽  
Gram Negative

As natural host defense compounds produced by numerous prokaryotic and eukaryotic life forms, antimicrobial peptides (AMPs) are now emerging as solid candidate chemotherapeutic drugs to fight against the various types of pathogenic Gram-positive and Gram-negative bacteria, especially those resistant to current antibiotics [...]

scholarly journals Physicochemical Properties That Enhance Discriminative Antibacterial Activity of Short Dermaseptin Derivatives

2006 ◽  
Vol 50 (8) ◽  
pp. 2666-2672 ◽  
Author(s):  
Shahar Rotem ◽  
Inna Radzishevsky ◽  
Amram Mor
Keyword(s):  
Antimicrobial Peptides ◽  
Physicochemical Properties ◽  
Culture Media ◽  
Gram Negative Bacteria ◽  
Terminal Sequence ◽  
Binding Properties ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Cytoplasmic Membranes

ABSTRACT Antimicrobial peptides are widely believed to exert their effects by nonspecific mechanisms. We assessed the extent to which physicochemical properties can be exploited to promote discriminative activity by manipulating the N-terminal sequence of the 13-mer dermaseptin derivative K4-S4(1-13) (P). Inhibitory activity determined in culture media against 16 strains of bacteria showed that when its hydrophobicity and charge were changed, P became predominantly active against either gram-positive or gram-negative bacteria. Thus, conjugation of various aminoacyl-lysin moieties (e.g., aminohexyl-K-P) led to inactivity against gram-positive bacteria (MIC50 > 50 μM) but potent activity against gram-negative bacteria (MIC50, 6.2 μM). Conversely, conjugation of equivalent acyls to the substituted analog M4-S4(1-13) (e.g., hexyl-M4-P) led to inactivity against gram-negative bacteria (MIC50 > 50 μM) but potent activity against gram-positive bacteria (MIC50, 3.1 μM). Surface plasmon resonance experiments, used to investigate peptides' binding properties to lipopolysaccharide-containing idealized phospholipid membranes, suggest that although the acylated derivatives have increased lipophilic properties with parallel antibacterial behavior, hydrophobic derivatives are prevented from reaching the cytoplasmic membranes of gram-negative bacteria. Moreover, unlike modifications that enhanced the activity against gram-positive bacteria, which also enhanced hemolysis, we found that modifications that enhanced activity against gram-negative bacteria generally reduced hemolysis. Thus, compared with the clinically tested peptides MSI-78 and IB-367, the dermaseptin derivative aminohexyl-K-P performed similarly in terms of potency and bactericidal kinetics but was significantly more selective in terms of discrimination between bacteria and human erythrocytes. Overall, the data suggest that similar strategies maybe useful to derive potent and safe compounds from known antimicrobial peptides.

scholarly journals DETERMINATION OF ANTIBACTERIAL ACTIVITY OF SOME IMPORTANT SPICES

2015 ◽  
Vol 3 (10) ◽  
pp. 57-64
Author(s):  
Ranganathan Kapilan
Keyword(s):  
Antimicrobial Activity ◽  
Antibacterial Activity ◽  
Pathogenic Bacteria ◽  
Maximum Activity ◽  
Gram Negative Bacteria ◽  
Alcoholic Extract ◽  
Gram Positive ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Wide Range

Wide range of plant extracts are used for medicinal purposes as they are very cheap, efficient, harmless and do not cause any side effects. Spices are parts of different plants and they add special aroma and taste to the food preparations. The aim of the study was to determine the antimicrobial activity of some important naturally grown spices against gram positive and gram negative pathogenic bacteria. Antibacterial activity of the spices was tested against gram positive bacteria Bacillus pumilus, Bacillus cereus and Staphylococcus aureus and gram negative bacteria Escherichia coli, Salmonella typhi and Pseudomonas aeruginosa using aqueous, ethanolic, methanolic and liquid nutrient extracts. Among all the extracts tested alcoholic extracts of Cardamom (Elettaria cardamom), clove (Eugenia caryophyllus) and lemongrass (Cymbopogoncitratus) showed maximum antimicrobial activity against gram negative bacteria while alcoholic extract of Cardamom (Elettaria cardamom) and lemongrass (Cymbopogoncitratus) showed maximum activity against gram positive bacteria. All the spices tested in this study proved that they have antibacterial activity and the maximum activity index (1.39) was exhibited by the ethanol extract of cardamom against E.coli.

scholarly journals Quaternary Ammonium Leucine-Based Surfactants: The Effect of a Benzyl Group on Physicochemical Properties and Antimicrobial Activity

Pharmaceutics ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 287 ◽  
Author(s):  
Diego Romano Perinelli ◽  
Dezemona Petrelli ◽  
Luca Agostino Vitali ◽  
Giulia Bonacucina ◽  
Marco Cespi ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Quaternary Ammonium ◽  
Cationic Surfactants ◽  
Cytotoxic Effect ◽  
Bacterial Species ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
Wide Range ◽  
Surface Active

Quaternary ammonium amphiphiles are a class of compounds with a wide range of commercial and industrial uses. In the pharmaceutical field, the most common quaternary ammonium surfactant is benzalkonium chloride (BAC), which is employed as a preservative in several topical formulations for ocular, skin, or nasal application. Despite the broad antimicrobial activity against Gram-positive and Gram-negative bacteria, as well as fungi and small enveloped viruses, safety concerns regarding its irritant and cytotoxic effect on epithelial cells still remain. In this work, quaternary ammonium derivatives of leucine esters (C10, C12 and C14) were synthesised as BAC analogues. These cationic surfactants were characterised in terms of critical micelle concentration (CMC, by tensiometry), cytotoxicity (MTS and LDH assays on the Caco-2 and Calu-3 cell lines) and antimicrobial activity on the bacterial species Staphylococcus aureus and Enterococcus faecalis among the Gram-positives, Escherichia coli and Pseudomonas aeruginosa among the Gram-negatives and the yeast Candida albicans. They showed satisfactory surface-active properties, and a cytotoxic effect that was dependent on the length of the hydrophobic chain. Lower minimum inhibiting concentration (MIC) values were calculated for C14-derivatives, which were comparable to those calculated for BAC toward Gram-positive bacteria and slightly higher for Gram-negative bacteria and C. albicans. Thus, the synthesised leucine-based quaternary ammonium cationic surfactants can potentially find application as promising surface-active compounds with antimicrobial activity.

scholarly journals Antimicrobial Peptide Resistance Genes in the Plant Pathogen Dickeya dadantii

2016 ◽  
Vol 82 (21) ◽  
pp. 6423-6430 ◽  
Author(s):  
Caroline Pandin ◽  
Martine Caroff ◽  
Guy Condemine
Keyword(s):  
Antimicrobial Peptides ◽  
Bacterial Resistance ◽  
Soft Rot ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Dickeya Dadantii ◽  
Gram Negative ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
New Genes

ABSTRACTModification of teichoic acid through the incorporation ofd-alanine confers resistance in Gram-positive bacteria to antimicrobial peptides (AMPs). This process involves the products of thedltXABCDgenes. These genes are widespread in Gram-positive bacteria, and they are also found in a few Gram-negative bacteria. Notably, these genes are present in all soft-rot enterobacteria (PectobacteriumandDickeya) whosedltDXBACoperons have been sequenced. We studied the function and regulation of these genes inDickeya dadantii.dltBexpression was induced in the presence of the AMP polymyxin. It was not regulated by PhoP, which controls the expression of some genes involved in AMP resistance, but was regulated by ArcA, which has been identified as an activator of genes involved in AMP resistance. However,arcAwas not the regulator responsible for polymyxin induction of these genes in this bacterium, which underlines the complexity of the mechanisms controlling AMP resistance inD. dadantii. Two other genes involved in resistance to AMPs have also been characterized,phoSandphoH.dltB,phoS,phoH, andarcAbut notdltDmutants were more sensitive to polymyxin than the wild-type strain. Decreased fitness of thedltB,phoS, andphoHmutants in chicory leaves indicates that their products are important for resistance to plant AMPs.IMPORTANCEGram-negative bacteria can modify their lipopolysaccharides (LPSs) to resist antimicrobial peptides (AMPs). Soft-rot enterobacteria (DickeyaandPectobacteriumspp.) possess homologues of thedltgenes in their genomes which, in Gram-positive bacteria, are involved in resistance to AMPs. In this study, we show that these genes confer resistance to AMPs, probably by modifying LPSs, and that they are required for the fitness of the bacteria during plant infection. Two other new genes involved in resistance were also analyzed. These results show that bacterial resistance to AMPs can occur in bacteria through many different mechanisms that need to be characterized.

scholarly journals Identification of Ly2 members as antimicrobial peptides from zebrafish Danio rerio

2017 ◽  
Vol 37 (1) ◽  
Author(s):  
Xuemin Liu ◽  
Xuwen Cao ◽  
Su Wang ◽  
Guangdong Ji ◽  
Shicui Zhang ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Recombinant Proteins ◽  
Mammalian Cells ◽  
Multidrug Resistant ◽  
Scatchard Analysis ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
E Coli ◽  
Gram Positive Bacteria

The emergence of multidrug-resistant (MDR) microbes caused by overuse of antibiotics leads to urgent demands for novel antibiotics exploration. Our recent data showed that Ly2.1–3 (a novel lymphocyte antigen 6 (Ly6) gene cluster) were proteins with cationic nature and rich in cysteine content, that are characteristic of antimicrobial peptides (AMPs) and their expression were all significantly up-regulated after challenge with lipopolysaccharide (LPS). These strongly suggested that Ly2.1–3 are potential AMPs, but firm evidence are lacking. Here, we clearly showed that the recombinant proteins of Ly2.1–3 were capable of killing Gram-negative bacteria Aeromonas hydrophila and Escherichia coli, while they had little bactericidal activity against the Gram-positive bacteria Staphylococcus aureus and Bacillus subtilis. We also showed that recombinant proteins Ly2.1–3 (rLy2.1–3) were able to bind to the Gram-negative bacteria A. hydrophila, E. coli and the microbial signature molecule LPS, but not to the Gram-positive bacteria S. aureus and B. subtilis as well as the microbial signature molecule LTA. Moreover, the Scatchard analysis revealed that rLy2.1–3 could specifically bind to LPS. Finally, we found that Ly2.1–3 were not cytotoxic to mammalian cells. All these together indicate that Ly2.1–3 can function as AMPs.

scholarly journals The intestinal microbiota of rats under the influence of biotechnological strains of microorganisms from various taxonomic groups

2021 ◽  
Vol 100 (3) ◽  
pp. 234-239
Author(s):  
Natalia I. Sheina ◽  
Elena V. Budanova ◽  
Valentina V. Kolesnikova ◽  
Lyubov I. Mjalina ◽  
Lyubov I. Sazonova
Keyword(s):  
Intestinal Microbiota ◽  
Ambient Air ◽  
Control Group ◽  
Gram Negative Bacteria ◽  
Gram Positive ◽  
Gram Negative ◽  
White Rats ◽  
Wide Range ◽  
Taxonomic Groups ◽  
Animal Feces

Introduction. The microbiota of the gastrointestinal tract (GIT) plays an essential role in maintaining human health. Many factors, including industrial pollutions with biotechnological strains of microbes, can affect the normal balance of intestinal microbiota. The biotechnological industry nowadays produces a wide range of products for medical and veterinary use, agriculture, food, chemical industries, etc. To develop hygienic standards that regulate the possible adverse effect of biotechnological strains of microorganisms on workers’ health, the intestinal microflora of rats in the experiment can be studied. The data obtained were used as the basic concept in elaborating state sanitary standards for limitations of the concentrations of biotechnological strains of microorganisms in the ambient air of the working area and settlements’ atmosphere. Materials and methods. We have tested 52 strains of microorganisms applied in biotechnology as producers of a variety of biological substances. They included members of different taxonomic groups: gram-positive and gram-negative bacteria, actinomycetes, molds, and yeasts. The experiments were carried out on conventional male and female white rats (290-320 g, body weight). Each test and control group of animals included eight animals. The strains of microorganisms mentioned above were given to animals by inhalation of minimal effective doses of microbes in the concentrations of 103-108 CFU/m3 during one month. To demonstrate possible adverse effects to gut microflora, the routine bacteriological examination of animal feces was performed. To do this, after the priming, the 10-fold dilutions of animal feces in sterile saline were inoculated onto a set of general-purpose and selective culture media for Enterobacteriaceae members, staphylococci, enterococci, clostridia, bifidobacteria, lactobacilli, and fungi, with subsequent identification of the genus of the isolated microorganism. After that, the concentrations of microorganisms were calculated and measured in lg of CFU/g of feces. The Institutional Ethical Committee of Animal Care and Use of the Pirogov Russian National Research Medical University approved all procedures involving animals. The results of experiments were analyzed with a simple t-test using Statistica (v.6.0, Stat Soft, USA) and Microsoft Office Excel 2007. Results were considered statistically significant when p < 0.05. Results. The most notable changes in the composition of the intestinal microbiota were observed after inhaling of yeasts of genus Candida at the level of 103-104 CFU/m3 and in cases of exposure to molds (Aspergillus awamori, Penicillium funiculosum, and Tolypocladium cylindrosporum) in the concentration of 2•104 CFU/m3, and gram-negative bacteria of the genus Alcaligenes and genus Pseudomonas at 5•105 CFU/m3. We observed a dramatic decrease of Escherichia coli and the increase of gram-positive bacteria (staphylococci, enterococci). For some genera of biotechnological strains, a significant decline in the content of lactobacilli was also shown. On the other hand, Rhodococcus did not cause any disturbances even at high concentrations in the ambient air. Conclusion. The obtained data can be used to develop biosafety and hygienic standards for industrial microbes to help decrease or minimize the occupational risk of infection or undesirable allergic effect when working with biotechnological strains of microbes in the ambient air of residential areas.

scholarly journals Broad Spectrum Anti-Quorum Sensing Activity of Tannin-Rich Crude Extracts of Indian Medicinal Plants

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Varsha Shukla ◽  
Zarine Bhathena
Keyword(s):  
Quorum Sensing ◽  
Medicinal Plants ◽  
Broad Spectrum ◽  
Gram Negative Bacteria ◽  
High Concentration ◽  
Gram Positive ◽  
Gram Negative ◽  
Medicinal Plant Extracts ◽  
Wide Range ◽  
Autoinducing Peptides

Quorum sensing (QS) mechanisms have been demonstrated to have significance in expression of pathogenicity in infectious bacteria. In Gram negative bacteria the autoinducer molecules that mediate QS are acyl homoserine lactones (AHL) and in Gram positive bacteria they are peptides called autoinducing peptides (AIP). A screening of tannin-rich medicinal plants was attempted to identify extracts that could interrupt the QS mechanisms in both Gram positive and Gram negative bacteria over a wide range of concentrations and therefore potentially be potent agents that could act as broad spectrum QS inhibitors. Six out of the twelve Indian medicinal plant extracts that were analyzed exhibited anti-QS activity inChromobacterium violaceum12472 and inS.aureusstrain withagr:blaZfusion over a broad range of subinhibitory concentrations, indicating that the extracts contain high concentration of molecules that can interfere with the QS mechanisms mediated by AHL as well as AIP.

scholarly journals Insights Into the Immune Response of the Black Soldier Fly Larvae to Bacteria

2021 ◽  
Vol 12 ◽  
Author(s):  
Daniele Bruno ◽  
Aurora Montali ◽  
Maristella Mastore ◽  
Maurizio Francesco Brivio ◽  
Amr Mohamed ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Health Status ◽  
Gram Negative Bacteria ◽  
Organic Substrates ◽  
Gram Positive ◽  
Black Soldier Fly ◽  
Gram Negative ◽  
Wide Range ◽  
Functional Features

In insects, a complex and effective immune system that can be rapidly activated by a plethora of stimuli has evolved. Although the main cellular and humoral mechanisms and their activation pathways are highly conserved across insects, the timing and the efficacy of triggered immune responses can differ among different species. In this scenario, an insect deserving particular attention is the black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae). Indeed, BSF larvae can be reared on a wide range of decaying organic substrates and, thanks to their high protein and lipid content, they represent a valuable source of macromolecules useful for different applications (e.g., production of feedstuff, bioplastics, and biodiesel), thus contributing to the development of circular economy supply chains for waste valorization. However, decaying substrates bring the larvae into contact with different potential pathogens that can challenge their health status and growth. Although these life strategies have presumably contributed to shape the evolution of a sophisticated and efficient immune system in this dipteran, knowledge about its functional features is still fragmentary. In the present study, we investigated the processes underpinning the immune response to bacteria in H. illucens larvae and characterized their reaction times. Our data demonstrate that the cellular and humoral responses in this insect show different kinetics: phagocytosis and encapsulation are rapidly triggered after the immune challenge, while the humoral components intervene later. Moreover, although both Gram-positive and Gram-negative bacteria are completely removed from the insect body within a few hours after injection, Gram-positive bacteria persist in the hemolymph longer than do Gram-negative bacteria. Finally, the activity of two key actors of the humoral response, i.e., lysozyme and phenoloxidase, show unusual dynamics as compared to other insects. This study represents the first detailed characterization of the immune response to bacteria of H. illucens larvae, expanding knowledge on the defense mechanisms of this insect among Diptera. This information is a prerequisite to manipulating the larval immune response by nutritional and environmental factors to increase resistance to pathogens and optimize health status during mass rearing.

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