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.

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Antimicrobial peptides isolated from the blood of farm animals

Animal Production Science ◽

10.1071/ea07185 ◽

2010 ◽

Vol 50 (7) ◽

pp. 660 ◽

Cited By ~ 8

Author(s):

Pak-Lam Yu ◽

Danitsja S. van der Linden ◽

Haryadi Sugiarto ◽

Rachel C. Anderson

Keyword(s):

Antimicrobial Peptides ◽

Pathogenic Bacteria ◽

Synergistic Effects ◽

Waste Product ◽

Pharmaceutical Products ◽

Farm Animals ◽

Antimicrobial Substances ◽

Spectrum Activity ◽

Conventional Antibiotics

The development of antimicrobial resistance by pathogenic bacteria has fuelled the search for alternatives to conventional antibiotics. Endogenous antimicrobial peptides have the potential to be used as new antimicrobial substances because they have low minimum inhibitory concentration in vitro, have broad-spectrum activity, neutralise lipopolysaccharides, promote wound healing and have synergistic effects with conventional antibiotics. Farm animals, in particular the blood that is a by-product of the meat and poultry industries, are an abundant, and currently underutilised, source of such antimicrobial peptides. These antimicrobial peptides could be isolated and developed into high-value products such as biopreservatives, topical neutraceutical products and pharmaceuticals. There have been some clinical trials of antimicrobial peptides as pharmaceutical products, but up to now, the trials have shown disappointing results. Further research and development is still needed before such peptides can be commercialised and full advantage taken of this waste product of the meat and poultry industries.

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A Mig-14-like protein (PA5003) affects antimicrobial peptide recognition in Pseudomonas aeruginosa

Microbiology ◽

10.1099/mic.0.049445-0 ◽

2011 ◽

Vol 157 (9) ◽

pp. 2647-2657 ◽

Cited By ~ 11

Author(s):

Nicholas Jochumsen ◽

Yang Liu ◽

Søren Molin ◽

Anders Folkesson

Keyword(s):

Pseudomonas Aeruginosa ◽

Antimicrobial Peptides ◽

Antimicrobial Peptide ◽

Pathogenic Bacteria ◽

Molecular Mechanisms ◽

Fluorescent Protein ◽

Flow Chamber ◽

Gene Encoding ◽

Conventional Antibiotics ◽

Green Fluorescent

The evolution of antibiotic resistance in pathogenic bacteria is a growing global health problem which is gradually making the treatment of infectious diseases less efficient. Antimicrobial peptides are small charged molecules found in organisms from the complete phylogenetic spectrum. The peptides are attractive candidates for novel drug development due to their activity against bacteria that are resistant to conventional antibiotics, and reports of peptide resistance are rare in the clinical setting. Paradoxically, many clinically relevant bacteria have mechanisms that can recognize and respond to the presence of cationic antimicrobial peptides (CAMPs) in the environment by changing the properties of the microbial surface thereby increasing the tolerance of the microbes towards the peptides. In Pseudomonas aeruginosa an essential component of this inducible tolerance mechanism is the lipopolysaccharide modification operon arnBCADTEF–PA3559 which encodes enzymes required for LPS alterations leading to increased antimicrobial peptide tolerance. The expression of the operon is induced by the presence of CAMPs in the environment but the molecular mechanisms underlying the cellular recognition of the peptides are poorly elucidated. In this work, we investigate the factors influencing arnB expression by transposon mutagenesis and arnB promoter green fluorescent protein reporters. We have identified a novel gene encoding a Mig-14-like protein that is required for recognition of the CAMPs colistin and Novispirin G10 by P. aeruginosa. Moreover, we show that this gene is also required for the formation of CAMP-tolerant subpopulations in P. aeruginosa hydrodynamic flow chamber biofilms.

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Prediction of Substrate-Enzyme-Product Interaction Based on Molecular Descriptors and Physicochemical Properties

BioMed Research International ◽

10.1155/2013/674215 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 9

Author(s):

Bing Niu ◽

Guohua Huang ◽

Linfeng Zheng ◽

Xueyuan Wang ◽

Fuxue Chen ◽

...

Keyword(s):

Physicochemical Properties ◽

Molecular Descriptors ◽

Solvent Accessibility ◽

Interaction Network ◽

Van Der Waals Volume ◽

Enzyme Product ◽

Novel Approach ◽

Encoding Method ◽

Enzyme Molecules ◽

Product Interaction

It is important to correctly and efficiently predict the interaction of substrate-enzyme and to predict their product in metabolic pathway. In this work, a novel approach was introduced to encode substrate/product and enzyme molecules with molecular descriptors and physicochemical properties, respectively. Based on this encoding method, KNN was adopted to build the substrate-enzyme-product interaction network. After selecting the optimal features that are able to represent the main factors of substrate-enzyme-product interaction in our prediction, totally 160 features out of 290 features were attained which can be clustered into ten categories: elemental analysis, geometry, chemistry, amino acid composition, predicted secondary structure, hydrophobicity, polarizability, solvent accessibility, normalized van der Waals volume, and polarity. As a result, our predicting model achieved an MCC of 0.423 and an overall prediction accuracy of 89.1% for 10-fold cross-validation test.

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Synergy pattern of short cationic antimicrobial peptides against multidrug-resistant Pseudomonas aeruginosa

10.1101/639286 ◽

2019 ◽

Author(s):

Serge Ruden ◽

Annika Rieder ◽

Thomas Schwartz ◽

Ralf Mikut ◽

Kai Hilpert

Keyword(s):

Pseudomonas Aeruginosa ◽

Antimicrobial Peptides ◽

Pathogenic Bacteria ◽

Synergistic Effects ◽

Polymyxin B ◽

Multidrug Resistant ◽

Multi Drug Resistance ◽

Resistant Bacteria ◽

Drug Resistant ◽

Conventional Antibiotics

AbstractWith the rise of various multi-drug resistance pathogenic bacteria, worldwide health care is under pressure to respond. Conventional antibiotics are failing and the development of novel classes or alternative strategies is a major priority. Antimicrobial peptides (AMPs) can not only kill multi-drug resistant bacteria, but also can be used synergistically with conventional antibiotics. We selected 30 short AMPs from different origins and measured their synergy in combination with Polymyxin B, Piperacillin, Ceftazidime, Cefepime, Meropenem, Imipenem, Tetracycline, Erythromycin, Kanamycin, Tobramycin, Amikacin, Gentamycin, and Ciprofloxacin. In total 403 unique combinations were tested against a multi-drug resistant Pseudomonas aeruginosa isolate (PA910). As a measure of the synergistic effects, fractional inhibitory concentrations (FICs) were determined using microdilution assays with FICs ranges between 0.25 and 2. A high number of combinations between peptides and Polymyxin B, Erythromycin and Tetracycline were found to be synergistic. Novel variants of Indolicidin also showed a high frequency in synergist interaction.

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Pembaharuan Pesantren: Arah dan Implikasi

Edugama: Jurnal Kependidikan dan Sosial Keagamaan ◽

10.32923/edugama.v4i1.663 ◽

2018 ◽

Vol 4 (1) ◽

pp. 67-84

Author(s):

Wahyudin Noor

Keyword(s):

Rapid Development ◽

The Other ◽

Learning Methods ◽

Technology Learning ◽

Other Hand ◽

The One ◽

Traditional Term

Abstract Pesantren are often associated with backwardness and traditionalism in everything: facilities, technology, learning methods, and even the curriculum. For now, it seems like the traditional term for pesantren is no longer relevant enough. The pace of movement in the era of renewal marked by the rapid development of technology has demanded pesantren to make adjustments. However, on the one hand, when viewed from the direction of change, the reform efforts pursued by pesantren are not to erase the old tradition, but merely to add something new so that the old tradition and conditions can be maintained while accepting the presence of a new one. On the other hand, the reform efforts undertaken by pesantren have implications for the fact that the typical values of the pesantren are fading away. Abstrak Pesantren seringkali diasosiasikan dengan keterbelakangan dan tradisional dalam segala hal: fasilitas, teknologi, metode pembelajaran, dan bahkan kurikulumnya. Untuk saat ini, sepertinya istilah tradisional untuk pesantren, sudah tidak lagi cukup relevan. Laju gerak pembaharuan zaman yang ditandai dengan pesatnya perkembangan teknologi telah menuntut pesantren untuk melakukan penyesuaian diri. Kendatipun demikian, di satu sisi, jika dilihat dari arah perubahan, upaya pembaharuan yang ditempuh pesantren tidaklah untuk menghapus tradisi yang lama, tetapi sekadar menambah dengan sesuatu yang baru sehingga tradisi maupun kondisi yang lama bisa dipertahankan sambil menerima kehadiran yang baru. Di sisi yang lain, upaya pembaharuan yang dilakukan pesantren ternyata berimplikasi pada kenyataan akan semakin pudarnya nilai-nilai khas yang dimiliki oleh pesantren.

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Recent Advances in the Development of Antimicrobial Peptides (AMPs): Attempts for Sustainable Medicine?

Current Medicinal Chemistry ◽

10.2174/0929867325666180117142142 ◽

2018 ◽

Vol 25 (21) ◽

pp. 2503-2519 ◽

Cited By ~ 4

Author(s):

Anne Kokel ◽

Marianna Torok

Keyword(s):

Side Effects ◽

Antimicrobial Peptides ◽

Potential Drug ◽

Green Technologies ◽

Specific Antibodies ◽

Structural Modifications ◽

Drug Candidates ◽

Induce Resistance ◽

Conventional Antibiotics

Background: Since the first isolation of antimicrobial peptides (AMPs) they have attracted extensive interest in medicinal chemistry. However, only a few AMP-based drugs are currently available on the market. Despite their effectiveness, biodegradability, and versatile mode of action that is less likely to induce resistance compared to conventional antibiotics, AMPs suffer from major issues that need to be addressed to broaden their use. Notably, AMPs can lack selectivity leading to side effects and cytotoxicity, and also exhibit in vivo instability. Several strategies are being actively considered to overcome the limitations that restrain the success of AMPs. Methods: In the current work, recent strategies reported for improving AMPs in the context of drug design and delivery were surveyed, and also their possible impact on patients and the environment was assessed. Results: As a major advantage AMPs possess an easily tunable skeleton offering opportunities to improve their properties. Strategic structural modifications and the beneficial properties of cyclic or branched AMPs in term of stability have been reported. The conjugation of AMPs with nanoparticles has also been explored to increase their in vivo stability. Other techniques such as the coupling of AMPs with specific antibodies aim to increase the selectivity of the potential drug towards the target. These strategies were evaluated for their effect on the environment highlighting green technologies. Conclusion: Although further research is needed taking into account both environmental and human health consequences of novel AMPs, several of these compounds are promising drug candidates for use in sustainable medicine.

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Antimicrobial Peptides and their Multiple Effects at Sub-Inhibitory Concentrations

Current Topics in Medicinal Chemistry ◽

10.2174/1568026620666200427090912 ◽

2020 ◽

Vol 20 (14) ◽

pp. 1264-1273 ◽

Cited By ~ 1

Author(s):

Bruno Casciaro ◽

Floriana Cappiello ◽

Walter Verrusio ◽

Mauro Cacciafesta ◽

Maria Luisa Mangoni

Keyword(s):

Antimicrobial Peptides ◽

Inhibitory Concentration ◽

Multidrug Resistant ◽

Mechanisms Of Action ◽

New Drugs ◽

Lead Compounds ◽

Bacterial Pathogenicity ◽

Growth Inhibitory ◽

Resistant Strains ◽

Conventional Antibiotics

The frequent occurrence of multidrug-resistant strains to conventional antimicrobials has led to a clear decline in antibiotic therapies. Therefore, new molecules with different mechanisms of action are extremely necessary. Due to their unique properties, antimicrobial peptides (AMPs) represent a valid alternative to conventional antibiotics and many of them have been characterized for their activity and cytotoxicity. However, the effects that these peptides cause at concentrations below the minimum growth inhibitory concentration (MIC) have yet to be fully analyzed along with the underlying molecular mechanism. In this mini-review, the ability of AMPs to synergize with different antibiotic classes or different natural compounds is examined. Furthermore, data on microbial resistance induction are reported to highlight the importance of antibiotic resistance in the fight against infections. Finally, the effects that sub-MIC levels of AMPs can have on the bacterial pathogenicity are summarized while showing how signaling pathways can be valid therapeutic targets for the treatment of infectious diseases. All these aspects support the high potential of AMPs as lead compounds for the development of new drugs with antibacterial and immunomodulatory activities.

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Biochemical studies on the production of neuraminidase by environmental isolates of Vibrio cholerae non-O1 from Bulgaria

Canadian Journal of Microbiology ◽

10.1139/w11-042 ◽

2011 ◽

Vol 57 (7) ◽

pp. 606-610 ◽

Cited By ~ 6

Author(s):

Rumyana Eneva ◽

Stephan Engibarov ◽

Tanya Strateva ◽

Radoslav Abrashev ◽

Ignat Abrashev

Keyword(s):

Vibrio Cholerae ◽

Pathogenic Bacteria ◽

Environmental Isolates ◽

Anaerobic Conditions ◽

Temperature Optimum ◽

Ph Optimum ◽

Cholera Vibrio ◽

Key Factor ◽

Aeration Conditions ◽

The One

Neuraminidase is a key factor in the infectious process of many viruses and pathogenic bacteria. The neuraminidase enzyme secreted by the etiological agent of cholera — Vibrio cholerae О1 — is well studied in contrast with the one produced by non-O1/non-O139 V. cholerae. Environmental non-O1/non-O139 V. cholerae isolates from Bulgaria were screened for production of neuraminidase. The presence of the neuraminidase gene nanH was detected in 18.5% of the strains. Тhe strain showing highest activity (30 U/mL), V. cholerae non-O1/13, was used to investigate the enzyme production in several media and at different aeration conditions. The highest production of extracellular neuraminidase was observed under microaerophilic conditions, which is possibly related to its role in the infection of intestine epithelium, where the oxygen content is low. On the other hand, this is another advantage of the microbe in such microaerophilic environments as sediments and lake mud. The highest production of intracellular neuraminidase was observed at anaerobic conditions. The ratio of extracellular to intracellular neuraminidase production in V. cholerae was investigated. The temperature optimum of the enzyme was determined to be 50 °C and the pH optimum to be 5.6–5.8.

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Sorting out the Superbugs: Potential of Sortase A Inhibitors among Other Antimicrobial Strategies to Tackle the Problem of Antibiotic Resistance

Antibiotics ◽

10.3390/antibiotics10020164 ◽

2021 ◽

Vol 10 (2) ◽

pp. 164 ◽

Cited By ~ 1

Author(s):

Nikita Zrelovs ◽

Viktorija Kurbatska ◽

Zhanna Rudevica ◽

Ainars Leonchiks ◽

Davids Fridmanis

Keyword(s):

Cell Wall ◽

Antibiotic Resistance ◽

Pathogenic Bacteria ◽

Resistance Mechanisms ◽

Surface Proteins ◽

Sortase A ◽

Inhibitory Compounds ◽

Alternative Means ◽

Alternative Approaches ◽

Conventional Antibiotics

Rapid spread of antibiotic resistance throughout the kingdom bacteria is inevitably bringing humanity towards the “post-antibiotic” era. The emergence of so-called “superbugs”—pathogen strains that develop resistance to multiple conventional antibiotics—is urging researchers around the globe to work on the development or perfecting of alternative means of tackling the pathogenic bacteria infections. Although various conceptually different approaches are being considered, each comes with its advantages and drawbacks. While drug-resistant pathogens are undoubtedly represented by both Gram(+) and Gram(−) bacteria, possible target spectrum across the proposed alternative approaches of tackling them is variable. Numerous anti-virulence strategies aimed at reducing the pathogenicity of target bacteria rather than eliminating them are being considered among such alternative approaches. Sortase A (SrtA) is a membrane-associated cysteine protease that catalyzes a cell wall sorting reaction by which surface proteins, including virulence factors, are anchored to the bacterial cell wall of Gram(+) bacteria. Although SrtA inhibition seems perspective among the Gram-positive pathogen-targeted antivirulence strategies, it still remains less popular than other alternatives. A decrease in virulence due to inactivation of SrtA activity has been extensively studied in Staphylococcus aureus, but it has also been demonstrated in other Gram(+) species. In this manuscript, results of past studies on the discovery of novel SrtA inhibitory compounds and evaluation of their potency were summarized and commented on. Here, we discussed the rationale behind the inhibition of SrtA, raised some concerns on the comparability of the results from different studies, and touched upon the possible resistance mechanisms as a response to implementation of such therapy in practice. The goal of this article is to encourage further studies of SrtA inhibitory compounds.

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A Synergic Potential of Antimicrobial Peptides against Pseudomonas syringae pv. actinidiae

Molecules ◽

10.3390/molecules26051461 ◽

2021 ◽

Vol 26 (5) ◽

pp. 1461

Author(s):

Nuno Mariz-Ponte ◽

Laura Regalado ◽

Emil Gimranov ◽

Natália Tassi ◽

Luísa Moura ◽

...

Keyword(s):

Flow Cytometry ◽

Antimicrobial Peptides ◽

Pseudomonas Syringae ◽

Pathogenic Bacteria ◽

High Efficiency ◽

Bacterial Canker ◽

Membrane Permeation ◽

Flow Cytometry Analysis ◽

Pathogenic Agent ◽

Peptide Mixtures

Pseudomonas syringae pv. actinidiae (Psa) is the pathogenic agent responsible for the bacterial canker of kiwifruit (BCK) leading to major losses in kiwifruit productions. No effective treatments and measures have yet been found to control this disease. Despite antimicrobial peptides (AMPs) having been successfully used for the control of several pathogenic bacteria, few studies have focused on the use of AMPs against Psa. In this study, the potential of six AMPs (BP100, RW-BP100, CA-M, 3.1, D4E1, and Dhvar-5) to control Psa was investigated. The minimal inhibitory and bactericidal concentrations (MIC and MBC) were determined and membrane damaging capacity was evaluated by flow cytometry analysis. Among the tested AMPs, the higher inhibitory and bactericidal capacity was observed for BP100 and CA-M with MIC of 3.4 and 3.4–6.2 µM, respectively and MBC 3.4–10 µM for both. Flow cytometry assays suggested a faster membrane permeation for peptide 3.1, in comparison with the other AMPs studied. Peptide mixtures were also tested, disclosing the high efficiency of BP100:3.1 at low concentration to reduce Psa viability. These results highlight the potential interest of AMP mixtures against Psa, and 3.1 as an antimicrobial molecule that can improve other treatments in synergic action.

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