scholarly journals The Hitchhiker’s Guide to the Periplasm: Unexpected Molecular Interactions of Antibiotics Revealed by Considering Crowding Effects in E. coli

2020 ◽  
Author(s):  
Conrado Pedebos ◽  
Iain P. S. Smith ◽  
Alister Boags ◽  
Syma Khalid
Keyword(s):  
Molecular Dynamics ◽  
Antibacterial Agents ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli ◽  
Crowding Effects ◽  
Therapeutic Mechanism ◽  
Target Membrane ◽  
Dynamics Simulations ◽  
Crowded Environment

AbstractThe periplasm of Gram-negative bacteria is a highly crowded environment comprised of many different molecular species. Antibacterial agents that causes lysis of Gram-negative bacteria by their action against the inner membrane must cross the periplasm to arrive at their target membrane. Very little is currently known about their route through the periplasm, and the interactions they experience. To this end, here atomistic molecular dynamics simulations are used to study the path taken by the antibiotic polymyxin B1 through a number of models of the periplasm which are crowded with proteins and osmolytes to different extents. The simulations reveal that PMB1 forms transient and long-lived interactions with proteins and osmolytes that are free in solution as well as lipoproteins anchored to the outer membrane and bound to the cell wall. We show that PMB1 may be able to ‘hitchhike’ within the periplasm by binding to lipoprotein carriers. Overall our results show that PMB1 is rarely uncomplexed within the periplasm; an important consideration for interpretations of its therapeutic mechanism of action. It is likely that this observation can be extended to other antibiotics that rely on diffusion to cross the periplasm.

scholarly journals Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq

Antibiotics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 257
Author(s):  
Florian Turbant ◽  
David Partouche ◽  
Omar El Hamoui ◽  
Sylvain Trépout ◽  
Théa Legoubey ◽  
...  
Keyword(s):  
Small Rnas ◽  
Antibacterial Agents ◽  
Amyloid Fibrils ◽  
Noncoding Rnas ◽  
Amyloid Formation ◽  
Gram Negative Bacteria ◽  
Translation Efficiency ◽  
Gram Negative ◽  
Bacterial Adaptation ◽  
E Coli

Hfq is a bacterial regulator with key roles in gene expression. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, thanks to its binding to small regulatory noncoding RNAs. This property is of primary importance for bacterial adaptation and survival in hosts. Small RNAs and Hfq are, for instance, involved in the response to antibiotics. Previous work has shown that the E. coli Hfq C-terminal region (Hfq-CTR) self-assembles into an amyloid structure. It was also demonstrated that the green tea compound EpiGallo Catechin Gallate (EGCG) binds to Hfq-CTR amyloid fibrils and remodels them into nonamyloid structures. Thus, compounds that target the amyloid region of Hfq may be used as antibacterial agents. Here, we show that another compound that inhibits amyloid formation, apomorphine, may also serve as a new antibacterial. Our results provide an alternative in order to repurpose apomorphine, commonly used in the treatment of Parkinson’s disease, as an antibiotic to block bacterial adaptation to treat infections.

scholarly journals Oxidative Stress and Antimicrobial Activity of Chromium(III) and Ruthenium(II) Complexes onStaphylococcus aureusandEscherichia coli

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Paulina L. Páez ◽  
Claudia M. Bazán ◽  
María E. Bongiovanni ◽  
Judith Toneatto ◽  
Inés Albesa ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Antimicrobial Activity ◽  
Antibacterial Agents ◽  
Antibacterial Activities ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli ◽  
Diimine Ligands

The prevalence of antibiotic resistance has resulted in the need for new approaches to be developed to combat previously easily treatable infections. The main aim of this work was to establish the potential of the syntheticα-diimine chromium(III) and ruthenium(II) complexes (where theα-diimine ligands are bpy = 2,2-bipyridine, phen = 1,10-phenanthroline, and dppz = dipyrido[3,2-a:2′,3′-c]-phenazine) like [Cr(phen)3]3+, [Cr(phen)2(dppz)]3+, [Ru(phen)3]2+, and [Ru(bpy)3]2+as antibacterial agents by generating oxidative stress. The [Cr(phen)3]3+and [Cr(phen)2(dppz)]3+complexes showed activity against Gram positive and Gram negative bacteria with minimum inhibitory concentrations (MICs) ranging from 0.125 μg/mL to 1 μg/mL, while [Ru(phen)3]2+and [Ru(bpy)3]2+do not exhibit antimicrobial activity against the two bacterial genera studied at the concentration range used. When ciprofloxacin was combined with [Cr(phen)3]3+for the inhibition ofStaphylococcus aureusandEscherichia coli, an important synergistic effect was observed, FIC 0.066 forS. aureusand FIC 0.064 forE. coli. The work described here shows that chromium(III) complexes are bactericidal forS. aureusandE. coli. Our results indicate thatα-diimine chromium(III) complexes may be interesting to open new paths for metallodrug chemotherapy against different bacterial genera since some of these complexes have been found to exhibit remarkable antibacterial activities.

scholarly journals 5-Bromo-1-(4-chlorobenzyl)-1H-indole-2-carboxamides as new potent antibacterial agents

2018 ◽  
Vol 24 (6) ◽  
pp. 327-332 ◽  
Author(s):  
Yogesh D. Mane ◽  
Smita S. Patil ◽  
Dhanraj O. Biradar ◽  
Bhimrao C. Khade
Keyword(s):  
Escherichia Coli ◽  
Antibacterial Activity ◽  
Antibacterial Agents ◽  
Inhibitory Concentration ◽  
Antibacterial Activities ◽  
Gram Negative Bacteria ◽  
Internal Standards ◽  
Gram Negative ◽  
E Coli ◽  
High Antibacterial Activity

Abstract Ten 5-bromoindole-2-carboxamides were synthesized, characterized and evaluated for antibacterial activity against pathogenic Gram-negative bacteria Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa and Salmonella Typhi using gentamicin and ciprofloxacin as internal standards. Compounds 7a–c, 7g and 7h exhibit high antibacterial activity with a minimum inhibitory concentration (MIC) of 0.35–1.25 μg/mL. Compounds 7a–c exhibit antibacterial activities that are higher than those of the standards against E. coli and P. aeruginosa.

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

2015 ◽  
Vol 43 (2) ◽  
pp. 162-167 ◽  
Author(s):  
Syma Khalid ◽  
Nils A. Berglund ◽  
Daniel A. Holdbrook ◽  
Yuk M. Leung ◽  
Jamie Parkin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Molecular Modelling ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Bacterial Membranes ◽  
Lipid Species ◽  
Membrane Models ◽  
Dynamics Simulations

Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have been studied using molecular dynamics simulations in simple models of membranes, usually only comprising one lipid species. Thus, traditionally, the simulations have reflected the majority of in vitro membrane experimental setups, enabling observations from the latter to be rationalized at the molecular level. In the last few years, the sophistication and complexity of membrane models have improved considerably, such that the heterogeneity of the lipid and protein composition of the membranes can now be considered both at the atomistic and coarse-grain levels of granularity. Importantly this means relevant biology is now being retained in the models, thereby linking the in silico and in vivo scenarios. We discuss recent progress in simulations of proteins in simple lipid bilayers, more complex membrane models and finally describe some efforts to overcome timescale limitations of atomistic molecular dynamics simulations of bacterial membranes.

scholarly journals Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Runrun Wu ◽  
Jeremy W. Bakelar ◽  
Karl Lundquist ◽  
Zijian Zhang ◽  
Katie M. Kuo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Single Unit ◽  
Outer Membrane Proteins ◽  
Conformational Dynamics ◽  
Accessory Proteins ◽  
Gram Negative Bacteria ◽  
Folding Intermediate ◽  
Gram Negative ◽  
Dynamics Simulations

AbstractIn Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins is mediated by the β-barrel assembly machinery (BAM). The mechanism employed by BAM is complex and so far- incompletely understood. Here, we report the structures of BAM in nanodiscs, prepared using polar lipids and native membranes, where we observe an outward-open state. Mutations in the barrel domain of BamA reveal that plasticity in BAM is essential, particularly along the lateral seam of the barrel domain, which is further supported by molecular dynamics simulations that show conformational dynamics in BAM are modulated by the accessory proteins. We also report the structure of BAM in complex with EspP, which reveals an early folding intermediate where EspP threads from the underside of BAM and incorporates into the barrel domain of BamA, supporting a hybrid-barrel budding mechanism in which the substrate is folded into the membrane sequentially rather than as a single unit.

scholarly journals Glucose transport via the pseudomonad porin OprB: implications for the design of Trojan Horse anti-infectives

2019 ◽  
Vol 21 (16) ◽  
pp. 8457-8463 ◽  
Author(s):  
Joan Coines ◽  
Silvia Acosta-Gutierrez ◽  
Igor Bodrenko ◽  
Carme Rovira ◽  
Matteo Ceccarelli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Glucose Transport ◽  
Trojan Horse ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Dynamical Features ◽  
Dynamics Simulations

Knowing the structural and dynamical features of specific porins from poor-permeable Gram-negative bacteria helps to design anti-infectives with optimal permeation. Molecular dynamics simulations can characterize and quantify the transport of substrates through these specific porins.

scholarly journals Explore the Potential of a Plant Phospholipase as an Antimicrobial

2020 ◽  
Author(s):  
Curtis Chen ◽  
Shanhui Xu ◽  
Yanran Li
Keyword(s):  
Antibacterial Agents ◽  
Gram Negative Bacteria ◽  
Global Public Health ◽  
Lower Efficiency ◽  
Gram Negative ◽  
E Coli ◽  
Gram Positive Bacteria ◽  
Plant Lipase ◽  
Plant Enzymes ◽  
Shed Light

AbstractGlobal public health is increasingly threatened by the fast emergence of antibiotic resistance, and novel types of antibiotics are urgently needed. Metazoans have evolved their own antimicrobial mechanism, such as human group IIA secreted phospholipase A (sPLA2), which can efficiently inhibit the growth of gram-positive bacteria, but with much lower efficiency toward gram-negative bacteria. Here, we verified the antibacterial activity of a plant lipase, PLIP1 from Arabidopsis thaliana, against the gram-negative bacteria Escherichia coli, which belongs to the WHO priority 1 (critical) pathogen Enterobacteriaceae family. We also explored the potential of evolving PLIP1 as a more potent antimicrobial agent towards E. coli. Our results imply the possibility of using plant lipases as a potential antimicrobial and shed light on the future exploration of plant enzymes for novel and more efficient antibacterial agents.

Disinfection of Fruits with Activated Water

2019 ◽  
Vol 10 ◽  
pp. 1864-1872
Author(s):  
Prof. Teodora P. Popova
Keyword(s):  
Antimicrobial Activity ◽  
Aqueous Solutions ◽  
Antimicrobial Properties ◽  
The Other ◽  
Gram Negative Bacteria ◽  
High Antimicrobial Activity ◽  
Gram Negative ◽  
E Coli ◽  
Number Of Microorganisms ◽  
Lower Effect

The effect of ionized aqueous solutions (anolytes and catholyte) in the processing of fruits (cherries, morellos, and strawberries) for decontamination has been tested. Freshly prepared analytes and catholyte without the addition of salts were used, as well as stored for 7 months anolytes, prepared with 0.5% NaCl and a combination of 0.5% NaCl and 0.5% Na2CO3. The anolyte prepared with a combination of 0.5% NaCl and 0.5% Na2CO3, as well as the anolyte obtained with 0.5% NaCl, exhibit high antimicrobial activity against the surface microflora of strawberries, cherries, and sour cherries. They inactivate E. coli for 15 minutes. The other species of the fam. Enterobacteriaceae were also affected to the maximum extent, as is the total number of microorganisms, especially in cherries and sour cherries. Even stored for 7 months, they largely retain their antimicrobial properties. Anolyte and catholyte, obtained without the addition of salts, showed a lower effect on the total number of microorganisms, but had a significant effect on Gram-negative bacteria, and especially with regard to the sanitary indicative E. coli.

Structure-Activity Relationship and Antimicrobial Evaluation of N-Phenylpyrazole Curcumin Derivatives

2020 ◽  
Vol 16 (4) ◽  
pp. 481-488
Author(s):  
Heli Sanghvi ◽  
Satyendra Mishra
Keyword(s):  
Antibacterial Activity ◽  
Gram Negative Bacteria ◽  
Pyrazole Derivatives ◽  
Gram Positive ◽  
Gram Negative ◽  
E Coli ◽  
Curcumin Derivatives ◽  
Structure Activity ◽  
Electron Donating Groups ◽  
Derivatives Of

Background: Curcumin, one of the most important pharmacologically significant natural products, has gained significant consideration among scientists for decades since its multipharmacological activities. 1, 3-Dicarbonyl moiety of curcumin was found to be accountable for the rapid degradation of curcumin molecule. The aim of present work is to replace 1, 3-dicarbonyl moiety of curcumin by pyrazole and phenylpyrazole derivatives with a view to improving its stability and to investigate the role of substitution in N-phenylpyrazole curcumin on its antibacterial activity against both Gram-positive as well as Gram-negative bacteria. Methods: Pyrazole derivatives of curcumin were prepared by heating curcumin with phenyhydrazine/ substituted phenyhydrazine derivatives in AcOH. The residue was purified by silica gel column chromatography. Structures of purified compounds were confirmed by 1H NMR and Mass spectroscopy. The synthesized compounds were evaluated for their antibacterial activity by the microdilution broth susceptibility test method against gram positive (S. aureus) and gram negative (E. coli). Results: Effects of substitution in N-phenylpyrazole curcumin derivatives against S. aureus and E. coli were studied. The most active N-(3-Nitrophenylpyrazole) curcumin (12) exhibits twenty-fold more potency against S. aureus (MIC: 10μg/mL)) and N-(2-Fluoroophenylpyrazole) curcumin (5) fivefold more potency against E. coli (MIC; 50 μg/mL) than N-phenylpyrazole curcumin (4). Whereas, a remarkable decline in anti-bacterial activity against S. aureus and E. coli was observed when electron donating groups were incorporated in N-phenylpyrazole curcumin (4). Comparative studies of synthesized compounds suggest the effects of electron withdrawing and electron donating groups on unsubstituted phenylpyrazole curcumin (4). Conclusion: The structure-activity relationship (SAR) results indicated that the electron withdrawing and electron donating at N-phenylpyrazole curcumin played key roles for their bacterial inhibitory effects. The results of the antibacterial evaluation showed that the synthesized pyrazole derivatives of curcumin displayed moderate to very high activity in S. aureus. In conclusion, the series of novel curcumin derivatives were designed, synthesized and tested for their antibacterial activities against S. aureus and E. coli. Among them, N-(3-Nitrophenylpyrazole curcumin; 12) was most active against S. aureus (Gram-positive) and N-(2-Fluoroophenylpyrazole) curcumin (5) against E. coli (Gram-negative) bacteria.

Quality Improvement of the DNA extracted by boiling method in Gram negative bacteria

2017 ◽  
Vol 6 (04) ◽  
pp. 5347 ◽  
Author(s):  
Omar B. Ahmed* ◽  
Anas S. Dablool
Keyword(s):  
Dna Extraction ◽  
Control Method ◽  
Extraction Procedure ◽  
Cost Effective ◽  
High Yield ◽  
Gram Negative Bacteria ◽  
Bacterial Dna ◽  
Gram Negative ◽  
E Coli

Several methods of Deoxyribonucleic acid (DNA) extraction have been applied to extract bacterial DNA. The amount and the quality of the DNA obtained for each one of those methods are variable. The study aimed to evaluate bacterial DNA extraction using conventional boiling method followed by alcohol precipitation. DNA extraction from Gram negative bacilli was extracted and precipitated using boiling method with further precipitation by ethanol. The extraction procedure performed using the boiling method resulted in high DNA yields for both E. coli and K. pneumoniae bacteria in (199.7 and 285.7μg/ml, respectively) which was close to control method (229.3 and 440.3μg/ml). It was concluded that after alcohol precipitation boiling procedure was easy, cost-effective, and applicable for high-yield quality of DNA in Gram-negative bacteria.

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