scholarly journals One drug multiple targets: An approach to predict drug efficacies on bacterial strains differing in membrane composition

2018 ◽  
Author(s):  
Ayan Majumder ◽  
Malay Ranjan Biswal ◽  
Meher K. Prakash
Keyword(s):  
Rational Design ◽  
Quantitative Model ◽  
Membrane Composition ◽  
Bacterial Strains ◽  
Activity Prediction ◽  
Bacterial Membranes ◽  
Complementary Approach ◽  
Single Target ◽  
Membrane Adaptation ◽  
Quantitative Structure Activity Relationships

AbstractRational design methodologies such as quantitative structure activity relationships (QSAR) have conventionally focused on screening through several drugs for their activity against a single target, either a bacterial protein or membrane. Recent concerns in drug design such as the development of drug resistance by membrane adaptation, or the undesirable damage to gut microbiota require a paradigm shift in activity prediction. A complementary approach capable of predicting the activity of a single drug against diverse targets, the diversity arising from bacterial adaptation or a heterogeneous composition with other helpful or harmful bacteria, is needed. As a first predictive step towards this goal, we develop a quantitative model for the activity of daptomycin onStreptococcus aureusstrains with different membrane compositions, mainly varying in lysylation. The results of the predictions are good, and within the limits of the scarcely available data, hint at an interaction of daptomycin with the inner membrane. The complementary approach may in principle be extended to estimate the activity against gut bacterial membranes, when systematic data can be curated for training the model.

scholarly journals An integrated microfluidic platform for quantifying drug permeation across biomimetic vesicle membranes

2019 ◽  
Author(s):  
Michael Schaich ◽  
Jehangir Cama ◽  
Kareem Al Nahas ◽  
Diana Sobota ◽  
Kevin Jahnke ◽  
...  
Keyword(s):  
Drug Transport ◽  
Membrane Composition ◽  
Drug Permeability ◽  
Bacterial Membranes ◽  
Drug Molecules ◽  
Total Analysis System ◽  
Transport Assay ◽  
Order Of Magnitude ◽  
Analysis System ◽  
The Individual

The low membrane permeability of candidate drug molecules is a major challenge in drug development and insufficient permeability is one reason for the failure of antibiotic treatment against bacteria. Quantifying drug transport across specific pathways in living systems is challenging since one typically lacks knowledge of the exact lipidome and proteome of the individual cells under investigation. Here, we quantify drug permeability across biomimetic liposome membranes, with comprehensive control over membrane composition. We integrate the microfluidic octanol-assisted liposome assembly platform with an optofluidic transport assay to create a complete microfluidic total analysis system for quantifying drug permeability. Our system enables us to form liposomes with charged lipids mimicking the negative charge of bacterial membranes at physiological salt and pH levels, which proved difficult with previous liposome formation techniques. Furthermore, the microfluidic technique yields an order of magnitude more liposomes per experiment than previous assays. We demonstrate the feasibility of the assay by determining the permeability coefficient of norfloxacin across biomimetic liposomes.

scholarly journals Insecticidal Activity of Bacteria from Larvae Breeding Site with Natural Larvae Mortality: Screening of Separated Supernatant and Pellet Fractions

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 486 ◽  
Author(s):  
Handi Dahmana ◽  
Didier Raoult ◽  
Florence Fenollar ◽  
Oleg Mediannikov
Keyword(s):  
Biological Control ◽  
Insecticidal Activity ◽  
Breeding Site ◽  
Bacterial Strains ◽  
Activity Prediction ◽  
Pcr Screening ◽  
Breeding Sites ◽  
Insecticide Activity ◽  
New Compounds

Mosquitoes can transmit to humans devastating and deadly pathogens. As many chemical insecticides are banned due to environmental side effects or are of reduced efficacy due to resistance, biological control, including the use of bacterial strains with insecticidal activity, is of increasing interest and importance. The urgent actual need relies on the discovery of new compounds, preferably of a biological nature. Here, we explored the phenomenon of natural larvae mortality in larval breeding sites to identify potential novel compounds that may be used in biological control. From there, we isolated 14 bacterial strains of the phylum Firmicutes, most of the order Bacillales. Cultures were carried out under controlled conditions and were separated on supernatant and pellet fractions. The two fractions and a 1:1 mixture of the two fractions were tested on L3 and early L4 Aedes albopictus. Two concentrations were tested (2 and 6 mg/L). Larvae mortality was recorded at 24, 48 and 72 h and compared to that induced by the commercialized B. thuringiensis subsp. israelensis. Of the 14 strains isolated, 11 were active against the A. albopictus larvae: 10 of the supernatant fractions and one pellet fraction, and mortality increased with the concentration. For the insecticide activity prediction in three strains of the Bacillus cereus complex, PCR screening of the crystal (Cry) and cytolytic (Cyt) protein families characteristic to B. thuringiensis subsp. israelensis was performed. Most of the genes coding for these proteins’ synthesis were not detected. We identified bacterial strains that exhibit higher insecticidal activity compared with a commercial product. Further studies are needed for the characterization of active compounds.

Discovery of vascular endothelial growth factor receptor tyrosine kinase inhibitors by quantitative structure–activity relationships, molecular dynamics simulation and free energy calculation

RSC Advances ◽  
2016 ◽  
Vol 6 (42) ◽  
pp. 35402-35415 ◽  
Author(s):  
Juan Wang ◽  
Mao Shu ◽  
Xiaorong Wen ◽  
Yuanliang Wang ◽  
Yuanqiang Wang ◽  
...  
Keyword(s):  
Rational Design ◽  
Kinase Inhibitors ◽  
Growth Factor Receptor ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Vascular Endothelial ◽  
Structure Activity ◽  
Quantitative Structure Activity Relationships ◽  
Combined Strategy ◽  
Endothelial Growth Factor

Employing the combined strategy to understand the features of KDR–ligands complexes, and provide a basis for rational design of inhibitors.

scholarly journals A New Natural Product Analog of Blasticidin S Reveals Cellular Uptake Facilitated by the NorA Multidrug Transporter

2017 ◽  
Vol 61 (6) ◽  
Author(s):  
Jack R. Davison ◽  
Katheryn M. Lohith ◽  
Xiaoning Wang ◽  
Kostyantyn Bobyk ◽  
Sivakoteswara R. Mandadapu ◽  
...  
Keyword(s):  
Efflux Pump ◽  
Bacterial Strains ◽  
Multidrug Efflux ◽  
Multidrug Efflux Pump ◽  
Gene Encoding ◽  
Content Type ◽  
Bacterial Membranes ◽  
Development Of Resistance ◽  
Antibiotic Compounds ◽  
Blasticidin S

ABSTRACT The permeation of antibiotics through bacterial membranes to their target site is a crucial determinant of drug activity but in many cases remains poorly understood. During screening efforts to discover new broad-spectrum antibiotic compounds from marine sponge samples, we identified a new analog of the peptidyl nucleoside antibiotic blasticidin S that exhibited up to 16-fold-improved potency against a range of laboratory and clinical bacterial strains which we named P10. Whole-genome sequencing of laboratory-evolved strains of Staphylococcus aureus resistant to blasticidin S and P10, combined with genome-wide assessment of the fitness of barcoded Escherichia coli knockout strains in the presence of the antibiotics, revealed that restriction of cellular access was a key feature in the development of resistance to this class of drug. In particular, the gene encoding the well-characterized multidrug efflux pump NorA was found to be mutated in 69% of all S. aureus isolates resistant to blasticidin S or P10. Unexpectedly, resistance was associated with inactivation of norA, suggesting that the NorA transporter facilitates cellular entry of peptidyl nucleosides in addition to its known role in the efflux of diverse compounds, including fluoroquinolone antibiotics.

scholarly journals Synthetic Gene Circuits for Antimicrobial Resistance and Cancer Research

2021 ◽  
Author(s):  
Kevin S. Farquhar ◽  
Michael Tyler Guinn ◽  
Gábor Balázsi ◽  
Daniel A. Charlebois
Keyword(s):  
Mammalian Cells ◽  
Rational Design ◽  
Study Drug ◽  
Quantitative Model ◽  
Synthetic Gene ◽  
Modeling Tools ◽  
Gene Circuits ◽  
Novel Treatments ◽  
Synthetic Gene Circuits ◽  
Temporal Dimensions

Mathematical models and synthetic gene circuits are powerful tools to develop novel treatments for patients with drug-resistant infections and cancers. Mathematical modeling guides the rational design of synthetic gene circuits. These systems are then assembled into unified constructs from existing and/or modified genetic components from a range of organisms. In this chapter, we describe modeling tools for the design and characterization of chemical- and light-inducible synthetic gene circuits in different organisms and highlight how synthetic gene circuits are advancing biomedical research. Specifically, we demonstrate how these quantitative model systems are being used to study drug resistance in microbes and to probe the spatial–temporal dimensions of cancer in mammalian cells.

scholarly journals Characterization and Antimicrobial Activity of Amphiphilic Peptide AP3 and Derivative Sequences

Antibiotics ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 20 ◽  
Author(s):  
Christina Chrom ◽  
Lindsay Renn ◽  
Gregory Caputo
Keyword(s):  
Antimicrobial Activity ◽  
Fluorescence Spectroscopy ◽  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Cd Spectroscopy ◽  
Membrane Permeabilization ◽  
Bacterial Membrane ◽  
Bacterial Strains ◽  
Bacterial Membranes ◽  
Model Lipid Membranes

The continued emergence of new antibiotic resistant bacterial strains has resulted in great interest in the development of new antimicrobial treatments. Antimicrobial peptides (AMPs) are one of many potential classes of molecules to help meet this emerging need. AMPs are naturally derived sequences, which act as part of the innate immune system of organisms ranging from insects through humans. We investigated the antimicrobial peptide AP3, which is originally isolated from the winter flounder Pleuronectes americanus. This peptide is of specific interest because it does not exhibit the canonical facially amphiphilic orientation of side chains when in a helical orientation. Different analogs of AP3 were synthesized in which length, charge identity, and Trp position were varied to investigate the sequence-structure and activity relationship. We performed biophysical and microbiological characterization using fluorescence spectroscopy, CD spectroscopy, vesicle leakage assays, bacterial membrane permeabilization assays, and minimal inhibitory concentration (MIC) assays. Fluorescence spectroscopy showed that the peptides bind to lipid bilayers to similar extents, while CD spectra show the peptides adopt helical conformations. All five peptides tested in this study exhibited binding to model lipid membranes, while the truncated peptides showed no measurable antimicrobial activity. The most active peptide proved to be the parent peptide AP3 with the highest degree of leakage and bacterial membrane permeabilization. Moreover, it was found that the ability to permeabilize model and bacterial membranes correlated most closely with the ability to predict antimicrobial activity.

scholarly journals The Host Defense Peptide LL-37 Selectively Permeabilizes Apoptotic Leukocytes

2008 ◽  
Vol 53 (3) ◽  
pp. 1027-1038 ◽  
Author(s):  
Åse Björstad ◽  
Galia Askarieh ◽  
Kelly L. Brown ◽  
Karin Christenson ◽  
Huamei Forsman ◽  
...  
Keyword(s):  
Host Defense ◽  
Acute Inflammation ◽  
Specific Activity ◽  
Apoptotic Cell ◽  
Density Lipoprotein ◽  
Eukaryotic Cells ◽  
Apoptotic Cells ◽  
Membrane Composition ◽  
Bacterial Membranes ◽  
Host Defense Peptide

ABSTRACT LL-37 is a cationic host defense peptide that is highly expressed during acute inflammation and that kills bacteria by poorly defined mechanisms, resulting in permeabilization of microbial membranes. High concentrations of LL-37 have also been reported to have cytotoxic effects against eukaryotic cells, but the peptide is clearly capable of differentiating between membranes with different compositions (eukaryotic versus bacterial membranes). Eukaryotic cells such as leukocytes change their membrane composition during apoptotic cell death, when they are turned into nonfunctional but structurally intact entities. We tested whether LL-37 exerted specific activity on apoptotic cells and found that the peptide selectively permeabilized the membranes of apoptotic human leukocytes, leaving viable cells unaffected. This activity was seemingly analogous to the direct microbicidal effect of LL-37, in that it was rapid, independent of known surface receptors and/or active cell signaling, and inhibitable by serum components such as high-density lipoprotein. A similar selective permeabilization of apoptotic cells was recorded for both NK cells and neutrophils. In the latter cell type, LL-37 permeabilized both the plasma and granule membranes, resulting in the release of both lactate dehydrogenase and myeloperoxidase. Apoptosis is a way for inflammatory cells to die silently and minimize collateral tissue damage by retaining tissue-damaging and proinflammatory substances within intact membranes. Permeabilization of apoptotic leukocytes by LL-37, accompanied by the leakage of cytoplasmic as well as intragranular molecules, may thus shift the balance between pro- and anti-inflammatory signals and in this way be of importance for the termination of acute inflammation.

scholarly journals Bactericidal Properties of Rod-, Peanut-, and Star-Shaped Gold Nanoparticles Coated with Ceragenin CSA-131 against Multidrug-Resistant Bacterial Strains

Pharmaceutics ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 425
Author(s):  
Sylwia Joanna Chmielewska ◽  
Karol Skłodowski ◽  
Joanna Depciuch ◽  
Piotr Deptuła ◽  
Ewelina Piktel ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Bactericidal Activity ◽  
Molecular Mechanisms ◽  
Covalent Bond ◽  
Multidrug Resistant ◽  
Host Cells ◽  
Cooh Group ◽  
Bacterial Strains ◽  
Au Nps ◽  
Bacterial Membranes

Background: The ever-growing number of infections caused by multidrug-resistant (MDR) bacterial strains requires an increased effort to develop new antibiotics. Herein, we demonstrate that a new class of gold nanoparticles (Au NPs), defined by shape and conjugated with ceragenin CSA-131 (cationic steroid antimicrobial), display strong bactericidal activity against intractable superbugs. Methods: For the purpose of research, we developed nanosystems with rod- (AuR NPs@CSA-131), peanut-(AuP NPs@CSA-131) and star-shaped (AuS NPs@CSA-131) metal cores. Those nanosystems were evaluated against bacterial strains representing various groups of MDR (multidrug-resistant) Gram-positive (MRSA, MRSE, and MLSb) and Gram-negative (ESBL, AmpC, and CR) pathogens. Assessment of MICs (minimum inhibitory concentrations)/MBCs (minimum bactericidal concentrations) and killing assays were performed as a measure of their antibacterial activity. In addition to a comprehensive analysis of bacterial responses involving the generation of ROS (reactive oxygen species), plasma membrane permeabilization and depolarization, as well as the release of protein content, were performed to investigate the molecular mechanisms of action of the nanosystems. Finally, their hemocompatibility was assessed by a hemolysis assay. Results: All of the tested nanosystems exerted potent bactericidal activity in a manner resulting in the generation of ROS, followed by damage of the bacterial membranes and the leakage of intracellular content. Notably, the killing action occurred with all of the bacterial strains evaluated, including those known to be drug resistant, and at concentrations that did not impact the growth of host cells. Conclusions: Conjugation of CSA-131 with Au NPs by covalent bond between the COOH group from MHDA and NH3 from CSA-131 potentiates the antimicrobial activity of this ceragenin if compared to its action alone. Results validate the development of AuR NPs@CSA-131, AuP NPs@CSA-131, and AuS NPs@CSA-131 as potential novel nanoantibiotics that might effectively eradicate MDR bacteria.

scholarly journals Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane

2018 ◽  
Vol 115 (14) ◽  
pp. 3704-3709 ◽  
Author(s):  
Antonella Caforio ◽  
Melvin F. Siliakus ◽  
Marten Exterkate ◽  
Samta Jain ◽  
Varsha R. Jumde ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Ether Lipid ◽  
Lipid Biosynthesis ◽  
Phosphate Ester ◽  
Membrane Composition ◽  
Glycerol Phosphate ◽  
Bacterial Membranes ◽  
E Coli ◽  
Phosphate Backbone ◽  
Archaeal Lipids

One of the main differences between bacteria and archaea concerns their membrane composition. Whereas bacterial membranes are made up of glycerol-3-phosphate ester lipids, archaeal membranes are composed of glycerol-1-phosphate ether lipids. Here, we report the construction of a stable hybrid heterochiral membrane through lipid engineering of the bacterium Escherichia coli. By boosting isoprenoid biosynthesis and heterologous expression of archaeal ether lipid biosynthesis genes, we obtained a viable E. coli strain of which the membranes contain archaeal lipids with the expected stereochemistry. It has been found that the archaeal lipid biosynthesis enzymes are relatively promiscuous with respect to their glycerol phosphate backbone and that E. coli has the unexpected potential to generate glycerol-1-phosphate. The unprecedented level of 20–30% archaeal lipids in a bacterial cell has allowed for analyzing the effect on the mixed-membrane cell’s phenotype. Interestingly, growth rates are unchanged, whereas the robustness of cells with a hybrid heterochiral membrane appeared slightly increased. The implications of these findings for evolutionary scenarios are discussed.

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