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Iliopoulos F, Tu D, Pence IJ, Li X, Ghosh P, Luke MC, Raney SG, Rantou E, Evans CL. Determining topical product bioequivalence with stimulated Raman scattering microscopy. J Control Release 2024; 367:864-876. [PMID: 38346503 DOI: 10.1016/j.jconrel.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024]
Abstract
Generic drugs are essential for affordable medicine and improving accessibility to treatments. Bioequivalence (BE) is typically demonstrated by assessing a generic product's pharmacokinetics (PK) relative to a reference-listed drug (RLD). Accurately estimating cutaneous PK (cPK) at or near the site of action can be challenging for locally acting topical products. Certain cPK approaches are available for assessing local bioavailability (BA) in the skin. Stimulated Raman scattering (SRS) microscopy has unique capabilities enabling continuous, high spatial and temporal resolution and quantitative imaging of drugs within the skin. In this paper, we developed an approach based on SRS and a polymer-based standard reference for the evaluation of topical product BA and BE in human skin ex vivo. BE assessment of tazarotene-containing formulations was achieved using cPK parameters obtained within different skin microstructures. The establishment of BE between the RLD and an approved generic product was successfully demonstrated. Interestingly, within the constraints of the current study design the results suggest similar BA between the tested gel formulation and the reference cream formulation, despite the differences in the formulation/dosage form. Another formulation containing polyethylene glycol as the vehicle was demonstrated to be not bioequivalent to the RLD. Compared to using the SRS approach without a standard reference, the developed approach enabled more consistent and reproducible results, which is crucial in BE assessment. The abundant information from the developed approach can help to systematically identify key areas of study design that will enable a better comparison of topical products and support an assessment of BE.
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Affiliation(s)
- Fotis Iliopoulos
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Dandan Tu
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Isaac J Pence
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Xiaolei Li
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA
| | - Priyanka Ghosh
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Markham C Luke
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Sam G Raney
- Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Elena Rantou
- Office of Biostatistics, Office of Translational Sciences, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring 20993, MD, USA
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown 02129, MA, USA.
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2
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Turbant F, Esnouf E, Rosaz F, Wien F, Węgrzyn G, Chauvet H, Arluison V. Role of the Bacterial Amyloid-like Hfq in Fluoroquinolone Fluxes. Microorganisms 2023; 12:53. [PMID: 38257880 PMCID: PMC10819720 DOI: 10.3390/microorganisms12010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Due to their two-cell membranes, Gram-negative bacteria are particularly resistant to antibiotics. Recent investigations aimed at exploring new target proteins involved in Gram-negative bacteria adaptation helped to identify environmental changes encountered during infection. One of the most promising approaches in finding novel targets for antibacterial drugs consists of blocking noncoding RNA-based regulation using the protein cofactor, Hfq. Although Hfq is important in many bacterial pathogens, its involvement in antibiotics response is still unclear. Indeed, Hfq may mediate drug resistance by regulating the major efflux system in Escherichia coli, but it could also play a role in the influx of antibiotics. Here, using an imaging approach, we addressed this problem quantitatively at the single-cell level. More precisely, we analyzed how Hfq affects the dynamic influx and efflux of ciprofloxacin, an antibiotic from the group of fluoroquinolones that is used to treat bacterial infections. Our results indicated that the absence of either whole Hfq or its C-terminal domain resulted in a more effective accumulation of ciprofloxacin, irrespective of the presence of the functional AcrAB-TolC efflux pump. However, overproduction of the MicF small regulatory RNA, which reduces the efficiency of expression of the ompF gene (coding for a porin involved in antibiotics influx) in a Hfq-dependent manner, resulted in impaired accumulation of ciprofloxacin. These results led us to propose potential mechanisms of action of Hfq in the regulation of fluoroquinolone fluxes across the E. coli envelope.
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Affiliation(s)
- Florian Turbant
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Emeline Esnouf
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
| | - Francois Rosaz
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Hugo Chauvet
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
- UFR SDV, Université Paris Cité, 75013 Paris, France
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3
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Ferrand A, Vergalli J, Bosi C, Pantel A, Pagès JM, Davin-Regli A. Contribution of efflux and mutations in fluoroquinolone susceptibility in MDR enterobacterial isolates: a quantitative and molecular study. J Antimicrob Chemother 2023; 78:1532-1542. [PMID: 37104818 DOI: 10.1093/jac/dkad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
OBJECTIVES The emergence of MDR strains is a public health problem in the management of associated infections. Several resistance mechanisms are present, and antibiotic efflux is often found at the same time as enzyme resistance and/or target mutations. However, in the laboratory routinely, only the latter two are identified and the prevalence of antibiotic expulsion is underestimated, causing a misinterpretation of the bacterial resistance phenotype. The development of a diagnostic system to quantify the efflux routinely would thus improve the management of patients. METHODS A quantitative technique based on detection of clinically used fluoroquinolones was investigated in Enterobacteriaceae clinical strains with a high or basal efflux activity. The detail of efflux involvement was studied from MIC determination and antibiotic accumulation inside bacteria. WGS was carried out on selected strains to determine the genetic background associated with efflux expression. RESULTS Only 1 Klebsiella pneumoniae isolate exhibited a lack of efflux whereas 13 isolates had a basal efflux and 8 presented efflux pump overexpression. The antibiotic accumulation evidenced the efficacy of the efflux mechanism in strains, and the contribution of dynamic expulsion versus target mutations in fluoroquinolone susceptibility. CONCLUSIONS We confirmed that phenylalanine arginine β-naphthylamide is not a reliable marker of efflux due to the affinity of the AcrB efflux pump for different substrates. We have developed an accumulation test that can be used efficiently on clinical isolates collected by the biological laboratory. The experimental conditions and protocols ensure a robust assay that with improvements in practice, expertise and equipment could be transferred to the hospital laboratory to diagnose the contribution of efflux in Gram-negative bacteria.
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Affiliation(s)
- Aurélie Ferrand
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France
| | - Julia Vergalli
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France
| | - Claude Bosi
- Laboratoire de Biologie Polyvalente, Centre Hospitalier d'Aubagne, Aubagne, France
| | - Alix Pantel
- Virulence Bactérienne et Infections Chroniques, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30900 Nîmes, France
| | - Jean-Marie Pagès
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France
| | - Anne Davin-Regli
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France
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4
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Pajović JD, Dojčilović RJ, Kaščáková S, Réfrégiers M, Božanić DK, Djoković V. Enhanced resonance energy transfer in gold nanoparticles bifunctionalized by tryptophan and riboflavin and its application in fluorescence bioimaging. Colloids Surf B Biointerfaces 2023; 227:113340. [PMID: 37201446 DOI: 10.1016/j.colsurfb.2023.113340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Gold nanoparticles were functionalized by amino acid tryptophan and vitamin riboflavin - a resonance energy transfer (RET) pair of biomolecules. The presence of the gold nanoparticles resulted in 65% increase in RET efficiency. Because of enhanced RET efficiency, the photobleaching dynamics of the fluorescent molecules at the surface of the nanoparticles is different from that of molecules in solution. The observed effect was used for detection of the functionalized nanoparticles within biological material rich with autofluorescent species. Synchrotron radiation deep-ultraviolet fluorescence microscopy is used to study the photobleaching dynamics of the fluorescence centers within human hepatocellular carcinoma Huh7.5.1 cells incubated with the nanoparticles. The fluorescent centers were classified according to their photobleaching dynamics, which enabled the discrimination of the cell areas where the accumulation of the nanoparticles takes place, even though the particles were smaller than the spatial resolution of the images.
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Affiliation(s)
- Jelena D Pajović
- DISCO Beamline, Synchrotron SOLEIL, BP 48, Gif sur Yvette 91192, France; University of Belgrade, Faculty of Physics, Studentski trg 12, Belgrade 11001, Serbia.
| | - Radovan J Dojčilović
- University of Belgrade, "VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Center of Excellence for Photoconversion, PO Box 522, Belgrade 11001, Serbia; Department of Experimental and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, Barcelona 08003, Spain
| | - Slávka Kaščáková
- Inserm, Unité 1193, Villejuif F-94800, France; University Paris-Sud XI, UMR-S1193, Villejuif F-94800, France
| | - Matthieu Réfrégiers
- DISCO Beamline, Synchrotron SOLEIL, BP 48, Gif sur Yvette 91192, France; Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, Orléans 45071, France
| | - Dušan K Božanić
- University of Belgrade, "VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Center of Excellence for Photoconversion, PO Box 522, Belgrade 11001, Serbia.
| | - Vladimir Djoković
- University of Belgrade, "VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Center of Excellence for Photoconversion, PO Box 522, Belgrade 11001, Serbia.
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5
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-Aryl-2(trifluoromethyl)benzo[][1,8]naphthyridin-4(1)-one as Convenient Platform to Design High Photostable and Long-Lived Dyad Fluorophore with Potential Application in Live-Cell Imaging. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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6
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Sousa CF, Kamal MAM, Richter R, Elamaldeniya K, Hartmann RW, Empting M, Lehr CM, Kalinina OV. Modeling the Effect of Hydrophobicity on the Passive Permeation of Solutes across a Bacterial Model Membrane. J Chem Inf Model 2022; 62:5023-5033. [PMID: 36214845 DOI: 10.1021/acs.jcim.2c00767] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Passive diffusion across biomembranes is an important mechanism of permeation for multiple drugs, including antibiotics. However, this process is frequently neglected while studying drug uptake and, in our view, warrants further investigation. Here, we apply molecular dynamics simulations to investigate the impact of changes in molecular hydrophobicity on the permeability of a series of inhibitors of the quorum sensing of Pseudomonas aeruginosa, previously discovered by us, across a membrane model. Overall, we show that permeation across this membrane model does not correlate with the molecule's hydrophobicity. We demonstrate that using a simple model for permeation, based on the difference between the maximum and minimum of the free energy profile, outperforms the inhomogeneous solubility-diffusion model, yielding a permeability ranking that better agrees with the experimental results, especially for hydrophobic permeants. The calculated differences in permeability could not explain differences in in bacterio activity. Nevertheless, substantial differences in molecular orientation along the permeation pathway correlate with the in bacterio activity, emphasizing the importance of analyzing, at an atomistic level, the permeation pathway of these solutes.
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Affiliation(s)
- Carla F Sousa
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Mohamed A M Kamal
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Robert Richter
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany
| | - Kalanika Elamaldeniya
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - Rolf W Hartmann
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany.,Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken66123, Germany
| | - Martin Empting
- Department of Pharmacy, Saarland University, Saarbrücken66123, Germany.,Antiviral & Antivirulence Drugs Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig, Saarbrücken66123, Germany
| | - Claus-Michael Lehr
- Department of Biological Barriers and Drug Delivery, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Department of Pharmacy, Saarland University, Saarbrücken66123, Germany
| | - Olga V Kalinina
- Drug Bioinformatics Group, Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken66123, Germany.,Center for Bioinformatics, Saarland University, Saarbrücken66123, Germany.,Medical Faculty, Saarland University, Homburg66421, Germany
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7
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Vergalli J, Chauvet H, Oliva F, Pajović J, Malloci G, Vargiu AV, Réfrégiers M, Ruggerone P, Pagès JM. A framework for dissecting affinities of multidrug efflux transporter AcrB to fluoroquinolones. Commun Biol 2022; 5:1062. [PMID: 36203030 PMCID: PMC9537517 DOI: 10.1038/s42003-022-04024-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022] Open
Abstract
Sufficient concentration of antibiotics close to their target is key for antimicrobial action. Among the tools exploited by bacteria to reduce the internal concentration of antibiotics, multidrug efflux pumps stand out for their ability to capture and expel many unrelated compounds out of the cell. Determining the specificities and efflux efficiency of these pumps towards their substrates would provide quantitative insights into the development of antibacterial strategies. In this light, we developed a competition efflux assay on whole cells, that allows measuring the efficacy of extrusion of clinically used quinolones in populations and individual bacteria. Experiments reveal the efficient competitive action of some quinolones that restore an active concentration of other fluoroquinolones. Computational methods show how quinolones interact with the multidrug efflux transporter AcrB. Combining experiments and computations unveils a key molecular mechanism acting in vivo to detoxify bacterial cells. The developed assay can be generalized to the study of other efflux pumps. A competitive efflux assay combined with computational approaches reveal how different quinolones interact with the prototypical bacterial multidrug efflux transporter AcrB, providing insights which may help optimise antibiotics.
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Affiliation(s)
- Julia Vergalli
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France
| | - Hugo Chauvet
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France
| | - Francesco Oliva
- Department of Physics, University of Cagliari, 09042, Monserrato, (CA), Italy
| | - Jelena Pajović
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France.,University of Belgrade, Faculty of Physics, 11001, Belgrade, Serbia
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042, Monserrato, (CA), Italy
| | | | - Matthieu Réfrégiers
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France.,Centre de Biophysique Moléculaire, CNRS UPR4301, Rue Charles Sadron, Orléans, France
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042, Monserrato, (CA), Italy
| | - Jean-Marie Pagès
- UMR_MD1, U-1261, Aix-Marseille Univ, INSERM, IRBA, MCT, Marseille, France.
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8
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Cephalosporin translocation across enterobacterial OmpF and OmpC channels, a filter across the outer membrane. Commun Biol 2022; 5:1059. [PMID: 36198902 PMCID: PMC9534850 DOI: 10.1038/s42003-022-04035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
Gram-negative porins are the main entry for small hydrophilic molecules. We studied translocation of structurally related cephalosporins, ceftazidime (CAZ), cefotaxime (CTX) and cefepime (FEP). CAZ is highly active on E. coli producing OmpF (Outer membrane protein F) but less efficient on cells expressing OmpC (Outer membrane protein C), whereas FEP and CTX kill bacteria regardless of the porin expressed. This matches with the different capacity of CAZ and FEP to accumulate into bacterial cells as quantified by LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometry). Furthermore, porin reconstitution into planar lipid bilayer and zero current assays suggest permeation of ≈1,000 molecules of CAZ per sec and per channel through OmpF versus ≈500 through OmpC. Here, the instant killing is directly correlated to internal drug concentration. We propose that the net negative charge of CAZ represents a key advantage for permeation through OmpF porins that are less cation-selective than OmpC. These data could explain the decreased susceptibility to some cephalosporins of enterobacteria that exclusively express OmpC porins. The translocation of cephalosporins across enterobacterial OmpF and OmpC channels is monitored in real-time, demonstrating differential permeation of some cephalosporins through OmpF and OmpC.
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9
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Besagarhally Shivappa S, Krishnegowda A. Spectrophotometric determination of glucose in human serum samples using para‐phenylenediamine and alpha‐naphthol as a chromogenic reagent. INT J CHEM KINET 2022. [DOI: 10.1002/kin.21605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Łapińska U, Voliotis M, Lee KK, Campey A, Stone MRL, Tuck B, Phetsang W, Zhang B, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S. Fast bacterial growth reduces antibiotic accumulation and efficacy. eLife 2022; 11:74062. [PMID: 35670099 PMCID: PMC9173744 DOI: 10.7554/elife.74062] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/08/2022] [Indexed: 12/11/2022] Open
Abstract
Phenotypic variations between individual microbial cells play a key role in the resistance of microbial pathogens to pharmacotherapies. Nevertheless, little is known about cell individuality in antibiotic accumulation. Here, we hypothesise that phenotypic diversification can be driven by fundamental cell-to-cell differences in drug transport rates. To test this hypothesis, we employed microfluidics-based single-cell microscopy, libraries of fluorescent antibiotic probes and mathematical modelling. This approach allowed us to rapidly identify phenotypic variants that avoid antibiotic accumulation within populations of Escherichia coli, Pseudomonas aeruginosa, Burkholderia cenocepacia, and Staphylococcus aureus. Crucially, we found that fast growing phenotypic variants avoid macrolide accumulation and survive treatment without genetic mutations. These findings are in contrast with the current consensus that cellular dormancy and slow metabolism underlie bacterial survival to antibiotics. Our results also show that fast growing variants display significantly higher expression of ribosomal promoters before drug treatment compared to slow growing variants. Drug-free active ribosomes facilitate essential cellular processes in these fast-growing variants, including efflux that can reduce macrolide accumulation. We used this new knowledge to eradicate variants that displayed low antibiotic accumulation through the chemical manipulation of their outer membrane inspiring new avenues to overcome current antibiotic treatment failures.
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Affiliation(s)
- Urszula Łapińska
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - Margaritis Voliotis
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Department of Mathematics, University of ExeterExeterUnited Kingdom
| | - Ka Kiu Lee
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - Adrian Campey
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - M Rhia L Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New JerseyPiscatawayUnited States
| | - Brandon Tuck
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - Wanida Phetsang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Bing Zhang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Department of Mathematics, University of ExeterExeterUnited Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of ExeterExeterUnited Kingdom
- Department of Bioinformatics and Mathematical Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of SciencesSofiaBulgaria
| | - Mark AT Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Stefano Pagliara
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
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11
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Richter R, Kamal MAM, Koch M, Niebuur B, Huber A, Goes A, Volz C, Vergalli J, Kraus T, Müller R, Schneider‐Daum N, Fuhrmann G, Pagès J, Lehr C. An Outer Membrane Vesicle-Based Permeation Assay (OMPA) for Assessing Bacterial Bioavailability. Adv Healthc Mater 2022; 11:e2101180. [PMID: 34614289 DOI: 10.1002/adhm.202101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/14/2021] [Indexed: 11/11/2022]
Abstract
When searching for new antibiotics against Gram-negative bacterial infections, a better understanding of the permeability across the cell envelope and tools to discriminate high from low bacterial bioavailability compounds are urgently needed. Inspired by the phospholipid vesicle-based permeation assay (PVPA), which is designed to predict non-facilitated permeation across phospholipid membranes, outer membrane vesicles (OMVs) of Escherichia coli either enriched or deficient of porins are employed to coat filter supports for predicting drug uptake across the complex cell envelope. OMVs and the obtained in vitro model are structurally and functionally characterized using cryo-TEM, SEM, CLSM, SAXS, and light scattering techniques. In vitro permeability, obtained from the membrane model for a set of nine antibiotics, correlates with reported in bacterio accumulation data and allows to discriminate high from low accumulating antibiotics. In contrast, the correlation of the same data set generated by liposome-based comparator membranes is poor. This better correlation of the OMV-derived membranes points to the importance of hydrophilic membrane components, such as lipopolysaccharides and porins, since those features are lacking in liposomal comparator membranes. This approach can offer in the future a high throughput screening tool with high predictive capacity or can help to identify compound- and bacteria-specific passive uptake pathways.
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Affiliation(s)
- Robert Richter
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Mohamed A. M. Kamal
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Marcus Koch
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
| | - Bart‐Jan Niebuur
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
| | - Anna‐Lena Huber
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Adriely Goes
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Carsten Volz
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Julia Vergalli
- UMR_MD1 U‐1261 Aix‐Marseille Université INSERM IRBA MCT Faculté de Pharmacie 27 Boulevard Jean Moulin Marseille 13005 France
| | - Tobias Kraus
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
- Colloid and Interface Chemistry Saarland University Campus D2.2 Saarbrücken 66123 Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Nicole Schneider‐Daum
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Gregor Fuhrmann
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Jean‐Marie Pagès
- UMR_MD1 U‐1261 Aix‐Marseille Université INSERM IRBA MCT Faculté de Pharmacie 27 Boulevard Jean Moulin Marseille 13005 France
| | - Claus‐Michael Lehr
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
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12
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Application of antibiotic-derived fluorescent probes to bacterial studies. Methods Enzymol 2022; 665:1-28. [DOI: 10.1016/bs.mie.2021.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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An LC-MS/MS assay and complementary web-based tool to quantify and predict compound accumulation in E. coli. Nat Protoc 2021; 16:4833-4854. [PMID: 34480129 PMCID: PMC8715754 DOI: 10.1038/s41596-021-00598-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 02/08/2023]
Abstract
Novel classes of broad-spectrum antibiotics have been extremely difficult to discover, largely due to the impermeability of the Gram-negative membranes coupled with a poor understanding of the physicochemical properties a compound should possess to promote its accumulation inside the cell. To address this challenge, numerous methodologies for assessing intracellular compound accumulation in Gram-negative bacteria have been established, including classic radiometric and fluorescence-based methods. The recent development of accumulation assays that utilize liquid chromatography-tandem mass spectrometry (LC-MS/MS) have circumvented the requirement for labeled compounds, enabling assessment of a substantially broader range of small molecules. Our unbiased study of accumulation trends in Escherichia coli using an LC-MS/MS-based assay led to the development of the eNTRy rules, which stipulate that a compound is most likely to accumulate in E. coli if it has an ionizable Nitrogen, has low Three-dimensionality and is relatively Rigid. To aid in the implementation of the eNTRy rules, we developed a complementary web tool, eNTRyway, which calculates relevant properties and predicts compound accumulation. Here we provide a comprehensive protocol for analysis and prediction of intracellular accumulation of small molecules in E. coli using an LC-MS/MS-based assay (which takes ~2 d) and eNTRyway, a workflow that is readily adoptable by any microbiology, biochemistry or chemical biology laboratory.
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14
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Clinical Status of Efflux Resistance Mechanisms in Gram-Negative Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10091117. [PMID: 34572699 PMCID: PMC8467137 DOI: 10.3390/antibiotics10091117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/05/2021] [Accepted: 09/15/2021] [Indexed: 01/25/2023] Open
Abstract
Antibiotic efflux is a mechanism that is well-documented in the phenotype of multidrug resistance in bacteria. Efflux is considered as an early facilitating mechanism in the bacterial adaptation face to the concentration of antibiotics at the infectious site, which is involved in the acquirement of complementary efficient mechanisms, such as enzymatic resistance or target mutation. Various efflux pumps have been described in the Gram-negative bacteria most often encountered in infectious diseases and, in healthcare-associated infections. Some are more often involved than others and expel virtually all families of antibiotics and antibacterials. Numerous studies report the contribution of these pumps in resistant strains previously identified from their phenotypes. The authors characterize the pumps involved, the facilitating antibiotics and those mainly concerned by the efflux. However, today no study describes a process for the real-time quantification of efflux in resistant clinical strains. It is currently necessary to have at hospital level a reliable and easy method to quantify the efflux in routine and contribute to a rational choice of antibiotics. This review provides a recent overview of the prevalence of the main efflux pumps observed in clinical practice and provides an idea of the prevalence of this mechanism in the multidrug resistant Gram-negative bacteria. The development of a routine diagnostic tool is now an emergency need for the proper application of current recommendations regarding a rational use of antibiotics.
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15
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Richter R, Lehr CM. Extracellular vesicles as novel assay tools to study cellular interactions of anti-infective compounds - A perspective. Adv Drug Deliv Rev 2021; 173:492-503. [PMID: 33857554 DOI: 10.1016/j.addr.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Sudden outbreaks of novel infectious diseases and the persistent evolution of antimicrobial resistant pathogens make it necessary to develop specific tools to quickly understand pathogen-cell interactions and to study appropriate drug delivery strategies. Extracellular vesicles (EVs) are cell-specific biogenic transport systems, which are gaining more and more popularity as either diagnostic markers or drug delivery systems. Apart from that, there are emerging possibilities for EVs as tools to study drug penetration, drug-membrane interactions as well as pathogen-membrane interactions. However, it appears that the potential of EVs for such applications has not been fully exploited yet. Considering the vast variety of cells that can be involved in an infection, vesicle-based analytical methods are just emerging and the number of reported applications is still relatively small. Aim of this review is to discuss the current state of the art of EV-based assays, especially in the context of antimicrobial research and therapy, and to present some new perspectives for a more exhaustive and creative exploration in the future.
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Affiliation(s)
- Robert Richter
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
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16
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Mastering the Gram-negative bacterial barrier - Chemical approaches to increase bacterial bioavailability of antibiotics. Adv Drug Deliv Rev 2021; 172:339-360. [PMID: 33705882 DOI: 10.1016/j.addr.2021.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
To win the battle against resistant, pathogenic bacteria, novel classes of anti-infectives and targets are urgently needed. Bacterial uptake, distribution, metabolic and efflux pathways of antibiotics in Gram-negative bacteria determine what we here refer to as bacterial bioavailability. Understanding these mechanisms from a chemical perspective is essential for anti-infective activity and hence, drug discovery as well as drug delivery. A systematic and critical discussion of in bacterio, in vitro and in silico assays reveals that a sufficiently accurate holistic approach is still missing. We expect new findings based on Gram-negative bacterial bioavailability to guide future anti-infective research.
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17
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Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
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Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
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18
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Boulant E, Cambon E, Vergalli J, Bernard R, Neulat-Ripoll F, Nolent F, Gorgé O, Girleanu M, Favier AL, Leonetti JP, Bolla JM. Tolerance engineering in Deinococcus geothermalis by heterologous efflux pumps. Sci Rep 2021; 11:4280. [PMID: 33608597 PMCID: PMC7896070 DOI: 10.1038/s41598-021-83339-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/28/2021] [Indexed: 11/21/2022] Open
Abstract
Producing industrially significant compounds with more environmentally friendly represents a challenging task. The large-scale production of an exogenous molecule in a host microfactory can quickly cause toxic effects, forcing the cell to inhibit production to survive. The key point to counter these toxic effects is to promote a gain of tolerance in the host, for instance, by inducing a constant flux of the neo-synthetized compound out of the producing cells. Efflux pumps are membrane proteins that constitute the most powerful mechanism to release molecules out of cells. We propose here a new biological model, Deinococcus geothermalis, organism known for its ability to survive hostile environment; with the aim of coupling the promising industrial potential of this species with that of heterologous efflux pumps to promote engineering tolerance. In this study, clones of D. geothermalis containing various genes encoding chromosomal heterologous efflux pumps were generated. Resistant recombinants were selected using antibiotic susceptibility tests to screen promising candidates. We then developed a method to determine the efflux efficiency of the best candidate, which contains the gene encoding the MdfA of Salmonella enterica serovar Choleraesuis. We observe 1.6 times more compound in the external medium of the hit recombinant than that of the WT at early incubation time. The data presented here will contribute to better understanding of the parameters required for efficient production in D. geothermalis.
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Affiliation(s)
- Erika Boulant
- Aix Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
- Deinove, Cap Sigma/ZAC Euromédecine II, Grabels, France
| | | | - Julia Vergalli
- Aix Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Rémi Bernard
- Deinove, Cap Sigma/ZAC Euromédecine II, Grabels, France
- Vilmorin SA, Centre de Recherche de La Costière, Ledenon, France
| | - Fabienne Neulat-Ripoll
- Institut de Recherche Biomédicale des Armées, Département Microbiologie et Maladies Infectieuses, Unité Bactériologie, Brétigny-sur-Orge, France
| | - Flora Nolent
- Institut de Recherche Biomédicale des Armées, Département Microbiologie et Maladies Infectieuses, Unité Bactériologie, Brétigny-sur-Orge, France
| | - Olivier Gorgé
- Institut de Recherche Biomédicale des Armées, Département Microbiologie et Maladies Infectieuses, Unité Bactériologie, Brétigny-sur-Orge, France
| | - Maria Girleanu
- Institut de Recherche Biomédicale des Armées, Département des Plateformes et Recherche Technologique, Unité Imagerie, Brétigny-sur-Orge, France
| | - Anne-Laure Favier
- Institut de Recherche Biomédicale des Armées, Département des Plateformes et Recherche Technologique, Unité Imagerie, Brétigny-sur-Orge, France
| | - Jean-Paul Leonetti
- Deinove, Cap Sigma/ZAC Euromédecine II, Grabels, France
- Institut de Recherche en Infectiologie de Montpellier, UMR 9004-CNRS/UM, Montpellier, France
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19
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Design and Clinical Application of an Integrated Microfluidic Device for Circulating Tumor Cells Isolation and Single-Cell Analysis. MICROMACHINES 2021; 12:mi12010049. [PMID: 33401770 PMCID: PMC7824094 DOI: 10.3390/mi12010049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/27/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022]
Abstract
Circulating tumor cells (CTCs) have been considered as an alternative to tissue biopsy for providing both germline-specific and tumor-derived genetic variations. Single-cell analysis of CTCs enables in-depth investigation of tumor heterogeneity and individualized clinical assessment. However, common CTC enrichment techniques generally have limitations of low throughput and cell damage. Herein, based on micropore-arrayed filtration membrane and microfluidic chip, we established an integrated CTC isolation platform with high-throughput, high-efficiency, and less cell damage. We observed a capture rate of around 85% and a purity of 60.4% by spiking tumor cells (PC-9) into healthy blood samples. Detection of CTCs from lung cancer patients demonstrated a positive detectable rate of 87.5%. Additionally, single CTCs, ctDNA and liver biopsy tissue of a representative advanced lung cancer patient were collected and sequenced, which revealed comprehensive genetic information of CTCs while reflected the differences in genetic profiles between different biological samples. This work provides a promising tool for CTCs isolation and further analysis at single-cell resolution with potential clinical value.
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20
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Skok Ž, Barančoková M, Benek O, Cruz CD, Tammela P, Tomašič T, Zidar N, Mašič LP, Zega A, Stevenson CEM, Mundy JEA, Lawson DM, Maxwell A, Kikelj D, Ilaš J. Exploring the Chemical Space of Benzothiazole-Based DNA Gyrase B Inhibitors. ACS Med Chem Lett 2020; 11:2433-2440. [PMID: 33329764 PMCID: PMC7734788 DOI: 10.1021/acsmedchemlett.0c00416] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/13/2020] [Indexed: 12/22/2022] Open
Abstract
![]()
We
designed and synthesized a series of inhibitors of the bacterial
enzymes DNA gyrase and DNA topoisomerase IV, based on our recently
published benzothiazole-based inhibitor bearing an oxalyl moiety.
To improve the antibacterial activity and retain potent enzymatic
activity, we systematically explored the chemical space. Several strategies
of modification were followed: varying substituents on the pyrrole
carboxamide moiety, alteration of the central scaffold, including
variation of substitution position and, most importantly, modification
of the oxalyl moiety. Compounds with acidic, basic, and neutral properties
were synthesized. To understand the mechanism of action and binding
mode, we have obtained a crystal structure of compound 16a, bearing a primary amino group, in complex with the N-terminal domain
of E. coli gyrase B (24 kDa) (PDB: 6YD9). Compound 15a, with a low molecular weight of 383
Da, potent inhibitory activity on E. coli gyrase
(IC50 = 9.5 nM), potent antibacterial activity on E. faecalis (MIC = 3.13 μM), and efflux impaired E. coli strain (MIC = 0.78 μM), is an important contribution
for the development of novel gyrase and topoisomerase IV inhibitors
in Gram-negative bacteria.
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Affiliation(s)
- Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Michaela Barančoková
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Ondřej Benek
- University of Hradec Králové, Faculty of Science, Department of Chemistry, Rokitanského 62, 500 03 Hradec Králové, Czech Republic
| | - Cristina Durante Cruz
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Päivi Tammela
- Centre for Drug Research, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Clare E. M. Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Julia E. A. Mundy
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - David M. Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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21
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Zhao S, Adamiak JW, Bonifay V, Mehla J, Zgurskaya HI, Tan DS. Defining new chemical space for drug penetration into Gram-negative bacteria. Nat Chem Biol 2020; 16:1293-1302. [PMID: 33199906 PMCID: PMC7897441 DOI: 10.1038/s41589-020-00674-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022]
Abstract
We live in the era of antibiotic resistance, and this problem will progressively worsen if no new solutions emerge. In particular, Gram-negative pathogens present both biological and chemical challenges that hinder the discovery of new antibacterial drugs. First, these bacteria are protected from a variety of structurally diverse drugs by a low-permeability barrier composed of two membranes with distinct permeability properties, in addition to active drug efflux, making this cell envelope impermeable to most compounds. Second, chemical libraries currently used in drug discovery contain few compounds that can penetrate Gram-negative bacteria. As a result of these challenges, intensive screening campaigns have led to few successes, highlighting the need for new approaches to identify regions of chemical space that are specifically relevant to antibacterial drug discovery. Herein we provide an overview of emerging insights into this problem and outline a general approach to addressing it using prospective analysis of chemical libraries for the ability of compounds to accumulate in Gram-negative bacteria. The overall goal is to develop robust cheminformatic tools to predict Gram-negative permeation and efflux, which can then be used to guide medicinal chemistry campaigns and the design of antibacterial discovery libraries.
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Affiliation(s)
- Shibin Zhao
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justyna W Adamiak
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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22
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Stone MRL, Łapińska U, Pagliara S, Masi M, Blanchfield JT, Cooper MA, Blaskovich MAT. Fluorescent macrolide probes - synthesis and use in evaluation of bacterial resistance. RSC Chem Biol 2020; 1:395-404. [PMID: 34458770 PMCID: PMC8341779 DOI: 10.1039/d0cb00118j] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/28/2020] [Indexed: 12/19/2022] Open
Abstract
The emerging crisis of antibiotic resistance requires a multi-pronged approach in order to avert the onset of a post-antibiotic age. Studies of antibiotic uptake and localisation in live cells may inform the design of improved drugs and help develop a better understanding of bacterial resistance and persistence. To facilitate this research, we have synthesised fluorescent derivatives of the macrolide antibiotic erythromycin. These analogues exhibit a similar spectrum of antibiotic activity to the parent drug and are capable of labelling both Gram-positive and -negative bacteria for microscopy. The probes localise intracellularly, with uptake in Gram-negative bacteria dependent on the level of efflux pump activity. A plate-based assay established to quantify bacterial labelling and localisation demonstrated that the probes were taken up by both susceptible and resistant bacteria. Significant intra-strain and -species differences were observed in these preliminary studies. In order to examine uptake in real-time, the probe was used in single-cell microfluidic microscopy, revealing previously unseen heterogeneity of uptake in populations of susceptible bacteria. These studies illustrate the potential of fluorescent macrolide probes to characterise and explore drug uptake and efflux in bacteria. Macrolide fluorescent probes illuminate the interactions between antibiotics and bacteria, providing new insight into mechanisms of resistance.![]()
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Affiliation(s)
- M Rhia L Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland 306 Carmody Road St Lucia 4072 Brisbane Australia
| | - Urszula Łapińska
- Living Systems Institute, University of Exeter Exeter EX4 4QD UK
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter Exeter EX4 4QD UK
| | - Muriel Masi
- Université Paris-Saclay, CEA, CNRS Institute for Integrative Biology of the Cell (I2BC) 911198 Gif-sur-Yvette France
| | - Joanne T Blanchfield
- School of Chemistry and Molecular Biosciences, The University of Queensland 68 Cooper Road St Lucia 4072 Brisbane Australia
| | - Matthew A Cooper
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland 306 Carmody Road St Lucia 4072 Brisbane Australia
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland 306 Carmody Road St Lucia 4072 Brisbane Australia
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23
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Winterhalter M. Antibiotic uptake through porins located in the outer membrane of Gram-negative bacteria. Expert Opin Drug Deliv 2020; 18:449-457. [PMID: 33161750 DOI: 10.1080/17425247.2021.1847080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Introduction: Making selective inhibitors of novel Gram-negative targets is not a substantial challenge - getting them into Gram-negative bacteria to reach their lethal target is the bottleneck. Poor permeability of the antibiotic requires high concentration causing off target activity. The lack of simple experimental techniques to measure antibiotic uptake as well as the local concentration at the target site creates a particular bottleneck in understanding and in improving the antibiotic activity.Areas covered: Here we recall current approaches to quantify the uptake. For a few antibiotics with known evidence for channel-limited permeation, the flux across a single OmpF or OmpC channel has been measured. For a typical concentration gradient of 1 µM of antibiotics the uptake varies between one up to few hundred molecules per second and per channel.Expert opinion: The current research effort is on quantifying the flux for a larger list of compounds on a cellular (mass spectra, fluorescence) or at single channel level (electrophysiology). A larger dataset of single channel permeabilities under various condition will be a powerful tool for understanding and improving the activity of antibiotics.
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24
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Cama J, Voliotis M, Metz J, Smith A, Iannucci J, Keyser UF, Tsaneva-Atanasova K, Pagliara S. Single-cell microfluidics facilitates the rapid quantification of antibiotic accumulation in Gram-negative bacteria. LAB ON A CHIP 2020; 20:2765-2775. [PMID: 32613221 PMCID: PMC7953842 DOI: 10.1039/d0lc00242a] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/15/2020] [Indexed: 06/01/2023]
Abstract
The double-membrane cell envelope of Gram-negative bacteria is a formidable barrier to intracellular antibiotic accumulation. A quantitative understanding of antibiotic transport in these cells is crucial for drug development, but this has proved elusive due to a dearth of suitable investigative techniques. Here we combine microfluidics and time-lapse auto-fluorescence microscopy to rapidly quantify antibiotic accumulation in hundreds of individual Escherichia coli cells. By serially manipulating the microfluidic environment, we demonstrated that stationary phase Escherichia coli, traditionally more refractory to antibiotics than growing cells, display reduced accumulation of the antibiotic ofloxacin compared to actively growing cells. Our novel microfluidic method facilitates the quantitative comparison of the role of the microenvironment versus that of the absence of key membrane transport pathways in cellular drug accumulation. Unlike traditional techniques, our assay is rapid, studying accumulation as the cells are dosed with the drug. This platform provides a powerful new tool for studying antibiotic accumulation in bacteria, which will be critical for the rational development of the next generation of antibiotics.
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Affiliation(s)
- Jehangir Cama
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
- Cavendish Laboratory
, Department of Physics
, University of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
| | - Margaritis Voliotis
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
| | - Jeremy Metz
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Ashley Smith
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Jari Iannucci
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Ulrich F. Keyser
- Cavendish Laboratory
, Department of Physics
, University of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
| | - Stefano Pagliara
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
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25
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Sabeti Azad M, Okuda M, Cyrenne M, Bourge M, Heck MP, Yoshizawa S, Fourmy D. Fluorescent Aminoglycoside Antibiotics and Methods for Accurately Monitoring Uptake by Bacteria. ACS Infect Dis 2020; 6:1008-1017. [PMID: 32195576 DOI: 10.1021/acsinfecdis.9b00421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Characterizing how multidrug-resistant bacteria circumvent the action of clinically used or novel antibiotics requires a detailed understanding of how the antibiotics interact with and cross bacterial membranes to accumulate in the cells and exert their action. When monitoring the interactions of drugs with bacteria, it remains challenging to differentiate functionally relevant internalized drug levels from nonspecific binding. Fluorescence is a method of choice for observing dynamics of biomolecules. In order to facilitate studies involving aminoglycoside antibiotics, we have generated fluorescently labeled aminoglycoside derivatives with uptake and bactericidal activities similar, albeit with a moderate loss, to those of the parent drug. The method combines fluorescence microscopy with fluorescence-activated cell sorting (FACS) using neomycin coupled to nonpermeable cyanine dyes. Fluorescence imaging allowed membrane-bound antibiotic to be distinguished from molecules in the cytoplasm. Patterns of uptake were assigned to different populations in the FACS analysis. Our study illustrates how fluorescent derivatives of an aminoglycoside enable a robust characterization of the three components of uptake: membrane binding, EDPI, and EDPII. Because EDPI levels are weak compared to the two other types of accumulation and critical for the action of these drugs, the three components of uptake must be taken into account separately when drawing conclusions about aminoglycoside function.
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Affiliation(s)
- Mahnaz Sabeti Azad
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maho Okuda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mélina Cyrenne
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mickael Bourge
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie-Pierre Heck
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et de Marquage, 91191 Gif-sur-Yvette, France
| | - Satoko Yoshizawa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Dominique Fourmy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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26
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Jamme F, Cinquin B, Gohon Y, Pereiro E, Réfrégiers M, Froissard M. Synchrotron multimodal imaging in a whole cell reveals lipid droplet core organization. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:772-778. [PMID: 32381780 PMCID: PMC7206545 DOI: 10.1107/s1600577520003847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
A lipid droplet (LD) core of a cell consists mainly of neutral lipids, triacylglycerols and/or steryl esters (SEs). The structuration of these lipids inside the core is still under debate. Lipid segregation inside LDs has been observed but is sometimes suggested to be an artefact of LD isolation and chemical fixation. LD imaging in their native state and in unaltered cellular environments appears essential to overcome these possible technical pitfalls. Here, imaging techniques for ultrastructural study of native LDs in cellulo are provided and it is shown that LDs are organized structures. Cryo soft X-ray tomography and deep-ultraviolet (DUV) transmittance imaging are showing a partitioning of SEs at the periphery of the LD core. Furthermore, DUV transmittance and tryptophan/tyrosine auto-fluorescence imaging on living cells are combined to obtain complementary information on cell chemical contents. This multimodal approach paves the way for a new label-free organelle imaging technique in living cells.
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Affiliation(s)
- Frédéric Jamme
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Bertrand Cinquin
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Yann Gohon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Eva Pereiro
- MISTRAL Beamline, ALBA Synchrotron, Cerdanyola del Vallès, Barcelona 08290, Spain
| | | | - Marine Froissard
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
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27
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Vergalli J, Atzori A, Pajovic J, Dumont E, Malloci G, Masi M, Vargiu AV, Winterhalter M, Réfrégiers M, Ruggerone P, Pagès JM. The challenge of intracellular antibiotic accumulation, a function of fluoroquinolone influx versus bacterial efflux. Commun Biol 2020; 3:198. [PMID: 32346058 PMCID: PMC7189378 DOI: 10.1038/s42003-020-0929-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/31/2020] [Indexed: 01/15/2023] Open
Abstract
With the spreading of antibiotic resistance, the translocation of antibiotics through bacterial envelopes is crucial for their antibacterial activity. In Gram-negative bacteria, the interplay between membrane permeability and drug efflux pumps must be investigated as a whole. Here, we quantified the intracellular accumulation of a series of fluoroquinolones in population and in individual cells of Escherichia coli according to the expression of the AcrB efflux transporter. Computational results supported the accumulation levels measured experimentally and highlighted how fluoroquinolones side chains interact with specific residues of the distal pocket of the AcrB tight monomer during recognition and binding steps.
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Affiliation(s)
- Julia Vergalli
- UMR_MD1, U-1261, Aix-Marseille University, INSERM, IRBA, MCT, Marseille, France
| | - Alessio Atzori
- Department of Physics, University of Cagliari, 09042, Monserrato, CA, Italy
| | - Jelena Pajovic
- DISCO beamline, Synchrotron Soleil, Saint-Aubin, France
- University of Belgrade, Faculty of Physics, 11001, Belgrade, Serbia
| | - Estelle Dumont
- UMR_MD1, U-1261, Aix-Marseille University, INSERM, IRBA, MCT, Marseille, France
- Institut National Supérieur d'Agronomie et de Biotechnologies (INSAB), Université des Sciences et Techniques de Masuku (USTM), BP941, Franceville, Gabon
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, 09042, Monserrato, CA, Italy
| | - Muriel Masi
- UMR_MD1, U-1261, Aix-Marseille University, INSERM, IRBA, MCT, Marseille, France
- Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris Saclay, CNRS, CEA, 91198, Gif-sur-Yvette, France
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719, Bremen, Germany
| | | | - Paolo Ruggerone
- Department of Physics, University of Cagliari, 09042, Monserrato, CA, Italy
| | - Jean-Marie Pagès
- UMR_MD1, U-1261, Aix-Marseille University, INSERM, IRBA, MCT, Marseille, France.
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Frei A, Amado M, Cooper MA, Blaskovich MAT. Light-Activated Rhenium Complexes with Dual Mode of Action against Bacteria. Chemistry 2020; 26:2852-2858. [PMID: 31788867 PMCID: PMC7687258 DOI: 10.1002/chem.201904689] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/12/2019] [Indexed: 12/20/2022]
Abstract
New antibiotics and innovative approaches to kill drug-resistant bacteria are urgently needed. Metal complexes offer access to alternative modes of action but have only sparingly been investigated in antibacterial drug discovery. We have developed a light-activated rhenium complex with activity against drug-resistant S. aureus and E. coli. The activity profile against mutant strains combined with assessments of cellular uptake and synergy suggest two distinct modes of action.
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Affiliation(s)
- Angelo Frei
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Maite Amado
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Matthew A. Cooper
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
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29
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Dumont E, Vergalli J, Conraux L, Taillier C, Vassort A, Pajovic J, Réfrégiers M, Mourez M, Pagès JM. Antibiotics and efflux: combined spectrofluorimetry and mass spectrometry to evaluate the involvement of concentration and efflux activity in antibiotic intracellular accumulation. J Antimicrob Chemother 2020; 74:58-65. [PMID: 30325444 DOI: 10.1093/jac/dky396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/04/2018] [Indexed: 11/14/2022] Open
Abstract
Background In Gram-negative bacteria, passing through the double membrane barrier to reach the inhibitory concentration inside the bacterium is a pivotal step for antibiotic activity. Spectrofluorimetry has been developed to follow fluoroquinolone accumulation inside bacteria using intrinsic bacterial fluorescence as an internal standard. However, adaptation for non-fluorescent antibiotics is needed; quantitative methods based on MS offer the possibility of expanding the detection range obtained by spectrofluorimetry. Objectives To validate, with spectrofluorimetry, the use of MS to measure antibiotic accumulation in cells and to determine the relationship between antibiotic concentrations and the amount of intrabacterial accumulation in different efflux backgrounds on the same batch of molecules. Methods Spectrofluorimetry was performed in parallel with MS on the same samples to measure the ciprofloxacin and fleroxacin accumulation in cells expressing various efflux pump levels. A microplate protocol was set up to determine the antibiotic accumulation as a function of external antibiotic concentrations. Results A correlation existed between the data obtained with spectrofluorimetry and MS, whatever the efflux pump or tested antibiotic. The results highlighted different dynamics of uptake between ciprofloxacin and fleroxacin as well as the relationship between the level of efflux activity and antibiotic accumulation. Conclusions We have developed a microplate protocol and cross-validated two complementary methods: spectrofluorimetry, which contains a reliable internal standard; and MS, which allows detection of low antibiotic amounts. These assays allow study of the dose effect and the efflux impact on the intrabacterial accumulation of antibiotics.
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Affiliation(s)
- Estelle Dumont
- UMR_MD1, Aix-Marseille Univ, U-1261 INSERM, SSA, IRBA, MCT, Marseille, France
| | - Julia Vergalli
- UMR_MD1, Aix-Marseille Univ, U-1261 INSERM, SSA, IRBA, MCT, Marseille, France
| | - Laurence Conraux
- Infectious Diseases Therapeutic Area, Sanofi R&D, Marcy l'Étoile, France
| | - Carine Taillier
- Infectious Diseases Therapeutic Area, Sanofi R&D, Marcy l'Étoile, France
| | - Aurélie Vassort
- Infectious Diseases Therapeutic Area, Sanofi R&D, Marcy l'Étoile, France
| | | | | | - Michael Mourez
- Infectious Diseases Therapeutic Area, Sanofi R&D, Marcy l'Étoile, France
| | - Jean-Marie Pagès
- UMR_MD1, Aix-Marseille Univ, U-1261 INSERM, SSA, IRBA, MCT, Marseille, France
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30
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Porins and small-molecule translocation across the outer membrane of Gram-negative bacteria. Nat Rev Microbiol 2019; 18:164-176. [DOI: 10.1038/s41579-019-0294-2] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
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Borselli D, Brunel JM, Gorgé O, Bolla JM. Polyamino-Isoprenyl Derivatives as Antibiotic Adjuvants and Motility Inhibitors for Bordetella bronchiseptica Porcine Pulmonary Infection Treatment. Front Microbiol 2019; 10:1771. [PMID: 31456758 PMCID: PMC6700233 DOI: 10.3389/fmicb.2019.01771] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/18/2019] [Indexed: 01/25/2023] Open
Abstract
The spreading of multidrug-resistant bacteria and the lack of novel antibiotic molecules leave clinicians and veterinarians with very limited options to treat bacterial infections, especially those caused by Gram-negative pathogens. To reduce the selection of antibiotic resistance mechanisms and their transfer to human pathogens, veterinary pharmaceutical companies have dramatically decreased the number of antibiotics used. Among all the investigated alternate solutions, chemosensitizers, which decrease the amount of the used drugs, appear to be one of the most promising strategies. In this study, we reported that polyamino-isoprenyl derivatives can potentiate florfenicol activity against veterinary sensitive reference strains as well as clinical isolates. These molecules induce inner membrane depolarization and subsequently inhibit efflux pumps by collapsing the proton-motive force (PMF). Considering that Bordetella bronchiseptica rotor flagellum is highly PMF dependent and that flagellar motility represents an important factor involved in colonization, we monitored the swimming and swarming motilities of bacteria and showed a strong inhibition in the presence of the lead selected compound. Taken together, our results suggest that this class of molecules are able to increase treatment efficacy and decrease drug consumption.
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Affiliation(s)
- Diane Borselli
- INSERM, SSA, IRBA, MCT, Aix-Marseille University, Marseille, France
| | | | - Olivier Gorgé
- INSERM, SSA, IRBA, MCT, Aix-Marseille University, Marseille, France
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32
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Breaching the Barrier: Quantifying Antibiotic Permeability across Gram-negative Bacterial Membranes. J Mol Biol 2019; 431:3531-3546. [DOI: 10.1016/j.jmb.2019.03.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/29/2019] [Accepted: 03/28/2019] [Indexed: 11/22/2022]
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33
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Enterobacter spp.: Update on Taxonomy, Clinical Aspects, and Emerging Antimicrobial Resistance. Clin Microbiol Rev 2019; 32:32/4/e00002-19. [PMID: 31315895 DOI: 10.1128/cmr.00002-19] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genus Enterobacter is a member of the ESKAPE group, which contains the major resistant bacterial pathogens. First described in 1960, this group member has proven to be more complex as a result of the exponential evolution of phenotypic and genotypic methods. Today, 22 species belong to the Enterobacter genus. These species are described in the environment and have been reported as opportunistic pathogens in plants, animals, and humans. The pathogenicity/virulence of this bacterium remains rather unclear due to the limited amount of work performed to date in this field. In contrast, its resistance against antibacterial agents has been extensively studied. In the face of antibiotic treatment, it is able to manage different mechanisms of resistance via various local and global regulator genes and the modulation of the expression of different proteins, including enzymes (β-lactamases, etc.) or membrane transporters, such as porins and efflux pumps. During various hospital outbreaks, the Enterobacter aerogenes and E. cloacae complex exhibited a multidrug-resistant phenotype, which has stimulated questions about the role of cascade regulation in the emergence of these well-adapted clones.
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34
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Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes. Nature 2019; 571:72-78. [PMID: 31217586 DOI: 10.1038/s41586-019-1315-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/21/2019] [Indexed: 01/07/2023]
Abstract
New antibiotics are needed to combat rising levels of resistance, with new Mycobacterium tuberculosis (Mtb) drugs having the highest priority. However, conventional whole-cell and biochemical antibiotic screens have failed. Here we develop a strategy termed PROSPECT (primary screening of strains to prioritize expanded chemistry and targets), in which we screen compounds against pools of strains depleted of essential bacterial targets. We engineered strains that target 474 essential Mtb genes and screened pools of 100-150 strains against activity-enriched and unbiased compound libraries, probing more than 8.5 million chemical-genetic interactions. Primary screens identified over tenfold more hits than screening wild-type Mtb alone, with chemical-genetic interactions providing immediate, direct target insights. We identified over 40 compounds that target DNA gyrase, the cell wall, tryptophan, folate biosynthesis and RNA polymerase, as well as inhibitors that target EfpA. Chemical optimization yielded EfpA inhibitors with potent wild-type activity, thus demonstrating the ability of PROSPECT to yield inhibitors against targets that would have eluded conventional drug discovery.
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Stone MRL, Masi M, Phetsang W, Pagès JM, Cooper MA, Blaskovich MAT. Fluoroquinolone-derived fluorescent probes for studies of bacterial penetration and efflux. MEDCHEMCOMM 2019; 10:901-906. [PMID: 31303987 PMCID: PMC6596217 DOI: 10.1039/c9md00124g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/16/2019] [Indexed: 12/21/2022]
Abstract
Fluorescent probes derived from the fluoroquinolone antibiotic ciprofloxacin were synthesised using a Cu(i)-catalysed azide–alkyne cycloaddition (CuAAC) to link a ciprofloxacin azide derivative with alkyne-substituted green and blue fluorophores.
Fluorescent probes derived from the fluoroquinolone antibiotic ciprofloxacin were synthesised using a Cu(i)-catalysed azide–alkyne cycloaddition (CuAAC) to link a ciprofloxacin azide derivative with alkyne-substituted green and blue fluorophores. The azide (2) and fluorophore (3 and 4) derivatives retained antimicrobial activity against Gram-positive and Gram-negative bacteria. The use of confocal fluorescent microscopy showed intracellular penetration, which was substantially enhanced in the presence of carbonyl cyanide 3-chlorophenylhydrazone as an efflux pump inhibitor in Escherichia coli.
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Affiliation(s)
- M Rhia L Stone
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Muriel Masi
- Membranes et Cibles Thérapeutiques , UMR_MD1 , Inserm U1261 , Aix-Marseille Univ & IRBA , Facultés de Médecine et de Pharmacie , 27 Bd Jean Moulin , 13005 Marseille , France
| | - Wanida Phetsang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Jean-Marie Pagès
- Membranes et Cibles Thérapeutiques , UMR_MD1 , Inserm U1261 , Aix-Marseille Univ & IRBA , Facultés de Médecine et de Pharmacie , 27 Bd Jean Moulin , 13005 Marseille , France
| | - Matthew A Cooper
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
| | - Mark A T Blaskovich
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia .
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Reversing resistance to counter antimicrobial resistance in the World Health Organisation's critical priority of most dangerous pathogens. Biosci Rep 2019; 39:BSR20180474. [PMID: 30910848 PMCID: PMC6465202 DOI: 10.1042/bsr20180474] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 02/07/2023] Open
Abstract
The speed at which bacteria develop antimicrobial resistance far outpace drug discovery and development efforts resulting in untreatable infections. The World Health Organisation recently released a list of pathogens in urgent need for the development of new antimicrobials. The organisms that are listed as the most critical priority are all Gram-negative bacteria resistant to the carbapenem class of antibiotics. Carbapenem resistance in these organisms is typified by intrinsic resistance due to the expression of antibiotic efflux pumps and the permeability barrier presented by the outer membrane, as well as by acquired resistance due to the acquisition of enzymes able to degrade β-lactam antibiotics. In this perspective article we argue the case for reversing resistance by targeting these resistance mechanisms – to increase our arsenal of available antibiotics and drastically reduce antibiotic discovery times – as the most effective way to combat antimicrobial resistance in these high priority pathogens.
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Abstract
The transport of small molecules across membranes is essential for the import of nutrients and other energy sources into the cell and, for the export of waste and other potentially harmful byproducts out of the cell. While hydrophobic molecules are permeable to membranes, ions and other small polar molecules require transport via specialized membrane transport proteins . The two major classes of membrane transport proteins are transporters and channels. With our focus here on porins-major class of non-specific diffusion channel proteins , we will highlight some recent structural biology reports and functional assays that have substantially contributed to our understanding of the mechanism that mediates uptake of small molecules, including antibiotics, across the outer membrane of Enterobacteriaceae . We will also review advances in the regulation of porin expression and porin biogenesis and discuss these pathways as new therapeutic targets.
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Affiliation(s)
- Muriel Masi
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | | | - Jean-Marie Pagès
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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38
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Dumont E, Vergalli J, Pajovic J, Bhamidimarri SP, Morante K, Wang J, Lubriks D, Suna E, Stavenger RA, Winterhalter M, Réfrégiers M, Pagès JM. Mechanistic aspects of maltotriose-conjugate translocation to the Gram-negative bacteria cytoplasm. Life Sci Alliance 2018; 2:e201800242. [PMID: 30620010 PMCID: PMC6311466 DOI: 10.26508/lsa.201800242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Small molecule accumulation in Gram-negative bacteria is a key challenge to discover novel antibiotics, because of their two membranes and efflux pumps expelling toxic molecules. An approach to overcome this challenge is to hijack uptake pathways so that bacterial transporters shuttle the antibiotic to the cytoplasm. Here, we have characterized maltodextrin-fluorophore conjugates that can pass through both the outer and inner membranes mediated by components of the Escherichia coli maltose regulon. Single-channel electrophysiology recording demonstrated that the compounds permeate across the LamB channel leading to accumulation in the periplasm. We have also demonstrated that a maltotriose conjugate distributes into both the periplasm and cytoplasm. In the cytoplasm, the molecule activates the maltose regulon and triggers the expression of maltose binding protein in the periplasmic space indicating that the complete maltose entry pathway is induced. This maltotriose conjugate can (i) reach the periplasmic and cytoplasmic compartments to significant internal concentrations and (ii) auto-induce its own entry pathway via the activation of the maltose regulon, representing an interesting prototype to deliver molecules to the cytoplasm of Gram-negative bacteria.
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Affiliation(s)
- Estelle Dumont
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Service de Santé des Armées, Institut de Recherche Biomédicale des Armées, Membranes et Cibles Thérapeutiques, Marseille, France
| | - Julia Vergalli
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Service de Santé des Armées, Institut de Recherche Biomédicale des Armées, Membranes et Cibles Thérapeutiques, Marseille, France
| | - Jelena Pajovic
- DISCO Beamline, Synchrotron Soleil, Saint-Aubin, France.,University of Belgrade, Faculty of Physics, Belgrade, Serbia
| | - Satya P Bhamidimarri
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Koldo Morante
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Jiajun Wang
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | | | - Edgars Suna
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert A Stavenger
- Antibacterial Discovery Performance Unit, Infectious Diseases Discovery, GlaxoSmithKline, Collegeville, PA, USA
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | | | - Jean-Marie Pagès
- Aix Marseille Univ, Institut National de la Santé et de la Recherche Médicale, Service de Santé des Armées, Institut de Recherche Biomédicale des Armées, Membranes et Cibles Thérapeutiques, Marseille, France
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