1
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Akshay SD, Deekshit VK, Mohan Raj J, Maiti B. Outer Membrane Proteins and Efflux Pumps Mediated Multi-Drug Resistance in Salmonella: Rising Threat to Antimicrobial Therapy. ACS Infect Dis 2023; 9:2072-2092. [PMID: 37910638 DOI: 10.1021/acsinfecdis.3c00408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Despite colossal achievements in antibiotic therapy in recent decades, drug-resistant pathogens have remained a leading cause of death and economic loss globally. One such WHO-critical group pathogen is Salmonella. The extensive and inappropriate treatments for Salmonella infections have led from multi-drug resistance (MDR) to extensive drug resistance (XDR). The synergy between efflux-mediated systems and outer membrane proteins (OMPs) may favor MDR in Salmonella. Differential expression of the efflux system and OMPs (influx) and positional mutations are the factors that can be correlated to the development of drug resistance. Insights into the mechanism of influx and efflux of antibiotics can aid in developing a structurally stable molecule that can be proficient at escaping from the resistance loops in Salmonella. Understanding the strategic responsibilities and developing policies to address the surge of drug resistance at the national, regional, and global levels are the needs of the hour. In this Review, we attempt to aggregate all the available research findings and delineate the resistance mechanisms by dissecting the involvement of OMPs and efflux systems. Integrating major OMPs and the efflux system's differential expression and positional mutation in Salmonella may provide insight into developing strategic therapies for one health application.
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Affiliation(s)
- Sadanand Dangari Akshay
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Bio & Nano Technology, Paneer Campus, Deralakatte, Mangalore-575018, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Infectious Diseases & Microbial Genomics, Paneer Campus, Deralakatte, Mangalore-575018, India
| | - Juliet Mohan Raj
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Infectious Diseases & Microbial Genomics, Paneer Campus, Deralakatte, Mangalore-575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research, Department of Bio & Nano Technology, Paneer Campus, Deralakatte, Mangalore-575018, India
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2
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Povinelli APR, de Carvalho Bertozo L, Zazeri G, Ximenes VF. A flaw in applying the FRET technique to evaluate the distance between ligands and tryptophan residues in human serum albumin: Proposal of correction. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 242:112693. [PMID: 36947916 DOI: 10.1016/j.jphotobiol.2023.112693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/23/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023]
Abstract
Due to its primordial function as a drug carrier, human serum albumin (HSA) is extensively studied regarding its binding affinity with developing drugs. Förster resonance energy transfer (FRET) is frequently applied as a spectroscopic molecular ruler to measure the distance between the binding site and the ligand. In this work, we have shown that most of the published results that use the FRET technique to estimate the distance from ligands to the binding sites do not corroborate the crystallography data. By comparing the binding affinity of dansyl-proline with HSA and ovotransferrin, we demonstrated that FRET explains the quenching provoked by the interaction of ligands in albumin. So, why does the distance calculation via FRET not corroborate the crystallography data? We have shown that this inconsistency is related to the fact that a one-to-one relationship between donor and acceptor is not present in most experiments. Hence, the quenching efficiency used for calculating energy transfer depends on distance and binding constant, which is inconsistent with the correct application of FRET as a molecular ruler. We have also shown that the indiscriminate attribution of 2/3 to the relative orientation of transition dipoles of the acceptor and donor (κ2) generates inconsistencies. We proposed corrections based on the experimental equilibrium constant and theoretical orientation of transition dipoles to correct the FRET results.
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Affiliation(s)
- Ana Paula Ribeiro Povinelli
- Federal Institute of Education, Science and Technology of Mato Grosso, Campo Novo do Parecis, 78360-000, MT, Brazil
| | - Luiza de Carvalho Bertozo
- Department of Chemistry, Faculty of Sciences, UNESP - São Paulo State University, 17033-360 Bauru, SP, Brazil
| | - Gabriel Zazeri
- Federal Institute of Education, Science and Technology of Mato Grosso, Campo Novo do Parecis, 78360-000, MT, Brazil
| | - Valdecir Farias Ximenes
- Department of Chemistry, Faculty of Sciences, UNESP - São Paulo State University, 17033-360 Bauru, SP, Brazil.
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3
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Ponmalar II, Swain J, Basu JK. Modification of bacterial cell membrane dynamics and morphology upon exposure to sub inhibitory concentrations of ciprofloxacin. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183935. [PMID: 35461827 DOI: 10.1016/j.bbamem.2022.183935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/13/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Ciprofloxacin (CPX), a second generation fluoroquinolone antibiotic, is used as a primary antibiotic for treatment against gastroenteritis, drug-resistant tuberculosis, and malignant otitis externa. CPX is a broad spectrum antibiotic that targets the DNA gyrase of both Gram-positive and Gram-negative bacteria. Irrational and improper usage of CPX results in emergence of CPX resistant organisms emphasizing the importance of using lethal doses of CPX. Here, we have systematically analysed the effect of CPX at sub lethal concentrations on live E. coli membrane and growth dynamics. As a result of CPX interaction at sub-lethal concentrations, we detected filamentation of the bacterial cells during cell division. Although CPX is a DNA targeting antibiotic and did not result in considerable increase of live E. coli cell surface roughness, we observed significant enhancement in the lipid diffusion coefficients possibly due to disrupted lipid packing or altered lipid composition. Interestingly, we seem to observe slightly higher extent of lipid diffusion alteration when bacterial inner membrane specific label FM4-64 was used in comparison to the non-specific membrane dye. Both these results are contrary to that observed in bacterial cells for colistin, a membrane targeting antibiotics. Our work highlights the need for using multiple, complementary surface and depth sensitive techniques to obtain information on the realistic nature of bacterial cell membrane remodelling due to non-membrane targeting antibiotics. Our work could have implications for identification of potential biomembrane markers at sub-lethal concentrations even for antibiotics which are non-membrane targeting that could help in unravelling pathways for emergence of antimicrobial resistance.
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Affiliation(s)
- Ilanila Ilangumaran Ponmalar
- Center for Biosystems Science and Engineering, Indian Institute of Science, C.V. Raman Avenue, Bengaluru, 560012, Karnataka, India
| | - Jitendriya Swain
- Department of Physics, Indian Institute of Science, C.V. Raman Avenue, Bengaluru, 560012, Karnataka, India
| | - Jaydeep K Basu
- Department of Physics, Indian Institute of Science, C.V. Raman Avenue, Bengaluru, 560012, Karnataka, India.
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4
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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 PMCID: PMC11468809 DOI: 10.1002/adhm.202101180] [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: 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 ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
| | - Mohamed A. M. Kamal
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Marcus Koch
- INM – Leibniz Institute for New MaterialsCampus D2.2Saarbrücken66123Germany
| | - Bart‐Jan Niebuur
- INM – Leibniz Institute for New MaterialsCampus D2.2Saarbrücken66123Germany
| | - Anna‐Lena Huber
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Adriely Goes
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Carsten Volz
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
| | - Julia Vergalli
- UMR_MD1U‐1261Aix‐Marseille UniversitéINSERMIRBAMCTFaculté de Pharmacie27 Boulevard Jean MoulinMarseille13005France
| | - Tobias Kraus
- INM – Leibniz Institute for New MaterialsCampus D2.2Saarbrücken66123Germany
- Colloid and Interface ChemistrySaarland UniversityCampus D2.2Saarbrücken66123Germany
| | - Rolf Müller
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Nicole Schneider‐Daum
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
| | - Gregor Fuhrmann
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
| | - Jean‐Marie Pagès
- UMR_MD1U‐1261Aix‐Marseille UniversitéINSERMIRBAMCTFaculté de Pharmacie27 Boulevard Jean MoulinMarseille13005France
| | - Claus‐Michael Lehr
- Helmholtz Centre for Infection ResearchHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.1Saarbrücken66123Germany
- Saarland UniversityDepartment of PharmacyCampus E8.1Saarbrücken66123Germany
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5
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Ferreira M, Gameiro P. Fluoroquinolone-Transition Metal Complexes: A Strategy to Overcome Bacterial Resistance. Microorganisms 2021; 9:microorganisms9071506. [PMID: 34361943 PMCID: PMC8303200 DOI: 10.3390/microorganisms9071506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 01/12/2023] Open
Abstract
Fluoroquinolones (FQs) are antibiotics widely used in the clinical practice due to their large spectrum of action against Gram-negative and some Gram-positive bacteria. Nevertheless, the misuse and overuse of these antibiotics has triggered the development of bacterial resistance mechanisms. One of the strategies to circumvent this problem is the complexation of FQs with transition metal ions, known as metalloantibiotics, which can promote different activity and enhanced pharmacological behaviour. Here, we discuss the stability of FQ metalloantibiotics and their possible translocation pathways. The main goal of the present review is to frame the present knowledge on the conjunction of biophysical and biological tools that can help to unravel the antibacterial action of FQ metalloantibiotics. An additional goal is to shed light on the studies that must be accomplished to ensure stability and viability of such metalloantibiotics. Potentiometric, spectroscopic, microscopic, microbiological, and computational techniques are surveyed. Stability and partition constants, interaction with membrane porins and elucidation of their role in the influx, determination of the antimicrobial activity against multidrug-resistant (MDR) clinical isolates, elucidation of the mechanism of action, and toxicity assays are described for FQ metalloantibiotics.
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6
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Warraich AA, Mohammed AUR, Gibson H, Hussain M, Rahman AS. Acidic amino acids as counterions of ciprofloxacin: Effect on growth and pigment production in Staphylococcus aureus NCTC 8325 and Pseudomonas aeruginosa PAO1. PLoS One 2021; 16:e0250705. [PMID: 33914790 PMCID: PMC8084218 DOI: 10.1371/journal.pone.0250705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 04/13/2021] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial resistance (AMR) is emerging as a global threat to public health. One of the strategies employed to combat AMR is the use of adjuvants which act to enhance or reinstate antimicrobial activity by inhibiting resistance mechanisms. However, these adjuvants are themselves not immune to selecting resistant phenotypes. Thus, there is a need to utilise mechanisms which are either less likely to or unable to trigger resistance. One commonly employed mechanism of resistance by microorganisms is to prevent antimicrobial uptake or efflux the antibiotic which manages to permeate its membrane. Here we propose amino acids as antimicrobial adjuvants that may be utilizing alternate mechanisms to fight AMR. We used a modified ethidium bromide (EtBr) efflux assay to determine its efflux in the presence of ciprofloxacin within Staphylococcus aureus (NCTC 8325) and Pseudomonas aeruginosa (PAO1). In this study, aspartic acid and glutamic acid were found to inhibit growth of both bacterial species. Moreover, a reduced production of toxic pigments, pyocyanin and pyoverdine by P. aeruginosa was also observed. As evident from similar findings with tetracycline, these adjuvants, may be a way forward towards tackling antimicrobial resistance.
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Affiliation(s)
- Annsar Ahmad Warraich
- Aston Pharmacy School, Aston University, Birmingham, United Kingdom
- School of Pharmacy, University of Wolverhampton, Wolverhampton, United Kingdom
| | | | - Hazel Gibson
- School of Pharmacy, University of Wolverhampton, Wolverhampton, United Kingdom
| | | | - Ayesha Sabah Rahman
- School of Pharmacy, University of Wolverhampton, Wolverhampton, United Kingdom
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7
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Ferreira M, Sousa CF, Gameiro P. Fluoroquinolone Metalloantibiotics to Bypass Antimicrobial Resistance Mechanisms: Decreased Permeation through Porins. MEMBRANES 2020; 11:membranes11010003. [PMID: 33375018 PMCID: PMC7822003 DOI: 10.3390/membranes11010003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022]
Abstract
Fluoroquinolones (FQs) are broad-spectrum antibiotics largely used in the clinical practice against Gram-negative and some Gram-positive bacteria. Nevertheless, bacteria have developed several antimicrobial resistance mechanisms against such class of antibiotics. Ternary complexes of FQs, copper(II) and phenanthroline, known as metalloantibiotics, arise in an attempt to counteract an antibiotic resistance mechanism related to low membrane permeability. These metalloantibiotics seem to use an alternative influx route, independent of porins. The translocation pathways of five FQs and its metalloantibiotics were studied through biophysical experiments, allowing us to infer about the role of OmpF porin in the influx. The FQ-OmpF interaction was assessed in mimetic membrane systems differing on the lipidic composition, disclosing no interference of the lipidic composition. The drug-porin interaction revealed similar values for the association constants of FQs and metalloantibiotics with native OmpF. Therefore, OmpF mutants and specific quenchers were used to study the location-association relationship, comparing a free FQ and its metalloantibiotic. The free FQ revealed a specific association, with preference for residues on the centre of OmpF, while the metalloantibiotic showed a random interaction. Thereby, metalloantibiotics may be an alternative to pure FQs, being able to overcome some antimicrobial resistance mechanism of Gram-negative bacteria related to decreased membrane permeability.
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8
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Ipte PR, Satpati AK. Probing the interaction of ciprofloxacin and E. coli by electrochemistry, spectroscopy and atomic force microscopy. Biophys Chem 2020; 266:106456. [PMID: 32835912 DOI: 10.1016/j.bpc.2020.106456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022]
Abstract
Under the present investigation, effect of ciprofloxacin (CIP) on Escherichia coli has been investigated using electrochemical, spectroscopic and atomic force microscope (AFM) measurements. Investigation reveals the interaction pattern of CIP with E. coli. The CIP essentially interacts with the outer membrane protein F (OmpF), the formation constant of the complex forms between CIP and the OmpF active sites over E. coli is obtained as log Kf of 12.1. Spectroscopic measurements are carried out, which supports the electrochemical measurements on the interaction between CIP and E. coli, at a higher concentration, CIP induces lysis of the E. coli cell membrane. Spectroscopic investigations further reveals that the FeS containing proteins present inside the E. coli cells released out through the ruptured cell membrane of E. coli. Different degrees of detrimental effects on E. coli has been observed when exposed to different concentrations of the drugs. The microscopic images obtained from the AFM scans of E. coli in presence of CIP shows deformation of the E. coli cell wall and its rupture with increasing concentrations of CIP.
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Affiliation(s)
- Priyanka R Ipte
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Ashis Kumar Satpati
- Analytical Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India.
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9
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Jaglińska K, Polak B, Klimek-Turek A, Pomastowski P, Buszewski B, Dzido TH. Retardation of some drugs in thin-layer chromatographic systems with impregnated silica gel plates with hen's egg white and bovine serum albumin. J Chromatogr A 2020; 1625:461277. [PMID: 32709329 DOI: 10.1016/j.chroma.2020.461277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 10/24/2022]
Abstract
The influence of impregnation the chromatographic plate adsorbent layer, silica, with hen's egg white albumin (OVA) or bovine serum albumin (BSA) on the retention of some popular medicines (paracetamol, aminophenazone, theophylline, caffeine, acetanilide, ciprofloxacin, tramadol, acetylsalicylic acid, acebutolol) is investigated. The effect of composition and buffer pH of the mobile phase on solute separation selectivity is also studied. The chromatographic systems with and without above mentioned albumins and their influence on investigated drug retention are compared. In general, it has been turned out that retention of tested medicines in systems with the sorbent impregnated with albumin significantly increase relative to those with non-impregnated.
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Affiliation(s)
- Kamila Jaglińska
- Physical Chemistry Department. Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland.
| | - Beata Polak
- Physical Chemistry Department. Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
| | - Anna Klimek-Turek
- Physical Chemistry Department. Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
| | - Paweł Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies. Nicolaus Copernicus University in Torun, 4 Wileńska Street, 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland; Centre for Modern Interdisciplinary Technologies. Nicolaus Copernicus University in Torun, 4 Wileńska Street, 87-100 Toruń, Poland
| | - Tadeusz H Dzido
- Physical Chemistry Department. Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland
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10
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Synergistic Antibacterial Effect of the Magnesium-Doped ZnO Nanoparticles with Chloramphenicol. BIONANOSCIENCE 2019. [DOI: 10.1007/s12668-019-00696-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Jelinkova P, Mazumdar A, Sur VP, Kociova S, Dolezelikova K, Jimenez AMJ, Koudelkova Z, Mishra PK, Smerkova K, Heger Z, Vaculovicova M, Moulick A, Adam V. Nanoparticle-drug conjugates treating bacterial infections. J Control Release 2019; 307:166-185. [DOI: 10.1016/j.jconrel.2019.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
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12
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Ramadurai S, Sarangi NK, Maher S, MacConnell N, Bond AM, McDaid D, Flynn D, Keyes TE. Microcavity-Supported Lipid Bilayers; Evaluation of Drug-Lipid Membrane Interactions by Electrochemical Impedance and Fluorescence Correlation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8095-8109. [PMID: 31120755 DOI: 10.1021/acs.langmuir.9b01028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Many drugs have intracellular or membrane-associated targets, thus understanding their interaction with the cell membrane is of value in drug development. Cell-free tools used to predict membrane interactions should replicate the molecular organization of the membrane. Microcavity array-supported lipid bilayer (MSLB) platforms are versatile biophysical models of the cell membrane that combine liposome-like membrane fluidity with stability and addressability. We used an MSLB herein to interrogate drug-membrane interactions across seven drugs from different classes, including nonsteroidal anti-inflammatories: ibuprofen (Ibu) and diclofenac (Dic); antibiotics: rifampicin (Rif), levofloxacin (Levo), and pefloxacin (Pef); and bisphosphonates: alendronate (Ale) and clodronate (Clo). Fluorescence lifetime correlation spectroscopy (FLCS) and electrochemical impedance spectroscopy (EIS) were used to evaluate the impact of drug on 1,2-dioleyl- sn-glycerophosphocholine and binary bilayers over physiologically relevant drug concentrations. Although FLCS data revealed Ibu, Levo, Pef, Ale, and Clo had no impact on lipid lateral mobility, EIS, which is more sensitive to membrane structural change, indicated modest but significant decreases to membrane resistivity consistent with adsorption but weak penetration of drugs at the membrane. Ale and Clo, evaluated at pH 5.25, did not impact the impedance of the membrane except at concentrations exceeding 4 mM. Conversely, Dic and Rif dramatically altered bilayer fluidity, suggesting their translocation through the bilayer, and EIS data showed that resistivity of the membrane decreased substantially with increasing drug concentration. Capacitance changes to the bilayer in most cases were insignificant. Using a Langmuir-Freundlich model to fit the EIS data, we propose Rsat as an empirical value that reflects permeation. Overall, the data indicate that Ibu, Levo, and Pef adsorb at the interface of the lipid membrane but Dic and Rif interact strongly, permeating the membrane core modifying the water/ion permeability of the bilayer structure. These observations are discussed in the context of previously reported data on drug permeability and log P.
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Affiliation(s)
- Sivaramakrishnan Ramadurai
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Nirod Kumar Sarangi
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Sean Maher
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Nicola MacConnell
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Alan M Bond
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
| | | | | | - Tia E Keyes
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
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13
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Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Savitski MM, Bork P, Göttig S, Typas A. Species-specific activity of antibacterial drug combinations. Nature 2018; 559:259-263. [PMID: 29973719 DOI: 10.1038/s41586-018-0278-9] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/24/2018] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance has become a serious public health concern, making once-treatable diseases deadly again and undermining the achievements of modern medicine1,2. Drug combinations can help to fight multi-drug-resistant bacterial infections, yet they are largely unexplored and rarely used in clinics. Here we profile almost 3,000 dose-resolved combinations of antibiotics, human-targeted drugs and food additives in six strains from three Gram-negative pathogens-Escherichia coli, Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa-to identify general principles for antibacterial drug combinations and understand their potential. Despite the phylogenetic relatedness of the three species, more than 70% of the drug-drug interactions that we detected are species-specific and 20% display strain specificity, revealing a large potential for narrow-spectrum therapies. Overall, antagonisms are more common than synergies and occur almost exclusively between drugs that target different cellular processes, whereas synergies are more conserved and are enriched in drugs that target the same process. We provide mechanistic insights into this dichotomy and further dissect the interactions of the food additive vanillin. Finally, we demonstrate that several synergies are effective against multi-drug-resistant clinical isolates in vitro and during infections of the larvae of the greater wax moth Galleria mellonella, with one reverting resistance to the last-resort antibiotic colistin.
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Affiliation(s)
- Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Anja Telzerow
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jacob Bobonis
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Emily Huth
- Institute of Medical Microbiology and Infection Control, Hospital of Goethe University, Frankfurt am Main, Germany
| | - Stefan Bassler
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jordi Zamarreño Beas
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Matylda Zietek
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Natalie Ng
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sunniva Foerster
- Institute of Social & Preventive Medicine, Institute of Infectious Diseases, University of Bern, Bern, Switzerland
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France
| | - Frédéric Barras
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS UMR 7283, Aix-Marseille Université, Marseille, France.,Institut Pasteur, Paris, France
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural & Computational Biology Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Stephan Göttig
- Institute of Medical Microbiology and Infection Control, Hospital of Goethe University, Frankfurt am Main, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,European Molecular Biology Laboratory, Structural & Computational Biology Unit, Heidelberg, Germany.
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14
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The Global Regulatory Cyclic AMP Receptor Protein (CRP) Controls Multifactorial Fluoroquinolone Susceptibility in Salmonella enterica Serovar Typhimurium. Antimicrob Agents Chemother 2017; 61:AAC.01666-17. [PMID: 28874380 DOI: 10.1128/aac.01666-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 08/30/2017] [Indexed: 12/29/2022] Open
Abstract
Fluoroquinolone antibiotics are prescribed for the treatment of Salmonella enterica infections, but resistance to this family of antibiotics is growing. Here we report that loss of the global regulatory protein cyclic AMP (cAMP) receptor protein (CRP) or its allosteric effector, cAMP, reduces susceptibility to fluoroquinolones. A Δcrp mutation was synergistic with the primary fluoroquinolone resistance allele gyrA83, thus able to contribute to clinically relevant resistance. Decreased susceptibility to fluoroquinolones could be partly explained by decreased expression of the outer membrane porin genes ompA and ompF with a concomitant increase in the expression of the ciprofloxacin resistance efflux pump gene acrB in Δcrp cells. Expression of gyrAB, which encode the DNA supercoiling enzyme GyrAB, which is blocked by fluoroquinolones, and expression of topA, which encodes the dominant supercoiling-relaxing enzyme topoisomerase I, were unchanged in Δcrp cells. Yet Δcrp cells maintained a more relaxed state of DNA supercoiling, correlating with an observed increase in topoisomerase IV (parCE) expression. Surprisingly, the Δcrp mutation had the unanticipated effect of enhancing fitness in the presence of fluoroquinolone antibiotics, which can be explained by the observation that exposure of Δcrp cells to ciprofloxacin had the counterintuitive effect of restoring wild-type levels of DNA supercoiling. Consistent with this, Δcrp cells did not become elongated or induce the SOS response when challenged with ciprofloxacin. These findings implicate the combined action of multiple drug resistance mechanisms in Δcrp cells: reduced permeability and elevated efflux of fluoroquinolones coupled with a relaxed DNA supercoiling state that buffers cells against GyrAB inhibition by fluoroquinolones.
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15
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Qin P, Pan X, Liu R, Qiu J, Fang X. Experimental and computational characterization on the binding of two fluoroquinolones to bovine hemoglobin. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2647] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/17/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Pengfei Qin
- College of Resources and Environment, Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection; Linyi University; Linyi China
| | - Xingren Pan
- School of Physics and Electronic Engineering; Linyi University; Linyi China
| | - Rutao Liu
- School of Environmental Science and Engineering; Shandong University; Jinan China
| | - Jicai Qiu
- College of Resources and Environment, Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection; Linyi University; Linyi China
| | - Xiaoyan Fang
- Linyi Agricultural Environmental Protection and Monitoring Station; Linyi China
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16
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Talukdar S, Bayan U, Saikia KK. In silico identification of vaccine candidates against Klebsiella oxytoca. Comput Biol Chem 2017; 69:48-54. [PMID: 28570984 DOI: 10.1016/j.compbiolchem.2017.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 05/06/2017] [Accepted: 05/20/2017] [Indexed: 01/10/2023]
Abstract
Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria. Subcellular localization of the protein sequences taken from the selected 36 pathways were predicted using PSORTb v3.0.2 and CELLO v2.5. Prediction of B cell epitope and the probability of the antigenicity were evaluated by using IEDB and Vaxijen respectively. BLASTp was done to find out the similarity of the selected proteins with the human proteome. Proteins failing to comply with the set parameters were filtered at each step. Finally, we identified 6 surface exposed proteins as potential vaccine candidates against Klebsiella oxytoca.
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Affiliation(s)
- Sandipan Talukdar
- Dept of Bioengineering & Technology, GUIST, Gauhati University, India
| | - Udeshna Bayan
- Dept of Bioengineering & Technology, GUIST, Gauhati University, India
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17
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Pan X, Qin P, Liu R, Li J, Zhang F. Molecular mechanism on two fluoroquinolones inducing oxidative stress: evidence from copper/zinc superoxide dismutase. RSC Adv 2016. [DOI: 10.1039/c6ra19454k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The combination of molecular and cellular analysis suggested that the structural and functional alterations of Cu/Zn-SOD were closely associated with increased risk of oxidative stress initiated by both CPFX and ENFX.
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Affiliation(s)
- Xingren Pan
- School of Science
- Linyi University
- Linyi
- P. R. China
| | - Pengfei Qin
- College of Resources and Environment
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection
- Linyi University
- Linyi
- P. R. China
| | - Rutao Liu
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- P. R. China
| | - Jianfeng Li
- College of Resources and Environment
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection
- Linyi University
- Linyi
- P. R. China
| | - Fucui Zhang
- Maternal and Child Care Service Centre of Junan
- Junan
- P. R. China
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18
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Suárez-Germà C, Hernández-Borrell J, Prieto M, Loura LMS. Modeling FRET to investigate the selectivity of lactose permease ofEscherichia colifor lipids. Mol Membr Biol 2014; 31:120-30. [DOI: 10.3109/09687688.2014.915351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Improved detection of antibiotic compounds by bacterial reporter strains achieved by manipulations of membrane permeability and efflux capacity. Appl Microbiol Biotechnol 2013; 98:2267-77. [PMID: 23963273 DOI: 10.1007/s00253-013-5176-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/20/2013] [Accepted: 08/02/2013] [Indexed: 10/26/2022]
Abstract
The occurrence of pharmaceuticals, including antibacterial compounds, in the environment has been acknowledged as an emerging and troubling issue in environmental safety; their usage is constantly on the rise, and their effects on the environment are only partially understood. Such compounds can accumulate, contaminate the ecosystem, and contribute to the spreading of antibiotic resistance among bacteria, hindering human health. Bioluminescent Escherichia coli reporter strains, engineered to detect antibiotic compounds by fusing the promoter of the global regulator soxS to the Photorhabdus luminescens luxCDABE cassette, were further modified by altering their membrane permeability and efflux capabilities. This was accomplished by introducing several mutations in the efflux system (ΔemrE, ΔacrB, and ΔtolC) and by overexpressing OmpF, a porin located in the outer membrane that allows passive diffusion of molecules. Combinations of these alterations had a cumulative effect in lowering the detection threshold of several antibiotics, in some of the cases to concentrations reported from pharmaceutical-polluted environments.
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20
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Qin P, Liu R. Oxidative stress response of two fluoroquinolones with catalase and erythrocytes: a combined molecular and cellular study. JOURNAL OF HAZARDOUS MATERIALS 2013; 252-253:321-9. [PMID: 23542600 DOI: 10.1016/j.jhazmat.2013.03.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/19/2013] [Accepted: 03/03/2013] [Indexed: 05/24/2023]
Abstract
Ciprofloxacin (CPFX) and enrofloxacin (ENFX), two representatives of fluoroquinolones (FQs), pose potential threats to health for their wide exposures in environment. The aim of the study is to characterize the harmful effects of oxidative stress induced by CPFX and ENFX from the structure and function of catalase (CAT), a vital enzyme involved in protection against oxidative damage. The cellular tests firstly confirmed an enhanced oxidative stress in FQs treated erythrocytes from the depletion of GSH contents and decrease of CAT activity. Besides, CPFX posed more of an oxidative threat than ENFX. During the spectroscopic and computational investigations, both FQs could bind into its central cavity with only one binding site and interact with Arg 65, Arg 362 and His 363 mainly through electrostatic forces. Furthermore, the binding of two FQs not only caused the conformational and micro-environmental changes of CAT, but also inhibited its molecular activity, consistent with the cellular activity measurements. All these results suggested that the structural and functional changes of CAT were closely associated with increased risk of oxidative stress induced by both FQs. The established methods in this work can help to comprehensively understanding the oxidative stress-induced cellular damage of other pollutants via antioxidant effects.
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Affiliation(s)
- Pengfei Qin
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, PR China
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21
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Mechanisms of ceftazidime and ciprofloxacin transport through porins in multidrug-resistance developed by extended-spectrum beta-lactamase E.coli strains. J Fluoresc 2011; 21:1421-9. [PMID: 21234661 DOI: 10.1007/s10895-010-0826-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 12/29/2010] [Indexed: 10/18/2022]
Abstract
Resistance towards antibiotics stands out today as a major issue in the clinical act of treatment of bacterial-generated infections. This process was characterized in proteoliposomes reconstituted from an E.coli strain isolated from invasive infections (blood culture) occurred in patients with a cardio-vascular device admitted for surgery. Fluorescence spectroscopy and patch-clamp technique have been used. Two types of antibiotics have been targeted: ceftazidime and ciprofloxacin. Antibiotics addition in proteoliposomes suspension undergoes a quenching in tryptophan residues from outer membrane porins structure, probably due to the formation of a transient non-fluorescent porin-antibiotic complex. Patch-clamp recordings revealed strong ion current blockages for both antibiotics, reflecting antibiotic-channel interactions but with varying strength of interaction. The present study puts forward the mechanism of multidrug-resistance in extended-spectrum beta-lactamase E.coli strains, as being caused by alterations of the antibiotics transport across the porins of the outer bacterial membrane.
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22
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Banoee M, Seif S, Nazari ZE, Jafari-Fesharaki P, Shahverdi HR, Moballegh A, Moghaddam KM, Shahverdi AR. ZnO nanoparticles enhanced antibacterial activity of ciprofloxacin against Staphylococcus aureus and Escherichia coli. J Biomed Mater Res B Appl Biomater 2010; 93:557-61. [PMID: 20225250 DOI: 10.1002/jbm.b.31615] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nanoparticle metal oxides offer a wide variety of potential applications in medicine due to the unprecedented advances in nanobiotechnology research. In this work, the effect of zinc oxide (ZnO) nanoparticles prepared by mechano-chemical method on the antibacterial activity of different antibiotics was evaluated using disk diffusion method against Staphylococcus aureus and Escherichia coli. The average size of ZnO nanoparticles was between 20 nm and 45 nm. Although ZnO nanoparticles (500 microg/disk) decreased the antibacterial activity of amoxicillin, penicillin G, and nitrofurantoin in S. aureus, the antibacterial activity of ciprofloxacin increased in the presence of ZnO nanoparticles in both test strains. A total of 27% and 22% increase in inhibition zone areas was observed for ciprofloxacin in the presence of ZnO nanoparticles in S. aureus and E. coli, respectively. The enhancing effect of this nanomaterial on the antibacterial activity of ciprofloxacin was further investigated at three different contents (500, 1000, and 2000 microg/disk) against various clinical isolates of S. aureus and E. coli The enhancing effect of ZnO nanoparticles on the antibacterial activity of ciprofloxacin was concentration-dependent against all test strains. The most enhancing activities were observed in the contents of the 2000 microg/disk.
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Affiliation(s)
- Maryam Banoee
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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23
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Ho MY, Chiou ML, Chang RC, Chen YH, Cheng CC. Outer membrane protein OmpF involved in the transportation of polypyridyl ruthenium complexes into Escherichia coli. J Inorg Biochem 2010; 104:614-7. [DOI: 10.1016/j.jinorgbio.2010.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 01/28/2010] [Accepted: 01/28/2010] [Indexed: 10/19/2022]
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24
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Loura LMS, Prieto M, Fernandes F. Quantification of protein-lipid selectivity using FRET. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2010; 39:565-78. [PMID: 20238256 PMCID: PMC2841278 DOI: 10.1007/s00249-009-0532-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 07/30/2009] [Accepted: 08/04/2009] [Indexed: 12/11/2022]
Abstract
Membrane proteins exhibit different affinities for different lipid species, and protein-lipid selectivity regulates the membrane composition in close proximity to the protein, playing an important role in the formation of nanoscale membrane heterogeneities. The sensitivity of Förster resonance energy transfer (FRET) for distances of 10 A up to 100 A is particularly useful to retrieve information on the relative distribution of proteins and lipids in the range over which protein-lipid selectivity is expected to influence membrane composition. Several FRET-based methods applied to the quantification of protein-lipid selectivity are described herein, and different formalisms applied to the analysis of FRET data for particular geometries of donor-acceptor distribution are critically assessed.
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Affiliation(s)
- Luís M. S. Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Centro de Química de Évora, Rua Romão Ramalho, 59, 7000-671 Evora, Portugal
| | - Manuel Prieto
- Centro de Química Física Molecular and Institute of Nanosciences and Nanotechnologies, Complexo I, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Fábio Fernandes
- Department of Membrane Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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25
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Pezeshki S, Chimerel C, Bessonov AN, Winterhalter M, Kleinekathöfer U. Understanding ion conductance on a molecular level: an all-atom modeling of the bacterial porin OmpF. Biophys J 2009; 97:1898-906. [PMID: 19804720 PMCID: PMC2756365 DOI: 10.1016/j.bpj.2009.07.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 07/08/2009] [Accepted: 07/14/2009] [Indexed: 10/20/2022] Open
Abstract
All-atom molecular dynamics simulations of the ion current through OmpF, the major porin in the outer membrane of Escherichia coli, were performed. Starting from the crystal structure, the all-atom modeling allows us to calculate a parameter-free ion conductance in semiquantitative agreement with experiment. Discrepancies between modeling and experiment occur, e.g., at salt concentrations above 1 M KCl or at high temperatures. At lower salt concentrations, the ions have separate pathways along the channel surface. The constriction zone in the channel contains, on one side, a series of positively charges (R42, R82, R132), and on the opposite side, two negatively charged residues (D113, E117). Mutations generated in the constriction zone by removing cationic residues enhance the otherwise small cation selectivity, whereas removing the anionic residues reverses the selectivity. Reduction of the negatively charged residues decreases the conductance by half, whereas cationic residues enhance the conductance. Experiments on mutants confirm the results of the molecular-level simulations.
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26
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Neves P, Sousa I, Winterhalter M, Gameiro P. Fluorescence quenching as a tool to investigate quinolone antibiotic interactions with bacterial protein OmpF. J Membr Biol 2009; 227:133-40. [PMID: 19148694 DOI: 10.1007/s00232-008-9152-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
Abstract
The outer membrane porin OmpF is an important protein for the uptake of antibiotics through the outer membrane of gram-negative bacteria; however, the possible binding sites involved in this uptake are still not recognized. Determination, at the molecular level, of the possible sites of antibiotic interaction is very important, not only to understand their mechanism of action but also to unravel bacterial resistance. Due to the intrinsic OmpF fluorescence, attributed mainly to its tryptophans (Trp(214), Trp(61)), quenching experiments were used to assess the site(s) of interaction of some quinolone antibiotics. OmpF was reconstituted in different organized structures, and the fluorescence quenching results, in the presence of two quenching agents, acrylamide and iodide, certified that acrylamide quenches Trp(61) and iodide Trp(214). Similar data, obtained in presence of the quinolones, revealed distinct behaviors for these antibiotics, with nalidixic acid interacting near Trp(214) and moxifloxacin near Trp(61). These studies, based on straightforward and quick procedures, show the existence of conformational changes in the protein in order to adapt to the different organized structures and to interact with the quinolones. The extent of reorganization of the protein in the presence of the different quinolones allowed an estimate on the sites of protein/quinolone interaction.
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27
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Synthesis of citrate-ciprofloxacin conjugates. Bioorg Med Chem Lett 2009; 19:1496-8. [PMID: 19179071 DOI: 10.1016/j.bmcl.2009.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/06/2009] [Accepted: 01/06/2009] [Indexed: 11/22/2022]
Abstract
Two regioisomeric citrate-functionalized ciprofloxacin conjugates have been synthesized and their antimicrobial activities against a panel of clinically-relevant bacteria have been determined. Cellular uptake mechanisms were investigated using wild-type and ompF deletion strains of Escherichia coli K-12.
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