1
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Ghai I. Electrophysiological Insights into Antibiotic Translocation and Resistance: The Impact of Outer Membrane Proteins. MEMBRANES 2024; 14:161. [PMID: 39057669 PMCID: PMC11279362 DOI: 10.3390/membranes14070161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/14/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
The alarming rise of antibiotic resistance in Gram-negative bacteria has emerged as a major global health challenge. A key factor contributing to this crisis is the low permeability of the bacterial outer membrane, which acts as a barrier that prevents antibiotics from entering the cell. Protein channels embedded in this outer membrane selectively regulate the influx of hydrophilic compounds, including antibiotics. To combat antibiotic resistance, understanding the molecular mechanisms governing antibiotic permeability through bacterial membrane channels is crucial. This knowledge is key towards elucidating their roles in studing antibiotic resistance. By compiling and analysing the flux data from multiple electrophysiological reversal potential experimental studies, which involves measuring zero-current potentials and the corresponding single-channel conductance, we can calculate the flux of charged antibiotics/compounds across different Gram-negative bacterial outer membrane channels. Through this comprehensive synthesis, this review aims to advance our understanding and stimulate discussions about the physicochemical factors influencing the flux of antibiotics through bacterial membrane protein channels, ultimately enhancing our knowledge in this area.
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Affiliation(s)
- Ishan Ghai
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
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2
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Ceccarelli M, Milenkovic S, Bodrenko IV. The Effect of Lipopolysaccharides on the Electrostatic Properties of Gram-Negative General Porins from Enterobacteriaceae. Chemphyschem 2024; 25:e202400147. [PMID: 38625051 DOI: 10.1002/cphc.202400147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
We investigated, by using all-atom molecular dynamics simulations, the effect of the outer membrane of Gram-negative bacteria, composed in the outer leaflet by polar/charged lipopolysaccharides (LPS), on the electrostatic properties of general porins from the Enterobacteriaceae family. General porins constitute the main path for the facilitated diffusion of polar antibiotics through the outer membrane. As model system we selected OmpK36 from Klebsiella pneumoniae, the ortholog of OmpC from Escherichia coli. This species presents high variability of amino acid composition of porins, with the effect to increase its resistance to the penetration of antibiotics. The various properties we analyzed seem to indicate that LPS acts as an independent layer without affecting the internal electrostatic properties of OmpK36. The only apparent effect on the microsecond time scale we sampled is the appearance of calcium ions, when present at moderate concentration in solution, inside the pore. However, we noticed increased fluctuations of the polarization density and only minor changes on its average value.
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Affiliation(s)
- Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, IT
| | - Stefan Milenkovic
- Department of Physics, University of Cagliari, Cittadella Universitaria, 09042, Monserrato, IT
| | - Igor V Bodrenko
- Istituto Nanoscienze, CNR, piazza San Silvestro 12, 56127, Pisa, Italy
- Lab NEST, Scuola Normale Superiore, piazza San Silvestro 12, 56127, Pisa, Italy
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3
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Milenkovic S, Boi S, Scorciapino MA, Bodrenko IV, Ceccarelli M. Machine Learning Prediction of Small Molecule Accumulation in Escherichia Coli Enhanced with Descriptor Statistics. J Chem Theory Comput 2024. [PMID: 38978185 DOI: 10.1021/acs.jctc.4c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Antibiotic resistance, particularly among Gram-negative bacteria, poses a significant healthcare challenge due to their ability to evade antibiotic action through various mechanisms. In this study, we explore the prediction of small molecule accumulation in Gram-negative bacteria by using machine learning techniques enhanced with statistical descriptors derived from molecular dynamics simulations. We begin by identifying a minimal set of molecular descriptors that maximize the model's predictive power while preserving human interpretability. We optimize model accuracy, precision, and the area under the receiver operating characteristic curve through an iterative process. We demonstrate that the inclusion of statistical descriptors significantly improves model performance across various prediction metrics. Particularly, the addition of statistical descriptors related to dipole moment and minimum projection radius enhances the model's predictive capabilities, shedding light on the physicochemical properties crucial for small molecule accumulation. Our findings highlight the importance of considering statistical moments beyond mean values in predictive modeling and suggest avenues for future research. Overall, our study provides insights into the complex dynamics of antibiotic accumulation in Escherichia coli bacterial cells, generalizable to other Gram-negative species, offering a promising approach for the discovery of effective antibacterial agents, identifying new hits, and improving them to define effective lead agents.
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Affiliation(s)
- Stefan Milenkovic
- Department of Physics, University of Cagliari, Cittadella Universitaria, Monserrato 09042, Italy
| | - Sara Boi
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, Monserrato 09042, Italy
| | - Mariano Andrea Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria, Monserrato 09042, Italy
| | | | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria, Monserrato 09042, Italy
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4
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Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Baslé A, Khalid S, Beloin C, Gribaldo S, van den Berg B. Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes. Nat Commun 2023; 14:7152. [PMID: 37932269 PMCID: PMC10628300 DOI: 10.1038/s41467-023-42601-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The outer membrane (OM) in diderm, or Gram-negative, bacteria must be tethered to peptidoglycan for mechanical stability and to maintain cell morphology. Most diderm phyla from the Terrabacteria group have recently been shown to lack well-characterised OM attachment systems, but instead have OmpM, which could represent an ancestral tethering system in bacteria. Here, we have determined the structure of the most abundant OmpM protein from Veillonella parvula (diderm Firmicutes) by single particle cryogenic electron microscopy. We also characterised the channel properties of the transmembrane β-barrel of OmpM and investigated the structure and PG-binding properties of its periplasmic stalk region. Our results show that OM tethering and nutrient acquisition are genetically linked in V. parvula, and probably other diderm Terrabacteria. This dual function of OmpM may have played a role in the loss of the OM in ancestral bacteria and the emergence of monoderm bacterial lineages.
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Affiliation(s)
- Augustinas Silale
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Yiling Zhu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Jerzy Witwinowski
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Robert E Smith
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Kahlan E Newman
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Satya P Bhamidimarri
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Arnaud Baslé
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Christophe Beloin
- Institut Pasteur, Université de Paris Cité, Genetics of Biofilms Laboratory, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Bert van den Berg
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, NE2 4HH, Newcastle upon Tyne, UK.
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5
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Bodrenko I, Ceccarelli M, Acosta-Gutierrez S. The mechanism of an electrostatic nanofilter: overcoming entropy with electrostatics. Phys Chem Chem Phys 2023; 25:26497-26506. [PMID: 37772905 DOI: 10.1039/d3cp02895j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
General porins are nature's sieving machinery in the outer membrane of Gram-negative bacteria. Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. The mechanism of transport through porins is of utmost and direct interest for drug discovery, extending toward nanotechnology applications for blue energy, separations, and sequencing. Here we present a theoretical framework for analysing the filter of general porins in relation to translocating molecules with the aid of enhanced molecular simulations quantitatively. Using different electrostatic probes in the form of a series of related molecules, we describe the nature of this filter and how to finely tune permeability by exploiting electrostatic interactions between the pore and the translocating molecule. Eventually, we show how enhanced simulations constitute today a valid tool for characterising the mechanism and quantifying energetically the transport of molecules through nanopores.
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Affiliation(s)
- Igor Bodrenko
- École Normale Supérieure, Département de Chimie - Laboratoire PASTEUR, Paris, France
- CNR-IOM, Sezione di Cagliari, Cittadella Universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy
| | - Matteo Ceccarelli
- CNR-IOM, Sezione di Cagliari, Cittadella Universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, S.P.8 - km 0.700, 09042 Monserrato (CA), Italy.
| | - Silvia Acosta-Gutierrez
- Institute for Bioengineering of Catalonia, Carrer Baldiri Reixac 10-12, 080028 Barcelona, Spain.
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6
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Tuveri GM, Ceccarelli M, Pira A, Bodrenko IV. The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway. Antibiotics (Basel) 2022; 11:antibiotics11070840. [PMID: 35884094 PMCID: PMC9311757 DOI: 10.3390/antibiotics11070840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022] Open
Abstract
We investigated the diffusion of three cyclic boronates formulated as beta-lactamase inhibitors through the porin OmpF to evaluate their potential to cross OM via the porin pathway. The three nonbeta-lactam molecules diffuse through the porin eyelet region with the same mechanism observed for beta-lactam molecules and diazobicyclooctan derivatives, with the electric dipole moment aligned with the transversal electric field. In particular, the BOH group can interact with both the basic ladder and the acidic loop L3, which is characteristic of the size-constricted region of this class of porins. On one hand, we confirm that the transport of small molecules through enterobacter porins has a common general mechanism; on the other, the class of cyclic boronate molecules does not seem to have particular difficulties in diffusing through enterobacter porins, thus representing a good scaffold for new anti-infectives targeting Gram-negative bacteria research.
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Affiliation(s)
- Gian Marco Tuveri
- Molecular Bionics, Institute for Bioengineering of Catalonia, Carrer de Baldiri Reixac, 10, 12, 08028 Barcelona, Spain;
| | - Matteo Ceccarelli
- Dipartimento di Fisica, University of Cagliari, Cittadella Universitaria, Monserrato, 09042-IT Cagliari, Italy;
- Centro Nazionale di Ricerca/Istituto Officina dei Materiali (CNR/IOM), Sezione di Cagliari, c/o Dipartimento di Fisica, Cittadella Universitaria, Monserrato, 09042-IT Cagliari, Italy
| | - Alessandro Pira
- Dipartimento di Scienze Chimiche e Geologiche, University of Cagliari, Cittadella Universitaria, Monserrato, 09042-IT Cagliari, Italy;
| | - Igor V. Bodrenko
- Centro Nazionale di Ricerca/Istituto Officina dei Materiali (CNR/IOM), Sezione di Cagliari, c/o Dipartimento di Fisica, Cittadella Universitaria, Monserrato, 09042-IT Cagliari, Italy
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759-DE Bremen, Germany
- Correspondence:
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7
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Berthoumieux H, Monet G, Blossey R. Dipolar Poisson models in a dual view. J Chem Phys 2021; 155:024112. [PMID: 34266284 DOI: 10.1063/5.0056430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this work, we study the continuum theories of dipolar-Poisson models. Both the standard dipolar-Poisson model and the dipolar-Poisson-Langevin model, which keeps the dipolar density fixed, are non-convex functionals of the scalar electrostatic potential ϕ. Applying the Legendre transform approach introduced by Maggs [Europhys. Lett. 98, 16012 (2012)], the dual functionals of these models are derived and are given by convex vector-field functionals of the dielectric displacement D and the polarization field P. We compare the convex functionals in P-space to the non-convex functionals in electric field E-space and apply them to the classic problem of the solvation of point-like ions. Since the dipolar-Poisson model does not properly describe polarization saturation, we argue that only the dipolar-Poisson-Langevin functional can be used to provide a nonlinear generalization of the harmonic polarization functional used in the theory of Marcus for the electron transfer rate to nonlinear regimes. We show that the model can be quantitatively parameterized by molecular dynamics simulations.
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Affiliation(s)
- Hélène Berthoumieux
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée (LPTMC, UMR 7600), F-75005 Paris, France
| | - Geoffrey Monet
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée (LPTMC, UMR 7600), F-75005 Paris, France
| | - Ralf Blossey
- University of Lille, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) CNRS UMR8576, 59000 Lille, France
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8
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The Influence of Permeability through Bacterial Porins in Whole-Cell Compound Accumulation. Antibiotics (Basel) 2021; 10:antibiotics10060635. [PMID: 34073313 PMCID: PMC8226570 DOI: 10.3390/antibiotics10060635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 01/09/2023] Open
Abstract
The lack of new drugs for Gram-negative pathogens is a global threat to modern medicine. The complexity of their cell envelope, with an additional outer membrane, hinders internal accumulation and thus, the access of molecules to their targets. Our limited understanding of the molecular basis for compound influx and efflux from these pathogens is a major bottleneck for the discovery of effective antibacterial compounds. Here we analyse the correlation between the whole-cell compound accumulation of ~200 molecules and their predicted porin permeability coefficient (influx), using a recently developed scoring function. We found a strong linear relationship (74%) between the two, confirming porins key in compound uptake in Gram-negative bacteria. The analysis of this unique dataset aids to better understand the molecular descriptors behind whole-cell accumulation and molecular uptake in Gram-negative bacteria.
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9
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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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10
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Pira A, Scorciapino MA, Bodrenko IV, Bosin A, Acosta-Gutiérrez S, Ceccarelli M. Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria. Molecules 2020; 25:E5747. [PMID: 33291474 PMCID: PMC7730927 DOI: 10.3390/molecules25235747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 11/16/2022] Open
Abstract
Modern medicine relies upon antibiotics, but we have arrived to the point where our inability to come up with new effective molecules against resistant pathogens, together with the declining private investment, is resulting in the number of untreatable infections increasing worldwide at worrying pace. Among other pathogens, widely recognized institutions have indicated Gram-negative bacteria as particularly challenging, due to the presence of the outer membrane. The very first step in the action of every antibiotic or adjuvant is the permeation through this membrane, with small hydrophilic drugs usually crossing through protein channels. Thus, a detailed understanding of their properties at a molecular level is crucial. By making use of Molecular Dynamics simulations, we compared the two main porins of four members of the Enterobacteriaceae family, and, in this paper, we show their shared geometrical and electrostatic characteristics. Then, we used metadynamics simulations to reconstruct the free energy for permeation of selected diazobicyclooctans through OmpF. We demonstrate how porins features are coupled to those of the translocating species, modulating their passive permeation. In particular, we show that the minimal projection area of a molecule is a better descriptor than its molecular mass or the volume. Together with the magnitude and orientation of the electric dipole moment, these are the crucial parameters to gain an efficient compensation between the entropic and enthalpic contributions to the free energy barrier required for permeation. Our results confirm the possibility to predict the permeability of molecules through porins by using a few molecular parameters and bolster the general model according to which the free energy increase is mostly due to the decrease of conformational entropy, and this can be compensated by a favorable alignment of the electric dipole with respect to the channel intrinsic electric field.
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Affiliation(s)
- Alessandro Pira
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (A.P.); (A.B.)
| | - Mariano Andrea Scorciapino
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy;
| | - Igor V. Bodrenko
- CNR/IOM Sezione di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy;
| | - Andrea Bosin
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (A.P.); (A.B.)
| | | | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (A.P.); (A.B.)
- CNR/IOM Sezione di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy;
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11
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Bafna JA, Sans-Serramitjana E, Acosta-Gutiérrez S, Bodrenko IV, Hörömpöli D, Berscheid A, Brötz-Oesterhelt H, Winterhalter M, Ceccarelli M. Kanamycin Uptake into Escherichia coli Is Facilitated by OmpF and OmpC Porin Channels Located in the Outer Membrane. ACS Infect Dis 2020; 6:1855-1865. [PMID: 32369342 DOI: 10.1021/acsinfecdis.0c00102] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Despite decades of therapeutic application of aminoglycosides, it is still a matter of debate if porins contribute to the translocation of the antibiotics across the bacterial outer membrane. Here, we quantified the uptake of kanamycin across the major porin channels OmpF and OmpC present in the outer membrane of Escherichia coli. Our analysis revealed that, despite its relatively large size, about 10-20 kanamycin molecules per second permeate through OmpF and OmpC under a 10 μM concentration gradient, whereas OmpN does not allow the passage. Molecular simulations elucidate the uptake mechanism of kanamycin through these porins. Whole-cell studies with a defined set of E. coli porin mutants provide evidence that translocation of kanamycin via porins is relevant for antibiotic potency. The values are discussed with respect to other antibiotics.
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Affiliation(s)
- Jayesh Arun Bafna
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719Bremen, Germany
| | | | | | - Igor V. Bodrenko
- IOM/CNR, Sezione di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy
| | - Daniel Hörömpöli
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
- German Center for Infection Research (DZIF) Partner Site, D-72076 Tübingen, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
- German Center for Infection Research (DZIF) Partner Site, D-72076 Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
- German Center for Infection Research (DZIF) Partner Site, D-72076 Tübingen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, D-28719Bremen, Germany
| | - Matteo Ceccarelli
- IOM/CNR, Sezione di Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy
- Department of Physics, University of Cagliari, and CNR/IOM, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy
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12
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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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13
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Coines J, Acosta-Gutierrez S, Bodrenko I, Rovira C, Ceccarelli M. Glucose transport via the pseudomonad porin OprB: implications for the design of Trojan Horse anti-infectives. Phys Chem Chem Phys 2019; 21:8457-8463. [PMID: 30951074 DOI: 10.1039/c9cp00778d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deciphering the transport through outer-membrane porins is crucial to understand how anti-infectives enter Gram-negative bacteria and perform their function. Here we elucidated the transport mechanism of substrates through the Pseudomonads sugar-specific porin OprB by means of multiscale modeling. We used molecular dynamics simulations to quantify the energetics of transport and thus a diffusion model to quantify the macroscopic flux of molecules through OprB. Our results show that Trp171 and several glutamate residues in the constriction region are key for the transport of glucose, the preferred natural substrate, through OprB. The unveiled transport mechanism suggests that 2-acetamido-1,2-dideoxynojirimycin (DNJ-NAc), an anti-infective structurally similar to glucose, can enter the cell via OprB. We quantified its energetics and macroscopic flux through OprB providing a comparative analysis with the natural substrate. Thus this pore can be considered as a promising gateway for exploiting the Trojan Horse strategy in pathogenic bacteria.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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14
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Samanta S, Bodrenko I, Acosta-Gutiérrez S, D’Agostino T, Pathania M, Ghai I, Schleberger C, Bumann D, Wagner R, Winterhalter M, van den Berg B, Ceccarelli M. Getting Drugs through Small Pores: Exploiting the Porins Pathway in Pseudomonas aeruginosa. ACS Infect Dis 2018; 4:1519-1528. [PMID: 30039960 DOI: 10.1021/acsinfecdis.8b00149] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Understanding molecular properties of outer membrane channels of Gram-negative bacteria is of fundamental significance as they are the entry point of polar antibiotics into bacteria. Outer membrane proteomics revealed OccK8 (OprE) to be among the five most expressed substrate specific channels of the clinically important Pseudomonas aeruginosa. The high-resolution X-ray structure and electrophysiology highlighted a very narrow pore. However, experimental in vitro methods showed the transport of natural amino acids and antibiotics, among them ceftazidime. We used molecular dynamics simulations to reveal the importance of the physicochemical properties of ceftazidime in modulating the translocation through OccK8, proposing a structure-function relationship. As in general porins, the internal electric field favors the translocation of polar molecules by gainful energy compensation in the central constriction region. Importantly, the comparatively narrow OccK8 pore can undergo a substrate-induced expansion to accommodate relatively large-sized substrates.
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Affiliation(s)
- Susruta Samanta
- Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
- Department of Chemistry, Manipal University Jaipur, VPO Dehmi Kalan, Jaipur, Rajasthan 303007, India
| | - Igor Bodrenko
- Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
| | - Silvia Acosta-Gutiérrez
- Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
| | - Tommaso D’Agostino
- Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
| | - Monisha Pathania
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Ishan Ghai
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Christian Schleberger
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Dirk Bumann
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Richard Wagner
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
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15
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Acosta-Gutiérrez S, Ferrara L, Pathania M, Masi M, Wang J, Bodrenko I, Zahn M, Winterhalter M, Stavenger RA, Pagès JM, Naismith JH, van den Berg B, Page MGP, Ceccarelli M. Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins. ACS Infect Dis 2018; 4:1487-1498. [PMID: 29962203 DOI: 10.1021/acsinfecdis.8b00108] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Small, hydrophilic molecules, including most important antibiotics in clinical use, cross the Gram-negative outer membrane through the water-filled channels provided by porins. We have determined the X-ray crystal structures of the principal general porins from three species of Enterobacteriaceae, namely Enterobacter aerogenes, Enterobacter cloacae, and Klebsiella pneumoniae, and determined their antibiotic permeabilities as well as those of the orthologues from Escherichia coli. Starting from the structure of the porins and molecules, we propose a physical mechanism underlying transport and condense it in a computationally efficient scoring function. The scoring function shows good agreement with in vitro penetration data and will enable the screening of virtual databases to identify molecules with optimal permeability through porins and help to guide the optimization of antibiotics with poor permeation.
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Affiliation(s)
- Silvia Acosta-Gutiérrez
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
| | - Luana Ferrara
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9RH, United Kingdom
| | - Monisha Pathania
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Muriel Masi
- UMR_MD1 Inserm U1261, Membranes et Cibles Thérapeutiques, Aix-Marseille Université, Facultés de Pharmacie et de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Jiajun Wang
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Igor Bodrenko
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
| | - Michael Zahn
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Robert A. Stavenger
- Antibacterial DPU, GlaxoSmithKline, 1250 Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jean-Marie Pagès
- UMR_MD1 Inserm U1261, Membranes et Cibles Thérapeutiques, Aix-Marseille Université, Facultés de Pharmacie et de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - James H. Naismith
- Division of Structural Biology, Nuffield Department of Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
- Research Complex at Harwell, Rutherford Laboratory, Didcot, OX11 0FA, United Kingdom
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Malcolm G. P. Page
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria di Monserrato, SP Monserrato-Sestu Km 0.8, Monserrato, 09042, Italy
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16
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Wilson J, Aksimentiev A. Water-Compression Gating of Nanopore Transport. PHYSICAL REVIEW LETTERS 2018; 120:268101. [PMID: 30004740 PMCID: PMC6262874 DOI: 10.1103/physrevlett.120.268101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/18/2018] [Indexed: 05/22/2023]
Abstract
Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.
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Affiliation(s)
- James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801 and Beckman Institute for Advanced Science and Technology
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17
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Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae. Structure 2018; 26:708-721.e4. [PMID: 29657131 DOI: 10.1016/j.str.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/15/2018] [Accepted: 03/16/2018] [Indexed: 01/26/2023]
Abstract
The outer membranes (OM) of many Gram-negative bacteria contain general porins, which form nonspecific, large-diameter channels for the diffusional uptake of small molecules required for cell growth and function. While the porins of Enterobacteriaceae (e.g., E. coli OmpF and OmpC) have been extensively characterized structurally and biochemically, much less is known about their counterparts in Vibrionaceae. Vibrio cholerae, the causative agent of cholera, has two major porins, OmpU and OmpT, for which no structural information is available despite their importance for the bacterium. Here we report high-resolution X-ray crystal structures of V. cholerae OmpU and OmpT complemented with molecular dynamics simulations. While similar overall to other general porins, the channels of OmpU and OmpT have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels. Together with electrophysiological and in vitro transport data, our results illuminate small-molecule uptake within the Vibrionaceae.
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18
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Abstract
Collective antibiotic drug resistance is a global threat, especially with respect to Gram-negative bacteria. The low permeability of the bacterial outer cell wall has been identified as a challenging barrier that prevents a sufficient antibiotic effect to be attained at low doses of the antibiotic. The Gram-negative bacterial cell envelope comprises an outer membrane that delimits the periplasm from the exterior milieu. The crucial mechanisms of antibiotic entry via outer membrane includes general diffusion porins (Omps) responsible for hydrophilic antibiotics and lipid-mediated pathway for hydrophobic antibiotics. The protein and lipid arrangements of the outer membrane have had a strong impact on the understanding of bacteria and their resistance to many types of antibiotics. Thus, one of the current challenges is effective interpretation at the molecular basis of the outer membrane permeability. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in solute influx. Moreover, it aims toward further understanding and exploration of prospects to improve our knowledge of physicochemical limitations that direct the translocation of antibiotics via bacterial outer membrane.
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Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen, Germany.,Consultation Division, RSGBIOGEN, New Delhi, India
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19
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Tran QT, Maigre L, D'Agostino T, Ceccarelli M, Winterhalter M, Pagès JM, Davin-Regli A. Porin flexibility in Providencia stuartii : cell-surface-exposed loops L5 and L7 are markers of Providencia porin OmpPst1. Res Microbiol 2017; 168:685-699. [DOI: 10.1016/j.resmic.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/10/2017] [Accepted: 05/19/2017] [Indexed: 12/16/2022]
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20
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Abstract
One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps) is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels.
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Affiliation(s)
- Ishan Ghai
- School of Engineering and Life Sciences, Jacobs University, Bremen
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21
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Bajaj H, Acosta Gutierrez S, Bodrenko I, Malloci G, Scorciapino MA, Winterhalter M, Ceccarelli M. Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules. ACS NANO 2017; 11:5465-5473. [PMID: 28485920 DOI: 10.1021/acsnano.6b08613] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.
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Affiliation(s)
- Harsha Bajaj
- Jacobs University Bremen , Campus Ring 1, D-28759 Bremen, Germany
| | | | - Igor Bodrenko
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
| | | | | | - Matteo Ceccarelli
- Department of Physics, University of Cagliari , 09124 Cagliari, Italy
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22
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Scorciapino MA, Acosta-Gutierrez S, Benkerrou D, D'Agostino T, Malloci G, Samanta S, Bodrenko I, Ceccarelli M. Rationalizing the permeation of polar antibiotics into Gram-negative bacteria. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:113001. [PMID: 28155846 DOI: 10.1088/1361-648x/aa543b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The increasing level of antibiotic resistance in Gram-negative bacteria, together with the lack of new potential drug scaffolds in the pipeline, make the problem of infectious diseases a global challenge for modern medicine. The main reason that Gram-negative bacteria are particularly challenging is the presence of an outer cell-protecting membrane, which is not present in Gram-positive species. Such an asymmetric bilayer is a highly effective barrier for polar molecules. Several protein systems are expressed in the outer membrane to control the internal concentration of both nutrients and noxious species, in particular: (i) water-filled channels that modulate the permeation of polar molecules and ions according to concentration gradients, and (ii) efflux pumps to actively expel toxic compounds. Thus, besides expressing specific enzymes for drugs degradation, Gram-negative bacteria can also resist by modulating the influx and efflux of antibiotics, keeping the internal concentration low. However, there are no direct and robust experimental methods capable of measuring the permeability of small molecules, thus severely limiting our knowledge of the molecular mechanisms that ultimately control the permeation of antibiotics through the outer membrane. This is the innovation gap to be filled for Gram-negative bacteria. This review is focused on the permeation of small molecules through porins, considered the main path for the entry of polar antibiotics into Gram-negative bacteria. A fundamental understanding of how these proteins are able to filter small molecules is a prerequisite to design/optimize antibacterials with improved permeation. The level of sophistication of modern molecular modeling algorithms and the advances in new computer hardware has made the simulation of such complex processes possible at the molecular level. In this work we aim to share our experience and perspectives in the context of a multidisciplinary extended collaboration within the IMI-Translocation consortium. The synergistic combination of structural data, in vitro assays and computer simulations has proven to give new insights towards the identification and description of physico-chemical properties modulating permeation. Once similar general rules are identified, we believe that the use of virtual screening techniques will be very helpful in searching for new molecular scaffolds with enhanced permeation, and that molecular modeling will be of fundamental assistance to the optimization stage.
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Affiliation(s)
- Mariano Andrea Scorciapino
- Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Cittadella Universitaria di Monserrato, S.P. 8 km 0.700-09042 Monserrato (CA), Italy
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23
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Ghai I, Pira A, Scorciapino MA, Bodrenko I, Benier L, Ceccarelli M, Winterhalter M, Wagner R. General Method to Determine the Flux of Charged Molecules through Nanopores Applied to β-Lactamase Inhibitors and OmpF. J Phys Chem Lett 2017; 8:1295-1301. [PMID: 28240914 DOI: 10.1021/acs.jpclett.7b00062] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A major challenge in the discovery of the new antibiotics against Gram-negative bacteria is to achieve sufficiently fast permeation in order to avoid high doses causing toxic side effects. So far, suitable assays for quantifying the uptake of charged antibiotics into bacteria are lacking. We apply an electrophysiological zero-current assay using concentration gradients of β-lactamase inhibitors combined with single-channel conductance to quantify their flux rates through OmpF. Molecular dynamic simulations provide in addition details on the interactions between the nanopore wall and the charged solutes. In particular, the interaction barrier for three β-lactamase inhibitors is surprisingly as low as 3-5 kcal/mol and only slightly above the diffusion barrier of ions such as chloride. Within our macroscopic constant field model, we determine that at a zero-membrane potential a concentration gradient of 10 μM of avibactam, sulbactam, or tazobactam can create flux rates of roughly 620 molecules/s per OmpF trimer.
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Affiliation(s)
- Ishan Ghai
- Department of Life Sciences and Chemistry, Jacobs University Bremen , 28719 Bremen, Germany
| | - Alessandro Pira
- Department of Physics, University of Cagliari , Cagliari 09124, Italy
| | | | - Igor Bodrenko
- Department of Physics, University of Cagliari , Cagliari 09124, Italy
| | - Lorraine Benier
- Department of Life Sciences and Chemistry, Jacobs University Bremen , 28719 Bremen, Germany
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari , Cagliari 09124, Italy
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen , 28719 Bremen, Germany
| | - Richard Wagner
- Department of Life Sciences and Chemistry, Jacobs University Bremen , 28719 Bremen, Germany
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24
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Ferrara LGM, Wallat GD, Moynié L, Dhanasekar NN, Aliouane S, Acosta-Gutiérrez S, Pagès JM, Bolla JM, Winterhalter M, Ceccarelli M, Naismith JH. MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca 2+ Ion Bound at the Constriction Zone. J Mol Biol 2016; 428:4528-4543. [PMID: 27693650 PMCID: PMC5090048 DOI: 10.1016/j.jmb.2016.09.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/26/2016] [Accepted: 09/26/2016] [Indexed: 11/11/2022]
Abstract
The Gram-negative organism Campylobacter jejuni is the major cause of food poisoning. Unlike Escherichia coli, which has two major porins, OmpC and OmpF, C. jejuni has one, termed major outer membrane protein (MOMP) through which nutrients and antibiotics transit. We report the 2.1-Å crystal structure of C. jejuni MOMP expressed in E. coli and a lower resolution but otherwise identical structure purified directly from C. jejuni. The 2.1-Å resolution structure of recombinant MOMP showed that although the protein has timeric arrangement similar to OmpC, it is an 18-stranded, not 16-stranded, β-barrel. The structure has identified a Ca2 + bound at the constriction zone, which is functionally significant as suggested by molecular dynamics and single-channel experiments. The water-filled channel of MOMP has a narrow constriction zone, and single-molecule studies show a monomeric conductivity of 0.7 ± 0.2 nS and a trimeric conductance of 2.2 ± 0.2 nS. The ion neutralizes negative charges at the constriction zone, reducing the transverse electric field and reversing ion selectivity. Modeling of the transit of ciprofloxacin, an antibiotic of choice for treating Campylobacter infection, through the pore of MOMP reveals a trajectory that is dependent upon the presence metal ion. The crystal structure of MOMP, the general diffusion porin of Campylobacter, has been determined. The protein is an 18-stranded β-barrel that is different than the 16-stranded OmpC and OmpF proteins from E. coli, but like them, MOMP is trimeric. The protein has a central pore size and conductivity intermediate between OmpC and OmpF. A Ca2 + ion bound at the constriction zone influences the biophysical properties of porin. The trajectory of the transit of the antibiotic ciprofloxacin through the pore is dependent on the presence of a metal ion.
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Affiliation(s)
- Luana G M Ferrara
- Biomedical Sciences Research Complex, University of St Andrews, 09042 St Andrews, UK
| | - Gregor D Wallat
- Biomedical Sciences Research Complex, University of St Andrews, 09042 St Andrews, UK
| | - Lucile Moynié
- Biomedical Sciences Research Complex, University of St Andrews, 09042 St Andrews, UK
| | - Naresh N Dhanasekar
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | | | - Silvia Acosta-Gutiérrez
- Department of Physics, University of Cagliari, Cittadella Universitaria Monserrato, S.P8-km 0.700, 09042 Monserrato, Cagliari (CA), Italy
| | | | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, 28719 Bremen, Germany
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cittadella Universitaria Monserrato, S.P8-km 0.700, 09042 Monserrato, Cagliari (CA), Italy
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, 09042 St Andrews, UK; State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.
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25
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Exploiting the porin pathway for polar compound delivery into Gram-negative bacteria. Future Med Chem 2016; 8:1047-62. [PMID: 27303954 DOI: 10.4155/fmc-2016-0038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND In Gram-negative bacteria, the outer-membrane represents an additional barrier for antibiotics to permeate inside pathogens. Our inability to come up with novel effective antibiotics mostly relies upon insufficient understanding of the molecular basis behind outer-membrane penetration. RESULTS Polar antibiotics can permeate through water-filled porins, such as OmpF and OmpC from Escherichia coli. Through molecular modeling, permeation of imipenem and meropenem was found to be strongly dependent upon capability of drugs to properly align their electric dipole to the internal electric field in the restricted region of the pore. Electrostatics differences between OmpF and OmpC, and modifications along a series of OmpC mutants from E. coli-resistant clinical strains identify a 'preorientation' region, which dramatically affects antibiotic pathway. CONCLUSION A novel perspective is presented, suggesting new molecular properties to be included in drug design.
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