1
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Bennett ID, Burns JR, Ryadnov MG, Howorka S, Pyne ALB. Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2207585. [PMID: 38840451 DOI: 10.1002/smll.202207585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/01/2024] [Indexed: 06/07/2024]
Abstract
Chemistry has the power to endow supramolecular nanostructures with new biomedically relevant functions. Here it is reported that DNA nanostructures modified with cholesterol tags disrupt bacterial membranes to cause microbial cell death. The lipidated DNA nanostructures bind more readily to cholesterol-free bacterial membranes than to cholesterol-rich, eukaryotic membranes. These highly negatively charged, lipidated DNA nanostructures cause bacterial cell death by rupturing membranes. Strikingly, killing is mediated by clusters of barrel-shaped nanostructures that adhere to the membrane without the involvement of expected bilayer-puncturing barrels. These DNA nanomaterials may inspire the development of polymeric or small-molecule antibacterial agents that mimic the principles of selective binding and rupturing to help combat antimicrobial resistance.
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Affiliation(s)
- Isabel D Bennett
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Division of Medicine, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- Department of Physics, King's College London, Strand Lane, London, WC2R 2LS, United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Sheffield, S1 3JD, United Kingdom
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2
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Roy A, Sarangi NK, Ghosh S, Prabhakaran A, Keyes TE. Leaflet by Leaflet Synergistic Effects of Antimicrobial Peptides on Bacterial and Mammalian Membrane Models. J Phys Chem Lett 2023; 14:3920-3928. [PMID: 37075204 PMCID: PMC10150393 DOI: 10.1021/acs.jpclett.3c00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Antimicrobial peptides (AMPs) offer significant hope in the fight against antibiotic resistance. Operating via a mechanism different from that of antibiotics, they target the microbial membrane and ideally should damage it without impacting mammalian cells. Here, the interactions of two AMPs, magainin 2 and PGLa, and their synergistic effects on bacterial and mammalian membrane models were studied using electrochemical impedance spectroscopy, atomic force microscopy (AFM), and fluorescence correlation spectroscopy. Toroidal pore formation was observed by AFM when the two AMPs were combined, while individually AMP effects were confined to the exterior leaflet of the bacterial membrane analogue. Using microcavity-supported lipid bilayers, the diffusivity of each bilayer leaflet could be studied independently, and we observed that combined, the AMPs penetrate both leaflets of the bacterial model but individually each peptide had a limited impact on the proximal leaflet of the bacterial model. The impact of AMPs on a ternary, mammalian mimetic membrane was much weaker.
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Affiliation(s)
- Arpita Roy
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nirod Kumar Sarangi
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Surajit Ghosh
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Amrutha Prabhakaran
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Tia E Keyes
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
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3
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Noble JE, Vila-Gómez P, Rey S, Dondi C, Briones A, Aggarwal P, Hoose A, Baran M, Ryadnov MG. Folding-Mediated DNA Delivery by α-Helical Amphipathic Peptides. ACS Biomater Sci Eng 2023; 9:2584-2595. [PMID: 37014978 DOI: 10.1021/acsbiomaterials.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The renaissance gene therapy experiences these days requires specialist biomaterials and a systemic understanding of major factors influencing their ability to deliver genetic material. Peptide transfection systems represent a major class of such biomaterials. Several peptidic reagents have been commercialized to date. However, a comparative assessment of peptide sequences alone without auxiliary support or excipients against a common determinant for their ability to complex and deliver DNA has been lacking. This study cross-compares commercial and experimental transfection reagents from the same family of helical amphiphiles. Factors defining the efficacy of DNA delivery including cell uptake and gene expression are assessed along with cytotoxicity and DNA complexation. The results show that despite differences in sequence composition, length, and origin, peptide reagents of the same structural family exhibit similar characteristics and limitations with common variability trends. The cross-comparison revealed that functional DNA delivery is independent of the peptide sequence used but is mediated by the ability of the reagents to co-fold with DNA. Peptide folding proved to be the common determinant for DNA complexation and delivery by peptidic transfection reagents.
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Affiliation(s)
- James E Noble
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Paula Vila-Gómez
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Brain Sciences, Imperial College London, London W12 0TR, U.K
| | - Stephanie Rey
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Camilla Dondi
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Andrea Briones
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Purnank Aggarwal
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maryana Baran
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Physics, King's College London, London WC2R 2LS, U.K
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4
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Zhang Y, Kepiro I, Ryadnov MG, Pagliara S. Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes. Microbiol Spectr 2023; 11:e0366722. [PMID: 36651776 PMCID: PMC9927147 DOI: 10.1128/spectrum.03667-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
With the spread of multidrug-resistant bacteria, there has been an increasing focus on molecular classes that have not yet yielded an antibiotic. A key capability for assessing and prescribing new antibacterial treatments is to compare the effects antibacterial agents have on bacterial growth at a phenotypic, single-cell level. Here, we combined time-lapse microscopy with microfluidics to investigate the concentration-dependent killing kinetics of stationary-phase Escherichia coli cells. We used antibacterial agents from three different molecular classes, β-lactams and fluoroquinolones, with the known antibiotics ampicillin and ciprofloxacin, respectively, and a new experimental class, protein Ψ-capsids. We found that bacterial cells elongated when treated with ampicillin and ciprofloxacin used at their minimum inhibitory concentration (MIC). This was in contrast to Ψ-capsids, which arrested bacterial elongation within the first two hours of treatment. At concentrations exceeding the MIC, all the antibacterial agents tested arrested bacterial growth within the first 2 h of treatment. Further, our single-cell experiments revealed differences in the modes of action of three different agents. At the MIC, ampicillin and ciprofloxacin caused the lysis of bacterial cells, whereas at higher concentrations, the mode of action shifted toward membrane disruption. The Ψ-capsids killed cells by disrupting their membranes at all concentrations tested. Finally, at increasing concentrations, ampicillin and Ψ-capsids reduced the fraction of the population that survived treatment in a viable but nonculturable state, whereas ciprofloxacin increased this fraction. This study introduces an effective capability to differentiate the killing kinetics of antibacterial agents from different molecular classes and offers a high content analysis of antibacterial mechanisms at the single-cell level. IMPORTANCE Antibiotics act against bacterial pathogens by inhibiting their growth or killing them directly. Different modes of action determine different antibacterial responses, whereas phenotypic differences in bacteria can challenge the efficacy of antibiotics. Therefore, it is important to be able to differentiate the concentration-dependent killing kinetics of antibacterial agents at a single-cell level, in particular for molecular classes which have not yielded an antibiotic before. Here, we measured single-cell responses using microfluidics-enabled imaging, revealing that a novel class of antibacterial agents, protein Ψ-capsids, arrests bacterial elongation at the onset of treatment, whereas elongation continues for cells treated with β-lactam and fluoroquinolone antibiotics. The study advances our current understanding of antibacterial function and offers an effective strategy for the comparative design of new antibacterial therapies, as well as clinical antibiotic susceptibility testing.
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Affiliation(s)
- Yuewen Zhang
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
- National Physical Laboratory, Teddington, United Kingdom
| | - Ibolya Kepiro
- National Physical Laboratory, Teddington, United Kingdom
| | - Maxim G. Ryadnov
- National Physical Laboratory, Teddington, United Kingdom
- Department of Physics, King’s College London, London, United Kingdom
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, United Kingdom
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5
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DANAMIC: Data analyzer of minimum inhibitory concentrations – Protocol to analyze antimicrobial susceptibility data. STAR Protoc 2022; 3:101782. [PMID: 36386890 PMCID: PMC9641264 DOI: 10.1016/j.xpro.2022.101782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This protocol describes an open-source software developed to analyze experimental data obtained using antimicrobial susceptibility assays. We first describe experimental procedures for testing the activity of antimicrobial agents in vitro based on reference standards (BS EN ISO 20776-1:2020). We then describe the software protocol to analyze and convert the data obtained using these procedures into minimum inhibitory concentrations. This approach enables automated data analysis for microdilution assays and can be adapted for high-throughput antimicrobial screening. Open-source software to analyze antimicrobial susceptibility data Detailed reference procedures for obtaining antimicrobial activity data Automated conversion of the obtained data into minimum inhibitory concentrations Automated data analysis compatible with high-throughput screening
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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6
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Fletcher M, Zhu J, Rubio-Sánchez R, Sandler SE, Nahas KA, Michele LD, Keyser UF, Tivony R. DNA-Based Optical Quantification of Ion Transport across Giant Vesicles. ACS NANO 2022; 16:17128-17138. [PMID: 36222833 PMCID: PMC9620405 DOI: 10.1021/acsnano.2c07496] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Accurate measurements of ion permeability through cellular membranes remains challenging due to the lack of suitable ion-selective probes. Here we use giant unilamellar vesicles (GUVs) as membrane models for the direct visualization of mass translocation at the single-vesicle level. Ion transport is indicated with a fluorescently adjustable DNA-based sensor that accurately detects sub-millimolar variations in K+ concentration. In combination with microfluidics, we employed our DNA-based K+ sensor for extraction of the permeation coefficient of potassium ions. We measured K+ permeability coefficients at least 1 order of magnitude larger than previously reported values from bulk experiments and show that permeation rates across the lipid bilayer increase in the presence of octanol. In addition, an analysis of the K+ flux in different concentration gradients allows us to estimate the complementary H+ flux that dissipates the charge imbalance across the GUV membrane. Subsequently, we show that our sensor can quantify the K+ transport across prototypical cation-selective ion channels, gramicidin A and OmpF, revealing their relative H+/K+ selectivity. Our results show that gramicidin A is much more selective to protons than OmpF with a H+/K+ permeability ratio of ∼104.
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Affiliation(s)
- Marcus Fletcher
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Roger Rubio-Sánchez
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Sarah E Sandler
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Kareem Al Nahas
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Lorenzo Di Michele
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Ulrich F Keyser
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
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7
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Al Nahas K, Fletcher M, Hammond K, Nehls C, Cama J, Ryadnov MG, Keyser UF. Measuring Thousands of Single-Vesicle Leakage Events Reveals the Mode of Action of Antimicrobial Peptides. Anal Chem 2022; 94:9530-9539. [PMID: 35760038 PMCID: PMC9280716 DOI: 10.1021/acs.analchem.1c03564] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Host defense or antimicrobial
peptides hold promise for providing
new pipelines of effective antimicrobial agents. Their activity quantified
against model phospholipid membranes is fundamental to a detailed
understanding of their structure–activity relationships. However,
classical characterization assays often lack the ability to achieve
this insight. Leveraging a highly parallelized microfluidic platform
for trapping and studying thousands of giant unilamellar vesicles,
we conducted quantitative long-term microscopy studies to monitor
the membrane-disruptive activity of archetypal antimicrobial peptides
with a high spatiotemporal resolution. We described the modes of action
of these peptides via measurements of the disruption of the vesicle
population under the conditions of continuous peptide dosing using
a range of concentrations and related the observed modes to the molecular
activity mechanisms of these peptides. The study offers an effective
approach for characterizing membrane-targeting antimicrobial agents
in a standardized manner and for assigning specific modes of action
to the corresponding antimicrobial mechanisms.
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Affiliation(s)
- Kareem Al Nahas
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Marcus Fletcher
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K.,London Centre for Nanotechnology, University College London, London WC1H 0AH, U.K
| | - Christian Nehls
- Research Center Borstel, Leibniz Lung Center, Parkallee 10, Borstel 23845, Germany
| | - Jehangir Cama
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K.,Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, North Park Road, Exeter EX4 4QF, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K.,Department of Physics, King's College London, Strand Lane, London WC2R 2LS, U.K
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, U.K
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8
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Łapińska U, Voliotis M, Lee KK, Campey A, Stone MRL, Tuck B, Phetsang W, Zhang B, Tsaneva-Atanasova K, Blaskovich MAT, Pagliara S. Fast bacterial growth reduces antibiotic accumulation and efficacy. eLife 2022; 11:e74062. [PMID: 35670099 PMCID: PMC9173744 DOI: 10.7554/elife.74062] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/08/2022] [Indexed: 12/11/2022] Open
Abstract
Phenotypic variations between individual microbial cells play a key role in the resistance of microbial pathogens to pharmacotherapies. Nevertheless, little is known about cell individuality in antibiotic accumulation. Here, we hypothesise that phenotypic diversification can be driven by fundamental cell-to-cell differences in drug transport rates. To test this hypothesis, we employed microfluidics-based single-cell microscopy, libraries of fluorescent antibiotic probes and mathematical modelling. This approach allowed us to rapidly identify phenotypic variants that avoid antibiotic accumulation within populations of Escherichia coli, Pseudomonas aeruginosa, Burkholderia cenocepacia, and Staphylococcus aureus. Crucially, we found that fast growing phenotypic variants avoid macrolide accumulation and survive treatment without genetic mutations. These findings are in contrast with the current consensus that cellular dormancy and slow metabolism underlie bacterial survival to antibiotics. Our results also show that fast growing variants display significantly higher expression of ribosomal promoters before drug treatment compared to slow growing variants. Drug-free active ribosomes facilitate essential cellular processes in these fast-growing variants, including efflux that can reduce macrolide accumulation. We used this new knowledge to eradicate variants that displayed low antibiotic accumulation through the chemical manipulation of their outer membrane inspiring new avenues to overcome current antibiotic treatment failures.
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Affiliation(s)
- Urszula Łapińska
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - Margaritis Voliotis
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Department of Mathematics, University of ExeterExeterUnited Kingdom
| | - Ka Kiu Lee
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - Adrian Campey
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - M Rhia L Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New JerseyPiscatawayUnited States
| | - Brandon Tuck
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
| | - Wanida Phetsang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Bing Zhang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Department of Mathematics, University of ExeterExeterUnited Kingdom
- EPSRC Hub for Quantitative Modelling in Healthcare, University of ExeterExeterUnited Kingdom
- Department of Bioinformatics and Mathematical Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of SciencesSofiaBulgaria
| | - Mark AT Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Stefano Pagliara
- Living Systems Institute, University of ExeterExeterUnited Kingdom
- Biosciences, University of ExeterExeterUnited Kingdom
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9
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Cama J, Al Nahas K, Fletcher M, Hammond K, Ryadnov MG, Keyser UF, Pagliara S. An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics. Sci Rep 2022; 12:4005. [PMID: 35256720 PMCID: PMC8901753 DOI: 10.1038/s41598-022-07973-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/28/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance challenges the ability of modern medicine to contain infections. Given the dire need for new antimicrobials, polypeptide antibiotics hold particular promise. These agents hit multiple targets in bacteria starting with their most exposed regions-their membranes. However, suitable approaches to quantify the efficacy of polypeptide antibiotics at the membrane and cellular level have been lacking. Here, we employ two complementary microfluidic platforms to probe the structure-activity relationships of two experimental series of polypeptide antibiotics. We reveal strong correlations between each peptide's physicochemical activity at the membrane level and biological activity at the cellular level. We achieve this knowledge by assaying the membranolytic activities of the compounds on hundreds of individual giant lipid vesicles, and by quantifying phenotypic responses within clonal bacterial populations with single-cell resolution. Our strategy proved capable of detecting differential responses for peptides with single amino acid substitutions between them, and can accelerate the rational design and development of peptide antimicrobials.
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Affiliation(s)
- Jehangir Cama
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, North Park Road, Exeter, EX4 4QF, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
| | - Kareem Al Nahas
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Marcus Fletcher
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
- Department of Physics, King's College London, Strand Lane, London, WC2R 2LS, UK
| | - Ulrich F Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
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10
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Hornemann A, Eichert DM, Hoehl A, Tiersch B, Ulm G, Ryadnov MG, Beckhoff B. Investigating Membrane‐Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far‐Infrared Spectroscopy. Chemphyschem 2022; 23:e202100815. [PMID: 35032089 PMCID: PMC9303692 DOI: 10.1002/cphc.202100815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/20/2021] [Indexed: 11/30/2022]
Abstract
Synchrotron radiation‐based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio‐molecular phenomena including folding‐mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near‐THz 400–40 cm−1 range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature‐dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane‐induced and folding‐mediated activity of AMPs. The far‐FTIR study offers a direct and information‐rich probe of membrane‐related antimicrobial interactions.
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Affiliation(s)
- Andrea Hornemann
- Department 7.1 Radiometry with Synchrotron Radiation and Department 7.2 X-Ray Metrology with Synchrotron Radiation Physikalisch-Technische Bundesanstalt (PTB) Abbestr. 2–12 10587 Berlin Germany
| | - Diane M. Eichert
- ELETTRA – Sincrotrone Trieste S.S.14 Km 163.5 in Area Science Park 34149 Basovizza Trieste Italy
| | - Arne Hoehl
- Department 7.1 Radiometry with Synchrotron Radiation and Department 7.2 X-Ray Metrology with Synchrotron Radiation Physikalisch-Technische Bundesanstalt (PTB) Abbestr. 2–12 10587 Berlin Germany
| | - Brigitte Tiersch
- Universität Potsdam Karl-Liebknecht-Str. 24–25 14476 Potsdam Germany
| | - Gerhard Ulm
- Department 7.1 Radiometry with Synchrotron Radiation and Department 7.2 X-Ray Metrology with Synchrotron Radiation Physikalisch-Technische Bundesanstalt (PTB) Abbestr. 2–12 10587 Berlin Germany
| | - Maxim G. Ryadnov
- National Physical Laboratory Hampton Rd Teddington Middlesex TW11 0LW UK
| | - Burkhard Beckhoff
- Department 7.1 Radiometry with Synchrotron Radiation and Department 7.2 X-Ray Metrology with Synchrotron Radiation Physikalisch-Technische Bundesanstalt (PTB) Abbestr. 2–12 10587 Berlin Germany
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11
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Timmons PB, Hewage CM. Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca. Sci Rep 2021; 11:22468. [PMID: 34789753 PMCID: PMC8599514 DOI: 10.1038/s41598-021-01769-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 01/13/2023] Open
Abstract
Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-\documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, and a cyclic disulfide-bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide’s interactions with sodium dodecyl sulfate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its \documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.
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Affiliation(s)
- Patrick B Timmons
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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12
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Lai Z, Jian Q, Li G, Shao C, Zhu Y, Yuan X, Chen H, Shan A. Self-Assembling Peptide Dendron Nanoparticles with High Stability and a Multimodal Antimicrobial Mechanism of Action. ACS NANO 2021; 15:15824-15840. [PMID: 34549935 DOI: 10.1021/acsnano.1c03301] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-assembling nanometer-scale structured peptide polymers and peptide dendrimers have shown promise in biomedical applications due to their versatile properties and easy availability. Herein, self-assembling peptide dendron nanoparticles (SPDNs) with potent antimicrobial activity against a range of bacteria were developed based on the nanoscale self-assembly of an arginine-proline repeat branched peptide dendron bearing a hexadecanoic acid chain. The SPDNs are biocompatible, and our most active peptide dendron nanoparticle, C16-3RP, was found to have negligible toxicity after both in vitro and in vivo studies. Furthermore, the C16-3RP nanoparticles showed excellent stability under physiological concentrations of salt ions and against serum and protease degradation, resulting in highly effective treatment in a mouse acute peritonitis model. Comprehensive analyses using a series of biofluorescence, microscopy, and transcriptome sequencing techniques revealed that C16-3RP nanoparticles kill Gram-negative bacteria by increasing bacterial membrane permeability, inducing cytoplasmic membrane depolarization and drastic membrane disruption, inhibiting ribosome biogenesis, and influencing energy generation and other processes. Collectively, C16-3RP nanoparticles show promising biocompatibility and in vivo therapeutic efficacy without apparent resistance development. These advancements may facilitate the development of peptide-based antibiotics in clinical settings.
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Affiliation(s)
- Zhenheng Lai
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Qiao Jian
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Guoyu Li
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Changxuan Shao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yongjie Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xiaojie Yuan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Hongyu Chen
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, People's Republic of China
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Al Nahas K, Keyser UF. Standardizing characterization of membrane active peptides with microfluidics. BIOMICROFLUIDICS 2021; 15:041301. [PMID: 34257793 PMCID: PMC8266397 DOI: 10.1063/5.0048906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial peptides (AMPs) are emerging as important players in the fight against antibiotic resistance. In parallel, the field of microfluidics has matured and its benefits are being exploited in applications of biomimetics and standardized testing. Membrane models are essential tools extensively utilized in studying the activity and modes of action of AMPs. Here, we describe how the utilization of microfluidic platforms in characterizing membrane active peptides can develop a reliable colorful image that classical techniques have rendered black and white.
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Affiliation(s)
- Kareem Al Nahas
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB30HE, United Kingdom
| | - Ulrich F. Keyser
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB30HE, United Kingdom
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