1
|
Xu Y, Wang X, Zaal EA, Berkers CR, Lorent JH, Heise T, Cox R, Pieters RJ, Breukink E. Specific labeling of newly synthesized lipopolysaccharide via metabolic incorporation of azido-galactose. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159467. [PMID: 38382574 DOI: 10.1016/j.bbalip.2024.159467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/12/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
Gram-negative bacteria possess an asymmetric outer membrane (OM) primarily composed of lipopolysaccharides (LPS) on the outer leaflet and phospholipids on the inner leaflet. The outer membrane functions as an effective permeability barrier to compounds such as antibiotics. Studying LPS biosynthesis is therefore helpful to explore novel strategies for new antibiotic development. Metabolic glycan labeling of the bacterial surface has emerged as a powerful method to investigate LPS biosynthesis. However, the previously reported methods of labeling LPS are based on radioactivity or difficult-to-produce analogs of bacterial sugars. In this study, we report on the incorporation of azido galactose into the LPS of the Gram-negative bacteria Escherichia coli and Salmonella typhi via metabolic labeling. As a common sugar analog, azido galactose successfully labeled both O-antigen and core of Salmonella LPS, but not E. coli LPS. This labeling of Salmonella LPS, as shown by SDS-PAGE analysis and fluorescence microscopy, differs from the previously reported labeling of either O-antigen or core of LPS. Our findings are useful for studying LPS biogenesis pathways in Gram-negative bacteria like Salmonella. In addition, our approach is helpful for screening for agents that target LPS biosynthesis as it allows for the detection of newly synthesized LPS that appears in the OM. Furthermore, this approach may also aid in isolating chemically modified LPS for vaccine development or immunotherapy.
Collapse
Affiliation(s)
- Yang Xu
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Esther A Zaal
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Celia R Berkers
- Division of Cell Biology, Metabolism & Cancer, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Torben Heise
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Ruud Cox
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Roland J Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| |
Collapse
|
2
|
Wang X, Xu Y, Martin NI, Breukink E. The enigmatic mode of action of the lantibiotic epilancin 15X. Biochim Biophys Acta Biomembr 2024; 1866:184282. [PMID: 38218577 DOI: 10.1016/j.bbamem.2024.184282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Epilancin 15X is a lantibiotic that has an antimicrobial activity in the nanomolar concentration range towards Staphylococcus simulans. Such low MICs usually imply that these peptides employ a mechanism of action (MoA) involving high affinity targets. Here we studied this MoA by using epilancin 15X's ability to dissipate the membrane potential of intact S. simulans cells. These membrane depolarization assays showed that treatment of the bacteria by antibiotics known to affect the bacterial cell wall synthesis pathway decreased the membrane depolarization effects of epilancin 15X. Disruption of the Lipid II cycle in intact bacteria using several methods led to a decrease in the activity of epilancin 15X. Antagonism-based experiments on 96-well plate and agar diffusion plate pointed towards a possible interaction between epilancin 15X and Lipid II and this was confirmed by Circular Dichroism (CD) based experiments. However, this interaction did not lead to a detectable effect on either carboxyfluorescein (CF) leakage or proton permeability. All experiments point to the involvement of a phosphodiester-containing target within a polyisoprene-based biosynthesis pathway, yet the exact identity of the target remains obscure so far.
Collapse
Affiliation(s)
- Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Yang Xu
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands; Zhejiang Provincial Key Laboratory of Food Microbiotechnology Research of China, the Zhejiang Gongshang University of China, Hangzhou, China.
| |
Collapse
|
3
|
Yekefallah M, van Aalst EJ, van Beekveld RAM, Eason IR, Breukink E, Weingarth M, Wylie BJ. Cooperative Gating of a K + Channel by Unmodified Biological Anionic Lipids Viewed by Solid-State NMR Spectroscopy. J Am Chem Soc 2024; 146:4421-4432. [PMID: 38334076 PMCID: PMC10885140 DOI: 10.1021/jacs.3c09266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Lipids adhere to membrane proteins to stimulate or suppress molecular and ionic transport and signal transduction. Yet, the molecular details of lipid-protein interaction and their functional impact are poorly characterized. Here we combine NMR, coarse-grained molecular dynamics (CGMD), and functional assays to reveal classic cooperativity in the binding and subsequent activation of a bacterial inward rectifier potassium (Kir) channel by phosphatidylglycerol (PG), a common component of many membranes. Past studies of lipid activation of Kir channels focused primarily on phosphatidylinositol bisphosphate, a relatively rare signaling lipid that is tightly regulated in space and time. We use solid-state NMR to quantify the binding of unmodified 13C-PG to the K+ channel KirBac1.1 in liposomes. This specific lipid-protein interaction has a dissociation constant (Kd) of ∼7 mol percentage PG (ΧPG) with positive cooperativity (n = 3.8) and approaches saturation near 20% ΧPG. Liposomal flux assays show that K+ flux also increases with PG in a cooperative manner with an EC50 of ∼20% ΧPG, within the physiological range. Further quantitative fitting of these data reveals that PG acts as a partial (80%) agonist with fivefold K+ flux amplification. Comparisons of NMR chemical shift perturbation and CGMD simulations at different ΧPG confirm the direct interaction of PG with key residues, several of which would not be accessible to lipid headgroups in the closed state of the channel. Allosteric regulation by a common lipid is directly relevant to the activation mechanisms of several human ion channels. This study highlights the role of concentration-dependent lipid-protein interactions and tightly controlled protein allostery in the activation and regulation of ion channels.
Collapse
Affiliation(s)
- Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Roy A M van Beekveld
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, Utrecht3584 CH, The Netherlands
| | - Isaac R Eason
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Markus Weingarth
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, Utrecht3584 CH, The Netherlands
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
4
|
Parmar A, Lakshminarayanan R, Iyer A, Goh ETL, To TY, Yam JKH, Yang L, Newire E, Robertson MC, Prior SH, Breukink E, Madder A, Singh I. Development of teixobactin analogues containing hydrophobic, non-proteogenic amino acids that are highly potent against multidrug-resistant bacteria and biofilms. Eur J Med Chem 2023; 261:115853. [PMID: 37857144 DOI: 10.1016/j.ejmech.2023.115853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/24/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023]
Abstract
Teixobactin is a cyclic undecadepsipeptide that has shown excellent potency against multidrug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). In this article, we present the design, synthesis, and antibacterial evaluations of 16 different teixobactin analogues. These simplified analogues contain commercially available hydrophobic, non-proteogenic amino acid residues instead of synthetically challenging expensive L-allo-enduracididine amino acid residue at position 10 together with different combinations of arginines at positions 3, 4 and 9. The new teixobactin analogues showed potent antibacterial activity against a broad panel of Gram-positive bacteria, including MRSA and VRE strains. Our work also presents the first demonstration of the potent antibiofilm activity of teixobactin analogoues against Staphylococcus species associated with serious chronic infections. Our results suggest that the use of hydrophobic, non-proteogenic amino acids at position 10 in combination with arginine at positions 3, 4 and 9 holds the key to synthesising a new generation of highly potent teixobactin analogues to tackle resistant bacterial infections and biofilms.
Collapse
Affiliation(s)
- Anish Parmar
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool, L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX, Liverpool, UK
| | - Rajamani Lakshminarayanan
- Singapore Eye Research Institute, The Academia, Discovery Tower Level 6, 20 College Road, 169857, Singapore
| | - Abhishek Iyer
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 (S4), B-9000, Ghent, Belgium
| | - Eunice Tze Leng Goh
- Singapore Eye Research Institute, The Academia, Discovery Tower Level 6, 20 College Road, 169857, Singapore
| | - Tsz Ying To
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool, L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX, Liverpool, UK
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore; School of Biological Sciences, Division of Structural Biology and Biochemistry, Nanyang Technological University, 639798, Singapore
| | - Enas Newire
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool, L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX, Liverpool, UK
| | - Maria C Robertson
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool, L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX, Liverpool, UK
| | - Stephen H Prior
- School of Chemistry, Joseph Banks Laboratories, University of Lincoln, Green Lane, Lincoln, LN6 7DL, United Kingdom
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584, CH, Utrecht, the Netherlands
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 (S4), B-9000, Ghent, Belgium
| | - Ishwar Singh
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool, L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX, Liverpool, UK.
| |
Collapse
|
5
|
Xie M, Koch EHW, van Walree CA, Sobota A, Sonnen AFP, Breukink E, Killian JA, Lorent JH. Two separate mechanisms are involved in membrane permeabilization during lipid oxidation. Biophys J 2023; 122:4503-4517. [PMID: 37905401 PMCID: PMC10719051 DOI: 10.1016/j.bpj.2023.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023] Open
Abstract
Lipid oxidation is a universal degradative process of cell membrane lipids that is induced by oxidative stress and reactive oxygen and nitrogen species (RONS) in multiple pathophysiological situations. It has been shown that certain oxidized lipids alter membrane properties, leading to a loss of membrane function. Alteration of membrane properties is thought to depend on the initial membrane lipid composition, such as the number of acyl chain unsaturations. However, it is unclear how oxidative damage is related to biophysical properties of membranes. We therefore set out to quantify lipid oxidation through various analytical methods and determine key biophysical membrane parameters using model membranes containing lipids with different degrees of lipid unsaturation. As source for RONS, we used cold plasma, which is currently developed as treatment for infections and cancer. Our data revealed complex lipid oxidation that can lead to two main permeabilization mechanisms. The first one appears upon direct contact of membranes with RONS and depends on the formation of truncated oxidized phospholipids. These lipids seem to be partly released from the bilayer, implying that they are likely to interact with other membranes and potentially act as signaling molecules. This mechanism is independent of lipid unsaturation, does not rely on large variations in lipid packing, and is most probably mediated via short-living RONS. The second mechanism takes over after longer incubation periods and probably depends on the continued formation of lipid oxygen adducts such as lipid hydroperoxides or ketones. This mechanism depends on lipid unsaturation and involves large variations in lipid packing. This study indicates that polyunsaturated lipids, which are present in mammalian membranes rather than in bacteria, do not sensitize membranes to instant permeabilization by RONS but could promote long-term damage.
Collapse
Affiliation(s)
- Min Xie
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Eveline H W Koch
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands; University College Utrecht, Campusplein 1, Utrecht, the Netherlands
| | - Ana Sobota
- Atmospheric Pressure Non-Thermal Plasmas and Their Interaction with Targets, Applied Physics Department, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Andreas F P Sonnen
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands; Pathology Department, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands; Cellular and Molecular Pharmacology, Translational Research from Experimental and Clinical Pharmacology to Treatment Optimization, Louvain Drug Research Institute, UCLouvain, Brussels, Belgium.
| |
Collapse
|
6
|
Shukla R, Peoples AJ, Ludwig KC, Maity S, Derks MGN, De Benedetti S, Krueger AM, Vermeulen BJA, Harbig T, Lavore F, Kumar R, Honorato RV, Grein F, Nieselt K, Liu Y, Bonvin AMJJ, Baldus M, Kubitscheck U, Breukink E, Achorn C, Nitti A, Schwalen CJ, Spoering AL, Ling LL, Hughes D, Lelli M, Roos WH, Lewis K, Schneider T, Weingarth M. An antibiotic from an uncultured bacterium binds to an immutable target. Cell 2023; 186:4059-4073.e27. [PMID: 37611581 DOI: 10.1016/j.cell.2023.07.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/01/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023]
Abstract
Antimicrobial resistance is a leading mortality factor worldwide. Here, we report the discovery of clovibactin, an antibiotic isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant Gram-positive bacterial pathogens without detectable resistance. Using biochemical assays, solid-state nuclear magnetic resonance, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C55PP, lipid II, and lipid IIIWTA). Clovibactin uses an unusual hydrophobic interface to tightly wrap around pyrophosphate but bypasses the variable structural elements of precursors, accounting for the lack of resistance. Selective and efficient target binding is achieved by the sequestration of precursors into supramolecular fibrils that only form on bacterial membranes that contain lipid-anchored pyrophosphate groups. This potent antibiotic holds the promise of enabling the design of improved therapeutics that kill bacterial pathogens without resistance development.
Collapse
Affiliation(s)
- Rhythm Shukla
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | | | - Kevin C Ludwig
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Maik G N Derks
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Stefania De Benedetti
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Annika M Krueger
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Bram J A Vermeulen
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Theresa Harbig
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Francesca Lavore
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Rodrigo V Honorato
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Kay Nieselt
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72070 Tübingen, Germany
| | - Yangping Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Alexandre M J J Bonvin
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ulrich Kubitscheck
- Clausius-Institute for Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | | | - Anthony Nitti
- NovoBiotic Pharmaceuticals, Cambridge, MA 02138, USA
| | | | | | | | - Dallas Hughes
- NovoBiotic Pharmaceuticals, Cambridge, MA 02138, USA
| | - Moreno Lelli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, MA 02115, USA
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany.
| | - Markus Weingarth
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| |
Collapse
|
7
|
Wang X, van Beekveld RAM, Xu Y, Parmar A, Das S, Singh I, Breukink E. Analyzing mechanisms of action of antimicrobial peptides on bacterial membranes requires multiple complimentary assays and different bacterial strains. Biochim Biophys Acta Biomembr 2023; 1865:184160. [PMID: 37100361 DOI: 10.1016/j.bbamem.2023.184160] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 04/28/2023]
Abstract
Antimicrobial peptides (AMPs) commonly target bacterial membranes and show broad-spectrum activity against microorganisms. In this research we used three AMPs (nisin, epilancin 15×, [R4L10]-teixobactin) and tested their membrane effects towards three strains (Staphylococcus simulans, Micrococcus flavus, Bacillus megaterium) in relation with their antibacterial activity. We describe fluorescence and luminescence-based assays to measure effects on membrane potential, intracellular pH, membrane permeabilization and intracellular ATP levels. The results show that our control peptide, nisin, performed mostly as expected in view of its targeted pore-forming activity, with fast killing kinetics that coincided with severe membrane permeabilization in all three strains. However, the mechanisms of action of both Epilancin 15× as well as [R4L10]-teixobactin appeared to depend strongly on the bacterium tested. In certain specific combinations of assay, peptide and bacterium, deviations from the general picture were observed. This was even the case for nisin, indicating the importance of using multiple assays and bacteria for mode of action studies to be able to draw proper conclusions on the mode of action of AMPs.
Collapse
Affiliation(s)
- Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Roy A M van Beekveld
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Yang Xu
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Anish Parmar
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX Liverpool, UK
| | - Sanjit Das
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool L7 8TX, UK; Antimicrobial Drug Discovery and Development, Department of Chemistry, The Robert Robinson Laboratories, University of Liverpool, L69 3BX Liverpool, UK
| | - Ishwar Singh
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, William Henry Duncan Building, 6 West Derby St, Liverpool L7 8TX, UK
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands; Zhejiang Provincial Key Laboratory of Food Microbiotechnology Research of China, the Zhejiang Gongshang University of China, Hangzhou, China.
| |
Collapse
|
8
|
Shukla R, Peoples AJ, Ludwig KC, Maity S, Derks MG, de Benedetti S, Krueger AM, Vermeulen BJ, Lavore F, Honorato RV, Grein F, Bonvin A, Kubitscheck U, Breukink E, Achorn C, Nitti A, Schwalen CJ, Spoering AL, Ling LL, Hughes D, Lelli M, Roos WH, Lewis K, Schneider T, Weingarth M. A new antibiotic from an uncultured bacterium binds to an immutable target. bioRxiv 2023:2023.05.15.540765. [PMID: 37292624 PMCID: PMC10245560 DOI: 10.1101/2023.05.15.540765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antimicrobial resistance is a leading mortality factor worldwide. Here we report the discovery of clovibactin, a new antibiotic, isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant bacterial pathogens without detectable resistance. Using biochemical assays, solid-state NMR, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C 55 PP, Lipid II, Lipid WTA ). Clovibactin uses an unusual hydrophobic interface to tightly wrap around pyrophosphate, but bypasses the variable structural elements of precursors, accounting for the lack of resistance. Selective and efficient target binding is achieved by the irreversible sequestration of precursors into supramolecular fibrils that only form on bacterial membranes that contain lipid-anchored pyrophosphate groups. Uncultured bacteria offer a rich reservoir of antibiotics with new mechanisms of action that could replenish the antimicrobial discovery pipeline.
Collapse
Affiliation(s)
- Rhythm Shukla
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | - Kevin C. Ludwig
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maik G.N. Derks
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefania de Benedetti
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Annika M Krueger
- Institute for Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Bram J.A. Vermeulen
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Francesca Lavore
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rodrigo V. Honorato
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Alexandre Bonvin
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ulrich Kubitscheck
- Institute for Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | - Anthony Nitti
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | | | - Amy L. Spoering
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Losee Lucy Ling
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Dallas Hughes
- NovoBiotic Pharmaceuticals, Cambridge, Massachusetts 02138, USA
| | - Moreno Lelli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Department of Biology, Boston, Massachusetts 02115, USA
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Markus Weingarth
- NMR Spectroscopy, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
9
|
van Beekveld R, Derks M, Kumar R, Smid L, Maass T, Medeiros-Silva J, Breukink E, Weingarth M. Specific Lipid Studies in Complex Membranes by Solid‐State NMR Spectroscopy. Chemistry 2022; 28:e202202472. [PMID: 36098094 PMCID: PMC10092488 DOI: 10.1002/chem.202202472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/11/2022]
Abstract
Specific interactions with phospholipids are often critical for the function of proteins or drugs, but studying these interactions at high resolution remains difficult, especially in complex membranes that mimic biological conditions. In principle, molecular interactions with phospholipids could be directly probed by solid-state NMR (ssNMR). However, due to the challenge to detect specific lipids in mixed liposomes and limited spectral sensitivity, ssNMR studies of specific lipids in complex membranes are scarce. Here, by using purified biological 13 C,15 N-labeled phospholipids, we show that we can selectively detect traces of specific lipids in complex membranes. In combination with 1 H-detected ssNMR, we show that our approach provides unprecedented high-resolution insights into the mechanisms of drugs that target specific lipids. This broadly applicable approach opens new opportunities for the molecular characterization of specific lipid interactions with proteins or drugs in complex fluid membranes.
Collapse
Affiliation(s)
| | - Maik Derks
- Utrecht University: Universiteit Utrecht Chemistry NETHERLANDS
| | - Raj Kumar
- Utrecht University: Universiteit Utrecht Chemistry NETHERLANDS
| | - Leanna Smid
- Utrecht University: Universiteit Utrecht Chemistry NETHERLANDS
| | - Thorben Maass
- Utrecht University: Universiteit Utrecht Chemistry NETHERLANDS
| | | | - Eefjan Breukink
- Utrecht University: Universiteit Utrecht Chemistry NETHERLANDS
| | | |
Collapse
|
10
|
Xu Y, Hernández-Rocamora VM, Lorent JH, Cox R, Wang X, Bao X, Stel M, Vos G, van den Bos RM, Pieters RJ, Gray J, Vollmer W, Breukink E. Metabolic labeling of the bacterial peptidoglycan by functionalized glucosamine. iScience 2022; 25:104753. [PMID: 35942089 PMCID: PMC9356107 DOI: 10.1016/j.isci.2022.104753] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/09/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
N-Acetylglucosamine (GlcNAc) is an essential monosaccharide required in almost all organisms. Fluorescent labeling of the peptidoglycan (PG) on N-acetylglucosamine has been poorly explored. Here, we report on the labeling of the PG with a bioorthogonal handle on the GlcNAc. We developed a facile one-step synthesis of uridine diphosphate N-azidoacetylglucosamine (UDP-GlcNAz) using the glycosyltransferase OleD, followed by in vitro incorporation of GlcNAz into the peptidoglycan precursor Lipid II and fluorescent labeling of the azido group via click chemistry. In a PG synthesis assay, fluorescent GlcNAz-labeled Lipid II was incorporated into peptidoglycan by the DD-transpeptidase activity of bifunctional class A penicillin-binding proteins. We further demonstrate the incorporation of GlcNAz into the PG layer of OleD-expressed bacteria by feeding with 2-chloro-4-nitrophenyl GlcNAz (GlcNAz-CNP). Hence, our labeling method using the heterologous expression of OleD is useful to study PG synthesis and possibly other biological processes involving GlcNAc metabolism in vivo. Peptidoglycan consists of N-acetylglucosamine, N-acetylmuramic acid, and amino acids We developed a one-step synthesis of azide-labeled UDP-N-acetylglucosamine In vivo generated azide-labeled UDP-N-acetylglucosamine gets incorporated into peptidoglycan Bacteria were fluorescently labeled on N-acetylglucosamine of peptidoglycan
Collapse
Affiliation(s)
- Yang Xu
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | | | - Joseph H. Lorent
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Ruud Cox
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Xue Bao
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Marjon Stel
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 Utrecht, the Netherlands
| | - Gaël Vos
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 Utrecht, the Netherlands
| | - Ramon M. van den Bos
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 Utrecht, the Netherlands
| | - Joe Gray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
- Corresponding author
| |
Collapse
|
11
|
Sassine J, Pazos M, Breukink E, Vollmer W. Lytic transglycosylase MltG cleaves in nascent peptidoglycan and produces short glycan strands. Cell Surf 2021; 7:100053. [PMID: 34036206 PMCID: PMC8135044 DOI: 10.1016/j.tcsw.2021.100053] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria encase their cytoplasmic membrane with peptidoglycan (PG) to maintain the shape of the cell and protect it from bursting. The enlargement of the PG layer is facilitated by the coordinated activities of PG synthesising and -cleaving enzymes. In Escherichia coli, the cytoplasmic membrane-bound lytic transglycosylase MltG associates with PG synthases and was suggested to terminate the polymerisation of PG glycan strands. Using pull-down and surface plasmon resonance, we detected interactions between MltG from Bacillus subtilis and two PG synthases; the class A PBP1 and the class B PBP2B. Using in vitro PG synthesis assays with radio-labelled or fluorophore-labelled B. subtilis-type and/or E. coli-type lipid II, we showed that both, BsMltG and EcMltG, are lytic tranglycosylases and that their activity is higher during ongoing glycan strand polymerisation. MltG competed with the transpeptidase activity of class A PBPs, but had no effect on their glycosyltransferase activity, and produced glycan strands with a length of 7 disaccharide units from cleavage in the nascent strands. We hypothesize that MltG cleaves the nascent strands to produce short glycan strands that are used in the cell for a yet unknown process.
Collapse
Affiliation(s)
- Jad Sassine
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre of Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
12
|
Zhao X, Wang X, Shukla R, Kumar R, Weingarth M, Breukink E, Kuipers OP. Brevibacillin 2V Exerts Its Bactericidal Activity via Binding to Lipid II and Permeabilizing Cellular Membranes. Front Microbiol 2021; 12:694847. [PMID: 34335524 PMCID: PMC8322648 DOI: 10.3389/fmicb.2021.694847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/28/2021] [Indexed: 11/14/2022] Open
Abstract
Lipo-tridecapeptides, a class of bacterial non-ribosomally produced peptides, show strong antimicrobial activity against Gram-positive pathogens, including antibiotic-resistant Staphylococcus aureus and Enterococcus spp. However, many of these lipo-tridecapeptides have shown high hemolytic activity and cytotoxicity, which has limited their potential to be developed into antibiotics. Recently, we reported a novel antimicrobial lipo-tridecapeptide, brevibacillin 2V, which showed no hemolytic activity against human red blood cells at a high concentration of 128 mg/L, opposite to other brevibacillins and lipo-tridecapeptides. In addition, brevibacillin 2V showed much lower cytotoxicity than the other members of the brevibacillin family. In this study, we set out to elucidate the antimicrobial mode of action of brevibacillin 2V. The results show that brevibacillin 2V acts as bactericidal antimicrobial agent against S. aureus (MRSA). Further studies show that brevibacillin 2V exerts its bactericidal activity by binding to the bacterial cell wall synthesis precursor Lipid II and permeabilizing the bacterial membrane. Combined solid-state NMR, circular dichroism, and isothermal titration calorimetry assays indicate that brevibacillin 2V binds to the GlcNAc-MurNAc moiety and/or the pentapeptide of Lipid II. This study provides an insight into the antimicrobial mode of action of brevibacillin 2V. As brevibacillin 2V is a novel and promising antibiotic candidate with low hemolytic activity and cytotoxicity, the here-elucidated mode of action will help further studies to develop it as an alternative antimicrobial agent.
Collapse
Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Rhythm Shukla
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.,NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| |
Collapse
|
13
|
van Eijk M, van Dijk A, van der Ent CK, Arets HGM, Breukink E, van Os N, Adrichem R, van der Water S, Lino Gómez R, Kristensen M, Hessing M, Jekhmane S, Weingarth M, Veldhuizen RAW, Veldhuizen EJA, Haagsman HP. PepBiotics, novel cathelicidin-inspired antimicrobials to fight pulmonary bacterial infections. Biochim Biophys Acta Gen Subj 2021; 1865:129951. [PMID: 34147544 DOI: 10.1016/j.bbagen.2021.129951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/28/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Antimicrobial peptides are considered potential alternatives to antibiotics. Here we describe the antibacterial properties of a family of novel cathelicidin-related (CR-) peptides, which we named PepBiotics, against bacteria typically present in cystic fibrosis (CF) patients. METHODS Broth dilution assays were used to determine antibacterial activity of PepBiotics under physiological conditions, as well as development of bacterial resistance against these peptides. Toxicity was tested in mice and cell cultures while molecular interactions of PepBiotics with bacterial membrane components was determined using CD, ITC and LPS/LTA induced macrophage studies. RESULTS A relatively small number of PepBiotics remained highly antibacterial against CF-related respiratory pathogens Pseudomonas aeruginosa and Staphylococcus aureus, at high ionic strength and low pH. Interestingly, these PepBiotics also prevented LPS/LTA induced activation of macrophages and was shown to be non-toxic to primary human nasal epithelial cells. Furthermore, both P. aeruginosa and S. aureus were unable to induce resistance against CR-163 and CR-172, two PepBiotics selected for their excellent antimicrobial and immunomodulatory properties. Toxicity studies in mice indicated that intratracheal administration of CR-163 was well tolerated in vivo. Finally, interaction of CR-163 with bacterial-type anionic membranes but not with mammalian-type (zwitterionic lipid) membranes was confirmed using ITC and 31P solid state NMR. CONCLUSIONS PepBiotics are a promising novel class of highly active antimicrobial peptides, of which CR-163 showed the most potential for treatment of clinically relevant (CF-) pathogens in physiological conditions. GENERAL SIGNIFICANCE These observations emphasize the therapeutic potential of PepBiotics against CF-related bacterial respiratory infections.
Collapse
Affiliation(s)
- Martin van Eijk
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| | - Albert van Dijk
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| | - Cornelis K van der Ent
- Department of Paediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Hubertus G M Arets
- Department of Paediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Nico van Os
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| | - Roy Adrichem
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| | - Sven van der Water
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| | - Rita Lino Gómez
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| | - Maartje Kristensen
- Department of Paediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Martin Hessing
- U-Protein Express B.V., Life Science Incubator, Utrecht Science Park, Yalelaan 62, 3584CM Utrecht, the Netherlands
| | - Shehrazade Jekhmane
- Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Markus Weingarth
- Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, the Netherlands
| | - Ruud A W Veldhuizen
- Department of Physiology and Pharmacology, Western University, London, Ontario, Canada
| | - Edwin J A Veldhuizen
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands; Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Immunology, Utrecht University, the Netherlands.
| | - Henk P Haagsman
- Faculty of Veterinary Medicine, Department of Biomolecular Health Sciences, Division Infectious Diseases & Immunology, Section Molecular Host Defence, Utrecht University, the Netherlands
| |
Collapse
|
14
|
Zhao X, Wang X, Shukla R, Kumar R, Weingarth M, Breukink E, Kuipers OP. Brevibacillin 2V, a Novel Antimicrobial Lipopeptide With an Exceptionally Low Hemolytic Activity. Front Microbiol 2021; 12:693725. [PMID: 34220785 PMCID: PMC8245773 DOI: 10.3389/fmicb.2021.693725] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial non-ribosomally produced peptides (NRPs) form a rich source of antibiotics, including more than 20 of these antibiotics that are used in the clinic, such as penicillin G, colistin, vancomycin, and chloramphenicol. Here we report the identification, purification, and characterization of a novel NRP, i.e., brevibacillin 2V (lipo-tridecapeptide), from Brevibacillus laterosporus DSM 25. Brevibacillin 2V has a strong antimicrobial activity against Gram-positive bacterial pathogens (minimum inhibitory concentration = 2 mg/L), including difficult-to-treat antibiotic-resistant Enterococcus faecium, Enterococcus faecalis, and Staphylococcus aureus. Notably, brevibacillin 2V has a much lower hemolytic activity (HC50 > 128 mg/L) and cytotoxicity (CC50 = 45.49 ± 0.24 mg/L) to eukaryotic cells than previously reported NRPs of the lipo-tridecapeptide family, including other brevibacillins, which makes it a promising candidate for antibiotic development. In addition, our results demonstrate that brevibacillins display a synergistic action with established antibiotics against Gram-negative bacterial pathogens. Probably due to the presence of non-canonical amino acids and D-amino acids, brevibacillin 2V showed good stability in human plasma. Thus, we identified and characterized a novel and promising antimicrobial candidate (brevibacillin 2V) with low hemolytic activity and cytotoxicity, which can be used either on its own or as a template for further total synthesis and modification.
Collapse
Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Rhythm Shukla
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.,NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| |
Collapse
|
15
|
Hernández-Rocamora VM, Baranova N, Peters K, Breukink E, Loose M, Vollmer W. Real-time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin-binding proteins. eLife 2021; 10:61525. [PMID: 33625355 PMCID: PMC7943195 DOI: 10.7554/elife.61525] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.
Collapse
Affiliation(s)
- Víctor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Natalia Baranova
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, Netherlands
| | - Martin Loose
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
16
|
Boes A, Kerff F, Herman R, Touze T, Breukink E, Terrak M. The bacterial cell division protein fragment EFtsN binds to and activates the major peptidoglycan synthase PBP1b. J Biol Chem 2020; 295:18256-18265. [PMID: 33109614 PMCID: PMC7939390 DOI: 10.1074/jbc.ra120.015951] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Peptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division, the machinery responsible for PG synthesis localizes mid-cell, at the septum, under the control of a multiprotein complex called the divisome. In Escherichia coli, septal PG synthesis and cell constriction rely on the accumulation of FtsN at the division site. Interestingly, a short sequence of FtsN (Leu75-Gln93, known as EFtsN) was shown to be essential and sufficient for its functioning in vivo, but what exactly this sequence is doing remained unknown. Here, we show that EFtsN binds specifically to the major PG synthase PBP1b and is sufficient to stimulate its biosynthetic glycosyltransferase (GTase) activity. We also report the crystal structure of PBP1b in complex with EFtsN, which demonstrates that EFtsN binds at the junction between the GTase and UB2H domains of PBP1b. Interestingly, mutations to two residues (R141A/R397A) within the EFtsN-binding pocket reduced the activation of PBP1b by FtsN but not by the lipoprotein LpoB. This mutant was unable to rescue the ΔponB-ponAts strain, which lacks PBP1b and has a thermosensitive PBP1a, at nonpermissive temperature and induced a mild cell-chaining phenotype and cell lysis. Altogether, the results show that EFtsN interacts with PBP1b and that this interaction plays a role in the activation of its GTase activity by FtsN, which may contribute to the overall septal PG synthesis and regulation during cell division.
Collapse
Affiliation(s)
- Adrien Boes
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium
| | - Frederic Kerff
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium
| | - Raphael Herman
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium
| | - Thierry Touze
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mohammed Terrak
- InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium.
| |
Collapse
|
17
|
Boes A, Brunel JM, Derouaux A, Kerff F, Bouhss A, Touze T, Breukink E, Terrak M. Squalamine and Aminosterol Mimics Inhibit the Peptidoglycan Glycosyltransferase Activity of PBP1b. Antibiotics (Basel) 2020; 9:antibiotics9070373. [PMID: 32630634 PMCID: PMC7400108 DOI: 10.3390/antibiotics9070373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is an essential polymer of the bacterial cell wall and a major antibacterial target. Its synthesis requires glycosyltransferase (GTase) and transpeptidase enzymes that, respectively, catalyze glycan chain elongation and their cross-linking to form the protective sacculus of the bacterial cell. The GTase domain of bifunctional penicillin-binding proteins (PBPs) of class A, such as Escherichia coli PBP1b, belong to the GTase 51 family. These enzymes play an essential role in PG synthesis, and their specific inhibition by moenomycin was shown to lead to bacterial cell death. In this work, we report that the aminosterol squalamine and mimic compounds present an unexpected mode of action consisting in the inhibition of the GTase activity of the model enzyme PBP1b. In addition, selected compounds were able to specifically displace the lipid II from the active site in a fluorescence anisotropy assay, suggesting that they act as competitive inhibitors.
Collapse
Affiliation(s)
- Adrien Boes
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Jean Michel Brunel
- UMR_MD1, U-1261, Aix Marseille Univ, INSERM, SSA, MCT, 13385 Marseille, France;
| | - Adeline Derouaux
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Frédéric Kerff
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (A.B.); (T.T.)
- Laboratoire Structure-Activite des Biomolecules Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Universite Paris-Saclay, 91025 Evry, France
| | - Thierry Touze
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (A.B.); (T.T.)
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands;
| | - Mohammed Terrak
- InBioS-Centre d’Ingénierie des Protéines, Liège University, 4000 Liège, Belgium; (A.B.); (A.D.); (F.K.)
- Correspondence: ; Tel.: +33-4366-3332
| |
Collapse
|
18
|
Caveney NA, Egan AJF, Ayala I, Laguri C, Robb CS, Breukink E, Vollmer W, Strynadka NCJ, Simorre JP. Structure of the Peptidoglycan Synthase Activator LpoP in Pseudomonas aeruginosa. Structure 2020; 28:643-650.e5. [PMID: 32320673 PMCID: PMC7267771 DOI: 10.1016/j.str.2020.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/15/2020] [Accepted: 03/24/2020] [Indexed: 12/23/2022]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall and is assembled from a lipid II precursor by glycosyltransferase and transpeptidase reactions catalyzed in particular by bifunctional class A penicillin-binding proteins (aPBPs). In the major clinical pathogen Pseudomonas aeruginosa, PBP1B is anchored within the cytoplasmic membrane but regulated by a bespoke outer membrane-localized lipoprotein known as LpoP. Here, we report the structure of LpoP, showing an extended N-terminal, flexible tether followed by a well-ordered C-terminal tandem-tetratricopeptide repeat domain. We show that LpoP stimulates both PBP1B transpeptidase and glycosyltransferase activities in vitro and interacts directly via its C terminus globular domain with the central UB2H domain of PBP1B. Contrary to the situation in E. coli, P. aeruginosa CpoB does not regulate PBP1B/LpoP in vitro. We propose a mechanism that helps to underscore similarities and differences in class A PBP activation across Gram-negative bacteria. Structural organization of LpoP has been resolved PaPBP1B is directly stimulated by LpoP but not by PaCpoB in vitro LpoP likely interacts between the GTase and UB2H domains of PaPBP1B
Collapse
Affiliation(s)
- Nathanael A Caveney
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver V6T 1Z3 BC, Canada
| | - Alexander J F Egan
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Isabel Ayala
- University of Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Cédric Laguri
- University of Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver V6T 1Z3 BC, Canada
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver V6T 1Z3 BC, Canada.
| | | |
Collapse
|
19
|
Wang X, Gu Q, Breukink E. Non-lipid II targeting lantibiotics. Biochim Biophys Acta Biomembr 2020; 1862:183244. [PMID: 32126235 DOI: 10.1016/j.bbamem.2020.183244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, China
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.
| |
Collapse
|
20
|
Banzhaf M, Yau HC, Verheul J, Lodge A, Kritikos G, Mateus A, Cordier B, Hov AK, Stein F, Wartel M, Pazos M, Solovyova AS, Breukink E, van Teeffelen S, Savitski MM, den Blaauwen T, Typas A, Vollmer W. Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli. EMBO J 2020; 39:e102246. [PMID: 32009249 PMCID: PMC7049810 DOI: 10.15252/embj.2019102246] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 12/20/2019] [Accepted: 01/14/2020] [Indexed: 12/16/2022] Open
Abstract
The peptidoglycan (PG) sacculus provides bacteria with the mechanical strength to maintain cell shape and resist osmotic stress. Enlargement of the mesh‐like sacculus requires the combined activity of peptidoglycan synthases and hydrolases. In Escherichia coli, the activity of two PG synthases is driven by lipoproteins anchored in the outer membrane (OM). However, the regulation of PG hydrolases is less well understood, with only regulators for PG amidases having been described. Here, we identify the OM lipoprotein NlpI as a general adaptor protein for PG hydrolases. NlpI binds to different classes of hydrolases and can specifically form complexes with various PG endopeptidases. In addition, NlpI seems to contribute both to PG elongation and division biosynthetic complexes based on its localization and genetic interactions. Consistent with such a role, we reconstitute PG multi‐enzyme complexes containing NlpI, the PG synthesis regulator LpoA, its cognate bifunctional synthase, PBP1A, and different endopeptidases. Our results indicate that peptidoglycan regulators and adaptors are part of PG biosynthetic multi‐enzyme complexes, regulating and potentially coordinating the spatiotemporal action of PG synthases and hydrolases.
Collapse
Affiliation(s)
- Manuel Banzhaf
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Hamish Cl Yau
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Jolanda Verheul
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Adam Lodge
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - George Kritikos
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Baptiste Cordier
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Paris, France
| | - Ann Kristin Hov
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Morgane Wartel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | | | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | | | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,European Molecular Biology Laboratory, Structural & Computational Unit, Heidelberg, Germany
| | - Tanneke den Blaauwen
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,European Molecular Biology Laboratory, Structural & Computational Unit, Heidelberg, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| |
Collapse
|
21
|
Kuru E, Radkov A, Meng X, Egan A, Alvarez L, Dowson A, Booher G, Breukink E, Roper DI, Cava F, Vollmer W, Brun Y, VanNieuwenhze MS. Mechanisms of Incorporation for D-Amino Acid Probes That Target Peptidoglycan Biosynthesis. ACS Chem Biol 2019; 14:2745-2756. [PMID: 31743648 PMCID: PMC6929685 DOI: 10.1021/acschembio.9b00664] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Bacteria exhibit a myriad of different morphologies,
through the
synthesis and modification of their essential peptidoglycan (PG) cell
wall. Our discovery of a fluorescent D-amino acid (FDAA)-based PG labeling approach provided a powerful method
for observing how these morphological changes occur. Given that PG
is unique to bacterial cells and a common target for antibiotics,
understanding the precise mechanism(s) for incorporation of (F)DAA-based
probes is a crucial determinant in understanding the role of PG synthesis
in bacterial cell biology and could provide a valuable tool in the
development of new antimicrobials to treat drug-resistant antibacterial
infections. Here, we systematically investigate the mechanisms of
FDAA probe incorporation into PG using two model organisms Escherichia coli (Gram-negative) and Bacillus subtilis (Gram-positive). Our in vitro and in vivo data unequivocally demonstrate
that these bacteria incorporate FDAAs using two extracytoplasmic pathways:
through activity of their D,D-transpeptidases, and,
if present, by their L,D-transpeptidases and not
via cytoplasmic incorporation into a D-Ala-D-Ala
dipeptide precursor. Our data also revealed the unprecedented finding
that the DAA-drug, D-cycloserine, can be incorporated into
peptide stems by each of these transpeptidases, in addition to its
known inhibitory activity against D-alanine racemase and D-Ala-D-Ala ligase. These mechanistic findings enabled
development of a new, FDAA-based, in vitro labeling approach that
reports on subcellular distribution of muropeptides, an especially
important attribute to enable the study of bacteria with poorly defined
growth modes. An improved understanding of the incorporation mechanisms
utilized by DAA-based probes is essential when interpreting results
from high resolution experiments and highlights the antimicrobial
potential of synthetic DAAs.
Collapse
Affiliation(s)
- Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Atanas Radkov
- Department of Biochemistry and Biophysics, UCSF School of Medicine, San Francisco, California 94158, United States
| | - Xin Meng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alexander Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Laura Alvarez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Amanda Dowson
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Garrett Booher
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Eefjan Breukink
- Department of Chemistry, Utrecht University, 3584 CH, Utrecht, Netherlands
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Felipe Cava
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Yves Brun
- Department of Microbiology, Infectious Diseases, and Immunology, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Michael S. VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
22
|
Medeiros-Silva J, Jekhmane S, Breukink E, Weingarth M. Towards the Native Binding Modes of Antibiotics that Target Lipid II. Chembiochem 2019; 20:1731-1738. [PMID: 30725496 PMCID: PMC6767406 DOI: 10.1002/cbic.201800796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 12/22/2022]
Abstract
The alarming rise of antimicrobial resistance (AMR) imposes severe burdens on healthcare systems and the economy worldwide, urgently calling for the development of new antibiotics. Antimicrobial peptides could be ideal templates for next‐generation antibiotics, due to their low propensity to cause resistance. An especially promising branch of antimicrobial peptides target lipid II, the precursor of the bacterial peptidoglycan network. To develop these peptides into clinically applicable compounds, detailed information on their pharmacologically relevant modes of action is of critical importance. Here we review the binding modes of a selection of peptides that target lipid II and highlight shortcomings in our molecular understanding that, at least partly, relate to the widespread use of artificial membrane mimics for structural studies of membrane‐active antibiotics. In particular, with the example of the antimicrobial peptide nisin, we showcase how the native cellular membrane environment can be critical for understanding of the physiologically relevant binding mode.
Collapse
Affiliation(s)
- João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
23
|
Mueller EA, Egan AJ, Breukink E, Vollmer W, Levin PA. Plasticity of Escherichia coli cell wall metabolism promotes fitness and antibiotic resistance across environmental conditions. eLife 2019; 8:40754. [PMID: 30963998 PMCID: PMC6456298 DOI: 10.7554/elife.40754] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 03/23/2019] [Indexed: 11/13/2022] Open
Abstract
Although the peptidoglycan cell wall is an essential structural and morphological feature of most bacterial cells, the extracytoplasmic enzymes involved in its synthesis are frequently dispensable under standard culture conditions. By modulating a single growth parameter-extracellular pH-we discovered a subset of these so-called 'redundant' enzymes in Escherichia coli are required for maximal fitness across pH environments. Among these pH specialists are the class A penicillin binding proteins PBP1a and PBP1b; defects in these enzymes attenuate growth in alkaline and acidic conditions, respectively. Genetic, biochemical, and cytological studies demonstrate that synthase activity is required for cell wall integrity across a wide pH range and influences pH-dependent changes in resistance to cell wall active antibiotics. Altogether, our findings reveal previously thought to be redundant enzymes are instead specialized for distinct environmental niches. This specialization may ensure robust growth and cell wall integrity in a wide range of conditions. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Collapse
Affiliation(s)
- Elizabeth A Mueller
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Alexander Jf Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| |
Collapse
|
24
|
Pazos M, Peters K, Casanova M, Palacios P, VanNieuwenhze M, Breukink E, Vicente M, Vollmer W. Publisher Correction: Z-ring membrane anchors associate with cell wall synthases to initiate bacterial cell division. Nat Commun 2019; 10:591. [PMID: 30700720 PMCID: PMC6353939 DOI: 10.1038/s41467-019-08410-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained errors in Figures 1 and 3. In Fig. 1b, the label 'IP-PBP3' above the second of the three blots incorrectly read 'IP-PBP1B'. In Fig. 3b, the label 'PBP1B' under the first bar of each chart incorrectly read 'PBP1A'. These errors have been corrected in both the PDF and HTML versions of the Article.
Collapse
Affiliation(s)
- Manuel Pazos
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Mercedes Casanova
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Pilar Palacios
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Michael VanNieuwenhze
- Molecular and Cellular Biochemistry Department, Biology Department, Indiana University, 212S. Hawthorne Dr, Bloomington, IN, 47405, USA
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Miguel Vicente
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| |
Collapse
|
25
|
Liu Y, Moura ECCM, Dörr JM, Scheidelaar S, Heger M, Egmond MR, Killian JA, Mohammadi T, Breukink E. Correction: Bacillus subtilis MraY in detergent-free system of nanodiscs wrapped by styrene-maleic acid copolymers. PLoS One 2018; 13:e0210135. [PMID: 30589887 PMCID: PMC6307741 DOI: 10.1371/journal.pone.0210135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
26
|
Pazos M, Peters K, Casanova M, Palacios P, VanNieuwenhze M, Breukink E, Vicente M, Vollmer W. Z-ring membrane anchors associate with cell wall synthases to initiate bacterial cell division. Nat Commun 2018; 9:5090. [PMID: 30504892 PMCID: PMC6269477 DOI: 10.1038/s41467-018-07559-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 11/08/2018] [Indexed: 12/29/2022] Open
Abstract
During the transition from elongation to septation, Escherichia coli establishes a ring-like peptidoglycan growth zone at the future division site. This preseptal peptidoglycan synthesis does not require the cell division-specific peptidoglycan transpeptidase PBP3 or most of the other cell division proteins, but it does require FtsZ, its membrane-anchor ZipA and at least one of the bi-functional transglycosylase-transpeptidases, PBP1A or PBP1B. Here we show that PBP1A and PBP1B interact with ZipA and localise to preseptal sites in cells with inhibited PBP3. ZipA stimulates the glycosyltransferase activity of PBP1A. The membrane-anchored cell division protein FtsN localises at preseptal sites and stimulates both activities of PBP1B. Genes zipA and ftsN can be individually deleted in ftsA* mutant cells, but the simultaneous depletion of both proteins is lethal and cells do not establish preseptal sites. Our data support a model according to which ZipA and FtsN-FtsA have semi-redundant roles in connecting the cytosolic FtsZ ring with the membrane-anchored peptidoglycan synthases during the preseptal phase of envelope growth. Proteins FtsZ, ZipA, and either PBP1A or PBP1B are required for the synthesis of preseptal peptidoglycan at the future cell division site in E. coli. Here, Pazos et al. provide evidence that ZipA and FtsA-FtsN connect the cytosolic FtsZ ring with the membrane-anchored PBPs.
Collapse
Affiliation(s)
- Manuel Pazos
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Mercedes Casanova
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Pilar Palacios
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Michael VanNieuwenhze
- Molecular and Cellular Biochemistry Department, Biology Department, Indiana University, 212S. Hawthorne Dr, Bloomington, IN, 47405, USA
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Miguel Vicente
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049, Madrid, Spain
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
| |
Collapse
|
27
|
Liu Y, Moura ECCM, Dörr JM, Scheidelaar S, Heger M, Egmond MR, Killian JA, Mohammadi T, Breukink E. Bacillus subtilis MraY in detergent-free system of nanodiscs wrapped by styrene-maleic acid copolymers. PLoS One 2018; 13:e0206692. [PMID: 30395652 PMCID: PMC6218056 DOI: 10.1371/journal.pone.0206692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/17/2018] [Indexed: 12/25/2022] Open
Abstract
As an integral membrane protein, purification and characterization of phospho-N- acetylmuramyl- pentapeptide translocase MraY have proven difficult. Low yield and concerns of retaining stability and activity after detergent solubilization have hampered the structure-function analysis. The recently developed detergent-free styrene-maleic acid (SMA) co-polymer system offers an alternative approach that may overcome these disadvantages. In this study, we used the detergent free system to purify MraY from Bacillus subtilis. This allowed efficient extraction of MraY that was heterologously produced in Escherichia coli membranes into SMA-wrapped nanodiscs. The purified MraY embedded in these nanodiscs (SMA-MraY) was comparable to the micellar MraY extracted with a conventional detergent (DDM) with regard to the yield and the purity of the recombinant protein but required significantly less time. The predominantly alpha-helical secondary structure of the protein in SMA-wrapped nanodiscs was also more stable against heat denaturation compared to the micellar protein. Thus, this detergent-free system is amenable to extract MraY efficiently and effectively while maintaining the biophysical properties of the protein. However, the apparent activity of the SMA-MraY was reduced compared to that of the detergent-solubilized protein. The present data indicates that this is caused by a lower accessibility of the enzyme in SMA-wrapped nanodiscs towards its polyisoprenoid substrate.
Collapse
Affiliation(s)
- Yao Liu
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Elisabete C. C. M. Moura
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Jonas M. Dörr
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Stefan Scheidelaar
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Michal Heger
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Maarten R. Egmond
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - J. Antoinette Killian
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Tamimount Mohammadi
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, the Netherlands
- * E-mail:
| |
Collapse
|
28
|
Egan AJF, Maya-Martinez R, Ayala I, Bougault CM, Banzhaf M, Breukink E, Vollmer W, Simorre JP. Induced conformational changes activate the peptidoglycan synthase PBP1B. Mol Microbiol 2018; 110:335-356. [PMID: 30044025 PMCID: PMC6220978 DOI: 10.1111/mmi.14082] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2018] [Indexed: 12/25/2022]
Abstract
Bacteria surround their cytoplasmic membrane with an essential, stress‐bearing peptidoglycan (PG) layer consisting of glycan chains linked by short peptides into a mesh‐like structure. Growing and dividing cells expand their PG layer using inner‐membrane anchored PG synthases, including Penicillin‐binding proteins (PBPs), which participate in dynamic protein complexes to facilitate cell wall growth. In Escherichia coli, and presumably other Gram‐negative bacteria, growth of the mainly single layered PG is regulated by outer membrane‐anchored lipoproteins. The lipoprotein LpoB is required to activate PBP1B, which is a major, bi‐functional PG synthase with glycan chain polymerising (glycosyltransferase) and peptide cross‐linking (transpeptidase) activities. In this work we show how the binding of LpoB to the regulatory UB2H domain of PBP1B activates both activities. Binding induces structural changes in the UB2H domain, which transduce to the two catalytic domains by distinct allosteric pathways. We also show how an additional regulator protein, CpoB, is able to selectively modulate the TPase activation by LpoB without interfering with GTase activation.
Collapse
Affiliation(s)
- Alexander J F Egan
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Roberto Maya-Martinez
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Catherine M Bougault
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| | - Manuel Banzhaf
- European Molecular Biology Laboratory Heidelberg, Genome Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany.,Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham , B15 2TT, UK
| | - Eefjan Breukink
- Bijvoet Center for Biomolecular Research, Department of Biochemistry of Membranes, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, 71 avenue des Martyrs, 38000, Grenoble, France
| |
Collapse
|
29
|
Medeiros-Silva J, Jekhmane S, Paioni AL, Gawarecka K, Baldus M, Swiezewska E, Breukink E, Weingarth M. High-resolution NMR studies of antibiotics in cellular membranes. Nat Commun 2018; 9:3963. [PMID: 30262913 PMCID: PMC6160437 DOI: 10.1038/s41467-018-06314-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/23/2018] [Indexed: 01/12/2023] Open
Abstract
The alarming rise of antimicrobial resistance requires antibiotics with unexploited mechanisms. Ideal templates could be antibiotics that target the peptidoglycan precursor lipid II, known as the bacterial Achilles heel, at an irreplaceable pyrophosphate group. Such antibiotics would kill multidrug-resistant pathogens at nanomolecular concentrations without causing antimicrobial resistance. However, due to the challenge of studying small membrane-embedded drug–receptor complexes in native conditions, the structural correlates of the pharmaceutically relevant binding modes are unknown. Here, using advanced highly sensitive solid-state NMR setups, we present a high-resolution approach to study lipid II-binding antibiotics directly in cell membranes. On the example of nisin, the preeminent lantibiotic, we show that the native antibiotic-binding mode strongly differs from previously published structures, and we demonstrate that functional hotspots correspond to plastic drug domains that are critical for the cellular adaptability of nisin. Thereby, our approach provides a foundation for an improved understanding of powerful antibiotics. Antibiotics that target the peptidoglycan precursor lipid II are promising templates for next-generation antibiotics. Here authors use solid-state NMR and monitor lipid II-binding antibiotics, such as nisin, directly in cell membranes.
Collapse
Affiliation(s)
- João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Katarzyna Gawarecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| |
Collapse
|
30
|
Montón Silva A, Otten C, Biboy J, Breukink E, VanNieuwenhze M, Vollmer W, den Blaauwen T. The Fluorescent D-Amino Acid NADA as a Tool to Study the Conditional Activity of Transpeptidases in Escherichia coli. Front Microbiol 2018; 9:2101. [PMID: 30233559 PMCID: PMC6131605 DOI: 10.3389/fmicb.2018.02101] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/17/2018] [Indexed: 01/01/2023] Open
Abstract
The enzymes responsible for the synthesis of the peptidoglycan (PG) layer constitute a fundamental target for a large group of antibiotics. The family of β-lactam antibiotics inhibits the DD-transpeptidase (TPase) activity of the penicillin binding proteins (PBPs), whereas its subgroup of carbapenems can also block the TPase activity of the LD-TPases. D-Ala fluorescent probes, such as NADA, are incorporated into the PG presumably by TPases in Escherichia coli and can be used to study conditions that are required for their function. Of all LD-TPases of E. coli, only LdtD was able to incorporate NADA during exponential growth. Overproduction of LdtD caused NADA to be especially inserted at mid cell in the presence of LpoB-activated PBP1b and the class C PBP5. Using the NADA assay, we could confirm that LpoB activates PBP1b at mid cell and that CpoB regulates the activity of PBP1b in vivo. Overproduction of LdtD was able to partly compensate for the inhibition of the cell division specific class B PBP3 by aztreonam. We showed that class A PBP1c and the class C PBP6b cooperated with LdtD for NADA incorporation when PBP1b and PBP5 were absent, respectively. Besides, we proved that LdtD is active at pH 7.0 whereas LdtE and LdtF are more active in cells growing at pH 5.0 and they seem to cooperate synergistically. The NADA assay proved to be a useful tool for the analysis of the in vivo activities of the proteins involved in PG synthesis and our results provide additional evidence that the LD-TPases are involved in PG maintenance at different conditions.
Collapse
Affiliation(s)
- Alejandro Montón Silva
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Christian Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Utrecht, Netherlands
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, United States
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
31
|
Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Håvarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun 2018; 9:3180. [PMID: 30093673 PMCID: PMC6085368 DOI: 10.1038/s41467-018-05602-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.
Collapse
Affiliation(s)
- Cécile Morlot
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Nolwenn Simon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Anne-Marie Villard
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | | | - Francisco Leisico
- Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands
| | - Christine Gravier-Pelletier
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Laurent Le Corre
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Nicolas Pietrancosta
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Leiv Sigve Håvarstein
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - André Zapun
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.
| |
Collapse
|
32
|
Jiang H, Tang X, Zhou Q, Zou J, Li P, Breukink E, Gu Q. Plantaricin NC8 from Lactobacillus plantarum causes cell membrane disruption to Micrococcus luteus without targeting lipid II. Appl Microbiol Biotechnol 2018; 102:7465-7473. [PMID: 29982926 DOI: 10.1007/s00253-018-9182-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/11/2018] [Accepted: 06/16/2018] [Indexed: 11/29/2022]
Abstract
Plantaricin NC8, a two-peptide non-lantibiotic class IIb bacteriocin composed of PLNC8α and PLNC8β and derived from Lactobacillus plantarum ZJ316, has been shown to be highly potent against a range of bacteria and fungi. In this study, we assessed the antimicrobial mechanism of plantaricin NC8 against the most sensitive bacterial strain, Micrococcus luteus CGMCC 1.193. The results showed that plantaricin NC8 induced membrane permeabilization and caused cell membrane disruption to M. luteus CGMCC 1.193 cells, as evidenced by electrolyte efflux, loss of proton motive force, and ATP depletion within a few minutes of plantaricin NC8 treatment. Furthermore, scanning and transmission electron microscopy showed that plantaricin NC8 had a drastic impact on the structure and integrity of M. luteus CGMCC 1.193 cells. In addition, we found that either PLNC8α or PLNC8β alone exhibited membrane permeabilization activity, but that PLNC8β had higher permeabilization activity, and their individual effects were not as strong as that of the combined compounds as plantaricin NC8. Finally, we showed that lipid II is not the specific target of plantaricin NC8 against M. luteus CGMCC 1.193. Our study reveals the antimicrobial mechanism of plantaricin NC8 against M. luteus CGMCC 1.193.
Collapse
Affiliation(s)
- Han Jiang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Department of Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China.,Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Xuan Tang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Department of Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Qingqing Zhou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Department of Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Jiong Zou
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, People's Republic of China
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Department of Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China.
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, 3584, CH, Utrecht, the Netherlands
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, Department of Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, People's Republic of China.
| |
Collapse
|
33
|
Hernández-Rocamora VM, Otten CF, Radkov A, Simorre JP, Breukink E, VanNieuwenhze M, Vollmer W. Coupling of polymerase and carrier lipid phosphatase prevents product inhibition in peptidoglycan synthesis. ACTA ACUST UNITED AC 2018; 2:1-13. [PMID: 30046664 PMCID: PMC6053597 DOI: 10.1016/j.tcsw.2018.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/30/2022]
Abstract
Peptidoglycan (PG) is an essential component of the bacterial cell wall that maintains the shape and integrity of the cell. The PG precursor lipid II is assembled at the inner leaflet of the cytoplasmic membrane, translocated to the periplasmic side, and polymerized to glycan chains by membrane anchored PG synthases, such as the class A Penicillin-binding proteins (PBPs). Polymerization of PG releases the diphosphate form of the carrier lipid, undecaprenyl pyrophosphate (C55-PP), which is converted to the monophosphate form by membrane-embedded pyrophosphatases, generating C55-P for a new round of PG precursor synthesis. Here we report that deletion of the C55-PP pyrophosphatase gene pgpB in E. coli increases the susceptibility to cefsulodin, a β-lactam specific for PBP1A, indicating that the cellular function of PBP1B is impaired in the absence of PgpB. Purified PBP1B interacted with PgpB and another C55-PP pyrophosphatase, BacA and both, PgpB and BacA stimulated the glycosyltransferase activity of PBP1B. C55-PP was found to be a potent inhibitor of PBP1B. Our data suggest that the stimulation of PBP1B by PgpB is due to the faster removal and processing of C55-PP, and that PBP1B interacts with C55-PP phosphatases during PG synthesis to couple PG polymerization with the recycling of the carrier lipid and prevent product inhibition by C55-PP.
Collapse
Affiliation(s)
- Víctor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Christian F Otten
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Atanas Radkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405-7102, USA
| | - Jean-Pierre Simorre
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405-7102, USA
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| |
Collapse
|
34
|
Parmar A, Iyer A, Prior SH, Lloyd DG, Leng Goh ET, Vincent CS, Palmai-Pallag T, Bachrati CZ, Breukink E, Madder A, Lakshminarayanan R, Taylor EJ, Singh I. Teixobactin analogues reveal enduracididine to be non-essential for highly potent antibacterial activity and lipid II binding. Chem Sci 2017; 8:8183-8192. [PMID: 29568465 PMCID: PMC5855875 DOI: 10.1039/c7sc03241b] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/04/2017] [Indexed: 11/25/2022] Open
Abstract
Leu10-teixobactin and Ile10-teixobactin have shown comparable activity to natural teixobactin.
Teixobactin is a highly promising antibacterial depsipeptide consisting of four d-amino acids and a rare l-allo-enduracididine amino acid. l-allo-Enduracididine is reported to be important for the highly potent antibacterial activity of teixobactin. However, it is also a key limiting factor in the development of potent teixobactin analogues due to several synthetic challenges such as it is not commercially available, requires a multistep synthesis, long and repetitive couplings (16–30 hours). Due to all these challenges, the total synthesis of teixobactin is laborious and low yielding (3.3%). In this work, we have identified a unique design and developed a rapid synthesis (10 min μwave assisted coupling per amino acid, 30 min cyclisation) of several highly potent analogues of teixobactin with yields of 10–24% by replacing the l-allo-enduracididine with commercially available non-polar residues such as leucine and isoleucine. Most importantly, the Leu10-teixobactin and Ile10-teixobactin analogues have shown highly potent antibacterial activity against a broader panel of MRSA and Enterococcus faecalis (VRE). Furthermore, these synthetic analogues displayed identical antibacterial activity to natural teixobactin (MIC 0.25 μg mL–1) against MRSA ATCC 33591 despite their simpler design and ease of synthesis. We have confirmed lipid II binding and measured the binding affinities of individual amino acid residues of Ala10-teixobactin towards geranyl pyrophosphate by NMR to understand the nature and strength of binding interactions. Contrary to current understanding, we have shown that a cationic amino acid at position 10 is not essential for target (lipid II) binding and potent antibacterial activity of teixobactin. We thus provide strong evidence contrary to the many assumptions made about the mechanism of action of this exciting new antibiotic. Introduction of a non-cationic residue at position 10 allows for tremendous diversification in the design and synthesis of highly potent teixobactin analogues and lays the foundations for the development of teixobactin analogues as new drug-like molecules to target MRSA and Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Anish Parmar
- School of Pharmacy , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK .
| | - Abhishek Iyer
- School of Pharmacy , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK . .,Organic and Biomimetic Chemistry Research Group , Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 (S4) , B-9000 Ghent , Belgium
| | - Stephen H Prior
- School of Chemistry , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK
| | - Daniel G Lloyd
- School of Life Sciences , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK
| | - Eunice Tze Leng Goh
- Singapore Eye Research Institute , The Academia, Discovery Tower Level 6, 20 College Road , Singapore 169857
| | - Charlotte S Vincent
- School of Life Sciences , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK
| | - Timea Palmai-Pallag
- School of Life Sciences , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK
| | - Csanad Z Bachrati
- School of Life Sciences , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics , Institute of Biomembranes , Utrecht University , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group , Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 (S4) , B-9000 Ghent , Belgium
| | - Rajamani Lakshminarayanan
- Singapore Eye Research Institute , The Academia, Discovery Tower Level 6, 20 College Road , Singapore 169857
| | - Edward J Taylor
- School of Life Sciences , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK
| | - Ishwar Singh
- School of Pharmacy , University of Lincoln , JBL Building, Beevor St. , Lincoln LN67DL , UK .
| |
Collapse
|
35
|
't Hart P, Wood TM, Tehrani KHME, van Harten RM, Śleszyńska M, Rentero Rebollo I, Hendrickx APA, Willems RJL, Breukink E, Martin NI. De novo identification of lipid II binding lipopeptides with antibacterial activity against vancomycin-resistant bacteria. Chem Sci 2017; 8:7991-7997. [PMID: 29568446 PMCID: PMC5853558 DOI: 10.1039/c7sc03413j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/29/2017] [Indexed: 12/20/2022] Open
Abstract
Lipid II binding lipopeptides discovered via bicyclic peptide phage display exhibit promising antibacterial activity.
Creative strategies for identifying new antibiotics are essential to addressing the looming threat of a post-antibiotic era. We here report the use of a targeted peptide phage display screen as a means of generating novel antimicrobial lipopeptides. Specifically, a library of phage displayed bicyclic peptides was screened against a biomolecular target based on the bacterial cell wall precursor lipid II. In doing so we identified unique lipid II binding peptides that upon lipidation were found to be active against a range of Gram-positive bacteria including clinically relevant strains of vancomycin resistant bacteria. Optimization of the peptide sequence led to variants with enhanced antibacterial activity and reduced hemolytic activity. Biochemical experiments further confirm a lipid II mediated mode of action for these new-to-nature antibacterial lipopeptides.
Collapse
Affiliation(s)
- Peter 't Hart
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Thomas M Wood
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Kamaleddin Haj Mohammad Ebrahim Tehrani
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Roel M van Harten
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Małgorzata Śleszyńska
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Inmaculada Rentero Rebollo
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne , Lausanne , Switzerland
| | - Antoni P A Hendrickx
- Department of Medical Microbiology , University Medical Center , Utrecht , The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology , University Medical Center , Utrecht , The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics Group , Department of Chemistry , Utrecht University , The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| |
Collapse
|
36
|
Calvez P, Breukink E, Roper DI, Dib M, Contreras-Martel C, Zapun A. Substitutions in PBP2b from β-Lactam-resistant Streptococcus pneumoniae Have Different Effects on Enzymatic Activity and Drug Reactivity. J Biol Chem 2017; 292:2854-2865. [PMID: 28062575 DOI: 10.1074/jbc.m116.764696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Pneumococcus resists β-lactams by expressing variants of its target enzymes, the penicillin-binding proteins (PBPs), with many amino acid substitutions. Up to 10% of the sequence can be modified. These altered PBPs have a much reduced reactivity with the drugs but retain their physiological activity of cross-linking the peptidoglycan, the major constituent of the bacterial cell wall. However, because β-lactams are chemical and structural mimics of the natural substrate, resistance mediated by altered PBPs raises the following paradox: how PBPs that react poorly with the drugs maintain a sufficient level of activity with the physiological substrate. This question is addressed for the first time in this study, which compares the peptidoglycan cross-linking activity of PBP2b from susceptible and resistant strains with their inhibition by different β-lactams. Unexpectedly, the enzymatic activity of the variants did not correlate with their antibiotic reactivity. This finding indicates that some of the numerous amino acid substitutions were selected to restore a viable level of enzymatic activity by a compensatory molecular mechanism.
Collapse
Affiliation(s)
- Philippe Calvez
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Eefjan Breukink
- the Department of Chemical Biology and Organic Chemistry, Institute of Biomembranes, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584 CH, The Netherlands, and
| | - David I Roper
- the School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mélanie Dib
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Carlos Contreras-Martel
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - André Zapun
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France,
| |
Collapse
|
37
|
Parmar A, Prior SH, Iyer A, Vincent CS, Van Lysebetten D, Breukink E, Madder A, Taylor EJ, Singh I. Defining the molecular structure of teixobactin analogues and understanding their role in antibacterial activities. Chem Commun (Camb) 2017; 53:2016-2019. [DOI: 10.1039/c6cc09490b] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we have for the first time defined the molecular structure of seven teixobactin analogues through the variation of the d/l configuration of its key residues.
Collapse
Affiliation(s)
- Anish Parmar
- School of Pharmacy
- JBL Building
- University of Lincoln
- Lincoln LN6 7DL
- UK
| | | | - Abhishek Iyer
- School of Pharmacy
- JBL Building
- University of Lincoln
- Lincoln LN6 7DL
- UK
| | - Charlotte S. Vincent
- School of Life Sciences
- Joseph Bank Laboratories
- University of Lincoln
- Lincoln LN6 7DL
- UK
| | - Dorien Van Lysebetten
- Organic and Biomimetic Chemistry Research Group
- Department of Organic Chemistry
- Ghent University
- B-9000 Ghent
- Belgium
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics
- Institute of Biomembranes
- Utrecht University
- 3584 CH Utrecht
- The Netherlands
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group
- Department of Organic Chemistry
- Ghent University
- B-9000 Ghent
- Belgium
| | - Edward J. Taylor
- School of Life Sciences
- Joseph Bank Laboratories
- University of Lincoln
- Lincoln LN6 7DL
- UK
| | - Ishwar Singh
- School of Pharmacy
- JBL Building
- University of Lincoln
- Lincoln LN6 7DL
- UK
| |
Collapse
|
38
|
van't Veer IL, Leloup NOL, Egan AJF, Janssen BJC, Martin NI, Vollmer W, Breukink E. Site-Specific Immobilization of the Peptidoglycan Synthase PBP1B on a Surface Plasmon Resonance Chip Surface. Chembiochem 2016; 17:2250-2256. [PMID: 27709766 PMCID: PMC5298014 DOI: 10.1002/cbic.201600461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 12/23/2022]
Abstract
Surface plasmon resonance (SPR) is one of the most powerful label-free methods to determine the kinetic parameters of molecular interactions in real time and in a highly sensitive way. Penicillin-binding proteins (PBPs) are peptidoglycan synthesis enzymes present in most bacteria. Established protocols to analyze interactions of PBPs by SPR involve immobilization to an ampicillin-coated chip surface (a β-lactam antibiotic mimicking its substrate), thereby forming a covalent complex with the PBPs transpeptidase (TP) active site. However, PBP interactions measured with a substrate-bound TP domain potentially affect interactions near the TPase active site. Furthermore, in vivo PBPs are anchored in the inner membrane by an N-terminal transmembrane helix, and hence immobilization at the C-terminal TPase domain gives an orientation contrary to the in vivo situation. We designed a new procedure: immobilization of PBP by copper-free click chemistry at an azide incorporated in the N terminus. In a proof-of-principle study, we immobilized Escherichia coli PBP1B on an SPR chip surface and used this for the analysis of the well-characterized interaction of PBP1B with LpoB. The site-specific incorporation of the azide affords control over protein orientation, thereby resulting in a homogeneous immobilization on the chip surface. This method can be used to study topology-dependent interactions of any (membrane) protein.
Collapse
Affiliation(s)
- Inge L. van't Veer
- Department of Membrane Biochemistry and BiophysicsUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Nadia O. L. Leloup
- Crystal and Structural ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Alexander J. F. Egan
- The Centre for Bacterial Cell BiologyNewcastle UniversityRichardson RoadNE2 4AX, Newcastle upon TyneUK
| | - Bert J. C. Janssen
- Crystal and Structural ChemistryUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUniversiteitsweg 993584 CGUtrechtThe Netherlands
| | - Waldemar Vollmer
- The Centre for Bacterial Cell BiologyNewcastle UniversityRichardson RoadNE2 4AX, Newcastle upon TyneUK
| | - Eefjan Breukink
- Department of Membrane Biochemistry and BiophysicsUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| |
Collapse
|
39
|
van't Veer IL, Leloup NOL, Egan AJF, Janssen BJC, Martin NI, Vollmer W, Breukink E. Inside Cover: Site-Specific Immobilization of the Peptidoglycan Synthase PBP1B on a Surface Plasmon Resonance Chip Surface (ChemBioChem 23/2016). Chembiochem 2016. [DOI: 10.1002/cbic.201600601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Inge L. van't Veer
- Department of Membrane Biochemistry and Biophysics; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Nadia O. L. Leloup
- Crystal and Structural Chemistry; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Alexander J. F. Egan
- The Centre for Bacterial Cell Biology; Newcastle University; Richardson Road NE2 4AX, Newcastle upon Tyne UK
| | - Bert J. C. Janssen
- Crystal and Structural Chemistry; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology and Drug Discovery; Utrecht Institute for Pharmaceutical Sciences; Utrecht University; Universiteitsweg 99 3584 CG Utrecht The Netherlands
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology; Newcastle University; Richardson Road NE2 4AX, Newcastle upon Tyne UK
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics; Utrecht University; Padualaan 8 3584 CH Utrecht The Netherlands
| |
Collapse
|
40
|
Cleverley RM, Rismondo J, Lockhart-Cairns MP, Van Bentum PT, Egan AJ, Vollmer W, Halbedel S, Baldock C, Breukink E, Lewis RJ. Subunit Arrangement in GpsB, a Regulator of Cell Wall Biosynthesis. Microb Drug Resist 2016; 22:446-60. [PMID: 27257764 PMCID: PMC5111876 DOI: 10.1089/mdr.2016.0050] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
GpsB, a key regulator of cell division in Gram-positive bacteria, interacts with a key peptidoglycan synthase at the cell division septum, the penicillin binding protein PBP1 (a.k.a. PonA). Bacillus subtilis GpsB has been reported to interact with other components of the cell division machinery, including EzrA, MreC, and PrkC. In this study, we report an analysis of the arrangement of subunits in Listeria monocytogenes GpsB by small-angle X-ray scattering. The resulting model has an elongated shape with residues critical for interaction with PBP1 and the cell membrane clustered at one end of the molecule. Mutations that destabilize the hexameric assembly of the wild-type protein have a gpsB null phenotype, indicating that oligomerization is critical for the correct function of GpsB. We suggest a model in which a single GpsB hexamer can interact with multiple PBP1 molecules and can therefore influence the arrangement of PBP1 molecules within the cell division machinery, a dynamic multiprotein complex called the divisome, consistent with a role for GpsB in modulating the synthesis of the cell wall.
Collapse
Affiliation(s)
- Robert M. Cleverley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Jeanine Rismondo
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Michael P. Lockhart-Cairns
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Paulien T. Van Bentum
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, the Netherlands
| | - Alexander J.F. Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sven Halbedel
- FG11 Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Clair Baldock
- Wellcome Trust Centre for Cell Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Utrecht, the Netherlands
| | - Richard J. Lewis
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| |
Collapse
|
41
|
Abstract
Peptidoglycan (PG) is an essential component in the cell wall of nearly all bacteria, forming a continuous, mesh-like structure, called the sacculus, around the cytoplasmic membrane to protect the cell from bursting by its turgor. Although PG synthases, the penicillin-binding proteins (PBPs), have been studied for 70 years, useful in vitro assays for measuring their activities were established only recently, and these provided the first insights into the regulation of these enzymes. Here, we review the current knowledge on the glycosyltransferase and transpeptidase activities of PG synthases. We provide new data showing that the bifunctional PBP1A and PBP1B from Escherichia coli are active upon reconstitution into the membrane environment of proteoliposomes, and that these enzymes also exhibit DD-carboxypeptidase activity in certain conditions. Both novel features are relevant for their functioning within the cell. We also review recent data on the impact of protein–protein interactions and other factors on the activities of PBPs. As an example, we demonstrate a synergistic effect of multiple protein–protein interactions on the glycosyltransferase activity of PBP1B, by its cognate lipoprotein activator LpoB and the essential cell division protein FtsN.
Collapse
Affiliation(s)
- Alexander J F Egan
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Inge van't Veer
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, University of Utrecht, Padualaan 8, 3584 Utrecht, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| |
Collapse
|
42
|
Liu Y, Rodrigues JPGLM, Bonvin AMJJ, Zaal EA, Berkers CR, Heger M, Gawarecka K, Swiezewska E, Breukink E, Egmond MR. New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies. J Biol Chem 2016; 291:15057-68. [PMID: 27226570 DOI: 10.1074/jbc.m116.717884] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Indexed: 01/01/2023] Open
Abstract
Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide.
Collapse
Affiliation(s)
- Yao Liu
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | | | | | - Esther A Zaal
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Celia R Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Michal Heger
- the Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands, and
| | - Katarzyna Gawarecka
- the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewa Swiezewska
- the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Eefjan Breukink
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands,
| | - Maarten R Egmond
- From Institute of Biomembranes, Department of Membrane Biochemistry and Biophysics, Utrecht University, 3584 CH, Utrecht, the Netherlands
| |
Collapse
|
43
|
Broekgaarden M, van Vught R, Oliveira S, Roovers RC, van Bergen en Henegouwen PMP, Pieters RJ, Van Gulik TM, Breukink E, Heger M. Site-specific conjugation of single domain antibodies to liposomes enhances photosensitizer uptake and photodynamic therapy efficacy. Nanoscale 2016; 8:6490-6494. [PMID: 26954515 DOI: 10.1039/c6nr00014b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Photodynamic therapy for therapy-resistant cancers will greatly benefit from targeted delivery of tumor photosensitizing agents. In this study, a strategy for the site-specific conjugation of single domain antibodies onto liposomes containing the photosensitizer zinc phthalocyanine was developed and tested.
Collapse
Affiliation(s)
- M Broekgaarden
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| | - R van Vught
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - S Oliveira
- Division of Cell Biology, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - R C Roovers
- Division of Cell Biology, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - R J Pieters
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, P. O. Box 80082, NL-3508 TB, Utrecht, The Netherlands
| | - T M Van Gulik
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| | - E Breukink
- Department of Membrane Biochemistry and Biophysics, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - M Heger
- Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| |
Collapse
|
44
|
Kleijn LHJ, Oppedijk SF, 't Hart P, van Harten RM, Martin-Visscher LA, Kemmink J, Breukink E, Martin NI. Total Synthesis of Laspartomycin C and Characterization of Its Antibacterial Mechanism of Action. J Med Chem 2016; 59:3569-74. [PMID: 26967152 DOI: 10.1021/acs.jmedchem.6b00219] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Laspartomycin C is a lipopeptide antibiotic with activity against a range of Gram-positive bacteria including drug-resistant pathogens. We report the first total synthesis of laspartomycin C as well as a series of structural variants. Laspartomycin C was found to specifically bind undecaprenyl phosphate (C55-P) and inhibit formation of the bacterial cell wall precursor lipid II. While several clinically used antibiotics target the lipid II pathway, there are no approved drugs that act on its C55-P precursor.
Collapse
Affiliation(s)
- Laurens H J Kleijn
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Sabine F Oppedijk
- Membrane Biochemistry and Biophysics Group, Department of Chemistry, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter 't Hart
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Roel M van Harten
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | | | - Johan Kemmink
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics Group, Department of Chemistry, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nathaniel I Martin
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| |
Collapse
|
45
|
Slootweg JC, van Herwerden EF, van Doremalen MFM, Breukink E, Liskamp RMJ, Rijkers DTS. Synthesis of nisin AB dicarba analogs using ring-closing metathesis: influence of sp(3) versus sp(2) hybridization of the α-carbon atom of residues dehydrobutyrine-2 and dehydroalanine-5 on the lipid II binding affinity. Org Biomol Chem 2016; 13:5997-6009. [PMID: 25940216 DOI: 10.1039/c5ob00336a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein the synthesis of two nisin AB dicarba analogs is described, focusing on amino acid modifications at positions 2 and 5. The nisin mimics were synthesized by a combination of solid phase synthesis of the linear peptides, followed by macrocyclization via ring-closing metathesis and fragment assembly by means of solution phase chemistry. The two N-terminal nisin AB-fragment mimics contain either the native dehydrobutyrine (Dhb)/dehydroalanine (Dha) amino acid residues or alanine at position 2 and 5, respectively. The native dehydrobutyrine at position 2 and dehydroalanine at position 5 were introduced as their precursors, namely threonine and serine, respectively, and subsequent dehydration was carried out by EDCI/CuCl as the condensing agent. Both AB-fragment mimics were analyzed in a lipid II binding assay and it was found that the Ala2/Ala5 AB-mimic (2) showed a reduced activity, while the Dhb2/Dha5 AB-mimic (3) was as active as the native AB-fragment (1).
Collapse
Affiliation(s)
- Jack C Slootweg
- Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
| | | | | | | | | | | |
Collapse
|
46
|
't Hart P, Oppedijk SF, Breukink E, Martin NI. New Insights into Nisin's Antibacterial Mechanism Revealed by Binding Studies with Synthetic Lipid II Analogues. Biochemistry 2015; 55:232-7. [PMID: 26653142 DOI: 10.1021/acs.biochem.5b01173] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nisin is the preeminent lantibiotic, and to date its antibacterial mechanism has been investigated using a variety of techniques. While nisin's lipid II-mediated mode of action is well-established, a detailed analysis of the thermodynamic parameters governing this interaction has not been previously reported. We here describe an approach employing isothermal titration calorimetry to directly measure the affinity of nisin for lipid II and a number of synthetic lipid II precursors and analogues. Our measurements confirm the pyrophosphate unit of lipid II as the primary site of nisin binding and also indicate that the complete MurNAc moiety is required for a high-affinity interaction. Additionally, we find that while the pentapeptide unit of the lipid II molecule is not required for strong binding by nisin, it does play an important role in stabilizing the subsequently formed nisin-lipid II pore complex, albeit at an entropic cost. The anchoring of lipid II in a membrane environment was also found to play a significant role in enhancing nisin binding and is required in order to achieve a high-affinity interaction.
Collapse
Affiliation(s)
- Peter 't Hart
- Department of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Sabine F Oppedijk
- Membrane Biochemistry and Biophysics Group, Department of Chemistry, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics Group, Department of Chemistry, Utrecht University , Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nathaniel I Martin
- Department of Medicinal Chemistry & Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University , Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| |
Collapse
|
47
|
Sosič I, Anderluh M, Sova M, Gobec M, Mlinarič Raščan I, Derouaux A, Amoroso A, Terrak M, Breukink E, Gobec S. Structure-Activity Relationships of Novel Tryptamine-Based Inhibitors of Bacterial Transglycosylase. J Med Chem 2015; 58:9712-21. [PMID: 26588190 DOI: 10.1021/acs.jmedchem.5b01482] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Penicillin-binding proteins represent well-established, validated, and still very promising targets for the design and development of new antibacterial agents. The transglycosylase domain of penicillin-binding proteins is especially important, as it catalyzes polymerization of glycan chains, using the peptidoglycan precursor lipid II as a substrate. On the basis of the previous discovery of a noncovalent small-molecule inhibitor of transglycosylase activity, we systematically explored the structure-activity relationships of these tryptamine-based inhibitors. The main aim was to reduce the nonspecific cytotoxic properties of the initial hit compound and concurrently to retain the mode of its inhibition. A focused library of tryptamine-based compounds was synthesized, characterized, and evaluated biochemically. The results presented here show the successful reduction of the nonspecific cytotoxicity, and the retention of the inhibition of transglycosylase enzymatic activity, as well as the ability of these compounds to bind to lipid II and to have antibacterial actions.
Collapse
Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Irena Mlinarič Raščan
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Adeline Derouaux
- Centre d'Ingénierie des Protéines, Université de Liège , Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Ana Amoroso
- Centre d'Ingénierie des Protéines, Université de Liège , Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Mohammed Terrak
- Centre d'Ingénierie des Protéines, Université de Liège , Allée de la Chimie, B6a, B-4000, Sart Tilman, Liège, Belgium
| | - Eefjan Breukink
- Department Biochemistry of Membranes, Bijvoet Centre, Institute of Biomembranes, Utrecht University , Utrecht 3584 CH, The Netherlands
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
| |
Collapse
|
48
|
Liu Y, Qin R, Zaat SAJ, Breukink E, Heger M. Antibacterial photodynamic therapy: overview of a promising approach to fight antibiotic-resistant bacterial infections. J Clin Transl Res 2015; 1:140-167. [PMID: 30873451 PMCID: PMC6410618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 11/22/2015] [Accepted: 12/28/2015] [Indexed: 10/28/2022] Open
Abstract
Antibacterial photodynamic therapy (APDT) has drawn increasing attention from the scientific society for its potential to effectively kill multidrug-resistant pathogenic bacteria and for its low tendency to induce drug resistance that bacteria can rapidly develop against traditional antibiotic therapy. The review summarizes the mechanism of action of APDT, the photosensitizers, the barriers to PS localization, the targets, the in vitro-, in vivo-, and clinical evidence, the current developments in terms of treating Gram-positive and Gram-negative bacteria, the limitations, as well as future perspectives. Relevance for patients: A structured overview of all important aspects of APDT is provided in the context of resistant bacterial species. The information presented is relevant and accessible for scientists as well as clinicians, whose joint effort is required to ensure that this technology benefits patients in the post-antibiotic era.
Collapse
Affiliation(s)
- Yao Liu
- Department of Membrane Biochemistry and Biophysics, Utrecht University, the Netherlands
| | - Rong Qin
- Department of Membrane Biochemistry and Biophysics, Utrecht University, the Netherlands
| | - Sebastian A. J. Zaat
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Eefjan Breukink
- Department of Membrane Biochemistry and Biophysics, Utrecht University, the Netherlands
| | - Michal Heger
- Department of Membrane Biochemistry and Biophysics, Utrecht University, the Netherlands, Department of Experimental Surgery, Academic Medical Center, University of Amsterdam, the Netherlands
| |
Collapse
|
49
|
Oppedijk SF, Martin NI, Breukink E. Hit 'em where it hurts: The growing and structurally diverse family of peptides that target lipid-II. Biochim Biophys Acta 2015; 1858:947-57. [PMID: 26523408 DOI: 10.1016/j.bbamem.2015.10.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 02/08/2023]
Abstract
Understanding the mode of action of antibiotics is becoming more and more important in the time that microorganisms start to develop resistance. One very well validated target of several classes of antibiotics is the peptidoglycan precursor lipid II. In this review different classes of lipid II targeting antibiotics will be discussed in detail, including the lantibiotics, human invertebrate defensins and the recently discovered teixobactin. By hitting bacteria where it hurts, at the level of lipid II, we expect to be able to develop efficient antibacterial agents in the future. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
Collapse
Affiliation(s)
- Sabine F Oppedijk
- Membrane biochemistry and Biophysics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nathaniel I Martin
- Medicinal Chemistry and Chemical Biology, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Eefjan Breukink
- Membrane biochemistry and Biophysics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| |
Collapse
|
50
|
Blanchaert B, Wyseure T, Breukink E, Adams E, Declerck P, Van Schepdael A. Development of a liquid chromatography/mass spectrometry assay for the bacterial transglycosylation reaction through measurement of Lipid II. Electrophoresis 2015; 36:2841-2849. [DOI: 10.1002/elps.201500201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Bart Blanchaert
- Department of Pharmaceutical and Pharmacological sciences, Pharmaceutical analysis; KU Leuven - University of Leuven; Leuven Belgium
| | - Tine Wyseure
- Department of Pharmaceutical and Pharmacological sciences, Therapeutic and Diagnostic Antibodies; KU Leuven - University of Leuven; Leuven Belgium
| | - Eefjan Breukink
- Department of Biochemistry of Membranes, Bijvoet Center for Biomolecular Research; University of Utrecht; Utrecht The Netherlands
| | - Erwin Adams
- Department of Pharmaceutical and Pharmacological sciences, Pharmaceutical analysis; KU Leuven - University of Leuven; Leuven Belgium
| | - Paul Declerck
- Department of Pharmaceutical and Pharmacological sciences, Therapeutic and Diagnostic Antibodies; KU Leuven - University of Leuven; Leuven Belgium
| | - Ann Van Schepdael
- Department of Pharmaceutical and Pharmacological sciences, Pharmaceutical analysis; KU Leuven - University of Leuven; Leuven Belgium
| |
Collapse
|