1
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Jekhmane S, Derks MGN, Maity S, Slingerland CJ, Tehrani KHME, Medeiros-Silva J, Charitou V, Ammerlaan D, Fetz C, Consoli NA, Cochrane RVK, Matheson EJ, van der Weijde M, Elenbaas BOW, Lavore F, Cox R, Lorent JH, Baldus M, Künzler M, Lelli M, Cochrane SA, Martin NI, Roos WH, Breukink E, Weingarth M. Host defence peptide plectasin targets bacterial cell wall precursor lipid II by a calcium-sensitive supramolecular mechanism. Nat Microbiol 2024; 9:1778-1791. [PMID: 38783023 PMCID: PMC11222147 DOI: 10.1038/s41564-024-01696-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 04/04/2024] [Indexed: 05/25/2024]
Abstract
Antimicrobial resistance is a leading cause of mortality, calling for the development of new antibiotics. The fungal antibiotic plectasin is a eukaryotic host defence peptide that blocks bacterial cell wall synthesis. Here, using a combination of solid-state nuclear magnetic resonance, atomic force microscopy and activity assays, we show that plectasin uses a calcium-sensitive supramolecular killing mechanism. Efficient and selective binding of the target lipid II, a cell wall precursor with an irreplaceable pyrophosphate, is achieved by the oligomerization of plectasin into dense supra-structures that only form on bacterial membranes that comprise lipid II. Oligomerization and target binding of plectasin are interdependent and are enhanced by the coordination of calcium ions to plectasin's prominent anionic patch, causing allosteric changes that markedly improve the activity of the antibiotic. Structural knowledge of how host defence peptides impair cell wall synthesis will likely enable the development of superior drug candidates.
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Affiliation(s)
- Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Maik G N Derks
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
- Membrane Biochemistry and Biophysics, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Kamaleddin H M E Tehrani
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Vicky Charitou
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Danique Ammerlaan
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Céline Fetz
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Naomi A Consoli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Rachel V K Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - Eilidh J Matheson
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - Mick van der Weijde
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Barend O W Elenbaas
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Francesca Lavore
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Ruud Cox
- Membrane Biochemistry and Biophysics, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Joseph H Lorent
- Membrane Biochemistry and Biophysics, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Moreno Lelli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast, UK
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Utrecht University, Utrecht, The Netherlands.
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2
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Karak M, Cloonan CR, Baker BR, Cochrane RVK, Cochrane SA. Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target. Beilstein J Org Chem 2024; 20:220-227. [PMID: 38352069 PMCID: PMC10862138 DOI: 10.3762/bjoc.20.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Lipid II is an essential glycolipid found in bacteria. Accessing this valuable cell wall precursor is important both for studying cell wall synthesis and for studying/identifying novel antimicrobial compounds. Herein, we describe optimizations to the modular chemical synthesis of lipid II and unnatural analogues. In particular, the glycosylation step, a critical step in the formation of the central disaccharide unit (GlcNAc-MurNAc), was optimized. This was achieved by employing the use of glycosyl donors with diverse leaving groups. The key advantage of this approach lies in its adaptability, allowing for the generation of a wide array of analogues through the incorporation of alternative building blocks at different stages of synthesis.
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Affiliation(s)
- Milandip Karak
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Cian R Cloonan
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Brad R Baker
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Rachel V K Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
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3
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Reid A, Erickson KM, Hazel JM, Lukose V, Troutman JM. Chemoenzymatic Preparation of a Campylobacter jejuni Lipid-Linked Heptasaccharide on an Azide-Linked Polyisoprenoid. ACS OMEGA 2023; 8:15790-15798. [PMID: 37151508 PMCID: PMC10157688 DOI: 10.1021/acsomega.3c01657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023]
Abstract
Complex poly- and oligosaccharides on the surface of bacteria provide a unique fingerprint to different strains of pathogenic and symbiotic microbes that could be exploited for therapeutics or sensors selective for specific glycans. To discover reagents that can selectively interact with specific bacterial glycans, a system for both the chemoenzymatic preparation and immobilization of these materials would be ideal. Bacterial glycans are typically synthesized in nature on the C55 polyisoprenoid bactoprenyl (or undecaprenyl) phosphate. However, this long-chain isoprenoid can be difficult to work with in vitro. Here, we describe the addition of a chemically functional benzylazide tag to polyisoprenoids. We have found that both the organic-soluble and water-soluble benzylazide isoprenoid can serve as a substrate for the well-characterized system responsible for Campylobacter jejuni N-linked heptasaccharide assembly. Using the organic-soluble analogue, we demonstrate the use of an N-acetyl-glucosamine epimerase that can be used to lower the cost of glycan assembly, and using the water-soluble analogue, we demonstrate the immobilization of the C. jejuni heptasaccharide on magnetic beads. These conjugated beads are then shown to interact with soybean agglutinin, a lectin known to interact with N-acetyl-galactosamine in the C. jejuni heptasaccharide. The methods provided could be used for a wide variety of applications including the discovery of new glycan-interacting partners.
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Affiliation(s)
- Amanda
J. Reid
- Nanoscale
Science Program, University of North Carolina
at Charlotte, 9201 University City Blvd., Charlotte, North Carolina 28223, United States
| | - Katelyn M. Erickson
- Nanoscale
Science Program, University of North Carolina
at Charlotte, 9201 University City Blvd., Charlotte, North Carolina 28223, United States
| | - Joseph M. Hazel
- Department
of Chemistry, University of North Carolina
at Charlotte, 9201 University
City Blvd., Charlotte, North
Carolina 28223, United States
- Department
of Chemistry, The Ohio State University, 281 W Lane Avenue, Columbus, Ohio 43210, United States
| | - Vinita Lukose
- Departments
of Chemistry and Biology, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jerry M. Troutman
- Nanoscale
Science Program, University of North Carolina
at Charlotte, 9201 University City Blvd., Charlotte, North Carolina 28223, United States
- Department
of Chemistry, University of North Carolina
at Charlotte, 9201 University
City Blvd., Charlotte, North
Carolina 28223, United States
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4
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Moreira R, Taylor SD. A54145 Factor D Is Not Less Susceptible to Inhibition by Lung Surfactant than Daptomycin. ACS Infect Dis 2022; 8:1935-1947. [PMID: 36001599 DOI: 10.1021/acsinfecdis.2c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A54145 factor D (A5D) is a cyclic lipopeptide antibiotic that shares several structural and mechanistic features with the clinically important antibiotic daptomycin, such as their requirement for calcium and phosphatidylglycerol (PG) for activity. Studies by others have suggested that daptomycin's activity is strongly inhibited by lung surfactant while A5D's activity is not. This finding has inspired efforts, albeit unsuccessful, to develop an A5D analogue that is highly active in the presence of lung surfactant and can be used for treating community acquired pneumonia (CAP). Here we demonstrate that A5D, like daptomycin, has a strong preference for the 1,2-diacyl-sn-glycero-3-phospho-1'-sn-glycerol stereoisomer (2R,2'S configuration) of PG. This PG stereoisomer was determined to be the only stereoisomer of PG in lung surfactant. Both antibiotics are completely antagonized by approximately 1-2 mol equiv of 2R,2'S-PG. Studies performed in the presence of lung surfactant revealed that the antagonism of these peptides by surfactant is mainly due to their interaction with PG and that A5D is not significantly less susceptible to inhibition by lung surfactant than daptomycin.
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Affiliation(s)
- Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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5
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Hsu TW, Fang JM. Effective assay of bacterial transglycosylation by molecular turn-on sensing and a second-order scattering effect. Analyst 2021; 146:5843-5847. [PMID: 34570849 DOI: 10.1039/d1an00941a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Instead of using the lipid II substrate that requires prior labelling with a radioactive isotope or fluorophore to probe the formation of peptidoglycan in bacterial transglycosylation, the released undecaprenyl pyrophosphate (UPP) product is quantitatively measured either using a terpyridine-zinc fluorescence turn-on sensor or simply by the second-order scattering effect of the in situ formed UPP-calcium complex. Both the assay methods are utilized to identify moenomycin A as a potent transglycosylase inhibitor with a consistent IC50 value.
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Affiliation(s)
- Tse-Wei Hsu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
| | - Jim-Min Fang
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan. .,The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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6
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Baker BR, Ives CM, Bray A, Caffrey M, Cochrane SA. Undecaprenol kinase: Function, mechanism and substrate specificity of a potential antibiotic target. Eur J Med Chem 2020; 210:113062. [PMID: 33310291 DOI: 10.1016/j.ejmech.2020.113062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
The bifunctional undecaprenol kinase/phosphatase (UdpK) is a small, prokaryotic, integral membrane kinase, homologous with Escherichia coli diacylglycerol kinase and expressed by the dgkA gene. In Gram-positive bacteria, UdpK is involved in the homeostasis of the bacterial undecaprenoid pool, where it converts undecaprenol to undecaprenyl phosphate (C55P) and also catalyses the reverse process. C55P is the universal lipid carrier and critical to numerous glycopolymer and glycoprotein biosynthetic pathways in bacteria. DgkA gene expression has been linked to facilitating bacterial growth and survival in response to environmental stressors, as well being implicated as a resistance mechanism to the topical antibiotic bacitracin, by providing an additional route to C55P. Therefore, identification of UdpK inhibitors could lead to novel antibiotic treatments. A combination of homology modelling and mutagenesis experiments on UdpK have been used to identify residues that may be involved in kinase/phosphatase activity. In this review, we will summarise recent work on the mechanism and substrate specificity of UdpK.
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Affiliation(s)
- Brad R Baker
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Callum M Ives
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland; Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Ashley Bray
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160, Pearse Street, Dublin 2, D02 R590, Ireland.
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK.
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