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Duprez W, Premkumar L, Halili MA, Lindahl F, Reid RC, Fairlie DP, Martin JL. Peptide inhibitors of the Escherichia coli DsbA oxidative machinery essential for bacterial virulence. J Med Chem 2014; 58:577-87. [PMID: 25470204 DOI: 10.1021/jm500955s] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
One approach to address antibiotic resistance is to develop drugs that interfere with bacterial virulence. A master regulator of virulence in Gram-negative bacteria is the oxidative folding machinery comprising DsbA and DsbB. A crystal structure at 2.5 Å resolution is reported here for Escherichia coli DsbA complexed with PFATCDS, a heptapeptide derived from the partner protein Escherichia coli DsbB. Details of the peptide binding mode and binding site provide valuable clues for inhibitor design. Structure-activity relationships for 30 analogues were used to produce short peptides with a cysteine that bind tightly to EcDsbA (Kd = 2.0 ± 0.3 μM) and inhibit its activity (IC50 = 5.1 ± 1.1 μM). The most potent inhibitor does not bind to or inhibit human thioredoxin that shares a similar active site. This finding suggests that small molecule inhibitors can be designed to exploit a key interaction of EcDsbA, as the basis for antivirulence agents with a novel mechanism of action.
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Affiliation(s)
- Wilko Duprez
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland , Brisbane, Queensland 4072, Australia
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Premkumar L, Kurth F, Duprez W, Grøftehauge MK, King GJ, Halili MA, Heras B, Martin JL. Structure of the Acinetobacter baumannii dithiol oxidase DsbA bound to elongation factor EF-Tu reveals a novel protein interaction site. J Biol Chem 2014; 289:19869-80. [PMID: 24860094 DOI: 10.1074/jbc.m114.571737] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The multidrug resistant bacterium Acinetobacter baumannii is a significant cause of nosocomial infection. Biofilm formation, that requires both disulfide bond forming and chaperone-usher pathways, is a major virulence trait in this bacterium. Our biochemical characterizations show that the periplasmic A. baumannii DsbA (AbDsbA) enzyme has an oxidizing redox potential and dithiol oxidase activity. We found an unexpected non-covalent interaction between AbDsbA and the highly conserved prokaryotic elongation factor, EF-Tu. EF-Tu is a cytoplasmic protein but has been localized extracellularly in many bacterial pathogens. The crystal structure of this complex revealed that the EF-Tu switch I region binds to the non-catalytic surface of AbDsbA. Although the physiological and pathological significance of a DsbA/EF-Tu association is unknown, peptides derived from the EF-Tu switch I region bound to AbDsbA with submicromolar affinity. We also identified a seven-residue DsbB-derived peptide that bound to AbDsbA with low micromolar affinity. Further characterization confirmed that the EF-Tu- and DsbB-derived peptides bind at two distinct sites. These data point to the possibility that the non-catalytic surface of DsbA is a potential substrate or regulatory protein interaction site. The two peptides identified in this work together with the newly characterized interaction site provide a novel starting point for inhibitor design targeting AbDsbA.
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Affiliation(s)
- Lakshmanane Premkumar
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Fabian Kurth
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Wilko Duprez
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Morten K Grøftehauge
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Gordon J King
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Maria A Halili
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Begoña Heras
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Jennifer L Martin
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St. Lucia, Queensland 4067, Australia
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Kurth F, Duprez W, Premkumar L, Schembri MA, Fairlie DP, Martin JL. Crystal structure of the dithiol oxidase DsbA enzyme from proteus mirabilis bound non-covalently to an active site peptide ligand. J Biol Chem 2014; 289:19810-22. [PMID: 24831013 DOI: 10.1074/jbc.m114.552380] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery.
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Affiliation(s)
- Fabian Kurth
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and
| | - Wilko Duprez
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and
| | - Lakshmanane Premkumar
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - David P Fairlie
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Jennifer L Martin
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland 4067, Australia
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Premkumar L, McMahon R, Kurth F, Duprez W, Martin J. Development of subclass‐specific antivirulence inhibitors against disulfide oxidoreductase DsbA (LB193). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.lb193] [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)
- Lakshmanane Premkumar
- Chemistry and Structural Biology Institute for Molecular Bioscience St LuciaAustralia
| | - Roisin McMahon
- Chemistry and Structural Biology Institute for Molecular Bioscience St LuciaAustralia
| | - Fabian Kurth
- Chemistry and Structural Biology Institute for Molecular Bioscience St LuciaAustralia
| | - Wilko Duprez
- Chemistry and Structural Biology Institute for Molecular Bioscience St LuciaAustralia
| | - Jennifer Martin
- Chemistry and Structural Biology Institute for Molecular Bioscience St LuciaAustralia
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Kurth F, Rimmer K, Premkumar L, Mohanty B, Duprez W, Halili MA, Shouldice SR, Heras B, Fairlie DP, Scanlon MJ, Martin JL. Comparative sequence, structure and redox analyses of Klebsiella pneumoniae DsbA show that anti-virulence target DsbA enzymes fall into distinct classes. PLoS One 2013; 8:e80210. [PMID: 24244651 PMCID: PMC3828196 DOI: 10.1371/journal.pone.0080210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022] Open
Abstract
Bacterial DsbA enzymes catalyze oxidative folding of virulence factors, and have been identified as targets for antivirulence drugs. However, DsbA enzymes characterized to date exhibit a wide spectrum of redox properties and divergent structural features compared to the prototypical DsbA enzyme of Escherichia coli DsbA (EcDsbA). Nonetheless, sequence analysis shows that DsbAs are more highly conserved than their known substrate virulence factors, highlighting the potential to inhibit virulence across a range of organisms by targeting DsbA. For example, Salmonella enterica typhimurium (SeDsbA, 86 % sequence identity to EcDsbA) shares almost identical structural, surface and redox properties. Using comparative sequence and structure analysis we predicted that five other bacterial DsbAs would share these properties. To confirm this, we characterized Klebsiella pneumoniae DsbA (KpDsbA, 81 % identity to EcDsbA). As expected, the redox properties, structure and surface features (from crystal and NMR data) of KpDsbA were almost identical to those of EcDsbA and SeDsbA. Moreover, KpDsbA and EcDsbA bind peptides derived from their respective DsbBs with almost equal affinity, supporting the notion that compounds designed to inhibit EcDsbA will also inhibit KpDsbA. Taken together, our data show that DsbAs fall into different classes; that DsbAs within a class may be predicted by sequence analysis of binding loops; that DsbAs within a class are able to complement one another in vivo and that compounds designed to inhibit EcDsbA are likely to inhibit DsbAs within the same class.
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Affiliation(s)
- Fabian Kurth
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Kieran Rimmer
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Lakshmanane Premkumar
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Biswaranjan Mohanty
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Wilko Duprez
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Maria A. Halili
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Stephen R. Shouldice
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Begoña Heras
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Martin J. Scanlon
- Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre of Excellence for Coherent X-ray Science, Monash University, Parkville, Victoria, Australia
- * E-mail: (JLM); (MJS)
| | - Jennifer L. Martin
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (JLM); (MJS)
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Premkumar L, Heras B, Duprez W, Walden P, Halili M, Kurth F, Fairlie DP, Martin JL. Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like disulfide oxidases. Acta Crystallogr D Biol Crystallogr 2013; 69:1981-94. [PMID: 24100317 PMCID: PMC3792642 DOI: 10.1107/s0907444913017800] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 12/16/2022]
Abstract
The bacterial disulfide machinery is an attractive molecular target for developing new antibacterials because it is required for the production of multiple virulence factors. The archetypal disulfide oxidase proteins in Escherichia coli (Ec) are DsbA and DsbB, which together form a functional unit: DsbA introduces disulfides into folding proteins and DsbB reoxidizes DsbA to maintain it in the active form. In Mycobacterium tuberculosis (Mtb), no DsbB homologue is encoded but a functionally similar but structurally divergent protein, MtbVKOR, has been identified. Here, the Mtb protein Rv2969c is investigated and it is shown that it is the DsbA-like partner protein of MtbVKOR. It is found that it has the characteristic redox features of a DsbA-like protein: a highly acidic catalytic cysteine, a highly oxidizing potential and a destabilizing active-site disulfide bond. Rv2969c also has peptide-oxidizing activity and recognizes peptide segments derived from the periplasmic loops of MtbVKOR. Unlike the archetypal EcDsbA enzyme, Rv2969c has little or no activity in disulfide-reducing and disulfide-isomerase assays. The crystal structure of Rv2969c reveals a canonical DsbA fold comprising a thioredoxin domain with an embedded helical domain. However, Rv2969c diverges considerably from other DsbAs, including having an additional C-terminal helix (H8) that may restrain the mobility of the catalytic helix H1. The enzyme is also characterized by a very shallow hydrophobic binding surface and a negative electrostatic surface potential surrounding the catalytic cysteine. The structure of Rv2969c was also used to model the structure of a paralogous DsbA-like domain of the Ser/Thr protein kinase PknE. Together, these results show that Rv2969c is a DsbA-like protein with unique properties and a limited substrate-binding specificity.
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Affiliation(s)
- Lakshmanane Premkumar
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Begoña Heras
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Wilko Duprez
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Patricia Walden
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Maria Halili
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Fabian Kurth
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Jennifer L. Martin
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
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