1
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Cao J, Belousoff MJ, Danev R, Christopoulos A, Wootten D, Sexton PM. Cryo-EM Structure of the Human Amylin 1 Receptor in Complex with CGRP and Gs Protein. Biochemistry 2024. [PMID: 38603770 DOI: 10.1021/acs.biochem.4c00114] [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] [Indexed: 04/13/2024]
Abstract
Inhibition of calcitonin gene-related peptide (CGRP) or its cognate CGRP receptor (CGRPR) has arisen as a major breakthrough in the treatment of migraine. However, a second CGRP-responsive receptor exists, the amylin (Amy) 1 receptor (AMY1R), yet its involvement in the pathology of migraine is poorly understood. AMY1R and CGRPR are heterodimers consisting of receptor activity-modifying protein 1 (RAMP1) with the calcitonin receptor (CTR) and the calcitonin receptor-like receptor (CLR), respectively. Here, we present the structure of AMY1R in complex with CGRP and Gs protein and compare it with the reported structures of the AMY1R complex with rat amylin (rAmy) and the CGRPR in complex with CGRP. Despite similar protein backbones observed within the receptors and the N- and C-termini of the two peptides bound to the AMY1R complexes, they have distinct organization in the peptide midregions (the bypass motif) that is correlated with differences in the dynamics of the respective receptor extracellular domains. Moreover, divergent conformations of extracellular loop (ECL) 3, intracellular loop (ICL) 2, and ICL3 within the CTR and CLR protomers are evident when comparing the CGRP bound to the CGRPR and AMY1R, which influences the binding mode of CGRP. However, the conserved interactions made by the C-terminus of CGRP to the CGRPR and AMY1R are likely to account for cross-reactivity of nonpeptide CGRPR antagonists observed at AMY1R, which also extends to other clinically used CGRPR blockers, including antibodies.
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Affiliation(s)
- Jianjun Cao
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Arthur Christopoulos
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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2
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Russell I, Zhang X, Bumbak F, McNeill SM, Josephs TM, Leeming MG, Christopoulos G, Venugopal H, Flocco MM, Sexton PM, Wootten D, Belousoff MJ. Lipid-Dependent Activation of the Orphan G Protein-Coupled Receptor, GPR3. Biochemistry 2024; 63:625-631. [PMID: 38376112 PMCID: PMC10919283 DOI: 10.1021/acs.biochem.3c00647] [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] [Received: 11/18/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
The class A orphan G protein-coupled receptor (GPCR), GPR3, has been implicated in a variety of conditions, including Alzheimer's and premature ovarian failure. GPR3 constitutively couples with Gαs, resulting in the production of cAMP in cells. While tool compounds and several putative endogenous ligands have emerged for the receptor, its endogenous ligand, if it exists, remains a mystery. As novel potential drug targets, the structures of orphan GPCRs have been of increasing interest, revealing distinct modes of activation, including autoactivation, presence of constitutively activating mutations, or via cryptic ligands. Here, we present a cryo-electron microscopy (cryo-EM) structure of the orphan GPCR, GPR3 in complex with DNGαs and Gβ1γ2. The structure revealed clear density for a lipid-like ligand that bound within an extended hydrophobic groove, suggesting that the observed "constitutive activity" was likely due to activation via a lipid that may be ubiquitously present. Analysis of conformational variance within the cryo-EM data set revealed twisting motions of the GPR3 transmembrane helices that appeared coordinated with changes in the lipid-like density. We propose a mechanism for the binding of a lipid to its putative orthosteric binding pocket linked to the GPR3 dynamics.
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Affiliation(s)
- Isabella
C. Russell
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Xin Zhang
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Fabian Bumbak
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Samantha M. McNeill
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Tracy M. Josephs
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Michael G. Leeming
- Bio21
Molecular Science & Biotechnology Institute, Melbourne Mass Spectrometry
and Proteomics Facility, The University
of Melbourne, Melbourne, VIC 3052, Australia
| | - George Christopoulos
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Hariprasad Venugopal
- Ramaciotti
Centre for Cryo Electron Microscopy, Monash University, Clayton 3800, Victoria Australia
| | - Maria M. Flocco
- Mechanistic
and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB20AA, United Kingdom
| | - Patrick M. Sexton
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Denise Wootten
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
| | - Matthew J. Belousoff
- Drug
Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
- Australian
Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins,
Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria Australia
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3
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Cao J, Belousoff MJ, Gerrard E, Danev R, Fletcher MM, Dal Maso E, Schreuder H, Lorenz K, Evers A, Tiwari G, Besenius M, Li Z, Johnson RM, Wootten D, Sexton PM. Structural insight into selectivity of amylin and calcitonin receptor agonists. Nat Chem Biol 2024; 20:162-169. [PMID: 37537379 DOI: 10.1038/s41589-023-01393-4] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 06/29/2023] [Indexed: 08/05/2023]
Abstract
Amylin receptors (AMYRs), heterodimers of the calcitonin receptor (CTR) and one of three receptor activity-modifying proteins, are promising obesity targets. A hallmark of AMYR activation by Amy is the formation of a 'bypass' secondary structural motif (residues S19-P25). This study explored potential tuning of peptide selectivity through modification to residues 19-22, resulting in a selective AMYR agonist, San385, as well as nonselective dual amylin and calcitonin receptor agonists (DACRAs), with San45 being an exemplar. We determined the structure and dynamics of San385-bound AMY3R, and San45 bound to AMY3R or CTR. San45, via its conjugated lipid at position 21, was anchored at the edge of the receptor bundle, enabling a stable, alternative binding mode when bound to the CTR, in addition to the bypass mode of binding to AMY3R. Targeted lipid modification may provide a single intervention strategy for design of long-acting, nonselective, Amy-based DACRAs with potential anti-obesity effects.
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Affiliation(s)
- Jianjun Cao
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Elliot Gerrard
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Madeleine M Fletcher
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- GlaxoSmithKline, Abbotsford, Victoria, Australia
| | - Emma Dal Maso
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Herman Schreuder
- Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Katrin Lorenz
- Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Andreas Evers
- Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
- Merck Healthcare KGaA, Darmstadt, Germany
| | - Garima Tiwari
- Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
- Janssen Vaccines and Prevention B.V., Leiden, the Netherlands
| | - Melissa Besenius
- Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Ziyu Li
- Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Rachel M Johnson
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- OMass Therapeutics, Oxford, UK
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
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4
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Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife 2023; 12:83477. [PMID: 37248726 DOI: 10.7554/elife.83477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4 muscarinic acetylcholine receptor (M4 mAChR) is a validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. In this study, we rigorously quantified the affinity, efficacy, and magnitude of modulation of two different positive allosteric modulators, LY2033298 (LY298) and VU0467154 (VU154), combined with the endogenous agonist acetylcholine (ACh) or the high-affinity agonist iperoxo (Ipx), at the human M4 mAChR. By determining the cryo-electron microscopy structures of the M4 mAChR, bound to a cognate Gi1 protein and in complex with ACh, Ipx, LY298-Ipx, and VU154-Ipx, and applying molecular dynamics simulations, we determine key molecular mechanisms underlying allosteric pharmacology. In addition to delineating the contribution of spatially distinct binding sites on observed pharmacology, our findings also revealed a vital role for orthosteric and allosteric ligand-receptor-transducer complex stability, mediated by conformational dynamics between these sites, in the ultimate determination of affinity, efficacy, cooperativity, probe dependence, and species variability. There results provide a holistic framework for further GPCR mechanistic studies and can aid in the discovery and design of future allosteric drugs.
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Affiliation(s)
- Ziva Vuckovic
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jesse I Mobbs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Mahmuda Yeasmin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Vindhya Nawaratne
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Emma T van der Westhuizen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Elham Khajehali
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Craig W Lindsley
- Department of Pharmacology, Warren Center for Neuroscience Drug Discovery and Department of Chemistry, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, United States
| | - Andrew Tobin
- The Centre for Translational Pharmacology, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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5
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Cary BP, Gerrard EJ, Belousoff MJ, Fletcher MM, Jiang Y, Russell IC, Piper SJ, Wootten D, Sexton PM. Molecular insights into peptide agonist engagement with the PTH receptor. Structure 2023:S0969-2126(23)00125-9. [PMID: 37148874 DOI: 10.1016/j.str.2023.04.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/30/2022] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
The parathyroid hormone (PTH) 1 receptor (PTH1R) is a G protein-coupled receptor (GPCR) that regulates skeletal development and calcium homeostasis. Here, we describe cryo-EM structures of the PTH1R in complex with fragments of the two hormones, PTH and PTH-related protein, the drug abaloparatide, as well as the engineered tool compounds, long-acting PTH (LA-PTH) and the truncated peptide, M-PTH(1-14). We found that the critical N terminus of each agonist engages the transmembrane bundle in a topologically similar fashion, reflecting similarities in measures of Gαs activation. The full-length peptides induce subtly different extracellular domain (ECD) orientations relative to the transmembrane domain. In the structure bound to M-PTH, the ECD is unresolved, demonstrating that the ECD is highly dynamic when unconstrained by a peptide. High resolutions enabled identification of water molecules near peptide and G protein binding sites. Our results illuminate the action of orthosteric agonists of the PTH1R.
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Affiliation(s)
- Brian P Cary
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Elliot J Gerrard
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Madeleine M Fletcher
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Yan Jiang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Isabella C Russell
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Sarah J Piper
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
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6
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Perlaza-Jiménez L, Tan KS, Piper SJ, Johnson RM, Bamert RS, Stubenrauch CJ, Wright A, Lupton D, Lithgow T, Belousoff MJ. A Structurally Characterized Staphylococcus aureus Evolutionary Escape Route from Treatment with the Antibiotic Linezolid. Microbiol Spectr 2022; 10:e0058322. [PMID: 35736238 PMCID: PMC9431193 DOI: 10.1128/spectrum.00583-22] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen that presents great health concerns. Treatment requires the use of last-line antibiotics, such as members of the oxazolidinone family, of which linezolid is the first member to see regular use in the clinic. Here, we report a short time scale selection experiment in which strains of MRSA were subjected to linezolid treatment. Clonal isolates which had evolved a linezolid-resistant phenotype were characterized by whole-genome sequencing. Linezolid-resistant mutants were identified which had accumulated mutations in the ribosomal protein uL3. Multiple clones which had two mutations in uL3 exhibited resistance to linezolid, 2-fold higher than the clinical breakpoint. Ribosomes from this strain were isolated and subjected to single-particle cryo-electron microscopic analysis and compared to the ribosomes from the parent strain. We found that the mutations in uL3 lead to a rearrangement of a loop that makes contact with Helix 90, propagating a structural change over 15 Å away. This distal change swings nucleotide U2504 into the binding site of the antibiotic, causing linezolid resistance. IMPORTANCE Antibiotic resistance poses a critical problem to human health and decreases the utility of these lifesaving drugs. Of particular concern is the "superbug" methicillin-resistant Staphylococcus aureus (MRSA), for which treatment of infection requires the use of last-line antibiotics, including linezolid. In this paper, we characterize the atomic rearrangements which the ribosome, the target of linezolid, undergoes during its evolutionary journey toward becoming drug resistant. Using cryo-electron microscopy, we describe a particular molecular mechanism which MRSA uses to become resistant to linezolid.
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Affiliation(s)
- Laura Perlaza-Jiménez
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Kher-Shing Tan
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Sarah J. Piper
- Drug Development Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
- Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Rachel M. Johnson
- Drug Development Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
- Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Rebecca S. Bamert
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Christopher J. Stubenrauch
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Alexander Wright
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - David Lupton
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Matthew J. Belousoff
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Drug Development Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
- Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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7
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Cao J, Belousoff MJ, Liang YL, Johnson RM, Josephs TM, Fletcher MM, Christopoulos A, Hay DL, Danev R, Wootten D, Sexton PM. A structural basis for amylin receptor phenotype. Science 2022; 375:eabm9609. [PMID: 35324283 DOI: 10.1126/science.abm9609] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amylin receptors (AMYRs) are heterodimers of the calcitonin (CT) receptor (CTR) and one of three receptor activity-modifying proteins (RAMPs), AMY1R, AMY2R, and AMY3R. Selective AMYR agonists and dual AMYR/CTR agonists are being developed as obesity treatments; however, the molecular basis for peptide binding and selectivity is unknown. We determined the structure and dynamics of active AMYRs with amylin, AMY1R with salmon CT (sCT), AMY2R with sCT or human CT (hCT), and CTR with amylin, sCT, or hCT. The conformation of amylin-bound complexes was similar for all AMYRs, constrained by the RAMP, and an ordered midpeptide motif that we call the bypass motif. The CT-bound AMYR complexes were distinct, overlapping the CT-bound CTR complexes. Our findings indicate that activation of AMYRs by CT-based peptides is distinct from their activation by amylin-based peptides. This has important implications for the development of AMYR therapeutics.
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Affiliation(s)
- Jianjun Cao
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M Johnson
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Tracy M Josephs
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Madeleine M Fletcher
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Debbie L Hay
- Department of Pharmacology and Toxicology, University of Otago, Dunedin 9054, New Zealand
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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8
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Dunstan RA, Bamert RS, Belousoff MJ, Short FL, Barlow CK, Pickard DJ, Wilksch JJ, Schittenhelm RB, Strugnell RA, Dougan G, Lithgow T. Mechanistic Insights into the Capsule-Targeting Depolymerase from a Klebsiella pneumoniae Bacteriophage. Microbiol Spectr 2021; 9:e0102321. [PMID: 34431721 PMCID: PMC8552709 DOI: 10.1128/spectrum.01023-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
The production of capsular polysaccharides by Klebsiella pneumoniae protects the bacterial cell from harmful environmental factors such as antimicrobial compounds and infection by bacteriophages (phages). To bypass this protective barrier, some phages encode polysaccharide-degrading enzymes referred to as depolymerases to provide access to cell surface receptors. Here, we characterized the phage RAD2, which infects K. pneumoniae strains that produce the widespread, hypervirulence-associated K2-type capsular polysaccharide. Using transposon-directed insertion sequencing, we have shown that the production of capsule is an absolute requirement for efficient RAD2 infection by serving as a first-stage receptor. We have identified the depolymerase responsible for recognition and degradation of the capsule, determined that the depolymerase forms globular appendages on the phage virion tail tip, and present the cryo-electron microscopy structure of the RAD2 capsule depolymerase at 2.7-Å resolution. A putative active site for the enzyme was identified, comprising clustered negatively charged residues that could facilitate the hydrolysis of target polysaccharides. Enzymatic assays coupled with mass spectrometric analyses of digested oligosaccharide products provided further mechanistic insight into the hydrolase activity of the enzyme, which, when incubated with K. pneumoniae, removes the capsule and sensitizes the cells to serum-induced killing. Overall, these findings expand our understanding of how phages target the Klebsiella capsule for infection, providing a framework for the use of depolymerases as antivirulence agents against this medically important pathogen. IMPORTANCE Klebsiella pneumoniae is a medically important pathogen that produces a thick protective capsule that is essential for pathogenicity. Phages are natural predators of bacteria, and many encode diverse "capsule depolymerases" which specifically degrade the capsule of their hosts, an exploitable trait for potential therapies. We have determined the first structure of a depolymerase that targets the clinically relevant K2 capsule and have identified its putative active site, providing hints to its mechanism of action. We also show that Klebsiella cells treated with a recombinant form of the depolymerase are stripped of capsule, inhibiting their ability to grow in the presence of serum, demonstrating the anti-infective potential of these robust and readily producible enzymes against encapsulated bacterial pathogens such as K. pneumoniae.
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Affiliation(s)
- Rhys A. Dunstan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Rebecca S. Bamert
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Matthew J. Belousoff
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Francesca L. Short
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christopher K. Barlow
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Derek J. Pickard
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J. Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
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9
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Zhang X, Belousoff MJ, Liang YL, Danev R, Sexton PM, Wootten D. Structure and dynamics of semaglutide- and taspoglutide-bound GLP-1R-Gs complexes. Cell Rep 2021; 36:109374. [PMID: 34260945 DOI: 10.1016/j.celrep.2021.109374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 11/15/2020] [Revised: 05/14/2021] [Accepted: 06/18/2021] [Indexed: 12/01/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) regulates insulin secretion, carbohydrate metabolism, and appetite and is an important target for treatment of type 2 diabetes and obesity. Multiple GLP-1R agonists have entered into clinical trials, with some, such as semaglutide, progressing to approval. Others, including taspoglutide, failed due to the high incidence of side effects or insufficient efficacy. GLP-1R agonists have a broad spectrum of signaling profiles, but molecular understanding is limited by a lack of structural information on how different agonists engage with the GLP-1R. Here, we report cryoelectron microscopy (cryo-EM) structures and cryo-EM 3D variability analysis of semaglutide- and taspoglutide-bound GLP-1R-Gs protein complexes. These reveal similar peptide interactions to GLP-1 but different motions within the receptor and bound peptides, providing insights into the molecular determinants of GLP-1R peptide engagement.
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Affiliation(s)
- Xin Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, S402, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan.
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
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10
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Zhang X, Johnson RM, Drulyte I, Yu L, Kotecha A, Danev R, Wootten D, Sexton PM, Belousoff MJ. Evolving cryo-EM structural approaches for GPCR drug discovery. Structure 2021; 29:963-974.e6. [PMID: 33957078 DOI: 10.1016/j.str.2021.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/10/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest class of cell surface drug targets. Advances in stabilization of GPCR:transducer complexes, together with improvements in cryoelectron microscopy (cryo-EM) have recently been applied to structure-assisted drug design for GPCR agonists. Nonetheless, limitations in the commercial application of these approaches, including the use of nanobody 35 (Nb35) to aid complex stabilization and the high cost of 300 kV imaging, have restricted broad application of cryo-EM in drug discovery. Here, using the PF 06882961-bound GLP-1R as exemplar, we validated the formation of stable complexes with a modified Gs protein in the absence of Nb35. In parallel, we compare 200 versus 300 kV image acquisition using a Falcon 4 or K3 direct electron detector. Moreover, the 200 kV Glacios-Falcon 4 yielded a 3.2 Å map with clear density for bound drug and multiple structurally ordered waters. Our work paves the way for broader commercial application of cryo-EM for GPCR drug discovery.
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Affiliation(s)
- Xin Zhang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Rachel M Johnson
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Ieva Drulyte
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, 5651 GG Eindhoven, the Netherlands
| | - Lingbo Yu
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, 5651 GG Eindhoven, the Netherlands
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord, 5651 GG Eindhoven, the Netherlands
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
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11
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Josephs TM, Belousoff MJ, Liang YL, Piper SJ, Cao J, Garama DJ, Leach K, Gregory KJ, Christopoulos A, Hay DL, Danev R, Wootten D, Sexton PM. Structure and dynamics of the CGRP receptor in apo and peptide-bound forms. Science 2021; 372:science.abf7258. [DOI: 10.1126/science.abf7258] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Tracy M. Josephs
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Matthew J. Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Sarah J. Piper
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Jianjun Cao
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Daniel J. Garama
- Hudson Institute of Medical Research, Clayton 3168, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton 3168, Victoria, Australia
| | - Katie Leach
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Karen J. Gregory
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Debbie L. Hay
- Department of Pharmacology and Toxicology, University of Otago, Dunedin 9054, New Zealand
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M. Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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12
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Malcolm TR, Belousoff MJ, Venugopal H, Borg NA, Drinkwater N, Atkinson SC, McGowan S. Active site metals mediate an oligomeric equilibrium in Plasmodium M17 aminopeptidases. J Biol Chem 2020; 296:100173. [PMID: 33303633 PMCID: PMC7948507 DOI: 10.1074/jbc.ra120.016313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 10/07/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/14/2023] Open
Abstract
M17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases from Plasmodium falciparum (PfA-M17) and Plasmodium vivax (Pv-M17) function as catalytically active hexamers to generate free amino acids from human hemoglobin and are drug targets for the design of novel antimalarial agents. However, the molecular basis for oligomeric assembly is not fully understood. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found that PfA-M17 and Pv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species that can be controlled by manipulating the identity and concentration of metals available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of Pv-M17 by cryoelectron microscopy and X-ray crystallography together with solution studies revealed that PfA-M17 and Pv-M17 bind metal ions and substrates in a conserved fashion, although Pv-M17 forms the active hexamer more readily and processes substrates faster than PfA-M17. On the basis of these studies, we propose a dynamic equilibrium between monomer ↔ dimer ↔ tetramer ↔ hexamer, which becomes directional toward the large oligomeric states with the addition of metal ions. This sophisticated metal-dependent dynamic equilibrium may apply to other M17 aminopeptidases and underpin the moonlighting capabilities of this enzyme family.
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Affiliation(s)
- Tess R Malcolm
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hariprasad Venugopal
- Ramacciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Nyssa Drinkwater
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Sheena McGowan
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
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13
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Zhang X, Belousoff MJ, Zhao P, Kooistra AJ, Truong TT, Ang SY, Underwood CR, Egebjerg T, Šenel P, Stewart GD, Liang YL, Glukhova A, Venugopal H, Christopoulos A, Furness SGB, Miller LJ, Reedtz-Runge S, Langmead CJ, Gloriam DE, Danev R, Sexton PM, Wootten D. Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists. Mol Cell 2020; 80:485-500.e7. [PMID: 33027691 DOI: 10.1016/j.molcel.2020.09.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [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: 06/15/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
Peptide drugs targeting class B1 G-protein-coupled receptors (GPCRs) can treat multiple diseases; however, there remains substantial interest in the development of orally delivered non-peptide drugs. Here, we reveal unexpected overlap between signaling and regulation of the glucagon-like peptide-1 (GLP-1) receptor by the non-peptide agonist PF 06882961 and GLP-1 that was not observed for another compound, CHU-128. Compounds from these patent series, including PF 06882961, are currently in clinical trials for treatment of type 2 diabetes. High-resolution cryoelectron microscopy (cryo-EM) structures reveal that the binding sites for PF 06882961 and GLP-1 substantially overlap, whereas CHU-128 adopts a unique binding mode with a more open receptor conformation at the extracellular face. Structural differences involving extensive water-mediated hydrogen bond networks could be correlated to functional data to understand how PF 06882961, but not CHU-128, can closely mimic the pharmacological properties of GLP-1. These findings will facilitate rational structure-based discovery of non-peptide agonists targeting class B GPCRs.
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Affiliation(s)
- Xin Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Peishen Zhao
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Tin T Truong
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sheng Yu Ang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | | | | | - Petr Šenel
- Apigenex, Poděbradská 173/5, Prague 9 190 00, Czech Republic
| | - Gregory D Stewart
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC 3168, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Sebastian G B Furness
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ 85259, USA
| | | | - Christopher J Langmead
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan.
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia.
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14
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Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA. Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res 2020; 48:8006-8021. [PMID: 32556302 PMCID: PMC7641305 DOI: 10.1093/nar/gkaa519] [Citation(s) in RCA: 16] [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: 02/24/2020] [Revised: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 02/02/2023] Open
Abstract
The poliovirus type I IRES is able to recruit ribosomal machinery only in the presence of host factor PCBP2 that binds to stem-loop IV of the IRES. When PCBP2 is cleaved in its linker region by viral proteinase 3CD, translation initiation ceases allowing the next stage of replication to commence. Here, we investigate the interaction of PCBP2 with the apical region of stem-loop IV (SLIVm) of poliovirus RNA in its full-length and truncated form. CryoEM structure reconstruction of the full-length PCBP2 in complex with SLIVm solved to 6.1 Å resolution reveals a compact globular complex of PCBP2 interacting with the cruciform RNA via KH domains and featuring a prominent GNRA tetraloop. SEC-SAXS, SHAPE and hydroxyl-radical cleavage establish that PCBP2 stabilizes the SLIVm structure, but upon cleavage in the linker domain the complex becomes more flexible and base accessible. Limited proteolysis and REMSA demonstrate the accessibility of the linker region in the PCBP2/SLIVm complex and consequent loss of affinity of PCBP2 for the SLIVm upon cleavage. Together this study sheds light on the structural features of the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional interaction is regulated following translation of the poliovirus genome.
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Affiliation(s)
- Simone A Beckham
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Mehdi Y Matak
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Matthew J Belousoff
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Hariprasad Venugopal
- The Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Neelam Shah
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Hans Elmlund
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Joseph H C Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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15
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Dong M, Deganutti G, Piper SJ, Liang YL, Khoshouei M, Belousoff MJ, Harikumar KG, Reynolds CA, Glukhova A, Furness SGB, Christopoulos A, Danev R, Wootten D, Sexton PM, Miller LJ. Structure and dynamics of the active Gs-coupled human secretin receptor. Nat Commun 2020; 11:4137. [PMID: 32811827 PMCID: PMC7435274 DOI: 10.1038/s41467-020-17791-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 03/13/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023] Open
Abstract
The class B secretin GPCR (SecR) has broad physiological effects, with target potential for treatment of metabolic and cardiovascular disease. Molecular understanding of SecR binding and activation is important for its therapeutic exploitation. We combined cryo-electron microscopy, molecular dynamics, and biochemical cross-linking to determine a 2.3 Å structure, and interrogate dynamics, of secretin bound to the SecR:Gs complex. SecR exhibited a unique organization of its extracellular domain (ECD) relative to its 7-transmembrane (TM) core, forming more extended interactions than other family members. Numerous polar interactions formed between secretin and the receptor extracellular loops (ECLs) and TM helices. Cysteine-cross-linking, cryo-electron microscopy multivariate analysis and molecular dynamics simulations revealed that interactions between peptide and receptor were dynamic, and suggested a model for initial peptide engagement where early interactions between the far N-terminus of the peptide and SecR ECL2 likely occur following initial binding of the peptide C-terminus to the ECD.
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Affiliation(s)
- Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Giuseppe Deganutti
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK.,Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Alison Gingell Building, Coventry University, CV1 2DS, Coventry, UK
| | - Sarah J Piper
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Maryam Khoshouei
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002, Basel, Switzerland
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Kaleeckal G Harikumar
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | | | - Alisa Glukhova
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Sebastian G B Furness
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, 113-0033, Tokyo, Japan
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, AZ, 85259, USA.
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16
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Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F. The architecture and stabilisation of flagellotropic tailed bacteriophages. Nat Commun 2020; 11:3748. [PMID: 32719311 PMCID: PMC7385642 DOI: 10.1038/s41467-020-17505-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 10/13/2019] [Accepted: 07/01/2020] [Indexed: 12/31/2022] Open
Abstract
Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary proteins form two nested chainmails that ensure the integrity of the bacteriophage head. Core stabilising structures are conserved in herpesviruses suggesting their ancestral origin. The structure of the tail also reveals a robust yet pliable assembly. Hexameric rings of the tail-tube protein are braced by the N-terminus and a β-hairpin loop, and interconnected along the tail by the splayed β-hairpins. By contrast, we show that the β-hairpin has an inhibitory role in the tail-tube precursor, preventing uncontrolled self-assembly. Dyads of acidic residues inside the tail-tube present regularly-spaced motifs well suited to DNA translocation into bacteria through the tail.
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Affiliation(s)
- Joshua M Hardy
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Rhys Grinter
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Jiawei Wang
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Fasséli Coulibaly
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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17
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Wright A, Deane-Alder K, Marschall E, Bamert R, Venugopal H, Lithgow T, Lupton DW, Belousoff MJ. Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM. ACS Pharmacol Transl Sci 2020; 3:425-432. [PMID: 32566908 DOI: 10.1021/acsptsci.0c00041] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 01/02/2023]
Abstract
Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the core phenyl oxazolidinone leads to drastic changes in biological activity. Consequently, the structure-activity relationship around the core oxazolidinone is constantly evolving, often reflected with new structural motifs present in nascent oxazolidinones. Herein we describe the use of cryo-electron microscopy to examine the differences in binding of several functionally different oxazolidinones in the hopes of enhanced understanding of their SAR. Tedizolid, radezolid, T145, and contezolid have been examined within the peptidyl transferase center (PTC) of the 50S ribosomal subunit from methicillin resistant Staphylococcus aureus. The ribosome-antibiotic complexes were resolved to a resolution of around 3 Å enabling unambiguous assignment of how each antibiotic interacts with the PTC.
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Affiliation(s)
- Alexander Wright
- School of Chemistry, Monash University, Wellington Road, Clayton, 3800 Victoria, Australia
| | - Kieran Deane-Alder
- Drug and Development Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, 3052 Victoria, Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, 3800 Victoria, Australia
| | - Rebecca Bamert
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Wellington Road, Clayton, 3800 Victoria, Australia
| | - Hari Venugopal
- Ramaciotti Center for Cryo-Electron Microscopy, Monash University, Wellington Road, Clayton, 3800 Victoria, Australia
| | - Trevor Lithgow
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Wellington Road, Clayton, 3800 Victoria, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Wellington Road, Clayton, 3800 Victoria, Australia
| | - Matthew J Belousoff
- Drug and Development Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, 3052 Victoria, Australia
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18
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Chang R, Zhang X, Qiao A, Dai A, Belousoff MJ, Tan Q, Shao L, Zhong L, Lin G, Liang YL, Ma L, Han S, Yang D, Danev R, Wang MW, Wootten D, Wu B, Sexton PM. Cryo-electron microscopy structure of the glucagon receptor with a dual-agonist peptide. J Biol Chem 2020; 295:9313-9325. [PMID: 32371397 DOI: 10.1074/jbc.ra120.013793] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 04/09/2020] [Revised: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Unimolecular dual agonists of the glucagon (GCG) receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R) are a new class of drugs that are potentially superior to GLP-1R-specific agonists for the management of metabolic disease. The dual-agonist, peptide 15 (P15), is a glutamic acid 16 analog of GCG with GLP-1 peptide substitutions between amino acids 17 and 24 that has potency equivalent to those of the cognate peptide agonists at the GCGR and GLP-1R. Here, we have used cryo-EM to solve the structure of an active P15-GCGR-Gs complex and compared this structure to our recently published structure of the GCGR-Gs complex bound to GCG. This comparison revealed that P15 has a reduced interaction with the first extracellular loop (ECL1) and the top of transmembrane segment 1 (TM1) such that there is increased mobility of the GCGR extracellular domain and at the C terminus of the peptide compared with the GCG-bound receptor. We also observed a distinct conformation of ECL3 and could infer increased mobility of the far N-terminal His-1 residue in the P15-bound structure. These regions of conformational variance in the two peptide-bound GCGR structures were also regions that were distinct between GCGR structures and previously published peptide-bound structures of the GLP-1R, suggesting that greater conformational dynamics may contribute to the increased efficacy of P15 in activation of the GLP-1R compared with GCG. The variable domains in this receptor have previously been implicated in biased agonism at the GLP-1R and could result in altered signaling of P15 at the GCGR compared with GCG.
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Affiliation(s)
- Rulue Chang
- School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Zhang
- Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology, Monash University, Parkville, Victoria, Australia
| | - Anna Qiao
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Antao Dai
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,The National Center for Drug Screening, Shanghai, China
| | - Matthew J Belousoff
- Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology, Monash University, Parkville, Victoria, Australia
| | - Qiuxiang Tan
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lijun Shao
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Li Zhong
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangyao Lin
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yi-Lynn Liang
- Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology, Monash University, Parkville, Victoria, Australia
| | - Limin Ma
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shuo Han
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dehua Yang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,The National Center for Drug Screening, Shanghai, China
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Ming-Wei Wang
- School of Pharmacy, Shanghai Medical College, Fudan University, Shanghai, China .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,The National Center for Drug Screening, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Denise Wootten
- Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology, Monash University, Parkville, Victoria, Australia
| | - Beili Wu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China .,University of Chinese Academy of Sciences, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Patrick M Sexton
- Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology, Monash University, Parkville, Victoria, Australia
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19
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Liang YL, Belousoff MJ, Fletcher MM, Zhang X, Khoshouei M, Deganutti G, Koole C, Furness SGB, Miller LJ, Hay DL, Christopoulos A, Reynolds CA, Danev R, Wootten D, Sexton PM. Structure and Dynamics of Adrenomedullin Receptors AM 1 and AM 2 Reveal Key Mechanisms in the Control of Receptor Phenotype by Receptor Activity-Modifying Proteins. ACS Pharmacol Transl Sci 2020; 3:263-284. [PMID: 32296767 PMCID: PMC7155201 DOI: 10.1021/acsptsci.9b00080] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [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: 10/08/2019] [Indexed: 12/14/2022]
Abstract
Adrenomedullin (AM) and calcitonin gene-related peptide (CGRP) receptors are critically important for metabolism, vascular tone, and inflammatory response. AM receptors are also required for normal lymphatic and blood vascular development and angiogenesis. They play a pivotal role in embryo implantation and fertility and can provide protection against hypoxic and oxidative stress. CGRP and AM receptors are heterodimers of the calcitonin receptor-like receptor (CLR) and receptor activity-modifying protein 1 (RAMP1) (CGRPR), as well as RAMP2 or RAMP3 (AM1R and AM2R, respectively). However, the mechanistic basis for RAMP modulation of CLR phenotype is unclear. In this study, we report the cryo-EM structure of the AM1R in complex with AM and Gs at a global resolution of 3.0 Å, and structures of the AM2R in complex with either AM or intermedin/adrenomedullin 2 (AM2) and Gs at 2.4 and 2.3 Å, respectively. The structures reveal distinctions in the primary orientation of the extracellular domains (ECDs) relative to the receptor core and distinct positioning of extracellular loop 3 (ECL3) that are receptor-dependent. Analysis of dynamic data present in the cryo-EM micrographs revealed additional distinctions in the extent of mobility of the ECDs. Chimeric exchange of the linker region of the RAMPs connecting the TM helix and the ECD supports a role for this segment in controlling receptor phenotype. Moreover, a subset of the motions of the ECD appeared coordinated with motions of the G protein relative to the receptor core, suggesting that receptor ECD dynamics could influence G protein interactions. This work provides fundamental advances in our understanding of GPCR function and how this can be allosterically modulated by accessory proteins.
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Affiliation(s)
- Yi-Lynn Liang
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Matthew J. Belousoff
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Madeleine M. Fletcher
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Xin Zhang
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Maryam Khoshouei
- Department
of Molecular Structural Biology, Max Planck
Institute of Biochemistry, 82152 Martinsried, Germany
| | - Giuseppe Deganutti
- School
of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Cassandra Koole
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Sebastian G. B. Furness
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Laurence J. Miller
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- Department
of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona 85259, United States
| | - Debbie L. Hay
- School
of Biological Sciences, and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - Arthur Christopoulos
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | | | - Radostin Danev
- Graduate
School of Medicine, University of Tokyo, S402, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Denise Wootten
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- School
of Pharmacy, Fudan University, Shanghai 201203, China
| | - Patrick M. Sexton
- Drug
Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
- School
of Pharmacy, Fudan University, Shanghai 201203, China
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20
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Liang YL, Belousoff MJ, Zhao P, Koole C, Fletcher MM, Truong TT, Julita V, Christopoulos G, Xu HE, Zhang Y, Khoshouei M, Christopoulos A, Danev R, Sexton PM, Wootten D. Toward a Structural Understanding of Class B GPCR Peptide Binding and Activation. Mol Cell 2020; 77:656-668.e5. [PMID: 32004469 DOI: 10.1016/j.molcel.2020.01.012] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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: 06/18/2019] [Revised: 10/03/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
Class B G protein-coupled receptors (GPCRs) are important therapeutic targets for major diseases. Here, we present structures of peptide and Gs-bound pituitary adenylate cyclase-activating peptide, PAC1 receptor, and corticotropin-releasing factor (CRF), (CRF1) receptor. Together with recently solved structures, these provide coverage of the major class B GPCR subfamilies. Diverse orientations of the extracellular domain to the receptor core in different receptors are at least partially dependent on evolutionary conservation in the structure and nature of peptide interactions. Differences in peptide interactions to the receptor core also influence the interlinked TM2-TM1-TM6/ECL3/TM7 domain, and this is likely important in their diverse signaling. However, common conformational reorganization of ECL2, linked to reorganization of ICL2, modulates G protein contacts. Comparison between receptors reveals ICL2 as a key domain forming dynamic G protein interactions in a receptor- and ligand-specific manner. This work advances our understanding of class B GPCR activation and Gs coupling.
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Affiliation(s)
- Yi-Lynn Liang
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Peishen Zhao
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Cassandra Koole
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Madeleine M Fletcher
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Tin T Truong
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Villy Julita
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - George Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Yan Zhang
- Departments of Biophysics and Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Maryam Khoshouei
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, S402, 7-3-1 Hongo, Bunkyo-ku, 113-0033 Tokyo, Japan.
| | - Patrick M Sexton
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; School of Pharmacy, Fudan University, Shanghai 201203, China.
| | - Denise Wootten
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; School of Pharmacy, Fudan University, Shanghai 201203, China.
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21
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Greenhill AR, Mutreja A, Bulach D, Belousoff MJ, Jonduo MH, Collins DA, Kas MP, Wapling J, Seemann T, Lafana A, Dougan G, Brown MV, Horwood PF. Wave 2 strains of atypical Vibrio cholerae El Tor caused the 2009-2011 cholera outbreak in Papua New Guinea. Microb Genom 2019; 5. [PMID: 30810520 PMCID: PMC6487313 DOI: 10.1099/mgen.0.000256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae is the causative agent of cholera, a globally important human disease for at least 200 years. In 2009–2011, the first recorded cholera outbreak in Papua New Guinea (PNG) occurred. We conducted genetic and phenotypic characterization of 21 isolates of V. cholerae, with whole-genome sequencing conducted on 2 representative isolates. The PNG outbreak was caused by an atypical El Tor strain harbouring a tandem repeat of the CTX prophage on chromosome II. Whole-genome sequence data, prophage structural analysis and the absence of the SXT integrative conjugative element was indicative that the PNG isolates were most closely related to strains previously isolated in South-East and East Asia with affiliations to global wave 2 strains. This finding suggests that the cholera outbreak in PNG was caused by an exotic (non-endemic) strain of V. cholerae that originated in South-East Asia.
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Affiliation(s)
- Andrew R Greenhill
- 2School of Health and Life Sciences, Federation University Australia, Churchill, Australia.,1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ankur Mutreja
- 3Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,4Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dieter Bulach
- 5Melbourne Bioinformatics, The University of Melbourne, Parkville, Australia.,6Department of Microbiology, Monash University, Clayton, Australia
| | | | - Marinjho H Jonduo
- 1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Deirdre A Collins
- 1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.,7School of Medicinal and Health Sciences, Edith Cowan University, Perth, Australia
| | - Monalisa P Kas
- 1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Johanna Wapling
- 1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Torsten Seemann
- 5Melbourne Bioinformatics, The University of Melbourne, Parkville, Australia
| | - Alice Lafana
- 1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Gordon Dougan
- 3Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mark V Brown
- 8School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Paul F Horwood
- 1Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea.,9Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
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22
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Belousoff MJ, Venugopal H, Wright A, Seoner S, Stuart I, Stubenrauch C, Bamert RS, Lupton DW, Lithgow T. cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria. ChemMedChem 2019; 14:527-531. [PMID: 30667174 DOI: 10.1002/cmdc.201900042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 01/20/2019] [Indexed: 11/09/2022]
Abstract
While the ribosome is a common target for antibiotics, challenges with crystallography can impede the development of new bioactives using structure-based drug design approaches. In this study we exploit common structural features present in linezolid-resistant forms of both methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) to redesign the antibiotic. Enabled by rapid and facile cryoEM structures, this process has identified (S)-2,2-dichloro-N-((3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide (LZD-5) and (S)-2-chloro-N-((3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl) acetamide (LZD-6), which inhibit the ribosomal function and growth of linezolid-resistant MRSA and VRE. The strategy discussed highlights the potential for cryoEM to facilitate the development of novel bioactive materials.
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Affiliation(s)
- Matthew J Belousoff
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Hari Venugopal
- Ramaciotti Centre for Electron Microscopy, Monash University, Clayton, 3800, Australia
| | - Alexander Wright
- School of Chemistry, Monash University, Clayton, 3800, Australia
| | - Samuel Seoner
- School of Chemistry, Monash University, Clayton, 3800, Australia
| | - Isabella Stuart
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Chris Stubenrauch
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Rebecca S Bamert
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - David W Lupton
- School of Chemistry, Monash University, Clayton, 3800, Australia
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
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23
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Zeng Z, Belousoff MJ, Spiccia L, Bond AM, Torriero AAJ. Macrocycles Bearing Ferrocenyl Pendants and their Electrochemical Properties upon Binding to Divalent Transition Metal Cations. Chempluschem 2018; 83:728-738. [PMID: 31950627 DOI: 10.1002/cplu.201700550] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/15/2018] [Indexed: 01/09/2023]
Abstract
Metal complexes of Cu2+ , Co2+ , Cd2+ , Zn2+ , and Ni2+ formed with the ligands [Fc(cyclen)] (1) and [Fc(cyclen)2 ] (2) (Fc=ferrocene, cyclen=1,4,7,10-tetraazacyclododecane) are synthesised and characterised. The X-ray structure of the Cu2+ complex of 2, Fc([Cu(cyclen)(CH3 CN)]2 (ClO4 )4 , is reported, and shows that the two positively charged Cu2+ -cyclen units have a coordination number of five, adopting a distorted trigonal-bipyramidal configuration. The Cu2+ -cyclen units are arranged in a trans-like configuration with respect to the Fc group, presumably to minimise electrostatic repulsion. The voltammetric oxidation of the free ligands 1 and 2 in a CH2 Cl2 /CH3 CN (1:4) solvent mixture yields two closely spaced oxidation processes. Both electron-transfer steps are associated with the ferrocenyl moiety, implying strong communication between the cyclen nitrogen atoms and the ferrocenyl group. In contrast, cyclic voltammograms display only a simple reversible one-electron process if 1 and 2 are complexed with Cd2+ , Cu2+ , Zn2+ , Ni2+ , or Co2+ . Binding of these metal ions produces a significant shift in the reversible midpoint potential (Em ). Except for Ni2+ , Em is linearly proportional to the charge density of the transition metal ion, demonstrating that 1 and 2 may undergo redox switching. The diffusion coefficients of Fc, DmFc, 1 and 2, and their metal ion complexes correlate well with their molecular weights.
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Affiliation(s)
- Zhanghua Zeng
- School of Chemistry, Monash University, Clayton, VIC, 3800, Australia
| | | | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, VIC, 3800, Australia
| | - Alan M Bond
- School of Chemistry, Monash University, Clayton, VIC, 3800, Australia
| | - Angel A J Torriero
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia
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Lupton D, Belousoff MJ. The redesign of oxazolidinone antibiotics in response to Staphylococcus aureus. Future Microbiol 2017; 12:1113-1117. [PMID: 28876083 DOI: 10.2217/fmb-2017-0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- David Lupton
- School of Chemistry, Monash University, Clayton 3800, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton 3800, Australia
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Kong B, Joshi T, Belousoff MJ, Tor Y, Graham B, Spiccia L. Neomycin B-cyclen conjugates and their Zn(II) complexes as RNA-binding agents. J Inorg Biochem 2016; 162:334-342. [DOI: 10.1016/j.jinorgbio.2015.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/09/2015] [Accepted: 11/30/2015] [Indexed: 11/26/2022]
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Stubenrauch C, Belousoff MJ, Hay ID, Shen HH, Lillington J, Tuck KL, Peters KM, Phan MD, Lo AW, Schembri MA, Strugnell RA, Waksman G, Lithgow T. Effective assembly of fimbriae in Escherichia coli depends on the translocation assembly module nanomachine. Nat Microbiol 2016; 1:16064. [DOI: 10.1038/nmicrobiol.2016.64] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/07/2016] [Indexed: 01/08/2023]
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Selkrig J, Belousoff MJ, Headey SJ, Heinz E, Shiota T, Shen HH, Beckham SA, Bamert RS, Phan MD, Schembri MA, Wilce MCJ, Scanlon MJ, Strugnell RA, Lithgow T. Conserved features in TamA enable interaction with TamB to drive the activity of the translocation and assembly module. Sci Rep 2015; 5:12905. [PMID: 26243377 PMCID: PMC4525385 DOI: 10.1038/srep12905] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 01/06/2015] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
The biogenesis of membranes from constituent proteins and lipids is a fundamental aspect of cell biology. In the case of proteins assembled into bacterial outer membranes, an overarching question concerns how the energy required for protein insertion and folding is accessed at this remote location of the cell. The translocation and assembly module (TAM) is a nanomachine that functions in outer membrane biogenesis and virulence in diverse bacterial pathogens. Here we demonstrate the interactions through which TamA and TamB subunits dock to bridge the periplasm, and unite the outer membrane aspects to the inner membrane of the bacterial cell. We show that specific functional features in TamA have been conserved through evolution, including residues surrounding the lateral gate and an extensive surface of the POTRA domains. Analysis by nuclear magnetic resonance spectroscopy and small angle X-ray scattering document the characteristic structural features of these POTRA domains and demonstrate rigidity in solution. Quartz crystal microbalance measurements pinpoint which POTRA domain specifically docks the TamB subunit of the nanomachine. We speculate that the POTRA domain of TamA functions as a lever arm in order to drive the activity of the TAM, assembling proteins into bacterial outer membranes.
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Affiliation(s)
- Joel Selkrig
- 1] Department of Microbiology, Monash University, Clayton 3800, Australia [2] Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | | | - Stephen J Headey
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Eva Heinz
- Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Takuya Shiota
- Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Hsin-Hui Shen
- 1] Department of Microbiology, Monash University, Clayton 3800, Australia [2] Department of Materials Engineering, Monash University, Clayton 3800, Australia
| | - Simone A Beckham
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Rebecca S Bamert
- Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Minh-Duy Phan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew C J Wilce
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Martin J Scanlon
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
| | - Richard A Strugnell
- Department of Microbiology &Immunology, University of Melbourne, Parkville 3052, Australia
| | - Trevor Lithgow
- Department of Microbiology, Monash University, Clayton 3800, Australia
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Abstract
Bacterial outer membrane proteins require the beta-barrel assembly machinery (BAM) for their correct folding and function. The central component of this machinery is BamA, an Omp85 protein that is essential and found in all Gram-negative bacteria. An additional feature of the BAM is the translocation and assembly module (TAM), comprised TamA (an Omp85 family protein) and TamB. We report that TamA and a closely related protein TamL are confined almost exclusively to Proteobacteria and Bacteroidetes/Chlorobi respectively, whereas TamB is widely distributed across the majority of Gram-negative bacterial lineages. A comprehensive phylogenetic and secondary structure analysis of the TamB protein family revealed that TamB was present very early in the evolution of bacteria. Several sequence characteristics were discovered to define the TamB protein family: A signal-anchor linkage to the inner membrane, beta-helical structure, conserved domain architecture and a C-terminal region that mimics outer membrane protein beta-strands. Taken together, the structural and phylogenetic analyses suggest that the TAM likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi.
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Affiliation(s)
- Eva Heinz
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Joel Selkrig
- Department of Biochemistry & Molecular Biology, Monash University, Melbourne, Victoria, Australia Present address: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Matthew J Belousoff
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Trevor Lithgow
- Department of Microbiology, Monash University, Melbourne, Victoria, Australia
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Krupkin M, Matzov D, Tang H, Metz M, Kalaora R, Belousoff MJ, Zimmerman E, Bashan A, Yonath A. A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome. Philos Trans R Soc Lond B Biol Sci 2012; 366:2972-8. [PMID: 21930590 PMCID: PMC3158926 DOI: 10.1098/rstb.2011.0146] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [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: 11/12/2022] Open
Abstract
Based on the presumed capability of a prebiotic pocket-like entity to accommodate substrates whose stereochemistry enables the creation of chemical bonds, it is suggested that a universal symmetrical region identified within all contemporary ribosomes originated from an entity that we term the ‘proto-ribosome’. This ‘proto-ribosome’ could have evolved from an earlier machine that was capable of performing essential tasks in the RNA world, called here the ‘pre-proto-ribosome’, which was adapted for producing proteins.
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Affiliation(s)
- Miri Krupkin
- Weizmann Institute of Science, Rehovot 76100, Israel
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Zeng Z, Torriero AAJ, Belousoff MJ, Bond AM, Spiccia L. Synthesis, X-ray structure of ferrocene bearing bis(Zn-cyclen) complexes and the selective electrochemical sensing of TpT. Chemistry 2009; 15:10988-96. [PMID: 19746486 DOI: 10.1002/chem.200901639] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The new ligand, [Fc(cyclen)(2)] (5) (Fc=ferrocene, cyclen=1,4,7,10-tetraazacyclododecane), and corresponding Zn(II) complex receptor, [Fc{Zn(cyclen)(CH(3)OH)}(2)](ClO(4))(4) (1), consisting of a ferrocene moiety bearing one Zn(II)-cyclen complex on each cyclopentadienyl ring, have been designed and prepared through a multi-step synthesis. Significant shifts in the (1)H NMR signals of the ferrocenyl group, cf. ferrocene and a previously reported [Fc{Zn(cyclen)}](2+) derivative, indicated that the two Zn(II)-cyclen units in 1 significantly affect the electronic properties of the cyclopentadienyl rings. The X-ray crystal structure shows that the two positively charged Zn(II)-cyclen complexes are arranged in a trans like configuration, with respect to the ferrocene bridging unit, presumably to minimise electrostatic repulsion. Both 5 and 1 can be oxidized in 1:4 CH(2)Cl(2)/CH(3)CN and Tris-HCl aqueous buffer solution under conditions of cyclic voltammetry to give a well defined ferrocene-centred (Fc(0/+)) process. Importantly, 1 is a highly selective electrochemical sensor of thymidilyl(3'-5')thymidine (TpT) relative to other nucleobases and nucleotides in Tris-HCl buffer solution (pH 7.4). The electrochemical selectivity, detected as a shift in reversible potential of the Fc(0/+) component, is postulated to result from a change in the configuration of bis(Zn(II)-cyclen) units from a trans to a cis state. This is caused by the strong 1:1 binding of the two deprotonated thymine groups in TpT to different Zn(II) centres of receptor 1. UV-visible spectrophotometric titrations confirmed the 1:1 stoichiometry for the 1:TpT adduct and allowed the determination of the apparent formation constant of 0.89+/-0.10x10(6) M(-1) at pH 7.4.
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Affiliation(s)
- Zhanghua Zeng
- School of Chemistry, Monash University, Clayton, Victoria, Australia
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Nickita N, Gasser G, Pearson P, Belousoff MJ, Goh LY, Bond AM, Deacon GB, Spiccia L. Ruthenium(II) Complexes Incorporating 2-(2′-Pyridyl)pyrimidine-4-carboxylic Acid. Inorg Chem 2009. [DOI: 10.1021/ic9004505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Reaction of terbium triflate with a heptadentate ligand derivative of cyclen, L1 = 2-[7-ethyl-4,10-bis(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, produced a new synthetic ribonuclease, [Tb(L1)(OTf)(OH(2))](OTf)(2).MeCN (C1). X-ray crystal structure analysis indicates that the terbium(III) center in C1 is 9-coordinate, with a capped square-antiprism geometry. While the terbium(III) center is tightly bound by the L1 ligand, two of the coordination sites are occupied by labile water and triflate ligands. In water, the triflate ligand is likely to be displaced, forming [Tb(L1)(OH(2))(2)](3+), which is able to effectively promote RNA cleavage. This complex greatly accelerates the rate of intramolecular transesterification of an activated model RNA phosphodiester, uridine-3'-p-nitrophenylphosphate (UpNP), with k(obs) = 5.5(1) x 10(-2) s(-1) at 21 degrees C and pH 7.5, corresponding to an apparent second-order rate constant of 277(5) M(-1) s(-1). By contrast, the analogous complex of an octadentate derivative of cyclen featuring only a single labile coordination site, [Tb(L2)(OH(2))](OTf)(3) (C2), where L2 = 2-[4,7,10-tris(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, is inactive. [Tb(L1)(OH(2))(2)](3+) is also capable of hydrolyzing short transcripts of the HIV-1 transactivation response (TAR) element, HIV-1 dimerization initiation site (DIS) and ribosomal A-site, as well as formyl methionine tRNA (tRNA(fMet)), albeit at a considerably slower rate than UpNP transesterification (k(obs) = 2.78(8) x 10(-5) s(-1) for TAR cleavage at 37 degrees C, pH 6.5, corresponding to an apparent second-order rate constant of 0.56(2) M(-1)s(-1)). Cleavage is concentrated at the single-stranded "bulge" regions of these RNA motifs. Exploiting this selectivity, [Tb(L1)(OH(2))(2)](3+) was successfully employed in footprinting experiments, in which binding of the Tat peptide and neomycin B to the bulge region of the TAR stem-loop was confirmed.
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Affiliation(s)
- Matthew J. Belousoff
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | - Phuc Ung
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
| | - Craig M. Forsyth
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
| | - Bim Graham
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
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Nickita N, Gasser G, Pearson P, Belousoff MJ, Goh LY, Bond AM, Deacon GB, Spiccia L. Ruthenium(II) Complexes Incorporating 2-(2′-Pyridyl)pyrimidine-4-carboxylic Acid. Inorg Chem 2008; 48:68-81. [DOI: 10.1021/ic800972x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nickita Nickita
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Gilles Gasser
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Pauline Pearson
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Matthew J. Belousoff
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Lai Y. Goh
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Alan M. Bond
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Glen B. Deacon
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
| | - Leone Spiccia
- School of Chemistry, Monash University, VIC 3800, Australia, and Department of Chemistry, National University of Singapore, Singapore
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Belousoff MJ, Gasser G, Graham B, Tor Y, Spiccia L. Binding of HIV-1 TAR mRNA to a peptide nucleic acid oligomer and its conjugates with metal-ion-binding multidentate ligands. J Biol Inorg Chem 2008; 14:287-300. [PMID: 19015900 DOI: 10.1007/s00775-008-0448-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [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] [Received: 07/10/2008] [Accepted: 10/30/2008] [Indexed: 11/27/2022]
Abstract
A peptide nucleic acid (PNA) oligomer and a series of PNA conjugates featuring covalently attached pendant 1,4,7,10-tetraazacyclododecane (cyclen) or bis((pyridin-2-yl)methyl)amine (DPA) moieties have been synthesized that are complementary to regions of the HIV-1 TAR messenger RNA stem-loop. Thermal denaturation studies, in conjunction win with native gel shift assays, suggest that the PNAs "invade" TAR to produce a mixture of two 1:1 PNA-TAR adducts, tentatively assigned as an "open-duplex" structure, in which the TAR stem-loop dissociates and the PNA hybridizes with its RNA complement via Watson-Crick base-pairing, and a triplex-type structure, in which the initially displaced RNA segment is bound to the PNA:RNA duplex through Hoogsteen base-pairing. Thermal denaturation experiments with the TAR sequence and single-stranded RNA and DNA oligonucleotides, both in the presence and in the absence of Zn(2+) ions, show that the introduction of cyclen or DPA ligand arms into the PNA oligomer leads to a small but reproducible increase in the T (m) values. This is attributed to hydrogen-bonding and/or electrostatic interactions between protonated forms of cyclen/DPA and the cognate RNA or DNA oligonucleotide targets. Contrary to expectations, the addition of Zn(2+) ions did not further enhance duplex formation through binding of Zn(II)-cyclen or Zn(II)-DPA moieties to the complementary RNA or DNA. Native gel shift assays further confirmed the stability increase of the metal-free cyclen- and DPA-modified PNA hybrids as compared with a control PNA sequence.
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Abstract
A number of aminoglycoside antibiotics, and in particular neomycin B, are demonstrated to promote strand cleavage of RNA oligonucleotides (minimised HIV-1 TAR element and prokaryotic ribosomal A-site), by binding and causing sufficient distortion to the RNA backbone to render it more susceptible to intramolecular transesterification.
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Belousoff MJ, Graham B, Spiccia L. Copper(II) Complexes ofN-Methylated Derivatives ofortho- andmeta-Xylyl-Bridged Bis(1,4,7-triazacyclononane) Ligands: Synthesis, X-ray Structure and Reactivity as Artificial Nucleases. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Belousoff MJ, Tjioe L, Graham B, Spiccia L. Synthesis, X-Ray Crystal Structures, and Phosphate Ester Cleavage Properties of bis(2-Pyridylmethyl)amine Copper(II) Complexes with Guanidinium Pendant Groups. Inorg Chem 2008; 47:8641-51. [DOI: 10.1021/ic8004079] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Matthew J. Belousoff
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia, and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
| | - Linda Tjioe
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia, and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
| | - Bim Graham
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia, and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
| | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia, and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
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Gasser G, Tjioe L, Graham B, Belousoff MJ, Juran S, Walther M, Künstler JU, Bergmann R, Stephan H, Spiccia L. Synthesis, Copper(II) Complexation, (64)Cu-Labeling, and Bioconjugation of a New Bis(2-pyridylmethyl) Derivative of 1,4,7-Triazacyclononane. Bioconjug Chem 2008; 19:719-30. [PMID: 18254581 DOI: 10.1021/bc700396e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new ligand derivative of 1,4,7-triazacyclononane (TACN), 2-[4,7-bis(2-pyridylmethyl)-1,4,7-triazacyclononan-1-yl]acetic acid ( 6), has been synthesized and its complexation behavior toward Cu2+ ions investigated. The ligand 6 has been characterized by spectroscopic methods, and a molecular structure of a corresponding Cu(II) complex has been elucidated by single-crystal X-ray analysis. The suitability of 6 for conjugation to peptide substrates has been shown by amide coupling of 6 to the stabilized derivative of bombesin (BN), beta Ala-beta Ala-[Cha13, Nle14]BN(7-14), to give the conjugate 8. The free ligand 6 and the bioconjugate 8 were labeled with 64Cu2+, and the resulting complexes, 64Cu subset6 and 64Cu subset8 , were found to be stable in the presence of a large excess of a competing ligand (cyclam) or copper-seeking superoxide dismutase (SOD), as well as in rat plasma. Biodistribution studies of 64Cu subset8 in Wistar rats showed a high activity uptake into the pancreas (5.76 +/- 0.25 SUV, 5 min p.i.; 3.93 +/- 0.25 SUV, 1 h p.i.), which is the organ with high levels of gastrin-releasing peptide receptor (GRPR). This receptor is overexpressed in a large number of breast and prostate carcinomas. The novel 64Cu subset6 complex had a dominating influence on the nonspecific activity biodistribution of its BN conjugate, since the distribution data of 64Cu subset6 are similar to those of 64Cu subset8 . The 64Cu complexes exhibited a low activity accumulation in the liver tissue and an extensive renal clearance, which was distinctively different to the biodistribution of 64CuCl 2, suggesting that 64Cu subset6 does not undergo significant demetalation, but rather exhibits high in vivo stability.
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Affiliation(s)
- Gilles Gasser
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
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Nickita N, Belousoff MJ, Bhatt AI, Bond AM, Deacon GB, Gasser G, Spiccia L. Synthesis, Structure, Spectroscopic Properties, and Electrochemical Oxidation of Ruthenium(II) Complexes Incorporating Monocarboxylate Bipyridine Ligands. Inorg Chem 2007; 46:8638-51. [PMID: 17880205 DOI: 10.1021/ic700796m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[Ru(bpy)(2)(Mebpy-COOH)](PF(6))(2).3H(2)O (1), [Ru(phen)(2)(Mebpy-COOH)](ClO(4))(2).5H(2)O (2), [Ru(dppz)(2)(Mebpy-COOH)]Cl(2).9H(2)O (3), and [Ru(bpy)(dppz)(Mebpy-COOH)](PF(6))(2).5H(2)O (4) (bpy = 2,2'-bipyridine, Mebpy-COOH = 4'-methyl-2,2'-bipyridine-4-carboxylic acid, phen = 1,10-phenanthroline, dppz = dipyrido[3,2,-a;2',3-c]phenazine) have been synthesized and characterized spectroscopically and by microanalysis. The [Ru(Mebpy-COOH)(CO)(2)Cl(2)].H(2)O intermediate was prepared by reaction of the monocarboxylic acid ligand, Mebpy-COOH, with [Ru(CO)(2)Cl(2)](n), and the product was then reacted with either bpy, phen, or dppz in the presence of an excess of trimethylamine-N-oxide (Me(3)NO), as the decarbonylation agent, to generate 1, 2, and 3, respectively. For compound 4, [Ru(bpy)(CO)Cl(2)](2) was reacted with Mebpy-COOH to yield [Ru(bpy)(Mebpy-COOH)(CO)Cl](PF(6)).H(2)O as a mixture of two main geometric isomers. Chemical decarbonylation in the presence of dppz gave 4 also as a mixture of two isomers. Electrochemical and spectrophotometric studies indicated that complexes 1 and 2 were present as a mixture of protonated and deprotonated forms in acetonitrile solution because of water of solvation in the isolated solid products. The X-ray crystal structure determination on crystals of [Ru(bpy)2(MebpyCOO)][Ru(bpy)(2)(MebpyCOOH)](3)(PF(6))(7), 1a, and [Ru(phen)(2)(MebpyCOO)](ClO(4)).6H(2)O, 2a, obtained from solutions of 1 and 2, respectively, revealed that 1a consisted of a mixture of protonated and deprotonated forms of the complex in a 1:3 ratio and that 2a consisted of the deprotonated derivative of 2. A distorted octahedral geometry for the Ru(II) centers was found for both complexes. Upon excitation at 450 nm, MeCN solutions of the protonated complexes 1-4 were found to exhibit emission bands in the 635-655 nm range, whereas the corresponding emission maxima of their deprotonated forms were observed at lower wavelengths. Protonation/deprotonation effects were also observed in the luminescence and electrochemical behavior of complexes 1-4. Comprehensive electrochemical studies in acetonitrile show that the ruthenium centers on 1, 2, 3, and 4 are oxidized from Ru(II) to Ru(III) with reversible potentials at 917, 929, 1052, and 1005 mV vs Fc(0/+) (Fc = ferrocene), respectively. Complexes 1 and 2 also exhibit an irreversible oxidation process in acetonitrile, and all compounds undergo ligand-based reduction processes.
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Affiliation(s)
- Nickita Nickita
- School of Chemistry and Centre for Green Chemistry, Monash University, Victoria 3800, Australia
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Gasser G, Belousoff MJ, Bond AM, Spiccia L. Facile synthesis and detailed characterization of a new ferrocenyl uracil peptide nucleic acid monomer. J Org Chem 2007; 71:7565-73. [PMID: 16995660 DOI: 10.1021/jo060868t] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new ferrocenyl uracil peptide nucleic acid (PNA) monomer, tert-butyl-2-(N-(2-(((9H-floren-9-yl)methoxy)carbonylamino)ethyl)-2-(5-(N-ferrocenylmethylbenzamido)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetate (1), has been successfully prepared in good yield by a procedure involving the one-pot reaction of the key synthon, 5-(ferrocenylmethylamino)pyrimidine-2,4(1H,3H)-dione (4), itself prepared from the reaction of (ferrocenylmethyl)trimethylammonium iodide and 5-aminouracil, with benzoyl chloride followed by ethyl bromoacetate. After hydrolysis of the ester, the acid was coupled with a protected PNA backbone to generate 1. NMR spectroscopy showed that 1 hydrogen bonds 9-ethyladenine (EA) in a 1:1 mixture of CD3CN:CDCl3 with an association constant Ka of 70 M(-1) at 30 degrees C. This value is comparable with those observed for model receptors and shows that the ferrocenyl moiety of 1 does not hinder the hydrogen bonding of our new PNA monomer to the complementary DNA base or if it does, not significantly. 1 is oxidized to 1+ with a reversible potential of +538 mV vs the DMFc(0/+) (decamethylferrocene) couple under voltammetric conditions in a 1:1 mixture of CH3CN:CHCl3 (0.1 M Bu4NPF6). For this reversible process, a slightly larger diffusion coefficient of 4.2 x 10(-6) cm(2).s(-1) than usually found for these compounds was determined from these electrochemical studies, which should be analytically useful as it will readily afford submicromolar voltammetric detection limits.
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Affiliation(s)
- Gilles Gasser
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
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Gasser G, Belousoff MJ, Bond AM, Spiccia L. Binding of Nitrate to a CuII−Cyclen Complex Bearing a Ferrocenyl Pendant: Synthesis, Solid-State X-ray Structure, and Solution-Phase Electrochemical and Spectrophotometric Studies. Inorg Chem 2007; 46:3876-88. [PMID: 17439114 DOI: 10.1021/ic061622+] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of Cu(NO3)2.3H2O with the ligand 1-(ferrocenemethyl)-1,4,7,10-tetraazacyclododecane (L) in acetonitrile leads to the formation of a blue complex, [Cu(L)(NO3)][NO3] (C1). The X-ray structure determination shows an unexpected binding of a nitrate anion in that the CuII center is surrounded by four N atoms of the 1,4,7,10-tetraazacyclododecane (cyclen) macrocycle and two O atoms from a chelating nitrate anion, both Cu-O distances being below the sums of the van de Waals radii. Hydrogen-bonding interactions in the crystal lattice and a weak interaction between a second nitrate O and the CuII center in C1 give rise to a highly distorted CuII geometry relative to that found in the known structure of [Cu(cyclen)(NO3)][NO3] (C5). Electrochemical studies in acetonitrile containing 0.1 M [Bu4N][NO3] as the supporting electrolyte showed that oxidation of C1 in this medium exhibits a single reversible one-electron step with a formal potential E degrees f of +85 mV vs Fc0/+ (Fc = ferrocene). This process is associated with oxidation of the ferrocenyl pendant group. Additionally, a reversible one-electron reduction reaction with an E degrees f value of -932 mV vs Fc0/+, attributed to the CuII/I redox couple, is detected. Gradual change of the supporting electrolyte from 0.1 M [Bu4N][NO3] to the poorly coordinating [Bu4N][PF6] electrolyte, at constant ionic strength, led to a positive potential shift in E degrees f values by +107 and +39 mV for the CuII/I(C1) and Fc0/+(C1) redox couples, respectively. Analysis of these electrochemical data and UV-vis spectra is consistent with the probable presence of the complexes C1, [Cu(L)(CH3CN)2]2+ (C2), [Cu(L)(CH3CN)(NO3)]+ (C3), and [Cu(L)(NO3)2] (C4) as the major species in nitrate-containing acetonitrile solutions. In weakly solvating nitromethane, the extent of nitrate complexation remains significant even at low nitrate concentrations, due to the lack of solvent competition.
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Affiliation(s)
- Gilles Gasser
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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Gasser G, Belousoff MJ, Bond AM, Kosowski Z, Spiccia L. Recognition of Thymine and Related Nucleosides by a ZnII-Cyclen Complex Bearing a Ferrocenyl Pendant. Inorg Chem 2007; 46:1665-74. [PMID: 17284025 DOI: 10.1021/ic061902p] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A cyclen derivative bearing a ferrocenyl arm (L) and a series of its ZnII complexes [ZnL(OH2)][ClO4]2 (C1), [ZnL(OH)][ClO4] (C2), and [ZnL(Cl)][ClO4].CH3CN (C3) (cyclen = 1,4,7,10-tetraazacyclododecane, L = 1-(ferrocenemethyl)-1,4,7,10-tetraazacyclododecane) have been prepared and characterized spectroscopically. An X-ray structure determination confirmed the formation of complex C1 and revealed that the coordinated water participates in hydrogen bonding with the perchlorate counter ions. The pKa value for deprotonation of the water molecule determined by potentiometric titration was found to be 7.36 +/- 0.09 at 25 degrees C and I = 0.1 (KNO3). The possibility of using complex C1 as a potential sensor for thymine derivatives in aqueous solution has been examined. Shifts in the 1H and 13C NMR resonances showed the binding occurred with thymine (T) and two thymine derivatives, thymidine (dT) and thymidine 5'-monophosphate (TMP2-). Significant shifts of the nuC=O and nuC=C vibrations of the thymine derivatives were also observed via IR spectroscopy upon complexation with the receptor. The thymine adduct, [ZnL(thymine anion)][ClO4].2H2O (C4), has been crystallized and characterized. The X-ray structure of C4 confirmed the thymine binding to the receptor, and the short Zn-N(thymine) distance of 1.975(5) A indicated clearly that the ferrocenyl arm does not affect the complexation of the DNA base. In contrast to the large spectral changes, electrochemical studies showed a small shift of the reversible potential of the redox couple Fc+/Fc (Fc = ferrocene) and subtle changes in voltammetry upon the addition of an excess of dT, TMP2-, and guanine (dG) at physiological pH, indicating the level of interaction is similar in both Fc and Fc+ forms.
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Affiliation(s)
- Gilles Gasser
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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Belousoff MJ, Battle AR, Graham B, Spiccia L. Syntheses, structures and hydrolytic properties of copper(II) complexes of asymmetrically N-functionalised 1,4,7-triazacyclononane ligands. Polyhedron 2007. [DOI: 10.1016/j.poly.2006.06.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Belousoff MJ, Graham B, Moubaraki B, Murray KS, Spiccia L. Oxalato-Bridged Dinuclear Copper(II) Complexes ofN-Alkylated Derivatives of 1,4,7-Triazacyclononane: Synthesis, X-ray Crystal Structures and Magnetic Properties. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200600570] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Belousoff MJ, Duriska MB, Graham B, Batten SR, Moubaraki B, Murray KS, Spiccia L. Synthesis, X-ray Crystal Structures, Magnetism, and Phosphate Ester Cleavage Properties of Copper(II) Complexes of N-Substituted Derivatives of 1,4,7-Triazacyclononane. Inorg Chem 2006; 45:3746-55. [PMID: 16634610 DOI: 10.1021/ic051983+] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two new N-substituted derivatives of the 1,4,7-triazacyclononane (tacn) macrocycle, 1-benzyl-4,7-dimethyl-1,4,7-triazacyclononane (L2) and 1,4,7-tris(3-cyanobenzyl)-1,4,7-triazacyclononane (L3), have been prepared and, together with 1,4-dimethyl-1,4,7-triazacyclononane (L1), have been used to synthesize the corresponding hydroxo-bridged binuclear copper (II) complexes, [Cu2(mu-OH)2L2](ClO4)2.xH2O (1 L = L1, x = 0; 2 L = L2, x = 1; 3 L = L3, x = 2). The X-ray crystal structures of all three complexes reveal the presence of [Cu2(mu-OH)2]2+ cores capped by pairs of facially coordinating tacn ligands so that the Cu(II) centers reside in distorted square pyramidal coordination environments. Variable-temperature magnetic susceptibility measurements indicate weak antiferromagnetic coupling (J = -36.4 cm(-1)) between the Cu(II) centers in 1, while the centers in 2 and 3 have been shown to interact ferromagnetically (J = 11.2 and 49.3 cm(-1), respectively). The variation in the strength and sign of these interactions has been rationalized in terms of the differing geometries of the [Cu2(mu-OH)2]2+ cores. The ability of the Cu(II) complexes to cleave phosphate ester bonds has been probed using the model phosphate ester bis(4-nitrophenyl)phosphate (BNPP) at pH 7.4 and a temperature of 50 degrees C. The measured rate constant for 3 (3 x 10(-4) s(-1)) is significantly greater than those previously reported for the Cu(II) complexes of the fully alkylated tacn ligands, Me3tacn and iPr3tacn, which until now have been rated as the most effective tacn-based phosphate ester cleavage agents.
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Fry FH, Fischmann AJ, Belousoff MJ, Spiccia L, Brügger J. Kinetics and Mechanism of Hydrolysis of a Model Phosphate Diester by [Cu(Me3tacn)(OH2)2]2+ (Me3tacn = 1,4,7-Trimethyl-1,4,7-triazacyclononane). Inorg Chem 2005; 44:941-50. [PMID: 15859272 DOI: 10.1021/ic049469b] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The kinetics of hydrolysis of bis(p-nitrophenyl)phosphate (BNPP) by [Cu(Me3tacn)(OH2)2]2+ has been studied by spectrophotometrical monitoring of the release of the p-nitrophenylate ion from BNPP. The reaction was followed for up to 8000 min at constant BNPP concentration (15 microM) and ionic strength (0.15 M) and variable concentration of complex (1.0-7.5 mM) and temperature (42.5-65.0 degrees C). Biphasic kinetic traces were observed, indicating that the complex promotes the cleavage of BNPP to NPP [(p-nitrophenyl)phosphate] and then cleavage of the latter to phosphate, the two processes differing in rate by 50-100-fold. Analysis of the more amenable cleavage of BNPP revealed that the rate of BNPP cleavage is among the highest measured for mononuclear copper(II) complexes and is slightly higher than that reported for the close analogue [Cu(iPr3tacn)(OH2)2]2+. Detailed analysis required the determination of the pKa for [Cu(Me3tacn)(OH2)2]2+ and the constant for the dimerization of the conjugate base to [(Me3tacn)Cu(OH)2Cu(Me3tacn)]2+ (Kdim). Thermodynamic parameters derived from spectrophotometric pH titration and the analysis of the kinetic data were in reasonable agreement. Second-order rate constants for cleavage of BNPP by [Cu(Me3tacn)(OH2)(OH)]+ and associated activation parameters were obtained from initial rate analysis (k = 0.065 M(-1) s(-1) at 50.0 degrees C, deltaH = 56+/-6 kJ mol(-1), deltaS = -95+/-18 J K(-1) mol(-1)) and biphasic kinetic analysis (k = 0.14 M(-1) s(-1) at 50.0 degrees C, deltaH = 55+/-6 kJ mol(-1), deltaS = -92+/-20 J K(-1) mol(-1)). The negative entropy of activation is consistent with a concerted mechanism with considerable associative character. The complex was found to catalyze the cleavage of BNPP with turnover rates of up to 1 per day. Although these turnover rates can be considered low from an application point of view, the ability of the complexes to catalyze phosphate ester cleavage is clearly demonstrated.
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Affiliation(s)
- Fiona H Fry
- School of Chemistry, Monash University, Victoria 3800, Australia
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