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Leśniak RK, Rydzik AM, Kamps JJAG, Kahn A, Claridge TDW, Schofield CJ. 19F NMR studies on γ-butyrobetaine hydroxylase provide mechanistic insights and suggest a dual inhibition mode. Chem Commun (Camb) 2019; 55:14717-14720. [PMID: 31702759 PMCID: PMC6927413 DOI: 10.1039/c9cc06466d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022]
Abstract
The final step in the biosynthesis of l-carnitine in humans is catalysed by the 2-oxoglutarate and ferrous iron dependent oxygenase, γ-butyrobetaine hydroxylase (BBOX). 1H and 19F NMR studies inform on the BBOX mechanism including by providing evidence for cooperativity between monomers in substrate/some inhibitor binding. The value of the 19F NMR methods is demonstrated by their use in the design of new BBOX inhibitors.
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Affiliation(s)
- Robert K. Leśniak
- The Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
;
| | - Anna M. Rydzik
- The Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
;
| | - Jos J. A. G. Kamps
- The Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
;
| | - Amjad Kahn
- The Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
;
| | - Timothy D. W. Claridge
- The Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
;
| | - Christopher J. Schofield
- The Department of Chemistry
, University of Oxford
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
.
;
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2
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van Groesen E, Lohans CT, Brem J, Aertker KMJ, Claridge TDW, Schofield CJ. 19 F NMR Monitoring of Reversible Protein Post-Translational Modifications: Class D β-Lactamase Carbamylation and Inhibition. Chemistry 2019; 25:11837-11841. [PMID: 31310409 PMCID: PMC6771976 DOI: 10.1002/chem.201902529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/11/2019] [Indexed: 11/05/2022]
Abstract
Bacterial production of β‐lactamases with carbapenemase activity is a global health threat. The active sites of class D carbapenemases such as OXA‐48, which is of major clinical importance, uniquely contain a carbamylated lysine residue which is essential for catalysis. Although there is significant interest in characterizing this post‐translational modification, and it is a promising inhibition target, protein carbamylation is challenging to monitor in solution. We report the use of 19F NMR spectroscopy to monitor the carbamylation state of 19F‐labelled OXA‐48. This method was used to investigate the interactions of OXA‐48 with clinically used serine β‐lactamase inhibitors, including avibactam and vaborbactam. Crystallographic studies on 19F‐labelled OXA‐48 provide a structural rationale for the sensitivity of the 19F label to active site interactions. The overall results demonstrate the use of 19F NMR to monitor reversible covalent post‐translational modifications.
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Affiliation(s)
- Emma van Groesen
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Christopher T Lohans
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.,Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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3
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de Las Rivas M, Coelho H, Diniz A, Lira-Navarrete E, Compañón I, Jiménez-Barbero J, Schjoldager KT, Bennett EP, Vakhrushev SY, Clausen H, Corzana F, Marcelo F, Hurtado-Guerrero R. Structural Analysis of a GalNAc-T2 Mutant Reveals an Induced-Fit Catalytic Mechanism for GalNAc-Ts. Chemistry 2018; 24:8382-8392. [PMID: 29601100 DOI: 10.1002/chem.201800701] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Indexed: 02/02/2023]
Abstract
The family of polypeptide N-acetylgalactosamine (GalNAc) transferases (GalNAc-Ts) orchestrates the initiating step of mucin-type protein O-glycosylation by transfer of GalNAc moieties to serine and threonine residues in proteins. Deficiencies and dysregulation of GalNAc-T isoenzymes are related to different diseases. Recently, it has been demonstrated that an inactive GalNAc-T2 mutant (F104S), which is not located at the active site, induces low levels of high-density lipoprotein cholesterol (HDL-C) in humans. Herein, the molecular basis for F104S mutant inactivation has been deciphered. Saturation transfer difference NMR spectroscopy experiments demonstrate that the mutation induces loss of binding to peptide substrates. Analysis of the crystal structure of the F104S mutant bound to UDP-GalNAc (UDP=uridine diphosphate), combined with molecular dynamics (MD) simulations, has revealed that the flexible loop is disordered and displays larger conformational changes in the mutant enzyme than that in the wild-type (WT) enzyme. 19 F NMR spectroscopy experiments reveal that the WT enzyme only reaches the active state in the presence of UDP-GalNAc, which provides compelling evidence that GalNAc-T2 adopts a UDP-GalNAc-dependent induced-fit mechanism. The F104S mutation precludes the enzyme from achieving the active conformation and concomitantly binding peptide substrates. This study provides new insights into the catalytic mechanism of the large family of GalNAc-Ts and how these enzymes orchestrate protein O-glycosylation.
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Affiliation(s)
- Matilde de Las Rivas
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain
| | - Helena Coelho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
| | - Ana Diniz
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Erandi Lira-Navarrete
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain
| | - Katrine T Schjoldager
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Eric P Bennett
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Filipa Marcelo
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Ramon Hurtado-Guerrero
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain
- Fundación ARAID, 50018, Zaragoza, Spain
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4
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Abboud MI, Kosmopoulou M, Krismanich AP, Johnson JW, Hinchliffe P, Brem J, Claridge TDW, Spencer J, Schofield CJ, Dmitrienko GI. Cyclobutanone Mimics of Intermediates in Metallo-β-Lactamase Catalysis. Chemistry 2018; 24:5734-5737. [PMID: 29250863 PMCID: PMC5947706 DOI: 10.1002/chem.201705886] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 01/25/2023]
Abstract
The most important resistance mechanism to β-lactam antibiotics involves hydrolysis by two β-lactamase categories: the nucleophilic serine and the metallo-β-lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β-lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM-1. NMR experiments using 19 F-labeled SPM-1 imply the cyclobutanone binds to SPM-1 with micromolar affinity. A crystal structure of the SPM-1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc-bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13 C-labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition-state and/or intermediate analogues as inhibitors of all β-lactamase classes.
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Affiliation(s)
- Martine I. Abboud
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Magda Kosmopoulou
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | - Anthony P. Krismanich
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
| | - Jarrod W. Johnson
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
| | - Philip Hinchliffe
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | - Jürgen Brem
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | | | - Gary I. Dmitrienko
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
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Abboud MI, Hinchliffe P, Brem J, Macsics R, Pfeffer I, Makena A, Umland KD, Rydzik AM, Li GB, Spencer J, Claridge TDW, Schofield CJ. 19
F-NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the São Paulo Metallo-β-Lactamase. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martine I. Abboud
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine; University of Bristol; Bristol UK
| | - Jürgen Brem
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Robert Macsics
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Inga Pfeffer
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Anne Makena
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Klaus-Daniel Umland
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Anna M. Rydzik
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - Guo-Bo Li
- Department of Chemistry; University of Oxford; 12 Mansfield Road OX1 3TA Oxford UK
| | - James Spencer
- School of Cellular and Molecular Medicine; University of Bristol; Bristol UK
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6
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Abboud MI, Hinchliffe P, Brem J, Macsics R, Pfeffer I, Makena A, Umland KD, Rydzik AM, Li GB, Spencer J, Claridge TDW, Schofield CJ. 19 F-NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the São Paulo Metallo-β-Lactamase. Angew Chem Int Ed Engl 2017; 56:3862-3866. [PMID: 28252254 PMCID: PMC5396265 DOI: 10.1002/anie.201612185] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/16/2016] [Indexed: 01/19/2023]
Abstract
Resistance to β‐lactam antibiotics mediated by metallo‐β‐lactamases (MBLs) is a growing problem. We describe the use of protein‐observe 19F‐NMR (PrOF NMR) to study the dynamics of the São Paulo MBL (SPM‐1) from β‐lactam‐resistant Pseudomonas aeruginosa. Cysteinyl variants on the α3 and L3 regions, which flank the di‐ZnII active site, were selectively 19F‐labeled using 3‐bromo‐1,1,1‐trifluoroacetone. The PrOF NMR results reveal roles for the mobile α3 and L3 regions in the binding of both inhibitors and hydrolyzed β‐lactam products to SPM‐1. These results have implications for the mechanisms and inhibition of MBLs by β‐lactams and non‐β‐lactams and illustrate the utility of PrOF NMR for efficiently analyzing metal chelation, identifying new binding modes, and studying protein binding from a mixture of equilibrating isomers.
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Affiliation(s)
- Martine I Abboud
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Robert Macsics
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Inga Pfeffer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Anne Makena
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Klaus-Daniel Umland
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Anna M Rydzik
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - Guo-Bo Li
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK
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7
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Hamark C, Landström J, Widmalm G. SEAL by NMR: Glyco‐Based Selenium‐Labeled Affinity Ligands Detected by NMR Spectroscopy. Chemistry 2014; 20:13905-8. [DOI: 10.1002/chem.201404933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Indexed: 11/05/2022]
Affiliation(s)
- Christoffer Hamark
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, 10691 Stockholm (Sweden)
| | - Jens Landström
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, 10691 Stockholm (Sweden)
| | - Göran Widmalm
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, 10691 Stockholm (Sweden)
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