1
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Swartjes A, White PB, Bruekers JPJ, Elemans JAAW, Nolte RJM. Paramagnetic relaxation enhancement NMR as a tool to probe guest binding and exchange in metallohosts. Nat Commun 2022; 13:1846. [PMID: 35388004 PMCID: PMC8986849 DOI: 10.1038/s41467-022-29406-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/21/2022] [Indexed: 11/11/2022] Open
Abstract
Paramagnetic metallohost systems can bind guest molecules and find application as biomimetic catalysts. Due to the presence of the paramagnetic metal center, rigorous characterization of these systems by NMR spectroscopy can be very difficult. We report here that metallohost-guest systems can be studied by using the paramagnetic relaxation enhancement (PRE) effect. Manganese(III) porphyrin cage compounds are shown through their PRE to thread and bind viologen guests, including a polymeric one. The binding constants and dethreading activation parameters are lower than those of the metal-free porphyrin cage compounds, which is proposed to be a result of charge repulsion of the trivalent metal center and dicationic viologen guest. The threading rate of the manganese(III) porphyrin cage onto the polymer is more than 10 times faster than that of the non-metallated one, which is ascribed to initial binding of the cage to the polymer chain prior to threading, and to an entron effect. Paramagnetic metallohost systems are difficult to characterize. Here the authors report that the paramagnetic relaxation enhancement effect can be used to prove by nuclear magnetic resonance experiments that Mn(III) porphyrin cage compounds can bind and thread low molecular weight and polymeric guests.
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Affiliation(s)
- Anne Swartjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul B White
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Jeroen P J Bruekers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Johannes A A W Elemans
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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2
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Affiliation(s)
- Pramod N. Rakendu
- Institute for Integrated Programmes and Research in Basic Sciences (IIRBS) Mahatma Gandhi University Priyadarsini Hills P.O Kottayam Kerala 686560 India
| | - Thaipparambil Aneeja
- School of Chemical Sciences Mahatma Gandhi University Priyadarsini Hills P.O Kottayam Kerala 686560 India
| | - Gopinathan Anilkumar
- Institute for Integrated Programmes and Research in Basic Sciences (IIRBS) Mahatma Gandhi University Priyadarsini Hills P.O Kottayam Kerala 686560 India
- School of Chemical Sciences Mahatma Gandhi University Priyadarsini Hills P.O Kottayam Kerala 686560 India
- Advanced Molecular Materials Research centre (AMMRC) Mahatma Gandhi University Priyadarsini Hills P.O Kottayam Kerala 686560 India
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3
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Rydzik AM, Brem J, Chandler SA, Benesch JLP, Claridge TDW, Schofield CJ. Monitoring protein-metal binding by 19F NMR - a case study with the New Delhi metallo-β-lactamase 1. RSC Med Chem 2020; 11:387-391. [PMID: 33479644 PMCID: PMC7484990 DOI: 10.1039/c9md00416e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/31/2019] [Indexed: 11/29/2022] Open
Abstract
19F NMR protein observed spectroscopy is evaluated as a method for analysing protein metal binding using the New Delhi metallo-β-lactamase 1. The results imply 19F NMR is useful for analysis of different metallated protein states and investigations on equilibrium states in the presence of inhibitors. One limitation is that 19F labelling may affect metal ion binding. The sensitive readout of changes in protein behaviour observed by 19F NMR spectra coupled with the broad scope of tolerated conditions (e.g. buffer variations) means 19F NMR should be further investigated for studying metal ion interactions and the inhibition of metallo-enzymes during drug discovery.
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Affiliation(s)
- Anna M Rydzik
- The Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Jürgen Brem
- The Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Shane A Chandler
- The Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Justin L P Benesch
- 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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4
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Taraban MB, Deredge DJ, Smith ME, Briggs KT, Li Y, Jiang ZX, Wintrode PL, Yu YB. Monitoring dendrimer conformational transition using 19 F and 1 H 2 O NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:861-872. [PMID: 30746779 DOI: 10.1002/mrc.4849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/25/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
The conformational transition of a fluorinated amphiphilic dendrimer is monitored by the 1 H signal from water, alongside the 19 F signal from the dendrimer. High-field NMR data (chemical shift δ, self-diffusion coefficient D, longitudinal relaxation rate R1 , and transverse relaxation rate R2 ) for both dendrimer (19 F) and water (1 H) match each other in detecting the conformational transition. Among all parameters for both nuclei, the water proton transverse-relaxation rate R2 (1 H2 O) displays the highest relative scale of change upon conformational transition of the dendrimer. Hydrogen/deuterium-exchange mass spectrometry reveals that the compact form of the dendrimer has slower proton exchange with water than the extended form. This result suggests that the sensitivity of R2 (1 H2 O) toward dendrimer conformation originates, at least partially, from the difference in proton exchange efficiency between different dendrimer conformations. Finally, we also demonstrated that this conformational transition could be conveniently monitored using a low-field benchtop NMR spectrometer via R2 (1 H2 O). The 1 H2 O signal thus offers a simple way to monitor structural changes of macromolecules using benchtop time-domain NMR.
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Affiliation(s)
- Marc B Taraban
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Margaret E Smith
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Katharine T Briggs
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Yu Li
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhong-Xing Jiang
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
| | - Yihua Bruce Yu
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, 21201, USA
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5
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Abstract
WaterLOGSY is a ligand-observed NMR method that is widely used for the studies of protein-small molecule interactions. The basis of waterLOGSY relies on the transfer of magnetization between water molecules, proteins, and small molecules via the nuclear Overhauser effect and chemical exchange. WaterLOGSY is used extensively for the screening of protein ligands, as it is a robust, relatively high-throughput, and reliable method to identify small molecules that bind proteins with a binding affinity (KD) in the μM to mM region. WaterLOGSY also enables the determination of KD via ligand titration, although careful optimization of the experimental setup is required to avoid overestimation of binding constants. Finally, waterLOGSY allows the water-accessible ligand protons of protein-bound ligands to be identified, thus providing structural information of the ligand binding orientation. In this chapter, we introduce and describe the waterLOGSY method, and provide a practical guide for ligand screening and KD determination. The use of waterLOGSY to study water accessibility is also discussed.
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Affiliation(s)
- Renjie Huang
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand.
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6
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Das M, Yang T, Dong J, Prasetya F, Xie Y, Wong KHQ, Cheong A, Woon ECY. Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3. Chem Asian J 2018; 13:2854-2867. [PMID: 29917331 DOI: 10.1002/asia.201800729] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/12/2018] [Indexed: 12/18/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC50 =2.6 μm) and ALKBH3 (8; IC50 =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.
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MESH Headings
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/antagonists & inhibitors
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics
- AlkB Homolog 5, RNA Demethylase/antagonists & inhibitors
- AlkB Homolog 5, RNA Demethylase/chemistry
- AlkB Homolog 5, RNA Demethylase/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Catalysis
- Combinatorial Chemistry Techniques/methods
- Enzyme Inhibitors/chemistry
- Fluorometry/methods
- Humans
- Hydrazones/chemistry
- Kinetics
- Ligands
- Molecular Structure
- Oxidoreductases, O-Demethylating/antagonists & inhibitors
- Oxidoreductases, O-Demethylating/chemistry
- Oxidoreductases, O-Demethylating/genetics
- Peptides/chemistry
- Peptides/genetics
- Protein Denaturation
- Protein Engineering
- Protein Structure, Secondary
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Transition Temperature
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Affiliation(s)
- Mohua Das
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Jinghua Dong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Fransisca Prasetya
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Yiming Xie
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Adeline Cheong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
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7
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Yeh TL, Leissing TM, Abboud MI, Thinnes CC, Atasoylu O, Holt-Martyn JP, Zhang D, Tumber A, Lippl K, Lohans CT, Leung IKH, Morcrette H, Clifton IJ, Claridge TDW, Kawamura A, Flashman E, Lu X, Ratcliffe PJ, Chowdhury R, Pugh CW, Schofield CJ. Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Chem Sci 2017; 8:7651-7668. [PMID: 29435217 PMCID: PMC5802278 DOI: 10.1039/c7sc02103h] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023] Open
Abstract
Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1-3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophysical, and biochemical studies comparing four PHD inhibitors currently in clinical trials for anaemia treatment, that describe their mechanisms of action, potency against isolated enzymes and in cells, and selectivities versus representatives of other human 2OG oxygenase subfamilies. The 'clinical' PHD inhibitors are potent inhibitors of PHD catalyzed hydroxylation of the HIF-α oxygen dependent degradation domains (ODDs), and selective against most, but not all, representatives of other human 2OG dependent dioxygenase subfamilies. Crystallographic and NMR studies provide insights into the different active site binding modes of the inhibitors. Cell-based results reveal the inhibitors have similar effects on the upregulation of HIF target genes, but differ in the kinetics of their effects and in extent of inhibition of hydroxylation of the N- and C-terminal ODDs; the latter differences correlate with the biophysical observations.
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Affiliation(s)
- Tzu-Lan Yeh
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Thomas M Leissing
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Martine I Abboud
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Cyrille C Thinnes
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Onur Atasoylu
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - James P Holt-Martyn
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Dong Zhang
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Anthony Tumber
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Kerstin Lippl
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher T Lohans
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Helen Morcrette
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Ian J Clifton
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Timothy D W Claridge
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Akane Kawamura
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Emily Flashman
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Xin Lu
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Peter J Ratcliffe
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
- The Francis Crick Institute , 1 Midland Road , London NW1 1AT , UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher W Pugh
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Christopher J Schofield
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
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8
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Mbenza NM, Vadakkedath PG, McGillivray DJ, Leung IKH. NMR studies of the non-haem Fe(II) and 2-oxoglutarate-dependent oxygenases. J Inorg Biochem 2017; 177:384-394. [PMID: 28893416 DOI: 10.1016/j.jinorgbio.2017.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 01/13/2023]
Abstract
The non-haem Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenases belong to a superfamily of structurally-related enzymes that play important biological roles in plants, microorganisms and animals. Structural, mechanistic and functional studies of 2OG oxygenases require efficient and effective biophysical tools. Nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study this enzyme superfamily. It has been applied to obtain information about enzyme kinetics, identify and characterise 2OG oxygenase-catalysed oxidation products, elucidate the catalytic mechanism, monitor ligand binding and study protein dynamics. This review summarises the types of information that NMR spectroscopy can provide in the studies of 2OG oxygenases, highlights the advantages of the technique and describes its drawbacks.
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Affiliation(s)
- Naasson M Mbenza
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand..
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9
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O’Neill ES, Kolanowski JL, Bonnitcha PD, New EJ. A cobalt(ii) complex with unique paraSHIFT responses to anions. Chem Commun (Camb) 2017; 53:3571-3574. [DOI: 10.1039/c7cc00619e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A cobalt(ii) complex can distinguish between anions by observing the paramagnetic 1H NMR shift.
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Affiliation(s)
- E. S. O’Neill
- School of Chemistry
- The University of Sydney
- Australia
| | | | - P. D. Bonnitcha
- Sydney Medical School
- Royal North Shore Hospital
- St. Leonards
- Australia
| | - E. J. New
- School of Chemistry
- The University of Sydney
- Australia
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10
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Koukourakis MI, Giatromanolaki A, Zois CE, Kalamida D, Pouliliou S, Karagounis IV, Yeh TL, Abboud MI, Claridge TDW, Schofield CJ, Sivridis E, Simopoulos C, Tokmakidis SP, Harris AL. Normal tissue radioprotection by amifostine via Warburg-type effects. Sci Rep 2016; 6:30986. [PMID: 27507219 PMCID: PMC4978965 DOI: 10.1038/srep30986] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/07/2016] [Indexed: 12/12/2022] Open
Abstract
The mechanism of Amifostine (WR-2721) mediated radioprotection is poorly understood. The effects of amifostine on human basal metabolism, mouse liver metabolism and on normal and tumor hepatic cells were studied. Indirect calorimetric canopy tests showed significant reductions in oxygen consumption and of carbon dioxide emission in cancer patients receiving amifostine. Glucose levels significantly decreased and lactate levels increased in patient venous blood. Although amifostine in vitro did not inhibit the activity of the prolyl-hydroxylase PHD2, experiments with mouse liver showed that on a short timescale WR-1065 induced expression of the Hypoxia Inducible Factor HIF1α, lactate dehydrogenase LDH5, glucose transporter GLUT2, phosphorylated pyruvate dehydrogenase pPDH and PDH-kinase. This effect was confirmed on normal mouse NCTC hepatocytes, but not on hepatoma cells. A sharp reduction of acetyl-CoA and ATP levels in NCTC cells indicated reduced mitochondrial usage of pyruvate. Transient changes of mitochondrial membrane potential and reactive oxygen species ROS production were evident. Amifostine selectively protects NCTC cells against radiation, whilst HepG2 neoplastic cells are sensitized. The radiation protection was correlates with HIF levels. These findings shed new light on the mechanism of amifostine cytoprotection and encourage clinical research with this agent for the treatment of primary and metastatic liver cancer.
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Affiliation(s)
- Michael I. Koukourakis
- Department of Radiotherapy/Oncology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | | | - Christos E. Zois
- Department of Radiotherapy/Oncology, Democritus University of Thrace, Alexandroupolis 68100, Greece
- Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Dimitra Kalamida
- Department of Radiotherapy/Oncology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Stamatia Pouliliou
- Department of Radiotherapy/Oncology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Ilias V. Karagounis
- Department of Radiotherapy/Oncology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Tzu-Lan Yeh
- The Chemistry Research laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Martine I. Abboud
- The Chemistry Research laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | | | | | - Efthimios Sivridis
- Department of Pathology, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Costantinos Simopoulos
- Laboratory of Experimental Surgery, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Savvas P. Tokmakidis
- Department of Physical Education and Sports Science. Democritus University of Thrace, Komotini, Greece
| | - Adrian L. Harris
- Cancer Research UK, Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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11
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Pharmacological targeting of the HIF hydroxylases--A new field in medicine development. Mol Aspects Med 2016; 47-48:54-75. [PMID: 26791432 DOI: 10.1016/j.mam.2016.01.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 12/13/2022]
Abstract
In human cells oxygen levels are 'sensed' by a set of ferrous iron and 2-oxoglutarate dependent dioxygenases. These enzymes regulate a broad range of cellular and systemic responses to hypoxia by catalysing the post-translational hydroxylation of specific residues in the alpha subunits of hypoxia inducible factor (HIF) transcriptional complexes. The HIF hydroxylases are now the subject of pharmaceutical targeting by small molecule inhibitors that aim to activate or augment the endogenous HIF transcriptional response for the treatment of anaemia and other hypoxic human diseases. Here we consider the rationale for this therapeutic strategy from the biochemical, biological and medical perspectives. We outline structural and mechanistic considerations that are relevant to the design of HIF hydroxylase inhibitors, including likely determinants of specificity, and review published reports on their activity in pre-clinical models and clinical trials.
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12
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Khan A, Leśniak RK, Brem J, Rydzik AM, Choi H, Leung IKH, McDonough MA, Schofield CJ, Claridge TDW. Development and application of ligand-based NMR screening assays for γ-butyrobetaine hydroxylase. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00004e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 1H NMR based dual-reporter binding assay for γ-butyrobetaine hydroxylase (BBOX) reveals unexpected structure–activity relationships for isoquinoline-derived inhibitors.
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Affiliation(s)
- A. Khan
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - R. K. Leśniak
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - J. Brem
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - A. M. Rydzik
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - H. Choi
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - I. K. H. Leung
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - M. A. McDonough
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - C. J. Schofield
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
| | - T. D. W. Claridge
- Department of Chemistry
- Chemistry Research Laboratory
- University of Oxford
- Oxford
- UK
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13
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Chan MC, Atasoylu O, Hodson E, Tumber A, Leung IKH, Chowdhury R, Gómez-Pérez V, Demetriades M, Rydzik AM, Holt-Martyn J, Tian YM, Bishop T, Claridge TDW, Kawamura A, Pugh CW, Ratcliffe PJ, Schofield CJ. Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain. PLoS One 2015; 10:e0132004. [PMID: 26147748 PMCID: PMC4492579 DOI: 10.1371/journal.pone.0132004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 01/01/2023] Open
Abstract
As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human hypoxic response can be achieved by the inhibition of the hypoxia sensors for the HIF system, i.e. the HIF prolyl-hydroxylases (PHDs). Here, we report studies on tricyclic triazole-containing compounds as potent and selective PHD inhibitors which compete with the 2-oxoglutarate co-substrate. One compound (IOX4) induces HIFα in cells and in wildtype mice with marked induction in the brain tissue, revealing that it is useful for studies aimed at validating the upregulation of HIF for treatment of cerebral diseases including stroke.
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Affiliation(s)
- Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Onur Atasoylu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Emma Hodson
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Verónica Gómez-Pérez
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marina Demetriades
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Ya-Min Tian
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Tammie Bishop
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Christopher W. Pugh
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Peter J. Ratcliffe
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
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14
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Tarhonskaya H, Chowdhury R, Leung IKH, Loik ND, McCullagh JSO, Claridge TDW, Schofield CJ, Flashman E. Investigating the contribution of the active site environment to the slow reaction of hypoxia-inducible factor prolyl hydroxylase domain 2 with oxygen. Biochem J 2014; 463:363-72. [PMID: 25120187 DOI: 10.1042/bj20140779] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
The prolyl hydroxylase domain proteins (PHDs) catalyse the post-translational hydroxylation of the hypoxia-inducible factor (HIF), a modification that regulates the hypoxic response in humans. The PHDs are Fe(II)/2-oxoglutarate (2OG) oxygenases; their catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that purified PHD2 reacts slowly with O2 compared with some other studied 2OG oxygenases, a property which may be related to its hypoxia-sensing role. PHD2 forms a stable complex with Fe(II) and 2OG; crystallographic and kinetic analyses indicate that an Fe(II)-co-ordinated water molecule, which must be displaced before O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. While disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the Fe(II)-binding aspartate for a glutamate residue (D315E) manifested significantly reduced Fe(II) binding, yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.
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Affiliation(s)
- Hanna Tarhonskaya
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Rasheduzzaman Chowdhury
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Ivanhoe K H Leung
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Nikita D Loik
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - James S O McCullagh
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy D W Claridge
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Christopher J Schofield
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Emily Flashman
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
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15
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Chen RL, Ogunshola OO, Yeoh KK, Jani A, Papadakis M, Nagel S, Schofield CJ, Buchan AM. HIF prolyl hydroxylase inhibition prior to transient focal cerebral ischaemia is neuroprotective in mice. J Neurochem 2014; 131:177-89. [PMID: 24974727 DOI: 10.1111/jnc.12804] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 06/19/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022]
Abstract
This study investigated the effects of 2-(1-chloro-4-hydroxyisoquinoline-3-carboxamido) acetic acid (IOX3), a selective small molecule inhibitor of hypoxia-inducible factor (HIF) prolyl hydroxylases, on mouse brains subject to transient focal cerebral ischaemia. Male, 8- to 12-week-old C57/B6 mice were subjected to 45 min of middle cerebral artery occlusion (MCAO) either immediately or 24 h after receiving IOX3. Mice receiving IOX3 at 20 mg/kg 24 h prior to the MCAO had better neuroscores and smaller blood-brain barrier (BBB) disruption and infarct volumes than mice receiving the vehicle, whereas those having IOX3 at 60 mg/kg showed no significant changes. IOX3 treatment immediately before MCAO was not neuroprotective. IOX3 up-regulated HIF-1α, and increased EPO expression in mouse brains. In an in vitro BBB model (RBE4 cell line), IOX3 up-regulated HIF-1α and delocalized ZO-1. Pre-treating IOX3 on RBE4 cells 24 h before oxygen-glucose deprivation had a protective effect on endothelial barrier preservation with ZO-1 being better localized, while immediate IOX3 treatment did not. Our study suggests that HIF stabilization with IOX3 before cerebral ischaemia is neuroprotective partially because of BBB protection, while immediate application could be detrimental. These results provide information for studies aimed at the therapeutic activation of HIF pathway for neurovascular protection from cerebral ischaemia. We show that IOX3, a selective small molecule (280.66 Da) HIF prolyl hydroxylase inhibitor, could up-regulate HIF-1α and increase erythropoietin expression in mice. We further demonstrate that HIF stabilization with IOX3 before cerebral ischaemia is neuroprotective partially because of blood-brain barrier (BBB) protection, while immediate application is detrimental both in vivo and in vitro. These findings provide new insights into the role of HIF stabilization in ischaemic stroke.
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Affiliation(s)
- Ruoli L Chen
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Institute for Science and Technology in Medicine, School of Pharmacy, Keele University, Staffordshire, UK
| | - O O Ogunshola
- Institute of Veterinary Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Karkheng K Yeoh
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Anant Jani
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michalis Papadakis
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Simon Nagel
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Neurology, University of Heidelberg, Heidelberg, Germany
| | | | - Alastair M Buchan
- Acute Stroke Programme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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16
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Tarhonskaya H, Szöllössi A, Leung IKH, Bush JT, Henry L, Chowdhury R, Iqbal A, Claridge TDW, Schofield CJ, Flashman E. Studies on Deacetoxycephalosporin C Synthase Support a Consensus Mechanism for 2-Oxoglutarate Dependent Oxygenases. Biochemistry 2014; 53:2483-93. [DOI: 10.1021/bi500086p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Hanna Tarhonskaya
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrea Szöllössi
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jacob T. Bush
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Luc Henry
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Aman Iqbal
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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17
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Tarhonskaya H, Rydzik AM, Leung IKH, Loik ND, Chan MC, Kawamura A, McCullagh JSO, Claridge TDW, Flashman E, Schofield CJ. Non-enzymatic chemistry enables 2-hydroxyglutarate-mediated activation of 2-oxoglutarate oxygenases. Nat Commun 2014; 5:3423. [PMID: 24594748 PMCID: PMC3959194 DOI: 10.1038/ncomms4423] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 01/08/2023] Open
Abstract
Accumulation of (R)-2-hydroxyglutarate in cells results from mutations to isocitrate dehydrogenase that correlate with cancer. A recent study reports that (R)-, but not (S)-2-hydroxyglutarate, acts as a co-substrate for the hypoxia-inducible factor prolyl hydroxylases via enzyme-catalysed oxidation to 2-oxoglutarate. Here we investigate the mechanism of 2-hydroxyglutarate-enabled activation of 2-oxoglutarate oxygenases, including prolyl hydroxylase domain 2, the most important human prolyl hydroxylase isoform. We observe that 2-hydroxyglutarate-enabled catalysis by prolyl hydroxylase domain 2 is not enantiomer-specific and is stimulated by ferrous/ferric ion and reducing agents including L-ascorbate. The results reveal that 2-hydroxyglutarate is oxidized to 2-oxoglutarate non-enzymatically, likely via iron-mediated Fenton-chemistry, at levels supporting in vitro catalysis by 2-oxoglutarate oxygenases. Succinic semialdehyde and succinate are also identified as products of 2-hydroxyglutarate oxidation. Overall, the results rationalize the reported effects of 2-hydroxyglutarate on catalysis by prolyl hydroxylases in vitro and suggest that non-enzymatic 2-hydroxyglutarate oxidation may be of biological interest.
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Affiliation(s)
- Hanna Tarhonskaya
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Anna M. Rydzik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Nikita D. Loik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Mun Chiang Chan
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - James S. O. McCullagh
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
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18
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Leung IKH, Demetriades M, Hardy AP, Lejeune C, Smart TJ, Szöllössi A, Kawamura A, Schofield CJ, Claridge TDW. Reporter ligand NMR screening method for 2-oxoglutarate oxygenase inhibitors. J Med Chem 2013; 56:547-55. [PMID: 23234607 DOI: 10.1021/jm301583m] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The human 2-oxoglutarate (2OG) dependent oxygenases belong to a family of structurally related enzymes that play important roles in many biological processes. We report that competition-based NMR methods, using 2OG as a reporter ligand, can be used for quantitative and site-specific screening of ligand binding to 2OG oxygenases. The method was demonstrated using hypoxia inducible factor hydroxylases and histone demethylases, and K(D) values were determined for inhibitors that compete with 2OG at the metal center. This technique is also useful as a screening or validation tool for inhibitor discovery, as exemplified by work with protein-directed dynamic combinatorial chemistry.
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Affiliation(s)
- Ivanhoe K H Leung
- Department of Chemistry, University of Oxford , Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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19
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Rydzik AM, Leung IKH, Kochan GT, Thalhammer A, Oppermann U, Claridge TDW, Schofield CJ. Development and Application of a Fluoride-Detection-Based Fluorescence Assay for γ-Butyrobetaine Hydroxylase. Chembiochem 2012; 13:1559-63. [DOI: 10.1002/cbic.201200256] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Indexed: 01/30/2023]
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20
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202000] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Demetriades M, Leung IKH, Chowdhury R, Chan MC, McDonough MA, Yeoh KK, Tian YM, Claridge TDW, Ratcliffe PJ, Woon ECY, Schofield CJ. Dynamic Combinatorial Chemistry Employing Boronic Acids/Boronate Esters Leads to Potent Oxygenase Inhibitors. Angew Chem Int Ed Engl 2012; 51:6672-5. [DOI: 10.1002/anie.201202000] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Indexed: 11/05/2022]
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22
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Rotili D, Altun M, Kawamura A, Wolf A, Fischer R, Leung IKH, Mackeen MM, Tian YM, Ratcliffe PJ, Mai A, Kessler BM, Schofield CJ. A photoreactive small-molecule probe for 2-oxoglutarate oxygenases. ACTA ACUST UNITED AC 2011; 18:642-654. [PMID: 21609845 DOI: 10.1016/j.chembiol.2011.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 11/29/2022]
Abstract
2-oxoglutarate (2-OG)-dependent oxygenases have diverse roles in human biology. The inhibition of several 2-OG oxygenases is being targeted for therapeutic intervention, including for cancer, anemia, and ischemic diseases. We report a small-molecule probe for 2-OG oxygenases that employs a hydroxyquinoline template coupled to a photoactivable crosslinking group and an affinity-purification tag. Following studies with recombinant proteins, the probe was shown to crosslink to 2-OG oxygenases in human crude cell extracts, including to proteins at endogenous levels. This approach is useful for inhibitor profiling, as demonstrated by crosslinking to the histone demethylase FBXL11 (KDM2A) in HEK293T nuclear extracts. The results also suggest that small-molecule probes may be suitable for substrate identification studies.
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Affiliation(s)
- Dante Rotili
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.,Pasteur Institute - Cenci Bolognetti Foundation, Department of Chemistry and Technologies of Drugs, University of Rome "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
| | - Mikael Altun
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Akane Kawamura
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Alexander Wolf
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Roman Fischer
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ivanhoe K H Leung
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Mukram M Mackeen
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ya-Min Tian
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Peter J Ratcliffe
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Antonello Mai
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Chemistry and Technologies of Drugs, University of Rome "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
| | - Benedikt M Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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23
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Flashman E, Hoffart LM, Hamed RB, Bollinger JM, Krebs C, Schofield CJ. Evidence for the slow reaction of hypoxia-inducible factor prolyl hydroxylase 2 with oxygen. FEBS J 2010; 277:4089-99. [PMID: 20840591 DOI: 10.1111/j.1742-4658.2010.07804.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The response of animals to hypoxia is mediated by the hypoxia-inducible transcription factor. Human hypoxia-inducible factor is regulated by four Fe(II)- and 2-oxoglutarate-dependent oxygenases: prolyl hydroxylase domain enzymes 1-3 catalyse hydroxylation of two prolyl-residues in hypoxia-inducible factor, triggering its degradation by the proteasome. Factor inhibiting hypoxia-inducible factor catalyses the hydroxylation of an asparagine-residue in hypoxia-inducible factor, inhibiting its transcriptional activity. Collectively, the hypoxia-inducible factor hydroxylases negatively regulate hypoxia-inducible factor in response to increasing oxygen concentration. Prolyl hydroxylase domain 2 is the most important oxygen sensor in human cells; however, the underlying kinetic basis of the oxygen-sensing function of prolyl hydroxylase domain 2 is unclear. We report analyses of the reaction of prolyl hydroxylase domain 2 with oxygen. Chemical quench/MS experiments demonstrate that reaction of a complex of prolyl hydroxylase domain 2, Fe(II), 2-oxoglutarate and the C-terminal oxygen-dependent degradation domain of hypoxia-inducible factor-α with oxygen to form hydroxylated C-terminal oxygen-dependent degradation domain and succinate is much slower (approximately 100-fold) than for other similarly studied 2-oxoglutarate oxygenases. Stopped flow/UV-visible spectroscopy experiments demonstrate that the reaction produces a relatively stable species absorbing at 320 nm; Mössbauer spectroscopic experiments indicate that this species is likely not a Fe(IV)=O intermediate, as observed for other 2-oxoglutarate oxygenases. Overall, the results obtained suggest that, at least compared to other studied 2-oxoglutarate oxygenases, prolyl hydroxylase domain 2 reacts relatively slowly with oxygen, a property that may be associated with its function as an oxygen sensor.
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Affiliation(s)
- Emily Flashman
- Department of Chemistry and Oxford Centre for Integrative Systems Biology, Oxford, UK
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