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Liu T, Abboud MI, Chowdhury R, Tumber A, Hardy AP, Lippl K, Lohans CT, Pires E, Wickens J, McDonough MA, West CM, Schofield CJ. Biochemical and biophysical analyses of hypoxia sensing prolyl hydroxylases from Dictyostelium discoideum and Toxoplasma gondii. J Biol Chem 2020; 295:16545-16561. [PMID: 32934009 PMCID: PMC7864055 DOI: 10.1074/jbc.ra120.013998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 04/22/2020] [Revised: 08/14/2020] [Indexed: 12/30/2022] Open
Abstract
In animals, the response to chronic hypoxia is mediated by prolyl hydroxylases (PHDs) that regulate the levels of hypoxia-inducible transcription factor α (HIFα). PHD homologues exist in other types of eukaryotes and prokaryotes where they act on non HIF substrates. To gain insight into the factors underlying different PHD substrates and properties, we carried out biochemical and biophysical studies on PHD homologues from the cellular slime mold, Dictyostelium discoideum, and the protozoan parasite, Toxoplasma gondii, both lacking HIF. The respective prolyl-hydroxylases (DdPhyA and TgPhyA) catalyze prolyl-hydroxylation of S-phase kinase-associated protein 1 (Skp1), a reaction enabling adaptation to different dioxygen availability. Assays with full-length Skp1 substrates reveal substantial differences in the kinetic properties of DdPhyA and TgPhyA, both with respect to each other and compared with human PHD2; consistent with cellular studies, TgPhyA is more active at low dioxygen concentrations than DdPhyA. TgSkp1 is a DdPhyA substrate and DdSkp1 is a TgPhyA substrate. No cross-reactivity was detected between DdPhyA/TgPhyA substrates and human PHD2. The human Skp1 E147P variant is a DdPhyA and TgPhyA substrate, suggesting some retention of ancestral interactions. Crystallographic analysis of DdPhyA enables comparisons with homologues from humans, Trichoplax adhaerens, and prokaryotes, informing on differences in mobile elements involved in substrate binding and catalysis. In DdPhyA, two mobile loops that enclose substrates in the PHDs are conserved, but the C-terminal helix of the PHDs is strikingly absent. The combined results support the proposal that PHD homologues have evolved kinetic and structural features suited to their specific sensing roles.
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Affiliation(s)
- Tongri Liu
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Adam P Hardy
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - James Wickens
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Christopher M West
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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2
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Holt‐Martyn JP, Chowdhury R, Tumber A, Yeh T, Abboud MI, Lippl K, Lohans CT, Langley GW, Figg W, McDonough MA, Pugh CW, Ratcliffe PJ, Schofield CJ. Structure-Activity Relationship and Crystallographic Studies on 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors. ChemMedChem 2020; 15:270-273. [PMID: 31751494 PMCID: PMC7496690 DOI: 10.1002/cmdc.201900557] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 09/30/2019] [Revised: 11/08/2019] [Indexed: 02/06/2023]
Abstract
The 2-oxoglutarate-dependent hypoxia inducible factor prolyl hydroxylases (PHDs) are targets for treatment of a variety of diseases including anaemia. One PHD inhibitor is approved for use for the treatment of renal anaemia and others are in late stage clinical trials. The number of reported templates for PHD inhibition is limited. We report structure-activity relationship and crystallographic studies on a promising class of 4-hydroxypyrimidine-containing PHD inhibitors.
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Affiliation(s)
- James P. Holt‐Martyn
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Rasheduzzaman Chowdhury
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Tzu‐Lan Yeh
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Martine I. Abboud
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Kerstin Lippl
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Christopher T. Lohans
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Gareth W. Langley
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - William Figg
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | - Michael A. McDonough
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Peter J. Ratcliffe
- NDM Research BuildingUniversity of OxfordOxfordOX3 7FZUK
- The Francis Crick InstituteLondonNW1 1ATUK
| | - Christopher J. Schofield
- Department of ChemistryUniversity of Oxford Chemistry Research Laboratory12 Mansfield RoadOxfordOX1 3TAUK
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3
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Cockman ME, Lippl K, Tian YM, Pegg HB, Figg WD, Abboud MI, Heilig R, Fischer R, Myllyharju J, Schofield CJ, Ratcliffe PJ. Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates. eLife 2019; 8:e46490. [PMID: 31500697 PMCID: PMC6739866 DOI: 10.7554/elife.46490] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 02/28/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.
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Affiliation(s)
| | - Kerstin Lippl
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Ya-Min Tian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - William D Figg
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Peter J Ratcliffe
- The Francis Crick InstituteLondonUnited Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
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4
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Roatsch M, Hoffmann I, Abboud MI, Hancock RL, Tarhonskaya H, Hsu KF, Wilkins SE, Yeh TL, Lippl K, Serrer K, Moneke I, Ahrens TD, Robaa D, Wenzler S, Barthes NPF, Franz H, Sippl W, Lassmann S, Diederichs S, Schleicher E, Schofield CJ, Kawamura A, Schüle R, Jung M. The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases. ACS Chem Biol 2019; 14:1737-1750. [PMID: 31287655 DOI: 10.1021/acschembio.9b00289] [Citation(s) in RCA: 20] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are "epigenetic eraser" enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox might provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.
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Affiliation(s)
- Martin Roatsch
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Inga Hoffmann
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Martine I Abboud
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Rebecca L Hancock
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kuo-Feng Hsu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Sarah E Wilkins
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tzu-Lan Yeh
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Serrer
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Isabelle Moneke
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
| | - Theresa D Ahrens
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Dina Robaa
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Sandra Wenzler
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Nicolas P F Barthes
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Henriette Franz
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Wolfgang Sippl
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
- Division of RNA Biology & Cancer , German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280 , 69120 Heidelberg , Germany
| | - Erik Schleicher
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Christopher J Schofield
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Roland Schüle
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
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5
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Holt-Martyn JP, Tumber A, Rahman MZ, Lippl K, Figg W, McDonough MA, Chowdhury R, Schofield CJ. Studies on spiro[4.5]decanone prolyl hydroxylase domain inhibitors. Medchemcomm 2019; 10:500-504. [PMID: 31057728 PMCID: PMC6482412 DOI: 10.1039/c8md00548f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/09/2019] [Indexed: 12/12/2022]
Abstract
The 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (PHDs) are targets for treatment of anaemia and other ischaemia related diseases. PHD inhibitors are in clinical trials; however, the number of reported templates for PHD inhibition is limited. We report structure-activity relationship and crystallographic studies on spiro[4.5]decanone containing PHD inhibitors. Together with other studies, our results reveal spiro[4.5]decanones as useful templates for generation of potent and selective 2OG oxygenase inhibitors.
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Affiliation(s)
- James P Holt-Martyn
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Anthony Tumber
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Mohammed Z Rahman
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Kerstin Lippl
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - William Figg
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Rasheduzzaman Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford , OX1 3TA , UK .
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6
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Lippl K, Boleininger A, McDonough MA, Abboud MI, Tarhonskaya H, Chowdhury R, Loenarz C, Schofield CJ. Born to sense: biophysical analyses of the oxygen sensing prolyl hydroxylase from the simplest animal Trichoplax adhaerens. Hypoxia (Auckl) 2018; 6:57-71. [PMID: 30519597 PMCID: PMC6235002 DOI: 10.2147/hp.s174655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background In humans and other animals, the chronic hypoxic response is mediated by hypoxia inducible transcription factors (HIFs) which regulate the expression of genes that counteract the effects of limiting oxygen. Prolyl hydroxylases (PHDs) act as hypoxia sensors for the HIF system in organisms ranging from humans to the simplest animal Trichoplax adhaerens. Methods We report structural and biochemical studies on the T. adhaerens HIF prolyl hydroxylase (TaPHD) that inform about the evolution of hypoxia sensing in animals. Results High resolution crystal structures (≤1.3 Å) of TaPHD, with and without its HIFα substrate, reveal remarkable conservation of key active site elements between T. adhaerens and human PHDs, which also manifest in kinetic comparisons. Conclusion Conserved structural features of TaPHD and human PHDs include those apparently enabling the slow binding/reaction of oxygen with the active site Fe(II), the formation of a stable 2-oxoglutarate complex, and a stereoelectronically promoted change in conformation of the hydroxylated proline-residue. Comparison of substrate selectivity between the human PHDs and TaPHD provides insights into the selectivity determinants of HIF binding by the PHDs, and into the evolution of the multiple HIFs and PHDs present in higher animals.
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Affiliation(s)
- Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Oxford, UK,
| | - Anna Boleininger
- Chemistry Research Laboratory, University of Oxford, Oxford, UK,
| | | | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Oxford, UK,
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7
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Abboud MI, Chowdhury R, Leung IKH, Lippl K, Loenarz C, Claridge TDW, Schofield CJ. Studies on the Substrate Selectivity of the Hypoxia-Inducible Factor Prolyl Hydroxylase 2 Catalytic Domain. Chembiochem 2018; 19:2262-2267. [PMID: 30144273 DOI: 10.1002/cbic.201800246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 05/08/2018] [Indexed: 12/19/2022]
Abstract
In animals, the response to chronic hypoxia is mediated by upregulation of the α,β-heterodimeric hypoxia-inducible factors (HIFs). Levels of HIFα isoforms, but not HIFβ, are regulated by their post-translational modification as catalysed by prolyl hydroxylase domain enzymes (PHDs). Different roles for the human HIF-1/2α isoforms and their two oxygen-dependent degradation domains (ODDs) are proposed. We report kinetic and NMR analyses of the ODD selectivity of the catalytic domain of wild-type PHD2 (which is conserved in nearly all animals) and clinically observed variants. Studies using Ala scanning and "hybrid" ODD peptides imply that the relatively rigid conformation of the (hydroxylated) proline plays an important role in ODD binding. They also reveal differential roles in binding for the residues on the N- and C-terminal sides of the substrate proline. The overall results indicate how the PHDs achieve selectivity for HIFα ODDs and might be of use in identifying substrate-selective PHD inhibitors.
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Affiliation(s)
- Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Department of Molecular and Cellular Physiology, University of Stanford, Stanford, CA, 94305-5345, USA
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany
| | - Christoph Loenarz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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8
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Abboud MI, McAllister TE, Leung IKH, Chowdhury R, Jorgensen C, Domene C, Mecinović J, Lippl K, Hancock RL, Hopkinson RJ, Kawamura A, Claridge TDW, Schofield CJ. 2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2. Chem Commun (Camb) 2018. [PMID: 29522057 PMCID: PMC5885369 DOI: 10.1039/c8cc00387d] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The binding of prolyl-hydroxylated HIF-α to PHD2 is hindered by prior 2OG binding; likely, leading to the inhibition of HIF-α degradation under limiting 2OG conditions.
Prolyl hydroxylation of hypoxia inducible factor (HIF)-α, as catalysed by the Fe(ii)/2-oxoglutarate (2OG)-dependent prolyl hydroxylase domain (PHD) enzymes, has a hypoxia sensing role in animals. We report that binding of prolyl-hydroxylated HIF-α to PHD2 is ∼50 fold hindered by prior 2OG binding; thus, when 2OG is limiting, HIF-α degradation might be inhibited by PHD binding.
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Affiliation(s)
- Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Tom E McAllister
- 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. and School of Chemical Sciences, The University of Auckland, New Zealand
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | | | - Carmen Domene
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Jasmin Mecinović
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Rebecca L Hancock
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Leicester Institute of Structural and Chemical Biology and Department of Chemistry, University of Leicester, Leicester, LE1 7RH, UK
| | - Akane Kawamura
- 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.
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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9
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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: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Chan MC, Ilott NE, Schödel J, Sims D, Tumber A, Lippl K, Mole DR, Pugh CW, Ratcliffe PJ, Ponting CP, Schofield CJ. Tuning the Transcriptional Response to Hypoxia by Inhibiting Hypoxia-inducible Factor (HIF) Prolyl and Asparaginyl Hydroxylases. J Biol Chem 2016; 291:20661-73. [PMID: 27502280 PMCID: PMC5034057 DOI: 10.1074/jbc.m116.749291] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [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: 07/20/2016] [Revised: 08/05/2016] [Indexed: 01/08/2023] Open
Abstract
The hypoxia-inducible factor (HIF) system orchestrates cellular responses to hypoxia in animals. HIF is an α/β-heterodimeric transcription factor that regulates the expression of hundreds of genes in a tissue context-dependent manner. The major hypoxia-sensing component of the HIF system involves oxygen-dependent catalysis by the HIF hydroxylases; in humans there are three HIF prolyl hydroxylases (PHD1-3) and an asparaginyl hydroxylase (factor-inhibiting HIF (FIH)). PHD catalysis regulates HIFα levels, and FIH catalysis regulates HIF activity. How differences in HIFα hydroxylation status relate to variations in the induction of specific HIF target gene transcription is unknown. We report studies using small molecule HIF hydroxylase inhibitors that investigate the extent to which HIF target gene expression is induced by PHD or FIH inhibition. The results reveal substantial differences in the role of prolyl and asparaginyl hydroxylation in regulating hypoxia-responsive genes in cells. PHD inhibitors with different structural scaffolds behave similarly. Under the tested conditions, a broad-spectrum 2-oxoglutarate dioxygenase inhibitor is a better mimic of the overall transcriptional response to hypoxia than the selective PHD inhibitors, consistent with an important role for FIH in the hypoxic transcriptional response. Indeed, combined application of selective PHD and FIH inhibitors resulted in the transcriptional induction of a subset of genes not fully responsive to PHD inhibition alone. Thus, for the therapeutic regulation of HIF target genes, it is important to consider both PHD and FIH activity, and in the case of some sets of target genes, simultaneous inhibition of the PHDs and FIH catalysis may be preferable.
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Affiliation(s)
- Mun Chiang Chan
- From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Nicholas E Ilott
- the Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, and
| | - Johannes Schödel
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - David Sims
- the Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, and
| | - Anthony Tumber
- the Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Kerstin Lippl
- From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA
| | - David R Mole
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Christopher W Pugh
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Peter J Ratcliffe
- the Centre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN
| | - Chris P Ponting
- the Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, and
| | - Christopher J Schofield
- From the Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA,
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11
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Schwarz J, Dietel D, Lippl K, Eickelberg O. Role of Mitochondrial Metabolism in Phenotypic Plasticity of Lung Fibroblasts. Pneumologie 2011. [DOI: 10.1055/s-0031-1296146] [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: 10/15/2022]
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