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Figg WD, Fiorini G, Chowdhury R, Nakashima Y, Tumber A, McDonough MA, Schofield CJ. Structural basis for binding of the renal carcinoma target hypoxia-inducible factor 2α to prolyl hydroxylase domain 2. Proteins 2023; 91:1510-1524. [PMID: 37449559 PMCID: PMC10952196 DOI: 10.1002/prot.26541] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023]
Abstract
The hypoxia-inducible factor (HIF) prolyl-hydroxylases (human PHD1-3) catalyze prolyl hydroxylation in oxygen-dependent degradation (ODD) domains of HIFα isoforms, modifications that signal for HIFα proteasomal degradation in an oxygen-dependent manner. PHD inhibitors are used for treatment of anemia in kidney disease. Increased erythropoietin (EPO) in patients with familial/idiopathic erythrocytosis and pulmonary hypertension is associated with mutations in EGLN1 (PHD2) and EPAS1 (HIF2α); a drug inhibiting HIF2α activity is used for clear cell renal cell carcinoma (ccRCC) treatment. We report crystal structures of PHD2 complexed with the C-terminal HIF2α-ODD in the presence of its 2-oxoglutarate cosubstrate or N-oxalylglycine inhibitor. Combined with the reported PHD2.HIFα-ODD structures and biochemical studies, the results inform on the different PHD.HIFα-ODD binding modes and the potential effects of clinically observed mutations in HIFα and PHD2 genes. They may help enable new therapeutic avenues, including PHD isoform-selective inhibitors and sequestration of HIF2α by the PHDs for ccRCC treatment.
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Affiliation(s)
- William D. Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
- Institute of Natural Medicine, University of ToyamaToyamaJapan
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Michael A. McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
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Mbenza NM, Nasarudin N, Vadakkedath PG, Patel K, Ismail AZ, Hanif M, Wright LJ, Sarojini V, Hartinger CG, Leung IKH. Carbon Monoxide is an Inhibitor of HIF Prolyl Hydroxylase Domain 2. Chembiochem 2021; 22:2521-2525. [PMID: 34137488 DOI: 10.1002/cbic.202100181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/16/2021] [Indexed: 11/11/2022]
Abstract
Hypoxia-inducible factor prolyl hydroxylase domain 2 (PHD2) is an important oxygen sensor in animals. By using the CO-releasing molecule-2 (CORM-2) as an in situ CO donor, we demonstrate that CO is an inhibitor of PHD2. This report provides further evidence about the emerging role of CO in oxygen sensing and homeostasis.
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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
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Nawal Nasarudin
- 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
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Kamal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - A Z Ismail
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
- Department of Chemistry, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Muhammad Hanif
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - L James Wright
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, 92019, Victoria Street West, Auckland, 1142, New Zealand
- School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
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Figg WD, McDonough MA, Chowdhury R, Nakashima Y, Zhang Z, Holt‐Martyn JP, Krajnc A, Schofield CJ. Structural Basis of Prolyl Hydroxylase Domain Inhibition by Molidustat. ChemMedChem 2021; 16:2082-2088. [PMID: 33792169 PMCID: PMC8359944 DOI: 10.1002/cmdc.202100133] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Human prolyl-hydroxylases (PHDs) are hypoxia-sensing 2-oxoglutarate (2OG) oxygenases, catalysis by which suppresses the transcription of hypoxia-inducible factor target genes. PHD inhibition enables the treatment of anaemia/ischaemia-related disease. The PHD inhibitor Molidustat is approved for the treatment of renal anaemia; it differs from other approved/late-stage PHD inhibitors in lacking a glycinamide side chain. The first reported crystal structures of Molidustat and IOX4 (a brain-penetrating derivative) complexed with PHD2 reveal how their contiguous triazole, pyrazolone and pyrimidine/pyridine rings bind at the active site. The inhibitors bind to the active-site metal in a bidentate manner through their pyrazolone and pyrimidine nitrogens, with the triazole π-π-stacking with Tyr303 in the 2OG binding pocket. Comparison of the new structures with other PHD inhibitor complexes reveals differences in the conformations of Tyr303, Tyr310, and a mobile loop linking β2-β3, which are involved in dynamic substrate binding/product release.
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Affiliation(s)
- William D. Figg
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Rasheduzzaman Chowdhury
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Cardiovascular Research InstituteUniversity of California, San Francisco555 Mission Bay Blvd.San FranciscoCA 94158USA
| | - Yu Nakashima
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Institute of Natural MedicineUniversity of Toyama2630 SugitaniToyama930–0194Japan
| | - Zhihong Zhang
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - Alen Krajnc
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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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: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [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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