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Ferens FG, Taber CC, Stuart S, Hubert M, Tarade D, Lee JE, Ohh M. Deficiency in PHD2-mediated hydroxylation of HIF2α underlies Pacak-Zhuang syndrome. Commun Biol 2024; 7:240. [PMID: 38418569 PMCID: PMC10902354 DOI: 10.1038/s42003-024-05904-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 02/09/2024] [Indexed: 03/01/2024] Open
Abstract
Pacak-Zhuang syndrome is caused by mutations in the EPAS1 gene, which encodes for one of the three hypoxia-inducible factor alpha (HIFα) paralogs HIF2α and is associated with defined but varied phenotypic presentations including neuroendocrine tumors and polycythemia. However, the mechanisms underlying the complex genotype-phenotype correlations remain incompletely understood. Here, we devised a quantitative method for determining the dissociation constant (Kd) of the HIF2α peptides containing disease-associated mutations and the catalytic domain of prolyl-hydroxylase (PHD2) using microscale thermophoresis (MST) and showed that neuroendocrine-associated Class 1 HIF2α mutants have distinctly higher Kd than the exclusively polycythemia-associated Class 2 HIF2α mutants. Based on the co-crystal structure of PHD2/HIF2α peptide complex at 1.8 Å resolution, we showed that the Class 1 mutated residues are localized to the critical interface between HIF2α and PHD2, adjacent to the PHD2 active catalytic site, while Class 2 mutated residues are localized to the more flexible region of HIF2α that makes less contact with PHD2. Concordantly, Class 1 mutations were found to significantly increase HIF2α-mediated transcriptional activation in cellulo compared to Class 2 counterparts. These results reveal a structural mechanism in which the strength of the interaction between HIF2α and PHD2 is at the root of the general genotype-phenotype correlations observed in Pacak-Zhuang syndrome.
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Affiliation(s)
- Fraser G Ferens
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Cassandra C Taber
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Sarah Stuart
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Mia Hubert
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Daniel Tarade
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Michael Ohh
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Department of Biochemistry, Faculty of Medicine, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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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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Guo Z, Yang Y, Li L, Zhao Q, Li Y, Liu Z, Hao L, Guo B, Diao A. The novel prolyl hydroxylase-2 inhibitor caffeic acid upregulates hypoxia inducible factor and protects against hypoxia. Eur J Pharmacol 2022; 934:175307. [DOI: 10.1016/j.ejphar.2022.175307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/26/2022]
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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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