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Thomas MG, Jaber Sathik Rifayee SB, Chaturvedi SS, Gorantla KR, White W, Wildey J, Schofield CJ, Christov CZ. The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A. Inorg Chem 2024. [PMID: 38781256 DOI: 10.1021/acs.inorgchem.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.
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Affiliation(s)
| | | | | | | | | | | | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12, Mansfield Road, Oxford OX1 5JJ, U.K
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Windsor P, Ouyang H, da Costa JAG, Damodaran AR, Chen Y, Bhagi-Damodaran A. Gas tunnel engineering of prolyl hydroxylase reprograms hypoxia signaling in cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.07.552357. [PMID: 37609209 PMCID: PMC10441328 DOI: 10.1101/2023.08.07.552357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cells have evolved intricate mechanisms for recognizing and responding to changes in oxygen (O2) concentrations. Here, we have reprogrammed cellular hypoxia (low O2) signaling via gas tunnel engineering of prolyl hydroxylase 2 (PHD2), a non-heme iron dependent O2 sensor. Using computational modeling and protein engineering techniques, we identify a gas tunnel and critical residues therein that limit the flow of O2 to PHD2's catalytic core. We show that systematic modification of these residues can open the constriction topology of PHD2's gas tunnel. Using kinetic stopped-flow measurements with NO as a surrogate diatomic gas, we demonstrate up to 3.5-fold enhancement in its association rate to the iron center of tunnel-engineered mutants. Our most effectively designed mutant displays 9-fold enhanced catalytic efficiency (kcat/KM = 830 ± 40 M-1 s-1) in hydroxylating a peptide mimic of hypoxia inducible transcription factor HIF-1α, as compared to WT PHD2 (kcat/KM = 90 ± 9 M-1 s-1). Furthermore, transfection of plasmids that express designed PHD2 mutants in HEK-293T mammalian cells reveal significant reduction of HIF-1α and downstream hypoxia response transcripts under hypoxic conditions of 1% O2. Overall, these studies highlight activation of PHD2 as a new pathway to reprogram hypoxia responses and HIF signaling in cells.
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Affiliation(s)
- Peter Windsor
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Haiping Ouyang
- Department of Biochemistry and Molecular Biology University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Joseph A G da Costa
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Anoop Rama Damodaran
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Yue Chen
- Department of Biochemistry and Molecular Biology University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
| | - Ambika Bhagi-Damodaran
- Department of Chemistry University of Minnesota, Twin Cities Minneapolis, MN, 55455, United States
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3
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Fiorini G, Schofield CJ. Biochemistry of the hypoxia-inducible factor hydroxylases. Curr Opin Chem Biol 2024; 79:102428. [PMID: 38330792 DOI: 10.1016/j.cbpa.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/10/2024]
Abstract
The hypoxia-inducible factors are α,β-heterodimeric transcription factors that mediate the chronic response to hypoxia in humans and other animals. Protein hydroxylases belonging to two different structural subfamilies of the Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenase superfamily modify HIFα. HIFα prolyl-hydroxylation, as catalysed by the PHDs, regulates HIFα levels and, consequently, α,β-HIF levels. HIFα asparaginyl-hydroxylation, as catalysed by factor inhibiting HIF (FIH), regulates the transcriptional activity of α,β-HIF. The activities of the PHDs and FIH are regulated by O2 availability, enabling them to act as hypoxia sensors. We provide an overview of the biochemistry of the HIF hydroxylases, discussing evidence that their kinetic and structural properties may be tuned to their roles in the HIF system. Avenues for future research and therapeutic modulation are discussed.
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Affiliation(s)
- Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom.
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4
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [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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5
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Foskolou IP, Cunha PP, Sánchez-López E, Minogue EA, Nicolet BP, Guislain A, Jorgensen C, Kostidis S, Zandhuis ND, Barbieri L, Bargiela D, Nathanael D, Tyrakis PA, Palazon A, Giera M, Wolkers MC, Johnson RS. The two enantiomers of 2-hydroxyglutarate differentially regulate cytotoxic T cell function. Cell Rep 2023; 42:113013. [PMID: 37632752 DOI: 10.1016/j.celrep.2023.113013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 08/28/2023] Open
Abstract
2-Hydroxyglutarate (2HG) is a byproduct of the tricarboxylic acid (TCA) cycle and is readily detected in the tissues of healthy individuals. 2HG is found in two enantiomeric forms: S-2HG and R-2HG. Here, we investigate the differential roles of these two enantiomers in cluster of differentiation (CD)8+ T cell biology, where we find they have highly divergent effects on proliferation, differentiation, and T cell function. We show here an analysis of structural determinants that likely underlie these differential effects on specific α-ketoglutarate (αKG)-dependent enzymes. Treatment of CD8+ T cells with exogenous S-2HG, but not R-2HG, increased CD8+ T cell fitness in vivo and enhanced anti-tumor activity. These data show that S-2HG and R-2HG should be considered as two distinct and important actors in the regulation of T cell function.
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Affiliation(s)
- Iosifina P Foskolou
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK; Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden; Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory Amsterdam University Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands.
| | - Pedro P Cunha
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK; Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
| | - Elena Sánchez-López
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333ZA Leiden, the Netherlands
| | - Eleanor A Minogue
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
| | - Benoît P Nicolet
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory Amsterdam University Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Aurélie Guislain
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory Amsterdam University Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Christian Jorgensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Sarantos Kostidis
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333ZA Leiden, the Netherlands
| | - Nordin D Zandhuis
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory Amsterdam University Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Laura Barbieri
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
| | - David Bargiela
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
| | - Demitris Nathanael
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
| | - Petros A Tyrakis
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
| | - Asis Palazon
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, 2333ZA Leiden, the Netherlands
| | - Monika C Wolkers
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory Amsterdam University Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; Oncode Institute, 3521 AL Utrecht, the Netherlands
| | - Randall S Johnson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3EG, UK; Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.
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6
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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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7
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Schild Y, Bosserhoff J, Droege F, Littwitz-Salomon E, Fandrey J, Wrobeln A. Hypoxia-Inducible Factor-Prolyl Hydroxylase Inhibitor Improves Leukocyte Energy Metabolism in Hereditary Hemorrhagic Telangiectasia. Life (Basel) 2023; 13:1708. [PMID: 37629565 PMCID: PMC10456096 DOI: 10.3390/life13081708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The interplay between hypoxia-inducible factors (HIFs) and transforming growth factor beta (TGF-β) is critical for both inflammation and angiogenesis. In hereditary hemorrhagic telangiectasia (HHT), we have previously observed that impairment of the TGF-β pathway is associated with downregulation of HIF-1α. HIF-1α accumulation is mandatory in situations of altered energy demand, such as during infection or hypoxia, by adjusting cell metabolism. Leukocytes undergo a HIF-1α-dependent switch from aerobic mitochondrial respiration to anaerobic glycolysis (glycolytic switch) after stimulation and during differentiation. We postulate that the decreased HIF-1α accumulation in HHT leads to a clinically observed immunodeficiency in these patients. Examination of HIF-1α and its target genes in freshly isolated peripheral blood mononuclear cells (PBMCs) from HHT patients revealed decreased gene expression and protein levels of HIF-1α and HIF-1α-regulated glycolytic enzymes. Treatment of these cells with the HIF-prolyl hydroxylase inhibitor, Roxadustat, rescued their ability to accumulate HIF-1α protein. Functional analysis of metabolic flux using a Seahorse FX extracellular flux analyzer showed that the extracellular acidification rate (indicator of glycolytic turnover) after Roxadustat treatment was comparable to non-HHT controls, while oxygen consumption (indicator of mitochondrial respiration) was slightly reduced. HIF stabilization may be a potential therapeutic target in HHT patients suffering from infections.
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Affiliation(s)
- Yves Schild
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Y.S.); (J.B.); (J.F.)
| | - Jonah Bosserhoff
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Y.S.); (J.B.); (J.F.)
| | - Freya Droege
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Elisabeth Littwitz-Salomon
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
- Institute for Translational HIV Research, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Joachim Fandrey
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Y.S.); (J.B.); (J.F.)
| | - Anna Wrobeln
- Institute of Physiology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany; (Y.S.); (J.B.); (J.F.)
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8
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Tumber A, Salah E, Brewitz L, Corner TP, Schofield CJ. Kinetic and inhibition studies on human Jumonji-C (JmjC) domain-containing protein 5. RSC Chem Biol 2023; 4:399-413. [PMID: 37292060 PMCID: PMC10246557 DOI: 10.1039/d2cb00249c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Jumonji-C (JmjC) domain-containing protein 5 (JMJD5) is a human 2-oxoglutarate (2OG) and Fe(ii)-dependent oxygenase which catalyses the post-translational C3 hydroxylation of arginyl-residues and which is linked to the circadian rhythm and to cancer biology through as yet unidentified mechanisms. We report robust solid phase extraction coupled to mass spectrometry (SPE-MS)-based JMJD5 assays which enable kinetic and high-throughput inhibition studies. The kinetic studies reveal that some synthetic 2OG derivatives, notably including a 2OG derivative with a cyclic carbon backbone (i.e. (1R)-3-(carboxycarbonyl)cyclopentane-1-carboxylic acid), are efficient alternative cosubstrates of JMJD5 and of factor inhibiting hypoxia-inducible transcription factor HIF-α (FIH), but not of the Jumonji-C (JmjC) histone Nε-methyl lysine demethylase KDM4E, apparently reflecting the closer structural similarity of JMJD5 and FIH. The JMJD5 inhibition assays were validated by investigating the effect of reported 2OG oxygenase inhibitors on JMJD5 catalysis; the results reveal that broad-spectrum 2OG oxygenase inhibitors are also efficient JMJD5 inhibitors (e.g. N-oxalylglycine, pyridine-2,4-dicarboxylic acid, ebselen) whereas most 2OG oxygenase inhibitors that are in clinical use (e.g. roxadustat) do not inhibit JMJD5. The SPE-MS assays will help enable the development of efficient and selective JMJD5 inhibitors for investigating the biochemical functions of JMJD5 in cellular studies.
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Affiliation(s)
- Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
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9
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Bai R, Li Y, Jian L, Yang Y, Zhao L, Wei M. The hypoxia-driven crosstalk between tumor and tumor-associated macrophages: mechanisms and clinical treatment strategies. Mol Cancer 2022; 21:177. [PMID: 36071472 PMCID: PMC9454207 DOI: 10.1186/s12943-022-01645-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/25/2022] [Indexed: 02/08/2023] Open
Abstract
Given that hypoxia is a persistent physiological feature of many different solid tumors and a key driver for cancer malignancy, it is thought to be a major target in cancer treatment recently. Tumor-associated macrophages (TAMs) are the most abundant immune cells in the tumor microenvironment (TME), which have a large impact on tumor development and immunotherapy. TAMs massively accumulate within hypoxic tumor regions. TAMs and hypoxia represent a deadly combination because hypoxia has been suggested to induce a pro-tumorigenic macrophage phenotype. Hypoxia not only directly affects macrophage polarization, but it also has an indirect effect by altering the communication between tumor cells and macrophages. For example, hypoxia can influence the expression of chemokines and exosomes, both of which have profound impacts on the recipient cells. Recently, it has been demonstrated that the intricate interaction between cancer cells and TAMs in the hypoxic TME is relevant to poor prognosis and increased tumor malignancy. However, there are no comprehensive literature reviews on the molecular mechanisms underlying the hypoxia-mediated communication between tumor cells and TAMs. Therefore, this review has the aim to collect all recently available data on this topic and provide insights for developing novel therapeutic strategies for reducing the effects of hypoxia.
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Affiliation(s)
- Ruixue Bai
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, People's Republic of China.,Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Yunong Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, People's Republic of China
| | - Lingyan Jian
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Yuehui Yang
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China. .,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, People's Republic of China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, People's Republic of China. .,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, China Medical University, Shenyang, 110122, People's Republic of China. .,Shenyang Kangwei Medical Laboratory Analysis Co. LTD, Shenyang, 110000, People's Republic of China.
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10
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Dong L, Yang B, Zhang Y, Wang S, Li F, Xing G, Farina M, Zhang Y, Appiah-Kubi K, Tinkov AA, Aschner M, Shi H, Liu T, Lu R. Ferroptosis contributes to methylmercury-induced cytotoxicity in rat primary astrocytes and Buffalo rat liver cells. Neurotoxicology 2022; 90:228-236. [DOI: 10.1016/j.neuro.2022.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/27/2022] [Accepted: 04/14/2022] [Indexed: 01/18/2023]
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11
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Differentiation of cancer stem cells into erythroblasts in the presence of CoCl 2. Sci Rep 2021; 11:23977. [PMID: 34907219 PMCID: PMC8671479 DOI: 10.1038/s41598-021-03298-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/29/2021] [Indexed: 12/25/2022] Open
Abstract
Cancer stem cells (CSCs) are subpopulations in the malignant tumors that show self-renewal and multilineage differentiation into tumor microenvironment components that drive tumor growth and heterogeneity. In previous studies, our group succeeded in producing a CSC model by treating mouse induced pluripotent stem cells. In the current study, we investigated the potential of CSC differentiation into blood cells under chemical hypoxic conditions using CoCl2. CSCs and miPS-LLCcm cells were cultured for 1 to 7 days in the presence of CoCl2, and the expression of VEGFR1/2, Runx1, c-kit, CD31, CD34, and TER-119 was assessed by RT-qPCR, Western blotting and flow cytometry together with Wright-Giemsa staining and immunocytochemistry. CoCl2 induced significant accumulation of HIF-1α changing the morphology of miPS-LLCcm cells while the morphological change was apparently not related to differentiation. The expression of VEGFR2 and CD31 was suppressed while Runx1 expression was upregulated. The population with hematopoietic markers CD34+ and c-kit+ was immunologically detected in the presence of CoCl2. Additionally, high expression of CD34 and, a marker for erythroblasts, TER-119, was observed. Therefore, CSCs were suggested to differentiate into erythroblasts and erythrocytes under hypoxia. This differentiation potential of CSCs could provide new insight into the tumor microenvironment elucidating tumor heterogenicity.
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Singh S, Anand R. Tunnel Architectures in Enzyme Systems that Transport Gaseous Substrates. ACS OMEGA 2021; 6:33274-33283. [PMID: 34926879 PMCID: PMC8674909 DOI: 10.1021/acsomega.1c05430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Molecular tunnels regulate delivery of substrates/intermediates in enzymes which either harbor deep-seated reaction centers or are for transport of reactive/toxic intermediates that need to be specifically delivered. Here, we focus on the importance of structural diversity in tunnel architectures, especially for the gaseous substrate translocation, in rendering differential substrate preferences and directionality. Two major types of tunnels have been discussed, one that transports stable gases from the environment to the active site, namely, external gaseous (EG) tunnels, and the other that transports molecules between active sites, namely, internal gaseous (IG) tunnels. Aspects as to how the gaseous tunnels have shaped during the course of evolution and their potential to modulate the substrate flow and enzymatic function are examined. In conclusion, the review highlights our perspective on the pulsation mechanism that could facilitate unidirectional translocation of the gaseous molecules through buried tunnels.
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13
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Wang H, Wang L, Li Y, Luo S, Ye J, Lu Z, Li X, Lu H. The HIF-2α/PPARα pathway is essential for liraglutide-alleviated, lipid-induced hepatic steatosis. Biomed Pharmacother 2021; 140:111778. [PMID: 34062416 DOI: 10.1016/j.biopha.2021.111778] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 02/06/2023] Open
Abstract
Liraglutide has been demonstrated to alleviate hepatic steatosis in clinical practice, but the underlying mechanism remains unclear. Our previous study indicated that the HIF-2α/PPARα pathway was involved in hepatic lipid accumulation induced by hypoxia.We aimed to investigate whether liraglutide could alleviate lipid-induced hepatic steatosis via the HIF-2α/PPARα pathway. Whole-body HIF-2α heterozygous knockout (HIF-2α+/-) mice and littermate wild-type (WT) mice were successfully established. Male mice challenged with a high-fat diet were treated with liraglutide (0.6 mg/kg/d) or normal saline by intraperitoneal injection for 4 weeks. We observed that, compared with WT mice, many indicators of HIF-2α+/- mice improved, including GTT, ITT, fasting blood glucose, body weight, liver weight, and lipid profile in serum or liver lipid deposition, and the expression level of PPARα, mitochondrial function genes, and fatty acid oxidation genes were upregulated, while those of HIF-2α and lipogenesis genes were downregulated significantly. After liraglutide treatment in WT mice, we found that significant improvements were observed in the fat mass, GTT, ITT, fasting blood glucose, body weight, liver weight, lipid profile in serum or liver lipid deposition; the β-oxidation genes were upregulated and the lipogenesis genes were downregulated; and the abundance of intestinal Akkermansia muciniphila increased significantly. However, the effects of liraglutide on WT mice were not observed in HIF-2α+/- mice. In addition, in the HepG2 steatotic hepatocyte model, liraglutide alleviated lipid deposits by repressing lipid synthesis and enhancing fatty acid β-oxidation, which were substantially suppressed by the HIF-2α modulators. Therefore, the HIF-2α/PPARα pathway is essential for liraglutide-alleviated lipid-induced hepatic steatosis.
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Affiliation(s)
- Hou Wang
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China
| | - Lingling Wang
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China
| | - Yun Li
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China; Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China
| | - Shunkui Luo
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China
| | - Jianfang Ye
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China
| | - Zhanjin Lu
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai 519000, Guangdong, China.
| | - Hongyun Lu
- Department of Endocrinology & Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, Guangdong, China; Department of Endocrinology & Metabolism, Zhuhai People's Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai 519000, Guangdong, China.
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14
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Wu Y, Li Z, McDonough MA, Schofield CJ, Zhang X. Inhibition of the Oxygen-Sensing Asparaginyl Hydroxylase Factor Inhibiting Hypoxia-Inducible Factor: A Potential Hypoxia Response Modulating Strategy. J Med Chem 2021; 64:7189-7209. [PMID: 34029087 DOI: 10.1021/acs.jmedchem.1c00415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is a JmjC domain 2-oxogluarate and Fe(II)-dependent oxygenase that catalyzes hydroxylation of specific asparagines in the C-terminal transcriptional activation domain of hypoxia-inducible factor alpha (HIF-α) isoforms. This modification suppresses the transcriptional activity of HIF by reducing its interaction with the transcriptional coactivators p300/CBP. By contrast with inhibition of the HIF prolyl hydroxylases (PHDs), inhibitors of FIH, which accepts multiple non-HIF substrates, are less studied; they are of interest due to their potential ability to alter metabolism (either in a HIF-dependent and/or -independent manner) and, provided HIF is upregulated, to modulate the course of the HIF-mediated hypoxic response. Here we review studies on the mechanism and inhibition of FIH. We discuss proposed biological roles of FIH including its regulation of HIF activity and potential roles of FIH-catalyzed oxidation of non-HIF substrates. We highlight potential therapeutic applications of FIH inhibitors.
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Affiliation(s)
- Yue Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Zhihong Li
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Xiaojin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
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15
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Banerjee R, Lipscomb JD. Small-Molecule Tunnels in Metalloenzymes Viewed as Extensions of the Active Site. Acc Chem Res 2021; 54:2185-2195. [PMID: 33886257 DOI: 10.1021/acs.accounts.1c00058] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Rigorous substrate selectivity is a hallmark of enzyme catalysis. This selectivity is generally ascribed to a thermodynamically favorable process of substrate binding to the enzyme active site based upon complementary physiochemical characteristics, which allows both acquisition and orientation. However, this chemical selectivity is more difficult to rationalize for diminutive molecules that possess too narrow a range of physical characteristics to allow either precise positioning or discrimination between a substrate and an inhibitor. Foremost among these small molecules are dissolved gases such as H2, N2, O2, CO, CO2, NO, N2O, NH3, and CH4 so often encountered in metalloenzyme catalysis. Nevertheless, metalloenzymes have evolved to metabolize these small-molecule substrates with high selectivity and efficiency.The soluble methane monooxygenase enzyme (sMMO) acts upon two of these small molecules, O2 and CH4, to generate methanol as part of the C1 metabolic pathway of methanotrophic organisms. sMMO is capable of oxidizing many alternative hydrocarbon substrates. Remarkably, however, it will preferentially oxidize methane, the substrate with the fewest discriminating physical characteristics and the strongest C-H bond. Early studies led us to broadly attribute this specificity to the formation of a "molecular sieve" in which a methane- and oxygen-sized tunnel provides a size-selective route from bulk solvent to the completely buried sMMO active site. Indeed, recent cryogenic and serial femtosecond ambient temperature crystallographic studies have revealed such a route in sMMO. A detailed study of the sMMO tunnel considered here in the context of small-molecule tunnels identified in other metalloenzymes reveals three discrete characteristics that contribute to substrate selectivity and positioning beyond that which can be provided by the active site itself. Moreover, the dynamic nature of many tunnels allows an exquisite coordination of substrate binding and reaction phases of the catalytic cycle. Here we differentiate between the highly selective molecular tunnel, which allows only the one-dimensional transit of small molecules, and the larger, less-selective channels found in typical enzymes. Methods are described to identify and characterize tunnels as well as to differentiate them from channels. In metalloenzymes which metabolize dissolved gases, we posit that the contribution of tunnels is so great that they should be considered to be extensions of the active site itself. A full understanding of catalysis by these enzymes requires an appreciation of the roles played by tunnels. Such an understanding will also facilitate the use of the enzymes or their synthetic mimics in industrial or pharmaceutical applications.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55391, United States
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16
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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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Li Z, Zhen S, Su K, Tumber A, Yu Q, Dong Y, McDonough M, Schofield CJ, Zhang X. A small-molecule probe for monitoring binding to prolyl hydroxylase domain 2 by fluorescence polarisation. Chem Commun (Camb) 2020; 56:14199-14202. [PMID: 33111730 DOI: 10.1039/d0cc06353c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inhibition of the dioxygen sensing hypoxia-inducible factor prolyl hydroxylases has potential therapeutic benefit for treatment of diseases, including anaemia. We describe the discovery of a small-molecule probe useful for monitoring binding to human prolyl hydroxylase domain 2 (PHD2) via fluorescence polarisation. The assay is suitable for high-throughput screening of PHD inhibitors with both weak and strong affinities, as shown by work with clinically used inhibitors and naturally occurring PHD inhibitors.
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Affiliation(s)
- Zhihong Li
- Laboratory of Drug Design and Discovery, Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China.
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