A photoreactive small-molecule probe for 2-oxoglutarate oxygenases

Chemistry and Biology

Volumn 18, Issue 5, 2011, Pages 642-654

  Rotili, Dante ^a,b   Altun, Mikael ^c   Kawamura, Akane ^a   Wolf, Alexander ^a   Fischer, Roman ^c   Leung, Ivanhoe K H ^a   MacKeen, Mukram M ^c   Tian, Ya Min ^c   Ratcliffe, Peter J ^c   Mai, Antonello ^b   Kessler, Benedikt M ^c   Schofield, Christopher J ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOISOCAPROATE OXYGENASE; ALPHA-KETOISOCAPROATE OXYGENASE; CROSS LINKING REAGENT; DIOXYGENASE; ENZYME INHIBITOR; F BOX PROTEIN; FBXL11 PROTEIN, HUMAN; HISTONE DEMETHYLASE; QUINOLINOL DERIVATIVE;

ARTICLE; CELL LINE; CHEMISTRY; DRUG ANTAGONISM; HUMAN; MASS SPECTROMETRY; METABOLISM; MOLECULAR LIBRARY; PHOTOCHEMISTRY; PROTEIN TERTIARY STRUCTURE;

CELL LINE; CROSS-LINKING REAGENTS; DIOXYGENASES; ENZYME INHIBITORS; F-BOX PROTEINS; HUMANS; HYDROXYQUINOLINES; JUMONJI DOMAIN-CONTAINING HISTONE DEMETHYLASES; PHOTOCHEMICAL PROCESSES; PROTEIN STRUCTURE, TERTIARY; SMALL MOLECULE LIBRARIES; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 79957487715     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2011.03.007     Document Type: Article

References (37)

1. R.J. Appelhoff, Y.M. Tian, R.R. Raval, H. Turley, A.L. Harris, C.W. Pugh, P.J. Ratcliffe, and J.M. Gleadle Differential function of the prolyl hydroxylases PHD1, PHD2, and PHD3 in the regulation of hypoxia-inducible factor J. Biol. Chem. 279 2004 38458 38465 (Pubitemid 39295997)
2. R. Chowdhury, M.A. McDonough, J. Mecinovic, C. Loenarz, E. Flashman, K.S. Hewitson, C. Domene, and C.J. Schofield Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases Structure 17 2009 981 989
3. A.C.R. Epstein, J.M. Gleadle, L.A. McNeill, K.S. Hewitson, J. O'Rourke, D.R. Mole, M. Mukherji, E. Metzen, M.I. Wilson, and A. Dhanda C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation Cell 107 2001 43 54 (Pubitemid 32972036)
4. M.J. Evans, and B.F. Cravatt Mechanism-based profiling of enzyme families Chem. Rev. 106 2006 3279 3301 (Pubitemid 44376936)
5. J.J. Fischer, O.Y. Graebner (neé Baessler), C. Dalhoff, S. Michaelis, A.K. Schrey, J. Ungewiss, K. Andrich, D. Jeske, F. Kroll, and M. Glinski Comprehensive identification of staurosporine-binding kinases in the hepatocyte cell line HepG2 using capture compound mass spectrometry (CCMS) J. Proteome Res. 9 2010 806 817
6. E. Flashman, S.L. Davies, K.K. Yeoh, and C.J. Schofield Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents Biochem. J. 427 2010 135 142
7. S.A. Fleming Chemical reagents in photoaffinity labeling Tetrahedron 51 1995 12479 12520
8. R.P. Hausinger Fe(II)/α-ketoglutarate-dependent hydroxylases and related enzymes Crit. Rev. Biochem. Mol. Biol. 39 2004 21 68
9. L.R. Jensen, M. Amende, U. Gurok, B. Moser, V. Gimmel, A. Tzschach, A.R. Janecke, G. Tariverdian, J. Chelly, and J.P. Fryns Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation Am. J. Hum. Genet. 76 2005 227 236 (Pubitemid 40129549)
10. W.G. Kaelin Jr., and P.J. Ratcliffe Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway Mol. Cell 30 2008 393 402 (Pubitemid 351681994)
11. B.M. Kessler, D. Tortorella, M. Altun, A.F. Kisselev, E. Fiebiger, B.G. Hekking, H.L. Ploegh, and H.S. Overkleeft Extended peptide-based inhibitors efficiently target the proteasome and reveal overlapping specificities of the catalytic β-subunits Chem. Biol. 8 2001 913 929 (Pubitemid 32863208)
12. O.N.F. King, X.S. Li, M. Sakurai, A. Kawamura, N.R. Rose, S.S. Ng, A.M. Quinn, G. Rai, B.T. Mott, and P. Beswick Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors PLoS One 5 2010 e15535
13. R.J. Klose, and Y. Zhang Regulation of histone methylation by demethylimination and demethylation Nat. Rev. Mol. Cell Biol. 8 2007 307 317
14. F. Laumonnier, S. Holbert, N. Ronce, F. Faravelli, S. Lenzner, C.E. Schwartz, J. Lespinasse, H. Van Esch, D. Lacombe, and C. Goizet Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate J. Med. Genet. 42 2005 780 786 (Pubitemid 41475255)
15. I.K.H. Leung, E. Flashman, K.K. Yeoh, C.J. Schofield, and T.D.W. Claridge Using NMR solvent water relaxation to investigate metalloenzyme-ligand binding interactions J. Med. Chem. 53 2010 867 875
16. E. Liepinsh, R. Vilskersts, D. Loca, O. Kirjanova, O. Pugovichs, I. Kalvinsh, and M. Dambrova Mildronate, an inhibitor of carnitine biosynthesis, induces an increase in γ-butyrobetaine contents and cardioprotection in isolated rat heart infarction J. Cardiovasc. Pharmacol. 48 2006 314 319 (Pubitemid 46066837)
17. C. Loenarz, and C.J. Schofield Expanding chemical biology of 2-oxoglutarate oxygenases Nat. Chem. Biol. 4 2008 152 156 (Pubitemid 351264133)
18. C. Loenarz, and C.J. Schofield Oxygenase catalyzed 5-methylcytosine hydroxylation Chem. Biol. 16 2009 580 583
19. M.A. McDonough, L.A. McNeill, M. Tilliet, C.A. Papamicael, Q.-Y. Chen, B. Banerji, K.S. Hewitson, and C.J. Schofield Selective inhibition of factor inhibiting hypoxia-inducible factor J. Am. Chem. Soc. 127 2005 7680 7681 (Pubitemid 40745948)
20. L.A. McNeill, E. Flashman, M.R.G. Buck, K.S. Hewitson, I.J. Clifton, G. Jeschke, T.D.W. Claridge, D. Ehrismann, N.J. Oldham, and C.J. Schofield Hypoxia-inducible factor prolyl hydroxylase 2 has a high affinity for ferrous iron and 2-oxoglutarate Mol. Biosyst. 1 2005 321 324 (Pubitemid 41579324)
21. S. Nagel, N.P. Talbot, J. Mecinovic, T.G. Smith, A.M. Buchan, and C.J. Schofield Therapeutic manipulation of the HIF hydroxylases Antioxid. Redox Signal. 12 2010 481 501
22. N. Pescador, Y. Cuevas, S. Naranjo, M. Alcaide, D. Villar, M.O. Landazuri, and L. Del Peso Identification of a functional hypoxia-responsive element that regulates the expression of the egl nine homologue 3 (egln3/phd3) gene Biochem. J. 390 2005 189 197 (Pubitemid 41192244)
23. P.J. Pollard, C. Loenarz, D.R. Mole, M.A. McDonough, J.M. Gleadle, C.J. Schofield, and P.J. Ratcliffe Regulation of Jumonji-domain-containing histone demethylases by hypoxia-inducible factor (HIF)-1α Biochem. J. 416 2008 387 394
24. M. Risteli, H. Ruotsalainen, A.M. Salo, R. Sormunen, L. Sipilä, N.L. Baker, S.R. Lamandé, L. Vimpari-Kauppinen, and R. Myllylä Reduction of lysyl hydroxylase 3 causes deleterious changes in the deposition and organization of extracellular matrix J. Biol. Chem. 284 2009 28204 28211
25. N.R. Rose, S.S. Ng, J. Mecinovic, B.M. Lienard, S.H. Bello, Z. Sun, M.A. McDonough, U. Oppermann, and C.J. Schofield Inhibitor scaffolds for 2-oxoglutarate-dependent histone lysine demethylases J. Med. Chem. 51 2008 7053 7056
26. N.R. Rose, E.C.Y. Woon, G.L. Kingham, O.N.F. King, J. Mecinovic, I.J. Clifton, S.S. Ng, J. Talib-Hardy, U. Oppermann, and M.A. McDonough Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometry screening and crystallographic approaches J. Med. Chem. 53 2010 1810 1818
27. A.M. Sadaghiani, S.H.L. Verhelst, and M. Bogyo Tagging and detection strategies for activity-based proteomics Curr. Opin. Chem. Biol. 11 2007 20 28 (Pubitemid 46216128)
28. C.M. Salisbury, and B.F. Cravatt Optimization of activity-based probes for proteomic profiling of histone deacetylase complexes J. Am. Chem. Soc. 130 2008 2184 2194 (Pubitemid 351287995)
29. S.A. Sieber, S. Niessen, H.S. Hoover, and B.F. Cravatt Proteomic profiling of metalloprotease activities with cocktails of active-site probes Nat. Chem. Biol. 2 2006 274 281
30. N.A. Smirnova, I. Rakhman, N. Moroz, M. Basso, J. Payappilly, S. Kazakov, F. Hernandez-Guzman, I.N. Gaisina, A.P. Kozikowski, and R.R. Ratan Utilization of an in vivo reporter for high throughput identification of branched small molecule regulators of hypoxic adaptation Chem. Biol. 17 2010 380 391
31. A. Spannhoff, A.T. Hauser, R. Heinke, W. Sippl, and M. Jung The emerging therapeutic potential of histone methyltransferase and demethylase inhibitors ChemMedChem 4 2009 1568 1582
32. C.J. Stubbs, C. Loenarz, J. Mecinovic, K.K. Yeoh, N. Hindley, B.M. Lienard, F. Sobott, C.J. Schofield, and E. Flashman Application of a proteolysis/mass spectrometry method for investigating the effects of inhibitors on hydroxylase structure J. Med. Chem. 52 2009 2799 2805
33. Y. Tsukada, J. Fang, H. Erdjument-Bromage, M.E. Warren, C.H. Borchers, P. Tempst, and Y. Zhang Histone demethylation by a family of JmjC domain-containing proteins Nature 439 2006 811 816 (Pubitemid 43255695)
34. N.C. Warshakoon, S. Wu, A. Boyer, R. Kawamoto, J. Sheville, S. Renock, K. Xu, M. Pokross, S. Zhou, and C. Winter Structure-based design, synthesis, and SAR evaluation of a new series of 8-hydroxyquinolines as HIF-1α prolyl hydroxylase inhibitors Bioorg. Med. Chem. Lett. 16 2006 5517 5522 (Pubitemid 44415462)
35. C.C. Wu, and M.J. MacCoss Shotgun proteomics: tools for the analysis of complex biological systems Curr. Opin. Mol. Ther. 4 2002 242 250 (Pubitemid 35282870)
36. C. Xu, E. Soragni, C.J. Chou, D. Herman, H.L. Plasterer, J.R. Rusche, and J.M. Gottesfeld Chemical probes identify a role for histone deacetylase 3 in Friedreich's ataxia gene silencing Chem. Biol. 16 2009 980 989
37. L. Yu, Y. Wang, S. Huang, J. Wang, Z. Deng, Q. Zhang, W. Wu, X. Zhang, Z. Liu, and W. Gong Structural insights into a novel histone demethylase PHF8 Cell Res. 20 2010 166 173