Mechanism of binding of the inhibitor (E)-3-(furan-2-yl)-N- hydroxyacrylamide to a histone deacetylase-like amidohydrolase

Biochemistry

Volumn 49, Issue 7, 2010, Pages 1418-1424

  Syuekora, Jaromir ^a   Meyer Almes, Franz Josef ^a  

^a UNIVERSITY OF APPLIED SCIENCES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ASSOCIATION CONSTANT; ASSOCIATION KINETICS; CONFORMATIONAL CHANGE; CUTANEOUS T-CELL LYMPHOMA; EQUILIBRIUM BINDING CONSTANT; EQUILIBRIUM TITRATIONS; FLUORESCENCE RESONANCE ENERGY TRANSFER; HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE; HISTONE DEACETYLASES; INTERMEDIATE COMPLEX; INTRINSIC TRYPTOPHANS; KINETIC DATA; LEAD STRUCTURE; SIDE EFFECT; STOPPED FLOW; THREE-STEP MECHANISM; TIME RANGE; TWO PHASIS; UNIMOLECULAR;

AMINO ACIDS; BINDING ENERGY; CHROMOPHORES; COMPLEXATION; ENERGY TRANSFER; FLUORESCENCE; OPTICAL COMMUNICATION; RATE CONSTANTS;

ENZYMES;

3 (FURAN 2 YL) N HYDROXYACRYLAMIDE; AMIDASE; HISTONE; HISTONE DEACETYLASE; HISTONE DEACETYLASE INHIBITOR; HISTONE DEACETYLASE LIKE AMIDOHYDROLASE; HYDROXAMIC ACID DERIVATIVE; TRYPTOPHAN; UNCLASSIFIED DRUG; VORINOSTAT;

ALCALIGENES; ARTICLE; BINDING KINETICS; BORDETELLA; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME INHIBITION; FLUORESCENCE RESONANCE ENERGY TRANSFER; PRIORITY JOURNAL; SKIN LYMPHOMA; T CELL LYMPHOMA;

ALCALIGENES; ANTINEOPLASTIC AGENTS; BACTERIAL PROTEINS; BENZOFURANS; BINDING SITES; BORDETELLA; CRYSTALLIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; HISTONE DEACETYLASE INHIBITORS; HISTONE DEACETYLASES; HYDROXAMIC ACIDS; KINETICS;

EID: 77449117126     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi901617w     Document Type: Article

References (33)

1. Mai, A., Massa, S., Rotili, D., Cerbara, I., Valente, S., Pezzi, R., Simeoni, S., and Ragno, R. (2005) Histone deacetylation in epigenetics: An attractive target for anticancer therapy. Med. Res. Rev. 25, 261-309.
2. Lehrmann, H., Pritchard, L. L., and Harel-Bellan, A. (2002) Histone acetyltransferases and deacetylases in the control of cell proliferation and differentiation. Adv. Cancer Res. 86, 41-65.
3. Grunstein, M. (1997) Histone acetylation in chromatin structure and transcription, Nature 389, 349-352.
4. Peterson, C. L. (2002) HDAC's at work: Everyone doing their part. Mol. Cell 9, 921-922.
5. Mariadason, J. M., Corner, G. A., and Augenlicht, L. H. (2000) Genetic reprogramming in pathways of colonic cell maturation, induced by short chain fatty acids: Comparison with trichostatin A, sulindac, and curcumin and implications for chemoprevention of colon cancer Cancer Res. 60, 4561-4572.
6. Peart, M. J., Smyth, G. K., van. Laar, R. K., Bowtell, D. D., Richon, V. M., Marks, P. A., Holloway, A. J., and Johnstone, R. W. (2005) Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors. Proc Natl. Acad. Sci. U.S.A. 102, 3697-3702.
7. Xu, W. S., Parmigiani, R. B., and Marks, P. A. (2007) Histone deacetylase inhibitors: Molecular mechanisms of action. Oncogene 26, 5541-5552.
8. Marks, P. A., and Dokmanovic, M. (2005) Histone deacetylase inhibitors: Discovery and development as anticancer agents. Expert Opin. Invest. Drugs 14, 1497-1511.
9. Minucci, S., and Pelicci, P. G. (2006) Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat. Rev. Cancer 6, 38-51.
10. Paris, M., Porcelloni, M., Binaschi, M., and Fattori, D. (2008) Histone deacetylase inhibitors: From bench to clinic. J. Med. Chem. 51, 1505-1529.
11. Riester, D., Hildmann, C., and Schwienhorst, A. (2007) Histone deacetylase inhibitors: Turning epigenic mechanisms of gene regulation into tools of therapeutic intervention in malignant and other diseases, Appl. Microbiol. Biotechnol. 75, 499-514.
12. Lee, M. J., Kim, Y. S., Kummar, S., Giaccone, G., and Trepei, J. B. (2008) Histone deacetylase inhibitors in cancer therapy, Curr. Opin. Oncol. 20, 639-649.
13. Nielsen, T. K., Hildmann, C., Dickmanns, A., Schwienhorst, A., and Ficner, R. (2005) Crystal structure of a bacterial class 2 histone deacetylase homologue. J. Mol. Biol. 354, 107-120.
14. Hildmann, C., Ninkovic, M., Dietrich, R., Wegener, D., Riester, D., Zimmermann, T., Birch, O. M., Bernegger, C., Loidl, P., and Schwienhorst, A. (2004) A new amidohydrolase from Bordetella or Alcaligenes strain FB188 with similarities to histone deacetylases. J. Bacteriol. 186, 2328-2339.
15. Hildmann, C., Wegener, D., Riester, D., Hempel, R., Schober, A., Merana, J., Giurato, L., Guccione, S., Nielsen, T. K., Ficner, R., and Schwienhorst, A. (2006) Substrate and inhibitor specificity of class 1 and class 2 histone deacetylases. J. Biotechnol. 124, 258-270.
16. Riester, D., Hildmann, C., Haus, P., Galetovic, A., Schober, A., Schwienhorst, A., and Mieyer-Almes, F. J. (2009) Non-isotopic dual parameter competition assay suitable for high-throughput screening of histone deacetylases. Bioorg. Med. Chem. Lett. 19, 3651-3656.
17. Schafer, S., Saunders, L., Eliseeva, E., Velena, A., Jung, M., Schwienhorst, A., Strasser, A., Dickmanns, A., Ficner, R., Schlimme, S., Sippl, W., Verdin, E., and Jung, M. (2008) Phenylalanine-containing hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs). Bioorg. Med. Chem. 16, 2011-2033.
18. Riester, D., Hildmann, C., Schwienhorst, A., and Meyer-Almes, F. J. (2007) Histone deacetylase inhibitor assay based on fluorescence resonance energy transfer. Anal. Biochem. 362, 136-141.
19. Bouchain, G., and Delorme, D. (2003) Novel hydroxamate and anilide derivatives as potent histone deacetylase inhibitors: Synthesis and antiproliferative evaluation. Curr. Med. Chem. 10, 2359-2372.
20. Munster, P. N., Troso-Sandoval, T., Rosen, N., Rifkind, R., Marks, P. A., and Richon, V. M. (2001) The histone deacetylase inhibitor suberoylanilide hydroxamic acid induces differentiation of human breast cancer cells, Cancer Res. 61, 8492-8497.
21. Bernasconi, C. (1976) Relaxation Kinetics Academic Press, Inc., New York.
22. Lasdon, L. S., Waren, A. D., Jain, A., and Ratner, M. (1978) Design and Testing of a Generalized Reduced Gradient Code for Nonlinear Programming, 4th ed., pp 34-50, Association for Computing Machinery, New York.
23. Foerster, T. (1948) Zwischenmolekulare Energiewanderung und Fluoreszenz, 2nd ed.; Annalen der Physik, 1948, Vol.437, pp 55-75.
24. Stein, S., Bohlen, P., and Udenfriend, S. (1974) Studies on the kinetics of reaction and hydrolysis of fluorescamine. Arch. Biochem. Biophys. 163, 403.
25. Kern, S., Riester, D., Hildmann, C., Schwienhorst, A., and Meyer-Almes, F. J. (2007) Inhibitor-mediated stabilization of the conformational structure of a histone deacetylase-like amidohydrolase. FEBSJ. 274, 3578-3588.
26. Navarro-Martinez, M. D., Cabezas-Herrera, J., Garcia-Canovas, F., and Rodriguez-Lopez, J. N. (2007) Inhibition of Stenotrophomonas maltophilia dihydrofolate reductase by methotrexate: A single slowbinding process. J. Enzyme Inhib. Med. Chem. 22, 377-382.
27. Wielgus-Kutrowska, B., Antosiewicz, J. M., Dlugosz, M., Holy, A., and Bzowska, A. (2007) Towards the mechanism of trimeric purine nucleoside phosphorylases: Stopped-flow studies of binding of multisubstrate analogue inhibitor -2-amino-9-[2-(phosphonomethoxy)ethyl]6-sulfanylpurine. Biophys. Chem. 125, 260-268.
28. Ploux, O., Breyne, O., Carillon, S., and Marquet, A. (1999) Slowbinding and competitive inhibition of 8-amino-7-oxopelargonate synthase, a pyridoxal-5′-phosphate-dependent enzyme involved in biotin biosynthesis, by substrate and intermediate analogs. Kinetic and binding studies. Eur. J. Biochem. 259, 63-70.
29. Faller, B., Cadene, M., and Bieth, J. G. (1993) Demonstration of a twostep reaction, mechanism for the inhibition of heparin-bound neutrophil elastase by α-proteinase inhibitor. Biochemistry 32, 9230-9235.
30. Furfine, E. S., D'Souza, E., Ingold, K. J., Leban, J. J., Spector, T., and Porter, D. J. (1992) Two-step binding mechanism for HIV protease inhibitors. Biochemistry 31, 7886-7891.
31. Rajagopalan, R., Misialek, S., Stevens, S., Myszka, D., Brandhuber, B., Ballard, J., Andrews, S., Seiwert, S., and Kossen, K. (2009) Inhibition and Binding Kinetics of the Hepatitis C Virus NS3 Protease Inhibitor ITMN-191 Reveals Tight Binding and Slow Dissociative Behavior. Biochemistry. 48, 2559-2568.
32. Isin, E. M., and Guengerich, F. P. (2007) Multiple sequential steps involved in the binding of inhibitors to cytochrome P450 3A4. J. Biol. Chem. 282, 6863-6874.
33. Jackman, M. P., Parry, M. A., Hofsteenge, J., and. Stone, S. R. (1992) Intrinsic fluorescence changes and rapid kinetics of the reaction of thrombin with hirudin. J. Biol. Chem. 267, 15375-15383.