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HDAC5 (620-1122), HDAC6, and HDAC7 (438-915) are N-terminal His-tagged.
The enzymeswere incubated withthe compounds inassaybuffer (25 mMHepes,
pH 8.0, 137 mM NaCl, 1 mM MgCl2 and 2.7 mM KCl) for 10 min at ambient
temperature in black 96-well plates. The substrate was added into enzyme-
compound mixture and incubated at 37 °C. Reaction was quenched by adding
trypsin and TSA to a final concentration of 1 mg/mL and 1
lM, respectively.
Fluorescence was measured using fluorimeter (SPECTRAMAX GeminiXS,
a
Molecular Devices). The 50% inhibitory concentrations (IC50) for inhibitors
were determined by analyzing dose–response inhibition curves with GraFit; (c)
At the time we were investigating different substrates for determining the
activity of HDAC class II enzymes, Jones et al. (Bioorg. Med. Chem. Lett. 2008, 18,
1814) published their obervations that purified mammalian HDAC class IIa
enzymes could not be isolated and are contaminated with other deacetylases.
Our results and those of Jones et al. demonstrated that the BOC-
L-Lys(e-
trifluoroacetyl)-MCA is selective class IIa substrate and allowed the
a
development of assays to measure HDAC class IIa activity even in the presence
of class I enzymes for naked enzymes and even in intact cells; (d) Our studies
7. (a) Lahm, A.; Paolini, C.; Pallaoro, M.; Nardi, M. C.; Jones, P.; Neddermann, P.;
Sambucini, S.; Bottomley, M. J.; Lo Surdo, P.; Carfí, A.; Koch, U.; De Francesco, R.;
Steinküler, C.; Gallinari, P. Proc. Natl, Acad. Sci. U.S.A. 2007, 104, 17335; (b)
Nielsen, T. K.; Hildmann, C.; Riester, D.; Wegener, D.; Schwienhorst, A.; Ficner,
R. Acta Cryst. 2007, F63, 270; (c) Jones, P.; Altamura, S.; De Francesco, R.;
Gallinari, P.; Lahm, A.; Neddermann, P.; Rowley, M.; Serafini, S.; Steinküler, C.
Bioorg. Med. Chem. Lett. 2008, 18, 1814; (d) Jones, P.; Bottomley, M. J.; Carfí, A.;
Cecchetti, O.; Ferrigno, F.; Lo Surdo, P.; Ontoria, J. M.; Rowley, M.; Scarpelli, R.;
Schultz-Fademrecht, C.; Steinküler, C. Bioorg. Med. Chem. Lett. 2008, 18, 3456;
(e) Scarpelli, R.; Di Marco, A.; Ferrigno, F.; Laufer, R.; Marcucci, I.; Muraglia, E.;
Ontoria, J. M.; Rowley, M.; Serafini, S.; Steinküler, C.; Jones, P. Bioorg. Med.
Chem. Lett. 2008, 18, 6078.
8. KrennHrubec, K.; Marshall, B. L.; Hedglin, M.; Verdin, E.; Ulrich, S. M. Bioorg.
Med. Chem. Lett. 2007, 17, 2874.
9. Fleming, I.; Iqbal, J.; Krebs, E.-P. Tetrahedron 1983, 39, 841.
10. Takahashi, Y.; Yoneda, N.; Nagai, H. Chem. Lett. 1985, 14, 1733.
11. Ling, C.; Minato, M.; Lahti, P. M.; van Willigen, H. J. Am. Chem. Soc. 1992, 114,
9959.
12. (a) For experimental details see: Tessier, P.; Leit, S.; Smil, D.; Deziel, R.; Ajamian,
A.; Chantigny, Y.A.; Dominguez, C. International Patent application WO 07/
122115, 2008; (b) The enzymatic assay followed the fluorescent signal obtained
from the HDAC catalyzed deacetylation of coumarin-labeled lysine. The
showed that human HDAC4,
trifluormethylacetyl)-MCA substrate at a much higher turn-over rate than
HDAC8 did. A plot of the enzyme reactivity (Kcat/Km
MÀ1 minÀ1) versus HDAC1,
2, 3, 4, 5, 7, and 8 enzymes utilizing both acetyl-Boc-Lysine and Boc-Lys-(
trifluormethylacetyl)-MCA substrates clearly demonstrated the extraordinary
5
and
7
processed the Boc-Lys-(e-
,
l
e-
specificity of the Boc-Lys-(e-trifluormethylacetyl)-MCA substrate for HDAC4, 5,
and 7 enzymes (class IIa).
13. Schuetz, A.; Min, J.; Allali-Hassani, A.; Schapira, M.; Shuen, M.; Loppnau, P.;
Mazitschek, R.; Kwiatkowski, N. P.; Lewis, T. A.; Maglathin, R. L.; McLean, T. H.;
Bochkarev, A.; Plotnikov, A. N.; Vedadi, M.; Arrowsmith, C. H. J. Biol. Chem.
2008, 283, 11355.
14. (a) For details of the HDAC class I whole cell assay see: Li, Z.; Besterman, J.M.;
and Bonfils, C. International Patent application WO 2007/135471 A1, 2007; (b)
For details of the HDAC class II whole cell assay see Jubrail Rahil, Aihua Lu
Patent Application US 2008/0199897, 2008; (c) The whole cell assay was done
in cultured Human Embryonic Kidney cells (293T), which were treated with
inhibitors for 16 h and then incubated with the substrate Boc-Ac-Lys-AMC, for
measuring class I HDAC activity or Boc-Lys-(
measuring HDAC class IIa activity. After 90 min at 37 °C, the reaction was
quenched with trypsin and TSA to a final concentration of 1 mg/mL and 1 M,
e-trifluormethylacetyl)-AMC for
l
respectively. The cells were lysed with 1% NP-40. Fluorescence was read at Ex
360 nm, Em 470 nm, using GeminiXS fluorimeter.
substrate used for HDAC1, 2, 3, 6, and 8 was Boc-Lys(
e
-acetyl)-AMC (Bachem
15. Campbell, K. J. Chem. Soc. 1946, 25.
Biosciences Inc.) and Boc-Lys-( -trifluormethylacetyl)-AMC (synthesized
in-house) for HDAC4, 5, and 7. Recombinant enzymes expressed in baculovirus
were used. HDAC1, and 2 were C-terminal FLAG-tagged and HDAC4 (612-1034),
e
16. Tanaka, K.; Matsuo, K.; Nakanishi, A.; Hatano, T.; Izeki, H. Chem. Pharm. Bull.
Engl. 1983, 31, 2810.