Chemistry - A European Journal
10.1002/chem.201605140
FULL PAPER
1
(
DCM/MeOH 10:1); m. p.: 155-158°C; H-NMR (300 MHz, CDCl
3
, 25°C):
); 4.37
); 4.25-4.11 (m, 0.5H, CH); 3.86-3.70 (m, 0.5H,
DIEA (35 µL, 200.93 µmol, 2.7 eq.), TBTU (27.3 mg, 85.02 µmol, 1.1 eq.)
and the amine 6 (39.2 mg, 75.32 µmol, 1.0 eq.) in anhydrous DMF (4.0
δ = 6.78 (bs, 0.5H, NH); 6.72-6.36 (2H, NH, CH); 6.11 (s, 2H, CH
2
3
(
q, J = 7.1 Hz, 4H, CH
CH); 3.61-3.20 (3H, CH
CH ); 2.52-2.32 (1.5H, CH, CH
.75 (m, 2.5H, CH ); 1.38 ppm (t, J= 7.1 Hz, 6H. CH
MHz, CDCl , 25°C): δ = 172.6 (1C, C=O); 172.2 (1C, C=O); 168.3 (1C,
C=O); 167.3 (1C, C=O); 161.9 (2C, C=O); 141.9 (2C, Cquart.); 141.2 (2C,
quart.); 110.9 (1C, CH); 110.7 (1C, CH); 103.2 (2C, Cquart.); 102.9 (1C,
CH ); 61.7 (2C, CH ); 42.2 (1C, CH ); 41.7 (1C, CH ); 40.3 (2C, CH );
9.6 (2C, CH ); 35.5 (1C, CH ); 34.1 (1C, CH ); 32.3 (1C, CH ); 31.5 (1C,
CH ); 18.1 (1C, CH ); 15.4 (1C, CH
MHz, CDCl
405, 2976, 1720, 1654, 1449, 1296, 1176, 1078, 1023 cm ; HRMS: (EI)
2
mL).
Purifying by silica gel chromatography (DCM/MeOH/TEA
3
2
); 3.02-2.88 (2H, CH
2
); 2.82 (t, J = 6.8 Hz, 1H,
); 2.27 (t, J = 7.0 Hz, 1H, CH ); 2.10-
); C-NMR (75
10:1:0.0→10:1:0.1) give the title compound as an orange solid (40.3 mg,
3
1
2
2
2
90 %). R
MHz, CDCl
5.3 Hz, 1H, CH); 6.11 (s, 2H, CH
f
= 0.53 (DCM/MeOH 10:1); m. p.: 185-186°C; H-NMR (300
3
13
3
1
2
3
3
, 25°C): δ = 6.72 (bt, 1H, NH); 6.60 (bt, 1H, NH); 6.59 (t, J =
); 3.47-3.36 (4H, CH ); 2.93-2.86 (6H,
); 2.22 (t, J = 7.4 Hz, 2H, CH ); 1.77-
); 0.97 ppm (t, J = 7.4 Hz, 6H,
, 25°C): δ = 196.6 (2C, C=O); 173.8 (1C,
C=O); 167.0 (1C, C=O); 141.2 (2C, Cquart.); 140.4 (2C, Cquart.); 110.6 (1C,
CH); 110.1 (2C, Cquart.); 102.6 (1C, CH ); 45.7 (2C, CH ); 42.2 (1C, CH );
40.2 (1C, CH ); 39.9 (1C, CH ); 36.1 (1C, CH ); 35.9 (1C, CH ); 28.2 (1C,
CH ); 25.0 (1C, CH ); 22.0 (1C, CH ); 17.1 (2C, CH
F-NMR (282 MHz, CDCl
275, 2933, 1710, 1658, 1557, 1451, 1293, 1262, 1155, 1079, 1051 cm
3
2
2
3
3
CH
2
); 2.71 (t, J = 7.1 Hz, 2H, CH
); 1.41-1.24 (m, 2H, CH
); C-NMR (75 MHz, CDCl
2
2
3
C
1.58 (8H, CH
2
2
13
2
2
2
2
2
CH
3
3
3
2
2
2
2
19
2
2
2
); 14.2 ppm (2C, CH
3
); F-NMR (282
2
2
2
3
, 25°C): δ = -77.9 (s, 3F); -79.9 ppm (s, 3F); IR (ATR): v
̅
=
2
2
2
2
-
1
3
2
2
2
2
3
); 13.7 (2C, CH );
+
19
m/z = 576.1548 [M ], calc.: 576.1567.
3
̅
, 25°C): δ = -79.8 ppm (s, 3F); IR (ATR): v =
-
3
;
1
+
HRMS: (EI) m/z = 600.2304 [M ], calc.: 600.2295.
N-(2-(2-(4,8-Dibutyrylbenzo[1,2-d:4,5-d']bis([1,3]dioxole)-2-
yl)acetamido)ethyl)-7,7,7-trifluoro-6-oxoheptanamide
(13b):
Following the procedure described above for 13a, the trifluoromethyl
ketone 13b was obtained from the carboxylic acid 12b (20.0 mg, 108.63
µmol, 1.5 eq.), DIEA (26 µL, 149.26 µmol, 2.0 eq.), TBTU (35.0 mg,
Diethyl 2-(2-oxo-2-((2-(8,8,8-trifluoro-7-oxooctanamido)ethyl)ami-
no)ethyl)benzo[1,2-d:4,5-d']bis([1,3]dioxole)-4,8-dicarboxylate (14c):
Following the procedure described above for 13a, the trifluoromethyl
ketone 14c was obtained from the carboxylic acid 12c (17.9 mg, 84.37
µmol, 1.1 eq.), DIEA (35 µL, 200.93 µmol, 2.7 eq.), TBTU (27.2 mg,
84.71 µmol, 1.1 eq.) and the amine 7 (39.2 mg, 74.75 µmol, 1.0 eq.) in
anhydrous DMF (4.0 mL). Purifying by silica gel chromatography
(DCM/MeOH/TEA 20:1:0.1) give the title compound as a yellow solid
109.00 µmol, 1.5 eq.) and the amine 6 (38.7 mg, 74.36 µmol) in
anhydrous DMF (1.5 mL). Purifying by silica gel chromatography
(
DCM/MeOH/TEA 100:1:0.1) give the title compound as an orange solid
26.8 mg, 71 %). R = 0.47 (DCM/MeOH 10:1); m. p.: decomp. at 175°C;
H-NMR (300 MHz, CDCl , 25°C): δ = 6.82 (bs, 1H, NH); 6.65 (bs, 1H,-
NH); 6.59 (t, J = 4.8 Hz, 1H, CH); 6.11 (s, 2H, CH ); 3.54-3.33 (4H,
CH ); 2.97-2.83 (6H, CH ); 2.73 (bt, 2H, CH ); 2.26 (bt, 2H, CH ); 1.88-
.56 (8H, CH ); 0.97 ppm (t, J = 7.3 Hz, 6H, CH ); C-NMR (75 MHz,
CDCl , 25°C): δ = 196.7 (2C, C=O); 173.3 (1C, C=O); 167.2 (1C, C=O);
41.2 (2C, Cquart.); 140.4 (2C, Cquart.); 110.6 (2C, Cquart.); 110.0 (1C, CH);
02.6 (1C, CH ); 45.7 (2C, CH ); 42.2 (1C, CH ); 40.0 (1C, CH ); 39.9
); 36.1 (1C, CH ); 35.7 (1C, CH ); 24.5 (1C, CH ); 21.8 (1C,
); 17.1 (2C, CH ); 13.7 ppm (2C, CH ); F-NMR (282 MHz, CDCl
= 3284, 2962, 2936, 2877,
678, 1642, 1560, 1436, 1281, 1089 cm ; HRMS: (EI) m/z = 586.2128
(
f
1
3
3
2
(44.4 mg, 98 %). R
f
= 0.48 (DCM/MeOH 10:1); m. p.: decomp. at 195°C;
H-NMR (300 MHz, CDCl , 25°C): δ = 6.75 (bt, 1H, NH); 6.64-6.56 (1H,
); 4.38
); 2.91 (d, J = 5.3 Hz, 2H,
1
2
2
2
2
3
3
13
3
1
2
3
NH); 6.60 (t, J = 5.3 Hz, 1H, CH); 6.11 (d, AB, J =1.6 Hz, 2H, CH
(q, J = 7.1 Hz, 4H, CH
2
3
3
3
2
); 3.49-3.34 (4H, CH
2
3
3
1
1
CH
2
); 2.71 (t, J = 7.0 Hz, 2H, CH
2
); 2.23 (t, J = 7.4 Hz, 2H, CH
2
); 1.73-
); 1.37 ppm (t, J = 7.1 Hz, 6H,
, 25°C): δ = 167.3 (1C, C=O); 161.8 (2C,
C=O); 141.9 (2C, Cquart.); 141.2 (2C, Cquart.); 110.8 (1C, CH); 103.2 (2C,
quart.); 102.9 (1C, CH ); 61.7 (2C, CH ); 42.1 (1C, CH ); 40.1 (1C, CH );
39.8 (1C, CH ); 36.1 (1C, CH ); 35.6 (1C, CH ); 28.2 (1C, CH ); 25.1 (1C,
CH ); 22.0 (1C, CH ); F-NMR (282 MHz, CDCl
= 3278, 2931, 1710, 1657,
3
2
2
2
2
1.58 (m, 4H, CH
2
); 1.41-1.28 (m, 2H, CH
2
13
(1C, CH
2
2
2
2
CH
3
); C-NMR (75 MHz, CDCl
3
1
9
CH
2
1
2
2
3
3
,
5°C): δ = -79.8 ppm (s, 3F); IR (ATR): v
̅
C
2
2
2
2
−
1
2
2
2
2
+
19
[M ], calc.: 586.2138.
2
2
); 14.2 ppm (2C, CH
3
3
,
2
1
6
5°C): δ = -79.5 ppm (s, 3F); IR (ATR): v
̅
-
1
557, 1450, 1293, 1261, 1155, 1079, 1051 cm ; HRMS: (EI) m/z =
Diethyl 2-(2-oxo-2-((2-(7,7,7-trifluoro-6-oxoheptanamido)ethyl)ami-
no)ethyl)benzo[1,2-d:4,5-d']bis([1,3]dioxole)-4,8-dicarboxylate (14b):
Following the procedure described above for 13a, the trifluoromethyl
ketone 14b was obtained from the carboxylic acid 12b (15.5 mg, 78.23
µmol, 1.1 eq.), DIEA (30 µL, 172.23 µmol, 2.5 eq.), TBTU (25.5 mg,
+
04.1869 [M ], calc.: 604.1880.
Protein expression and purification of HDACs
7
9.42 µmol, 1.1 eq.) and the amine 7 (36.6 mg, 69.79 µmol, 1.0 eq.) in
anhydrous DMF (3.0 mL). Purifying by silica gel chromatography
DCM/MeOH/TEA 10:1:0.0→10:1:0.1) give the title compound as a
yellow solid (36.5 mg, 89 %). R = 0.45 (DCM/MeOH 10:1); m. p.:
decomp. at 182°C; H-NMR (300 MHz, CDCl , 25°C): δ = 6.72 (bs, 1H,
NH); 6.67-6.46 (2H, NH, CH); 6.11 (s, 2H, CH
The genes encoding the catalytical domains of HDAC4 (amino acids 648-
1057), HDAC5 (amino acids 655-1122), HDAC7 (amino acids 518-952)
(
and full length HDAC8 were codon optimised and ordered from
GenScribt. The genes were delivered in a pUC57 plasmid and cloned
into a pET14b-SUMO (HDAC8) or a pET14b-SUMO-CPD (HDAC4, 5
and 7) vector. All proteins were recombinantly expressed in E.coli
f
1
3
3
2
); 4.38 (q, J = 7.1 Hz, 4H,
); 3.02-2.83 (m, 2H, CH ); 2.82-2.65 (m, 2H,
); 2.36-2.12 (m, 2H, CH ); 1.77-1.58 (m, 4H, CH
); C-NMR (126 MHz, CDCl , 25°C): δ = 161.9 (2C,
C=O); 141.9 (2C, Cquart.); 141.2 (2C, Cquart.); 110.8 (1C, CH); 103.2 (2C,
quart.); 102.9 (1C, CH ); 61.7 (2C, CH ); 42.2 (1C, CH ); 40.0 (1C, CH );
); 36.1 (1C, CH ); 35.7 (1C, CH ); 24.5 (1C, CH ); 21.8 (1C,
); F-NMR (282 MHz, CDCl , 25°C): δ = -79.8
= 3276, 2943, 1710, 1659, 1557, 1451, 1294,
CH
CH
2
); 3.57-3.30 (4H, CH
2
2
BL21(DE3) as fusion proteins, whereby they were N-terminally fused to a
3
); 1.37 ppm (t, J =
[43]
2
2
2
6xHis-SUMO tag.
HDACs 4, 5 and 7 were additionally fused to a C-
13
7.2 Hz, 6H, CH
3
3
terminal cysteine protease domain (CPD), which possess an
autocatalytic activity and cuts itself from the HDAC upon induction by
C
2
2
2
2
[44]
phytic acid. Bacterial cultures were grown at 37 °C in LB media to an
39.9 (1C, CH
2
2
2
2
optical density at 600 nm of 0.6 - 0.8. The protein expression was
induced by addition of 1 mM isopropyl-β-D-thiogalactopyranoside and the
cells were further cultured overnight at 25 °C. Cells were harvested by
centrifugation (15 min, 15.000xg, 4 °C) and the pellet was resuspended
in lysis buffer (50 mM HEPES, pH 8.0, 300 mM NaCl). Cells were lysed
by sonication and cell fragments were removed by centrifugation (30 min,
25000xg, 4 °C). The supernatant was loaded onto an immobilised metal
affinity chromatography using a cOmplete His-Tag purification resin
(Roche) which was equilibrated with lysis buffer. The resin was washed
with 20 volumes of lysis buffer. For the CPD fusion constructs the resin
19
CH
2
); 14.2 ppm (2C, CH
3
3
ppm (s, 3F); IR (ATR): v
̅
-
1
+
1
5
262, 1156, 1080, 1025 cm ; HRMS: (EI) m/z = 590.1739 [M ], calc.:
90.1723.
N-(2-(2-(4,8-Dibutyrylbenzo[1,2-d:4,5-d']bis([1,3]dioxole)-2-
yl)acetamido)ethyl)-8,8,8-trifluoro-7-oxooctanamide (13c): Following
the procedure described above for 13a, the trifluoromethyl ketone 13c
was obtained from the carboxylic acid 12c (18.2 mg, 85.78 µmol, 1.1 eq.),
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