In Silico-Guided Target Identification
Journal of Medicinal Chemistry, 2006, Vol. 49, No. 23 6775
with ethyl acetate as eluent to yield 3 (39 mg, 25%) as a white
powder. C15H19N3O4, white solid, C18-RP-HPLC (A: 0.1% TFA
in H2O, B: 0.08% TFA in MeCN, 0-100% B, 1.2 mL/min, 20
min): tR ) 11.45 min; IR(solid): νmax (cm-1) ) 3286, 3182 (NH),
4.36 (d, J ) 15.6 Hz, NCHN, 1H), 4.45 (br., NH), 4.53-4.59 (m,
NCH2CH, NCHCO, 3H), 5.24 (d, J ) 15.6 Hz, NCHN, 1H), 5.83-
5.87 (m, CHCHCO, 1H), 6.12 (td, J ) 7.1, 11.4 Hz, CH2CHCH,
1H), 7.24-7.36 (m, CH-Ar, 5H); 13C NMR (75 MHz, CDCl3, 298
K): δ ) 28.14, 34.28 (CH3), 38.43, 45.86 (CH2), 56.27 (CH), 61.53
(CH2), 81.09 (Cq), 123.98 (CH), 127.31, 129.00, 129.31 (CH-Ar),
136.18 (Cq-Ar), 143.12 (CH), 157.20, 169.89, 189.05 (CO); HRMS
(ESI): m/z: calculated for C20H28N3O4: 374.2074, found: 374.2069.
E isomer: C18-RP-HPLC (A: 0.1% TFA in H2O, B: 0.08% TFA
1
3027 (Csp2), 2922 (Csp3), 1750, 1681, 1638 (CO); H NMR (300
MHz, CDCl3, 298 K): δ ) 2.81 (dd, J ) 9, 14.4 Hz, CH2Ph, 1H),
3.13 (s, NCH3, 3H), 3.36 (dd, J ) 4.5, 14.4 Hz, CH2Ph, 1H), 3.73
(s, OCH3, 3H), 4.01 (d, J ) 17.8 Hz, NCH2, 1H), 4.17 (d, J )
15.7 Hz, NCH2N, 1H), 4.35 (d, J ) 17.8 Hz, NCH2, 1H), 4.58-
4.64 (m, NCHCO, 1H), 4.65 (br., NH), 5.45 (d, J ) 15.7 Hz,
NCH2N, 1H), 7.27-7.36 (m, H-Ar, 5H); HRMS(ESI): m/z:
calculated for C15H20N3O4: 306.1448, found: 306.1436.
1
in MeCN, 0-100% B, 1.2 mL/min, 20 min): tR ) 15.18 min; H
NMR (300 MHz, CDCl3, 298 K): δ ) 1.46 (s, (CH3)3, 9H), 2.80
(dd, J ) 9.0, 14.4 Hz, CH2Ph, 1H), 3.07 (s, NCH3, 3H), 3.35 (dd,
J ) 4.8, 14.4 Hz, CH2Ph, 1H), 4.36 (d, J ) 15.6 Hz, NCHN, 1H),
4.13-4.17 (m, NCH2CH, 2H), 4.55-4.60 (m, NCHCO, 1H), 4.75
(d, J ) 1.8 Hz, NH, 1H), 5.24 (d, J ) 15.6 Hz, NCHN, 1H), 5.82
(td, J ) 1.4, 15.7 Hz, CHCHCO, 1H), 6.71 (td, J ) 5.4, 15.9 Hz,
CH2CHCH, 1H), 7.25-7.34 (m, CH-Ar, 5H); 13C NMR (75 MHz,
CDCl3, 298 K): δ ) 28.08, 34.60 (CH3), 38.27, 43.38 (CH2), 56.27
(CH), 61.31 (CH2), 80.89 (Cq), 125.05 (CH), 127.31, 128.98, 129.35
(CH-Ar), 136.15 (Cq-Ar), 143.69 (CH), 157.09, 164.89, 169.83
(CO); HRMS (ESI): m/z: calculated for C20H28N3O4: 374.2074,
found:374.2071.
7-Benzyl-3-(2-hydroxy-ethyl)-5-methyl-[1,3,5]triazepan-2,6-
dione (6). Acid 5 (410 mg, 1.41 mmol) was dissolved in THF (20
mL) under inert atmosphere, and NMM (186µL, 1.69 mmol) was
added. The solution was cooled to -20 °C, and iBuOCOCl (222µL,
1.69 mmol) was added. The reaction mixture was stirred 25 min at
-20 °C. Salts were quickly filtered at room temperature, and the
mixture was replaced in the -20 °C bath. A solution of NaBH4
(160 mg, 4.23 mmol) in H2O (5 mL) was added. After 20 min at
-20 °C, the mixture was allowed to warm to room temperature.
Dilution in ethyl acetate was followed by a workup with brine.
The organic layer was dried over Na2SO4 and evaporated. The crude
residue was purified by silica gel column chromatography (CH2-
Cl2/MeOH/AcOH 95:5:1, v/v/v) to afford 6 (196 mg, 50%) as a
white powder. C14H19N3O3, C18-RP-HPLC (A: 0.1% TFA in H2O,
B: 0.08% TFA in MeCN, 0-100% B, 1.2 mL/min, 20 min): tR )
13.34 min; IR(solid): νmax (cm-1) ) 3397 (NH), 3279 (OH), 3023
(Csp2), 2918 (Csp3), 1644, 1620 (CO); 1H NMR (300 MHz, CDCl3,
298 K): δ ) 2.96 (dd, J ) 8.3, 14.3 Hz, CH2Ph, 1H), 3.23 (s,
NCH3, 3H), 3.42-3.53 (m, CH2Ph, NCH2CH2, 2H), 3.71-3.81 (m,,
NCH2CH2, HOCH2CH2, 3H), 4.42 (d, J ) 15.7 Hz, NCHN, 1H),
4.70-4.75 (m, NCHCO, 1H), 5.40-5.45 (m, NCHN, NH, 2H),
7.38-7.48 (m, CH-Ar, 5H); 13C NMR (75 MHz, CDCl3, 298 K):
δ ) 30.40 (CH3), 33.94, 48.01 (CH2), 52.08 (CH), 57.64, 58.91
(CH2), 123.11, 124.80, 124.98, 125.41 (CH-Ar), 132.60 (Cq-Ar),
154.38, 166.10 (CO); HRMS(ESI): m/z: calculated for C14H20N3O3:
278.1499, found: 278.1475.
4-(6-Benzyl-1-methyl-4,7-dioxo-[1,3,5]triazepan-3-yl)-butyr-
ic Acid tert-Butyl Ester (9). 8 (110 mg, 0.29 mmol) was dissolved
in EtOH (20 mL). Pd/C 10wt % (20 mg) was added. The system
was stirred for 16 h under hydrogen atmosphere. Filtration over
Celite yielded 9 (105 mg, 97%) as a white powder. C20H29N3O4,
C18-RP-HPLC (A: 0.1% TFA in H2O, B: 0.08% TFA in MeCN,
0-100% B, 1.2 mL/min, 20 min): tR ) 15.33 min; IR(solid): νmax
(cm-1) ) 3270, 3020 (NH), 3066 (Csp2), 2973, 2934 (Csp3), 1722,
1711, 1686, 1674, 1646, 1630 (CO); 1H NMR (300 MHz, CDCl3,
298 K): δ ) 1.42 (s, (CH3)3, 9H), 1.77-1.82 (m, NCH2CH2, 2H),
2.21-2.26 (m, COCH2CH2, 2H), 2.78 (dd, J ) 9.3, 14.3 Hz, CH2-
Ph, 1H), 3.13 (s, NCH3, 3H), 3.31-3.37 (m, CH2Ph, NCH2CH2,
2H), 3.42-3.47 (m, NCH2CH2, 1H), 4.25 (d, J ) 15.6 Hz, NCH2N,
1H), 4.40 (br., NH), 4.51-4.56 (m, NCHCO, 1H), 5.23 (d, J )
15.6 Hz, NCH2N, 1H), 7.24-7.32 (m, CH-Ar, 5H); 13C NMR
(75 MHz, CDCl3, 298 K): δ ) 24.38 (CH2), 28.07 (CH3), 32.23
(CH2), 34.52 (CH3), 38.56, 48.25 (CH2), 56.47 (CH), 61.85 (CH2),
80.55 (Cq), 127.28, 128.98, 129.32 (CH-Ar), 156.48, 169.89,
172.51 (CO); HRMS (ESI): m/z: calculated for C20H30N3O4:
376.2231, found: 376.2210.
4-(6-Benzyl-1-methyl-4,7-dioxo-[1,3,5]triazepan-3-yl)-butyr-
ic Acid (10). 9 (48 mg, 0.13 mmol) was dissolved in TFA/CH2Cl2
(1:1, v/v), (1 mL), and the reaction was stirred at room temperature
for 30 min. Solvents were evaporated and afforded 10 (22 mg, 55%)
as a white powder. C16H21N3O4, C18-RP-HPLC (A: 0.1% TFA in
H2O, B: 0.08% TFA in MeCN, 0-100% B, 1.2 mL/min, 20 min):
tR ) 11.52 min; IR(solid): νmax (cm-1) ) 3301 (OH), 2946, 2923,
2853 (Csp3), 1686, 1613 (CO); HRMS (ESI): m/z: calculated for
C16H22N3O4: 320.1605, found: 320.1618.
4-(6-Benzyl-1-methyl-4,7-dioxo-[1,3,5]triazepan-3-yl)-butyra-
mide (11). Sieber resin (0.084 mmol) was swollen in DMF and
rinced twice prior to use. Removal of the Fmoc group was achieved
by treatment with a mixture of DMF/ piperidine (1:1, v/v) (1 mL)
for 20 min (repeated twice), followed by washings with DMF (×6).
A solution of 10 (18 mg, 0.056 mmol), BOP (26 mg, 0.059 mmol),
and HOBt (8 mg, 0.059 mmol) dissolved in DMF was prepared
and added onto the resin. DIPEA (30µL, 0.17 mmol) was then
added, and the mixture was stirred at room temperature for 1.5 h.
The resin was filtered, washed with DMF (×4) and CH2Cl2 (×4)
and dried under high vaccum. Cleavage by treatment with TFA/
CH2Cl2 (1:9, v/v) (1 mL) was performed at room temperature in
40 min. The filtrate was collected, and the resin was washed with
CH2Cl2. The solvents were evaporated. The crude residue was
purified by flash column chromatography (CHCl3/MeOH 10:1, v/v)
to afford 11 (12 mg, 68%) as a white powder. C16H22N4O3, C18-
RP-HPLC (A: 0.1% TFA in H2O, B: 0.08% TFA in MeCN,
0-100% B, 1.2 mL/min, 20 min): tR ) 9.55 min; IR(solid): νmax
(cm-1) ) 3334 (NH), 2934 5Csp3), 1630 (CO); 1H NMR (300 MHz,
CDCl3, 298 K): δ ) 1.82-1.89 (m, NCH2CH2, 2H), 2.19-2.24
4-(6-Benzyl-1-methyl-4,7-dioxo-[1,3,5]triazepan-3-yl)-but-2-
enoic Acid tert-Butyl Ester (8). Under inert atmosphere, CH2Cl2
(0.5 mL) was introduced in a flask. Oxalyl chloride (57µL, 0.65
mmol) was added via a hypodermic syringe, and the mixture was
cooled to -20 °C. DMSO (91µL, 1.29 mmol) was added, and the
mixture was stirred at -20 °C for 10 min. A solution of alcohol 6
(120 mg, 0.43 mmol) in CH2Cl2 (1.5 mL) was added dropwise,
and the mixture was stirred at -20 °C for an additional 20 min.
DIPEA (450 µL, 2.6 mmol) was then added. After 5 min at -20
°C, the mixture was allowed to warm to room temperature. H2O
(10 mL) was added, and the system was stirred at r.t. for 10 min.
Extraction with CH2Cl2 (4 × 25 mL) provided the organic layer
which was washed with KHSO4 1 N and brine. The organic layer
was dried over Na2SO4 and evaporated to give the aldehyde 7.
Formation of 7 was followed by TLC, and the compound was
directly used in the next step. (Ph)3PdCHCOOtBu (244 mg, 0.65
mmol) was added to a solution of 7 in CH2Cl2 under inert
atmosphere, and the reaction mixture was stirred at room temper-
ature for 2.5 h. The reaction was quenched by addition of water.
After separation, the organic layer was dried over Na2SO4 and
evaporated. The crude residue was purified by flash column
chromatography (AcOEt/cyclohexane/AcOH, 1:1:0.1 v/v/v) to
afford Z-8 (18,6 mg, 11,6%) as a white powder and E-8 contami-
nated by (Ph)3PO. E-8 was isolated after selective precipitation of
(Ph)3PO in Et2O and subsequent filtration. Evaporation of solvent
yielded pure E-8 (93.5 mg, 58.2%) as a white powder. Global yield
of the reaction was calculated: 70%, Z/E ratio: 1/6. C20H27N3O4.
Z isomer: C18-RP-HPLC (A: 0.1% TFA in H2O, B: 0.08% TFA
in MeCN, 0-100% B, 1.2 mL/min, 20 min): tR ) 15.85 min; IR-
(solid): νmax (cm-1) ) 3281, 3211 (NH), 3070 (Csp2), 2919, 2851
1
(Csp3), 1705, 1683, 1645 (CO); H NMR (300 MHz, CDCl3, 298
K): δ ) 1.46 (s, (CH3)3, 9H), 2.80 (dd, J ) 9.3, 14.4 Hz, CH2Ph,
1H), 3.09 (s, NCH3, 3H), 3.35 (dd, J ) 4.5, 14.4 Hz, CH2Ph, 1H),