Small Molecule Inhibitors for 3CLpro
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 8 1857
for 1.5 h, after which the reaction mixture was concentrated in vacuo
and the residue was triturated with Et2O to yield the trifluoroacetate
salt. To a solution of trifluoroacetate salt in DMF (4 mL) at rt was
added Ac-Val-Thr(OBn)-Leu-OH (30.6 mg, 0.045 mmol), DIPEA
(16 µL, 0.090 mmol), and HBTU (17.7 mg, 0.045 mmol). After 4
h of stirring, the solvent was removed in vacuo. The crude product
was purified by HPLC (Waters C18 Bondpak 10 µm, 125 Å; 100
× 25 mm, 15 mL/min, 5 min elution of 20% acetonitrile, followed
by a linear gradient elution over 25 min of 20 to 100% acetonitrile
in 0.075% TFA/H2O, tR ) 26 min) to afford 7 (13.6 mg, 45% yield).
[R]25D ) -49.4 (c 0.05, DMSO); IR (microscope) 3064, 2958, 1740,
a solution of 10 (33.8 mg, 0.1 mmol) was added TFA/CH2Cl2 (3
mL, 1:1 ratio) at 0 °C. The resulting solution was stirred for 1.5 h,
after which the reaction mixture was concentrated in vacuo and
the residue was triturated with Et2O to yield the trifluoroacetate
salt. To a solution of trifluoroacetate salt in DMF (5 mL) at rt was
added Ac-Val-Thr(OBn)-Leu-OH (46.4 mg, 0.1 mmol), DIPEA (35
uL, 0.2 mmol), and HBTU (39.5 mg, 0.1 mmol). After 4 h of
stirring, the solvent was removed in vacuo. The crude product was
purified by HPLC (Waters C18 Bondpak 10 µm, 125 Å; 100 × 25
mm, 15 mL/min, 10 min elution of 10% acetonitrile followed by
linear gradient elution over 45 min of 10 to 100% acetonitrile in
0.075% TFA/H2O, tR ) 34 min) to afford 11 (23.4 mg, 34% yield).
[R]25D ) +2.8 (c 0.07, MeOH); IR (microscope) 3280, 3070, 2960,
1
1655, 1625, 1535, 1493 cm-1; H NMR (CD3OD, 500 MHz) δ
8.30 (ddd, 1H, J ) 7.8, 1.4, 0.70 Hz), 8.10 (ddd, 1H, J ) 7.8, 1.4,
0.64 Hz), 7.83 (dd, 1H, J ) 7.8, 0.5 Hz), 7.63 (dd, 1H, J ) 7.8,
0.5 Hz), 7.36-7.12 (m, 10H), 5.12 (d, 1H, J ) 17.0 Hz), 5.04 (d,
1H, J ) 17.0 Hz), 4.58 (d, 1H, J ) 11.3 Hz), 4.42 (d, 1H, J )
11.3 Hz), 4.40-4.33 (m, 2H), 4.13 (dd, 1H, J ) 6.4, 3.1 Hz), 4.07
(d, 1H, J ) 6.4 Hz), 3.48 (dd, 1H, J ) 14.0, 7.1 Hz), 3.26-3.18
(m, 1H), 2.94 (dd, 1H, J ) 14.0, 9.7 Hz), 2.12 (dd, 1H, J ) 13.4,
6.7 Hz), 1.95 (s, 3H), 1.57-1.46 (m, 2H), 1.40-1.28 (m, 1H), 1.22
(d, 3H, J ) 6.4 Hz), 0.99 (d, 3H, J ) 4.2 Hz), 0.98 (d, 3H, J ) 4.2
Hz), 0.83 (d, 3H, J ) 6.3 Hz), 0.79 (d, 3H, J ) 6.3 Hz); HRMS
(ES) calcd for C42H52N6O8Na, 791.3739; found, 791.3736.
(S)-tert-Butyl-1-(methoxy(methyl)amino)-1-oxo-3-((S)-2-ox-
opyrrolidin-3-yl)propan-2-ylcarbamate (9). To a solution of
cyclic glutamic acid 815 (200 mg, 0.73 mmol) in DCM (5 mL) at
0 °C was added Weinreb amine23 (71 mg, 0.73 mmol), EDCI (141
mg, 0.73 mmol), HOBt (99 mg, 0.73 mmol), and NMM (0.16 mL,
1.46 mmol). The resulting solution was stirred overnight while
allowing to warm slowly to rt. Then the reaction mixture was diluted
with DCM (50 mL) and washed with water and brine. The
combined organic layers were dried over MgSO4 and then
concentrated in vacuo. Purification of the crude product by flash
chromatography on silica gel (90/10, EtOAc/MeOH) afforded 5 as
a white foam (151 mg, 66%). [R]25D ) -0.22 (c 0.27, CHCl3); IR
(CHCl3, cast) 3293, 2976, 1693 cm-1; 1H NMR (CDCl3, 500 MHz)
δ 6.85 (br, 1H, NH), 5.45 (br, 1H, NH), 4.60 (t, 1H, J ) 8.0 Hz),
3.77 (s, 3H), 3.33 (dd, 2H, J ) 8.7, 4.0 Hz), 3.20 (s, 1H), 3.28-
3.16 (m, 2H), 2.54-2.42 (m, 2H), 2.15-2.02 (m, 1H), 1.89-1.77
(m, 1H), 1.72-1.62 (m, 1H), 1.42 (s, 9H); 13C NMR (CDCl3, 125
MHz) δ 179.6, 172.6, 155.8, 79.6, 61.6, 49.3, 40.3, 38.0, 34.4, 32.1,
28.3, 28.0; HRMS (ES) calcd for C14H25N3O5Na, 338.1686; found,
338.1688.
1
2873, 1635, 1517, 1438 cm-1; H NMR (CD3OD, 500 MHz) δ
7.93 (dd, 1H, J ) 3.8, 1.0 Hz), 7.83 (dd, 1H, J ) 4.9, 1.0 Hz),
7.34-7.26 (m, 5H), 7.16 (dd, 1H, J ) 4.9, 3.8 Hz), 5.14 (dd, 1H,
J ) 11.0, 4.0 Hz), 4.55 (d, 1H, J ) 11.5 Hz), 4.46 (d, 1H, J )
11.5 Hz), 4.40 (d, 2H, J ) 4.3 Hz), 4.23 (d, 1H, J ) 7.2 Hz), 4.03
(dd, 1H, J ) 6.3, 4.3 Hz), 3.28-3.16 (m, 2H), 2.32-2.18 (m, 3H),
2.14-2.04 (m, 1H), 2.05 (s, 3H), 1.86-1.72 (m, 2H), 1.64-1.52
(m, 3H), 1.19 (d, 3H, J ) 6.3 Hz), 0.97 (d, 3H, J ) 6.8 Hz), 0.93
(d, 3H, J ) 6.8 Hz), 0.87 (d, 3H, J ) 6.0 Hz), 0.85 (d, 3H, J ) 6.0
Hz); 13C NMR (CD3OD, 125 MHz) δ 192.6, 182.1, 174.8, 174.0,
173.9, 171.9, 142.8, 139.8, 136.1, 134.5, 129.6, 129.5, 129.1, 128.8,
75.9, 72.4, 60.5, 59.4, 55.7, 53.2, 41.9, 41.6, 40.0, 33.7, 31.6, 29.3,
25.8, 23.6, 22.5, 21.4, 19.9, 18.6, 16.5; HRMS (ES) calcd for
C35H49N5O7SNa, 706.3245; found, 706.3247.
(S)-2-((2S,3R)-2-((S)-2-Acetamido-3-methylbutanamido)-3-hy-
droxybutanamido)-4-methyl-N-((S)-1-oxo-3-((S)-2-oxopyrrolidin-
3-yl)-1-(thiophen-2-yl)propan-2-yl)pentanamide (12). To a so-
lution of 10 (9.5 mg, 0.028 mmol) was added TFA/CH2Cl2 (1 mL,
1:1 ratio) at 0 °C. The resulting solution was stirred for 1.5 h, after
which the reaction mixture was concentrated in vacuo and the
residue was triturated with Et2O to yield the trifluoroacetate salt.
To a solution of trifluoroacetate salt in DMF (1 mL) at rt was added
Ac-Val-Thr(OBn)-Leu-OH (10.9 mg, 0.028 mmol), DIPEA (10 uL,
0.056 mmol), and HBTU (11.1 mg, 0.028 mmol). After 4 h of
stirring, the solvent was removed in vacuo. The crude product was
purified by HPLC (Waters C18 Bondpak 10 µm, 125 Å; 100 × 25
mm, 15 mL/min, 10 min elution of 10% acetonitrile followed by
linear gradient elution over 45 min of 10 to 100% acetonitrile in
0.075% TFA/H2O, tR ) 26 min) to afford 11 (8.3 mg, 48% yield).
[R]25D ) -53.1 (c 0.11, MeOH); IR (microscope) 3277, 3083, 2962,
1632, 1537, 1438 cm-1; 1H NMR (CD3OD, 400 MHz) δ 7.98 (dd,
1H, J ) 3.9, 1.0 Hz), 7.88 (dd, 1H, J ) 5.0, 1.0 Hz), 7.21 (dd, 1H,
J ) 5.0, 3.9 Hz), 5.33 (dd, 1H, J ) 11.4, 4.0 Hz), 4.40 (dd, 1H, J
) 8.5, 6.2 Hz), 4.36 (d, 1H, J ) 4.4 Hz), 4.18 (d, 1H, J ) 7.1 Hz),
4.14 (dd, 1H, J ) 6.4, 4.4 Hz), 3.36-3.31 (m, 2H), 2.64-2.55 (m,
1H), 2.42-2.32 (m, 1H), 2.24 (ddd, 1H, J ) 14.0, 11.4, 4.0 Hz),
2.11-2.01 (m, 1H), 2.00 (s, 3H), 1.92-1.74 (m, 2H), 1.66-1.54
(m, 3H), 1.16 (d, 3H, J ) 6.4 Hz), 0.96 (d, 6H, J ) 6.8 Hz), 0.91
(d, 3H, J ) 6.2 Hz), 0.86 (d, 3H, J ) 6.2 Hz); 13C NMR (CD3OD,
125 MHz) δ 192.1, 181.7, 174.5, 173.9, 173.6, 171.9, 142.7, 136.0,
134.4, 129.4, 68.2, 60.7, 59.5, 54.3, 53.1, 41.4, 41.3, 39.4, 34.0,
31.3, 28.8, 25.6, 23.2, 22.2, 21.7, 19.7, 19.5, 18.5; HRMS (ES)
calcd for C28H43N5O7SNa, 616.2775; found, 616.2775.
(S)-tert-Butyl-1-oxo-3-((S)-2-oxopyrrolidin-3-yl)-1-(thiophen-
2-yl)propan-2-ylcarbamate (10). To a solution of 9 (120 mg, 0.38
mmol) in THF (2 mL) at -15 °C was charged i-PrMgCl (0.37 mL,
2 M solution in THF, 0.74 mmol) dropwise to afford a clear
solution. After stirring for 10 min, thiophen-2-yl-magnesium
bromide (1.2 mL, 1.0 M solution in THF, 1.2 mmol) was added
slowly, and the temperature was maintained lower than -5 °C.
The cooling bath was removed, and the mixture was allowed to
warm to rt over 30 min. After 4 h of stirring at rt, the reaction was
complete, which was monitored by TLC. The reaction mixture was
cooled on an ice bath, and 1.0 N HCl (2 mL) was added slowly,
followed by an EtOAc extraction. The combined organic layer was
dried over MgSO4, and the solvent was removed in vacuo to obtain
the crude mixture, which was purified by flash column chroma-
tography on silica gel (EtOAc) to obtain product 10 (81 mg, 63%)
as a white foam and recovered starting material 9 (18 mg, 15%).
[R]25D ) +33.7 (c 0.25, CHCl3); IR (CHCl3, cast) 3283, 2977, 1663,
(2S,5S,8S,11S)-8-((R)-1-(Benzyloxyl)ethyl)-5-isobutyl-11-iso-
propyl-4,7,10,13-tetraoxo-2-((S)-2-oxopyrrolidin-3-yl)methyl-
3,6,9,12-tetraazatetradecan-1-oic Acid (15). To a solution of 1415
(45 mg, 0.071mmol) in THF/H2O (10 mL, 1:1 ratio) at 0 °C was
added LiOH (4.0 mg, 0.092 mmol). After 2 h of stirring, the solvent
was removed in vacuo. Water (10 mL) and citric acid were added
to adjust the pH of the solution to 3. The mixture was extracted
with EtOAc and washed with water and brine. The combined
organic layers were dried over MgSO4 and then the solvent was
removed in vacuo to afford the product 15 (42 mg, quant.) as a
white foam. [R]25D ) -22.9 (c 0.30, MeOH); IR (microscope) 3276,
1
1515, 1440 cm-1; H NMR (CDCl3, 500 MHz) δ 7.84 (m, 1H),
7.66 (d, 1H, J ) 4.8 Hz), 7.12 (dd, 1H, J ) 4.8, 3.8 Hz), 6.29 (br,
1H, NH), 5.68 (br, 1H, NH), 5.10 (dd, 1H, J ) 6.5, 0.6 Hz), 3.38-
3.30 (m, 2H), 2.58-2.46 (m, 2H), 2.22-2.14 (m, 1H), 1.94-1.84
(m, 2H), 1.42 (s, 9H); 13C NMR (CDCl3, 125 MHz) δ 191.5, 179.5,
155.6, 141.2, 134.8, 133.2, 128.4, 79.9, 54.9, 40.3, 38.2, 35.3, 35.2,
28.3; HRMS (ES) calcd for C16H22N2O4SNa, 361.1193; found,
361.1190.
1
3089, 2961, 2873, 1633, 1545, 1438, 1404 cm-1; H NMR (CD3-
(S)-2-((2S,3R)-2-((S)-2-Acetamido-3-methylbutanamido)-3-
(benzyloxy)butanamido)-4-methyl-N-((S)-1-oxo-3-((S)-2-oxopy-
rrolidin-3-yl)-1-(thiophen-2-yl)propan-2-yl)pentanamide (11). To
OD, 400 MHz) δ 7.38-7.20 (m, 5H), 4.59 (d, 1H, J ) 11.1 Hz),
4.47 (d, 1H, J ) 11.1 Hz), 4.47 (d, 2H, J ) 3.7 Hz), 4.18 (d, 1H,
J ) 6.8 Hz), 4.16-4.06 (m, 1H), 3.28-3.10 (m, 2H), 2.54-2.42