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10. Molecular modeling was performed starting from the 1.95 Å MR structure with
bound corticosterone (PDB code 2A3I: Li, Y.; Suino, K.; Daugherty, J.; Xu, H. E.
Mol. Cell, 2005, 19, 367). The structure was prepared by removal of waters,
addition of hydrogens, and restrained energy minimization using Macromodel
(Macromodel 9.8.107, Schrödinger LLC, New York, NY). Electrophilic and
hydrophobic potentials were generated with Maestro (Maestro 9.1.107,
Scheme 1. Reagents and conditions: (a) CsF, DMF, 40 °C to rt, 3 days, 71%; (b) KOH,
EtOH, 46%, rt, overnight; (c) chiral SFC (OJ-H, 4.6 Â 100 mm, 5% MeOH/0.1% TFA/
CO2, 2.5 mL/min, 100 bar); (d) HATU, iPr2NEt, 3,5-dimethoxybenzylamine, DMF,
2 h, 72%; (e) 11, NaOH, THF, rt, overnight, 57%.
Schrödinger LLC, New York, NY) in
a
6 Å grid centered on the
crystallographic ligand. Molecular docking was performed by employing our
in-house docking routine FLOG (Miller, M. D.; Kearsley, S. K.; Underwood, D. J.;
Sheridan, R. P. J. Comput. Aided Mol. Des. 1994, 8, 153), which ranks pre-
calculated conformations of the target molecules in a 6 Å grid centered on the
crystallographic ligand. Conformations were generated using our in-house
metric matrix distance geometry algorithm JG (Kearsley, S. K. Merck & Co., Inc.,
unpublished). The conformations were subjected to energy minimization with
Macromodel using the MMFFs force field (Halgren, T. A. J. Comput. Chem. 1999,
20, 720). The representative docking pose reported in Figure 2 was selected by
visual inspection using SAR and was subjected to restrained energy
minimization (using Macromodel) to produce the model shown. Figure 2
was generated using Pymol (The Pymol Molecular Graphics System, version
1.4, Schrödinger LLC, New York, NY).
placement of the R2/R3 benzyl rings in the ligand binding pocket,
reducing its activity. Furthermore, the reported binding mode has
strain energy of 2 kcal/mol, which is thermally accessible at room
temperature.
The selectivity profiles of representative analogs 3f and 3j
against several nuclear hormone receptors, including AR, GR, ERa,
ERb, and PRb, are shown in Table 5. Compounds 3f and 3j demon-
strated acceptable selectivity, in particular, superior selectivity in
the AR antagonist mode assay with respect to spironolactone.
The rat pharmacokinetic (PK) profiles of compounds 1g, 3f and
3j are shown in Table 6. All compounds exhibited modest to high
clearance and acceptable IV exposure, with 1g showing poor oral
bioavailability. Interestingly, the structurally closely related and
more conformationally constrained analog 3g, improved the oral
bioavailability to 28%. The best oral bioavailability was observed
with 3j (63%). The preliminary PK studies demonstrated that the
oxazolidinedione represented a promising lead series.
12. The mixture of diethyl a-benzylmalonate (41 g, 164 mmol) and CsF (49.8 g) in
90 mL of DMF was heated at 40 °C with vigorous air bubbling for 3 days. The
resulting mixture was diluted with ethyl acetate (800 mL) and washed with
water (1 L Â 3). The organic layer was concentrated and then purified by
biotage (5–20% ethyl acetate in hexanes) to give the diethyl
a-benzyl a-
hydroxy malonate (31 g, 117 mmol, 71%) as a colorless oil. 1H NMR (300 MHz,
CDCl3) d: 7.22–7.26 (m, 5H), 4.23 (q, J = 7.2 Hz, 4H), 3.80 (br, 1H), 3.35 (s, 2H),
1.26 (t, J = 7.2 Hz, 6H). To diethyl
a-benzyl a-hydroxy malonate (6.3 g,
24 mmol) in 50 mL of EtOH (anhydrous) was added KOH (1.5 g). The mixture
was stirred at rt over night. After removing the solvent in vacuo, the residue
was taken up with 100 mL of ethyl acetate and 150 mL of water. The organic
layer was removed. To the aqueous layer containing the potassium salt of the
desired product was added 0.2 N HCl until pH = 2. The mixture was extracted
with 200 mL ethyl acetate. The organic layer was dried with magnesium
sulfate and concentrated to give the acid (2.6 g, 11 mmol, 46%) as a colorless
oil. The racemic acid was then purified by chiral SFC (OJ-H, 4.6 Â 100 mm, 5%
MeOH/0.1% TFA/CO2, 2.5 mL/min, 100 bar) to give (2R)-2-benzyl-3-ethoxy-2-
hydroxy-3-oxopropanoic acid as a single enantiomer (1.0 g, the first eluting
peak). The assignment of the absolute configuration is based on vibrational
circular dichroism (details in supporting information). LC/MS 261.1 (M+23). To
a mixture of (2R)-2-benzyl-3-ethoxy-2-hydroxy-3-oxopropanoic acid (112 mg,
0.47 mmol), 3,5-dimethoxybenzylamine (86 mg, 0.51 mmol) and HATU
(197 mg, 0.52 mmol) was added DMF (4 mL) and Hünig base (67 mg,
0.52 mmol). The mixture was stirred at rt for 2 h. To the mixture was added
ethyl acetate and water. The organic layer was washed with water twice, and
dried with magnesium sulfate. After removal of the solvent, the residue was
purified by biotage (10–30% ethyl acetate in hexanes) to give ethyl (2R)-2-
benzyl-3-[(3,5-dimethoxybenzyl)amino]-2-hydroxy-3-oxopropanoate
(132 mg, 0.34 mmol, 72%) as a colorless oil. To a mixture of ethyl (2R)-2-
benzyl-3-[(3,5-dimethoxybenzyl)amino]-2-hydroxy-3-oxopropanoate (40 mg,
0.10 mmol) and isocyanate 11 (80 mg, 0.54 mmol) in 4 mL of THF was added
NaOH (solid, 50 mg) at rt. The mixture was under vigorous stirring for
overnight. Filtered, and washed with ethyl acetate. The filtrate was
concentrated, taken up by DMSO, and purified by Gilson (30–100%
acetonitrile/water/0.05% TFA) to give 1g (28 mg, 0.057 mmol, 57%) as a white
solid. LC/MS 489.0 (M+1). 1H NMR (300 MHz, CDCl3) d: 7.20–7.29 (m, 8H), 7.01
(d, J = 7.0 Hz, 2H), 6.80 (t, J = 5.5 Hz, 1H), 6.42 (t, J = 2.0 Hz, 1H), 6.35 (d,
J = 2.0 Hz, 2H), 5.06 (q, J = 7.0 Hz, 1H), 4.44 (dd, J = 5.5, 14.5 Hz, 1H), 4.36 (dd,
J = 5.5, 15.0 Hz, 1H), 3.79 (s, 6H), 3.65 (d, J = 14.0 Hz, 1H), 3.40 (d, J = 14.5 Hz,
1H), 1.54 (d, J = 7.0 Hz, 3H).
A representative synthesis of oxazolidinedione analogs is illus-
trated in Scheme 1.12 The
a-hydroxylation of malonate 6 occurred
by applying vigorous air bubbling over 3 days, to afforded desired
hydroxylated intermediate 7, which then underwent a monohy-
drolysis to yield monocarboxylic acid 8. Chiral super critical fluid
chromatography (SFC) separation provided the chiral acid 9, which
subsequently coupled with 3,5-dimethoxybenzylamine to gener-
ate amide 10. The final oxazolidinedione formation was accom-
plished by using isocyanate 11 in the presence of solid NaOH in
THF. It should be noted that the oxazolidinedione is particularly
unstable under basic aqueous conditions.
In conclusion, we have identified novel oxazolidinedione
amides as potent antagonists for MR. Systematic SAR studies led
to several compounds with excellent selectivity over other nuclear
hormone receptors, and representative compounds also displayed
reasonable PK profiles in rats. Further investigations of the series
will be reported in due course.
References and notes