Design of oxobenzimidazoles and oxindoles as novel androgen receptor antagonists

Article abstract of DOI:10.1016/j.bmcl.2012.01.116

Oxobenzimidazoles (e.g., 1), a novel series of androgen receptor (AR) antagonists, were discovered through de novo design guided by structure-based drug design. The compounds in this series were reasonably permeable and metabolically stable, but suffered

Full text of DOI:10.1016/j.bmcl.2012.01.116

Bioorganic & Medicinal Chemistry Letters 22 (2012) 2572–2578
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design of oxobenzimidazoles and oxindoles as novel androgen
receptor antagonists
⇑
⇑
Chuangxing Guo , Mason Pairish , Angelica Linton, Susan Kephart, Martha Ornelas, Asako Nagata,
Benjamin Burke, Liming Dong, Jon Engebretsen, Andrea N. Fanjul
Oncology Medicinal Chemistry, Pfizer PharmaTherapeutics R&D, San Diego, CA 92121, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Oxobenzimidazoles (e.g., 1), a novel series of androgen receptor (AR) antagonists, were discovered
through de novo design guided by structure-based drug design. The compounds in this series were rea-
sonably permeable and metabolically stable, but suffered from poor solubility. The incorporation of three
dimensional structural features led to improved solubility. In addition, the observation of a ‘flipped’ bind-
ing mode of an oxobenzimidazole analog in an AR ligand binding domain (LBD) model, led to the design
and discovery of the novel oxindole series (e.g., 2) that is a potent full antagonist of AR.
Received 14 December 2011
Revised 26 January 2012
Accepted 30 January 2012
Available online 7 February 2012
Keywords:
Androgen receptor
AR antagonist
Prostate cancer
Ligand efficiency
CRPC
CF3
O
NC
NC
O
N
LBD
NHR
N
N
N
O
O
2
1
oxindole
oxobenzimidazole
Ó 2012 Elsevier Ltd. All rights reserved.
Most prostate cancer patients receiving hormonal therapies
progress to more aggressive castration-resistant prostate cancer
(CRPC).1 Recently, full AR antagonists such as MDV3100 and
BMS-641988 (Fig. 1) have demonstrated efficacy against CRPC in
preclinical models2 and more importantly in patients.3 These
encouraging results instigated our interest4 in searching for new,
non-steroidal full AR antagonists.
facilitates binding of a coactivator (shown in blue) to ER and
triggers downstream gene transcription. In Figure 2B, an ER antag-
onist (4-hydroxytamoxifen) (shown in orange) ‘pushes’ H12 open
and prevents the binding of the coactivator. As a result, gene
transcription is not initiated.
It was rationalized that since the LBD domain of NHRs have a
highly conserved structure,6 a full antagonist of AR may require
There are no reported crystal structures of a full antagonist
bound to AR, but the crystal structure of a full antagonist bound
to the closely related estrogen receptor (ER) may be illustrative
of the conformational changes responsible for full antagonism to
a nuclear hormone receptor (NHR). As shown in Figure 2A5 when
an agonist (diethylstilbestrol) (shown in orange) binds to ER, helix
12 (H12) (shown in yellow) adopts a ‘closed’ conformation, which
CF3
CF3
NC
NC
F
O
S
O
H
O
N
N
N
HN
NH
S
O
O
O
H
O
MDV-3100
BMS-641988
(Phase I)
(Phase II/III)
⇑
Corresponding authors.
E-mail addresses: alexguo01@gmail.com (C. Guo), mason.pairish@pfizer.com
(M. Pairish).
Figure 1. Androgen receptor antagonists.
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2012.01.116

C. Guo et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2572–2578
2573
Figure 2. Crystal structures of estrogen receptor. Helix 12 in yellow. Coactivator in blue. Ligand in orange. (A) ER with agonist (diethylstilbestrol) (PDB: 3ERD). (B) ER with
antagonist (4-hydroxytamoxifen) (PDB: 3ERT).
A
B
C
CF3
O
CF3
CN
H
N
H
H
H
H
H
F
CN
O
S
H
O
O
N
O
O
HO
S
O
N
H
O
O
OH
DHT
bicalutamide
BMS-641988
Figure 3. Crystal structures and truncated model of AR. Helix 12 in yellow. Ligand in orange. (A) AR with agonist (DHT) (PDB: 3L3X). (B) AR with partial-antagonist
(bicalutamide) (PDB: 1Z95). (C) Model of truncated AR with full antagonist BMS-641988).
H12 movement7 similar to that seen in ER. In co-crystal structures8
of AR with its natural agonist 5-alpha-dihydrotestosterone (DHT)
(Fig. 3 A) and the co-crystal structures9 of a mutant AR with a
partial antagonist10 (bicalutamide) (Fig. 3B), H12 adopts a closed
conformation. Our docking11 of the reported full antagonist BMS-
641988 (Fig. 3C) into the truncated12 ligand binding domain
(LBD) suggests that it would keep H12 from closing and prevent
the binding of coactivator, thereby inhibiting gene transcription.
Comparison of the possible binding modes of BMS-641988 and
compound 3 (an AR antagonist previously reported by Pfizer13),
suggested that an oxobenzimidazole (e.g., 1) could be used as a no-
vel core which would provide rigid vectors for attaching the left
hand side group and the right hand side group (Fig. 4). In particular,
the right hand side benzyl group may be able to push H12 into an
open form for achieving full antagonism. To test this design, ana-
logs 1, 7–9 were synthesized by the methods shown in Scheme
1.14 Nucleophilic displacement of commercially available aryl fluo-
ride 4 with urea 5 yielded product 6, which was then alkylated or
coupled with boronic acids to provide compounds 1, 7–9 in good
yields. Compounds 1, 7–9 were tested in a cell-based (CRPC model)
AR antagonism assay.15 Compound 1 was found to be a full AR
antagonist (Table 1) with reasonable potency. Interestingly, more
rigid analogs 7 and 8 were inactive in the same assay, implying
the vector coming off the right hand side nitrogen may be different
from that of MDV3100.
Despite its high lipophilicity, the metabolic stability (HLM
ER = 0.46)16 of 1 is good. The major drawback of this molecule is
its poor aqueous solubility. In order to improve solubility, we
looked into two initial strategies: truncation and substitution.
The effect on potency with the change in polarity was monitored
with the measure of lipophilicity ligand efficiency (LipE).17 LipE ac-
counts for compound lipophilicity and antagonism potency (in one
term). First, truncation of the right-hand region was investigated.
Although this was an effective way to improve solubility, either in-
creased agonism18 and/or decreased potency was observed with
the changes (Table 2). A second strategy to improve solubility
was the introduction of nitrogen atoms into the benzene rings of
our lead compounds to give pyridyl analogs (Table 3). Unfortu-
nately, potency and solubility did not track together with these
substitutions.
A third approach to improve aqueous solubility was to disrupt
molecular planarity and symmetry.19 Branching in the right-hand
region (Table 4) was effective in increasing solubility but the
resulting compounds were either less potent (20/21) or prone to

2574
C. Guo et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2572–2578
O
NC
O
NC
H
O
NC
F3C
H
N
N
N
N
N
O
F3C
F3C
O
S
(R)
O
O
O
H
BMS-641988
Compound 3
Compound 1
O
O
NC
O
NC
F3C
N
N
N
+
N
F3C
Figure 4. Design of oxobenzimidazole core.
H
N
BnBr, K2CO3
O
F3C
NC
O
N
DMSO
61%
HN
O
N
F3C
NC
R
CF3
NH
5
N
NC
K2CO3
DMSO
71%
OR
F
R-B(OH)2
Cu(OAc)2
TEA, DCM
47%
6
4
1,7-9
Scheme 1. Synthesis of compounds 1, 7–9.
Table 1
Initial SAR of oxobenzimidazole series
F3C
O
NC
R
N
N
Compd
R
cLogP
Antagonism IC50, nM (or% @1.0
170
lM)
Agonism fold induction @1.0
lM
Sol (
lM)
LipE
1.34
1
5.43
1.04Â
<0.16
0.79
7
8
6.38
4.66
(12.6%)
(28.7%)
0.88Â
1.44Â
O
F
N
H
8.81
9.9
F
H
N
9
4.08
(72.5%)
1.08Â
O

C. Guo et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2572–2578
2575
Table 2
SAR of analogs with truncated right-hand substituents
F3C
O
NC
R
N
N
Compd
R
cLogP
Antagonism IC50, nM (or% @1.0
l
M)
Agonism fold induction @ 1.0
lM
Sol (lM)
10
11
12
13
CH2CN
iPr
H
3.39
4.86
4.18
4.55
(94.8%)
373
(60.1%)
293
1.42Â
0.965Â
6.2Â
18.9
9.3
7.9
Et
1.08Â
3.47
Table 3
SAR of pyridyl isomers
4
5
A
A
O
N
F3C
NC
N
3
A
A
1
A
2
Compd
N position
cLogP
Antagonism IC50, nM (or% @1.0
lM)
Agonism fold induction @ 1.0
lM
LipE
Sol (l
M)
14
15
16
17
18
19
A1
A2
A3
A4
A5
A1, A2
4.4
(91%)
60.6
588
301
389
1.04Â
1.13Â
0.951Â
1.03Â
0.984Â
1.1Â
5.3
<0.500
4.27
4.27
3.93
3.93
3.23
2.95
1.96
2.59
2.48
12
2.5
1.7
(96.3%)
Table 4
SAR of analogs with branched right-hand groups
R1
O
NC
R2
N
N
Compd
R1
R2
Optical rotation
NA
cLogP
Antag. IC50 (nM)
170
Agonism fold induction @1.0
lM
LipE
1.34
Sol (lM)
1
CF3
5.43
1.04Â
<0.16
5.58
20
CF3
(À)
5.74
363
0.833Â
0.70
21
22
CF3
Cl
(+)
NA
5.74
3.38
292
126
0.904Â
0.941Â
0.79
3.52
4.41
5.9
N
O
O
O
N
N
N
N
N
23
24
Cl
Cl
(À)
3.68
3.68
189
178
0.945Â
0.874Â
3.04
3.07
N
N
(+)
9.45
N

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C. Guo et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2572–2578
O
N
O
N
O
N
F3C
NC
F3C
NC
F3C
NC
R
R
N
25
Antagonism % @ 1.0 uM = (75.70%)
Agonism fold induction @ 1.0 uM = 1.96x
cLogP = 3.3
Figure 5. Design of dimethyloxindole core.
hypothesized. In the second, ‘flipped’ conformation (shown in or-
ange), the benzyl group binds deeper in the LBD and the 5-position
of the oxobenzimidazole is oriented toward H12. This suggested a
new vector for the introduction of H12 disrupting extensions.
We reasoned that the extended oxindole structure such as 26
would dock well in this conformation (Fig. 7). Therefore it was syn-
thesized by the method shown in Scheme 2.14 Nucleophilic dis-
placement of commercially available aryl fluoride
4 with
oxindole 27 yielded product 28. Suzuki cross-coupling with boro-
nic acid 29 provided compound 26 which was found to be a potent
AR full antagonist.
To improve ADME properties of 26, we wanted to reduce lipo-
philicity by replacing the trifluoromethyl group with a methoxy
group. The aryl methoxy group was introduced via a copper cata-
lyzed cross coupling (Scheme 3)14 of arylbromide 30 and oxindole
31 to give compound 32. Bromination of 32 proceeded regiospecif-
ically to afford 33 as the only product. Subsequent Suzuki cou-
plings provided 35 and 2. Both compounds have improved
solubility over the original lead (1) and good pharmacology and
ADME profiles (Table 5). Lipophilicity ligand efficiency (LipE).17
was also significantly improved (3.58/3.79 for 35 and 2 vs 1.34
for 1). The oxindole has been established as a novel core for AR full
antagonists.
In summary, a series of novel, non-steroidal full AR antagonists
have been discovered through design of AR LBD binders possessing
sufficient length and rigidity to force H12 movement. The initial
oxobenzimidazole leads suffered from low solubility that is likely
due to high lipophilicity and the planarity of the oxobenzimidazole
core. The crystallinity of the oxobenzimidazole core was reduced
by introduction of three dimensional structural features (sp3 cen-
ters), most notably, by replacing oxobenzimidazole with the less
planar dimethyloxindole. The design idea was inspired by detailed
analysis of ligand binding conformations docked into a truncated
AR LBD model. The discovery of the dimethyloxindole series not
Figure 6. Two different binding modes observed when docking compound 1.
epimerization (23/24).20 Lipophilicity ligand efficiency (LipE).17
was improved in the case of compounds 23/24. Therefore, we
turned our attention to adding a three dimensional structural fea-
ture to the oxobenzimidazole core.
Figure 5 illustrates how replacement of one of the nitrogens of
the oxobenzimidazole core with a carbon would introduce a non-
planar sp3 center. The dimethyl-substituted oxindole analog 25
had submicromolar antagonism, but unfortunately proved to pos-
sess significant AR agonism.18
In order to suppress the agonism, computer modeling was em-
ployed to design oxindole molecules which would have the poten-
tial to push AR H12 open. As a surrogate for the oxindole core, the
modeled bound conformations of the closely related oxobenzimi-
dazole 1 were examined for hints of a suitable vector to extend
out for interaction with the H12. Docking11 of 1 into a truncated
AR model ( Fig. 6).12 suggested that the oxobenzimidazole ring
could adopt two conformations. In one conformation (shown in
yellow), the benzyl group extends towards H12 as originally
O
N
H
F3C
NC
F
N
O
26
Figure 7. Docking experiment of extended dimethyloxindole structure 26 suggested that the ‘flipped conformation’ is preferred.

C. Guo et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2572–2578
2577
O
N
O
F
H
HO
N
H
O
N
F3C
NC
F
B
OH
KOtBu
DMSO
CF3
F3C
29
O
Br
NC
HN
83%
PdCl2(PPh3)2
NC
N
O
F
CsF, DMF, H2O
Br
70%
3
27
28
26
Scheme 2. Synthesis of oxindole analogs bearing trifluoromethyl groups.
HO
R2
B
O
N
O
N
CuI
MeO
NC
MeO
NC
OH
R2
Br2
DMCHDA
K2CO3
OMe
MeO
NC
34
NaOAc
O
NC
+
HN
N
O
PdCl2(PPh3)2
AcOH
dioxane
Br
Br
CsF, DMF, H2O
41-88%
30
31
32
33
35
for 3 steps
Scheme 3. Synthesis of oxindole analogs bearing methoxy groups.
Table 5
SAR of extended dimethyloxindole series
N
R2
R1
N
O
Compd
R1
R2
cLogP
Antag. IC50 (nM)
Agonism fold induction @1.0
lM
Sol (l
M)
HLMa
LipE
O
N
H
26
CF3
3.84
197
0.941Â
6.25
0.4
2.87
F
O
N
H
35
OMe
OMe
3.2
165
0.884Â
1.04Â
9.7
9.8
<0.25
3.58
3.79
F
b
N
2
3.31
79.6
O
a
see Ref. 16.
b
Compound 2 ionizes poorly under the MS conditions used in the HLM assays, so reliable data for this compound could not be obtained from this assay.
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nists, but also sheds light on the AR protein conformation changes
responsible for full antagonism.
References and notes
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15. CRPC cell-based HTS assay: In this assay, prostate cancer refractory cells
(LNAR), stably expressing an AR Response Element DNA sequence (ARE)-
luciferase reporter gene construct (PSA-LUC), were treated with the testing
compounds in the absence (agonistic mode) or the presence (antagonistic
mode) of a potent agonist (R1881). Upon activation and binding of the AR to
the ARE, the luciferase gene transcribed and translated into active luciferase
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compounds were docked into a LBD binding pocket of the truncated AR
model (see Ref. 12).
12. Although many agonist-bound NHR crystal structures have been published in
the last decade, only a few antagonist-bound structures have been reported in
the PDB. The AR modeling was based on three ER co-crystal structures that
have antagonistic actions in some cells (PDB code: 1ERR, 3ERT, 1NDE). These
never exceeded 0.1%. For agonism, values obtained from the compounds under
study were compared to those of untreated cells, which were assigned an
arbitrary number of 1.0 to indicate no agonism. For antagonism, cells were
treated with 0.1 nM R1881 alone (corresponding to max receptor
activation = 100%) or in combination with the various compounds.
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18. The cut-off for significant residual AR agonism was set to >1.11 fold induction
in CRPC cell-based assay (agonism mode, see Ref. 7) based on statistic analysis
of multiple test results (n = 176) of RD-162 in the same assay. RD-162, a full AR
antagonist reported in literature (Refs. 4a,b), was used as a reference standard.
In the agonism assay, the averaged agonism fold induction of RD-162 (n = 176)
is 0.876 with a standard deviation of 0.0779. An AR ligand with an agonism fold
induction >1.11 (0.876 + 3 Â 0.0779) is likely (>99.7% confidence) to have more
residual agonism than RD-162.
co-crystal structures bound to these modulators displayed
a different ER
conformation from the ‘‘closed’’ agonist-bound form. Instead, these structures
adopted a conformation where the C-terminal alpha helix (helix12; H12) was
changed dramatically and H12 blocked its co-activator binding site. When
developing
a model for our antagonist designs, we made two main
assumptions. We assumed that the agonist-bound crystal structures were
not proper for modeling since antagonists would bump H12 in the agonist-
bound ‘closed’ conformation. We also assumed that AR would have a similar
inactive conformation to ER when AR antagonists were bound. However, since
the C-terminal residues were not well conserved among NHRs and uncertainty
remained regarding its exact conformation in AR, we built an AR model based
on AR crystal structure (PDB code: 3B5R) with
a
truncated C-terminus
19. Ishikawa, M.; Hashimoto, Y. J. Med. Chem. 2011, 54, 1539.
(Leu881ꢀ) where H12 was absent. We applied this truncated, antagonist-
ligand-accepting model for evaluating our designed molecules by docking
simulations.
20. The benzylic methyl in compounds 23/24 was found to epimerize during chiral
separation by preparative HPLC.