1-Benzylbenzimidazoles: The discovery of a novel series of bradykinin B1 receptor antagonists

Article abstract of DOI:10.1016/j.bmcl.2008.08.014

The design, synthesis, and structure-activity studies of a novel series of BK B₁ receptor antagonists based on a 1-benzylbenzimidazole chemotype are described. A number of compounds, for example, 38g, with excellent affinity for the cynomolgus

Full text of DOI:10.1016/j.bmcl.2008.08.014

Bioorganic & Medicinal Chemistry Letters 18 (2008) 5027–5031
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
1-Benzylbenzimidazoles: The discovery of a novel series of bradykinin B1
receptor antagonists
Qin Guo, Jayaraman Chandrasekhar, David Ihle, David J. Wustrow, Bertrand L. Chenard, James E. Krause,
Alan Hutchison, Dawn Alderman, Charles Cheng, Daniel Cortright, Daniel Broom, Mark T. Kershaw,
*
Jean Simmermacher-Mayer, Yao Peng, Kevin J. Hodgetts
Neurogen Corporation, 35 NE Industrial Road, Branford, CT 06405, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The design, synthesis, and structure–activity studies of a novel series of BK B1 receptor antagonists based
on a 1-benzylbenzimidazole chemotype are described. A number of compounds, for example, 38g, with
excellent affinity for the cynomolgus macaque and rat bradykinin B1 receptor were discovered.
Ó 2008 Elsevier Ltd. All rights reserved.
Received 29 May 2008
Revised 3 August 2008
Accepted 5 August 2008
Available online 9 August 2008
Keywords:
Bradykinin B1
P-glycoprotein
1-Benzylbenzimidazole
The kinins, bradykinin (BK) and kallidin (KD) and their metabo-
lites [des-Arg9]bradykinin (DABK) and [des-Arg10]kallidin (DAKD)
provoke a number of acute and chronic inflammatory pathways
resulting in pain, edema and vasodilation.1 These effects are med-
iated by the G-protein coupled receptors BK B1 and B2.2 The BK B2
receptor is constitutively expressed, whereas the BK B1 receptor
expression in peripheral tissues is induced following injury.3 Re-
cent studies in mice however, suggest that the BK B1 receptor is
constitutively expressed in the central nervous system, suggesting
a potential central role for this receptor as well.4 BK B1 receptor
null mice exhibit decreased inflammatory response and hyperalge-
sia supporting the hypothesis that BK B1 receptor antagonists will
be effective anti-inflammatory analgesic drugs. A number of selec-
tive, non-peptide, potent BK B1 receptor antagonists have been de-
scribed.5 Early disclosures were dominated by relatively high
molecular weight aryl sulfonamides including the extensively
studied SSR2406126 and NVP-SAA164.7 Recently, a number of
non-sulfonamide templates have emerged including the pyrazole
1,8 cyclopropane-carboxamide 29 and the benzodiazepine 310a
(Fig. 1). The biaryl 2 exhibited a large difference between its re-
ported human and rat affinity whereas the benzodiazepine 3 dis-
played similar potency at both human and rat receptors.
Planning to study the in vivo efficacy of the compounds prepared
in the present study in rodent models of pain, the benzodiazepine
3 appeared to be an excellent starting point in this regard,
O
CF3
NH
O
N
Cl
O
H
N
N
N
O
NH
F
H
H
N
CO2Me
Cl
N
Me
1 hBK1 IC50 = 1.8 nM
rBK1 not reported
2 hBK1 Ki = 0.44 nM
rBK1 Ki = 1600 nM
O
N
N
O
N
N
N
N
N
H
H
Ph
3 hBK1 Ki = 0.59 nM
rBK1 Ki = 0.92 nM
Figure 1. Structures of non-sulfonamide BK B1 receptor antagonists.
although, the molecular weight of 3 was high (MW = 601) and the
oral bioavailability10a in rodent was low (F < 4%).10b We considered
that replacement of the phenethylbenzodiazepine moiety of 3 by a
lower molecular weight surrogate could lead to compounds potent
at both human and rat BK B1 receptors and with improved oral
bioavailability.
* Corresponding author. Tel.: +1 2034888201.
E-mail address: kjhodgetts@aol.com (K. J. Hodgetts).
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.08.014

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Q. Guo et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5027–5031
The benzimidazole core has been considered to be a privileged
O
O
structure, being found in compounds that modulate a number of
GPCRs and ligand-gated ion channels and in marketed drugs such
as omeprazole.11 We considered that the benzodiazepine core 4
could be replaced by a suitably substituted benzimidazole-2-car-
boxamide, for example, 5 (Fig. 2) and that exploration of the cen-
tral linker and the basic tail (R) could lead to a novel series of BK
B1 receptor antagonists. Our endeavors in this regard are reported
herein.
Potential alignments of low-energy conformers of the BK B1
receptor antagonist 4 and the proposed new template 5 were first
examined to better understand the relative dispositions of the
pharmacophores of the two templates. The analyses were per-
formed using the GASP algorithm.12 The results were encouraging
and revealed that there was significant, although by no means per-
fect, overlap between 4 and 5 with respect to several of the pre-
sumed key pharmacophore features over the entire surface of the
two templates (Fig. 3). In particular, the pyridylpiperazine moiety
at one end overlapped well. At the opposite end, the aromatic ring
of the benzyl substituent of 5 matched with the aryl ring of the
benzodiazepine, both in the location of the ring centroids and rel-
OH
N
N
OH
N
H
ii, iii
N
N
O
Ph
6
Ph
8
i
i
N
O
O
N
N
N
N
N
N
N
N
H
N
O
N
Ph
Ph
7
9
Scheme 1. Reagents and conditions: (i) DMC, DIEA, 4-pyridylpiperazine, MeCN
(96%); (ii) DMC, DIEA, NH2CH2CO2Et, MeCN (87%); (iii) NaOH, MeOH (95%).
analogous sequences to those outlined in Scheme 1, but using
alternate amino esters as the linkers and the appropriate terminal
amine moiety, the compounds described in Tables 1–3 were pre-
pared. BK B1 receptor antagonist potency was determined using
cynomolgus macaque BK B1 receptor-expressing CHO cells and a
fluorescent imaging plate reader (FLIPR) to measure intracellular
Ca2+ transients. Inhibition of 0.1 nM (approximate EC50 concentra-
tion) DAKD-induced fluorescence was measured at multiple com-
pound concentrations to determine a functional IC50 at the BK B1
receptor. Compound potency at the rat BK B1 receptor was deter-
mined in an analogous manner. A number of analogues made dur-
ing the study were also evaluated as potential substrates for the
xenobiotic efflux pump P-glycoprotein (P-gp), this was important
because a Pgp substrate may limit access to central nervous system
BK B1 receptors which may be critical for analgesic activity.4 The P-
gp efflux ratio was assessed by calculating the ratio of the apparent
permeability (Papp) in the basolateral to apical direction versus Papp
in the apical to basolateral direction across a monolayer of MDR1
transfected MDCK cells.15
Given the basic character of the endogenous B1 receptor ligands
DABK and DAKD, and that of a number of reported small molecule
BK B1 ligands, we initially chose to keep the terminal amine region
of the targets as 4-pyridylpiperazine, 1-(1-methyl-4-piperidin-4-
yl)piperazine or N-methylbenzylimidazoline and varied the nature
of the linker between this group and the benzimidazole. Direct
attachment of 4-pyridylpiperazine or 1-(1-methyl-4-piperidin-4-
yl)piperazine to the 2-carboxylbenzimidazole gave analogues 7
and 10, which were inactive but the imidazoline analogue 11
was the first active compound in the series, albeit in the low micro-
molar range. Attachment of the amines to the benzimidazole via a
glycine linker, however, gave compounds with sub micromolar
activity (9, IC50 = 310 nM and 12, IC50 = 686 nM) and in the case
of the imidazoline 13 potency under 10 nM. To capitalize upon this
promising activity, the effects of substitutions to the glycine linker
were examined (compounds 14–24). C-alkylation brought about a
loss in activity, for example, 14 and 15 and N-methylation resulted
in a loss in activity for the 4-pyridyl analogue 16 but a boost in
activity for the 4-methylpiperidine analogue 17 relative to their
parent analogues 9 and 12. The N-ethyl and N-propyl analogues,
however, were considerably more active, in particular the 4-meth-
ylpiperidine analogues 19 and 22 (IC50 = 16 and 18 nM, respec-
tively), while the imidazoline 20 was as active as its un-alkylated
parent (IC50 = 6 nM). Branching of the alkyl chain, for example,
23 and 24 resulted in a significant reduction in potency. Increasing
the length of the linker (e.g., b-alanine analogues 25 and 26) ren-
dered compounds of similar activity to their glycine counterparts,
whereas imidazoline 27 was an order of magnitude weaker. Con-
ative orientation of the p-planes. In the middle portion of the mol-
ecule, the imine nitrogen of benzimidazole overlapped with that of
the benzodiazepine, while the oxygen of the carboxamide had
good correspondence with that of the urea. Although the two sets
of hydrogen bond acceptors are slightly displaced from each other,
the lone pairs point in similar directions. Consequently, template 5
appeared to be a promising mimic of 4 in its ability to interact with
the BK B1 receptor.
The compounds described in the study were synthesized from
the readily available 1-benzyl-benzimidazol-2-carboxylic acid
(6)13 as exemplified by the synthesis of the final compounds 7
and 9 (Scheme 1). 2-Chloro-1,3-dimethylimidazolinium chloride
(DMC)14 coupling of the acid 6 with commercially available 4-pyr-
idylpiperazine directly gave the amide 7. Alternatively, DMC or
benzotriazolyloxytris(dimethylamino) phosphonium hexafluoro-
phosphate (BOP) mediated coupling of the acid 6 with glycine ethyl
ester followed by saponification with aqueous sodium hydroxide
gave the acid 8. A second amide coupling reaction with 4-pyridyl-
piperazine gave the target amide 9 in good overall yield. Following
O
O
N
N
O
O
N
H
N
H
N
R
R
N
N
H
N
H
Ph
Ph
4
5
Figure 2. 1-Benzylbenzimidazoles as potential BK B1 receptor antagonists.
Figure 3. Common pharmacophore features in aligned low energy conformations
of benzodiazepine and benzimidazole cores. Shared hydrogen bond acceptors are
shown in red, centroids of aromatic rings in purple, and hydrophobic units in gray.

Table 1
Effects of the linker (X) and the amine tail (R) on cBK B1 receptor potency
P-gpb
Papp (10À6 cm/s)
Compound key
a
a
c
Compound
X
R
cBK B1 IC50 (nM)
rBK B1 IC50 (nM)
7
A
A
A
B
B
B
i
>5000
>5000
1016
310
686
5
X
N
R
10
11
9
12
13
ii
iii
i
ii
iii
N
417
155
Ph
23
1.0
14
15
16
17
18
C
C
D
D
E
i
ii
i
ii
i
>5000
1303
1176
268
O
O
O
O
X =
N
H
N
H
N
O
O
O
278
B
A
D
C
O
19
20
21
22
23
24
E
E
F
F
G
G
ii
iii
i
ii
i
16
6.0
355
18
>5000
465
15
55
0.6
O
O
O
O
345
396
23
N
N
N
N
H
O
O
O
ii
E
F
G
H
25
26
27
28
29
30
31
H
H
H
I
I
I
i
962
601
54
2311
4021
188
4074
ii
iii
i
ii
iii
i
O
O
O
O
O
N
N
N
N
O
J
O
I
J
L
K
N
32
33
34
35
36
J
ii
i
ii
i
3219
>5000
884
>5000
>5000
N
H
K
K
L
L
N
N
N
N
N
R =
N
N
i
ii
iii
ii
a
IC50 values are means of at least two determinations.
MDR1 directional transport ratio (B to A)/(A to B).
Passive permeability (A to B).
b
c

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Q. Guo et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5027–5031
Table 2
Table 3
Imidazoline bioisosteres
b-Alanine linked analogues
R
O
O
O
N
N
N
H
R
N
N
H
N
N
O
Ph
Ph
38a-g
37a-l
a
Compound
R
cBK B1 IC50
Compound
R
cBK B1
Compound
R
cBK B1
IC50, nMa
IC50, nMa
38a
38b
38c
>5000
N
N
N
O
O
O
37a
>5000
37g
407
NH2
N
N
1990
2912
N
37b
37c
37d
37e
>5000
>5000
14
37h
37i
37j
37k
37l
330
N
N
N
N
N
CN
196
NH
38d
38e
>5000
744
O
O
N
N
N
1167
2130
>5000
N
N
S
N
H
N
H
O
N
N
N
N
N
718
N
H
N
38f
524
N
N
H
N
H
37f
626
N
N
H
N
a
IC50 values are means of at least two determinations.
N
H
38g
2
N
N
H
straint of the linker into a cyclic system (compounds 28–34) gave a
large decrease in activity and the importance of the 2-carbonyl was
underscored by the lack of activity observed for the 2-methylene
analogues 35 and 36. A number of the compounds were further
characterized. The pyridine 9 was evaluated at the rat receptor
and encouragingly was found to be of similar potency (rBK1
IC50 = 417 nM) as at the cynomolgus macaque receptor. The 4-
methylpiperidine 19 was also of similar potency at the rat receptor
(rBK1 IC50 = 15 nM) as at the cynomolgus macaque receptor. De-
spite a relatively high molecular weight (MW = 502), compound
a
IC50 values are means of at least two determinations.
compounds 37a–l). Examples included basic, acidic and neutral
heterocycles but a significant reduction in potency was the result
of all modifications of this type. Examination of the 4-cyano ana-
logue 37c (which lacks a basic amine moiety) in MDR1 transfected
MDCK cells revealed reduced P-gp susceptibility (BA/AB = 3) and
reasonable permeability [Papp = 7 (10À6 cm/s)] indicating, that at
least in part, the P-gp liability of the series was related to the pres-
ence of a basic moiety in the molecule.
19 had excellent aqueous solubility (120 lg/mL at pH 7.4) and
was also found to be stable in rat liver microsomes.16 The pharma-
cokinetic properties of 19 were examined in rodents (10 mpk PO,
0.5% MC/0.1% TA) but poor oral exposure (F < 5%) was observed.
In addition, compound 19 demonstrated both poor permeability
[Papp = 0.6 (10À6 cm/s)] and a potential P-gp liability (BA/AB = 55).
The imidazolines 13 and 20 were also evaluated at the rat receptor,
and in contrast to the 4-pyridine and 4-methylpiperidine ana-
logues (9, 19, 21, and 22) were found to be considerably weaker
(rBK1 IC50 = 155 and 345 nM, respectively) than at the cynomolgus
receptor. Compound 13 also had a potential P-gp liability (BA/
AB = 23). To confirm that 13 was a P-gp substrate, the compound
The b-alanine linked compounds 25–27 had shown encouraging
in vitro activity and a number of additional analogues with this lin-
ker were also prepared (Table 3). The spirocyclic and bicyclic ana-
logues 38a–f had weak activity but the 2-imidazoline-5-
aminopyridine analogue 38g had excellent cynomolgus potency
(IC50 = 2 nM) and in contrast to the benzyl linked imidazolines
(e.g., 13 and 20)
a similar activity in the rat assay (rBK1
IC50 = 0.8 nM). As with all previous imidazolines, compound 38g
had a high P-gp susceptibility (BA/AB = 42).
In summary, the hypothesis of replacing the benzodiazepine
core of a known BK B1 receptor antagonist was investigated and
a novel series of benzimidazoles were discovered. The 2-carboxyl
group was important for activity and a number of different linkers
and amine groups were studied. Pyridine and piperidine moieties
displayed little difference between cynomolgus and rat activity
(e.g., 9, 19, 21, and 22) but the analogues with phenyl-imidazoline
moieties were generally an order of magnitude weaker at the rat
receptor (e.g., 13 and 20). The combination of b-alanine linker
and 2-imidazoline-5-aminopyridine group, however, led to the
was also tested in the presence of 25 lM cyclosporine, a potent
P-gp inhibitor.17 An improvement in both apparent permeability
[Papp = 11 (10À6 cm/s)] and efflux ratio (BA/AB = 1.5) was the result,
confirming 13 to be a P-gp substrate.
To capitalize on the excellent cynomolgus macaque receptor
potency observed for the imidazoline analogues, and in an attempt
to increase rat receptor potency and reduce P-gp liability, a num-
ber of bioisosteres for the imidazoline were prepared (Table 2,

Q. Guo et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5027–5031
5031
9. Wood, M. R.; Books, K. M.; Kim, J. J.; Wan, B.-L.; Murphy, K. L.; Ransom,
R. W.; Chang, R. S. L.; Tang, C.; Prueksaritanont, T.; Detwiler, T. J.;
Hettrick, L. A.; Landis, E. R.; Leonard, Y. M.; Krueger, J. A.; Lewis, S. D.;
Pettibone, D. J.; Freidinger, R. M.; Bock, M. G. J. Med. Chem. 2006, 48,
1231.
10. (a) Wood, M. R.; Kim, J. J.; Han, W.; Dorsey, B. D.; Homnick, C. F.; DiPardo, R. M.;
Kuduk, S. D.; MacNeil, T.; Murphy, K. L.; Lis, E. V.; Ransom, R. W.; Stump, G. L.;
Lynch, J. J.; O’Malley, S. S.; Miller, P. J.; Chen, T.-B.; Harrell, C. M.; Chang, R. S. L.;
Sandhu, P.; Ellis, J. D.; Bondiskey, P. J.; Pettibone, D. J.; Freidinger, R. M.; Bock,
M. G. J. Med. Chem. 2003, 46, 1803; b A closely related analog of 3 (h BK1
Ki = 13 nM and MW = 592) has a reported oral bioavailability in rat of 32% with
t1/2 = 4.3 h.10a
identification of a compound 38g of excellent potency at both
cynomolgus and rat receptors. A number of compounds were as-
sessed in MDR1 transfected MDCK cells and found to be P-gp sub-
strates. The hydrogen bond acceptor located in the tail of these
compounds appeared to facilitate the efflux. Further optimization
of the benzimidazole series with respect to improving pharmacoki-
netic properties will be reported in due course.
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