Pyrrolidin-3-yl-N-methylbenzamides as potent histamine 3 receptor antagonists

Article abstract of DOI:10.1016/j.bmcl.2011.07.061

On the basis of the previously reported benzimidazole 1,3′- bipyrrolidine benzamides (1), a series of related pyrrolidin-3-yl-N- methylbenzamides were synthesized and evaluated as H₃ receptor antagonists. In particular, compound 32 exhibits pot

Full text of DOI:10.1016/j.bmcl.2011.07.061

Bioorganic & Medicinal Chemistry Letters 21 (2011) 5957–5960
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Pyrrolidin-3-yl-N-methylbenzamides as potent histamine 3
receptor antagonists
Dahui Zhou a, , Jonathan L. Gross b, Jean Y. Sze b, Adedayo B. Adedoyin b, Mark Bowlby b, Li Di a,
⇑
Brian J. Platt b, Guoming Zhang a, Nicholas Brandon a, Thomas A. Comery a, Albert J. Robichaud b
a Pfizer Global Research and Development, 445 Eastern Point Road, Groton, CT 06340, United States
b Pfizer Global Research and Development, CN 8000, Princeton, NJ 08543, United States
a r t i c l e i n f o
a b s t r a c t
On the basis of the previously reported benzimidazole 1,30-bipyrrolidine benzamides (1), a series of
related pyrrolidin-3-yl-N-methylbenzamides were synthesized and evaluated as H3 receptor antagonists.
In particular, compound 32 exhibits potent H3 receptor binding affinity, improved pharmaceutical prop-
erties and a favorable in vivo profile.
Article history:
Received 30 June 2011
Revised 16 July 2011
Accepted 19 July 2011
Available online 27 July 2011
Ó 2011 Elsevier Ltd. All rights reserved.
Keyword:
H3 receptor antagonist
The histamine 3 (H3) receptor is a G-protein coupled receptor
expressed in the CNS in regions associated with learning and mem-
ory such as the cerebral cortex, hippocampus, and striatum.1 Treat-
ment with H3 receptor antagonists has been shown to modulate
neurotransmitters that are associated with cognitive function and
improve memory, attention and vigilance in preclinical animal
models.2–4 As such, H3 receptor antagonists may prove to be useful
in the treatment of a variety of CNS disorders including schizo-
phrenia, Alzheimer’s disease and attention deficit hyperactivity
disorder (ADHD). Indeed several H3 receptor antagonists have ad-
vanced to clinical trials for cognitive disorders and dementia.5
Researchers from our laboratories recently reported the lead
optimization of a series of benzimidazole analogs that originated
from a screen of our focused biogenic amine library using a com-
pyrrolidin-3-yl-N-methylbenzamide analogs that demonstrated
potent activities as H3 receptor antagonists.
We begin our SAR study from the right-hand side of the molecule
(A-region, 2, Fig. 1) by examining the effects of substitutions at two
nitrogens and the stereochemical preference, while maintaining the
2-methylbenzimidazole moiety in the B-region (2, Fig. 1). Our gen-
eral synthetic approach to compounds 3–20 is outlined in Scheme
1. Nucleophilic aromatic substitution of corresponding methyl-4-
fluorobenzoate (21) with 2-methylbenzimidazole in the presence
of potassium carbonate, followed by methyl ester hydrolysis affor-
ded benzoic acid 22, which was coupled to commercially available
(R)- or (S)-N-Boc-3-aminopyrrolidine using 2-(1H-benzotriazol-1-
yl)-1,1,3,3-tetramethyluronium tetra-fluoroborate (TBTU) as a cou-
pling reagent. Alkylation of the intermediate 23 with a correspond-
ing alkyl iodide generated intermediate 24. Removal of the Boc
protecting group, followed by reductive alkylation provided the
desired products 3–20.
petitive binding assay with [3H]-(R)-
a-methylhistamine and cell
membranes from HEK293T cells over-expressing human H3 (hH3)
receptors. A few compounds (1, Fig. 1) were identified as advanced
discovery leads with single digit nanomolar potency and efficacy in
both water intake and novel object recognition models in ro-
dents.6–8 However, the potential mutagenic liability associated
with the lead compound prompted us to expand our efforts to in-
clude analogs devoid of the 1,30-bipyrrolidine moiety. Therefore,
our initial efforts focused on investigating the SAR of a series of
molecules (2, Fig. 1), in which the heteroaryl–phenyl scaffold (B-
region, 2, Fig. 1) is conserved and the amide nitrogen is pendant
to a pyrrolidine ring system (A-region, 2, Fig. 1). Herein, we de-
scribe the synthesis and biological evaluation of a series of novel
Table
1 illustrates the SAR data for the 2-methyl-1H-
benzo[d]imidazol-1-yl analogs 3–20. Substitutents at the basic
nitrogen had a dramatic impact on the human H3 receptor binding
affinity, compounds only bearing isopropyl (7), cyclobutyl (9),
cyclopentyl (11), and cyclohexyl (13) displayed potent affinities
for the human H3 receptor binding. As the size of substituent get-
ting bigger (i.e., cycloheptyl 15), the analog started to lose human
H3 binding affinity.9 In addition, a clear trend emerged with the (R)
absolute configuration being preferred when compared to the four
enantiomeric pairs (i.e., 7 vs 8; 9 vs 10; 11 vs 12 and 13 vs 14) for
the human H3 receptor binding affinity, suggesting that there was a
specific and well-defined binding pocket at the basic amine region.
Exploration of the amide nitrogen substitution showed little
⇑
Corresponding author. Tel.: +1 860 686 9219.
E-mail address: dahui.zhou@pfizer.com (D. Zhou).
0960-894X/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2011.07.061

5958
D. Zhou et al. / Bioorg. Med. Chem. Lett. 21 (2011) 5957–5960
A-region
N
O
O
R1
R3
N
(S)
N
N
N
n
N
N
N
R2
R
n
Discovery Leads (1)
2
hH3 Ki = 10 nM when R = H, n = 1
hH3 Ki = 5 nM when R = CH3, n = 1
hH3 Ki = 0.4 nM when R = CH3, n = 0
B-region
Figure 1. Design strategy.
O
O
O
NBoc
OH
N
H
a, b
c
OCH3
N
N
F
N
N
23
21
22
CH3
CH3
O
O
R1
N
NBoc
N
e, f
d
N
CH3
CH3
N
N
N
N
CH3
CH3
3-20
24
Scheme 1. Reagents and conditions: (a) 2-methylbenzimidazole, K2CO3, DMSO, 80 °C, 72 h; (b) LiOH, rt, 18 h; (c) (R)- or (S)-N-Boc-3-aminopyrrolidine, TBTU, 4-
methylmorpholine, rt, 2 h; (d) MeI, NaH, DMF, rt, 18 h; (e) TFA, CH2Cl2, rt, 18 h; (f) ketones, NaBH(OAc)3, HOAc, ClCH2CH2Cl, rt, 18 h.
analogs demonstrated reduced human H3 receptor binding affinity
when compared to corresponding methyl analogs (7, 9, and 11).
Having successfully identified the best substitutents at both
nitrogens and the stereochemical preference, we next focused
our attention on the left-hand side of the molecule (B-region, 2,
Fig. 1). In this exercise we first investigated the effect of a methy-
lene spacer between the benzimidazole and the phenyl core on hu-
man H3 receptor binding affinity. As shown in Scheme 2,
compounds 25–30 were readily prepared, starting from commer-
cially available methyl 4-(bromomethyl)-benzoate (31).
Table 1
Biding affinity of compounds 3–20
O
R1
N
N
R2
N
N
CH3
Compds
R1
R2
Stereochemistry
hH3 binding
Kia (nM)
Encouragingly, as summarized in Table 2, insertion of a methy-
lene spacer between the benzimidazole and the phenyl core re-
sulted in increased binding affinity for the human H3 receptor.
The exceptions were the cyclopentyl derivatives 27 and 30, which
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
H
Me
Et
n-Pr
i-Pr
i-Pr
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
H
(R)
(R)
(R)
(R)
(R)
(S)
(R)
(S)
(R)
(S)
(R)
(S)
(R)
(R)
(R)
(R)
(R)
(R)
>10
252
15
lM
17
4.2
26
6.7
21
3.5
5.2
4.7
49
32
173
19
15
197
26
Cyclobutyl
Cyclobutyl
Cyclopentyl
Cyclopentyl
Cyclohexyl
Cyclohexyl
Cycloheptyl
i-Pr
O
O
R3
N
a
OCH3
OCH3
N
Br
32
31
i-Pr
Et
Et
H
Et
O
Cyclobutyl
Cyclopentyl
Cyclopentyl
R1
R3
N
b-f
N
N
N
CH3
a
Displacement of [3H]-(R)-
a-methylhistamine binding to cloned hH3 receptors
stably expressed in HEK293T cells. Ki values were determined in triplicate.
25-30
Scheme 2. Reagents and conditions: (a) 2-methylbenzimidazole or benzimidazole,
K2CO3, DMSO, 80 °C, 72 h; (b) LiOH, rt, 18 h; (c) (R)-N-Boc-3-aminopyrrolidine,
TBTU, 4-methylmorpholine, rt, 2 h; (d) MeI, NaH, DMF, rt, 18 h; (e) TFA, CH2Cl2, rt,
18 h; (f) ketones, NaBH(OAc)3, HOAc, ClCH2CH2Cl, rt, 18 h.
opportunity for modification. The methyl group at the amide nitro-
gen was essential for binding at the human H3 receptor. Both non-
substituted (16 and 19) and ethyl substituted (17, 18, and 20)

D. Zhou et al. / Bioorg. Med. Chem. Lett. 21 (2011) 5957–5960
5959
Table 2
Table 4
Binding affinity of compounds 25–30
Biding affinity of compounds 31–36
O
O
R1
R1
N
R3
N
N
N
CH3
N
N
N
CH3
N
n
Compds
R1
n
hH3 binding
Compds
R1
R3
hH3 binding
Kia (nM)
Kia (nM)
31
32
33
34
35
36
i-Pr
0
0
0
1
1
1
7
25
26
27
28
29
30
i-Pr
Me
Me
Me
H
H
H
1.6
2.7
9
4
7.3
15
Cyclobutyl
Cyclopentyl
i-Pr
Cyclobutyl
Cyclopentyl
1.8
3.6
184
144
210
Cyclobutyl
Cyclopentyl
i-Pr
Cyclobutyl
Cyclopentyl
a
Displacement of [3H]-(R)-
a-methylhistamine binding to cloned hH3 receptors
a
Displacement of [3H]-(R)-
a-methylhistamine binding to cloned hH3 receptors
stably expressed in HEK293T cells. Ki values were determined in triplicate.
stably expressed in HEK293T cells. Ki values were determined in triplicate.
right stereochemistry, compounds 31–36 were prepared according
to Schemes 1 and 2 by substituting the 2-methylbenzimidazole
with 1H-pyrazole.
As shown in Table 4, compounds 31–36 maintained potent hu-
man H3 receptor binding affinity. Notably, compound 32 demon-
strated a 3.7-fold improvement in human H3 receptor binding
compared to compound 9. In contrast, decreased human H3 recep-
showed a 2- to 4-fold decrease in binding affinity for the human H3
receptor.
By now we had identified a few compounds which exhibited
good binding affinity at the human H3 receptor, we then proceeded
with the assessment of their drug-likeness in vitro. To this end, six
compounds (7, 9, 11, 13, 25, and 26) were evaluated in human liver
microsomal stability assay,10 hERG inhibition assay11 and MDCK
assay.12
As shown in Table 3, compounds 7 and 9 were metabolically
unstable in the presence of human liver microsomes, resulting in
a short half-life. Although compounds 11 and 13 displayed good
microsomal stability, they exhibited strong hERG inhibition with
Table 5
Calculated and measured properties of compound 32
Compd
MW
c log P
Microsomal stabilitya
t1/2 (min)
hERG
MDCK
IC50 < 3 l
M in the IonWorks HT assay,11 suggesting the potential
IC50
(
l
M)
Effluxb
risk of cardiac arrhythmia. In addition, in the MDCK assay com-
pounds 25 and 26 exhibited high P-gp-mediated efflux ratios
(B?A/A?B = 38 and 7.8, respectively), suggesting the potential
for poor brain penetration. Subsequent in vivo studies (rats,
10 mg/kg, po) validated these in vitro results, as compounds 25
and 26 demonstrated poor brain/plasma ratios with B/P = 0.21
and 0.18, respectively.
B?A/A?B
32
324
2.27
>30
25
0.9
a
Microsomal protein concentration: 0.5 mg/mL.
b
A, apical; B, basolateral; B?A/A?B is the ratio of the basolateral to-apical
permeation rate divided by the A?B permeation rate.
Having encountered problems with poor metabolic stability and
brain penetration, we returned our attention to the left-hand side
of the molecule (B-region, Fig. 1), focusing on the benzimidazole
moiety replacement, reasoning that the high molecular weight
and c log P value may be contributing to these issues. It appeared
that the replacement of a benzimidazole moiety with a five mem-
bered heterocycle was a logical move. Since imidazole-containing
H3 receptor ligands are associated with inhibition of cytochrome
P450 enzymes,13,14 a pyrazolyl heterocycle would be a suitable
choice.
6
*
4
The syntheses of pyrazole analogs 31–36 were straightforward.
Combining the preferred substituents at the basic nitrogen with a
2
Table 3
#
#
Calculated and measured properties of selected compounds
Compds MW
c log P Microsomal stabilitya hERG
MDCK
t1/2 (min)
IC50
(l
M) Effluxb
B?A/A?B
7
376.5
4
14
45
na
9
388.5 3.8
402.5 4.4
416.6 4.9
390.5 3.3
402.5 3.2
15
>30
2.3
2.8
>30
>30
0.7
0.9
1.3
38
0
11
13
25
26
>30
>30
>30
>30
veh
veh
3 mg/kg
10 mg/kg
+ Ramh (2.5 mg/kg, i.p.)
7.8
a
Microsomal protein concentration: 0.5 mg/mL.
A, apical; B, basolateral; B?A/A?B is the ratio of the basolateral to-apical
Figure 2. Effect of 32 on (R)-a-methylhistamine (Ramh) induced water consump-
b
tion in rats. Compound 32 was administered 30 min prior to Ramh. ⁄p < 0.05 versus
vehicle; #p < 0.05 versus Ramh alone.
permeation rate divided by the A?B permeation rate.

5960
D. Zhou et al. / Bioorg. Med. Chem. Lett. 21 (2011) 5957–5960
tor binding affinity was observed upon the insertion of a methy-
lene linker between the phenyl core and the pyrozole moiety
(compounds 34–36).
References and notes
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drug-like properties. Furthermore, compound 32 exhibited good
brain exposure in vivo (rats, 10 mg/kg, po) with the B/P ratio = 1.6.
We then examined the pharmacokinetics of compound 32 in rat
at 2 mg/kg, iv and observed a high plasma clearance of 68 mL/min/
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