In vitro SAR of pyrrolidine-containing histamine H3 receptor antagonists: Trends across multiple chemical series

Article abstract of DOI:10.1016/j.bmcl.2007.10.067

Structure-activity relationships (SAR) were analyzed within a library of diverse yet simple compounds prepared as histamine H₃ antagonists. The libraries were constructed with a variety of low molecular weight pyrrolidines, selected from (R)-2-methylpyrrolidine, (S)-2-methylpyrrolidine, and pyrrolidine.

Full text of DOI:10.1016/j.bmcl.2007.10.067

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 18 (2008) 355–359
In vitro SAR of pyrrolidine-containing histamine H3 receptor
antagonists: Trends across multiple chemical series
Diana L. Nersesian,* Lawrence A. Black, Thomas R. Miller, Timothy A. Vortherms,
Timothy A. Esbenshade, Arthur A. Hancock and Marlon D. Cowart
Neuroscience Research, Global Pharmaceutical Research and Development, Abbott Laboratories,
100 Abbott Park Road, Abbott Park, IL 60064, USA
Received 21 August 2007; revised 17 October 2007; accepted 19 October 2007
Available online 24 October 2007
Abstract—Structure–activity relationships (SAR) were analyzed within a library of diverse yet simple compounds prepared as his-
tamine H3 antagonists. The libraries were constructed with a variety of low molecular weight pyrrolidines, selected from (R)-2-meth-
ylpyrrolidine, (S)-2-methylpyrrolidine, and pyrrolidine.
Ó 2007 Elsevier Ltd. All rights reserved.
CN
The histamine H3 receptor (H3R), primarily located in
the CNS, is a presynaptic auto-receptor that has been
shown to regulate the release of histamine and other
important neurotransmitters such as serotonin, dopa-
mine, and acetylcholine.1 Due to the wide distribution
of H3R in the mammalian CNS, many therapeutic tar-
gets have been proposed and explored in animal models
of disease, including attention-deficit hyperactivity dis-
order (ADHD), Alzheimer’s disease (AD), schizophre-
O
NO2
Ar
N
N
N
O
R
(c) R=H, (R)-2-Me, (S)-2-Me
(a) ABT-239
(b) UCL 1972
Figure 1. (a) The structure of a benzofuran (ABT-239) with potent
in vitro activity and behavioral efficacy. (b) The structure of UCL 1972
one of the first examples of a potent non-imidazole H3 antagonists.3a
(c) General structure of histamine H3 antagonists prepared in library
form, specifically with pyrrolidines as the amine moiety.
nia, and obesity.2 The efforts of
a number of
laboratories have been directed toward discovering po-
tent H3 antagonists for the treatment of these and other
indications, with a wide variety of structural motifs
found to have potent histamine H3 antagonist activity.3
Recent efforts focus on so- called non-imidazoles. Most
H3 antagonists under active investigation share some
common broad structural elements: a basic amine, con-
nected through a flexible propyloxy or alkyl chain to a
lipophilic aromatic group.4
ABT-239, had particularly high potency, in both
in vitro and in vivo behavioral efficacy models. An early
SAR study examining receptor binding potencies sug-
gested that (R)-2-methylpyrrolidine was a superior
amine in the benzofuran-2-ethylamine series.5b To better
understand the SAR trends in other pyrrolidine-contain-
ing non-imidazoles outside the benzofuran-2-ethylamine
series, in more diverse structural families, we made and
tested libraries of new analogs spanning many different
core moieties (Fig. 1c). For each core moiety, three
Previous studies of histamine H3 receptor antagonists
have often incorporated either piperidine or pyrrolidine
moieties (Fig. 1a and b). The SAR of these basic amine
moieties was examined in a benzofuran series of H3
antagonists, and it was found that the methylated pyr-
rolidine had high in vitro potency.5 One compound,
Pyrrolidine
MsCl, NEt3
2(
R
)-MePyr
)-MePyr
HO
MsO
N
Ar
Ar
Ar
CH2Cl2 0°C to RT
R
2(
S
R= H
R
-methyl
-methyl
Keywords: Histamine H3; ADHD; Serotonin; Imidazoles.
*
S
Corresponding author. Tel.: +1 847 937 9669; fax: +1 847 935
5466; e-mail: diana.nersesian@abbott.com
Scheme 1. Synthesis of aryl amines.
0960-894X/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2007.10.067

356
D. L. Nersesian et al. / Bioorg. Med. Chem. Lett. 18 (2008) 355–359
Table 1. The in vitro H3 affinity (nM) of the compounds of the library7
#
Structure
R = H Ki (nM)
R = (S)-CH3 Ki (nM)
R = (R)-CH3 Ki (nM)
Hum
Rat
Hum
Rat
Hum
Rat
N
R
N
1
>350
>340
350
230
190
>360
>360
360
270
400
200
81
320
340
>330
200
>320
N
N
N
R
2
>320
320
>330
140
300
33
>320
>320
>320
160
340
230
260
220
72
300
70
320
320
150
81
N
R
3
N
R
N
4
160
34
N
S
N
R
5
>320
>340
>340
>340
340
17
S
N
R
6
110
43
34
140
43
N
7
6.0
96
N
R
NO2
8
20
280
240
35
N
R
N
R
9
96
21
OH
N
R
10
11
12
13
14
15
16
230
10
11
N
R
>340
>340
260
32
240
330
240
170
63
5.0
5.0
35
30
N
R
27
37
N
R
340
260
41
31
110
160
12
O
N
R
O
O
>330
370
65
16
8.9
18
2.3
132
N
R
219
>340
340
>340
N
H
N
R

D. L. Nersesian et al. / Bioorg. Med. Chem. Lett. 18 (2008) 355–359
357
Table 1 (continued)
#
Structure
R = H Ki (nM)
R = (S)-CH3 Ki (nM)
R = (R)-CH3 Ki (nM)
Hum
Rat
Hum
Rat
Hum
Rat
O
17
230
>360
100
>360
15
41
N
N
H
R
O
N
18
19
20
26
30
5.0
210
>240
40
28
14
1.6
440
89
3.5
62
N
R
N
N
1.3
7.1
3.9
R
O
5.9
0.39
R
amine analogs were made, with (R)-2-methylpyrrolidine
(2(R)-MePyr), (S)-2-methylpyrrolidine (2(S)-MePyr),
and pyrrolidine (Pyr) installed to allow direct compari-
son of in vitro potency across series.
containing (S)-2-methylpyrrolidine were more potent
(average of 4-fold) than the corresponding unmethylat-
ed pyrrolidine analogs. Analogs containing (R)-2-meth-
ylpyrrolidine were yet more potent (up to 14-fold) than
the corresponding non-methylated pyrrolidine analogs.
In the great majority of the series (18 of 20 series) the
(R)-2-methylpyrrolidine analogs exceeded the potency
of the (S)-2-methylpyrrolidine analogs.
To develop the SAR in the most timely and efficient
manner, molecular simplicity and synthetic tractability
were priorities. The compounds in each core series were
prepared in two steps as shown in Scheme 1, using com-
mercially available arylethylalcohols and the three target
pyrrolidines. The (R)-2-methylpyrrolidine and (S)-2-
methylpyrrolidine were prepared in enantiomerically
pure form (>98% ee) by fractional crystallization of
the tartrate salts.5d The alcohols were converted to
mesylates in high yields using mesyl chloride and trieth-
ylamine in CH2Cl2. The reaction was efficient, so the
mesylates were typically not purified. Mesylates were
found to react directly and cleanly with each of the three
amines in CH3CN at ambient temperature. Final prod-
ucts were purified to >90% (95% NMR or HPLC) by re-
versed phase HPLC, elution with acetonitrile/aqueous
CF3CO2H. Compounds were all assayed for in vitro his-
tamine H3 potency in competition binding assays using
human H3R from cell membranes and rat H3 receptors
from membranes derived from cortical homogenates.6
In all a total of 60 new analogs were prepared compris-
ing 20 different core moieties, each incorporating Pyr,
2(R)-MePyr, or 2(S)-MePyr (Table 1).
Next we examined SAR trends at the rat H3R and found
them similar to the human H3 receptor. Compounds
containing (R)-2-methylpyrrolidine were up to 9-fold
more potent than the corresponding unmethylated pyr-
rolidine analogs. (S)-2-Methylpyrrolidine containing
compounds were up to 2.5-fold more potent than unme-
thylated analogs. Overall, binding potencies at the hu-
man receptor in the present series were generally
greater than those at the rat receptor (as much as 10-
fold), consistent with some previous reports on other
non-imidazole structures.5c,d,8
Moving beyond the SAR analysis of the pyrrolidine
moiety, to an examination of the SAR of the core moi-
eties of the 20 series, the data in Table 1 point to weak
human H3R affinity for small polar aromatic groups
(e.g., compounds 1–3). However, compounds with polar
substituents in the para position show moderate affinity
(e.g., compounds 7 and 8). Enhanced affinity for the hu-
man H3 receptor is clearly seen with non-polar aromatic
groups (e.g., compounds 10–15) which show 10- to 100-
fold increases in potency compared to compounds
containing heterocycles and polar substituents (e.g.,
compounds 1–3 and 17). Of all the series made, those
with large non-polar groups show the highest affinity
(e.g., 18–20).
The three series incorporating pyrrolidine (Pyr), 2(S)-
methylpyrrolidine (2(S)-MePyr), and 2(R)-methylpyr-
rolidine (2(R)-MePyr) were compared using the data in
Table 1 (values are reported as nonamolar potencies;
n P 3 SEM typically <0.08) and Fig. 2. We first exam-
ined the SAR at the human H3 receptor, where several
important trends became clear.9 In no series did any
of the pyrrolidine analogs exceed the potency of either
the (R) or the (S)-methylpyrrolidine analogs, leading
to the conclusion that methylation of pyrrolidine moie-
ties increased the in vitro potency across all series. Aver-
ages of the ratios calculated from human H3 binding
assays indicated that for 18 of the 20 series, compounds
GTPcS binding using H3 receptor-transfected cells dem-
onstrated that compounds 19-(S)-CH3 and 20-(R)-CH3
function as antagonists at both the human (h) and rat
(r) H3 receptor subtypes (pKb = 7.75 0.06 (h),
6.98 0.06 (r); 8.93 0.04 (h), 8.24 0.05 (r), respec-
tively). The GTPcS functional data were consistent with

358
D. L. Nersesian et al. / Bioorg. Med. Chem. Lett. 18 (2008) 355–359
10
9
Pyr
2(S)-MePyr
2(R)-MePyr
Human H3
Binding
Affinity
(pKi)
8
7
6
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15 16 17 18 19 20
Compounds
9
8
7
6
Pyr
2(S)-MePyr
2(R)-MePyr
Rat H3
Binding
Affinity
(pKi)
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15 16 17 18 19 20
Compounds
Figure 2. Graphical illustration of SAR trends. Compound chemical series are shown on the x-axis, with the H3 receptor binding potency values on
the y-axis, expressed as pKi values for better graphical display. The pyrrolidine base groups are shown on the z-axis. (a) human histamine H3
receptor, (b) rat histamine H3 receptor.
R.; Haas, H. L. Pharmacol. Rev. 1997, 49, 253; (b) Arrang,
J.-M.; Garbarg, M.; Schwartz, J.-C. Nature 1983, 302, 832;
(c) Leurs, R.; Blandina, P.; Tedford, C.; Timmerman, H.
Trends Pharmacol. Sci. 1998, 19, 177; (d) Lovenberg, T. W.;
Roland, B. L.; Wilson, S. J.; Jiang, X.; Pyati, J.; Huvar, A.;
Jackson, M. R.; Erlander, M. G. Mol. Pharmacol. 1999, 55,
1101; (e) Leurs, R.; Bakker, R. A.; Timmerman, H.; de
Esch, I. J. P. Nat. Rev. Drug Discov. 2005, 4, 107.
the radioligand binding data where 19-(S)-CH3 had low-
er affinity than 20-(R)-CH3 for the H3 receptor. The
selectivity of these compounds was also tested at the
other histamine receptor subtypes. Compounds 19-(S)-
CH3 and 20-(R)-CH3 had Ki > 1000 nM at H1, H2,
and H4 receptors indicating that these compounds are
selective for the H3 receptor subtype.
2. (a) Stark, H.; Schlincher, E.; Schunack, W. Drugs Fut. 1996,
21, 507; (b) Tozer, M. J.; Kalindjian, S. B. Exp. Opin. Ther.
Patents 2000; (c) Bennani, Y. L.; Black, L. A.; Faghih, R.;
Hancock, A. A.; Decker, M. W. Behav. Brain Res. 2002,
131, 151; (d) Halpern, M. T. Curr. Opin. Cent. Peripher,
Nerv. Syst. Invest. Drugs 1999, 1, 524; (e) Ali, S. M.;
Tedford, C. E.; Gregory, R.; Handley, M. K.; Yates, S. L.;
Hirth, W. W.; Phillips, J. G. J. Med. Chem. 1999, 42, 903;
(f) Fox, G. B.; Pan, J. G.; Esbenshade, T. A.; Switzerland,
2004; p 97; (g) Babier, A. J.; Berridge, C.; Dugovic, C.;
Laposky, A. D.; Wilson, S. J.; Boggs, J.; Aluisio, L.; Lord,
B.; Mazur, C.; Pudiak, C. M.; Langlois, X.; Xiao, W.;
Apodaca, R.; Carruthers, N. I.; Lovenberg, T. W. Br. J.
Pharmacol. 2004, 143, 649; (h) Hancock, A. A. Curr. Opin.
Investig. Drugs 2003, 4, 1190; (i) Hancock, A. A.; Bennani,
Y. L.; Bush, E. N.; Esbenshade, T. A.; Faghih, R.; Fox, G.
B.; Jacobson, P.; Knourek-Segal, V.; Krueger, K. M.; Nuss,
M. E.; Pan, J. B.; Shapiro, R.; Witte, D. G.; Yao, B. B. Eur.
J. Pharmacol. 2004, 487, 183; (j) Malmolof, K.; Zaragoza,
F.; Golozoubova, V.; Refsgaard, H. H. F.; Cremers, T.;
Raun, K.; Wulff, B. S.; Johansen, P. B.; Westerink, B.;
Rimvall, K. Int. J. Obesity 2005, 29, 1402.
Results of this extensive SAR study of 60 compounds in
the presently examined 20 new series showed that the
substitution of the pyrrolidine moiety with a methyl
group at the 2-position reliably enhances in vitro po-
tency over unsubstituted analogs at both human and
rat histamine H3 receptors. (R)-2-Methylpyrrolidine
(95%) analogs were more potent than the (S)-2-methyl-
pyrrolidine analogs. The results thus support the
hypothesis that 2-methylpyrrolidine generally enhances
in vitro potency across diverse chemical classes, and that
the (R)-configuration is superior to the (S)-configura-
tion. We posit that this finding will prove useful to de-
sign new histamine H3 antagonists.
References and notes
1. (a) Hill, S. J.; Ganellin, C. R.; Timmerman, H.; Schwartz,
J.-C.; Shankley, N. P.; Young, J. M.; Schunack, W.; Levi,

D. L. Nersesian et al. / Bioorg. Med. Chem. Lett. 18 (2008) 355–359
359
3. (a) Celanire, S.; Wijtmans, M.; Talaga, P.; Leurs, R.; de
Esch, I. J. P. Drug Discov. Today 2005, 10, 1613; (b)
Esbenshade, T. A.; Fox, G. B.; Cowart, M. D. Mol.
Interventions 2006, 6, 77; (c) Arrang, J. M.; Morisset, S.;
Rouleau, A.; Gbahou, F.; Ligneau, X.; Tardivel-Lacombe,
J.; Stark, H.; Schunack, W.; Ganellin, C. R.; Schwartz, J.-
C. Int. Congr. Ser. 2003, 1249, 139; (d) Stark, H. Exp. Opin.
Ther. Pat. 2003, 13, 851.
5. (a) Cowart, M.; Faghih, R.; Curtis, M. P.; Gfesser, G. A.;
Bennani, Y. L.; Black, L. A.; Pan, L.; Marsh, K. C.;
Sullivan, J. P.; Esbenshade, T. A.; Fox, G. B.; Hancock, A.
A. J. Med. Chem. 2005, 48, 38; (b) Cowart, M. D.; Pratt, J.
K.; Stewart, A. O.; Bennani, Y. L.; Esbenshade, T. A.;
Hancock, A. A. Bioorg. Med. Chem. Lett. 2004, 14, 689; (c)
Black, L. A.; Nersesian, D. L.; Sharma, P.; Ku, Y.-Y.;
Bennani, Y. L.; Marsh, K. C.; Miller, T. R.; Esbenshade, T.
A.; Hancock, A. A.; Cowart, M. D. Bioorg. Med. Chem.
Lett. 2007, 17, 1443; (d) Gfesser, G. A.; Faghih, R.;
Bennani, Y. L.; Curtis, M. C.; Esbenshade, T. A.; Hancock,
A. A.; Cowart, M. D. Biorg. Med. Chem. Lett. 2005, 15,
2559; (e) Cowart, M. D.; Gfesser, G. A.; Browman, K. E.;
Faghih, R.; Miller, T. R.; Milicic, I.; Baranowski, J. L.;
Krueger, K. M.; Witte, D. G.; Molesky, A. L.; Komater, V.
A.; Buckley, M. J.; Diaz, B. J.; Gagne, G. D.; Zhou, D.;
Deng, X.; Pan, L.; Roberts, E. M.; Diehl, M. S.; Wetter, J.
M.; Marsh, K. C.; Fox, G. B.; Brioni, J. D.; Esbenshade, T.
A.; Hancock, A. A. J. Biochem. Pharmacol. 2007, 73, 1243.
6. Esbenshade, T. A.; Fox, G. B.; Krueger, L. M.; Miller, T.
R.; Kang, C. H.; Denny, L. I., et al. J. Pharmacol Exp.
Ther. 2005, 313, 165.
4. (a) Meier, G.; Apelt, J.; Reichert, U.; Grassman, S.; Ligneau,
X.; Elz, S.; Leurquin, F.; Ganellin, C. R.; Schwartz, J.-C.;
Schunack, W.; Stark, H. Eur. J. Pharmacol. Sci. 2001, 12,
249; (b) Faghih, R.; Dwight, W.; Vasudevan, A.; Dinges, J.;
Conner, S. E.; Esbenshade, T. A.; Bennani, Y. L.; Hancock,
A. A. Bioorg. Med. Chem. Lett. 2002, 12, 3077; (c) Apodaca,
R.; Dvorak, C. A.; Xiao, W.; Barbier, A. J.; Boggs, J. D.;
Wilson, S. J.; Lovenberg, T. W.; Carruthers, N. I. J. Med.
Chem. 2003, 46, 3938; (d) sbenshade, T. A.; Fox, G. B.;
Krueger, K. M.; Miller, T. R.; Kang, C. J.; Denny, L. I.;
Witte, D. G.; Yao, B. B.; Pan, L.; Wetter, J.; Marsh, K.;
Bennani, Y. L.; Cowart, M. D.; Sullivan, J. P.; Hancock, A.
A. J. Pharmacol. Exp. Ther. 2005, 313, 165; (e) Fox, G. B.;
Esbenshade, T. A.; Pan, J. B.; Radek, R. J.; Krueger, K. M.;
Yao, B. B.; Browman, K. E.; Buckley, M. J.; Ballard, M. E.;
Komater, V. A.; Miner, H.; Zhang, M.; Faghih, R.; Rueter,
L. E.; Bitner, R. S.; Drescher, K. U.; Wetter, J.; Marsh, K.;
Lemaire, M.; Porsolt, R. D.; Bennani, Y. L.; Sullivan, J. P.;
Cowart, M. D.; Decker, M. W.; Hancock, A. A. J. Pharma-
col. Exp. Ther. 2005, 313, 176; (f) Veber, D. F.; Johnson, S.
R.; Chen, H.-Y.; Smith, B. R.; Ward, K. W.; Kopple, K. D. J.
Med. Chem. 2002, 45, 2615; (g) Wenlock, M. C.; Austin, R.
P.; Barton, P.; Davis, A. M.; Leeson, P. D. J. Med. Chem.
2003, 46, 1250.
7. These were determined from the mean of at least three pKi
determinations, for the compounds, the standard error of
the mean pKi (SEM) were typically <0.08.
8. Faghih, R.; Dwight, W.; Pan, J. B.; Fox, G. B.; Krueger, K.
M.; Esbenshade, T. A.; McVey, J. M.; Marsh, K.; Bennani,
Y. L.; Hancock,A.A. Bioorg. Med. Chem.Lett.2002, 13, 1325.
9. Potencies were compared by calculation of the ratio of
potencies across series according to these formulae:
2ðRÞꢀMePyr 2ðRÞꢀMePyr 2ðSÞꢀMePyr
;
;
.
2ðSÞꢀMePyr
Pyr
Pyr