Novel 1H-pyrrolo[2,3-c]pyridines as acid pump antagonists (APAs)

Article abstract of DOI:10.1016/j.bmcl.2010.06.143

A series of 1H-pyrrolo[2,3-c]pyridines as acid pump antagonists (APAs) was synthesized and the inhibitory activities against H⁺/K⁺ ATPase isolated from hog gastric mucosa were determined. After elaborating on substituents at N1, C5, and C7 position of 1H-pyrrolo[2,3-c]pyridine scaffold, we have observed that compounds 14f and 14g are potent APAs with H ⁺/K⁺ ATPase IC₅₀ = 28 and 29 nM, respectively.

Full text of DOI:10.1016/j.bmcl.2010.06.143

Bioorganic & Medicinal Chemistry Letters 20 (2010) 5237–5240
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Novel 1H-pyrrolo[2,3-c]pyridines as acid pump antagonists (APAs)
Young Ae Yoon, Dong Hoon Kim, Byoung Moon Lee, Tae Kyun Kim, Myung Hun Cha, Jae Young Sim,
*
Jae Gyu Kim
Yuhan Research Institute, 416-1, Gongse-dong, Giheung-gu, Yongin-si, Gyeonggi-do, Korea 446 902, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of 1H-pyrrolo[2,3-c]pyridines as acid pump antagonists (APAs) was synthesized and the inhibi-
tory activities against H+/K+ ATPase isolated from hog gastric mucosa were determined. After elaborating
on substituents at N1, C5, and C7 position of 1H-pyrrolo[2,3-c]pyridine scaffold, we have observed that
compounds 14f and 14g are potent APAs with H+/K+ ATPase IC50 = 28 and 29 nM, respectively.
Ó 2010 Elsevier Ltd. All rights reserved.
Received 5 February 2010
Revised 11 June 2010
Accepted 30 June 2010
Available online 23 July 2010
Keywords:
Gastroesophageal reflux disease
Ulcer
H+/K+ ATPase
Acid pump antagonist (APA)
Gastroesophageal reflux disease (GERD) is a common acid-
related disorder that occurs in approximately 10–20% of Western
people and about 5% of people in Asia, it is defined as at least a
weekly episode of heartburn and/or acid regurgitation.1 The severity
of the symptoms and esophageal mucosal damage were correlated
well with the exposure of the esophagus to gastric acid.2 Therefore,
acid suppression is considered as the first-line therapy for GERD, and
many drugs that suppress the acid secretion are now available.
These conventional agents are histamine 2 receptor antagonists
(H2RAs) and proton pump inhibitors (PPIs). Presently, PPIs are recog-
nized as the ‘treatment of choice’ in most countries.3 However, PPIs
still continue to have their set of limitations. The currently available
PPIs require around 3–5 days to achieve maximum acid inhibition at
existent therapeutic doses, primarily due to their chemical struc-
tures and irreversible inhibition of H+/K+ ATPase.4 Failure to demon-
strate a sustained acid inhibition throughout the day and night, in
spite of twice daily administration, and nocturnal acid breakthrough
(NAB) are found to be common in patients taking PPIs.5 Therefore,
many novel strategies to address the unmet needs of existent PPI
therapy have been investigated, and acid pump antagonists (APAs)
could play a promising role, as they provide faster onset and longer
duration of action than conventional PPIs by virtue of their ability to
reversibly bind to the proton pump.6
R3
R6
N
R2
N
X
R'
1
R2 = substituted small alkyl, etc.
R3 = substituted small alkyl, etc.
R6 = H, amide, etc.
R' = alkyl, halogen, etc.
X = O, N, etc.
Figure 1. Structure of imidazo[1,2-a]pyridine APAs 1.
were shown to inhibit the gastric acid secretion by reversible and K+
competitive binding to H+/K+ ATPase, and they also displayed excel-
lent antisecretory properties.7–9
In the course of our efforts to develop novel and potent APAs,
we were able to identify APAs that have a novel heterocyclic scaf-
fold different from the well-known imidazo[1,2-a]pyridine. Here,
we report the synthesis and pharmacological evaluation of 1H-pyr-
rolo[2,3-c]pyridine derivatives of the general formula 2 as APAs
(Fig. 2).
APAs are lipophilic and weak bases that have diverse structures
such as, imidazopyridines, pyrimidines, imidazonaphthyridines,
quinolines, etc.6 The APAs studied most extensively so far rely on
substituted imidazo[1,2-a]pyridine derivatives (1) (Fig. 1). And they
Reaction of commercially available 2-chloro-3-nitropyridine 3
with respective benzyl alcohols using tris[2-(2-methoxyethoxy)-
ethyl]amine (TDA) as a phase transfer catalyst led to 2-benzyloxy
* Corresponding author.
E-mail address: yayoon@yuhan.co.kr (J.G. Kim).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.06.143

5238
Y. A. Yoon et al. / Bioorg. Med. Chem. Lett. 20 (2010) 5237–5240
Cl
N
Cl
R5
a
b
N
N
NO2
NO2
N
Cl
O
R1
O
7
R
F
8
2
R1 = H, substituted alkyl, alkenyl, benzyl, etc.
Cl
NC
R5 = H, amide
c
d
R = H, F, Cl
N
F
N
N
N
H
Figure 2. Structure of 1H-pyrrolo[2,3-c]pyridine APAs 2.
H
O
O
substituted 3-nitropyridines 4 in good yield (84–95%). Subse-
quently, substituted 1H-pyrrolo[2,3-c]pyridines 5 was prepared by
Bartoli reaction as described in the literature.10 Reaction of 2-ben-
zyloxy substituted 3-nitropyridines 4 with 1-methyl-1-propenyl
magnesium bromide 0.5 M in anhydrous THF under nitrogen
atmosphere at ꢀ78 °C provided 7-benzyloxysubstituted 1H-pyrrolo-
[2,3-c]pyridines 5 in moderate yield (12–39%). After deprotonation of
7-benzyloxy substituted 1H-pyrrolo[2,3-c]pyridines 5 with potas-
sium t-butoxide and 18-crown-6, transformation with respective
substituted alkyl or benzyl halide afforded corresponding N-1-alkyl-
ated pyrrolo[2,3-c]pyridine derivatives 6 in moderate to good yield
(41–76%, Scheme 1).
F
9
10
O
NC
H2N
e
N
N
F
N
N
R1
R1
O
O
5-Amide substituted 1H-pyrrolo[2,3-c]pyridine derivatives
were obtained starting from commercially available 2,6-dichloro-
F
11
12
11a: R1=CH2CH=CH2
11b: R1=CH2Ph
12a: R1=CH2CH=CH2
12b: R1=CH2Ph
a
b
N
N
NO2
NO2
f
Cl
O
O
O
N
3
R5'
HO
g
N
R5''
N
N
N
R
R1
R1
O
O
4(R=H, 2-F, 4-F, 4-Cl)
c
F
F
N
N
N
N
R1
13
14
H
14a: R1=CH2CH=CH2, R5'=H, R5''=CH3
14b: R1=CH2CH=CH2, R5'=H, R5''=cPro
14c: R1=CH2CH=CH2, R5'=H, R5''=4-pyridyl
14d: R1=CH2Ph, R5'=H, R5''=CH3
13a: R1=CH2CH=CH2
13b: R1=CH2Ph
O
R
O
14e: R1=CH2Ph, R5'=H, R5''=cPro
14f: R1=CH2Ph, R5'=R5''=CH3
R
14g: R1=CH2Ph, NR5'R5''=morpholinyl
6
5
Scheme 2. Reagents and conditions: (a) benzyl alcohol, TDA, KOH, K2CO3, toluene,
rt, 40 min, 69%; (b) 1-methyl-1-propenyl magnesium bromide, THF, ꢀ78 °C, 1 h,
30%; (c) CuCN, DMF, 160 °C, 2 days, 15%; (d) alkyl halide, NaH, DMF, rt, 45–60%; (e)
6a: R1 = CH2CH=CH2, R = 4-F
6b: R1 = CH2CH(CH3)2, R = 4-F
6c: R1 = CH2CH(CH3)2, R = 4-Cl
6d: R1 = CH2CH2CH3, R = 4-F
6e: R1 = CH2[1,3]dioxolane, R = 4-F
6f: R1 = CH2cPro, R = 4-F
5a: R=H
5b: R=2-F
5c: R=4-F
5d: R=4-Cl
KOH, EtOH/H2O, reflux, 2 h, 80–84%; (f) KOH, EtOH/H2O, reflux, 3 days, 75–80%; (g)
0
EDC, HOBT, DIPEA, R5 R5 NH, CH2Cl2, overnight, 50–77%.
00
6g: R1 = CH2Ph, R = 4-Cl
3-nitropyridine 7 (Scheme 2). 5-Chloro-7-(4-fluorobenzyloxy)-2,3-
dimethyl-1H-pyrrolo[2,3-c]pyridine intermediate 9 was synthe-
sized following the same procedures as shown in Scheme 1. For
the introduction of nitrile group at C5, compound of formula 9 was
Scheme 1. Reagents and conditions: (a) benzyl alcohols, TDA, KOH, K2CO3, toluene,
rt, 40 min, 84–95%; (b) 1-methyl-1-propenyl magnesium bromide, THF, ꢀ78 °C, 1 h,
12–39%; (c) alkyl halide, KOtBu, 18-crown-6, THF, rt, 12 h, 41–76%.

Y. A. Yoon et al. / Bioorg. Med. Chem. Lett. 20 (2010) 5237–5240
5239
Table 1
compounds with significantly increased inhibitory activity were
obtained. Compounds 6a–b and 6d–f were shown to have dramat-
ically increased activity compared to that of the compound of for-
mula 5c devoid of substituent at N1 (R1 = H). Among them, 6a
substituted by allyl group at N1 showed much higher activity
H+/K+ ATPase inhibition assay results for 5, 6, 12, and 14
R5
N
N
(IC50 = 0.125 lM) than other compounds 6b, 6d, 6e, and 6f substi-
R1
O
tuted with alkyl groups of the same length at N1, which means that
the substituents with sp2 character at N1 of 1H-pyrrolo[2,3-c]pyr-
idine are favored. The same trend was also exhibited by com-
pounds 6c (R1 = CH2CH(CH3)2) and 6g (R1 = CH2Ph). Moderate
improvement in inhibitory activity against H+/K+ ATPase was made
by 6g substituted by benzyl group at N1 compared to that of 6c
(IC50 = 0.187 and 0.205 lM, respectively).
Based on the results above, we focused on the substitution at C5.
Various C5-amide substituted 1H-pyrrolo[2,3-c]pyridines (R = 4-F,
R
5, 6, 13
Compds
R1
R5
R
H+/K+ ATPase
IC50 M)
(
l
5a
5b
5c
6a
6b
6c
6d
6e
H
H
H
H
H
H
H
H
H
H
H
H
50.9%a
32.1%a
60.3%a
0.125
0.196
0.205
0.302
0.173
0.181
0.187
80.3%a
16.1%a
78.4%a
0.408
0.735
39.4%b
0.738
0.028
0.029
2-F
4-F
4-F
4-F
4-Cl
4-F
4-F
4-F
4-Cl
4-F
4-F
4-F
4-F
4-F
4-F
4-F
4-F
4-F
100
80
CH2CH@CH2
CH2CH(CH3)2
CH2CH(CH3)2
CH2CH2CH3
CH2[1,3] dioxolane
CH2cPro
CH2Ph
CH2CH@CH2
CH2Ph
CH2CH@CH2
CH2CH@CH2
CH2CH@CH2
CH2Ph
6f
6g
H
H
60
12a
12b
14a
14b
14c
14d
14e
14f
14g
CONH2
CONH2
40
CONH(CH3)
CONH(cPro)
CONH(4-pyridyl)
CONH(CH3)
CONH(cPro)
CON(CH3)2
CO(morpholinyl)
14g
14f
20
CH2Ph
CH2Ph
CH2Ph
0
-8.5
-8.0
-7.5
Log (M)
-7.0
-6.5
a
Inhibition percentage at 4
Inhibition percentage at 1
l
l
M.
M.
b
Figure 3. Dose-dependent inhibitions of H+/K+ ATPase by 1H-pyrrolo[2,3-c]pyri-
dine APAs 14f and 14g.
treated with excess copper (I) cyanide in DMF at 160 °C. The low
yield (15%) for 10 was to due to the low reactivity of Cl at C5. Depro-
tonation of 10 with NaH, and subsequent reaction with respective
substitutedalkylor benzylhalide afforded N-1-alkylated derivatives
18.0
13.0
11 (45–60%). The hydrolysis of 11 under basic condition yielded
5
00
carboxylic acid derivatives 13 via carboxamides (12, R5 = R = H)
in good yield (75–80%). Finally, coupling of compounds of formula
13 with respective amines using 1-(3-dimethylaminopropyl)-3-
ethylcarbodiimide hydrochloride (EDC), 1-hydroxybenzotriazole
hydrate (HOBT), and diisopropylethylamine (DIPEA) led C5-amide
substituted derivatives 14 (50–77%).
0
25nM
8.0
3.0
12.5nM
6.25nM
3.125nM
control
Table 1 enlists the inhibitory activities of 1H-pyrrolo [2,3-c]pyr-
idines 5, 6, 12, 14 against H+/K+ ATPase isolated from hog gastric
mucosa.11
-0.1
-2.0 0
0.1
0.2
1/[KCl](mM-1
)
-7.0
The inhibitory activity against H+/K+ ATPase of compounds
without substituents at N1 and C5 (R1 = R5 = H) was evaluated as
a starting point. Compounds 5a–c were shown to have near micro-
molar inhibitory concentration. After exploring the substituents of
benzyloxy groups at C7 to improve inhibitory activity against H+/K+
ATPase, we discovered the compound of formula 5c which substi-
tuted by 4-fluorobenzyloxy group at C7 of 1H-pyrrolo[2,3-c]-
pyridine (R = 4-F) with moderately increased inhibitory activity
Figure 4. Lineweaver–Burk plot showing H+/K+ ATPase activity versus K+ concen-
tration for various concentrations of 14f.
70.0
50.0
50nM
25nM
(inhibition percentage at 4 lM = 60.3%) compared to other substit-
30.0
10.0
12.5nM
6.25nM
3.125nM
control
uents (R = H and 2-F), indicating that the substituents at para-posi-
tion of the benzyloxy group are favored. And the replacement of F
with Cl at para-position of the benzyloxy group had no notable
change in the inhibitory activity against H+/K+ ATPase exemplified
-0.08 -0.04
0
0.04 0.08 0.12 0.16 0.2 0.24
1/[KCl](mM-1
-0.12
-10.0
by compounds 6b and 6c (IC50 = 0.196 and 0.205 lM, respectively).
)
Therefore, with F at para-position of the benzyloxy group of
1H-pyrrolo[2,3-c]pyridines held constant (R = 4-F), we further
elaborated on the effect of substituents at N1 on the inhibitory
activity against H+/K+ ATPase (6a–b, 6d–f). By alkylating at N1,
-30.0
Figure 5. Lineweaver–Burk plot H+/K+ ATPase activity versus K+ concentration for
various concentrations of 14g.

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Y. A. Yoon et al. / Bioorg. Med. Chem. Lett. 20 (2010) 5237–5240
R1 = allyl or benzyl) were synthesized and their inhibitory activity
against H+/K+ ATPase was tested. C5-primary amide (R5 = CONH2)
and secondary amide (R5 = CONH(CH3), CONH(cPro), and CONH(4-
pyridyl)) substituted 1H-pyrrolo[2,3-c]pyridines 12a, 14a, 14b,
and 14c were shown to have lower inhibitory activity than that of
unsubstituted one 6a. However, it was notable that C5-secondary
amide substituted compounds were more potent than C5-primary
amide substituted compounds: 14b (R5 = CONH(cPro)), and 14c
(R5 = CONH(4-pyridyl)) were shown to have more improved inhib-
3. Robinson, M. Eur. J. Gastroenterol. Hepatol. 2001, 13, S43.
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5. (a) Hatlebakk, J. G.; Katz, P. O.; Kuo, B.; Castell, D. O. Aliment. Pharmacol. Ther.
1998, 12, 1235; (b) Katz, P. O.; Hatlebakk, J. G.; Castell, D. O. Aliment. Pharmacol.
Ther. 2000, 14, 709; (c) Katz, P. O.; Anderson, C.; Khoury, R.; Castell, D. O.
Aliment. Pharmacol. Ther. 1998, 12, 1231.
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7. (a) Ene, M. D.; Khan-Daneshmend, T.; Roberts, C. J. Br. J. Pharmacol. 1982, 76,
389; (b) Long, J. F.; Chiu, P. J.; Derelanko, M. J.; Steinberg, M. J. Pharmacol. Exp.
Ther. 1983, 226, 114; (c) Keeling, D. J.; Laing, S. M.; Senn-Bilfinger, J. Biochem.
Pharmacol. 1988, 37, 2231; (d) Van der Hijden, H. T.; Koster, H. P.; Swarts, H. G.;
De Pont, J. J. Biochim. Biophys. Acta 1991, 1061, 141.
8. (a) Kaminski, J. J.; Bristol, J. A.; Puchalski, C.; Lovey, R. G.; Elliott, A. J.; Guzik, H.;
Solomon, D. M.; Conn, D. J.; Domalski, M. S. J. Med. Chem. 1985, 28, 876; (b)
Kaminski, J. J.; Hilbert, J. M.; Pramanik, B. M.; Solomon, D. M.; Conn, D. J.; Rizvi,
R. K.; Elliott, A. J.; Guzik, H.; Lovey, R. G.; Domalski, M. S.; Wong, S. C.; Puchalski,
C.; Gold, E. H.; Long, J. F.; Chiu, P. J. S.; McPhail, A. T. J. Med. Chem. 1987, 30,
2031; (c) Kaminski, J. J.; Perkins, D. G.; Frantz, J. D.; Solomon, D. M.; Elliott, A. J.;
Chiu, P. J. S.; Long, J. F. J. Med. Chem. 1987, 30, 2047; (d) Kaminski, J. J.;
Puchalski, C.; Solomon, D. M.; Rizvi, R. K.; Conn, D. J.; Elliott, A. J.; Lovey, R. G.;
Guzik, H.; Chiu, P. J. S. J. Med. Chem. 1989, 32, 1686; (e) Kaminski, J. J.;
Wallmark, B.; Briving, C.; Andersson, B. M. J. Med. Chem. 1991, 34, 533; (f)
Kaminski, J. J.; Doweyko, A. M. J. Med. Chem. 1997, 40, 427.
itory activity than 12a (R5 = CONH2, IC50 = 0.408 and 0.735
inhibition percentage at 4 M = 80.3%). A similar trend was also ob-
lM, vs
l
served for N-1-benzyl substituted 1H-pyrrolo[2,3-c]pyridines 12b
(R5 = CONH2), 14d (R5 = CONH(CH3)) and 14e (R5 = CONH(cPro)).
Therefore, C5-tertiary amide substituted 1H-pyrrolo[2,3-c]pyri-
dines was expected to show more improved inhibitory activity
against H+/K+ ATPase compared to C5-secondary amide substituted
ones, which were proved by the compounds 14f and 14g. Com-
pounds 14f (R5 = CON(CH3)2) and 14g (R5 = CO(morpholinyl))
showed dose-dependent inhibitory activity against H+/K+ ATPase
with IC50 = 28 and 29 nM, respectively (Fig. 3).
9. (a) Gedda, K.; Briving, C.; Svensson, K.; Maxvall, I.; Andersson, K. Biochem.
Pharmacol. 2007, 73, 198; (b) Kirchhoff, P.; Andersson, K.; Socrates, T.; Sidani,
S.; Kosiek, O.; Geibel, J. P. Am. J. Physiol. Gastrointest. Liver Physiol. 2006, 291,
G838.
10. Zhang, Z.; Yang, Z.; Meanwell, N. A.; Kadow, J. F.; Wang, T. J. Org. Chem. 2002,
67, 2345.
Compounds 14f and 14g inhibited H+/K+ ATPase activity in a K+-
competitive manner with Ki = 13.6 and 10.7 nM, respectively (Figs.
4 and 5).12 The Lineweaver–Burk plots showed H+/K+ ATPase activ-
ity versus K+ concentration for various concentrations of 14f and
14g, and demonstrated a common intercept with the Y-axis, which
is characteristic of competitive inhibition.
In summary, we have prepared a series of novel 1H-pyrrolo [2,3-
c]pyridines as APAs. Optimization of substituents at N1, C5, and C7
led to some potent 1H-pyrrolo[2,3-c]pyridines APAs. Especially,
compounds 14f and 14g were shown to have excellent inhibitory
activity against H+/K+ ATPase (IC50 = 28 and 29 nM, respectively).
Therefore, compounds 14f and 14g are promising leads for further
development as APAs, and this series of 1H-pyrrolo[2,3-c]pyridine
derivatives would be explored for further optimization.
11. Ion-leaky membrane vesicle enriched in gastric H+/K+-ATPase was derived
from pig stomach as per the method described by Saccomani et al. with
suitable modifications (Saccomani, G.; Stewart, H. B.; Show, D.; Lewin, M.;
Sachs, G. Biochem. Biophy. Acta 1977, 465, 311). The inhibitory effects of the K+
specific H+/K+-ATPase activity was calculated based on the difference between
the activity of H+/K+-ATPase activity with and without K+ ion. The lyophilized
vesicle in 5 mM pipes/Tris buffer (pH 6.1) was pre-incubated in the presence of
various concentrations of compounds. After 5 min of preincubation, negative
and positive buffers were respectively added to the previous reaction mixture.
As a substrate ATP was added to the reaction buffer, and incubated for 30 min
at 37 °C. Enzymatic activity was stopped by adding colorimetric reagent and
the amount of mono phosphate (Pi) in the reaction was measured at 620 nm
using the micro plate reader. The difference between the Pi production with
and without K+ is taken as K+ stimulated H+/K+-ATPase activity. The IC50s of test
compounds were calculated from each % inhibition value of compounds using
the method as described be Litchfield–Wilcoxon (Litchfield, J. T.; Wilcoxon, F. J.
Pharmacol. Exp. Ther. 1949, 95).
Acknowledgment
12. The inhibition kinetics were determined in relation to the activation of H+/K+-
ATPase activity by K+. The lyophilized vesicle in 5 mM pipes/Tris buffer (pH
6.1) was pre-incubated in the presence of various concentrations of
compounds. Compounds were examined for its ability to inhibit the
generation of inorganic phosphate induced by various concentrations of KCl.
The difference between the Pi production with K+ and without K+ is taken as K+
stimulated H+/K+-ATPase activity. The K+-stimulated H+/K+-ATPase activities
were analyzed by Lineweaver–Burk plot.
This study was supported by Ministry for Health, Welfare and
Family Affairs, Republic of Korea (A081052).
References and notes
1. Dent, J.; El-Serag, H. B.; Wallander, M. A.; Johansson, S. Gut 2005, 54, 710.
2. Bell, N.; Burget, D.; Howden, C.; Wilkinson, J.; Hunt, R. Digestion 1992, 51, 59.