A reverse method for diversity introduction of benzimidazole to synthesize H+/K+-ATP enzyme inhibitors

Article abstract of DOI:10.1016/j.bmcl.2011.05.080

A series of 2-[(2-pyridylmethyl)sulfinyl]benzimidazole derivatives were synthesized via a solution phase synthetic route using a reversal method of diversity introduction. Using this synthetic strategy, we obtained two key intermediates (4-A and 4-B) simultaneously, which allows us to introduce diversity points onto the benzimidazole part of the final product under reliable reaction conditions to identify potent H⁺/K⁺-ATP enzyme inhibitors. Compound 14l (IC₅₀ = 1.6 × 10^-5 M) was comparable with H⁺/K⁺-ATP enzyme inhibitor in vitro.

Full text of DOI:10.1016/j.bmcl.2011.05.080

Bioorganic & Medicinal Chemistry Letters 21 (2011) 4189–4192
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
A reverse method for diversity introduction of benzimidazole to synthesize
H+/K+-ATP enzyme inhibitors
Yu Yan a, Zijie Liu a, Jianjun Zhang a, Ruiming Xu a, Xiao Hu a, Gang Liu a,b,
⇑
a Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, 2 Nanwei Rd., Xicheng Dist., Beijing 100050, PR China
b Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Haidian Dist., Beijing 100084, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of 2-[(2-pyridylmethyl)sulfinyl]benzimidazole derivatives were synthesized via a solution phase
synthetic route using a reversal method of diversity introduction. Using this synthetic strategy, we
obtained two key intermediates (4-A and 4-B) simultaneously, which allows us to introduce diversity
points onto the benzimidazole part of the final product under reliable reaction conditions to identify
potent H+/K+-ATP enzyme inhibitors. Compound 14l (IC50 = 1.6 Â 10À5 M) was comparable with H+/K+-
ATP enzyme inhibitor in vitro.
Received 26 March 2011
Revised 21 May 2011
Accepted 23 May 2011
Available online 27 May 2011
Keywords:
Ó 2011 Elsevier Ltd. All rights reserved.
Benzimidazole
H+/K+-ATP enzyme inhibitors
DFDNB
Solution phase synthesis
Proton pump inhibitors (PPIs) belong to a class of therapeutic
agents for most acid-related diseases, including gastroesophageal
reflux disease, peptic ulcer diseases, and acute gastrointestinal
bleeding.1–3 Benzimidazole-type agents contribute significantly to
these agents, such as omeprazole and pantoprazole.4–7 Current
benzimidazole-type PPIs, which consist of two fragments of benz-
imidazole and pyridine, act as prodrugs owing to protonation of
the pyridine ring under a gastrointestinal acid environment, result-
ing in a chemical rearrangement of the entire molecule (Fig. 1).8–10
Recently, PPIs have been investigated using various substitutions
on the pyridine ring, but there has been less effort on modifying
the benzimidazole moiety. Our laboratory has developed a highly
efficient method to generate benzimidazoles at four diversity
points using 1,5-difluoro-2,4-dinitrobenzene (DFDNB, 1),11,12
where the 2,4-dinitro groups were simultaneously reduced. In this
Letter, a selective reduction of the dinitro groups is optimized to al-
low two disparate intermediates to occur simultaneously (4-A and
4-B), which enables us to generate subsequent substituent diversi-
ties with anticipated diversification of benzimidazole under reli-
able reaction conditions.
Two disparate intermediates (4-A and 4-B) were successfully ob-
tained at the same time (Scheme 1).
From intermediate 4-A in Scheme 2, an imidazole ring could be
constructed in the next reaction step from the cyclocondensation
of 4-A with a sulfur-bearing reagent, such as potassium ethyl xan-
thate,15 sodium ethyl xanthate,15 di(1H-imidazol-1-yl)methanethi-
one,16 or carbon disulfide (CS2).17 In our work, CS2 was selected to
react with intermediate 4-A, on taking availability and postpro-
cessing into consideration. Crude intermediate 2-mercapto
benzimidazole derivative 5 was obtained with a purity >95%
determined using HPLC–MS analysis, which was reacted directly
with 2-chloromethyl pyridine hydrochloride to obtain 6. The
2-chloromethyl pyridine hydrochlorides that appeared in the
structure of omeprazole and pantoprazole were chosen to investi-
gate the influence of the diverse substituents of benzimidazole
pharmacophore on the antiulcer activity.
Various oxidation conditions were tested that did not give the
anticipated product 7 from 6, including UHP (an adduct of peroxide
and urea)/anhydride,18 sodium hypochlorite (NaClO),19,20 hydro-
gen peroxide (H2O2),21 AcOOH, Na2CO3/iPrOH, and DMSO. It was
presumed that the oxidative capability of these oxidants was too
high. Therefore, the mild oxidant m-chloroperbenzoic acid
(mCPBA) was investigated in a treatment with 6 in a two-phase
mixed solution of dichloromethane (DCM) and a weakly alkaline
(KHCO3) saturated aqueous solution maintained near to 0 °C22 that
showed the capability to generate 7 in a high yield. The remaining
nitro group of 7 was fully reduced by Na2S2O4/K2CO323 to give 8 in
both a high yield and a purity as determined by HPLC analysis. The
anticipated final product of 9 was attained through the acylation of
8 at the final step. Compound 9 was purified from recrystallization
Briefly, the two fluorine atoms of 1 were selectively and quan-
titatively replaced first by ammonia and subsequently by alcohols,
phenols, or primary or secondary amines to give 3 as described
previously.11,12 A stepwise reduction of the 2,4-dinitro groups is
proposed in this Letter using sodium hydrosulfide (NaHS).13,14
⇑
Corresponding author. Tel.: +86 10 63167165/62797740; fax: +86 10 6316
5246/62797740.
E-mail address: gliu@imm.ac.cn (G. Liu).
0960-894X/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2011.05.080

4190
Y. Yan et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4189–4192
From 4-B, a reversal route of R2 introduction was performed
(Scheme 3). The difference between 4-A and 4-B allowed us to
choose the reaction conditions to introduce the 4-position R2 group
before, or after connection of the pyridine moiety. Interestingly,
the acylation of 4-B only occurred at the 4-NH2 site rather than
at the 1-NH2 site in the preparation of 10 in the presence of an
equivalent amount of the previously mentioned anhydride or acyl
chloride. In this route, crude 10, without any further purification,
could be reduced directly using Pd-C/HCOONH4, affording 11
quickly and in high purity. The filtrate of 11 was consequently re-
acted with CS2 in the presence of TEA to obtain 12 in 2–3 h at 45 °C
with a purity >95% as determined by HPLC–MS analysis. Therefore,
the crude product of 12 was further reacted with 2-chloromethyl
pyridine hydrochloride under the conditions shown in Scheme 2,
to give 13. Finally, 13 was oxidized by m-chloroperbenzoic acid
(mCPBA) to obtain the final product 14 (Table 1 and Fig. 3).
Each synthetic route had an impact on its own sequel. Scheme 2
allowed us to introduce the diversity in the final step, and im-
proved the synthetic throughput of R2 introduction. Scheme 3
had the advantage of an easy work-up without further purification
of the intermediates. Most importantly, the reversal strategy of
diversity introduction allowed us to select the reaction conditions
to synthesize various molecules.
R3
R4
O
R3
R4
N
R5
H+
R1
S
H
N
N
R5
N
H
R1
N
S
N
H
O
b
R3
R3
N
H2O
N
N
R1
N
R4
R1
N
R4
N
H
-H2O
S
R5
S
R5
OH
d
c
-H2O
R3
Enz SH
Enz SH
N
N
R1
N
R4
H
S
R5
All the 2-[(2-pyridylmethyl)sulfinyl]benzimidazole derivatives
(9a–r and 14a–r) were investigated for in vitro inhibitory activity
against the H+/K+-ATP enzyme from porcine gastric mucosa. The
primary inhibitory rate (in %) on the H+/K+-ATP enzyme was deter-
mined at a concentration of 10 M, whereas the positive control of
omeprazole exhibited an inhibition of 39% (Table 1). Among these
compounds, 14g, 14b, 14l, 14n, and 14d exhibited an inhibitory
percentage of 48%, 58%, 62%, 39%, and 41%, respectively, at the con-
centration level used. Compound 14l was tested further to obtain
its IC50 value at a concentration of 1.6 Â 10À5 M (Fig. 4).
S
Enz
Figure 1. Mechanism of acid transformation of 2-[(2-pyridylmethyl)sulfinyl]benz-
imidazole derivatives. First, the gastrointestinal acid environment results in the
protonation of the pyridine ring to give an intermediate, b. Subsequently, the
reaction proceeds via a chemical rearrangement, and sulfenic acid c is obtained,
forming sulfenamide d by dehydration. Either the sulfenic acid c or the sulfenamide
d is the active enzyme inhibitor, and this reacts with cysteine from the gastric H+/
K+-ATP enzyme.8–10
From the data shown in Table 1, the variability of benzimid-
azole moiety provided potent compounds that efficiently inhibited
the H+/K+-ATP enzymatic activity.
or silica gel column chromatography, and was fully characterized
using HRMS (TOF) and 1H NMR (see Table 1 and Fig. 2).
R1
NH2
NH2
R1
NH2
NO2
O2N
F
F
F
NH2
NO2
a
b
c
4-A
4-B
O2N
O2N
R1
NH2
NO2
O2N
NO2
1
2
3
H2N
3a R1=MeO
3b R1=ArO
3c R1=R6R7N
Scheme 1. Synthesis of 4-A and 4-B. Reagents and conditions: (a) NH3ÁH2O, THF, rt, 30 min; (b) CH3OH, 1 M KOH, THF, rt, 30 min, ArOH, K2CO3, acetone, 50 °C, 5–10 h, or
R6R7NH, DIPEA, THF, 65 °C, 5–10 h; (c) NaHS, CH3OH, H2O, reflux, 3–5 h.
R1
R3
R4
R1
R1
NH2
NH2
N
N
d
e
f
S
SH
R5
N
H
N
H
O2N
O2N
O2N
N
4-A
5
6
R1
R1
R1
H2N
R3
R4
O
R3
R4
N
O
R3
R4
O
N
N
g
h
S
S
S
R2
R5
R5
R5
N
H
N
H
N
H
N
O2N
H
N
N
N
7
8
9
R2= RCO
R4
Scheme 2. Synthesis of benzimidazole derivatives using 4-A. Reagents and conditions: (d) CS2, Et3N, CH3OH, 45 °C, 3 h; (e)
R3
, K2CO3, KI, C2H5OH and acetone,
R5
Cl
N
HCl
45 °C, 4 h; (f) mCPBA, KHCO3, DCM and H2O, 0 °C, 15 min; (g) Na2S2O4, K2CO3, THF, C2H5OH, H2O, 50 °C, 30 min; (h) (RCO)2O or RCOCl, Et3N, DCM, rt, 1–5 h.

Y. Yan et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4189–4192
4191
Table 1
Structural information and inhibitory rate on the H+/K+-ATP enzyme of 9a–ra and 14a–rb at a concentration of 10 M
Compd.
R1
R2
Inhibitory rate (%)
Compd.
R1
R2
Inhibitory rate (%)
9a
14a
8
10
9j
14j
*
*
1
35
∗
∗
N
N
O
O
O
CH3
CH3
O
O
9b
14b
32
58
9k
14k
0
10
∗
∗
O
∗
O
9c
14c
32
34
9l
14l
28
62
∗
N
∗
∗
∗
∗
N
N
CH3
9d
14d
F
38
41
9m
14m
11
33
F
F
N
∗
9e
14e
*
*
6
37
9n
14n
0
39
∗
N
CH3
∗
O
O
O
F
9f
14f
2
18
9o
14o
24
3
∗
N
∗
∗
F
F
∗
9g
14g
*
9
48
9p
14p
4
4
CH3O
CH3O
CH3
O
N
∗
O
9h
14h
O
17
15
9q
14q
16
16
∗
∗
∗
N
N
CH3
O
O
9i
14i
4
21
9r
14r
13
13
N
∗
CH3O
O
O
Omeprazole
39
Rabeprazole sodium
90
a
Compound 9 was synthesized from 4-A.
Compound 14 was synthesized from 4-B.
b
O
O
O
O
O
O
R1
R1
N
N
N
N
O
O
F
S
N
S
N
S
N
S
N
R2
N
H
N
H
O
N
H
O
R2
N
H
N
H
O
O
N
H
O
F
O
9a-9r
Pantoprazole
14a-14r
Omprazole
Figure 2. Synthesis of 9a–r: diversity introduction to benzimidazoles.
Figure 3. Synthesis of 14a–r: diversity introduction to benzimidazoles.
In conclusion, we have developed a method for the synthesis of
make various molecules, and this was helpful in identifying more
potent H+/K+-ATP enzyme inhibitors. A new compound, 14l dem-
onstrated an IC50 value of 1.6 Â 10À5 M, which is comparable with
the drug omeprazole.
2-[(2-pyridylmethyl)sulfinyl]benzimidazole derivatives that inhi-
bit H+/K+-ATP enzymatic activity as potential proton pump inhibi-
tors. The reversal strategy of the diversity introduction of R2 on the
benzimidazole moiety allows us to select the reaction conditions to
R1
NH2
NO2
R1
NH2
NH2
R1
R1
NH2
NO2
N
h
i
j
SH
R2
R2
R2
N
H
N
H
N
H
N
H
H2N
4-B
10
R2= RCO
11
12
R1
R1
R3
R4
N
O R3
R4
N
e
f
S
S
R2
R2
R5
N
H
R5
N
H
N
H
N
H
N
N
13
14
Scheme 3. Synthesis of benzimidazole derivatives using 4-B. Reagents and conditions: (h) (RCO)2O or RCOCl, Et3N, DCM, rt, 1–5 h; (i) Pd/C, HCOONH4, THF and C2H5OH, rt,
R4
R3
15–30 min; (j) CS2, Et3N, THF and C2H5OH, 45 °C, 3 h; (e)
R5
, K2CO3, KI, C2H5OH and acetone, 45 °C, 4 h; (f) mCPBA, KHCO3, DCM and H2O, 0 °C, 15 min.
Cl
N
HCl

4192
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