3-Benzimidazol-2-yl-1H-indazoles as potent c-ABL inhibitors

Article abstract of DOI:10.1016/j.bmcl.2006.04.043

The 3-benzimidazol-2-yl-1H-indazole scaffold was developed as an alternate scaffold for our receptor tyrosine kinase (RTK) inhibitor program. In exploring the SAR of this series, it was discovered that a subset of these compounds potently inhibit the enzy

Full text of DOI:10.1016/j.bmcl.2006.04.043

Bioorganic & Medicinal Chemistry Letters 16 (2006) 3789–3792
3-Benzimidazol-2-yl-1H-indazoles as potent c-ABL inhibitors
Christopher M. McBride, Paul A. Renhowe, Thomas G. Gesner, Johanna M. Jansen,
Julie Lin, Sylvia Ma, Yasheen Zhou and Cynthia M. Shafer*
Small Molecule Drug Discovery, Medicinal Chemistry Department, Chiron Corporation, 4560 Horton Street,
Emeryville, CA 94608, USA
Received 29 March 2006; revised 14 April 2006; accepted 14 April 2006
Available online 5 May 2006
Abstract—The 3-benzimidazol-2-yl-1H-indazole scaffold was developed as an alternate scaffold for our receptor tyrosine kinase
(RTK) inhibitor program. In exploring the SAR of this series, it was discovered that a subset of these compounds potently inhibit
the enzyme c-ABL. The SAR of these compounds is described.
Ó 2006 Elsevier Ltd. All rights reserved.
The tyrosine protein kinase, c-ABL, is ubiquitously
expressed in mammalian cells and is involved in cell
cycle regulation.1 A chromosomal translocation between
the bcr and abl genes results in a fusion protein with
constitutive ABL kinase activity, leading to expansion
of cells of the hematopoietic lineage and the disease,
chronic myelogenous leukemia (CML).2,3 The clinical
development of imatinib mesylate (STI571, GleevecTM,
1) has resulted in unprecedented response rates for the
treatment of chronic phase CML patients.4 Patients in
the blast crisis stage of CML, however, have a less dura-
ble response.4 The primary mechanism of acquired
GleevecTM resistance occurs through kinase domain
mutations in BCR-ABL.5 Other small molecule inhibi-
tors are currently under development to treat
GleevecTM-resistant CML.5
the benzimidazole, and, when located at C5’, most
substituents were found to be tolerated. Typically, basic
amines improved physiochemical properties, and thus
were evaluated more closely. Compounds containing
the piperidinylpiperidine amine inhibited other RTKs
potently and exhibited good inhibition of cellular prolif-
eration.9 This moiety, then, was used in expanding the
SAR around the subset of compounds shown to exhibit
potent c-ABL activity. Compound 4 (Table 1), with no
functionality on ring A, moderately inhibits c-ABL
phosphorylation at 0.60 lM similar to the potency
exhibited by GleevecTM (1, 0.43 lM). Analysis of the
SAR of the indazole benzimidazoles indicated that
c-ABL affinity was dependent on being substituted at
C5 or C6.10 Incorporating a methoxy at C-5 (5) im-
proves the in vitro potency against c-ABL somewhat,
but a nearly 10-fold improvement is seen when the much
larger benzyloxy (7) moiety is incorporated at C5. This
improvement in affinity increases to 19-fold when C5
is substituted with phenoxy (6). Furthermore, a 200-fold
improvement in enzymatic inhibition is seen when a
methoxy is incorporated at C6, ortho to the
C-5 benzyloxy, (8). Attempts to incorporate two large
groups such as in compound 10 (5,6-dibenzyloxy) or
move the benzyloxy substituent to C6 as in compound
9 result in significant loss of affinity compared to 8.
During the course of our RTK program, we desired an
alternate scaffold to the 4-amino-3-benzimidazol-2-yl-
hydroquinolin-2-one series (Fig. 1, 2).6–8 The 3-ben-
zimidazol-2-yl-1H-indazole (3, hereafter referred to as
indazole benzimidazole) series was designed, and the
SAR explored.9 During the course of that work, a subset
of compounds was identified as potent c-ABL inhibitors.
This SAR was developed and is presented here.
In evaluating the indazole benzimidazole scaffold, a
number of substituents were assessed on the D ring of
Because of the observation that a large substituent at C5
of the indazole ring significantly improved potency
against c-ABL, effects of substitution on the phenoxy
were evaluated. Incorporation of a methoxy on the
ortho- positon of the phenoxy ring (11) yielded
similar affinity as the unsubstituted phenoxy (6), while
Keywords: Protein tyrosine kinase; c-ABL; Chronic myelogenous
leukemia (CML); Indazole; Benzimidazole.
*
Corresponding author. Tel.: +1 510 923 8086; e-mail:
cynthia_shafer@chiron.com
0960-894X/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.04.043

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C. M. McBride et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3789–3792
CH3
NH
O
D
H3C
D
NH2
N
O
N
N
H
N C
C
NH
N
N
N
N
H
A
B
N
A
N
N
B
H
N
H
1
2
3
Figure 1. Imatinib mesylate (GleevecTM, 1), 4-amino-3-benzimidazol-2-ylhydroquinolin-2-one (2), and 3-benzimidazol-2-yl-1H-indazole (3).
Table 1. Structure–activity relationship of the indazole benzimidazole
series against c-ABL
Analogs with amino-linked substituents at C-5 were
synthesized and evaluated. The benzylamino substituted
analog (14) was less potent than the oxy analog (7), but
the more structurally constrained 1-benzyl-4-piperidyl-
amine (15) exhibited potent enzymatic inhibitory activi-
ty. The tert-butyl urea moiety (16) also conferred potent
enzymatic affinity to the molecule. The amide (17)
showed less potent c-ABL inhibition, but removal of
the carbonyl to give 2-furylmethylamine (18) improved
affinity. And, finally, replacement of the furan (18) with
a thiazole (19) gave an additional 5-fold potency
improvement.
N
N
5'
N
5
4
R
6
NH
N
7
N
H
A subset of the analogs screened in the enzymatic
assay were further evaluated in the CML cell line
K562 which expresses the Bcr-Abl protein (Table
2).11 The 5-benzyl analog (7) inhibited K562 cellular
proliferation with an EC50 of 0.97 lM which was
11-fold less potent than GleevecTM (1, 0.09 lM). The
amino-linked benzyl analog (14) exhibited poorer cell
growth inhibition than 7, while the 1-benzyl-4-piper-
idylamine analog (15) had 14-fold improvement in
cellular inhibitory activity compared to 7 and was
on par with that of GleevecTM’s (1). The tert-butyl
urea compound (16) had slightly improved cell
potency compared to 7 but significantly worse cellular
potency compared to 15. Comparing 17, 18, and 19,
the anti-proliferative effect followed the same trend as
the enzymatic data in that the 2-furylmethylamine
(18) was more potent against the K562 cells than
17, while the 2-thiazolylmethylamine (19) is the most
potent analog tested on this cell line. The potency of
18 on cell is greater than the c-ABL in vitro activity,
while the cellular potency of 19 is equipotent to the
enzymatic affinity indicating that the inhibition of
K562 proliferation is most likely influenced by
potency against other kinases.12
Compound
R
c-ABL IC50 (lM)
1 (GleevecTM
)
—
H
0.43
0.60
0.23
0.03
0.06
0.003
0.20
0.90
4
5
5-OMe
5-OPh
5-OBn
6
7
8
5-OBn, 6-OMe
6-OBn
5-OBn, 6-OBn
9
10
OMe
5-
11
12
0.02
0.06
O
MeO
5-
O
13
14
15
0.22
0.13
0.007
MeO
O
5-
5-NHBn
Bn
N
N
H
5-
16
17
5-NH(CO)NHt-Bu
0.03
0.15
Synthesis of the indazole benzimidazole core from an in-
dazole aldehyde and a phenylenediamine has been previ-
ously described.9 For the aryloxy analogs (Scheme 1, 6,
11–13), the indoles were synthesized by SNAr of the
anion of phenol or substituted phenol on 4-fluoro-2-
methyl-1-nitrobenzene followed by condensation with
DMF Æ DMA, reduction, and in situ cyclization to the
indole.13,14 The anion of phenol (and substituted phe-
nols) could be made by combining the molten phenol
with KOH at 110 °C.13 The indazole aldehydes were
synthesized as previously described.9,15,16 For the
nitrogen-linked analogs (14–19), the nitro was carried
O
O
5-
HN
O
18
19
0.06
0.01
5-
5-
HN
HN
S
N
substitution at the meta- (12) and para-positions (13) led
to a decrease in activity. A similar trend was seen with a
fluoro substituent.10

C. M. McBride et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3789–3792
3791
O
O
a) DMF·DMA, DMF, 110˚C
b) Pd/C, H2, EtOH
OH
a) KOH, 110˚C
F
N
H
NO2
NO2
b) 130˚C, 1 h
N
O
H
N
N
NaNO2 (aq, pH 2)
Dioxane
EtOH, Toluene, 80˚C
O
+
H2N
H2N
N
N
O
N
N
H
NH
N
N
H
6
Scheme 1. Synthetic scheme for the 5-phenoxy-substituted indazole benzimidazole, 6.
Table 2. Cellular proliferation data for selected compounds
N
N
5'
N
5
4
R
6
NH
N
7
N
H
Compound
R
c-ABL IC50 K562 EC50
(lM)
Figure 2. Compound 6 docked at the ATP binding site of c-ABL. The
protein structure is taken from Brookhaven Protein Data Bank, entry
1M52, where the kinase adopts an inactive conformation with the P-
loop residues wrapping around the ATP site (not shown in the picture)
and the Phe382 flanking out at the DFG loop. Surface of the binding
site is colored by atom-type (Oxygen, red; Nitrogen, blue; and Carbon,
white), and hydrogen bonds to hinge residues are also labeled.
(lM)
1 (GleevecTM
)
—
5-OBn
5-NHBn
0.43
0.06
0.13
0.09
0.97
1.8
7
14
Bn
N
N
H
5-
15
16
17
0.007
0.03
0.15
0.07
0.36
0.56
5-NH(CO)NHt-Bu
O
O
5-
5-
5-
HN
Glu316 and Met318 at the hinge of the kinase. The
basic piperidinopiperidine group of the ligand stretch-
es into the solvent and is in close contact with two
acidic residues Asp325 and Glu329. The phenoxy
group at C5 occupies the kinase specificity pocket
consisting mainly of the side chains of Val256,
Met290, Phe382, Ile313, Glu286, and Lys271.
Although, this docking model could explain the
general SAR that C5 substitution leads to more
active compounds, it is not representative of all the
C5 substituted compounds. For example, one of the
more active compounds, 15, would probably bind
to a different conformation of the enzyme (model
shown in Supplemental Material). It is also worth
noting that this series of compounds do not seem
to form the H-bond with the side chain of Thr315
as GleevecTM does, therefore they are expected to
overcome one of the major GleevecTM-resistance
mutations, T315I.17
O
18
19
0.06
0.01
0.03
0.01
HN
HN
S
N
through the reaction sequence from the commercially
available 5-nitroindole. Subsequent catalytic reduction
followed by reaction with an electrophile (16–17) or by
reductive amination (14–15 and 18–19) gave the desired
products.
Figure 2 shows a docking model of compound 6 at
the ATP binding site of c-ABL. In this proposed
binding mode, the indazole benzimidazole core of
compound
6 forms three H-bonds with residue

3792
C. M. McBride et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3789–3792
8. Lopes de Menezes, D. E.; Peng, J.; Garrett, E. N.; Louie,
Supplementary data
S. G.; Lee, S. H.; Wiesmann, M.; Tang, Y.; Shephard, L.;
Goldbeck, C.; Oei, Y.; Ye, H.; Aukerman, S. L.; Heise, C.
Clin. Cancer Res. 2005, 11, 5281.
Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/j.bmcl.
2006.04.043.
9. McBride, C. M.; Renhowe, P. A.; Heise, C.; Jansen, J. M.;
Lapointe, G.; Ma, S.; Pin˜eda, R.; Vora, J.; Wiesmann, M.;
Shafer, C. M. Biorg. Med. Chem. Lett., in press,
doi:10.1016/j.bmcl.2006.03.069.
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