Aminoimidazo[1,2-a]pyridines as a new structural class of cyclin-dependent kinase inhibitors. Part 1: Design, synthesis, and biological evaluation

Article abstract of DOI:10.1016/j.bmcl.2004.09.053

Synthesis of 2-aminoimidazo[1,2-a]pyridines 1 and their evaluation as CDK2 inhibitors is described. We have identified a novel structural class of protein serine/threonine kinase inhibitors comprised of an aminoimidazo[1,2-a]pyridine nucleus. Compounds from this family are shown to potently inhibit cyclin-dependent kinases by competing with ATP for binding to a catalytic subunit of the protein. Structure-based design approach was used to direct this chemical scaffold toward generating potent and selective CDK2 inhibitors. The discovery of this new class of ATP-site directed protein kinase inhibitors, aminoimidazo[1,2-a]pyridines, provides the basis of new medicinal chemistry tool in search for an effective treatment of cancer and other diseases that involve protein kinase signaling pathways.

Full text of DOI:10.1016/j.bmcl.2004.09.053

Bioorganic & Medicinal Chemistry Letters 14 (2004) 6095–6099
Aminoimidazo[1,2-a]pyridines as a new structural class of
cyclin-dependent kinase inhibitors. Part 1: Design, synthesis,
and biological evaluation
Carlos Jaramillo,a,* J. Eugenio de Diego,a Chafiq Hamdouchi,b Elizabeth Collins,b
b
a
a
b
´
´
Heather Keyser, Concha Sanchez-Martınez, Miriam del Prado, Bryan Norman,
Harold B. Brooks,b Scott A. Watkins,b Charles D. Spencer,b Jack Alan Dempsey,b
Bryan D. Anderson,b Robert M. Campbell,b Tellie Leggett,b Bharvin Patel,b
Richard M. Schultz,b Juan Espinosa,a Michal Vieth,b Faming Zhangb and David E. Timmb
a
´
Centro de Investigacion Lilly, Avenida de la Industria, 30, 28108 Alcobendas, Madrid, Spain
bLilly ResearchLaboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46385, USA
Received 15 June 2004; revised 14 September 2004; accepted 20 September 2004
Available online 12 October 2004
Abstract—We have identified a novel structural class of protein serine/threonine kinase inhibitors comprised of an aminoimid-
azo[1,2-a]pyridine nucleus. Compounds from this family are shown to potently inhibit cyclin-dependent kinases by competing with
ATP for binding to a catalytic subunit of the protein. Structure-based design approach was used to direct this chemical scaffold
toward generating potent and selective CDK2 inhibitors. The discovery of this new class of ATP-site directed protein kinase inhibi-
tors, aminoimidazo[1,2-a]pyridines, provides the basis of new medicinal chemistry tool in search for an effective treatment of cancer
and other diseases that involve protein kinase signaling pathways.
Ó 2004 Elsevier Ltd. All rights reserved.
The primary function of the cell cycle is to manage
the process of replication of DNA.1–4 Alterations
in the key regulatory elements that control the phases
of the cell cycle often result in uncontrolled prolifera-
tion, the basis of neoplastic disease.5 The basic cell cycle
is divided into four phases, known as G1, S, G2, and M.
When cells cease proliferation, they exit the cycle and
enter a nondividing, quiescent state known as G0.
Because of the CDKs critical role in the regulation of
cell cycle and the observed expression/activity pattern
in most human cancers, considerable effort has been
focused on the development of small molecule inhibi-
tors6,7 that block CDK activity.8–17 However, the num-
ber of structural classes that act as CDKs inhibitors is
limited and most of them derive from relatively nonspe-
cific protein kinase inhibitor scaffolds that also inhibit
CDKs such as staurosporins,18 flavonoids,19 indigoids,20
paullones,21 and purines.22 Flavopiridol,23 a flavonoid
derived from an indigenous plant from India, was the
first CDK modulator tested in clinical trials. Early-
phase trials have shown activity in some patients with
non-HodgkinÕs lymphoma, renal, prostate, colon, and
gastric carcinomas.24
Cyclin-dependent kinases (CDKs) are the key players in
the control of this complex process. Family members of
this class of serine/threonine kinases include at least nine
CDKs and over 12 different cyclin families. The most
relevant enzymes for cell cycle control are CDK4 and
CDK6 (involved in early G1), CDK2 (required to com-
plete G1 and initiate S phase), and CDK1 (controls the
G2 checkpoint and regulates entry into mitosis).
We have recently showed25 that 2-aminoimidazo[1,2-a]-
pyridine scaffold 1 represents a new structural class of
protein serine/threonine kinase inhibitors. These kind
of compounds potently inhibit cyclin-dependent kinases
by competing with ATP for binding to a catalytic
subunit of the protein. The initial lead identification,
Keywords: Cyclin-dependent kinase; CDK; Imidazopyridine; Kinase.
*
Corresponding author. Tel.: +34 916633408; fax: +34 916233591;
e-mail: c.jaramillo@lilly.com
0960-894X/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2004.09.053

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C. Jaramillo et al. / Bioorg. Med. Chem. Lett. 14 (2004) 6095–6099
structure-based analog design, kinase inhibition data,
and X-ray crystallographic structures of CDK2/inhibi-
tor complexes were reported. We now disclose a detailed
SAR study of 2-aminoimidazo[1,2-a]pyridines around
substituents 3 and 6 of the aromatic bicyclic nucleus.
3. Halogen–metal exchange of 5,27 followed by reaction
with the appropriate aryl aldehyde, gave alcohols 29,
bearing the desired R6 functionality. Further protection
of alcohol functional group, and then metalation at
position 3, afforded, by reaction of the required electro-
phile, 3,6-disubstituted 2-aminoimidazo[1,2-a]pyridines,
which were transformed into targets 30–41 by subse-
quent deprotection of the silyl ether, oxidation of the
resulting alcohol, and final trifluoroacetamide removal.
N
NH2
R6
N
X6
Y6
X3
Y3
Our initial lead (14) proved to be quite potent as CDK2
inhibitor, and it was proved that its inhibitory activity
was effected to competing with ATP for binding to cata-
lytic subunit of the protein.25 Initial SAR studies around
R6 (Table 1) were focused to determine the best aryl sub-
stitution pattern, and it was found that the presence of
at least one substituent at position 2 was necessary to
keep the potency below 1lM. Disubstitution with elec-
tron-withdrawing functional groups at positions 2 and
6 provided the most active molecules and, among them,
fluorine and chlorine (compounds 14, 12, and 31)
proved to be the best. The use of other functional
groups, or substitution at other positions of the aryl
ring, led to a significant loss in activity.
R3
1
Our initial research effort was directed to create a diver-
sity of substituents at positions 3 and 6 of the imid-
azo[1,2-a]pyridine nucleus. The approaches for the
synthesis of molecules described in this letter are based
on two different routes: one makes use26 of the reaction
of 2-chloropyridines 2 with cyanamide 3 and a-bromo-
acetophenones 4 (route A, Scheme 1), while the other
focuses on the selective and sequential functionaliza-
tion27 of 2-trifluoroamido-6-iodoimidazo[1,2-a]pyridine
528 (route B, Scheme 2).
Route A started (Scheme 1) from 2-chloronicotinic
acidÕs Weinreb amide 2a,28 which was provided with
the adequate functionality at R6 by treatment with the
appropriate aryl lithium reagent, to give ketones 2b.
Targets 6–29 were directly prepared from 2b using our
one-pot procedure26 for the formation of the 2-amino-
imidazo[1,2-a]pyridine nucleus, by effecting chloride
atom displacement with cyanamide, followed by N-alkyl-
ation with bromoacetophenone, and final ring-closure to
target compounds.
We next studied position 6 (Table 2) to map the optimal
spacer X6–Y6 between phenyl and imidazopyridine
rings. The presence of an sp2 was shown to be critical
to maintain activity. Carbonyl, vinyl, or Z-configurated
cyanovinyl substituents, were equally efficient, but activ-
ity was partially lost when either E-configurated olefins
(27) or bulkier Y6 such as tetrazole (28) substituents
were introduced.
SAR around R3–Y3 (Table 3) was performed taking into
consideration that the presence of a Y3 substituent bear-
ing a lone pair might lead to a conformational change in
the molecule, by the formation of a hydrogen acceptor
On the other hand, route B was based (Scheme 2) on the
stepwise introduction of substituents at positions 6 and
Br
N
O
R3
NH2
3
Cl
4
F
Cl
R6M, THF
N
OMe
NH2
R6
N
N
N
N
X6
Y6
F
O
F
O
O
2a
2b
F
25-28
F
N
N
NH2
NH2
R6
N
N
F
N
F
NH2
O
O
F
N
O
O
Y3
O
F
F
R3
R
21-24
6-12
13-20
Scheme 1. Synthesis of 2-aminoimidazo[1,2-a]pyridines (route A).

C. Jaramillo et al. / Bioorg. Med. Chem. Lett. 14 (2004) 6095–6099
6097
N
N
1. i-PrMgCl
NHCOCF3
R6
N
NHCOCF3
N
2. RCHO
I
OH
5
29
F
N
N
1. TBSOTf
1. TBAF
2. IBX
NH2
NHCOCF3
R6
N
N
2. n-BuLi
3. E+
NH /MeOH
3.
3
E
O
O
F
OTBS
R3
30
38-42
F
N
N
NH2
NH2
R6
N
N
F
O
O
F
O
O
F
R
31-32
33-37
Scheme 2. Synthesis of 2-aminoimidazo[1,2-a]pyridines (route B).
Table 1. Enz. assay (IC50) CDK229
Table 2. Enz. assay (IC50) CDK229
F
N
N
NH2
NH2
R6
N
N
X6
Y6
F
F
O
O
O
F
F
F
X6–Y6
IC50 (nM)
Compound
R6
IC50 (nM)
Compound
14
6
2,6-Di-F–Ph
Ph
2-Cl–Ph
122
1927
428
14
25
26
27
28
C@O
C@CH2
(Z)-C@CHCN
(E)-C@CHCN
(E,Z)-C@CH(1H-tetrazol-5-yl)
122
63
7
160
896
1691
8
2-CF3–Ph
2-Me–Ph
1068
1294
603
9
10
11
12
31
2-MeO–Ph
2-CF3O–Ph
2,6-Di-Cl–Ph
2-Cl–6-F–Ph
2171
53
33
electron-withdrawing groups (18 and 20) was present.
On the other hand, it was also discovered that subtle
changes in R3 had a profound effect in the activity of
the molecule. In this case, the presence of an electron-
donating group at position 4 was well tolerated (16
and 20). We took advantage of this to introduce poten-
tially solubilizing groups in the molecule.
with one of the hydrogen atoms at N-2.30 On the other
hand, according to our modeling and X-ray studies,25
this part of the molecule would need to fit in a narrow,
hydrophobic pocket, and, therefore, a profound effect
on activity should be expected in this region. It was
found that substitution at positions 2 with electron-
donating methoxy (38), or at positions 2 and 6 elec-
tron-withdrawing fluorine and chlorine (14, 42, and
15) functional groups, provided the most active mole-
cules. In this regard, we also found that, when X was
a sulfur atom, a fivefold improvement in activity
was obtained with respect to the oxygenated analog,
but only when a 2,6-disubstitution pattern containing
For the introduction of potentially solubilizing side
chains at 4-position of R3 (Table 4), 2,6-dichlorophenyl
substitution was used as R3. It was found, as we had
expected, that only small substituents (21, 36, and 37)
would fit in the molecule without losing activity; bulkier
functional groups showed reduced activity (22 and 23).
On the other hand, the nature of the substituent seemed
to have little effect on the activity.

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C. Jaramillo et al. / Bioorg. Med. Chem. Lett. 14 (2004) 6095–6099
Table 3. Enz. assay (IC50) CDK229
We finally studied the selectivity profile of selected com-
pounds against a variety of kinases. The results are sum-
marized in Table 5. Most compounds proved to be
selective for CDKs versus PKA, CAMKII, and GSK-
3b, with selectivity ranging from 4 to >400-fold. Among
the CDKs, all compounds showed less activity against
CDK4 than against either CDK1 or CDK2; the best
selectivity for CDK1 versus CDK2 was observed for
14, 26, and 28 (2–18-fold), while CDK2 versus CDK1
selectivity was achieved with 38, 31, 18, 20, and 37 (3–
7-fold). In this sense, 20 was >5-fold selective for
CDK2 versus CDK1 and CDK4, and >100-fold selec-
tive for CDK2 versus PKA, CAMKII, and GSK-3b.
Overall, these results provided us with useful tools for
the preparation of either selective or dual CDK
inhibitors.
F
N
NH2
N
Y3
O
F
R3
Compound
R3
Ph
Y3
IC50 (nM)
13
14
38
39
40
41
42
15
16
17
18
19
20
O
O
O
O
O
O
O
O
O
S
324
122
68
2,6-Di-F–Ph
2-MeO–Ph
2-Thienyl
547
1711
2538
121
102
91
4-Cl–Ph
4-Piridyl
2,6-Di-Cl–Ph
2-Cl–6-F–Ph
2,6-Di-F–4-MeO–Ph
Ph
2,6-Di-F–Ph
214
26
In summary, we have found a new structural class of
protein serine/threonine kinase inhibitors based on the
novel 2-aminoimidazo[1,2-a]pyridine core. Compounds
from this family are shown to potently inhibit either
CDK1 or CDK2 by competing with ATP for binding
to catalytic subunit of the protein. The discovery of this
new class of ATP-site directed protein kinase inhibitors,
aminoimidazo[1,2-a]pyridines, provides a new medicinal
chemistry tool in the search for an effective treatment of
cancer and other diseases that involve protein kinase
signaling pathways.
S
2,6-Di-MeO–Ph
2,6-Di-F–4-MeO–Ph
S
462
29
S
Table 4. Enz. assay (IC50) CDK229
Cl
N
NH2
N
F
O
Cl
O
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