Concise, flexible syntheses of 4-(4-imidazolyl)pyrimidine cyclin-dependent kinase 2 (CDK2) inhibitors

Article abstract of DOI:10.1016/j.tetlet.2010.09.074

A flexible six-step synthesis of potential cyclin-dependent kinase 2 (CDK2) inhibitors is reported. The synthesis involves the condensation between 3-chloro-4,4-dimethoxy-2-butanone and amidines, which provides acetyl-imidazoles and late stage palladium-catalyzed N-arylation to give the target pyrimidine derivatives.

Full text of DOI:10.1016/j.tetlet.2010.09.074

Tetrahedron Letters 51 (2010) 6126–6128
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Concise, flexible syntheses of 4-(4-imidazolyl)pyrimidine cyclin-dependent
kinase 2 (CDK2) inhibitors
Mathieu Toumi, Marion Barbazanges, Sebastian H. B. Kroll, Hetal Patel, Simak Ali, R. Charles Coombes,
⇑
Anthony G. M. Barrett
Departments of Chemistry and Cancer Medicine, Imperial College, London SW7 2AZ, UK
a r t i c l e i n f o
a b s t r a c t
Article history:
A flexible six-step synthesis of potential cyclin-dependent kinase 2 (CDK2) inhibitors is reported. The
synthesis involves the condensation between 3-chloro-4,4-dimethoxy-2-butanone and amidines, which
provides acetyl-imidazoles and late stage palladium-catalyzed N-arylation to give the target pyrimidine
derivatives.
Received 9 July 2010
Revised 24 August 2010
Accepted 17 September 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Protein kinases play important regulating roles in cellular pro-
cesses such as transcription, cell cycle, metabolism, apoptosis
and neuronal development.1 Mutations which deregulate the func-
tion of these kinases result in many diseases, such as cancer, and
neurodegenerative and cardiovascular disorders. Among the 11
members of the CDK family identified, cyclin-dependent kinase 2
(CDK2) is known to play important roles in the cell cycle.2,3
Recently, these protein kinases have attracted increased attention
and small molecule CDK inhibitors have been identified as poten-
tial therapeutic agents. In this context, a number of CDK inhibitors
such as flavopiridol (1) and (R)-roscovitine (CYC202) (2) have
proved their efficacy for the treatment of cancer (Fig. 1). More
recently, flavopiridol (1) was investigated for the treatment of
oesophageal, lung and liver cancers and was demonstrated to have
a strong effect against lymphatic leukaemia.4
Due to growing interest in CDKs as potential targets for cancer
chemotherapy, several pharmaceutical companies have developed
new classes of CDK2 inhibitors. Following earlier studies,5
AstraZeneca scientists found that replacement of the imi-
dazo[1,2-a]pyridine in 3 or imidazo[1,2-b]pyridazine in 4 with an
imidazole-pyrimidine sulfone 5 gave rise to inhibitors with supe-
rior physicochemical properties and cellular potency (Fig. 2).6 This
group reported the synthesis of imidazole-pyrimidine sulfone 5
and its analogues using derivatives of 5-methyl-isoxazoles 8 as
the synthetic equivalent of acetyl-imidazoles 9 and the key trans-
formations are outlined in Scheme 1.7
is present in BS-181, which is the most selective CDK7 inhibitor, re-
ported to date.8
Condensation of 3-chloro-4,4-dimethoxy-2-butanone (10)9 with
the amidines 11a–c10,11 gave the imidazoles 12a–c. These reactions
were optimally carried out using an excess of amidines 11 with
sodium acetate and chloro-ketone 10 in anhydrous 1,4-dioxane at
reflux for 16 h (12a, 12b) or 36 h (12c) (Scheme 3).
Subsequent N-iso-propylation of 12 proved to be more compli-
cated than expected.12 Whilst the use of basic conditions in polar
Me
N
NH
N
N
OH
O
N
HO
HN
N
Cl
HO
OH
1
2
Figure 1. CDK2 inhibitors flavopiridol (1) and (R)-roscovitine (2).
H
N
N
H
N
N
N
N
N
N
N
Herein, we report an alternative synthesis of the regioisomeric
4-acetylimidazoles 13a–c by the condensation of 3-chloro-4,4-
dimethoxy-2-butanone (10) and amidines 11 (Scheme 2). Subse-
quent N-alkylation and conversion into imidazole-pyrimidine
sulfones 21a–c, afforded novel CDK2 inhibitors, which contained
an unusual hexamethylenediamine side chain. This functionality
NMe2
N
N
3
4
H
N
Me2N
N
N
Me
S
O
O
N
N
5
⇑
Corresponding author. Tel.: +44 20 7 59 4 5766; fax: +44 20 7 59 4 5805.
E-mail address: agm.barrett@imperial.ac.uk (A.G.M. Barrett).
Figure 2. CDK2 inhibitors developed by AstraZeneca.
0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2010.09.074

M. Toumi et al. / Tetrahedron Letters 51 (2010) 6126–6128
6127
NH .HCl
NH2
NH2
MeO
MeO
regioselective
nitration /
N
O
H2N
NMe
C
2 Me2N
H2N
N
N
N
O
O
7
reduction
130 º
MeONa / MeOH
13a-c
N
6
neat
16 h to 5 d
n-propanol
reflux, 12 h
N
R
N
reduction
and
acylation
R
N
R1
15a: R = Me, 84%
15b: R = Ph, 92%
16a: R = Me, 74%
16b: R = Ph, 93%
O
O
i
i
15c: R = Pr, 98%
16c: R = Pr, 92%
R2
R1
catalytic
N
R2
N
hydrogenation /
Scheme 5. Synthesis of the 4-substitued 2-aminopyrimidines 16.
N
N
cyclization
O
9
8
After developing an efficient synthesis of the 4-acetylimidazoles
13, we next examined the introduction of the 2-aminopyrimidine
moiety. Acetyl-imidazoles 13 were converted into enones 15 by
reaction with neat DMF-dimethyl acetal. Subsequent reaction with
excess guanidine hydrochloride and sodium methoxide in n-propa-
nol at reflux gave the desired 4-substitued 2-amino-pyrimidines
16 in excellent yields over the two-step sequence (Scheme 5).
The sulfonamide unit 19 (Scheme 6) was readily prepared in 95%
yield by condensation of 4-iodobenzenesulfonyl chloride (18) with
mono-Boc-protected 1,6-diaminohexane 1713 using a biphasic sys-
tem of dichloromethane and saturated aqueous sodium hydrogen
carbonate at room temperature for 24 h.14
Scheme 1. Six-step synthesis of N-alkylated acetyl-imidazoles 9 from 5-methyl-
isoxazole 6.
O
O
HN
Cl
N
condensation
MeO
R1.
+
HCl
H2N
HN
OMe
R1
10
11
12
N-alkylation
O
Attempted copper-catalyzed Ullmann arylation of 2-aminopyr-
imidines 16a–c with 4-iodobenzenesulfonamide 19 using cop-
per(I) iodide (25–100 mol %) and N,N0-dimethylethylenediamine
(25–100 mol %), potassium or caesium carbonate in 1,4-dioxane
at 100 °C15 was unsuccessful and gave no coupled product. In con-
trast, palladium-catalyzed coupling with Pd2dba3 (1 mol %), Xant-
phos (2.2 mol %) and caesium carbonate in 1,4-dioxane at 100 °C
N
N
R1
R2
13
Scheme 2. Two step synthesis of N-alkylated acetyl-imidazoles from building
blocks 10 and 11.
gave the desired products 20 in excellent yields (Scheme 7),16
,
which were Boc-deprotected using methanolic hydrogen chloride
to provide amines 21a–c.
O
With amines 21a–c in hand, we evaluated their ability to inhibit
several kinases and also their cellular activity. Initially we hoped to
see good CDK7 inhibition, because we observed excellent CDK7
selectivity and potency with the hexamethylene diamine side
chain in BS-181, containing the pyrazolo[1,5-a]pyrimidine core.8
Changing this functionality on the pyrazolopyrimidine scaffold
for more drug-like moieties resulted in diminished potency and
selectivity. Therefore we decided to incorporate the BS-181
side chain in this new series of inhibitors, to seek to introduce
CDK7-selectivity. Computational studies suggested that this side
chain could form the same interaction with CDK7 as in BS-181
and analogues of BS-181. In addition, substituent changes at the
imidazole C-2 position were expected to improve CDK7 selectivity.
Unfortunately, these predictions were not confirmed by the exper-
imental data. Table 1 shows the effects of imidazole C-2 substitu-
tion on activity. The imidazole 21a with the small methyl group
(entry 1) showed moderate CDK7 potency and low nM CDK2
inhibition. Changing to the iso-propyl group (21c, entry 3), resulted
in decreased activity for CDK2 by 10-folds with hardly any
inhibition of CDK7. Further increasing the steric bulk to a phenyl
in imidazole 21b completely suppressed inhibition (entry 2). The
data shows good selectivity for CDK2 over CDK7 in the first two
cases, with moderate IC50 values.
AcONa,
HN
N
1,4-dioxane reflux
16 h to 36 h
R. HCl
+
10
HN
H2N
R
11a: R = Me
11b: R = Ph
11c: R = iPr
12a: R = Me, 88%
12b: R = Ph, 78%
12c: R = iPr, 81%
Scheme 3. Condensation reaction between the chloride 10 and amidines 11.
solvents failed to give any alkylation products, we found that
reaction of imidazoles 12 with iso-propyl iodide in the presence
of copper(I) iodide, 1,10-phenanthroline and caesium carbonate
in 1,4-dioxane or without solvent gave the expected N-iso-pro-
pyl-4-acetylimidazoles 13 in good yields and with excellent levels
of regioselectivity. The minor regioisomers (14a, 14c), detected and
quantified by 1H NMR spectroscopy, were easily removed by flash
chromatography (Scheme 4). The structures of the imidazoles 13
were assigned unambiguously by NOE or NOESY experiments.
O
I
O
This observed influence of the size of the 2-position substitu-
ent is in good agreement with compounds prepared in the Astra-
N
CuI
N
1,10-phenanthroline
N
Zeneca laboratories,6 suggesting
a
similar binding mode.
12a-c
+
R
N
Cs2CO3
R
Imidazole-pyrimidines 21a and 21c showed moderate growth
inhibition of MCF-7 cells but this effect was at reduced levels
for analogue 21b. In general, the cellular data did not follow
the kinase data, suggesting that imidazolyl-pyrimidines 21a–c
may also inhibit other targets.
1,4-dioxane or neat
110 ºC or 80 ºC
13a: R = Me, 78%
13b: R = Ph, 81%
13c: R = Pr, 69%
14a: R = Me, 6%
14b: R = Ph, 0%
i
i
14c: R = Pr, 4%
Scheme 4. Copper-catalyzed N-alkylation of imidazoles 12.

6128
M. Toumi et al. / Tetrahedron Letters 51 (2010) 6126–6128
I
I
H
N
CH2Cl2 / NaHCO3
BocHN
NH2
+
BocHN
Cl
S
S
rt, 24 h
95%
4
4
19
O
O
O
O
17
18
Scheme 6. Formation of 4-iodobenzene-sulfonamide 19.
19
H
N
endowment (to A.G.M.B.) and P.R. Haycock and R.N. Sheppard,
both at Imperial College London, for high-resolution NMR
spectroscopy.
N
Pd2dba3 (1 mol%)
Xantphos (2.2 mol%)
H
N
N
16a-c
BocHN
S
Cs CO (1.4 eq.)
2
3
4
1,4-dioxane 100 ºC, 16 h
O
O
N
Supplementary data
N
R
20a: R = Me, 96%
20b: R = Ph, 93%
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.tetlet.2010.09.074.
i
20c: R = Pr, 95%
HCl / MeOH
rt , 1 h
References and notes
1. Noble, M. E. M.; Endicott, J. A.; Johnson, L. N. Science 2004, 303, 1800.
2. Pines, J. Adv. Cancer Res. 1995, 66, 181.
3. Morgan, D. O. Annu. Rev. Cell Dev. Biol. 1997, 13, 261.
H
N
N
H
N
N
4. Byrd, J. C.; Lin, T. S.; Dalton, J. T.; Wu, D.; Phelps, M. A.; Fischer, B.; Moran,
M.; Blum, K. A.; Rovin, B.; Brooker-McEldowney, M.; Broering, S.; Schaaf, L.
J.; Johnson, A. J.; Lucas, D. M.; Heerema, N. A.; Lozanski, G.; Young, D. C.;
Suarez, J.-R.; Colevas, A. D.; Grever, M. R. Blood 2007, 15, 399.
5. (a) Anderson, M.; Beattie, J. F.; Breault, G. A.; Breed, J.; Byth, K. F.; Culshaw, J. D.;
Ellston, R. P. A.; Green, S.; Minshull, C. A.; Norman, R. A.; Pauptit, R. A.; Stanway,
J.; Thomas, A. P.; Jewsbury, P. J. Bioorg. Med. Chem. Lett. 2003, 13, 3021; (b) Byth,
K. F.; Culshaw, J. D.; Green, S.; Oakes, S. E.; Thomas, A. P. Bioorg. Med. Chem. Lett.
2004, 14, 2245.
H2N
S
4
O
O
N
21a: R = Me, 86%
21b: R = Ph, 92%
N
R
i
21c: R = Pr, 72%
Scheme 7. Palladium-catalyzed N-arylation and completion of the synthesis.
6. Jones, D. C.; Andrews, D. M.; Barker, A. J.; Blades, K.; Byth, K. F.; Finlay, M. R. V.;
Geh, C.; Green, C. P.; Johannsen, M.; Walker, M.; Weir, H. M. Bioorg. Med. Chem.
Lett. 2008, 18, 6486.
Table 1
CDK2, CDK7 and cellular inhibition by amines 21
7. Reiter, L. A. J. Org. Chem. 1987, 52, 2714.
a
a
a
Entry Amine IC50 CDK2
(nM)
IC50 CDK7
(nM)
GI50
M)
TGIa
M)
LC50
8. Ali, S.; Heathcote, D.; Kroll, S. H. B.; Scheiper, B.; Jogalekar, A. S.; Patel, H.;
Brackow, J.; Siwicka, A.; Periyasamy, M.; Tolhurst, T. S.; Kanneganti, S. K.;
Snyder, J. P.; Liotta, D.; Aboagye, E. O.; Barrett, A. G. M.; Coombes, R. C. Cancer
Res. 2009, 69, 6208.
(
l
(
l
(l
M)
1
2
3
21a
21b
21c
26
4800
225
1139
3425
3402
33
37
28
36
75
34
45
>100
41
9. Reiter, L. A. J. Org. Chem. 1984, 49, 3494.
10. For the synthesis of amidines via trihaloethyl imidates, see: Caron, S.; Wei, L.;
Douville, J.; Ghosh, A. J. Org. Chem. 2010, 75, 945; by reduction of amidoximes
with potassium formate, see: Nadrah, K.; Dolenc, M. S. Synlett 2007, 1257; by
addition of amines to amides, see: Charette, A. B.; Grenon, M. Tetrahedron Lett.
2000, 41, 1677.
a
IC50: concentration that inhibits 50% of enzyme activity; GI50: concentration
that inhibits 50% of cell growth; TGI: concentration when cell growth stops; LC50
concentration with 50% cell death.
:
11. Schaefer, F. C.; Krapcho, A. P. J. Org. Chem. 1961, 27, 1255.
12. (a) Seto, M.; Miyamoto, N.; Aikawa, K.; Aramaki, Y.; Kanzaki, N.; Iizawa, Y.;
Baba, M.; Shiraishi, M. Bioorg. Med. Chem. 2005, 13, 363; (b) Kaur, N.; Monga,
V.; Josan, S. J.; Lu, X.; Gershengorn, M. C.; Jain, R. Bioorg. Med. Chem. 2006, 14,
5981; (c) Barrow, J. C.; Nantermet, P. G.; Stauffer, S. R.; Ngo, P. L.; Steinbeiser,
M. A.; Mao, S. S.; Carroll, S. S.; Bailey, C.; Colussi, D.; Bosserman, M.; Burlein, C.;
Cook, J. J.; Sitko, G.; Tiller, P. R.; Miller-Stein, C. M.; Rose, M.; McMasters, D. R.;
Vacca, J. P.; Selnick, H. G. J. Med. Chem. 2004, 46, 5294.
13. Gardner, R. A.; Ghobrial, G.; Naser, S. A.; Phanstiel, O., IV J. Med. Chem. 2004, 47,
4933.
14. Christy, S. J.; Lim, B. B.; Vilner, B. J.; Geyer, B. C.; Bowen, W. D. J. Med. Chem.
1998, 41, 2445.
In summary, the synthesis of the target imidazolyl-pyrimidines
21 have been achieved in six steps with overall yields ranging from
35% (R = Me, iPr) to 46% for (R = Ph). Our synthetic approach uses a
condensation reaction leading to 4-acetyl-imidazoles and palla-
dium-catalyzed N-arylation of substituted 2-aminopyrimidines.
Further applications of this methodology are under investigation
and will be reported in due course.
15. Liu, Y.; Bai, Y.; Zhang, J.; Li, Y.; Jiao, J.; Qi, X. Eur. J. Org. Chem. 2007, 36,
6084.
16. Yin, J.; Zhao, M. M.; Huffman, M. A.; McNamara, J. M. Org. Lett. 2002, 4,
3481.
Acknowledgements
We thank Cancer Research UK for generous support of our
cancer medicinal chemistry, GlaxoSmithKline for the generous