Synthesis of an aryloxy oxo pyrimidinone library that displays ALK-selective inhibition

Article abstract of DOI:10.1016/j.bmcl.2011.05.103

We report the synthesis of a pyrimidinone library that targets anaplastic lymphoma kinase (ALK), an oncogenic receptor tyrosine kinase. This library was generated in three steps from a versatile commercially available starting material. Some compounds wit

Full text of DOI:10.1016/j.bmcl.2011.05.103

Bioorganic & Medicinal Chemistry Letters 21 (2011) 4592–4596
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis of an aryloxy oxo pyrimidinone library that displays ALK-selective
inhibition
P. Jake Slavish a, Jeanine E. Price a, Qin Jiang b, Xiaoli Cui b, Stephan W. Morris b,c, Thomas R. Webb a,
⇑
a Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, United States
b Department of Pathology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, United States
c Department of Oncology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, United States
a r t i c l e i n f o
a b s t r a c t
Article history:
We report the synthesis of a pyrimidinone library that targets anaplastic lymphoma kinase (ALK), an
oncogenic receptor tyrosine kinase. This library was generated in three steps from a versatile commer-
cially available starting material. Some compounds within this library showed single digit micromolar
inhibition of ALK in vitro, while showing minimal inhibition of other homologous insulin receptor family
kinases including the human insulin receptor kinase (IRK), at the highest concentrations investigated. We
also present initial ALK structure–activity relationships for this library.
Received 11 April 2011
Revised 25 May 2011
Accepted 26 May 2011
Available online 12 June 2011
Keywords:
Anaplastic lymphoma kinase (ALK)
Kinase inhibitor
Ó 2011 Elsevier Ltd. All rights reserved.
Small library synthesis
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase
(RTK) and a member of the insulin receptor superfamily.1,2 Mutant
forms of ALK, for example, NPM (nucleophosmin) -ALK and EML4
(echinoderm microtubule-associated protein-like 4) -ALK, have
been identified as oncogenic drivers in ALCL (anaplastic large cell
lymphoma),3,4 non-small-cell lung cancer,5,6 and neuroblastoma7–9
among other malignancies. Furthermore, ALK knock-out mice show
no phenotypic abnormalities,10 suggesting that inhibition of ALK for
the treatment of ALK-driven cancers should not be associated
with significant target-associated toxicity. The initial clinical
success of Pfizer’s dual ALK/MET inhibitor PF-234106611–14
(crizotinibÒ 1, Fig. 1) for the therapy of ALK-driven subsets of lung
cancer6,15 has confirmed the efficacy and safety of ALK inhibition for
the management of ALK-driven tumors.
We set out to generate a small library of ALK-selective kinase
inhibitors from a flexible and commercially available starting
material. Given the ALK-inhibitory activity of PF-2341066, Chem-
Bridge’s ALK inhibitor16 (2, Fig. 1), our previously published ALK
‘hit’ compound17 (3, Fig. 1), and other amino-pyrimidine/pyridines
recently reviewed,18 we envisioned that a pyridone or pyrimidi-
N
Cl
N
N
O
O
O
N
O
HN
F
N
H
Cl
N
1
NH2
N
H
O
2
Ph
N
Diversification
Cl
N
N
O
N
N
H
O
H
Masked OH source
Cl
3
4
Figure 1. Literature examples of ALK inhibitors.
⇑
Corresponding author.
E-mail address: thomas.webb@stjude.org (T.R. Webb).
0960-894X/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2011.05.103

P. J. Slavish et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4592–4596
4593
Scheme 1. Reagents and conditions: (a) 1-(triphenylphosphoranylidene)propan-2-one or ethyl 2-(triphenylphosphoranylidene)acetate, THF, 67 °C, 4 h; (b) para-methoxy
benzyl alcohol, potassium carbonate, neat, 50 °C, 16 h; (c) substituted phenol, potassium carbonate, DME, 80 °C, 16 h; (d) TFA, DCM, rt, 16 h.
Table 1
Yields of phenoxy-displacement/PMB-cleavage reactions and biochemical evaluation of pyrimidinone library versus ALK, IRK and MET using the in vitro enzymatic kinase assay
previously reported17
OR2
O
N
R1
N
H
O
Yielda (%)
ALK IC50
IRK IC50
MET IC50
b
ID
R1
R2
9a
10a
CH3
OEt
48
59
3.03
>40
>40
>40
4.01
>40
O
O
9b
10b
CH3
OEt
51
66
>40
>40
>40
>40
>40
>40
9c
10c
CH3
OEt
49
64
>40
>40
>40
>40
>40
>40
9d
10d
CH3OEt
35
63
>40
>40
>40
>40
>40
>40
Cl
9e
10e
CH3
OEt
33
60
>40
>40
>40
>40
>40
>40
F
9f
10f
CH3
OEt
53
60
>40
>40
>40
>40
>40
>40
O
O
O
9g
10g
CH3
OEt
50
25
>40
>40
>40
>40
>40
>40
O
O
O
9h
10h
CH3
OEt
27
84
>40
>40
>40
>40
>40
>40
CN
9i
10i
CH3
OEt
36
68
>40
>40
>40
>40
>40
>40
Cl
9j
10j
CH3
OEt
57
79
>40
>40
>40
>40
>40
>40
O
9k
10k
CH3
OEt
25
12
>40
>40
>40
>40
>40
>40
Cl
Cl
1
0.6
0.65
0.00078
a
Yields determined after reverse phase HPLC purification.
All IC50 value determinations were done in triplicate and are reported in lM.
b
none-based library could serve as the starting template for
selective ALK-targeted compounds. Since chloropyrimidines are
generally more reactive than their pyridine counterpart, we started
with the commercially available 2,4-dichloro-pyrimidin-5-carbal-
dehyde (4, Fig. 1). We envisioned that the initial chloride displace-
ment of 4 would allow for the introduction of the masked oxygen
component of the pyrimidine, followed by subsequent selective
diversification by displacement of the other chloride with various

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P. J. Slavish et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4592–4596
Table 2
nucleophiles. Additionally, the 5-carbaldehyde provided additional
varied avenues for diversification. Since enones, enoates and
derivatives thereof have been found to have anticancer and/or
antibacterial activity as thymidylate synthase inhibitors,19 dihy-
drofolate reductase inhibitor20 and bacterial enoyl-ACP reductase
inhibitors,21 we initially diversified the 5-pyrimidinyl position
Yields of selected phenoxy-displacement/PMB-cleavage reactions and biochemical
evaluation of pyrimidinone library versus ALK, IRK and MET. R1 = CH3 in all cases for
this Table
Yielda (%)
18
ALK IC50
IRK IC50
>40
MET IC50
>40
b
ID
R2
with a,b-unsaturated keto- and ester functionality, respectively.
O
Our synthetic efforts towards both the keto- and ester series are
illustrated in Scheme 1. Treatment of dichloropyrmidin-5-carbalde-
hyde (4) with commercially available 1-(triphenylphosphoranylid-
ene)propan-2-one or ethyl 2-(triphenylphosphoranylidene)acetate
under reflux conditions produced the corresponding ketone 5, or
ester 6, in 60% and 75% yield, respectively. 4-methoxyl benzyl alco-
hol displacement provided the PMB-protected chloro pyrimidinone
7 and 8 in 52% and 63% yield, respectively. Chloride displacement
with various phenols, followed by TFA-PMB cleavage, gave pyrimid-
inones 9 and 10a–m in 15–92% yield. Specific yields and IC50 values
of all pyrimidinones versus ALK and two kinases homologous to
ALK–IRK (insulin receptor kinase) and MET, are provided in Table 1.
As shown in Table 1, we observed that 9a exhibited single-digit
micromolar ALK-selective inhibition. The ester series suffered from
limited solubility, which was noted at the highest concentrations
used in these initial assays. With these data in hand, we prepared
and screened a larger library, based on the more active enone tem-
plate. The yields of the selected pyrimidinone compounds and their
respective activities versus ALK, IRK, and MET are displayed in
Table 2. (Additional data on less active enone compounds synthe-
sized (mostly bearing halo- or alkyl-aryl substituents) are available
in the Supplementary data.)
9l
6.64
N
H
O
9m
58
6.25
>40
>40
9n
9o
26
16
7.57
6.91
>40
>40
>40
>40
OH
CN
O
9p
39
7.54
>40
>40
O
O
9q
9r
9s
48
64
74
>40
>40
>40
>40
>40
>40
>40
O
O
F
>40
O
Several compounds from the enone series exhibited IC50s in the
single-digit micromolar range for ALK and no detectable inhibition
at the highest concentration tested (40 lM) for the highly homol-
O
ogous kinase IRK. This selectivity is clinically relevant due to the
possibility of iatrogenic diabetes resulting from IRK inhibition. It
appears that the 3-oxo aryl compounds (9a and m) exhibited the
greatest ALK-selective inhibition in this series, though 9a inhibited
MET in the single-digit micromolar range as well. 2-Oxo aryl enon-
es also displayed ALK-selectivity. 2-Ethyl ester 9u displayed
ALK-selective inhibition; however, the more lipophilic 2-hexyl es-
ter 9x showed no ALK inhibition. The ALK inhibition of the afore-
mentioned oxo-aryl compounds tolerated additional aryl-
substituents at times, but the presence of alkyl–aryl substitution
appears to render compounds inactive with respect to ALK.
We next evaluated additional R1 substituents, while keeping the
3-methyl ester aryl oxy constant (Scheme 2). Selective saponifica-
tion of the unsaturated ester in the presence of the aryl ester of 9a
10.18
O
9t
74
61
>40
>40
>40
>40
>40
O
EtO
9u
7.54
O
9v
48
>40
>40
>40
could not be achieved. Using
a similar synthetic route, as
O
illustrated in Scheme 1 carbaldehyde 4 was reacted with tert-butyl
2-(triphenylphosphoranylidene)acetate or 1-phenyl-2-(triphenyl-
phosphoranylidene)ethanone to give ester 11 or ketone 12 in
75% and 55% yield, respectively. Initial displacement with 4-meth-
oxyl benzyl alcohol provided the PMB-protected chloro pyrimidi-
none 13 and 14 in 66% and 43% yield, respectively. Subsequent
phenoxide displacement, followed by TFA cleavage, gave the
unsaturated acid 15 and phenyl ketone 16, both in 35% yield.
Unfortunately, both of these compounds were inactive in our
focused kinase screen.
We then concentrated on alternative substituents at the 5-pyri-
midinone position to elucidate the importance of the enone unit.
Reduction of the alkene using palladium on carbon with 1,4-cyclo-
hexadiene as the hydrogen source with microwave heating22 gave
the saturated pyrimidinone 17 (Scheme 3). Attempts to generate
5-pyrazolo analogues from 9a were explored as well. The 5-dihydro-
pyrazolo analogues 18 and 19 could be generated from 9a. However,
attempts to oxidize 18 using DDQ23,24 gave no reaction and the alter-
nate approach employing ceric ammonium nitrate25 gave the deacy-
O
9w
9x
9y
43
83
>40
>40
>40
>40
>40
>40
>40
>40
>40
Cl
O
C6H13
O
O
OEt
61
25
O
CF3
9z
1
9.87
0.6
>40
>40
Cl
0.65
0.00078
a
Yields determined after reverse phase HPLC purification.
All IC50 value determinations were done in triplicate and are reported in lM.
b

P. J. Slavish et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4592–4596
4595
O
Cl
N
O
Cl
N
Cl
N
13
14
O
O
O
b
c, d
a
O
N
R1
N
N
R1
O
N
R1
Cl
Cl
OPMB
N
H
O
, R1 = OtBu
, R1 = Ph
11, R1 = OtBu
12, R1 = Ph
4
15
, R1 = OH
16, R1 = Ph
Scheme 2. Reagents and conditions: (a) tert-butyl 2-(triphenylphosphoranylidene)acetate or 1-phenyl-2-(triphenylphosphoranylidene)ethanone, THF, 67 °C, 4 h; (b) para-
methoxy benzyl alcohol, potassium carbonate, neat, 50 °C, 16 h; (c) phenol, potassium carbonate, DME, 80 °C, 16 h; (d) TFA, DCM, rt, 16 h.
R1
O
O
O
N
N
O
N
O
O
O
O
HN
O
O
O
b
a
O
c
9a
N
N
N
N
H
N
H
17
O
N
H
20
18, R1 = Ac
19, R1 = CH3
O
O
Cl
N
Cl
N
O
O
N
O
R1
O
Br
Cl
Br
OPMB
e
N
f
d
N
N
O
Br
OPMB
N
H
N
Scheme 3. Reagents and conditions: (a) Pd (C), 1,4-cyclohexadiene, methanol, MW, 140 °C, 1 h; (b) hydrazine (where R1 = acetyl) or methyl hydrazine, HOAc, 90 °C, 16 h, (c)
ceric ammonium nitrate, methanol, rt, 4 h. (d) para-methoxy benzyl alcohol, potassium tert-butoxide, THF, 50 °C, 16 h; (e) phenol, potassium carbonate, DME, 80 °C, 16 h; (f)
arylboronic acid, tetrakis(triphenylphosphine) palladium, sodium carbonate, DMF/H2O (5:1), 130 °C, 16 h.
33% yield. Finally, Suzuki coupling using previously published
conditions26 gave the 5-aryl pyrimidinone products 24a–e. The
yields and ALK-inhibitory activities of each analogue are provided
in Table 3.
Table 3
Yields and biochemical evaluation of compounds 17–20, 24a–e versus ALK, IRK and
MET
ID
R1
Yielda (%)
ALK IC50
IRK IC50
MET IC50
b
Conclusion
17
18
19
20
40
75
49
30
>40
9.0
>40
>40
>40
>40
>40
>40
>40
>40
>40
>40
Ac
CH3
We report the synthesis and biochemical evaluation of a 5-
enone pyrimidinone library in four steps (three pots) that selec-
tively inhibits ALK when compared to the highly homologous ki-
nase, IRK. Compounds from the methyl enone series exhibit
single-digit micromolar ALK inhibition and two compounds from
that series demonstrated MET-inhibitory activity as well. The ac-
tive compounds from the methyl enone series generally bore
carbonyl substituents on the aryl ring, preferring the 2- or 3-aryl
positions. When the methyl group of the enone was replaced
with a phenyl group, ALK-inhibitory activity was lost. Com-
pounds with other functional groups at the terminal position
of the pyrimidinone, for example, ethyl ester or carboxylic acid,
were inactive versus ALK as well. Enone derivatives were syn-
thesized and only the N-acyl dihyrdropyrazole derivative exhib-
ited ALK-selective inhibition.
N
24a
24b
2
9
>40
>40
>40
>40
>40
>40
NH2
O
24c
24d
24e
5
8
3
>40
>40
>40
>40
>40
>40
>40
>40
>40
a
Yields determined after reverse phase HPLC purification.
All IC50 value determinations were done in triplicate and are reported in lM.
Acknowledgments
b
The authors would like to thank the staff in the High
Throughput Analytical Center in the Department of Chemical
Biology & Therapeutics, St. Jude Children’s Research Hospital—
Bing Yan, Andy Lemoff, Cynthia Jefferies and Lei Yang—for their
purification and quality control work for most of the compounds
described in this manuscript. This work was supported by the
American Lebanese Syrian Associated Charities (ALSAC), St. Jude
Children’s Research Hospital.
lated compound 20. The yields and ALK-inhibitory activities of each
analogue are shown in Table 3.
Additionally, we generated a small 5-aryl pyrimidinone library
starting with commercially available 5-bromo-2,4-dichloro pyrimi-
dine (21). Initial chloro displacement with para-methoxyl benzyl
alcohol, followed by phenolic displacement gave bromide 22 in

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P. J. Slavish et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4592–4596
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