3-Hydroxychromones as cyclin-dependent kinase inhibitors: Synthesis and biological evaluation

Article abstract of DOI:10.1016/j.bmcl.2006.12.011

A novel series of 3-hydroxychromones were prepared and found to be CDK inhibitors. Isothiazolidine 1,1-dioxide analogues showed potent CDK1 and CDK2 inhibitory activities and inhibited proliferation of EJ, HCT116, SW620, and MDAMB468 cancer cells.

Full text of DOI:10.1016/j.bmcl.2006.12.011

Bioorganic & Medicinal Chemistry Letters 17 (2007) 1284–1287
3-Hydroxychromones as cyclin-dependent kinase inhibitors:
Synthesis and biological evaluation
Jinho Lee,a,* Taesik Park,b Shinwu Jeong,b, Kyoung-Hee Kimb and Changyong Hongb
aDepartment of Chemistry, Keimyung University, 1000 Sindang-Dong, Dalseo-Gu, Daegu 704-701, South Korea
bLG Life Sciences, Science Town, Taejon 305-380, South Korea
Received 1 September 2006; revised 20 November 2006; accepted 4 December 2006
Available online 15 December 2006
Abstract—A novel series of 3-hydroxychromones were prepared and found to be CDK inhibitors. Isothiazolidine 1,1-dioxide ana-
logues showed potent CDK1 and CDK2 inhibitory activities and inhibited proliferation of EJ, HCT116, SW620, and MDAMB468
cancer cells.
Ó 2006 Elsevier Ltd. All rights reserved.
Cyclin-dependent kinases (CDKs) play significant roles
in cell cycle progression, and their activities are regulat-
ed precisely by multiple mechanisms.1 The activities of
CDKs are regulated positively by the various cyclin pro-
teins and negatively by the CDK inhibitors such as the
Cip/Kip and INK protein families. In various human tu-
mors, the abnormal high expression of the cyclins and/
or loss of the CDK inhibitors are known to cause the
dysregulation of the activities of CDKs.2 Such altered
activations of CDKs in tumorigenesis have instigated
intensive searches for CDK inhibitors as a potential
anti-cancer drug.3,4
inhibitory activities against CDK2 (Table 1). As far as
the hydroxyl group was present at R1, any additional
hydroxyl group at R2 or R3 did not affect the inhibitory
activities (1, 2, 6). Since flavopiridol has the hydroxyl
group at R2 which is involved in H-bond interactions
with the enzyme,9 compounds having hydroxyl group
at R1 instead of R2 were expected to have different bind-
ing orientations, compared to flavopiridol, and to show
different structure–activity relationships.
Efforts to improve the potency of the 3-hydroxychro-
mone 6 initially focused on the modification of R4 with
amine derivatives. 3-Hydroxychromones were prepared
in two steps.11 However, two different synthetic routes
were used depending on the type of R4 as shown in
Flavonoids are phenylchromone derivatives that are
ubiquitous in all plants. It has been shown that they
have a variety of biological activities including anticarci-
nogenic activity.5,6 Flavonoids displayed either inhibi-
tion or induction of the enzymes involved in the
regulation of the cell proliferation;7 for example, flavo-
piridol showed inhibitory activity against multiple ki-
nases and was the first small molecule that went to the
clinical trial as a CDK inhibitor.8 In an effort to search
for CDK inhibitors, flavonol had been found as a hit.
Preliminary screening of the commercially available fla-
vonoids showed that at least one hydroxyl group at
either R1 or R2 of chromone was needed to have the
Table 1. Structure and CDK2 inhibitory activity of flavonesa
R2
O
R1
OH
OH
R3
O
R4
R2
b
Compound
R1
R3
R4
CDK2 IC50 (lM)
1
2
3
4
5
6
OH
OH
H
OH
H
OH
OH
OH
OH
H
H
40
5
H
OH
H
H
20
Keywords: 3-Hydroxychromone; Isothiazolidine 1,1-dioxide; CDK2.
*
H
OH
H
>500
>500
4
Corresponding author. Tel.: +82 53 580 5183; fax: +82 53 580
5164; e-mail: jinho@kmu.ac.kr
H
OH
H
H
H
H
Present address: USC/Norris Comprehensive Cancer Center, Keck
School of Medicine, University of Southern California, 1441 East
Lake Avenue, Los Angeles, CA 90089, USA.
a The CDK2 inhibitory assays were performed as described in Ref. 10.
b Values are means of three experiments.
0960-894X/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.12.011

J. Lee et al. / Bioorg. Med. Chem. Lett. 17 (2007) 1284–1287
1285
O
O
O
O
O
O
CH3
a
a, b, c
O
O
O
OH
OH
OH
NO2
Br
NO2
Br
O
8
d
7
b, c
O
O
O
O
O
O
OH
O
O
O
CH3
e
CH3
CH3
d
OH
OH
O
O
O
O
O
O
O
O
R7
R7
NH2
NO2
12c, d, e
9
10
Scheme 2. General synthetic route for 3-hydroxychromones. Reagents
and conditions: (a) piperonal, NaOH, 80% aq EtOH (65%); (b) H2O2,
10% aq NaOH, MeOH (78%); (c) CH3I, K2CO3, acetone (79%); (d)
Pd2(DBA)3, DPPF toluene; 12c: pyrrolidine (82%), 12d: piperidine
(68%), 12e: N-methylpiperazine (63%); (e) BBr3, DCM (75–81%).
e
O
O
O
O
OH
CH3
f
OH
OH
O
O
O
N
N
R5
R6
R5
R6
Alternatively, cyclic amines were introduced at R4 by
the palladium-catalyzed coupling reactions12 of 8-brom-
ochromone with the corresponding amines as shown in
Scheme 2.
11
12a,b, 13a-e
Scheme 1. General synthetic route for 3-hydroxychromones. Reagents
and conditions: (a) piperonal, NaOH, 80% aq EtOH (95%); (b) H2O2,
10% aq NaOH, MeOH (62%); (c) CH3I, K2CO3, acetone (94%); (d)
Pd/C, H2, MeOH/DCM (1:1) (quantitative); (e) 12b: CH3CHO,
NaBH(AcO)3, 1,2-DCE (42%), 13a: (1) Cl(CH2)3COCl, Et3N, DCM;
(2) NaH, DMF (26%, two steps yield), 13b: succinic anhydride, Et3N,
DMF (55%), 13c: ClCO(CH2)3COCl, K2CO3, DMF (37%), 13d: (1)
CbzNHCH2CO2H, i-PrOCOCl, N-methylmorpholine, THF (75%); (2)
(n-Bu)4NF, THF (59%), 13e: Cl3COCCl3, CH3NH(CH2)2OCH3, Et3N,
DMF (61%); (f) BBr3, DCM (30–84%).
Alkylation and amidation of amine either open-chains
or cyclic forms did not improve the potency against
CDK2, 12a–e, 13a–d (Table 2). However, the presence
of methyl group at the nitrogen of hydantoin improved
the activity by 2 order of magnitude compared to hydan-
toin itself (13d vs 13e). 1k6-Isothiazolidine-1,1-dione 15a
provided a similar enzymatic potency with N-meth-
ylhydantoin, but showed improved cellular activity.
Schemes 1 and 2. 8-Amino-3-hydroxychromone 10
was prepared according to the procedure outlined in
Scheme 1. The coupling reaction between 1-(2-hydroxy-
5-methyl-3-nitro-phenyl)-ethanone and benzo[1,3]diox-
ole-5-carbaldehyde provided compound 8 which was
converted to 3-hydroxychromone by NaOH in the pres-
ence of hydrogen peroxide. Protection of the hydroxyl
group followed by reduction of nitro group produced
the compound 10 which was converted to various func-
tionalities either by alkylation or amide coupling
reaction. Compound 13b was obtained by treatment of
11, product of the reaction between 10 and succinic anhy-
dride, with BBr3.
An X-ray crystal structure analysis showed that the
binding mode of 3-hydroxychromone was different from
that of flavopiridol, as expected (Fig. 1).
The binding mode was analogous to that of fisetin
bound to CDK6.14 3-Hydroxyl and 4-keto groups made
two hydrogen bonds with carbonyl oxygen of Glu 81
and the amide nitrogen of Leu 83, respectively. In con-
trast, flavopiridol used its 5-hydroxyl group for the
hydrogen bond with Glu 81. The chromone ring made
many van der Waals contacts with the hinge region of
CDK2. The dihydroxyphenyl ring rotated about 30 de-
Table 2. CDK2 inhibitory activities of 3-hydroxychromones
R5, R6, or R7
CDK2 IC50 (lM)
EJ cytotoxicityb GI50 (lM)
a
Compound
12a
12b
12c
12d
12e
13a
13b
13c
13d
13e
15a
H, H
0.63
1.6
CH3CH2, CH3CH2
CH2(CH2)2CH2
CH2(CH2)3CH2
CH2CH2N(CH3)CH2CH2
CH2(CH2)2CO
CO(CH2)2CO
3.0
2.6
0.64
1.6
1.5
4.4
1.2
CO(CH2)3CO
CONHCH2CO
CON(CH3)CH2CO
SO2(CH2)2CH2
4.0
0.056
0.087
1.1
0.6
a Values are means of three experiments.
b Exponentially growing cells were treated with test compounds at various concentrations for 48 h, and then the cell numbers were measured. The
compound concentration with 50% growth inhibition activity was determined.13 Values are means of three experiments.

1286
J. Lee et al. / Bioorg. Med. Chem. Lett. 17 (2007) 1284–1287
O
O
O
OBn
a, b, c, d
R8
R8
OH
O
NH
O
H
NH2
OBn
OBn
e
O
O
OH
OBn
f
R9
R8
OBn
O
O
O
O
N
N
OH
S
S
O
O
R8 = 14a: OBn
14c: Cl
15a-f
Figure 1. Comparison of the binding mode of 3-hydroxychromone 15a
(in green) and deschloro-flavopiridol (in gray) in the CDK2 ATP-
binding site.
14d: Br
Scheme 3. General synthetic route for 3-hydroxychromones bearing
isothiazolidine-1,1-dione. Reagents and conditions: (a) NaOH, 80% aq
EtOH (59–78%); (b) H2O2, 10% aq. NaOH, MeOH (59–93%); (c)
C6H5CH2Br, K2CO3, acetone (47–56%), (d) 1—(Boc)2O, DMAP,
DCM; 2—NaOH, MeOH; (3) AcCl, MeOH (52–94%, three steps
yield); (e) 1—Cl(CH2)3SO2Cl, Et3N, DMAP, DCM; 2—1N aq NaOH,
DMF (14a: 74%, 14c: 82%, 14d: 67%, two steps yield); (f) 15a: Pd/C,
H2, MeOH/DCM (1:1) (54%), 15b: Pd/C, H2 (82% from 14d), 15c: Pd/
C, H2 (58%), 15d: BBr3, DCM (69%), 15e: (1) Pd2(dba)3, DPPF,
Zn(CN)2, DMF (33% from 14d); (2) Pd/C, H2 (86%), 15f: (1)
FSO2CF2CO2CH3, CuI, DMF (76% from 14d); (2) Pd/C, H2 (91%).
grees from the plane of chromone and bound comple-
mentarily to the pocket formed by Lys 33, Val 64, Phe
80, and Ala 144. Its 2-hydroxyl group formed third
hydrogen bond with the side chain of Asp 145. 1k6-Iso-
thiazolidine-1,1-dione rotated about 80 deg from the
plane of chromone making close contacts with side
chains of Gly 11, Val 18, and Gln 131.15
Since the introduction of 1k6-isothiazolidine-1,1-dione at
R4 improved the potency in both CDK2 enzyme and EJ
cell line, further modifications of catechol had been per-
formed while keeping 1k6-isothiazolidine-1,1-dione.
the presence of CuI according to the procedure de-
scribed by Njoroge et al.17
The substitution of the hydroxyl group with Cl or Br
(15c, 15d, respectively) provided highly potent com-
pounds against both CDK1 and CDK2 and the prolifer-
ation of various human cancer cell lines, such as EJ
(bladder carcinoma), HCT116, SW620 (colon carci-
noma), and MDAMB468 (breast carcinoma) (Table 3).
The introduction of CF3 15f increased the selectivity on
CDK1 over CDK2 but caused poor cellular activity.
The results described in Table 3 indicate that inhibition
of both CDK1 and CDK2 may be required to achieve
potent anti-proliferative activity in cancer cells.
The synthetic methods for the modification of catechol
are outlined in Scheme 3. The synthesis of 1k6-isothiaz-
olidine-1,1-dione was performed in two consecutive
steps without purification of intermediate.
Compound 15e was obtained by palladium-catalyzed
cyanation of 14d according to the procedure described
by Maligres et al.16 Introduction of trifluoromethyl moi-
ety was accomplished by treatment of aryl bromide 14d
with methyl 2,2-difluoro-2-(fluorosulfonyl)-acetate in
Table 3. CDK2 inhibitory activities of 3-hydroxychromones bearing 1k6-isothiazolidine-1,1-dione
O
OH
R9
OH
O
O
O
N
S
R9
IC50 (lM)
Cytotoxicityb GI50 (lM)
a
Compound
CDK1
CDK2
EJ
HCT116
SW620
MDAMB468
15a
15b
15c
15d
15e
15f
OH
H
0.13
0.45
0.087
0.25
0.19
0.075
1.4
0.6
0.28
0.34
0.037
0.9
1.0
0.27
0.065
0.064
0.57
0.064
0.052
0.62
0.18
Cl
Br
0.033
0.019
0.16
0.017
c
0.23
c
c
c
CN
CF3
c
c
0.063
1.7
1.3
0.91
a Values are means of three experiments.
b Tests were performed as shown in Table 2. Values are means of three experiments.
c Not determined.

J. Lee et al. / Bioorg. Med. Chem. Lett. 17 (2007) 1284–1287
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3-hydroxychromone derivatives that were effective cy-
clin-dependent kinase inhibitors and potent growth
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