Novel pyrrolyllactone and pyrrolyllactam indolinones as potent cyclin-dependent kinase 2 inhibitors

Article abstract of DOI:10.1016/S0960-894X(03)00312-3

Cyclin-dependent kinases (CDKs) are essential in the control of cell cycle progression. Inhibition of CDKs represents a new approach for pharmacological intervention in the treatment of a variety of proliferative diseases, especially cancer. Based on the crystal structure of CDK2 in complex with an imidazole indolinone compound 1 (SU9516), lead optimization through modeling, synthesis, and SAR studies has led to the discovery of a novel series of pyrrolyllactone and pyrrolyllactam indolinones as potent CDK2 inhibitors.

Full text of DOI:10.1016/S0960-894X(03)00312-3

Bioorganic & Medicinal Chemistry Letters 13 (2003) 1939–1942
Novel Pyrrolyllactone and Pyrrolyllactam Indolinones as Potent
Cyclin-Dependent Kinase 2 Inhibitors
Xiaoyuan Li,* Ping Huang, Jingrong Jean Cui, Jennifer Zhang and Cho Tang*
SUGEN, Inc., 230 East Grand Ave., South San Francisco, CA 94080, USA
Received 4 November 2002;accepted 27 January 2003
Abstract—Cyclin-dependent kinases (CDKs) are essential in the control of cell cycle progression. Inhibition of CDKs represents a
new approach for pharmacological intervention in the treatment of a variety of proliferative diseases, especially cancer. Based on
the crystal structure of CDK2 in complex with an imidazole indolinone compound 1 (SU9516), lead optimization through model-
ing, synthesis, and SAR studies has led to the discovery of a novel series of pyrrolyllactone and pyrrolyllactam indolinones as
potent CDK2 inhibitors.
#
2003 Elsevier Science Ltd. All rights reserved.
Cyclin-dependent kinases (CDKs) play important roles
in cell cycle regulation.
1ꢀ4
CDKs activate host proteins
through phosphorylation of serine or threonine residues
using adenosine triphosphate (ATP) as a phosphate
donor. Inhibitors of CDKs are anticipated to possess
therapeutic potential in the treatment of proliferative
1ꢀ9
disorders, including cancer.
Over the past few years,
a large variety of small-molecule inhibitors have been
reported in the literature which target the ATP-binding
site of CDKs (see reviews in refs 5–9 and references
cited therein). Some inhibitors have been co-crystallized
with CDK2. These crystallographic investigations have
provided a wealth of structural information for the
design of inhibitors of CDKs. In the study reported
here, we chose CDK2 as a target since both cyclin E/
CDK2 and cyclin A/CDK2 complexes were suggested
Figure 1. Chemical structures of SU9516 (1) and SU5402 (2).
As part of a continuing effort to optimize the indolinone
scaffold in order to increase the CDK2 inhibitory activ-
ity, structure-based design and modeling studies have
been performed using the co-crystal structure of CDK2
in complex with 1 (Fig. 2). The design considerations
resulting from these studies are summarized in Figure 3.
5
to play an important role in cell cycle regulation. We
1
1
have previously reported 1 (SU9516, Fig. 1), an imida-
zole indolinone compound identified as CDK2 inhibitor
by screening of collections of synthetic organic mole-
Like SU5402, the oxindole (C¼O)NH moiety and the
pyrrole or imidazole NH are essential for binding. They
make three hydrogen bonds with the backbone motif in
the kinase hinge region. Appropriate substituents at the
1
0
cules. Subsequently, this compound was successfully
0
1
0
0
co-crystallized with CDK2.
The crystal structure
4-, 5-, 3 -, and 4 -positions of the indolinone core are
favorable for CDK2 inhibition, as shown in Figure 3.
revealed that the binding mode of 1 in CDK2 is similar
to SU5402 bound to FGFR1. SU5402 is a pyrrole
indolinone compound 2 (Fig. 1) that has been co-crys-
0
The 5 -position is, however, not suitable for substitution
since it is very close to the peptide backbone of His84
and Gln85. Substitutions are not tolerated at either the
1
1
tallized with FGFR1 previously.
6
3
- or 7-positions because they are close to Phe80 (Fig.
0
). The 5 -steric exclusion of indolinone is unique to
0
CDK2, while generally 5 -methylpyrrole indolinones
1
2
13
such as SU5416, SU6668, and tetrahydroindole
1
*Corresponding author. Tel.: +1-650-837-3418;e-mail: sharon-li@
sugen.com
4
indolinones are favorable for the inhibition of VEGF-
0
960-894X/03/$ - see front matter # 2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0960-894X(03)00312-3

1940
X. Li et al. / Bioorg. Med. Chem. Lett. 13 (2003) 1939–1942
With this promising result, the pyrrolyllactone indoli-
none scaffold was subsequently expanded to pyrro-
lyllactam indolinone (16a–n) since pyrrolyllactam was
expected to have better pharmaceutical properties.
The general syntheses of pyrrolyllactone (15a–n) and
pyrrolyllactam indolinones (16a–n) are illustrated in
Schemes 1–3. The pyrrolyllactone (5) was prepared
using commercially available valerolactone (3) that was
treated with tosylmethyl isocyanide and followed with a
Vilsmeier reaction to afford the corresponding pyrrolyl-
aldehyde (5, Scheme 1). For the synthesis of pyrro-
lyllactam (13, Scheme 2), the key intermediate t-boc
protected dihydro-pyridone 10 was synthesized from
2
-piperidone (6) in four steps with an overall yield of
2%. The final indolinone compounds 15 and 16 were
5
prepared via a condensation reaction (Scheme 3) of
Figure 2. Co-crystal structure of CDK2 in complex with 1. Color
coding: oxygen, red;nitrogen, dark blue;carbons in CDK2, green;
carbons in 1, gray;hydrogen, white. Non-polar hydrogens are gen-
erally omitted for clarity. Light blue ribbon represents the backbone of
CDK2.
pyrrolaldehydes (5, 13) in ethanol with the oxindoles 14
12ꢀ14
reported previously.
All new compounds were
characterized by 300 MHz NMR and MS. The final
products were purified by either re-crystallization or
1
6
column chromatography.
R2, FGF-R1, PDGF-Rb, and some other kinases. Fur-
ther pair-wise comparisons of 5 -H and 5 -methyl pyr-
0
role indolinones clearly demonstrated that 5 -H
0
Pyrrolyllactone indolinones with various substituents at
the 4-, 5-, and 6-positions in the oxindole core are
shown in Table 2. Among the 5-substituted analogues
(15a–i), 5-N-methylsulfonamide (15b) and 5-carboxyl
(15f) compounds are the most potent and selective,
consistent with their favorable interactions with the side
chain of Lys33 (Fig. 3). In addition, 5-sulfonamide
analogues (15b–e) are more potent than the 5-halo ana-
logues (15g–i). Substitution at the 4-position was con-
sidered well tolerated from modeling study.
Appropriate substituent at this position can further
interact with the side chain of Gln131 or Asn132 (Fig.
3). In fact, compounds with a polar substituent at the 4-
position (15k, 15l) are significantly more potent than the
4-methyl analogue 15j (Table 2). Compound 15l is the
most potent analogue among the three. In this com-
pound, a piperidine was introduced to the 4-position
based on modeling study of flavopiridol, the most
0
analogues were significantly more potent in CDK2
0
inhibitory activity than the corresponding 5 -methyl
0
1
5
analogues, fully supporting the prediction of 5 -H
preference of CDK2 based on modeling.
With the rationale discussed above, a novel pyrro-
lyllactone indolinone scaffold (15a–n) was designed and
synthesized. In this scaffold, the lactone moiety can
make additional hydrogen bonding and electrostatic
interactions with the side chain of Lys89 in CDK2. Such
interactions were absent in the co-crystal structure of
CDK2 in complex with 1 (Fig. 2). Consistent with this
hypothesis, a direct comparison of pyrrolyllactone
indolinone 15a with imidazole indolinone 1 in Table 1
revealed that the pyrrolyllactone compound is more
potent and selective than the imidazole compound.
Figure 3. Design considerations for lead optimization. X is a carbon or nitrogen in the structure.

X. Li et al. / Bioorg. Med. Chem. Lett. 13 (2003) 1939–1942
1941
Table 1. Biochemical screening dataa [IC50 (mM)] for a direct com-
parison of pyrrollylactone indolinone 15a with imidazole indolinone 1
Compd
Structure
CDK2
FLK
PDGF-Rb
SRC
1
0.11
0.13
18
11
15a
0.040
>20
>20
>20
aAssay procedures are provided in ref 16. All experiments were con-
ducted in duplicate.
Figure 4. A comparison of 15l with flavopiridol by docking in the
ATP binding site of CDK2, suggesting that their piperidine moieties
are in a similar position. Color coding: oxygen, red;nitrogen, dark
blue;carbons in 15l, gray;carbons in flavopiridol, green;chlorine,
light green;hydrogen, white. Non-polar hydrogens are generally
omitted for clarity.
Scheme 1. Synthesis of pyrrolyllactone.
advanced CDK inhibitor in clinical trials.17 The piperi-
dine moiety of 15l was in a similar position to that of
flavopiridol when the two molecules were docked in the
ATP binding site of CDK2, as shown in Figure 4. The
6-position is not suitable for substitution (Fig. 3). As
shown in Table 2, 15m and 15n are clearly less potent
than the 4- or 5-substituted compounds 15a–l.
Similar to the results of pyrrolyllactone indolinones,
among the 5-substituted pyrrolyllactam indolinones
(
16a–i) in Table 3, 5-sulfonamide (16b, 16e) and 5-car-
boxyl (16f) analogues are more potent than the 5-halo
analogues (16g, 16i). Like 15l, the 4-piperidine com-
pound (16l) exhibits potent inhibitory activity. The
6-phenyl analogue (16n) is significantly less active than
the 5- or 4-substitued analogues (16a–l). However, pyr-
rolyllactams are generally 2–10-fold less potent than the
corresponding pyrrolyllactones, as seen in the pair-wise
comparisons of 16a versus 15a, 16b versus 15b, 16e ver-
sus 15e, 16f versus 15f, 16g versus 15g, 16i versus 15i,
16k versus 15k, and 16l versus 15l. The better activity of
pyrrolyllactone is attributed to its lactone moiety that
makes favorable electrostatic interaction with the side
chain of Lys89 (Fig. 3) in addition to hydrogen bond-
ing. In pyrrolyllactam, the lactam amide NH is unfa-
vorable in electrostatic interaction with Lys89, while the
amide C¼O can form hydrogen bonds with Lys89.
Scheme 2. Synthesis of pyrrolyllactam.
In summary, based on the crystal structure of CDK2 in
complex with 1, lead optimization through modeling,
synthesis, and SAR studies has led to the discovery of a
novel series of pyrrolyllactone and pyrrolyllactam indo-
linones as potent CDK2 inhibitors. The 4- and 5-sub-
stitutions in these indolinones are important to their
CDK2 inhibitory activity, and pyrrolyllactone indoli-
nones are generally more potent than pyrrolyllactam
indolinones.
Scheme 3. General synthesis of indolinones.

1942
X. Li et al. / Bioorg. Med. Chem. Lett. 13 (2003) 1939–1942
a
Table 2. Biochemical screening data [IC50 (mM)] of pyrrollylactone indolinones 15a–n
Compd
R
CDK2
FLK
PDGF-Rb
SRC
1
1
1
1
1
1
1
1
1
1
1
5a
5b
5c
5d
5e
5f
5g
5h
5i
5-OCH
3
0.040
0.004
0.012
0.064
0.033
0.004
0.082
0.088
0.19
>20
6.6
6.6
>20
>20
>20
>20
>20
>20
>20
2.1
>20
>20
13
5-SO
5-SO
5-SO NH(
5-SO N(CH
2
NHCH
NH
Pr)
3
2
2
2
i
6.7
>20
>20
>20
>20
>20
>20
>20
>20
2
3
)
2
>20
6.2
10
>20
11
5-COOH
5-F
5-Cl
5-Br
18
>20
>20
5j
5k
4-CH
4-CH CH
3
0.27
0.030
>20
1.2
2
2
OH
15l
0.009
0.49
1.1
1.1
1
1
5m
5n
6-OCH
6-Ph
3
1.5
>10
>20
2.0
1.4
1.1
>20
8.4
aAssay procedures are provided in ref 16. All experiments were conducted in duplicate.
References and Notes
a
Table 3. Biochemical screening data [IC50 (mM)] of pyrrollylactam
indolinones 16a–n
1
9
2
3
1
4
5
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0
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2
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