Design and synthesis of aminopropyl tetrahydroindole-based indolin-2-ones as selective and potent inhibitors of Src and Yes tyrosine kinase

Article abstract of DOI:10.1016/j.bmcl.2003.09.069

A novel series of substituted 3-[3-(aminopropyl)-4,5,6,7-tetrahydro-1H- indol-2-ylmethylene]-1,3-dihydro-indole-2-ones was discovered as potent inhibitors of the non-receptor tyrosine kinase Src and Yes. A structure-activity relationship was developed in order to optimize their potency and selectivity. Syntheses of these compounds are also described herein.

Full text of DOI:10.1016/j.bmcl.2003.09.069

Bioorganic & Medicinal Chemistry Letters 14(2004) 187–190
Design and synthesis of aminopropyl tetrahydroindole-based
indolin-2-ones as selective and potent inhibitors of Src and Yes
tyrosine kinase
Huiping Guan,a A. Douglas Laird,b Robert A. Blake,c Cho Tanga and Chris Lianga,*
aDepartment of Chemistry, SUGEN, Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA
bPre-clinical Research and Exploratory Development, SUGEN, Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA
cDiscovery Technology, SUGEN, Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA
Received 14May 2003; revised 20 September 2003; accepted 27 September 2003
Abstract—A novel series of substituted 3-[3-(aminopropyl)-4,5,6,7-tetrahydro-1H-indol-2-ylmethylene]-1,3-dihydro-indole-2-ones
was discovered as potent inhibitors of the non-receptor tyrosine kinase Src and Yes. A structure–activity relationship was developed
in order to optimize their potency and selectivity. Syntheses of these compounds are also described herein.
# 2003 Elsevier Ltd. All rights reserved.
Src and its close kinase sub-family members, such as
Yes, Fyn, Lyn and Lck, are non-receptor protein tyr-
osine kinases which function as early upstream signal
transduction proteins.1,2 Src and Yes are widely expres-
sed and activated in a great number of tumor types. In
particular, Src has been identified as a prototype onco-
gene and is considered to be a validated therapeutic
target for cancer, osteoporosis and other diseases.3
Extensive research has been directed to discover Src
efforts were focused on (1) the C-5 position of the oxi-
ndole ring, (2) the tetrahydroindole moiety and (3) the
30-amino side chain as shown in Figure 1.
In general, the syntheses consist of three steps: (1) pre-
paration of substituted oxindole core (2) preparation of
functionalized pyrrole aldehydes (3) aldol-condensation
of the two moieties under basic conditions13 to furnish
final indolinones 1, 2, 3, and 4. Most of the oxindoles
with C-5 substitution were either commercially available
or prepared by published methods.14 Oxindole sulfones
7 and sulfonamides 8 were prepared by sulfonation of
2-oxindoles 5 into 6 followed by alkylation or amidation
of the sulfonyl chloride group of 6, respectively (Scheme
1). Compound 14 was synthesized via procedures illu-
strated in Scheme 1. Intermediate 11 was obtained by
reduction of 9 to its sodium methylsulfonite 10 followed
by reaction with 4-bromomethyl nitrobenzene. Reduction
of the nitro group of 11 led to 12, which was condensed
inhibitors and
a
number of them have been
reported,4ꢀ11 though none has been reported in clinical
trials to date.12
Screening of a proprietary compound collection showed
several tetrahydroindole based indolinones as potent
and selective Src inhibitors. In particular, 3-[3-(3-dime-
thylamino-propyl)-4,5,6,7-tetrahydro-1H-indol-2-ylme-
thylene]-2-oxo-2,3-dihydro-1H-indole-5-sulfonic
acid
methylamide (1a) was identified as a potent inhibitor of
Src kinase activity (0.1 mM in an enzymatic assay and a
functional cellular phosphorylation assay) with over
10-fold selectivity against closely related kinases such as
Lck and PDGFRb. The present study reports the
synthesis and initial structure–activity relationship
(SAR) on this novel class of compounds. Our chemistry
* Corresponding author at present address: 729 W. Remington Drive,
Sunnyvale, CA 94087, USA. Tel./fax: +1-408-746-0486; e-mail:
chrisliang03@yahoo.com
Figure 1. Lead compound and SAR focus.
0960-894X/$ - see front matter # 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2003.09.069

188
H. Guan et al. / Bioorg. Med. Chem. Lett. 14 (2004) 187–190
Scheme 1. Synthesis of substituted indolin-2-ones.
Scheme 3. Synthesis of functionalized tetrahydroindole aldehydes.
Scheme 2. Synthesis of analogues of tetrahydroindole aldehydes.
Scheme 4. Diversification of the piperazine moiety.
with ethyl(methylthio)acetate to produce the key inter-
mediate 13. Reductive cleavage of the methylthio group
of 13 furnished 14.
indole aldehyde shown in Scheme 2. Series 3 and 4 were
prepared from the two oxindoles condensed with the
tetrahydroindole aldehydes in Schemes 3 and 4.
Analogues of 4,5,6,7-tetrahydroindole-2-carbaldehydes
16 were made by amidation, reduction and Vilsmeier
formylation of commercially available 15. 18 was
synthesized by reducing both the amido and ethoxy
carbonyl groups of 1714 followed by formylation
(Scheme 2).
An initial SAR study revealed that the substituents at
the C-5 position of the oxindole core had a dramatic
impact on the inhibitory activity against Src kinase
(Table 1). Larger alkyl secondary sulfonamides (1c–f)
and tertiary sulfonamides (1g) reduced Src inhibitory
activity. Replacing the sulfonamide with a sulfonyl
group of similar size (1i) slightly improved Src potency.
Varying the size of the alkyl led to weaker Src inhibitors
(1h,j). These results depict that methylsulfonamide of 1a
or ethylsulfonyl of 1i have favorable size and that the
acidic proton of sulfonamide is not critical to Src activ-
ity. However, the sulfone moiety was essential to
potency towards Src. Its removal (1l) or replacement
with carbonyl (1m,n), phenyl (1o), fluorine (1p), or
methoxy (1q) all diminished Src inhibitory activity.
Insertion of a methylene between the sulfonyl and oxi-
ndole abolished Src activity (1k), suggesting that the
sulfonyl group needs to be directly attached to the oxi-
ndole core.
Syntheses of derivatives of tetrahydroindole aldehydes
are illustrated in Scheme 3, where R1R2N represents
different amines. 3-(2-Formyl-4,5,6,7-tetrahydroindol-3-
yl)-propionamides 20 was derived from 19.13 Com-
pounds 22 were made from intermediate 2115,16 via
amidation and reduction. Formylation of 22 afforded
23. Mannich type of reaction to attach a morpholino-
methyl moiety to the C-30 position of 4,5,6,7-tetra-
hydroindole-2-carbaldehydes 26 was achieved in a
microwave reactor. The terminal amino group of piper-
azine moiety in 23a was further diversified by amidation
or alkylation to furnish 28a–e (Scheme 4).
Finally, different oxindoles prepared according to
Scheme 1 were reacted with the tetrahydroindoles 23
(R1=R2=methyl) in Scheme 3 to yield series 1. Series 2
compounds were derived from the reaction of the 5-N-
methylsulfonamide oxindole with substituted pyrrole or
The tetrahydroindole moiety was found to be favorable
for Src activity. Replacing it with indole (2a) or opening
the six-membered ring (2b) decreased the inhibitory
potency towards Src kinase activity (Fig. 2).

H. Guan et al. / Bioorg. Med. Chem. Lett. 14 (2004) 187–190
189
Table 1. Biochemical Src kinase inhibitory activity of compounds
1a–q
Table 2. Biochemical Src kinase inhibitory activity of compounds
3a–p and 4a–p
Compd
R
Src IC50 (mM)*
Compd
R
Src IC50 (mM)*
3a
4a
4b
3c
4c
3d
4d
3e
4e
3f
H
2.1
0.7
0.4
0.01
0.07
0.03
0.04
0.3
1a
1b
1c
1d
1e
1f
1g
1h
1i
1j
1k
1l
1m
1n
1o
1p
1q
SO2NHCH3
SO2NH2
0.10
0.6
0.24
0.23
1.2
0.3
2.6
0.3
0.06
0.23
10
3.3
0.7
1.1
2.3
0.5
1.0
H
(CH2)2CO2H
CH2N(CH2CH2)2O
CH2N(CH2CH2)2O
SO2NHCH2CH2OH
SO2NHCH(CH3)2
SO2NHCH2(4-F–Ph)
SO2NH(2-Cl–Ph)
SO2N(CH3)2
SO2CH3
(CH2)2CONH2
(CH2)2CONH2
(CH2)2CON(CH2CH2)2NCH3
(CH2)2CON(CH2CH2)2NCH3
(CH2)3N(CH2CH2)2O
0.5
SO2C2H5
0.06
0.15
0.07
0.21
0.2
0.3
0.8
0.3
0.4
SO2CH(CH3)2
CH2SO2CH3
H
CO2H
CO2NHCH3
Ph
4f
(CH2)3N(CH2CH2)2O
3g
4g
3h
3i
4i
3j
(CH2)3N(CH2CH2)2NCH3
(CH2)3N(CH2CH2)2NCH3
(CH2)3N(CH2CH2)2NH
(CH2)3N(CH2CH2)2NCO2C2H5
(CH2)3N(CH2CH2)2NCO2C2H5
(CH2)3N(CH2CH2)2NCOCH3
(CH2)3N(CH2CH2)2NCOCH3
(CH2)3N(CH2CH2)2NCOCH2OH
(CH2)3N(CH2CH2)2NCOCH2OH
(CH2)3N(CH2CH2)2NCH2CO2C2H5
(CH2)3N(CH2CH2)2NCH2CO2H
(CH2)3N(CH2CH2)2NCH2CO2H
(CH2)3N(CH2CH2)2CHOH
(CH2)3N(CH2CH2)2CHOH
(CH2)3N(CH2CH2)2NCH2CH2OH
(CH2)3N(CH2CH2)2NCH2CH2OH
F
OCH3
4j
3k
4k
3l
3m
4m
3n
4n
3o
4o
0.4
*IC50 values were determined by at least two separate tests with
deviation less than 20% and are reported as mean values.
0.22
0.07
0.02
0.07
0.05
0.07
0.03
0.07
*IC50 values were determined by at least two separate tests with
deviation less than 20% and are reported as mean values.
Lck, Fyn, VEGFR2, FGFR1, or PDGFRb according
to previously reported methods.13,17 Inhibition of cel-
lular Src function was evaluated using the actin ring
assay which assesses the Src-dependent cytoskeletal re-
organization of podosome rosettes in fibroblast cells
transformed with an activated mutant of Src.17,18 Selec-
ted data for the most potent compounds are listed in
Table 3. It shows that this class of compounds is very
potent against Yes as well as Src. But they displayed
about 10-fold selectivity for Src over Lck and sometimes
Fyn. The selectivity with respect to VEGFR2 and
FGFR1 was moderate in some cases, but the potent
compounds with amido side chains (3d, 4d) were not
very selective against FGFR1. Most compounds exhib-
ited high selectivity for Src over PDGFRb.
Figure 2. Structure of 2a and 2b and their Src kinase inhibitory activity.
With the optimized oxindole substituents (5-ethylsul-
fone and 5-methylsulfonamide) and the tetra-
hydroindole moiety fixed, we further examined
variations on the C-30 position of the tetrahydroindole
core (Table 2). The results indicated that the C-30 side
chain was required since its deletion impaired the activ-
ity by over 10-fold (3a and 4a, compared to 1a and 1i,
respectively). Replacing the basic head group by an
acidic group reduced potency (4b). However, there is no
obvious trend regarding the length or basicity of the
C-30 substituents. For example, shortening the linker
improved activity by 10-fold in 3c over the initial lead
1a, but did not affect 4c compared to 1i. Replacing the
amino chain by amido chain afforded more potent
compounds 3d and 4d as well as less potent compounds
3e, 4e. Varying the basicity of the side chain has little
effect on Src activity as well (3f–h, vs 1a). Further
diversification of piperazylpropyl chain produced mixed
results. Some (3l–o) are more potent than 1a, while
others (3i–k) are weaker, with the largest difference as
high as 20-fold in inhibiting Src enzymatic activity
(Table 2).
Although most compounds in Table 3 are more potent
in Src biochemical assay than the initial lead 1a, this did
not necessary translate into improved cellular potency.
In fact, most of these compounds were much less potent
in cells than 1a and only the close analogues 3f–g have
comparable cellular potency. The lack of cellular
potency for enzymatically potent Src inhibitors was also
observed in other series of compounds.5,6,10,11 It is
interesting to note that the zwitterion 3m was inactive in
cells (perhaps because of poor cell membrane perme-
ability), while its ester analogue (3l) had moderate cel-
lular activity. All of the inhibitors with relatively good
Most compounds were also evaluated for their inhibi-
tory activity against tyrosine phosphorylation by Yes,

190
H. Guan et al. / Bioorg. Med. Chem. Lett. 14 (2004) 187–190
Table 3. Biochemical selectivity and cellular Src activity of selected
compounds
References and notes
1. Courtneidge, S. A. Biochm. Soc. Trans. 2002, 30, 11.
2. Sura, M.; Teti, A. Drug News Perspec. 2000, 133, 169.
3. Susa, M.; Missbach, M.; Green, J. Trends Pharmacol. Sci.
2000, 21, 489.
Compd
Biochemical activity (IC50, mM)a
Cellular
(IC50
,
Src Yes Lck Fyn VEGFR2 FGFR1 PDGFRb mM)a
4. Rapecki, S.; Allen, R. J. Pharmacol. Exp. Ther. 2002, 303,
1325.
5. Berger, D.; Dutia, M.; Powell, D.; Wissner, A.; DeMorin,
F.; Raifeld, Y.; Weber, J.; Boschelli, F. Bioorg. Med.
Chem. Lett. 2002, 12, 2989.
6. Berger, D.; Dutia, M.; Powell, D.; Wu, B.; Wissner, A.;
DeMorin, F.; Weber, J.; Boschelli, F. Bioorg. Med. Chem.
Lett. 2002, 12, 2761.
7. Wilson, M. B.; Schreiner, S. J.; Choi, H.-J.; Kamens, J.;
Smithgall, T. E. Oncogene 2002, 21, 8075.
8. Myers, M. R.; Setzer, N. N.; Spada, A. P.; Zulli, A. L.;
Hsu, C.-Y. J.; Zilberstein, A.; Johnson, S. E.; Hook, L. E.;
Jacoski, M. V. Bioorg. Med. Chem. Lett. 1997, 7, 417.
9. Wang, Y.; Miller, K.; Boschelli, D.; Ye, F.; Wu, B.;
Floyd, M.; Powell, D.; Wissner, A.; Webber, J.; Boschelli,
F. Bioorg. Med. Chem. Lett. 2000, 10, 2477.
10. Widler, L.; Green, J.; Missbach, M.; Susa, M.; Altmann,
E. Bioorg. Med. Chem. Lett. 2001, 11, 849.
11. Altmann, E.; Missbach, M.; Green, J.; Susa, M.; Wagen-
knecht, H.-A.; Widler, L. Bioorg. Med. Chem. Lett. 2001,
11, 853.
1a
1i
0.1 0.01 1.6 0.06
0.06 0.02 0.2 0.3
0.01 0.040.08 0.4
0.07 0.16 0.8 1.40.1
0.03 0.01 0.1 0.05
1.1
2.7
0.06
0.7
0.42.5
0.2
0.4 NT
0.07
3.3
0.5
b
0.1
3c
4c
3d
4d
3f
3g
4g
3l
3m
4m
3n
4n
3o
4o
NT
1.0
5.0
>10
>10
0.1
b
0.5
0.3
2.3
0.3
2.6
0.5
6.6
5.1
18
10
11
0.040.03
—
0.2
0.08
1.7
1.2
NTb
0.08
8
13
0.06 0.03 0.7 0.7
0.07 0.01 0.7 0.8
0.16 0.03 0.6 1.2
0.07 0.02 0.6 0.5
0.02 0.01 0.1 0.40.4 0.2
0.07 0.01 0.40.4 0.8
0.05 0.01 0.3 0.2
0.07 0.02 0.7 0.6
0.03 0.01 0.40.1
0.07 0.040.5 0.4
0.1
0.2
0.9
>20
>10
0.4
10
2.3
7.1
0.5
0.4
0.4
.7 3.44 0.9
0.5
0.8
0.6
1.1
5.6
9
3
1.7
a IC50 values were determined by at least two separate tests with
deviation less than 20% and are reported as mean values.
b NT, not tested.
12. Sawyer, T.; Boyce, B.; Dalgarno, D.; Iuliucci, J. Expert
Opin. Investig. Drugs 2001, 10, 1327.
13. Sun, L.; Tran, N.; Liang, C.; Hubbard, S.; Tang, F.; Lip-
son, K.; Schreck, R.; Zhou, Y.; McMahon, G.; Tang, C.
J. Med. Chem. 2000, 43, 2655.
cellular activity (1a, 1i, 3f, 3g, 4g, IC50<0.5 mM) con-
tained a basic (3-amino)propyl side chain attached to
the C-30 of the tetrahydroindole moiety, suggesting that
it confers to cellular potency.
14. Sun, L.; Tran, N.; Liang, C.; Tang, F.; Rice, A.; Schreck,
R.; Waltz, K.; Shawver, L.; McMahon, G.; Tang, C. J.
Med. Chem. 1999, 42, 5120.
15. Tang, P. C.; Sun, L.; Miller, T.; Liang, C.; Tran, N.; Nguyen,
A.; Nematalla, A. PCT Patent WO 0008202 A2, 2000.
16. Brown, E.; Butler, A. J. Chem. Res. 1998, 458.
17. Blake, R. A.; Broome, M. A.; Liu, X.; Wu, J.; Gishisky,
M.; Sun, L.; Courtneidge, S. A. Mol. Cell. Biol. 2000, 20,
9018.
In conclusion, we have explored substituted 3-[3-(ami-
nopropyl)-4,5,6,7-tetrahydro-1H-indol-2-ylmethylene]-
1,3-dihydro-indole-2-ones as potent and selective inhi-
bitors of Src and Yes kinases. Initial SAR study sug-
gested that the 5-sulfonyl substitution, tetrahydroindole
ring, and 3-aminopropyl side chain of the initial lead 1a
are all critical to biochemical and cellular potency and
kinase selectivity for Src.
18. Blake, R. A. Curr. Opin. Pharmacol. 2001, 1, 533.