A new class of highly cytotoxic diketopiperazines

Article abstract of DOI:10.1016/S0960-894X(00)00152-9

The discovery of a novel class of diketopiperazines possessing potent cytotoxic activity is described. (C) 2000 Elsevier Science Ltd. All rights reserved.

Full text of DOI:10.1016/S0960-894X(00)00152-9

Bioorganic & Medicinal Chemistry Letters 10 (2000) 1019±1020
A New Class of Highly Cytotoxic Diketopiperazines
Dale L. Boger,* Brian E. Fink and Michael P. Hedrick
Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute,
10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Received 1 February 2000; accepted 25 February 2000
AbstractÐThe discovery of a novel class of diketopiperazines possessing potent cytotoxic activity is described. # 2000 Elsevier
Science Ltd. All rights reserved.
DNA binding/alkylating agents that exhibit selective
cytotoxic activity are commonly used as therapeutics for
the treatment of cancer. During the course of preparing
a combinatorial library of DNA minor groove binding
agents, a novel class of diketopiperazines possessing
potent cytotoxic activity and DNA binding anity was
discovered.1 Herein is reported the discovery, synthesis
and biological properties of these agents.
Synthesis
During the course of preparing a library of heterocyclic
dipeptides by solution phase parallel synthesis,1 the
indole carboxylic acid 11 was found to provide the
diketopiperazine 2, rather than the expected dipeptide
(Scheme 1). Further elaboration of this core unit
through BOC deprotection (4.0 M HCl/EtOAc, 25 ꢀC,
3 h) a€orded the free diamine 3, which was converted to
the more water soluble bis(dimethylamino)diketopiper-
azine 4 (EDCI/DMAP, 25 ꢀC, 24 h). Along with the
core diketopiperazine, two extended agents were pre-
pared in order to probe the possibility of developing
more extended agents with increased biological activity
and/or better DNA binding properties. Because of the
low solubility of the diketopiperazine core itself and to
facilitate the characterization of intermediates, an alter-
native route was employed for these agents that con-
Scheme 1.
structed the core diketopiperazine at the ®nal step
allowing the isolation of more soluble intermediates at
each step (Scheme 2). The aminoindole 51 was coupled to
two di€erent aromatic amino acids used extensively in the
preparation of previously reported DNA binding agents
to a€ord 6 and 7. BOC deprotection (4.0 M HCl/EtOAc,
25 ꢀC, 2 h) and coupling to 4-(dimethylamino)butyric acid
a€orded the two amines 8 and 9. Hydrolysis of the
esters (LiOH, 1:1 MeOH/H2O, 60 ꢀC, 4 h) and treat-
ment of the crude acids with EDCI/DMAP a€orded the
two extended diketopiperazines 10 and 11.
Biological Activity
The diketopiperazines were assayed for cytotoxic activ-
ity using a standard L1210-cell based cytotoxicity assay
*Corresponding author. Tel.: +1-858-784-7522; fax: +1-858-784-78550;
e-mail: boger@scripps.edu
0960-894X/00/$ - see front matter # 2000 Elsevier Science Ltd. All rights reserved.
PII: S0960-894X(00)00152-9

1020
D. L. Boger et al. / Bioorg. Med. Chem. Lett. 10 (2000) 1019±1020
While the striking di€erence in cytotoxic activity may be
in part due to the low solubility of 2 and 3 compared to
4, it may also arise from the increased anity of 4 for
the polyanionic backbone of DNA. Analysis of the
DNA binding properties of 4, 10 and 11 using quanti-
tative titration with displacement of prebound ethidium
bromide showed that only 4 bound to DNA to an
appreciable extent (Table 1).2,3
Acknowledgements
We gratefully acknowledge the ®nancial support of the
National Institutes of Health (CA78045), Novartis, and
the award of a NIH postdoctoral fellowship (BEF, F32
CA76718, 1998±2000)
References and Notes
1. Boger, D. L.; Fink, B. E.; Hedrick, M. P. J. Am. Chem. Soc.
submitted for publication.
2. Boger, D. L.; Invergo, B. J.; Coleman, R. S.; Zarrinmayeh,
H.; Kitos, P. A.; Thompson, S. C.; Leong, T.; McLaughlin, L.
W. Chem±Biol. Interact. 1990, 73, 29. Boger, D. L.; Sakya, S.
M. J. Org. Chem. 1992, 57, 1277.
3. Spectroscopic data. 2: 1H NMR (DMSO-d6, 500 MHz) d
9.62 (s, 1H), 8.30 (d, 1H, J=8.9 Hz), 8.06 (s, 1H), 7.76 (s, 1H),
7.56 (d, 1H, J=8.9 Hz), 1.50 (s, 9H). 4: 1H NMR (DMSO-d6,
500 MHz) d 10.23 (s, 1H), 8.41 (d, 1H, J=9.2 Hz), 8.34 (d,
1H, J=1.9 Hz), 7.87 (s, 1H), 7.70 (dd, 1H, J=8.8, 1.9 Hz),
2.45 (t, 4H, J=7.4 Hz), 2.30 (s, 6H), 1.84 (pent, 2H, J=7.2
Hz). FABHRMS (DHB) m/z 543.2716 (M+H+, C30H34N6O4
1
requires 543.2720. 6: H NMR (acetone-d6, 500 MHz) d 9.39
(s, 1H), 8.24 (s, 1H), 7.86 (s, 1H), 7.58 (dd, 1H, J=8.8, 1.8
Hz), 7.50 (d, 1H, J=8.8 Hz), 4.34 (q, 2H, J=7.4 Hz), 1.52 (s,
9H), 1.35 (t, 3H, J=7.0 Hz). 7: 1H NMR (DMF-d7, 500 MHz)
d 10.30 (s, 1H), 9.48 (s, 1H), 8.33 (s, 1H), 7.80 (d, 2H, J=11.1
Hz), 7.65 (s, 2H), 7.47 (d, 2H, J=11.0 Hz), 3.78 (s, 3H), 1.23
(s, 9H); FABHRMS (NBA) m/z 412.1519 (M+H+,
C21H21N3O6 requires 412.1519). 8: 1H NMR (CD3OD, 500
MHz) d 7.92 (s , 1H), 7.74 (s , 1H), 7.35 (m , 2H), 7.06 (s, 1H),
4.28 (d, 2H, J=7.0 Hz), 2.42 (m, 4H), 2.25 (s , 6H), 1.83 (pent,
2H, J=7.4 Hz), 1.30 (t, 3H, J=7.0 Hz). 9: 1H NMR (CD3OD,
500 MHz) d 7.97 (d, 1H, J=1.8 Hz), 7.93 (d, 2H, J=12.4 Hz),
7.73 (d, 2H, J=11.0 Hz), 7.50 (dd, 1H, J=2.5, 11.4 Hz), 7.48
(d, 1H, J=11.0 Hz), 7.15 (s, 1H), 4.38 (q, 2H, J=7.4 Hz), 2.52
(t, 2H, J=7.6 Hz), 2.48 (t, 2H, J=7.4 Hz), 2.36 (s, 6H), 1.92
Scheme 2.
(Table 1). While both the BOC-protected and free
amino derivatives 2 and 3 as well as the two extended
agents 10 and 11 showed low activity, IC50=29, 30, 4,
and 7 mM, respectively, the dimethylamino compound 4
showed remarkably potent activity, IC50=34 nM.
Table 1. Cytotoxic activity and DNA binding anity
IC50 (nM)
(L1210)
K (Â105)a
poly[dA]-poly[dT]
1
(pent, 2H, J=7.6 Hz), 1.41 (t, 3H, J=7.0 Hz). 10: H NMR
2
3
4
10
11
29,000
30,000
34
4000
7000
NDb
ND
2.03
NAc
NA
(CF3CO2D, 500 MHz) d 8.78 (br s, 2H), 8.43 (br s, 2H), 8.15
(br s, 2H), 7.80 (br s, 4H), 3.68 (br s, 4H), 3.35 (s, 16H), 2.62
(br s, 4H); FABHRMS (DHB) m/z 795.2495 (M+H+,
C38H38N10O6S2 requires 795.2495). 11: 1H NMR (DMF-d7,
500 MHz) d 8.60 (m, 12H), 8.02 (s, 2H), 7.46 (s, 2H), 2.87 (t,
4H, J=7.6 Hz), 2.78 (s, 12H), 2.68 (t, 4H, J=7.1 Hz), 2.32
(pent, 4H, J=7.0 Hz); FABHRMS (DHB) m/z 781.3455
(M+H+, C44H44N8O6 requires 781.3462).
aBinding constants calculated from K=Ketbr[EtBr]/[Agent].
bNot determined due to poor solubility of agent.
cDemonstrated no decrease in ¯uorescence up to 10 mM.