Design and synthesis of bis 1-chloromethyl-5-hydroxy-1,2- dihydro-3H-benz[e]indole (seco-CBI)-pyrrole polyamide conjugates.

Article abstract of DOI:10.1021/ol020047k

[carbohydrate structure: see text] The design and synthesis of bis 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI)-pyrrole polyamide conjugates (13, 17) as DNA minor groove binding agents are described.

Full text of DOI:10.1021/ol020047k

ORGANIC
LETTERS
2002
Vol. 4, No. 11
1851-1854
Design and Synthesis of Bis
1-Chloromethyl-5-hydroxy-1,2-
dihydro-3H-benz[e]indole
(seco-CBI)-Pyrrole Polyamide
Conjugates
Rohtash Kumar and J. William Lown*
Department of Chemistry, UniVersity of Alberta, Edmonton, AB, Canada T6G 2G2
annabelle.wiseman@ualberta.ca
Received March 1, 2002
ABSTRACT
The design and synthesis of bis 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI)-pyrrole polyamide conjugates (13, 17) as
DNA minor groove binding agents are described.
Sequence-specific DNA alkylating agents have played an
important role in molecular biology and human medicine in
cancer chemotherapy. The cyclopropylindole class of anti-
tumor antibiotics, exemplified by CC-1065 and duocarmycin
A (Figure 1), is the parent member of a potent class of
naturally occurring antitumor antibiotics that exert their
biological properties through the sequence-selective alkyl-
ation of DNA.1-10 Cellular investigations have shown that
CC-1065 alkylates B-DNA reversibly with a high sequence
selectivity at AT regions of the minor groove sites of 5′-d
(A/GNTTA)-3′ and 5′-d (AAAAA)-3′, by the N-3 position
of the 3′-adenine by the cyclopropylindole unit present in
the molecule.11-12
Compared with other anticancer agents (+)-CC-1065 has
a high bioactivity and is 400 times more potent than
(7) Hurley, L. H.; Needham-VanDevanter, D. R. Acc. Chem. Res. 1986,
19, 230.
* To whom correspondence should be addressed. Tel. 780-492-3646.
Fax: 780-492-8231.
(1) Boger, D. L.; Johnson, D. S. Angew. Chem., Int. Ed. Engl. 1996, 35,
1439.
(8) Warpehoski, M. A. In AdVances in DNA Sequence Specific Agents;
Hurley, L. H., Ed.; JAI: Greenwich, CT, 1992; Vol. 1, p 315.
(9) Aristoff, P. A. In AdVances in Medicinal Chemistry; Maryanoff, B.
E., Ed.; JAI: Greenwich, CT, 1993; Vol. 2, p 67.
(2) Boger, D. L.; Boyce, C. W.; Garbaccio, R. M.; Goldberg, J. Chem.
ReV. 1997, 97, 787.
(10) Warpehoski, M. A.; McGovren, P.; Mitchell, M. A. In Molecular
Basis of Specificity in Nucleic Acid-Drug Interactions; Pullman, B., Jortner,
J., Eds.; Kluwer: Dordrecht, The Netherlands, 1990; p 531.
(11) Reynolds, V. L.; Molineux, I.; Kaplan, D. J.; Swenson, D. H.;
Hurley, L. H. Biochemistry 1985, 24, 6228.
(12) Hurley, L. H.; Reynolds, V. L.; Swenson, D. H.; Petzold, G. L.;
Scahill, T. A. Science 1984, 226, 843.
(3) Boger, D. L.; Johnson, D. S. Proc. Natl. Acad. Sci. U.S.A. 1995, 92,
3642.
(4) Boger, D. L. Acc. Chem. Res. 1995, 28, 20.
(5) Boger, D. L. Chemtracts: Org. Chem. 1991, 4, 329.
(6) Warpehoski, M. A.; Hurley, L. H. Chem. Res. Toxicol. 1988, 1, 315.
10.1021/ol020047k CCC: $22.00 © 2002 American Chemical Society
Published on Web 05/01/2002

10 000 times higher than that of CC-1065 against KB human
cancer cells.16 Studies also have shown that some synthetic
compounds, which contain two CPI moieties linked from
two positions by a flexible methylene chain of variable
length, are significantly more potent than CC-1065 both in
vitro and in vivo.18
Prevously we reported the synthesis and biological evalu-
ation of seco-CBI dimers against nine types of cancer cells.
Certain examples showed significant activity against CCRT-
CEM, HL-60 (TB), MOLT-4, leukemia, CNS cancer,
melanoma, and prostate cancer cell lines with Gl50 values
<0.01 µm.19
To our knowledge no attempt has been made to synthesize
bis 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole
(seco-CBI)-pyrrole polyamide conjugates 13, 17 (bis seco-
CBI pyrrole polyamide dimers). To investigate the structure-
activity relationship systematically, we have designed and
synthesized bis seco-CBI pyrrole polyamide dimers, which
contain two racemic CBI moieties linked from two different
positions with pyrrole polyamide by a flexible methylene
chain of variable length.
Figure 1.
doxorubicin, 80 times more potent than actinomycin D, and
about twice as potent as maytansine against L1210 leukemia
cells in vitro. Despite its high potency CC-1065 cannot be
used in humans because it was found that it caused delayed
death in the experimental animals. Because of the unique
structure and properties of these natural products, many
chemists were stimulated to synthesize derivatives and
analogues of CC-1065 and duocarmycins with better anti-
tumor selectivity and DNA-sequence-specific binding prop-
erties,13 in an attempt to avoid the undesired side effects while
retaining potency against tumor cells.13 As a successful
example of modification of 1,2,8,8a-tetrahydro-7-methyl
cyclopropa[c]pyrrolo[3,2-e]indole-4-one (CPI), the DNA
alkylating moiety of CC-1065, Boger first reported that the
simplified moiety, 1,2,9,9a-tetrahydrocyclo-propa[c]benzo-
[e]indole-4-one (CBI) and its analogues were more stable
and more potent than the CPI counterparts.14
In our previous work the seco-CBI moiety was synthesized
by using the following convenient route in good yield.
Deprotonation of carbamate 1,17 using NaH, followed by
alkylation of the resulting anion with 1,3-dichloropropene
in the presence of phase transfer catalyst Bu4NI gave an
mixture of Z and E isomers of vinyl chloride 2. Selective
reduction of the nitro group of 2 using hydrazine provided
amine 3, the desired precursor for the intramolecular aryl
radical cyclization on to a tethered vinyl chloride. A
deoxygenated solution of 3 in dry benzene was heated at
reflux for 15 h in the presence of 2 equiv of Bu3SnH and a
catalytic amount of AIBN to give the bifunctionalized seco-
CBI prodrug 4. To deactivate the amine group at the C7
position by reaction with acetyl chloride almost quantitatively
to afford its acetyl derivative 5 (Scheme 1).
In addition, studies on netropsin, distamycin, and related
compounds have led to the concept of polyamides as
information reading agents.15 A predominantly 4-5 AT base
pair sequence is recognized by netropsin and distamycin in
the minor groove of DNA. In our group attempts have been
made to link CPI16 and CBI17 with polyamides, which are
well-established DNA minor groove binders, to improve their
pharmacological properties and potencies. We found that
certain CPI-polyamide conjugates exhibit potency up to
Scheme 1a
(13) (a) Boger, D. L.; Colemon, R. S. J. Am. Chem. Soc. 1988, 110,
4796. (b) Lin, C. H.; Sun, D.; Hurley, L. H. Chem. Res. Toxicol. 1991, 4,
21.
(14) (a) Boger, D. L.; Ishizaki, T.; Wysocki, R. J.; Munk, S. A.; Kitos,
P. A.; Suntornwat, O. J. Am. Chem. Soc. 1989, 111, 6461. (b) Boger, D.
L.; Ishizaki, T. J. Org. Chem. 1990, 55, 5823. (c) Aristoff, P. A.; Johnson,
P. D. J. Org. Chem. 1992, 57, 6234.
(15) (a) Lown, J. W. Synthesis of Sequence-specific Agents: Lexitrop-
sins. In Molecular Aspects of Anticancer Drug-DNA Interactions; Neidle,
S., Waring, M., Eds.; CRC Press: Boca Raton, FL, 1993; Vol. 1, p 322.
(b) Dervan, P. B. Science 1986, 232, 464. (c) Trauger, J. W.; Baird, E. E.;
Dervan, P. B. Angew. Chem., Int. Ed. 1998, 37, 1421. (d) Mrksich, M.;
Parks, M. E.; Dervan, P. B. J. Am. Chem. Soc. 1994, 116, 7983.
(16) (a) Fregeau, N. L.; Wang, Y.; Pon, R. T.; Wylie, W. A.; Lown, J.
W. J. Am. Chem. Soc. 1995, 117, 8917. (b) Iida, H.; Lown, J. W. Recent
Res. DeV. Synth. Org. Chem. 1998, 1, 17.
a (i) NaH; (ii) ClCHdCHCH2Cl, Bu4NI; (iii) hydrazine hydrate,
FeCl3, C; (iv) Bu3SnH, AIBN; (v) CH3COCl, DIEA.
(17) (a) Jia, G.; Iida, H.; Lown, J. W. Hetrocycl. Commun. 1998, 4, 557.
(b) Jia, G.; Iida, H.; Lown, J. W. Chem. Commun. 1999, 119. (c) Jia, G.;
Iida, H.; Lown, J. W. Synth. Lett. 2000, 5, 603.
Treatment of the seco-CBI 4 with 1.0 equiv succinic
anhydride in the presence of triethylamine in dry THF at
1852
Org. Lett., Vol. 4, No. 11, 2002

60 °C provided acid 6 in 80% yield. This acid 6 was then
coupled with the amine moiety of pyrrole polyamide 7,20
using EDCI and HOBt as the coupling agents, in dry DMF
at room temperature for about 12 h to afford the correspond-
ing coupled seco-CBI polyamide methyl ester 8 in 80% yield,
which upon hydrolysis with 1 N NaOH at room temperature
produced the corresponding seco-CBI polyamide acid com-
pound 9 in 70% yield. The corresponding amino compound
was then prepared by hydrogenation of the corresponding
nitro polyamide. This seco-CBI polyamide acid 9 was treated
with the seco-CBI prodrug 4 under standard EDCI/HOBt
coupling conditions and via its acid chloride route (Scheme
2). Unfortunately both reactions failed to produce the
introducing a more nucleophilic primary amine moiety in
the seco-CBI 4 through a suitable linker.
Condensation of the seco-CBI 4 in the presence of EDCI
and HOBt in dry DMF at room temperature with 1.0 equiv
N-Fmoc glycine gave compound 10 in 70% yield. Detach-
ment of the Fmoc group from 10 with TBAF in dry THF,
followed by coupling with 1.0 equiv of seco-CBI poly-
amide acid 9 using EDCI and HOBt as the coupling agents
in dry DMF at room temperature for about 12 h afforded
the corresponding coupled bis seco-CBI polyamide 12 in
70% yield. Hydrogenolysis of the bis seco-CBI polyamide
12 in THF with 4.0 equiv of ammonium formate in the
presence of Pd-C for about 2 h to remove the benzyl ether
almost quantitatively provided the final C7-C7 bis seco-
21
CBI pyrrole polyamide dimer 13
in 80-90% yield
(Scheme 3).
Scheme 2a
Scheme 3a
a (i) N-FmOC glycine, EDCI, HOBt, DMF, rt; (ii) TBAF, THF,
rt; (iii) 9, EDCI, HOBt, DMF, rt; (iv) HCOONH4, Pd/C,
THF, rt.
a (i) Succinic anhydride, THF, rt; (ii) EDCI, HOBt, DMF, rt;
(iii) 1 N NaOH, THF/MeOH (1:1), rt; (iv) EDCI, HOBt, DMF, rt;
(v) DCC, HOBt, DMF, rt; (vi) EDCI, DMF, rt; (viii) (1) TBDMS,
imidazole, rt, (2) oxalyl chloride/DCM 0 °C, (3) Et3N, THF, rt.
Acid-mediated deprotection of the Boc group from 5
followed by coupling with 1.0 equiv of N-Boc glycine under
standard EDCI/HOBt coupling conditions in dry DMF
desired product because of the less reactive aromatic amino
group of the seco-CBI 4. In that case we needed to increase
the reactivity of the amino group at the C7 position by
(21) Spectral data for compound 13: 1H NMR (300 MHz, DMSO-d6) δ
1.52 (s, 18H, 2 × Boc-H), 2.56-2.70 (m, 4H, 2 × CH2CO-), 3.81 (s, 3H,
-NCH3), 3.82 (s, 3H, -NCH3), 3.85 (s, 3H, -NCH3), 3.90-4.10 (m, 12H,
Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2), 6.88 (d, 1H, J ) 1.8 Hz, Py-H),
6.96 (d, 1H, J ) 1.8 Hz, Py-H), 7.05 (d, 1H, J ) 1.8 Hz, Py-H), 7.18 (d,
1H, J ) 1.8 Hz, Py-H), 7.24 (d, 1H, J ) 1.8 Hz, Py-H), 7.26 (d, 1H,
J ) 1.8 Hz, Py-H), 7.59-7.75 (m, 6H, 2 × C4-H, C7-H, C8-H),
8.32 (m, 1H, NHCH2), 8.40 (s, 2H, 2 × C6-H), 9.89 (s, 1H), 9.91 (s, 1H),
9.95 (s, 1H), 10.09 (s, 1H), 10.12 (s, 1H), 10.30 (s, 1H), 10.32 (s, 1H).
ES-MS m/z calcd for C60H65N11O12Cl2Na 1224.40, found 1224.40 (M +
Na+).
(18) (a) Mitchell, M. A.; Johnson, P. D.; Williams, M. G.; Aristoff, P.
A. J. Am. Chem. Soc. 1989, 111, 6428. (b) Mitchell, M. A.; Kelly, R. C.;
Wicniensky, N. A.; Hatzenbuhler, N. T.; Williams, M. G.; Petzold, G. L.;
Slihgtom, J. L.; Siemieniak, D. R. J. Am. Chem. Soc. 1991, 113, 8994.
(19) (a) Jia, G.; Iida, H.; Lown, J. W. Hetrocycl. Commun. 1999, 5, 467.
(b) Jia, G.; Lown, J. W. Bioorg. Med. Chem. 2000, 8, 1607.
(20) (a) Lown, J. W.; Krowicki, K. J. Org. Chem. 1985, 50, 3774. (b)
Zhao, R.; Lown, J. W. Heterocycles 1995, 41, 337.
Org. Lett., Vol. 4, No. 11, 2002
1853

CBI polyamide acid 9 using EDCI and HOBt as the coupling
agents in dry DMF produced benzyl-protected C7-N3 bis
seco-CBI pyrrole polyamide dimer 16 in 60-70% yield.
Treatment of 16 with ammonium formate in the presence of
Pd-C for about 2 h provided the final C7-N3 bis seco-
CBI pyrrole polyamide dimer 1722 in 80% yield (Scheme
4).
Scheme 4a
In summary, we have described the first synthesis of the
bis 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole
(seco-CBI)-pyrrole polyamide conjugates 13 and 17 (bis
seco-CBI pyrrole polyamide dimers). Results on the DNA
sequence preferences and biological evaluation will be
reported in due course.
Acknowledgment. The research was supported by a grant
to J.W.L. from the Natural Sciences and Engineering
Research Council of Canada.
OL020047K
(22) Spectral data for compound 17: 1H NMR (300 MHz, DMSO-d6) δ
1.52 (s, 9H, Boc-H), 2.04 (s, 3H, CH3CON), 2.58-2.70 (m, 4H, 2 ×
CH2CO-), 3.81 (s, 3H, -NCH3), 3.82 (s, 3H, -NCH3), 3.85 (s, 3H,
-NCH3), 3.90-4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2),
6.88 (d, 1H, J ) 1.5 Hz, Py-H), 6.96 (d, 1H, J ) 1.5 Hz, Py-H), 7.05 (d,
1H, J ) 1.5 Hz, Py-H), 7.16 (d, 1H, J ) 1.5 Hz, Py-H), 7.23 (d, 1H, J )
1.5 Hz, Py-H), 7.26 (d, 1H, J ) 1.5 Hz, Py-H), 7.60-7.79 (m, 5H, 2 ×
C8, C9-H, C4-H), 7.90 (d, 1H, C4-H), 8.20-8.30 (m, 1H, NHCH2),
8.35-8.42 (m, 2H, 2 × C6-H), 9.91 (s, 1H), 9.94 (s, 1H), 10.03 (s, 1H),
10.05 (s, 1H), 10.07 (s, 1H), 10.14 (s, 1H), 10.32 (s, 1H). HR-ESMS m/z
calcd for C57H59N11O11Cl2Na 1166.367, found 1166.368 (M + Na+).
a (i) 4 M HCl in dioxane, rt, 2 h; (ii) N-Boc glycine, EDCI, HOBt,
NaHCO3, DMF, rt; (iii) 4 M HCl in dioxane, rt, 2 h; (iv) 9, EDCI,
HOBt, NaHCO3, DMF, rt; (v) HCOONH4, Pd/C, THF, rt.
afforded compound 14 in good yield. Detachment of the Boc
group from 14, followed by coupling with 1.0 equiv of seco-
1854
Org. Lett., Vol. 4, No. 11, 2002