Synthesis and cytotoxicity evaluation of novel C7-c7, C7-N3 and N3-N3 dimers of 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benzo[e]indole (seco-CBI) with pyrrole and imidazole polyamide conjugates.

Article abstract of DOI:10.1039/b303650m

The C7-C7, C7-N3 and N3-N3 dimers of 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benzo[e]indole (seco-CBI) with pyrrole and imidazole polyamides were synthesized and preliminary anti-cancer evaluation carried out by NCI against three types of cancer cells.

Full text of DOI:10.1039/b303650m

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Synthesis and cytotoxicity evaluation of novel C7–C7, C7–N3 and
N3–N3 dimers of 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-
benzo[e]indole (seco-CBI) with pyrrole and imidazole polyamide
conjugates
Rohtash Kumar and J. William Lown*
Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
Received (in Pittsburgh, PA, USA) 1st April 2003, Accepted 13th June 2003
First published as an Advance Article on the web 27th June 2003
The C7–C7, C7–N3 and N3–N3 dimers of 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benzo[e]indole (seco-CBI) with
pyrrole and imidazole polyamides were synthesized and preliminary anti-cancer evaluation carried out by NCI
against three types of cancer cells.
DNA.14–22 CC-1065 and some of its derivatives irreversibly
alkylate DNA and some of compounds reversibly alkylate
Introduction
DNA has for many years been a traditional target for chemo-
therapeutic intervention1 in human cancers, especially for those
where high proliferation rates of some tumor cell types have
resulted in sensitivity to drugs, which block replication and
transcription of their DNA.2 Substantial progress has been
made in understanding the fundamental principles responsible
for the sequence-selective recognition of DNA by small organic
molecules3 including a range of naturally occurring antitumor
antibiotics. Three fundamental issues that arise in the examin-
ation of DNA binding agents are the origin of binding affinity,
binding selectivity and reaction selectivity including DNA
alkylation or cleavage. Each factor can independently assert
levels of control on the sequence-selective recognition of DNA
and the relative role and origin of these effects remain a pri-
mary objective of many investigations. A powerful complement
to such tools in the examination of naturally derived DNA
binding agents is the preparation and subsequent examination
of key partial structure modifications or variations in the nat-
ural product and their corresponding unnatural enantiomers.
In addition, DNA sequence specificity or selectivity has
recently become recognized as an important component of
many cytotoxic agents,4,5 CC-1065 and duocarmycins,6 sara-
mycin,7 distamycin,8–10 netropsin,8–10 pyrrolo[1,4]benzodiaze-
pinone,11 bleomycin,12,13 several of which are of clinical
interest in the treatment of human malignancies. CC-1065 and
the duocarmycins represent members of a class of exceptionally
potent antitumor antibiotics that derive their biological effects
through the reversible, sequence selective alkylation of duplex
DNA. Subsequent to their disclosure, extensive efforts have
been devoted to establish their duplex DNA alkylation selectiv-
ity and its structural origin,14–22 to establish the link between
DNA alkylation and the concomitant biological properties,23
and to define the fundamental principles underlying the rel-
ationships between structure, chemical reactivity, and biological
properties.24–33
Compared with other anticancer agents (ϩ)-CC-1065 has a
high bioactivity, and is 400 times more potent than doxo-
rubicin, 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 to cause delayed death in
experimental animals. Because of the unique structure and
properties of these natural products, many chemists were inter-
ested in synthesizing derivatives and analogues of CC-1065 and
duocarmycins with better antitumor selectivity and DNA-
sequence specific binding properties,34 in an attempt to avoid
the undesired side effects while retaining their potency against
tumor cells.34 As a successful example of the modification of
1,2,8,8a-tetrahydro-7-methylcyclopropa[c]pyrrolo[3,2-e]indole-
4-one (CPI), the DNA alkylating moiety of CC-1065, Boger
first reported the synthesis of 1,2,9,9a-tetrahydrocyclo-propa[c]-
benzo[e]indole-4-one (CBI).35
Studies of the CBI-based analogues of CC-1065 have
shown that they are chemically more stable, biologically more
potent, and considerably more synthetically accessible than
the corresponding agents incorporating the natural CPI
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
T h i s j o u r n a l i s © T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 3
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Scheme 1 Reagents and conditions: i. NaH; ii. ClCH=CHCH2Cl, Bu4NI; iii. hydrazine hydrate, FeCl3, activated carbon; iv. Bu3SnH, AlBN; v.
CH3COCl, DIEA; vi. succinic anhydride, THF, Et3N, RT.
(cyclopropapyrroloindolone) alkylation subunit of CC-1065.29
Moreover, the natural enantiomers of the CBI based analogs
alkylate DNA with an unaltered sequence selectivity at an
enhanced rate and with a greater efficiency than the corre-
sponding CPI analogs, indicating that they possess character-
istics that make them especially attractive to pursue.36 These
observations have prompted us to study certain CBI-based
analogs of CC-1065 in detail.
Results and discussion
In our previous work the seco-CBI moiety was synthesized43
using the following convenient route in good yield. Deproton-
ation of carbamate 1, (Scheme 1)43 using NaH, followed by
alkylation of the resulting anion with 1,3-dichloropropene in
the presence of phase transfer catalyst Bu4NI gave a 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 cycliz-
ation 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 equivalents of Bu3SnH and a catalytic amount of AIBN to
give the bifunctionalized seco-CBI prodrug 4. Treatment of
the seco-CBI 4 with 1.0 equivalent of succinic anhydride in
the presence of triethylamine in dry THF at 60 ЊC afforded
acid seco-CBI acid 5 in 80% yield. Treatment of the amine
group at the C7 position with acetyl chloride almost quanti-
tatively gave its acetyl derivative 6. Acid mediated deprotection
of the Boc group from compound 6 followed by reaction with
1.0 equivalent of succinic anhydride in the presence of triethyl-
amine in dry THF at 60 ЊC provided acid 7 in 80% yield.
(Scheme 1).
In addition studies on netropsin, distamycin and related
compounds have led to the concept of polyamides as inform-
ation reading agents.37 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 CPI38 and CBI39 with polyamides, the well established
DNA minor groove binders. It was found that some optimized
CPI-polyamide conjugates exhibit up to 10000 times higher
potency than CC-1065 against KB human cancer cells.38
Studies have also shown that some synthetic compounds, which
contain two CPI moieties linked from two possible positions by
a flexible methylene chain of variable length, are significantly
more potent than CC-1065 both in vitro and in vivo.40 In fact
many antitumor agents act by cross-linking DNA. Recently a
C8-linked pyrrolo[1,4]benzodiazepinone dimer was prepared41
which forms a symmetrical interstrand cross link with duplex
DNA involving a four base pairs bonding site but spanning six
base pairs overall.42 To date only a few CPI dimers have been
prepared to examine the interstrand cross-linking of DNA.40
We have also reported the synthesis and biological evaluation
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 Gl 50 values < 0.01 µm.43
In view of the commonly observed activity of these PBD,
CPI and seco-CBI dimers and some CPI polyamide conjugates
we attempted to conjugate two seco-CBI units with pyrrole and
imidazole polyamide from both sides by a flexible methylene
chain of varible length. In our previous studies, we reported the
synthesis of bis 1-chloromethyl-5-hydroxy-1,2-dihydro-3H-
benzo[e]indole (seco-CBI)–pyrrole polyamide conjugates44
which contain two racemic CBI moieties linked from two differ-
ent positions to a polyamide by a flexible methylene chain of
variable length. In order to investigate the structure–activity
relationships systematically as well as their cytotoxicity against
human cancer cells, we herein describe the synthesis and testing
of novel C7–C7, C7–N3 and N3–N3 dimers of 1-chloromethyl-
5-hydroxy-1,2-dihydro-3H-benzo[e]indole (seco-CBI) with poly-
amide conjugates which contain two racemic CBI moieties
linked from two different positions with pyrrole and imidazole
bearing polyamides by a flexible methylene chain of variable
length.
The seco-CBI acid 5 was then coupled with the amine moiety
of pyrrole polyamides, using EDCI and HOBt as the coupling
agents, in dry DMF at room temperature for about 12 h to
afford the corresponding coupled seco-CBI polyamide methyl
esters 8–10 in 80% yield which upon hydrolysis with 0.5 M
NaOH at room temperature produced the corresponding
seco-CBI polyamide acids 11–13 in 70% yield. The corre-
sponding amino compounds were then prepared by hydro-
genation of the nitro polyamides. These seco-CBI polyamide
acids 11–13 were treated with the seco-CBI prodrug 4 under
standard EDCI, HOBt coupling conditions via its acid chloride
route (Scheme 2). Unfortunately both reactions failed to pro-
duce the desired product, owing to the less reactive aromatic
amino group of the seco-CBI 4. In this case we needed to
increase the reactivity of the amino group at the C7 and N3
positions by introducing a more nucleophilic primary amine
moiety in 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 temp with 1.0 equiv N-Fmoc
glycine gave compound 14 in 70% yield. Detachment of the
Fmoc group from 14 with TBAF in dry THF gave the free
amine 15 in 70% yield. Acid mediated deprotection of the Boc
group from compound 6 followed by coupling with 1.0 equiv.
N-Boc glycine under standard EDCI, HOBt coupling condi-
tions in dry DMF afforded compound 16 in good yield.
Detachment of the Boc group from 16 gave the free amine 17
(Scheme 3).
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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Scheme 2 Reagents and conditions: i. 5, EDCl, HOBt, DMF, RT; ii. 1 M NaOH, THF–MeOH (1 : 1), RT; 111. EDCI, HOBt, DMF, RT; iv. DCC,
HOBt, DMF, RT; v. EDCI, DMF, RT; vi. a) TBDMS, imidazole, RT; b) oxalyl chloride–DCM, 0 ЊC; c) Et3N, THF, RT.
Scheme 3 Reagents and conditions: i. N-FmOC glycine, EDCI, HOBt, DMF, RT; ii. TBAF, THF, RT; iii. 4 M HCl in dioxane, RT, 2 h; iv. N-BOC
glycine, EDCl, HOBt, NaHCO3, DMF, RT; v. 4 M HCl in dioxane, RT, 2 h.
Scheme 4 Reagents and conditions: i. EDCl, HOBt, DMF, RT; ii. 10% HCOONH4, Pd/C, THF, RT.
The reaction of amines 15 and 17 with 1.0 equivalent of the
seco-CBI polyamide acids 11–13 using EDCI, HOBt (and
NaHCO3 in the case of amine 17) as the coupling agents in dry
DMF at room temperature for about 12 h, afforded the corre-
sponding coupled bis seco-CBI polyamides 18–23 in 70% yield.
Hydrogenolysis of the bis seco-CBI polyamides 18–23 in THF
with 4.0 equiv. of 10% aqueous ammonium formate in the pres-
ence of Pd–C for about 2 h to remove the benzyl ether provided
almost quantitatively the final C7–C7 and C7–N3 bis seco-CBI
pyrrole polyamide dimers 24–29 in 80–90% yield (Scheme 4).
The reaction of seco-CBI acid 7 with the amine moiety of
pyrrole polyamide methyl ester, using standard EDCI and
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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HOBt coupling conditions gave the corresponding coupled N3
seco-CBI polyamide methyl ester 30 in 80% yield. This ester 30
was treated with 0.5 M NaOH at room temp. and with aq.
LiOH to produce the desired acid (Scheme 5). Unfortunately
both reactions failed to produce the desired product, due to
the acetate group at the C7 position. In this case we need to
employ an acid labile deprotecting group in the nitropolyamides
e.g. tert-butyl group.
treated with the 4-nitro-2-(trichloroacetyl)-1-methyl pyrrole 32
in the presence of triethylamine to give compound 37 in good
yield (Scheme 6).
Coupling of the seco-CBI acid 7 with the amine moiety of
tert-butyl ester pyrrole polyamides 35–37, using EDCI and
HOBt as coupling agents in dry DMF afforded the corre-
sponding coupled N3 seco-CBI polyamide tert-butyl esters 38–
40 in 80% yield which were hydrolyzed under acidic conditions
by using 1 M solution of TiCl4 in dichloromethane to give the
corresponding N3 seco-CBI polyamide acid compounds 41–43
in fair yield. The corresponding amino compounds were then
prepared by hydrogenation of the corresponding nitro poly-
amides 35–37. Coupling of these N3 seco-CBI polyamide acids
41–43 with the seco-CBI amine 17 using EDCI, HOBt and
NaHCO3 as coupling agents in dry DMF afforded the corre-
sponding coupled N3–N3 bis seco-CBI pyrrole polyamides 44–
46 in good yield. Treatment of 44–46 with ammonium formate
in the presence of Pd–C for about 2 h provided the final N3–N3
bis-seco-CBI pyrrole polyamide dimers 47–49 in fair yield
(Schemes 7 and 8).
Scheme 5 Reagents and conditions: i. 7, EDCl, HOBt, DMF, RT; ii. a)
1 M NaOH, THF–MeOH (1 : 1), RT; b) LiOH, THF–MeOH (1 : 1),
RT.
Treatment of the 4-nitro-2-(trichloroacetyl)-1-methyl pyrrole
32 with methanol gave methyl ester 33 in quantitative yield.
Basic hydrolysis of compound 33 gave the corresponding acid
compound 34, which was converted into an acidic labile tert-
butyl ester compound 35 by treating the acid 34 with isobutyl-
ene under acidic conditions. The nitro group of compound 35
was reduced with hydrogen in the presence of Pd/C catalyst into
the corresponding amino compound which was then treated
with the 4-nitro-2-(trichloroacetyl)-1-methyl pyrrole 32 in the
presence of triethylamine and gave compound 36. The nitro
group of compound 36 was reduced, using the same procedure,
into its corresponding amino compound and then the latter was
Scheme 7 Reagents and conditions: i. H2, Pd/C, MeOH, RT; ii. 7,
EDCl, HOBt, DMF, RT; iii. 1 M TiCl4, DCM, RT, 12 h.
Condensation of the seco-CBI acid 5 with the amine moiety
of 1-methyl-4-nitro-1H-imidazole-2-carboxylic acid methyl
ester polyamide, using EDCI and HOBt as the coupling agents,
in dry DMF afforded the corresponding coupled seco-CBI
imidazole polyamide methyl ester 50 in 80% yield which
upon hydrolysis with 1 M NaOH produced the corresponding
seco-CBI polyamide acid compound 51 in 70% yield. The
Scheme 6 Reagents and conditions: i. MeOH, 80 ЊC; ii. 1 M NaOH, THF–MeOH (1 : 1), RT; iii. isobutylene, H2SO4, RT, 12 h; iv. H2 Pd/C, 32, Et3N,
THF, RT; v. H2 Pd/C, 32, ET3N, THF, RT.
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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Scheme 8 Reagents and conditions: i. EDCl, HOBt, DMF, RT; ii. 10% HCOONH4, Pd/C, THF, RT.
Scheme 9 Reagents and conditions: i. 5, EDCl, HOBt, DMF, RT; ii. 1 M NaOH, THF–MeOH (1 : 1), RT; iii. EDCl, HOBt, DMF, RT; iv. DCC,
HOBt, DMF, RT; v. EDCl, DMF, RT; vi. a) TBDMS, imidazole, RT; b) oxalyl chloride–DCM 0 ЊC; c) Et3N, THF, RT.
Scheme 10 Reagents and conditions: i. glycine methyl ester hydrochloride, THF, Et3N, RT; ii. H2 Pd/C, MeOH or DMF, 52, Et3N, THF, RT; iii. H2
Pd/C 52, Et3N, THF, RT.
corresponding amino compounds were then prepared by
hydrogenation of the nitropolyamides. The seco-CBI polyamide
acid 51 was then coupled with the seco-CBI amines 15 or 17,
containing a more nucleophilic primary amine group, under
EDCI, HOBt coupling conditions and via its acid chloride
derivative (Scheme 9). Unfortunately both reactions failed to
produce the desired products, due to the less reactive carboxyl
group in the seco-CBI imidazole polyamide acid 51 residing
between two nitrogen functions. In this case we needed to
increase the reactivity of the carboxyl group in the imidazole
polyamide esters by introducing a more electrophilic primary
carboxylic group through a suitable linker.
Treatment of the 4-nitro-2-(trichloroacetyl)-1-methyl imid-
azole 52 with glycine methyl ester hydrochloride in the presence
of triethylamine afforded compound 53 in good yield. The nitro
group of compound 53 was reduced with hydrogen in the pres-
ence of Pd/C catalyst into the corresponding amino compound
which was then treated with the 4-nitro-2-(trichloroacetyl)-1-
methyl imidazole 52 in the presence of triethylamine and to give
compound 54. The nitro group of compound 54 was reduced,
using the same procedure, into its corresponding amino com-
pound and then the latter was treated with the 4-nitro-2-
(trichloroacetyl)-1-methyl imidazole 52 in the presence of tri-
ethylamine to give compound 55 in good yield (Scheme 10).
Coupling of the acid 5 with the amine moiety of imidazole
polyamides 53–55, using EDCI and HOBt coupling conditions,
in dry DMF afforded the corresponding coupled seco-CBI
polyamide methyl esters 56–58 in 80% yield which upon
hydrolysis with 1 M NaOH produced the corresponding
seco-CBI polyamide acid compounds 59–61 in 70% yield. The
corresponding amino compounds were then prepared by
hydrogenation of the nitropolyamides. Coupling of these C7
seco-CBI polyamide acids 59–61 with the seco-CBI amines 15
and 17 using EDCI and HOBt (and NaHCO3 in the case of
amine 17) as coupling agents in dry DMF afforded the corre-
sponding coupled C7–C7 and C7–N3 bis seco-CBI imidazole
polyamides 62–66 in 60% yield. Treatment of 62–67 with
ammonium formate in the presence of Pd–C for about 2 h
provided the final C7–C7 and C7–N3 bis-seco-CBI imidazole
polyamide dimers 68–73 in fair yield (Schemes 11 and 12).
Basic hydrolysis of compound 53 gave the corresponding
acid compound 74, which was converted into an acid labile
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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tert-butyl ester compound 75 by treating the acid 74 with iso-
butylene under acidic conditions. The nitro group of com-
pound 75 was reduced with hydrogen in the presence of Pd/C
catalyst into the corresponding amino compound which was
then treated with the 4-nitro-2-(trichloroacetyl)-1-methyl imid-
azole 52 in the presence of triethylamine to give compound 76.
The nitro group of compound 76 was reduced, using the same
procedure, into its corresponding amino compound and then
the latter was treated with the 4-nitro-2-(trichloroacetyl)-1-
methyl imidazole 52 in the presence of triethylamine to give
compound 77 in good yield (Scheme 13).
Coupling of the seco-CBI acid 7 with the amine moiety of
tert-butyl ester imidazole polyamides 75–77, using EDCI and
HOBt as coupling agents in dry DMF afforded the corre-
sponding coupled N3 seco-CBI polyamide tert-butyl esters 78–
80 in 75% yield which was hydrolyzed under acidic conditions
by using a 1 M solution of TiCl4 in dichloromethane to give
the corresponding N3 seco-CBI imidazole polyamide acid
compounds 81–83 in fair yield. The corresponding amino com-
pounds were then prepared by hydrogenation of the nitro poly-
amides 75–77. Coupling of these N3 seco-CBI polyamide acids
81–83 with the seco-CBI amine 17 using EDCI, HOBt and
NaHCO3 as coupling agents in dry DMF afforded the corre-
sponding coupled N3–N3 bis seco-CBI imidazole polyamides
84–86 in good yield. Hydrogenolysis of the bis seco-CBI poly-
amides 84–86 in THF with 4.0 equiv of 10% aqueous ammo-
nium formate in the presence of Pd–C for about 2 h to remove
the benzyl ether provided almost quantitatively the final N3–N3
bis seco-CBI imidazole polyamide dimers 87–89 in 80% yield
(Schemes 14 and 15).
The bis-seco-CBI pyrrole and imidazole polyamide conju-
gates 24–29 and 68–73 containing one or more pyrrole and
imidazole units were selected by the US National Cancer Insti-
tute for evaluation in an in vitro preclinical antitumor screening
program for primary anticancer assays against three human
tumor cell lines consisting of MCF7 (Breast), NCI-H460
(Lung), and SF-268 (CNS) cells. In the current protocol, each
cell line is inoculated and preincubated on a mirotiter plate. Test
agents are then added at a single concentration and the culture
incubated for 48 hours. End-point determinations are made
with alamar blue. Results of each test agent are reported as the
percent of growth of the treated cells when compared to the
untreated control cells. The compounds listed in Table 1 have
been evaluated in the 3-cell line, one dose primary anticancer
assay. It is observed from the initial cytotoxic data (Table 1) that
all compounds have varying cytotoxic potency activity against
these three cancer cell lines. Very surprising from this prelimin-
ary data and our previously reported data43 is that the mono-
mer compounds and alkyl linked seco-CBI dimer give the
higher cytotoxicity. It has been suggested by a reviewer that
from the initial biological data it can be concluded that if the
compound is too long, it might be out of the phase in the minor
groove of DNA, which lowers the DNA-binding affinity or due
Scheme 11 Reagents and conditions: i. H2 Pd/C, MeOH or DMF, RT;
ii. 5, EDCl, HOBt, DMF, RT; iii. 1 M NaOH, THF–MeOH (1 : 1), RT.
Scheme 12 Reagents and conditions: i. EDCl, HOBt, DMF, RT; ii. 10% HCOONH4, Pd/C, THF, RT.
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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Table 1 In vitro preclinical cytotoxic data of bis-seco-CBI-polyamides
Growth percentage
(Breast) MCF-7
Compound no.
Concentration/M
(Non-small cell lung) NCI-H460
(CNS) SF-268
24
25
26
27
28
29
68
69
70
71
72
73
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
1.000EϪ04
69
77
53
55
70
61
64
71
71
56
73
103
91
80
75
82
78
88
87
89
75
97
78
78
110
98
93
94
99
86
86
98
93
71
91
92
Scheme 13 Reagents and conditions:i. 1 M NaOH, THF–MeOH (1 : 1); ii. isobutylene, H2SO4, RT; iii. H2 Pd/C, 52, Et3N, THF, RT.
Scheme 14 Reagents and conditions:i. H2 Pd/C, MeOH, RT; ii. 7, EDCl, HOBt, DMF, RT; iii. 1 M TiCl4, DCM, RT, 12 h.
Scheme 15 Reagents and conditions:i. EDCl, HOBt, DMF, RT; ii. 10% HCOONH4, Pd/C, THF, RT.
to the large size of the molecule might lead to low binding
affinity. We are now in the course of performing cellular uptake
studies of these types of compounds, which bear fluorescent
tags. Cellular uptake results and more extensive cytotoxicity
data will be published in due course.
In summary, we have described the first synthesis of the C7–
C7, C7–N3 and N3–N3 dimers of 1-chloromethyl-5-hydroxy-
1,2-dihydro-3H-benzo[e]indole (seco-CBI) with pyrrole and
imidazole polyamides and also their preliminary anti-cancer
evaluation.
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filtration through a Celite pad. The filtrate was concentrated to
Experimental
dryness under reduced pressure (at RT) to afford the corre-
sponding amine. Owing to the sensitivity of the amine to
oxidation, it was used for the next reaction immediately. It was
dissolved in dry DMF and a mixture of the seco-CBI acid 5
(1.0 equivalent), hydroxybenzotriazole (1.0 equivalent), and
EDCI (2.5 equivalent), in dry DMF was added. This mixture
was stirred at RT for 12 h and after completion of the reaction
the solvent was removed under reduced pressure to afford a
dark oil which was purified by flash column chromatography on
silica gel by using methanol–dichloromethane as eluent to
afford the seco-CBI pyrrole or imidazole polyamide esters as
white solids in good yield.
Kieselgel 60 (230–400 mesh) of E. Merck was used for flash
column chromatography, and precoated silica gel 60F-254
sheets of E-Merck were used for TLC, with the solvent system
indicated in the procedure. TLC plates were visualized by using
uv light. All compounds obtained commercially were used
without further purification unless otherwise stated. Methanol
was freshly distilled over magnesium turnings; tetrahydrofuran
was distilled over sodium benzophenone ketyl under an atmos-
phere of dry argon, ether was dried over sodium; methylene
chloride was freshly distilled from calcium hydride, triethyl-
amine was treated with potassium hydroxide then distilled from
barium oxide and stored over 3Å molecular sieves, Dry di-
methylformamide and all commercially available chemicals
were purchased from Aldrich Chemical Co. The 1H NMR
spectra were recorded on a Bruker WH-300 spectrometer.
Proton chemical shifts are reported in parts per million
(δ) downfield from tetramethylsilane (SiMe4) as an internal
standard. Coupling constants (J values) are given in hertz and
spin multiplicates are described as follows: s (singlet), d (doub-
let), dd (doublet of doublets), t (triplet), q (quartet), p (pentet)
or m (multiplet). FAB (fast atom bombardment) mass spectra
with glycerol as the matrix were determined on Associate
Electrical Ind. (AEI) MS – 9 and MS – 50 focusing high-
resolution mass spectrometers.
5-Benzyloxy-1-chloromethyl-7-[3-(5-methoxycarbonyl-1-methyl-
1H-pyrrol-3-ylcarbamoyl)propionylamino]-1,2-dihydrobenzo[e]-
indole-3-carboxylic acid tert-butyl ester (8)
This compound was prepared starting from 1-methyl-4-nitro-
1H-pyrrole-2-carboxylic acid methyl ester (0.410 g, 2.22 mmol)
and the acid 5 (1.0 g, 1.85 mmol) according to general
procedure A (1.0 g, 80% yield) as a white solid. 1H NMR
(300 MHz, DMSO-d6) δ 1.52 (s, 9H, Boc-H), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.85 (s, 3H, – OCH3), 3.90–
4.10 (m, 5H, –CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5),
6.96 (d, 1H, J = 1.8 Hz, Py–H), 7.20 (d, 1H, J = 1.8 Hz, Py–H),
7.52–7.90 (m, 8H, Ar–H), 8.40 (s, 1H, C6–H), 9.80 (s, 1H,
–NH–), 10.20 (s, 1H, –NH–). HR–MS m/z calculated for
C36H39N4O7Cl 674.25, found 697.22 (M ϩ Na).
5-Benzyloxy-7-(3-carboxypropionylamino)-1-chloromethyl-1,2-
dihydrobenzo[e]indole-3-carboxylic acid tert-butyl ester (5)
A
solution of 7-amino-5-benzyloxy-1-chloromethyl-1,2-di-
5-Benzyloxy-1-chloromethyl-7-{3-[5-(5-methoxycarbonyl-1-
methyl-1H-pyrrol-3-ylcarbamoyl)-1-methyl-1H-pyrrol-3-ylcarb-
amoyl]propionylamino}-1,2-dihydrobenzo[e]indole-3-carboxylic
acid tert-butyl ester (9)
hydro-benzo[e]indole-3-carboxylic acid tert-butyl ester (4)
(2.5g, 5.70 mmol) in THF (50.0 ml) was added dropwise to a
stirred solution of succinic anhydride (0.63 g, 6.3 mmol) and
triethylamine (1 ml) in dry THF at 0 ЊC. The reaction mixture
was stirred for 12 h at room temperature. After the completion
of the reaction, as indicated by TLC, the mixture was concen-
trated under reduced pressure and the residue was purified by
column chromatography using MeOH–DCM, 1 : 9 to give 5 as
Prepared according to general procedure
A by using
1-methyl-4-[(1-methyl-4-nitro-1H-pyrrole-2-carbonyl)amino]-
1H-pyrrole-2-carboxylic acid methyl ester (0.68 g, 2.22 mmol)
and the acid 5 (1.0 g, 1.85 mmol) in 81% yield (1.2 g) as a white
1
1
a solid (2.8 g, 91% yield). H NMR (300 MHz, CDCl3) δ 1.57
solid. H NMR (300 MHz, DMSO-d6) δ 1.53 (s, 9H, Boc–H),
(s, 9H, Boc–H), 2.60–2.75 (m, 4H, 2 × –CH2CO–), 3.56–4.20
(m, 5H, –CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5), 7.07
(dd, 1H, J = 2.4, 8.8 Hz), 7.37–7.46 (m, 4H, Ar–H), 7.56–7.76
(m, 4H, Ar–H), 9.50 (s, 1H, –NH–). HR–MS m/z calculated for
C29H31N2O6Cl 538.00, found 539.02 (M ϩ 1).
2.52–2.71 (m, 4H, 2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.85 (s,
3H, –NCH3), 3.88 (s, 3H, –OCH3), 3.91–4.15 (m, 5H, –CH,
CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5), 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), 7.45 (d, 1H, J = 1.8 Hz, Py–H), 7.50–7.90
(m, 8H, Ar–H), 8.45 (s, 1H, C6–H), 10.00 (s, 1H, –NH–), 10.12
(s, 1H, –NH–), 10.20 (s, 1H, –NH–). HR–MS m/z calculated for
C42H45N6O8Cl 796.30, found 819.28 (M ϩ Na).
4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-dihydro-
benzo[e]indol-3-yl)-4-oxo-butyric acid (7)
7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-dihydrobenzo-
[e]indole-3-carboxylic acid tert-butyl ester (6) (2.5 g, 5.20 mmol)
was added to a solution of 4 M HCl in dioxane (20 ml) at 0 ЊC
under argon. The reaction mixture was stirred at 23 ЊC for 5 h
before the solvent was removed. After being dried in vacuo, the
residue, triethylamine (1 ml) and succinic anhydride (0.57 g,
5.70 mmol) were dissolved in anhydrous THF (50 ml), and the
reaction mixture was stirred at 23 ЊC for 12 h then the solvent
was removed and the residue was purified by column chrom-
atography 10% MeOH–DCM as a eluting solvent in 80%
yield (2.0 g) as a white solid. 1H NMR (300 MHz, acetone-d6) δ
1.80–1.86 (m, 2H, –CH2CO–), 2.05 (s, 3H, –NHCOCH3), 2.56–
2.66 (m, 2H, –NCOCH2–), 3.59–4.22 (m, 5H, –CH, CH2Cl,
CH2N), 5.26 (s, 2H, –OCH2C6H5), 7.37–7.57 (m, 5H, Ar–H),
7.76–7.84 (m, 3H, Ar–H), 8.33 (s, 1H, Ar–H), 10.05 (s, 1H,
–NH–). HR–MS m/z calculated for C26H25N2O5Cl 480.15,
found 480.18.
5-Benzyloxy-1-chloromethyl-7-(3-{5-[5-(5-methoxycarbonyl-1-
methyl-1H-pyrrol-3-ylcarbamoyl)-1-methyl-1H-pyrrol-3-ylcarb-
amoyl]-1-methyl-1H-pyrrol-3-ylcarbamoyl}propionylamino)-1,2-
dihydrobenzo[e]indole-3-carboxylic acid tert-butyl ester (10)
This compound was prepared according to the method
described for the compounds 8 by employing 1-methyl-4-
({1-methyl-4-[(1-methyl-4-nitro-1H-pyrrole-2-carbonyl)amino]-
1H-pyrrole-2-carbonyl}amino)-1H-pyrrole-2-carboxylic acid
methyl ester (0.95 g, 2.22 mmol) and the acid 5 (1.0 g,
1.85 mmol) in 80% yield (1.40 g) as a white solid. 1H
NMR (300 MHz, DMSO-d6) δ 1.52 (s, 9H, Boc–H), 2.56–2.70
(m, 4H, 2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.84 (s, 3H,
–NCH3), 3.86 (s, 3H, –NCH3), 3.89 (s, 3H, –OCH3), 3.92–4.20
(m, 5H, –CH, CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5), 6.81
(d, 1H, J = 1.8 Hz, Py–H), 6.96 (d, 1H, J = 1.8 Hz, Py–H), 7.15
(d, 1H, J = 1.8 Hz, Py–H), 7.25 (d, 1H, J = 1.8 Hz, Py–H), 7.31
(d, 1H, J = 1.8 Hz, Py–H), 7.41 (d, 1H, J = 1.8 Hz, Py–H), 7.46–
7.91 (m, 8H, Ar–H), 8.45 (s, 1H, C6–H), 9.95 (s, 1H, –NH–),
10.12 (s, 1H, –NH–), 10.20 (s, 1H, –NH–), 10.30 (s, 1H, –NH–).
HR–MS m/z Calculated for C48H51N8O9Cl 918.35, found
941.32 (M ϩ Na).
General procedure A
A solution of the nitropolyamides (pyrrole or imidazole) in
MeOH or DMF was hydrogenated over 10% Pd/C at 50 psi
pressure for two hours and the catalyst was removed by
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
2637

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General procedure B
was dissolved in dry DMF (10 ml) and added to a mixture of
the N-Fmoc glycine (0.746 g, 2.50 mmol), HOBT (0.308 g, 2.27
mmol), and EDCI (1.09 g, 5.68 mmol) in DMF (15 ml). This
mixture was stirred at RT for 12 h and the solvent was removed
under reduced pressure to afford a dark oil which was purified
by flash chromatography on silica gel (2% methanol–dichloro-
methane) to afford compound 14 as a white solid in 80% yield
A mixture of seco-CBI pyrrole or imidazole polyamide methyl
esters in methanol and 10 ml of 0.5 M NaOH was placed in a
flask, then the reaction mixture was stirred at room temperature
until the ester completely disappeared as shown by TLC. The
reaction was cooled in ice with stirring and neutralized with 0.5
M HCl slowly to pH 2. The reaction mixture was extracted with
ethyl acetate and THF (1 : 1) three times and dried over sodium
sulfate and the solvent was removed under reduced pressure.
The residue was purified by column chromatography using
MeOH–dichloromethane as eluent to afford the seco-CBI
pyrrole or imidazole polyamide acids in good yield.
1
(1.31 g). H NMR (300 MHz, CDCl3) δ 1.58 (s, 9H, Boc–H),
3.71 (dd, J = 8.4, 10.0 Hz, 1H), 3.75 (m, 2H, –CH2NH–), 4.01
(dd, J = 3.1, 11.1 Hz, 1H), 4.05–4.22 (m, 3H), 4.30 (t, J = 6.9 Hz,
1H), 4.50 (d, J = 6.9 Hz, 2H), 5.29 (s, 2H, –OCH2C6H5), 7.30–
7.88 (m, 16H, Ar–H), 8.38 (s, 1H, C6–H), 9.10 (s, 1H, –NH–),
10.0 (s, 1H, –NH–). HR–MS m/z Calculated for C42H40N3O6Cl
717.26, found 740.25 (M ϩ Na).
5-Benzyloxy-7-[3-(5-carboxy-1-methyl-1H-pyrrol-3-ylcarbamoyl)-
propionylamino]-1-chloromethyl-1,2-dihydrobenzo[e]indole-
3-carboxylic acid tert-butyl ester (11)
7-(2-Aminoacetylamino)-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indole-3-carboxylic acid tert-butyl ester (15)
This compound was prepared according to general procedure B
To a solution of 5-benzyloxy-1-chloromethyl-7-[2-(9H-fluoren-
9-ylmethoxycarbonylamino)acetylamino]-1,2-dihydrobenzo[e]-
indole-3-carboxylic acid tert-butyl ester (14) (2.5 g, 3.48 mmol)
in dry THF (100 ml) was added tetrabutylammonium fluoride
(3.12 ml, 1.0 M in THF) and the mixture was stirred at room
temperature for 2 h. After the completion of the reaction as
indicated by TLC, the mixture was concentrated under reduced
pressure and the residue was purified by column chromato-
graphy using 10% MeOH–DCM as a eluting solvent to give 15
in 73% yield (1.25 g). 1H NMR (300 MHz, DMSO-d6) δ 1.57 (s,
9H, Boc–H), 3.60–3.65 (m, 1H), 3.75 (m, 2H, –CH2NH–), 3.95–
4.20 (m, 4H, –CH2Cl, –CH2N), 4.82 (m, 2H, –CH2NH2–), 5.26
(s, 2H, –OCH2C6H5), 7.07 (dd, 1H, J = 2.4, 8.8 Hz, 1-H), 7.37–
7.45 (m, 4H, Ar–H), 7.56–7.61 (m, 4H, Ar–H), 9.05 (s, 1H,
–NH–). HR–MS m/z calculated for C27H30N3O4Cl 495.19,
found 496.00 (M ϩ 1).
by employing compound 8 (1.0 g, 1.48 mmol) and 0.5 M NaOH
1
in 76% yield (0.75 g) as a white solid. H NMR (300 MHz,
DMSO-d6)
δ 1.52 (s, 9H, Boc–H), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.90–4.10 (m, 5H,
–CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5), 7.18 (d, 1H,
J = 1.8 Hz, Py–H), 7.25 (d, 1H, J = 1.8 Hz, Py–H), 7.56–7.90
(m, 8H, Ar–H), 8.40 (s, 1H, C6–H), 10.0 (s, 1H, –NH–), 10.20
(s, 1H, –NH–), 12.52 (br s, 1H, –COOH). HR–MS m/z
calculated for C35H37N4O7Cl 660.24, found 683.22 (M ϩ Na).
5-Benzyloxy-7-{3-[5-(5-carboxy-1-methyl-1H-pyrrol-3-ylcarb-
amoyl)-1-methyl-1H-pyrrol-3-ylcarbamoyl]propionylamino}-1-
chloromethyl-1,2-dihydrobenzo[e]indole-3-carboxylic acid
tert-butyl ester (12)
Prepared according to general procedure B by using compound
9 (1.0 g, 1.25 mmol) and 0.5 M NaOH solution in 77% yield
(0.76 g) as a white solid. 1H NMR (300 MHz, DMSO-d6) δ 1.51
(s, 9H, Boc–H), 2.52–2.72 (m, 4H, 2 × CH2CO–), 3.81 (s, 3H,
–NCH3), 3.84 (s, 3H, –NCH3), 3.90–4.20 (m, 5H, –CH, CH2Cl,
CH2N), 5.25 (s, 2H, –OCH2C6H5), 6.93 (d, 1H, J = 1.8 Hz,
Py–H), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.22 (d, 1H, J = 1.8 Hz,
Py–H), 7.42 (d, 1H, J = 1.8 Hz, Py–H), 7.51–7.86 (m, 8H,
Ar–H), 8.45 (s, 1H, C6–H), 10.00 (s, 1H, –NH–), 10.12 (s, 1H,
–NH–), 10.25 (s, 1H, –NH–), 12.60 (br s, 1H, –COOH).
HR–MS m/z calculated for C41H43N6O8Cl 782.25, found 805.22
(M ϩ Na).
[2-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-dihydro-
benzo[e]indol-3-yl)-2-oxo-ethyl]carbamic acid tert-butyl ester
(16)
Compound (6) (1.2 g, 2.5 mmol) was added to a solution of
4 M HCl in dioxane (20 ml) at 0 ЊC under argon. The reaction
mixture was stirred at 23 ЊC for 5 h before the solvent was
removed. After being dried in vacuo, the residue, was dissolved
in dry DMF (10 ml) and added to a mixture of the N-Boc
glycine (0.438 g, 2.50 mmol), HOBT (0.338 g, 2.50 mmol),
EDCI (1.2 g, 6.25 mmol) and NaHCO3 (0.525 g, 6.24 mmol) in
DMF (15 ml). This mixture was stirred at RT for 12 h and the
solvent was removed under reduced pressure to afford a col-
oured oil which was purified by column chromatography on
silica gel (3% methanol–dichoromethane) to afford compound
5-Benzyloxy-7-(3-{5-[5-(5-carboxy-1-methyl-1H-pyrrol-3-yl-
carbamoyl)-1-methyl-1H-pyrrol-3-ylcarbamoyl]-1-methyl-1H-
pyrrol-3-ylcarbamoyl}propionylamino)-1-chloromethyl-1,2-di-
hydrobenzo[e]indole-3-carboxylic acid tert-butyl ester (13)
1
14 as a white solid in 78% yield (1.05 g). H NMR (300 MHz,
DMSO-d6) δ 1.54 (s, 9H, Boc–H), 2.05 (s, 3H, NHCOCH3),
3.78–4.20 (m, 7H, –CH2NH–, –CH2Cl, –CH2N, –CH–), 5.26 (s,
2H, –OCH2C6H5), 7.37–7.57 (m, 5H, Ar–H), 7.76–7.84 (m, 3H,
Ar–H), 8.34 (s, 1H, Ar–H), 9.80 (s, 1H, –NH–), 10.09 (s, 1H,
–NH–). HR–MS m/z calculated for C29H32N3O5Cl 537.20,
found 560.15 (M ϩ Na).
This compound was prepared according to general method B
by using compound 10 (1.0 g, 1.08 mmol) and 0.5 M NaOH
1
solution in 81% yield (0.80 g) as a white solid. H NMR (300
MHz, DMSO-d6) δ 1.56 (s, 9H, Boc–H), 2.54–2.68 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.88
(s, 3H, –NCH3), 3.92–4.20 (m, 5H, –CH, CH2Cl, CH2N), 5.24
(s, 2H, –OCH2C6H5), 6.83 (d, 1H, J = 1.8 Hz, Py–H), 6.96 (d,
1H, J = 1.8 Hz, Py–H), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.20 (d,
1H, J = 1.8 Hz, Py–H), 7.35 (d, 1H, J = 1.8 Hz, Py–H), 7.42 (d,
1H, J = 1.8 Hz, Py–H), 7.49–7.90 (m, 8H, Ar–H), 8.40 (s, 1H,
C6–H), 9.95 (s, 1H, –NH–), 10.12 (s, 1H, –NH–), 10.20 (s, 1H,
–NH–), 10.31 (s, 1H, –NH–) 12.59 (br s, 1H, –COOH).
HR–MS m/z calculated for C47H49N8O9Cl 904.33, found 927.32
(M ϩ Na).
N-[3-(2-Aminoacetyl)-5-benzyloxy-1-chloromethyl-2,3-dihydro-
1H-benzo[e]indol-7-yl]acetamide hydrochloride (17)
[2-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-2-oxoethyl]carbamic acid tert-butyl
ester (16) was added to a solution of 4 M HCl in dioxane
(20 ml) at 0 ЊC under argon. The reaction mixture was stirred at
23 ЊC for 5 h before the solvent was removed. After drying the
residue at high vaccum it was used imidiately in the next step
reaction without purification.
5-Benzyloxy-1-chloromethyl-7-[2-(9H-fluoren-9-ylmethoxy-
carbonylamino)acetylamino]-1,2-dihydrobenzo[e]indole-3-
carboxylic acid tert-butyl ester (14)
General procedure C
7-Amino-5-benzyloxy-1-chloromethyl-1,2-dihydro-benzo[e]-
indole-3-carboxylic acid tert-butyl ester (4) (1.0 g, 2.28 mmol)
To a solution of seco-CBI pyrrole or imidazole polyamide acids
in dry DMF (20 ml) were added EDCI (2.5 mol), HOBt (1.0
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
2638

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mol), and seco-CBI amine 15 (1.1 mol) or seco-CBI amine 17
(1.1 mol) and NaHCO3 (3.0 mol) in the case of amine 17 under
a nitrogen atmosphere and the mixture was stirred for 12 h.
When TLC indicated the absence of starting material, DMF
was removed under reduced pressure. The dark residue was
purified by column chromatography on silica gel using MeOH–
dichloromethane as eluent to afford the coupled conjugates as
white solids in good yields.
HR-ESMS m/z calculated for C59H59N7O9Cl2 1079.38, found
1102.40 (M ϩ Na).
Compound 22
This compound was prepared according to the method
described for the compound 21, employing seco-CBI polyamide
acid 12 (0.3 g, 0.383 mmol) and the amine 17 (0.25 g, 0.572
1
mmol) in 70% yield (0.321 g) as a white solid. H NMR (300
MHz, DMSO-d6) δ 1.54 (s, 9H, Boc–H), 2.04 (s, 3H,
CH3CON), 2.58–2.72 (m, 4H, 2 × CH2CO–), 3.82 (s, 3H,
–NCH3), 3.85 (s, 3H, –NCH3), 3.90–4.35 (m, 12H, Cl, 2-H,
2 × CH2Cl, 2 × CH2N, NHCH2), 5.22 (s, 2H, –OCH2C6H5),
5.24 (s, 2H, –OCH2C6H5), 6.85 (d, 1H, J = 1.5 Hz, Py–H), 7.06
(d, 1H, J = 1.5 Hz, Py–H), 7.19 (d, 1H, J = 1.5 Hz, Py–H), 7.26
(d, 1H, J = 1.5 Hz, Py–H), 7.50–7.85 (m, 16H, Ar–H), 8.25–8.32
(m, 1H, NHCH2), 8.35–8.42 (m, 2H, 2 × C6–H), 9.91 (s, 1H,
–NH–), 10.05 (s, 1H, –NH–), 10.09 (s, 1H, –NH–), 10.20 (s, 1H,
–NH–). HR-ESMS m/z calculated for C65H65N9O10Cl2 1201.42,
found 1224.41 (M ϩ Na).
Compound 18
Prepared according to general procedure C by using compound
11 (0.25 g, 0.378 mmol) and seco-CBI amine 15 (0.2 g, 0.404
mmol) in 70% yield (0.30 g) as a white solid. H NMR (300
1
MHz, DMSO-d6) δ 1.52 (s, 18H, 2 × Boc–H), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.89–4.10 (m, 12H, Cl,
2-H, 2 × CH2Cl, 2 × CH2N, NHCH2), 5.24 (s, 2H, –OCH2-
C6H5), 5.25 (s, 2H, –OCH2C6H5), 6.86 (d, 1H, J = 1.8 Hz,
Py–H), 7.18 (d, 1H, J = 1.8 Hz, Py–H), 7.59–7.75 (m, 16H,
Ar–H), 8.30 (m, 1H, NHCH2), 8.40 (s, 2H, 2 × C6–H), 9.91 (s,
1H, –NH–), 10.09 (s, 1H, –NH–), 10.27 (s, 1H, –NH–). ES–MS
m/z calculated for C62H65N7O10Cl2 1137.42, found 1160.40
(M ϩ Na).
Compound 23
Prepared according to general procedure C using compound 13
(0.3 g, 0.331 mmol) and seco-CBI amine 17 (0.213 g, 0.487
Compound 19
1
mmol) in 72% yield (0.32 g) as a white solid. H NMR (300
This compound was prepared according to the method
described for the compound 18, employing seco-CBI pyrrole
polyamide acid 12 (0.25 g, 0.319 mmol) and the amine 15 (0.175
MHz, DMSO-d6) δ 1.52 (s, 9H, Boc–H), 2.05 (s, 3H,
CH3CON), 2.58–2.70 (m, 4H, 2 × CH2CO–), 3.81 (s, 3H,
–NCH3), 3.83 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.89–
4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2), 5.25
(s,2H, –OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 6.88 (d, 1H,
J = 1.5 Hz, Py–H), 6.98 (d, 1H, J = 1.5 Hz, Py–H), 7.08 (d, 1H,
J = 1.5 Hz, Py–H), 7.18 (d, 1H, J = 1.5 Hz, Py–H), 7.24 (d, 1H,
J = 1.5 Hz, Py–H), 7.27 (d, 1H, J = 1.5 Hz, Py–H), 7.59–7.85
(m, 16H, Ar–H), 8.20–8.30 (m, 1H, NHCH2), 8.35–8.42 (m,
2H, 2 × C6–H), 9.89 (s, 1H, –NH–), 9.92 (s, 1H, –NH–), 10.15
(s, 1H, –NH–), 10.18 (s, 1H, –NH–), 10.22 (s, 1H, –NH–).
HR-ESMS m/z calculated for C71H71N11O11Cl2 1323.47, found
1346.50 (M ϩ Na).
1
g, 0.353 mmol) in 70% yield (0.28 g) as a solid. H NMR (300
MHz, DMSO-d6) δ 1.56 (s, 18H, 2 × Boc–H), 2.52–2.70 (m, 4H,
2 × CH2CO–), 3.81 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.90–
4.20 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2), 5.23 (s,
2H, –OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 6.85 (d, 1H,
J = 1.8 Hz, Py–H), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.24 (d, 1H,
J = 1.8 Hz, Py–H), 7.28 (d, 1H, J = 1.8 Hz, Py–H), 7.60–7.85
(m, 16H, Ar–H), 8.35 (m, 1H, NHCH2), 8.40 (s, 2H, 2 × C6–H),
9.91 (s, 1H, –NH–), 9.94 (s, 1H, –NH–), 10.09 (s, 1H, –NH–),
10.12 (s, 1H, –NH–). ES–MS m/z calculated for C68H71N9O11Cl2
1259.47, found 1282.45 (M ϩ Na).
General procedure D
Compound 20
To a solution of bis-seco-CBI pyrrole or imidazole dimers with
benzyl group in THF or DMF was added 10% Pd/C under
argon. The mixture was cooled to 0 ЊC and 10% aqueous
ammonium formate was added. The mixture was stirred at
23 ЊC until the reaction was complete (TLC). The mixture was
then filtered through a pad of Celite, and concentrated in vacuo.
The crude product was purified by flash column chromato-
graphy using MeOH–dichloromethane as eluent to afford the
C7–C7, C7–N3 bis-seco-CBI-pyrrole or imidazole polyamide
conjugates compounds as white solids in good yield.
This compound was prepared starting from seco-CBI amine 15
(0.180 g, 0.363 mmol) and the acid 13 (0.30 g, 0.331 mmol)
according to general procedure described for compound 19 as a
white solid (0.30 g, 65% yield).1H NMR (300 MHz, DMSO-d6)
δ 1.54 (s, 18H, 2 × Boc–H), 2.52–2.72 (m, 4H, 2 × CH2CO–),
3.81 (s, 3H, –NCH3), 3.83 (s, 3H, –NCH3), 3.86 (s, 3H, –NCH3),
3.91–4.15 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2),
5.25 (s, 2H, –OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 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), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.25 (d,
1H, J = 1.8 Hz, Py–H), 7.28 (d, 1H, J = 1.8 Hz, Py–H), 7.60–
7.85 (m, 16H, Ar–H), 8.35 (m, 1H, NHCH2), 8.40 (s, 2H,
2 × C6–H), 9.91 (s, 1H, –NH–), 9.95 (s, 1H, –NH–), 10.09 (s,
1H, –NH–), 10.12 (s, 1H, –NH–), 10.32 (s, 1H, –NH–). ES–MS
m/z calculated for C74H77N11O12Cl2 1381.51, found 1404.50
(M ϩ Na).
Compound 24
Prepared according to general procedure D by using compound
18 (0.2 g, 0.175 mmol), 0.2 ml of 10% aqueous ammonium
formate and 0.2 g of 10% Pd/C in 15 ml of THF to give com-
pound 24 as a white solid in 89% yield (0.15 g). 1H NMR (300
MHz, DMSO-d6) δ 1.52 (s, 18H, 2 × Boc–H), 2.50–2.71 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.90–4.10 (m, 12H, Cl, 2-
H, 2 × CH2Cl, 2 × CH2N, NHCH2), 6.85 (d, 1H, J = 1.8 Hz, Py–
H), 7.18 (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),
9.91 (s, 1H), 10.09 (s, 1H), 10.12 (s, 1H), 10.25 (s, 1H), 10.30 (s,
1H). ES–MS m/z calculated for C48H53N7O10Cl2 957.32, found
980.30 (M ϩ Na).
Compound 21
This compound was prepared starting from seco-CBI amine 17
(0.290 g, 0.663 mmol) and the acid 11 (0.30 g, 0.454 mmol)
according to general procedure C (0.30 g, 61% yield) as a white
solid. 1H NMR (300 MHz, DMSO-d6) δH 1.52 (s, 9H, Boc–H),
2.05 (s, 3H, CH3CON), 2.56–2.70 (m, 4H, 2 × CH2CO–),
3.82 (s, 3H, –NCH3), 3.90–4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl,
2 × CH2N, NHCH2), 5.25 (s, 2H, –OCH2C6H5), 5.26 (s, 2H,
–OCH2C6H5), 6.81 (d, 1H, J = 1.5 Hz, Py–H), 7.16 (d, 1H,
J = 1.5 Hz, Py–H), 7.55–7.89 (m, 16H, Ar–H), 8.21–8.30
(m, 1H, NHCH2), 8.35–8.42 (m, 2H, 2 × C6–H), 9.95 (s,
1H, –NH–), 10.07 (s, 1H, –NH–), 10.14 (s, 1H, –NH–).
Compound 25
This compound was prepared according to the method
described for the compound 24, employing compound 19 (0.2 g,
0.158 mmol) and aq. ammonium formate (0.2 ml) in 90% yield
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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1
(0.154 g) as a white solid. H NMR (300 MHz, DMSO-d6)
Hz, Py–H), 7.26 (d, 1H, J = 1.5 Hz, Py–H), 7.60–7.79 (m, 5H,
δ 1.56 (s, 18H, 2 × Boc–H), 2.54–2.72 (m, 4H, 2 × CH2CO–),
3.82 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.89–4.20 (m, 12H,
Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2), 6.85 (d, 1H, J = 1.8
Hz, Py–H), 6.96 (d, 1H, J = 1.8 Hz, Py–H), 7.15 (d, 1H, J = 1.8
Hz, Py–H), 7.25 (d, 1H, J = 1.8 Hz, Py–H), 7.55–7.85 (m, 6H,
2 × C4–H, C7–H, C8–H), 8.32 (m, 1H, NHCH2), 8.43 (s, 2H,
2 × C6–H), 9.89 (s, 1H), 10.05 (s, 1H), 10.09 (s, 1H), 10.12 (s,
1H), 10.22 (s, 1H), 10.28 (s, 1H). ES–MS m/z calculated for
C54H59N9O11Cl2 1079.37, found 1102.30 (M ϩ Naϩ).
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 calculated for C57H59N11O11Cl2
1143.38 found 1166.36 (M ϩ Na).
4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-dihydro-
benzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-pyrrole-
2-carboxylic acid methyl ester (30)
This compound was prepared starting from 1-methyl-4-nitro-
1H-pyrrole-2-carboxylic acid methyl ester (0.421 g, 2.28 mmol)
and the seco-CBI acid 7 (1.0 g, 2.08 mmol) according to general
procedure A (0.90 g, 70% yield) as a white solid. 1H NMR (300
MHz, DMSO-d6) δ 2.04 (s, 3H, CH3CON), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.89 (s, 3H, –OCH3), 3.90–
4.10 (m, 5H, –CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5),
6.96 (d, 1H, J = 1.8 Hz, Py–H), 7.18 (d, 1H, J = 1.8 Hz, Py–H),
7.52–7.90 (m, 7H, Ar–H), 8.14 (s, 1H, Ar–H), 8.37 (s, 1H,
Ar–H), 9.99 (s, 1H, –NH–),10.0 (s, 1H, –NH–). ES–MS m/z
calculated for C33H33N4O6Cl 616.21, found 639.22 (M ϩ Na).
Compound 26
This compound was prepared starting from compound 20
(0.20 g, 0.144 mmol) and aq. ammonium formate (0.2 ml)
according to general procedure D (0.155 g, 90% yield) as a
1
white solid. H 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), 9.93 (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 calculated for C60H65N11O12Cl2 1201.42, found 1224.40
(M ϩ Na).
1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid tert-butyl ester
(35)
1-Methyl-4-nitro-1H-pyrrole-2-carboxylic acid (34) was
obtained from the basic hydrolysis of the corresponding
1-methyl-4-nitro-1H-pyrrole-2-carboxylic acid methyl ester (33)
from the above described reported procedure. Compound 34
(5.0 g, 29.41 mmol) was added to 200 ml of diethyl ether and
6 ml of concentrated sulfuric acid in a round bottom pressure
bottle. The colloidal solution was cooled to Ϫ60 ЊC and a slow
stream of isobutylene was bubbled through this solution for
several minutes. The solution was capped tightly with a teflon
cork and allowed to warm to room temperature and stirred for
36 h. The crude reaction mixture was washed with saturated
NaHCO3 repeatedly. The crude product was further purified by
column chromatography using using pure DCM as eluent to
Compound 27
This compound was prepared starting from compound 21
(0.20 g, 0.185 mmol) and aq. ammonium formate (0.2 ml)
according to general procedure D (0.15 g, 90% yield) as a white
1
solid. H NMR (300 MHz, DMSO-d6) δ 1.53 (s, 9H, Boc–H),
2.04 (s, 3H, CH3CON), 2.56–2.72 (m, 4H, 2 × CH2CO–), 3.82
(s, 3H, –NCH3), 3.90–4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl,
2 × CH2N, NHCH2), 6.80 (d, 1H, J = 1.7 Hz, Py–H), 7.16 (d,
1H, J = 1.7 Hz, Py–H), 7.60–7.79 (m, 5H, 2 × C8, C9–H, C4–
H), 7.90 (d, 1H, C4–H), 8.15–8.25 (m, 1H, NHCH2), 8.35–8.42
(m, 2H, 2 × C6–H), 9.91 (s, 1H), 10.05 (s, 1H), 10.07 (s, 1H),
10.14 (s, 1H), 10.32 (s, 1H). HR-ESMS m/z calculated for
C45H47N7O9Cl2 899.28, found 922.31 (M ϩ Na).
1
give compound 35 in 82% yield (5.5 g) as a white solid. H
NMR (300 MHz, CDCl3) δ 1.59 (s, 9H, –C(CH3)3), 3.85 (s,
3H, –NCH3), 7.36 (d, 1H, J = 1.8 Hz, Py–H), 7.76 (d, 1H,
J = 1.8 Hz, Py–H). HR–MS m/z calculated for C10H14N2O4
226.10, found 226.20.
Compound 28
1-Methyl-4-[(1-methyl-4-nitro-1H-pyrrole-2-carbonyl)amino]-
1H-pyrrole-2-carboxylic acid tert-butyl ester (36)
Prepared according to general procedure for compounds B by
using compound 22 (0.20 g, 0.166 mmol) and aq. ammonium
1
formate (0.25 ml) in 88% yield (0.15 g) as a white solid. H
To a solution of compound 35 (1.0 g, 4.42 mmol) in 25.0 ml of
methanol was added 0.200 g of 10% Pd/C. The reaction mixture
was hydrogenated in a Parr shaker at 50 psi for 2 h. The catalyst
was removed by filtration and the solvent was evaporated in
vacuo. The residue was dissolved in dry THF (10.0 ml), Et3N
(1.0 ml) and a solution of compound 32 (1.32 g, 4.86 mmol) in
THF (5.0 ml), was added slowly with stirring at 0 ЊC under a
nitrogen atmosphere. The reaction mixture was brought to
room temperature and stirred for 2 h. After completion of the
reaction the residue was concentrated to dryness under reduced
pressure and was purified by column chromatography eluting
with 5% MeOH–DCM to give 36, 1.3 g in 85% yield as a
NMR (300 MHz, DMSO-d6) δ 1.54 (s, 9H, Boc–H), 2.05 (s, 3H,
CH3CON), 2.60–2.72 (m, 4H, 2 × CH2CO–), 3.82 (s, 3H,
–NCH3), 3.84 (s, 3H, –NCH3), 3.91–4.40 (m, 12H, Cl, 2-H,
2 × CH2Cl, 2 × CH2N, NHCH2), 6.89 (d, 1H, J = 1.7 Hz,
Py–H), 6.96 (d, 1H, J = 1.7 Hz, Py–H), 7.18 (d, 1H, J = 1.7 Hz,
Py–H), 7.23 (d, 1H, J = 1.7 Hz, Py–H), 7.60–7.79 (m, 5H,
2 × C8, C9–H, C4–H), 7.91 (d, 1H, C4–H), 8.20–8.30 (m, 1H,
NHCH2), 8.35–8.42 (m, 2H, 2 × C6–H), 9.90 (s, 1H), 10.03 (s,
1H), 10.05 (s, 1H), 10.07 (s, 1H), 10.14 (s, 1H), 10.30 (s, 1H).
HR-ESMS m/z calculated for C51H53N9O10Cl2 1021.33, found
1044.31 (M ϩ Na).
1
white solid. H NMR : (300 MHz, DMSO-d6) δ 1.60 (s, 9H,
Compound 29
–C(CH3)3), 3.82 (s, 3H, –NCH3), 3.86 (s, 3H, –NCH3), 6.81 (d,
1H, J = 1.8 Hz, Py–H), 6.96 (d, 1H, J = 1.8 Hz, Py–H), 7.10 (d,
1H, J = 1.8 Hz, Py–H), 7.25 (d, 1H, J = 1.8 Hz, Py–H), 9.99 (s,
1H, –NH–) HR–MS m/z calculated for C16H20N4O5 348.14,
found 348.28.
This compound was prepared according to the method
described for the compound 27, employing compound 23
(0.20 g, 0.151 mmol) and the aq. ammonium formate (0.2 ml) in
90% yield (0.156 g) as a white solid. 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 = 1.7 Hz,
Py–H), 6.96 (d, 1H, J = 1.7 Hz, Py–H), 7.05 (d, 1H, J = 1.7 Hz,
Py–H), 7.16 (d, 1H, J = 1.5 Hz, Py–H), 7.23 (d, 1H, J = 1.5
1-Methyl-4-({1-methyl-4-[(1-methyl-4-nitro-1H-pyrrole-2-carb-
onyl)amino]-1H-pyrrole-2-carbonyl}amino)-1H-pyrrole-2-carb-
oxylic acid tert-butyl ester (37)
This compound was prepared according to the method
described for the compound 36, employing compound 36 (1.0 g,
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
2640

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2.87 mmol) and 32 (0.85 g, 3.13 mmol) and the crude product
was purified by column chromatography by using 7% MeOH–
DCM as eluting solvent in 75% yield (1.0 g) as a white solid. 1H
NMR : (300 MHz, DMSO-d6) δ 1.61 (s, 9H, –C(CH3)3), 3.81 (s,
3H, –NCH3), 3.83 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 6.86
(d, 1H, J = 1.8 Hz, Py–H), 7.05 (d, 1H, J = 1.8 Hz, Py–H), 7.14
(d, 1H, J = 1.8 Hz, Py–H), 7.23 (d, 1H, J = 1.8 Hz, Py–H), 7.31
(d, 1H, J = 1.8 Hz, Py–H), 7.39 (d, 1H, J = 1.8 Hz, Py–H), 9.98
(s, 1H, –NH–), 10.15 (s, 1H, –NH–) HR–MS m/z calculated for
C22H26N6O6 470.19, found 470.28.
General procedure E
A solution of the compounds 38, 39, or 40 was prepared in dry
dichloromethane or dry THF and to it 1.0 molar TiCl4 solution
in dichloromethane was added slowly dropwise with constant
stirring at room temperature. After complete addition the stir-
ring was continued for 24 h. The TLC observation at this time
indicated completion of the reaction. The reaction mixture was
concentrated in vacuo and purified by column chromatography.
Elution with 7% MeOH–DCM gave pure compounds 41–43 in
50% yield.
4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-dihydro-
benzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-pyrrole-
2-carboxylic acid tert-butyl ester (38)
4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-dihydro-
benzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-pyrrole-
2-carboxylic acid (41)
This compound was prepared starting from 1-methyl-4-nitro-
1H-pyrrole-2-carboxylic acid tert-butyl ester (35) (0.517 g, 2.28
mmol) and the seco-CBI acid 7 (1.0 g, 2.08 mmol) according to
general procedure A (1.0 g, 73% yield) as a solid. 1H NMR (300
MHz, DMSO-d6) δ 1.59 (s, 9H, –C(CH3)3), 2.04 (s, 3H,
CH3CON), 2.54–2.70 (m, 4H, 2 × CH2CO–), 3.82 (s, 3H,
–NCH3), 3.90–4.20 (m, 5H, –CH, CH2Cl, CH2N), 5.26 (s,
2H, –OCH2C6H5), 6.96 (d, 1H, J = 1.8 Hz, Py–H), 7.15 (d, 1H,
J = 1.8 Hz, Py–H), 7.56–7.89 (m, 7H, Ar–H), 8.14 (s, 1H,
Ar–H), 8.35 (s, 1H, Ar–H), 9.98 (s, 1H, –NH–), 10.10 (s, 1H,
–NH–). HR–MS m/z calculated for C36H39N4O6Cl 658.26,
found 681.30 (M ϩ Na).
Prepared according to general method E by using compound 38
(1.0g, 1.51 mmol) and 1.0 M solution of TiCl4 (3.0 ml) in di-
chloromethane to give compound 41 as a solid in 65% yield
(0.60g). 1H NMR (300 MHz, DMSO-d6) δ 2.05 (s, 3H,
CH3CON), 2.58–2.72 (m, 4H, 2 × CH2CO–), 3.82 (s, 3H,
–NCH3), 3.92–4.20 (m, 5H, –CH, CH2Cl, CH2N), 5.24 (s, 2H,
–OCH2C6H5), 6.98 (d, 1H, J = 1.8 Hz, Py–H), 7.20 (d, 1H,
J = 1.8 Hz, Py–H), 7.52–7.90 (m, 7H, Ar–H), 8.18 (s, 1H,
Ar–H), 8.39 (s, 1H, Ar–H), 10.00 (s, 1H, –NH–), 10.20 (s, 1H,
–NH–), 12.52 (br s, 1H, –COOH). HR–MS m/z calculated for
C32H31N4O6Cl 602.19, found 625.22 (M ϩ Na).
4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carboxylic
acid (42)
4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carboxylic
acid tert-butyl ester (39)
Prepared, according to general procedure E using compound 39
(1.0g, 1.28 mmol) and 1.0 M solution of TiCl4 (3.0 ml) solution,
in 65% yield (0.60 g) as solid. 1H NMR (300 MHz, DMSO-d6)
δ 2.04 (s, 3H, CH3CON), 2.54–2.75 (m, 4H, 2 × CH2CO–), 3.82
(s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.91–4.20 (m, 5H, –CH,
CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5), 6.96 (d, 1H, J = 1.8
Hz, Py–H), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.23 (d, 1H, J = 1.8
Hz, Py–H), 7.33 (d, 1H, J = 1.8 Hz, Py–H), 7.52–7.96 (m, 7H,
Ar–H), 8.15 (s, 1H, Ar–H), 8.35 (s, 1H, Ar–H), 10.05 (s, 1H,
–NH–), 10.12 (s, 1H, –NH–), 10.20 (s, 1H, –NH–), 12.52 (br s,
1H, –COOH). HR–MS m/z calculated for C38H37N6O7Cl
724.24, found 747.25 (M ϩ Na).
Prepared according to general procedure A by using 1-methyl-4-
[(1-methyl-4-nitro-1H-pyrrole-2-carbonyl)amino]-1H-pyrrole-2-
carboxylic acid tert-butyl ester (36) (0.797 g, 2.28 mmol) and the
acid 7 (1.0 g, 2.08 mmol) in 80% yield (1.30g) as a white solid.
1H NMR (300 M Hz, DMSO-d6) δ 1.59 (s, 9H, –C(CH3)3),
2.04 (s, 3H, CH3CON), 2.54–2.70 (m, 4H, 2 × CH2CO–),
3.82 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.91–4.20 (m, 5H,
–CH, CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5), 6.96 (d, 1H,
J = 1.8 Hz, Py–H), 7.05 (d, 1H, J = 1.8 Hz, Py–H), 7.26 (d, 1H,
J = 1.8 Hz, Py–H), 7.31 (d, 1H, J = 1.8 Hz, Py–H), 7.55–7.92
(m, 7H, Ar–H), 8.18 (s, 1H, Ar–H), 8.38 (s, 1H, Ar–H), 9.98 (s,
1H, –NH–), 10.12 (s, 1H, –NH–), 10.20 (s, 1H, –NH–).
HR–MS m/z calculated for C42H45N6O7Cl 780.30, found 803.31
(M ϩ Na).
4-{[4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]-
amino}-1-methyl-1H-pyrrole-2-carboxylic acid (43)
4-{[4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]-
amino}-1-methyl-1H-pyrrole-2-carboxylic acid tert-butyl ester
(40)
Prepared according to general method E by using compound 40
(1.0g, 1.10 mmol) and 1.0 M solution of TiCl4 (3.0 ml) to give
1
compound 43 as a light yellow solid in 58% yield (0.55g). H
NMR (300 MHz, DMSO-d6) δ 2.04 (s, 3H, CH3CON), 2.58–
2.73 (m, 4H, 2 × CH2CO–), 3.81 (s, 3H, –NCH3), 3.84 (s, 3H,
–NCH3), 3.86 (s, 3H, –NCH3), 3.91–4.20 (m, 5H, –CH, CH2Cl,
CH2N), 5.24 (s, 2H, –OCH2C6H5), 6.81 (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), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.24 (d, 1H, J = 1.8 Hz,
Py–H), 7.32 (d, 1H, J = 1.8 Hz, Py–H), 7.49–7.90 (m, 7H,
Ar–H), 8.18 (s, 1H, Ar–H), 8.35 (s, 1H, Ar–H), 9.95 (s, 1H,
–NH–), 10.12 (s, 1H, –NH–), 10.22 (s, 1H, –NH–), 10.30 (s, 1H,
–NH–), 12.56 (br s, 1H, –COOH). HR–MS m/z calculated for
C44H43N8O8Cl 846.29, found 869.31 (M ϩ Na).
This compound was prepared according to the method
described for the compounds 38–40, employing 1-methyl-4-
({1-methyl-4-[(1-methyl-4-nitro-1H-pyrrole-2-carbonyl)amino]-
1H-pyrrole-2-carbonyl}amino)-1H-pyrrole-2-carboxylic acid
tert-butyl ester (37) (1.07 g, 2.27 mmol) and the seco-CBI acid 7
1
(1.0 g, 2.08 mmol) in 72% yield (1.35 g) as a white solid. H
NMR (300 MHz, DMSO-d6) δ 1.60 (s, 9H, –C(CH3)3), 2.05 (s,
3H, CH3CON), 2.56–2.70 (m, 4H, 2 × CH2CO–), 3.81 (s, 3H,
–NCH3), 3.84 (s, 3H, –NCH3), 3.87 (s, 3H, –NCH3), 3.92–4.20
(m, 5H, –CH, CH2Cl, CH2N), 5.26 (s, 2H, –OCH2C6H5), 6.89
(d, 1H, J = 1.8 Hz, Py–H), 6.98 (d, 1H, J = 1.8 Hz, Py–H), 7.05
(d, 1H, J = 1.8 Hz, Py–H), 7.15 (d, 1H, J = 1.8 Hz, Py–H), 7.25
(d, 1H, J = 1.8 Hz, Py–H), 7.31 (d, 1H, J = 1.8 Hz, Py–H), 7.45–
7.90 (m, 7H, Ar–H), 8.20 (s, 1H, Ar–H), 8.35 (s, 1H, Ar–H),
9.98 (s, 1H, –NH–), 10.15 (s, 1H, –NH–), 10.22 (s, 1H, –NH–),
10.35 (s, 1H, –NH–). HR–MS m/z calculated for C48H51N8O8Cl
902.35, found 925.40 (M ϩ Na).
Compound 44
This compound was prepared starting from seco-CBI amine 17
(0.239 g, 0.546 mmol) and the acid 41 (0.30g, 0.498 mmol)
according to general procedure C (0.310 g, 61% yield) as a
1
white solid. H NMR (300 MHz, DMSO-d6) δ 2.04 (s, 6H,
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
2641

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2 × –CH3CON), 2.58–2.70 (m, 4H, 2 × CH2CO–), 3.83 (s, 3H,
–NCH3), 3.92–4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N,
NHCH2), 5.24 (s, 2H, –OCH2C6H5), 5.25 (s, 2H, –OCH2C6H5),
6.94 (d, 1H, J = 1.7 Hz, Py–H), 7.16 (d, 1H, J = 1.7 Hz, Py–H),
7.60–7.90 (m, 14H, Ar–H), 8.13 (s, 2H, Ar–H), 8.21–8.30 (m,
1H, NHCH2), 8.35 (s, 2H, Ar–H), 10.03 (s, 1H, –NH–), 10.07 (s,
1H, –NH–), 10.14 (s, 1H, –NH–). HR-ESMS m/z calculated for
C56H53N7O8Cl2 1021.33, found 1044.45 (M ϩ Na).
Ar–H), 9.98 (s, 1H), 10.05 (s, 1H), 10.07 (s, 1H), 10.08 (s, 1H),
10.14 (s, 1H), 10.35 (s, 1H). HR-ESMS m/z calculated for
C48H47N9O9Cl2 963.29, found 986.31 (M ϩ Na).
Compound 49
This compound was prepared according to the method
described for compound 47, employing compound 46 (0.3 g,
0.237 mmol) and 10% aq. ammonium formate (0.35 ml) in 81%
yield (0.21 g) as a white solid. 1H NMR (300 MHz, DMSO-d6)
δ 2.04 (s, 6H, 2 × –CH3CON), 2.61–2.72 (m, 4H, 2 × CH2CO–),
3.81 (s, 3H, –NCH3), 3.82 (s, 3H, –NCH3), 3.84 (s, 3H, –NCH3),
3.91–4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2),
6.81 (d, 1H, J = 1.7 Hz, Py–H), 6.96 (d, 1H, J = 1.7 Hz, Py–H),
7.06 (d, 1H, J = 1.7 Hz, Py–H), 7.16 (d, 1H, J = 1.7 Hz, Py–H),
7.24 (d, 1H, J = 1.7 Hz, Py–H), 7.27 (d, 1H, J = 1.7 Hz, Py–H),
7.65 (d, J = 8.8 Hz, 2H, Ar–H), 7.75 (d, J = 8.8 Hz, 2H, Ar–H),
7.95 (s, 2H, Ar–H), 8.20–8.30 (m, 1H, NHCH2), 8.35 (s, 2H,
Ar–H), 9.95 (s, 1H), 10.02 (s, 1H), 10.06 (s, 1H), 10.09 (s, 1H),
10.14 (s, 1H), 10.28 (s, 1H), 10.35 (s, 1H). HR-ESMS m/z calcu-
lated for C54H53N11O10Cl2 1085.34 found 1108.40 (M ϩ Na).
Compound 45
This compound was prepared according to the method
described for the compound 44, employing seco-CBI N-3 poly-
amide acid 42 (0.3 g, 0.414 mmol) and the amine 17 (0.20 g,
0.457 mmol) in 63% yield (0.30g). 1H NMR (300 M Hz,
DMSOd6) δ 2.04 (s, 6H, 2 × –CH3CON), 2.58–2.74 (m, 4H,
2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.85 (s, 3H, –NCH3), 3.90–
4.35 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2), 5.22
(s, 2H, –OCH2C6H5), 5.24 (s, 2H, –OCH2C6H5), 6.89 (d, 1H,
J = 1.7 Hz, Py–H), 7.05 (d, 1H, J = 1.7 Hz, Py–H), 7.19 (d, 1H,
J = 1.7 Hz, Py–H), 7.26 (d, 1H, J = 1.7 Hz, Py–H), 7.61–7.95
(m, 14H, Ar–H), 8.15 (s, 2H, Ar–H), 8.25–8.30 (m, 1H,
NHCH2), 8.38 (s, 2H, Ar–H), 10.02 (s, 1H, –NH–), 10.10 (s, 1H,
–NH–), 10.15 (s, 1H, –NH–), 10.18 (s, 1H, –NH–). HR-ESMS
m/z calculated for C62H59N9O9Cl2 1143.38 found 1166.40
(M ϩ Na).
5-Benzyloxy-1-chloromethyl-7-[3-(2-methoxycarbonyl-1-methyl-
1H-imidazol-4-ylcarbamoyl)propionylamino]-1,2-dihydro-
benzo[e]indole-3-carboxylic acid tert-butyl ester (50)
This compound was prepared starting from 1-methyl-4-nitro-
1H-imidazole-2-carboxylic acid methyl ester (0.190 g, 1.02
mmol) and the acid 5 (0.5g, 0.929 mmol) according to general
procedure A (0.9 g, 79% yield) as a white solid. 1H NMR
(300 MHz, DMSO-d6) δ 1.53 (s, 9H, Boc–H), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.84 (s, 3H, –NCH3), 3.85 (s, 3H, –OCH3), 3.90–
4.15 (m, 5H, –CH, CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5),
7.55 (s, 1H, Im–H), 7.61–7.90 (m, 8H, Ar–H), 8.40 (s, 1H, C6–
H), 10.15 (s, 1H, –NH–), 10.55 (s, 1H, –NH–). HR–MS m/z
calculated for C35H38N5O7Cl 675.25, found 698.23 (M ϩ Na).
Compound 46
Prepared according to general procedure C by using compound
43 (0.30 g, 0.354 mmol) and seco-CBI amine 17 (0.17 g, 0.388
mmol) in 69% yield (0.31 g). 1H NMR (300 M Hz, DMSO-d6)
δ 2.04 (s, 6H, 2 ×-CH3CON), 2.55–2.72 (m, 4H, 2 × CH2CO–),
3.81 (s, 3H, –NCH3), 3.82 (s, 3H, –NCH3), 3.82 (s, 3H, –NCH3),
3.89–4.40 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2),
5.25 (s,2H, –OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 6.81 (d,
1H, J = 1.7 Hz, Py–H), 6.98 (d, 1H, J = 1.7 Hz, Py–H), 7.08 (d,
1H, J = 1.7 Hz, Py–H), 7.18 (d, 1H, J = 1.7 Hz, Py–H), 7.24 (d,
1H, J = 1.7 Hz, Py–H), 7.27 (d, 1H, J = 1.7 Hz, Py–H), 7.59–
7.85 (m, 14H, Ar–H), 8.10 (s, 2H, Ar–H), 8.20–8.30 (m, 1H,
NHCH2), 8.37 (s, 2H, Ar–H), 10.00 (s, 1H, –NH–), 10.07 (s, 1H,
–NH–), 10.10 (s, 1H, –NH–), 10.18 (s, 1H, –NH–), 10.25 (s, 1H,
–NH–). HR-ESMS m/z calculated for C68H65N11O10Cl2 1265.43
found 1288.40 (M ϩ Na).
5-Benzyloxy-7-[3-(2-carboxy-1-methyl-1H-imidazol-4-ylcarb-
amoyl)propionylamino]-1-chloromethyl-1,2-dihydrobenzo[e]-
indole-3-carboxylic acid tert-butyl ester (51)
This compound was prepared according to general procedure B
by employing compound 50 (0.4g, 0.592 mmol) and 0.5 M NaOH
in 76% yield (0.30 g) as a white solid. 1H NMR (300 MHz,
DMSO-d6) δ 1.52 (s, 9H, Boc–H), 2.56–2.70 (m, 4H, 2 ×
CH2CO–), 3.82 (s, 3H, –NCH3), 3.90–4.20 (m, 5H, –CH, CH2Cl,
CH2N), 5.24 (s, 2H, –OCH2C6H5), 7.45 (s, 1H, Im–H), 7.58–7.90
(m, 8H, Ar–H), 8.40 (s, 1H, C6–H), 10.12 (s, 1H, –NH–), 10.40 (s,
1H, –NH–), 12.52 (br s, 1H, –COOH). HR–MS m/z calculated
for C34H36N5O7Cl 661.23, found 662.13 (M ϩ 1).
Compound 47
This compound was prepared starting from compound 44
(0.25 g, 0.244 mmol) and 10% aq. ammonium formate (0.2 ml)
according to general procedure D in (0.17 g, 82% yield)
as a white solid.1H NMR (300 MHz, DMSO-d6) δ 2.04 (s, 6H,
2 × –CH3CON), 2.56–2.72 (m, 4H, 2 × CH2CO–), 3.81 (s,
3H, –NCH3), 3.90–4.35 (m, 12H, Cl, 2-H, 2 × CH2Cl,
2 × CH2N, NHCH2), 6.94 (d, 1H, J = 1.7 Hz, Py–H), 7.19 (d,
1H, J = 1.7 Hz, Py–H), 7.65 (d, J = 8.9 Hz, 2H, Ar–H), 7.73 (d,
J = 8.9 Hz, 2H, Ar–H), 7.96 (s, 2H, Ar–H), 8.20–8.30 (m, 1H,
NHCH2), 8.35 (s, 2H, Ar–H), 9.94 (s, 1H), 10.05 (s, 1H), 10.07
(s, 1H), 10.14 (s, 1H). HR-ESMS m/z calculated for C42H41N7-
O8Cl2 841.24, found 864.19 (M ϩ Na).
[(1-Methyl-4-nitro-1H-imidazole-2-carbonyl)amino]acetic acid
methyl ester (53)
To a solution of glycine methyl ester hydrochloride (1.0 g,
7.96 mmol) in dry THF (50.0 ml), Et3N (1.0 ml) and a solution
of compound 52 (2.38 g, 8.73 mmol) in THF (5.0 ml), was
added slowly with stirring at 0 ЊC under nitrogen atmosphere.
The reaction mixture was brought to room temperature and
stirred for 4 h. After completion of the reaction the residue was
concentrated to dryness under reduced pressure and the residue
was purified by column chromatography in 87% yield (1.85 g) as
Compound 48
1
a solid. H NMR (300 MHz, DMSO-d6) δ 3.55–3.82 (m, 2H,
Prepared according to general procedure D by using compound
–NHCH2), 3.85 (s, 3H, –OCH3), 3.87 (s, 3H, –NCH3), 7.45 (s,
1H, Im–H), 8.20 (m, 1H, –NHCH2). HR–MS m/z calculated for
C8H10N4O5 242.07, found 242.20.
45 (0.25 g, 0.218 mmol) and 10% aq. ammonium formate
1
(0.3 ml) in 82% yield (0.172 g) as a white solid. H NMR (300
MHz, DMSO-d6) δ 2.04 (s, 6H, 2 × –CH3CON), 2.60–2.72 (m,
4H, 2 × CH2CO–), 3.82 (s, 3H, –NCH3), 3.84 (s, 3H, –NCH3),
3.91–4.42 (m, 12H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N, NHCH2),
6.94 (d, 1H, J = 1.7 Hz, Py–H), 7.16 (d, 1H, J = 1.7 Hz, Py–H),
7.23 (d, 1H, J = 1.7 Hz, Py–H), 7.26 (d, 1H, J = 1.7 Hz, Py–H),
7.64 (d, J = 8.9 Hz, 2H, Ar–H), 7.75 (d, J = 9.0 Hz, 2H, Ar–H),
7.96 (s, 2H, Ar–H), 8.20–8.30 (m, 1H, NHCH2), 8.35 (s, 2H,
({1-Methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-carbonyl)-
amino]-1H-imidazole-2-carbonyl}amino)acetic acid methyl ester
(54)
To a solution of compound 53 (1.0 g, 4.13 mmol) in 25.0 ml
of methanol was added 0.200 g of 10% Pd–C. The reaction
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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mixture was hydrogenated in a Parr shaker at 50 psi for 2 h. The
catalyst was removed by filtration and the solvent was evapor-
ated in vacuo. The residue was dissolved in dry THF (20.0 ml),
Et3N (1.0 ml) and a solution of compound 52 (1.12 g, 4.11
mmol) in THF (5.0 ml), was added slowly with stirring at 0 ЊC
under nitrogen atmosphere. The reaction mixture was brought
to room temperature and stirred for 2 h. After completion
of the reaction the residue was concentrated to dryness under
reduced pressure and the residue was purified by column
chromatography eluting with 3% MeOH–DCM to give 54, as a
yellow solid 1.3 g in 86% yield. 1H NMR (300 MHz, DMSO-d6)
δ 3.56–3.80 (m, 2H, –NHCH2), 3.85 (s, 3H, –OCH3), 3.87 (s,
3H, –NCH3), 3.89 (s, 3H, –NCH3), 7.75 (s, 1H, Im–H),
8.15–8.20 (m, 1H, –NHCH2), 8.60 (s, 1H, Im–H), 10.90 (s, 1H,
–NH–). HR–MS m/z calculated for C13H15N7O6 365.11, found
365.32.
5-Benzyloxy-1-chloromethyl-7-(3-{2-[2-(2-methoxycarbonyl-
methylcarbamoyl)-1-methyl-1H-imidazol-4-ylcarbamoyl)-1-
methyl-1H-imidazol-4-ylcarbamoyl]-1-methyl-1H-imidazol-4-
ylcarbamoyl}propionylamino)-1,2-dihydrobenzo[e]indole-3-
carboxylic acid tert-butyl ester (58)
This compound was prepared according to the method
described for compounds 56, 57 by employing {[1-methyl-4-({1-
methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-carbonyl)-amino]-
1H-imidazole-2-carbonyl}-amino)-1H-imidazole-2-carbonyl]-
amino}acetic acid methyl ester (55) (0.998 g, 2.04 mmol) and
the acid 5 (1.0 g, 1.85 mmol) in 80% yield (1.45 g) as a white
1
solid. H NMR (300 MHz, DMSO-d6) δ 1.55 (s, 9H, Boc–H),
2.56–2.70 (m, 4H, 2 × CH2CO–), 3.57–3.80 (m, 2H, –NHCH2),
3.83 (s, 3H, –OCH3), 3.86 (s, 3H, –NCH3), 3.87 (s, 3H, –NCH3),
3.89 (s, 3H, –NCH3), 3.92–4.20 (m, 5H, –CH, CH2Cl, CH2N),
5.25 (s, 2H, –OCH2C6H5), 7.45 (s, 1H, Im–H), 7.65 (s, 1H,
Im–H), 7.69–7.98 (m, 9H, Ar–H, Im–H), 8.20–8.35 (m, 1H,
–NHCH2), 8.48 (s, 1H, C6–H), 9.70 (s, 1H, –NH–), 9.80 (s, 1H,
–NH–), 10.15 (s, 1H, –NH–), 10.50 (s, 1H, –NH–). HR–MS m/z
calculated for C47H51N12O10Cl 978.35, found 979.36 (M ϩ 1).
{[1-Methyl-4-({1-methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-
carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-imid-
azole-2-carbonyl]amino}acetic acid methyl ester (55)
This compound was prepared according to the method
described for compound 54, employing compounds 54 (1.0 g,
2.73 mmol) and 52 (0.746 g, 2.73 mmol) and the crude prod-
uct was purified by column chromatography using 7%
MeOH–DCM as eluting solvent. Compound 55 was obtained
in 75% yield (1.0 g) as a solid. 1H NMR (300 MHz, DMSO-d6)
δ 3.58–3.80 (m, 2H, –NHCH2), 3.86 (s, 3H, –OCH3), 3.87
(s, 3H, –NCH3), 3.89 (s, 3H, –NCH3), 3.91 (s, 3H, –NCH3), 7.58
(s, 1H, Im–H), 7.76 (s, 1H, Im–H), 8.15–8.26 (m, 1H,
–NHCH2), 8.58 (s, 1H, Im–H), 10.10 (s, 1H, –NH–), 10.60 (s,
1H, –NH–). HR–MS m/z calculated for C18H20N10O7 488.15,
found 488.40.
5-Benzyloxy-7-{3-[2-(carboxymethylcarbamoyl)-1-methyl-1H-
imidazol-4-ylcarbamoyl]propionylamino}-1-chloromethyl-1,2-di-
hydrobenzo[e]indole-3-carboxylic acid tert-butyl ester (59)
This compound was prepared in 81% yield as a solid according
to general procedure B by employing compound 56 (1.0 g, 1.36
mmol) and 0.5 M NaOH (0.80 g). 1H NMR (300 MHz, DMSO-
d6) δ 1.54 (s, 9H, Boc–H), 2.55–2.72 (m, 4H, 2 × CH2CO–),
3.57–3.80 (m, 2H, –NHCH2), 3.87 (s, 3H, –NCH3), 3.92–4.15
(m, 5H, –CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5), 7.45
(s, 1H, Im–H), 7.58–7.90 (m, 8H, Ar–H), 8.18–8.35 (m, 1H,
–NHCH2), 8.40 (s, 1H, C6–H), 10.15 (s, 1H, –NH–), 10.38 (s,
1H, –NH–), 12.56 (br s, 1H, –COOH). HR–MS m/z calculated
for C36H39N6O8Cl 718.25, found 741.24 (M ϩ Na).
5-Benzyloxy-1-chloromethyl-7-{3-[2-(methoxycarbonylmethyl-
carbamoyl)-1-methyl-1H-imidazol-4-ylcarbamoyl]propionyl-
amino}-1,2-dihydrobenzo[e]indole-3-carboxylic acid tert-butyl
ester (56)
5-Benzyloxy-7-(3-{2-[2-(carboxymethylcarbamoyl)-1-methyl-
1H-imidazol-4-ylcarbamoyl]-1-methyl-1H-imidazol-4-ylcarb-
amoyl}propionylamino)-1-chloromethyl-1,2-dihydrobenzo[e]-
indole-3-carboxylic acid tert-butyl ester (60)
This compound was prepared starting from [(1-methyl-4-nitro-
1H-imidazole-2-carbonyl)amino]acetic acid methyl ester (53)
(0.494 g, 2.04 mmol) and the acid 5 (1.0 g, 1.85 mmol) accord-
ing to general procedure A (1.0 g, 73% yield) as a white solid.
1H NMR (300 MHz, DMSO-d6) δ 1.56 (s, 9H, Boc–H),
2.56–2.70 (m, 4H, 2 × CH2CO–), 3.58–3.78 (m, 2H, –NHCH2),
3.84 (s, 3H, –OCH3), 3.87 (s, 3H, –NCH3), 3.92–4.15 (m, 5H,
–CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5), 7.47 (s, 1H,
Im–H), 7.52–7.90 (m, 8H, Ar–H), 8.18–8.30 (m, 1H, –NHCH2),
8.40 (s, 1H, C6–H), 10.15 (s, 1H, –NH–), 10.25 (s, 1H, –NH–).
HR–MS m/z calculated for C37H41N6O8Cl 732.27, found 733.30
(M ϩ 1).
Prepared according to general procedure B by using compound
57 (1.0 g, 1.16 mmol) and 0.5 M NaOH solution in 81% yield
1
(0.80 g) as a solid. H NMR (300 MHz, DMSO-d6) δ 1.54 (s,
9H, Boc–H), 2.56–2.72 (m, 4H, 2 × CH2CO–), 3.55–3.80 (m,
2H, –NHCH2), 3.86 (s, 3H, –NCH3), 3.88 (s, 3H, –NCH3),
3.91–4.20 (m, 5H, –CH, CH2Cl, CH2N), 5.25 (s, 2H,
–OCH2C6H5), 7.42 (s, 1H, Im–H), 7.55 (s, Im–H), 7.58–7.89
(m, 8H, Ar–H), 8.20–8.35 (m, 1H, –NHCH2), 8.47 (s, 1H, C6–
H), 9.80 (s, 1H, –NH–), 10.15 (s, 1H, –NH–), 10.50 (s, 1H,
–NH–), 12.60 (br s, 1H, –COOH). HR–MS m/z calculated for
C41H44N9O9Cl 841.30, found 842.31 (M ϩ 1).
5-Benzyloxy-1-chloromethyl-7-(3-{2-[2-(methoxycarbonyl-
methylcarbamoyl)-1-methyl-1H-imidazol-4-ylcarbamoyl]-1-
methyl-1H-imidazol-4-ylcarbamoyl}propionylamino)-1,2-di-
hydrobenzo[e]indole-3-carboxylic acid tert-butyl ester (57)
5-Benzyloxy-7-(3-{2-[2-(2-(carboxymethylcarbamoyl)-1-methyl-
1H-imidazol-4-ylcarbamoyl)-1-methyl-1H-imidazol-4-ylcarb-
amoyl]-1-methyl-1H-imidazol-4-ylcarbamoyl}propionylamino)-
1-chloromethyl-1,2-dihydrobenzo[e]indole-3-carboxylic acid tert-
butyl ester (61)
Prepared according to general procedure A by using ({1-
methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-carbonyl)amino]-
1H-imidazole-2-carbonyl}amino)acetic acid methyl ester (54)
(0.746 g, 2.04 mmol) and the acid 5 (1.0 g, 1.85 mmol) in 80%
This compound was prepared according to general method B
by using compound 58 (1.0 g, 1.02 mmol) and 0.5 M NaOH
1
solution in 81% yield (0.80 g) as a white solid. H NMR (300
1
yield (1.2 g) as a white solid. H NMR (300 MHz, DMSO-d6)
MHz, DMSO-d6) δ 1.52 (s, 9H, Boc–H), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.56–3.80 (m, 2H, –NHCH2), 3.86 (s, 3H,
–NCH3), 3.87 (s, 3H, –NCH3), 3.89 (s, 3H, –NCH3), 3.92–4.20
(m, 5H, –CH, CH2Cl, CH2N), 5.24 (s, 2H, –OCH2C6H5), 7.47
(s, 1H, Im–H), 7.55 (s, 1H, Im–H), 7.58–7.98 (m, 9H, Ar–H,
Im–H), 8.15–8.35 (m, 1H, –NHCH2), 8.40 (s, 1H, C6–H), 9.56
(s, 1H, –NH–), 9.89 (s, 1H, –NH–), 10.20 (s, 1H, –NH–), 10.51
(s, 1H, –NH–), 12.59 (br s, 1H, –COOH). HR–MS m/z calcu-
lated for C46H49N12O10Cl 964.34, found 965.34 (M ϩ 1).
δ 1.53 (s, 9H, Boc–H), 2.52–2.71 (m, 4H, 2 × CH2CO–), 3.56–
3.79 (m, 2H, –NHCH2), 3.82 (s, 3H, –OCH3), 3.86 (s, 3H,
–NCH3), 3.88 (s, 3H, – NCH3), 3.91–4.15 (m, 5H, –CH, CH2Cl,
CH2N), 5.26 (s, 2H, –OCH2C6H5), 7.47 (s, 1H, Im–H), 7.50–
7.95 (m, 9H, Ar–H, Im–H), 8.20–8.30 (m, 1H, –NHCH2), 8.42
(s, 1H, C6–H), 9.55 (s, 1H, –NH–), 10.15 (s, 1H, –NH–), 10.48
(s, 1H, –NH–). HR–MS m/z calculated for C42H46N9O9Cl
855.31, found 856.31 (M ϩ 1).
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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Compound 62
7.50–7.95 (m, 17H, Ar–H, Im–H), 8.25–8.32 (m, 2H,
2 × –NHCH2), 8.30–8.40 (m, 2H, 2 × C6–H), 9.45 (s, 1H,
–NH–), 10.12 (s, 1H, –NH–), 10.18 (s, 1H, –NH–), 10.45 (s, 1H,
–NH–). HR-ESMS m/z calculated for C65H66N12O11Cl2 1260.44
found 1261.40 (M ϩ 1).
Prepared according to general procedure C by using compound
59 (0.25 g, 0.348 mmol) and seco-CBI amine 15 (0.189 g, 0.381
mmol) in 72% yield (0.30 g) as a white solid. H NMR (300
1
MHz, DMSO-d6) δ 1.52 (s, 18H, 2 × Boc–H), 2.56–2.70 (m, 4H,
2 × CH2CO–), 3.55–3.79 (m, 4H, 2 × –NHCH2), 3.85 (s, 3H,
–NCH3), 3.91–4.20 (m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N),
5.24 (s, 2H, –OCH2C6H5), 5.25 (s, 2H, –OCH2C6H5), 7.48
(s, 1H, Im–H), 7.59–7.75 (m, 16H, Ar–H), 8.30 (m, 2H,
2 × –NHCH2), 8.40 (s, 2H, 2 × C6–H), 10.10 (s, 1H, –NH–),
10.20 (s, 1H, –NH–), 10.40 (s, 1H, –NH–). ES–MS m/z calcu-
lated for C63H67N9O11Cl2 1195.43, found 1218.40 (M ϩ Na).
Compound 67
Prepared according to general procedure C using compound 61
(0.3 g, 0.311 mmol) and seco-CBI amine 17 (0.183 g, 0.369
1
mmol) in 69% yield (0.30 g) as a white solid. H NMR (300
MHz, DMSO-d6) δ 1.56 (s, 9H, Boc–H), 2.05 (s, 3H,
CH3CON), 2.56–2.70 (m, 4H, 2 × CH2CO–), 3.56–3.80 (m,
4H, 2 × –NHCH2), 3.86 (s, 3H, –NCH3), 3.87 (s, 3H, –NCH3),
3.89 (s, 3H, –NCH3), 3.91–4.40 (m, 10H, Cl, 2-H, 2 × CH2Cl,
2 × CH2N), 5.25 (s,2H, –OCH2C6H5), 5.26 (s, 2H, –OCH2-
C6H5), 7.48 (s, 1H, Im–H), 7.57 (s, 1H, Im–H), 7.60–7.95 (m,
17H, Ar–H, Im–H), 8.20–8.30 (m, 2H, 2 × –NHCH2), 8.32–
8.42 (m, 2H, 2 × C6–H), 9.62 (s, 1H, –NH–), 9.85 (s, 1H, –NH–),
10.15 (s, 1H, –NH–), 10.18 (s, 1H, –NH–), 10.48 (s, 1H, –NH–).
HR-ESMS m/z calculated for C70H71N15O12Cl2 1383.48 found
1384.50 (M ϩ 1).
Compound 63
This compound was prepared according to the method
described for compound 62, by employing seco-CBI imidazole
polyamide acid 60 (0.25 g, 0.297 mmol) and the amine 15 (0.161
1
g, 0.325 mmol) in 76% yield (0.30 g) as a solid. H NMR (300
MHz, DMSO-d6) δ 1.56 (s, 18H, 2 × Boc–H), 2.52–2.70 (m, 4H,
2 × CH2CO–), 3.56–3.79 (m, 4H, 2 × –NHCH2), 3.85 (s, 3H,
–NCH3), 3.87 (s, 3H, –NCH3), 3.90–4.20 (m, 10H, Cl, 2-H,
2 × CH2Cl, 2 × CH2N), 5.24 (s, 2H, –OCH2C6H5), 5.26 (s, 2H,
–OCH2C6H5), 7.48 (s, 1H, Im–H), 7.60–7.95 (m, 17H, Ar–H,
Im–H), 8.20–8.35 (m, 2H, 2 × –NHCH2), 8.40 (s, 2H, 2 × C6–
H), 9.51 (s, 1H, –NH–), 10.10 (s, 1H, –NH–), 10.18 (s, 1H,
–NH–), 10.25 (s, 1H, –NH–) ES–MS m/z calculated for
C68H72N12O12Cl2 1318.48, found 1319.50 (M ϩ 1).
Compound 68
Prepared according to general procedure D by using compound
62 (0.2 g, 0.167 mmol), 0.2 ml of 10% aqueous ammonium form-
ate and 0.2 g of 10% Pd/C in 15 ml of THF to give compound 68
as a white solid in 88% yield (0.15 g). 1H NMR (300 MHz,
DMSO-d6) δ 1.52 (s, 18H, 2 × Boc–H), 2.50–2.71 (m, 4H, 2 ×
CH2CO–), 3.52–3.70 (m, 4H, 2 × –NHCH2), 3.86 (s, 3H,
–NCH3), 3.92–4.20 (m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N),
7.59–7.85 (m, 7H, 2 × C4–H, C7–H, C8–H, Im–H), 8.20–8.32 (m,
2H, 2 × –NHCH2), 8.40 (s, 2H, 2 × C6–H), 9.95 (s, 1H), 10.05 (s,
1H), 10.12 (s, 1H), 10.25 (s, 1H), 10.30 (s, 1H). ES–MS m/z calcu-
lated for C49H55N9O11Cl2 1015.34, found 1038.30 (M ϩ Na).
Compound 64
This compound was prepared starting from seco-CBI amine 15
(0.169 g, 0.341 mmol) and the acid 61 (0.30 g, 0.311 mmol)
according to general procedure described for compound 63
(0.30 g, 66% yield) as a white solid. 1H NMR (300 MHz,
DMSO-d6) δ 1.54 (s, 18H, 2 × Boc–H), 2.56–2.72 (m, 4H, 2 ×
CH2CO–), 3.52–3.76 (m, 4H, 2 × –NHCH2), 3.86 (s, 3H,
–NCH3), 3.87 (s, 3H, –NCH3), 3.88 (s, 3H, –NCH3), 3.91–4.15
(m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 5.25 (s, 2H,
–OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 7.45 (s, 1H, Im–H),
7.52 (s, 1H, Im–H), 7.60–7.85 (m, 17H, Ar–H, Im–H), 8.15–
8.31 (m, 2H, 2 × –NHCH2), 8.40 (s, 2H, 2 × C6–H), 9.68 (s, 1H,
–NH–), 9.80 (s, 1H, –NH–), 10.05 (s, 1H, –NH–), 10.19 (s, 1H,
–NH–), 10.49 (s, 1H, –NH–). ES–MS m/z calculated for
C73H77N15O13Cl2 1441.52, found 1442.50 (M ϩ 1).
Compound 69
This compound was prepared according to the method
described for the compound 68, employing compound 63 (0.2 g,
0.151 mmol) and the aq. ammonium formate (0.2 ml) in 87%
yield (0.15 g) as a white solid. 1H NMR (300 MHz, DMSO-d6) δ
1.56 (s, 18H, 2 × Boc–H), 2.54–2.72 (m, 4H, 2 × CH2CO–),
3.55–3.76 (m, 4H, 2 × –NHCH2), 3.86 (s, 3H, –NCH3), 3.88
(s, 3H, –NCH3), 3.91–4.20 (m, 10H, Cl, 2-H, 2 × CH2Cl,
2 × CH2N), 7.45 (s, 1H, Im–H), 7.55–7.95 (m, 7H, 2 × C4–H,
C7–H, C8–H, Im–H), 8.20–8.32 (m, 2H, 2 × –NHCH2), 8.43 (s,
2H, 2 × C6–H), 9.50 (s, 1H), 9.98 (s, 1H), 10.05 (s, 1H), 10.12 (s,
1H), 10.32 (s, 1H), 10.48 (s, 1H). ES–MS m/z calculated for
C54H59N12O12Cl2 1138.38, found 1139.40 (M ϩ 1).
Compound 65
This compound was prepared starting from seco-CBI amine 17
(0.246 g, 0.562 mmol) and the acid 59 (0.30 g, 0.417 mmol)
according to general procedure C (0.30 g, 63% yield) as a white
1
Compound 70
solid. H NMR (300 MHz, DMSO-d6) δ 1.52 (s, 9H, Boc–H),
2.05 (s, 3H, CH3CON), 2.56–2.70 (m, 4H, 2 × CH2CO–), 3.55–
3.79 (m, 4H, 2 × –NHCH2), 3.87 (s, 3H, –NCH3), 3.90–4.40
(m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 5.25 (s, 2H,
–OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 7.46 (s, 1H, Im–H),
7.56–7.89 (m, 16H, Ar–H), 8.18–8.30 (m, 2H, 2 × –NHCH2),
8.35–8.42 (m, 2H, 2 × C6–H), 10.15 (s, 1H, –NH–), 10.18 (s,
1H, –NH–), 10.40 (s, 1H, –NH–). HR-ESMS m/z calculated for
C60H61N9O10Cl2 1137.39, found 1138.40 (M ϩ 1).
This compound was prepared starting from compound 64
(0.20 g, 0.138 mmol) and aq. ammonium formate (0.2 ml)
according to general procedure D (0.155 g, 88% yield) as a
solid. 1H NMR (300 MHz, DMSO-d6) δ 1.50 (s, 18H, 2 × Boc–
H), 2.50–2.70 (m, 4H, 2 × CH2CO–), 3.55–3.80 (m, 4H, 2 ×
NHCH2), 3.91 (s, 3H, –NCH3), 3.94 (s, 3H, –NCH3), 3.99 (s,
3H, –NCH3), 4.00–4.10 (m, 10H, Cl, 2-H, 2 × CH2Cl, 2 ×
CH2N), 7.47 (s, 1H, Im–H), 7.53 (s, 1H, Im–H), 7.55–7.80 (m,
7H, 2 × C4–H, C7–H, C8–H, Im–H), 8.32 (m, 2H, 2 ×
NHCH2), 8.40 (s, 2H, 2 × C6–H), 9.69 (s, 1H), 9.81 (s, 1H), 9.90
(s, 1H), 10.09 (s, 1H), 10.12 (s, 1H), 10.30 (s, 1H), 10.42 (s, 1H).
HR-ESMS m/z calculated for C59H66N15O13Cl2 1262.40, found
1262.40 (M ϩ H).
Compound 66
This compound was prepared according to the method
described for compound 65, employing seco-CBI polyamide
acid 60 (0.3 g, 0.356 mmol) and the amine 17 (0.210 g, 0.424
1
mmol) in 71% yield (0.320 g) as a white solid. H NMR (300
Compound 71
MHz, DMSO-d6) δ 1.54 (s, 9H, Boc–H), 2.04 (s, 3H,
CH3CON), 2.56–2.72 (m, 4H, 2 × CH2CO–), 3.56–3.79 (m, 4H,
2 × –NHCH2), 3.84 (s, 3H, –NCH3), 3.89 (s, 3H, –NCH3), 3.90–
4.30 (m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 5.24 (s, 2H,
–OCH2C6H5), 5.25 (s, 2H, –OCH2C6H5), 7.47 (s, 1H, Im–H),
This compound was prepared starting from compound 65
(0.20 g, 0.175 mmol) and aq. ammonium formate (0.2 ml)
according to general procedure D (0.15 g, 89% yield) as a white
1
solid. H NMR (300 MHz, DMSO-d6) δ 1.53 (s, 9H, Boc–H),
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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2.05 (s, 3H, CH3CON), 2.56–2.72 (m, 4H, 2 × CH2CO–), 3.55–
3.78 (m, 4H, 2 × NHCH2), 3.86 (s, 3H, –NCH3), 3.95–4.25 (m,
10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 7.55–7.79 (m, 6H, 2 × C8,
C9–H, C4–H, Im–H), 7.90 (d, 1H, C4–H), 8.15–8.25 (m, 1H,
–NHCH2), 8.35–8.42 (m, 3H, 2 × C6–H, –NHCH2), 9.98 (s,
1H), 10.05 (s, 1H), 10.07 (s, 1H), 10.14 (??s, 1H), 10.40 (s, 1H).
HR-ESMS m/z calculated for C46H49N9O10Cl2 957.30, found
980.30 (M ϩ Na).
Et3N (1.0 ml) and a solution of compound 52 (1.05 g, 3.85
mmol) in THF (5.0 ml), was added slowly with stirring at 0 ЊC
under a nitrogen atmosphere. The reaction mixture was
brought to room temperature and was stirred for 2 h. After
completion of the reaction the residue was concentrated to
dryness under reduced pressure and was purified by column
chromatography eluting with 5% MeOH–DCM to give 76, as a
1
solid 1.25 g in 87% yield. H NMR (300 MHz, DMSO-d6)
δ 1.56 (s, 9H, –C(CH3)3), 3.56–3.72 (m, 2H, NHCH2), 3.85
(s, 3H, –NCH3), 3.87 (s, 3H, –NCH3), 7.45 (s, 1H, Im–H), 7.75
(s, 1H, Im–H), 8.25 (m, 1H, NHCH2), 10.10 (s, 1H, –NH–).
HR–MS m/z calculated for C16H21N7O6 407.16, found 407.30.
Compound 72
Prepared according to general procedure D by using compound
66 (0.20 g, 0.158 mmol) and aq. ammonium formate (0.25 ml)
in 87% yield (0.15 g) as a white solid. H NMR (300 MHz,
1
{[1-Methyl-4-({1-methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-
carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-
imidazole-2-carbonyl]amino}acetic acid tert-butyl ester (77)
DMSO-d6) δ 1.54 (s, 9H, Boc–H), 2.05 (s, 3H, CH3CON), 2.56–
2.72 (m, 4H, 2 × CH2CO–), 3.52–3.78 (m, 4H, 2 × NHCH2),
3.86 (s, 3H, –NCH3), 3.87 (s, 3H, –NCH3), 3.95–4.25 (m, 10H,
Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 7.48 (s, 1H, Im–H), 7.60–7.79
(m, 6H, 2 × C8, C9–H, C4–H, Im–H), 7.91 (d, 1H, C4–H),
8.20–8.30 (m, 1H, NHCH2), 8.35–8.42 (m, 3H, 2 × C6–H,
Im–H), 9.50 (s, 1H), 10.03 (s, 1H), 10.05 (s, 1H), 10.35 (s, 1H),
10.37 (s, 1H), 10.48 (s, 1H). HR-ESMS m/z calculated for
C51H54N12O11Cl2 1080.34, found 1081.30 (M ϩ 1).
This compound was prepared according to the method
described for compound 76, by employing compounds 76
(1.0 g, 2.45 mmol) and 52 (0.736 g, 2.70 mmol) and the crude
product was purified by column chromatography using 7%
MeOH–DCM as eluting solvent in 77% yield (1.0 g). 1H NMR
(300 MHz, DMSO-d6) δ 1.56 (s, 9H, –C(CH3)3), 3.58 (m, 2H,
NHCH2), 3.86 (s, 3H, –NCH3), 3.88 (s, 3H, –NCH3), 3.89 (s,
3H, –NCH3), 7.43 (s, 1H, Im–H), 7.61 (s, 1H, Im–H), 7.79 (s,
1H, Im–H), 8.19–8.30 (m, 1H, NHCH2), 10.05 (s, 1H, –NH–),
10.25 (s, 1H, –NH–). HR–MS m/z calculated for C21H26N10O7
530.20, found 530.40.
Compound 73
This compound was prepared according to the method
described for the compound 71, by employing compound 67
(0.20 g, 0.144 mmol) and aq. ammonium formate (0.2 ml) in
86% yield (0.15 g) as a white solid. 1H NMR (300 MHz,
DMSO-d6). δ 1.52 (s, 9H, Boc–H), 2.03 (s, 3H, CH3CON),
2.58–2.70 (m, 4H, 2 × CH2CO–), 3.57–3.80 (m, 4H, 2 ×
NHCH2), 3.84 (s, 3H, –NCH3), 3.87 (s, 3H, –NCH3), 3.89 (s,
3H, –NCH3), 4.04–4.40 (m, 10H, Cl, 2-H, 2 × CH2Cl, 2 ×
CH2N), 7.45 (s, 1H, Im–H), 7.57 (s, 1H, Im–H), 7.60–7.75 (m,
6H, 2 × C8, C9–H, C4–H, Im–H), 7.90 (d, 1H, C4–H), 8.16–
8.25 (m, 1H, NHCH2), 8.35–8.42 (m, 3H, 2 × C6–H, NHCH2),
9.64 (s, 1H), 9.81 (s, 1H), 10.02 (s, 1H), 10.05 (s, 1H), 10.10 (s,
1H), 10.29 (s, 1H), 10.45 (s, 1H). HR-ESMS m/z calculated for
C56H59N15O12Cl2Na 1226.40 found 1226.40(M ϩ Na).
({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
imidazole-2-carbonyl}amino)acetic acid tert-butyl ester (78)
This compound was prepared starting from [(1-methyl-4-nitro-
1H-imidazole-2-carbonyl)amino]acetic acid tert-butyl ester (75)
(0.650 g, 2.28 mmol) and the seco-CBI acid 7 (1.0 g, 2.08 mmol)
according to general procedure A (1.2 g, 80% yield) as a white
solid. 1H NMR (300 MHz, DMSO-d6) δ 1.59 (s, 9H, –C(CH3)3),
2.05 (s, 3H, CH3CON), 2.56–2.72 (m, 4H, 2 × CH2CO–), 3.57
(m, 2H, NHCH2), 3.86 (s, 3H, –NCH3), 3.90–4.20 (m, 5H,
–CH, CH2Cl, CH2N), 5.26 (s, 2H, –OCH2C6H5), 7.47 (s, 1H,
Im–H), 7.56–7.89 (m, 7H, Ar–H), 8.14 (s, 1H, Ar–H), 8.25–8.35
(m, 2H, Ar–H, NHCH2), 10.00 (s, 1H, –NH–), 10.30 (s, 1H,
–NH–). HR–MS m/z calculated for C37H41N6O7Cl 716.27,
found 717.20 (M ϩ 1).
[(1-Methyl-4-nitro-1H-imidazole-2-carbonyl)amino]acetic acid
tert-butyl ester (75)
[(1-Methyl-4-nitro-1H-imidazole-2-carbonyl)amino]acetic acid
(74) was obtained from the basic hydrolysis of the corre-
sponding [(1-Methyl-4-nitro-1H-imidazole-2-carbonyl)amino]-
acetic acid methyl ester (53) from the reported procedure.
Compound 74 (3.0 g, 13.15 mmol) was added to 300 ml of THF
and 3 ml of concentrated sulfuric acid in a round bottom pres-
sure bottle. The colloidal solution was cooled to Ϫ40 ЊC and a
slow stream of isobutylene was bubbled through this solution
for several minutes. The solution was capped tightly with a
Teflon cork and was allowed to warm to room temperature and
was stirred for 36 h. The crude reaction mixture was dissolved
in ethyl acetate and was washed with saturated NaHCO3
repeatedly. The crude product was further purified by column
chromatography using pure 2% EtOAc–DCM as eluent to give
{[4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
imidazole-2-carbonyl}amino)-1-methyl-1H-imidazole-2-
carbonyl]amino}acetic acid tert-butyl ester (79)
Prepared according to general procedure A by using ({1-methyl-
4-[(1-methyl-4-nitro-1H-imidazole-2-carbonyl)amino]-1H-imid-
azole-2-carbonyl}amino)acetic acid tert-butyl ester (76) (0.932
g, 2.28 mmol) and the acid 7 (1.0 g, 2.08 mmol) in 74% yield
(1.30 g) as a white solid. 1H NMR (300 MHz, DMSO-d6) δ 1.59
(s, 9H, –C(CH3)3), 2.04 (s, 3H, CH3CON), 2.54–2.70 (m, 4H,
2 × CH2CO–), 3.55–3.75 (m, 2H, NHCH2), 3.86 (s, 3H,
–NCH3), 3.88 (s, 3H, –NCH3), 3.91–4.20 (m, 5H, –CH, CH2Cl,
CH2N), 5.26 (s, 2H, –OCH2C6H5), 7.46 (s, 1H, Im–H), 7.55–
7.92 (m, 8H, Ar–H, Im–H), 8.18 (s, 1H, Ar–H), 8.23–8.38 (m,
2H, Ar–H, NHCH2), 10.05 (s, 1H, –NH–), 10.20 (s, 1H, –NH–),
10.37 (s, 1H, –NH–). HR–MS m/z calculated for C42H46N9O8Cl
839.32, found 840.30 (M ϩ 1).
1
compound 75 in 72% yield (2.7 g) as a white solid. H NMR
(300 MHz, CDCl3) δ 1.53 (s, 9H, –C(CH3)3), 3.55–3.75 (m, 2H,
NHCH2), 3.86 (s, 3H, –NCH3), 7.76 (s, 1H, Im–H), 8.15–8.28
(m, 1H, NHCH2). HR–MS m/z calculated for C11H16N4O5
284.11, found 284.20.
({1-Methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-carbonyl)-
amino]-1H-imidazole-2-carbonyl}amino)acetic acid tert-butyl
ester (76)
4-{[4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
imidazole-2-carbonyl}amino)-1-methyl-1H-imidazole-2-
carbonyl]amino}-1-methyl-1H-imidazole-2-carbonyl]amino}-
acetic acid tert-butyl ester (80)
To a solution of compound 75 (1.0 g, 3.51 mmol) in 25.0 ml of
methanol was added 0.200 g of 10% Pd–C. The reaction mix-
ture was hydrogenated in a Parr shaker at 50 psi for 2 h. The
catalyst was removed by filtration and the solvent was evapor-
ated in vacuo. The residue was dissolved in dry THF (20.0 ml),
This compound was prepared according to the method
described for compounds 79, by employing {[1-methyl-4-({1-
methyl-4-[(1-methyl-4-nitro-1H-imidazole-2-carbonyl)-amino]-
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
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1
1H-imidazole-2-carbonyl}amino)-1H-imidazole-2-carbonyl]-
amino}acetic acid tert-butyl ester (77) (1.21 g, 2.28 mmol) and
the seco-CBI acid 7 (1.0 g, 2.08 mmol) in 75% yield (1.2 g)
white solid. H NMR (300 MHz, DMSO-d6) δ 2.05 (s, 6H,
2 × –CH3CON), 2.58–2.70 (m, 4H, 2 × CH2CO–), 3.55–
3.80 (m, 4H, 2 × –NHCH2), 3.86 (s, 3H, –NCH3), 3.95–4.40
(m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 5.24 (s, 2H,
–OCH2C6H5), 5.25 (s, 2H, –OCH2C6H5), 7.46 (s, 1H, Im–H),
7.60–7.90 (m, 14H, Ar–H), 8.13 (s, 2H, Ar–H), 8.21–8.30
(m, 2H, 2 × –NHCH2), 8.35 (s, 2H, Ar–H), 10.03 (s, 1H,
–NH–), 10.10 (s, 1H, –NH–), 10.35 (s, 1H, –NH–). HR-ESMS
m/z calculated for C57H55N9O9Cl2 1079.35, found 1102.30
(M ϩ Na).
1
as a white solid. H NMR (300 MHz, DMSO-d6) δ 1.58 (s,
9H, –C(CH3)3), 2.05 (s, 3H, CH3CON), 2.56–2.72 (m, 4H,
2 × CH2CO–), 3.56–3.72 (m, 2H, NHCH2), 3.85 (s, 3H,
–NCH3), 3.87 (s, 3H, –NCH3), 3.89 (s, 3H, –NCH3), 3.90–4.20
(m, 5H, –CH, CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5), 7.45
(s, 1H, Im–H), 7.61 (s, 1H, Im–H), 7.75–7.95 (m, 8H, Ar–H,
Im–H), 8.17 (s, 1H, Ar–H), 8.25–8.35 (m, 2H, Ar–H, NHCH2),
9.98 (s, 1H, –NH–), 10.15 (s, 1H, –NH–), 10.25 (s, 1H, –NH–),
10.40 (s, 1H, –NH–). HR–MS m/z calculated for C47H51N12-
O9Cl 962.36, found 963.40 (M ϩ 1).
Compound 85
This compound was prepared according to the method
described for compound 84, by employing seco-CBI N-3 poly-
amide acid 82 (0.3 g, 0.383 mmol) and the amine 17 (0.226 g,
({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
imidazole-2-carbonyl}amino)acetic acid (81)
1
0.420 mmol) in 65% yield (0.30 g) as a solid. H NMR (300
MHz, DMSOd6) δ 2.05 (s, 6H, 2 × –CH3CON), 2.52–2.74 (m,
4H, 2 × CH2CO–), 3.52–3.78 (m, 4H, 2 × –NHCH2), 3.86 (s,
3H, –NCH3), 3.88 (s, 3H, –NCH3), 3.95–4.35 (m, 10H, Cl, 2-H,
2 × CH2Cl, 2 × CH2N), 5.23 (s, 2H, –OCH2C6H5), 5.24 (s, 2H,
–OCH2C6H5), 7.49 (s, 1H, Im–H), 7.56 (s, 1H, Im–H), 7.65–
7.95 (m, 14H, Ar–H), 8.15 (s, 2H, Ar–H), 8.25–8.30 (m, 2H,
2 × –NHCH2), 8.38 (s, 2H, Ar–H), 10.02 (s, 1H, –NH–), 10.16
(s, 1H, –NH–), 10.25 (s, 1H, –NH–), 10.38 (s, 1H, –NH–).
HR-ESMS m/z calculated for C62H60N12O10Cl2 1202.39 found
1225.40 (M ϩ Na).
This compound was prepared according to general method E
by using compound 78 (1.0 g, 1.39 mmol) and 1.0 M solution of
TiCl4 (3.0 ml) in dichloromethane to give compound 81 as a
white solid in 70% yield (0.65 g). 1H NMR (300 MHz, DMSO-
d6) δ 2.05 (s, 3H, CH3CON), 2.56–2.72 (m, 4H, 2 × CH2CO–),
3.55–3.70 (m, 2H, NHCH2), 3.86 (s, 3H, –NCH3), 3.92–4.20 (m,
5H, –CH, CH2Cl, CH2N), 5.25 (s, 2H, –OCH2C6H5), 7.50 (s,
1H, Im–H), 7.60–7.90 (m, 7H, Ar–H), 8.18 (s, 1H, Ar–H), 8.20–
8.39 (m, 2H, Ar–H, NHCH2), 10.10 (s, 1H, –NH–), 10.27 (s,
1H, –NH–), 12.56 (br s, 1H, –COOH). HR–MS m/z calculated
for C33H33N6O7Cl 660.21, found 683.25 (M ϩ Na).
Compound 86
{[4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
imidazole-2-carbonyl}amino)-1-methyl-1H-imidazole-2-
carbonyl]amino}acetic acid (82)
Prepared according to general procedure C by using compound
83 (0.30 g, 0.331 mmol) and seco-CBI amine 17 (0.195 g,
1
0.215 mmol) in 66% yield (0.29 g) as a white solid. H NMR
(300 MHz, DMSO-d6) δ 2.05 (s, 6H, 2 × –CH3CON), 2.56–2.72
(m, 4H, 2 × CH2CO–), 3.54–3.77 (m, 4H, 2 × –NHCH2), 3.87
(s, 3H, –NCH3), 3.88 (s, 3H, –NCH3), 3.89 (s, 3H, –NCH3),
3.92–4.40 (m, 10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 5.25 (s,2H,
–OCH2C6H5), 5.26 (s, 2H, –OCH2C6H5), 7.44 (s, 1H, Im–H),
7.57 (s, 1H, Im–H), 7.62–7.90 (m, 15H, Ar–H, Im–H), 8.15
(s, 2H, Ar–H), 8.20–8.30 (m, 2H, 2 × –NHCH2), 8.38 (s, 2H,
Ar–H), 10.00 (s, 1H, –NH–), 10.10 (s, 1H, –NH–), 10.15 (s, 1H,
–NH–), 10.25 (s, 1H, –NH–), 10.35 (s, 1H, –NH–). HR-ESMS
m/z calculated for C67H65N15O11Cl2 1325.44 found 1348.40 (M
ϩ Na).
Prepared according to general procedure E by using compound
79 (1.0 g, 1.19 mmol) and 1.0 M solution of TiCl4 (3.0 ml)
1
solution in 76% yield (0.71 g) as a solid. H NMR (300 MHz,
DMSO-d6) δ 2.04 (s, 3H, CH3CON), 2.54–2.75 (m, 4H,
2 × CH2CO–), 3.56–3.75 (m, 2H, NHCH2), 3.86 (s, 3H,
–NCH3), 3.88 (s, 3H, –NCH3), 3.95–4.20 (m, 5H, –CH, CH2Cl,
CH2N), 5.25 (s, 2H, –OCH2C6H5), 7.46 (s, 1H, Im–H), 7.53
(s, 1H, Im–H), 7.59–7.96 (m, 8H, Ar–H, Im–H), 8.15 (s, 1H,
Ar–H), 8.19–8.36 (m, 2H, Ar–H, NHCH2), 10.05 (s, 1H, –NH–),
10.22 (s, 1H, –NH–), 10.35 (s, 1H, –NH–), 12.56 (br s, 1H,
–COOH). HR–MS m/z calculated for C38H38N9O8Cl 783.25,
found 806.30 (M ϩ Na).
Compound 87
This compound was prepared starting from compound 84
(0.25 g, 0.231 mmol) and 10% aq. ammonium formate (0.2 ml)
according to general procedure D in (0.15 g, 72% yield)
as a white solid. 1H NMR (300 MHz, DMSO-d6) δ 2.04 (s, 6H,
2 × –CH3CON), 2.54–2.72 (m, 4H, 2 × CH2CO–), 3.52–3.71
(m, 4H, 2 × –NHCH2), 3.87 (s, 3H, –NCH3), 3.95–4.35 (m,
10H, Cl, 2-H, 2 × CH2Cl, 2 × CH2N), 7.49 (s, 1H, Im–H), 7.66
(d, J = 8.9 Hz, 2H, Ar–H), 7.75 (d, J = 8.9 Hz, 2H, Ar–H), 7.96
(s, 2H, Ar–H), 8.18–8.30 (m, 2H, 2 × –NHCH2), 8.35 (s, 2H,
Ar–H), 9.94 (s, 1H), 10.06 (s, 1H), 10.07 (s, 1H), 10.24 (s, 1H).
HR-ESMS m/z calculated for C43H43N9O9Cl2 899.26, found
922.30 (M ϩ Na).
4-{[4-({4-[4-(7-Acetylamino-5-benzyloxy-1-chloromethyl-1,2-di-
hydrobenzo[e]indol-3-yl)-4-oxo-butyrylamino]-1-methyl-1H-
imidazole-2-carbonyl}amino)-1-methyl-1H-imidazole-2-
carbonyl]amino}-1-methyl-1H-imidazole-2-carbonyl]amino}-
acetic acid (83)
This compound was prepared according to general method E
by using compound 80 (1.0 g, 1.03 mmol) and 1.0 M solution of
TiCl4 (3.0 ml) to give compound 83 as a white solid in 63% yield
(0.60 g). 1H NMR (300 MHz, DMSO-d6) δ 2.04 (s, 3H,
CH3CON), 2.56–2.75 (m, 4H, 2 × CH2CO–), 3.52–3.75 (m, 2H,
NHCH2), 3.85 (s, 3H, –NCH3), 3.87 (s, 3H, –NCH3), 3.89 (s,
3H, –NCH3), 3.91–4.20 (m, 5H, –CH, CH2Cl, CH2N), 5.24 (s,
2H, –OCH2C6H5), 7.44 (s, 1H, Im–H), 7.56 (s, 1H, Im–H),
7.62–7.90 (m, 8H, Ar–H, Im–H), 8.18 (s, 1H, Ar–H), 8.21–8.35
(m, 2H, Ar–H, NHCH2), 9.98 (s, 1H, –NH–), 10.08 (s, 1H,
–NH–), 10.25 (s, 1H, –NH–), 10.40 (s, 1H, –NH–), 12.56 (br s,
1H, –COOH). HR–MS m/z calculated for C43H43N12O9Cl
906.30, found 929.32 (M ϩ Na).
Compound 88
Prepared according to general procedure D by using compound
85 (0.25 g, 0.207 mmol) and 10% aq. ammonium formate
1
(0.3 ml) in 81% yield (0.172 g) as a white solid. H NMR (300
MHz, DMSO-d6) δ 2.04 (s, 6H, 2 × –CH3CON), 2.56–2.72 (m,
4H, 2 × CH2CO–), 3.51–3.75 (m, 4H, 2 × –NHCH2), 3.86 (s,
3H, –NCH3), 3.88 (s, 3H, –NCH3), 3.95–4.42 (m, 10H, Cl, 2-H,
2 × CH2Cl, 2 × CH2N), 7.43 (s, 1H, Im–H), 7.56 (s, 1H, Im–H),
7.65 (d, J = 8.9 Hz, 2H, Ar–H), 7.75 (d, J = 9.0 Hz, 2H, Ar–H),
7.96 (s, 2H, Ar–H), 8.20–8.30 (m, 2H, 2 × –NHCH2), 8.35 (s,
2H, Ar–H), 9.98 (s, 1H), 10.06 (s, 1H), 10.08 (s, 1H), 10.09 (s,
Compound 84
This compound was prepared starting from seco-CBI amine 17
(0.268 g, 0.50 mmol) and the acid 81 (0.30 g, 0.454 mmol)
according to general procedure C (0.320 g, 65% yield) as a
O r g . B i o m o l . C h e m . , 2 0 0 3 , 1, 2 6 3 0 – 2 6 4 7
2646

View Article Online
20 D. L. Boger, W. Yun, S. Terashima, Y. Fukuda, K. Nakatani,
1H), 10.24 (s, 1H), 10.35 (s, 1H). HR-ESMS m/z calculated for
C48H48N12O10Cl2 1022.30, found 1045.50 (M ϩ Na).
P. A. Kitos and Q. Jin, Bioorg. Med. Chem. Lett., 1992, 2, 759.
21 D. L. Boger, D. S. Johnson and W. Yun, J. Am. Chem. Soc., 1994,
116, 1635.
22 K. Yamamoto, H. Sugiyama and S. Kawanishi, Biochemistry, 1993,
32, 1059; A. Asai, S. Nagamura and H. Saito, J. Am. Chem. Soc.,
1994, 116, 4171.
23 D. L. Boger, D. S. Johnson and W. Wrasidlo, Bioorg. Med. Chem.
Lett., 1994, 4, 631.
24 D. L. Boger and R. S. Coleman, J. Am. Chem. Soc., 1988, 110, 4796;
L. F. Tietze and T. Grote, J. Org. Chem., 1994, 59, 192.
25 M. A. Warpehoski, I. Gebhard, R. C. Kelly, W. C. Krueger, L. H. Li,
J. P. Mc Govren, M. D. Prairie, N. Wicnienski and W. Wierenga,
J. Med. Chem., 1988, 31, 590.
26 Y. Fukuda, Y. Itoh, K. Nakatani and S. Terashima, Tetrahedron,
1994, 50, 2793; Y. Fukuda, K. Nakatani and S. Terashima,
Tetrahedron, 1994, 50, 2809; Y. Fukuda, K. Nakatani and
S. Terashima, Bioorg. Med. Chem. Lett., 1992, 2, 755.
27 D. L. Boger, K. Machiya, D. L. Hertzog, P. A. Kitos and
D. J. Holmes, J. Am. Chem. Soc., 1993, 115, 9025; D. L. Boger and
K. Machiya, J. Am. Chem. Soc., 1992, 114, 10056.
28 D. L. Boger, H. Zarrinmayeh, S. A. Munk, P. A. Kitos and
O. Suntornwat, Proc. Natl. Acad. Sci. U.S.A., 1991, 88, 1431;
Y. Wang and J. W. Lown, Hetrocycles, 1993, 36, 1399; Y. Wang,
R. Gupta, L. Huang and J. W. Lown, J. Med. Chem., 1993, 36, 4172.
29 D. L. Boger and S. A. Munk, J. Am. Chem. Soc., 1992, 114, 15487;
D. L. Boger and W. Yun, J. Am. Chem. Soc., 1994, 116, 7996;
P. A. Aristof and P. D. Johnson, J. Org. Chem., 1992, 57, 6234;
P. A. Aristof, P. D. Johnson and P. D. Sun, J. Med. Chem., 1993, 36,
1956.
Compound 89
This compound was prepared according to the method
described for compound 87, by employing compound 86 (0.3 g,
0.226 mmol) and 10% aq. ammonium formate (0.35 ml) in 77%
yield (0.20 g) as a white solid. 1H NMR (300 MHz, DMSO-d6)
δ 2.05 (s, 6H, 2 × –CH3CON), 2.61–2.72 (m, 4H, 2 × CH2CO–),
3.55–3.75 (m, 4H, 2 × –NHCH2), 3.86 (s, 3H, –NCH3), 3.88 (s,
3H, –NCH3), 3.91 (s, 3H, –NCH3), 3.95–4.40 (m, 10H, Cl, 2-H,
2 × CH2Cl, 2 × CH2N), 7.44 (s, 1H, Im–H), 7.57 (s, 1H, Im–H),
7.68 (d, J = 8.8 Hz, 2H, Ar–H), 7.75 (d, J = 8.8 Hz, 2H, Ar–H),
7.95 (s, 2H, Ar–H), 8.20–8.30 (m, 2H, 2 × –NHCH2), 8.36 (s,
2H, Ar–H), 9.95 (s, 1H), 10.04 (s, 1H), 10.05 (s, 1H), 10.08 (s,
1H), 10.24 (s, 1H), 10.31 (s, 1H), 10.40 (s, 1H). HR-ESMS
m/z calculated for C53H53N15O11Cl2 1145.34 found 1168.40
(M ϩ Na).
Acknowledgements
We gratefully acknowledge the financial support of the Natural
Sciences and Engineering Research Council of Canada
(to J. W. Lown).
30 D. L. Boger and M. S. S. Palanki, J. Am. Chem. Soc., 1992, 114,
9318; D. L. Boger, D. S. Johnson, M. S. S. Palanki, P. A. Kitos,
J. Chang and P. Dowell, Bioorg. Med. Chem., 1993, 1, 27.
31 D. L. Boger, P. Mesini and C. M. Tarby, J. Am. Chem. Soc., 1994,
116, 6461; D. L. Boger and P. Mesini, J. Am. Chem. Soc., 1994, 116,
11335.
32 F. Mohamadi, M. M. Spees, G. S. Staten, P. Marder, J. K. Kipka,
D. A. Johnson, D. L. Boger and H. Zarrinmayeh, J. Med. Chem.,
1994, 37, 232.
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