Optimization of the indenone ring of indenoisoquinoline topoisomerase I inhibitors

Article abstract of DOI:10.1021/jm070307+

Two series of indenoisoquinoline topoisomerase I inhibitors have been prepared to investigate optimal substituents on the indenone ring at the 9-position. The more exhaustive series was prepared using a nitrated isoquinoline ring that has been previously demonstrated to enhance biological activity. After preliminary biological evaluation, a more focused series of inhibitors was prepared utilizing a 2,3-dimethoxy-substituted isoquinoline ring. The results of the two series indicate the existence of superior functional groups such as methoxy, fluorine, and cyano for the indenoisoquinoline 9-position. Interestingly, these functional groups coincide with established structure-activity relationships for the 11-position of camptothecin.

Full text of DOI:10.1021/jm070307+

4388
J. Med. Chem. 2007, 50, 4388-4404
Optimization of the Indenone Ring of Indenoisoquinoline Topoisomerase I Inhibitors
Andrew Morrell,† Michael Placzek,† Seth Parmley,† Brian Grella,† Smitha Antony,‡ Yves Pommier,‡ and Mark Cushman*,†
Department of Medicinal Chemistry and Molecular Pharmacology, School of Pharmacy and Pharmaceutical Sciences, and the Purdue
Cancer Center, Purdue UniVersity, West Lafayette, Indiana 47907, Laboratory of Molecular Pharmacology, Center for Cancer Research,
National Cancer Institute, Bethesda, Maryland 20892-4255
ReceiVed March 17, 2007
Two series of indenoisoquinoline topoisomerase I inhibitors have been prepared to investigate optimal
substituents on the indenone ring at the 9-position. The more exhaustive series was prepared using a nitrated
isoquinoline ring that has been previously demonstrated to enhance biological activity. After preliminary
biological evaluation, a more focused series of inhibitors was prepared utilizing a 2,3-dimethoxy-substituted
isoquinoline ring. The results of the two series indicate the existence of superior functional groups such as
methoxy, fluorine, and cyano for the indenoisoquinoline 9-position. Interestingly, these functional groups
coincide with established structure-activity relationships for the 11-position of camptothecin.
Introduction
Camptothecin (1, Figure 1) was first discovered in 1966 by
Wall and Wani utilizing bioassay-guided fractionation from the
tree Camptotheca acuminata.1 Camptothecin was found to be
highly cytotoxic toward leukemia cells and a potent tumor
inhibitor. Consequently, it served as the structural core for the
synthesis of a new class of anticancer agents.1,2 Research interest
in camptothecin and its derivatives increased dramatically after
1985 when it was determined that camptothecin was a selective
mammalian topoisomerase I (Top1) inhibitor.3 Although camp-
tothecin displayed potent biological activity, initial drug devel-
opment was hindered due to poor aqueous solubility.4 In an
attempt to engineer an improved solubility profile for camp-
tothecin, topotecan and irinotecan were designed.4-8 Both of
these molecules possess basic functionalities that are protonated
at physiological pH and serve to enhance the solubility of the
camptothecin core structure.4-8 The engineered solubility profile
was a great success for the camptothecins, as irinotecan and
topotecan are the only Top1 inhibitors currently approved by
the Food and Drug Administration for the treatment of cancer.4-8
Unfortunately, camptothecin derivatives are not ideal drug
molecules. They are compromised by their inability to com-
pletely stabilize the ternary (DNA-enzyme-drug) complex,
necessitating long infusion times to achieve maximum activity.7
Furthermore, the camptothecins are inherently unstable and
suffer from lactone ring opening (which is favored at physi-
ological pH) to form a hydroxy-acid that has a high affinity for
human serum albumin.9-12 Additionally, certain cancers have
been found to be unresponsive to camptothecin treatment and
have either developed Top1 mutations limiting the sensitivity
of the enzyme to the drug or have evolved P-glycoprotein drug
efflux pumps to remove the drug from the cancer cell.13,14 As
a result of the pharmacokinetic problems with the camptothecins,
there is great interest in the development of noncamptothecin
Top1 inhibitors as anticancer agents.
Figure 1. Representative Top1 inhibitors.
predicted that indenoisoquinoline 2 (Figure 1) should be a Top1
inhibitor based upon a comparison of its cytotoxicity profile to
that of camptothecin in the NCI cell screen.16 Subsequent in
vitro testing of 2 indicated that it did induce DNA cleavage in
the presence of Top1 (albeit at micromolar concentrations),
thereby confirming the biological target prediction by the
COMPARE analysis.16 Despite the indenoisoquinoline’s
relatively modest potency, there were differences between the
DNA cleavage products for both the indenoisoquinoline and
the camptothecin that warranted the further development of
this new class of Top1 inhibitors.16 Additionally, the Top1
ternary cleavage complex formed in the presence of indenoiso-
quinoline 2 was more stable than that formed from camptoth-
ecin.16
Lead optimization of the indenoisoquinolines has provided
several compounds with improved cytotoxicity profiles and
Top1 inhibitory activities.17-30 Recently, an investigation was
undertaken to explore the improvement in biological activity
previously reported for indenoisoquinolines possessing a nitrated
isoquinoline ring and a methylenedioxy-substituted indenone
ring.23,30 This investigation led to the identification of a highly
potent series of indenoisoquinolines (3-5) possessing a nitrated
isoquinoline ring and a 9-methoxy-substituted indenone ring
(Figure 1). Utilizing the nitrated indenoisoquinolines as a
In the 1990s, the National Cancer Institute (NCI) developed
a COMPARE algorithm to facilitate the prediction of biological
targets from data generated by the 60 human cancer cell
cytotoxicity screen.15 Utilizing the COMPARE algorithm, it was
* To whom correspondence should be addressed. Tel.: 765-494-1465.
Fax: 765-494-6790. E-mail: cushman@pharmacy.purdue.edu.
† Purdue University
‡ National Cancer Institute, NIH.
10.1021/jm070307+ CCC: $37.00 © 2007 American Chemical Society
Published on Web 08/04/2007

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4389
Scheme 1a
a Reagents and conditions: (a) CHCl3, rt; (b) (i) SOCl2, benzene, reflux; (ii) AlCl3, nitrobenzene, 100 °C; (c) MCPBA, CHCl3; (d) NaN3, DMSO, 100 °C;
(e) (i) P(OEt)3, benzene, reflux; (ii) 3 M HCl in MeOH, benzene, reflux.
platform for lead development, an effort was orchestrated to
optimize the 9-position of the indenoisoquinolines in order to
discover functionalities that exhibit improved biolo-
gical activity (both cytotoxicity and Top1 inhibition) similar to
that observed for the methoxy substituent at the 9-position.
After preliminary biological evaluation and noting the difficulties
encountered during the preparation of certain 9-position deriva-
tives (such as strong electron-withdrawing substituents and
aniline derivatives), a second series of analogues were pre-
pared utilizing a 2,3-dimethoxy-substituted isoquinoline ring.
Collectively, the two series of compounds allow for the
identification of new lead substituents at the 9-position of the
indenoisoquinolines.
bases 7-20 provided cis-carboxylic acids 21-34. It has
previously been demonstrated that the ratio of cis- to trans-
diastereomers afforded by condensations between homophthalic
anhydrides and Schiff bases is dictated, in part, by the electronic
nature of the Schiff base’s substituents.32 Generally speaking,
electron-donating substituents favor the formation of greater
amounts of the cis-diasteromer, whereas electron-withdrawing
substituents increase the formation of the trans-product.32 This
was a critical consideration for the successful outcome of
analogue syntheses in this study because the oxidative Friedel-
Crafts acylation used to convert carboxylic acids 21-34 into
indenoisoquinolines 35-48 only proceeds with the cis-diaste-
reomer.33,34 As a result of diminished formation and difficulty
separating the desired cis-stereoisomers from their trans-
diastereomers, cis-carboxylic acids 31 and 32 were carried
through the subsequent oxidative Friedel-Crafts acylation in
crude form. Furthermore, the use of a more electron-deficient
substituent (such as a nitro group) on the Schiff base could not
Chemistry
The nitrated indenoisoquinolines utilized in this investigation
were prepared according to the conditions outlined in Scheme
1. Treatment of 4-nitrohomophthalic anhydride (6)31 with Schiff

4390 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
Scheme 2a
a Reagents and conditions: (a) CHCl3, rt; (b) (i) SOCl2, benzene, reflux; (ii) AlCl3, nitrobenzene, 100 °C; (c) NaN3, DMSO, 100 °C; (d) 6 M HCl, THF,
reflux; (e) H2CO, NaCNBH3; (f) (i) P(OEt)3, benzene, reflux; (ii) 3 M HCl in MeOH, benzene, reflux.
be performed at this juncture due to its formation of the trans-
carboxylic acid and no observed formation of the desired
cis-stereoisomer.32
observed for the reactions involving 4-nitrohomophthalic an-
hydride.32 However, there was a definite reduction in the amount
of cis-carboxylic acid afforded by the condensation of Schiff
bases with strong electron-withdrawing substituents.32 With the
desired cis-carboxylic acids prepared, compounds 78-85 were
subjected to oxidative Friedel-Crafts acylation utilizing thionyl
chloride and aluminum chloride to provide indenoisoquinolines
86-93 (although sufficient microanalyses of compounds 88 and
93 could not be obtained and they were carried through the
next transformation in crude form).23,33,34 Treatment of com-
pounds 86-93 with sodium azide in DMSO afforded analogues
94 and 97-103. The aniline amide bond in 94 was then cleaved
under acidic conditions to yield the corresponding aniline
analogue 95, which was subjected to reductive amination to
provide compound 96. Reduction of compounds 95-103
ultimately afforded analogues 104-112 upon isolation as their
respective hydrochloride salts.
With an array of cis-carboxylic acids prepared, compounds
21-34 were subjected to oxidative Friedel-Crafts acylation
utilizing thionyl chloride and aluminum chloride to provide
indenoisoquinolines 35-48.23,33,34 Compound 38 was then
oxidized with MCPBA to provide analogue 49, a compound
whose synthesis was not envisioned to be amenable to the Schiff
base-homophthalic anhydride condensation for the stereoelec-
tronic reasons indicated above. Indenoisoquinolines 35-46 were
then converted into analogues 50-61 by treatment with sodium
azide in DMSO and reduced with triethyl phosphite to afford
analogues 62-73 upon isolation as their respective hydrochlo-
ride salts. It is worth noting that compounds 47-49 were not
elaborated further due to their poor performance in the initial
biological assays and undesirable interactions in hypothetical
ternary complex models.
The 2,3-dimethoxy-substituted indenoisoquinolines utilized
in this study were prepared according to the conditions outlined
in Scheme 2. 4,5-Dimethoxyhomophthalic anhydride (74)35 was
condensed with Schiff bases 8, 12, 13, 17, 18, and 75-77 to
provide cis-carboxylic acids 78-85. Fortunately, cis-carboxylic
acids with strong electron-withdrawing substituents (including
the previously unavailable nitro group) were obtained from the
condensation, as the stereoelectronic outcome dictated by the
substituents on the Schiff bases was less pronounced than that
Biological Results and Discussion
The indenoisoquinolines were examined for antiproliferative
activity against the human cancer cell lines in the National
Cancer Institute screen, in which the activity of each compound
was evaluated with approximately 55 different cancer cell lines
of diverse tumor origins.36,37 The GI50 values obtained with
selected cell lines, along with the mean graph midpoint (MGM)
values, are summarized in Table 1. The MGM is based on a
calculation of the average GI50 for all of the cell lines tested

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4391
Table 1. Cytotoxicities and Topoisomerase I Inhibitory Activities of Indenoisoquinoline Analogues
cytotoxicity (GI50 in µM)a
lung
HOP-62
colon
HCT-116
CNS
SF-539
melanoma
UACC-62
ovarian
OVCAR-3
renal
SN12C
prostate
DU-145
breast
MDA-MB-435
Top1
cmpd
MGMb
cleavagec
1
2
3
4
5
0.01
1.3
0.295
<0.001
<0.010
5.75
21.4
24.5
1.05
18.2
0.03
35
0.794
<0.001
<0.010
6.03
>50.1
18.6
2.24
>50.1
3.63
7.24
3.47
0.01
41
0.027
<0.001
<0.010
5.62
28.2
>100
4.57
0.01
4.2
<0.010
0.22
73
0.02
68
<0.010
0.01
37
0.036
<0.001
0.04
96
0.0405 ( 0.0187
20.0
0.178 ( 0.012
0.198 ( 0.18
0.027 ( 0.008
15.1
38.0
42.0
8.91
34.5 ( 8.2
18.2
14.8
7.76
++++
++
++++
+++
++++
0/+
0
0
0
0
++
++
++
++
++++
+++
+++
0
3.39
0.155
2.82
23.4
>50.1
70.8
>100
>50.1
4.90
46.8
36.3
0.575
3.24
0.251
3.31
30.9
>50.1
>100
30.9
>50.1
31.6
37.2
14.8
0.282
<0.010
5.75
32.4
26.3
3.09
49.0
20.4
2.29
3.47
<0.010
11.7
>50.1
46.8
0.891
>50.1
26.9
27.5
2.51
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
86
87
89
90
91
92
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
4.27
>50.1
50.1
3.89
>50.1
40.7
3.39
3.98
0.214
16.6
43.6
2.29
2.45
3.63
3.72
0.661
3.72
0.017
0.019
0.241 ( 0.022
43.7
2.57
27.5
7.59
8.13
3.02
>50.1
72.4
0.603
>100
>100
0.251
41.7
1.82
81.3
>100
7.41
1.82
>50.1
20.4
0.776
>100
8.13
83.2
2.63
56.2
50.1
24.0
3.89
>50.1
>100
0.891
>100
27.5
1.12
33.9
23.4
4.27
2.88
>50.1
30.2
95.5
8.71
>100
81.3
28.8
20.0
>50.1
>100
3.89
>100
NT
>100
5.89
>100
>100
6.92
5.25
>50.1
58.9
37.2
2.75
>100
58.9
6.31
3.89
>50.1
>100
1.15
>100
>100
0.437
>100
>100
>100
>100
83.2
66.1
7.08
58.9
42.7
10.2
5.62
49.0
49.0
0
++
0/+
0
0
0/+
0
39.8
>50.1
>100
6.03
>100
>100
2.88
0.708
>100
29.5
1.05
>100
72.4
5.05 ( 2.03
82.3 ( 1.0
13.5
++
++++
0
+++
+++
0
+++
++++
+
++++
++++
0
++++
++++
+++
++++
+++
++++
+++
0
0.309
0.457
0.380
3.47
0.302
1.76 ( 0.53
56.2
1.82
25.7
15.1
0.012
1.38
0.191
<0.010
0.186
3.02
2.14
47.9
3.89
>100
2.24
53.7
>50.1
0.035
1.58
0.603
<0.010
1.62
0.138
0.028
<0.010
0.011
0.044
>100
3.31
37.1
3.63
0.055
1.48
>100
18.2
>100
>50.1
0.457
1.58
0.324
0.170
1.82
0.083
0.052
>100
3.89
>100
46.8
0.055
1.48
0.229
0.162
0.437
0.009
0.034
<0.010
<0.010
<0.010
14.8
1.78
70.8
7.08
>100
34.7
>100
>50.1
0.200
1.55
0.316
0.204
0.468
0.123
0.081
51.3
6.03
55.0
18.6
0.104 ( 0.006
1.07
0.244 ( 0.025
0.063 ( 0.010
0.646 ( 0.096
0.146 ( 0.100
0.040 ( 0.004
0.021 ( 0.005
0.030 ( 0.002
0.152 ( 0.067
0.174
0.575
0.229
0.023
0.178
<0.005
<0.010
<0.010
0.048
<0.010
0.011
0.776
0.115
<0.010
0.200
0.014
<0.010
<0.010
<0.010
<0.010
<0.010
1.51
0.028
<0.010
<0.010
<0.010
<0.010
<0.010
<0.010
0.033
0.295
1.20
0.162
0.224
0.021
1.29
4.07
4.47
4.17
>100
14.8
50.1
0.051
>100
11.5
56.2
3.55
4.17
>100
14.1
89.1
2.57
8.32
2.46
5.75
>100
15.1
50.1
0.047
3.80
6.76
14.1
3.55
2.09
3.02
12.3
3.89
>100
6.76
50.1
0.026
>100
20.9
91.2
2.63
5.25
>100
12.3
69.2
1.38
21.9
0.427
1.82
2.88
3.39
17.4
17.0
11.5
4.36
70.8
10.7
24.5
>100
12.9
50.1
0.214
>100
49.0
>100
4.57
6.17
>100
17.0
>100
1.82
17.8
0.389
1.51
0.085
6.31
16.6
19.1
16.6
13.8
5.50
>100
15.5
>100
22.9
50.1
0.148
>100
64.6
>100
13.8
8.32
>100
15.5
>100
2.57
17.0
4.68
4.07
>100
4.36
>100
10.7
50.1
0.059
>100
26.3
>100
28.2
4.17
>100
33.9
34.7
2.40
2.40
<0.010
1.62
2.63
0.575
17.8
12.3
2.09
13.8
37.2
>100
43.7
>100
>100
50.1
0.214
>100
>100
>100
9.77
6.76
17.2 ( 2.8
23.4
12.3
81.3
11.2
41.7
0.231 ( 0.124
97.7
38.9
81.3
11.7
12.0
79.4
34.7
0
++
+
+
7.24
50.1
0.050
>100
56.2
57.5
4.68
3.24
>100
17.4
38.9
0.316
1.90
0.115
1.62
2.82
1.12
15.8
++
0
0
++
0
27.5
0
1.82
4.17
>100
24.0
>100
0.263
3.63
++
0/+
0
38.0
>100
>100
>100
4.17
17.8
1.70
2.00
0.631
6.03
18.2
18.6
+
57.5
2.19
9.77 ( 0
0.186 ( 0.042
1.74
0/+
+
17.0
<0.010
1.82
0.151
0.603
3.72
3.98
0.617
-
0.054
0.141
1.74
0.794
4.36
15.1
16.6
+++
0
<0.010
1.38
16.6
15.9
1.32
1.35
+++
+++
0/+
+
2.61 ( 0.21
13.0 ( 0.45
10.0
3.72
11.7
15.8
4.40
+
a The cytotoxicity GI50 values are the concentrations corresponding to 50% growth inhibition. b Mean graph midpoint for growth inhibition of all human
cancer cell lines successfully tested. c The compounds were tested at concentrations ranging up to 10 µM. The activity of the compounds to produce Top1-
mediated DNA cleavage was expressed semiquantitatively as follows: +, weak activity; ++ and +++, modest activity; ++++, similar activity as 1 µM
camptothecin.

4392 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
(approximately 55) in which GI50 values below and above the
test range (10-8 to 10-4 molar) are taken as the minimum (10-8
molar) and maximum (10-4 molar) drug concentrations used
in the screening test. For comparison purposes, the activities of
the previously reported lead camptothecin (1) and compounds
2-5 are also included in the table. The relative potencies of
the compounds in the production of Top1-mediated DNA
cleavage are also listed in the table. These results were expressed
semiquantitatively as follows: 0, no detectable activity; +, weak
activity; ++, similar activity as compound 2; +++ and
++++, greater activity than compound 2; ++++, similar
activity as 1 µM camptothecin.
The analogues whose biological data are reported in Table 1
can be readily divided into two categories: nitrated indenoiso-
quinolines (compounds 3-5 and 35-73) and dimethoxy-
substituted indenoisoquinolines (compounds 86-112). With
such a division, inferences can be made from the data regarding
the effects of 9-position substituents on both Top1 inhibition
and cytotoxicity for each category of analogues. If one defines
the criteria to be considered an “active” compound as an MGM
value less than 1 µM or a Top1 inhibitory value of “+++” or
greater, then the two categories of analogues can be readily
evaluated. In general, the nitrated indenoisoquinolines prepared
in this study were usually more cytotoxic and better Top1
inhibitors than the dimethoxy-substituted derivatives. This result
was not surprising, however, given the previously observed
biological results for nitrated indenoisoquinolines (especially
compounds 3-5) and the features imparted by the nitro group
believed to be responsible for the enhanced activity (such as
improved π-stacking interactions with the DNA base pairs and
hydrogen-bonding interactions with Asn722).23,27,30,38
Figure 2. Ligand overlay of the crystal structures of camptothecin
(red) and an indenoisoquinoline (colored by atom type). Numbers in
red correspond to camptothecin atom numbering and numbers in white
correspond to indenoisoquinoline atom numbering.
propylamino lactam subsituent’s effects are included in the
analysis, only compounds 63 and 66, with their respective
9-position ethyl and phenyl substituents, did not display potent
Top1 inhibition.
Even in the absence of increased Top1 inhibition, the
analogues in this study indicate important features about the
binding pocket in the vicinity of the 9-position of the inde-
noisoquinolines. A comparison of compounds 3-5 (9-position
methoxy) and 36, 51, and 63 (9-position ethyl) indicate an
important feature about the methoxy group. These six com-
pounds differ only by the replacement of an ether oxygen atom
with a methylene unit, but this small difference results in a
dramatic change in the biological activity of the compounds,
with 36, 51, and 63 being virtually inactive in the biological
assays (relative to 3-5). Therefore, the ether oxygen atom must
have an important role in stabilizing the ternary complex. It
has previously been postulated that the ether oxygen of the
methoxy group contributes to electrostatic charge complemen-
tarity with the DNA base pairs in the ternary complex.
Additionally, molecular modeling using a hydrated binding
pocket has indicated a hypothetical hydrogen bond network
between water molecules and the oxygen atom. Given that the
analysis of a 9-position ethyl substituent resulted in a complete
loss in biological activity, it is evident that the postulated roles
of the methoxy group are highly important for stabilizing the
ternary complex. Furthermore, analogues possessing 9-position
substituents such as methyl and thiomethyl (37, 52, 38, and 53)
generally displayed poor biological activity until the lactam side
chain functionality compensated (compounds 64 and 65). These
results collectively support the role of the 9-position methoxy
group regarding charge complementarity and hydrogen bonding.
Additionally, electrostatic charge complementarity and the
ability to participate in hydrogen-bonding interactions help to
rationalize the discovery that fluorine and nitrile substituents
at the 9-position tend to confer potent Top1 inhibition.
The inactivity of previously reported 8,9-dimethoxy-substi-
tuted indenoisoquinolines was rationalized utilizing a crystal
structure overlay of ternary complexes for camptothecin and
an indenoisoquinoline and noting the conserved positioning of
the aromatic rings of the two ligands (Figure 2).30 Once again,
the use of the crystal structure overlay in Figure 2 illustrates
Nitroindenoisoquinolines. One of the more surprising results
for the nitrated indenoisoquinolines in Table 1 was the deter-
mination that the previously identified methoxy substituent is
optimally suited for enhancing the biological activity of the
indenoisoquinoline 9-position (indenoisoquinolines 3-5). In-
deed, the methoxy substituent was the only functional group at
the 9-position that consistently produced both cytotoxic and
potent Top1 inhibitors regardless of the lactam nitrogen’s
functionality. Substituents on the lactam nitrogen (such as a
propylamino group) have previously been identified to improve
the biological activity of the indenoisoquinolines and this
improvement is hypothesized to result from more efficient DNA
targeting and the formation of hydrogen-bonding interactions
within the ternary complex.24 Thus, the identification of
9-position substituents that can improve the biological activity
of the indenoisoquinolines in the absence of enhancement from
the lactam nitrogen should in theory be useful for “mixing and
matching” with lactam substituents known to confer greater
potency than an amino group.28
Although the methoxy group was the only substituent
identified in this study to enhance both the cytotoxicity and the
Top1 inhibition of the analogues, several functional groups were
identified that improved Top1 inhibition. A fluorine atom in
the 9-position (analogues 41, 56, and 68) provided compounds
with potent Top1 inhibition equal in magnitude to camptothecin,
regardless of the lactam substituent. Furthermore, when the
9-position fluorine atom was combined with a propylamino-
substituted lactam nitrogen, the resulting analogue 68 was
equally as cytotoxic as camptothecin. Additional functional
groups at the 9-position that resulted in potent Top1 inhibition
in the absence of the propylamino lactam substituent’s effects
included an iodine atom (44 and 59), a methyl ester (45), a
nitrile (46 and 61), and a bromine atom (58). When the

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4393
two important points for the camptothecin and indenoisoquino-
line classes of Top1 inhibitors. First, the existence of such a
conserved overlap for the aromatic rings between the two classes
of compounds indicates that the rings are optimally positioned
to stabilize the ternary complex and minimize detrimental steric
interactions between the ligand and the non-scissile DNA strand.
Thus, 9-position substituents that are sterically demanding (such
as phenyl, p-toluenesulfonyl, and methyl sulfone) would not
be expected to demonstrate potent Top1 inhibition. Indeed this
is the result as compounds 39, 54, 66, 47, 48, and 49 were all
rather poor Top1 inhibitors. Furthermore, a close examination
of 3 with 35 and 4 with 50 illustrates that even though sterically
more demanding substituents have a detrimental effect on
biological activity, the negative biological effects can be
overcome by incorporation of a more potent functional group
on the lactam side chain, illustrated by compound 62. The
second point that Figure 2 indicates is that because the 9-position
of the indenoisoquinolines and the 11-position of the camp-
tothecins occupy a similar space in the ternary complex, then
substituents at these positions that result in potent Top1
inhibition for one class should demonstrate inhibition in the other
class. This is indeed the case given the fact that fluorine
(indenoisoquinolines 41, 56, and 68) and nitrile (indenoiso-
quinolines 46, 61, and 73) substituents at the indenoisoquinoline
9-position or the camptothecin 11-position demonstrated potent
Top1 inhibition regardless of the lactam substituent on the
indenoisoquinoline.8,9,39-41 Therefore, in addition to the “steric”
and “electrostatic charge complementarity” hypotheses that have
been invoked to rationalize the biological results of the
indenoisoquinolines, it appears that substituents conferring
potent Top1 inhibition (located on the spatially conserved
aromatic rings in the ternary complexes for both classes of
inhibitors) could theoretically be swapped between classes and
still retain Top1 inhibition. Thus, the structure-activity relation-
ships for the conserved rings of both classes should be mutually
inclusive. Furthermore, it has been established that indolocar-
bazoles orient one aromatic ring to occupy the similarly
conserved space with the camptothecins and indenoisoquino-
lines, and the SAR for all three classes of Top1 inhibitors may
be applicable to each other and could aid the design of hybrid
inhibitors.8,42
results for the propylamino-substituted analogues presumably
highlight the importance of effectively targeting DNA in a
cellular system and its ability to aid in the stabilization of the
ternary complex. Furthermore, it seems reasonable to conclude
that the general ability of the propylamino substituent to confer
potent Top1 inhibition and cytotoxicity regardless of the
9-position substituent emphasizes that it has a more dominant
effect than the 9-position in contributing to the biological activity
of the indenoisoquinolines.
Dimethoxyindenoisoquinolines. Due to several problems
encountered during the synthesis of nitrated indenoisoquinoline
analogues, a second series of compounds was prepared using a
2,3-dimethoxy-substituted isoquinoline ring. Utilizing this plat-
form, analogues 86-112 were prepared and included both
previously utilized (methoxy, ethyl, hydrogen, fluorine, methyl
ester, and nitrile) and novel (acetamide, amino, dimethylamino,
and nitro) 9-position substituents. This analogue platform was
not envisioned to be as active as the nitrated series of
compounds, and the biological results for analogues with novel
9-position substituents were envisioned to guide their incorpora-
tion into the nitrated series of analogues. Of the newly examined
analogues, only 89, 99, 106, 108, and 109 demonstrated potent
Top1 inhibition. The fact that the 9-position methoxy and
fluorine substituents (106 and 109) appeared in the analysis of
active Top1 inhibitors emphasizes their prominence as superior
functional groups important for Top1 inhibition. Demonstrating
a consistent theme with the nitrated series of analogues, the
substitution of the ether oxygen atom of the methoxy group
(compounds 97 and 106) with a methylene subunit (providing
compounds 98 and 107) had a detrimental effect on Top1
inhibition, and this continues to highlight the importance of
electrostatics and hydrogen-bonding interactions in the ternary
complex. Reinvestigating the extrapolation of structure-activity
relationships between the camptothecin and the indenoisoquino-
line classes of Top1 inhibitors, the results for the new 9-position
substituents in this current series are not surprising. For
camptothecin analogues, 11-position nitro, amino, and dim-
ethylamino substituents are generally not very active.40 Thus,
the absence of Top1 inhibition conferred by these substituents
at the indenoisoquinoline 9-position is not surprising and lends
support to the hypothesis of a universal nature of SAR for
interfacial Top1 inhibitors.
A comparison of the 9-position substituent’s effect on
cytotoxicity of the corresponding analogues was equally as
intriguing as their effect on Top1 inhibition. In the absence of
the propylamino-substituted lactam nitrogen, only a 9-position
methoxy group (3 and 4) or a bromine atom (43) displayed
submicromolar MGM values. This result was rather disappoint-
ing, especially given that none of the newly examined 9-position
substituents that displayed enhanced cytotoxicity also displayed
potent Top1 inhibition. This inconsistency has been previously
observed and attributed to differential uptake, distribution, and
metabolism in a cellular assay.24 When the effects of the
propylamino-substituted lactam nitrogen are considered (ana-
logues 62-71), only compound 63 (with its 9-position ethyl
substituent) did not show potent cytotoxicity. Furthermore,
several of the compounds (65 and 68-70) have MGM values
comparable to camptothecin. With the exception of compound
66, all of the analogues displaying potent cytotoxicity were
effective Top1 inhibitors and it seems reasonable to attribute
their cytotoxicity principally to the inhibition of Top1. Obvi-
ously, compound 66 has Top1-independent cytotoxicity, and
hypothetical modeling of the compound in ternary complex with
DNA and Top1 indicates that there is simply not enough space
to accommodate a phenyl ring at the 9-position. Yet again, the
Upon examining the cytotoxicity of the new series of
compounds (86-112), discrepancies between Top1 inhibition
and cytotoxicity are evident. Compounds 89, 99, 108, and 109
are poor cytotoxic agents in comparison to their ability to inhibit
Top1. Indeed, the only compound to display both potent
cytotoxicity and Top1 inhibition in the new series (86-112)
was 106, with its 9-position methoxy group. Demonstrating a
consistent theme with the nitrated series of analogues, the
substitution of the ether oxygen atom of the methoxy group
(106) with a methylene subunit (107) resulted in a 10-fold loss
in cytotoxicity. Thus, a methoxy group at the 9-position appears
to be the most optimal substituent for the 9-position that has
thus far been discovered.
The indenoisoquinolines 66 and 95 are inactive as Top1
inhibitors, yet they display cytotoxicities in the submicromolar
range. Obviously, their cytotoxicities must be Top1-independent,
and this raises the question of whether or not the indenoiso-
quinolines in the present series that are potent Top1 inhibitors
also have additional targets that contribute to their cytotoxicities.
This question was previously investigated with the indenoiso-
quinoline MJ-III-65 (113, Figure 3) in the murine cell line P388/
CPT45, which does not have any detectable Top1. The results

4394 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
perfect correlation between Top1 inhibition and cellular
cytotoxicity is not surprising and is attributed to differential
uptake, distribution, and metabolism in a cellular assay, as
well as the possibility of additional targets as discussed
above.
The DNA cleavage patterns produced by camptothecin (1,
lane 3 of each gel), the indenoisoquinoline NSC 314622 (2),
and compounds 5, 65, 68, 69, 70, and 106 are displayed in
Figure 4. The following points are apparent from inspection of
the gels: (1) The potencies of the indenoisoquinolines as Top1
inhibitors are reflected in the intensities of the DNA cleavage
bands. The bands produced by compounds 69 (Top1: +++)
and 106 (Top1: +++) are slightly weaker in comparison with
the other analogues and camptothecin. (2) Top1 inhibitors can
be classified as Top1 suppressors, which inhibit DNA cleavage
and Top1 poisons, which inhibit the re-ligation reaction after
DNA cleavage. Many of the Top1-mediated DNA cleavages
are trapped at lower compound concentrations and suppressed
at higher concentrations, and therefore, the indenoisoquinolines
act as Top1 poisons at lower concentrations and Top1 suppres-
sors at higher concentrations. The suppression could result from
binding of the drug to the DNA, rendering it a poorer enzyme
substrate at high drug concentration, or from a direct effect on
the enzyme to suppress its ability to cleave DNA. Interestingly,
all of the analogues presented in Figure 4 demonstrate this effect.
(3) There are differences in the cleavage pattern of camptothecin
versus the indenoisoquinolines. For example, the cleavage at
base pair 44 seen with the indenoisoquinolines is absent with
camptothecin. This difference may indicate that the indenoiso-
quinolines might display antitumor spectra different from
camptothecin or its clinically useful derivatives irinotecan and
topotecan.
Figure 3. Structure of MJ-III-65.
demonstrated that P388/CPT45 cells showed considerable
resistance to compound 113 at low drug concentrations (<1
µM), but not at higher doses.43 Indenoisoquinoline 113 cyto-
toxicity is therefore mediated by Top1 inhibition at low drug
concentrations, but additional targets are implied at higher
concentrations. The potent Top1 inhibitors in the present series
are consequently likely to have additional targets that may
contribute to their observed cytotoxicities. Compound 113 can
intercalate with DNA at high concentrations, and this ability
may account for the additional targets that mediate cytotoxic-
ity.18 Previous studies have shown that some of the indenoiso-
quinolines can intercalate with DNA in the absence of Top1,
while others require the action of Top1 to intercalate.17
To compare the 3-nitro and 2,3-dimethoxy series, pairs of
compounds that were identical except for 3-nitro versus 2,3-
dimethoxy substitution were identified. If one considers the
cytotoxicity MGM values of the 10 pairs for which there are
complete data (40/89, 41/90, 46/92, 51/98, 55/99, 56/100, 60/
101, 61/102, 63/107, and 68/109), the MGM values are close
for nine of them. Only the 68/109 pair shows a large difference
in cytotoxicity, with the nitro compound 68 being significantly
more cytotoxic. This indicates that, in general, changing from
the 3-nitro to the 2,3-dimethoxy substitution does not make a
large difference in cytotoxicity. On the other hand, the Top1
inhibition data are similar for 8 of the 12 pairs (40/89, 41/90,
55/99, 46/92, 51/98, 60/101, 63/107, and 68/109), with signifi-
cant differences evident in the remaining four pairs (56/100,
61/102, 72/110, and 73/111). Of the pairs that show significant
differences in Top1 inhibitory activity, the nitro compounds are
more potent in all of the cases. The results are hypothesized to
be the consequence of improved charge-complementarity be-
tween the nitrated indenoisoquinolines and the DNA base pairs
at the site of intercalation and are fully consistent with our
models of the ternary complexes formed from the indenoiso-
quinolines, DNA, and Top1.30 The lack of a universal,
Conclusion
In conclusion, two series of indenoisoquinoline Top1 inhibi-
tors have been prepared to investigate and identify optimal
substituents on the indenone ring at the 9-position of the
indenoisoquinolines. An extensive series was prepared using a
nitrated isoquinoline ring. After preliminary biological evalu-
ation and encountering difficulties preparing 9-position ana-
logues with functional groups such as nitro and aniline
derivatives, a more focused series of inhibitors was prepared
utilizing a 2,3-dimethoxy-substituted isoquinoline ring. The
results of the two series indicate the existence of superior
Figure 4. Lane 1, DNA alone; lane 2, Top1 alone; lane 3, +CPT (1 µM); In the first panel, lane 4, Top1 + NSC 314622 (100 µM); lanes 5-8
(for compound 5) and lanes 4-7 (for compounds 65, 68, 69, 70, and 106), Top1 + indicated compound at 0.1, 1, 10, and 100 µM, respectively.
Number on left and arrows indicate cleavage site positions.

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4395
was heated at 100 °C for 1 h. Water (100 mL) was added and the
solution was extracted with CHCl3 (3 × 100-200 mL). The
combined organic layer was washed with satd NaHCO3 (3 × 50-
100 mL) and satd NaCl (50-100 mL) and dried over sodium
sulfate. The solution was concentrated, hexanes (800 mL) were
added, and the liquid was decanted. The solid was washed with
hexanes (100 mL), and the liquid was again decanted. The solid
was purified with flash column chromatography (SiO2), eluting with
chloroform, to provide the pure compound.
General Procedure for the Preparation of Indenoisoquino-
lines 50-61, 94, and 97-103. Sodium azide (0.002-0.242 g,
0.031-3.714 mmol, 1-3 equiv) and the appropriate indenoiso-
quinoline (0.013-0.529 g, 0.301-1.238 mmol, 1 equiv) were
diluted with DMSO (10-100 mL), and the mixture was heated at
100 °C for 1 h. The reaction mixture was diluted with CHCl3 (50-
300 mL), washed with water (4 × 50-100 mL) and satd NaCl
(50-100 mL), and dried over sodium sulfate. The solution was
concentrated to provide a crude solid that was purified by flash
column chromatography (SiO2), eluting with chloroform, to provide
the desired compound.
General Procedure for the Preparation of Indenoisoquino-
lines 62-73 and 104-112. Triethyl phosphite (0.089-0.180 mL,
0.52-1.05 mmol, 2.5 equiv) was added to a solution of the
appropriate azido-substituted indenoisoquinoline (0.090-0.167 g,
0.208-0.425 mmol, 1 equiv) in benzene (30-40 mL), and the
reaction mixture was heated at reflux for 16 h. The reaction mixture
was allowed to cool to room temperature, 3 M HCl in methanol
(10 mL) was added, and the reaction mixture was heated at reflux
for 2 h. The reaction mixture was allowed to cool to room
temperature and the precipitate was filtered to provide the desired
compound.
4-Ethoxybenzylidene-(3-bromo-1-propylamine) (7). The gen-
eral procedure provided the desired compound as a viscous yellow
oil (3.516 g, 99%). IR (film) 1645, 1606, 1511, 1248, 1167, and
1045 cm-1; 1H NMR (CDCl3) δ 8.25 (s, 1 H), 7.67 (d, J ) 8.6 Hz,
2 H), 6.93 (d, J ) 8.6 Hz, 2 H), 4.13 (q, J ) 7.0 Hz, 2 H), 3.73
(t, J ) 6.1 Hz, 2 H), 3.51 (t, J ) 6.4 Hz, 2 H), 2.29 (pent, J ) 6.3
Hz, 2 H), 1.48 (t, J ) 7.0 Hz, 3 H); ESIMS m/z (rel intensity)
270/272 (MH+, 100/98). Anal. (C12H16BrNO) C, H, N.
functional groups such as methoxy, fluoro, and nitrile that have
a greater tendency to confer potent Top1 inhibition for the
indenoisoquinolines (especially the nitrated series) when sub-
stituted at the 9-position. Interestingly, several of the functional
groups observed to confer potent Top1 inhibition to the
indenoisoquinolines support established structure-activity re-
lationships for the 11-position of camptothecin derivatives.
Additionally, indenoisoquinoline 9-position substituents that
were relatively inactive (or detrimental to Top1 inhibition) were
also observed to be detrimental within the camptothecin class
of Top1 inhibitors. The results of the present study with the
indenoisoquinolines have been further utilized to help define
steric limitations of functional groups protruding toward the
nonscissile DNA strand and they also highlight the importance
of hydrogen-bonding and substituent electrostatic interactions
with the DNA base pairs in the ternary complex. More
importantly, the results of this study indicate a universal nature
for structure-activity relationships between the camptothecins
and the indenoisoquinolines, and this relationship may be useful
for the design of hybrid Top1 inhibitors.
Experimental Section
General. Melting points were determined using capillary tubes
with a Mel-Temp apparatus and are uncorrected. Infrared spectra
were obtained using CHCl3 as the solvent unless otherwise
specified. The proton nuclear magnetic resonance (1H NMR) spectra
were recorded using an ARX300 300 MHz Bruker NMR spec-
trometer. IR spectra were recorded using a Perkin-Elmer 1600 series
FTIR spectrometer. Combustion microanalyses were performed at
the Purdue University Microanalysis Laboratory and the reported
values were within 0.4% of the calculated values. All of the
indenoisoquinolines are amorphous solids that in many cases retain
water even after prolonged heating in vacuo in a drying pistol.
Analytical thin-layer chromatography was carried out on Baker-
flex silica gel IB2-F plates and compounds were visualized with
short wavelength UV light. Silica gel flash chromatography was
performed using 230-400 mesh silica gel.
General Procedure for the Preparation of Schiff Bases 7-20
and 75-77. The hydrobromide (or hydrochloride) salt of 3-bro-
mopropylamine (or 3-chloropropylamine; 1.646-9.646 g, 7.520-
46.00 mmol, 1.5-2.0 equiv) was treated with triethylamine (1.31-
9.85 mL, 9.40-70.7 mmol, 3.0 equiv) in CHCl3 (50-200 mL),
and the mixture was allowed to stir at room temperature for 5 min.
The appropriate aldehyde (1.454-5.200 g, 6.267-30 mmol, 1
equiv) and magnesium sulfate (4.000-20.00 g) were added, and
the reaction mixture was allowed to stir at room temperature for
16 h. The reaction mixture was filtered and the filter pad was
washed with CHCl3 (50-100 mL). The filtrate was washed with
water (3 × 30-100 mL) and satd NaCl (30-100 mL), dried over
sodium sulfate, and concentrated to provide the desired compound.
General Procedure for the Preparation of Carboxylic Acids
21-34 and 78-85. 4-Nitrohomophthalic anhydride [(6) or 4,5-
dimethoxyhomophthalic anhydride (74); 1.177-7.300 g, 5.681-
33.00 mmol, 1 equiv] was added to a chloroform (50-300 mL)
solution of the appropriate Schiff base (2.000-7.200 g, 5.681-
33.00 mmol, 1 equiv), and the reaction mixture was allowed to stir
at room temperature for 2-72 h. The precipitate was filtered,
washed with chloroform (30-100 mL), and dried to provide the
desired compound.
General Procedure for the Preparation of Indenoisoquino-
lines 35-48 and 86-93. Thionyl chloride (1-20 mL) was added
to a solution of the appropriate carboxylic acid (0.250-2.000 g,
0.447-4.832 mmol, 1 equiv) in benzene (40 mL). The reaction
mixture was heated at reflux for 30 min, allowed to cool to room
temperature, and concentrated. The residue was diluted with
nitrobenzene (20-100 mL), chilled in an ice bath, and aluminum
chloride (0.119-1.288 g, 0.894-9.666 mmol, 2 equiv) was added.
The reaction mixture was removed from the bath and the mixture
4-(Ethyl)benzylidene-(3-bromo-1-propylamine) (8). The gen-
eral procedure provided the desired compound as a yellow viscous
oil (5.655 g, 94%). IR (film) 2965, 2841, 1646, 1609, and 829 cm-1
;
1H NMR (CDCl3) δ 8.31 (s, 1 H), 7.66 (d, J ) 8.1 Hz, 2 H), 7.26
(d, J ) 7.9 Hz, 2 H), 3.76 (dt, J ) 6.3 and 1.2 Hz, 2 H), 3.51
(t, J ) 6.5 Hz, 2 H), 2.72 (q, J ) 7.6 Hz, 2 H), 2.30 (pent, J ) 6.4
Hz, 2 H), 1.28 (t, J ) 7.6 Hz, 3 H); ESIMS m/z (rel intensity)
254/256 (MH+, 73/73). Anal. (C12H16BrN) C, H, N.
4-Methylbenzylidene-(3-bromo-1-propylamine) (9). The gen-
eral procedure provided the desired compound as a yellow oil (6.320
1
g, 99%). IR (film) 2840, 1646, 1609, and 813 cm-1; H NMR
(CDCl3) δ 8.30 (s, 1 H), 7.63 (d, J ) 8.1 Hz, 2 H), 7.21 (d, J )
7.9 Hz, 2 H), 3.76 (dt, J ) 6.3 and 1.2 Hz, 2 H), 3.51 (t, J ) 6.5
Hz, 2 H), 2.35 (s, 3 H), 2.21 (pent, J ) 6.4 Hz, 2 H); CIMS m/z
(rel intensity) 240/242 (MH+, 43/43), 160 (MH+ - HBr, 100). Anal.
(C11H14BrN) C, H, N.
4-(Thiomethyl)benzylidene-(3-bromo-1-propylamine) (10). The
general procedure provided the desired compound as a light yellow
oil (5.231 g, 98%). IR (film) 1642, 1594, 1091, and 815 cm-1; 1H
NMR (CDCl3) δ 8.27 (s, 1 H), 7.65-7.62 (m, 2 H), 7.27-7.24
(m, 2 H), 3.75 (dt, J ) 6.3 and 1.2 Hz, 2 H), 3.51 (t, J ) 6.5 Hz,
2 H), 2.51 (s, 3 H), 2.21 (pent, J ) 6.4 Hz, 2 H); CIMS m/z (rel
intensity) 272/274 (MH+, 70/71), 192 (MH+ - HBr, 100). Anal.
(C11H14BrNS) C, H, N.
4-(Phenyl)benzylidene-(3-bromo-1-propylamine) (11). The
general procedure provided the desired compound as a yellow
viscous oil (4.879 g, 100%). IR (film) 2841, 1644, 1487, 836, 763,
1
and 697 cm-1; H NMR (CDCl3) δ 8.38 (s, 1 H), 7.82 (m, 2 H),
7.67 (m, 4 H), 7.49 (m, 2 H), 7.44 (m, 1 H), 3.80 (dt, J ) 6.3 and
1.2 Hz, 2 H), 3.54 (t, J ) 6.5 Hz, 2 H), 2.33 (pent, J ) 6.4 Hz, 2
H); ESIMS m/z (rel intensity) 302/304 (MH+, 100/94). Anal.
(C16H16BrN) C, H, N.

4396 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
Benzylidene-(3-chloro-1-propylamine) (12).44 The general pro-
cedure provided the desired compound as a yellow oil (8.560 g,
100%). 1H NMR (CDCl3) δ 8.33 (s, 1 H), 7.76 (m, 2 H), 7.46 (m,
3 H), 3.79 (dt, J ) 6.3 and 1.2 Hz, 2 H), 3.66 (t, J ) 6.4 Hz, 2 H),
2.23 (pent, J ) 6.4 Hz, 2 H).
2.29 (pent, J ) 6.4 Hz, 2 H); ESIMS m/z (rel intensity) 314/316
(MH+, 28/27). Anal. (C13H16BrNO3) C, H, N.
4-(Toluene-4-sulfonyloxy)benzylidene-(3-bromo-1-propy-
lamine) (20). The general procedure provided the desired compound
as a yellow viscous oil (4.303 g, 100%). IR (film) 1646, 1598,
4-Fluorobenzylidene-(3-bromo-1-propylamine) (13). The gen-
eral procedure provided the desired compound as a yellow oil (5.780
1500, 1374, 1198, 1173, 1154, 1093, and 865 cm-1 1H NMR
;
(CDCl3) δ 8.29 (s, 1 H), 7.72 (d, J ) 8.4 Hz, 2 H), 7.70 (d, J )
8.6 Hz, 2 H), 7.32 (d, J ) 8.4 Hz, 2 H), 7.05 (m, 2 H), 3.76 (dt,
J ) 6.3 and 1.1 Hz, 2 H), 3.50 (t, J ) 6.4 Hz, 2 H), 2.45 (s, 3 H),
2.28 (pent, J ) 6.4 Hz, 2 H); ESIMS m/z (rel intensity) 396/398
(MH+, 95/100). Anal. (C17H18BrNO3S) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3-(4-ethoxyphenyl)-3,4-di-
hydro-7-nitro-1(2H)isoquinolone (21). The general procedure
provided the desired compound as a white solid (4.166 g, 69%):
mp 167-171 °C. IR (KBr) 3081, 1741, 1633, 1528, 1348, and 1178
cm-1; 1H NMR (CD3OD) δ 8.92 (d, J ) 2.5 Hz, 1 H), 8.41 (dd, J
) 8.6 and 2.6 Hz, 1 H), 8.01 (dd, J ) 8.6 and 2.9 Hz, 1 H), 6.99
(d, J ) 11.7 Hz, 2 H), 6.77 (d, J ) 8.7 Hz, 2 H), 5.28 (d, J ) 5.9
Hz, 1 H), 4.93 (m, 1 H), 4.04 (m, 1 H), 3.95 (q, J ) 7.0 Hz, 2 H),
3.54 (m, 2 H), 3.28 (m, 1 H), 2.30-2.10 (m, 2 H), 1.36 (t, J ) 7.0
Hz, 3 H); ESIMS m/z (rel intensity) 477/479 (MH+, 24/23). Anal.
(C21H21BrN2O6‚0.5H2O) C, H, N.
g, 98%). IR (film) 1649, 1602, 1508, 1230, 1152, and 835 cm-1
;
1H NMR (CDCl3) δ 8.30 (s, 1 H), 7.76 (dd, J ) 7.9 and 5.6 Hz, 2
H), 7.14 (m, 2 H), 3.77 (dt, J ) 6.3 and 0.9 Hz, 2 H), 3.52 (t, J )
6.4 Hz, 2 H), 2.30 (pent, J ) 6.4 Hz, 2 H); CIMS m/z (rel intensity)
244/246 (MH+, 38/34), 164 (MH+ - HBr, 100). Anal. (C10H11-
BrFN) C, H, N.
4-Chlorobenzylidene-(3-bromo-1-propylamine) (14). The gen-
eral procedure provided the desired compound as a yellow oil (5.375
g, 97%). IR (film) 1646, 1596, 1489, 1088, 1014, and 822 cm-1
;
1H NMR (CDCl3) δ 8.30 (s, 1 H), 7.69 (dd, J ) 8.5 and 1.8 Hz, 2
H), 7.41 (dd, J ) 8.5 and 1.8 Hz, 2 H), 3.77 (dt, J ) 6.3 and 1.2
Hz, 2 H), 3.51 (t, J ) 6.4 Hz, 2 H), 2.30 (pent, J ) 6.4 Hz, 2 H);
CIMS m/z (rel intensity) 260/262/264 (MH+, 71/100/20). Anal.
(C10H11BrClN) C, H, N.
4-Bromobenzylidene-(3-chloro-1-propylamine) (15). The gen-
eral procedure provided the desired compound as a yellow oil (5.311
g, 94%). IR (film) 2844, 1646, 1589, 1486, 1295, 1067, 1010, and
818 cm-1; 1H NMR (CDCl3) δ 8.27 (s, 1 H), 7.62-7.53 (m, 4 H),
3.77 (dt, J ) 6.4 and 1.3 Hz, 2 H), 3.63 (t, J ) 6.3 Hz, 2 H), 2.21
(quin, J ) 6.4 Hz, 2 H); CIMS m/z (rel intensity) 260/262/264
(MH+, 84/100/24). Anal. (C10H11BrClN) C, H, N.
4-Iodobenzylidene-(3-bromo-1-propylamine) (16). The general
procedure provided the desired compound as a yellow oil (2.182
g, 99%). IR (film) 1645, 1585, 1482, 1006, and 814 cm-1; 1H NMR
(CDCl3) δ 8.26 (s, 1 H), 7.78-7.74 (m, 2 H), 7.47-7.43 (m, 2 H),
3.76 (dt, J ) 6.3 and 1.3 Hz, 2 H), 3.51 (t, J ) 6.4 Hz, 2 H), 2.29
(pent, J ) 6.4 Hz, 2 H); CIMS m/z (rel intensity) 352/354 (MH+,
57/50), 272 (MH+ - HBr, 100); CIMS m/z (rel intensity) 352/354
(MH+, 57/59). Anal. (C10H11BrIN) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3-[4-(ethyl)phenyl]-3,4-di-
hydro-7-nitro-1(2H)isoquinolone (22). The general procedure
provided the desired compound as an off-white solid (7.386 g,
79%): mp 157-161 °C. IR (KBr) 3446, 1745, 1636, 1522, 1351,
1
and 1188 cm-1; H NMR (CD3OD) δ 8.89 (d, J ) 2.5 Hz, 1 H),
8.38 (dd, J ) 8.6 and 2.5 Hz, 1 H), 7.98 (dd, J ) 8.7 and 1.0 Hz,
1 H), 7.06 (d, J ) 8.2 Hz, 2 H), 6.96 (d, J ) 8.2 Hz, 2 H), 5.28 (d,
J ) 6.3 Hz, 1 H), 4.94 (d, J ) 6.4 Hz, 1 H), 4.00 (m, 1 H), 3.51
(m, 2 H), 3.26 (m, 1 H), 2.59 (q, J ) 7.5 Hz, 2 H), 2.25-2.10 (m,
2 H), 1.16 (t, J ) 7.6 Hz, 3 H); ESIMS m/z (rel intensity) 461/463
(MH+, 82/81). Anal. (C21H21BrN2O5‚0.75H2O) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3,4-dihydro-3-(4-methylphe-
nyl)-7-nitro-1(2H)isoquinolone (23). The general procedure pro-
vided the desired compound as an off-white solid (6.099 g, 56%):
mp 164-168 °C. IR (KBr) 3079, 1740, 1633, 1527, 1347, and 1180
cm-1; 1H NMR (CD3OD) δ 8.89 (d, J ) 2.5 Hz, 1 H), 8.38 (dd, J
) 8.6 and 2.5 Hz, 1 H), 7.98 (m, 1 H), 7.03 (d, J ) 8.0 Hz, 2 H),
6.93 (d, J ) 8.3 Hz, 2 H), 5.27 (d, J ) 6.2 Hz, 1 H), 4.91 (d, J )
6.2 Hz, 1 H), 4.00 (m, 1 H), 3.51 (m, 2 H), 3.26 (m, 1 H), 2.27-
2.07 (m, 2 H), 2.20 (s, 3 H); ESIMS m/z (rel intensity) 367
(MH+ - HBr, 100). Anal. (C20H19BrN2O5‚0.5H2O) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3,4-dihydro-7-nitro-3-[4-
(thiomethyl)phenyl]-1(2H)isoquinolone (24). The general proce-
dure provided the desired compound as an off-white solid (6.854
g, 78%): mp 168-170 °C. IR (KBr) 3079, 1737, 1632, 1527, 1492,
4-Methoxycarbonylbenzylidene-(3-chloro-1-propylamine) (17).
The general procedure provided the desired compound as a yellow
oil (7.2 g, 95%). IR (film) 2948, 2601, 2496, 1723, and 1644 cm-1
;
1H NMR (CDCl3) δ 8.37 (s, 1 H), 8.12-8.07 (m, 2 H), 7.85-7.61
(m, 2 H), 3.93 (s, 3 H), 3.82 (t, J ) 6.0 Hz, 2 H), 3.64 (t, J ) 6.0
Hz, 2 H), 2.25-2.19 (m, 2 H); ESIMS m/z 240 (MH+, 100). Anal.
(C12H14ClNO2) C, H, N.
4-Cyanobenzylidene-(3-chloropropylamine) (18). The general
procedure provided the desired compound as a yellow oil (6.8 g,
86%). IR (film) 2979, 2601, 2228, 1646, 1480, and 1445 cm-1; 1H
NMR (CDCl3) δ 8.35 (s, 1 H), 7.84-7.81 (m, 2 H), 7.71-7.68
(m, 2 H), 3.80 (t, J ) 6.0 Hz, 2 H), 3.63 (t, J ) 6.0 Hz, 2 H), 2.18
(quin, J ) 6.0 Hz, 2 H); ESIMS m/z (rel intensity) 207 (MH+,
100). Anal. (C11H11ClN2) C, H, N.
1
1347, and 1176 cm-1; H NMR (CD3OD) δ 8.89 (d, J ) 2.5 Hz,
1 H), 8.38 (dd, J ) 8.7 and 2.56 Hz, 1 H), 7.98 (m, 1 H), 7.10 (d,
J ) 8.4 Hz, 2 H), 6.98 (d, J ) 8.5 Hz, 2 H), 5.28 (d, J ) 5.7 Hz,
1 H), 4.87 (m, 1 H), 4.01 (m, 1 H), 3.52 (m, 2 H), 3.29 (m, 1 H),
2.39 (s, 3 H), 2.28-2.10 (m, 2 H); ESIMS m/z (rel intensity) 355
(MH+ - HBr - CO2, 100). Anal. (C20H19BrN2O5S‚0.5H2O) C, H,
N.
4-(Methoxycarbonyloxymethyl)benzaldehyde. Methyl chlo-
roformate (3.363 g, 35.59 mmol) was added to a solution of
4-hydroxymethylbenzaldehyde6 (3.230 g, 23.72 mmol) in dichlo-
romethane (50 mL) at 0 °C. DMAP (6.522 g, 53.39 mmol) was
added, and the solution was allowed to warm to room temperature.
After 3 h, the solution was diluted with dichloromethane (150 mL),
washed with water (3 × 50 mL) and satd NaCl (50 mL), and dried
over sodium sulfate. Concentration provided a crude oil that was
purified by flash column chromatography (SiO2), eluting with a
gradient of hexanes to 25% EtOAc in hexanes, to provide a colorless
oil (3.057 g, 66%) that solidified upon standing: mp 29-32 °C.
cis-N-(3-Bromopropyl)-4-carboxy-3,4-dihydro-3-(4-phenyl)-
1(2H)isoquinolone (25). The general procedure provided the
desired compound as an off-white solid (5.160 g, 77%): mp 168-
171 °C. IR (KBr) 3083, 1740, 1634, 1527, 1487, 1347, and 1175
cm-1; 1H NMR (CD3OD) δ 8.92 (d, J ) 2.5 Hz, 1 H), 8.39 (dd, J
) 8.6 and 2.6 Hz, 1 H), 8.01 (m, 1 H), 7.54 (m, 4 H), 7.40 (m, 2
H), 7.29 (m, 1 H), 7.14 (d, J ) 8.4 Hz, 2 H), 5.37 (d, J ) 6.1 Hz,
1 H), 4.99 (d, J ) 6.0 Hz, 1 H), 4.06 (m, 1 H), 3.54 (m, 2 H), 3.27
(m, 1 H), 2.29 (m, 1 H), 2.17 (m, 1 H); ESIMS m/z (rel intensity)
509/511 (MH+, 100/87). Anal. (C25H21BrN2O5‚0.5H2O) C, H, N.
cis-4-Carboxy-3,4-dihydro-N-(3-chloropropyl)-3-phenyl-7-ni-
tro-1(2H)isoquinolone (26). The general procedure provided the
desired compound as an off-white solid (5.865 g, 62%): mp 158-
159 °C. IR (KBr) 3062, 1745, 1643, 1520, 1485, 1450, 1350, 1191,
1
IR (film) 1750, 1701, and 1270 cm-1; H NMR (CDCl3) δ 10.02
(s, 1 H), 7.91 (dd, J ) 6.5 and 1.7 Hz, 2 H), 7.55 (d, J ) 8.1 Hz,
2 H), 5.24 (s, 2 H), 3.83 (s, 3 H); CIMS m/z (rel intensity) 195
(MH+, 100). Anal. (C10H10O4) C, H.
4-(Methoxycarbonyloxymethyl)benzylidene-(3-bromo-1-pro-
pylamine) (19). The general procedure provided the desired
compound as a yellow viscous oil (4.375 g, 84%). IR (film) 1749,
1
1
1646, 1442, and 1268 cm-1; H NMR (CDCl3) δ 8.33 (s, 1 H),
and 704 cm-1; H NMR (CD3OD) δ 8.82 (d, J ) 2.5 Hz, 1 H),
7.76 (d, J ) 7.7 Hz, 2 H), 7.44 (d, J ) 8.1 Hz, 2 H), 5.19 (s, 2 H),
3.81 (s, 3 H), 3.77 (t, J ) 5.8 Hz, 2 H), 3.51 (t, J ) 6.4 Hz, 2 H),
8.30 (dd, J ) 8.6 and 2.5 Hz, 1 H), 7.89 (dd, J ) 8.6 and 1.9 Hz,
1 H), 7.20-7.10 (m, 3 H), 6.98-6.95 (m, 2 H), 5.23 (d, J ) 6.0

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4397
Hz, 1 H), 4.87 (d, J ) 5.8 Hz, 1 H), 3.97-3.88 (m, 1 H), 3.58-
3.50 (m, 2 H), 3.21-3.11 (m, 1 H), 2.11-1.90 (m, 2 H).
cis-3-[4-(Methoxycarbonyloxymethylphenyl)]-N-(3-bromopro-
pyl)-4-carboxy-3,4-dihydro-1(2H)isoquinolone (33). The general
procedure provided the desired compound as an off-white solid
(4.059 g, 59%): mp 138-142 °C. IR (KBr) 3438, 1747, 1633,
1522, 1351, and 1276 cm-1; 1H NMR (CD3OD) δ 8.90 (d, J ) 2.5
Hz, 1 H), 8.39 (dd, J ) 8.7 and 2.54 Hz, 1 H), 7.97 (m, 1 H), 7.25
(d, J ) 8.3 Hz, 2 H), 7.08 (d, J ) 8.3 Hz, 2 H), 5.35 (d, J ) 5.8
Hz, 1 H), 5.05 (s, 2 H), 4.96 (d, J ) 6.4 Hz, 1 H), 4.02 (m, 1 H),
3.71 (s, 3 H), 3.52 (m, 2 H), 3.26 (m, 1 H), 2.28 (m, 1 H), 2.11 (m,
1 H); ESIMS m/z (rel intensity) 521/523 (MH+, 32/31). Anal.
(C22H21BrN2O8) C, H, N.
cis-4-Carboxy-N-(3-bromopropyl)-3,4-dihydro-3-[4-(toluene-
4-sulfonyloxy)phenyl]-1(2H)isoquinolone (34). The general pro-
cedure provided the desired compound as an off-white solid (4.678
g, 77%): mp 166-169 °C. The product was insoluble at room
temperature in all common NMR solvents, but when heated in
deuterated methanol, it epimerized and went into solution. The
corresponding NMR spectrum of the trans-isomer is reported
here: 1H NMR (CD3OD) δ 8.86 (d, J ) 2.50 Hz, 1 H), 8.39 (dd,
J ) 8.65 and 2.55 Hz, 1 H), 7.95 (d, J ) 8.65 Hz, 1 H), 7.56 (d,
J ) 8.36 Hz, 2 H), 7.34 (d, J ) 8.01 Hz, 2 H), 7.02 (dd, J ) 6.71
and 2.01 Hz, 2 H), 6.83 (dd, J ) 6.74 and 2.07 Hz, 2 H), 5.29 (s,
1 H), 4.85 (s, 1 H), 3.96 (m, 1 H), 3.49 (m, 2 H), 3.29 (m, 1 H),
2.39 (s, 3 H), 2.24 (m, 1 H), 2.07 (m, 1 H).
cis-N-(3-Bromopropyl)-4-carboxy-3,4-dihydro-3-(4-fluorophe-
nyl)-7-nitro-1(2H)isoquinolone (27). The general procedure pro-
vided the desired compound as an off-white solid (5.687 g, 77%):
mp 175-176 °C. IR (KBr) 3060, 1742, 1641, 1520, 1484, 1350,
1
1236, and 1190 cm-1; H NMR (CD3OD) δ 8.90 (d, J ) 2.5 Hz,
1 H), 8.39 (dd, J ) 8.6 and 2.6 Hz, 1 H), 7.97 (dd, J ) 8.7 and 1.0
Hz, 1 H), 7.10-7.05 (m, 2 H), 6.98-6.92 (m, 2 H), 5.33 (d, J )
6.4 Hz, 1 H), 4.97 (d, J ) 6.4 Hz, 1 H), 4.02 (m, 1 H), 3.53 (m,
2 H), 3.28 (m, 1 H), 2.26 (m, 1 H), 2.10 (m, 1 H); ESIMS m/z (rel
intensity) 406/408 (M+ - CO2, 34/27), 327 (M+ - CO2 - Br,
100). Anal. (C19H16BrFN2O5) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3-(4-chlorophenyl)-3,4-di-
hydro-7-nitro-1(2H)isoquinolone (28). The general procedure
provided the desired compound as a yellow solid (7.490 g, 83%):
mp 163-165 °C. IR (KBr) 3437, 1744, 1639, 1522, 1354, and 1191
cm-1; 1H NMR (CD3OD) δ 8.89 (d, J ) 2.4 Hz, 1 H), 8.39 (dd, J
) 8.7 and 2.6 Hz, 1 H), 7.96 (m, 1 H), 7.24-7.21 (m, 2 H), 7.05-
7.02 (m, 2 H), 5.32 (d, J ) 6.4 Hz, 1 H), 4.95 (d, J ) 6.8 Hz, 2
H), 4.02 (m, 1 H) 3.53 (m, 2 H), 3.23 (m, 1 H), 2.26-2.11 (m, 2
H); ESIMS m/z (rel intensity) 343/345 (MH+ - HBr - CO2, 100/
33). Anal. (C19H16BrClN2O5‚1.0H2O) C, H, N.
cis-3-(4-Bromophenyl)-N-(3-chloropropyl)-4-carboxy-3,4-di-
hydro-7-nitro-1(2H)isoquinolone (29). The general procedure
provided the desired compound as a yellow solid (4.824 g, 85%):
mp 169-171 °C. IR (KBr) 3078, 1737, 1638, 1527, 1487, 1407,
1347, 1186, and 742 cm-1; 1H NMR (CD3OD) δ 8.89 (d, J ) 2.5
Hz, 1 H), 8.37 (dd, J ) 8.6 and 2.5 Hz, 1 H), 7.96 (dd, J ) 5.6
and 3.1 Hz, 1 H), 7.39 (d, J ) 8.5 Hz, 2 H), 6.99 (d, J ) 8.5 Hz,
2 H), 5.30 (d, J ) 5.6 Hz, 1 H), 4.95 (d, J ) 6.1 Hz, 1 H), 4.01
(m, 1 H), 3.65 (m, 2 H), 3.29 (m, 1 H), 2.17 (m, 1 H), 2.05 (m, 1
H); negative ion ESIMS m/z (rel intensity) 465/467 [(M - H+)-,
94/100]. Anal. (C19H16BrClN2O5‚1.0H2O) C, H, N.
6-(3-Bromopropyl)-9-ethoxy-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (35). The general procedure pro-
vided the desired compound as a red solid (0.441 g, 46%): mp
230-234 °C. IR (KBr) 1667, 1614, 1507, 1456, 1335, 1337, and
1
1229 cm-1; H NMR (CDCl3) δ 9.16 (d, J ) 2.4 Hz, 1 H), 8.80
(d, J ) 9.0 Hz, 1 H), 8.48 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.79 (d,
J ) 8.4 Hz, 1 H), 7.26 (1 H buried under residual solvent), 6.93
(dd, J ) 8.4 and 2.6 Hz, 1 H), 4.70 (m, 2 H), 4.19 (q, J ) 7.0 Hz,
2 H), 3.69 (t, J ) 6.1 Hz, 2 H), 2.51 (m, 2 H), 1.50 (t, J ) 7.0 Hz,
3 H); ESIMS m/z (rel intensity) 457/459 (MH+, 18/14). Anal.
(C21H17N2O5) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3,4-dihydro-3-(4-iodophe-
nyl)-7-nitro-1(2H)isoquinolone (30). The general procedure pro-
vided the desired compound as a yellow solid (2.390 g, 75%): mp
178-180 °C. IR (KBr) 3082, 1735, 1527, 1484, 1347, and 1186
cm-1; 1H NMR (CD3OD) δ 8.88 (d, J ) 2.5 Hz, 1 H), 8.38 (dd, J
) 8.6 and 2.5 Hz, 1 H), 7.96 (d, J ) 8.5 Hz, 1 H), 7.58 (d, J ) 8.5
Hz, 2 H), 6.85 (d, J ) 8.5 Hz, 2 H), 5.27 (s, 1 H), 4.95 (s, 1 H),
4.02 (m, 1 H), 3.52 (m, 2 H), 3.23 (m, 1 H), 2.26-2.10 (m, 2 H);
6-(3-Bromopropyl)-9-ethyl-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (36). The general procedure pro-
vided the desired compound as an orange solid (0.338 g, 35%):
mp 227-231 °C. IR (film) 1671, 1612, 1558, 1501, and 1337 cm-1
;
1H NMR (CDCl3) δ 9.18 (d, J ) 2.4 Hz, 1 H), 8.86 (d, J ) 9.0
Hz, 1 H), 8.50 (dd, J ) 9.0 and 2.5 Hz, 1 H), 7.81 (d, J ) 7.8 Hz,
1 H), 7.57 (d, J ) 1.5 Hz, 1 H), 7.38 (dd, J ) 7.8 and 1.7 Hz, 1
H), 4.72 (m, 2 H), 3.69 (t, J ) 6.1 Hz, 2 H), 2.78 (q, J ) 7.6 Hz,
2 H), 2.52 (m, 2 H), 1.33 (t, J ) 7.6 Hz, 3 H); ESIMS m/z (rel
intensity) 441/443 (MH+, 13/11). Anal. (C21H17BrN2O4‚0.5H2O)
C, H, N.
ESIMS m/z (rel intensity) 479 (MH+ - HBr, 54), 435 (MH+
HBr - CO2, 100). Anal. (C19H16BrIN2O5) C, H, N.
-
cis-4-Carboxy-N-(3-chloropropyl)-3,4-dihydro-3-(4-methoxy-
carbonylphenyl)-7-nitro-1(2H)isoquinolone (31). The general
procedure provided the desired compound as a white solid (5.186
g, 65%). The product was highly insoluble in CD3OD and required
heating to obtain a suitable 1H NMR sample. The experiment
revealed a mixture of cis- and trans-isomers in a ratio of ∼40:60,
respectively. However, it is unclear whether this was the result of
sample preparation because the cis-isomer readily epimerizes to
the trans-isomer upon heating. Further complicating matters, the
product is readily soluble in DMSO-d6, but decarboxylates to
undermine the stereochemical information at the centers in question.
As a result, the material was carried forward in the reaction scheme
without characterization.
6-(3-Bromopropyl)-5,6-dihydro-9-methyl-7-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (37). The general procedure pro-
vided the desired compound as an orange-red solid (0.479 g,
50%): mp 224-227 °C (dec). IR (film) 1675, 1610, 1556, 1501,
1
and 1331 cm-1; H NMR (CDCl3) δ 9.19 (d, J ) 2.4 Hz, 1 H),
8.86 (d, J ) 9.0 Hz, 1 H), 8.51 (dd, J ) 9.0 and 2.5 Hz, 1 H), 7.79
(d, J ) 7.8 Hz, 1 H), 7.54 (s, 1 H), 7.36 (d, J ) 8.0 Hz, 1 H), 4.73
(m, 2 H), 3.69 (t, J ) 6.0 Hz, 2 H), 2.52 (m, 2 H), 2.45 (s, 3 H);
CIMS m/z (rel intensity) 427/429 (MH+, 96/100). Anal. (C20H15-
BrN2O4‚0.5H2O) C, H, N.
6-(3-Bromopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-thiomethyl-
11H-indeno[1,2-c]isoquinoline (38). The general procedure pro-
vided the desired compound as a red solid (0.160 g, 33%): mp
cis-4-Carboxy-N-(3-chloropropyl)-3-(4-cyanophenyl)-3,4-di-
hydro-7-nitro-1(2H)isoquinolone (32). The general procedure
provided the desired compound as a white solid (6.083 g, 61%).
The product was highly insoluble in CD3OD and required heating
242-245 °C. IR (film) 1665, 1610, 1502, 1429, and 1336 cm-1
;
1H NMR (CDCl3) δ 9.17 (d, J ) 2.4 Hz, 1 H), 8.82 (d, J ) 9.0
Hz, 1 H), 8.50 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.80 (d, J ) 8.1 Hz,
1 H), 7.54 (d, J ) 1.9 Hz, 1 H), 7.31 (dd, J ) 8.0 and 2.0 Hz, 1
H), 4.71 (m, 2 H), 3.69 (t, J ) 6.1 Hz, 2 H), 2.59 (s, 3 H), 2.49 (m,
1
to obtain a suitable H NMR sample. The experiment revealed a
mixture of cis- and trans-isomers, with the major product being
the trans-isomer. However, it is unclear whether this was the result
of sample preparation, because the cis-isomer readily epimerizes
to the trans-isomer upon heating. Further complicating matters, the
product is readily soluble in DMSO-d6 but decarboxylates to
undermine the stereochemical information at the centers in question.
As a result, the material was carried forward in the reaction scheme
without characterization.
2 H); EIMS m/z (rel intensity) 458/460 (M+, 35/37), 379 (M+
Br, 25). Anal. (C20H15BrN2O4S‚1.0H2O) C, H, N.
-
6-(3-Bromopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-phenyl-
11H-indeno[1,2-c]isoquinoline (39). The general procedure pro-
vided the desired compound as an orange solid that was precipitated
cleanly from EtOAc/hexanes (0.168 g, 35%): mp 253-256 °C.
IR (film) 1674, 1612, 1498, 1435, and 1338 cm-1 1H NMR
;

4398 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
(CDCl3) δ 9.21 (d, J ) 2.4 Hz, 1 H), 8.90 (d, J ) 8.9 Hz, 1 H),
8.53 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.99 (d, J ) 1.5 Hz, 1 H), 7.98
(d, J ) 4.4 Hz, 1 H), 7.80 (dd, J ) 8.1 and 1.8 Hz, 1 H), 7.70 (m,
2 H), 7.54 (m, 3 H), 4.78 (m, 2 H), 3.72 (t, J ) 6.1 Hz, 2 H), 2.56
(m, 2 H); EIMS m/z (rel intensity) 488/500 (M+, 7/7). Anal. (C25H17-
BrN2O4‚0.5H2O) C, H, N.
(DMSO-d6) δ 8.90 (d, J ) 2.2 Hz, 1 H), 8.74 (d, J ) 8.9 Hz, 1 H),
8.63 (dd, J ) 8.9 and 2.5 Hz, 1 H), 8.19 (dd, J ) 8.0 and 1.6 Hz,
1 H), 8.10 (d, J ) 8.0 Hz, 1 H), 8.07 (d, J ) 1.4 Hz, 1 H), 4.68
(m, 2 H), 3.92 (t, J ) 6.5 Hz, 2 H), 2.31 (m, 2 H). Anal. (C20H12-
ClN3O4‚0.5H2O) C, H, N.
9-(Methoxycarbonyloxymethyl)-6-(3-bromopropyl)-5,6-dihy-
dro-3-nitro-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (47). The
general procedure provided the desired compound as an orange solid
(0.038 g, 16%) that was precipitated cleanly from EtOAc-
6-(3-Chloropropyl)-5,6-dihydro-5,11-dioxo-3-nitro-11H-indeno-
[1,2-c]isoquinoline (40). The general procedure provided the
desired compound as an orange solid (1.081 g, 57%): mp 260 °C
1
(dec). IR (film) 1677, 1612, 1505, 1338, and 668 cm-1; H NMR
hexanes: mp 233-236 °C. IR (film) 1749, 1684, and 1502 cm-1
;
(CDCl3) δ 9.20 (d, J ) 2.4 Hz, 1 H), 8.89 (d, J ) 9.0 Hz, 1 H),
8.52 (dd, J ) 8.9 and 2.5 Hz, 1 H), 7.90 (d, J ) 6.8 Hz, 1 H), 7.75
(dd, J ) 6.5 and 1.7 Hz, 1 H), 7.57-7.52 (m, 2 H), 4.77 (m, 2 H),
3.87 (t, J ) 6.0 Hz, 2 H), 2.46 (m, 2 H); EIMS m/z (rel intensity)
368/370 (M+, 100/34). Anal. (C19H13ClN2O4‚0.25H2O) C, H, N.
6-(3-Bromopropyl)-9-fluoro-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (41). The general procedure pro-
vided the desired compound as a red-orange solid (0.593 g, 41%):
mp 265-267 °C (dec). IR (KBr) 1702, 1683, 1611, 1501, 1335,
and 1217 cm-1; 1H NMR (DMSO-d6) δ 8.89 (d, J ) 2.4 Hz, 1 H),
8.71 (d, J ) 8.9 Hz, 1 H), 8.60 (dd, J ) 9.0 and 2.5 Hz, 1 H), 8.00
(dd, J ) 8.4 and 4.5 Hz, 1 H), 7.56 (dd, J ) 7.0 and 2.5 Hz, 1 H),
7.50 (dt, J ) 8.5 and 2.8 Hz, 1 H), 4.65 (t, J ) 7.4 Hz, 2 H), 3.79
(t, J ) 6.6 Hz, 2 H), 2.39 (t, J ) 7.5 Hz, 2 H); ESIMS m/z (rel
intensity) 431/433 (MH+, 1.6/1.4). Anal. (C19H12BrFN2O4) C, H,
N.
1H NMR (CDCl3) δ 9.20 (d, J ) 2.3 Hz, 1 H), 8.88 (d, J ) 9.0
Hz, 1 H), 8.53 (dd, J ) 8.9 and 2.4 Hz, 1 H), 7.94 (d, J ) 7.9 Hz,
1 H), 7.72 (s, 1 H), 7.59 (d, J ) 7.9 Hz, 1 H), 5.23 (s, 2 H), 4.74
(m, 2 H), 3.84 (s, 3 H), 3.70 (t, J ) 6.1 Hz, 2 H), 2.52 (m, 2 H);
ESIMS m/z (rel intensity) 501/503 (MH+, 99/100). Anal. (C22H17-
BrN2O7) C, H, N.
6-(3-Bromopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-[4-(toluene-
4-sulfonyloxy)phenyl]-11H-indeno[1,2-c]isoquinoline (48). The
general procedure provided the desired compound as an orange solid
(0.099 g, 17%) that was precipitated cleanly from EtOAc-
hexanes: mp 232-233 °C. IR (film) 1673, 1501, and 1353 cm-1
;
1H NMR (CDCl3) δ 9.19 (d, J ) 2.4 Hz, 1 H), 8.83 (d, J ) 8.9
Hz, 1 H), 8.52 (dd, J ) 8.9 and 2.4 Hz, 1 H), 7.92 (d, J ) 8.2 Hz,
1 H), 7.80 (d, J ) 8.4 Hz, 2 H), 7.39 (d, J ) 8.3 Hz, 2 H), 7.33
(dd, J ) 8.2 and 2.3 Hz, 1 H), 7.28 (d, J ) 2.4 Hz, 1 H), 4.71 (m,
2 H), 3.69 (t, J ) 6.0 Hz, 2 H), 2.48 (s, 3 H), 2.48 (m, 2 H); EIMS
m/z (rel intensity) 582/584 (M+, 1/1). Anal. (C26H19BrN2O7S‚
0.5H2O) C, H, N.
6-(3-Bromopropyl)-9-chloro-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (42). The general procedure pro-
vided the desired compound as a red-orange solid (0.642 g, 45%):
6-(3-Bromopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-meth-
anesulfonyl-11H-indeno[1,2-c]isoquinoline (49). 3-Chloroperben-
zoic acid (77%; 0.300 g, 1.339 mmol) was added to a solution of
6-(3-bromopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-thiomethyl-
11H-indeno[1,2-c]isoquinoline (38; 0.123 g, 0.268 mmol) in CHCl3
(40 mL). After 30 min, the reaction mixture was concentrated,
diluted with diethyl ether (50 mL), and filtered. The solid was
washed with diethyl ether (100 mL) to provide an orange solid
(0.100 g, 76%): mp 240-242 °C (dec). IR (KBr) 1682, 1611, 1504,
mp 273-275 °C. IR (film) 1678, 1614, 1557, 1504, and 1336 cm-1
;
1H NMR (CDCl3) δ 9.20 (d, J ) 2.4 Hz, 1 H), 8.86 (d, J ) 9.0
Hz, 1 H), 8.53 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.89 (d, J ) 8.1 Hz,
1 H), 7.69 (d, J ) 2.1 Hz, 1 H), 7.53 (dd, J ) 8.1 and 2.1 Hz, 1
H), 4.72 (m, 2 H), 3.70 (t, J ) 6.0 Hz, 2 H), 2.51 (m, 2 H); EIMS
m/z (rel intensity) 446/448/450 (M+, 17/22/6). Anal. (C19H12-
BrClN2O4) C, H, N.
9-Bromo-6-(3-chloropropyl)-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (43). The general procedure pro-
vided the desired compound as an orange solid (0.367 g, 38%):
1
1344, 1312, and 1145 cm-1; H NMR (DMSO-d6) δ 8.93 (d, J )
2.5 Hz, 1 H), 8.79 (d, J ) 8.9 Hz, 1 H), 8.65 (dd, J ) 8.9 and 2.5
Hz, 1 H), 8.18 (s, 2 H), 8.07 (s, 1 H), 4.70 (m, 2 H), 3.80 (t, J )
6.8 Hz, 2 H), 3.38 (s, 3 H), 2.41 (m, 2 H); ESIMS m/z (rel intensity)
411 (MH+ - HBr, 100). Anal. (C20H15BrN2O6S) C, H, N.
6-(3-Azidopropyl)-9-ethoxy-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (50). The general procedure pro-
vided the desired compound as a red solid (0.399 g, 99%): mp
170-173 °C. IR (KBr) 2095, 1666, 1616, 1509, 1337, and 1229
cm-1; 1H NMR (CDCl3) δ 9.17 (d, J ) 2.4 Hz, 1 H), 8.81 (d, J )
9.0 Hz, 1 H), 8.48 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.73 (d, J ) 8.5
Hz, 1 H), 6.95 (dd, J ) 8.3 and 2.4 Hz, 1 H), 4.63 (m, 2 H), 4.19
(q, J ) 7.2 Hz, 2 H), 3.69 (t, J ) 6.0 Hz, 2 H), 2.17 (m, 2 H), 1.50
(t, J ) 7.0 Hz, 3 H); ESIMS m/z (rel intensity) 426 [(MLi+, 13].
Anal. (C21H17N5O5) C, H, N.
mp 246-249 °C. IR (film) 1669, 1613, 1500, 1429, and 1339 cm-1
;
1H NMR (DMSO-d6) δ 8.89 (d, J ) 2.5 Hz, 1 H), 8.71 (d, J ) 9.0
Hz, 1 H), 8.61 (dd, J ) 8.9 and 2.5 Hz, 1 H), 7.85 (bs, 2 H), 7.77
(s, 1 H), 4.65 (t, J ) 6.3 Hz, 2 H), 3.91 (t, J ) 6.5 Hz, 2 H), 2.30
(m, 2 H); MALDIMS m/z (rel intensity) 447/449/451 (MH+, 100/
95/45). Anal. (C19H12BrClN2O4) C, H, N.
6-(3-Bromopropyl)-5,6-dihydro-9-iodo-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (44). The general procedure pro-
vided the desired compound as an orange solid (0.130 g, 54%):
mp 252-255 °C. IR (film) 1678, 1613, 1498, 1430, and 1347 cm-1
;
1H NMR (CDCl3) δ 9.19 (d, J ) 2.4 Hz, 1 H), 8.85 (d, J ) 9.0
Hz, 1 H), 8.53 (dd, J ) 8.9 and 2.4 Hz, 1 H), 8.01 (d, J ) 1.7 Hz,
1 H), 7.96 (dd, J ) 8.0 and 1.7 Hz, 1 H), 7.68 (d, J ) 8.0 Hz, 1
H), 4.71 (m, 2 H), 3.69 (t, J ) 5.9 Hz, 2 H), 2.48 (m, 2 H); EIMS
m/z (rel intensity) 538/540 (M+, 47/46), 459 (M+ - Br, 43). Anal.
(C19H12BrIN2O4) C, H, N.
6-(3-Azidopropyl)-9-ethyl-5,6-dihydro-3-nitro-5,11-dioxo-11H-
indeno[1,2-c]isoquinoline (51). The general procedure provided
the desired compound as a red-orange solid (0.583 g, 90%): mp
190-192 °C. IR (film) 2099, 1670, 1613, 1557, 1502, and 1336
cm-1; 1H NMR (CDCl3) δ 9.19 (d, J ) 2.1 Hz, 1 H), 8.86 (d, J )
9.0 Hz, 1 H), 8.50 (dd, J ) 9.0 and 2.5 Hz, 1 H), 7.74 (d, J ) 8.0
Hz, 1 H), 7.58 (d, J ) 1.5 Hz, 1 H), 7.39 (d, J ) 7.8 Hz, 1 H),
4.66 (m, 2 H), 3.70 (t, J ) 6.0 Hz, 2 H), 2.76 (q, J ) 7.6 Hz, 2 H),
2.19 (m, 2 H), 1.33 (t, J ) 7.6 Hz, 3 H); EIMS m/z (rel intensity)
403 (M+, 100). Anal. (C21H17N5O4) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-9-methyl-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (52). The general procedure pro-
vided the desired compound as a red-orange solid (0.388 g, 80%):
mp 225-229 °C. IR (film) 2088, 1671, 1613, 1556, 1503, and 1335
cm-1; 1H NMR (CHCl3) δ 9.19 (d, J ) 2.3 Hz, 1 H), 8.56 (d, J )
8.9 Hz, 1 H), 8.50 (dd, J ) 8.9 and 2.4 Hz, 1 H), 7.71 (d, J ) 7.8
Hz, 1 H), 7.54 (s, 1 H), 7.37 (d, J ) 7.8 Hz, 1 H), 4.66 (t, J ) 7.4
Hz, 2 H), 3.69 (t, J ) 6.0 Hz, 2 H), 2.45 (s, 3 H), 2.20 (m, 2 H).
Anal. (C20H15N5O4) C, H, N.
6-(3-Chloropropyl)-5,6-dihydro-9-methoxycarbonyl-3-nitro-
5,11-dioxo-11H-indeno[1,2-c]isoquinoline (45). The general pro-
cedure provided the desired compound as a red-orange solid (0.112
g, 12%) upon precipitation with diethyl ether: mp 249-251 °C.
IR (KBr) 1722, 1679, 1614, 1504, 1436, and 1342 cm-1; 1H NMR
(CDCl3) δ 9.22 (d, J ) 2.2 Hz, 1 H), 8.92 (d, J ) 8.9 Hz, 1 H),
8.55 (dd, J ) 9.0 and 2.4 Hz, 1 H), 8.32 (d, J ) 1.4 Hz, 1 H), 8.29
(dd, J ) 8.0 and 1.7 Hz, 1 H), 8.02 (d, J ) 7.8 Hz, 1 H), 4.79 (m,
2 H), 3.98 (s, 3 H), 3.88 (t, J ) 5.8 Hz, 2 H), 2.43 (m, 2 H); ESIMS
m/z (rel intensity) 427/429 (MH+, 25/10). Anal. (C21H15ClN2O6‚
1.1H2O) C, H, N.
6-(3-Chloropropyl)-9-cyano-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (46). The general procedure pro-
vided the desired compound as a yellow-orange solid (0.182 g, 10%)
upon precipitation with diethyl ether: mp 272-276 °C. IR (KBr)
1
1709, 1676, 1613, 1557, 1505, 1339, and 1174 cm-1; H NMR

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4399
6-(3-Azidopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-thiomethyl-
11H-indeno[1,2-c]isoquinoline (53). The general procedure pro-
vided the desired compound as a red solid (0.362 g, 45%): mp
210-213 °C (dec). IR (film) 2093, 1672, 1613, 1504, 1427, and
1336 cm-1; 1H NMR (DMSO-d6) δ 8.83 (s, 1 H), 8.61 (d, J ) 9.1
Hz, 1 H), 8.52 (d, J ) 9.2 Hz, 1 H), 7.77 (d, J ) 8.6 Hz, 1 H),
7.40-7.38 (m, 2 H), 4.54 (t, J ) 6.7 Hz, 2 H), 3.66 (t, J ) 6.6 Hz,
2 H), 2.59 (s, 3 H), 2.07 (m, 2 H); ESIMS m/z (rel intensity) 428
(MLi+, 100). Anal. (C20H15N5O4S‚0.5CH3OH) C, H, N.
1 H), 8.68 (d, J ) 9.0 Hz, 1 H), 8.59 (dd, J ) 8.9 and 2.5 Hz, 1
H), 7.85 (m, 2 H), 7.75 (d, J ) 1.5 Hz, 1 H), 4.58 (t, J ) 6.8 Hz,
2 H), 3.65 (t, J ) 6.6 Hz, 2 H), 2.07 (pent, J ) 7.2 Hz, 2 H). Anal.
(C19H12BrN5O4) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-9-iodo-3-nitro-5,11-dioxo-11H-
indeno[1,2-c]isoquinoline (59). The general procedure provided
the desired compound as a red solid (0.292 g, 78%): mp 225-
227 °C (dec). IR (film) 2099, 1670, 1613, 1503, 1430, and 1338
cm-1; 1H NMR (CDCl3) δ 9.19 (d, J ) 2.1 Hz, 1 H), 8.85 (d, J )
8.9 Hz, 1 H), 8.52 (dd, J ) 8.9 and 2.4 Hz, 1 H), 8.01 (d, J ) 1.6
Hz, 1 H), 7.97 (dd, J ) 8.0 and 1.7 Hz, 1 H), 7.61 (d, J ) 8.1 Hz,
1 H), 4.63 (m, 2 H), 3.71 (t, J ) 6.0 Hz, 2 H), 2.16 (m, 2 H);
ESIMS m/z (rel intensity) 502 (MH+, 100). Anal. (C19H12IN5O4)
C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-phenyl-
11H-indeno[1,2-c]isoquinoline (54). Thionyl chloride (10 mL) was
added to a solution cis-N-(3-bromopropyl)-4-carboxy-3,4-dihydro-
3-(4-biphenyl)-1(2H)isoquinolone (39; 1.500 g, 2.945 mmol) in
benzene (75 mL). The reaction mixture was heated at reflux for 30
min, allowed to cool to room temperature, and concentrated. The
residue was diluted with nitrobenzene (50 mL), chilled in an ice
bath, and aluminum chloride (0.785 g, 5.890 mmol) was added.
The reaction mixture was removed from the bath and heated at
reflux for 1 h. Ice water (100 mL) was added and the solution was
extracted with CHCl3 (3 × 100 mL). The combined organic layer
was washed with satd NaHCO3 (3 × 100 mL), satd NaCl (100
mL), and dried over sodium sulfate. The solution was concentrated
and sodium azide (0.191 g, 2.945 mmol) was added. The reaction
mixture was diluted with DMSO (200 mL) and the mixture was
heated at 100 °C for 1 h. The reaction mixture was diluted with
CHCl3 (500 mL), washed with water (3 × 100 mL) and satd NaCl
(100 mL), and dried over sodium sulfate. The solution was
concentrated to provide a crude solid that was purified by flash
column chromatography (SiO2), eluting with chloroform, and
precipitated from CHCl3-EtOAc-hexanes to afford a red solid
(0.641 g, 48%): mp 219-221 °C. IR (film) 2092, 1666, 1612, 1500,
1435, and 1337 cm-1; 1H NMR (CDCl3) δ 9.20 (d, J ) 2.4 Hz, 1
H), 8.89 (d, J ) 8.9 Hz, 1 H), 8.52 (dd, J ) 8.9 and 2.4 Hz, 1 H),
7.98 (d, J ) 1.8 Hz, 1 H), 7.91 (d, J ) 8.0 Hz, 1 H), 7.81 (dd, J
) 8.0 and 1.8 Hz, 1 H), 7.69 (m, 2 H), 7.54 (m, 3 H), 4.70 (m, 2
H), 3.73 (t, J ) 6.0 Hz, 2 H), 2.23 (m, 2 H). Anal. (C25H17N5O4‚
0.5H2O) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-11H-indeno-
[1,2-c]isoquinoline (55). The general procedure provided the
desired compound as an orange-red solid (0.179 g, 98%): mp
214 °C (dec). IR (film) 2090, 1673, 1614, 1560, 1505, and 1336
cm-1; 1H NMR (CDCl3) δ 9.20 (d, J ) 2.4 Hz, 1 H), 8.89 (d, J )
8.9 Hz, 1 H), 8.52 (dd, J ) 9.0 and 2.0 Hz, 1 H), 7.85 (d, J ) 7.4
Hz, 1 H), 7.74 (d, J ) 6.9 Hz, 1 H), 7.60-7.50 (m, 2 H), 4.69
(t, J ) 7.6 Hz, 2 H), 3.71 (t, J ) 6.3 Hz, 2 H), 2.20 (m, 2 H);
CIMS m/z (rel intensity) 376 (MH+, 100). Anal. (C19H13N5O4) C,
H, N.
6-(3-Azidopropyl)-9-fluoro-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (56). The general procedure pro-
vided the desired compound as an orange-red solid (0.0115 g,
98%): mp 195-200 °C (dec). IR (film) 2101, 1670, 1610, 1503,
1438, and 1338 cm-1; 1H NMR (CDCl3) δ 9.19 (d, J ) 2.4 Hz, 1
H), 8.84 (d, J ) 8.9 Hz, 1 H), 8.52 (dd, J ) 8.9 and 2.42 Hz, 1 H),
7.88 (dd, J ) 9.3 and 4.0 Hz, 1 H), 7.45 (dd, J ) 6.7 and 2.4 Hz,
1 H), 7.23 (dd, J ) 8.4 and 2.6 Hz, 1 H), 4.65 (m, 2 H), 3.72
(t, J ) 5.9 Hz, 2 H), 2.20 (m, 2 H); CIMS m/z (rel intensity) 394
(MH+, 74). Anal. (C19H12FN5O4‚0.3H2O) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-9-methoxycarbonyl-3-nitro-5,-
11-dioxo-11H-indeno[1,2-c]isoquinoline (60). The general pro-
cedure provided the desired compound as a red-orange solid (0.083
g, 73%): mp 233-235 °C. IR (KBr) 2092, 1722, 1675, 1615, 1504,
1
and 1343 cm-1; H NMR (CDCl3) δ 9.21 (d, J ) 2.4 Hz, 1 H),
8.91 (d, J ) 8.9 Hz, 1 H), 8.54 (dd, J ) 8.9 and 2.4 Hz, 1 H), 8.30
(m, 2 H), 7.97 (d, J ) 8.2 Hz, 1 H), 4.69 (m, 2 H), 3.99 (s, 3 H),
3.73 (t, J ) 6.0 Hz, 2 H), 2.20 (m, 2 H); ESIMS m/z (rel intensity)
434 (MH+, 23). Anal. (C21H15N5O6‚0.75H2O) C, H, N.
6-(3-Azidopropyl)-9-cyano-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (61). The general procedure pro-
vided the desired compound as a red solid (0.155 g, 84%) that was
washed with EtOAc and Et2O: mp 237 °C (dec). IR (KBr) 2088,
1675, 1615, 1504, and 1343 cm-1; 1H NMR (DMSO-d6) δ 8.83 (s,
1 H), 8.66 (d, J ) 8.8 Hz, 1 H), 8.58 (dd, J ) 8.7 and 2.1 Hz, 1
H), 8.17 (d, J ) 7.9 Hz, 1 H), 8.07 (d, J ) 7.9 Hz, 1 H), 8.04 (s,
1 H), 4.59 (t, J ) 7.4 Hz, 2 H), 3.66 (t, J ) 6.5 Hz, 2 H), 2.07
(pent, J ) 6.6 Hz, 2 H). Anal. (C20H12N6O4‚0.5H2O) C, H, N.
6-(3-Aminopropyl)-9-ethoxy-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (62). The general
procedure provided the desired compound as a red solid (0.126 g,
85%): mp 262-265 °C (dec). IR (KBr) 1672, 1614, 1557, 1505,
and 1336 cm-1; 1H NMR (DMSO-d6) δ 8.85 (d, J ) 2.4 Hz, 1 H),
8.65 (d, J ) 9.0 Hz, 1 H), 8.55 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.88
(bs, 2 H), 7.81 (d, J ) 8.7 Hz, 1 H), 7.15 (d, J ) 2.5 Hz, 1 H),
7.06 (dd, J ) 8.5 and 2.5 Hz, 1 H), 4.56 (m, 2 H), 4.22 (q, J ) 7.0
Hz, 2 H), 3.01 (m, 2 H), 2.15 (m, 2 H), 1.40 (t, J ) 6.9 Hz, 3 H);
ESIMS m/z (rel intensity) 394 (MH+, 30), 377 (MH+ - NH3, 100).
Anal. (C21H20ClN3O5‚1.0H2O) C, H, N.
6-(3-Aminopropyl)-9-ethyl-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (63). The general
procedure provided the desired compound as an orange solid (0.088
g, 85%): mp 268-270 °C (dec). IR (KBr) 3438, 1669, 1614, 1558,
1504, and 1338 cm-1; 1H NMR (DMSO-d6) δ 8.87 (d, J ) 2.4 Hz,
1 H), 8.71 (d, J ) 9.0 Hz, 1 H), 8.58 (dd, J ) 9.0 and 2.5 Hz, 1
H), 7.93 (bs, 2 H), 7.82 (d, J ) 7.9 Hz, 1 H), 7.52 (d, J ) 1.5 Hz,
1 H), 7.48 (d, J ) 7.8 Hz, 1 H), 4.60 (t, J ) 7.0 Hz, 2 H), 3.01 (bs,
2 H), 2.73 (q, J ) 7.6 Hz, 2 H), 2.16 (m, 2 H), 1.25 (t, J ) 7.6 Hz,
3 H); ESIMS m/z (rel intensity) 378 (MH+, 100). Anal. (C21H20-
ClN3O4‚0.75H2O) C, H, N.
6-(3-Aminopropyl)-5,6-dihydro-9-methyl-5,11-dioxo-11H-in-
deno[1,2-c]isoquinoline Hydrochloride (64). The general
procedure provided the desired compound as an orange solid
(0.078 g, 76%): mp 275 °C (dec). IR (KBr) 3435, 1674, 1615,
1504, and 1338 cm-1; 1H NMR (DMSO-d6) δ 8.90 (d, J ) 2.4 Hz,
1 H), 8.74 (d, J ) 9.0 Hz, 1 H), 8.61 (dd, J ) 9.0 and 2.4 Hz, 1
H), 7.80 (d, J ) 7.3 Hz, 1 H), 7.44 (bs, 2 H), 7.52 (s, 1 H), 7.47
(d, J ) 7.7 Hz, 1 H), 4.58 (m, 2 H), 3.03 (m, 2 H), 2.43 (s, 3 H),
2.11 (m, 2 H); ESIMS m/z (rel intensity) 364 (MH+, 100). Anal.
(C20H18ClN3O4‚0.5H2O) C, H, N.
6-(3-Azidopropyl)-9-chloro-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (57). The general procedure pro-
vided the desired compound as a red-orange solid (0.446 g, 99%):
mp 238-240 °C (dec). IR (film) 2091, 1674, 1615, 1556, and 1339
cm-1; 1H NMR (CDCl3) δ 9.20 (d, J ) 2.4 Hz, 1 H), 8.86 (d, J )
8.9 Hz, 1 H), 8.53 (dd, J ) 8.9 and 2.4 Hz, 1 H), 7.82 (d, J ) 8.1
Hz, 1 H), 7.68 (d, J ) 2.1 Hz, 1 H), 7.56 (dd, J ) 8.1 and 2.1 Hz,
1 H), 4.65 (m, 2 H), 3.72 (t, J ) 6.0 Hz, 2 H), 2.17 (m, 2 H). Anal.
(C19H12ClN5O4) C, H, N.
6-(3-Azidopropyl)-9-bromo-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (58). The general procedure
provided the desired compound as an orange-red solid
(0.243 g, 80%): mp 230 °C (dec). IR (film) 2082, 1671, 1613,
1503, and 1339 cm-1; 1H NMR (DMSO-d6) δ 8.87 (d, J ) 2.4 Hz,
6-(3-Aminopropyl)-5,6-dihydro-5,11-dioxo-9-thiomethyl-11H-
indeno[1,2-c]isoquinoline Hydrochloride (65). The general pro-
cedure provided the desired compound as a red-brown solid (0.103
g, 93%): mp 267-269 °C (dec). IR (KBr) 3433, 1654, 1613, 1548,
1
1497, 1431, and 1336 cm-1; H NMR (DMSO-d6) δ 8.88 (d, J )
2.4 Hz, 1 H), 8.70 (d, J ) 9.0 Hz, 1 H), 8.59 (dd, J ) 9.0 and 2.5
Hz, 1 H), 7.85 (bs, 2 H), 7.81 (d, J ) 8.2 Hz, 1 H), 7.49 (d, J )

4400 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
1.9 Hz, 1 H), 7.43 (dd, J ) 8.2 and 1.8 Hz, 1 H), 4.59 (t, J ) 7.0
Hz, 2 H), 3.01 (m, 2 H), 2.62 (s, 3 H), 2.17 (m, 2 H); ESIMS m/z
(rel intensity) 396 (MH+, 100). Anal. (C20H18ClN3O4S) C, H, N.
2.15 (m, 2 H); ESIMS m/z (rel intensity) 408 (MH+, 35), 391 (MH+
- NH3, 100). Anal. (C21H18N3O6‚1.0H2O) C, H, N.
6-(3-Aminopropyl)-9-cyano-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (73). The general
procedure provided the desired compound as an orange solid (0.086
g, 93%): mp 275-280 °C (dec). IR (KBr) 1706, 1682, 1615, 1558,
1501, and 1347 cm-1; 1H NMR (DMSO-d6) δ 8.90 (d, J ) 2.4 Hz,
1 H), 8.75 (dd, J ) 9.0 and 3.2 Hz, 1 H), 8.64-8.58 (m, 1 H),
8.17-8.07 (m, 3 H), 8.06-7.95 (m, 3 H), 4.60 (m, 2 H), 3.02 (bs,
2 H), 2.13 (bs, 2 H); negative ion ESIMS m/z (rel intensity) 373
[(M - H+)-, 72]. Anal. (C20H15ClN4O4‚2.0H2O) C, H, N.
4-(Acetamido)benzylidene-(3-bromo-1-propylamine) (75). The
general procedure provided the desired compound as an off-white
solid (5.149 g, 99%): mp 118-121 °C. IR (film) 3305, 1670, 1643,
6-(3-Aminopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-9-phenyl-
11H-indeno[1,2-c]isoquinoline Hydrochloride (66). The general
procedure provided the desired compound as an orange solid (0.090
g, 88%): mp 260 °C (dec). IR (KBr) 3422, 1668, 1615, 1557, 1501,
1437, and 1336 cm-1; 1H NMR (DMSO-d6) δ 8.88 (d, J ) 2.4 Hz,
1 H), 8.75 (d, J ) 9.0 Hz, 1 H), 8.61 (dd, J ) 9.0 and 2.5 Hz, 1
H), 8.00 (m, 5 H), 7.82 (m, 2 H), 7.56 (m, 3 H), 4.65 (t, J ) 6.8
Hz, 2 H), 3.04 (bs, 2 H), 2.20 (m, 2 H); ESIMS m/z (rel intensity)
426 (MH+, 66), 409 (MH+ - NH3, 100). Anal. (C25H20ClN3O4‚
1.25H2O) C, H, N.
6-(3-Aminopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-11H-indeno-
[1,2-c]isoquinoline Hydrochloride (67). The general procedure
provided the desired compound as an orange solid (0.133 g, 86%):
mp 268 °C (dec). IR (film) 2843, 1614, 1557, and 1329 cm-1; 1H
NMR (DMSO-d6) δ 8.90 (d, J ) 2.4 Hz, 1 H), 8.76 (d, J ) 9.0
Hz, 1 H), 8.61 (dd, J ) 9.0 and 2.4 Hz, 1 H), 7.93-7.91 (m, 3 H),
7.70-7.61 (m, 3 H), 4.63 (m, 2 H), 3.05 (m, 2 H), 2.17 (m, 2 H);
ESIMS m/z (rel intensity) 350 (MH+, 100). Anal. (C19H16ClN3O4)
C, H, N.
1
1597, 1536, and 1317 cm-1; H NMR (CDCl3) δ 8.28 (s, 1 H),
7.71 (d, J ) 8.6 Hz, 2 H), 7.59 (d, J ) 8.4 Hz, 2 H), 7.40 (bs, 1
H), 3.76 (dt, J ) 6.3 and 1.2 Hz, 2 H), 3.51 (t, J ) 6.5 Hz, 2 H),
2.30 (pent, J ) 6.4 Hz, 2 H), 2.20 (s, 3 H); ESIMS m/z (rel intensity)
283/285 (MH+, 100/99). Anal. (C12H15BrN2O) C, H, N.
4-Methoxybenzylidene-(3-chloro-1-propylamine) (76).44 The
general procedure provided the desired compound as a yellow
1
viscous oil (4.664 g, 100%). H NMR (CDCl3) δ 8.25 (s, 1 H),
7.68 (dd, J ) 6.0 and 2.0 Hz, 2 H), 6.94 (dd, J ) 6.8 and 2.0 Hz,
2 H), 3.84 (s, 3 H), 3.75 (dt, J ) 6.4 and 1.2 Hz, 2 H), 3.65 (t, J
) 6.4 Hz, 2 H), 2.20 (pent, J ) 6.38 Hz, 2 H).
6-(3-Aminopropyl)-9-fluoro-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (68). The general procedure pro-
vided the desired compound as a red-orange solid (0.175 g,
100%): mp 248-251 °C (dec). IR (KBr) 2951, 1672, 1614, 1557,
4-(Nitro)benzylidene-(3-bromo-1-propylamine) (77). The gen-
eral procedure provided the desired compound as a yellow viscous
1
1504, 1440, 1338, and 1219 cm-1; H NMR (DMSO-d6) δ 8.90
oil (10.700 g, 99%). IR (KBr) 1644, 1602, 1521, and 1346 cm-1
;
(d, J ) 2.4 Hz, 1 H), 8.73 (d, J ) 9.0 Hz, 1 H), 8.63 (dd, J ) 8.9
and 2.4 Hz, 1 H), 7.99 (dd, J ) 8.6 and 4.3 Hz, 1 H), 7.87 (bs, 2
H), 7.59 (dd, J ) 7.1 and 2.6 Hz, 1 H), 7.50 (dt, J ) 8.6 and 2.7
Hz, 1 H), 4.61 (t, J ) 6.8 Hz, 2 H), 3.02 (m, 2 H), 2.15 (m, 2 H);
negative ion ESIMS m/z (rel intensity) 366 [(M - H+)-, 100]. Anal.
(C19H15ClFN3O4‚1.25H2O) C, H, N.
1H NMR (CDCl3) δ 8.42 (s, 1 H), 8.28-8.25 (m, 2 H), 7.91-7.88
(m, 2 H), 3.84 (dt, J ) 6.3 and 1.3 Hz, 2 H), 3.53 (t, J ) 6.4 Hz,
2 H), 2.33 (pent, J ) 6.4 Hz, 2 H); ESIMS m/z (rel intensity) 191
(MH+ - HBr, 100). Anal. (C10H11BrN2O2) C, H, N.
cis-3-(4-Acetamido)-N-(3-bromopropyl)-4-carboxy-3,4-dihy-
dro-6,7-dimethoxy-1(2H)isoquinolone (78). The general
procedure provided the desired compound as an off-white solid
(4.548 g, 73%): mp 179 °C. IR (KBr) 3384, 1739, 1690, 1598,
1528, 1285, 1216, and 1183 cm-1; 1H NMR (DMSO-d6) δ 8.91 (s,
1 H), 7.53 (s, 1 H), 7.40 (d, J ) 8.6 Hz, 2 H), 7.12 (s, 1 H), 6.95
(d, J ) 8.6 Hz, 2 H), 5.04 (d, J ) 6.3 Hz, 1 H), 4.70 (d, J ) 6.1
Hz, 1 H), 3.89 (m, 2 H), 3.83 (s, 3 H), 3.74 (s, 3 H), 3.56 (m, 2 H),
2.96 (m, 1 H), 2.13 (m, 1 H), 1.99 (s, 3 H); negative ion
ESIMS m/z (rel intensity) 503/505 [(M - H+)-, 44/43]. Anal.
(C23H25BrN2O6‚0.5H2O) C, H, N.
6-(3-Aminopropyl)-9-chloro-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (69). The general
procedure provided the desired compound as an orange solid (0.035
g, 34%): mp 265-268 °C (dec). IR (KBr) 3413, 1674, 1615, 1556,
1
1503, 1432, and 1339 cm-1; H NMR (DMSO-d6) δ 8.89 (d, J )
2.4 Hz, 1 H), 8.71 (d, J ) 9.0 Hz, 1 H), 8.62 (dd, J ) 9.0 and 2.5
Hz, 1 H), 7.93 (m, 3 H), 7.71-7.69 (m, 2 H), 4.60 (t, J ) 7.1 Hz,
2 H), 3.02 (m, 2 H), 2.15 (m, 2 H); ESIMS m/z (rel intensity) 384/
386 (MH+, 100/33). Anal. (C19H15Cl2N3O4‚0.75H2O) C, H, N.
6-(3-Aminopropyl)-9-bromo-5,6-dihydro-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (70). The general
procedure provided the desired compound as a red-orange solid
(0.084 g, 82%): mp 275-277 °C (dec). IR (KBr) 3258, 3071, 2822,
cis-4-Carboxy-N-(3-chloropropyl)-3,4-dihydro-6,7-dimethoxy-
3-(4-methoxyphenyl)-1(2H)isoquinolone (79). The general pro-
cedure provided the desired compound as an off-white solid (5.659
g, 69%): mp 200-202 °C. IR (KBr) 3073, 1745, 1616, 1595, 1572,
1708, 1662, 1614, 1552, 1499, 1428, 1347, 1200, and 1088 cm-1
;
1
1516, 1486, 1297, 1264, 1189, and 1178 cm-1; H NMR (CD3-
1H NMR (DMSO-d6) δ 8.90 (d, J ) 2.4 Hz, 1 H), 8.73 (d, J ) 8.9
Hz, 1 H), 8.63 (dd, J ) 8.9 and 2.4 Hz, 1 H), 7.84-7.80 (m, 5 H),
4.60 (t, J ) 7.3 Hz, 2 H), 3.02 (m, 2 H), 2.14 (m, 2 H); ESIMS
m/z (rel intensity) 428/430 (MH+, 100/96). Anal. (C19H15BrClN3O4)
C, H, N.
OD) δ 7.62 (s, 1 H), 7.23 (s, 1 H), 7.00 (d, J ) 8.8 Hz, 2 H), 6.76
(d, J ) 8.8 Hz, 2 H), 5.10 (d, J ) 6.3 Hz, 1 H), 4.68 (d, J ) 5.8
Hz, 1 H), 3.97 (m, 1 H), 3.59 (s, 3 H), 3.80 (s, 3 H), 3.71 (s, 3 H),
3.61 (m, 2 H), 3.18 (m, 1 H), 2.12-1.99 (m, 2 H); ESIMS m/z (rel
intensity) 434/436 (MH+, 90/28), 398 (MH+ - Cl, 100). Anal.
(C22H24ClNO6) C, H, N.
6-(3-Aminopropyl)-5,6-dihydro-9-iodo-3-nitro-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (71). The general
procedure provided the desired compound as an orange solid (0.086
g, 80%): mp 270 °C (dec). IR (KBr) 3428, 1661, 1614, 1553, 1499,
1427, and 1347 cm-1; 1H NMR (DMSO-d6) δ 8.90 (d, J ) 2.4 Hz,
1 H), 8.73 (d, J ) 9.0 Hz, 1 H), 8.63 (dd, J ) 9.0 and 2.5 Hz, 1
H), 8.04 (d, J ) 8.0 and 1.6 Hz, 1 H), 7.93 (d, J ) 1.7 Hz, 1 H),
7.80 (bs, 2 H), 7.69 (d, J ) 8.0 Hz, 1 H), 4.59 (t, J ) 7.0 Hz, 2 H),
3.01 (m, 2 H), 2.13 (m, 2 H); negative ion ESIMS m/z (rel intensity)
474 [(M - H+)-, 100]. Anal. (C19H15ClIN3O4) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3-(4-ethyl)-3,4-dihydro-6,7-
dimethoxy-1(2H)isoquinolone (80). The general procedure pro-
vided the desired compound as a white solid (2.859 g, 43%): mp
207-211 °C. IR (KBr) 3434, 2967, 1735, 1620, 1595, 1576, 1294,
1
and 1175 cm-1; H NMR (DMSO-d6) δ 7.53 (s, 1 H), 7.14 (s, 1
H), 7.07 (d, J ) 8.1 Hz, 2 H), 6.95 (d, J ) 8.2 Hz, 2 H), 5.07 (d,
J ) 6.3 Hz, 1 H), 4.74 (d, J ) 6.2 Hz, 1 H), 3.91 (m, 1 H), 3.83
(s, 3 H), 3.74 (s, 3 H), 3.57 (m, 2 H), 2.91 (m, 1 H), 2.55 (q, J )
7.6 Hz, 2 H), 2.12-1.99 (m, 2 H), 1.13 (t, J ) 7.6 Hz, 3 H); ESIMS
m/z (rel intensity) 396 (MH+ - HBr, 100). Anal. (C23H26BrNO5‚
0.2CHCl3) C, H, N.
6-(3-Aminopropyl)-5,6-dihydro-9-methoxycarbonyl-3-nitro-
5,11-dioxo-11H-indeno[1,2-c]isoquinoline Hydrochloride (72).
The general procedure provided the desired compound as an orange
solid (0.092 g, 100%): mp 257-262 °C (dec). IR (KBr) 3434,
cis-4-Carboxy-N-(3-chloropropyl)-3,4-dihydro-6,7-dimethoxy-
3-phenyl-1(2H)isoquinolone (81). The general procedure provided
the desired compound as an off-white solid (2.026 g, 49%). IR
(KBr) 2940, 1744, 1615, 1594, 1572, 1488, 1455, 1292, 1186, and
1
2951, 1726, 1674, 1614, 1504, 1434, and 1342 cm-1; H NMR
(DMSO-d6) δ 8.83 (d, J ) 2.1 Hz, 1 H), 8.67 (d, J ) 9.0 Hz, 1 H),
8.57 (dd, J ) 8.8 and 2.2 Hz, 1 H), 8.17 (d, J ) 8.2 Hz, 1 H), 8.06
(m, 4 H), 7.87 (s, 1 H), 4.59 (m, 2 H), 3.91 (s, 3 H), 3.06 (m, 2 H),
1
1170 cm-1; H NMR (DMSO-d6) δ 7.54 (s, 1 H), 7.24 (m, 3 H),
7.13 (s, 1 H), 7.05 (m, 2 H), 5.10 (d, J ) 6.3 Hz, 1 H), 4.74 (d, J

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4401
) 6.2 Hz, 1 H), 3.94 (m, 1 H), 3.83 (s, 3 H), 3.74 (s, 3 H), 3.69
(m, 2 H), 2.98 (m, 1 H), 2.05-1.88 (m, 2 H); CIMS m/z (rel
intensity) 404/406 (MH+, 38/9), 360/362 (MH+ - CO2, 100/24).
Anal. (C21H22ClNO5) C, H, N.
(m, 2 H), 4.07 (s, 3 H), 3.99 (s, 3 H), 3.66 (t, J ) 6.3 Hz, 2 H),
2.73 (q, J ) 7.6 Hz, 2 H), 2.49 (m, 2 H), 1.30 (t, J ) 7.6 Hz, 3 H);
ESIMS m/z (rel intensity) 456/458 (MH+, 41/38).
6-(3-Chloropropyl)-5,6-dihydro-2,3-dimethoxy-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (89). The general procedure pro-
vided the desired compound as a red solid (349 mg, 49%): mp
230-233 °C. IR (film) 1652, 1564, 1500, 1464, 1444, 1253, and
cis-N-(3-Bromopropyl)-4-carboxy-3-(4-fluoro)-3,4-dihydro-
6,7-dimethoxy-1(2H)isoquinolone (82). The general procedure
provided the desired compound as a white solid (2.420 g, 32%):
mp 198-201 °C. IR (KBr) 3455, 2972, 1742, 1593, 1572, 1510,
1
1037 cm-1; H NMR (CDCl3) δ 8.14 (s, 1 H), 7.74-7.58 (m, 3
1
1296, 1231, 1184, 1170 and 1106 cm-1; H NMR (DMSO-d6) δ
H), 7.45-7.35 (m, 2 H), 6.10 (s, 2 H), 4.70 (m, 2 H), 3.83 (t, J )
6.1 Hz, 2 H), 2.42 (m, 2 H); CIMS m/z (rel intensity) 384/386
(MH+, 100/30). Anal. (C21H18ClNO4) C, H, N.
7.53 (s, 1 H), 7.11-7.06 (m, 5 H), 5.13 (d, J ) 6.2 Hz, 1 H), 4.75
(d, J ) 6.2 Hz, 1 H), 3.90-3.75 (m, 7 H), 3.56-3.50 (m, 2 H),
2.97-2.91 (m, 1 H), 2.14-1.96 (m, 2 H); negative ion ESIMS m/z
(rel intensity) 464/466 [(M - H+)-, 10/10]. Anal. (C21H21BrFNO5)
C, H, N.
6-(3-Bromopropyl)-9-fluoro-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline (90). The general procedure
provided the desired compound as a red solid that was precipitated
from EtOAc-hexanes (0.060 g, 13%): mp 251-253 °C (dec). IR
cis-N-(3-Chloropropyl)-4-carboxy-6,7-dimethoxy-3-(4-meth-
oxycarbonylphenyl)-3,4-dihydro-1(2H)isoquinolone (83). The
general procedure provided the desired compound as a white solid
(7.0 g, 48%): mp 210-211 °C. IR (film) 2932, 1736, 1718, 1622,
1
(film) 2937, 1644, 1466, 1432, 1270, 1249, and 1213 cm-1; H
NMR (CDCl3) δ 8.04 (s, 1 H), 7.71 (dd, J ) 4.2 and 8.4 Hz, 1 H),
7.64 (s, 2 H), 7.29 (dd, J ) 2.6 and 6.9 Hz, 1 H), 7.26 (s, 1 H),
7.11 (dt J ) 2.5 and 8.4, 1 H), 4.64-4.59 (m, 2 H), 4.05 (s, 3 H),
3.99 (s, 3 H), 3.67 (t, J ) 6.2 Hz, 2 H), 2.48 (m, 2 H); ESIMS m/z
(rel intensity) 446/448 (MH+, 100/91). Anal. (C21H17BrNO4) C,
H, N.
6-(3-Chloropropyl)-5,6-dihydro-2,3-dimethoxy-9-methoxycar-
bonyl-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (91). The general
procedure provided the desired compound as a purple solid (3.5 g,
52%): mp 253-254 °C. IR (film) 3014, 2950, 1727, 1697, 1648,
and 1479 cm-1. 1H NMR (CDCl3) δ 8.16-8.08 (m, 3 H), 7.78 (d,
J ) 7.7 Hz, 1 H), 7.65 (s, 1 H), 4.70-4.64 (m, 2 H), 4.06 (s, 3 H),
3.99 (s, 3 H), 3.95 (s, 3 H), 3.82 (t, J ) 6.0 Hz, 2 H), 2.41-2.35
(m, 2 H); EIMS m/z (rel intensity) 441 (MH+, 100). Anal. (C23H20-
ClNO6) C, H, N.
6-(3-Chloropropyl)-9-cyano-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinolone (92). The general procedure
provided the desired compound as a purple solid (0.17 g, 18%):
mp 246-249 °C (dec). IR (film) 3585, 3077, 2970, 2229, 1695,
1651, 1609, 1480, 1434, and 1269 cm-1; 1H NMR (CDCl3) δ 8.10
(s, 1 H), 7.88-7.85 (m, 1 H), 7.79-7.76 (m, 2 H), 7.69 (s, 1 H),
4.69-4.64 (m, 2 H), 4.07 (s, 3 H), 4.00 (s, 3 H), 3.84-3.80 (m, 2
H), 2.42-2.33 (m, 2 H); ESIMS m/z (rel intensity) 380 (MH+, 100).
Anal. (C22H17ClN2O4‚0.5H2O) C, H, N.
1
1596, and 1574 cm-1; H NMR (DMSO-d6) δ 7.82-7.79 (m, 2
H), 7.53 (s, 1 H), 7.18-7.16 (m, 2 H), 7.07 (s, 1 H). 5.19 (d, J )
6.0 Hz, 1 H), 4.76 (d, J ) 6.0, 1 H), 3.91-3.80 (m, 7 H), 3.72 (s,
3 H), 3.66-3.59 (m, 2 H), 2.97-2.91 (m, 1 H), 2.08-1.81 (m, 2
H); ESIMS m/z 426 (MH+ - HCl, 100). Anal. (C23H24ClNO7) C,
H, N.
cis-4-Carboxy-2-(3-chloropropyl)-3-(4-cyanophenyl)-3,4-dihy-
dro-6,7-dimethoxy-1(2H)isoquinolone (84). The general procedure
provided the desired compound as a white solid (5.0 g, 35%): mp
220-222 °C. IR (film) 2966, 2227, 1736, 1625, 1597, and 1579
1
cm-1; H NMR (DMSO-d6) δ 7.74-7.72 (m, 2 H), 7.53 (s, 1 H),
7.22-7.19 (m, 2 H), 7.05 (s, 1 H), 5.22 (d, J ) 6.0 Hz, 1 H), 4.80
(d, J ) 6.0 Hz, 1 H), 3.91-3.61 (m, 9 H), 2.94-2.89 (m, 1 H),
2.01-1.90 (m, 2 H); ESIMS m/z 393 (MH+ - HCl, 100). Anal.
(C22H21ClN2O5) C, H, N.
cis-N-(3-Bromopropyl)-4-carboxy-3,4-dihydro-6,7-dimethoxy-
3-[4-(nitro)phenyl]-1(2H)isoquinolone (85). The general procedure
provided the desired compound as an off-white solid (4.438 g,
35%): mp 203-207 °C. IR (KBr) 3449, 2940, 1736, 1623, 1598,
1578, 1520, 1488, 1347, 1293, and 1183 cm-1; 1H NMR (DMSO-
d6) δ 8.14 (d, J ) 8.6 Hz, 2 H), 7.55 (s, 1 H), 7.32 (d, J ) 8.7 Hz,
2 H), 7.06 (s, 1 H), 5.31 (d, J ) 6.3 Hz, 1 H), 4.86 (d, J ) 6.1 Hz,
1 H), 3.93 (m, 1 H), 3.88 (s, 3 H), 3.74 (s, 3 H), 3.54 (m, 2 H),
2.96 (m, 1 H), 2.15-1.97 (m, 2 H); ESIMS m/z (rel intensity) 493/
495 (MH+, 3/3), 413 (MH+ - HBr, 100). Anal. (C21H21BrN2O7‚
1.0H2O) C, H, N.
9-Acetamido-6-(3-bromopropyl)-5,6-dihydro-2,3-dimethoxy-
5,11-dioxo-11H-indeno[1,2-c]isoquinoline (86). The general pro-
cedure provided the desired compound as crude purple solid that
was precipitated cleanly from EtOAc-hexanes (0.070 g, 15%): mp
249-251 °C (dec). IR (film) 3306, 1649, 1548, 1481, 1421, and
1263 cm-1; 1H NMR (CDCl3) δ 8.07 (s, 1 H), 7.90 (d, J ) 9.5 Hz,
1 H), 7.67 (m, 2 H), 7.47 (d, J ) 2.1 Hz, 1 H), 7.33 (s, 1 H), 4.66
(m, 2 H), 4.06 (s, 3 H), 3.99 (s, 3 H), 3.66 (t, J ) 6.3 Hz, 2 H),
2.48 (m, 2 H), 2.24 (s, 3 H); ESIMS m/z (rel intensity) 485/487
(MH+, 34/45), 405 (MH+-HBr, 100). Anal. (C23H21BrN2O5‚0.5H2O)
C, H, N.
6-(3-Bromopropyl)-5,6-dihydro-2,3-dimethoxy-9-nitro-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline (93). The general procedure
provided the desired compound as a purple solid that was
precipitated cleanly from Et2O (0.479 g, 50%): mp 268-272 °C.
IR (film) 1655, 1605, 1528, 1508, 1480, 1434, 1338, and 1262
1
cm-1; H NMR (CDCl3) δ 8.39 (dd, J ) 8.3 and 2.3 Hz, 1 H),
8.32 (d, J ) 2.2 Hz, 1 H), 8.12 (s, 1 H), 7.97 (t, J ) 8.0 Hz, 1 H),
7.70 (s, 1 H), 4.73 (m, 2 H), 4.09 (s, 3 H), 4.02 (s, 3 H), 3.86 (t,
J ) 5.9 Hz, 1 H), 3.70 (t, J ) 6.0 Hz, 1 H), 2.50 (m, 2 H); ESIMS
m/z (rel intensity) 473/475 (MH+, 55/52).
9-Acetamido-6-(3-azidopropyl)-5,6-dihydro-2,3-dimethoxy-5,-
11-dioxo-11H-indeno[1,2-c]isoquinoline (94). The general pro-
cedure provided the desired compound as a red solid (0.460 g,
57%): mp 178-179 °C (dec). IR (film) 3307, 2097, 1640, 1481,
and 1264 cm-1; 1H NMR (CDCl3) δ 8.04 (s, 1 H), 7.87 (d, J ) 7.3
Hz, 1 H), 7.64 (s, 1 H), 7.59 (d, J ) 8.2 Hz, 1 H), 7.46 (d, J ) 2.2
Hz, 1 H), 7.38 (s, 1 H), 4.58 (t, J ) 7.3 Hz, 2 H), 4.05 (s, 3 H),
3.99 (s, 3 H), 3.65 (t, J ) 6.2 Hz, 2 H), 2.24 (s, 3 H), 2.17 (m, 2
H); negative ion ESIMS m/z (rel intensity) 446 [(M - H+)-, 100].
Anal. (C23H21N5O5‚0.5H2O) C, H, N.
6-(3-Chloropropyl)-5,6-dihydro-2,3,9-trimethoxy-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (87). The general procedure pro-
vided the desired compound as a purple-red solid that was
precipitated from EtOAc-hexanes (0.597 g, 63%): mp 244-245
1
°C. IR (film) 1650, 1553, 1475, 1424, 1265, and 1023 cm-1; H
NMR (CDCl3) δ 8.10 (s, 1 H), 7.66 (s, 1 H), 7.63 (dd, J ) 7.7 and
2.8 Hz, 1 H), 7.19 (d, J ) 2.5 Hz, 1 H), 6.85 (dd, J ) 8.3 and 2.7
Hz, 1 H), 4.67 (m, 2 H), 4.06 (s, 3 H), 3.99 (s, 3 H), 3.89 (s, 3 H),
3.83 (t, J ) 6.0 Hz, 2 H), 2.41 (m, 2 H); ESIMS m/z (rel intensity)
414/416 (MH+, 100/28). Anal. (C22H20ClNO5) C, H, N.
9-Amino-6-(3-azidopropyl)-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline (95). 9-Acetamido-6-(3-azi-
dopropyl)-5,6-dihydro-3-nitro-5,11-dioxo-11H-indeno[1,2-c]iso-
quinoline (94; 0.050 g, 0.108 mmol) was diluted with THF (10
mL) and 6 M aq HCl (10 mL). The reaction mixture was heated at
reflux for 16 h, allowed to cool to room temperature, and extracted
with CHCl3 (3 × 30 mL). The combined organic layer was washed
with satd NaHCO3 (3 × 30 mL), dried over sodium sulfate, and
concentrated to provide a black solid (0.038 g, 84%): mp 238 °C
(dec). IR (film) 3352, 2098, 1644, 1550, 1477, and 1264 cm-1; 1H
NMR (CDCl3) δ 8.06 (s, 1 H), 7.63 (s, 1 H), 7.39 (d, J ) Hz, 1
6-(3-Bromopropyl)-9-ethyl-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline (88). The general procedure
provided the desired compound as a red solid that was precipitated
from Et2O (0.234 g, 49%): mp 219-221 °C. IR (film) 1646, 1481,
1
1468, and 1266 cm-1; H NMR (CDCl3) δ 8.11 (s, 1 H), 7.67 (s,
1 H), 7.61 (m, 1 H), 7.44 (d, J ) 1.6 Hz, 1 H), 7.25 (m, 1 H), 4.67

4402 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
Morrell et al.
H), 6.93 (s, 1 H), 6.59 (d, J ) Hz, 1 H), 4.56 (m, 2 H), 4.05 (s, 3
H), 3.98 (s, 3 H), 3.60 (m, 2 H), 2.17 (m, 2 H); ESIMS m/z (rel
intensity) 406 (MH+, 100). Anal. (C21H19N5O4) C, H, N.
cm-1; 1H NMR (CDCl3) δ 8.08 (s, 1 H), 7.78-7.80 (m, 2 H), 7.76
(s, 1 H), 7.68 (s, 1 H), 4.60-4.55 (m, 2 H), 4.07 (s, 3 H), 4.00 (s,
3 H), 3.69-3.65 (m, 2 H), 2.14-2.09 (m, 2 H); ESIMS m/z (rel
intensity) 422 (MLi+, 42). Anal. (C22H17N5O4‚0.25H2O) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-2,3-dimethoxy-9-nitro-5,11-di-
oxo-11H-indeno[1,2-c]isoquinoline (103). The general procedure
provided the desired compound as a green solid (0.187 g, 81%)
that was precipitated from Et2O: mp 235-238 °C. IR (film) 2121,
6-(3-Azidopropyl)-5,6-dihydro-2,3-dimethoxy-9-dimethylamino-
5,11-dioxo-11H-indeno[1,2-c]isoquinoline (96). 9-Amino-6-(3-
azidopropyl)-5,6-dihydro-2,3-dimethoxy-5,11-dioxo-11H-indeno-
[1,2-c]isoquinoline (95; 0.141 g, 0.336 mmol) was dissolved in
HOAc (100 mL). Formaldehyde (15 mL, 37% aq) was added,
followed by NaBH3CN (0.106 g, 1.681 mmol) and the reaction
mixture was allowed to stir at room temperature for 16 h. The
reaction mixture was concentrated, dissolved in CHCl3 (200 mL),
washed with satd NaHCO3 (3 × 50 mL) and satd NaCl (50 mL),
and dried over sodium sulfate. The solution was concentrated and
purified by flash column chromatography (SiO2), eluting with
chloroform, to provide a blue-green solid (0.141 g, 94%): mp 218-
220 °C. IR (film) 2097, 1551, 1505, 1394, and 1263 cm-1; 1H NMR
(CDCl3) δ 8.06 (s, 1 H), 7.62 (s, 1 H), 7.42 (d, J ) 8.5 Hz, 1 H),
7.04 (d, J ) 2.6 Hz, 1 H), 6.49 (dd, J ) 8.3 and 2.6 Hz, 1 H), 4.55
(t, J ) 7.1 Hz, 2 H), 4.06 (s, 3 H), 3.98 (s, 3 H), 3.63 (t, J ) 6.2
Hz, 2 H), 3.09 (s, 6 H), 2.16 (m, 2 H); ESIMS m/z (rel intensity)
434 (MH+, 61). Anal. (C23H23N5O4‚0.5H2O) C, H, N.
1
1662, 1605, 1523, 1478, 1432, 1340, and 1276 cm-1; H NMR
(CDCl3) δ 8.41 (dd, J ) 8.3 and 2.3 Hz, 1 H), 8.34 (d, J ) 2.2 Hz,
1 H), 8.13 (s, 1 H), 7.91 (d, J ) 8.3 Hz, 1 H), 7.71 (s, 1 H), 4.65
(t, J ) 8.0 Hz, 2 H), 4.09 (s, 3 H), 4.02 (s, 3 H), 3.71 (t, J ) 6.0
Hz, 2 H), 2.17 (m, 2 H); ESIMS m/z (rel intensity) 436 (MH+,
100). Anal. (C21H17N5O6‚0.5H2O) C, H, N.
9-Amino-6-(3-aminopropyl)-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline Dihydrochloride (104).
The general procedure provided the desired compound as a
black solid (0.100 g, 90%): mp 245-250 °C (dec). IR (KBr) 3432,
2912, 1636, 1552, 1514, 1479, and 1269 cm-1; 1H NMR (DMSO-
d6) δ 7.93 (s, 1 H), 7.90 (bs, 2 H), 7.49 (s, 1 H), 7.40 (d, J ) 8.2
Hz, 1 H), 6.87 (d, J ) 2.2 Hz, 1 H), 6.58 (dd, J ) 8.1 and 2.2 Hz,
1 H), 4.45 (m, 2 H), 3.91 (s, 3 H), 3.85 (s, 3 H), 2.92 (M, 2 H),
2.09 (m, 2 H); ESIMS m/z (rel intensity) 380 (MH+, 65). Anal.
(C21H23Cl2N3O4‚2H2O) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-2,3,9-trimethoxy-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline (97). The general procedure pro-
vided the desired compound as a purple-red solid (0.237 g, 93%):
mp 222-223 °C. IR (film) 2098, 1649, 1482, 1266, and 1024 cm-1
;
6-(3-Aminopropyl)-5,6-dihydro-2,3-dimethoxy-9-dimethy-
lamino-5,11-dioxo-11H-indeno[1,2-c]isoquinoline Dihydrochlo-
ride (105). The general procedure provided the desired compound
as a black solid (0.087 g, 88%): mp 200-203 °C (dec). IR (KBr)
3418, 2939, 2627, 1705, 1651, 1552, 1510, 1480, 1433, 1395, and
1H NMR (CDCl3) δ 8.08 (s, 1 H), 7.65 (s, 1 H), 7.55 (d, J ) 8.4
Hz, 1 H), 7.18 (d, J ) 2.6 Hz, 1 H), 6.85 (dd, J ) 8.4 and 2.6 Hz,
1 H), 4.59 (t, J ) 7.7 Hz, 2 H), 4.06 (s, 3 H), 3.99 (s, 3 H), 3.89
(s, 3 H), 3.65 (t, J ) 6.2 Hz, 2 H), 2.16 (m, 2 H); ESIMS m/z (rel
intensity) 421 (MH+, 31). Anal. (C20H20N4O5) C, H, N.
1
1267 cm-1; H NMR (DMSO-d6) δ 7.99 (bs, 2 H), 7.85 (s, 1 H),
6-(3-Azidopropyl)-9-ethyl-5,6-dihydro-2,3-dimethoxy-5,11-di-
oxo-11H-indeno[1,2-c]isoquinoline (98). The general procedure
provided the desired compound as a red solid that was precipitated
from Et2O-hexanes (0.715 g, 80%): mp 170-172 °C (dec). IR
7.45 (d, J ) 8.4 Hz, 1 H), 7.43 (s, 1 H), 6.86 (d, J ) 2.6 Hz, 1 H),
6.54 (dd, J ) 8.5 and 2.5 Hz, 1 H), 4.46 (t, J ) 6.4 Hz, 2 H), 3.89
(s, 3 H), 3.83 (s, 3 H), 3.03 (s, 6 H), 2.92 (m, 2 H), 2.11 (m, 2 H);
ESIMS m/z (rel intensity) 408 (MH+, 100). Anal. (C23H27Cl2N3O4)
C, H, N.
1
(film) 2098, 1650, 1613, 1554, 1481, 1469, and 1266 cm-1; H
NMR (CDCl3) δ 8.12 (s, 1 H), 7.68 (s, 1 H), 7.55 (d, J ) 7.8 Hz,
1 H), 7.45 (d, J ) 1.5 Hz, 1 H), 7.27 (m, 1 H), 4.62 (m, 2 H), 4.07
(s, 3 H), 4.00 (s, 3 H), 3.64 (t, J ) 6.2 Hz, 2 H), 2.73 (q, J ) 7.5
Hz, 2 H), 2.17 (m, 2 H), 1.30 (t, J ) 7.6 Hz, 3 H); ESIMS m/z (rel
intensity) 419 (MH+, 100). Anal. (C23H22N4O4‚0.75H2O) C, H, N.
6-(3-Azidopropyl)-5,6-dihydro-2,3-dimethoxy-5,11-dioxo-11H-
indeno[1,2-c]isoquinoline (99). The general procedure provided
the desired compound as a red solid (0.420 g, 98%): mp 200-
202 °C (dec). IR (film) 2099, 1652, 1513, 1478, 1429, and 1266
cm-1; 1H NMR (CDCl3) δ 8.14 (s, 1 H), 7.69 (s, 1 H), 7.66-7.59
(m, 2 H), 7.46-7.32 (m, 2 H), 4.64 (m, 2 H), 4.06 (s, 3 H), 4.00
(s, 3 H), 3.66 (t, J ) 6.2 Hz, 2 H), 2.19 (m, 2 H); ESIMS m/z (rel
intensity) 391 (MH+, 100). Anal. (C21H18N4O4) C, H, N.
6-(3-Azidopropyl)-9-fluoro-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline (100). The general procedure
provided the desired compound as a red solid (0.074 g, 62%) that
was precipitated from Et2O-hexanes: mp 214-218 °C (dec). IR
(film) 2097, 1646, 1479, and 1267 cm-1; 1H NMR (CDCl3) δ 8.10
(s, 1 H), 7.68 (s, 1 H), 7.66 (dd, J ) 4.2 and 8.5 Hz, 1 H), 7.32
(dd, J ) 2.6 and 6.8 Hz, 2 H), 7.14 (dt, 2.7 and 8.4 1H), 4.61-
4.56 (m, 2 H), 4.07 (s, 3 H), 4.00 (s, 3 H), 3.67 (t, J ) 6.2, 2 H),
2.18-2.11 (m, 2 H); ESIMS m/z (rel intensity) 409 (MH+, 100).
Anal. (C21H17FN4O4) C, H, N.
6-(3-Azidopropyl)-5,11-dihydro-2,3-dimethoxy-9-methoxycar-
bonyl-5,11-dioxo-11H-indeno[1,2-c]isoquinoline (101). The gen-
eral procedure provided the desired compound as a purple solid
(208 mg, 68%): mp 252-254 °C. IR (film) 2950, 2096, 1717, 1650,
and 1480 cm-1; 1H NMR (CDCl3) δ 8.16-8.13 (m, 1 H), 8.10 (s,
1 H), 8.07 (s, 1 H), 7.72 (d, J ) 7.7 Hz, 1 H), 7.65 (s, 1 H), 4.59
(t, J ) 7.7 Hz, 2 H), 4.06 (s, 3 H), 3.99 (s, 3 H), 3.95 (s, 3 H), 3.65
(t, J ) 6.0 Hz, 2 H), 2.18-2.11 (m, 2 H); EIMS m/z (rel intensity)
448 (MH+, 100). Anal. (C23H20N4O6) C, H, N.
6-(3-Azidopropyl)-9-cyano-2,3-dimethoxy-5,6-dioxo-5,11-di-
hydro-11H-indeno[1,2-c]isoquinoline (102). The general proce-
dure provided the desired compound as a red solid (188 mg,
62%): mp 238-240 °C. IR (film) 2967, 2229, 1695, 1655, 1609
6-(3-Aminopropyl)-5,6-dihydro-2,3,9-trimethoxy-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (106). The general
procedure provided the desired compound as a light purple solid
(0.088 g, 86%): mp 268-270 °C (dec). IR (KBr) 3430, 2942, 1644,
1
1554, 1482, 1266, 1244, and 1019 cm-1; H NMR (DMSO-d6) δ
7.94 (s, 1 H), 7.82 (bs, 2 H), 7.66 (d, J ) 8.4 Hz, 1 H), 7.51 (s, 1
H), 7.07 (d, J ) 2.5 Hz, 1 H), 6.99 (dd, J ) 8.3 and 2.6 Hz, 1 H),
4.54 (t, J ) 6.7 Hz, 2 H), 3.92 (s, 1 H), 3.88 (s, 3 H), 3.87 (s, 3 H),
2.96 (t, J ) 7.7 Hz, 2 H), 2.11 (m, 2 H); ESIMS m/z (rel intensity)
395 (MH+, 56), 378 (MH+ - NH3, 100). Anal. (C22H23ClN2O5)
C, H, N.
6-(3-Aminopropyl)-9-ethyl-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline Hydrochloride (107). The
general procedure provided the desired compound as a red
solid (0.93 g, 73%): mp 275 °C (dec). IR (KBr) 3438, 1636, 1551,
1
1482, 1385, and 1269 cm-1; H NMR (DMSO) δ 7.97 (s, 1 H),
7.86 (bs, 2 H), 7.65 (d, J ) 7.6 Hz, 1 H), 7.53 (s, 1 H), 7.38-7.35
(m, 2 H), 4.55 (t, J ) 6.5 Hz, 2 H), 3.93 (s, 3 H), 3.87 (s, 3 H),
2.96 (m, 2 H), 2.69 (q, J ) 7.6 Hz, 2 H), 2.12 (m, 2 H), 1.23 (t, J
) 7.6 Hz, 3 H); ESIMS m/z (rel intensity) 393 (MH+, 96). Anal.
(C23H25ClN2O4) C, H, N.
6-(3-Aminopropyl)-5,6-dihydro-2,3-dimethoxy-5,11-dioxo-
11H-indeno[1,2-c]isoquinoline Hydrochloride (108). The general
procedure provided the desired compound as an orange solid (0.214
g, 84%): mp 280 °C (dec). IR (KBr) 2974, 1692, 1651, 1556, 1522,
1512, 1478, 1429, 1397, 1265, and 1019 cm-1; 1H NMR (DMSO-
d6) δ 8.02 (s, 1 H), 7.81 (bs, 2 H), 7.77 (d, J ) 7.4 Hz, 1 H),
7.57-7.48 (m, 4 H), 4.59 (t, J ) 6.1 Hz, 2 H), 3.94 (s, 3 H), 3.89
(s, 3 H), 2.97 (t, J ) 6.9 Hz, 2 H), 2.13 (m, 2 H); ESIMS m/z (rel
intensity) 365 (MH+, 88), 348 (MH+ - NH3). Anal. (C21H21-
ClN2O4) C, H, N.
6-(3-Aminopropyl)-9-fluoro-5,6-dihydro-2,3-dimethoxy-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline Hydrochloride (109). The
general procedure provided the desired compound as a purple solid
(0.090 g, 87%): mp 265-269 °C. IR (KBr) 3438, 1636, 1551,
1
1482, 1385, and 1269 cm-1; H NMR (DMSO-d6) δ 7.93 (bs, 2

Indenone Ring of Indenoisoquinoline Top1 Inhibitors
Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18 4403
H), 7.87 (s, 1 H), 7.77 (dd, J ) 4.0 and 13.1 Hz, 1 H), 7.48 (s, 1
H), 7.36-7.29 (m, 2 H), 4.53 (t, J ) 6.9 Hz, 2 H), 3.91 (s, 3 H),
3.86 (s, 3 H), 2.94 (m, 2 H), 2.12-2.07 (m, 2 H); ESIMS m/z (rel
intensity) 383 (MH+, 60). Anal. (C21H20ClFN2O4‚0.75H2O) C, H,
N.
94-112. This material is available free of charge via the Internet
at http://pubs.acs.org.
References
(1) Wall, M. E.; Wani, M. C.; Cook, C. E.; Palmer, K. H.; A. T. M.;
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Antitumor Agents. 18. Synthesis and Biological Activity of Camp-
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(7) Pommier, Y.; Pourquier, P.; Fan, Y.; Strumberg, D. Mechanism of
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Produces Growth Inhibition Equivalent to Continuous Exposure.
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(13) Chrencik, J. E.; Staker, B. L.; Burgin, A. B., Jr.; Pourquier, P.;
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(16) Kohlhagen, G.; Paull, K. D.; Cushman, M.; Nagafuji, P.; Pommier,
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Pommier, Y.; Cushman, M. Synthesis of New Dihydroindeno[1,2-
c]isoquinoline and Indenoisoquinolinium Chloride Topoisomerase I
Inhibitors Having High In Vivo Anticancer Acitivity in the Hollow
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(20) Antony, S.; Jayaraman, M.; Laco, G.; Kohlhagen, G.; Kohn, K. W.;
Cushman, M.; Pommier, Y. Differential Induction of Topoisomerase
I-DNA Cleavage Complexes by the Indenoisoquinoline MJ-III-65
(NSC 706744) and Camptothecin: Base Sequence Analysis and
Activity against Camptothecin-Resistant Topoisomerase I. Cancer
Res. 2003, 63, 7428-7435.
6-(3-Aminopropyl)-5,6-dihydro-2,3-dimethoxy-9-methoxycar-
bonyl-5,11-dioxo-11H-indeno[1,2-c]isoquinoline Hydrochloride
(110). The general procedure provided the desired compound as a
purple solid (0.095 g, 93%): mp 268-270 °C. IR (film) 1719, 1632,
1
1481, 1269, and 1254 cm-1; H NMR (D2O) δ 7.54 (d, J ) 6.6
Hz, 1 H), 7.03 (d, J ) 6.6 Hz, 1 H), 6.71 (s, 1 H), 6.62 (s, 1 H),
6.34 (s, 1 H), 4.12-4.06 (m, 2 H), 3.77 (s, 3 H), 3.47 (s, 3 H),
3.45 (s, 3 H), 3.11 (t, J ) 7.2 Hz, 1 H); ESIMS m/z (rel intensity)
422 (MH+, 100). Anal. (C23H23ClN2O‚1.0H2O) C, H, N.
6-(3-Aminopropyl)-9-cyano-2,3-dimethoxy-5,11-dioxo-5,6-di-
hydro-11H-indeno[1,2-c]isoquinoline Hydrochloride (111). The
general procedure provided the desired compound as a purple solid
(0.066 g, 65%): mp 266-267 °C. IR (film) 1637, 1610, 1511, 1479
1
cm-1; H NMR (DMSO-d6) δ 8.02-7.79 (m, 6 H), 7.48 (s, 1 H),
4.51-4.49 (m, 2 H), 3.91 (s, 3 H), 3.86 (s, 3 H), 2.96-2.93 (m, 2
H), 2.09-2.08 (m, 2 H); ESIMS m/z (rel intensity) 391 (MH+
HCl, 100). Anal. (C22H20ClN3O4‚1.25H2O) C, H, N.
-
6-(3-Aminopropyl)-5,6-dihydro-2,3-dimethoxy-9-nitro-5,11-
dioxo-11H-indeno[1,2-c]isoquinoline Hydrochloride (112). The
general procedure provided the desired compound as a black solid
(0.091 g, 85%): mp 197-200 °C (dec). IR (KBr) 3433, 1643, 1607,
1
1523, 1478, 1342, and 1273 cm-1; H NMR (DMSO-d6) δ 8.39
(dd, J ) 8.5 and 2.2 Hz, 1 H), 8.08 (d, J ) 2.3 Hz, 1 H), 8.01-
7.98 (m, 2 H), 7.82 (bs, 2 H), 7.59 (s, 1 H), 4.59 (m, 2 H), 3.96 (s,
3 H), 3.91 (s, 3 H), 2.99 (m, 2 H), 2.10 (m, 2 H); ESIMS m/z (rel
intensity) 410 (MH+, 100). Anal. (C21H20ClN3O6‚2.5H2O) C, H,
N.
Topoisomerase I-Mediated DNA Cleavage Reactions. Human
recombinant Top1 was purified from Baculovirus as described
previously.45 The 161 bp fragment from pBluescript SK(-) phagemid
DNA (Stratagene, La Jolla, CA) was cleaved with the restriction
endonuclease Pvu II and Hind III (New England Biolabs, Beverly,
MA) in supplied NE buffer 2 (50 µL reactions) for 1 h at 37 °C,
and separated by electrophoresis in a 1% agarose gel made in 1×
TBE buffer. The 161 bp fragment was eluted from the gel slice
using the QIAEX II kit (QIAGEN Inc., Valencia, CA). Ap-
proximately 200 ng of the fragament was 3′-end-labeled at the Hind
III site by fill-in reaction with [alpha-32P]-dGTP and 0.5 mM dATP,
dCTP, and dTTP, in React 2 buffer (50 mM Tris-HCl, pH 8.0, 100
mM MgCl2, 50 mM NaCl) with 0.5 unit of DNA polymerase I
(Klenow fragment). Unincorporated 32P-dGTP was removed using
mini Quick Spin DNA columns (Roche, Indianapolis, IN), and the
eluate containing the 3′-end-labeled 161 bp fragment was collected.
Aliquots (approximately 50 000 dpm/reaction) were incubated with
Top1 at 22 °C for 30 min in the presence of the tested drug.
Reactions were terminated by adding SDS (0.5% final concentra-
tion). The samples (10 µL) were mixed with 30 µL of loading buffer
(80% formamide, 10 mM sodium hydroxide, 1 mM sodium EDTA,
0.1% xylene cyanol, and 0.1% bromophenol blue, pH 8.0). Aliquots
were separated in denaturing gels (16% polyacrylamine, 7 M urea).
Gels were dried and visualized by using a Phosphoimager and
ImageQuant software (Molecular Dynamics, Sunnyvale, CA).
Acknowledgment. This work was made possible by the
National Institutes of Health (NIH) through support of this work
with Research Grant UO1 CA89566, Training Grant ST32
CA09634-12, and by an ACS Medicinal Chemistry Predoctoral
Fellowship sponsored by Pfizer Global Research and Develop-
ment (A.M.). The in vitro testing was conducted through the
Developmental Therapeutics Program, DCTD, NCI under
Contract NO1-CO-56000. This research was supported in part
by the Intramural Research Program of the NIH, National
Cancer Institute, Center for Cancer Research.
Supporting Information Available: Elemental analyses for
compounds 7-11, 13-25, 27-30, 33-73, 75, 77-87, 89-92, and

4404 Journal of Medicinal Chemistry, 2007, Vol. 50, No. 18
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