Design, synthesis and docking study of 5-amino substituted indeno[1,2-c]isoquinolines as novel topoisomerase i inhibitors

Article abstract of DOI:10.1016/j.bmc.2011.01.064

Various 5-amino group-substituted indeno[1,2-c]isoquinolines 7a-f were synthesized based on the previous QSAR study as rigid structures of 3-arylisoquinolines. Amino group-substituted compounds, especially 5-piperazinyl indeno[1,2-c]isoquinoline 7f, displayed potent topoisomerase I inhibitory activity as well as cytotoxicities against five different tumor cell lines. A Surflex-Dock docking model of 7f was also studied.

Full text of DOI:10.1016/j.bmc.2011.01.064

Bioorganic & Medicinal Chemistry 19 (2011) 1924–1929
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry
journal homepage: www.elsevier.com/locate/bmc
Design, synthesis and docking study of 5-amino substituted
indeno[1,2-c]isoquinolines as novel topoisomerase I inhibitors
Daulat Bikram Khadka a, Quynh Manh Le a, Su Hui Yang a, Hue Thi My Van a, Thanh Nguyen Le a,
Suk Hee Cho a, Youngjoo Kwon b, Kyung-Tae Lee c, Eung-Seok Lee d, Won-Jea Cho a,
⇑
a College of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 500-757, Republic of Korea
b College of Pharmacy, Ewha Womans University, Seoul 120-750, Republic of Korea
c College of Pharmacy, Kyung-Hee University, Seoul 130-701, Republic of Korea
d College of Pharmacy, Yeungnam University, Kyongsan 712-749, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history:
Various 5-amino group-substituted indeno[1,2-c]isoquinolines 7a–f were synthesized based on the
Received 30 December 2010
Revised 28 January 2011
Accepted 29 January 2011
Available online 3 February 2011
previous QSAR study as rigid structures of 3-arylisoquinolines. Amino group-substituted compounds,
especially 5-piperazinyl indeno[1,2-c]isoquinoline 7f, displayed potent topoisomerase
I inhibitory
activity as well as cytotoxicities against five different tumor cell lines. A Surflex-Dock docking model
of 7f was also studied.
Ó 2011 Elsevier Ltd. All rights reserved.
Keywords:
Indeno[1,2-c]isoquinolines
Topoisomerase I
Cytotoxicity
Docking study
1. Introduction
synthesized analogs, ethylenediamino-substituted compound 3
exhibited strong cytotoxicities and showed a potent topo I poison.
Camptothecin derivatives, which were approved as anticancer
drugs, have been investigated over the last decade as selective
DNA topoisomerase I (topo I) inhibitors.1–3 However, several limi-
tations,4 such as their chemically unstable structure and rapid ef-
flux from the cell by membrane pumps, prompted us to search
for new topo I inhibitors and we have therefore studied 3-aryliso-
quinolines as topo I inhibitors.5–8
Cushman’s group has also investigated indeno[1,2-c]isoquino-
line derivatives10–13 and identified an indeno[1,2-c]isoquinoline
analog, NSC 314622, as a clinical drug that could serve as a novel
compound to overcome some of the limitations of camptothecin-
like drugs.14
So far, no structural modification of indeno[1,2-c]isoquinoline
at the C-5 position has been reported except our preparation of
compound 3. In this paper, we introduced various amino groups
at the C-5 position because the docking model indicated that the
amino group could hydrogen bond with topo I–DNA ternary com-
plex via the carbonyl group.
In 1999, we synthesized 6,11-dimethyl-6,11-dihydro-5H-inde-
no[1,2-c]isoquinolin-5-one via radical cyclization of a 3-aryliso-
quinoline analog.9 Surprisingly, indenoisoquinoline
1 (Fig. 1)
showed potent cytotoxicities against tumor cell lines (less than
0.001 mg/mL against SK-MEL-2 cells). With this compound as a
seed, we designed and synthesized more than 40 indeno[1,2-c]iso-
quinoline analogs and found some of them were potent topo I poi-
sons and had strong cytotoxicities against various tumor cell lines.8
Through a docking study of these indenoisoquinoline derivatives in
the topo I–DNA ternary complex, we realized the flatness of the
compounds favored their function as DNA intercalators. Moreover,
a carbonyl group at the C-11 position also contributed to strong
interaction between the ligand and the topo I–DNA complex
through hydrogen bonding with Arg 364 of topo I.7 Among the
2. Chemistry
3-Chloroindenoisoquinoline 68 was treated with various amines
such as N-methylpiperazine, morpholine, N-ethylpiperazine,
N-methyldiazepane, n-butylamine and piperazine in the presence
of K2CO3 in DMF to afford the corresponding amines 7 in good
yields. Reaction of compounds 7a–d with BH3 gave the correspond-
ing reduced amines 8a–d in moderate yields. Compounds 7a–c
were reacted with NaBH4 in MeOH to give the alcohols 10a–c.
Alcohol 10b was acetylated with Ac2O and 4-dimethylaminopyri-
dine in methylene chloride to afford the acetylated 11 in 87% yield.
Compound 7a was treated with MeMgBr or n-hexylMgBr to afford
⇑
Corresponding author. Tel.: +82 62 530 2933; fax: +82 62 530 2911.
E-mail address: wjcho@jnu.ac.kr (W.-J. Cho).
0968-0896/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmc.2011.01.064

D. B. Khadka et al. / Bioorg. Med. Chem. 19 (2011) 1924–1929
1925
O
R'
O
O
R'
MeO
R
R
NH
NH
N
MeO
Me
O
O
O
Indeno[1,2-c]isoquinolinone (2)
3-Arylisoquinoline (1)
NSC 314622
O
11
X
1
4
N
5
N
HN
HN
R
NH2
4
3
Figure 1. Structures of NSC 314622 and indeno[1,2-c]isoquinolines.
O
O
O
POCl3
amine
BH3
THF
K2CO3, DMF
N
NH
N
N
Cl
6
O
R
R
8
5
7
R1MgBr
NaBH4, MeOH
AcO
R1
HO
HO
Ac2O, DMAP
CH2Cl2
N
N
N
N
N
R
O
9a R1 = Me
9b R1 = n-Hexyl
10
11
N
Me
R=
HN
N
N
N
N
N
O
N
N
H
N
N
Me
Me
Et
f
a
b
c
d
e
Scheme 1. The synthesis of indeno[1,2-c]isoquinolines.
the corresponding alcohols 9a or 9b in 76% and 65% yield, respec-
tively, as shown in Scheme 1.
(lung), Col2 (colon), SNU-638 (stomach), HT1080 (fibro sarcoma)
cell lines and MTT assay for HL-60 (myeloid leukemic) cells.15
To determine topo I catalytic activity, assays were carried out
with supercoiled pBR322 DNA as the substrate according to proto-
col. 500 ng of supercoiled pBR322 DNA was incubated with 1 unit
topo I in the absence or presence of camptothecin or the synthe-
sized compounds for 30 min at 37 °C. The reaction mixtures were
analyzed on 1% agarose gel with ethidium bromide staining.16
Semi-quantitative comparisons of the inhibitory activities are
shown in Table 1. The IC50 cytotoxicity values obtained with cell
3. Results and discussion
3.1. Biological evaluation
The in vitro cytotoxicity experiments with the synthesized
compounds were performed by sulforhodamine B (SRB) for A549

1926
D. B. Khadka et al. / Bioorg. Med. Chem. 19 (2011) 1924–1929
lines and the relative potencies of the compounds are expressed
semi-quantitatively as follows: +, weak activity; +++, lower activity
biological activities. In case of morpholine substituted compounds,
7b and 10b showed poor cytotoxicities. On the other hand, 9b
than 0.1
0.1 M camptothecin.
As expected, indenoisoquinolines 7a, 7c, 7d and 7f exhibited
more potent topo I inhibitory activities than 8a–e because the
C11 carbonyl group could have hydrogen bond with Arg 364 of
topo I as shown in Figure 2. This result is consistent with our pre-
vious reports.8 Overall, the C5 amino groups did not influence the
l
M camptothecin; ++++, similar or greater activity than
exhibited high cytotoxicity (2.57–12.36 lM) as well as strong topo
l
I poison as shown in Table 1. N-Methypiperazine substituted com-
pounds such as 7a, 8a and 9a did not show any correlation be-
tween C5 amino group and biological activities. However, topo I
potencies were highly affected by C11 carbonyl group of the com-
pounds. Compound 7d showed cytotoxicities ranging from 0.27 to
1.36
duced carbonyl group also displayed potent cytotoxicities. In par-
ticular, compound 8d exhibited 0.25–8.24 M potencies against
lM against the tumor cells and the compounds 8a–e with re-
l
five different cell lines. This discrepancy indicates that topo I
may not be the sole biological target for these compounds. Similar
results were found in other reports and were explained by the
ability of the compounds to penetrate the cell membrane and reach
the target, as well as by distribution differences within the cell. The
most potent topo I inhibitor, compound 7f, also exhibited relatively
Table 1
IC50 cytotoxicity (
lM and topo I activity of the compounds
a
No. Compound A549
Col2
7.77
96.88
6.45
SNU-638 HL-60
HT1080 Topo I
1
2
3
4
5
6
7
8
7a
7b
7c
7d
7e
7f
8a
8b
8c
8d
8e
9a
8.19
>100
7.10
7.98
>100
5.85
6.35
>100
4.21
5.36
69.25
1.23
0.54
48.24
2.01
3.85
1.24
18.98
0.25
4.39
22.22
2.57
4.87
>100
8.66
58.32
9.60
0.080
4.3
+++
À
strong cytotoxicities, ranging from 2.01 to 8.55 lM against tumor
+++
+++
À
1.05
0.27
1.36
1.28
cells. 11-Hydroxy analogs 10a–b exhibited weak or moderate
cytotoxicities against the tumor cell lines and displayed poor topo
I poison. These results were not unexpected due to the fact that the
hydroxyl group does not work well as a hydrogen bonding donor
with Arg 364 of topo I. On the other hand, compound 9b showed
>100
8.52
>100
7.99
>100
8.25
>100
4.68
+++++
À
11.36
5.69
10.12
4.42
19.75
2.58
5.87
8.65
À
9
8.19
7.74
3.25
9.98
À
10
11
12
13
14
15
16
17
18
19
20
5.46
2.13
8.24
3.33
À
relatively strong (2.57–12.36
activity. 11-Acetoxy compound 11 exhibited weak cytotoxicity
(6.99–58.32 M) or even worse activity than 9b. Furthermore, this
lM) cytotoxicities and topo I
27.69
92.49
7.21
18.12
93.33
20.94
8.30
0.85
0.069
1.9
75.21
57.98
6.24
28.26
>100
19.25
7.87
1.43
0.045
2.3
22.21
58.24
12.36
9.01
>100
18.88
6.99
1.68
0.098
2.2
19.57
79.87
8.55
13.36
99.25
29.37
15.88
10.40
0.018
5.8
À
À
l
9b
+++
À
compound did not have any topo I–DNA inhibitory activity.
10a
10b
10c
11
À
À
3.2. Docking study
À
3
+++++
+++
ntb
In order to determine the binding mode of action of the most
potent topo I inhibitor 7f, we performed a docking study. The
resulting docking model revealed a different binding mode than
the former indeno[1,2-c]isoquinoline model. In this model, the iso-
quinoline ring intercalated between the À1 and +1 bases, parallel
to the plane of the base pairs, and the carbonyl group of C-11
CPT
Ellipticine
a
Activity is expressed semi-quantitatively as follows: À very weak activity, +
weak activity, +++similar activity to camptothecin, +++++ stronger activity than
camptothecin.
b
nt means not tested.
Figure 2. Topo I inhibitory activities of the compounds. Lane P: pBR322; lane T: pBR322 + topo I; lane C: pBR322 + topo I + camptothecin (0.01 mg/mL); lane 55–76 (prepared
compound number, 0.1 mg/mL): 55 (11), 56 (7d), 57 (7c), 58 (7f), 59 (7e), 60 (7d), 61 (7a), 62 (9b), 63 (9a), 64 (10a), 65 (8e), 69 (8a), 70 (10b), 71 (8b), 72 (8d), 73 (8c), 75
(10a), 76 (10c).
Figure 3. Space filling (left) and top view (right) models of compound 7f.

D. B. Khadka et al. / Bioorg. Med. Chem. 19 (2011) 1924–1929
1927
Figure 4. Wall-eyed viewing docked model of compound 7f.
position had a H-bond to Asp 533, which is considered an impor-
tant amino acid that interacts with the ligand in the DNA-topo I ac-
tive site. In this model, the indenoisoquinoline ring functioned as a
DNA intercalator as a blocker of the rejoining process of the phos-
phoester. In the previous study, the binding geometry of campto-
thecin in the DNA–topo I complex was studied with an ab initio
Science Institute and were reported in ppm, downfield from the
peak of the internal standard, tetramethylsilane. The data are re-
ported as follows: chemical shift, number of protons, multiplicity
(s: singlet, d: doublet, t: triplet, q: quartet, m: multiplet, b: broad-
ened). IR spectra were recorded on JASCO-FT IR spectrometer using
CHCl3 or KBr pellets. Mass spectra were obtained on JEOL JNS-DX
303 using the electron-impact (EI) method. Column chromatogra-
phy was performed on Merck silica gel 60 (70–230 mesh). TLC was
performed using plates coated with silica gel 60 F254 that were
purchased from Merck.
quantum mechanics calculation and indicated that the p–p stack-
ing interactions contributed much more than the hydrogen bond-
ing effect of the ligand.17 From this molecular docking study, the
importance of the DNA intercalation of 7f and the hydrogen bond
was clarified through the molecular docking study. Space filling
model of 7f and the stereoview picture are shown in Figures 3
and 4.
5.1.1. 5-(4-Methylpiperazin-1-yl)indeno[1,2-c]isoquinolin-11-
one (7a)
The mixture of compound 6 (100 mg, 0.38 mmol), N-methylpi-
perazine (57 mg, 0.56 mmol) and K2CO3 (156 mg, 1.13 mmol) in
10 mL of DMF was refluxed for 2 h. After the reaction was com-
pleted, the reaction mixture was diluted with 40 mL of water,
and the aqueous phase was extracted with diethyl ether. The or-
ganic layer was washed with water and brine and dried over anhy-
drous Na2SO4. Evaporation of the solvent in vacuo gave the residue
which was purified by column chromatography on silica gel with
CH2Cl2/methanol (10:1) to afford the desired amine 7a (80 mg,
64%) as a yellow solid. mp: 176–177 °C. IR cmÀ1: 1678. 1H NMR
(CDCl3): d 8.68–8.65 (m, 1H), 7.86 (d, J = 8.4 Hz, 1H), 7.62–7.28
(m, 6H), 3.83 (t, J = 4.8 Hz, 4H), 2.66 (t, J = 4.9 Hz, 4H), 2.40 (s,
3H). EIMS: m/z 329 (M+, 100).
4. Conclusion
In conclusion, based on the previous QSAR investigation of the
indeno[1,2-c]isoquinolines, we designed and synthesized various
amino group-substituted analogs at the C-5 position. The newly
synthesized indeno[1,2-c]isoquinolines were also structurally
modified. As expected, molecules containing the 11-carbonyl
group exhibited potent topo I inhibitory activities with relatively
strong cytotoxicities against five different tumor cell lines. On
the other hand, 11-hydrogenated compounds showed no topo I
poison even though they exhibited strong cytotoxicities. Alkyl
group introduction at the C11 position did not enhance the biolog-
ical activities, except for the compound containing the n-hexyl
group, which showed moderate topo I activity. For an explanation
of the topo I activity of 7f, molecular docking studies were per-
formed with the Surflex-Dock program to provide the reasonable
binding mode of the compound into the binding sites of the
DNA–topo I complex.
5.1.2. 5-Morpholin-4-yl-indeno[1,2-c]isoquinolin-11-one (7b)
The procedure described for the preparation of 7a gave 7b (92%)
as a yellow solid. mp: 204–206 °C. 1H NMR (CDCl3): d 8.67–8.64
(m, 1H), 7.90–7.30 (m, 7H), 3.95 (t, J = 4.6 Hz, 4H), 3.80 (t,
J = 4.7 Hz, 4H). EIMS: m/z 316 (M+, 86).
In further studies of the other constrained structures of 3-aryl-
isoquinolines, diverse structural modifications such as 4-arylation
or heterocyclization of 3-arylisoquinolines are currently being
carried out and these will be reported in due course.
5.1.3. 5-(4-Ethylpiperazin-1-yl)indeno[1,2-c]isoquinolin-11-one
(7c)
The procedure described for the synthesis of 7a gave 7c (93%) as
a yellow solid. mp: 134–135 °C. 1H NMR (CDCl3): d 8.67–8.64 (m,
1H), 7.93–7.90 (m, 1H), 7.66–7.32 (m, 6H), 3.88 (t, J = 4.9 Hz, 4H),
2.71 (t, J = 4.9 Hz, 4H), 2.54 (m, 2H), 1.16 (t, J = 7.2 Hz, 3H). EIMS:
m/z 343 (M+, 54).
5. Experimental section
5.1. Chemistry
5.1.4. 5-(4-Methyl[1,4]diazepan-1-yl)indeno[1,2-c]isoquinolin-
11-one (7d)
Melting points were determined by the capillary method on
Electrothermal IA9200 digital melting point apparatus and were
uncorrected. Nuclear magnetic resonance (NMR) data for 1H NMR
were collected on Varian 300 FT spectrometer of Korea Basic
The procedure described for the preparation of 7a provided 7d
(83%) as a yellow solid. mp: 107–108 °C.1H NMR (CDCl3): d 8.66–

1928
D. B. Khadka et al. / Bioorg. Med. Chem. 19 (2011) 1924–1929
8.63 (m, 1H), 7.96–7.93 (m, 1H), 7.60–7.30 (m, 6H), 4.17–4.14 (m,
2H), 4.11–4.07 (m, 2H), 2.94–2.91 (m, 4H), 2.67–2.64 (m, 2H), 2.41
(s, 3H). EIMS: m/z 343 (M+, 100).
5.1.12. 11-Methyl-5-(4-methylpiperazin-1-yl)-11H-indeno[1,2-
c]isoquinolin-11-ol (9a)
To a stirred solution of 7a (100 mg, 0.27 mmol) in THF (10 mL),
1 M CH3MgBr in n-butyl ether (0.6 mL, 0.54 mmol) was added at
0 °C and the reaction mixture was continuously stirred while the
temperature increased to room temperature. After 12 h, the reac-
tion was quenched with water and the mixture was filtered
through celite. The filtrate was washed with CH2Cl2 and brine,
dried over anhydrous Na2SO4 and concentrated to dryness. The res-
idue was purified by column chromatography on silica gel with
hexane/ethyl acetate (2:1) to yield 9a (82 mg, 79%) as a yellow so-
lid. mp: 201–202 °C. IR cmÀ1: 3421. 1H NMR (CDCl3): d 8.28 (d,
J = 8.0 Hz, 1H), 7.96–7.35 (m, 7H), 3.13 (m, 4H), 2.46 (m, 4H),
2.21 (s, 3H), 1.87 (s, 3H). EIMS: m/z 345 (M+, 85).
5.1.5. 5-Butylaminoindeno[1,2-c]isoquinolin-11-one (7e)
The procedure described for the preparation of 7a afforded 7e
(98%) as a yellow solid. mp: 215–218 °C. 1H NMR (CDCl3): d
8.72–8.69 (m, 1H), 7.68–7.26 (m, 7H), 5.99 (s, 1H), 3.88–3.82 (m,
2H), 1.83–1.73 (m, 2H), 1.58–1.48 (m, 2H), 1.03 (t, J = 7.3 Hz, 3H).
EIMS: m/z 302 (M+, 55).
5.1.6. 5-Piperazin-1-ylindeno[1,2-c]isoquinolin-11-one (7f)
The procedure described for the preparation of 7a gave 7f (73%)
as a yellow solid. mp: 188–189 °C. 1H NMR (CDCl3): d 8.73–8.70
(m, 1H), 7.89–7.28 (m, 7H), 3.80 (t, J = 4.9 Hz, 4H), 3.14 (t,
J = 4.9 Hz, 4H), 1.98 (s, 1H). EIMS: m/z 315 (M+, 66).
5.1.13. 11-Hexyl-5-(4-methylpiperazin-1-yl)-11H-indeno[1,2-
c]isoquinolin-11-ol (9b)
5.1.7. 5-(4-Methylpiperazin-1-yl)-11H-indeno[1,2-c]isoquinolin
(8a)
The procedure described for the preparation of 9a gave 9b (70%)
as a yellow solid. mp: 83–84 °C. 1H NMR (CDCl3): d 8.27 (d,
J = 8.1 Hz, 1H), 8.00–7.27 (m, 7H), 4.50 (s, 1H), 3.22 (s, 4H), 2.53
(s, 4H), 2.48–2.30 (m, 2H), 2.24 (s, 3H), 1.08–0.96 (m, 6H), 0.71
(t, J = 6.9 Hz, 3H), 0.66–0.61 (m, 2H). EIMS: m/z 415 (M+, 100).
A reaction mixture of compound 7a (475 mg, 1.79 mmol) and
1 M borane–tetrahydrofuran complex (4 mL) in dry THF (10 mL)
was refluxed for 6 h. After cooling to room temperature, the
mixture was concentrated in vacuo and the residue was diluted
with EtOAc (100 mL). Glacial acetic acid was added dropwise to
the reaction mixture until pH 5. The organic layer was washed
with saturated sodium bicarbonate (100 mL) and brine, dried
over Na2SO4 and concentrated to give the residue which was
purified by short silica gel column with CH2Cl2/methanol
(15:1) to yield the dehydrogenated compound 8a (315 mg,
56%) as a yellow solid. mp: 178–180 °C. 1H NMR (CDCl3): d
8.01 (d, J = 8.4 Hz, 1H), 8.02–7.99 (m, 1H), 7.91 (d, J = 8.3 Hz,
1H), 7.68–7.34 (m, 5H), 4.03 (s, 2H), 3.86–3.83 (m, 2H), 3.68–
3.65 (m, 2H), 3.36–3.33 (m, 2H), 3.12–3.05 (m, 2H), 2.77 (s,
3H). EIMS: m/z 315 (M+, 92).
5.1.14.5-(4-Methylpiperazin-1-yl)-11H-indeno[1,2-c]isoquinolin-
11-ol (10a)
To a stirred solution of 7a (100 mg, 0.27 mmol) in 10 mL MeOH
was added NaBH4 (31 mg, 0.82 mmol) at 0 °C and the reaction mix-
ture was stirred at room temperature for 4 h. The reaction was
quenched with water and extracted with CH2Cl2. The CH2Cl2 layer
was washed with brine, dried over anhydrous Na2SO4 and concen-
trated to dryness. The residue was purified by column chromatog-
raphy on silica gel with hexane/ethyl acetate (2:1) to yield the
alcohol 10a (68 mg, 77%) as a white solid. mp: 195–197 °C. 1H NMR
(CDCl3): d 8.21–8.18 (m, 1H), 7.91 (t, J = 8.2 Hz, 2H), 7.68–7.60 (m,
2H), 7.45–7.27 (m, 3H), 5.75 (s, 1H), 3.16 (m, 4H), 2.53–2.38 (m,
4H), 2.31 (s, 3H). EIMS: m/z 331 (M+, 78).
5.1.8. 5-Morpholin-4-yl-11H-indeno[1,2-c]isoquinolin (8b)
The procedure described for the preparation of 8a yielded 8b
(91%) as a yellow solid. mp: 159–160 °C. 1H NMR (CDCl3): d
8.17–8.14 (m, 1H), 8.03–8.00 (m, 1H), 7.87–7.84 (m, 1H),
7.64–7.31 (m, 5H), 4.04–3.99 (m, 4H), 3.97 (s, 2H), 3.52–3.48 (m,
4H). EIMS: m/z 302 (M+, 100).
5.1.15. 5-Morpholin-4-yl-11H-indeno[1,2-c]isoquinolin-11-ol
(10b)
The procedure described for the preparation of 10a afforded
10b (78%) as a white solid. mp: 149–151 °C. IR cmÀ1: 3382.
1H NMR (CDCl3): d 8.23–7.34 (m, 8H), 5.82 (d, J = 5.8 Hz, 1H),
3.95 (t, J = 4.7 Hz, 4H), 3.50–3.45 (m, 4H). EIMS: m/z 318 (M+, 67).
5.1.9. 5-(4-Ethylpiperazin-1-yl)-11H-indeno[1,2-c]isoquinolin
(8c)
The procedure described for the preparation of 8a gave 8c (69%)
as a yellow solid. mp: 176–179 °C. 1H NMR (CDCl3): d 8.11–8.08
(m, 1H), 8.02–7.99 (m, 1H), 7.92–7.89 (m, 1H), 7.68–7.34 (m,
5H), 4.02 (s, 2H), 3.91–3.87 (m, 2H), 3.69–3.67 (m, 2H), 3.29–
3.27 (m, 2H), 3.14–3.09 (m, 2H), 3.07–3.00 (m, 2H), 1.36 (t,
J = 7.3 Hz, 3H). EIMS: m/z 329 (M+, 87).
5.1.16. 5-(4-Ethylpiperazin-1-yl)-11H-indeno[1,2-c]isoquinolin-
11-ol (10c)
The procedure described for the preparation of 9a gave 9c (87%)
as a white solid. mp: 203–207 °C. 1H NMR (CDCl3): d 8.22–8.19 (m,
1H), 7.99–7.35 (m, 7H), 5.79 (s, 1H), 3.32 (m, 2H), 3.21 (m, 2H),
2.68–2.62 (m, 4H), 2.52–2.45 (m, 2H), 1.59 (t, J = 7.2 Hz, 3H). EIMS:
m/z 345 (M+, 100).
5.1.10. 5-(4-Methyl-[1,4]diazepan-1-yl)-11H-indeno[1,2-
c]isoquinolin (8d)
5.1.17. Acetic acid 5-morpholin-4-yl-11H-indeno[1,2-
The procedure described for the preparation of 8a gave 8d (82%)
as a yellow solid. mp: 147–149 °C. 1H NMR (CDCl3): d 8.07 (d,
J = 8.5 Hz, 1H), 7.99–7.96 (m, 1H), 7.90–7.87 (m, 1H), 7.66–7.35
(m, 5H), 4.00 (s, 2H), 3.99–3.92 (m, 2H), 3.81–3.76 (m, 2H),
3.50–3.35 (m, 3H), 3.15–3.07 (m, 1H), 3.12 (s, 3H), 2.34–2.32 (m,
1H), 2.21–2.13 (m, 1H). EIMS: m/z 329 (M+, 54).
c]isoquinolin-11-yl ester (11)
To a solution of 10b (331 mg, 1.04 mmol) in 10 mL CH2Cl2, pyr-
idine (107 mg, 1.35 mmol) and 4-dimethylaminopyridine (40 mg)
was added anhydride acetic acid (127 mg, 1.25 mmol) at 0 °C un-
der nitrogen. The reaction mixture was stirred overnight and then
poured into water followed by extraction with ether and the ether
layer was washed with brine, dried over Na2SO4 and concentrated
in vacuo. The residue was purified by column chromatography
with n-hexane/ethyl acetate (6:1) on silica gel to afford 11
(278 mg, 74%) as a yellow solid. mp: 164–166 °C. IR cmÀ1: 1726.
1H NMR (CDCl3): d 8.14 (d, J = 8.4 Hz, 1H), 7.90 (d, J = 7.4 Hz, 1H),
7.78–7.75 (m, 1H), 7.68–7.33 (m, 5H), 7.14 (s, 1H), 4.02–3.99 (m,
4H), 3.58–3.55 (m, 4H), 2.23 (s, 3H). EIMS: m/z 360 (M+, 57).
5.1.11. n-Butyl(11H-indeno[1,2-c]isoquinolin-5-yl)amine(8e)
The procedure described for the preparation of 8a gave 8e (55%)
as a yellow solid. 1H NMR (CDCl3): d 8.00 (d, J = 7.4 Hz, 1H),
7.81–7.77 (m, 2H), 7.62–7.55 (m, 2H), 7.42–7.31 (m, 3H), 5.27 (s,
1H), 3.93 (s, 2H), 3.78 (q, J = 6.5 Hz, 2H), 1.77 (m, 2H), 1.53 (m,
2H), 1.03 (t, J = 7.3 Hz, 3H). EIMS: m/z 288 (M+, 100).

D. B. Khadka et al. / Bioorg. Med. Chem. 19 (2011) 1924–1929
1929
5.2. Molecular modeling
References and notes
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The docking study was performed using Surflex-Dock in Sybyl
version 8.1.1 by Tripos Associates, operating under Red Hat Li-
nux 4.0 with an IBM computer (Intel Pentium 4, 2.8 GHz CPU,
1 GB memory). The structure of compound 7f was sketched in
the Sybyl package and minimized using the conjugate gradient
method until the gradient was 0.001 kcal/mol with the Tripos
force field with Gasteiger-Huckel charge. The 1SC7 (PDB code)
structure in Protein Data Bank was taken and the structure
was refined as follows. After the phosphoester bond of G12 in
1SC7 was produced, the SH of G11 on the scissile strand was
modified to OH. With this DNA–topo I complex, Surflex-Dock
was carried out with 7f. After the protomol generation, which
was positioned to scissile bond cavity between the À1 and +1
bases, Surflex-Dock was operated to afford 10 docked conform-
ers. The conformer with the best total score (7.89) was chosen
for speculation regarding the detailed binding patterns in the
cavity.
Acknowledgment
This work was supported by Korea Research Foundation grant
(KRF-2009-0071379).
16. Cho, W. J.; Min, S. Y.; Le, T. N.; Kim, T. S. Bioorg. Med. Chem. Lett. 2003, 13, 4451.
17. Xiao, X.; Cushman, M. J. Am. Chem. Soc. 2005, 127, 9960.