Synthesis of novel β-carbolines with efficient DNA-binding capacity and potent cytotoxicity

Article abstract of DOI:10.1016/j.bmcl.2010.05.034

A series of water-soluble β-carbolines, bearing a flexible amino side chain, was prepared and evaluated in vitro against a panel of human tumor cell lines. The N⁹-arylated alkyl substituted β-carbolines represented the most interesting cytotoxic activities, and compound 7b was found to be the most potent antitumor agent with IC₅₀ values lower than 10 μM against eight human tumor cell lines. The results confirmed that the N⁹-arylated alkyl substituents of β-carboline nucleus played an important role in the modulation of the cytotoxic potencies. In addition, these compounds were found to exhibit significant DNA-binding affinity.

Full text of DOI:10.1016/j.bmcl.2010.05.034

Bioorganic & Medicinal Chemistry Letters 20 (2010) 3876–3879
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis of novel b-carbolines with efficient DNA-binding capacity and
potent cytotoxicity
a
a
a
a,
b
b
Zhiyong Chen a, Rihui Cao a, , Buxi Shi , Wei Yi , Liang Yu , Huacan Song , Zhenhua Ren , Wenlie Peng
*
*
a School of Chemistry and Chemical Engineering, Sun Yat-sen University, 135 Xin Gang West Road, Guangzhou 510275, PR China
b School of Life Science, Sun Yat-sen University, 135 Xin Gang West Road, Guangzhou 510275, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of water-soluble b-carbolines, bearing a flexible amino side chain, was prepared and evaluated
in vitro against a panel of human tumor cell lines. The N9-arylated alkyl substituted b-carbolines repre-
sented the most interesting cytotoxic activities, and compound 7b was found to be the most potent anti-
Received 12 January 2010
Revised 30 April 2010
Accepted 12 May 2010
Available online 15 May 2010
tumor agent with IC50 values lower than 10 lM against eight human tumor cell lines. The results
confirmed that the N9-arylated alkyl substituents of b-carboline nucleus played an important role in
the modulation of the cytotoxic potencies. In addition, these compounds were found to exhibit significant
DNA-binding affinity.
Keywords:
b-Carboline
Synthesis
Cytotoxic
Intercalating
Tm
Ó 2010 Published by Elsevier Ltd.
The b-carboline alkaloids have been characterized as a class of
potential antitumor agents, which was discovered to function their
antitumor activity through multiple mechanisms, such as interca-
lating into DNA,1 inhibiting topoisomerase I and II,2 CDK,3 MAP-
KAP-K2,4 MK-25 and kinesin Eg5.6 We also observed that the
ability of b-carbolines to act as DNA intercalating agents and topo-
isomerase I inhibitors was related to their potent antitumor activ-
ities,7 and some b-carbolines can induce apoptosis in HepG2 cells
and down-regulate the expression of Bcl-2 gene and upregulate
the expression of death receptor Fas without altering the level of
Bax and P53.8
Recently, our group described the syntheses of numerous b-
carboline derivatives bearing various substituents at position-1,
2, 3, 7 and 9 of b-carboline nucleus and evaluated their antitumor
activities in vitro9–15 and in vivo.9,11 The structure–activity rela-
tionships (SARs) analysis revealed that the introduction of appro-
priate substituents into position-3 and 9 of b-carboline nucleus
facilitated the antitumor activity; and the n-butyl, benzyl or phen-
ylpropyl substituents at position-9 were optimal pharmacophoric
group giving rise to some potent antitumor agents.
vious SARs analysis,16 and the choice of the amino substituents
was limited to diethylaminoethylamino, diethylaminopropylami-
no and diethylaminobutylamino moiety. The focus of this investi-
gation was to probe the optimal structural requirement of these
compounds with regard to antitumor activities, and further devel-
op new antitumor b-carbolines with improved water solubility and
bioavailability.
The synthetic routes of novel b-carbolines 1a, 2a–c, 3a–c, 4a–c,
5a–c, 6a–c and 7a–c were outlined in Scheme 1. 3-Carboxalde-
hyde-b-carbolines 1–7 were prepared from the L-tryptophan via
six steps including the Pictet–Spengler condensation, esterifica-
tion, aromatization, N-alkylation or N-arylation, reduction and
oxidation as previously described.9–11 The reaction of 3-carboxal-
dehyde-b-carbolines 1–7 with the corresponding diamines to form
schiff bases took place readily at room temperature in good yield.
The crude schiff bases were reduced with NaBH3CN in anhydrous
methanol to give the target b-carbolines 1a, 2a–c, 3a–c, 4a–c,
5a–c, 6a–c and 7a–c in 30–65% yields.17 The chemical structures
of all the synthesized novel compounds were characterized by
MS, HRMS, IR, 1H NMR and 13C NMR spectra.
In continuing search for novel and effective antitumor agents,
we designed and synthesized a series of water-soluble b-carbolines
bearing a flexible alkylamino side chain at position-3. The design of
substituents at position-9 of b-carboline ring was based on the pre-
The cytotoxic potential of all newly synthesized b-carboline
derivatives was evaluated in vitro against a panel of human tumor
cell lines according to procedures described in our previous re-
ports.9 As predicted, all compounds showed significantly improved
water solubility (more than 500 mg/ml). The tumor cell line panel
consisted of renal carcinoma (769-P), epidermoid carcinoma of the
nasopharynx (KB), gastric carcinoma (BGC-823), renal carcinoma
(786-0 and OS-RC-2), liver carcinoma (HepG2), melanoma
* Corresponding authors. Tel.: +86 20 84110918; fax: +86 20 84112245.
E-mail addresses: caorihui@mail.sysu.edu.cn (R. Cao), yjhxhc@mail.sysu.edu.cn
(H. Song).
0960-894X/$ - see front matter Ó 2010 Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2010.05.034

Z. Chen et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3876–3879
3877
H2N
N
1)
m
CHO
CH3OH/CH2Cl2 (2:1 V:V)
N
N
N
H
m
N
N
2)
3)
NaBH3CN/CH3OH
4N HCl/CH3CH2OH
N
R9
R9
1 R9=H
2 R9=CH3
1a, 2a-c, 3a-c, 4a-c,
5a-c, 6a-c, 7a-c
3 R9=n-C4H9
4 R9=CH2C6H5
5 R9=CH2C6H4(p-F)
6 R9=CH2C6H4(m-Cl)
)
7 R9= CH2)3C6H5
Scheme 1. Synthesis of b-carboline derivatives.
(A375), colon carcinoma (HT-29), prostate carcinoma (22RV1) and
breast carcinoma (MCF-7). The results were summarized in Table
1.
As shown in Table 1, compound 1a without substituent at posi-
tion-9 and compounds 2a–c bearing a methyl substituent at posi-
tion-9 of b-carboline core only exhibited weak cytotoxic activities
tent cytotoxic activities than the N9-alkylated substituted
compounds 2a–c and 3a–c. The N9-(3-phenyl)propyl substituted
b-carbolines 7a–c represented the most interesting cytotoxic activ-
ities, and compound 7b was found to be the most potent cytotoxic
agent with IC50 values lower than 10 lM against eight human
tumor cell lines. These results suggested that the arylated alkyl
substituents might be a favorable group to exploit in searching
for new antitumor leading compounds. Interestingly, compounds
3b, 4b, 5b, 6b and 7b, bearing a diethylaminopropylamino moiety,
all displayed more potent cytotoxic activity than those compounds
having a diethylaminoethylamino or diethylaminobutylamino sub-
stituents. The results suggested that the length of the alkylamino
side chain moiety also affected their cytotoxic potencies, and three
CH2 units were more favorable.
with IC50 values of more than 50 lM. Whereas, compounds 3a–c,
4a–c, 5a–c, 6a–c and 7a–c, bearing N9-n-butyl, benzyl, 4-fluorob-
enzyl, 3-chlorobenzyl and 3-phenylpropyl substituents, respec-
tively, all exhibited excellent cytotoxic activities against most of
human tumor cell lines with IC50 values of lower than 10 lM. As
a whole, 769-P, KB, BGC-823,786-0, HepG2, HT-29 and 22RV1 cell
lines were more sensitive to such compounds than A375, OS-RC-2
and MCF-7 cell lines.
Of all 9-substituted b-carbolines, the N9-arylated alkyl substi-
tuted compounds 4a–c, 5a–c, 6a–c and 7a–c exhibited more po-
The interaction of compounds 1a and 7b with calf thymus DNA
(CT-DNA) was examined by UV–vis spectroscopy.7 Figure 1 illus-
Table 1
Cytotoxicity of b-carboline derivatives in vitroc (IC50
,
a lM)
N
N
m
H
N
N
R9
Compd
R9
m
769-Pb
KB
BGC-823
786-0
HepG2
A375
HT-29
OS-RC-2
22RV1
MCF-7
1a
2a
2b
2c
3a
3b
3c
4a
4b
4c
5a
5b
5c
6a
6b
6c
7a
7b
7c
H
CH3
CH3
CH3
n-C4H9
n-C4H9
n-C4H9
CH2C6H5
CH2C6H5
CH2C6H5
CH2C6H4(p-F)
CH2C6H4(p-F)
CH2C6H4(p-F)
CH2C6H4(m-Cl)
CH2C6H4(m-Cl)
CH2C6H4(m-Cl)
(CH2)3C6H5
(CH2)3C6H5
(CH2)3C6H5
Cisplatin
Paclitaxel
Adriamycin
1
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
0
1
2
75.3
>100
>100
>100
7.4
2.2
8.0
2.0
1.5
31.0
8.8
8.5
>100
>100
59.7
70.6
13.7
6.2
10.2
8.2
4.9
>100
75.7
>100
>100
20.2
5.9
23.4
9.7
2.8
29.3
10.9
2.6
9.4
37.9
8.1
>100
>100
87.6
>100
37.6
19.5
14.1
14.4
6.4
93.7
>100
96.1
>100
10.1
4.6
8.0
13.1
4.4
3.0
9.1
8.0
2.5
17.7
11.7
10.8
7.2
3.8
3.4
>100
>100
>100
>100
>100
41.1
35.7
33.1
7.8
2.6
27.4
5.2
67.4
>100
>100
>100
>100
35.7
71.7
>100
14.5
55.0
93.6
13.6
31.7
52.3
8.0
>100
>100
>100
>100
25.7
8.8
13.5
15.9
7.3
8.9
9.0
3.6
9.6
58.5
8.4
8.6
8.2
7.7
>100
>100
>100
>100
92.8
64.2
23.4
68.1
32.5
13.4
43.6
31.8
20.2
42.2
17.4
19.8
27.7
13.8
9.1
75.9
44.2
15.2
39.1
17.5
16.2
35.0
13.7
6.5
22.7
14.7
12.6
5.9
8.9
5.8
9.4
0.81
17.2
3.7
8.2
6.2
13.1
6.1
27.0
36.2
10.2
10.1
19.7
9.3
12.2
4.2
2.6
6.4
85.7
0.38
4.2
37.1
33.1
6.5
21.6
7.8
4.2
9.7
4.8
6.1
2.9
5.8
19.3
14.3
8.2
7.3
5.1
10.9
19.2
7.1
47.6
13.0
19.4
11.2
8.3
9.2
4.9
<0.08
3.1
9.8
14.2
7.4
8.8
13.4
1.5
6.7
43.9
13.1
27.7
3.4
<0.08
<1.0
7.6
4.6
0.08
<1.0
4.6
0.08
0.6
16.0
<0.08
<1.0
12.4
1.3
5.1
11.5
<1.0
a
Cytotoxicity as IC50 for each cell line is the concentration of compound, which reduced by 50% the optical density of treated cells with respect to untreated using the MTT
assay.
b
Cell lines include renal carcinoma (769-P), epidermoid carcinoma of the nasopharynx (KB), gastric carcinoma (BGC-823), renal carcinoma (786-0 and OS-RC-2), liver
carcinoma (HepG2), melanoma (A375), colon carcinoma (HT-29), prostate carcinoma (22RV1) and breast carcinoma (MCF-7).
c
The data represent the mean values of three independent determinations.

3878
Z. Chen et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3876–3879
trates the absorption spectra of compounds 1a and 7b in the PE
buffer (1 mM Na2HPO4, 0.1 mM EDTA, pH 7.4) in the presence of
increasing amounts of CT-DNA. In all cases, the binding of the
drugs to CT-DNA results in considerable spectral changes, charac-
terized by a slight bathochromic shift and a marked hypochro-
mism. The results indicated that such compounds possessed an
effective interaction with CT-DNA double helix.
35
30
25
20
15
10
5
In order to confirm the DNA-binding ability of those com-
pounds, we investigated the stabilization of the DNA helix by the
selected b-carbolines 1a, 2b, 3b, 4b and 7b using melting temper-
ature (Tm) studies to evaluate relative affinity for DNA of the se-
lected compounds. The Tm of CT-DNA in the presence and
absence of compounds 1a, 2b, 3b, 4b and 7b were obtained from
melting curves (not shown) and the results of Tm analysis per-
formed with CT-DNA are shown in Figure 2. CT-DNA which melt
at a low temperature (53.5 °C in PE buffer) affords a sensitive
determination of the DNA-binding capacity of the studied mole-
cules. As indicated in Figure 2, compound 1a without substituent
at position-9 stabilized CT-DNA against heat denaturation with
0
1a
2b
3b
4b
7b
Adr
Compound
Figure 2. Variation of the
DTm of the complexes between the tested compounds
and CT-DNA. Melting temperature measurements were performed in PE buffer
(1 mM Na2HPO4, 0.1 mM EDTA) at pH 7.4 with a drug/DNA ratio of 0.2. Adr is
abbreviation of adriamycin (doxorubicin hydrochloride).
D
Tm value ð
D
Tm ¼ Tdmrug—DNA complex ꢀ TmDNA aloneÞ of 12.6 °C. 9-Methyl
(compound 2b) and 9-n-butyl (compound 3b) substituted b-carb-
ation with
DTm value of 24.5 and 20.6 °C, respectively. Whereas
oline congeners markedly stabilized CT-DNA against heat denatur-
9-benzyl (compound 4b) and 9-phenylpropyl (compound 7b)
substituted b-carboline congeners exhibited more weaker effect
on CT-DNA thermal stability with
DTm value of 15.6 and 18.8 °C,
0.5
respectively. The results suggested that (1) these compounds could
significantly stabilize the double helix of CT-DNA; (2) the introduc-
tion of substituent into position-9 of b-carboline nucleus facilitated
the intercalating potency, and short alkyl group was superior to
arylated aklyl substituent. Because the cytotoxic effects of such
compounds on human tumor cell lines were involved in absorp-
tion, metabolism and bioclearance, there were no correlation be-
tween their cytotoxic activities and DNA-binding potencies.
In addition, the effects of CT-DNA on the fluorescence intensity
of compounds 1a and 7b were also determined by the use of fluo-
rescence spectroscopy. In the determinations, a solution of com-
pounds 1a and 7b in PE buffer (1 mM Na2HPO4, 0.1 mM EDTA,
0.4
1a
0.3
0.2
0.1
0.0
pH 7.4) was titrated with 10
ll of solution containing serial
concentrations (0, 40, 80, 120, 160, 200, 240, 280, 320
lM) of
CT-DNA in PE buffer. The changes in fluorescence intensities (fluo-
rescence quenching) of 1a and 7b were recorded on a Shimadzu
RF-5310PC spectrofluorometer at a fluorescence excitation wave-
length of 372 nm. Figure 3 illustrates the typical course of the fluo-
rescence quenching of 1a and 7b, the emission maxima undergone
a slight red shift after binding to increasing concentration of CT-
DNA. The gradual decrease of the fluorescence intensities indicated
a marked quenching upon binding to CT-DNA. These data implied
that these compounds could significantly interact with DNA.
In summary, a series of water-soluble b-carbolines bearing a
flexible amino side chain described in this Letter were proved to
be significantly cytotoxic activities. The N9-arylated alkyl substi-
tuted b-carbolines represented the most interesting cytotoxic
activities. These results confirmed that the N9-arylated alkyl sub-
stituents of b-carboline nucleus played an important role in the
modulation of the cytotoxic potencies. On the basis of the signifi-
250
300
350
Wavelength (nm)
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
7b
cant spectral changes (red-shift and hypochromism),
DTm value
and fluorescence quenching effects, these compounds revealed a
significantly DNA-binding potency. However, different DNA bind-
ing modes can account for the spectral perturbation and it is
impossible to distinguish the mode of interaction of a drug with
DNA from absorption measurements alone and DNA intercalation
and groove binding can lead to similar and important spectral var-
iation. Undoubtedly, further investigation on the DNA binding
mechanisms of this class of b-carbolines is needed.
250
300
350
Wavelength (nm)
Figure 1. Absorption spectra for compounds 1a and 7b in 1 mL PE buffer (1 mM
Na2HPO4, 0.1 mM EDTA, pH 7.4) at different molarities of CT-DNA: top curve (0.0)
and bottom curve (0.2 mM) were recorded in quartz cells (10 mm path length) by a
UV spectrophotometer at room temperature.

Z. Chen et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3876–3879
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6a–c and 7a–c. A mixture of 3-carboxaldehyde-b-carboline (1 mmol), diamine
(1.2 mmol), anhydrous methanol (6 mL) and anhydrous CH2Cl2 (3 mL) was
stirred at room temperature overnight. The solvent was evaporated under
vacuum to give the crude schiff base which was used directly in the next step
without further purification. NaBH3CN (10 mmol) was added to a solution of
the above-mentioned crude schiff base in anhydrous CH3OH (10 mL) at 0 °C.
The mixture was stirred at room temperature for 24 h and then concentrated
under vacuum. The residue was dissolved in CH2Cl2 (50 mL) and washed with
aqueous Na2CO3 (pH 10, 50 mL). The organic layer was separated, dried over
anhydrous Na2SO4, filtered, and concentrated under vacuum. The residue was
purified by flash chromatography on silica gel (CH2Cl2/CH3OH/NH4OH, 95:5:1)
to gain yellow oil. The oil was dissolved in 4 N HCl/ethanol (20 mL) and stirred
at room temperature for 30 min, then removed the solvent under reduced
pressure to obtain yellow solid. The solid were dried in vacuo at 100 °C for
3 days to give the target compounds 1a, 2a–c, 3a–c, 4a–c, 5a–c, 6a–c and 7a–c
400
450
500
/ nm
550
Figure 3. Fluorescence spectra of the selected compounds 1a and 7b upon
incubation with graded concentration of CT-DNA. fixed concentration of
compounds 1a and 7b (10 M) was incubated with increasing concentration of
CT-DNA from 0 to 90 M in PE buffer (1 mM Na2HPO4, 0.1 mM EDTA, pH 7.4).
A
l
in 30–65% yields. Compound 7b: Yield 56%, IR (KBr, cmꢀ1
) m: 2940, 2626, 1633,
1508, 1459, 1378, 1342, 755; 1H NMR (500 MHz, D2O): d 8.75 (s, 1H), 8.46 (s,
1H), 8.08–8.10 (d, J = 10 Hz, 1H), 7.61 (t, J = 9.5 Hz, 1H), 7.27–7.33 (m, 2H),
6.96–6.98 (m, 3H), 6.76–6.78 (m, 2H), 4.72 (s, 2H), 4.19 (t, J = 8.5 Hz, 2H), 3.34
(t, J = 10 Hz, 2H), 3.32–3.28 (m, 6H), 2.43 (t, J = 8.5 Hz, 2H), 2.19–2.27 (m, 2H),
1.98–2.05 (m, 2H), 1.27 (t, J = 9 Hz, 6H); 13C NMR (125 MHz, D2O): d 144.0,
140.7, 135.0, 133.1, 132.4, 131.2, 128.4, 128.1, 126.3, 126.1, 123.3, 122.2, 119.4,
118.9, 111.1, 48.6, 48.2, 47.8, 45.0, 43.4, 32.2, 28.8, 21.0, 8.4; HRMS (EI) calcd
for C28H36N4: 428.2934, found: 428.2928.
l
Acknowledgments
This work was supported by MEGA-Project (2009ZX09103-015)
and Xinjiang Huashidan Pharmaceutical Co. Ltd.
References and notes
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