Design, synthesis, molecular docking and biological evaluation of new dithiocarbamates substituted benzimidazole and chalcones as possible chemotherapeutic agents

Article abstract of DOI:10.1016/j.bmcl.2012.03.018

A series of novel dithiocarbamates with benzimidazole and chalcone scaffold have been designed synthesised and evaluated for their antimitotic activity. Compounds 4c and 9d display the most promising antimitotic activity with IC ₅₀ of 1.66 μM and 1.52 μM respectively.

Full text of DOI:10.1016/j.bmcl.2012.03.018

Bioorganic & Medicinal Chemistry Letters 22 (2012) 3274–3277
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design, synthesis, molecular docking and biological evaluation of new
dithiocarbamates substituted benzimidazole and chalcones as possible
chemotherapeutic agents
Keerthana Bacharaju a, Swathi Reddy Jambula a, Sreekanth Sivan b, Saritha JyostnaTangeda a,
Vijjulatha Manga b,
⇑
a Sarojini Naidu Vanitha Pharmacy Maha Vidyalaya, Osmania University, Hyderabad 500001, Andhra Pradesh, India
b Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, Nizam College, Osmania University, Hyderabad 500001, Andhra Pradesh, India
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of novel dithiocarbamates with benzimidazole and chalcone scaffold have been designed syn-
Received 29 December 2011
Revised 3 March 2012
Accepted 6 March 2012
Available online 11 March 2012
thesised and evaluated for their antimitotic activity. Compounds 4c and 9d display the most promising
antimitotic activity with IC50 of 1.66
l
M and 1.52
l
M respectively.
Ó 2012 Elsevier Ltd. All rights reserved.
Keywords:
Benzimidazole
Chalcone
Dithiocarbamate
Antimitotic
Molecular docking
Benzimidazoles are one of the most extensively studied classes
of heterocyclic compounds known for their wide range of biologi-
cal activities.1,2 Extensive studies have been carried out on benzim-
idazoles and their chemotherapeutic activity.3,4 On the other side,
dithiocarbamates are a common class of organic molecules, that
form mono and bidentate coordination with transition metals.
Transition metal complexes of dithiocarbamate present a wide
range of biological activities5 and are recently applied in the treat-
ment of cancer.6,7 Since brassinin (Fig. 1), a phytoalexin first iso-
lated from cabbage had cancer preventive activity, structural
modification on this compound led to the synthesis of isobrassinin
(Fig. 1)8 and a series of dithiocarbamates, some of these were found
to have antitumor activity.9
Beside the compounds mentioned above chalcones are the bio-
genetic precursors of all known flavonoids and isoflavanoids and
are abundant in edible plants.10 They exhibit a broad spectrum of
pharmacological activities such as anticancer,11 antiinflamma-
tary,12 antimalarial,13 antifungal,14 antilipidemic,15 antiviral,16
antileshmanial,17 antiulcer18 and antioxidant activities.19 Recently
Yong Qian and coworkers reported a series of chalcone derivatives
(Fig. 1), with dithiocarbamate moieties which possessed potential
antiproliferative and anti-tubulin properties.20 Microtubules are
among the most important molecular targets for cancer chemo-
therapeutic agents. These small molecules bind to the tubulin,
interfering with the polymerisation or depolymerisation of micro-
tubules and there by inducing cell cycle arrest, resulting in cell
death or apoptosis.
Although many new chalcone derivatives have been synthesized
as potential antitumor agents, there is very scarce recent literature
data on antitumor potentials of dithiocarbamate-substituted
chalcones. This combination should provide favourable structural
properties of both dithiocarbamate and chalcone moieties.
It improves their binding affinities with the protein via
hydrogen bonding, hydrophobic contact and to further explore
their chemotherapeutic properties. New molecules were designed
in which indole moiety, is isosterically replaced with benzimid-
azole. A series of novel derivatives containing both benzimidazole
nucleus and dithiocarbamate as side chain possessing different
substituents on nitrogen linked through methylene group at
second position of benzimidazole were synthesized.
Route applied for the synthesis of a various dithiocarbamate
analogues is summarized in Schemes 1 and 2. Key intermediate
2-chloromethylbenzimidazole (2) (Scheme 1) was prepared by
the addition of chloroaceticacid to o-phenylenediamine in 4 N
hydrochloric acid as reported earlier.21 Dithiocarbamates were
synthesized from various amines and carbon disulfide, using
dimethylformamide as solvent and anhydrous potassium
phosphate as base, followed by treatment with 2-chloromethyl-
benzimidazoles.22 Chalconedithiocarbamates were obtained by
⇑
Corresponding author. Tel.: +91 040 23234321; fax: +91 040 23240806.
E-mail address: vijjulathamanga@gmail.com (V. Manga).
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2012.03.018

K. Bacharaju et al. / Bioorg. Med. Chem. Lett. 22 (2012) 3274–3277
3275
Among the series compound 4c (piperidine) showed highest po-
tency with IC50 of 1.66 M. Compounds 4a (pyrrolidine) and 4b
(morpholine) were found to be equipotent with IC50 1.8 M and
1.89 M respectively. In case of the compounds with alkyl substi-
tuted aminodithiocarbamates, compound with diethyl (4e) substi-
tution showed greater potency than the corresponding dimethyl
H
N
l
SCH3
S
l
S
N
N
l
H
H
N
H
SR
Brassinin
Isobrassinin
amine (4d) with IC50 values 1.86 and 2.12 lM respectively. How-
ever compound 4f and 4g with propyl amine and butyl amine
exhibited similar activity like 4d as evidenced from the IC50 values
2.29 and 2.11 lM respectively. Overall results indicate that the
cyclic amines have higher activity when compared to aliphatic
amines.
O
S
Cl
H3C
H3C
N
S
Antimitotic activity of 9a–9f series, compound 9d (2-amino
benzothiazole side chain) showed highest potency of 1.52
Compound 9a (pyrrolidine) and 9c (morpholine) were equipotent
with IC50 1.67 and 1.65 M respectively. On the contrary com-
pound 9b (piperidine) showed slight decrease in potency
(1.85 M). In case of the compounds with dialkyl amine side chain
the compound 9f (diethyl amine) showed greater potency than the
corresponding compound 9e (dimethyl amine) with IC50 1.84
and 2.43 M, respectively.
lM.
3-(4-chlorophenyl)-3-oxo-1-phenylpropyl diethylcarbamodithioate
l
Figure 1. Structure of known chalcone derivatives.
l
one pot reaction of various amines, carbondisulfide and intermedi-
ate chalcone23 (Scheme 2).
lM
l
Synthesized compounds were evaluated for their biological
activity using chick pea seeds (Cicer arietinum)24 for their potential
antimitotic activity, it is a rapid and inexpensive cytotoxicity test
for the preliminary screening of new drugs.25,26 Synthesized com-
pounds were found to inhibit the growth of the germinating roots
from the seeds. Inhibitory activity values (IC50) are listed in Table 1.
In order to gain more insight into the interaction between these
new series of dithiocarbamate derivatives and b-tubulin that is in-
volved in assembly of microtubules. Crystal structure of b-tubulin
of bovine (pdb id: 1SA0) was download from the protein data bank
(Since the plant b-tubulin experimental structure is not available
and it has 94% sequence similarity with bovine). GLIDE 5.6 was
R1
NH2
ClCH2COOH
4N HCl, 100 ºC
Cl
N
HN
+
R2
NH2
N
H
3
1
2
CS2,
DMF,
4a:
4b:
4c:
4d:
4e:
4f:
NR1R2 = Pyrrolidinyl
NR1R2 = morpholinyl
NR1R2 = piperdinyl
NR1R2 = N,N-dimethyl
NR1R2 = N,N-diethyl
NR1= H, R2 = N-propyl
NR1= H, R2 = N-butyl
RT 2Hrs
Anhydrous K3PO4
R1
N
H
N
R2
S
S
4g:
N
4a - g
Scheme 1. Synthetic route to the benzimidazole dithiocarbamates (4a–4g).
O
CH3
O
R1
KOH, MeOH
HN
+
+
RT
R2
5
6
3
O
7
CS2, CH2Cl2
9a:
9b:
9c:
9d:
9e:
9f:
NR1R2 = pyrrolidinyl
NR1R2 = piperidinyl
NR1R2 = morpholinyl
NR1= H, R2 = benzothiazolyl
NR1R2 = N,N-dimethyl
NR1R2 = N,N-diethyl
O
S
S
N
R1
R2
9 a - f
Scheme 2. Synthetic route to the chalcone dithiocarbamates (9a–9f).

3276
K. Bacharaju et al. / Bioorg. Med. Chem. Lett. 22 (2012) 3274–3277
Table 1
The antimitotic activity and GlideScore of title compounds 4a–g and 9a–f
R1
N
S
R2
H
O
S
S
S
N
N
R1
R2
N
4a - 4g
9 a - f
Compound
R1R2
Antimitotic activity IC50 SDa
(
lM)
GlideScore (SP docking) Kcal/mol
GlideScore (XP docking) Kcal/mol
Cisplatin*
4a
4b
4c
4d
4e
4f
4g
9a
9b
9c
9d
9e
—
1.21 0.21
1.8 0.45
—
—
Pyrrolidinyl
Morpholinyl
Piperdinyl
À6.656
À6.726
À6.546
À5.814
À6.060
À5.764
À5.914
À6.506
À6.504
À6.999
À7.774
À5.587
À6.107
À7.090
À7.119
À6.354
À6.594
À6.756
À7.085
À7.787
À7.192
À7.945
À6.983
À8.637
À7.246
À8.004
1.89 0.47
1.66 0.44
2.12 0.50
1.86 0.51
2.29 0.47
2.11 0.49
1.67 0.42
1.85 0.44
1.65 0.39
1.52 0.40
2.43 0.48
1.84 0.43
N,N-Dimethyl
N,N-Diethyl
R1 = H, R2 = N-Propyl
R1 = H, R2 = N-butyl
Pyrrolidinyl
Piperdinyl
Morpholinyl
R1 = H, R2 = Benzothiazolyl
N,N-Dimethyl
N,N-Diethyl
9f
*
Cisplatin was taken as a standard, as it inhibits tubulin assembly into microtubules.
IC50 values are average of three replicate assays.
a
Figure 2. Dock pose of 9d in the active site of bovine b-tubulin showing a hydrogen bond interaction with Val 315. All the aromatic rings are deeply embedded into the
hydrophobic pockets.
used for molecular docking. Protein was prepared using protein
preparation wizard in Maestro 9.0 applying default parameters; a
grid was generated around the active site by selecting the cocrys-
talized ligand. Receptor van der Waals scaling for non polar atoms
was kept at 0.9. Molecules were built using Maestro build panel
and prepared by LigPrep 2.0 application. Low energy conformation
of the ligands were selected and docked into the grid generated for
the protein using both standard precision (SP) and extra precision
(XP) docking modes. Dock pose of each ligand was analysed for
interactions with the receptor. Molecules showed purely

K. Bacharaju et al. / Bioorg. Med. Chem. Lett. 22 (2012) 3274–3277
3277
12. Javier, R.; Jose, N. D.; Jaime, E. C.; Gricela, L.; Miguel, P. M.; Luisa, F. Eur. J. Med.
Chem. 2002, 37, 699.
13. Satish, K. A.; Nidhi, M.; Rajesh, K. B.; Manish, S.; Amit, B.; Lokesh, C. M.;
Virendra, K. B. Med. Chem. Res. 2009, 18, 407.
14. Lathchev, K. L.; Batovska, D. J.; Parushev, St. P.; Ubiyvovk, V. M.; Sibirny, A. A.
Eur. J. Med. Chem. 2008, 43, 2220.
15. Santos, L.; Curi, P. R.; Correa, R.; Cechinel, F. V.; Nunes, R. J.; Yunes, R. A. Arch.
Pharm. 2006, 339, 541.
16. Mallikarjuni, K. G. E-J. Chem. 2005, 2, 58.
17. Simon, F. N.; Saren, B. C.; Gabriele, C.; Arsalan, K.; Tommy, L. J. Med. Chem. 1998,
41, 4819.
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19. Belsare, D. P.; Pal, S. C.; Kazi, A. A.; Kankate, R. S.; Vanjari, S. S. Int. J. ChemTech
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Bioorg. Med. Chem. 2010, 18, 4310.
hydrophobic interactions with the protein active site. Molecules
were deeply embedded into the hydrophobic pocket formed by
Cys241, Leu245 and Leu255 amino acids in the active site (Fig. 2).
Most active molecule in the series (9d) showed high dockscore
of À7.774 and À8.637 kcal/mol in SP and XP docking protocol
respectively, this can be explained in terms of hydrophobic interac-
tion of the phenyl rings, specifically benzothiazole ring that is
occupying the extended hydrophobic cavity, it also showed one
hydrogen bond interaction with Val315 (Fig. 2). Molecules 4a–c
and 9a–c showed moderate dockscore ranging from À6.504 to
À6.999 kcal/mol, this is due to the hydrophobic interaction of cyc-
lic systems, but lack of hydrogen bond interaction has reduced the
dockscore compared to 9d this is also evident from the IC50 values.
Molecules 4d and 9e having a dimethyl group instead of cyclic sys-
tem has least activity and dockscores due to reduced hydrophobic
characteristics. Molecule 4e and 9f having diethyl substitution that
increases hydrophobic nature showed improved dockscore than
dimethyl substituted 4d and 9e molecules similar to the experi-
mental IC50 values. In molecules 4f and 4g only single substitution
of N-propyl and N-butyl groups is present that resulted in consid-
erable decrease in dockscore in accordance to the IC50 values. A
regression analysis between the SP dockscore and IC50 values gave
a regression coefficient (r2) value of 0.761 representing the signif-
icant correlation between the biological activities and docking
analysis.
21. U.S. Patent 4714764, 1987; Chem. Abstr. 1983, 98, 46775h.
22. General procedure for synthesis of benzimadazoledithiocarbmates 4a–g:
Equimolar mixture of amine
3 and anhydrous potassium phosphate in
dimethyl formamide was stirred at room temperature for 5 min, and then
carbondisulfide (2 equiv) was added. The reaction mixture was stirred for
additional 20 min, and then appropriate 2-chloromethylbenzimidazole 2,
(1 equiv) was added. Stirring was continued at room temperature until the
reaction was completed as monitored by TLC. The mixture was poured into
cold water then extracted with ethylacetate (3 Â 30 mL), organic phase was
washed once with water and dried over sodium sulfate and filtered. Solvent
was evaporated under reduced pressure and the resultant residue was
chromatographed over silica gel using mixture of petroleum ether and
ethylacetate as eluent.
Compound (4a): Yield: 92%; Melting point:160–162 °C; IR (KBr) cmÀ1
:
3394(NH), 2921(CH); 1H NMR [CDCl3,400 MHz]:
d
(ppm) 2.0–2.11(m, 4H,
(CH2)2), 3.62–3.65(t, 2H, NCH2), 3.97–4.01(t, 2H, NCH2), 4.88(s, 2H, CH2S),
7.21–7.26 (m, 4H, Ar-H); EI-MS: 278(M+1)+.
In conclusion, a novel class of benzimidazoledithiocarbamate
and chalcone dithiocarbamate derivatives were synthesized by
introducing various amines on dithiocarbamate side chain. Acyclic
amines showed less potency compared to cyclic groups. The main
aim of the study was to evaluate these compounds for their antimi-
totic activity and screen them for further invitro studies. Although
these molecules showed less potency compared to Cisplatin, toxic-
ity wise these molecules can be considered as potent antimitotic
derivatives.
Compound (4b): Yield: 96%; Melting point:186–188 °C; IR (KBr) cmÀ1
:
3221(NH), 2921(CH); 1H NMR [DMSO, 200 MHz]:
d (ppm) 3.66 (m, 4H,
O(CH2)2), 3.98–4.18 (br s, 4H, N(CH2)2), 4.76 (s, 2H, CH2S), 7.12–7.47 (m, 4H,
Ar-H), 12.37 (br s, 1H, NH); EI-MS: 294[M+1]+.
Compound (4c): Yield: 91%; Melting point:168–170 °C; IR (KBr) cmÀ1: 3451
(NH), 2936 (CH); 1H NMR (CDCl3, 400 MHz):
d (ppm) 1.67–1.73 (d, 6H,
piperidine (CH2)3), 3.86 (s, 2H, NCH2) 4.34 (s, 2H, NCH2), 4.91 (s, 2H, CH2S),
7.22–7.26 (m, 4H, Ar-H).
23. General procedure for synthesis of chalconedithiocarbamates 9a–f:
Carbondisulfide (0.15 mL, 2.5 mM) and chalcone
7 (0.42 g, 2 mM) was
dissolved in dichloromethane (10 mL) and the solution was cooled to 0 °C in
an ice bath. Amine 3 (2.25 mM) was slowly added and the reaction mixture
was stirred at 0 °C for 30 min. Then, the solution was warmed to room
temperature and stirred for another 24 h, and the reaction was monitored by
TLC. After the end of the reaction, solvents were removed in vaccum and the
residue was purified by column chromatography on silica gel (ethyl acetate–
petroleum ether) affording compound dithiocarbamates.
Acknowledgments
We gratefully acknowledge support for this research from
Council of Scientific and Industrial Research (Project No. 01/
(2436)/10/EMR-II), Department of Science and Technology, New
Delhi, India, University Grants Commission, New Delhi, India. We
also acknowledge Sarojini Naidu Vanitha Pharmacy Maha Vidya-
laya and Department of chemistry, Nizam College, Hyderabad, In-
dia. We also acknowledge Schrödinger Inc. for GLIDE software,
Tripos Inc. for SYBYLX-1.2.
Compound (9a): Yield: 92%; Melting point:116–118 °C; IR (KBr) cmÀ1: 1679
(C@O), 2869 (aliphatic); 1H NMR [CDCl3, 400 MHz]: 1.94–2.06 (m, 4H,
pyrrolidine (CH2)2), 3.57–3.63 (m, 2H, NCH2), 3.71–3.78 (m, 1H, CH2 of CO
gp), 3.90–3.94 (t, 2H, NCH2), 4.10–4.16 (m, 1H, CH2 of CO gp), 5.74–5.77 (dd,
1H, SCH), 7.25–7.96 (m, 10H, Ar-H); MASS (ESI): 378 [M+Na]+.
Compound (9b): Yield: 82%; Melting point:118–120 °C; IR (KBr) cmÀ1: 1681
(C@O), 2939 (aliphatic); 1H NMR [CDCl3, 400 MHz]: 1.69 (s, 6H, piperidine
(CH2)3), 3.72–3.78 (m, 1H, CH2 of CO gp), 3.83 (br s, 2H, NCH2), 4.12–4.17 (m,
1H, CH2 of CO gp), 4.27 (br s, 2H, NCH2), 5.70–5.74 (dd, 1H, SCH), 7.22–7.53 (m,
10H, Ar-H); MASS (ESI):392 [M+Na]+
References and notes
Compound (9d): Yield: 85%; Melting point:148–150 °C; IR (KBr) cmÀ1:1667
(C@O), 3341 (N–H), 2856 (aliphatic); 1H NMR [CDCl3, 300 MHz]: 3.55 (s, 1H,
CH2), 3.76 (s, 1H, CH2), 5.44 (s, 1H, SCH), 6.79 (br s, 1H, NH), 7.05-7.85 (m, 14H,
Ar-H).
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Procedure: Chick pea seeds (Cicer arietinum) of good quality were soaked
overnight with water to hasten the germinating process. These were
distributed in a group of 10 each in Petri dishes on moistened filter paper.
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and added to the filter paper in the Petri dishes. One Petri dish served as
control (DMSO) and one served as standard (cisplatin). The seeds were allowed
to germinate for 7 days and care was taken to moisten the filter paper with
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