Original Article
Synthesis and Characterization of Novel
N-Benzylbenzimidazole Linked Pyrimidine Derivatives
as Anticancer Agents
Gopal Krishna Padhy1,2, Jagadeesh Panda3, Ajaya Kumar Behera1,*
1
Organic Synthesis Laboratory, School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, INDIA.
Department of Pharmaceutical Chemistry, Maharajah's College of Pharmacy, Phool Baugh, Vizianagaram, Andhra Pradesh, INDIA.
3
Department of Pharmaceutical Chemistry, Raghu College of Pharmacy, Dakamarri, Visakhapatnam, Andhra Pradesh, INDIA.
2
ABSTRACT
Background: Emergence of resistance to accessible anticancer drugs became a threat
to human lives in the recent time. To address this issue, discovery of novel anticancer
agents becomes very essential. Benzimidazoles and pyrimidines have been reported to
possess potent anticancer activity. Materials and Methods: A hybrid approach has been
used, in which core structure of potentially active N-benzyl benzimidazole and pyrimidine
derivatives are brought together in to a single molecule. The desired compounds were
prepared by the condensation of N-benzyl benzimidazole chalcones with guanidine
hydrochloride. The synthesized compounds were characterized using spectral studies
(IR, 1H, 13C-NMR techniques and mass spectrometry). All the compounds were screened
for their anticancer activity against human breast cancer cell line MDA-MB-231. Results:
The spectral data’s are in well agreement with the synthesized compounds 5a-e.
Compounds 5b (GI50 = 39.6 μM) and 5a (GI50=84.0 μM) exhibited significant anticancer
activity. Conclusion: Owing to the anticancer activity, compound 5b can be used as lead
structure in the development of yet more potent anticancer agents.
Key words: Chalcone, Benzimidazole, Pyrimidine, Anticancer activity, SRB assay.
INTRODUCTION
In present situation cancer became a cruel
reality to human lives due to their resistance
to accessible drugs. Thus, discovery of new
types of anticancer drugs becomes very
critical. Benzimidazoles are exceptionally
valuable for the development of anticancer agent as they inhibits several enzymes
involved in pathology of cancer including
tyrosine kinase,1 Raf kinase,2 phosphatidylinositol 3-kinase3 and insulin-like growth
factor I receptor kinase.4 In addition,
N-benzyl substituted benzimidazoles have
been synthesized exhibiting potent anticancer activity in which the PPTMB5 and
BPB6 are examples (Figure 1). The pyrimidine motif is a core structure in numerous
biologically active compounds. Some representatives of this heterocycle exhibited anti-
cancer activity.7-9 Moreover compounds like
GNE-47710 and certinib11 were reported as
potential anticancer agents (Figure 1).
The hybrid of N-benzyl benzimidazole and
pyrimidine moieties is anticipated to be a
good approach to design promising anticancer agents. Thus in present work an efficient
synthesis of some new N-benzyl benzimidazole linked pyrimidine derivatives were
synthesized and evaluated against human
breast cancer cell line MDA-MB-231.
Submission Date: 11-09-2018;
Revision Date: 08-01-2019;
Accepted Date: 20-03-2019.
DOI: 10.5530/ijper.53.2s.57
Correspondence:
Dr. Ajaya Kumar Behera
Organic Synthesis Laboratory, School of Chemistry,
Sambalpur University, Jyoti
Vihar, Burla 768019, Odisha,
INDIA.
Phone: +91-663-2430114
E-mail: ajay.behera1962@
gmail.com
MATERIALS AND METHODS
Materials and Instrumentation
The chemicals used were procured from
Merck (India) and Finar (India). 1H and 13C
NMR spectra were recorded on a Bruker
Indian Journal of Pharmaceutical Education and Research | Vol 53 | Issue 2 (Suppl)| Apr-Jun, 2019
www.ijper.org
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Padhy, et al.: Anticancer N-Benzylbenzimidazole Linked Pyrimidines
Avance III 500 MHz (AV 500), spectrometer using TMS
as internal standard. The mass spectra were recorded on
Varian Inc 410 prostar Binary LC-MS. IR spectra were
obtained on a Bruker Alpha-T FT-IR spectrometer.
Melting points were determined by open tube capillary
method and are uncorrected. Progress of the reaction
and purity of the products was checked by TLC under
iodine vapors/UV light.
General Method for the Synthesis of 4-(1-benzyl1H-benzo[d]imidazol-2-yl)-6-(Substituted Phenyl)
Pyrimidin-2-amine (5a-e)
Appropriate N-benzyl benzimidazole chalcone 4a-e
(2 mmol) was dissolved in mixture of absolute alcohol
(10 ml) and aqueous sodium hydroxide solution (10%,
1 ml). Guanidine hydrochloride (4 mmol) was added
to the reaction mixture and the contents were refluxed
until completion of reaction (10-12 h). The progress
of the reaction was monitored by TLC (Benzene-ethyl
acetate, 4:1). The reaction mixture was cooled and the
precipitate formed was filtered and washed with rectified spirit.
4-(1-benzyl-1H-benzo[d]imidazol-2-yl)-6phenylpyrimidin-2-amine (5a)
Yield: 72 %; cream colour solid; m.p. 204-206°C; FTIR
(KBr) cm-1 3404 (br, -NH2), 1628 (C=N); 1H-NMR (500
MHz, DMSO-d6, δ / ppm): 8.15-8.13 (2H, m, H-2՛ and
H-6՛), 7.97 ( 1H, s, H-15), 7.80 (1H, d, J = 7 Hz, H-4)
7.71 (1H, d, J = 7.5 Hz, H-7), 7.54-7.53 ( 3H, m, H-3՛,
H-5՛ and H-4՛), 7.35-7.29 (2H, m, H-5 and H-6), 7.267.23 (2H, m, H-3՛՛ and H-5՛՛), 7.20-7.16 (3H, m, H-2՛՛,
H-6՛՛ and H-4՛՛), 7.02 (2H, s, -NH2), 6.37 (2H, s, H-10);
13
C NMR (125 MHz, DMSO-d6): 165.49 (C12), 163.86
(C16), 159.18 (C14), 148.21 (C2), 142.52 (C8), 138.46
(C1՛՛), 137.30 (C1՛), 137.23 (C9), 131.22 (C4՛), 129.28
(C3՛ and C5՛), 128.98 (C3՛՛ and C5՛՛), 127.74 (C4՛՛),
127.44 (C2՛՛ and C6՛՛), 127.28 (C2՛ and C6՛), 124.48
(C6), 123.33 (C5), 120.41 (C4), 112.04 (C7), 104.90
(C15), 48.42 (C10); ESI-MS m/z: 378.1 [M+H]..
4-(1-benzyl-1H-benzo[d]imidazol-2-yl)-6-(p-tolyl)
pyrimidin-2-amine (5b)
Yield: 62 %; cream colour solid; m.p. 180-182°C; FTIR
(KBr) cm-1 3306 (-NH2), 1624 (C=N); 1H-NMR (500
MHz, DMSO-d6, δ / ppm): 8.05 (2H, d, J = 10 Hz, H-2՛
and H-6՛ ), 7.94 (1H, s, H-15), 7.79 (1H, dd, J = 5 Hz, J
= 10 Hz, H-4), 7.70 (1H, dd, J = 5 Hz, J = 10 Hz, H-7),
7.35-7.29 ( 4H, m, H-3՛, H-5՛, H-5 and H-6 ), 7.26-7.23
(2H, m, H-3՛՛ and H-5՛՛), 7.19-7.16 (3H, m, H-2՛՛, H-6՛՛
and H-4՛՛), 6.98 (2H, s, -NH2), 6.37 (2H, s, H-10), 2.38
(3H, s, -CH3); ESI-MS m/z: 392.1 [M+H].
S130
4-(1-benzyl-1H-benzo[d]imidazol-2-yl)-6-(4chlorophenyl)pyrimidin-2-amine (5c)
Yield: 66 %; cream colour solid; m.p. 186--188°C;
FTIR (KBr) cm-1 3321 and 3201(-NH2), 1627 (C=N);
1
H-NMR (500 MHz, DMSO-d6, δ / ppm): 8.18 (2H, d, J
= 8.5 Hz, H-2՛ and H-6՛), 7.98 ( 1H, s, H-15), 7.80 (1H,
d, J = 7 Hz, H-4) 7.77 (1H, d, J = 7.5 Hz, H-7), 7.6 (2H,
d, J = 9 Hz, H-3՛ and H-5՛), 7.35-7.29 (2H, m, H-5 and
H-6), 7.26-7.23 (2H, m, H-3՛՛ and H-5՛՛), 7.20-7.17 (3H,
m, H-2՛՛, H-6՛՛ and H-4՛՛), 7.04 (2H, s, -NH2), 6.37 (2H,
s, H-10); 13C NMR (125 MHz, DMSO-d6): 164.19 (C12),
163.81 (C16), 159.37 (C14), 148.05 (C2), 142.49 (C8),
138.44 (C1՛՛), 137.24 (C9), 136.09 (C4՛), 136.00 (C1՛),
129.35 (C2՛ and C6՛), 129.10 (C3՛ and C5՛), 128.98 (C3՛՛
and C5՛՛), 127.75 (C4՛՛), 127.43 (C2՛՛ and C6՛՛), 124.53
(C6), 123.36 (C5), 120.41 (C4), 112.06 (C7), 104.74
(C15), 48.41 (C10); ESI-MS m/z: 411.9 [M+H].
4-(1-benzyl-1H-benzo[d]imidazol-2-yl)-6-(4bromophenyl)pyrimidin-2-amine (5d)
Yield: 58 %; light yellow colour solid; m.p. 216-218°C;
FTIR (KBr) cm-1 3330 and 3205 (-NH2), 1627 (C=N);
1
H-NMR (500 MHz, DMSO-d6, δ / ppm): 8.10 (2H, d,
J = 8.5 Hz, H-2՛ and H-6՛), 7.97 (1H, s, H-15), 7.80 (1H,
dd, J = 1.5 Hz, J = 7.5 Hz, H-4), 7.75-7.70 (3H, m, H-3՛,
H-5՛ and H-7), 7.36-7.29 (2H, m, H-5 and H-6), 7.267.23 (2H, m, H-3՛՛ and H-5՛՛), 7.20-7.17 (3H, m, H-2՛՛,
H-6՛՛ and H-4՛՛), 7.04 (2H, s, -NH2), 6.36 (2H, s, H-10);
ESI-MS m/z: 455.9 [M+H], 457.9 [M+2].
4-(1-benzyl-1H-benzo[d]imidazol-2-yl)-6-(4fluorophenyl)pyrimidin-2-amine (5e)
Yield: 68 %.; cream colour solid; m.p. 210-212°C;
FTIR (KBr) cm-1 3373 and 3294 (-NH2), 1633 (C=N);
1
H-NMR (500 MHz, DMSO-d6, δ / ppm): 8.23-8.20
(2H, m, H-2՛ and H-6՛), 7.98 (1H, s, H-15), 7.81 (1H, d,
J = 7.5 Hz, H-4), 7.71 (1H, d, J = 8 Hz, H-7), 7.36-7.29
(4H, m, H-5, H-6, H-3՛ and H-5՛), 7.25-7.16 (5H, m,
H-3՛՛, H-5՛՛, H-2՛՛, H-6՛՛ and H-4՛՛), 7.05 (2H, s, -NH2),
6.38 (2H, s, H-10); 13C NMR (125 MHz, DMSO-d6):
165.23-163.26 (C4՛), 164.37 (C12), 163.80 (C16), 159.25
(C14), 148.16 (C2), 142.52 (C8), 138.45 (C1՛՛), 137.23
(C9), 133.77-133.75 (C2՛ and C6՛), 129.74-129.67 (C1՛),
128.97 (C3՛՛ and C5՛՛), 127.74 (C4՛՛), 127.43 (C2՛՛ and
C6՛՛), 124.49 (C6), 123.34 (C5), 120.40 (C4), 116.27 (C3՛
and C5՛), 116.10 (C5՛), 112.03 (C7), 104.69 (C15), 48.42
(C10); ESI-MS m/z: 396.1 [M+H].
Anticancer activity
The in vitro cytotoxicity activities (cell viability assay) of
the compounds were evaluated by SRB assay12 against
Human breast cancer cell line MDA-MB-231. The cell
Indian Journal of Pharmaceutical Education and Research | Vol 53 | Issue 2 (Suppl)| Apr-Jun, 2019
Padhy, et al.: Anticancer N-Benzylbenzimidazole Linked Pyrimidines
line was grown in RPMI 1640 medium containing 2
mM L-glutamine and 10% fetal bovine serum. Cells
were inoculated into 96 well microtiter plates in 90 µL
medium at 5000 cells per well and incubated at 37°C,
5% CO2, 95% air and 100% relative humidity for 24
h. Subsequent to the addition of drugs (0.1–100 μM),
the culture plate was incubated for additional 48 h. Cells
were fixed in situ by slowly adding 25 µL of 10% trichloroacetic acid and then incubated for 60 min at 4°C.
After discarding the supernatant, the plate was washed
five times with tap water. Finally, 50 µL of sulforhodamine in 1% acetic acid solution was added to each
well for staining. The stained cells were solubilized using
10 mM trizma base and the absorbance was noted at a
wavelength of 515 nm. The % viability was calculated
for each compound at different concentration using the
formula: (Absorbance of Test/Absorbance of control)
× 100
The GI50 (Concentration required to cause 50% inhibition in growth) for the synthesized compounds were
calculated from a non-linear sigmoidal dose–response
(Variable slope) curve by using GraphPad Prism v.4.03
software.
RESULTS AND DISCUSSION
Synthesis
The desired compounds were prepared as outlined in
the (Scheme 1). 2-hydroxyethylbenzimidazole 1 was
obtained by condensation of o-phenylenediamine with
lactic acid under acidic condition. Oxidation of the 1
followed by neutralization with ammonia gave 2-acetylbenzimidazole 2.13 The required chalcones 3a-e were
obtained by claisen-schmidt condensation of 2-acetylbenzimidazole 2 with substituted aromatic aldehydes in
presence of NaOH.14 N-Benzyl substituted benzimidazole chalocones (4a-e) were obtained by nucleophilic
substitution reactions of 1H-Benzimidazole chalcones
(3a-e) with benzyl chloride.15 Condensation of the
N-benzyl benzimidazole chalcones with guanidine
hydrochloride resulted in novel pyrimidine derivatives
(5a-e).
The scheme of synthesis 1: Synthetic route to 1-benzyl2-(1-substituted-5-aryl-4,5-dihydro-1H-pyrazol-3-yl)1H-benzo[d]imidazoles. Reagents and conditions: i) 4N
HCl, reflux, 8 h; ii) K2Cr2O7, dil. H2SO4, r.t., 2h; iii) ArCHO, 10 % aq NaOH, ethanol, r.t., 4-8 h; iv) Benzyl
chloride, anhydrous K2CO3, dry acetone, reflux, 22-26
h; v) Guanidine. HCl, NaOH, EtOH, H2O, reflux, 10-12
h.
Spectral Study
The structures of synthesized compounds 5a-e were
assigned via spectroscopic analysis: IR, 1H-NMR, 13CNMR and mass spectrometry. The spectral study of
compound 5a is described as an example. IR spectrum
of compound 5a showed the characteristic peak at
3404 cm-1 corresponding to N-H stretching. In 1HMR
spectrum of 5a, the doublets due to arylidene protons
disappeared, instead a singlet at δ 7.97 is observed due
to proton at C15 ensuring the formation of pyrimidine
ring. The phenyl protons H-2՛ and H-6՛ appeared as
a multiplet at δ 8.15-8.13. The benzimidazole protons
(H-4 and H-7) appeared as two separate doublets at δ
7.80 and 7.71 (J = 7.5 Hz) respectively. One multiplet
at δ 7.54-7.53 was attributed to three aromatic protons
of phenyl group (H-3՛, H-5՛ and H-4՛). Two benzimidazole protons (H-5 and H-6) were observed as a multiplet at δ 7.35-7.29. Two separate multiples at δ 7.26-7.23
and δ 7.20-7.16 were assigned to aromatic benzyl protons (H-3՛՛, H-5՛՛, H-2՛՛, H-6՛՛ and H-4՛՛). The amino
protons appeared as a singlet at δ 7.02. The methylene
protons at C10 appeared as a singlet at δ 6.37.
The 13C NMR spectrum of compound 5a, the peaks at δ
165.49, 163.86, 159.18, 104.90 are attributed to pyrimidine carbons (C12, C16, C14 and C15). The peaks at
δ 148.21, 142.52, 137.23, 124.48, 123.33, 120.41 and
112.04 are assigned to benzimidazole carbons (C2,
C8, C9, C6, C5, C4 and C7). The aromatic benzyl carbons (C1՛՛), (C3՛՛ and C5՛՛), (C2՛՛ and C6՛՛) and (C4՛՛)
appeared at δ 138.46, 128.98, 127.44 and 127.74 respectively. The peaks at δ 131.22, 137.30, 127.28 and 129.28
are assigned to (C4՛), (C1՛), (C2՛ and C6՛) and (C3՛ and
C5՛) respectively. A peak at 48.42 confirms the presence of methylene carbon (C10). Additionally, ESI-MS
spectrum showed a peak at 378.1 (M+H). Hence, the
above spectral data are compatible with the structure of
desired product 5a.
Anticancer Activity
The in vitro anticancer activities (cell viability assay) of
compounds were evaluated by SRB assay against Human
breast cancer cell line MDA-MB-231. Compounds 5a
Indian Journal of Pharmaceutical Education and Research | Vol 53 | Issue 2 (Suppl)| Apr-Jun, 2019
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Padhy, et al.: Anticancer N-Benzylbenzimidazole Linked Pyrimidines
Table 1: In vitro anticancer activity of synthesized
compounds 5a-e (GI50 µM).
Compound
GI50 (µM)
5a
84.0
5b
39.6
5c
>100
5d
>100
5e
>100
Positive control Adriamycin (GI50= 0.04 µM).
(GI50 = 84.0 μM) and 5b (GI50 = 39.6 μM) exhibited
weak activity. Compound 5a-b clearly inhibited the
proliferation of Human breast cancer cell line MDAMB-23 as shown in (Figure 2). All the other compounds
found inactive (GI50 >100 μM) as compared to standard
drug adriamycin. The results obtained from cytotoxicity
testing are represented in (Table 1).
CONCLUSION
Figure 1: Rational Design of the Benzimidazole Linked Pyrimidine via Hybriding Potent Anticancer Agents.
Five novel benzimidazole derivatives containing pyrimidine ring were synthesized. The structures of new compounds were confirmed by spectral data (IR, 1H-NMR,
13
C-NMR and mass spectrometry). Our anticancer
study results revealed that the most active compound
5b possessed GI50 value of 39.6 µM. Based on the GI50
values presented by the tested compounds, it could be
concluded that, presence of electron releasing group on
the phenyl ring enhanced the active.
ACKNOWLEDGEMENT
The authors gratefully acknowledge the Sophisticated
Instrumentation Facility (SAIF), IIT Madras and SAIF,
IIT Bombay for providing spectral data. The authors
also acknowledge Anti-cancer drug screening facility
(ACDSF) at ACTREC, Tata Memorial Centre, Navi
Mumbai for evaluating anti-cancer activity. Gopal is
thankful to Sri. P. Ashok Gajapathi Raju, Chairman,
MANSAS, Vizianagaram and Dr. P. Udaya Shankar,
Principal Maharajah’s College of pharmacy, Vizianagaram for providing necessary infrastructure and facility.
CONFLICT OF INTEREST
The authors declare no conflict of interest.
ABBREVIATIONS
Figure 2: Images of Phase Contrast Microscopy. Cells were
treated with 100 μM 5a-e, for 48 h. Negative Control Included
cells treated with DMSO.
S132
NMR: Nuclear magnetic resonance spectroscopy;
TMS: Tetramethylsilane; DMSO-d6: Deuterated
Dimethyl Sulfoxide; LC-MS: Liquid Chromatography-
Indian Journal of Pharmaceutical Education and Research | Vol 53 | Issue 2 (Suppl)| Apr-Jun, 2019
Padhy, et al.: Anticancer N-Benzylbenzimidazole Linked Pyrimidines
Mass spectrometry; ESI-MS: Electro spray ionizationMass Spectrometer; FT-IR: Fourier transform infrared
spectroscopy; TLC: Thin layer chromatography; UV:
Ultraviolet spectroscopy; SRB: Sulforhodamine B;
RPMI: Roswell Park Memorial Institute.
7.
Ma LY, Pang LP, Wang B, Zhang M, Hu B, Xue DQ, et al. Design and synthesis
of novel 1, 2, 3-triazole-pyrimidine hybrids as potential anticancer agents. Eur
J Med Chem. 2014;86:368-80.
8.
El-Deeb IM, Lee SH. Design and synthesis of new anticancer pyrimidines
with multiple kinase inhibitory effect. Bioorg Med Chem. 2010;18(11):386074.
9.
Wang S, Griffiths G, Midgley CA, Barnett AL, Cooper M, Grabarek
J, et al. Discovery and Characterization of 2-Anilino-4-(thiazol-5-yl)
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SUMMARY
PICTORIAL ABSTRACT
•
Identification of lead molecules against cancer
is a vital area of today’s research. In this study a
new series of N-benzyl benzimidazole and pyrimidine derivatives were synthesized, characterized
and evaluated for in vitro anticancer activity. Compound 5b showed significant activity. Hence it can
be used as a lead structure in the advance of yet
more potent anticancer agents.
ABOUT AUTHORS
Dr. Ajaya Kumar Behera was born in Nayagarh District of Odisha, India, in 1962. He
received his M.Sc. degree from Utkal University in 1984 and M.Phil. and Ph.D. degrees from
Berhampur University in 1990 and 1996, respectively. After working for a few years at Government College, he joined the PG Department of Chemistry, Sambalpur University, in 1997
as Senior Lecturer and became Reader in 2003. His research interest includes synthesis of
pharamacologically active heterocycles, spiroheterocycles and natural products.
Dr. Jagadeesh Panda received his M.Pharm. degree from Andhra University in 1995 and
Ph.D. degrees from Berhampur University in 2004 respectively. Currently he is working as a
Professor and Principal of Raghu College of Pharmacy, Visakhapatnam. His research interest
includes synthesis of pharamacologically active heterocycles and natural products.
Indian Journal of Pharmaceutical Education and Research | Vol 53 | Issue 2 (Suppl)| Apr-Jun, 2019
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Padhy, et al.: Anticancer N-Benzylbenzimidazole Linked Pyrimidines
Dr. Gopal Krishna Padhy obtained his M.Pharm. degree in Pharmaceutical Chemistry from
Poona College of Pharmacy, Bharati Vidyapeeth University, in 2007. He had carried out his
Ph.D. work under joint supervision of Dr. Ajaya Kumar Behera and Dr. Jagadeesh Panda in
Sambalpur University. Currently, he is working as an associate professor in Maharajah’s College of Pharmacy, Phool Baugh.
Cite this article: Padhy GK, Panda J, Behera AK. Synthesis and Characterization of Novel N-Benzylbenzimidazole
Linked Pyrimidine Derivatives as Anticancer Agents. Indian J of Pharmaceutical Education and Research.
2019;53(2S):s129-s134.
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