Synthesis pharmacological evaluation and docking studies of pyrimidine derivatives

Article abstract of DOI:10.1016/j.ejmech.2012.09.050

A new group of pyrimidine derivatives of indane-1,3-dione were synthesized aiming at the synthesis of new compounds acting as analgesic, anti-inflammatory and antimicrobial activity in a single component. The title compounds (3a-l) were synthesized from c

Full text of DOI:10.1016/j.ejmech.2012.09.050

European Journal of Medicinal Chemistry 58 (2012) 478e484
Contents lists available at SciVerse ScienceDirect
European Journal of Medicinal Chemistry
journal homepage: http://www.elsevier.com/locate/ejmech
Short communication
Synthesis pharmacological evaluation and docking studies of pyrimidine
derivatives
,
a
b
a
a
a
D. Giles a , Karki Roopa , F.R. Sheeba , P.M. Gurubasavarajaswamy , Goli Divakar , Thomas Vidhya
*
a Acharya & B.M. Reddy College of Pharmacy, Bangalore, Karnataka, India
b Mallige College of Pharmacy, Bangalore, Karnataka, India
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 2 July 2012
Received in revised form
27 September 2012
Accepted 28 September 2012
Available online 16 October 2012
A new group of pyrimidine derivatives of indane-1,3-dione were synthesized aiming at the synthesis of
new compounds acting as analgesic, anti-inflammatory and antimicrobial activity in a single component.
The title compounds (3a-l) were synthesized from chalcone derivatives of indane-1,3-dione (2a-l)
through cyclization reaction with urea. The synthesized compounds were characterized by FT-IR, 1H
NMR, mass spectral data, elemental analysis and evaluated for anti-inflammatory, analgesic, antibacterial
and antifungal activities. The most active compound 3e, was evaluated for its ulcerogenicity. Good anti-
inflammatory property was observed for chlorophenyl substituted pyrimidine derivatives. It mainly
binds with Pro 218 of 1CX2, and the ligand could have caused much conformational changes in the
protein structure than other derivatives. It also exhibits good analgesic and antimicrobial agent in
a single component.
Keywords:
Analgesic activity
Anti-Inflammatory activity
Antimicrobial activity
Cyclooxygenase
Ó 2012 Elsevier Masson SAS. All rights reserved.
Indane-1,3-dione
Pyrimidine
Ulcerogenic activity
1. Introduction
containing the pyrimidine heterocyclic have demonstrated a wide
range of biological activity viz. anti-inflammatory [11e14], anal-
Inflammation is a complex defensive mechanism of the body to
any noxious stimulus [1]. Non-steroidal anti-inflammatory drugs
are of huge benefit in the treatment of inflammatory disease [2,3].
The most common side effect associated with all currently available
non-steroidal anti-inflammatory drugs are gastrointestinal hem-
orrhagica and ulceration [4e6]. In fact, while a number of mecha-
nisms have been proposed to explain the pharmacological effects of
non-steroidal anti-inflammatory drugs, it is believed that the
inhibition of cyclooxygenase (COX) is one of the greatest impor-
tance. The discovery of isoform of the COX-1 and COX-2 enzymes
opens a new perspective of COX-2 inhibitors used in therapeutics
[7e9]. Consequently, a new generation of COX-2 selective inhibitors
has been clinically used with the hope that they would exhibit
a reduced risk in gastrointestinal events [10].
gesic [11e13,15,16], antipyretic [16], antimicrobial [14,17e20] and
anticancer [21e25] activities. Indane-1,3-dione exhibits wide range
of biological activities covering anti-inflammatory [26e28], anal-
gesic [26,29], anticoagulant [26,30], antimicrobial [26,31] and
anticancer [26,32,33] activities.
Co-administration of multiple drugs for treatment of pain,
inflammatory conditions associated with microbial infection is
a major risk factor for the patients with impaired liver or kidney
functions.
A mono therapy of a drug with analgesic, anti-
inflammatory and antimicrobial activity would be preferred form
of the pharmacoeconomic and patient compliance point of view.
This premise was one of the goals of our research aimed at the
discovery of new pyrimidine derivatives that would possess anal-
gesic, anti-inflammatory and antimicrobial agent in a single
component. Combination of two or more biological active moieties
increases or decreases the biological activity. Being involved in
a research program aiming at finding out new structural leads that
would act as potent anti-inflammatory, analgesic and antimicrobial
agents, we have reported the synthesis, anti-inflammatory, anal-
gesic and antimicrobial activities of some lead compounds
comprising mainly pyrimidine derivatives of indane-1,3-dione.
Pyrimidine ring system has attracted significant interest
in medicinal chemistry over the past few decades. Scaffolds
* Corresponding author. Department of Pharmaceutical Chemistry, Acharya &
B.M. Reddy College of Pharmacy, Soladevanahalli, Chikkabanavara Post, Bangalore
560 090, Karnataka, India. Tel.: þ91 94487 36917.
E-mail address: sahayagiles@yahoo.com (D. Giles).
0223-5234/$ e see front matter Ó 2012 Elsevier Masson SAS. All rights reserved.
http://dx.doi.org/10.1016/j.ejmech.2012.09.050

D. Giles et al. / European Journal of Medicinal Chemistry 58 (2012) 478e484
479
2. Results and discussion
CH and CH2 protons which was not observed in the chalcone
derivatives. The CH proton adjacent to carbonyl carbon of indane-
1,3-dione appeared as a singlet. All these results established the
formation of target compounds. It was further confirmed by mass
spectral data and elemental analysis.
2.1. Chemistry
Synthesis of the target compounds were performed according to
the reactions illustrated in Scheme 1. 2-Acetylindane-1,3-dione (1)
was treated with different aldehydes (a-l) to form chalcones of
indane-1,3-dione (2a-l). The chalcones (2a-l) were further treated
with urea to form pyrimidine derivatives of indane-1,3-dione (3a-l).
The desired pyrimidine analogs (3a-l) were confirmed by the
spectral data. The IR spectra of products exhibited absorption bands
at 3226e3394 cmꢀ1, assigned to NH group stretching vibration
which was not observed for chalcone derivatives (2a-l). The
stretching frequency at 1671e1709 cmꢀ1 was assigned to C]O
vibrations and the characteristic absorptions for C]N was also
present. The main characteristic of the 1H NMR for the pyrimidine
series was the presence of a three doublet of doublet attributed by
2.2. Molecular modeling studies
2.2.1. Docking studies
Molecular docking studies of compounds 3a-l were carried out
using Molegro Virtual Docker 2010 in order to rationalize biological
activity results. Docking also helps in understanding the various
interactions between ligand and enzyme in the active site in detail.
The crystal structure of COX-2 (PDB: 1CX2) and COX-1 (PDB: 2OYE)
were used for docking study.
As per the docking study with 1CX2 the following results can be
drawn. The synthesized series 3a-l had MolDock score ranging
from ꢀ130.970 to ꢀ150.445. Five hydrogen bonds were present in
the derivative 3j, which was the highest among the series. The
carbonyl group of indane-1,3-dione mainly binds with NH2 of Arg
44 in compounds 3b, 3d, 3g, 3h, 3i, 3j and 3k which had hydrogen
ꢀ
bond of 3.032, 3.038, 3.083, 2.824, 3.033, 3.105 and 2.538 A
respectively. Chloro group in phenyl ring binds with NH2 of Pro 218
which was not observed in any other derivatives. Pyrimidine ring in
this series binds mainly with OH of Ser 439, C]O of Lys 468, NH2 of
Arg 150, OH of Ser 471, NH2 of Lys 468, C]O of Glu 465, C]O of Lys
465, NH2 of Asn 43, NH of Gln 461, NH2 of Arg 44. It was a clear
indication that the pyrimidine ring had an enough role in binding of
the drug with the COX-2. Oxygen of NO2 binds with NH of Arg 44 in
ꢀ
3c derivative with a bond length of 3.434 A. Oxygen in furan ring of
ꢀ
3h binds with NH2 of Asn 43 with a bond length of 3.158 A. In 3j the
OH in phenyl ring binds with C]O of Cys 141 and Gly 145 with
ꢀ
ꢀ
bond length of 2.639 A and 3.187 A respectively. NH in indole ring of
3k binds with C]O of Arg 469. OH and OCH3 in 3l binds with Cys 36
ꢀ
ꢀ
and Gln 461 with bond length of 3.552 A and 3.520 A respectively.
This indicates the effect of substituent in phenyl ring.
The synthesized series 3a-l had MolDock score ranging
from ꢀ110.682 to ꢀ155.055 for 2OYE. Seven hydrogen bonds were
present in the derivative 3j, which was the highest among the
series. The MolDock score for the compound was ꢀ110.682. The
carbonyl group of indane-1,3-dione mainly binds with NH2 of Gln
44 in compounds 3a, 3b, 3d, 3f, 3g, 3h, 3i, 3j and 3l which had good
hydrogen bonding with the target. All the compounds except 3k
were binding with indane-1,3-dione. Pyrimidine ring in this series
binds mainly with NH of His 43, NH of Gln 42, NH of Lys 468, OH of
Tyr 64, OH of Tyr 130, NH of Gly 471, NH of Gln 44, OH of Thr 129.
This clearly indicates the effect of indane-1,3-dione and pyrimidine
ring in the ring system. The substituent’s also binds with the target
indicating the effect of substituent. Compound 3e has a MolDock
Score of ꢀ127.314 with three hydrogen bonds.
2.3. Biological evaluation
2.3.1. Anti-inflammatory activity
All the synthesized compounds were screened for their anti-
inflammatory activity by carrageenan induced rat paw edema
method. The results of anti-inflammatory activity indicated that
compounds in pyrimidine series except 3g and 3k exhibited
significant activity than that of control. None of the compounds in
this series were much effective as standard. Steady increase in paw
edema inhibition was observed for 3e than other synthesized
derivatives. Compound 3c showed significant anti-inflammatory
activity at 1 and 2 h of drug administration but the effect started
decreasing from 3 h. The anti-inflammatory effect produced by 3c
at 1 h was higher than standard. Whereas, other compounds
Scheme 1. General scheme for the synthesis of pyrimidine derivatives of indane-1,3-dione.

480
D. Giles et al. / European Journal of Medicinal Chemistry 58 (2012) 478e484
showed moderate anti-inflammatory activity compared to that of
standard drug indomethacin. Edema inhibition of 3e at 3h was
found to be similar to that of standard at 4 h of drug administration.
All these results indicate that pyrimidine series of indane-1,3-dione
possess moderate anti-inflammatory activity.
investigation and derivatization for the development of a new class
of drugs in a single component.
4. Experimental
The molecular modeling studies correlates well with pharmaco-
logical activity. In this regard, the compound 3e showed selective
inhibition of COX-2 than COX-1. Docking results were in concordance
with the anti-inflammatory activity. Molecules binding with Arg 44
possess significant anti-inflammatory activity which could be
possible because of the presence of both indane-1,-3-dione and
pyrimidine ring. At the same time, binding of 3e with Pro 218 in
1CX2 could have caused much conformational changes in the
protein structure than other derivatives. This could be the reason for
its good anti-inflammatory activity.
Melting point was determined by conventional melting point
apparatus and was uncorrected. The progress of the reaction was
monitored on readymade silica gel plates (Merck). Infrared spectra
were recorded by FT-IR technique using Tensor 27 spectropho-
tometer, Bruker Optic (Germany) by ATR technique. 1H NMR spectra
of synthesized compounds were recorded using AMX-400 at
400 MHz using DMSO as solvent. Mass spectra was recorded using
Qstar Elite, LC MS. Animal experimentation was approved by IAEC
of Acharya & B.M. Reddy College of Pharmacy.
4.1. Chemistry
2.3.2. Ulcerogenic effect
The compounds 3e showed good anti-inflammatory. So it was
screened for ulcerogenicity. The tested 3e showed significant
reduction in ulcerogenic activity when compared to that of stan-
dard. This indicates that compound 3e does not induce ulcer.
Docking results also confirms the less affinity towards COX-1.
4.1.1. Synthesis of chalcones derivatives of 2-acetylindane-1,3-dione
A
mixture of 2-acetylindane-1,3-dione (0.01 mol) and
substituted aromatic aldehyde (0.01 mol) were stirred in ethanol
(25 mL) and then an aqueous solution of sodium hydroxide (10 mL)
was added to it. The mixture was then kept overnight at room
temperature and then poured into crushed ice. The solution was
acidified with dilute hydrochloric acid. The chalcone derivatives of
indane-1,3-dione precipitates out [34]. The product was filtered
and recrystallized form ethanol.
2.3.3. Analgesic activity
All the compounds were screened for analgesic activity by acetic
acid induced writhing method in mice. The results indicate that
some of the compounds in the series 3a-l possess good activity.
The percentage activity in this series ranges from 16% to 52%.
Compound 3f showed excellent analgesic activity whereas 3a, 3b,
3c, 3d, 3e, 3g, 3j, 3k and 3l showed moderate to good analgesic
activity. The activity of these compounds ranges from 21% to 44%.
Least active analgesic in this series was 3i. Presence of dimethyl
amino group as substituent emerged as a most active analgesic
agent among the synthesized series. Moderate analgesic activity
was observed for the compounds possessing nitro, chloro, methoxy,
hydroxyl groups as substituent. Increase the length of the chain
diminished the analgesic activity. Presence of fused heterocyclic
ring provides good analgesic activity than single ring system.
4.1.2. Synthesis of 2-(2-oxo-6-substituted-1,2,5,6-tetrahydro
pyrimidin-4-yl)indane-1,3-dione (3a-l)
A mixture of chalcones 2a-l (0.01 mol), urea (0.01 mol), and
sodium hydroxide (0.025 mol) in ethanol (25 mL) were refluxed for
6 h. The reaction mixture was cooled and acidified with dilute
hydrochloric acid. The precipitate formed was filtered and recrys-
tallized form ethanol to give 3a-l.
4.1.2.1. 2-(2-oxo-6-phenyl-1,2,5,6-tetrahydropyrimidin-4-yl)-
indane-1,3-dione (3a). Yield 59%; mp 182e185 ꢁC; IR (cmꢀ1): 3226
(NeH stretching), 3021 (CeH aromatic stretching), 2944 (CeH
aliphatic stretching), 1689 (C]O stretching), 1642 (C]N stretching),
2.3.4. Antimicrobial activity
1587 (C]C stretching); 1H NMR
d (ppm): 10.821 (s, IH, NH), 7.422e
Some of the compounds in the series 3a-l showed promising
antimicrobial activity against Escherichia coli and Bacillus subtilis.
7.438 (m, 2H), 7.456e7.502 (m, 2H) 7.653e7.675 (m, 1H), 7.678e
7.689 (m, 2H),7.792e8.059 (m, 2H), 6.023e6.063 (dd, J ¼ 9.6 Hz,
J ¼ 4.4 Hz, 1H), 3.421 (s, 1H), 2.210e2.253 (dd, J ¼ 4.4 Hz, J ¼ 11.2 Hz,
1H),1.932e1.986 (dd, J ¼ 11.2 Hz, J ¼ 9.6 Hz, 1H); 13C NMR (125 MHz,
Compounds 3b and 3h showed good inhibition at 31.2
mg/mL
against E. coli and 3e and 3h showed good inhibition at the same
concentration against B. subtilis. Compounds 3e, 3f, 3h and 3i
showed good inhibition against Pseudomonas aeruginosa, Staphy-
lococcus aureus, Aspergillus niger and Candida albicans. Among this
series 3h was the most active one, since it shows good inhibition
against all the tested bacterial and fungal strains except
P. aeruginosa.
DMSO-d6)
d 210.59, 209.98, 160.83, 137.84, 136.74, 136.41, 127.61,
129.41, 129.01, 128.34, 128.14, 127.37, 124.41, 123.31, 123.02, 119.43,
65.43, 57.85, 36.44; MS (m/z) (%): 318 [Mþ, 12%]. Anal. Calcd for
C19H14N2O3: C, 71.69; H, 4.43; N, 8.80. Found: C, 71.34; H, 4.33; N, 8.53.
4.1.2.2. 2-[6-(2-nitrophenyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-4-
yl]-indane-1,3-dione (3b). Yield 60%; mp 166e167 ꢁC; IR (cmꢀ1):
3283 (NeH stretching), 3044 (CeH aromatic stretching), 2941 (CeH
aliphatic stretching),1698 (C]O stretching),1633 (C]N stretching),
3. Conclusion
In conclusion, a series of pyrimidine analogs of indane-1,3-dione
were synthesized in good yields. From docking studies it was true
that the compound 3e display a high degree of selectivity towards
COX-2 than COX-1. It was further proved by its pharmacological
activity. In addition to this binding with Pro 218 could be the
possible reason for its good anti-inflammatory activity. This binding
was not observed in any other derivatives. This clearly indicates
that, binding with specific amino acids causes good confirmation
change in the protein structure, there by good pharmacological
effect was observed. Since the same compound possess good
analgesic and antimicrobial activity the product was worthy for
additional studies in view of their therapeutic potential for further
1588 (C]C stretching); 1H NMR
d (ppm): 10.621 (s, IH, NH), 7.047e
7.098 (m, 2H), 7.135e7.236 (m, 2H) 7.352e7.395 (m, 1H), 7.528e
7.692 (m, 2H),7.923e8.981 (m, 1H), 6.211e6.261 (dd, J ¼ 10.4 Hz,
J ¼ 5.2 Hz,1H), 3.351 (s,1H), 2.436e2.486 (dd, J ¼ 5.2 Hz, J ¼ 12.8 Hz,
1H),1.852e1.859 (dd, J ¼ 12.8 Hz, J ¼ 10.4 Hz,1H); MS (m/z) (%): 362
[Mþ ꢀ 1, 34%]. Anal. Calcd for C19H13N3O5: C, 62.81; H, 3.61; N, 11.57.
Found: C, 62.55; H, 3.23; N, 11.12.
4.1.2.3. 2-[6-(3-nitrophenyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-4-
yl]-indane-1,3-dione (3c). Yield 62%; mp 173e174 ꢁC; IR (cmꢀ1):
3346.59 (NeH stretching), 3002 (CeH aromatic stretching), 2881
(CeH aliphatic stretching), 1701 (C]O stretching), 1619 (C]N

D. Giles et al. / European Journal of Medicinal Chemistry 58 (2012) 478e484
481
stretching), 1583 (C]C stretching); 1H NMR
d (ppm): 10.203 (s, IH,
NH), 7.315e7.385 (m, 2H), 7.402e7.466 (m, 2H) 7.523e7.599 (m,1H),
7.652e7.792 (m, 2H), 7.899e7.974 (m, 1H),7.315e7.974 (m, 8H,
aromatic), 6.410e6.452 (dd, J ¼ 10.0 Hz, J ¼ 5.6 Hz,1H), 3.321 (s,1H),
2.501e2.550 (dd, J ¼ 5.6 Hz, J ¼ 12.4 Hz, 1H), 1.842e1.895 (dd,
J ¼ 12.4 Hz, J ¼ 10.0 Hz,1H); 13C NMR (125 MHz, DMSO-d6)
d 210.64,
209.87, 160.75, 137.17, 136.72, 136.42, 127.65, 127.38, 125.12, 125.14,
124.44, 123.34, 123.15, 120.11, 119.35, 115.48, 65.41, 57.97, 36.58; MS
(m/z) (%): 363 [Mþ, 23%]. Anal. Calcd for C19H13N3O5: C, 62.81; H,
3.61; N, 11.57. Found: C, 62.58; H, 3.24; N, 11.22.
4.1.2.4. 2-[6-(4-nitrophenyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-4-
yl]-indane-1,3-dione (3d). Yield 43%; mp 182e183 ꢁC; IR (cmꢀ1):
3362 (NeH stretching), 3000 (CeH aromatic stretching), 2901 (CeH
aliphatic stretching), 1698 (C]O stretching), 1621 (C]N stretching),
1582 (C]C stretching); 1H NMR
d (ppm): 10.181 (s, IH, NH), 7.021e
Fig. 2. Binding mode of 3h into the binding site of 1CX2.
7.152 (m, 2H), 7.256e7.351 (m, 2H) 7.482e7.586 (m, 1H), 7.681e
7.735 (m, 2H), 7.832e7.952 (m, 1H), 7.021e7.952 (m, 8H, aromatic),
6.251e6.294 (dd, J ¼ 10.0 Hz, J ¼ 5.2 Hz,1H), 3.494 (s,1H), 2.632e2.674
(dd, J¼ 5.2Hz,J¼ 12.0Hz,1H),1.848e1.896(dd, J¼ 12.0Hz, J¼ 10.0 Hz,
1H); MS (m/z) (%): 364 [Mþ þ 1, 22%]. Anal. Calcd for C19H13N3O5: C,
62.81; H, 3.61; N, 11.57. Found: C, 62.63; H, 3.23; N, 11.11.
J ¼ 9.8 Hz, 1H); 13C NMR (125 MHz, DMSO-d6)
d 210.57, 209.87,
160.81, 136.41, 136.21, 135.80, 127.57, 127.47, 127.27, 126.01, 125.57,
123.54, 123.21, 123.07, 120.88, 119.48, 65.44, 57.74, 36.44, 28.37,
28.21; MS (m/z) (%): 362 [Mþ þ 1, 11%]. Anal. Calcd for C21H19N3O3:
C, 69.79; H, 5.30; N, 11.63. Found: C, 69.56; H, 5.14; N, 11.42.
4.1.2.5. 2-[6-(4-chlorophenyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-4-
yl]-indane-1,3-dione (3e). Yield 56%; mp 176e178 ꢁC; IR (cmꢀ1):
3328.57 (NeH stretching), 3192 (CeH aromatic stretching), 2921
(CeH aliphatic stretching), 1702 (C]O stretching), 1640 (C]N
4.1.2.7. 2-[6-(4-methoxyphenyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-
4-yl]-indane-1,3-dione (3g). Yield 64%; mp 210e212 ꢁC; IR (cmꢀ1):
3355 (NeH stretching), 3071 (CeH aromatic stretching), 2881 (CeH
aliphatic stretching), 1702 (C]O stretching), 1642 (C]N stretch-
stretching), 1562 (C]C stretching); 1H NMR
d
(ppm): 10.901 (s, IH,
ing), 1586 (C]C stretching); 1H NMR
d (ppm): 9.951 (s, 1H, NH),
NH), 6.932e7.052 (m, 2H), 7.159e7.256 (m, 2H) 7.361e7.422 (m,
1H), 7.582e7.627 (m, 2H), 7.698e7.785 (m, 1H), 6.402e6.452 (dd,
J ¼ 9.6 Hz, J ¼ 5.6 Hz, 1H), 3.521 (s, 1H), 2.342e2.684 (dd, J ¼ 5.6 Hz,
J ¼ 11.2 Hz, 1H), 1.622e4.672 (dd, J ¼ 11.2 Hz, J ¼ 9.6 Hz, 1H); 13C
7.414e7.472 (m, 2H), 7.552e7.599 (m, 2H) 7.621e7.665 (m, 1H),
7.682e7.702 (m, 2H), 7.705e7.751 (m, 1H), 6.521e6.565 (dd,
J ¼ 10.4 Hz, J ¼ 5.2 Hz, 1H), 3.401 (s, 1H), 3.157 (s, 3H), 2.632e2.685
(dd, J ¼ 5.2 Hz, J ¼ 12.4 Hz, 1H), 2.052e2.096 (dd, J ¼ 12.4 Hz,
J ¼ 10.4 Hz, 1H); MS (m/z) (%): 349 [Mþ þ 1, 21%]. Anal. Calcd
for C20H16N2O4: C, 68.98; H, 4.63; N, 8.04. Found: C, 38.66; H, 4.52;
N, 8.22.
NMR (125 MHz, DMSO-d6)
d 210.69, 209.74, 160.77, 136.84, 136.75,
135.78, 127.68, 127.34, 127.15, 126.01, 125.37, 123.48, 123.31, 123.01,
120.98, 119.48, 65.47, 57.88, 36.47; MS (m/z) (%) : 354 [Mþ þ 2, 10%].
Anal. Calcd for C19H13ClN2O3: C, 64.69; H, 3.71; N, 7.94. Found: C,
64.52; H, 3.55; N, 7.46.
4.1.2.8. 2-[6-(2-furyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-4-yl]-
indane-1,3-dione (3h). Yield 69%; mp 145e146 ꢁC; IR (cmꢀ1): 3359
(NeH stretching), 3064 (CeH aromatic stretching), 2882 (CeH
aliphatic stretching), 1701 (C]O stretching), 1620 (C]N stretch-
4.1.2.6. 2-{6-[4-(dimethylamino)phenyl]-2-oxo-1,2,5,6-
tetrahydropyrimidin-4-yl}-indane-1,3-dione (3f). Yield 59%; mp
162e163 ꢁC; IR (cmꢀ1): 3312.41 (NeH stretching), 3055 (CeH
aromatic stretching), 2912 (CeH aliphatic stretching), 1662 (C]N
ing), 1586 (C]C stretching); 1H NMR
d (ppm): 10.382 (s, IH, NH),
7.211e7.252 (m, 2H), 7.256e7.358 (m, 2H) 7.452e7.505 (m, 1H),
7.658e7.765 (m, 2H) 6.820e6.868 (dd, J ¼ 9.6 Hz, J ¼ 5.6 Hz, 1H),
3.504 (s,1H), 2.401e2.452 (dd, J ¼ 5.6 Hz, J ¼ 11.6 Hz,1H), 2.056 (dd,
J ¼ 11.6 Hz, J ¼ 9.4 Hz, 1H); MS (m/z) (%): 309 [Mþ þ 1, 12%]. Anal.
Calcd for C17H12N2O4: C, 66.23; H, 3.92; N, 9.09. Found: C, 66.05; H,
3.59; N, 8.95.
stretching), 1591 (C]C stretching); 1H NMR
d (ppm): 9.674 (s, 1H,
NH), 7.045e7.154 (m, 2H), 7.232e7.366 (m, 2H) 7.488e7.592 (m,
1H), 7.601e7.652 (m, 2H), 7.689e7.724 (m, 1H), 6.693e6.767 (dd,
J ¼ 9.8 Hz, J ¼ 5.2 Hz, 1H), 3.384 (s, 1H), 2.970e3.045 (dd, J ¼ 5.2 Hz,
J ¼ 12.4 Hz, 1H), 2.516 (s, 6H), 2.315e2.392 (dd, J ¼ 12.2 Hz,
Fig. 1. Binding mode of indomethacin into the binding site of 1CX2.
Fig. 3. Binding mode of indomethacin into the binding site of 2OYE.

482
D. Giles et al. / European Journal of Medicinal Chemistry 58 (2012) 478e484
3373 (NeH stretching), 3083 (CeH aromatic stretching), 2989 (CeH
aliphatic stretching), 1702 (C]O stretching), 1620 (C]N stretch-
ing), 1586 (C]C stretching); 1H NMR
(ppm): 12.142 (s, IH, NH),
d
10.025 (s, IH, NH), 7.211e7.302 (m, 2H), 7.352e7.415 (m, 2H) 7.424e
7.501 (m, 1H), 7.689e7.756 (m, 2H) 7.852e7.921 (m, 1H), 8.226e
8.306 (m, 1H), 6.761e6.810 (dd, J ¼ 9.4 Hz, J ¼ 5.4 Hz, 1H), 3.125
(s, 1H), 2.610e2.690 (dd, J ¼ 5.4 Hz, J ¼ 11.8 Hz, 1H), 2.462e2.502
(dd, J ¼ 11.8 Hz, J ¼ 9.4 Hz, 1H); MS (m/z) (%): 358 [Mþ þ 1, 23%].
Anal. Calcd for C21H15N3O3: C, 70.58; H, 4.23; N, 11.76. Found: C,
70.52; H, 4.13; N, 11.59.
4.1.2.12. 2-[6-(4-hydroxy-3-methoxyphenyl)-2-oxo-1,2,5,6-
tetrahydropyrimidin-4-yl]-indane-1,3-dione (3l). Yield 53%; mp
165e168 ꢁC; IR (cmꢀ1): 3545 (OeH stretching) 3331 (NeH stretch-
ing), 3034 (CeH aromatic stretching), 2942 (CeH aliphatic stretch-
ing), 1709 (C]O stretching), 1641 (C]N stretching), 1576 (C]C
Fig. 4. Binding mode of 4j into the binding site of 2OYE.
stretching); 1H NMR
d (ppm): 11.212 (s, IH, OH), 10.211 (s, IH, NH),
6.955e7.121 (m, 2H), 7.221e7.311 (m, 2H) 7.426e7.521 (m, 1H),
7.625e7.721 (m, 1H) 7.921e8.052 (m, 1H), 6.754e6.822 (dd,
J ¼ 10.4 Hz, J ¼ 5.2 Hz,1H), 3.411 (s,1H), 3.221 (s, 3H) 2.521e2.593 (dd,
J ¼ 5.2 Hz, J ¼ 12.4 Hz, 1H), 2.221e2.286 (dd, J ¼ 12.4 Hz, J ¼ 10.4 Hz,
1H; MS (m/z) (%): 364 [Mþ, 22%). Anal. Calcd for C20H16N2O5: C, 65.93;
H, 4.43; N, 7.69. Found: C, 65.65; H, 4.29; N, 7.49.
4.1.2.9. 2-{2-oxo-6-[2-phenylvinyl]-1,2,5,6-tetrahydropyrimidin-4-
yl}-indane-1,3-dione (3i). Yield 49%; mp 186e187 ꢁC; IR (cmꢀ1):
3394 (NeH stretching), 3085 (CeH aromatic stretching), 2863 (Ce
H
aliphatic stretching), 1692 (C]O stretching), 1642 (C]N
stretching), 1544 (C]C stretching); 1H NMR
d
(ppm): 10.052 (s, IH,
NH), 6.932e7.052 (m, 2H), 7.122e7.252 (m, 2H) 7.289e7.321
(m, 1H), 7.356e7.452 (m, 2H), 7.521e7.602 (m, 2H), 7.952e8.021
(m, 2H), 6.851e6.898 (dd, J ¼ 10.8 Hz, J ¼ 5.2 Hz, 1H), 3.402
(s, 1H), 2.652e2.699 (dd, J ¼ 5.2 Hz, J ¼ 12.8 Hz, 1H), 1.921e1.970
(dd, J ¼ 12.8 Hz, J ¼ 10.4 Hz, 1H); MS (m/z) (%): 344 [Mþ, 22%].
Anal. Calcd for C21H16N2O3: C, 73.24; H, 4.68; N, 8.13. Found: C,
73.02; H, 4.52; N, 8.08.
4.2. Docking studies
Molecular docking studies of the synthesized compounds were
performed in order to rationalize the obtained biological results.
Molecular docking studies further help in understanding the various
interactions between the ligand and enzyme active site in detail.
Docking study was carried out for the target compounds using
Molegro Virtual docker version 2010. MolDock scoring function is
used by MVD program is defined by
4.1.2.10. 2-[6-(2-hydroxyphenyl)-2-oxo-1,2,5,6-tetrahydropyrimidin-
4-yl]-indane-1,3-dione (3j). Yield 58%; mp 189e191 ꢁC; IR (cmꢀ1):
3373 (OeH stretching), 3361 (NeH stretching), 3083 (CeH
aromatic stretching), 2925 (CeH aliphatic stretching), 1641 (C]O
stretching), 1641 (C]N stretching), 1542 (C]C stretching); 1H NMR
Escore ¼ Einter þ Eintra
d
(ppm): 12.152 (s, 1H, OH), 9.942 (s, IH, NH), 7.321e7.388 (m, 2H),
Where, Escore ¼ MolDock score.
7.402e7.483 (m, 2H) 7.525e7.608 (m, 1H), 7.898e8.086 (m, 2H)
8.126e8.289 (m, 1H), 7.105e7.152 (dd, J ¼ 10.4 Hz, J ¼ 4.8 Hz, 1H),
3.478 (s, 1H), 2.654e2.692 (dd, J ¼ 4.8 Hz, J ¼ 12.0 Hz, 1H), 2.458e
2.499 (dd, J ¼ 12.0 Hz, J ¼ 10.4 Hz, 1H); MS (m/z) (%): 335 [Mþ þ 1,
12%]. Anal. Calcd for C19H14N2O4: C, 68.26; H, 4.22; N, 8.38. Found:
C, 68.06; H, 4.12; N, 8.12.
Einter ¼ ligandeProtein interaction
Eintra ¼ internal energy of the ligand.
The ligand structure was drawn in Marvin Sketch 5.4. Hydrogen
atoms were viewed. The 2D structure was then converted into 3D
and saved as PDB file type. It was then imported into Molegro
Virtual Docker. The Pdb codes 1CX2 and 2OYE were downloaded
from the protein data bank www.pdb.org then docking was carried
4.1.2.11. 2-[6-(1H-indol-2-yl)-2-oxo-1,2,5,6-tetrahydropyrimidin-4-
yl]-indane-1,3-dione (3k). Yield 59%; mp 110e112 ꢁC; IR (cmꢀ1):
Table 1
Anti-inflammatory activity of the synthesized compounds.
Compound
Change in paw volume (in mL) after drug administration (Mean ꢂ SEMa)
Percentage inhibition of edema volume after
1 h
2 h
3 h
4 h
1 h
2 h
3 h
4 h
Control
Standard
3a
3b
3c
3d
3e
3f
3g
3h
3i
0.76 ꢂ 0.03
0.58 ꢂ 0.06*
0.61 ꢂ 0.04
0.68 ꢂ 0.05
0.56 ꢂ 0.06*
0.64 ꢂ 0.02
0.64 ꢂ 0.03
0.65 ꢂ 0.02
0.60 ꢂ 0.05
0.63 ꢂ 0.06
0.63 ꢂ 0.07**
0.58 ꢂ 0.04
0.62 ꢂ 0.03
0.61 ꢂ 0.05
0.83 ꢂ 0.02
0.66 ꢂ 0.02
0.41 ꢂ 0.02**
0.52 ꢂ 0.03
0.49 ꢂ 0.05*
0.53 ꢂ 0.03
0.53 ꢂ 0.06
0.46 ꢂ 0.03**
0.53 ꢂ 0.03
0.51 ꢂ 0.04
0.53 ꢂ 0.03
0.55 ꢂ 0.03
0.54 ꢂ 0.03
0.58 ꢂ 0.02
0.49 ꢂ 0.03*
0.60 ꢂ 0.02
0.39 ꢂ 0.02*
0.53 ꢂ 0.03
0.41 ꢂ 0.03*
0.52 ꢂ 0.03
0.49 ꢂ 0.06
0.39 ꢂ 0.04*
0.50 ꢂ 0.05
0.54 ꢂ 0.04
0.56 ꢂ 0.02
0.50 ꢂ 0.04
0.50 ꢂ 0.05
0.52 ꢂ 0.06
0.53 ꢂ 0.04
e
e
e
e
0.43 ꢂ 0.02**
0.55 ꢂ 0.03**
0.58 ꢂ 0.03**
0.53 ꢂ 0.03**
0.61 ꢂ 0.05**
0.68 ꢂ 0.06
23
20
11
27
16
15
15
22
18
17
24
19
20
48
33
30
36
26
19
29
21
25
32
22
21
33
39
21
26
21
19
31
20
22
20
18
19
12
26
34
11
32
12
18
34
16
10
7
16
16
12
11
0.59 ꢂ 0.03**
0.66 ꢂ 0.03
0.62 ꢂ 0.02**
0.57 ꢂ 0.02**
0.65 ꢂ 0.05*
0.66 ꢂ 0.07
3j
3k
3l
0.56 ꢂ 0.02**
*P < 0.05; **P < 0.01; ***P < 0.001.
a
Standard Error Mean.

D. Giles et al. / European Journal of Medicinal Chemistry 58 (2012) 478e484
483
Table 3
out for the structural proteins [35]. Figs. 1e4 represent the binding
Analgesic activity of the synthesized compounds.
modes of indomethacin, 3h and 4j with 1CX2 and 2OYE.
Compound
No. of writhing in 15 min
Percentage inhibition
of pain
(Mean ꢂ SEMa)
4.3. Biological activities
Control
Standard
3a
3b
3c
3d
3e
3f
3g
3h
3i
36.20 ꢂ 0.84
e
16.50 ꢂ 1.18**
25.33 ꢂ 1.76**
23.83 ꢂ 1.13**
23.33 ꢂ 1.56**
22.66 ꢂ 0.98**
20.50 ꢂ 2.09**
17.50 ꢂ 1.20**
25.33 ꢂ 1.89**
27.66 ꢂ 1.90*
30.83 ꢂ 1.97
55
31
35
36
38
44
52
31
25
16
37
21
28
4.3.1. Anti-inflammatory activity
Rats weighing between 150e200 g were selected randomly
(excluding pregnant female rats) for the test [12]. Animals were
housed with food and water for two days before testing. A mark
was made on hind paw just beyond tibiotarsal junction, to ensure
constant paw volume. The initial paw volume of each rat was noted
by mercury displacement method. Animals were divided into
groups with six animals in each group. The first groups of rats were
treated with 0.1 mL of 1% carboxy methylcellulose suspension
orally (control). The second group was administered with at a dose
of 10 mg/kg of the suspension of indomethacin (standard) and the
other groups were treated with 10 mg/kg of the suspension of test
compounds. After 30 min 0.1 mL of 1% (w/v) carrageenan was
injected in the plantar region of the left paw of control, standard
and test groups. The paw volumes were noted for 1, 2, 3 and 4 h
after carrageenan challenge. The percent difference in paw volumes
were calculated and expressed as percent edema inhibition by the
drugs. It was calculated by using the formula
3j
3k
3l
23.00 ꢂ 2.11**
29.00 ꢂ 1.77*
26.5 ꢂ 1.33**
*P < 0.05; **P < 0.01; ***P < 0.001.
a
Standard Error Mean.
such response during a period of 10 min was recorded. The stan-
dard and test compounds were injected to the other group of
animals at the dose of 10 mg/kg. Fifteen minutes later, acetic acid
solution was administered to these animals. The onset and severity
of writhing response were noted. The mean writhing scores in
control and compound treated groups were calculated and inhibi-
tion of pain response by compounds was noted.
Vt
Vc
1 ꢀ
ꢃ 100
Where
Vt
Vc
Percentage inhibition of pain ¼ 1 ꢀ
ꢃ 100
Vt: e edema volume in drug treated group.
Vc: e edema volume in the control group.
Where,
The results of anti-inflammatory activity of the synthesized
compounds were specified in Table 1.
Vt: e number of writhing (mean) in drug treated group.
Vc: e number of writhing (mean) in control group.
4.3.2. Ulcerogenic effect
The results of analgesic activity of synthesized compounds were
tabulated in Table 3.
Ulceration in rats was induced as described by Goyal et al.
Wistar albino rats weighing 150e200 g of either sex were divided
into various groups of six animals. Control group of animals were
treated with 10% v/v Tween 80 suspension intraperitoneally [12].
One group was administered with indomethacin intraperitoneally
in a dose of 10 mg/kg once daily for three days. The remaining
group was administered with test compounds intraperitoneally at
the dose of 10 mg/kg. On the fourth day, pylorus was ligated and the
animals were fasted for 36 h before the ligation procedure. Four
hours after ligation, animals were sacrificed. The stomach was
removed along with the greater curvature. Ulcer index was deter-
mined. The results were reported in Table 2.
4.3.4. Antimicrobial activity
Minimum inhibitory concentration (MIC) of any compound is
defined as the lowest concentration, which completely inhibits
growth (turbidity on liquid media). In vitro antimicrobial activities
of the compounds were tested by using the tube dilution method.
The medium was prepared and the sterile broth was then poured
in each sterile tube followed by addition of compound in first
tube. Two-fold serial dilution was carried out from the tubes and
excess broth was discarded from the last tube. McFarland stan-
dard was compared visually to
a microbial suspension of
4.3.3. Analgesic activity
Table 4
Antimicrobial activity of the synthesized compounds.
Compound Minimum inhibitory concentration (
E. coli P. aeruginosa B. subtilis S. aureus A. niger C. albicans
The mice were weighed and numbered. Animals were divided
into different groups, each containing at least six mice [12].
Appropriate volume of acetic acid solution was administered to the
first group (which serves as control) and placed individually under
glass jar for observation. The onset on writhes was noted. The
number of abdominal contractions, trunk twist response and
extension of hind limbs as well as the number of animals showing
m
g/mL)
Ampicillin
3.9
3.9
3.9
3.9
e
e
Fluconazole
e
e
e
e
7.8
7.8
3a
3b
3c
3d
3e
3f
3g
3h
3i
62.5
31.2
250
500
125
125
250
31.2
125
500
250
500
125
250
250
250
62.5
62.5
250
500
250
125
125
250
250
250
250
250
31.2
125
125
31.2
125
250
250
250
125
125
125
125
125
125
500
62.5
62.5
125
250
125
500
500
125
500
125
500
250
62.5
250
500
125
125
500
500
500
500
125
500
250
62.5
250
250
500
250
Table 2
Evaluation of ulcerogenicity index.
Compound
Ulcer index (Mean ꢂ SEMa)
Control
Indomethacin
3e
0.13 ꢂ 0.22
1.70 ꢂ 0.32**
1.28 ꢂ 0.32*
3j
3k
3l
*P < 0.05; **P < 0.01; ***P < 0.001.
a
Standard Error Mean.

484
D. Giles et al. / European Journal of Medicinal Chemistry 58 (2012) 478e484
approximately 1.5 ꢃ 108 cells/mL. To each tube, standard inocu-
lums were added [36].
The test compounds, ampicillin and fluconazole were diluted to
get 1000, 500, 250, 125, 62.5, 31.2, 15.6, 7.8, 3.9, 1.9, 0.97 mg/mL
concentration. 10% DMSO was used as a solvent. All determinations
were done in duplicate and the average was taken as final reading.
In order to ensure that the solvent had no effect on the growth
a control test was performed containing inoculated broth sus-
pended with 10% DMSO. Then it was kept for incubation.
[4] P. David A, Am. J. Med. 117 (2004) S63eS71.
[5] F. Buttgereit, G.R. Burmester, L.S. Simon, Am. J. Med. 110 (2001) S13eS19.
[6] M. Denis, Am. J. Med. 105 (1998) 3Se9S.
[7] C. Charlier, C. Michaux, Eur. J. Med. Chem. 38 (2003) 645e659.
[8] X.-P. Miao, Q. Ouyang, H.-Y. Li, Z.-H. Wen, D.-K. Zhang, X.-Y. Cui, Curr. Ther.
Res. 69 (2008) 181e191.
[9] S. Ronald S, Semin. Arthritis Rheum. 26 (1996) 435e446.
[10] B. Cryer, M. Feldman, Am. J. Med. 104 (1998) 413e421.
[11] A.A. Abu-Hashem, M.M. Youssef, Molecules 16 (2011) 1956e1972.
[12] V. Alagarsamy, S. Meena, K.V. Ramseshu, V.R. Solomon, K. Thirumurugan,
K. Dhanabal, M. Murugan, Eur. J. Med. Chem. 41 (2006) 1293e1300.
[13] K.M. Amin, M.M. Hanna, H.E. Abo-Youssef, R.F. George, Eur. J. Med. Chem.
44 (2009) 4572e4584.
[14] N. Kumar, A. Chauhan, S. Drabu, Biomed. Pharmacother. 65 (2011) 375e380.
[15] G. Amr Ael, H.H. Sayed, M.M. Abdulla, Arch. Pharm. 338 (2005) 433e440.
[16] R.S. Keri, K.M. Hosamani, R.V. Shingalapur, M.H. Hugar, Eur. J. Med. Chem.
45 (2010) 2597e2605.
[17] N.M. Abunada, H.M. Hassaneen, N.G. Kandile, O.A. Miqdad, Molecules 13 (2008)
1501e1517.
4.3.4.1. Antibacterial. The antibacterial activities of the synthesized
compounds were tested against E. coli (MTCC-4351), P. aeruginosa,
(MTCC-424), B. subtilis, (MTCC-441) and S. aureus (MTCC-3160)
using MullereHinton medium. The pH was maintained at 7.4. The
incubation was carried out at 37 ꢂ 1 ꢁC for 24 h. After incubation for
24 h, the tube with no growth of microorganism was recorded to
[18] E.S. Al-Abdullah, A.R. Al-Obaid, O.A. Al-Deeb, E.E. Habib, A.A. El-Emam, Eur. J.
Med. Chem. 46 (2011) 4642e4647.
[19] G. Auzzi, A. Costanzo, F. Bruni, M. Clauser, G. Guerrini, S. Selleri, L. Pecori
Vettori, Farmaco 45 (1990) 1193e1205.
[20] A.A. Bekhit, H.T.Y. Fahmy, S.A.F. Rostom, A.M. Baraka, Eur. J. Med. Chem. 38
(2003) 27e36.
represent MIC, which was expressed in mg/mL. At the end of the
incubation period, the MIC values were determined. The results
were reported in Table 4.
[21] O.M. Ahmed, M.A. Mohamed, R.R. Ahmed, S.A. Ahmed, Eur. J. Med. Chem.
44 (2009) 3519e3523.
[22] A.G. Amr, A.M. Mohamed, S.F. Mohamed, N.A. Abdel-Hafez, F. Hammam Ael,
Bioorg. Med. Chem. 14 (2006) 5481e5488.
[23] M. Debi, Indian J. Exp. Biol. 35 (1997) 1208e1213.
[24] A. Kamal, J.S. Reddy, M.J. Ramaiah, E.V. Bharathi, D. Dastagiri, M.K. Reddy,
S.N. Pushpavalli, M. Pal-Bhadra, Bioorg. Med. Chem. Lett. 20 (2010)
5232e5236.
4.3.4.2. Antifungal activities. The antifungal activities of the
synthesized compounds were tested against A. niger (MTCC-282)
and C. albicans (MTCC-183) using sabouraud dextrose broth main-
tained at pH 7.4. The tubes were incubated at 25 ꢂ 1 ꢁC for 48 h. The
tube with no growth of fungi was recorded to represent MIC
expressed in mg/mL. The results were reported in Table 4.
[25] S. Kim, D.H. Park, T.H. Kim, M. Hwang, J. Shim, FEBS J. 276 (2009) 4715e4726.
[26] D. Giles, M. Prakash, K. Ramsesu, E-J Chem 4 (2007) 428e433.
[27] W. He, F.-C. Huang, B. Hanney, J. Souness, B. Miller, G. Liang, J. Mason, S. Djuric,
J. Med. Chem. 41 (1998) 4216e4223.
Acknowledgment
[28] S. Robert-Piessard, D. Leblois, P. Kumar, J. Robert, G.L. Baut, L. Sparfel,
B.R.E.K.R. Sanchez, J. Petit, L. Welin, Eur. J. Med. Chem. 25 (1990) 735e747.
[29] P. Crooks, R. Sommeerville, J. Pharm. Sci. 71 (1982) 291e294.
[30] S.L. Shapiro, K. Geiger, L. Freedman, J. Org. Chem. 25 (1960) 1860e1865.
[31] S. Jubie, S. Meena, K.V. Ramaseshu, N. Jawahar, S. Vijayakumar. Sect. B, Indian
J. Chem. 49 (2010) 1261e1263.
Authors are thankful to Sri. B. Premnath Reddy, Chairman,
Acharya Institutes for providing facilities for the successful comple-
tion of the project. We also thank Dr. Rene Thomsen for providing
Molegro trial license.
[32] S. Inayama, K. Mamoto, T. Shibata, M. Hirose, J. Med. Chem. 19 (1976)
433e436.
[33] T. Matsuo, T. Takagi, K. Saito, H. Yuki, T. Yamaguchi, Yakugaku Zasshi 101
(1981) 960e964.
References
[34] Y. Rajendraprasad, A. Laxshnamarao, R. Rambabu, E-J Chem 5 (2008) 461e466.
[35] B. Sandhya, D. Giles, V. Mathew, G. Basavarajaswamy, R. Abraham, Eur. J. Med.
Chem. 46 (2011) 4696e4701.
[1] V. Vassileva, M. Piquette-Miller, Clin. Pharmacol. Ther. 87 (2010) 375e379.
[2] A. Lanas, Dig. Liver Dis. 33 (2001) S29eS34.
[36] J.M. Andrews, J. Antimicrob. Chemother. 48 (suppl. S1) (2001) 5e16.
[3] B.M.D.F. Peter, Am. J. Med. 104 (1998) 9Se13S.