Synthesis, screening for antitubercular activity and 3D-QSAR studies of substituted N-phenyl-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydro-pyrimidine-5-carboxamides

Article abstract of DOI:10.1016/j.ejmech.2007.08.004

Multi-drug resistance to commonly used antitubercular drugs has propelled the development of new structural classes of antitubercular agents. This paper reports the synthesis, evaluation and 3D-QSAR analysis of a set of substituted N-phenyl-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydropyrimidine-5-carboxamides as antitubercular agents. Substituted acetoacetanilides were reacted with various aromatic aldehydes and urea which yielded the tetrahydropyrimidine derivatives with a phenyl carbamoyl group at C₅ position, and with various substitutions on the 4-phenyl and the N-phenyl aromatic rings. All compounds were screened for antitubercular activity against Mycobacterium tuberculosis H₃₇Rv strain. The QSAR models were generated on a training set of 23 molecules. The molecules were aligned using the atom-fit and field-fit techniques. The CoMFA and CoMSIA models generated on the molecules aligned by the atom-fit method show a correlation coefficient (r²) of 0.98 and 0.95 with cross-validated r²(q²) of 0.68 and 0.58, respectively. The 3D-QSAR models were externally validated against a test set of 7 molecules for which the predictive r² (r_pred²) is recorded as 0.41 and 0.32 for the CoMFA and CoMSIA models, respectively. The CoMFA and CoMSIA contours helped to design some new molecules with improved activity.

Full text of DOI:10.1016/j.ejmech.2007.08.004

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European Journal of Medicinal Chemistry 43 (2008) 2103e2115
http://www.elsevier.com/locate/ejmech
Original article
Synthesis, screening for antitubercular activity and 3D-QSAR
studies of substituted N-phenyl-6-methyl-2-oxo-4-phenyl-
1,2,3,4-tetrahydro-pyrimidine-5-carboxamides
Vijay Virsodia a, Raghuvir R.S. Pissurlenkar b, Dinesh Manvar c, Chintan Dholakia d,
Priti Adlakha e, Anamik Shah a, , Evans C. Coutinho
*
b,**
a Department of Chemistry, Saurashtra University, Rajkot 360 005, Gujarat, India
b Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, Maharashtra, India
c Calyx Chemicals and Pharmaceuticals Ltd., Mumbai 400 072, Maharashtra, India
d Unimark Remedies Ltd., Bavla, Ahemdabad 382 220, Gujarat, India
e Institute of Applied Synthetic Chemistry, Vienna University of Technology, Vienna, Austria
Received 29 May 2007; received in revised form 26 June 2007; accepted 20 August 2007
Available online 11 September 2007
Abstract
Multi-drug resistance to commonly used antitubercular drugs has propelled the development of new structural classes of antitubercular
agents. This paper reports the synthesis, evaluation and 3D-QSAR analysis of a set of substituted N-phenyl-6-methyl-2-oxo-4-phenyl-1,2,3,4-
tetrahydropyrimidine-5-carboxamides as antitubercular agents. Substituted acetoacetanilides were reacted with various aromatic aldehydes
and urea which yielded the tetrahydropyrimidine derivatives with a phenyl carbamoyl group at C5 position, and with various substitutions on
the 4-phenyl and the N-phenyl aromatic rings. All compounds were screened for antitubercular activity against Mycobacterium tuberculosis
H37Rv strain. The QSAR models were generated on a training set of 23 molecules. The molecules were aligned using the atom-fit and field-
fit techniques. The CoMFA and CoMSIA models generated on the molecules aligned by the atom-fit method show a correlation coefficient
(r2) of 0.98 and 0.95 with cross-validated r2(q2) of 0.68 and 0.58, respectively. The 3D-QSAR models were externally validated against
a test set of 7 molecules for which the predictive r2 (rp2red) is recorded as 0.41 and 0.32 for the CoMFA and CoMSIA models, respectively.
The CoMFA and CoMSIA contours helped to design some new molecules with improved activity.
Ó 2007 Elsevier Masson SAS. All rights reserved.
Keywords: Tetrahydropyrimidines; Antitubercular activity; CoMFA; CoMSIA
1. Introduction
Multi-drug resistance tuberculosis (MDR-TB), defined as
resistance to at least isoniazid and rifampicin [4], is a serious
threat to tuberculosis control and prevention. Isoniazid blocks
the biosynthesis of mycolic acids, essential components of
mycobacterial cell wall, and is believed to be oxidized by cat-
alase peroxidase (KatG) to the active form [5]. Mutations in
the KatG and the InhA genes are associated with 70e80%
of INH resistant M. tuberculosis isolates [6]. Resistance to ri-
fampicin has been associated with mutations in the 81-bp core
region of the rpoB gene encoding the b-subunit of RNA poly-
merase [7,8], in over 90% cases. The development of resis-
tance by M. tuberculosis to commonly used antitubercular
One-third of the world’s population is infected with Myco-
bacterium tuberculosis which is the leading cause of death
[1,2] in the developing world. Approximately 2 million people
die every year [3].
* Corresponding author. Tel.: þ91 281 2581013; fax: þ91 281 2576802.
** Corresponding author. Tel.: þ91 22 2667 0871; fax: þ91 22 2667 0816.
E-mail addresses: anamik_shah@hotmail.com (A. Shah), evans@bcpindia.
org (E.C. Coutinho).
0223-5234/$ - see front matter Ó 2007 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.ejmech.2007.08.004

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V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
drugs necessitates a longer duration of therapy. The emergence
of multi-drug resistance has forced the development of new
structural classes of antitubercular agents, with several of
them showing promising activity against M. tuberculosis [9].
There are several reports in the literature of new structural
classes of antitubercular agents. Derivatives of imidazoles
have MIC values between 0.015 and 0.25 mg/mL against var-
ious drug-resistant strains of M. tuberculosis, and are highly
active both in vitro and in vivo [10,11]. Acyclic deoxy mono-
saccharide derivatives, from the carbohydrate class, have
MIC value of 3.125 mg/mL against H37Rv strain [12]. The
most effective derivative from the benzoic acid hydrazone
class with a MIC of 2.0 mg/mL is a good lead for further
drug design studies [13]. Calanolide A, a naturally occurring
coumarin derivative and an inhibitor of HIV-1 reverse tran-
scriptase also shows promising in vitro activity against M.
tuberculosis with MIC value of 3.13 mg/mL [14,15]. The pu-
rine derivatives are quite potent against M. tuberculosis
H37Rv strain with MIC of 0.78 mg/mL [16,17]. The most
effective compounds of the pyrrole class exhibit MIC values
of 0.4 mg/mL and 0.7 mg/mL against Mycobacterium avium
and M. tuberculosis, respectively [18,19]. MIC value of
0.5 mcmol/L has been reported for benzoxazine derivatives,
against M. tuberculosis [20]. Various diterpenoids derived
from plants have been described to possess tuberculosis activ-
ity against M. tuberculosis [21,22]. These new structural clas-
ses build important plots for the focused development of new
antitubercular drugs.
Pyridines and pyrimidines have also been identified with
antitubercular activity and can be developed as new structural
classes of antitubercular agents. Amongst the pyridines, N-
alkyl-1,2-dihydro-2-thioxo-3-pyridine carbothioamides have
been recognized as a novel class of compounds with good an-
titubercular activity. Two compounds in this series have an
MIC of 0.50 mg/mL [23]. N-Pyridinylsalicylamides which
also belong to the pyridine class of compounds have an
MIC of 2.0 mg/mL. The effect of various substitutions on
activity of this class was studied by QSAR [24]. Within the
pyrimidine group, 2,4-diaminopyrimidines have been identi-
fied with IC50 of 0.0058 mM and a safety index >600 [25].
The most effective derivative in the chloropyrimidine series
has an MIC of 0.78 mg/mL [26], while the most successful
compound from the anilinopyrimidine series displays an
MIC of 3.12 mg/mL [27]. Thymidine monophosphate deriva-
tives have been evaluated for binding to thymidine monophos-
phate kinase of M. tuberculosis. The most effective inhibitor
has a Ki of 10.5 mM [28]. Thus, this structural class holds
great hope for development of new and effective antitubercu-
lar agents.
continuation of this work, we sought to explore and modify
the 1,4-dihydropyridines to tetrahydropyrimidines (which can
be viewed as aza analogs of pyridines) for development of
new antitubercular agents and to subject them to a QSAR anal-
ysis to understand the relationships between structure and activ-
ity for this class. This paper describes the synthesis, evaluation
and 3D-QSAR studies of a series of N-phenyl-6-methyl-2-oxo-
4-phenyl-1,2,3,4-tetrahydro-pyrimidine-5-carboxamides.
2. Results and discussion
2.1. Chemistry
Various substituted acetoacetanilides (2aen) were prepared
by reacting substituted amines and ethyl acetoacetate in tolu-
ene with a catalytic amount of NaOH or KOH (Scheme 1).
The reaction mixture was heated at 120 ꢀC for 10e15 h.
Fourteen different acetoacetanilides were synthesized bearing
various electron donating and electron withdrawing groups
like 2,3-diCH3; 3,4-diCH3; 4-CH3; H; 2,5-diCH3; 2,4-diCH3;
3-Cl-4-F; 4-F; 4-Cl; 2-Cl; 2-F; 4-OCH3; 2,5-diCl and 3-NO2
on the phenyl ring. Acetoacetanilides, thus obtained, were
used as 1,3-diketone adducts for the multi-component Bigi-
nelli reaction.
The acetoacetanilides (2aen) were reacted with substituted
aldehydes and urea in methanol using conc. HCl in catalytic
amount to obtain the title compounds (3aev, 4aeg) depicted
in Scheme 2. The reaction time was found to vary from 5 to
10 h depending upon the substitutions on the aldehydes and
the 1,3-diketones.
The structures of the synthesized compounds were con-
firmed by spectral analysis. The carbonyl group of NHeCO
(amide) was observed at 1650e1690 cmꢁ1 and the cyclic
ketone was observed at 1700e1720 cmꢁ1 in the IR spectra.
In the NMR spectra, the proton attached to C4 was observed
between d 4.2 and 6.0 ppm. The protons attached to the methyl
group on C6 are deshielded and were observed at d 1.8e3.8
ppm. The signals of N1H, N3H and the NH of the carbamoyl
group were observed downfield (d ¼ 7.2e10.0 ppm). The
molecular ion peaks (Mþ) were in total agreement with the
molecular weight. The elemental analysis was found to match
the calculated elemental composition within the permissible
error limits.
2.2. Antitubercular activity
Synthesized compounds (3aev, 4aeg) were tested for their
antitubercular activity against M. tuberculosis H37Rv strain.
Percentage inhibition data of compounds (3aev, 4aeg) are
reported in Tables 1 and 2. Compounds 3c and 4f, with 2,3-
dimethylphenyl and 3,4-dimethyl carbamoyl side chain, re-
spectively, showed 65% and 63% inhibition. Thus, methyl
group at these positions showed higher potency. But substitu-
tions on 4-phenyl ring also alter the activity of compound.
Compound 3m is having 3,4-dimethylphenyl carbamoyl side
chain as in compound 4f, but NO2 group is at meta position
in compound 3c and at para position in compound 3m which
We had synthesized and evaluated several 1,4-dihydropyr-
idines bearing a lipophilic group, as antitubercular agents,
on the assumption that these compounds could act as pro-
drugs, which after penetration would be converted to the
3,5-carboxylate anions by enzymatic hydrolysis. The most
effective analogs show more than 97% inhibition of myco-
bacterium at a concentration of 2.50 mg/mL, and this series
was examined in detail by QSAR analysis [29,30]. In

V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
2105
H
N
O
O
R4
R3
NH2
R1
R4
R3
a
O
O
O
R1
R2
R2
1a-n
2a-n
Scheme 1. Reagents and conditions: (a) NaOH/KOH, toluene, 110 ꢀC, 10e15 h.
leads to decrease in % inhibition from 63% to 13%. Thus,
compound with methyl substitution on phenyl carbamoyl
side chain with eOPh or eNO2 substitution at meta position
of 4-phenyl ring were more potent than same substitution on
para position. The replacement of methyl groups in phenyl
ring of phenyl carbamoyl side chain with halogen result in
loss of potency. Compounds with halogen substituted at differ-
ent position of phenyl ring of phenyl carbamoyl side chain do
not showed good potency either with meta or para substituted
4-phenyl ring. Thus, it can be concluded that methyl groups on
phenyl ring of C5 side chain with meta substituted 4-phenyl
ring showed good potency. To find out structural requirement
and better activity data, the results obtained were subjected to
3D-QSAR analysis.
2.3. QSAR study
2.3.1. Computational details
The 3D-QSAR techniques of CoMFA and CoMSIAwere car-
ried out with Sybyl 7.1 (Tripos Inc., USA) [31] running on a Pen-
tium IV computer under the Red Hat Linux Enterprise WS4.
2.3.2. Ligand preparation
The dataset was divided into a training set (23 molecules,
Table 1) and a test set (7 molecules, Table 2) on the basis of
chemical and biological diversity using the Tanimoto similar-
ity coefficient [32].
For the QSAR study, the activity values were transformed
as follows [33]:
H
R4
R3
N
O
R
O
O
R1
H2N
NH2
R2
CHO
2a-n
b
R4
R
R3
R2
O
N
H
NH
R1
N
H
O
3a-v
4a-g
Scheme 2. Reagents and conditions: (b) HCl, methanol, reflux, 5e10 h.

2106
V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
Table 1
Molecules used in the training set for CoMFA and CoMSIA studies
The molecules were built using the Builder module in Sybyl
7.1. The crystal structure of methyl-4-(3-methoxyphenyl)-6-
methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate [34]
was used as the template (Fig. 1) to built the molecules in
the dataset. The template structure has the pyrimidine ring in
the boat conformation with the 4-phenyl ring in the axial orien-
tation and the C4 atom of the pyrimidine ring in an S-configu-
ration. The ligand geometries were optimized by energy
minimization with the Powel method using MMFF94 forcefield
R4
R3
O
N
H
R2
NH
˚
and charges for the atoms, till a gradient of 0.005 kcal/mol/A
was reached, maintaining the template structure rigid during
the minimization.
R1
N
H
O
Compound
R
R1
R2
R3
R4
% Inhibition log
(mg/mL)
2.3.3. Molecular alignment
activitya
The molecules of the dataset were aligned by two techniques.
First by the atom-fit technique, using atoms common with the
crystal structure of methyl-4-(3-methoxyphenyl)-6-methyl-2-
oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (Fig. 2a). In
the second approach, the molecules were aligned by the field-
fit technique where the steric and electrostatic fields of the
most active molecule in the series were extracted and used for
the alignment of the fields of the other molecules (Fig. 2b).
3a
3b
3c
3d
3e
3f
4-OCH3 CH3
H
H
H
CH3 2
CH3 27
3.08
4.40
5.10
3.88
3.40
3.54
4.08
3.14
3.88
3.08
4.77
3.39
3.96
3.92
4.34
4.42
4.27
4.55
4.21
4.40
4.36
4.40
3-OPh
3-OPh
2-NO2
4-NO2
4-Cl
CH3
H
CH3 CH3
H
H
H
CH3
H
H
Cl
H
H
H
H
H
H
H
H
H
H
H
H
H
H
65
11
4
Cl
CH3
H
H
H
H
H
H
H
6
3g
3h
3i
4-OH
4-NO2
4-OH
4-OH
3-Cl
F
H
H
18
18
12
2
Cl
CH3
H
H
H
H
CH3
H
3j
NO2
Cl
H
3k
3l
H
F
48
4
2.3.4. CoMFA and CoMSIA studies
4-NO2
4-NO2
4-NO2
3-NO2
3-NO2
3-NO2
3-Cl
F
H
CoMFA (Comparative Molecular Field Analysis) [35] and
CoMSIA (Comparative Molecular Similarity Indices Analy-
sis) [36e38] studies were carried out with the default settings
for the 3D cubic lattice, the grid spacing, the probe atom, and
the energy cutoff.
3m
3n
3o
3p
3q
3r
3s
H
CH3 CH3
13
12
26
29
24
38
21
29
28
30
CH3
Cl
H
H
H
Cl
H
H
H
H
H
H
CH3
H
F
F
H
H
F
For CoMSIA, five physicochemical properties (steric, elec-
trostatic, hydrophobic, and hydrogen-bond donor and accep-
tor) were explored, and the attenuation factor was set to the
default value of 0.3. The CoMFA and CoMSIA descriptors
were used as independent variables and the log activities as
the dependent variable in a partial least squares (PLS) regres-
sion analysis [39] to derive the 3D-QSAR models. The models
were internally evaluated by leave-one-out (LOO) cross-vali-
dation. The optimal number of components was determined
by the SAMPLS [40] method which was subsequently used
to derive the final QSAR models. In addition to the q2, the con-
ventional correlation coefficient r2, and standard errors (SE)
were also computed. The robustness of the models was gauged
by cross-validation using leave-group-out (LGO) of 10 groups
and bootstrapping [41] carried out with 100 runs. The CoMFA
4-NO2
3-NO2
3-NO2
3-NO2
H
OCH3
Cl
3t
H
3u
3v
H
CH3
F
H
MIC > 6.25 mg/mL.
a
log acitivity calculated as described in text.
log activity ¼ ꢁlogc þ logit
where c is molar concentration ¼ concentration (mg/mL) ꢂ
0.001/(molecular weight) and log it ¼ log [% inhibition/
(100ꢁ% inhibition)].
Table 2
Molecules used in the test set for CoMFA and CoMSIA studies
Compound
R
R1
R2
R3
R4 % Inhibition log activitya
(mg/mL)
4a
4b
4c
4d
4e
4f
3-NO2 CH3
H
H
H
H
H
H
H
H
H
H
H
6
26
9
3.57
4.33
3.79
4.51
4.29
5.02
4.26
4-Cl
Cl
H
H
H
H
H
H
Cl
4-NO2
3-OPh
4-NO2
3-NO2
4-NO2
CH3 CH3
H
32
25
63
22
H
CH3 CH3
Cl
4g
F
MIC > 6.25 mg/mL.
a
log acitivity calculated as described in text.
Fig. 1. Template structure for building the molecules in the training and test
sets.

V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
2107
Fig. 2. (a) Atom-fit and (b) field-fit alignment for the dataset.
and CoMSIA models were also validated for their predictivity
on an external dataset of 7 molecules. The statistical data are
reported in Table 3.
The molecules that exhibited large residuals were reintro-
duced into the dataset with alternate conformations and the
QSAR models regenerated. The statistical parameters e q2
and rp2red of the CoMFA and CoMSIA models obtained by
atom-fit alignment are better than the corresponding values
for the models obtained by field-fit alignment (Table 3).
(STDEV ꢂ COEFF) set at 80% and 20% for favored and dis-
favored levels, respectively. The CoMFA and CoMSIA con-
tours are depicted for the atom-fit alignment models in Figs.
3 and 4, respectively. The CoMFA model has equal steric
and electrostatic contribution to the activity while electrostatic
and hydrophobicity contributions are seen to dominate in the
CoMSIA model.
The 3D-QSAR contours and their relation with the biolog-
ical activity of molecules are described in Figs. 3e5. The
CoMFA steric fields (green contours, Fig. 3a) favor substitu-
tion of bulky groups at the meta position of both the 5N-phenyl
and the 4-phenyl moieties, while disfavored steric fields (yel-
low contours) are seen at the para position of the 4-phenyl
group, which is also supported by the CoMSIA steric contours
(Fig. 4a). In addition, disfavored steric CoMSIA contours are
also seen at the meta0-position of the 5N-phenyl residue.
The CoMFA electrostatic contours depict that electroposi-
tive groups (blue contour, Fig. 3b) are favored at the meta po-
sition of the 5N-phenyl group and at the ortho0, meta and para
positions of the 4-phenyl group. However, electronegative
groups (red contour) at the meta0-position of the 4-phenyl moi-
ety are likely to increase the activity. The CoMSIA electro-
static contours (Fig. 4b) also favor electropositive groups at
the para and ortho0 positions of the 4-phenyl ring and in addi-
tion, electronegative groups at the para position of 5N-phenyl
group. The hydrophobic contours of CoMSIA indicate desired
and undesired hydrophobic regions around the two phenyl
rings. The hydrophobic groups (white contours, Fig. 4c) would
cause the activity to decrease when placed at the meta0 posi-
tion of the 5N-phenyl ring or the meta0 and para positions of
the 4-phenyl ring; small hydrophobic groups (yellow fields)
are accepted at the meta position of the 5N-phenyl ring.
The H-bond donor fields are absent in the CoMSIA model.
The disfavored fields of the H-bond acceptor are seen as red
2.3.5. Graphical analysis
The CoMFA and CoMSIA contour maps were generated
using scalar products of coefficients and standard deviation
Table 3
The statistics of the CoMFA and CoMSIA models
Atom-fit alignment
Field-fit alignment
CoMFA
CoMSIA
CoMFA
CoMSIA
PLS statistics
n
23
23
0.95
23
23
0.96
r2
0.98
0.68
0.64
0.99
0.41
184.85
0.08
6
0.97
0.38
0.45
0.98
0.60
234.60
0.10
3
q2 (LOO)
0.58
0.50
0.98
0.32
45.85
0.15
6
0.23
0.26
0.99
0.36
70.78
0.13
6
q2 (LGO)
rb2ootstrap
rp2red
F
SE
PLS components
Field contribution
Steric
0.49
0.51
e
0.13
0.31
0.33
0.08
0.15
0.43
0.57
e
0.09
0.34
0.25
0.16
0.16
Electrostatic
Hydrophobic
Donor
e
e
Acceptor
e
e

2108
V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
Fig. 3. The CoMFA contours around molecule 3c (a) steric contours e favored (green); disfavored (yellow) (b) electrostatic contours e electropositive (blue);
electronegative (red).
contours in Fig. 4e, in the vicinity of the 5-carboxamide, the
ortho and meta position of the 5N-phenyl ring, while the
favored magenta contours are found to encapsulate the para
and meta0 positions of the 4-phenyl ring.
4. Experimental
4.1. Synthesis
Melting points were determined in open glass capillaries in
1
a paraffin bath and are uncorrected. H NMR spectra were
2.4. New molecules designed with improved activity
recorded on a BRUKER AC 300 MHz FT-NMR spectropho-
tometer using tetramethylsilane as an internal standard. Mass
spectra were recorded on JEOL SX 102/DA-6000 by the
FAB (Fast Atom Bombardment) technique for ionization.
Thin layer chromatography was performed on Merck Kiesel-
gel 60F254 (Merck 5549, USA) plates.
New molecules were designed on the basis of the contour
maps seen around the most active molecule (3c). Variations
(R1, Table 4) were made on the 4-phenyl ring, at the meta
position. Modifications (R2, Table 4) were also made at the
5-carbamoyl group. It is seen that the molecules with R2
groups of the type e 3-pyridyl and 4-pyridyl rings with suit-
able substituents, are predicted with higher activity than the
correspondingly substituted phenyl rings. Further, molecules
with pyridyl rings bearing nitro, dimethylaminocarbonyl, car-
bonyl or methoxy have greater activity than the molecules
with unsubstituted pyridyl rings. Some of the newly designed
molecules are depicted in Table 4.
4.2. General method for the preparation of
N-phenyl-6-methyl-2-oxo-4-phenyl-1,2,3,4-tetrahydro-
pyrimidine-5-carboxamide
Urea (0.9 g, 15 mmol), aldehyde (10 mmol) and acetoaceta-
nilide (10 mmol) were taken in 10 mL of methanol in a 100 mL
round bottom flask. The mixture was refluxed for 10 min when
a clear solution resulted. Then 3e4 drops of conc. HCl were
added to the solution. The reaction mixture was refluxed in
a water bath for 5e10 h. The progress of the reaction was mon-
itored by TLC. When the reaction was complete, the flask was
removed from the water bath and allowed to cool to room tem-
perature. The separated solid was collected by suction, washed
with methanol and recrystallized from DMF.
3. Conclusions
The title compounds were obtained using the Biginelli reac-
tion by reacting acetoacetanilide derivatives, substituted alde-
hydes and urea in methanol with a catalytic amount of conc.
HCl. The synthesized compounds showed a range of antituber-
cular activity, extending from 2% to 63% inhibition of M. tu-
berculosis. The molecules were aligned in two ways, by the
atom-fit and field-fit methods, and CoMFA and CoMSIA was
carried out to map the structural features that modulate the
inhibitory activity of these molecules. The CoMFA and CoM-
SIA models generated with the atom-fit alignment were better
in terms of the statistical parameters (r2, q2 and rp2red) over the
field-fit models. Analysis of the CoMFA and CoMSIA con-
tours provide details on the fine relationship linking structure
and activity, and offer clues for structural modifications that
can improve the activity.
4.2.1. N-(2,5-Dimethylphenyl)-6-methyl-2-
oxo-4-(4-methoxyphenyl)-1,2,3,4-tetrahydro-
pyrimidine-5-carboxamide (3a)
Mp 240e241 ꢀC; yield 59%; 1H NMR (DMSO-d6, d ppm):
1.59 (s, 3H), 1.78 (s, 3H), 2.67 (s, 3H), 3.04 (s, 3H), 5.33 (s,
1H), 6.79 (d, 2H; J ¼ 7.82), 7.23 (m, 3H), 7.92 (dd, 2H;
J ¼ 8.14), 7.56 (s, 1H), 8.80 (s, 1H), 9.78 (s, 1H); IR
(cmꢁ1): 3389 (NeH str.), 1667, 1710 (CO str.); Mass (m/z):
365 (Mþ, 62%), 245 (100%); 13C NMR (d ppm): 11.39,

V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
2109
Fig. 4. The CoMSIA contours around molecule 3c (a) steric contours e favored (green), disfavored (yellow) (b) electrostatic contours e electropositive (blue)
electronegative (red) (c) hydrophobic contours e favored (yellow), disfavored (white) (d) H-donor contours e favored (cyan) (e) H-acceptor contours e favored
(magenta), disfavored (purple), disfavored (red).

2110
V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
(t, 1H, J ¼ 7.84, 2.12), 7.59 (s, 1H), 7.88 (m, 4H), 8.19 (dd,
1H; J ¼ 8.16, 1.79), 8.26 (dd, 1H; J ¼ 8.10, 2.13), 8.40 (s,
1H), 9.66 (s, 1H); IR (cmꢁ1): 3404 (NeH str.), 1669, 1711
(CO str.); Mass (m/z): 386 (Mþ, 66%), 260 (100%); 13C
NMR (d ppm): 13.17, 53.18, 106.34, 117.18, 122.34, 124.67,
125.97, 128.36, 129.34, 131.47, 134.25, 138.78, 142.15,
143.64, 148.57, 149.78, 153.62, 164.76. Anal. Calcd for
C18H15ClN4O4: C 55.89, H 3.91, N 14.49; found: C 55.90,
H 3.92, N 14.50.
4.2.5. N-(2,5-Dimethylphenyl)-6-methyl-2-oxo-4-
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
Fig. 5. The figure is used for explaining the CoMFA and CoMSIA.
carboxamide (3e)
Mp 140e142 ꢀC; yield 56%; 1H NMR (DMSO-d6, d ppm):
1.67 (s, 3H), 1.98 (s, 3H), 2.81 (s, 3H), 5.33 (s, 1H), 7.26 (dd,
2H; J ¼ 7.59, 2.21), 7.68 (m, 5H), 7.99 (s, 1H), 8.37 (s, 1H),
9.92 (s, 1H); IR (cmꢁ1): 3440 (NeH str.), 1656, 1720 (CO
str.); Mass (m/z): 380 (Mþ, 62%), 260 (100%); 13C NMR (d
ppm): 10.18, 14.47, 18.78, 58.27, 107.29, 112.86, 115.49,
120.37, 123.17, 124.88, 127.37, 129.19, 132.57, 135.71,
136.93, 141.48, 145.24, 148.68, 155.62, 171.68. Anal. Calcd
for C20H20N4O4: C 63.15, H 5.30, N 14.73; found: C 63.19,
H 5.32, N 14.76.
17.23, 19.68, 49.12, 56.32, 109.31, 117.36, 117.88, 122.27,
123.39, 124.72, 126.39, 128.14, 134.32, 137.19, 138.43,
139.18, 148.13, 151.29, 152.32, 165.18. Anal. Calcd for
C21H23N3O3: C 69.02, H 6.34, N 11.50; found: C 69.07, H
6.39, N 11.52.
4.2.2. N-(2,5-Dimethylphenyl)-6-methyl-2-oxo-4-
(3-phenoxyphenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3b)
Mp 258e261 ꢀC; yield 60%; 1H NMR (DMSO-d6, d ppm):
2.53 (s, 3H), 2.88 (s, 3H), 3.16 (s, 3H), 5.14 (s, 1H), 7.11 (d,
2H; J ¼ 7.69), 7.53 (m, 4H), 7.82 (dd, 1H; J ¼ 7.82), 7.96 (m,
2H), 8.14 (d, 1H; J ¼ 1.87), 8.32 (dd, 2H; J ¼ 7.92, 2.14), 8.03
(s, 1H), 8.61 (s, 1H), 9.79 (s, 1H); IR (cmꢁ1): 3411 (NeH str.),
1650, 1709 (CO str.); Mass (m/z): 427 (Mþ, 82%), 307
(100%); 13C NMR (d ppm): 12.18, 16.11, 20.32, 53.18,
110.54, 116.32, 116.89, 118.18, 119.39, 123.88, 125.39,
125.92, 127.18, 128.92, 130.18, 130.72, 131.93, 134.35,
136.82, 137.13, 141.32, 148.19, 159.25, 163.18, 166.18,
168.32. Anal. Calcd for C26H25N3O3: C 73.05, H 5.89, N
9.83; found: C 73.08, H 5.92, N 9.85.
4.2.6. N-(Phenyl)-6-methyl-2-oxo-4-(4-chlorophenyl)-
1,2,3,4-tetrahydro-pyrimidine-5-carboxamide (3f)
Mp 157e158 ꢀC; yield 68%; 1H NMR (CDCl3, d ppm): 2.45
(s, 3H), 5.22 (s, 1H), 6.78 (d, 2H; J ¼ 7.61), 7.14 (m, 5H), 7.35
(d, 2H; J ¼ 8.37), 7.44 (s, 1H), 8.55 (s, 1H), 9.36 (s, 1H); IR
(cmꢁ1): 3472 (NeH str.), 1669, 1701 (CO str.); Mass (m/z):
341 (Mþ, 77%), 249 (100%); 13C NMR (d ppm): 12.38,
61.29, 114.25, 123.27, 126.28, 127.33, 130.41, 132.26,
136.38, 137.78, 139.33, 144.23, 145.56, 148.26, 151.22,
155.28, 160.18, 167.28. Anal. Calcd for C18H16ClN3O2: C
63.25, H 4.72, N 12.29; found: C 63.29, H 4.75, N 12.30.
4.2.3. N-(2,3-Dimethylphenyl)-6-methyl-2-oxo-4-
(3-phenoxyphenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3c)
4.2.7. N-(2-Flourophenyl)-6-methyl-2-oxo-4-
(4-hydroxyphenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3g)
Mp 220e222 ꢀC; yield 63%; 1H NMR (DMSO-d6, d ppm):
2.12 (s, 3H), 2.42 (s, 3H), 2.53 (s, 3H), 5.56 (s, 1H), 7.54 (dd,
1H; J ¼ 8.22), 7.89 (m, 7H), 8.12 (d, 1H; J ¼ 2.08), 8.29 (d,
2H, J ¼ 7.78), 8.40 (dd, 1H; J ¼ 7.61), 7.72 (s, 1H), 8.86 (s,
1H), 9.23 (s, 1H); IR (cmꢁ1): 3439 (NeH str.), 1672, 1712
(CO str.); Mass (m/z): 427 (Mþ, 68%), 307 (100%); 13C
NMR (d ppm): 11.56, 15.28, 17.39, 50.23, 107.46, 112.34,
114.15, 116.29, 119.22, 122.78, 124.27, 125.39, 127.66,
129.32, 131.25, 132.34, 135.23, 136.11, 138.45, 140.10,
141.40, 147.18, 155.73, 159.27, 163.17, 170.42. Anal. Calcd
for C26H25N3O3: C 73.05, H 5.89, N 9.83; found: C 73.11,
H 5.92, N 9.91.
1
Mp 244e245 ꢀC; yield 64%; H NMR (CDCl3-d6, d ppm):
3.79 (s, 3H), 5.19 (s, 1H), 6.84 (d, 2H; J ¼ 9.12), 7.23 (m, 3H),
7.44 (t, 1H; J ¼ 8.81, 2.13), 7.52 (d, 2H; J ¼ 9.53), 7.60 (s,
1H), 8.95 (s, 1H), 9.39 (s, 1H), 10.41 (s, 1H); IR (cmꢁ1):
3393 (NeH str.), 1660, 1718 (CO str.); Mass (m/z): 341
(Mþ, 67%), 231 (100%); 13C NMR (d ppm): 10.45, 57.24,
111.45, 116.76, 119.34, 127.34, 129.45, 133.56, 134.34,
137.24, 139.56, 140.22, 144.27, 145.39, 154.34, 159.36,
166.89, 173.26. Anal. Calcd for C18H16FN3O3: C 63.34, H
4.72, N 12.31; found: C 63.35, H 4.75, N 12.35.
4.2.8. N-(2,5-Dichlorophenyl)-6-methyl-2-oxo-4-
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3h)
Mp 246e247 ꢀC; yield 56%; 1H NMR (CDCl3, d ppm): 2.17
(s, 3H), 5.48 (s, 1H), 7.25 (m, 5H), 8.21 (d, 2H; J ¼ 7.76), 7.82
(s, 1H), 9.00 (s, 1H), 9.27 (s, 1H); IR (cmꢁ1): 3214 (NeH str.),
1652, 1707 (CO str.); Mass (m/z): 421 (Mþ, 59%), 260 (100%);
4.2.4. N-(2-Chlorophenyl)-6-methyl-2-oxo-4-
(2-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3d)
1
Mp 196e198 ꢀC; yield 60%; H NMR (CDCl3, d ppm):
2.78 (s, 3H), 5.20 (s, 1H), 7.13 (t, 1H; J ¼ 8.26, 1.96), 7.49

V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
2111
Table 4
New molecules with improved predicted activity
R1
H
N
O
NH
R2
HN
O
Sr. no.
Molecule
N001
R1
H
R2
Predicted activity (CoMFA)a
Predicted activity (CoMSIA)a
1
5.36
4.65
NO2
O
2
3
4
5
N002
N003
N004
N005
N006
eOCONHCH3
eCOCH3
eCN
5.57
5.36
5.61
5.52
5.61
4.63
4.55
4.47
4.35
4.37
N(CH3)2
N(CH3)2
N(CH3)2
N
O
O
O
O
N
N
N
N
eNHSO2CH3
N(CH3)2
N(CH3)2
6
eCF3
a
Also see Tables 1 and 2 for comparison.
13C NMR (d ppm): 11.89, 48.35, 110.56, 118.39, 121.28,
126.34, 126.95, 130.24, 131.57, 134.25, 135.89, 137.43,
137.79, 145.28, 148.27, 150.28, 156.35, 167.37. Anal. Calcd
for C18H14Cl2N4O4: C 51.32, H 3.35, N 13.30; found: C
51.39, H 3.39, N 13.38.
4.2.9. N-(2,4-Dimethylphenyl)-6-methyl-2-oxo-4-
(4-hydroxyphenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3i)
Mp 215e216 ꢀC; yield 56%; 1H NMR (DMSO-d6, d ppm):
1.47 (s, 3H), 1.73 (s, 3H), 3.14 (s, 3H), 5.23 (s, 1H), 6.69e7.92

2112
V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
(m, 7H), 7.54 (s, 1H), 8.12 (s, 1H), 9.58 (s, 1H), 10.34 (s, 1H);
IR (cmꢁ1): 3425 (NeH str.), 1655, 1717 (CO str.); Mass (m/z):
351 (Mþ, 54%), 231 (100%); 13C NMR (d ppm): 13.34, 17.25,
19.28, 64.23, 118.23, 118.78, 122.34, 126.36, 127.58, 133.23,
134.74, 136.47, 138.49, 140.25, 141.28, 144.24, 148.35,
158.13, 159.37, 165.36. Anal. Calcd for C20H21N3O3: C
68.36, H 6.02, N 11.96; found: C 68.38, H 6.03, N 11.98.
(cmꢁ1): 3289 (NeH str.), 1678, 1706 (CO str.); Mass (m/z):
380 (Mþ, 54%), 260 (100%); 13C NMR (d ppm): 11.68,
14.38, 19.45, 62.67, 108.57, 117.68, 118.95, 121.33, 124.52,
128.88, 130.07, 130.68, 134.78, 138.42, 141.38, 142.39,
145.49, 147.22, 154.79, 167.58. Anal. Calcd for C20H20N4O4:
C 63.15, H 5.30, N 14.73; found: C 63.19, H 5.31, N 14.75.
4.2.14. N-(2,4-Dimethylphenyl)-6-methyl-2-oxo-4-
4.2.10. N-(3-Nitrophenyl)-6-methyl-2-oxo-4-
(4-hydroxyphenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3j)
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3n)
Mp 215e216 ꢀC; yield 56%; 1H NMR (DMSO-d6, d ppm):
1.08 (s, 3H), 1.93 (s, 3H), 2.79 (s, 3H), 5.69 (s, 1H), 6.92 (d,
1H; J ¼ 7.64), 7.29 (m, 4H), 7.78 (d, 2H; J ¼ 8.35), 7.94 (s,
1H), 8.72 (s, 1H), 9.48 (s, 1H); IR (cmꢁ1): 3321 (NeH str.),
1689, 1709 (CO str.); Mass (m/z): 380 (Mþ, 62%), 260
(100%); 13C NMR (d ppm): 14.63, 17.28, 18.39, 65.61,
112.78, 117.28, 121.37, 122.84, 123.35, 124.19, 130.68,
134.24, 137.82, 138.27, 140.21, 142.56, 143.93, 147.41,
152.84, 161.84. Anal. Calcd for C20H20N4O4: C 63.15, H
5.30, N 14.73; found: C 63.17, H 5.33, N 14.75.
1
Mp 206e208 ꢀC; yield 52%; H NMR (CDCl3, d ppm):
2.55 (s, 3H), 5.34 (s, 1H), 7.19 (t, 1H; J ¼ 8.67), 7.48 (m,
5H), 7.69 (dd, 2H, J ¼ 7.19, 2.19), 7.85 (s, 1H), 8.33 (s,
1H), 9.47 (s, 1H), 10.78 (s, 1H); IR (cmꢁ1): 3239 (NeH
str.), 1662, 1711 (CO str.); Mass (m/z): 368 (Mþ, 52%), 231
(100%); 13C NMR (d ppm): 10.37, 46.18, 108.27, 118.25,
119.59, 126.27, 128.36, 131.26, 135.38, 136.72, 139.37,
139.88, 142.36, 146.78, 152.46, 158.48, 163.59, 172.48.
Anal. Calcd for C18H16N4O5: C 58.69, H 4.38, N 15.21; found:
C 58.74, H 4.43, N 15.27.
4.2.15. N-(2-Chlorophenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3o)
4.2.11. N-(3-Chloro-4-flourophenyl)-6-methyl-2-oxo-4-
(3-chlorophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3k)
1
Mp 245e246 ꢀC; yield 62%; H NMR (CDCl3, d ppm):
1
Mp 270e272 ꢀC; yield 65%; H NMR (CDCl3, d ppm):
2.79 (s, 3H), 5.59 (s, 1H), 7.02 (t, 1H; J ¼ 8.18), 7.45 (m,
7H), 8.53 (s, 1H), 8.79 (s, 1H), 9.70 (s, 1H); IR (cmꢁ1):
3447 (NeH str.), 1659, 1701 (CO str.); Mass (m/z): 386
(Mþ, 72%), 260 (100%); 13C NMR (d ppm): 13.72, 45.74,
104.27, 112.35, 113.86, 118.25, 119.20, 124.37, 127.81,
130.34, 133.16, 136.68, 137.28, 139.50, 142.47, 151.74,
158.58, 167.38. Anal. Calcd for C18H15ClN4O4: C 55.89, H
3.91, N 14.49; found: C 55.95, H 3.98, N 14.55.
3.12 (s, 3H), 5.12 (s, 1H), 6.85 (d, 1H; J ¼ 9.92), 7.34 (m,
4H), 7.45 (dd, 1H; J ¼ 7.25, 3.87), 7.78 (d, 1H; J ¼ 9.43),
7.93 (s, 1H), 8.21 (s, 1H), 9.03 (s, 1H); IR (cmꢁ1): 3256
(NeH str.), 1658, 1708 (CO str.); Mass (m/z): 394 (Mþ,
68%), 249 (100%); 13C NMR (d ppm): 14.26, 67.37, 110.38,
117.35, 118.27, 121.29, 125.26, 125.81, 129.69, 130.33,
133.16, 135.93, 138.24, 140.36, 144.28, 147,84, 154.29,
166.73. Anal. Calcd for C18H15Cl2FN3O2: C 54.84, H 3.58,
N 10.66; found: C 54.88, H 3.59, N 10.70.
4.2.16. N-(3-Chloro-4-flourophenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
4.2.12. N-(2-Flourophenyl)-6-methyl-2-oxo-4-
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3l)
carboxamide (3p)
Mp 208e209 ꢀC; yield 67%; 1H NMR (CDCl3, d ppm): 2.89
(s, 3H), 5.47 (s, 1H), 7.12 (t, 1H; J ¼ 9.18), 7.38 (m, 5H), 7.89
(d, 1H; J ¼ 9.37), 7.98 (s, 1H), 8.78 (s, 1H), 9.82 (s, 1H); IR
(cmꢁ1): 3439 (NeH str.), 1672, 1720 (CO str.); Mass (m/z):
404 (Mþ, 70%), 260 (100%); 13C NMR (d ppm): 15.27,
57.16, 110.47, 118.24, 119.37, 122.49, 123.62, 128.89,
129.17, 134.58, 136.83, 139.42, 140.07, 146.47, 149.85,
157.31, 159.40, 171.37. Anal. Calcd for C18H14ClFN4O3: C
53.41, H 3.49, N 13.84; found: C 53.48, H 3.54, N 13.86.
1
Mp 254e255 ꢀC; yield 60%; H NMR (CDCl3, d ppm):
2.79 (s, 3H), 5.07 (s, 1H), 6.70 (dd, 2H; J ¼ 8.94, 2.31),
7.29 (s, 1H), 7.54 (m, 5H), 7.90 (t, 1H; J ¼ 9.85), 8.66 (s,
1H), 9.89 (s, 1H); IR (cmꢁ1): 3405 (NeH str.), 1678, 1702
(CO str.); Mass (m/z): 370 (Mþ, 67%), 260 (100%); 13C
NMR (d ppm): 12.44, 49.24, 112.23, 115.44, 118.37, 122.18,
126.28, 131.28, 134.54, 138.55, 139.83, 140.89, 142.57,
148.29, 149.70, 153.46, 158.36, 170.78. Anal. Calcd for
C18H15FN4O4: C 58.38, H 4.08, N 15.13; found: C 58.42, H
4.09, N 15.15.
4.2.17. N-(2-Flourophenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3q)
4.2.13. N-(3,4-Dimethylphenyl)-6-methyl-2-oxo-4-
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3m)
Mp 254e256 ꢀC; yield 58%; 1H NMR (DMSO-d6, d ppm):
1.23 (s, 3H), 1.67 (s, 3H), 2.78 (s, 3H), 5.48 (s, 1H), 6.89 (dd,
1H; J ¼ 8.11, 2.32), 7.11 (m, 3H), 7.38 (d, 2H; J ¼ 8.94), 7.54
(s, 1H), 8.14 (d, 1H; J ¼ 7.17), 8.52 (s, 1H), 9.84 (s, 1H); IR
Mp 210e212 ꢀC; yield 62%; 1H NMR (CDCl3, d ppm): 2.81
(s, 3H), 5.27 (s, 1H), 7.12 (s, 1H), 7.22 (t, 1H; J ¼ 9.18), 7.39 (t,
1H; J ¼ 8.62), 7.80 (m, 4H), 8.11 (dd, 1H; J ¼ 7.14, 2.10), 8.28
(dd, 1H; J ¼ 9.23, 3.92), 8.40 (s, 1H), 9.90 (s, 1H); IR (cmꢁ1):
3419 (NeH str.), 1667, 1712 (CO str.); Mass (m/z): 370 (Mþ,
72%), 260 (100%); 13C NMR (d ppm): 13.48, 53.41, 113.68,
115.27, 121.57, 122.31, 127.63, 128.93, 132.30, 132.78,

V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
2113
136.74, 137.96, 143.52, 148.58, 150.41, 156.84, 163.45,
173.37. Anal. Calcd for C18H15FN4O3: C 58.38, H 4.08, N
15.13; found: C 58.45, H 4.11, N 15.16.
4.2.22. N-(4-Flourophenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3v)
1
Mp 256e258 ꢀC; yield 60%; H NMR (CDCl3, d ppm):
2.86 (s, 3H), 5.62 (s, 1H), 6.92 (d, 2H; J ¼ 9.82), 7.34 (m,
6H), 7.81 (s, 1H), 8.65 (s, 1H), 9.14 (s, 1H); IR (cmꢁ1):
3382 (NeH str.), 1669, 1716 (CO str.); Mass (m/z): 370
(Mþ, 76%), 260 (100%); 13C NMR (d ppm): 14.27, 51.62,
111.64, 118.20, 118.94, 120.69, 121.38, 124.51, 125.82,
129.48, 130.26, 132.19, 136.29, 137.74, 138.15, 146.58,
154.27, 168.18. Anal. Calcd for C18H15FN4O4: C 58.38, H
4.08, N 15.13; found: C 58.40, H 4.10, N 15.17.
4.2.18. N-(4-Flourophenyl)-6-methyl-2-oxo-4-
(3-chlorophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3r)
Mp 270e272 ꢀC; yield 65%; 1H NMR (CDCl3, d ppm): 2.86
(s, 3H), 5.35 (s, 1H), 6.88 (d, 2H; J ¼ 9.36), 7.03 (t, 1H;
J ¼ 7.84, 1.78), 7.11 (d, 1H; J ¼ 9.17), 7.45 (m, 3H), 7.62 (d,
2H; J ¼ 9.75), 7.97 (s, 1H), 8.81 (s, 1H), 9.43 (s, 1H); IR
(cmꢁ1): 3266 (NeH str.), 1652, 1713 (CO str.); Mass (m/z):
359 (Mþ, 68%), 249 (100%); 13C NMR (d ppm): 12.84,
62.38, 105.25, 116.26, 117.83, 120.38, 121.26, 127.58,
129.38, 130.87, 133.28, 133.86, 137.39, 139.16, 141.29,
142.64, 157.49, 168.31; Anal. Calcd for C18H15ClFN3O2: C
60.09, H 4.20, N 11.68; found: C 60.14, H 4.25, N 11.70.
4.2.23. N-(2-Methylphenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (4a)
Mp 176e177 ꢀC; yield 60%; 1H NMR (DMSO-d6, d ppm):
1.82 (s, 3H), 2.28 (s, 3H), 5.40 (s, 1H), 7.06 (t, 1H; J ¼ 9.72,
1.86), 7.23 (m, 5H), 7.49 (t, 1H; J ¼ 7.29, 2.13), 7.71 (t, 1H;
J ¼ 8.12, 1.76), 7.81 (s, 1H), 8.78 (s, 1H), 9.08 (s, 1H); IR
(cmꢁ1): 3449 (NeH str.), 1662, 1707 (CO str.); Mass (m/z):
366 (Mþ, 80%), 260 (100%); 13C NMR (d ppm): 15.27,
17.80, 59.68, 107.28, 116.69, 117.25, 119.95, 120.31,
122.86, 124.58, 125.97, 129.47, 130.62, 132.61, 135.82,
138.14, 141.37, 152.81, 166.73. Anal. Calcd for C19H18
N4O4: C 62.29, H 4.95, N 15.29; found: C 62.32, H 4.97, N
14.33.
4.2.19. N-(4-Methoxy-phenyl)-6-methyl-2-oxo-4-
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3s)
1
Mp 268e270 ꢀC; yield 62%; H NMR (CDCl3, d ppm):
1.96 (s, 3H), 2.69 (s, 3H), 5.46 (s, 1H), 6.82 (d, 2H;
J ¼ 9.12), 7.52 (m, 4H), 7.79 (d, 2H; J ¼ 7.93), 7.97 (s, 1H),
8.57 (s, 1H), 9.52 (s, 1H); IR (cmꢁ1): 3418 (NeH str.),
1675, 1713 (CO str.); Mass (m/z): 382 (Mþ, 74%), 260
(100%); 13C NMR (d ppm): 15.74, 42.78, 56.82, 104.28,
110.28, 113.64, 116.92, 117.31, 119.48, 124.51, 127.75,
128.82, 129.30, 132.41, 136.78, 137.92, 144.58, 154.83,
168.91. Anal. Calcd for C19H18N4O5: C 59.68, H 4.74, N
14.65; found: C 59.73, H 4.75, N 14.68.
4.2.24. N-(2-Chlorophenyl)-6-methyl-2-oxo-4-
(4-chlorophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (4b)
1
4.2.20. N-(4-Chlorophenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3t)
Mp 208e210 ꢀC; yield 66%; H NMR (CDCl3, d ppm):
2.13 (s, 3H), 5.89 (s, 1H), 7.11 (d, 2H; J ¼ 9.18), 7.43 (t,
1H; J ¼ 7.13), 7.67 (m, 5H), 7.82 (s, 1H), 8.64 (s, 1H),
9.92 (s, 1H); IR (cmꢁ1): 3376 (NeH str.), 1660, 1718 (CO
str.); Mass (m/z): 376 (Mþ, 81%), 249 (100%); 13C NMR
(d ppm): 12.38, 65.82, 112.45, 115.28, 117.95, 120.32,
121.37, 124.53, 125.78, 128.13, 129.60, 130.27, 134.27,
137.82, 138.69, 140.24, 157.22, 169.41. Anal. Calcd for
C18H15Cl2N3O2: C 57.46, H 4.02, N 11.17; found: C 57.49,
H 4.05, N 11.20.
Mp 210e212 ꢀC; yield 62%; 1H NMR (CDCl3, d ppm): 2.51
(s, 3H), 5.21 (s, 1H), 6.78 (d, 2H; J ¼ 8.89), 7.13 (m, 5H), 7.36
(t, 1H; J ¼ 9.17, 2.18), 7.61 (s, 1H), 8.37 (s, 1H), 9.60 (s, 1H);
IR (cmꢁ1): 3413 (NeH str.), 1654, 1702 (CO str.); Mass (m/z):
386 (Mþ, 72%), 260 (100%); 13C NMR (d ppm): 16.28, 49.53,
110.25, 114.38, 114.88, 123.47, 124.63, 127.36, 128.29,
130.05, 130.62, 135.58, 136.91, 138.43, 140.04, 152.36,
160.13, 167.33. Anal. Calcd for C18H15ClN4O4: C 55.89, H
3.91, N 14.49; found: C 55.94, H 3.94, N 14.56.
4.2.25. N-(4-Chlorophenyl)-6-methyl-2-oxo-4-
(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (4c)
4.2.21. N-(4-Methylphenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (3u)
1
Mp 294e295 ꢀC; yield 64%; H NMR (CDCl3, d ppm):
Mp 210e212 ꢀC; yield 62%; 1H NMR (DMSO-d6, d ppm):
2.91 (s, 3H), 5.48 (s, 1H), 6.79 (d, 2H; J ¼ 8.52), 7.28 (m, 5H),
7.70 (t, 1H; J ¼ 9.13, 1.88), 7.92 (s, 1H), 8.28 (s, 1H), 9.19 (s,
1H); IR (cmꢁ1): 3323 (NeH str.), 1680, 1700 (CO str.); Mass
(m/z): 366 (Mþ, 72%), 260 (100%); 13C NMR (d ppm): 12.73,
18.38, 58.91, 108.64, 117.83, 118.07, 122.38, 124.08, 127.48,
128.35, 131.26, 132.82, 135.37, 137.39, 139.70, 140.16,
142.47, 156.30, 171.04. Anal. Calcd for C19H18N4O4: C
62.29, H 4.95, N 15.29; found: C 62.34, H 4.96, N 15.31.
2.92 (s, 3H), 5.56 (s, 1H), 6.78 (m, 2H), 7.26 (m, 4H),
7.92 (d, 2H; J ¼ 7.80), 7.45 (s, 1H), 8.78 (s, 1H), 9.44 (s,
1H); IR (cmꢁ1): 3444 (NeH str.), 1652, 1719 (CO str.);
Mass (m/z): 386 (Mþ, 61%), 260 (100%); 13C NMR (d
ppm): 14.92, 48.51, 104.38, 111.92, 114.68, 118.79,
119.27, 120.27, 125.31, 126.84, 128.38, 129.48, 131.18,
135.39, 136.35, 145.28, 153.14, 163.89. Anal. Calcd for
C18H15ClN4O4: C 55.89, H 3.91, N 14.49; found: C 55.92,
H 3.94, N 14.51.

2114
V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
4.2.26. N-(3,4-Dimethylphenyl)-6-methyl-2-oxo-4-
(3-phenoxyphenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (4d)
4.3. Antitubercular activity
Antitubercular activity was determined using the BACTEC
460 system [42] modified as described below. Stock solutions
as test compounds were prepared in dimethylsulfoxide
(DMSO) at 1 mg/mL and sterilized by passage through
0.22 mm PFTE filters (Millex-FG, Millipore, Bedford MA).
Fifty microliters was added to 4 mL radiometric 7H12 broth
(BACTEC 12B; Bectron Dickinson Diagnostic Instrument sys-
tem, Sparks, MD) to achieve a final concentration of 6.25 mg/
mL. Controls received 50 mL DMSO. Rifampin (Sigma Chem-
ical Co., St. Louis, MO) was included as a positive drug con-
trol. Rifampin was solubilized and diluted in DMSO and
added to BACTEC-12 broth to achieve minimum inhibitory
concentration (MIC, lowest concentration inhibiting 99% of
the inoculums).
Mp 224e225 ꢀC; yield 59%; 1H NMR (DMSO-d6, d ppm):
2.24 (s, 3H), 2.67 (s, 3H), 3.12 (s, 3H), 5.76 (s, 1H), 7.12 (dd,
1H; J ¼ 7.35, 2.12), 7.39 (d, 1H; J ¼ 9.72), 7.43 (m, 6H), 7.58
(m, 3H), 7.68 (s, 1H), 7.79 (t, 1H; J ¼ 8.15), 8.46 (s, 1H), 9.12
(s, 1H); IR (cmꢁ1): 3378 (NeH str.), 1664, 1710 (CO str.);
Mass (m/z): 427 (Mþ, 62%), 307 (100%); 13C NMR (d
ppm): 13.58, 17.25, 19.46, 56.82, 108.25, 112.38, 113.39,
116.78, 118.29, 121.57, 122.36, 126.28, 127.92, 128.47,
132.31, 134.83, 135.79, 138.26, 139.41, 140.66, 142.28,
143.86, 152.42, 155.82, 160.12, 169.31. Anal. Calcd for
C26H25N3O3: C 73.05, H 5.89, N 9.83; found: C 73.08, H
5.90, N 9.89.
M. tuberculosis H37Rv strain (ATCC 27294; American
type culture collection, Rockville, MD) was cultured at
37 ꢀC on a rotary shaker in middle brook 7H9 broth (Difco
Laboratories, Detroit, MI) supplemented with 0.2 v/v glycerol
and 0.05% v/v Tween 80 until the culture turbidity achieved an
optical density of 0.45e0.55 at 550 nm. Bacteria were pelleted
by centrifugation, washed twice and resuspended in one-fifth
of the original volume in Dulbecoo’s phosphate buffered sa-
line [PBS, Irvine Scientific, Santa Ana, (A)]. Large bacterial
clumps were removed by passage through an 8 mm filter (Mal-
gene, Rochester, NY) and aliquots were frozen at ꢁ80 ꢀC. The
cultures were thawed and an appropriate dilution performed
such that a BACTEC-12B vial inoculated with a 0.1 mL would
reach a growth index (GI) of 999 in 5 days. One-tenth of the
diluted inoculum was used to inoculate 4 mL fresh BAC-
TEC-12B broth containing the test compounds. An additional
control vial was included which received a further 1:100
diluted inoculum (as well as 50 mL DMSO) for use in calcu-
lating the MIC of rifampicin, respectively, by established
procedures.
Cultures were incubated at 37 ꢀC and the Growth of In-
hibition (GI) determined daily until control cultures
acheived a GI of 999. Assays were usually completed in
5e8 days. Percentage inhibition was defined as 1ꢁ(GI of
test sample/GI of control) 10. Minimum inhibitory concen-
tration of compound effecting a reduction in daily change
in GI, which was less than that observed with a 1:100 di-
luted control culture on day the later reached a GI of at
least 30.
4.2.27. N-(Phenyl)-6-methyl-2-oxo-4-(4-nitrophenyl)-
1,2,3,4-tetrahydro-pyrimidine-5-carboxamide (4e)
1
Mp 304e306 ꢀC; yield 64%; H NMR (CDCl3, d ppm):
1.83 (s, 3H), 5.23 (s, 1H), 6.69 (dd, 2H; J ¼ 8.49, 1.82),
7.04 (m, 2H), 7.38 (m, 3H), 7.59 (t, 2H; J ¼ 7.47, 2.31),
7.88 (s, 1H), 8.29 (s, 1H), 9.57 (s, 1H); IR (cmꢁ1): 3337
(NeH str.), 1684, 1712 (CO str.); Mass (m/z): 352 (Mþ,
67%), 260 (100%); 13C NMR (d ppm): 11.73, 58.12, 103.67,
114.57, 115.69, 121.73, 122.98, 126.26, 128.94, 129.24,
132.16, 133.83, 135.78, 138.38, 139.21, 145.73, 151.69,
164.47. Anal. Calcd for C18H16N4O4: C 61.36, H 4.58, N
15.90; found: C 61.40, H 4.60, N 15.94.
4.2.28. N-(3,4-Dimethylphenyl)-6-methyl-2-oxo-4-
(3-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-5-
carboxamide (4f)
Mp 220e222 ꢀC; yield 63%; 1H NMR (DMSO-d6, d ppm):
2.07 (s, 3H), 2.59 (s, 3H), 2.90 (s, 3H), 5.59 (s, 1H), 6.89 (m,
3H), 7.56 (m, 4H), 7.74 (s, 1H), 8.66 (s, 1H), 9.41 (s, 1H); IR
(cmꢁ1): 3429 (NeH str.), 1662, 1707 (CO str.); Mass (m/z):
380 (Mþ, 68%), 260 (100%); 13C NMR (d ppm): 12.35,
14.78, 18.24, 50.12, 111.37, 117.45, 118.28, 120.28, 123.52,
124.85, 125.89, 131.25, 134.58, 135.80, 136.27, 138.62,
139.36, 147.48, 153.45, 168.21. Anal. Calcd for C20H20
N4O4: C 63.15, H 5.30, N 14.73; found: C 63.17, H 5.31, N
14.76.
4.2.29. N-(3-Chloro-4-flouro-phenyl)-6-methyl-2-
oxo-4-(4-nitrophenyl)-1,2,3,4-tetrahydro-pyrimidine-
5-carboxamide (4g)
1
Mp 262e264 ꢀC; yield 59%; H NMR (CDCl3, d ppm):
Acknowledgement
1.96 (s, 3H), 5.67 (s, 1H), 6.90 (d, 1H; J ¼ 9.12), 7.27 (m,
2H), 7.48 (m, 2H), 7.67 (s, 1H), 7.87 (d, 2H; J ¼ 7.14), 8.77
(s, 1H), 9.94 (s, 1H); IR (cmꢁ1): 3312 (NeH str.), 1657,
1705 (CO str.); Mass (m/z): 404 (Mþ, 63%), 260 (100%);
13C NMR (d ppm): 14.56, 53.58, 112.37, 117.28, 119.48,
120.31, 122.89, 125.37, 126.19, 128.25, 129.39, 130.17,
134.68, 135.69, 137.27, 148.16, 152.84, 164.64. Anal. Calcd
for C18H14ClFN4O4: C 53.41, H 3.49, N 13.84; found: C
53.45, H 3.53, N 13.90.
Authors are thankful to the Tuberculosis Antimicrobial
Acquisition and Coordinating Facility (TAACF), USA for
antitubercular screening and to the Department of Chemis-
try, Saurashtra University, Rajkot for providing laboratory
facilities. The computational facilities at Bombay College
of Pharmacy, Mumbai were supported by All India Council
of Technical Education (F. No. 8022/RID/NPROJ/RPS-5/
2003-04).

V. Virsodia et al. / European Journal of Medicinal Chemistry 43 (2008) 2103e2115
2115
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