Design, synthesis and antibacterial activity of fluoroquinolones containing bulky arenesulfonyl fragment: 2D-QSAR and docking study

Article abstract of DOI:10.1016/j.ejmech.2011.09.011

Here in, we report the design, synthesis, and antibacterial activity of series of bulky arenesulfonamido derivatives using ciprofloxacin and norfloxacin as scaffolds. All the synthesized compounds were investigated in vitro for their antibacterial activit

Full text of DOI:10.1016/j.ejmech.2011.09.011

European Journal of Medicinal Chemistry 46 (2011) 5487e5497
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European Journal of Medicinal Chemistry
journal homepage: http://www.elsevier.com/locate/ejmech
Original article
Design, synthesis and antibacterial activity of fluoroquinolones containing bulky
arenesulfonyl fragment: 2D-QSAR and docking study
,
b
,
c
d
Alaa A.-M. Abdel-Aziza , Yousif A. Asiri , Mohamed H.M. Al-Agamy
*
a Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
b Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
c Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
d Department of Pharmaceutics and Microbiology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
a r t i c l e i n f o
a b s t r a c t
Article history:
Here in, we report the design, synthesis, and antibacterial activity of series of bulky arenesulfonamido
derivatives using ciprofloxacin and norfloxacin as scaffolds. All the synthesized compounds were
investigated in vitro for their antibacterial activities against two Gram-positive and two Gram-negative
organisms using dilution broth method. Among the tested compounds examined, compounds 3e7
showed significance difference from the standard drug ciprofloxacin. 2D-QSAR study provides details on
the fine relationship linking structure and activity and offers clues for structural modifications that can
improve the activity. Docking study of the compound 3b into the active site of the topoisomerase II DNA-
Received 15 July 2011
Received in revised form
5 September 2011
Accepted 7 September 2011
Available online 16 September 2011
Keywords:
gyrase enzymes revealed
a
similar binding mode to ciprofloxacin with additional classical and
Fluoroquinolones
Arenesulfonamido
Antibacterial
nonclassical hydrogen bonds.
Ó 2011 Elsevier Masson SAS. All rights reserved.
2D-QSAR
Molecular docking
1. Introduction
[17e20] characterized by having a piperazine moiety at C-7, which
represented a site of significant modification. Recently, benzene-
sulfonamidofluoroquinolones (BSFQs) are a new class of fluo-
roquinolones (Fig. 1A and B) reported previously by Manzo et al.
[21,22]. Some of those BSFQs have exhibited high in vitro activity
against Staphylococcus aureus ATCC 29213 [23,24] and also against
other Gram-positive clinical strains [25]. The new compounds
would exert their biological action through a quinolone-like
mechanism of action [23]. It was also reported that BSFQs have
displayed a more favorable kinetics of access to the bacterial cell in
S. aureus ATCC 29213 [23]. Studies on Staphylococcus pneumoniae
and S. aureus have identified the BSFQs as “dual targeting” agents
[26,27]. It was reported that the new analogs with a sulfa moiety on
piperazinyl group inhibit Escherichia coli DNA gyrase in similar way
as ciprofolxacin [23]. According to the proposed mechanisms of
action of fluoroquinolones, substituent at 7-position of quinolone
ring would be involved in the interaction with the enzyme through
electrostatic forces [12,19,28].
The fluoroquinolone antibacterial agents have been found to be
one of the fastest growing groups of drugs in recent years [1e7].
They are compounds of intense interest because of their broad
antibacterial spectrum against both Gram-positive and Gram-
negative bacteria and their in vivo chemotherapeutic efficacy
[8e10]. The fluoroquinolones are the only direct inhibitors of DNA
synthesis by binding to the enzyme- DNA complex; they stabilize
DNA strand breaks created by DNA gyrase and topoisomerase IV.
Ternary complexes of drug, enzyme, and DNA block progress of the
replication fork [7]. The inhibition of DNA gyrase and cell perme-
ability of quinolones is greatly influenced by the nature of C-7
substituent on the standard structure of 4-quinolone-3-carboxylic
acid [11,12]. During recent years a number of quinolones with
substitution on piperazine ring at C-7 position of the basic structure
of quinolones were synthesized and evaluated for antibacterial
activities [13e16]. Most of these agents are substituted at the 7
position by a nitrogen heterocycle. Ciprofolxacin and norfloxacin
In this context, the present work describes the synthesis, the
investigation of the antibacterial properties of new bulky arene-
sulfonylquinolones (Fig. 1CeG) and the achievement of a better
antibacterial profile at lower concentrations. The strategy is
intended to obtain potent broad spectrum antibacterial activity
using traditional medicinal chemistry techniques motivated by the
comparative modeling of quinolones (AeG) together with the
* Corresponding author. Department of Pharmaceutical Chemistry, College of
Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia. Tel.: þ966 56 2947305;
fax: þ966 1 4676220.
E-mail address: alaa_moenes@yahoo.com (A.A.-M. Abdel-Aziz).
0223-5234/$ e see front matter Ó 2011 Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.ejmech.2011.09.011

5488
A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
Fig. 1. Reported benzenesulfonamidonorfloxacin (A) and ciprofloxacin (B) and designed bulky arenesulfonyl derivatives (CeG).
available pharmacophore. Our strategy for synthesis such deriva-
tives based on the modification of the structure of the known
potent norfloxacin and ciprofloxacin. Moreover we describe a 2D-
QSAR analysis for the complete series of arenesulfonylquinolones
as well. Multiple linear regression analysis correlates biological
activity values with various descriptors. Computer docking tech-
nique plays an important role in the drug design and discovery, as
well as in the mechanistic study by placing a molecule into the
binding site of the target macromolecule in a non-covalent fashion
[29e33], and to predict the correct binding geometry for each
ligand at the active site, which reveals the MOE score values and
hydrogen bonds formed with the surrounding amino acids. MOE as
flexible docking program enable us to predict favorable pro-
teineligand complex structures with reasonable accuracy and
speed [34].
2.2. Biological activity
2.2.1. Antibacterial activities and structuraleactivity relationships
Compounds 1e11 in addition to the reference ciprofloxacin were
tested for their in vitro antibacterial activity against two Gram-
negative (E. coli ATCC 25922 and Pseudomonas aeruginosa ATCC
27853) and two Gram-positive (S. aureus ATCC 29213 and Bacillus
subtilis ATCC 10400) microorganisms. The minimal inhibitory
concentrations (MIC in
mg/mL and mmol/mL) or the lowest drug
concentrations that prevent visible growth of bacteria (Table 1), were
determined by a standard broth micro-dilution technique using the
European Committee for Antimicrobial Susceptibility Testing
(EUCAST) and Laboratory Standards method [35]. The results of MIC
tests against Gram-positive and Gram-negative bacteria revealed
that ciprofloxacin derivatives (R ¼ cyclopropyl) were usually more
active than norfloxacin derivatives (R ¼ ethyl) especially against
Gram-positive pathogens. From the obtained data (Table 1), the 3,4-
and 2,4-disubstiuted benzenesulfonyl derivatives 3e4 and 6e7
exhibited potential activity against all the tested Gram-positive
2. Results and discussion
2.1. Chemistry
organism (MIC; 0.000463e0.000481
mmol/mL), which was more
2.1.1. Synthesis of compounds 1e11
pronounced than that exhibited by the reference, ciprofloxacin (MIC;
Scheme 1 outlines the synthetic pathway used to obtain
compounds (1e11). Derivatives 1e7 were prepared by allowing
norfloxacin (a) or ciprofloxacin (b) to react with the appropriate
arenesulfonyl chloride in the presence of acetone and K2CO3 at
room temperature for 24 h. On the other hand compounds 8e11
were obtained in relatively good yields by addition of the appro-
priate arenesulfonyl chloride to a stirred solution of norfloxacin (a)
or ciprofloxacin (b) and K2CO3 in DMF at 50 ꢀC for 12 h.
0.000758
0.000479
than ciprofloxacin (MIC; 0.000758
m
m
mol/mL). The 1-naphthalenesulfonyl derivative 2b (MIC;
mol/mL) revealed a better activity two times more active
mol/mL) against B. subtilis while
the inhibition was moderate to weak with other tested strains.
Similarly compounds 5b (MIC; 0.000493 mol/ml), 8a (MIC;
0.000444 mol/ml) and 8b (MIC; 0.000435 mol/ml), showed
m
m
m
m
selective activity against B. subtilis two times more active than
ciprofloxacin with lower activity against other strain. Other

A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
5489
Scheme 1. Synthesis of bulky arenesulfonylquinolones.
compounds showed variable inhibition activities against the used
strains. Moreover, in vitro assay results revealed that the antibacterial
potency of target quinolone 9e11 was mild for Gram-positive and
important role in the antibacterial potency as the activity decreased
when the number of alkyl group or steric bulkiness increased from
compounds 9 to compounds 11 which were the least active deriva-
tives. However, the antibacterial potencies of the disubstitued are-
nesulfonylquinolones 3e7 were all superior to that of trisubstituted
Gram-negative strains (MIC; 0.00798 to ꢁ0.473
mmol/mL). These
results indicated that the aliphatic substitution did not play an
Table 1
Minimum inhibitory concentrations of the designed arenesulfonylquinolones.
Compd. no.
S. aureus ATCC 29213
B.subtilis ATCC 10400
E. coli ATCC 25922
P. aeruginosa ATCC 27853
MIC (
m
g/ml)
MIC (
m
mol/ml)
MIC (
m
g/ml)
MIC (
m
mol/ml)
MIC (
m
g/ml)
MIC (
m
mol/ml)
MIC (
m
g/ml)
MIC (mmol/ml)
1a
1b
2a
2b
3a
3b
4a
4b
5a
5b
6a
6b
7a
7b
8a
8b
1
1
1
1
0.00196
0.00192
0.00196
0.00192
0.000481
ꢂ0.000470
0.000962
ꢂ0.000470
0.00807
0.00394
ꢂ0.000473
ꢂ0.000463
ꢂ0.000473
ꢂ0.000463
0.001776
0.00174
0.00798
0.062
0.5
1
0.5
0.25
0.25
0.000981
0.00192
0.000981
0.000479
0.000481
ꢂ0.000470
0.000962
0.000470
0.00404
0.000493
0.000473
ꢂ0.000463
ꢂ0.000473
ꢂ0.000463
0.000444
0.000435
0.00798
0.031
128
64
128
32
ꢂ0.25
ꢂ0.25
ꢂ0.25
ꢂ0.25
4
0.251
0.123
0.251
0.0613
64
0.126
0.245
0.251
0.123
0.00385
0.000470
0.00385
0.00376
0.129
128
128
64
2
0.25
2
2
64
32
1
0.25
ꢂ0.000481
ꢂ0.000470
ꢂ0.000481
ꢂ0.000470
0.00807
0.00788
ꢂ0.000473
ꢂ0.000463
ꢂ0.000473
ꢂ0.000463
ꢁ0.455
ꢂ0.25
ꢂ0.25
0.5
0.5
ꢂ0.25
4
2
0.25
ꢂ0.25
ꢂ0.25
ꢂ0.25
1
0.25
2
0.25
0.25
ꢂ0.25
ꢂ0.25
ꢂ0.25
0.25
0.25
4
4
0.063
ꢂ0.25
ꢂ0.25
ꢂ0.25
ꢂ0.25
ꢁ256
64
0.00139
0.00185
0.00189
0.00185
ꢁ0.455
0.111
1
1
1
ꢁ256
1
4
32
0.111
0.032
0.062
64
9a
9b
16
32
32
64
0.064
0.125
16
10a
10b
11a
11b
Ciprof.
32
0.055
0.214
0.242
32
64
128
128
ꢂ0.25
0.055
0.107
0.242
0.236
32
2
128
0.055
0.00335
0.242
64
0.109
128
128
ꢁ256
ꢂ0.25
ꢁ256
128
ꢁ256
0.25
ꢁ0.428
0.242
ꢁ0.473
ꢁ256
ꢁ0.473
ꢁ0.473
0.000758
ꢂ0.000758
ꢂ0.000758
ꢂ0.25
ꢂ0.000758

5490
A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
arenesulfonylquinolones 8e11 such as compounds 6e7 are broad
spectrum antibacterial compared with compounds 8 which are
selective only for B. subtilis. The activities of quinolones 3e4 and 6e7
were comparable to quinolones 5, and the results indicated that the
fluoro group at the 2,4-position of the arenesulfonyl fragment did
not play an essential role in influencing the potency except for its
This observation showed that test set was interpolative and
derived within the minimumemaximum range of training set. The
mean and standard deviation of ꢃlog 1/MIC values of sets of
training and test provide insights to relative difference of mean and
point density distribution of two sets. 2D-QSAR models were
generated for training set of 18 compounds using multiple linear
regression (MLR) method. The best QSAR model was selected on
the basis of value of statistical parameters like r2 (square of corre-
lation coefficient for training set of compounds), q2 (cross-validated
r2), and pred_r2 (predictive r2 for the test set of compounds). All
QSAR model was validated and tested for its predictability using an
external test set of five compounds. Statistical results generated by
2D-QSAR analysis showed that QSAR models have good internal as
well as external predictability (Table 3). The results obtained for
actual and predicted activity are presented in Table 2 and the
residuals were found to be minimal. The regression equation ob-
tained for the different series of compounds is given below.
selectivity to B. subtilis in which 5b (MIC; 0.000493 mmol/mL) is two
times active than ciprofloxacin regarding this strain. More interest-
ingly, the 2,4-dimethoxybenzenesulfonylquinolone 3b exhibited
excellent activities against all the strains. It provided the most
effective antibacterial activity against S. aureus ATCC 29213 (MIC;
ꢂ0.000470
mL), E. coli ATCC 25922 (MIC; ꢂ0.000470
ATCC 27853 (MIC; 0.000470 mol/mL) and was more potent than
m
mol/mL), B. subtilis ATCC 10400 (MIC; ꢂ0.000470
mmol/
m
mol/mL) and P. aeruginosa
m
the reference drug ciprofloxacin (MIC; ꢂ0.000758
mmol/mL).
2.3. Molecular modeling results
2.3.1. 2D-QSAR study
ꢄ 2D-QSAR model for antibacterial activity against S. aureus
(Model 1)
The antibacterial activities of the tested compounds, presented
in ꢃlog 1/MIC (Table 2), were used in the 2D-QSAR studies using
VLife Molecular Design Suite [36]. Compounds were divided into
training and test set. This was achieved by setting aside five
compounds as test set which have regularly distributed activity.
Selection of molecules in the training set and test is a key and
important feature of any QSAR model. Therefore the care was taken
in such a way that biological activities of all compounds in test set
lie within the maximum and minimum value range of biological
activities of training set of compounds. A Uni-Column statistics for
training set and test set were generated to check correctness of
selection criteria for trainings and test set molecules. The
maximum and minimum value in training and set were compared
in a way that:
ꢃLog 1/MIC ¼ ꢃ0.2078(ꢅ 0.0085)
SsCH3E-index þ 0.0971(ꢅ0.0136) SssOE-index ꢃ 0.3033(ꢅ0.0974)
T_C_F_7 þ 0.1830(ꢅ0.0777) T_2_Cl_5 þ 3.4353
ꢄ 2D-QSAR model for antibacterial activity against B. subtilis
(Model 2)
ꢃLog 1/MIC ¼ ꢃ0.2098(ꢅ0.0192) SsCH3E-index þ 0.0815(ꢅ0.0201)
SssOE-index þ 3.2329
ꢄ 2D-QSAR model for antibacterial activity against E. coli
(Model 3)
1. The maximum value of ꢃlog 1/MIC of test set should be less
than or equal to maximum value of ꢃlog 1/MIC of training
set.
ꢃLog 1/MIC-
E. coli ¼ ꢃ0.4727(ꢅ0.0010) T_C_C_1 ꢃ0.9587(ꢅ0.0127)
T_Cl_Cl_4 þ1.9205(ꢅ0.0326) k3alpha þ 13.8546(ꢅ1.6427) SdsCHE-
index þ 0.1435(ꢅ0.0023) SaaCHcount ꢃ 14.8499
2. The minimum value of ꢃlog 1/MIC of test set should be higher
than or equal to minimum value of ꢃlog 1/MIC of training set.
Table 2
Observed and predicted antibacterial activity (ꢃlog 1/MIC) of the designed arenesulfonylquinolones.
Compd. no.
S. aureus
B. Subtillus
E. coli
P. aeruginosa
Observed
Predicted
Observed
Predicted
Observed
Predicted
Observed
Predicted
1a
1b
2a
2b
3a
3b
4a
4b
5a
5b
6a
6b
7a
7b
8a
8b
2.71
2.72
2.71
2.72
3.32
3.33
3.02
3.33
2.09
2.41
3.33
3.33
3.33
3.33
2.75
2.76
2.09
1.21
1.26
0.67
0.62
0.33
3.12
2.76
2.83
2.76
2.83
3.17
3.24
3.17
3.24
2.16
2.22
2.94
3.01
3.30
3.38
2.94
3.01
1.59
1.66
Outlier
0.25
0.74
0.81
2.83
3.01
2.72
3.01
3.32
3.32
3.33
3.02
3.33
2.39
3.31
3.33
3.33
3.33
3.33
3.35
3.36
2.09
1.51
1.26
0.97
0.62
0.63
3.12
2.85
3.23
2.85
3.10
3.10
3.48
3.10
3.47
2.87
3.23
2.85
3.23
2.85
3.23
2.85
3.23
1.68
2.06
Outlier
0.63
0.82
1.20
3.23
0.60
0.91
0.60
1.21
3.32
3.33
3.32
3.33
2.09
2.10
3.33
3.33
3.33
3.33
0.34
0.95
1.49
1.21
1.26
2.47
0.62
0.33
3.12
0.68
1.05
0.87
0.87
3.38
3.52
3.39
3.53
1.86
2.01
2.45
3.40
2.32
3.26
0.71
0.87
1.46
1.63
1.32
1.45
0.27
0.46
3.28
0.90
0.61
0.60
0.91
2.14
3.33
2.14
2.42
0.89
1.20
2.86
2.73
2.72
2.73
0.34
0.95
1.19
0.90
0.96
0.37
0.62
0.33
3.12
0.99
1.16
0.41
0.58
1.85
2.03
2.30
2.48
1.15
1.32
1.57
1.74
2.77
2.94
0.98
1.15
0.55
0.72
Outlier
0.22
0.39
0.56
3.10
9a
9b
10a
10b
11a
11b
Ciprof.

A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
5491
Table 3
anti-S. aureus activity (11%) which revealed the increased activity
with the presence of chlorine atoms on arenesulfonyl moiety such as
compounds 6 and 7.
Statistical results of 2D-QSAR models for arenesulfonylquinolones obtained by
multiple linear regression method.
Entry
Statistical
S. aureus
B. Subtillus
E. Coli
P. Aureognosa
2.3.1.1.2. For Gram-negative bacteria. The statistical best models
(Model 3) for antibacterial activity against E. coli with a coefficient of
determination (r2) ¼ 0.9404 was considered, as the model showed
an internal predictive power (q2 ¼ 0.8727) of 87% and a predictivity
for the external test set (pred_r2 ¼ 0.5677) of about 57%. Alignment
Independent (AI) descriptors T_C_C_1 which mean the count of
number of carbon atoms (single double or triple bonded) separated
from carbon atom by 1 bond distances in a molecule and T_Cl_Cl_4
which mean the count of number of chlorine atoms (single double or
triple bonded) separated from chlorine atom by 4 bond distances in
a molecule. These two descriptors showed negative contribution
toward antibacterial activity against E. coli in selected QSAR model-3
and the contributions are approx 35% and 20% respectively. Negative
contributions of these descriptors revealed the decrease of anti-
bacterial activity against E. coli of arenesulfonylquinolones with the
presence of methyl and chlorine groups such as compounds 8e11.
K3alpha is a descriptor signifies third alpha modified shape index
and is positively contributing descriptor toward anti-E. coli activity
and its contribution is approx 22%. While SdsCHE-index is Electro-
topological state indices for number of eCH group connected with
one double and one single bond in a molecule. This is the positively
contributing toward antibacterial activity against E. coli and it
contributes approx 16%. Lastly SaaCHcount is a descriptor defines
the total number of carbon atoms connected with hydrogen along
with two aromatic bonds and is 7% positively contributing
descriptor toward anti-E. coli activity. Positive contributions of these
descriptors were clearly signifying that the presence of quinolone
pharmacophore was important for biological activity.
parameters
(Model 1)
(Model 2)
(Model 3)
(Model 4)
1
2
3
4
5
6
7
8
9
r2
0.9268
0.8695
0.6734
0.2853
0.3550
0.3674
0.14369
2.05333
41.1690
0.9026
0.8569
0.6160
0.2973
0.3737
0.2915
0.21319
7.83318
64.8589
0.9404
0.8727
0.5677
0.3512
0.4133
0.5355
0.48605
6.40195
41.0142
0.7940
0.6728
0.5259
0.4225
0.5586
0.6164
0.29079
2.86240
17.9911
q2
Pred_r2
r2_se
q2_se
Pred_r2se
Best-Ran Q2
Z-score Q2
F-test
ꢄ 2D-QSAR model for antibacterial activity against P. aeruginosa
(Model 4)
ꢃLog 1/MIC ¼ ꢃ0.3388 T_T_N_4 þ 0.1364 SssOE-index þ 0.3572
T_2_Cl_5 ꢃ 0.4756 T_C_S_5 þ 5.8340
The statistical result of 2D-QSAR models is tabulated in Table 3.
A brief idea of the requirement of different physicochemical
parameters and their contributions (positive or negative influence
on biological activity), required for potential antibacterial activity
was obtained. The regression equation so obtained will be useful for
the prediction of biological activities of the designed series of
compounds, in future.
2.3.1.1. Contribution of descriptors
2.3.1.1.1. For Gram-positive bacteria. The statistical best models
(Model 1) for antibacterial activity against S. aureus with a coefficient
of determination (r2) ¼ 0.9268 was considered, as the model showed
an internal predictive power (q2 ¼ 0.8695) of 86% and a predictivity
for the external test set (pred_r2 ¼ 0.6734) of about 67%. Moreover
the statistical best model for antibacterial activity against B. subtilis
(Model 2) showed similar pattern with a coefficient of determination
(r2) ¼ 0.9026 was considered, as the model showed an internal
predictive power (q2 ¼ 0.8569) of 86% and a predictivity for the
external test set (pred_r2 ¼ 0.6160) of about 62%. The descriptor
SsCH3E-index is electrotopological state indices for number of eCH3
group connected with one single bond. This descriptor showed
negative contribution toward Gram-positive S. aureus and B. subtilis
in selected models (Model 1 and Model 2) and its contributions are
approx 54% and 73% respectively. Negative contribution of this
descriptor revealed the decrease of anti-Gram-positive bacteria of
arenesulfonylquinolones with the presence of CH3 group such as
compounds 10a and 10b. On the other hand descriptor such as
SssOE-index which is electrotopological state indices for number of
oxygen atom connected with two single bonds showed positive
contribution toward both strain of Gram-positive with contribution
of 20% and 27% for S. aureus and B. subtilis, respectively. Such positive
effect indicated that the antibacterial activity was increased with the
presence of methoxy groups such as compounds 3 and 4. Moreover
Model 1 for S. aureus showed two additional descriptors, one is
T_C_F_7 which is the count of umber of carbon atom (single, double
or triple bonded) separated from fluorine by seven bonds and the
second is T_2_Cl_5 which is the count of number of double bounded
atoms (i.e. any double bonded atom, T_2) separated from chlorine
atom by five bonds in a molecule. The first descriptor showed
negative contribution and its value was 15% which revealed the
decrease in anti-S. aureus activity with the presence of fluorine
atoms on arenesulfonyl fragment as indicated with compounds 5a.
On contrary the second descriptor is positively contributed with
The statistical best models (Model 4) for antibacterial activity
against P. aeruginosa with a coefficient of determination (r2) ¼
0.7940 was considered, as the model showed an internal predictive
power (q2 ¼ 0.6728) of 67% and a predictivity for the external test
set (pred_r2 ¼ 0.5259) of about 53%. Alignment Independent (AI)
descriptors T_T_N_4 which mean the count of number of double
bonds separated from nitrogen atom by four bond distances in
a molecule and T_C_S_5 which mean the count of number of carbon
atoms (single double or triple bonded) separated from sulphur
atom by five bond distances in a molecule. These two descriptors
showed negative contributions toward antibacterial activity against
P. aeruginosa in selected QSAR Model 4 and the contributions are
approx 27% and 21% respectively. Negative contributions of these
descriptors revealed the decrease of antibacterial activity against
P. aeruginosa of arenesulfonylquinolones with the presence of
methyl group such as compounds 9e11. Moreover descriptors, such
as SssOE-index which are electrotopological state indices for
number of oxygen atom connected with two single bonds and
Alignment Independent (AI) descriptors T_2_Cl_5 which mean the
count of number of double bond separated from chlorine atom by
five bond distances in a molecule, showed positive contribution
toward P. aeruginosa with contributions of 35% and 17% respec-
tively. Such positive effect indicates that the antibacterial activity
was increase with the presence of methoxy and chlorine moieties
such as compounds 3 and 6.
2.3.2. Field alignment
FieldAlign [37] was used to align the synthesized ligands to the
most active arenesulfonylquinolone 3b. The idea behind this type of
alignment is that two molecules which bind to a common active
site tend to make similar interactions with the protein and hence
have highly similar field properties. Field alignment was used;
taking into consideration the excluded volume provided by the
binding site amino acid residues, to align the ligands to the most

5492
A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
ꢀ
ꢀ
ꢀ
active arenesulfonylquinolone 3b, Fig. 2. The main constraints
which have been used were the field points representing the
hydrophobic moiety, the hydrogen bond donor and that repre-
senting the hydrogen bond acceptor. The compounds which are top
ranked in similarity index turned to have potent antibacterial
activity (Table 4). Investigating the alignment of these compounds
show high degree of compliance with the essential features which
were constrained (hydrogen bond donor and hydrogen bond
acceptor and hydrophobic aromatic feature). Investigating the
compounds which are the least active reveal a high score of
excluded volume clash penalty (compounds 9e11) or in general
they show no perfect mapping with the constrained field points.
with Ser-1084 (2.80 A), Gly-459 (2.84 A, 2.56 A) in addition to five
ꢀ
ꢀ
nonclassical hydrogen bonds [31] with DC-13 (2.55 A, 2.57 A), Glu-
ꢀ
ꢀ
ꢀ
477 (3.38 A), Asn-475 (2.61 A) and DC-14 (2.64 A) (Fig. 3; lower left
panel). Moreover both compounds 3b and 10b showed coordination
bonds with Mnþþ similar to ciprofloxacin. In short, compound 3b can
be bind in the active site of enzyme in approximately similar
fashion of ciprofloxacin with an additional classical and nonclassical
hydrogen bonds as described above, confirming the molecular design
of the reported class of arenesulfonyl derivatives [21,22,39,40].
3. Conclusion
In the present investigation, 22 different bulky arenesulfo-
nylquinolones based ciprofloxacin and norfloxacin scaffold were
synthesized and evaluated for their antibacterial activity. Most
compounds exhibited significant antibacterial activity. A remarkable
activity was found in compounds 3 and 4 that carrying methoxy
moieties. Compounds 6 and 7 with chloro substitution also exhibi-
ted excellent antibacterial activity. Amongst the compounds tested,
3b and 6b were found to be most potent, while 1, 2, and 8 were
found to have an average activity. On the other hand series 9e11 was
found to be the least active as antibacterial agents in this study. From
the detailed analysis of the results of above studies, we conclude that
antibacterial activity of the synthesized compounds significantly
depends on the electronic effect of methoxy and chloro groups and
this activity diminishes by methyl substitution which may attributed
to steric reason. Various physicochemical indices are helpful for the
understanding of microbiological results, as shown by our 2D-QSAR
study. The 2D-QSAR results could not be addressed to a concrete
drugereceptor interaction, but they can reveal trends in the rela-
tionship between ligand structures and their activities for our set of
antibacterial agents. Analysis of 2D-QSAR models provides details on
the fine relationship linking structure and activity and offers clues
for structural modifications that can improve the activity. These
trends should prove to be an essential guide for the future work.
Molecular docking studies further supported the potent antibacte-
rial inhibitory activity of 3b compared to 10b and ciprofloxacin and
further help understanding the various interactions between the
ligands and enzyme active sites in detail and thereby help to design
novel potent quinolone derivatives.
2.3.3. Docking studies
To predict the antimicrobial data on a structural basis, automated
docking studies were carried out using MOE 2008.10 program [34]
installed on 2.0G Core 2 Duo. The scoring functions and hydrogen
bonds formed with the surrounding amino acids are used to predict
the binding modes, the binding affinities and orientation of the
docked compounds at the active site of the topoisomerase II DNA-
gyrase enzymes. The proteineligand complex was constructed
based on the X-ray structure of topoisomerase II DNA-gyrase with its
bound inhibitor ciprofloxacin that available through the RCSB Protein
Data Bank (PDB entry 2XCT) [38]. The active site of the enzyme was
ꢀ
defined to include residues within a 10.0 A radius to any of the
inhibitor atoms. The scoring functions of the compounds were
calculated from minimized ligand protein complexes. In order to
compare the binding affinity of the newly synthesized arenesulfonyl
analogs, we docked compounds 3b and 10b with different activity
into the empty binding site of topoisomerase II DNA gyrase (2XCT),
with its bound inhibitor ciprofloxacin. Fig. 3 showed the docking
solutions with the highest predicted binding affinity for topoisom-
erase II DNA gyrase, binding mode of the original ligand into its
binding site and binding modes of compounds 3b and 10b as well. As
a results of molecular docking and as shown from Fig. 3, the following
results can be drawn: ciprofloxacin (the original ligand) reveals
dockingscore ofꢃ16.50 kca/mol and forms twohydrogenbonds with
ꢀ
ꢀ
Arg-458 (2.81 A) and Ser-1084 (2.79 A) and another two co-ordinate
bonds with Mnþþ (Fig. 3; upper right panel). Compound 10b which is
the least active exhibits relatively weak binding affinity with docking
score of ꢃ5.11 kca/mol but similarly forms one hydrogen bond with
ꢀ
ꢀ
Ser-1084 (2.79 A), and another bond with Gly-459 (3.31 A) (Fig. 3;
lower right panel). The weak binding affinity of such compound 10b
may be attributed to steric clash of tri-isopropyl moieties with the
adjacent residue and base pair. Compound 3b which is the most
active compound as antibacterial agent possess docking scores
of ꢃ25.35 kca/mol and forms three classical hydrogen bonds [31]
4. Experimental
4.1. Chemistry
Melting points (uncorrected) were recorded on Barnstead
Electrothermal 9100 melting apparatus. IR spectra were recorded
Fig. 2. Left panel showed that the most active arenesulfonylquinolones 3b and 6b were aligned together. Three constraints were applied. The first is the hydrophobic field point in
the center of the arenesulfonyl fragment (yellow sphere), the second is the negative field point which represents H-bond donor on the protein (blue sphere) and the third is the
positive field point which represents H-bond acceptor on the protein (red sphere). The field points interpretation is: blue, negative field points; red, positive field points; yellow, van
der Waals surface field points; gold/orange, hydrophobic field points (describe regions with high polarisability/hydrophobicity). Right panel showed that the least active arene-
sulfonylquinolone 10b aligned on the most active 3b with steric and hydrophobic clash with applied filed and lead to the noncompliance with the negative constrain and the
hydrophobic constrain (for interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article).

A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
5493
Table 4
on precoated (0.25 mm) silica gel GF254 plates (E. Merck, Ger-
many), compounds were detected with 254 nm UV lamp. Silica gel
(60e230 mesh) was employed for routine column chromatography
separations. Compounds 1b and 9b were prepared following their
procedures reported in the literature [40].
Fieldalign similarity score of the newly synthesized ligands to that of the most active
antibacterial arenesulfonylquinolone 3b.a
Compound no.
Similarity score
Compound No.
Similarity score
3a
6b
7b
6a
4b
8b
8a
7a
7a
4a
2b
0.757
0.755
0.752
0.749
0.742
0.742
0.739
0.736
0.733
0.729
0.708
5a
5b
2a
1b
11b
1a
11a
9b
9a
10b
10a
0.708
0.707
0.685
0.684
0.684
0.683
0.679
0.671
0.667
0.651
0.644
4.1.1. General procedure for the synthesis of compounds 1e7
A mixture of norfloxacin (a) or ciprofloxacin (b) (1 mmol)
(Scheme 1) and K2CO3 (152 mg, 1.1 mmol) was stirred in acetone
(20 mL) at room temperature for 20 min. To the resulted mixture,
the appropriate arenesulfonyl chloride (1.2 mmol) in acetone
(5 mL) was added dropwise over a period of 20 min. The reaction
mixture was further stirred at room temperature for 24 h. The
separated solid was then filtered, washed with cold water, dried
and crystallized from the appropriate solvent.
a
The top ranked ligands turned to have broad spectrum antibacterial. In general,
scores are high and we focus on three major essential features in quinolones and
neglect others.
4.1.1.1. 1-Ethyl-6-fluoro-7-(4-(naphthalen-2-ylsulfonyl)piperazin-1-
yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (1a). Yield, 88%;
mp 290e291 ꢀC (MeOH); IR(KBr) nmax/cmꢃ1 3446 (OH), 1718 (C]O),
on a FT-IR PerkineElmer spectrometer. 1H NMR and 13C NMR were
recorded in DMSO‑d6 and/or CDCl3 on a Bruker 500 MHz instru-
1640 (C]O).1H NMR (DMSO-d6);
d 15.24 (s, br,1H), 8.92 (s,1H), 8.51
ment using TMS as internal standard (chemical shifts in
d ppm).
Microanalytical data (C, H, and N) were performed on Per-
kineElmer 240 B analyzer and they agreed with proposed struc-
tures within ꢅ0.4% of the calculated values. Mass spectra were
recorded on on a PerkineElmer, Clarus 600 GC/MS and Varian, TQ
320 GC/MS/MS mass spectrometers. Solvent evaporation was per-
formed under reduced pressure using Buchan Rotatory Evaporator
unless otherwise stated. Thin layer chromatography was performed
(s, 1H), 8.24e8.19 (m, 2H), 8.10e8.08 (d, 1H, J ¼ 7.5 Hz), 7.86e7.80
(m, 2H), 7.75e7.71 (m, 2H), 7.17e7.16 (d, 1H, J ¼ 7.0 Hz), 4.55e4.54
(d, 2H, J ¼ 6.0 Hz), 3.41 (s, 4H), 3.19 (s, 4H), 1.36e1.33 (t, 3H,
J ¼ 7.0 Hz). 13CMR;
d 176.08, 165.97, 153.69, 151.70, 148.54, 144.71,
144.63, 136.95, 134.52, 132.05, 131.80, 129.47, 129.37, 128.89, 127.72,
122.80, 119.69, 111.26, 111.08, 107.08, 106.57, 79.13, 49.01, 48.83,
45.65, 14.27 MS m/z (%); 509.60 (8.0, Mþ).
Fig. 3. The orientation of 3b (color yellow) in DNA-gyrase active pocket (upper left panel; ciprofloxacin is shown as red). The docked ciprofloxacin (upper right panel; color red), 3b
(lower left panel; color yellow) and 10b (lower right panel; color cyan) in DNA-gyrase active pocket (H bonds are shown as green) (for interpretation of the references to colour in
this figure legend, the reader is referred to the web version of this article.)

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A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
4.1.1.2. 1-Cyclopropyl-6-fluoro-7-(4-(naphthalen-2-ylsulfonyl)piper-
azin-1-yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (1b).
Yield, 85%; IR(KBr) [39] nmax/cmꢃ1 3448 (OH),1720 (C]O),1633 (C]
O). 1H NMR (DMSO-d6);
15.08 (s, br, 1H), 8.61 (s, 1H), 8.51 (s, 1H),
56.13, 55.81, 49.34, 45.32, 35.87, 7.55. MS m/z (%); 531.60 (7.0, Mþ).
Anal. calcd. For C25H26FN3O7S: C, 56.49; H, 4.93; N, 7.91; S, 6.03.
Found: C, 55.27; H, 5.42; N, 8.03; S, 6.14.
d
8.24e8.19 (m, 2H), 8.10e8.08 (d, 1H, J ¼ 7.5 Hz), 7.82e7.79 (m, 2H),
7.76e7.69 (m, 2H), 7.53e7.51 (d, 1H, J ¼ 7.0 Hz), 3.76 (s, 1H), 3.41 (s,
4H), 3.20 (s, 4H), 1.30e1.29 (d, 2H, J ¼ 5.5 Hz), 1.11 (s, 2H). 13C NMR;
4.1.1.7. 7-(4-((3,4-Dimethoxyphenyl)sulfonyl)piperazin-1-yl)-1-ethyl-
6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (4a). Yield,
78%; mp 272e273 ꢀC (MeOH/CH2Cl2); IR(KBr) nmax/cmꢃ1 3449 (OH),
d
176.24, 165.77, 153.79, 151.80, 147.96, 144.37, 144.29, 138.91, 134.52,
1738 (C]O), 1630 (C]O). 1H NMR (DMSO-d6);
d 15.24 (s, br, 1H),
132.07, 131.80, 129.48, 129.36, 128.90, 127.87, 127.72, 122.80, 119.01,
111.00, 110.82, 106.95, 106.78, 79.14, 48.74, 45.61, 35.79, 7.50. MS m/z
(%); 521.90 (4.0, Mþ).
8.92 (s, 1H), 7.85e7.83 (d, 1H, J ¼ 13.0 Hz), 7.39e7.37 (dd, 1H, J ¼ 6.5,
10.0 Hz), 7.22e7.16 (td, 3H, J ¼ 6.0, 7.0 Hz), 4.56e4.55 (d, 2H,
J ¼ 6.5 Hz), 3.86 (s, 6H), 3.40 (s, 4H), 3.10 (s, 4H), 1.39e1.36 (t, 3H,
J ¼ 6.5 Hz). 13C NMR;
d 176.06, 165.97, 153.69, 152.67, 151.71, 148.74,
4.1.1.3. 1-Ethyl-6-fluoro-7-(4-(naphthalen-1-ylsulfonyl)piperazin-1-
yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (2a). Yield, 90%;
mp 218e219 ꢀC (MeOH); IR(KBr) nmax/cmꢃ1 3446 (OH),1735 (C]O),
148.50, 144.73, 144.65, 136.95, 125.92, 123.85, 121.49, 119.64, 111.43,
110.13,107.08,106.49, 62.92, 55.85, 49.02, 48.77, 45.62,14.29. MS m/z
(%); 519.90 (10.0, Mþ).
1631 (C]O). 1H NMR (DMSO-d6);
d 15.24 (s, br, 1H), 8.90 (s, 1H),
8.71e8.69 (d, 1H, J ¼ 8.5 Hz), 8.32e8.31 (t, 1H, J ¼ 8.0 Hz), 8.22e8.21
(d, 1H, J ¼ 6.5 Hz), 8.13e8.11 (d, 1H, J ¼ 8.0 Hz), 7.83e7.67 (m, 4H),
7.14e7.12 (d, 1H, J ¼ 7.0 Hz), 4.53e4.52 (d, 2H, J ¼ 6.5 Hz), 3.40 (s,
4.1.1.8. 1-Cyclopropyl-7-(4-((3,4-dimethoxyphenyl)sulfonyl)piperazin-
1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (4b).
Yield, 75%; mp 268e269 ꢀC (MeOH/CH2Cl2); IR(KBr) nmax/cmꢃ1
4H), 3.32 (s, 4H), 1.35e1.33 (t, 3H, J ¼ 6.5 Hz). 13C NMR;
d
176.04,
3447 (OH), 1738 (C]O), 1630 (C]O). 1H NMR (DMSO-d6);
d 15.09
165.96, 153.68, 151.69, 148.47, 144.64, 136.92, 134.80, 133.98, 131.80,
130.34, 129.35, 128.89, 128.32, 127.02, 124.52, 119.71, 119.65, 111.21,
111.03, 107.07, 106.53, 79.13, 48.99, 45.65, 14.30. MS m/z (%); 509.20
(5.0, Mþ). Anal. calcd. For C26H24FN3O5S: C, 61.29; H, 4.75; N, 8.25; S,
6.29. Found: C, 61.32; H, 5.00; N, 8.44; S, 6.25.
(s, br, 1H), 8.63 (s, 1H), 7.85e7.83 (d, 1H, J ¼ 13.0 Hz), 7.55e7.54 (d,
1H, J ¼ 12.0 Hz), 7.40e7.38 (dd, 1H, J ¼ 6.5, 10.0 Hz), 7.22e7.21 (t,
2H, J ¼ 8.0 Hz), 3.86 (s, 6H), 3.79 (s, 1H), 3.41 (s, 4H), 3.12 (s, 4H),
1.32e1.31 (d, 2H, J ¼ 5.0 Hz), 1.15 (s, 2H). 13C NMR;
d 176.27, 165.77,
152.68, 151.85, 148.76, 147.99, 144.43, 144.35, 138.95, 125.93,
121.50, 119.06, 119.00, 111.45, 111.02, 110.83, 110.13, 106.95, 106.74,
62.93, 55.85, 48.67, 45.58, 35.83, 7.52. MS m/z (%); 531.10 (14.0,
Mþ).
4.1.1.4. 1-Cyclopropyl-6-fluoro-7-(4-(naphthalen-1-ylsulfonyl)piper-
azin-1-yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (2b). Yield,
87%; mp 249e250 ꢀC (MeOH); IR(KBr) nmax/cmꢃ1 3446 (OH), 1723
(C]O), 1628 (C]O). 1H NMR (DMSO-d6);
d
15.11 (s, br, 1H),
4.1.1.9. 7-(4-((2,4-Difluorophenyl)sulfonyl)piperazin-1-yl)-1-ethyl-6-
fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (5a). Yield,
90%; mp 199e200 ꢀC (MeOH); IR(KBr) nmax/cmꢃ1 3448 (OH), 1728
8.72e8.70 (d, 1H, J ¼ 8.5 Hz), 8.63 (s, 1H), 8.34e7.32 (d, 1H,
J ¼ 8.5 Hz), 8.23e8.21 (d, 1H, J ¼ 6.5 Hz), 8.15e8.13 (d, 1H,
J ¼ 8.0 Hz), 7.86e7.84 (d, 1H, J ¼ 13.0 Hz), 7.77e7.70 (m, 3H),
7.53e7.51 (d, 1H, J ¼ 7.5 Hz), 3.76 (s, 1H), 3.36 (s, 8H), 1.28e1.27 (d,
(C]O), 1629 (C]O). 1H NMR (DMSO-d6);
d 15.14 (s, br, 1H), 8.99 (s,
1H), 7.99 (s, 1H), 7.76e7.74 (d, 2H, J ¼ 7.5 Hz), 7.55e7.54 (d, 1H,
J ¼ 8.0 Hz), 7.14 (s, 1H), 4.44 (s, 2H), 3.40 (s, 4H), 3.29 (s, 4H), 1.41 (s,
3H). MS m/z (%); 495.20 (5.0, Mþ)
2H, J ¼ 5.5 Hz),1.16 (s, 2H). 13C NMR;
d 176.30, 165.79,153.83,151.85,
148.02, 144.43, 144.36, 138.95, 134.83, 134.00, 131.80, 130.37, 129.16,
128.34, 128.14, 127.05, 124.52, 119.09, 110.85, 107.01, 106.75, 62.93,
49.02, 45.06, 35.82, 30.65, 7.50. MS m/z (%); 521.90 (8.0, Mþ). Anal.
calcd. For C27H24FN3O5S: C, 62.18; H, 4.64; N, 8.06; S, 6.15. Found: C,
62.04; H, 4.46; N, 8.22; S, 6.52.
4.1.1.10. 1-Cyclopropyl-7-(4-((2,4-difluorophenyl)sulfonyl)piperazin-
1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (5b).
Yield, 86%; mp 186e187 ꢀC (EtOH); IR(KBr) nmax/cmꢃ1 3448 (OH),
1728 (C]O),1630 (C]O). 1H NMR (DMSO-d6);
d 15.11 (s, br, 1H), 8.68
4.1.1.5. 7-(4-((2,4-Dimethoxyphenyl)sulfonyl)piperazin-1-yl)-1-ethyl-
6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (3a). Yield,
80%; mp 261e262 ꢀC (Hexane/CH2Cl2); IR(KBr) nmax/cmꢃ1 3446
(s, 1H), 8.16 (s, 1H), 7.98e7.96 (d, 1H, J ¼ 8.5 Hz), 7.89e7.87 (d, 2H,
J ¼ 13.5 Hz), 7.76e7.75 (d, 1H, J ¼ 8.0 Hz), 3.88e3.87 (d, 1H,
J ¼ 5.5 Hz), 3.45 (s, 4H), 3.26 (s, 4H), 1.31e1.30 (d, 2H, J ¼ 6.5 Hz), 1.17
(s, 2H). MS m/z (%); 507.60 (12.0, Mþ).
(OH), 1728 (C]O), 1629 (C]O). 1H NMR (CDCl3);
d 15.07 (s, br, 1H),
8.69 (s, 1H), 8.15e8.13 (d, 1H, J ¼ 11.5 Hz), 7.86e7.85 (d, 1H,
J ¼ 9.0 Hz), 7.28 (s, 1H), 6.91e6.90 (d, 1H, J ¼ 6.0 4H), 6.56e6.55 (t,
1H, J ¼ 6.0 Hz), 4.36e4.28 (t, 2H, J ¼ 7.0 Hz), 3.95 (s, 3H), 3.90 (s, 3H),
3.46 (s, 4H), 3.38 (s, 4H), 1.62e1.55 (t, 3H, J ¼ 6.5 Hz). 13C NMR;
4.1.1.11. 7-(4-((2,4-Dichlorophenyl)sulfonyl)piperazin-1-yl)-1-ethyl-
6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (6a). Yield,
77%; mp 255e256 ꢀC (EtOH); IR(KBr) nmax/cmꢃ1 3448 (OH), 1719
d
176.99, 167.01, 165.06, 158.59, 154.52, 152.52, 147.28, 145.77, 145.68,
(C]O), 1615 (C]O). 1H NMR (DMSO-d6);
d
8.99 (s, 1H), 8.33 (s, 1H),
8.03 (s, 2H), 7.96 (s, 1H), 7.79 (s, 1H), 4.58 (s, 2H), 3.43 (s, 8H,
overlapped with DMSO), 1.40 (s, 3H). 13C NMR;
176.00, 166.00,
137.06, 133.57, 121.31, 117.85, 113.04, 112.86, 108.55, 104.56, 99.62,
56.09, 55.77, 50.11, 49.79, 45.77, 14.50. MS m/z (%); 519.10 (2.5, Mþ).
Anal. calcd. For C24H26FN3O7S: C, 55.48; H, 5.04; N, 8.09; S, 6.17.
Found: C, 55.90; H, 4.73; N, 8.23; S, 6.09.
d
148.50, 144.50, 139.00,133.00,132.50, 132.00,127.50,114.00,112.00,
106.50, 79.14, 62.92, 48.00, 45.15, 14.00. MS m/z (%); 527.80 (2.0,
Mþ). Anal. calcd. For C22H20Cl2FN3O5S: C, 50.01; H, 3.82; N, 7.95; S,
6.07. Found: C, 50.86; H, 3.82; N, 7.96; S, 5.25.
4.1.1.6. 1-Cyclopropyl-7-(4-((2,4-dimethoxyphenyl)sulfonyl)piperazin-
1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (3b).
Yield, 83%; mp 276e277 ꢀC (MeOH/CH2Cl2); IR(KBr) nmax/cmꢃ1 3447
4.1.1.12. 1-Cyclopropyl-7-(4-((2,4-dichlorophenyl)sulfonyl)piperazin-
1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (6b).
Yield, 76%; mp 304e305 ꢀC (AcOH); IR(KBr) nmax/cmꢃ1 3448 (OH),
(OH), 1736 (C]O), 1627 (C]O). 1H NMR (DMSO-d6);
d 15.15 (s, br,
1H), 8.66 (s, 1H), 7.92e7.89 (d, 1H, J ¼ 8.0 Hz), 7.71e7.69 (d, 1H,
J ¼ 9.0 Hz), 7.59e7.58 (d, 1H, J ¼ 7.5 Hz), 6.76 (s, 1H), 6.70e6.68 (dd,
1H, J ¼ 6.5,10.5 Hz), 3.91 (s, 3H), 3.86 (s, 3H), 3.81 (s,1H), 3.37 (s, 4H),
3.28 (s, 4H), 1.33e1.32 (d, 2H, J ¼ 6.0 Hz), 1.17 (s, 2H). 13C NMR;
1719 (C]O), 1630 (C]O). 1H NMR (DMSO-d6);
d 15.15 (s, br, 1H),
8.68 (s, 1H), 8.32 (s, 1H), 8.04e8.02 (d, 1H, J ¼ 8.5 Hz), 7.95e7.92 (d,
1H, J ¼ 13.5 Hz), 7.71e7.69 (dd,1H, J ¼ 6.5,10.5 Hz), 7.61e7.60 (d,1H,
J ¼ 6.0 Hz), 3.76 (s, 1H), 3.44 (s, 4H), 3.40 (s, 4H), 1.33e1.31 (d, 2H,
J ¼ 5.5 Hz), 1.18 (s, 2H). MS m/z (%); 540.50 (3.0, Mþ). Anal. calcd. For
d
176.33, 165.83, 164.61, 158.41, 148.07, 144.72, 139.04, 132.64, 118.99,
117.07, 111.07, 110.89, 106.97, 106.76, 105.24, 99.550, 79.14, 62.92,

A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
5495
C23H20Cl2FN3O5S: C, 51.12; H, 3.73; N, 7.78; S, 5.93. Found: C, 50.31;
H, 3.58; N, 7.93; S, 6.29.
4.2.4. 1-Cyclopropyl-6-fluoro-7-(4-(mesitylsulfonyl)piperazin-1-
yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (9b)
Yield, 78% [39]; mp 238e239 ꢀC (EtOH); IR(KBr) nmax/cmꢃ1 3446
4.1.1.13. 7-(4-((3,4-Dichlorophenyl)sulfonyl)piperazin-1-yl)-1-ethyl-
6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (7a). Yield,
72%; mp 285e286 ꢀC (AcOH); IR(KBr) nmax/cmꢃ1 3446 (OH), 1729
(OH), 1741 (C]O), 1635 (C]O). 1H NMR (DMSO-d6);
d 15.15 (s, br,
1H), 8.67 (s, 1H), 8.32 (s, 1H), 7.94e7.92 (d, 1H, J ¼ 13.5 Hz),
7.60e7.59 (d, 1H, J ¼ 7.0 Hz), 7.13 (s, 1H), 3.80 (s, 1H), 3.37 (s, 4H),
3.28 (s, 4H), 2.60 (s, 6H), 2.30 (s, 3H), 1.32e1.31 (d, 2H, J ¼ 5.5 Hz),
(C]O), 1630 (C]O). 1H NMR (DMSO-d6);
d 15.19 (s, br, 1H), 8.96 (s,
1H), 7.97e7.94 (t, 2H, J ¼ 8.0 Hz), 7.79e7.77 (t, 2H, J ¼ 7.0 Hz),
1.17 (s, 2H). 13C NMR;
d 165.83,148.07,142.80,139.83,131.95,130.89,
7.10e7.08 (d, 1H, J ¼ 9.5 Hz), 4.59e4.58 (d, 2H, J ¼ 6.5 Hz), 3.43 (s,
111.10, 107.06, 106.78, 79.14, 62.93, 48.89, 43.76, 35.89, 22.42, 20.44,
4H), 3.20 (s, 4H), 1.40 (s, 3H). 13C NMR;
d
166.00, 149.58, 148.65,
7.55. MS m/z (%); 513.6 (11.0, Mþ).
137.03, 136.68, 136.09, 135.33, 132.62, 131.91, 129.19, 127.64, 123.87,
111.34, 107.13, 106.69, 62.92, 49.05, 48.82, 45.53, 14.32. MS m/z (%);
528.90 (5.5, Mþ).
4.2.5. 1-Ethyl-6-fluoro-4-oxo-7-(4-((2,4,6-tri-isopropylphenyl)
sulfonyl)piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid
(10a)
4.1.1.14. 1-Cyclopropyl-7-(4-((3,4-dichlorophenyl)sulfonyl)piperazin-
1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (7b).
Yield, 70%; mp 316e317 ꢀC (AcOH); IR(KBr) nmax/cmꢃ1 3447 (OH),
Yield, 64%; mp 301e302 ꢀC (Hexane/CH2Cl2); IR(KBr) nmax/cmꢃ1
3447 (OH), 1728 (C]O), 1628 (C]O). 1H NMR (CDCl3);
d 15.01 (s, br,
1H), 8.64 (s, 1H), 8.02e7.99 (d, 1H, J ¼ 12.5 Hz), 7.21 (s, 2H), 6.87 (s,
1H), 4.21e4.18 (t, 2H, J ¼ 6.5 Hz), 3.45 (s, 5H), 3.40 (s, 5H), 2.94e2.92
(t, 1H, J ¼ 6.5 Hz), 1.58 (s, 3H), 2.94e2.92 (d, 18H, J ¼ 6.0 Hz). 13C
1736 (C]O),1645 (C]O).1H NMR (DMSO-d6);
d 15.14 (s, br,1H), 8.67
(s, 1H), 8.02 (s, 1H), 7.97e7.96 (d, 1H, J ¼ 8.5 Hz), 7.93e7.91 (d, 1H,
J ¼ 13.0 Hz), 7.79e7.77 (d, 1H, J ¼ 8.5 Hz), 7.59e7.58 (d, 1H,
J ¼ 6.0 Hz), 3.82e3.81 (d, 1H, J ¼ 5.0 Hz), 3.43 (s, 4H), 3.22 (s, 4H),
1.33e1.31 (d, 2H, J ¼ 6.0 Hz), 1.16 (s, 2H).. MS m/z (%); 540.20 (17.0,
Mþ).
NMR; d 176.84, 167.02, 154.44, 153.76, 152.44, 151.88, 147.22, 145.55,
145.47, 137.03, 129.22, 124.11, 121.01, 120.95, 112.93, 112.74, 108.31,
104.43, 49.79, 49.48, 44.03, 34.22, 29.43, 24.92, 23.56, 14.52. MS m/z
(%); 586.0 (4.0, Mþ). Anal. calcd. For C31H40FN3O5S: C, 63.57; H,
6.88; N, 7.17; S, 5.47. Found: C, 63.96; H, 6.64; N, 7.40; S, 5.86.
4.2. Synthesis of compounds 8e11
4.2.6. 1-Cyclopropyl-6-fluoro-4-oxo-7-(4-((2,4,6-tri-
isopropylphenyl)sulfonyl)piperazin-1-yl)-1,4-dihydroquinoline-3-
carboxylic acid (10b)
A mixture of arenesulfonyl chloride (1.2 mmol) (Scheme 1),
norfloxacin or ciprofloxacin (1 mmol) and K2CO3 (152 mg,
1.1 mmol) in dimethylformamide (DMF) (5 ml) was heated at
50 ꢀC for 12 h. The solvent was removed under reduced pres-
sure. Water was added to the residue; the solids were filtered,
washed with H2O and crystallized from the appropriate
solvent.
Yield, 67%; mp 293e294 ꢀC (hexane/CH2Cl2); IR(KBr) nmax/cmꢃ1
3447 (OH), 1727 (C]O), 1631 (C]O) 1H NMR (CDCl3);
d 14.87 (s, br,
1H), 8.65 (s, 1H), 7.91e7.89 (d, 1H, J ¼ 12.5 Hz), 7.37e7.35 (d, 1H,
J ¼ 6.5 Hz), 7.21 (s, 2H), 4.20e4.18 (t, 2H, J ¼ 6.5 Hz), 3.44 (s, 5H),
3.41 (s, 4H), 2.94e2.92 (t, 1H, J ¼ 6.5 Hz), 1.40e1.39 (d, 2H,
J ¼ 5.0 Hz), 1.30e1.28 (d, 18H, J ¼ 6.5 Hz), 1.20 (s, 2H). 13C NMR;
4.2.1. 1-Ethyl-6-fluoro-4-oxo-7-(4-((2,4,6-trichlorophenyl)sulfonyl)
piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid (8a)
Yield, 68%; mp 323e324 ꢀC (AcOH); IR(KBr) nmax/cmꢃ1 3446
d 176.87, 166.73, 154.56, 153.74, 152.56, 151.87, 147.44, 145.30,
145.22,138.96, 129.24, 124.11, 120.12, 120.06, 112.43,112.24, 107.93,
105.36, 49.35, 49.33, 44.03, 35.40, 34.21, 29.42, 24.92, 23.56, 9.24.
MS m/z (%); 597.7 (7.0, Mþ). Anal. calcd. For C32H40FN3O5S: C,
64.30; H, 6.75; N, 7.03; S, 5.36. Found: C, 64.70; H, 6.56; N, 7.15; S,
5.44.
(OH), 1738 (C]O), 1628 (C]O). 1H NMR (DMSO-d6);
d 15.23 (s, br,
1H), 8.93 (s, 1H), 7.95e7.92 (d, 1H, J ¼ 13.0 Hz), 7.33 (s, 2H),
7.23e7.22 (d, 1H, J ¼ 6.0 Hz), 4.14e4.12 (t, 2H, J ¼ 6.0 Hz), 3.36 (s,
4H), 3.28 (s, 4H), 1.39e1.38 (d, 3H, J ¼ 6.0 Hz). 13C NMR;
d 176.06,
166.05, 153.74, 153.42, 151.21, 148.55, 144.75, 137.03, 129.29, 123.99,
120.03,111.36,111.18,106.50, 49.08, 43.61, 28.80, 24.58, 23.33,14.40.
MS m/z (%); 562.6 (13.0, Mþ).
4.2.7. 1-Ethyl-6-fluoro-4-oxo-7-(4-((2,3,4,5,6-pentamethylphenyl)
sulfonyl)piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid
(11a)
Yield, 59%; mp 309e310 ꢀC (MeOH); IR(KBr) nmax/cmꢃ1 3446
4.2.2. 1-Cyclopropyl-6-fluoro-4-oxo-7-(4-((2,4,6-trichlorophenyl)
sulfonyl)piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid (8b)
Yield, 63%; mp 331e332 ꢀC (AcOH); IR(KBr) nmax/cmꢃ1 3446
(OH), 1728 (C]O), 1629 (C]O). 1H NMR (DMSO-d6);
d 15.30 (s, br,
1H), 8.97 (s, 1H), 7.95 (s, 1H), 7.36 (s, 1H), 4.60 (s, 2H), 3.33 (s, 4H,
overlaped with DMSO), 3.27 (s, 4H), 2.55 (s, 6H), 2.28 (s, 3H), 2.24 (s,
6H), 1.40 (s, 3H). MS m/z (%); 529.2 (10.0, Mþ). Anal. calcd. For
C27H32FN3O5S: C, 61.23; H, 6.09; N, 7.93; S, 6.05. Found: C, 61.59; H,
6.31; N, 8.13; S, 6.33.
(OH), 1740 (C]O), 1628 (C]O). 1H NMR (DMSO-d6);
d 15.10 (s, br,
1H), 8.78 (s, 1H), 8.12 (s, 1H), 7.95 (s, 1H), 7.89e7.87 (d, 1H,
J ¼ 8.5 Hz), 7.23 (s, 1H), 3.87 (s, 1H), 3.37 (s, 4H), 3.29 (s, 4H),
1.33e1.31 (d, 2H, J ¼ 5.0 Hz), 1.19 (s, 2H). MS m/z (%); 574.2 (4.0,
Mþ).
4.2.8. 1-Cyclopropyl-6-fluoro-4-oxo-7-(4-((2,3,4,5,6-
pentamethylphenyl)sulfonyl)piperazin-1-yl)-1,4-dihydroquinoline-
3-carboxylic acid (11b)
4.2.3. 1-Ethyl-6-fluoro-7-(4-(mesitylsulfonyl)piperazin-1-yl)-4-
oxo-1,4-dihydroquinoline-3-carboxylic acid (9a)
Yield, 58%; mp 316e317 ꢀC (Hexane/CH2Cl2); IR(KBr) nmax/cmꢃ1
Yield, 76%; mp 250e251 ꢀC (EtOH); IR(KBr) nmax/cmꢃ1 3449
3447 (OH), 1727 (C]O), 1630 (C]O). 1H NMR (CDCl3);
d 14.88 (s, br,
(OH), 1721 (C]O), 1632 (C]O). 1H NMR (DMSO-d6);
d
15.28 (s, br,
1H, exchange with D2O), 8.70 (s, 1H), 7.96e7.93 (d, 1H, J ¼ 8.0 Hz),
7.36e7.35 (d, 1H, J ¼ 6.5 Hz), 3.55 (s, 1H), 3.44 (s, 4H), 3.38 (s, 4H)
2.60 (s, 6H), 2.32 (s, 3H), 2.27 (s, 6H), 1.40e139 (d, 4H, J ¼ 5.5 Hz).
1H), 8.96 (s, 1H), 8.32 (s, 2H), 7.94e7.92 (d, 1H, J ¼ 13.0 Hz),
7.23e7.22 (d, 1H, J ¼ 6.0 Hz), 4.59e4.57 (d, 2H, J ¼ 6.0 Hz), 3.35 (s,
4H), 3.26 (s, 4H), 2.60 (s, 6H), 2.30 (s, 3H), 1.41e1.38 (t, 3H,
13C NMR;
d 176.97, 166.71, 147.47, 145.30, 140.64, 138.96, 136.02,
J ¼ 6.0 Hz). 13C NMR;
d
176.16, 166.00, 153.85, 151.86, 148.59, 145.03,
135.08, 132.81, 112.39, 108.16, 105.31, 49.37, 44.05, 35.31, 18.86,
17.92, 17.85, 17.08, 8.23. MS m/z (%); 541.9 (4.6, Mþ). Anal. calcd. For
C28H32FN3O5S: C, 62.09; H, 5.95; N, 7.76; S, 5.92. Found: C, 62.31; H,
5.93; N, 7.91; S, 5.92.
144.94, 142.77, 139.80, 137.05, 131.92, 130.93, 119.85, 111.29, 111.11,
107.13, 106.68, 79.14, 62.92, 49.03, 43.77, 22.40, 20.43, 14.39. MS m/z
(%); 501.6 (3.5, Mþ).

5496
A.A.-M. Abdel-Aziz et al. / European Journal of Medicinal Chemistry 46 (2011) 5487e5497
4.3. Antibacterial methodology
independent variables (i.e., 2D descriptors) was done by removing
invariable (constant column).
MIC of the arenesulfonyl derivatives 1e11 and the reference
drug ciprofloxacin were performed by broth dilution method as
proposed by Clinical and Laboratory Standards Institute [35] and
interpreted using its guidelines. Briefly, the compounds were dis-
solved in dimethylsulphoxide to give final concentration 5120 mg/
mL, and then tenfold dilution was made in the MuellereHinton
4.4.2.2. Statistical analysis. The descriptors were taken as inde-
pendent variables and biological activity as dependent variable.
Multiple Linear Regression (MLR) method of analysis was used to
derive the 2D-QSAR equations. The developed QSAR models are
evaluated using the following statistical measures: r2, (the squared
correlation coefficient); r2se, (standard error of squared correlation
coefficient); F test, (Fischer’s value) for statistical significance; q2,
(cross-validated correlation coefficient); q2_se, (standard error of
cross-validated square correlation coefficient); pred_r2, (r2 for
external test set); pred_r2se, (standard error of predicted squared
regression); Z-score, (Z-score calculated by the randomization test);
best_ran_q2, (highest q2 value in the randomization test). The
regression coefficient r2 is a relative measure of fit by the regression
equation. It represents the part of the variation in the observed data
that is explained by the regression. However, a QSAR model is
considered to be predictive, if the following conditions are satis-
fied: r2 > 0.6, q2 > 0.6 and pred_r2 > 0.5 [42]. The F-test reflects the
ratio of the variance explained by the model and the variance due
to the error in the regression. High values of the F-test indicate that
the model is statistically significant. The low standard error of r2
(r2_se), q2 (q2_se) and pred_r2 (Pred_r2se) shows absolute quality of
fitness of the model.
broth (MHB), which was supplied from Oxoid Chemical Co. UK., to
give final concentration 512
was dispensed into wells of sterile 96 microtitre plate. A 100
the tested compounds (512 g/mL) was pipetted into the wells in
first column and mixed the contents by using multipippetor by
sucking up and down 6e8 times. Then 100 L from the first column
m
g/mL. Mueller-Hinton broth 100
mL
mL of
m
m
was withdrawn and added to the second column to makes
a twofold dilution. This procedure was repeated down to 12th
column to reach the concentration of 0.25 mg/mL. A 100mL was
discarding from 12th column. The standard strains, S. aureus ATCC
29213, Bacillus subtilis ATCC 10400, E. coli ATCC 25922 and
P. aeruginosa ATCC 27853 were grown in the tryptone soy broth to
the right A600. Five m
L of bacterial inoculums (104e105 CFU/mL)
was dispensed into wells. The plates were incubated at 35 ꢀC for
18 h. After the incubation period, the results of MIC were recorded
manually and interpreted according to the recommendations of
Laboratory Standards Institute [35]. MIC is defined as the lowest
concentration of the drug that kills or inhibits visible growth of
microorganism.
4.4.3. Docking methodology
Docking studies have been performed using MOE 2008.10. With
this purpose, crystal structure of topoisomerase II DNA gyrase, with
its bound inhibitor ciprofloxacin (PDB codes: 2XCT) was obtained
from the Protein Data Bank in order to prepare protein for docking
studies. Docking procedure was followed using the standard
protocol implemented in MOE 2008.10 and the geometry of
resulting complexes was studied using the MOE’s Pose Viewer
utility.
4.4. Molecular modeling methods
4.4.1. Energy minimization and alignment of molecules
All 23 compounds were built on workspace of molecular
modeling software VLife MDS 3.5 [36]. The structures were then
converted to three-dimensional space for further analysis. All mole-
cules were batch optimized for the minimization of energies using
Merck molecular force field (MMFF) [41] followed by considering
distance-dependent dielectric constant of 1.0, convergence criterion
Acknowledgments
ꢀ
or root mean-square (RMS) gradient at 0.01 kcal/molA and the iter-
ation limit to 10,000. The energy-minimized geometry was used for
the calculation of fieldalign and the various 2D descriptors. All
molecules were aligned by an atom based alignment technique using
a common structure as a template. The mostactive compound 3bwas
used as the template for alignment of molecule. The alignment is
useful for studying shape variation with respect to the base structure
selected for alignment.
The authors extend their appreciation to the Deanship of
Scientific Research at King Saud University for funding the work
through the research group project no. RGP-VPP-163. Our sincere
acknowledgments to Chemical Computing Group Inc, 1010 Sher-
brooke Street West, Suite 910, Montreal, H3A 2R7, Canada, for its
valuable agreement to use the package of MOE 2008.10 software.
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