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Scientific paper
Received: 14-03-2012
Abstract
A quantitative structure activity relationship (QSAR) has been carried out on a series of benzimidazole derivatives to
identify the structural requirements for their inhibitory activity against yeast Saccharomyces cerevisiae. A multiple linear regression (MLR) procedure was used to model the relationships between various physicochemical, steric, electronic, and structural molecular descriptors and antifungal activity of benzimidazole derivatives. The QSAR expressions
were generated using a training set of 16 compounds and the predictive ability of the resulting models was evaluated
against a test set of 8 compounds. The best QSAR models were further validated by leave one out technique as well as
by the calculation of statistical parameters for the established theoretical models. Therefore, satisfactory relationships
between antifungal activity and molecular descriptors were found. QSAR analysis reveals that lipophilicity descriptor
(logP), dipole moment (DM) and surface area grid (SAG) govern the inhibitory activity of compounds studied against
Saccharomyces cerevisiae.
Keywords: Benzimidazole derivatives; QSAR, molecular descriptors; antifungals; Saccharomyces cerevisiae
1. Introduction
Benzimidazoles and their derivatives are well known
to the chemists mainly because of the broad spectrum of the
antimicrobial properties exhibited by this class of compounds.1-13 Interest in the chemistry, synthesis and microbiology of this pharmacophore continues to be fuelled by
their biological properties such as antifungal,14 antitubercular,15 antioxidant,16,17 antiallergic,18,19 and antiparasitic.20 It
is also well known that these molecules are present in a variety of antitumoural,21 anthelmintic22 and herbicidal
agents23. Many derivatives of benzimidazole show antihistaminic, cytostatic, local analgesic, hypotensive and antiinflammatory activity.24 In recent years, benzimidazole derivatives have been attracted particular interest due to their anticancer activity or may act as in vitro anti-HIV agents.25,26
Predictions of biological and physicochemical properties of molecules based on their structure are the fundamental and most interesting objectives of chemistry. The
conception that there exists a close relationship between
27
2. 1. Molecular Modeling
The molecular modeling study was performed using
HyperChem 7.5 software (HyperCube Inc, Version 7.5)
running on P-III processor.34 HyperChem includes a model builder that turns a rough 2Dsketch of a molecule into
3D. The created 3-D models were cleaned up and subjected to energy minimization using molecular mechanics
(MM2). The minimization is executed until the root mean
square (RMS) gradient value reaches a value smaller than
0.1 kcal/mol. The Austin Model-1 (AM-1) method was
used for re-optimization until the RMS gradient attains a
Compound
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17*
18*
19*
20*
21*
22*
23*
24*
25*
26*
27*
28*
R1
NH2
NH2
NH2
NH2
NH2
NH2
NH2
NH2
NH2
NH2
CH3
CH3
CH3
CH3
CH3
CH3
H
H
H
H
NH2
NH2
NH2
NH2
NH2
CH3
NH2
CH3
R2
C6H5CH2
4CH3C6H4CH2
4ClC6H4CH2
C6H5CO
4CH3C6H4CO
4ClC6H4CO
3CH3C6H4CH2
3ClC6H4CH2
3FC6H4CH2
3OCH3C6H4CH2
C6H5CH2
4CH3C6H4CH2
4ClC6H4CH2
C6H5CO
4CH3C6H4CO
4ClC6H4CO
3CH3C6H4CH2
3ClC6H4CH2
3FC6H4CH2
3OCH3C6H4CH2
3CH3C6H4CH2
3ClC6H4CH2
3FC6H4CH2
3OCH3C6H4CH2
H
H
H
H
R3
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
H
H
CH3
CH3
R4
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
H
H
CH3
CH3
MIC (g/ml)
100.00
25.00
25.00
100.00
50.00
50.00
25.00
25.00
50.00
100.00
25.00
12.50
12.50
50.00
12.50
12.50
6.25
6.25
12.50
25.00
6.25
6.25
12.50
25.00
3000.00
2500.00
1000.00
500.00
28
2. 2. Descriptors Generation
The numerical descriptors were calculated for each
compound in the data set, using the software HyperChem,34
Dragon37 and CS Chem Office Software version 7.0.38 Since
there was a 78 different descriptors for each compound (electronic, constitutional, hydrophobic, and topological),
Pearsons correlation matrix was used as a qualitative model,
in order to select the suitable descriptors for MLR analysis.
One way to avoid data redundancy is to exclude descriptors
that are highly intercorrelated with each other before performing statistical analysis. The values of descriptors selected for
MLR model are presented in Table 2 (molar refractivity (MR),
polarizability (P), molar volume (MV), hydration energy
(HE), molar weight (MW), total energy (TE), surface area grid
(SAG), dipole moment (DM) and partition coefficient (logP)).
(1)
formula
(2)
(3)
formula
formula
2. 3. Statistical Methods
(4)
(5)
formula
Table 2. Values of inhibitory activities and molecular descriptors used in the regression analysis
Cmpd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
Log
(1/cMIC)
3.349
3.977
4.013
3.375
3.701
3.735
3.977
4.013
3.683
3.403
3.949
4.276
4.312
3.674
4.301
4.336
4.603
4.637
4.308
4.028
4.628
4.659
4.333
4.051
1.647
1.723
2.207
2.505
MR
77.28
81.56
81.99
77.21
81.49
80.61
81.56
81.99
77.40
83.65
78.48
82.76
83.19
78.41
82.69
81.81
87.25
87.69
83.10
89.34
90.12
89.24
85.97
92.27
43.63
44.83
49.54
49.95
P
26.63
28.46
28.55
26.71
28.55
28.64
28.46
28.55
26.53
29.10
27.11
28.94
29.04
27.20
29.03
29.12
30.78
30.87
28.85
31.42
32.13
32.22
30.20
32.77
15.13
15.62
17.55
19.83
MV
675.88
728.44
712.38
666.31
720.15
710.59
744.54
736.31
704.51
771.05
693.35
745.41
737.17
686.80
741.13
731.39
811.60
804.81
777.39
841.79
844.29
833.57
802.16
871.99
430.33
450.85
478.26
492.38
HE
7.12
5.95
6.72
7.67
6.52
7.35
6.39
7.16
7.31
8.95
2.73
1.61
2.44
3.68
2.53
3.36
1.00
1.86
2.23
3.68
4.26
5.38
5.21
6.83
11.28
4.75
5.28
6.32
MW
223.28
237.30
257.72
237.29
251.29
271.71
237.30
257.72
241.27
253.30
222.29
236.32
256.73
236.27
250.30
270.71
250.34
270.76
254.34
266.38
265.36
285.36
269.32
281.36
133.15
132.16
161.15
160.16
TE
9.75
9.81
9.81
29.80
29.61
30.38
26.35
26.03
26.07
27.94
1.34
1.23
1.63
53.89
53.68
54.42
27.17
26.87
27.02
28.92
27.67
27.18
27.46
29.38
1.21
10.35
5.59
14.14
SAG
416.78
442.99
437.70
409.30
437.71
434.96
458.41
450.08
433.17
470.97
423.77
453.96
448.98
422.33
452.01
447.07
490.32
429.54
477.14
507.17
503.71
498.16
480.77
517.74
292.48
304.78
328.57
372.35
DM
1.45
1.53
1.48
2.16
2.13
2.88
4.46
4.43
4.43
4.42
1.32
1.45
1.69
2.40
2.42
2.86
3.98
3.97
3.98
3.97
4.43
4.40
4.41
4.40
1.04
1.56
2.05
2.58
logP
2.96
3.44
3.52
2.84
3.32
3.39
3.44
3.52
3.12
2.83
3.45
3.94
4.01
3.33
3.81
3.89
4.24
4.31
3.91
3.63
4.42
4.49
4.09
3.80
0.99
1.05
1.54
2.02
29
Table 3. Correlation (r) matrix for the molecular descriptors calculated for benzimidazole derivatives
Log (1/cMIC)
Log (1/cMIC)
1
MR
0.6021
P
0.6308
MV
0.5009
HE
0.7526
MW
0.3352
TE
0.0303
SAG
0.4721
DM
0.1718
logP
0.9706
MR
MV
HE
MW
TE
SAG
DM
logP
1
0.9719
0.9122
0.2181
0.5657
0.0141
0.8888
0.1151
0.5731
1
0.8569
0.2448
0.6732
0.1221
0.8302
0.0883
0.6196
1
0.1197
0.4387
0.0965
0.9945
0.4043
0.4289
1
0.1138
0.06065
0.0792
0.4971
0.8079
1
0.3903
0.4302
0.3007
0.3448
1
0.1087
0.4931
0.0193
1
0.4608
0.3944
1
0.2755
Model
1
Coefficient
Intercept
0.6758
logP
0.9134
DM
0.0289
Intercept
0.0174
logP
0.8491
SAG
0.0022
n
16
r
0.9756
s
0.0787
F
128.6225
16
0.9754
0.0794
127.3676
30
Model
1
2
PRESS
0.1101
0.1349
SSY
1.6864
1.6864
PRESS/SSY
0.0653
0.0800
SPRESS
0.0829
0.0918
r2CV
0.9347
0.9200
r2adj
0.9445
0.9440
worthy that all these equations were derived using the entire data set of compounds (n = 16) and no outliers were
identified. The F-value presented in Table IV is found statistically significant at 99% level since all the calculated F
values are higher as compared to tabulated values.
For the testing the quality of the predictive power of
selected MLR models the LOO procedure was used
(Table 5). The PRESS value above can be used to compute an r2CV statistic, called r2 cross validated, which reflects the prediction ability of the model. This is a good
way to validate the prediction of a regression model without selecting another sample or splitting your data. In this
study, r2adj and r2CV is taken as a proof of the high predictive ability of QSAR models. A high value of these statistical characteristic (> 0.5) is considered as a proof of the
high predictive ability of the models. Adjustable correlation coefficient (r2adj) tells us the statistical significance of
incorporated physicochemical descriptor in MLR. r2adj
takes into account the adjustment of conventional correlation coefficient (r2).
Table 6. Predicted log1/cMIC values of training set with residual
Compound
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Residuals
Model 1
Model 2
0.072
0.085
0.115
0.079
0.079
0.058
0.043
0.059
0.068
0.084
0.120
0.103
0.030
0.045
0.006
0.031
0.030
0.078
0.015
0.038
0.084
0.084
0.040
0.071
0.075
0.083
0.113
0.086
0.075
0.069
0.025
0.047
However, the high r2CV does not imply automatically a high predictive ability of the model. Thus, the high
value of LOO r2CV is the necessary condition for a model
to have a high predictive power, it is not a sufficient condition. In order to verify the predictive power of the developed models, the predicted (log1/cMIC) values of the training set of compounds were calculated and compared with
the experimental values (Table 6, Fig. 1).
Fig 1. Plots of predicted versus the experimentally observed antifungal activity of training set
Compound
17
18
19
20
21
22
23
24
25
26
27
28
4.696
4.622
4.387
4.215
4.878
4.926
4.548
4.383
1.501
1.580
2.048
2.551
Residuals
Model 1
Model 2
0.061
0.09
0.054
0.078
0.213
0.245
0.206
0.223
0.037
0.043
0.065
0.090
0.093
0.015
0.079
0.187
0.250
0.267
0.215
0.332
0.146
0.143
0.159
0.046
4. Conclusion
From the results discussed above, it can be concluded that the different substituted benzimidazole derivatives
showed in vitro considerable inhibitory activity against
the yeast Saccharomyces cerevisiae. Molecular modeling
Fig 2. Plots of predicted versus the experimentally observed antifungal activity of test set
and QSAR analysis were performed to find the quantitative effects of the molecular structure of the compounds
on their antifungal activity. Various physicochemical parameters, especially partition coefficient, ionization constant and water solubility can be used successfully for
modeling antifungal activity of benzimidazoles. Two best
QSAR mathematical models are used to predict inhibitory
activity of the benzimidazoles investigated and close
agreement between experimental and predicted values
was obtained. The low residual activity and high crossvalidated r2 values (r2CV) observed indicated the predictive
ability of the developed QSAR models. It indicates that
these models can be successfully applied to predict the antifungal activity of these class of molecules.
5. Acknowledgement
These results are the part of the project No.172012
and No.172014, supported by the Ministry of Science and
Technological Development of the Republic of Serbia and
31
32
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Povzetek
QSAR metoda je bila uporabljena v seriji novih benzimidazolskih derivatov razli~nih struktur s ciljem ugotavljanja njihovih inhibitorskih aktivnosti na kvasovke Saccharomyces cerevisiae. Postopek multiple linearne regresije (MLR) je bil
uporabljen za modeliranje odnosa med razli~nimi fizikalno-kemi~nimi, sternimi, elektronskimi in strukturnimi molekularnimi deskriptorji in antifugalne aktivnosti preizku{enih benzimidazolnih derivatov. QSAR odvisnosti so bile dobijene
iz poskusnega seta sestavljenega iz 16 spojin. Mo`nost uporabe dobijenih ena~b za predvidevanje inhibitorske aktivnosti je bila nato preizku{ena z uporabo testnega niza iz 8 derivatov benzimidazola. Najbolj{i QSAR model je preverjen z
izra~unom statisti~nih parametrov ugotovljenega teoreti~nega modela. Tako je dolo~en odgovarjajo~ odnos odvisnosti
med antifugalno aktivnostjo in molekularnimi deskriptorji. Ugotovljeno je da ima na inhibitorsko aktivnost derivatov
benzimidazola na kvasovke Saccharomyces cerevisiae najve~ji vpliv deskriptor lipofilnosti (logP), dipolni moment
(DM) in mre`a povr{inskega podro~ja (SAG).
33