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Abstract
Several physiochemical, structural and quantum-mechanics based descriptors were derived for a set of anilide derivatives, using DFT-B3LYP/6-311G (d, p) level of theory. The aim of this study was to develop QSAR model using
multiple linear regression to predict the antimicrobial activity of anilides towards E. Coli in terms of several electronic
and molecular descriptors. The best-fit model involved electrophilicity index (w) in conjunction with molecular weight
(W) and logarithm of the octanol-water partition co-efficient (Log P) as antimicrobial activity descriptors. A comparison of the QSARs [ pIMC = -2.163 ELUMO+ 0.050 log P + 0.81, R2adj = 0.738, RSS = 0.109, F = 110.743], [ pIMC= 0.058
w + 0.047 Log P+ 0.772, R2adj = 0.771, RSS =0.095, F= 132.361], [ pIMC = -0.088ELUMO+ 0.012 + 0.248, R2adj = 0.688,
RSS = 0.129, F = 87.307] and [ pIMC = 0.053w +0.011 + 0.253, R2adj = 0.722, RSS = 0.115, F = 102.235] suggesting
that w is marginally a better descriptor than ELUMO and Log P is slightly a superior descriptor than for parameterization of electrophilic reactivity and hydrophobicity of molecules respectively.
Keywords: Electrophilicity, Hydrophobicity, QSAR, Escherichia Coli, DFT
Introduction
Antimicrobial drugs that help to rid our body of a bacterial infection are either microbiocidal or
microbiostatic. Most of the microbiologists classify
antimicrobial agents into two groups, antibiotics and
chemotherapeutic. Antibiotic are natural substances
produced by certain groups of microorganisms,
whereas chemotherapeutic agents are chemically synthesized. A hybrid antimicrobial substance is a semi
synthetic antibiotic produced by modifying a natural
derivative by the chemist to achieve desired properties. With the development of new antimicrobials, microorganisms have become resistant to various anti-
71
I N T E R N AT I O N A L
72
larizability () and logarithm of the octanol-water partition co-efficient (Log P ). Further, our aim was to investigate whether major chemical properties such as
electrophilic reactivity or hydrophobicity, which are
generally considered responsible for bio-availability
and biological action of chemical molecules at target
cell, can be parameterized in terms of single structural
descriptors s reported in many previous studies or it
requires a combined effect of a set of related descriptors to represent such molecular properties for developing efficient QSAR models.
X
O
NH
R4
R1
R3
R2
01-11; X = C6H5;
12-22; X = CH3(CH2)9CH2;
23-33; X = CH3(CH2)11CH2;
34-40; X = CH3(CH2)15CH2
1, 12, 23, 34; R1, R2, R3, R4=H
2, 13, 24, 35; R2, R3, R4 =H, R1=Cl
3, 14, 25, 36; R1, R3, R4 =H, R2=Cl
4, 15, 26, 37; R1, R2, R4=H, R3 =Cl
5, 16, 27, 38; R1, R3, R4 =H, R2 =CH3
6, 17, 28, 39; R1, R2, R4=H, R3 =CH3
7, 18, 29, 40; R2, R3, R4 =H, R1=OCH3
8, 19, 30; R1, R2, R4 =H, R3=OCH3
9, 20, 31; R1, R3, R4 =H, R2=NO2
10, 21, 32; R1, R2, R4 =H, R3=NO2
11, 22, 33; R1, R2, R4 =H, R3 =Br
Theoretical Background
(a) Quantum Chemical Descriptors
According to the Koopmans theorem, the IP and A are
the eigen value of the HOMO and LUMO with change
of sign49
I E HOMO A E LUMO
Chemical potential 48, hardness50 and softness51 can be
expressed in terms of ionization energy (I) and electron affinity (A) as given below:
-1+A,
1
-1+A and
1
E
-1
=
=
S=(
v(r)
v(r)
v(r)) (2)
2
2 N
2
2 N
N
2
=
2
(3)
(4)
73
I N T E R N AT I O N A L
Table 1: Calculated HOMO energies, LUMO energies, ionization energies, electron affinities, electronegativities, hardness,
softness, chemical potential, weight, volume, total Energy and polarizability of compounds
Comp.
no.
HOMO
(au)
LUMO
(au)
I(eV)
A(eV)
-0.2267
-0.0379
6.17
-0.2459
-0.0511
6.69
74
(eV)
(eV)
S(eV)
(eV)
Weight
Volume
T(au)
1.03
-3.6
2.57
0.19
2.52
197.24
215.79
-632.14
57.8
1.39
-4.04
2.65
0.19
3.08
231.68
229.80
-1091.77
58.8
-0.2440
-0.0401
6.64
1.09
-3.87
2.78
0.18
2.69
231.68
228.97
-1091.76
58.7
-0.2308
-0.0588
6.28
1.6
-3.94
2.34
0.21
3.32
231.68
229.48
-1091.77
58.9
-0.2238
-0.0511
6.09
1.39
-3.74
2.35
0.21
2.98
211.26
234.08
-671.47
59.3
-0.2198
-0.0507
5.98
1.38
-3.68
2.3
0.22
2.94
211.26
234.07
-671.47
59.3
-0.2139
-0.0478
5.82
1.3
-3.56
2.26
0.22
2.80
227.26
242.65
-746.70
60.0
-0.2205
-0.0426
6.0
1.16
-3.58
2.42
0.21
2.65
227.26
242.48
-746.69
59.9
-0.2539
-0.1000
6.91
2.72
-4.82
2.1
0.24
5.53
242.23
236.78
-836.69
59.6
10
-0.2569
-0.0974
6.99
2.65
-4.82
2.17
0.23
5.35
242.23
236.73
-836.69
59.6
11
-0.2289
-0.0592
6.23
1.61
-3.92
2.31
0.22
3.33
276.13
233.96
-3205.69
59.3
12
-0.2352
-0.0250
6.4
0.68
-3.54
2.86
0.17
2.19
275.44
334.36
-833.58
67.1
13
-0.2422
-0.0353
6.59
0.96
-3.78
2.82
0.18
2.53
309.88
347.91
-1293.20
68.3
14
-0.2477
-0.0386
6.74
1.05
-3.9
2.85
0.18
2.67
309.88
348.25
-1293.20
68.3
15
-0.2308
-0.0305
6.28
0.83
-3.56
2.73
0.18
2.32
309.88
348.21
-1293.21
68.3
16
-0.2231
-0.0176
6.07
0.48
-3.28
2.8
0.18
1.92
303.49
371.14
-912.23
70.2
17
-0.2370
-0.0327
6.45
0.89
-3.67
2.78
0.18
2.42
289.46
352.82
-872.95
68.7
18
-0.2271
-0.0257
6.18
0.7
-3.44
2.74
0.18
2.16
305.46
362.00
-948.18
69.4
19
-0.2062
-0.0125
5.61
0.34
-2.98
2.64
0.19
1.68
305.46
360.76
-948.13
69.4
20
-0.2495
-0.0908
6.79
2.47
-4.63
2.16
0.23
4.96
320.43
356.00
-1038.14
69.2
21
-0.2547
-0.0908
6.93
2.47
-4.7
2.23
0.22
4.95
320.43
355.96
-1038.14
69.2
22
-0.2282
-0.0301
6.21
0.82
-3.52
2.7
0.19
2.29
354.33
352.74
-3407.13
68.7
23
-0.2374
-0.0257
6.46
0.7
-3.58
2.88
0.17
2.23
303.49
371.30
-912.22
70.1
24
-0.2403
-0.0265
6.54
0.72
-3.63
2.91
0.17
2.26
303.49
371.44
-912.22
70.1
25
-0.2440
-0.0379
6.64
1.03
-3.84
2.81
0.18
2.62
408.07
467.89
-1568.45
78.7
26
-0.2418
-0.0382
6.58
1.04
-3.81
2.77
0.18
2.62
337.94
384.98
-1371.84
71.3
27
-0.2308
-0.0232
6.28
0.63
-3.46
2.83
0.18
2.11
317.52
389.39
-951.55
71.6
28
-0.2326
-0.0228
6.33
0.62
-3.48
2.86
0.18
2.11
317.52
389.52
-951.54
71.6
29
-0.2084
-0.0209
5.67
0.57
-3.12
2.55
0.20
1.91
333.52
398.12
-1026.77
72.5
30
-0.2315
-0.0257
6.3
0.7
-3.5
2.8
0.18
2.19
333.52
398.36
-1026.77
72.4
31
-0.2576
-0.1036
7.01
2.82
-4.92
2.1
0.24
5.77
348.49
392.76
-1116.78
72.2
32
-0.2580
-0.1011
7.02
2.75
-4.89
2.14
0.23
5.59
348.49
391.80
-1116.78
72.2
33
-0.2370
-0.0375
6.45
1.02
-3.74
2.72
0.18
2.57
382.39
389.32
-3485.76
71.7
34
-0.2370
-0.0261
6.45
0.71
-3.58
2.87
0.17
2.23
359.60
444.92
-1069.50
76.1
35
-0.2392
-0.0261
6.51
0.71
-3.61
2.9
0.17
2.25
359.60
444.92
-1069.51
76.1
36
-0.2389
-0.0364
6.5
0.99
-3.75
2.76
0.18
2.55
394.04
458.34
-1529.13
77.3
37
-0.2418
-0.0382
6.58
1.04
-3.81
2.77
0.18
2.62
394.04
458.66
-1529.14
77.3
38
-0.2319
-0.0220
6.31
0.6
-3.46
2.86
0.18
2.09
373.63
463.07
-1108.84
77.6
39
-0.2337
-0.0228
6.36
0.62
-3.49
2.87
0.17
2.12
373.63
463.31
-1108.84
77.6
40
-0.2436
-0.0246
6.63
0.67
-3.65
2.98
0.17
2.24
389.62
472.65
-1183.86
78.1
Equations
R2
RSS
0.5062
0.2057
40.0734
0.6201
0.1582
64.6613
0.034 + 1.092
0.7128
0.1196
97.8039
0.001W + 0.860
0.6254
0.1219
66.1072
0.007V + 0.943
0.5491
0.1470
48.4698
0.5818
0.5475
0.1361
0.1472
55.2727
48.1833
R2
0.738
0.771
0.689
0.722
RSS
0.109
0.095
0.129
0.116
F
110.742
132.361
87.307
102.235
0.777
0.859
0.925
0.945
0.867
0.914
0.093
0.059
0.031
0.022
0.056
0.036
136.809
238.663
478.898
671.493
254.098
413.213
(a)
(b)
(b)
75
I N T E R N AT I O N A L
2 and Figure-3.The corresponding experimentally observed and the calculated antimicrobial activity values
(a)
(b)
Figure 3: Observed and calculated pIMC values (a) using ELUMO, and W descriptors and (b) using
and W descriptor in three parameter regression model for complete set of molecules.
These results indicate that the two parameter regression equations using electrophilicity index () and Log
P give superior results as compared to using ELUMO and
polarizability(a). The extent of microbiocidal activity
of a given chemical derivative is expected to be governed by the extent of its electrophilic reactivity towards vital cellular components of a given microbe and
its bio-concentration and bioavailability at the target
cell. Our results indicates that electrophilicity index ()
better parameterizes electrophilic reactivity than ELUMO
for this set of test molecules and Log P shows improved
results in modeling lipophilicity than polarizability
parameter (a).However, by introducing addition structural parameter such as molecular weight (W) the resultant three parameter regression equation show better predicatively behavior for the antimicrobial activity of anilides towards E. Coli. The role of molecular
weight can be understood in terms of its effects on stabilization mechanism of the possible intermediates and
metabolites of the antimicrobial species, and also on
the steric properties of derivatives in in-vivo environments.
76
Conclusions
We have derived several physiochemical, structural
and quantum-mechanics based descriptors for a diverse set of organic derivatives compounds using DFTB3LYP/6-311G (d, p) level of theory to develop model
QSAR equations for predicting antimicrobial activity
of anilide derivatives towards E. Coli. Our main focus
has been to investigate the cumulative and synergistic
interplay of effects represents by a set of descriptors to
quantifies a major molecular property of a chemical
compound related to its antibacterial activity. Our main
conclusion is that the antimicrobial activity of compounds considered in this study cannot be completely
explained on the basis of considering only one or two
parameters. In fact, model QSAR equations with improved antimicrobial activity predictability can be developed by using a combination of structural,
physiochemical and electronic descriptors representing a range of chemical and physical properties of compounds responsible for their antimicrobial action.
Among these, the more important ones are related to
their ability to penetrate the cell membrane and their
Table 4: Observed and predicated antimicrobial activity of substituted anilides against E. coli using the best QSAR models
Observed
Comp.
no.
M. Formula
Log P*
pIMC*
( ELUMO,
Log P, W)
Calculated
( , Log P,
W)
pIMC
( ELUMO, ,
W)
( , ,
W)
C13H11NO
2.81
1.09
1.088
1.088
1.087
1.087
C13H10NOCl
3.33
1.16
1.147
1.157
1.130
1.140
C13H10NOCl
3.33
1.06
1.082
1.082
1.064
1.070
C13H10NOCl
3.33
0.97
1.010
1.001
1.018
1.014
C14H13NO
3.28
1.18
1.145
1.156
1.147
1.158
C14H13NO
3.28
1.1
1.110
1.099
1.097
1.096
C14H13NO2
2.56
1.01
1.066
1.028
1.089
1.088
C14H13NO2
2.56
1.06
1.053
1.049
1.074
1.079
C13H10N2O3
2.76
1.18
1.211
1.225
1.218
1.230
10
C13H10N2O3
2.76
1.24
1.205
1.214
1.212
1.220
11
C13H10NOBr
3.6
1.14
1.150
1.139
1.136
1.134
12
C18H29NO
5.09
1.14
1.129
1.137
1.134
1.136
1.190
13
C18H28NOCl
5.61
1.2
1.184
1.183
1.179
14
C18H28NOCl
5.61
1.2
1.193
1.191
1.187
1.197
15
C18H28NOCl
5.61
1.09
1.172
1.171
1.130
1.129
16
C19H31NO
5.56
1.21
1.176
1.185
1.180
1.187
17
C19H31NO
5.56
1.06
1.072
1.072
1.128
1.126
18
C19H31NO2
4.84
1.18
1.164
1.169
1.161
1.162
1.166
19
C19H31NO2
4.84
1.18
1.141
1.152
1.150
20
C18H28N2O3
5.04
1.4
1.382
1.400
1.359
1.379
21
C18H28N2O3
5.04
1.41
1.382
1.399
1.354
1.379
22
C18H28NOBr
5.88
1.15
1.170
1.167
1.161
1.167
23
C20H33NO
5.88
1.25
1.180
1.186
1.169
1.202
24
C20H32NOCl
6.4
1.13
1.190
1.188
1.161
1.155
25
C20H32NOCl
6.4
1.19
1.221
1.216
1.253
1.245
26
C20H32NOCl
6.4
1.27
1.251
1.266
1.213
1.239
27
C21H35NO
6.35
1.1
1.118
1.102
1.181
1.184
28
C21H35NO
6.35
1.16
1.180
1.172
1.180
1.184
29
C21H35NO2
5.09
1.1
1.128
1.125
1.176
1.164
30
C21H35NO2
5.09
1.14
1.140
1.140
1.193
1.190
5.84
1.4
1.385
1.393
1.382
1.386
31
C20H32N2O3
32
C20H32N2O3
5.84
1.24
1.259
1.243
1.265
1.256
33
C20H32NOBr
6.67
1.24
1.248
1.241
1.225
1.236
34
C24H41NO
7.47
1.3
1.282
1.292
1.273
1.282
35
C24H40NOCl
7.99
1.29
1.275
1.275
1.270
1.272
36
C24H40NOCl
7.99
1.25
1.277
1.267
1.281
1.274
37
C24H40NOCl
7.99
1.39
1.385
1.391
1.386
1.378
38
C25H43NO
7.94
1.27
1.265
1.266
1.261
1.261
39
C25H43NO
7.94
1.27
1.267
1.268
1.263
1.263
40
C25H43NO2
7.22
1.25
1.249
1.251
1.263
1.256
*reference 46
Vol. 1 (1) Jan - March 2012
77
I N T E R N AT I O N A L
Acknowledgment
We are thankful Prof. Khaliquz Zaman Khan, Head,
Department of Chemistry, University of Kashmir, for
his constant encouragement, and helpful suggestions.
We would also like to thank Prof. P. K. Chattaraj, Department of chemistry, IIT Kharagpur, Kharagpur for
his assistance and inspiration
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