A.A. El-Bindary et al. / Journal of Molecular Liquids 211 (2015) 256–267
259
Table 2
The bond length for (HL
1.6 million new cases in 2010. The incidence or prevalence rate of the
breast cancer in India is expected to be more than 90,000 in the coming
years and over 50,000 women die each year.
n
).
Bond length (Å)
Docking study showed the binding affinity, number of hydrogen
bonds. It is interesting to note that the binding affinities have
negative values. This reveals the high feasibility of this reaction.
Molecular docking is a key tool in computer drug design [26,27].
The focus of molecular docking is to simulate the molecular recog-
nition process. Molecular docking aims to achieve an optimized
conformation for both the protein and drug with relative orienta-
tion between them such that the free energy of the overall system
is minimized.
The study simulates the actual docking process in which the ligand–
protein pair-wise interaction energies are calculated using Docking
Server [28]. The MMFF94 Force field was used for energy minimization
of ligand molecules using Docking Server. Gasteiger partial charges
were added to the ligand atoms. Non-polar hydrogen atoms were
merged, and rotatable bonds were defined. Docking calculations were
carried out on 2q7k and 3hb5-oxidoreductase–Hormone protein
model. Essential hydrogen atoms, Kollman united atom type charges,
and solvation parameters were added with the aid of AutoDock tools
[29]. Affinity (grid) maps of 0.375 Å spacing were generated using
the Autogrid program [30]. AutoDock parameter set- and distance-
dependent dielectric functions were used in the calculation of the van
der Waals and the electrostatic terms, respectively.
HL
1
HL
2
HL
3
C(17)–H(30)
C(17)–H(29)
C(17)–H(28)
O(14)–H(27)
N(13)–H(26)
N(13)–H(25)
C(12)–H(24)
C(11)–H(23)
C(9)–H(22)
C(8)–H(21)
C(6)–H(20)
C(3)–H(19)
C(2)–H(18)
N(15)–N(16)
C(11)–C(12)
C(10)–C(17)
C(10)–C(11)
C(9)–C(10)
C(8)–C(9)
C(7)–N(16)
C(7)–C(12)
C(7)–C(8)
C(5)–O(14)
C(5)–C(6)
C(4)–N(15)
C(4)–C(5)
C(3)–C(4)
1.114
1.114
1.113
0.971
1.049
1.049
1.103
1.103
1.103
1.105
1.104
1.105
1.103
1.251
1.343
1.510
1.344
1.343
1.342
1.269
1.347
1.347
1.363
1.347
1.270
1.354
1.349
N(15)–N(16)
O(14)–H(27)
N(13)–H(26)
N(13)–H(25)
C(12)–H(24)
C(11)–H(23)
C(11)–C(12)
C(10)–H(22)
C(10)–C(11)
C(9)–H(21)
C(9)–C(10)
C(8)–H(20)
C(8)–C(9)
N(16)–C(7)
C(7)–C(12)
C(7)–C(8)
C(6)–H(19)
C(5)–O(14)
C(5)–C(6)
C(4)–N(15)
C(4)–C(5)
C(3)–H(18)
C(3)–C(4)
C(2)–H(17)
C(2)–C(3)
C(1)–N(13)
C(1)–C(6)
1.248
0.972
1.050
1.050
1.100
1.100
1.420
1.100
1.420
1.100
1.420
1.100
1.420
1.456
1.420
1.420
1.100
1.355
1.420
1.456
1.420
1.100
1.420
1.100
1.420
1.462
1.420
N(15)–N(16)
O(14)–H(27)
N(13)–H(26)
N(13)–H(25)
C(12)–H(24)
C(11)–H(23)
C(11)–C(12)
C(10)–Cl(17)
C(10)–C(11)
C(9)–H(22)
C(9)–C(10)
C(8)–H(21)
C(8)–C(9)
C(7)–N(16)
C(7)–C(12)
C(7)–C(8)
C(6)–H(20)
C(5)–O(14)
C(5)–C(6)
C(4)–N(15)
C(4)–C(5)
C(3)–H(19)
C(3)–C(4)
C(2)–H(18)
C(2)–C(3)
C(1)–N(13)
C(1)–C(6)
1.251
0.971
1.049
1.049
1.103
1.103
1.343
1.727
1.342
1.103
1.341
1.105
1.342
1.269
1.348
1.348
1.104
1.363
1.347
1.270
1.354
1.105
1.349
1.103
1.341
1.267
1.341
Docking simulations were performed using the Lamarckian genetic
algorithm (LGA) and the Solis & Wets local search method [31]. Initial
position, orientation, and torsions of the ligand molecules were set
randomly. All rotatable torsions were released during docking. Each
docking experiment was derived from 10 different runs that were set
to terminate after a maximum of 250,000 energy evaluations. The
population size was set to 150. During the search, a translational step
of 0.2 Å, and quaternion and torsion steps of 5 were applied.
Breast cancer is one of the most recurring worldwide diagnosed and
deadliest cancers next to lung cancer with a high number of mortality
rates among females [25]. At global level, it accounted for more than
In this context, the docked ligands were analysis with the prostate
cancer mutant 2q7k-Hormone and breast cancer 3hb5 as shown in
Fig. 4(A, C, E) and (B, D, F) and Fig. 5(A
, C , E ) and (B , D , F ). The
1 1 1 1 1 1
Table 3
The selected geometric parameters bond angle for (HL
n
).
study simulates the actual docking process in which the ligand–protein
pair-wise interaction energies are calculated in Tables 5 and 6. Accord-
ing to our results, HB plot curve indicates that, azo compound binds to
Bond angles (°)
HL
1
H
2
HL
3
H(26)–C(15)–C(16)
H(26)–C(15)–C(14)
C(16)–C(15)–C(14)
C(15)–C(14)–C(13)
H(25)–C(13)–C(14)
C(14)–C(13)–C(12)
H(27)–C(16)–C(9)
H(27)–C(16)–C(15)
C(9)–C(16)–C(15)
H(24)–C(12)–C(13)
C(13)–C(12)–C(9)
C(16)–C(9)–C(12)
C(16)–C(9)–N(10)
C(12)–C(9)–N(10)
N(11)–N(10)–C(9)
H(21)–N(7)–C(6)
C(1)–C(6)–C(5)
C(1)–C(6)–N(7)
C(5)–C(6)–N(7)
C(6)–C(5)–C(4)
C(3)–N(11)–N(10)
C(5)–C(4)–C(3)
C(5)–C(4)–O(8)
C(3)–C(4)–O(8)
C(4)–C(3)–C(2)
119.435
119.296
121.27
117.919
119.983
120.824
121.85
117.101
121.049
118.209
121.53
117.408
125.954
116.637
119.84
120.107
118.987
120.399
120.614
122.406
121.157
118.569
117.646
123.785
118.657
127.28
114.063
122.092
120.833
119.878
119.289
109.265
119.181
118.414
120.033
119.644
120.323
119.392
120.289
119.982
121.886
117.026
121.088
120.124
121.479
117.736
125.829
116.436
119.902
120.3
118.988
120.409
120.603
122.405
121.129
118.571
117.639
123.79
119.326
120.487
120.188
119.509
120.73
119.847
121.799
117.009
121.191
118.139
121.583
117.682
125.849
116.469
119.87
120.111
118.991
120.401
120.609
122.404
121.153
118.566
117.658
123.776
118.663
127.253
114.084
122.087
120.835
119.876
119.289
109.299
119.187
118.409
n
the two proteins with hydrogen bond interactions of ligands (HL )
with 2q7k and 3hb5 as shown in Figs. 6 and 7. The calculated efficiency
is favorable, Ki values estimated by AutoDock were compared with
experimental Ki values, when available, and the Gibbs free energy is
negative. Also, based on this data, we can propose that interaction
between the 2q7k, 3hb5 receptors and the ligands (HL
2D plot curve of docking with ligands (HL ) is shown in Figs. 8 and 9.
This interaction could activate apoptosis in cancer cell energy of interac-
tions with ligands (HL ). From the analysis of the values, it is evident
that the binding energy of (HL ) decreases. So that is decrease in
binding energy of HLn on transpiration of mutation for prostate cancer
q7k whereas increase with HLn for breast cancer. Binding energies
n
) is possible.
n
n
n
2
are most widely used mode of measuring binding affinity of a ligand.
Thus, the decrease in binding energy due to mutation will increase the
binding affinity of the azo phenol towards the receptor. The charac-
teristic feature of azo phenols represents the presence of several ac-
tive sites available for hydrogen bonding. This feature gives them the
ability to be good binding inhibitors to the protein and will help to
produce augmented inhibitory compounds. The results confirm that,
the azo ligand derived from 3-aminophenol is an efficient inhibitor of
prostate cancer mutant 2q7k-Hormone and 3hb5-oxidoreductase
breast cancer.
118.655
127.271
114.074
122.092
120.487
117.422
119.29
C(4)–C(3)–N(11)
C(2)–C(3)–N(11)
C(3)–C(2)–C(1)
H(18)–C(1)–C(6)
H(18)–C(1)–C(2)
C(6)–C(1)–C(2)
H(23)–O(8)–C(4)
H(20)–C(5)–C(6)
H(20)–C(5)–C(4)
3.4. Potentiometric studies
The average number of the protons associated with ligands (HL
n
) at
different pH values, nA , was calculated from the titration curves of