In Silico Geometry Optimization, Excited – State Properties of
(2E)-N-Hydroxy-3-[3-(Phenylsulfamoyl) Phenyl] prop-2-Enamide (Belinostat) and
its Molecular Docking Studies with Ebola Virus Glycoprotein
I.E. Otuokere1,
F.J. Amaku1 and C.O. Alisa2
1Department of Chemistry, Michael Okpara University of Agriculture, Umudike,
Nigeria
2Department of Chemistry, Federal University of Technology, Owerri, Nigeria
ABSTRACT:
The histone deacetylase
inhibitor (2E)-N-hydroxy-3-[3-(phenylsulfamoyl)phenyl]prop-2-enamide (belinostat) is a drug designed for the treatment of hematological
malignancies and solid tumors. Geometry optimization of (2E)-N-hydroxy-3-[3-(phenylsulfamoyl)phenyl]prop-2-enamide (belinostat)
using Argus lab software was performed. Molecular mechanics calculations were
based on specific interactions within the molecule. These interactions included
stretching or compressing of bond beyond their equilibrium lengths and angles.
The excited states of belinostat were created. The final self- consistent field
(SCF) energy was found to be be -126.3659168682
au (-79295.8815 kcal/mol). This is the
average interaction between a given belinostat particle and other belinostat particles of a
quantum-mechanical system consisting of many particles. The most energetically favourable conformation of belinostat
was found to have a heat of formation of 581.1137 kcal/mol via PM3
(NDDO) RHF SCF Type. The steric energy calculated for
belinostat was 0.64665673 a.u.(405.78359283 kcal/mol). Molecular docking result revealed
the binding free energy. The
global binding energy value -28.87 Kcal/mole was
ranked first because it had the least energy. The most feasible position for belinostat to inhibit ebola virus glycoprotein
was predicted to be -28.87 kcal/mol.
KEY WORDS:
Belinostat, molecular mechanics, Arguslab
software, docking, ebola vius
INTRODUCTION:
The histone deacetylase inhibitor belinostat is a drug designed for the treatment of hematological
malignancies and solid tumors. It can be used to treat ovarian cancer when
combined with carboplatin and paclitaxel for
relapsed ovarian cancer[1].
Pharmacodynamics
analyses have been conducted to describe the effect of belinostat
on the acetylation of histones
3 and 4 (H3 and H4), the acetylation
activity of both of these histones after belinostat exposure showed an increase in the level of acetylation both in vivo and in vitro [2-4].
Growth inhibition and apoptosis of the malignant cells were associated with
these increased levels of acetylation, and no
noticeable toxicity was seen in mice[5].
Belinostat has shown encouraging effect against peripheral T-cell lymphoma[6-
8]. This medication is available for intravenous administration only[9] .
Local charges
such as Mulliken charges and ZDO charges are also
generated from arguslab using the AM1 parameterized
method. In the zero deferential overlap (ZDO) approximation, the product of two
deferent atomic orbitals is set to zero. The integra which survives the ZDO approximation was partly
computed using the uniform charge sphere and the rest parameterized. The result
produced is the integrated form of Hückel Theory
which takes into account electron repulsion. Mulliken charges arise from the Mulliken population analysis [10, 11] and
provide a means of estimating partial atomic charges from calculations carried out by the
methods of computational chemistry, particularly
those based on the linear combination of atomic orbitals molecular
orbital method, and are routinely used as variables in linear
regression (QSAR) procedures[12,13]. The energies computed by molecular
mechanics are usually conformational energies. This means that the energy
computed is meant to be an energy that will reliably predict the diference in energy from one conformation to the next. The
effect of strained bond lengths or angles is also included in this energy. This
is not the same as the total energies obtained from ab
initio programs or the heat of formation from semiempirical
programs. Molecular mechanics methods are not generally applicable to
structures very far from equilibrium, such as transition structures. Arguslab is the electronic structure program that is based
on the quantum mechanics, it predicts the potential energies, molecular
structures; geometry optimization of structure, vibration frequencies of
coordinates of atoms, bond length, bond angle and reactions pathway[14].
Conformational analysis of molecule is based on molecular mechanics, it is a
method for the calculation of molecular structures, conformational energies and
other molecular properties using concept from classical mechanics. The energy
(E) of the molecule is calculated as a sum of terms as in equation (1).
E = Estretching + Ebending
+ Etorsion + EVander
Waals + Eelectrostatic + Ehydrogen bond + cross term (Equation 1)
These terms are
of importance for the accurate calculation of geometric properties of
molecules. The set of energy functions and the corresponding parameters are
called force field [15]
.
MATERIALS AND METHODS:
All
conformational analysis (geometry optimization) study was performed on a window
based computer using Arguslab[16] and ACDlab
Chemsketch software’s[17]. Belinostat molecule
was built with ACDlab and saved as mol file. The
saved mol file of belinostat was generated by Arguslab, and minimization was performed with the semi-empirical Austin Model
1 (AM1) parameterization[18,19].
The minimum potential energy was calculated by using geometry convergence
function in Arguslab software. In order to determine
the allowed conformation, the contact distance between the atoms in adjacent
residues is examined using criteria for minimum Vander Waal contact distance [20
– 23]. Surfaces created to visualize ground state properties as well as
excited state properties such as orbital, electron densities, electrostatic
potentials (ESP) spin densities generated the grid data used to make molecular
orbital surfaces. The minimum potential energy was calculated for drug receptor
interaction through the geometry convergence map. Retrieval of ebola virus envelop glycoprotein Crystal
structure of ebola virus envelop glycoprotein from
the organism Homo sapiens with
the PDB ID 2EBO was retrieved from the Protein Data Bank (PDB).
Molecular docking:
Molecular docking was performed using patchdock
online server[25]. Patchdock is a molecular docking algorithm based on shape complementarity principles. The Receptor (ebola
virus) and ligand molecule (belinostat) were uploaded in PDB format
in Patchdock
server, an automatic server for molecular docking. Clustering RMSD was chosen
as 1.5 Ĺ. E-mail address to retrieve the result was given. Complex type was
chosen as enzyme – inhibitor type. The docking job was submitted to the Patchdock server and refined in firedock
online server[26,27]. The best
conformation result was processed using Swiss PDB viewer software[28].
At the end of each docking run, interactions are shown in the form of
"poses" with the energy values given in kcal/mol for each pose.
Global energy and atomic contact energy scoring function of the firedock result were used to evaluate the stable
interactions as indicated by lowest global energy (the binding energy of the ligand and the protein target). The lowest energy poses
indicate the highest binding affinity as high energy produces unstable conformations.
RESULTS
AND DISCUSSION:
Prospective
view and calculated properties of belinostat molecule
are shown in Figure1. The active conformation and electron density mapped of belinostat by ACD labs-3D viewer software are shown in
Figure 2 and 3 respectively. Figures 4 and 5 shows the
highest occupied molecular orbital’s
and lowest unoccupied molecular orbital’s of belinostat.
Figure 6 shows electrostatic potential mapped density of belinostat
calculated with the AM1 (NDDO) RHF SCF type . The potential energy convergence map of belinostat is shown in Figure 7. UFF (molecular mechanics)
geometry optimized atomic coordinates of belinostat
is given in Table 1. Bond length and bond angles are given in Tables 2 and 3
respectively, which were calculated after geometry optimization of molecule
from Arguslab by using molecular mechanics
calculation. Tables 4 and 5 shows the dihedral angles and
improper torsion angles of belinostat respectively.
Table 6 shows calculated Final energy evaluation of belinostat
molecule. The Ground State Dipole (debye) of belinostat
is presented in Table 7. List of Mulliken atomic charges and ZDO atomic charges of belinostat is shown in Table 8 while the relative
interaction energy values of belinostat docked unto ebola virus is presented in Table 9.
Figure-1:
Prospective view of (2E)-N-Hydroxy-3-[3-(Phenylsulfamoyl)
Phenyl] prop-2-Enamide (Belinostat)
ArgusLab
was used to see what happened to the electrons in molecules when it absorbed
light. Surfaces were made to explore this fascinating phenomenon. Molecules absorbsed energy in the form of UV/visible light, it made a
transition from the ground electronic state to an excited electronic state. The
excited and ground states have different distributions of electron
density. This property is often valuable and sought after by chemists who
are interested in molecules that are useful as dyes, sunscreens, etc[16]. The HOMO is localized to the
plane of the molecule and is a non-bonding molecular orbital. The LUMO is perpendicular to the plane of the
molecule and is a combination of the pz
atomic orbitals. The n -> π*
transition is dominated by the excitation from the HOMO to the LUMO. The
positive and negative phases of the orbital are represented by the two colors,
the red regions represent an increase in electron density and the blue regions
a decrease in electron density. However, these calculations were examined in
the ground state and also in vacuum [16]. The electrostatic
potential is a physical property of a molecule that relates to how a molecule
is first “seen” or “felt” by a positive "test" charge at a particular
point in space. A distribution of electric charge creates an electric potential
in the surrounding space. A positive electric potential means that a positive
charge will be repelled in that region of space. A negative electric potential
means that a positive charge will be attracted. A portion of a molecule that
has a negative electrostatic potential will be susceptible to electrophilic attack – the more negative the better[16]. QuickPlot
ESP mapped density generates an electrostatic potential map on the total
electron density contour of the molecule. The electron density surface depicts
locations around the molecule where the electron probability density is equal[14]. This gives an idea of the
size of the molecule and its susceptibility to electrophilic
attack. Electron density surface shows
the complete surface with the color map. The surface color reflects the
magnitude and polarity of the electrostatic potential. The color map shows the
ESP energy (in hartrees) for the various colors. The
red end of the spectrum shows regions of highest stability for a positive test
charge, magenta/ blue show the regions of least stability for a positive test charge[16]. These images show that the
triple and double bonded end of the molecule is electron rich relative to the
single bonded end[16]. The self-consistent field (SCF) energy
is the average interaction between a given particle and other particles of a
quantum-mechanical system consisting of many particles. Because the problem of
many interacting particles is very complex and has no exact solution;
calculations are done by approximate methods. One of the most often used
approximated methods of quantum mechanics is based on the interaction of a
self-consistent field, which permits the many-particle problem to be reduced to
the problem of a single particle moving in the average self-consistent field
produced by the other particles[24]. The final SCF energy of belinostat was found to be -126.3659168682 au (-79295.8815
kcal/mol) as calculated by RHF/PM3 method using ArgusLab
4.0.1 suite. It should be noted that the Mulliken
charges do not reproduce the electrostatic potentials of a molecule very well. Mulliken charges were calculed by
determining the electron population of each atom as defined by the basis functions[21].
The standard heat of formation of a
compound is the enthalpy change for the formation of 1mole of the compound from
its constituent elements in their standard states at 1 atmosphere. Its symbol
is ΔHfθ. The most energetically favourable conformation of belinostat
was found to have a heat of formation of 581.1137 kcal/mol via PM3 (NDDO) RHF SCF Type. The steric
energy calculated for belinostat was 0.64665673 a.u. (405.78359283 kcal/mol). The
docked poses of the derivatives were ranked according to the docking scores
i.e. the lowest global energy values was
the top ranked and best fitted conformations of the docked pose were analyzed
for the study. The complex models generated after successful docking of the belinostat and ebola was based on
the parameters such as hydrogen bond interactions, global energy, atractive Vander Waals energy, repulsive Vander Waals
energy, and atomic contact energy of the docked compound within the active
site. These parameters play important roles in the biological activity of a
compound. The molecular docking result predicted the most feasible position for
belinostat to inhibit ebola
virus glycoprotein. This was found to be -28.87 kcal/mol.
Table
1: Geometry optimised atomic coordinates of belinostat.
Atoms |
X |
Y |
Z |
Atomic
No. |
C |
13.57317552 |
-12.00779349 |
0.00000000 |
6 |
C |
13.21151122 |
-13.44904618 |
0.00000000 |
6 |
C |
12.57270712 |
-11.10713415 |
0.00000000 |
6 |
C |
11.93206519 |
-13.84091147 |
0.00000000 |
6 |
C |
11.15804759 |
-11.53396071 |
0.00000000 |
6 |
C |
10.85335140 |
-12.83488810 |
0.00000000 |
6 |
N |
14.86409519 |
-11.55954248 |
0.00000000 |
7 |
S |
16.39167960 |
-12.48565335 |
0.00000000 |
16 |
O |
17.22478053 |
-11.18014456 |
0.00000000 |
8 |
O |
15.77692566 |
-13.90436742 |
0.00000000 |
8 |
C |
18.09236292 |
-13.31137288 |
0.00000000 |
6 |
C |
20.56974473 |
-13.12559106 |
0.00000000 |
6 |
C |
20.64708363 |
-14.60208976 |
0.00000000 |
6 |
C |
19.37191193 |
-12.52967171 |
0.00000000 |
6 |
C |
19.52798805 |
-15.32807618 |
0.00000000 |
6 |
C |
18.21278750 |
-14.65778439 |
0.00000000 |
6 |
C |
21.77993020 |
-12.28996022 |
0.00000000 |
6 |
C |
23.00952118 |
-12.81216498 |
0.00000000 |
6 |
C |
24.21756830 |
-11.96550048 |
0.00000000 |
6 |
N |
25.44123886 |
-12.54390926 |
0.00000000 |
7 |
O |
24.11241288 |
-10.70543889 |
0.00000000 |
8 |
O |
26.54007519 |
-11.80284723 |
0.00000000 |
8 |
H |
14.98310302 |
-10.51320864 |
0.00000000 |
1 |
H |
25.53413263 |
-13.58974246 |
0.00000000 |
1 |
Table 2: Bond length of belinostat
Atoms |
Length |
(C1)-(C2) |
1.458000 |
(C1)-(C3) |
1.323387 |
(C1)-(N7) |
1.343384 |
(C2)-(C4) |
1.323387 |
(C3)-(C5) |
1.458000 |
(C4)-(C6) |
1.458000 |
(C5)-(C6) |
1.323387 |
(N7)-(S8) |
1.749002 |
(S8)-(O9) |
1.546726 |
(S8)-(O10) |
1.546726 |
(S8)-(C11) |
1.800077 |
(C11)-(C14) |
1.458000 |
(C11)-(C16) |
1.323387 |
(C12)-(C13) |
1.458000 |
(C14)-(C14) |
1.323387 |
(C12)-(C17) |
1.461000
|
(C13)-(C15) |
1.323387
|
(C15)-(C16) |
1.458000
|
(C17)-(C18) |
1.328833
|
(C18)-(C19) |
1.464000
|
(C19)-(N20) |
1.346235
|
(C19)-(O22) |
1.260307
|
(N20)-(O21) |
1.323604
|
Table 3: Bond
angles of belinostat
Atoms |
Angles |
Alternate
angles |
(C2)-(C1)-(C3) |
120.000000 |
216.488007 |
(C2)-(C1)-(N7) |
120.000000 |
282.167276 |
(C1)-(C2)-(C4) |
120.000000 |
216.488007 |
(C3)-(C1)-(N7) |
120.000000 |
327.778708 |
(C1)-(C3)-(C5) |
120.000000 |
216.488007 |
(C1)-(N7)-(S8) |
120.000000 |
218.427741 |
(C2)-(C4)-(C6) |
120.000000 |
216.488007 |
(C3)-(C5)-(C6) |
120.000000 |
216.488007 |
(C4)-(C6)-(C5) |
120.000000 |
216.488007 |
(N7)-(S8)-(O9) |
92.100000 |
425.732935 |
(N7)-(S8)-(O10) |
92.100000 |
425.732935 |
(N7)-(S8)-(C11) |
92.100000 |
286.724350 |
(O9)-(S8)-(O10) |
92.100000 |
471.223100 |
(O9)-(S8)-(C11) |
92.100000 |
303.587174 |
(O10)-(S8)-(C11) |
92.100000 |
303.587174 |
(S8)-(C11)-(C14) |
120.000000 |
188.274860 |
(S8)-(C11)-(C16) |
120.000000 |
210.303144 |
(C14)-(C11)-(C16) |
120.000000 |
216.488007 |
(C11)-(C14)-(C12) |
120.000000 |
216.488007 |
(C11)-(C16)-(C15) |
120.000000 |
216.488007 |
(C13)-(C12)-(C14) |
120.000000 |
216.488007 |
(C13)-(C12)-(C17) |
120.000000 |
187.861407 |
(C12)-(C13)-(C15) |
120.000000 |
216.488007 |
(C14)-(C12)-(C17) |
120.000000 |
215.760874 |
(C12)-(C17)-(C18) |
120.000000 |
214.555074 |
(C13)-(C15)-(C16) |
120.000000 |
216.488007 |
(C17)-(C18)-(C19) |
120.000000 |
213.837163 |
(C18)-(C19)-(N20) |
120.000000 |
279.479738 |
(C18)-(C19)-(O22) |
120.000000 |
275.966448 |
(N20)-(C19)-(O22) |
120.000000 |
421.698151 |
(C19)-(N20)-(O21) |
120.000000 |
295.314382 |
Table 4: Dihedral angles of belinostat.
Atoms |
Dihedral Angles |
(C4)-(C2)-(C1)-(C3) |
5.000000
2 |
(C2)-(C1)-(C3)-(C5) |
19.486776
2 |
(C4)-(C2)-(C1)-(N7) |
5.000000
2 |
(C2)-(C1)-(N7)-(S8) |
13.474221
2 |
(C1)-(C2)-(C4)-(C6) |
38.973552 2 |
(C5)-(C3)-(C1)-(N7) |
19.486776
2 |
(C3)-(C1)-(N7)-(S8) |
13.474221
2 |
(C1)-(C3)-(C5)-(C6) |
10.000000 2 |
(C1)-(7N)-(S8)-(O9) |
2.635231
2 |
(C1)-(N7)-(S8)-(O10) |
2.635231 2 |
(C1)-(N7)-(S8)-(C11) |
2.635231 2 |
(C2)-(C4)-(C6)-(C5) |
10.000000 2 |
(C3)-(C5)-(C6)-(C4) |
38.973552 2 |
(N7)-(S8)-(C11)-(C14) |
1.317616 2 |
(N7)-(S8)-(C11)-(C16) |
1.317616 2 |
(O9)-(S8)-(C11)-(C14) |
1.317616
2 |
(O9)-(S8)-(C11)-(C16) |
1.317616 2 |
(O10)-(S8)-(C11)-(C14) |
1.317616
2 |
(O10)-(S8)-(C11)-(C16) |
1.317616 2 |
(S8)-(C11)-(C14)-(C12) |
5.000000 2 |
(S8)-(C11)-(C16)-(C15) |
19.486776 2 |
(C12)-(C14)-(C11)-(C16) |
5.000000 2 |
(C14)-(C11)-(C16)-(C15) |
19.486776 2 |
(C11)-(C14)-(C12)-(C13) |
19.486776 2 |
(C11)-(C14)-(C12)-(C17) |
19.486776 2 |
(C11)-(C16)-(C15)-(C13) |
10.000000 2 |
(C15)-(C13)-(C12)-(C14) |
5.000000 2 |
(C15)-(C13)-(C12)-(C17) |
5.000000 2 |
(C13)-(C12)-(C17)-(C18) |
5.000000 2 |
(C12)-(C13)-(C15)-(C16) |
38.973552 2 |
(C14)-(C12)-(C17)-(C18) |
5.000000 2 |
(C12)-(C17)-(C18)-(C19) |
38.973552 2 |
(C17)-(C18)-(C19)-(N20) |
5.000000 2 |
(C17)-(C18)-(C19)-(O22) |
5.000000 2 |
(C18)-(C19)-(N20)-(O21) |
13.474221 2 |
(O21)-(N20)-(C19)-(O22) |
13.474221 2 |
Table 5: Improper
torsions of belinostat
Atoms |
Improper torsions |
3
7 1 2
(C)-(N)-(C)-(C) |
2.000000 |
8 23
7 1 (S)-(H)-(N)-(C) |
2.000000 |
14 16
11 8 (C)-(C)-(C)-(S) |
2.000000 |
14 17
12 13 (C)-(C)-(C)-(C) |
2.000000 |
20 21
19 1 ( N)-(O)-(C)-(C) |
16.666667 |
22 24
20 19 (O)-(H)-(N)-(C) |
2.000000 |
Table 6: Final energy evaluation.
S.No. |
Force field |
Energy components (au) |
1 |
Molecular mechanics
bond (Estr) |
0.00453750 |
2 |
Molecular mechanics
angle (Ebend)+ (Estr‑bend) |
0.57603306 |
3 |
Molecular mechanics
dihedral (Etor) |
0.02519703 |
4 |
Molecular mechanics ImpTor (Eoop) |
0.00000000 |
5 |
Molecular mechanics
vdW (EVdW) |
0.04088915 |
6 |
Molecular mechanics
coulomb (Eqq) |
0.00000000 |
Total |
0.64665673a.u.
(405.78359283 kcal/mol) |
Table 7 : Ground State Dipole (debye)
X |
Y |
Z |
Length |
-4.83698520 |
-5.04353016 |
-0.00000000 |
6.98810577 |
Table 8: List of Mulliken atomic charges and ZDO
atomic charges of belinostat
S/NO |
Atoms |
ZDO
Atomic Charges |
Mulliken Atomic Charges |
1 |
C |
0.1477 |
0.1604 |
2 |
C |
0.2007 |
0.1952 |
3 |
C |
-0.0041 |
-0.0204 |
4 |
C |
-0.1060 |
-0.0791 |
5 |
C |
-0.0040 |
-0.0338 |
6 |
C |
0.0580 |
0.0459 |
7 |
N |
-1.0977 |
-1.3370 |
8 |
S |
3.382 |
4.2811 |
9 |
O |
-0.9370
|
-0.8867 |
10 |
O |
-0.8667 |
-0.9706 |
11 |
C |
-1.2220 |
-1.8037 |
12 |
C |
-0.1185 |
-0.1673 |
13 |
C |
0.2448 |
0.2833 |
14 |
C |
0.2815 |
0.3526 |
15 |
C |
-0.2352 |
-0.2464 |
16 |
C |
0.2651 |
0.2591 |
17 |
C |
0.1380 |
0.1564 |
18 |
C |
-0.0962 |
-0.0989 |
19 |
C |
0.1896 |
0.2325 |
20 |
N |
0.1035 |
0.0772
|
21 |
O |
-0.1212 |
-0.1243 |
22 |
O |
-0.2533 |
-0.2661 |
Table 9 :
Relative interaction energy values of belinostat
docked unto Ebola Virus
Rank |
||||||
Kcal/mol |
||||||
1 |
1 |
-28.87 |
-12.55
|
6.57
|
-10.85 |
0.00 |
2 |
6 |
-28.42 |
-12.46
|
4.98
|
-9.65 |
0.00 |
3 |
5 |
-28.02 |
-12.37
|
6.51
|
-10.53 |
0.00 |
4 |
8 |
-27.89 |
-12.60
|
8.85
|
-10.31 |
0.00 |
5 |
9 |
-26.53 |
-12.66
|
12.37
|
-11.16 |
0.00 |
6 |
10 |
-26.34 |
-13.64
|
15.39
|
-12.07 |
0.00 |
7 |
4 |
-25.28 |
-12.80
|
12.47
|
-10.90 |
0.00 |
8 |
2 |
-21.85 |
-12.01
|
12.96
|
-10.01 |
0.00 |
9 |
3 |
-16.55 |
-12.63
|
21.22
|
-10.78 |
0.00 |
10 |
7 |
-13.52 |
-6.91
|
3.68
|
-5.47 |
0.00 |
CONCLUSION:
Geometry optimization of (2E)-N-hydroxy-3-[3-(phenylsulfamoyl) phenyl]prop-2-enamide (belinostat)
using Argus lab software was performed. Molecular mechanics calculations were
based on specific interactions within the molecule. These interactions included
stretching or compressing of bond beyond their equilibrium lengths and angles.
The excited states of belinostat
were created. The final self- consistent field (SCF) energy was found to be be -126.3659168682 au (-79295.8815 kcal/mol). This is the average
interaction between a given belinostat
particle and other belinostat
particles of a quantum-mechanical system consisting of
many particles. The most energetically favourable
conformation of belinostat was found to have a heat
of formation of 581.1137 kcal/mol via PM3 (NDDO) RHF
SCF Type. The steric energy calculated for belinostat was 0.64665673 a.u.(405.78359283 kcal/mol). Molecular docking result revealed
the binding free energy. The
global binding energy value -28.87 Kcal/mole was
ranked first because it had the least energy. The most feasible position for belinostat to inhibit ebola virus glycoprotein
was predicted to be -28.87 kcal/mol.
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Received on 10.08.2015 Accepted on 05.09.2015
© Asian Pharma
Press All Right Reserved
Asian J. Pharm.
Res. 5(3): July- Sept.,
2015; Page 131-137
DOI: 10.5958/2231-5691.2015.00020.9