A. Barakat et al. / Journal of Molecular Structure 1098 (2015) 365e376
367
reaction, the crud product directly subjected to column chroma-
tography using 100e200 mesh silica gel and ethyl acetate/n-hexane
referenced to the TMS calculations were carried out at the same
level of theory. The natural bond orbital analyses were performed
using the NBO calculations as implemented in the Gaussian 03
package [38] at the DFT/B3LYP level.
(
2:8, v/v) as an eluent to afford the racemic mixture of products 3.
1
3 3
H NMR (400 MHz, CDCl ) d: 3.07 (s, 3H, eNCH ), 3.16 (s, 3H,
eNCH
3
), 3.59 & 3.63 (dd, 1H, J ¼ 18.32 Hz, 5.84 Hz, CH2(a)), 3.98 (d,
1
H, J ¼ 3.68 Hz, CH), 4.05 & 4.10 (dd, 1H, J ¼ 18.32 Hz, 8.08 Hz,
2.6. Homology modeling and molecular docking study of compound
3
CH2(e)), 4.45e4.55 (m,1H, CH), 7.39e7.49 (m, 3H, AreH), 7.56 (d, 2H,
J ¼ 8.80 Hz, AreH), 7.97 (d, 2H, J ¼ 7.36 Hz, AreH), 8.06e8.12 (m, 2H,
AreH); 13C NMR (100 MHz, CDCl
)
d: 28.3, 28.3, 40.5, 42.7, 52.6,
The study was designed to dock compound 3 against a-gluco-
3
(
R)
1
22.3, 123.1, 128.0, 128.7, 129.7, 133.6, 134.3, 136.3, 141.4, 148.3,
sidase enzyme with the following communications; Intel xen-
ꢁ
1
(R)
1
1
6
50.7, 167.3, 167.4, 197.3; IR (KBr, cm
689, 1526, 1449, 1346, 1298, 1270; [Anal. Calcd. for C21
1.61; H, 4.68; N, 10.26; Found: C, 61.49; H, 4.52; N, 10.11]; LC/MS
)
n
max ¼ 3420, 3083, 2953,
on CPU E5620@2.40GHz system having 3.8 GB RAM with the
open 11.4 (X 86_64) operating platform. Protein-Ligand docking
was carried out using the Molecular Operating Environment (MOE
H
19
N
3
O
6
: C,
þ
(
ESI, m/z): [M ], found 409.10, C21
H
19
N
3
O
6
requires 409.13.
2010.11) software package. The three dimensional structure for a-
glucosidase of S. cerevisiae has not been solved up-to yet, although
only few homology models has been reported [39e42]. In the
2.3. Single-crystal X-ray diffraction studies
current study we predict 3D structure for
evisiae by using same protocol as described by (Burke et al.) of
homology modeling [42]. The primary sequence of -glucosidase
a-glucosidase of S. cer-
Compound 3 was obtained as crystals by slow diffusion of
diethyl ether solution of compounds 3 in dichloromethane at room
a
temperature for 24 h. Diffraction data was collected on a Bruker
for S. cerevisiae was retrieved from UniProt (Access code P53341).
Template search was performed using MOE-Search tools against
the PDB implemented in MOE v2010.11. The crystallographic
structure of S. cerevisiae isomaltase (PDB code 3AJ7; Resolution
1.30 Å) with 72.4% of sequence identity with the target was selected
APEX-II D8 Venture area diffractometer, equipped with graphite
ꢀ
monochromatic Cu K
a
radiations at 293 (2) K. Cell refinement and
data reduction were carried out by Bruker SAINT. SHELXS-97
33,34] was used to solve structure. The final refinement was car-
[
ried out by full-matrix least-squares techniques with anisotropic
thermal data for nonhydrogen atoms on 3. All the hydrogen atoms
were placed at calculated positions.
The structure of 3 was determined by X-ray crystal structure
analysis (Bruker AXS GmbH). CCDC- 1024287; contains the sup-
plementary crystallographic data for this compound. These data
as a template [43]. The 3D structure of a-glucosidase for S. cerevisiae
was predicted using MOE homology modeling tools. The developed
model was then subjected to energy minimization up to 0.05
gradients.
Before docking, ligands and protein were prepared using MOE
v2010.11. 3D structure of compound 3 was built by using Molec-
ular Builder Module program implemented in MOE and save as a
(.mdb) file for molecular docking. Subsequently, the energy of
compound 3 was minimized up to 0.05 Gradient using MMFF 94x
force field. Energy minimization of the compound 3 was followed
by the preparation of protein for docking purposes. Most macro-
molecular crystal structures contain little or no hydrogen coordi-
nate data due to limited resolution and thus protonation was done
prior to docking using Protonate 3D tools. Protonation was fol-
lowed by energy minimization up to 0.05 Gradient using Amber
99 force field. The compound 3 was docked into the active site of
protein using the Triangular Matching docking method and 30
conformations of compound 3 and protein complex were gener-
ated with docking score (S). The complex was analyzed for in-
teractions and their 3D images were taken by using visualizing
tool PyMol.
2.4. a-Glucosidase inhibition assay
Glucosidase inhibition assay was performed spectrophotomet-
rically. -Glucosidase from Saccharomyces cerevisiae (G0660-
50UN, Sigma Aldrich) was dissolved in phosphate buffer (pH 6.8.,
0 mM). Compound 3 was dissolved in 70% DMSO. In 96-well
a
7
5
plates, 20
m
L of test compound, 20
m
L of enzyme and 135
m
L of
ꢀ
buffer were added, and incubated for 15 min at 37 C. After incu-
bation, 25
Aldrich) was added and change in absorbance was monitored for
0 min at 400 nm. Test compound was replaced with DMSO (7.5%
mL of p-nitrophenyl-a-D-glucopyranoside (0.7 mM, Sigma
3
final) as a control. Acarbose (Sigma Aldrich) was used as a standard
inhibitor.
3. Results and discussion
2.5. Computational study
3.1. Synthesis
All the quantum chemical calculations of the studied compound
were performed by applying DFT method with the B3LYP functional
and 6‒311G (d,p) basis set using Gaussian 03 software [35]. The
input file was taken from the CIF obtained from the X‒ray single
crystal measurement. The geometry was optimized by minimizing
the energies with respect to all the geometrical parameters without
imposing any molecular symmetry constraints. GaussView4.1 [36]
and Chemcraft [37] programs were used to draw the structure of
the optimized geometry. Frequency calculations at the optimized
geometry were aimed out to confirm the optimized structure to be
an energy minimum. The true energy minimum at the optimized
geometry of the studied compound was confirmed by absence of
any imaginary frequency modes. The electronic spectra of the
studied compound were calculated by the TD‒DFT method. The
gauge including atomic orbital (GIAO) method was used for the
The synthetic pathway to the title compound is summarized in
Scheme 1. The starting compounds, N,N-dimethyl barbituric acid
(1) is commercially available, (E)-3-(3-nitrophenyl)-1-phenylprop-
2-en-1-one (2) was obtained by the condensation of m-nitro-
benzaldehyde with acetophenone [25,26]. The reaction of (1) with
2
equimolar amount of enone 2 in DCM using NHEt as a base
afforded the target compound 3 in 93% yield. The desired com-
pound (±) 3 was obtained as a racemic mixture. The compound was
1
13
characterized by a combined application of H, and C and GCeMS
spectroscopy.
3.2. Single e crystal X-ray diffraction study
A
specimen of
C
21
H
19
N
3
O
6
,
approximate dimensions
1
13
NMR calculations. The H and the C isotropic shielding tensors
0.367 mm ꢂ 0.451 mm ꢂ 0.841 mm was used for the X-ray