Inversion kinetics of someE/Z3-(benzylidene)-2-oxo-indoline derivatives and theirin silicoCDK2 docking studies

Article abstract of DOI:10.1039/d0ra10672k

The structure-based design of some CDK2 inhibitors with a 3-(benzylidene)indolin-2-one scaffold as potential anticancer agents was realized. Target compounds were obtained asE/Zmixtures and were resolved to correspondingE- andZ-diastereomers.In silicostudies using MOE 2019.01 software revealed better docking on the targeted enzyme for theZ-diastereomer compared to theE-one. A time-dependent kinetic isomerization study was carried out for the inversion ofE/Zdiastereomers in DMSO-d₆at room temperature, and were found to obey the first order kinetic reactions. Furthermore, a determination of the kinetic inter-conversion rate order by graphical analysis method and calculation of the rate constant and half-life of this kinetic process were carried out. For the prediction of the stability of the diastereomer(s), a good multiple regression equation was generated between the reaction rates of isomerization and some QM parameters with significantpvalue.

Full text of DOI:10.1039/d0ra10672k

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Inversion kinetics of some E/Z 3-(benzylidene)-2-
oxo-indoline derivatives and their in silico CDK2
docking studies†‡
Cite this: RSC Adv., 2021, 11, 7839
*
Hany S. Mansour, Hend A. A. Abd El-wahab, Ahmed M. Ali and Tarek Aboul-Fadl
The structure-based design of some CDK2 inhibitors with a 3-(benzylidene)indolin-2-one scaffold as
potential anticancer agents was realized. Target compounds were obtained as E/Z mixtures and were
resolved to corresponding E- and Z-diastereomers. In silico studies using MOE 2019.01 software
revealed better docking on the targeted enzyme for the Z-diastereomer compared to the E-one. A time-
dependent kinetic isomerization study was carried out for the inversion of E/Z diastereomers in DMSO-
d6 at room temperature, and were found to obey the first order kinetic reactions. Furthermore,
a determination of the kinetic inter-conversion rate order by graphical analysis method and calculation
of the rate constant and half-life of this kinetic process were carried out. For the prediction of the
stability of the diastereomer(s), a good multiple regression equation was generated between the reaction
rates of isomerization and some QM parameters with significant p value.
Received 19th December 2020
Accepted 1st February 2021
DOI: 10.1039/d0ra10672k
rsc.li/rsc-advances
tyrosine kinase (RTK) inhibitor for the treatment of advanced
renal cell carcinoma and gastrointestinal stromal tumours,14
Introduction
in addition to semaxanib, toceranib phosphate, and
SU9516.11,14 They possess the capacity to bind the receptor
tyrosine kinase (RTK), CDK2 enzyme and Aurora B with high
affinity.14 Orantinib is a receptor tyrosine kinase inhibitor
that was approved as an antiproliferating agent, and ninte-
danib is an inhibitor of PDGF, FGF and VEGF receptors and
was approved for the treatment of non-small-cell lung
cancer,18,19 Fig. 1.
It has been established for more than half a century that
stereochemistry is fundamental in biological activities.20,21
The stereoselection, which has been extensively studied, was
almost exclusively explained in terms of diastereoselective
interactions for sunitinib and related compounds. Interest-
ingly, these molecules were bound as the Z-diastereomer,
even though they were the E-diastereomer in solution. The E
form must be converted to the Z form before binding, as all E-
diastereomers were inactive. Apparently, this conversion was
shown to be mediated by acid, base or light.22 Removing such
unsaturation and/or designing stereochemically stable
compounds may be feasible, provided that activities are not
compromised. This would avoid the issue of E/Z isomeriza-
tion however, the vinyl proton was determined to be essential
for activity.17,22
The 2-oxo-indoline scaffold is strongly associated with the
anticancer activity through multiple targets as cyclin-
dependent kinases (CDKs) and receptor tyrosine kinases
(RTKs).1–4 Cyclin-dependent kinases (CDKs) are the key
regulators of the cell cycle,5–8 the complex process by which
cells divide. The recognition of the importance of CDKs to the
process of cell division has stimulated an interest in them as
potential targets for the management of cancer.9,10 Molecules
having the 2-oxo-indoline scaffold usually compete with ATP
for binding in the enzyme active site, and prevent phosphate
transfer from ATP to the appropriate residue (Tyr, Ser, Thr).
Thus, they block auto- and substrate phosphorylation, and
therefore signal transduction and oncogenic activity.11 The
selectivity of these classes of compounds to the subclasses of
CDKs and RTKs is determined by other interactions between
substituents on the scaffold and residues found around this
hinge region at the interaction site.12,13 3-Arylidene-2-oxo-
indoline derivatives are at the heart of a wide range of clini-
cally,
medicinally
and
biologically
important
compounds.14–17 A number of 3-arylidene-2-oxo-indolines
have been approved for clinical application. Of particular
signicance is sunitinib, which is a clinically used receptor
Molecular modeling revealed that the oxindole moiety of
sunitinib is crucial for binding to the ATP binding site of
RTKs and CDKs.23,24 Additionally, the pyrrole functionality
and the C(5)-F element of (2-oxoindolin-3-ylidene)
methylpyrrole in the sunitinib structure both enhance
affinity by inducing further hydrophobic interactions.19,20,22
Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut,
Egypt. E-mail: fadl@aun.edu.eg
† Presented in 18th Austrian Chemistry Days, Linz – Austria, September 24 to 27,
2019.
‡ Electronic supplementary information (ESI) available. See DOI:
10.1039/d0ra10672k
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Fig. 1 Clinically approved 2-oxo-indoline derivatives.
synthesis of a series of some 3-benzylidene substituted oxindole
derivatives (Fig. 2).
Recent studies have been made for its effective synthesis,
and also for the stereoselective synthesis of (E) and (Z) diaste-
reomers.27–31 Accordingly, the kinetics of the E/Z isomerization
of the designed molecules seemed to be of interest.
Fig. 2 General structure for 3-benzylidene-substituted oxindoles.
Results and discussion
Chemistry
In contrast, the water-soluble diethyl amino ethyl tail of
sunitinib lies on the protein surface. The RTK inhibitory
activity
and
selectivity
of
(2-oxo-indolin-3-ylidene)
3-Benzylidenes 6(a–c) were obtained using the Wolff–Kishner-
methylpyrrole derivatives revealed strong relationships with like reduction of indolin-2,3-dione, 1 (isatin), with hydrazine
structural modications.25
hydrate, followed by reaction with an appropriate benzalde-
In view of the above facts, and in continuation of our interest hyde.32,33 5-Nitro derivatives 4(a–c) were obtained by nitration at
in the synthesis and in silico investigation of the CDK activities position 5 of the 2-oxo-indoline moiety with potassium nitrate
of 2-oxo-indoline derivatives,26 the current work describes the
in cold concentrated sulfuric acid.34,35 N-Substituted derivatives
[5(a–d) and 7(a–b)] were obtained by reacting [4(a–c) and 6(a–c)]
Scheme 1 (a) NH2NH2$H2O, reflux at 140 ꢀC/4 h; (b) KNO3/H2SO4, stir at 0–5 ꢀC/1.5 h; (c) substituted benzaldehydes, piperidine, ethanol, reflux
at 90 ꢀC/4–5 h; (d) K2CO3/KI, DMF, alkyl halides/stir at 60–80 ꢀC/4–12 h.
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Table 1 E : Z diastereomeric ratios of the synthesized compounds 5(a–d), 6a, 6c and 7(a–b) and the yield (%)
Substituents
R1
Chemical shis (d ppm)
vinyl H
20 and 60-Hs
Initial E : Z
ratio
Yield
(%)
Compd
R2
R3
E
Z
E
Z
5a
NO2
NO2
NO2
NO2
NO2
H
H
H
H
H
40-F
Benzyl
Propyl
Propyl
Propyl
Propyl
H
8.02
7.93
7.86
7.86
7.87
7.57
7.59
7.8
8.38
8.29
8.19
8.19
8.30
7.78
7.75
7.96
7.89
7.89
7.91
7.87
7.78
7.78
7.71
7.72
7.72
7.83
7.79
7.79
8.60
8.58
8.56
8.56
8.06
8.32
8.48
8.54
8.51
8.51
6 : 94
67
77
45
45
62
80
75
67
55
55
5b
5c1
5c2
5d
6a
6c
7a
7b1
7b2
40-F
17 : 83
30 : 70
65 : 35
93 : 7
100 : 0
98 : 2
18 : 82
2 : 98
88 : 12
40-OCH3
40-OCH3
20-Cl
40-Br
40-OCH3
40-F
H
Benzyl
Propyl
Propyl
40-F
7.7
7.7
40-F
0
0
with benzyl chloride or propyl bromide according to the re- The ortho-benzylidene protons (H2 ,6 ) were found to be more
ported procedures,26,27 Scheme 1.
shielded in the E-diastereomers for the same reason, as
All of the synthesized compounds 4(a–c), 5(a–d), 6(a–c) shown in Fig. 3. The 1H NMR spectra of 5c is shown in Fig. 4
and 7(a–b) were obtained as mixtures of the E and Z dia- as a representative example. The chemical shis of the major
stereomers in different ratios, as identied with their diastereomer (Z) revealed signals of Hvinyl at 8.25 ppm, H4 at
vinyl-H and 20 and 60-Hs chemical shis (ppm) of E and Z, 8.72 ppm and H2 ,6 at 8.59 ppm, while those of the minor
0
0
Table 1.
diastereomer (E) resonated at 7.9, 8.52 and 7.82 ppm,
The conguration of the major diastereomer was conrmed respectively.
by 2D NOE analysis, within the time of measurement. The E-
The conguration of the E/Z diastereomers of 5c was further
congured compounds showed NOE between the proton at C4 conrmed by the NOESY 2D-1H NMR. The NOE interaction
and the protons at C-20 and C-60 (Fig. 3A), whereas the Z- between Hvinyl and H4 was shown in the Z-diastereomer, Fig. 5A,
0
0
congured compounds showed NOE between the proton at the while the NOE interaction between H2 ,6 and H4 was shown in
C-4 and the vinyl proton (Fig. 3B).
the E-diastereomer, Fig. 5B.
The assignment of the E/Z diastereomers were conrmed
by 1H-NMR, where the vinyl protons resonated at a slight
downeld shi in the Z-diastereomer compared to the E-
diastereomer due to the inuence of the 2-carbonyl group.
Kinetics of the isomerization study
It has been reported that the E/Z diastereomers of 3-
benzylidene-2-oxo-indolines both can undergo isomerization to
0
0
Fig. 3 General configuration of E and Z diastereomers. (A) NOE interaction between H2 ,6 and H4 in E-diastereomer. (B) NOE interaction
between vinyl-H and H4 in Z-diastereomer.
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Fig. 4 1H-NMR chart (aromatic region) of compound 5c1, mixture of the E/Z diastereomers with a ratio ¼ 35 : 65.
each other.28,29 This phenomenon is also observed in the change
The diastereomeric ratios of the tested compounds were
1
of the initial E : Z product ratios for the synthesized compounds monitored using H NMR by measuring the integral height
listed in Table 1 during the measurement of the 1H NMR spectra in values of the vinyl and 20,60-protons of the respective E and Z
DMSO-d6. To acquire knowledge on the rates of the congura- diastereomers. With the exception of compounds 5b, 5c1
tional isomerization of the E/Z diastereomers for compounds 5a, and 7b2 that revealed no or insignicant isomerization at
5b, 5c1, 5c2, 5d, 6a, 6c, 7a, 7b1 and 7b2, the change of the initial the reaction conditions, the rate of the isomerization reac-
diastereomeric ratios at time intervals was measured in DMSO-d6 tions of the other tested compounds were found to display
at room temperature, and are listed in Table 2.
rst-order kinetics over the investigated solvent and
Fig. 5 NOESY 1H–1H 2D NMR interactions of the E/Z-diastereomers of 5c. (A) The major diastereomer (Z). (B) The minor diastereomer (E).
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Table 2 Time-dependent isomerization of E and Z diastereomers in DMSO-d6
E : Z ratio
E : Z ratio
E : Z ratio
E : Z ratio
E : Z ratio
Substituents
Compd
R1
R2
R3
Time: 0 h
1 h
2 h
3 h
5 h
Isomerization
5a
NO2
NO2
NO2
NO2
NO2
H
H
H
H
H
40-F
Benzyl
Propyl
Propyl
Propyl
Propyl
H
5.7 : 94.3
17 : 83
30.1 : 69.9
64.9 : 35.1
92.6 : 7.4
100 : 0
98.0 : 2.0
18.0 : 82.0
2.0 : 98.0
87.7 : 12.3
8.3 : 91.7
17 : 83
12.3 : 87.7
17 : 83
13.0 : 87.0
17 : 83
17.4 : 82.6
17 : 83
From Z to E
No isomeriz.
From Z to E
From E to Z
From E to Z
From E to Z
From E to Z
From Z to E
From Z to E
From E to Z
5b
5c1
5c2
5d
6a
6c
7a
7b1
7b2
40-F
40-OCH3
40-OCH3
20-Cl
34.6 : 65.4
61.3 : 38.7
88.5 : 11.5
96.2 : 3.8
96.2 : 3.8
30.1 : 69.9
13.0 : 87.0
87.0 : 13.0
33.8 : 66.2
55.2 : 44.8
84.0 : 16.0
94.3 : 5.7
93.5 : 6.5
35.1 : 64.9
15.3 : 84.7
87.0 : 13.0
35.1 : 64.9
51.3 : 48.7
82.0 : 18.0
91.7 : 8.3
91.7 : 8.3
38.3 : 61.7
20.6 : 79.4
87.0 : 13.0
35.1 : 64.9
44.4 : 55.6
80.6 : 19.4
90.1 : 9.9
90.1 : 9.9
42.9 : 57.1
29.1 : 70.9
87.0 : 13.0
40-Br
40-OCH3
40-F
H
Benzyl
Propyl
Propyl
40-F
40-F
Fig. 6 Graphical representation of first-order kinetic isomerization of the E/Z diastereomers for representative compounds 5c2 and 5d.
temperature. Representative rst-order kinetics plots for compounds using other solvents, such as CDCl3, failed due
the isomerization of the tested compounds are shown in to solubility issues. No attempts were made to investigate
Fig. 6. From the slopes of the linear correlations, it can be the mechanism of isomerization; however, this observed
seen that the potential for isomerization proceeds with phenomenon is consistent with previously reported
varied rates, and the rate data obtained for the tested ones.28,29,36,37
compounds are recorded in Table 3.
No general behavior pattern for the isomerization of the
tested compounds was observed. Compounds 5b and 5c
showed no signicant Z/E isomerization, but the rate of E/Z
Molecular structure and modeling studies
Molecular orbital calculations were carried out to investi-
gate the structure and stability of the E/Z-diastereomers of
the subjected molecules. The investigated benzylidene
oxindole structures were optimized in the ground state
using AM1 and PM3, and MNDO semi-empirical methods
with default Hartree–Fock (RHF) basis using MOE 2019.01
soware.
isomerization of 5c (t1/2 ¼ 8.3 h) revealed more stability for
the Z isomer. On the other hand, compound 7b showed no
E/Z isomerization, but the rate of Z/E isomerization (t1/2
12.53 h) revealed that the E diastereomer is more stable.
¼
Attempts to carry out additional studies on these
To determine which diastereomer is more stable ((E) or (Z)),
the heat of formation (HF, kcal molꢁ1) was calculated for each
diastereomer by three different methods, AM1, MNDO and
PM3. The results are recorded in Table 4.
Table 3 Rate data for the isomerization of the tested compounds in
DMSO-d6 at room temperature
From the results recorded in Table 4, the AM1 Hamilto-
nian shows that the (E) diastereomers are more stable than
(Z) diastereomers for compounds 5a, 5b, 6a, 7a and 7b.
However, the (Z) diastereomers are more stable than (E)
diastereomers for compounds 5c, 5d and 6c. This is consis-
tent with the observed rate of isomerization of the tested
compounds (5c2 and 7b1 compared to the other tested
compounds). The MNDO model showed that the (Z) diaste-
reomers are slightly more stable, while the PM3 model
Compd
k ꢂ 103 (minꢁ1) (r2, r)
t1/2 (h)
5a
0.461 (0.969, 0.984)
1.382 (0.995, 0.997)
0.461 (0.878, 0.937)
0.230 (0.930, 0.964)
0.230 (0.951, 0.975)
0.415 (0.996, 0.998)
0.921 (0.969, 0.984)
25.08
8.37
5c2
5d
6a
6c
7a
25.08
50.15
50.15
27.85
12.53
7b1
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Table 4 Heat of formation, total energy and potential energy calculated for the E/Z diastereomers of the 3-benzylidene-2-oxo-indoline
derivatives by quantum mechanics (QM) methods
Compd
and
Heat of formation (kcal molꢁ1
)
Total energy (kcal molꢁ1
)
Potential energy (kcal molꢁ1
)
cong.
AM1
MNDO
PM3
11.693
6.627
ꢁ21.439
ꢁ31.127
ꢁ26.998
ꢁ25.804
5.746
10.397
40.929
41.925
ꢁ4.928
ꢁ3.910
15.403
AM1
MNDO
PM3
AM1
MNDO
PM3
5a
5b
5c
5d
6a
6c
7a
7b
E
Z
E
Z
E
Z
E
Z
E
Z
E
Z
E
Z
E
Z
37.256
37.340
ꢁ1.852
ꢁ1.635
5.382
31.578
30.934
ꢁ7.613
ꢁ8.351
ꢁ0.8790
ꢁ1.486
32.169
31.458
33.937
33.491
ꢁ8.195
ꢁ8.622
25.706
15.488
ꢁ22.279
ꢁ22.891
ꢁ112 488.86
ꢁ112 488.77
ꢁ100 700.08
ꢁ100 699.96
ꢁ100 804.24
ꢁ100 803.59
ꢁ98 132.34
ꢁ98 132.13
ꢁ67 732.13
ꢁ67 731.67
ꢁ70 874.54
ꢁ70 874.59
ꢁ93 328.44
ꢁ93 326.40
ꢁ81 539.30
ꢁ81 537.63
ꢁ112 511.38
ꢁ112 512.03
ꢁ100 751.77
ꢁ100 752.5
ꢁ101 053.02
ꢁ101 053.63
ꢁ97 872.59
ꢁ97 873.28
ꢁ67 673.79
ꢁ67 674.24
ꢁ71 014.01
ꢁ71 014.44
ꢁ93 289.73
ꢁ93 290.25
ꢁ81 529.20
ꢁ81 529.82
ꢁ103 287
93.276
95.959
77.165
80.214
92.313
94.633
80.254
85.874
59.044
60.866
69.970
71.709
86.114
89.310
65.373
67.784
89.752
92.903
72.529
75.271
91.605
93.192
73.658
77.747
60.917
61.366
72.328
73.687
79.532
80.142
62.142
62.867
94.042
96.041
84.174
85.692
92.963
95.918
88.894
90.804
64.915
65.561
74.772
75.343
97.061
97.613
79.378
81.496
ꢁ103 286.73
ꢁ92 381.56
ꢁ92 380.82
ꢁ92 797.19
ꢁ92 795.82
ꢁ89 533.23
ꢁ89 532.20
ꢁ63 169.75
ꢁ63 168.77
ꢁ65 587.71
ꢁ65 586.70
ꢁ86 419.95
ꢁ86 418.98
ꢁ75 514.30
ꢁ75 513.34
4.534
37.420
37.414
52.500
52.959
9.479
9.435
33.941
41.257
ꢁ4.797
ꢁ3.140
21.588
ꢁ22.610
ꢁ21.660
Table 5 Modeling and QM calculations variables of the optimized structuresa
Topological
polar
Electrostatic
interaction
Heat of
formation
Dipole
moment
Electrostatic Strain
vdW
energy
Torsion
energy
energy
energy
surface area
vdW area energy
t1/2
Compd (h)
vdW_
area
AM1_H
AM1_dipole
E_ele
E_strain
E_vdW
TPSA
E_rele
E_tor
5c
5d
6a
6c
5a
7a
7b
8.37 5.382
25.08 37.420
2.939
3.400
2.349
3.308
3.895
3.532
3.621
ꢁ1.068
9.667
ꢁ13.894
ꢁ18.750
7.004
0.3197
ꢁ1.1060
15.948
14.098
10.470
12.762
15.010
14.470
12.974
7.525
5.785
4.959
6.472
9.655
7.020
4.445
75.360
66.130
29.100
38.330
66.130
20.310
20.310
335.918 20 118.777
321.263 19 081.748
243.157 10 623.542
246.036 11 923.694
344.125 21 515.154
315.987 12 584.364
279.953 10 202.203
0.914
ꢁ0.052
7.366
7.411
4.774
5.612
0.011
50.15 52.500
50.15 9.479
25.08 37.340
27.85 41.257
12.53 ꢁ3.140
a
AM1_H: heat of formation, AM1_dipole: dipole moment, E_ele: electrostatic energy, E_strain: strain energy, E_vdW: vdW energy, TPSA:
topological polar surface area, vdW_area: vdW area, E_rele: electrostatic interaction energy, E_tor: torsion energy.
Table 6 The correlation matrix of t1/2 of the E/Z isomerization with modeling and QM calculation variables of the optimized structures
Variable
t1/2 (E/Z)
AM1_H
AM1_dipole
E_ele
E_strain
E_vdW
TPSA
vdW_area
E_rele
E_tor
t1/2
1.000
0.632
AM1_H
AM1_dipole
E_ele
E_strain
E_vdW
TPSA
vdW_area
E_rele
E_tor
1.000
0.200
0.000
0.800
ꢁ1.000
0.800
0.800
0.800
0.000
ꢁ0.211
ꢁ0.736
ꢁ0.949a
0.632
1.000
0.400
0.400
0.200
0.400
0.400
0.400
ꢁ0.400
1.000
0.600
0.000
0.600
0.600
0.600
ꢁ1.000
1.000
0.800
1.000
1.000
1.000
1.000
0.800
0.800
0.000
ꢁ1.000
ꢁ0.949a
ꢁ0.949a
ꢁ0.948a
0.738
1.000
1.000
1.000
ꢁ0.600
1.000
1.000
ꢁ0.600
1.000
ꢁ0.600
ꢁ0.600
1.000
a
Signicant p value (0.05).
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Table 7 Estimated and found t1/2 values, and their corresponding
significant QM parameters
geometry optimization of the investigated 3-benzylidene oxin-
dole molecules.
For a better understanding of the factors affecting the rate of
E/Z or Z/E isomerization, the Spearmen correlation (2-tailed)
was studied between t1/2 and 9 selected physicochemical
parameters, Table 5. Data were recorded and analyzed with IBM
SPSS V22, and the P-value was considered signicant if it was
equal to or less than 0.05.
Accordingly, the cross correlation coefficient between t1/2 (E/
Z isomerization) and E_strain, TPSA, vdW_area and electro-
static interaction energy was high (0.949) with a signicant p
value (0.05), Table 6. However, when studying the cross corre-
lation between t1/2 (Z/E isomerization), no signicant correla-
tion was obtained between the t1/2 (Z/E isomerization) and
calculated descriptors.
Compd
Estimated t1/2 (h)
Found t1/2 (h)
5c2
5d
6a
6c
5a
7.57
21.33
47.27
49.32
30.67
19.72
23.32
34.36
7.57
8.37
25.08
50.15
50.15
25.08
27.85
12.53
NDa
7a
7b1
5b
5c1
7b2
ND
ND
23.32
a
Not Determined.
A good multiple regression equation was generated between
the half-life (t1/2) of the isomerization and the QM parameters
with signicant p value, eqn (1): multiple regression equation
between t1/2 and signicant QM parameters.
revealed that the (E) diastereomers are more stable, except for
compounds 5a and 5b.
In order to disclose this inconsistency between the three
methods and the additional calculations of the total energy and
potential energy of each diastereomer, these calculations
were also computed by three different methods (AM1,
MNDO and PM3), and the results are recorded in Table 4.
According to the total energy calculations, the (E) diaste-
reomers are more stable than the (Z) diastereomers
according to AM1 and PM3 for all compounds except
compound 6c, as the AM1 calculations reveal that the (Z)
diastereomer is slightly more stable. The MNDO calcula-
tions for the total energy still shows that the (Z) diastereo-
mers are slightly more stable than the (E) diastereomer.
However, based on the potential energy calculations by the
three methods (AM1, MNDO and PM3), it is clear that the (E)
diastereomers are more stable than (Z) isomers for all
compounds.
t1/2 ¼ 187.5378 + 1.542499 ꢂ E_strain ꢁ 1.63343 ꢂ TPSA
ꢁ 1.0012 ꢂ vdW-area + 0.012667 ꢂ E_rele,
n ¼ 7, R2 ¼ 0.8536
(1)
The isomerization rate and stability of the diastereomers can
be estimated using this equation. Matching the experimental
data with the estimated ones, Table 7 and Fig. 7, revealed
a quite good relationship.
Molecular docking study on CDK2
The molecular docking study was performed to predict the
binding and effect of the investigated molecules on the CDK2
enzyme, and the results are recorded in Table 8. As a general
pattern, it is clear from the obtained data that the Z-diastereomers
revealed better binding affinity to the active site of CDK2. In most
of the tested compounds, the binding scores are quite close to that
of the reference drug sunitunib [redocking rmsd of sunitinib ¼ 2].
Further computational studies together with biological activity are
In conclusion, the AM1 method has shown better perfor-
mance compared to PM3 and MNDO methods for the molecular
Fig. 7 Correlation between found t1/2 and estimated t1/2
.
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Table 8 The scores of the docked ligands
Conclusion
Compd
Score (S, kcal molꢁ1
)
Compd
Score (S, kcal molꢁ1
)
A series of 3-benzylideneindolin-2-ones and 5-nitro 3-benzyli-
dene indolin-2-ones have been synthesized and obtained as E/Z-
diastereomers. The compounds have been assigned as Z or E
congurations by 1H NMR analysis. The conguration of the
separated E- and Z-diastereomers were conrmed by 2D NOE. A
kinetic study of the E/Z isomerization was carried out in DMSO-
d6 at room temperature, and they were found to obey rst-order
kinetic reactions. To justify the stability of (E) or (Z), the heat of
formation (HF, kcal molꢁ1) was calculated for each diaste-
reomer by three different methods, AM1, MNDO and PM3. No
clear justication could be obtained; however, the AM1 method
has shown better performance compared to PM3 and MNDO.
Furthermore, a good multiple regression equation was gener-
ated between the reaction rates of isomerization and some QM
parameters with signicant p value for prediction of stability of
Sunitinib
5a-E
5b-E
5c-E
5d-E
6a-E
6c-E
7a-E
7b-E
ꢁ7.8956
ꢁ7.8976
ꢁ7.3031
ꢁ7.5347
ꢁ6.7651
ꢁ6.3125
ꢁ6.3683
ꢁ6.5126
ꢁ6.9255
5a-Z
5b-Z
5c-Z
5d-Z
6a-Z
6c-Z
7a-Z
7b-Z
ꢁ8.0125
ꢁ7.2988
ꢁ7.1837
ꢁ7.1422
ꢁ6.6100
ꢁ6.7596
ꢁ7.7525
ꢁ6.8315
currently in progress. Fig. 8 illustrates the 2D and 3D interactions
of the co-crystallized sunitinib, the Z-diastereomer of 5a, and the E-
diastereomer 6c.
Fig. 8 2D and 3D ligand interactions of (A) co-crystallized sunitinib (Z) with CDK2, (B) 5a (Z-diastereomer), (C) compound 6c (E-diastereomer).
All ligands are docked into the active site of CDK2 (PDB ID: 3TI1).
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the diastereomer(s). In silico docking studies using MOE
2019.01 soware revealed better docking on the targeted CDK2
enzyme for the Z-diastereomer compared to the E-one, and
comparable docking scores to sunitinib as a reference drug.
General procedure for the synthesis of target compounds (6a
and 6c) as reported33,39
Piperidine (0.01 mmol) was added to a solution of compound 2
or 3 (10 mmol) and appropriate substituted benzaldehyde (11
mmol) in ethanol (15 ml). The mixture was reuxed for 3–5 h,
and then the reaction mixture was cooled to room temperature
and le overnight. The precipitate was ltered, washed with
ethanol, and dried at room temperature to give the titled
compounds. The obtained crude products were puried by
column chromatography.
Experimental section
Chemicals were obtained commercially, and were used as
received. TLC was carried out on Merck 0.2 mm pre-coated silica
gel (60 F-254) aluminum sheets. The spots were visualized by
UV. Synthesized compounds were puried by column chroma-
(E/Z)-3-(4-Bromobenzylidene)indolin-2-one (6a).36 Orange-
ꢀ
tography using methanol/CH2Cl2 as the mobile phase. Melting yellow solid crystals; yield: 80%; mp: 193–195 C;
points were measured with a capillary melting point SMP1
IR: 3472 and 1708.2 cmꢁ1
.
apparatus (Stuart Scientic), and are uncorrected. H and 13C
1H-NMR (DMSO-d6, 400 MHz) d:
1
NMR spectra were recorded on a Brucker-400 MHz at the NMR
unit, Faculty of Pharmacy El-Mansoura University, El-
Mansoura, Egypt. The chemical shis are expressed in parts
per million (d) downeld relative to tetramethylsilane as an
internal standard (0 ppm). Coupling constants are reported in
E-Diastereomer: 10.65 (s, 1H, NH), 7.72 (d, J ¼ 8.3 Hz, 2H,
0
0
0
0
H2 ,6 ), 7.66 (d, J ¼ 8.3 Hz, 2H, H3 ,5 ), 7.57 (s, 1H, ]CH–), 7.49 (d,
J ¼ 7.7 Hz, 1H, H4), 7.24 (t, J ¼ 7.7 Hz, 1H, H5), 6.87 (m, 2H,
H6,7) ppm.
Z-Diastereomer: 10.69 (s, 1H, NH), 8.32 (d, J ¼ 8.3 Hz, 2H,
0
0
0
0
hertz (Hz). Elemental analyses were performed on a Perkin H2 ,6 ), 7.78 (s, 1H, ]CH–), 7.71 (m, 1H, H4), 7.68 (m, 2H, H3 ,5 ),
Elmer 2400 CHN elemental analyzer at the Regional Center for 7.22 (t, J ¼ 7.7 Hz, 1H, H5), 6.99 (t, J ¼ 7.7 Hz, 1H, H6), 6.82 (m,
Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt. 1H, H7) ppm.
All calculations based on semi-empirical molecular orbital
theory have been carried out using Molecular Operating Envi-
ronment (MOE 2019.01, 2019; Chemical Computing Group,
Canada) soware at the Medicinal Chemistry Department,
Faculty of Pharmacy, Assiut University, Assiut, Egypt.
(E/Z)-3-(4-Methoxybenzylidene)indolin-2-one (6c).36 Bright
ꢀ
yellow solid crystals; yield: 75%; mp: 160–162 C;
IR: 3452.5 and 1703.5 cmꢁ1
.
1H-NMR (DMSO-d6, 400 MHz) d:
0
0
E-Diastereomer: 10.58 (s, 1H, NH), 7.72 (d, J ¼ 8.5, 2H, H2 ,6 ),
7.66 (d, J ¼ 7.8 Hz, 1H, H4), 7.59 (s, 1H, ]CH–), 7.22 (t, J ¼
0
0
7.7 Hz, 1H, H5), 7.09 (d, J ¼ 8.5 Hz, 2H, H3 ,5 ), 6.87 (m, 2H, H6,7),
Synthesis of indolin-2-one (oxindole) (2)
3.84 (s, 3H, –OCH3) ppm.
A stirred solution of isatin 1 (0.01 mol; 1.47 g) in hydrazine
0
0
Z-Diastereomer: 10.61 (s, 1H, NH), 8.48 (d, J ¼ 8.5, 2H, H2 ,6 ),
ꢀ
hydrate (15 ml) was heated to 140 C for 4 h. The reaction was
7.75 (s, 1H, ]CH–), 7.66 (d, J ¼ 7.8 Hz, 1H, H4), 7.18 (t, J ¼
cooled to room temperature, poured into ice-cold water, then
acidied to pH 2 with 6 N hydrochloric acid and kept at room
temperature for 2 days. The solution was extracted with CH2Cl2
(5 ꢂ 20), dried over anhydrous sodium sulfate, ltered, and
then re-crystallized from water to give the pure compound. Yield
0
0
7.7 Hz, 1H, H5), 7.04 (d, J ¼ 8.5 Hz, 2H, H3 ,5 ), 6.98 (t, J ¼ 7.7 Hz,
1H, H6), 6.82 (d, J ¼ 8.0 Hz, 1H, H7), 3.84 (s, 3H, –OCH3) ppm.
General procedure for the synthesis of target compounds [5(a–
d) & 7(a–b)]
¼ 80% (1.18 g), mp: 126–128 C (lit.,38 127–129 ꢀC).
ꢀ
1H-NMR (DMSO-d6, 60 MHz) d:
9.15 (bs, 1H, NH), 7.4–6.7 (m, 5H, H4,5,6,7), 3.48 (s, 2H,
H3,3) ppm.
The appropriate compound [4(a–c) and 6(a–c)] (10 mmol.) was
dissolved in anhydrous DMF (5–10 ml), and cooled on ice with
stirring. Solid K2CO3 (12 mmol) was added in one portion, and
the dark colored suspension was brought to room temperature
and stirred for an additional 1 h. Alkyl chloride or bromide (11
Synthesis of 5-nitroindolin-2-one (3)
To a stirred solution of 2-oxo-indoline 2 (30 mol; 4 g) in cold mmol) and KI (2 mmol) were added, and the reaction mixture
ꢀ
concentrated sulfuric acid at 0 ꢀC (28 ml), a cold solution of was stirred at 60–80 C for 5–24 h, until the starting material
potassium nitrate (30 mmol; 3.87 g) in concentrated sulfuric acid had been consumed (monitored by TLC). The reaction mixture
(28 ml) was added in one portion. Stirring was continued for 1.5 h was poured into HCl (0.5 M, 50 ml) and extracted with ethyl
in an ice bath (the temperature of the mixture must not exceed 5 acetate (2 ꢂ 25 ml). The ethyl acetate portion was washed with
ꢀC), and the mixture was then added to 250 ml of crushed ice. The brine and dried over anhydrous Na2SO4. The crude product was
buffy-colored precipitate was collected by ltration, washed with puried by column chromatography using CH2Cl2.
water, and dried. The raw product was puried by recrystallization
(E/Z)-3-(4-Fluorobenzylidene)-1-benzyl-5-nitroindolin-2-one
from acetic acid (50%) to give the pure product. Yield: 70% (3.75 g), (5a). E : Z ratio ¼ 6 : 94.
mp: 247–250 ꢀC (lit.,34 249–254 ꢀC).
Yellow solid powder; yield: 67%; mp: 218–221 C;
1H-NMR (DMSO-d6, 400 MHz) d:
ꢀ
1H-NMR (DMSO-d6, 60 MHz) d:
11.25 (bs, 1H, NH), 8.3–8 (m, 2H, H4,6), 7.01 (d, J ¼ 7.7 Hz,
Z-Diastereomer: 8.77 (d, J ¼ 2.2 Hz, 1H, H4), 8.60 (dd, J ¼ 8.9,
0
0
1H, H7), 3.66 (s, 2H, H3,3) ppm.
1.8 Hz, 2H, H2 ,6 ), 8.38 (s, 1H, ]CH–), 8.20 (dd, J ¼ 8.7, 1.8 Hz,
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0
0
1H, H6), 7.43–7.23 (m, 7H, benzylic Hs, H3 ,5 ), 7.20 (d, J ¼
Elemental analysis calculated/found for C19H18N2O4: C
67.44/67.71; H 5.36/5.49; N 8.28/8.57.
9.4 Hz, 1H, H7), 5.09 (s, 2H, –CH2–) ppm.
E-Diastereomer: 8.34 (d, J ¼ 2.2 Hz, 1H, H4), 8.22 (dd, J ¼ 8.7,
(E/Z)-3-(4-Methoxybenzylidene)-1-propyl-5-nitroindolin-2-
2.2 Hz, 1H, H6), 8.02 (s, 1H, ]CH-), 7.91 (dd, J ¼ 8.9,1.8 Hz, 2H, one (5c2). E : Z ratio ¼ 65 : 35.
ꢀ
0
0
0
0
H2 ,6 ), 7.47–7.25 (m, 7H, benzylic Hs, H3 ,5 ), 7.22 (d, J ¼ 9.4 Hz,
Yellow solid powder; yield: 77%; mp: 147–150 C;
1H, H7), 5.10 (s, 2H, –CH2–) ppm.
1H-NMR (DMSO-d6, 400 MHz) d:
13C-NMR (DMSO-d6, 100 MHz) d:
E-Diastereomer: 8.47 (d, J ¼ 1.3 Hz, 1H, H4), 8.21 (dd, J ¼
Z-Diastereomer: 166.2, 165.5, 146.3, 143.1, 140.9, 136.5, 136, 8.7 Hz, 2.2 Hz, 1H, H6), 7.86 (s, 1H, ]CH–), 7.78 (d, J ¼ 8.8, 2H,
0
0
0
0
135.9, 130.7, 129.2 (2C), 128, 127.8 (2C), 125.6, 123, 117.6, 116.2, H2 ,6 ), 7.33 (d, J ¼ 8.8 Hz, 1H, H7),7.14 (d, J ¼ 8.9 Hz, 2H, H3 ,5 ),
116, 115.9, 109.5, 43.6 ppm. 3.88 (s, 3H, –OCH3), 3.79 (t, 2H, –CH2–CH2–CH3), 1.63 (m, 2H,
E-Diastereomer: 168.1, 162.9, 148.6, 142.6, 140.1, 136.2, –CH2–CH2–CH3), 0.90 (t, 3H, –CH2–CH2–CH3) ppm.
132.8, 132.7, 130.6, 129.3 (2C), 128.1, 127.7 (2C), 126.9, 125.2,
123.1, 121.1, 116.7, 116.5, 110, 43.5 ppm.
Z-Diastereomer: 8.68 (d, J ¼ 1.3 Hz, 1H, H4), 8.57 (d, J ¼ 8.9,
0
0
2H, H2 ,6 ), 8.19 (s, 1H, ]CH–), 8.18 (dd, J ¼ 8.7 Hz, 2.2 Hz, 1H,
0
0
Elemental analysis calculated/found for C22H15FN2O3: C H6), 7.27 (d, J ¼ 8.8 Hz, 1H, H7),7.08 (d, J ¼ 8.9 Hz, 2H, H3 ,5 ),
70.58/70.41; H 4.04/4.23; N 7.48/7.29. 3.88 (s, 3H, –OCH3), 3.79 (t, 2H, –CH2–CH2–CH3), 1.63 (m, 2H,
(E/Z)-1-Propyl-3-(40-uorobenzylidene)-5-nitro indolin-2-one –CH2–CH2–CH3), 0.90 (t, 3H, –CH2–CH2–CH3) ppm.
(5b). E : Z ratio ¼ 17 : 83.
13C-NMR (DMSO-d6, 100 MHz) d:
E-Diastereomer: 168.3, 161.9, 148.7, 142.2, 140.8, 132.6 (2C),
126.3, 126.2, 122.8, 121.3, 117.2, 114.9 (2C), 109.4, 56, 41.7, 21,
ꢀ
Bright yellow solid powder; yield: 77%; mp: 177–180 C;
1H-NMR (DMSO-d6, 400 MHz) d:
Z-Diastereomer: 8.72 (d, J ¼ 2.2 Hz, 1H, H4), 8.58 (dd, J ¼ 8.8, 11.6 ppm.
0
0
1.8 Hz, 2H, H2 ,6 ), 8.29 (s, 1H, ]CH–), 8.23 (dd, J ¼ 1.8, 8.8 Hz,
Z-Diastereomer: 166.3, 162.6, 146.2, 142.7, 141.6, 135.8 (2C),
0
0
1H, H6), 7.37 (t, J ¼ 9.2 Hz, 2H, H3 ,5 ), 7.31 (d, J ¼ 9.2 Hz, 1H, 127, 125.6, 124.8, 120.7, 115.1, 114.4 (2C), 108.8, 56, 41.6, 21.1,
H7), 3.80 (t, 2H, –CH2–CH2–CH3), 1.65 (m, 2H, –CH2–CH2–CH3), 11.6 ppm.
0.89 (t, 3H, –CH2–CH2–CH3) ppm.
E-Diastereomer: 8.68 (d, J ¼ 2.2 Hz, 1H, H4), 8.37 (dd, J ¼ 1.8, 67.44/67.71; H 5.36/5.49; N 8.28/8.57.
8.8 Hz, 1H, H6), 7.93 (s, 1H, ]CH–), 7.87 (dd, J ¼ 8.8, 1.8 Hz, 2H, (E/Z)-3-(2-Chlorobenzylidene)-1-propyl-5-nitroindolin-2-one
Elemental analysis calculated/found for C19H18N2O4: C
0
0
0
0
H2 ,6 ), 7.53 (d, J ¼ 8.9 Hz, 1H, H7), 7.44 (t, J ¼ 9.2 Hz, 2H, H3 ,5 ), (5d). E : Z ratio ¼ 93 : 7.
ꢀ
3.80 (t, 2H, –CH2–CH2–CH3), 1.65 (m, 2H, –CH2–CH2–CH3), 0.89
(t, 3H, –CH2–CH2–CH3) ppm.
Yellow solid powder; yield: 62%; mp: 136–139 C;
1H-NMR (DMSO-d6, 400 MHz) d:
E-Diastereomer: 8.25 (dd, J ¼ 7.8, 2.2 Hz, 1H, H6), 7.97 (d, J ¼
0
13C-NMR (DMSO-d6, 100 MHz) d:
Z-Diastereomer: 167.9, 166.1, 146.8, 142.8, 140.3, 135.9, 135.8, 2.2 Hz, 1H, H4), 7.87 (s, 1H, ]CH–), 7.85 (d, J ¼ 7.8 Hz, 1H, H3 ),
0
130.8, 125.7, 123.3, 117.5, 116.1, 115.9, 115.8, 109.1, 41.7, 21, 11.5 ppm. 7.71 (d, J ¼ 8.8 Hz, 1.1 Hz, 1H, H6 ), 7.62 (td, J ¼ 7.5 Hz, 0.8 Hz,
0
0
E-Diastereomer: 165.4, 162.9, 149.1, 142.3, 139.5, 132.7, 1H, H4 ), 7.55 (t, J ¼ 2.4 Hz, 1H, H5 ), 7.38 (d, J ¼ 8.8 Hz, 1H, H7),
132.6, 130.6, 126.8, 125.1, 123.3, 117.5, 116.7, 116.5, 109.7, 41.8, 3.80 (t, J ¼ 2.4 Hz, 2H, –CH2–CH2–CH3), 1.65 (m, 2H, –CH2–
20.8, 11.6 ppm.
CH2–CH3), 0.91 (t, J ¼ 2.4 Hz, 3H, –CH2–CH2–CH3) ppm.
Z-Diastereomer: 8.76 (d, J ¼ 2.2 Hz, 1H, H4), 8.30 (s, 1H, ]
CH–), 8.25 (dd, J ¼ 7.8, 2.2 Hz, 1H, H6), 8.06 (dd, J ¼ 8.0, 1.2 Hz,
Elemental analysis calculated/found for C18H15FN2O3: C
66.25/66.47; H 4.63/4.75; N 8.58/8.8.
(E/Z)-3-(4-Methoxybenzylidene)-1-propyl-5-nitroindolin-2-
one (5c1). E : Z ratio ¼ 30 : 70.
0
0
0
1H, H6 ), 7.59–7.52 (m, 1H, H3 ), 7.48 (t, J ¼ 7.5 Hz, 1H, H5 ), 7.39
0
(t, J ¼ 7.5 Hz, 1H, H4 ), 7.31 (d, J ¼ 8.8 Hz, 1H, H7), 3.72 (t, J ¼
ꢀ
Yellow solid powder; yield: 45%; mp: 150–153 C;
2.4 Hz, 2H, –CH2–CH2–CH3), 1.61 (m, 2H, –CH2–CH2–CH3), 0.87
(t, J ¼ 2.4 Hz, 3H, –CH2–CH2–CH3) ppm.
1H-NMR (DMSO-d6, 400 MHz) d:
Z-Diastereomer: 8.67 (d, J ¼ 1.3 Hz, 1H, H4), 8.56 (d, J ¼ 8.9,
13C-NMR (DMSO-d6, 100 MHz) d:
0
0
2H, H2 ,6 ), 8.19 (s, 1H, ]CH–), 8.17 (dd, J ¼ 8.7 Hz, 2.2 Hz, 1H,
E-Diastereomer: 167.5, 149.4, 142.3, 136.1, 133.6, 132.7,
0
0
H6),7.25 (d, J ¼ 8.8 Hz, 1H, H7), 7.06 (d, J ¼ 8.9 Hz, 2H, H3 ,5 ), 132.5, 130.9, 130.6, 128.1, 127.3, 127.2, 120.6, 117.9, 109.9, 41.9,
3.86 (s, 3H, –OCH3), 3.78 (t, 2H, –CH2–CH2–CH3), 1.63 (m, 2H, 21, 11.6 ppm.
–CH2–CH2–CH3), 0.89 (t, 3H, –CH2–CH2–CH3) ppm.
Z-Diastereomer: 165.6, 147.6, 142.9, 136.8, 134, 132.8, 132.2,
E-Diastereomer: 8.47 (d, J ¼ 1.3 Hz, 1H, H4), 8.21 (dd, J ¼ 131.9, 129.6, 126.9, 126.6, 126.2, 123.8, 116.7, 109.2, 41.6, 21,
8.7 Hz, 2.2 Hz, 1H, H6), 7.86 (s, 1H, ]CH–), 7.78 (d, J ¼ 8.8, 2H, 11.6 ppm.
0
0
0
0
H2 ,6 ), 7.31 (d, J ¼ 8.8 Hz, 1H, H7),7.13 (d, J ¼ 8.9 Hz, 2H, H3 ,5 ),
Elemental analysis calculated/found for C18H15ClN2O3: C
3.87 (s, 3H, –OCH3), 3.78 (t, 2H, –CH2–CH2–CH3), 1.63 (m, 2H, 63.07/62.89; H 4.41/4.58; N 8.17/8.45.
–CH2–CH2–CH3), 0.89 (t, 3H, –CH2–CH2–CH3) ppm.
13C-NMR (DMSO-d6, 100 MHz) d:
Z-Diastereomer: 166.3, 162.6, 146.2, 142.7, 141.6, 135.8 (2C), 127,
125.6, 124.8, 120.7, 115.1, 114.4 (2C), 108.8, 56, 41.6, 21.1, 11.6 ppm.
E-Diastereomer: 168.3, 161.9, 148.7, 142.2, 140.8, 132.6 (2C),
(E/Z)-3-(4-Fluorobenzylidene)-1-benzyl-indolin-2-one
(7a).
E : Z ratio ¼ 18 : 82.
Yellow semisolid; yield: 67%;
1H-NMR (DMSO-d6, 400 MHz) d:
0
0
Z-Diastereomer: 8.54 (dd, J ¼ 8.5, 1.8 Hz, 2H, H2 ,6 ), 7.96 (s,
126.3, 126.2, 122.8, 121.3, 117.2, 114.9 (2C), 109.4, 56, 41.7, 21, 1H, ]CH–), 7.79 (d, J ¼ 8.5 Hz, 1H, H4), 7.42–7.22 (m, 8H,
11.6 ppm.
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0
0
Benzylic Hs, H5, H3 ,5 ), 7.06 (t, J ¼ 8.7 Hz, 1H, H6), 6.98 (d, J ¼
Elemental analysis calculated/found for C18H16FNO: C 76.85/
76.59; H 5.73/5.89; N 4.98/5.13.
8.9 Hz, 1H, H7), 5.00 (s, 2H, –CH2–) ppm.
0
0
E-Diastereomer: 7.83 (dd, J ¼ 8.5, 1.8 Hz, 2H, H2 ,6 ), 7.80 (s,
1H, ]CH–), 7.56 (d, J ¼ 8.5 Hz, 1H, H4), 7.42–7.22 (m, 8H,
Kinetic measurements
0
0
Benzylic Hs, H5, H3 ,5 ), 6.99 (d, J ¼ 8.9 Hz, 1H, H7), 6.92 (t, J ¼
Isomerization rates of the tested compounds (5a, 5b, 5c1, 5c2,
5d, 6a, 6c, 7a, 7b1, 7b2) in DMSO-d6 were determined at room
temperature. The reactions were initiated by dissolving 10 mg of
the tested compound to 0.3 ml of DMSO-d6 in NMR tubes. At
appropriate intervals, the 1H-NMR spectrum for each sample
was measured, and the integral height values of the vinyl and
20,60-protons chemical shis of the respective E and Z diaste-
reomers were determined. The residual heights displayed
a rst-order rate of kinetics. The results of the kinetic
measurements are given in Tables 2 and 3.
8.7 Hz, 1H, H6), 5.00 (s, 2H, –CH2–) ppm.
13C-NMR (DMSO-d6, 100 MHz) d:
Z-Diastereomer: 165.7, 164.9, 162.4, 143.5, 136.5, 135.3,
132.4, 131.2, 130.6, 129.1 (2C), 127.9, 127.8 (2C), 125.4, 122.7,
122.3, 120.2, 116.5, 115.7, 109.5, 43.1 ppm.
E-Diastereomer: 167.8, 164.4, 161.9, 141.3, 137.2, 137, 135.2,
132.3, 129.4, 129.2 (2C), 127.9, 127.7 (2C), 126.9, 124.4, 122.4,
102.7, 116.3, 115.9, 110.1, 43 ppm.
Elemental analysis calculated/found for C22H16FNO: C 80.23/
79.97; H 4.90/5.12; N 4.25/4.48.
(E/Z)-1-Propyl-3-(40-uorobenzylidene)-indolin-2-one (7b1).
E : Z ratio ¼ 2 : 98.
Molecular modeling studies
Yellow semisolid; yield: 55%;
The molecular docking studies were performed (Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University,
Egypt) using Molecular Operating Environment (MOE 2019.01,
2019; Chemical Computing Group, Canada) as the computa-
tional soware. The three-dimensional structures and confor-
mations of the enzyme, cyclin-dependent kinase enzyme
(CDK2) in complex with sunitinib (PDB ID: 3TI1), was acquired
from the Protein Data Bank (PDB) web site.40 The binding
affinity of the docked molecules was expressed as binding score
(S, kcal molꢁ1). Briey, docking of the investigated molecules
was performed in four steps: preparation of the 3D structure of
the target, preparation of the ligands, running docking, and
interpretation of the results. Docking was performed using the
default settings of the MOE program [Placement, triangular
Matcher; Rescoring 1, London dG with retain ¼ 30; Renement,
Forceeld; Rescoring 2, GBVI/WSA dG with retain ¼ 30]. The key
amino acids involved in the interaction of sunitinib with CDK2
in the co-crystalized target are Ile10, Glu81, Leu83, Gln85 and
Asp86. Re-docking of sunitinib was performed to accurately
evaluate the efficiency of the method (rmsd ¼ 2).
1H-NMR (DMSO-d6, 400 MHz) d:
0
0
Z-diastereomer: 8.51 (dd, J ¼ 7.8, 1.8 Hz, 2H, H2 ,6 ), 7.89 (s,
0
0
1H, ]CH-), 7.77 (d, J ¼ 8.5 Hz, 1H, H4), 7.36–7.26 (m, 3H, H3 ,5
,
H6), 7.07 (m, 2H, H5,7), 3.72 (t, 2H, –CH2–CH2–CH3), 1.64 (m,
2H, –CH2–CH2–CH3), 0.89 (t, 3H, –CH2–CH2–CH3) ppm.
0
0
E-Diastereomer: 7.79 (dd, J ¼ 7.8, 1.8 Hz, 2H, H2 ,6 ), 7.7 (s,
0
0
1H, ]CH–), 7.54 (d, J ¼ 8.5 Hz, 1H, H4), 7.40–7.28 (m, 3H, H3 ,5
,
H6), 7.11 (d, J ¼ 8.8 Hz, 1H, H7), 6.92 (t, J ¼ 8.9 Hz, 1H, H5), 3.72
(t, 2H, –CH2–CH2–CH3), 1.64 (m, 2H, –CH2–CH2–CH3), 0.89 (t,
3H, –CH2–CH2–CH3) ppm.
13C-NMR (DMSO-d6, 100 MHz) d:
Z-Diastereomer: 167.6, 165.7, 162.3, 141.8, 136.4, 135.2,
135.1, 129.5, 125.7, 122.6, 122, 120.1, 115.8, 115.6, 109.1, 41.2,
21, 11.7 ppm.
E-Diastereomer: 164.8, 164.3, 161.8, 143.9, 135.9, 132.4,
132.3, 130.7, 127.1, 124.3, 122.1, 120.6, 116.5, 116.2, 109.6, 41.3,
20.9, 11.7 ppm.
Elemental analysis calculated/found for C18H16FNO: C 76.85/
76.59; H 5.73/5.89; N 4.98/5.13.
(E/Z)-1-Propyl-3-(40-uorobenzylidene)-indolin-2-one (7b2).
E : Z ratio ¼ 88 : 12.
1
Yellow semisolid; yield: 55%; H-NMR (DMSO-d6, 400 MHz)
Conflicts of interest
d:
The authors declare no conict of interest.
0
0
E-Diastereomer: 7.79 (dd, J ¼ 7.8, 1.8 Hz, 2H, H2 ,6 ), 7.7 (s,
0
0
1H, ]CH–), 7.54 (d, J ¼ 8.5 Hz, 1H, H4), 7.40–7.28 (m, 3H, H3 ,5
,
H6), 7.11 (d, J ¼ 8.8 Hz, 1H, H7), 6.92 (t, J ¼ 8.9 Hz, 1H, H5), 3.71
(t, 2H, –CH2–CH2–CH3), 1.64 (m, 2H, –CH2–CH2–CH3), 0.90 (t,
3H, –CH2–CH2–CH3) ppm.
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7850 | RSC Adv., 2021, 11, 7839–7850
© 2021 The Author(s). Published by the Royal Society of Chemistry