Synthesis, Docking, and Bioavailability of 2′-Oxo-3-phenylspiro[cyclopropane-1,3′-indoline]-2,2-dicarbonitriles as Antibacterial Agents In Silico

Article abstract of DOI:10.1002/jhet.3396

An efficient method has been developed for the synthesis of N-alkylated 2′-oxo-3-phenylspiro[cyclopropane-1,3′-indoline]-2,2-dicarbonitrile from 3-chloroindolin-2-one and 2-benzylidenemalononitrile by using triethylamine as a base at room temperature and obtained the products in moderate to good yields. In extension, the scope of the reaction has been investigated by stepwise and one-pot methods. Furthermore, in silico antibacterial activity was carried out in order to understand possible binding modes of novel derivatives with the active site of DNA gyrase A enzyme, and the results were well complemented. Additionally, absorption, distribution, metabolism, and excretion properties of compounds have shown drug likeness with good oral absorption and moderate blood–brain barrier permeability.

Full text of DOI:10.1002/jhet.3396

0
Month 2018
Synthesis, Docking, and Bioavailability of 2 -Oxo-3-
0
phenylspiro[cyclopropane-1,3 -indoline]-2,2-dicarbonitriles as
Antibacterial Agents In Silico
a,b
c
b
c
b
Vijay Kumar Reddy Avula,
Venkata Ramaiah Chintha,
Swetha Vallela,
Jaya Shree Anireddy,
a
Naga Raju Chamarthi, *
and Rajendra Wudayagiri
a
Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
b
Centre for Chemical Sciences and Technology, Institute of Science and Technology, Jawaharlal Nehru Technological
University, Hyderabad, Kukatpally, Telangana 500085, India
c
Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh 517502, India
*
E-mail: rajuchamarthi10@gmail.com
Received May 27, 2018
DOI 10.1002/jhet.3396
Published online 00 Month 2018 in Wiley Online Library (wileyonlinelibrary.com).
0
An efficient method has been developed for the synthesis of N-alkylated 2 -oxo-3-
0
phenylspiro[cyclopropane-1,3 -indoline]-2,2-dicarbonitrile
from
3-chloroindolin-2-one
and
2-
benzylidenemalononitrile by using triethylamine as a base at room temperature and obtained the products
in moderate to good yields. In extension, the scope of the reaction has been investigated by stepwise and
one-pot methods. Furthermore, in silico antibacterial activity was carried out in order to understand pos-
sible binding modes of novel derivatives with the active site of DNA gyrase A enzyme, and the results
were well complemented. Additionally, absorption, distribution, metabolism, and excretion properties of
compounds have shown drug likeness with good oral absorption and moderate blood–brain barrier
permeability.
J. Heterocyclic Chem., 00, 00 (2018).
INTRODUCTION
The spirooxindole framework has remained
display a variety of biological activities and many of them
used as starting materials for alkaloid synthesis [7].
Spirooxindoles are one of the most important classes of
naturally occurring substances, characterized by highly
pronounced biological properties. These molecules are
also the core structure of many synthetic pharmaceuticals
[8]. While the synthesis of spirocyclic oxindoles has
continued to gain attention, the development of
enantioselective methods to access spirooxindoles remains
an ongoing synthetic challenge. This review features
recent strategies for the enantioselective synthesis of
spirocyclic oxindoles, focusing on reports from 2010 and
2011 [9]. An extensive investigation on this aspect of
isatins’ chemistry during the past decade has led to
successful design and synthesis of diverse types of
heterocyclic and carbocyclic compounds with a spiro-
fused 2-oxindole ring containing many stereocenters on
one hand and discovery of many interesting facts of
organic synthesis design on the other hand that need to be
comprehensively reviewed [10].
a
synthetically challenging and privileged architectural
motif that is prevalent in many pharmaceuticals and
bioactive natural products [1]. This class of frameworks
has attracted more interest from chemists because of
their biological importance and the challenge embedded in
their synthesis [2]. The unique structures and the highly
pronounced pharmacological activity displayed by the
spirooxindoles have made them attractive synthetic targets
[
3]. As part of a medicinal chemistry project, we have
0
been focusing on the synthesis of novel 3 -spirocyclo-
oxindoles, and we recently reported the preparation of
0
3
-spiropentacyclo-oxindole derivatives using phosphine-
2]-cycloaddition reactions [4].
catalyzed [3
+
Interestingly, when diphenyldiazomethane was employed,
0
the desired 3,3-diphenyl-3 -spirocyclopropyloxindole-2-
carboxylic ester [5] was obtained.
As synthetic tools, nitrile-substituted cyclopropanes
are versatile templates for the rapid formation of
biologically active and synthetically useful functionalized
cyclopropane derivatives [6]. The synthesis of
spirocycloindolones has shown great interest because they
On the other hand, the general synthetic routes to
1-arylcyclopropane-1,2-dicarboxylate derivatives involve
the reaction of α-bromophenylacetates with acrylic esters
under strong basic conditions [11]. Organocatalytic
©
2018 Wiley Periodicals, Inc.

V. K. R. Avula, V. R. Chintha, S. Vallela, J. S. Anireddy, N. R. Chamarthi, and W. Rajendra
Vol 000
approaches to spiro-annulation of oxindoles offer a
high degree of stereoenantio control and have become
extremely popular for the construction of five-membered
and six-membered spiro-rings [12–18]. Artur Noole et al.
and excretion (ADME) properties, in order to suggest the
suitability of the new compounds for further drug
development with respect to antibacterial activity.
[
19] reported highly enantio and diastereoselective
generation of two quaternary centers in
RESULTS AND DISCUSSION
spirocyclopropanation of oxindole derivatives. Artur Nool
et al. [20] described asymmetric organometalic synthesis
of spiro cyclopropaneoxindoles using thiourea-based
catalyst emerged as the most suitable, providing the
spiro-cyclopropaneoxindole in excellent enantioselectivity
and diastereoselectivity and in almost quantitative yield.
Erin et al. [21] described stereochemical implications in
the synthesis of spirocyclopropyl oxindoles from β-aryl/
alkyl-substituted alkylidene. Rong Zhou et al. [22]
reported P(NMe ) -mediated model reaction between and
Chemistry.
Based on the earlier literature, we
developed a new method for the synthesis of spiro
cyclopropane indoline derivatives using different solvents
and bases. The simple and commercially available
starting materials aniline and chloroacetyl chloride were
reacted by using K CO base in dichloromethane (DCM)
2
3
solvent in the presence of aluminium trichloride to
give corresponding 3 [25] was shown in Scheme 1.
On further treatment of 3 with CMOBSC (chloromethoxy
benzenesulfonic acid) in acetonitrile solvent to obtain
chloro oxindole 4 [26]. Further, it was treated with
substituted 2-benzylidenemalononitriles in the presence of
triethylamine in toluene solvent at room temperature for
overnight to afford the corresponding title compounds
(8a–g) in very poor yield. In order to improve the yields
and optimize the reaction conditions, different solvents
and bases were tried. Among those conditions,
triethylamine as a base and DCM as a solvent at room
temperature for overnight gave an excellent yield; hence,
2
3
afforded the expected cyclopropanation product. Wen-Jie
et al. [23] reported a new method for the synthesis of
functionalized spiro cyclopropane indoline. John et al.
[24] reported the synthesis of gem-dimethyl cyclopropane
using isopropyl triphenylphoshorane as a catalyst and
MeI as an alkylating agent in tetrahydrofuran solvent.
The synthesized molecules are subjected to the molecular
docking active binding pocket of the DNA gyrase A
enzyme. Moreover, we have also used an in silico
method to predict absorption, distribution, metabolism,
0
0
Scheme 1. Stepwise and one-pot synthesis of 2 -oxo-3-phenylspiro[cyclopropane-1,3 -indoline]-2,2-dicarbonitriles (8a–g). DCM, dichloromethane; RT,
room temperature. [Color figure can be viewed at wileyonlinelibrary.com]
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet

Month 2018
Synthesis, Docking, and Bioavailability of Spirooxindoles as Antibacterial Agents
this methodology has been adopted for the synthesis of
other derivatives. The structures of title compounds were
confirmed by NMR and mass spectral data.
Table 3
Comparative parameters of stepwise and one-pot method.
Compound
8a
8b
8c
8d
8e
8f
8g
The title compounds could also be prepared in one-pot
0
% of yield in stepwise 90
method
89
85
80
70
80 80
65 65
method as shown in Scheme 1. The synthesis of 2 -oxo-3-
0
phenylspiro [cyclopropane-1,3 -indoline]-2,2-dicarbonitrile
%
of yield in one-pot
80
75
70
65
60
via one-pot and three-component method using starting
method
materials substituted benzaldehydes, malononitrile, and
3
-chloro oxindole in the presence of ammonium acetate,
the same binding pocket using Auto Dock 4.2 in PyRx
with default parameters. It showed a root-mean-square
deviation value of 0.689 Å, to obtain from all atoms
and heteroatom coordinates between experimental and
redocked confirmations. Moreover, the docked native
ligand is bound tightly to DNA gyrase A involving
almost the same residues as in the co-crystallized
structure. This indicates that these parameters are
adequate in reproducing the experimental structure and
can be extended to do docking studies on our synthesized
compounds. The molecular docking results revealed
that all the compounds 8a–g tend to bind within the
binding pocket of DNA gyrase A and show good binding
energies ranging from ꢀ7.2 to ꢀ6.4 kcal/mol. The
docking results are summarized in Table 4.
triethylamine as a base in DCM solvent, and acetic acid
under reflux conditions to obtain moderate to good yields.
Stepwise synthesis gave good yields compared with
one-pot, three-component method, and these results are
given in Tables 1 and 2. The detailed comparative yields
were tabulated in Table 3, respectively, for stepwise and
one-pot methods.
Molecular docking.
The docking protocol was
validated using redocking experiments by removing the
native ligand from DNA gyrase A and redocked into
Table 1
Optimization of reaction conditions at RT with TEA base (conc: 0.2 mole
equiv).
Compound 8a showed the highest binding energy of
ꢀ7.2 kcal/mol and the lowest inhibition constant of 0.82
followed by compounds 8b, 8d, and 8g, which showed
binding energies of ꢀ7.0, ꢀ6.8, and ꢀ6.8 kcal/mol and
inhibition constants of 1.13 and 1.53, respectively.
The low inhibition constant and more negative value of
binding energy indicate good binding affinity of the
ligand towards the target enzyme. Thus, the results
correlate well with the observed in silico antibacterial
activity. The three-dimensional visualization of the
interactions of the most active compounds 8a, 8b, 8d, 8f,
and 8g within the binding pocket of DNA gyrase A is
shown in Figure 1.
S. no.
Solvent
Time (h)
Yield (%)
1
2
3
4
5
6
7
8
9
Toluene
Acetonitrile
DMF
DMSO
Ethanol
Methanol
THF
1,4-Dioxane
12
12
12
12
12
12
12
12
12
12
20
50
35
40
25
20
35
25
75
90
CHCl
DCM
3
10
DCM, dichloromethane; DMF, dimethylformamide; DMSO, dimethyl
sulfoxide; RT, room temperature; TEA, triethylamine; THF,
tetrahydrofuran.
The binding models indicate that the compounds are
held in the active site by a combination of various
hydrogen bonding and hydrophobic interactions. Single
hydrogen bond was present in the derivative of 8a, which
has the highest binding energy among the series. It
showed hydrogen bonding interaction with amino acid
residue Asp 104 at the bond distances of 2.3 Å,
respectively. This is evidence for the requirement of
hydrophilic groups to bind strongly to the protein active
site. Whereas the remaining active compounds such as
8d, 8b, 8g, and 8f showed the interactions with amino
acids Val 103, Glu 139, Tyr 50, and Arg 126 at a bond
distance 2.7, 2.2, 2.5, 2.1, 2.5, 2.4, and 2.7, respectively.
Table 2
Optimization of reaction conditions with different bases at RT in DCM
solvent.
S. no.
Base (equiv 0.2)
Time (h)
Yield (%)
1
2
3
4
5
6
7
8
9
Pyridine
Morpholine
N,N-Diethylamine
Piperidine
Triphenylphosphine
Ammonium acetate
Sulfamic acid
L-Proline
12
12
12
12
12
12
12
12
12
12
10
15
20
25
Nil
Nil
Nil
20
Nil
90
Bioavailability of compounds 8a–g. Nowadays, many
potential drugs fail to reach the clinic because of
ADMET liabilities. Absorption, distribution, metabolism,
excretion, and toxicity (ADMET) processes play a pivotal
Ammonia
TEA
10
DCM, dichloromethane; RT, room temperature; TEA, triethylamine.
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet

V. K. R. Avula, V. R. Chintha, S. Vallela, J. S. Anireddy, N. R. Chamarthi, and W. Rajendra
Vol 000
Table 4
Bonding characterization of synthesized compounds (8a–g) and Nfx (one reference drug) against Escherichia coli DNA gyrase A protein.
Compound
Rank
BE (kcal/mol)
Binding interaction
Bond length (Å)
Bond angle (°)
Bond type
8
8
a
b
1
3
ꢀ7.2
ꢀ6.8
Asp 104 CG···HN
Glu 139 CD···HN
Tyr 50 CZ···HN
Met 101 CG···HN
Val 103 CA···HN
Glu 141 CZ···HN
Arg 126 CB···HN
Glu 139 CD···HN
Tyr 50 CZ···HN
Phe 213 CB···HN
Asp 104 CG···HO
Trp 59 CA···HO
2.3
2.2
2.5
2.1
2.7
2.3
2.7
2.5
2.4
2.6
1.8
2.1
108.4
126.2
120.5
112.8
122.8
128.8
118.6
126.2
120.5
104.7
116.6
120.5
H– don
H– don
H– don
H– don
H– don
H– don
H– don
H– don
H– don
H– don
H– don
H– don
8
8
8
8
8
c
d
e
f
7
2
6
5
4
ꢀ6.4
ꢀ7.0
ꢀ6.5
ꢀ6.7
ꢀ6.8
g
Nfx
R
ꢀ6.6
BE, binding energy.
Figure 1. Diagram representing the three-dimensional modeled binding modes of compounds 8a, 8b, 8d, 8f, 8g, and Nfx (standard) within the binding
domain of DNA gyrase A. [Color figure can be viewed at wileyonlinelibrary.com]
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet

Month 2018
Synthesis, Docking, and Bioavailability of Spirooxindoles as Antibacterial Agents
Table 5
Physicochemical properties of compounds 8a–g.
Compound
Rule
MW
MV
NRB
NHBD
NHBA
LROWPC
TPSA
LV
PA
≤500
390.2
378.6
349.8
422.6
450.4
347.8
340.6
—
—
5
6
5
5
5
5
5
≤5
0
0
0
0
0
0
0
≤10
8
7
8
77
8
≤5
—
≤1
0
0
0
0
0
0
0
—
8
8
8
8
8
8
8
a
b
c
d
e
f
336.6
354.0
373.4
372.4
313.9
341.0
303.3
3.42
3.26
3.28
3.35
3.45
3.96
4.10
80.46
82.18
88.42
84.66
86.12
90.36
82.14
90.5
90.5
97.3
90.5
74.7
90.5
90.5
7
7
g
MW, molecular weight; MV, molecular volume; NRB, number of rotatable bonds; NHBD, number of hydrogen bond donors (–OH and –NH); NHBA,
number of hydrogen bond acceptors; LROWPC, logarithmic ratio of the octanol–water partitioning coefficient; TPSA, topological polar surface area; LV,
Lipinski’s violation; PA, percentage of absorption %ABS = 109 ꢀ (0.3459 TPSA).
role in defining the therapeutic efficacy of a drug. Drug
likeness appears as promising paradigm of
bond acceptors, the molecular weight is greater than
500, and the calculated log p (logarithmic ratio of the
octanol–water partitioning coefficient) is greater than 5.
Molecules violating more than one of these parameters
may have problems with bioavailability and a high
probability of failure to display drug likeness [28].
Further, the topological polar surface area (TPSA),
which is another key property in estimating drug
bioavailability, was also calculated. Generally,
a
a
compound that optimizes their ADME in the human
body [27]. With the aim of estimating the drug
likeness of the compounds, we have determined the
compliance of the synthesized molecules to the
Lipinski’s “rule of five.” According to this rule, poor
absorption or permeation is more likely when there are
more than five hydrogen bond donors and 10 hydrogen
2
compounds with a TPSA ≥ 140 Å are thought to
have low bioavailability [29]. As shown in Table 5, all
the synthesized compounds comply with these rules.
Table 6
Moreover, the compounds exhibited
a
greater
Prediction of pharmacokinetic properties of compounds 8a–g.
percentage of absorption (%ABS) ranging from 74.70
to 90.5%. Hence, theoretically, all of these compounds
have good passive oral absorption and drug likeness.
In addition to this, some ADME predictions such as
blood–brain barrier (BBB) penetration, % of human
intestinal absorption (HIA), Caco-2 permeability, and % of
PPB were predicted for all compounds. Analysis of
ADME predictions (Table 6) reveals that all the
compounds showed high % of HIA in the range of
98.14–99.36% and is well absorbed. The Caco-2 cell
permeability is moderate, ranging from 20.36 to 26.24 nm/
Caco-2
permeability
HIA
(%)
PPB
(%)
Compound
BBB
8
8
8
8
8
8
8
a
b
c
d
e
f
20.36
22.18
21.12
20.86
26.24
23.86
22.14
98.14
98.6
94.16
92.28
93.36
93.38
94.46
98.88
100.00
0.112
0.452
0.444
0.136
0.432
0.224
0.428
98.46
99.12
99.36
98.89
98.84
g
Caco-2, colon adenocarcinoma; HIA, human intestinal absorption; PPB,
plasma protein binding; BBB, blood–brain barrier (Cbrain
C
blood).
Figure 2. Plausible reaction mechanism for the formation of spirooxindoles. [Color figure can be viewed at wileyonlinelibrary.com]
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet

V. K. R. Avula, V. R. Chintha, S. Vallela, J. S. Anireddy, N. R. Chamarthi, and W. Rajendra
Vol 000
s. Furthermore, all of them are strongly bound to plasma
proteins with %PPB penetration more than 92.28%,
and they were also found to have moderate penetration
was concentrated under vacuum and purified by column
chromatography (1:9 ethyl acetate and hexane).
General procedure for the synthesis of title compounds
(0.112–0.452) to the central nervous system through the
(8a–g) in one-pot method. A solution of chloro oxindole
BBB. Hence, it can be stated that, theoretically, all the
compounds exhibited good absorption and bioavailability
with reasonable permeability through the BBB.
(4, 10 mmol), substituted benzaldehyde (5a–g 10 mmol),
malononitrile (6, 10 mmol), and triethylamine catalytic
amount (0.2 mmol) in the presence of acetic acid
(10 mL) in DCM solvent was taken in a 100-mL round
bottom flask and refluxed for 12 h. The consumption
of starting material was monitored by TLC. After
completion of the reaction, obtained mass was
concentrated under vacuum and purified by column
chromatography (1:9 ethyl acetate and hexane). The
plausible reaction mechanism was provided in Figure 2.
CONCLUSION
We have developed a new synthetic methodology for
spiro cyclopropane indoline derivatives (8a–g) by using a
new and stable and economically affordable chlorinating
reagent (N-chloro-N-methozxybenzenesulfonamide) and
compared the yields in both stepwise and one-pot
methods by using optimized conditions. As an addition,
molecular docking studies of the synthesized compounds
0
Spectral data of title compounds (8a–g). 2-(2 -Oxo-2-
0
phenylspiro[cyclopropane-1,3 -indolin]-3-yl)malononitrile
(
(
8a).
White solid, yield = (92%); mp 147–149°C, IR
ꢀ
1
KBr) (νmax/cm ): 3033, 2952, 2242, 1725, 1619, 1491,
445, 1351, 1272, 1181, 1124, 1016, 821, 695 cm ;
H-NMR (400 MHz, CDCl /TMS): δ 3.9 (s, 1H, CH),
ꢀ
1
1
8
a–g against DNA gyrase A enzyme revealed that
1
compounds such as 8a, 8d, 8b, 8g, and 8f showed higher
binding affinities and many more interactions when
compared with other compounds. In addition, in silico
ADME prediction showed that all the compounds
fulfilled Lipinski’s rule of five with moderate potential to
penetrate the BBB. These results suggested that
compounds 8a, 8d, 8b, 8g, and 8f can be considered as
promising candidates for further development of potential
antibacterial drugs.
3
6
7
.89–7.04 (m, 1H, Ar–H), 7.18–7.25 (m, 2H, Ar–H),
.32–7.44 (m, 6H, Ar–H), 8.90 (s, 1H, –NH); C-NMR
13
(400 MHz, CDCl ): 20.04, 39.84, 42.83, 110.1, 111.4,
3
116.2, 116.5, 121.2, 121.8, 122.7, 123.2, 125.5, 130.5,
131.2, 141.4, 142.0, 168.4: MS (negative mode): m/
+
z = 284 [M + H] . Anal. Calcd (%) for C18
H
N
11
O:
3
C, 75.78; H, 3.89; N, 14.73. Found: C, 75.68; H, 3.82;
N, 14.65.
0
0
2
-(2-(4-Bromophenyl)-2 -oxospiro[cyclopropane-1,3 -
indolin]-3-yl)malononitrile (8b).
yield = (90%); mp 202–204°C, IR (KBr) (νmax/cm ):
Pale yellow solid,
ꢀ
1
EXPERIMENTAL
3
1
029, 2949, 2241, 1719, 1620, 1489, 1446, 1352, 1271,
ꢀ
1 1
179, 1124, 1019, 826, 691 cm ; H-NMR (400 MHz,
/TMS): δ 2.09 (s, 1H, CH), 6.34–6.35 (d, 1H,
All the starting materials and solvents were purchased
in reagent grade and used as such, and products were
purified by column chromatography (silica gel 200–300).
Melting points were determined in open capillary
tubes using Guna digital melting point apparatus
Hyderabad, India). Thin-layer chromatography (TLC)
analyses were run on silica gel-G, and visualization was
performed using UV lamp (Hyderabad, India) or iodine.
H-NMR and C-NMR spectra were recorded on Bruker
00-MHz instrument (Ettlingen, Germany) in CDCl or
DMSO-d using tetramethylsilane (TMS) as an internal
standard at 400 and 100 MHz, respectively. Chemical
shifts were recorded on δ scale in parts per million
CDCl
3
Ar–H), 6.95–6.98 (t, 2H, Ar–H), 7.09–7.12 (t, 2H,
Ar–H), 7.37–7.40 (t, 2H, Ar–H), 7.56–7.57 (d, 2H,
13
Ar–H), 8.50 (s, 1H, –NH); C-NMR (400 MHz, CDCl3):
32.91, 39.91, 65.90, 110.1, 110.0, 116.1, 116.5, 118.1,
121.9, 122.8, 125.5, 130.6, 131.3, 131.8, 132.0, 170.4:
(
+2
MS (positive mode): m/z = 366 [M + H] . Anal. Calcd
1
13
(%) for C H BrN O: C, 59.36; H, 2.77; N, 11.54.
18
10
3
4
3
Found: C, 59.42; H, 2.72; N, 11.45.
0
0
6
2-(2-(4-Chlorophenyl)-2 -oxospiro[cyclopropane-1,3 -
indolin]-3-yl)malononitrile
yield = (90%); mp 181–182°C, IR (KBr) (νmax/cm ):
(8c).
White
solid,
ꢀ
1
(
ppm). Mass spectra were recorded on Agilent LCMS
3021, 2915, 2235, 1718, 1622, 1451, 1461, 1352, 1252,
1150, 1109, 1028, 820, 693 cm ; H-NMR (400 MHz,
ꢀ
1 1
instrument (Ettlingen, Germany).
CDCl /TMS): δ 3.97 (s, 1H, CH), 7.02–7.04 (m, 1H,
General procedure for the synthesis of title compounds
3
(8a–g) in stepwise method. A solution of chloro oxindole
Ar–H), 7.15–7.19 (m, 2H, Ar–H), 7.28–7.30 (m, 2H,
(
4, 10 mmol), substituted benzonitriles (7a–g, 10 mmol),
Ar–H), 7.52–7.59 (m, 4H, Ar–H), 9.19 (s, 1H, –NH);
C-NMR (400 MHz, CDCl ): 20.52, 40.21, 41.62,
3
13
and triethylamine catalytic amount (0.2 mmol) in DCM
solvent was taken in a 100-mL round bottom flask
reacted at RT and monitored the progress of the reaction
by TLC. After completion of reaction, the reaction mass
111.4, 111.9, 115.5, 117.1, 120.9, 121.1, 122.5, 123.4,
123.9, 131.4, 133.1, 143.5, 144.0, 170.9: MS (positive
+2
mode): m/z = 321 [M + H] . Anal. Calcd (%) for
Journal of Heterocyclic Chemistry
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Month 2018
Synthesis, Docking, and Bioavailability of Spirooxindoles as Antibacterial Agents
C H ClN O: C, 67.61; H, 3.15; N, 13.14. Found: C,
In silico studies. Docking studies. Molecular docking
was used to determine the binding free energy and
binding mode of the synthesized compounds 16–22 with
DNA gyrase A. Molecular docking was performed with
PyRx 0.8 implementation of Auto Dock 4.2 [29] using an
empirical free energy force field and Lamarckian genetic
algorithm conformational search with the default
parameters. The grid box was set around the binding
pocket in DNA gyrase A with a 45, 942, and 946 Å grid
box having 0.375 Å grid point spacing.
1
8
10
3
6
7.56; H, 3.13; N, 13.21.
0
0
2
-(2-(4-Fluorophenyl)-2 -oxospiro[cyclopropane-1,3 -
indolin]-3-yl)malononitrile
yield = (90%); mp 149–150°C, IR (KBr) (νmax/cm ):
(8d).
White
solid,
ꢀ
1
3
1
012, 2931, 2236, 1720, 1625, 1461, 1451, 1332,
ꢀ
1
1
222, 1170, 1106, 1029, 821, 691 cm
;
H-NMR
(
400 MHz, CDCl /TMS): δ 3.99 (s, 1H, CH), 6.92–
3
6
.98 (m, 1H, Ar–H), 7.12–7.42 (m, 8H, Ar–H), 9.21
1
3
(
s, 1H, –NH);
C-NMR (400 MHz, CDCl ): 19.92,
3
39.21, 40.62, 111.3, 111.2, 114.5, 115.1, 119.9, 120.1,
Target structure and ligand dataset preparation.
The
1
22.5, 123.5, 124.3, 130.4, 132.1, 142.5, 142.0, 168.9: MS
three-dimensional coordinates of the crystal structure
DNA gyrase A were selected from the RCSB Protein
Data Bank (PDB code: 3LPX) as the receptor model
[30]. Water molecules and hetero atoms were removed
from the co-crystal structure. Hydrogen atoms and
Gasteiger partial charges were added to the target protein
using UCSF Chimera 1.10.2 [31]. The compounds were
subjected to energy minimization using the Open Babel
+
(positive mode): m/z = 304 [M + H] . Anal. Calcd (%) for
C H FN O: C, 71.28; H, 3.32; N, 13.85 Found: C,
1
8
10
3
71.18; H, 3.29; N, 13.92.
0
0
2
-(2-(4-Nitrophenyl)-2 -oxospiro[cyclopropane-1,3 -indolin]-
3
1
1
8
3
-yl)malononitrile (8e). White solid, yield = (90%); mp
83–185°C, IR (KBr) (νmax/cm ): 3025, 2948, 2231,
718, 1621, 1469, 1441, 1342, 1262, 1180, 1109, 1023,
ꢀ
1
ꢀ
1
1
25, 681 cm ; H-NMR (400 MHz, CDCl /TMS): δ
3
module in PyRx program.
In silico absorption, distribution, metabolism, and excretion
.89 (s, 1H, CH), 7.02–7.09 (m, 1H, Ar–H), 7.15–7.19
(
2
m, 3H, Ar–H), 7.91–7.97 (m, 2H, Ar–H), 8.31–8.35 (m,
H, Ar–H), 9.12 (s, 1H, –NH); C-NMR (400 MHz,
prediction.
The synthesized compounds were
1
3
subjected to prediction of ADME properties. The various
ADME properties including TPSA, molecular weight,
number of rotatable bonds, molecular volume, number
of hydrogen bond donors, number of hydrogen bond
acceptors, miLog P, and violations of Lipinski rule
were calculated by the Mol inspiration online property
toolkit. %ABS was calculated by using the formula:
CDCl ): 20.3, 39.3, 41.9, 112.1, 112.9, 115.5, 116.2,
1
1
Anal. Calcd (%) for C H N O : C, 65.45; H, 3.05; N,
1
3
20.2, 120.8, 123.7, 124.2, 125.5, 131.5, 132.2, 143.4,
+
44.0, 169.4: MS (positive mode): m/z = 331 [M + H] .
1
8 10 4 3
6.96 Found: C, 65.37; H, 3.12; N, 16.85.
0
0
2
-(2 -Oxo-2-(p-tolyl)spiro[cyclopropane-1,3 -indolin]-3-yl)
malononitrile (8f). White solid, yield = (90%); mp 164–
%
ABS = 109 ꢀ (0.3459 TPSA) [32]. ADME prediction
ꢀ
1
1
1
8
3
65°C, IR (KBr) (νmax/cm ): 3230, 3023, 2952, 2335,
properties like %HIA, Caco-2 permeability, %PPB, and
BBB were predicted by using pre-ADMET online server
721, 1722, 1651, 1462, 1321, 1272, 1170, 1107, 1027,
ꢀ
1
1
27, 683 cm ; H-NMR (400 MHz, CDCl /TMS): δ
3
(http://preadmet.bmdrc.org/).
.97 (s, 1H, CH), 3.57 (s, 3H, CH ), 6.95–7.00 (m, 1H,
3
Structure–activity relationship studies.
The detailed
Ar–H), 7.17–7.20 (m, 2H, Ar–H), 7.39–7.44 (m, 6H,
Ar–H), 9.5 (s, 1H, –NH); C-NMR (400 MHz, CDCl3):
1
1
1
1
3
analysis of the structure of spirooxindole compounds is
envisaging that the compound exhibits equilibrium due to
enolization, where both the isomers are in dynamic
interconversion from one form to another. Here, the
indolyl nitrogen atom is adjunction point for the
continuous conjugation in the indole moiety and phenyl-
substituted cyclopropyl spiro system. In this way, nitrogen
is protecting the continuous conjugation of π-electron
density over entire molecule with its empty p orbital and
7.3, 20.2, 40.2, 41.7, 111.6, 116.9, 116.5, 117.6, 120.3,
21.5, 122.6, 123.5, 123.6, 132.4, 133.1, 142.5, 143.0,
+2
71.9: MS (positive mode): m/z = 321 [M + H] . Anal.
Calcd (%) for C H N O: C, 76.24; H, 4.38; N, 14.04
Found: C, 76.20; H, 4.35; N, 13.28.
19 13 3
0
0
2
-(2-(4-Methoxyphenyl)-2 -oxospiro[cyclopropane-1,3 -
indolin]-3-yl)malononitrile
yield = (90%); mp 171–173°C, IR (KBr) (νmax/cm ):
3
1
(
(8g).
White
solid,
ꢀ
1
2
221, 3031, 2992, 2326, 1725, 1728, 1642, 1468, 1345,
remaining SP orbitals of carbon atoms. Hence, this is
ꢀ
1
1
278, 1176, 1105, 1057, 877, 673 cm
;
H-NMR
creating two active groups –NH and –OH that are acting
as hydrogen bond donors to the active proteins of DNA
gyrase A.
400 MHz, CDCl /TMS): δ 3.87 (s, 1H, CH), 3.57 (s, 3H,
3
CH ), 6.85–6.88 (m, 2H, Ar–H), 7.18–7.25 (m, 2H,
3
Ar–H), 7.29–7.35 (m, 6H, Ar–H), 9.5 (s, 1H, –NH);
The detailed structure–activity relationship study had
revealed that active amino-acid ending groups of Asp
104, Glu 139, Tyr 50, Met 101, Val 103, Glu 141,
Arg 126, Glu 139, Tyr 50, and Phe 213 are strongly
binding with the –NH group of the spirooxindole
compounds in structure I, and Asp 104 and Trp 59
are strongly binding with the –OH group of the
1
3
C-NMR (400 MHz, CDCl ): 18.3, 19.2, 39.3, 42.7,
3
1
1
11.8, 116.2, 115.5, 116.6, 119.3, 120.8, 121.6, 123.8,
24.6, 132.9, 133.5, 143.5, 144.0, 172.9: MS (positive
+
2
mode): m/z = 316 [M + H] . Anal. Calcd (%) for
C H N O : C, 72.37; H, 4.16; N, 13.33 Found: C,
1
9 13 3 2
76.27; H, 4.21; N, 13.33.
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet

V. K. R. Avula, V. R. Chintha, S. Vallela, J. S. Anireddy, N. R. Chamarthi, and W. Rajendra
Vol 000
Figure 3. Structure–activity relationship analysis for compounds 8a–g for binding with DNA gyrase A. [Color figure can be viewed at wileyonlinelibrary.
com]
spirooxindole compounds in structure II, respectively,
and establishing ꢀ7.2 to ꢀ6.4 kcal/mole of binding
energy. This is making these molecules active and
competent to act as potent antibacterial agents as
revealed by the molecular docking and other in silico
parameters. The remaining molecular docking and
Lipinski properties are also supporting this type of
molecular interaction of the molecules with the target
proteins and supporting them to report as antibacterial
agents (Fig. 3).
Chem Soc 1973, 95, 4230; (e) Gnad, F.; Reiser, O. Chem Rev 2003,
103, 1603.
[7] (a) Kokkinos, A. M. P.; Hassila, H. Acta Chem Scand 1996,
50, 323; (b) Flann, C. J.; Overman, L. E.; Sarkar, A. K. Tetrahedron Lett
1991, 32, 6993; (c) Benson, D. A.; Karsch-Mizrachi, I.; Shanmugam, P.
Tetrahedron 2006, 62, 4342.
[
8] (a) Deng, H. P.; Wei, Y.; Shi, M. Org Lett 2011, 13, 3348;
b) Zhang, X. C.; Cao, S. H.; Wei, Y.; Shi, M. Chem Commun 2011,
7, 1548.
[9] Presset, M.; Mohanan, K.; Hamann, M.; Coquerel, Y.;
Rodriguez, J. Org Lett 2011, 13, 4124.
(
4
[
[
10] Girija, S.; Singh, Z.; Desta, Y. Chem Rev 2012, 112, 6104.
11] (a) Bonavent, G.; Causse, M.; Guitard, M.; Fraisse-Jullien,
R. Bull Soc Chim Fr 1964 2462; (b) Epstein, J. W.; Rabander, H. J.;
Fanshawe, W. J.; Hofmann, C. M.; McKenzie, T. C.; Safir, S. R.;
Osterberg, A. C.; Cosulich, D. B.; Lovell, F. M. J Med Chem 1981,
24, 481; (c) Mangelinckx, S.; De Kimpe, N. Tetrahedron Lett 2003,
44, 1771.
Acknowledgments. We acknowledge the University Grants
Commission (UGC), New Delhi, India, for providing the labora-
tory facilities at Prof. R. Nagarajan’s research laboratory, School
of Chemistry, University of Hyderabad, Hyderabad, to work
under Visiting Researcher Programme of UGC Networking
Resource Center Program.
[12] Sun, W.; Zhu, G.; Wu, C.; Hong, L.; Wang, R. Eur J Chem
2
1
3
012, 18, 6737.
[13] Albertshofer, K.; Tan, B.; Barbas, C. F. Org Lett 2012,
4, 1834.
[14] Tan, B.; Candeias, N. R.; Barbas, C. F. Nat Chem 2011,
, 473.
[
15] Chen, W. B.; Wu, Z. J.; Pei, Q. L.; Cun, L. F.; Zhang, X. M.;
Yuan, W. C. Org Lett 2010, 12, 3132.
16] Jiang, K.; Jia, Z. J.; Yin, X.; Wu, L.; Chen, Y. C. Org Lett
010, 12, 2766.
17] Bencivenni, G.; Wu, L. Y.; Mazzanti, A.; Giannichi, B.;
Pesciaioli, F.; Song, M. P.; Bartoli, G.; Melchiorre, P. Angew Chem
009, 121, 7336.
18] Duan, S. W.; Li, Y.; Liu, Y. Y.; Zou, Y. Q.; Shi, D. Q.; Xiao,
W. J. Chem Commun 2012, 48, 5160.
19] Artur Noole, N.; Sucman, S.; Mikhail, A.; Kabeshov, T.;
Kanger Fliur, Z.; Macaev, A.; Malkov, V. Eur J Chem 2012, 18,
4929.
REFERENCES AND NOTES
[
2
[
1] (a) Xia, M.; Ma, R. Z. J. Heterocyclic Chem 2014, 51, 539;
b) Cheng, D.; Ishihara, Y.; Tan, B.; Barbas, C. F. ACS Catal 2014, 4,
43; (c) Trost, B. M.; Bringley, D. A.; Zhang, T.; Cramer, N. J Am
Chem Soc 2013, 135, 16720; (d) Hanhan, N. V.; Ball-Jones, N. R.;
Tran, N. T.; Franz, A. K. Angew Chem Int Ed 2012, 51, 989; (e)
Dugal-Tessier, J.; O’Bryan, E. A.; Schroeder, T. B. H.; Cohen, D. T.;
Scheidt, K. A. Angew Chem Int Ed 2012, 51, 4963; (f) Ball-Jones,
N. R.; Badillo, J. J.; Franz, A. K. Org Biomol Chem 2012, 10, 5165;
g) Madin, A.; O’Donnell, C. J.; Oh, T.; Old, D. W.; Overman, L. E.;
Sharp, M. J. J Am Chem Soc 2005, 127, 18054.
2] (a) Hong, L.; Wang, R. Adv Synth Catal 2013, 355, 1023; (b)
Ball-Jones, N. R.; Badillo, J. J.; Franz, A. K. Org Biomol Chem 2012, 10,
165; (c) Cao, Z.-Y.; Wang, Y.-H.; Zeng, X.-P.; Zhou, J. Tetrahedron Lett
014, 55, 2571; (d) Liu, Y. L.; Wang, X.; Zhao, Y. L.; Zhu, F.; Zeng, X.
P.; Chen, L.; Wang, C. H.; Zhao, X. L.; Zhou, J. Angew Chem Int Ed
013, 52, 13735.
3] (a) Singh, G. S.; Desta, Z. Y. Chem Rev 2012, 112, 6104;
b) Ball-Jones, N. R.; Badillo, J. J.; Franz, A. K. Org Biomol Chem
012, 10, 5165; (c) Hong, L.; Wang, R. Adv Synth Catal 2013, 355,
023.
[
(
7
2
[
[
1
(
[
[
20] Artur, N.; Andrei, V.; Malkov, T. K. Synthesis 2013, 45, 2520.
21] Erin, E.; Wilson, K.; Rodriguez, X.; Brandon, L. A. Tetrahe-
[
dron 2015, 71, 5765.
[22] Rong, Z.; Changjiang, Y.; Yiyi, L.; Ruifeng, L.; Zhengjie, H. J
5
2
Org Chem 2014, 79, 10709.
[23] Wen-Jie, Q.; Ying, H.; Chao-Guo, Y. Tetrahedron 2016, 72,
5057.
[24] John, L.; Alexandra, W.; Holubec, A.; Brian, M.; Matthew, S.;
Weiss, M.; Julie, A.; Brian, D.; Doan, D.; Mohammed, F.; Jennifer, S.;
Chen, M.; Timothy, P. H. J Am Chem Soc 1999, 121, 6326.
[25] Yuan, L.; Yu-Liang, W.; Yi-Ying, Z. Asian J Chem 2015,
27, 491.
2
[
(
2
1
[
4] Yong, S. R.; Williams, M. C.; Pyne, S. G.; Ung, A. T.;
Skelton, B. W.; White, A. H.; Turner, P. Tetrahedron 2005, 61, 8120.
[26] Xiaoqiu, P.; Qingwei, L.; Zehai, L.; Xianjin, Y. Eur J Org
Chem 2016, 5937.
[27] Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew,
R. K.; Goodsell, D. S.; Olson, A. J. J Comput Chem 2009, 30, 2785.
[28] Haar, E.; Coll, J. T.; Austen, D. A.; Hsiao, H. M.; Swenson, L.;
Jain, J. Nat Struct Biol 2009, 8, 593.
[
[
5] Franke, A.; Liebigs, A. Chem 1978, 5, 717.
6] (a) Jaegli, S.; Vors, J.-P.; Neuville, L.; Zhu, J. Tetrahedron
2
2
4
010, 66, 911; (b) Wurz, R. P.; Lin, W.; Charette, A. B. Tetrahedron Lett
003, 44, 8845; (c) Brackmann, F.; de Meijere, A. Chem Rev 2007, 107,
538; (d) Yankee, E. W.; Spencer, B.; Howe, N. E.; Cram, D. J. J Am
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet

Month 2018
Synthesis, Docking, and Bioavailability of Spirooxindoles as Antibacterial Agents
[
29] Pettersen, E. F.; Goddard, T. D.; Huang, C. C. J Comput Chem
SUPPORTING INFORMATION
2
004, 25, 1605.
[
30] Zhao, Y.; Abraham, M. H.; Lee, J.; Hersey, A.; Luscombe, N.
C.; Beek, G.; Sherborne, B.; Cooper, I. Pharm Res 2002, 19, 1446.
31] Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeny, P. J.
Adv Drug Deliv Rev 1997, 23, 3.
32] Clark, D. E.; Pickett, S. D. Drug Discov 2000, 5, 49.
Additional supporting information may be found online
in the Supporting Information section at the end of the
article.
[
[
Journal of Heterocyclic Chemistry
DOI 10.1002/jhet