Synthesis, Biological Evaluation, and Molecular Docking of 1,4-Benzodioxan Derivatives as Potential Antibacterial Agents

Article abstract of DOI:10.1134/S1070363218120228

A series of novel 1,4-benzodioxan derivatives containing Schiff base are synthesized by the method of splicing active substructures. All compounds are assayed for antimicrobial activity. The preliminary results indicate that most of the products demonstrate higher antibacterial activity against Gram-negative bacteria strains than Gram-positive bacteria strains. Compounds 4d and 4m exhibit better antibacterial activity against E. coli (MIC = 0.78 and 0.17 μg/mL), respectively; compound 4g displays better antibacterial activity against P. aeruginosa (MIC = 0.78 μg/mL). Eleven common antibacterial targets are selected for molecular docking of target compounds. The results demonstrate that all target compounds have the strongest binding energy to Tyrosine-tRNA synthetase (-CDOCKER_INTERACTION_ENERGY, kcal/mol: 47.1486 and 47.3776). Therefore, it is speculated that the target compounds can be used as novel tyrosine-tRNA synthetase inhibitors.

Full text of DOI:10.1134/S1070363218120228

ISSN 1070-3632, Russian Journal of General Chemistry, 2018, Vol. 88, No. 12, pp. 2601–2610. © Pleiades Publishing, Ltd., 2018.
Synthesis, Biological Evaluation, and Molecular Docking
1,2
of 1,4-Benzodioxan Derivatives as Potential Antibacterial Agents
a
a
a
a
a,b
H.-Y. Liu , T.-R. Wang , G.-H. Sheng *, J. Qin *, and J. Sun *
a
School of Life Sciences, Shandong University of Technology, Zibo, 255049 China
b
Elion Nature Biological Technology Co., Ltd., Nanjing, 210046 China
*
e-mail: sunreiyi86@163.com
Received July 29, 2018
Revised November 13, 2018
Accepted November 13, 2018
Abstract—A series of novel 1,4-benzodioxan derivatives containing Schiff base are synthesized by the method
of splicing active substructures. All compounds are assayed for antimicrobial activity. The preliminary results
indicate that most of the products demonstrate higher antibacterial activity against Gram-negative bacteria
strains than Gram-positive bacteria strains. Compounds 4d and 4m exhibit better antibacterial activity against
E. coli (MIC = 0.78 and 0.17 μg/mL), respectively; compound 4g displays better antibacterial activity against
P. aeruginosa (MIC = 0.78 μg/mL). Eleven common antibacterial targets are selected for molecular docking of
target compounds. The results demonstrate that all target compounds have the strongest binding energy to
Tyrosine-tRNA synthetase (-CDOCKER_INTERACTION_ENERGY, kcal/mol: 47.1486 and 47.3776).
Therefore, it is speculated that the target compounds can be used as novel tyrosine-tRNA synthetase inhibitors.
Keywords: 1,4-benzodioxan derivatives, Schiff base, antimicrobial activity, molecular docking
DOI: 10.1134/S1070363218120228
INTRODUCTION
In the first step 2,3-dihydrobenzo[b][1,4]dioxine-6-car-
boxylic acids 1 were refluxed with concentrated
sulfuric acid in methanol to give methyl 2,3-di-
hydrobenzo[b][1,4]dioxine-6-carboxylate 2. Concen-
trated sulfuric acid acted there as a catalyst. In the
second step 2,3-dihydrobenzo[b][1,4]dioxine-6-carbo-
hydrazides 3 were prepared by treatment of compound
High bacteria resistance to the originally powerful
antibiotics [1] initiates a proactive effort in developing
novel antibacterial agents with excellent antimicrobial
pharmacophores.
1
,4-Benzodioxane is a type of structural moieties
2
with hydrazine hydrate (85%) in ethanol. Finally, the
that contains multiple substitution sites and can
promote the developed of a variety of derivatives. 1,4-
Benzodioxane derivatives demonstrate a wide range of
biological activities, such as anti-tumor, anti-bacterial,
anti-inflammatory, and anti-adrenergic [2–4]. Owing to
the broad spectrum of chemotherapeutic properties of
mixture of 2,3-dihydrobenzo[b][1,4]dioxine-6-carbo-
hydrazides 3 with different substituents aldehydes in
methanol was refluxed for 2 h. Upon removal of the
solvent under reduced pressure the target compounds
4
a–4s were isolated as white powders with high yields.
1
,4-benzodioxane and Schiff bases [5–10], their
Crystal structure of compound 4b. Crystals of
combination in one molecule could result in creating
potentially strong antimicrobial agents. This approach
is promoted in the current study. Molecular docking
allowed to explore the binding ability of the target
compounds with the classical antibacterial active sites.
compound 4b (CCDC: 1847855) were obtained from a
methanol solution. The perspective view of the
monomeric unit with the atomic numbering scheme is
presented in Fig. 1. The crystal structure with inter-
and intramolecular H-bonds is presented in Fig. 2. The
crystallographic data and structure refinement
parameters are listed in Table 1. Hydrogen bond
lengths and angles are listed in Table 2.
RESULTS AND DISCUSSION
The developed three steps synthetic approach to
new target compounds 4a–4s is presented in Scheme 1.
Antibacterial activity. The MIC (Minimum
inhibitory concentration, μg/mL) of compounds 4a–4s
against the bacterial strains were tested by MTT
1
The text was submitted by the authors in English.
2
Supplementary materials are available from authors.
2
601

2
602
LIU et al.
Scheme 1. Synthesis of the title compounds.
O
H N
2
O
O
H C
3
NH
O
OH
O
O
O
b
a
O
O
O
1
2
3
O
R
c
HN N
O
O
H
O
R
4a−4s
OCH3
(4d),
Br
R =
(4a),
Br (4b),
CH (4c),
(4e),
3
HO
H
(
4f),
(4g),
OH
(4h),
OCH3
(4i), H C
(4j),
3
O
O N
HO
2
CH3
OCH3
(
4n),
NO2
(4o),
(
4k),
(
4l),
(4m),
H C
3
Cl
Cl
(
4p),
Cl (4q),
(4r),
(
4s).
S
Reagents and conditions: (a) concentrated sulfuric acid, methanol, reflux; (b) hydrazinehydrate (85%), ethanol; (c) different
substituents aldehydes, methanol, refluxing.
method (Table 3). Compounds 4a–4s demonstrated
significant selectivity and high antibacterial activity.
Among those compounds 4d and 4m exhibited the
highest antibacterial activity against E. coli (MIC =
ring (4s). The compound 4c (MIC =10.21 μg/mL for E.
coli) with the methyl group located on the benzene
ring was more active than the compounds 4j (MIC =
16.25 μg/mL for E. coli) and 4n (MIC > 20 μg/mL for
E. coli) that contained butane or isobutane fragments.
The compounds 4q and 4r with Cl on the benzene ring
were more active than the compounds 4b and 4e with
Br. The compounds containing Cl or Br atom in
p-position demonstrated stronger inhibitory activity
than their analogues with o-position of the same
substituents.
0
.78 and 0.17 μg/mL), and the compound 4g was the
most active against P. aeruginosa (MIC = 0.78 μg/mL).
Activities of the tested compounds could be
correlated with their molecular structures. According
to the accumulated data (Table 3), most of compounds
demonstrated better selectivity and inhibitory activity
against Gram-negative bacteria (E. coli and P.
aeruginosa). The compounds containing the benzene
ring exhibited higher inhibitory activity than those
containing the naphthalene ring (4p) and the thiophene
Introduction of the aldehyde group in p-position of
the benzene ring promoted the inhibitory activity (4g:
MIC = 3.12 μg/mL for E. coli and MIC = 0.78 μg/mL
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

SYNTHESIS, BIOLOGICAL EVALUATION, AND MOLECULAR DOCKING
2603
Fig. 1. Molecular structure of the compound 4b with atomic numbering scheme.
Fig. 2. Crystal packing and H-bonds in the compound 4b.
for P. aeruginosa). The compound 4m with the
methoxy group in p-position of the benzene ring
exhibited higher inhibitory activity (MIC = 0.17 μg/mL
for E. coli and MIC = 1.22 μg/mL for P. aeruginosa)
than the compound 4d, and was significantly higher
than the positive control penicillin.
the designed compounds could be more potent against
E. coli Tyrosyl-tRNA synthetase (PDB code: 1VBM).
The 2D and 3D simulations of compounds 4d and
4
m with the highest binding ability to the target
protein Tyrosine-tRNA synthetase were resolved using
DS 4.5 software (Fig. 3). According to these data
(Figs. 3c, 3d) the benzyl group of compound 4m
formed the carbon hydrogen bond with HIS98 and
PHE236 of the target protein; the benzene ring formed
Pi–Pi T-shaped with His 51, and Pi-alkyl forms with
LEU227 and PRO54. The oxygen atom in 1,4-
benzodioxan formed the conventional hydrogen bond
with the THR76, and the hydrogen atom formed the
Docking study. Molecular docking was performed
for validating antibacterial target proteins interaction
with the designed compounds. The molecular
structures of the synthesized compounds were fitted
into several antibacterial target protein, including
4
1
ALM, 3S1Y, 3FY8, 2VVT, 1PFY, 4HEJ, 3G75,
HNJ, 2VAM, 1JIJ, 1VBM. The results indicated that
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

2
604
LIU et al.
Table 1. Crystallographic data for compound 4b
Parameter Value
EXPERIMENTAL
All chemicals and reagents used were of analytical
grade. The reactions were monitored by TLC on
Merck precoated silica gel GF254 plates. Melting
points (uncorrected) were determined on a Digital
Melting Point apparatus (Shenguang, Shanghai, China).
Formula
16 13 2 3
C H N O Br
Formula weight
Crystal system
Space group
a, Å
361.18
Monoclinic
P21
ESI mass spectra were measured on a Mariner System
1
5
304 mass spectrometer. H NMR spectra were
5.0735(6)
17.9043(18)
16.2456(18)
90
measured on a Bruker DPX300 spectrometer at room
b, Å
temperature using DMSO-d as a solvent and TMS as
6
an internal standard. Elemental analyses were
performed on a CHN-O-Rapid instrument, and were
within ±0.4% of the theoretical values.
c, Å
α, deg
β, deg
90
(
E)-N'-Benzylidene-2,3-dihydrobenzo[b][1,4]-
1
γ, deg
90
dioxine-6-carbohydrazide (4a). mp 181–183°C. H
NMR spectrum, δ, ppm: 11.67 s (1H); 8.44 s (1H);
.70 s (2H); 7.44–7.47 m (5H); 6.97–7.00 d (J =
V, Å
1475.7(3)
4
7
5
Z
.58 Hz, 1H); 4.39–4.33 m (4H). MS: m/z: 282.1 [M +
3
+
D
calc, g/cm
1.626
H] . Found, %: C 68.13; H 5.06; N 9.87. C H N O .
16
14
2
3
Calculated, %: C 68.07; H 5.00; N 9.92.
θ range, deg
2.3–28.3
728
(
E)-N'-(4-Bromobenzylidene)-2,3-dihydrobenzo-
F(000)
1
[
b][1,4]-6-carbohydrazide(4b). mp 244–246°C. H
Reflections collected/unique
Date/restraints/parameters
14170/6650
2989/0.044/200
0.71073
0.0855/0.1428
0.0855/0.1428
1.010
NMR spectrum, δ, ppm: 11.75 s (1H); 8.41 s (1H);
7.66 s (4H); 7.43–7.47 m (2H); 6.97–7.00 d (J =
8.4 Hz, 1H); 4.29–4.33 m (4H). MS: m/z: 360.01 [M +
–
1
Absorption coefficient, mm
+
H] . Found, %: C 53.27; H 3.59; Br, 22.17; N 7.71.
R
1
1
/wR
2
2
[I > 2σ(I)]
C H BrN O . Calculated, %: C 53.21; H 3.63; Br,
1
6
13
2
3
R
/wR
(all date)
22.12; N 7.76.
GOOF
(E)-N'-(4-Methylbenzylidene)-2,3-dihydrobenzo-
[
b][1,4]dioxine-6-carbohydrazide(4c). mp 205–207°C.
1
H NMR spectrum, δ, ppm: 11.61 s (1H); 8.40 s (1H);
carbon hydrogen bond with the THR76. The
compounds 4d and 4m could fully bind to the active
pocket of the target protein, in which the benzene ring
site was located inside the active pocket, and the 1,4-
benzodioxane site was located in the opening of the
active pocket.
7
.46–7.62 m (2H); 7.45–7.44 m (2H); 7.25–7.28 m
(2H); 6.96–6.99 d (J = 8.22 Hz, 1H); 4.29–4.32 m
(4H); 2.34–2.49 d (J = 4.2 Hz, 3H). MS: m/z: 296.12
[M + H] . Found, %: C 68.96; H 5.40; N 9.49.
+
C H N O . Calculated, %: C 68.91; H 5.44; N 9.45.
17 16 2 3
Table 2. Hydrogen bonds length and bond angles values for compound 4b
D–H···A
d(D–H), Å
0.86
d(H···A), Å
d(D···A), Å
2.961(9)
∠DHA, deg
143
2
2
1
N ···H ···O
2.33
2.24
2.48
2.59
2.45
2.57
4B
4B
4
N ···H ···O
0.86
2.953(9)
141
3T
3T
2
C ···H ···O
0.93
3.305(10)
3.213(10)
3.291(11)
3.211(9)
149
7
7
1
C ···H ···O
0.93
125
21
21
5
C ···H ···O
0.93
150
23O
23O
4
C
···H ···O
0.93
127
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

SYNTHESIS, BIOLOGICAL EVALUATION, AND MOLECULAR DOCKING
2605
Table 3. Antibacterial activity (MIC) of the synthesized compounds
MIC±SD, μg/mL
gram-negative bacteria
Escherichia coli Pseudomonas aeruginosa
gram-positive bacteria
Staphylococcus aureus Bacillus subtilis
Compound
4
a
b
c
d
e
f
12.52±1.235
7.22±0.986
10.21±1.669
0.78±0.079
10.12±1.593
>20
15.00±1.996
6.68±0.981
13.79±1.967
3.78±0.468
8.17±0.963
18.03±
>20
>20
>20
>20
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
>20
>20
12.50±1.654
12.50±1.364
>20
>20
>20
>20
g
h
i
3.12±0.997
12.58±1.596
15.32±1.779
16.25±1.489
12.58±1.566
>20
0.78±0.083
12.11±1.649
>20
>20
>20
>20
>20
12.50±1.265
12.50±1.469
>20
>20
j
12.56±1.648
13.66±1.934
>20
>20
k
l
>20
>20
>20
m
n
o
p
q
r
s
0.17±0.029
>20
1.22±0.352
>20
>20
>20
>20
>20
12.15±1.569
>20
8.08±0.978
18.71±1.679
5.56±0.966
8.12±0.987
16.97±1.689
1.89±0.647
12.50±1.349
>20
>20
>20
3.56±0.966
5.18±0.998
12.24±1.795
1.56±0.467
>20
>20
12.50±1.497
>20
12.50±1.675
>20
Penicillin
6.25±0.976
6.25±0.996
+
(
E)-N'-(3-methoxybenzylidene)-2,3-dihydro-
[M + H] . Found, %: C 53.27; H 3.60; Br, 22.16; N
benzo[b][1,4]-6-carbohydrazide (4d). mp 179–181°C.
H NMR spectrum, δ, ppm: 11.69 s (1H); 8.41 s (1H);
7.70. C H BrN O . Calculated, %: C 53.21; H 3.63;
Br, 22.12; N 7.76.
1
6
13
2
3
1
7
.40–7.47 m (2H); 7.35–7.3707 m (1H); 7.01–7.26 m
(
E)-N'-(2-Hydroxybenzylidene)-2,3-dihydro-
(
2H); 6.97–7.00 m (2H); 4.29–4.32 m (4H); 3.75–3.81
benzo[b][1,4]-6-carbohydrazide (4f). mp 176–177°C.
H NMR spectrum, δ, ppm: 11.95 s (1H), 11.34 s (1H);
.61 s (1H); 7.30–7.53 m (3H); 7.28–7.27 m (1H);
.00–7.02 m (1H); 6.90–6.95 m (2H); 4.29–4.34 m
4H). MS: m/z: 298.1 [M + H] . Found, %: C 64.47H,
4.69; N 9.34. C16
.73; N 9.39.
+
d (J = 16.44 Hz, 3H). MS: m/z: 312.11 [M + H] .
Found, %: C 65.42; H 5.11; N 8.92. C H N O .
Calculated, %: C 65.38; H 5.16; N 8.97.
1
1
7
16
2
4
8
7
(
+
(
E)-N'-(2-Bromobenzylidene)-2,3-dihydrobenzo-
1
H N O . Calculated, %: C 64.42 H
14 2 4
[
b][1,4]-6-carbohydrazide (4e). mp 232–235°C. H
4
NMR spectrum, δ, ppm: 11.94 s (1H); 8.80 s (1H);
7
7
7
.98–8.00 d (J = 4.11 Hz, 1H); 7.67–7.71 m (1H); 7.44–
.50 m (3H); 7.33–7.39 m (1H); 6.98–7.01 d (J =
.62 Hz, 1H); 4.29–4.34 m (4H). MS: m/z: 360.01
(E)-N'-(4-Formylbenzylidene)-2,3-dihydrobenzo-
[b][1,4]-6-carbohydrazide (4g). mp 330–337°C. H
NMR spectrum, δ, ppm: 11.77 s (1H); 8.46 s (1H);
1
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

2
606
LIU et al.
(b)
(
a)
(
c)
(
d)
Fig. 3. (a) The best pose of 4m (blue) obtained from the docking study in the active site of E. coil Tyrosyl-tRNA synthetase
1VBM), (b) 4d (red) And 4m (blue) in 1VBM, (c) 2D schematic presentation of compound 4m, and (d) important amino acid
(
residues associated with compound 4m. Green is the conventional hydrogen bond, cyan is the carbon hydrogen bond, and purple is
the Alkyl and Pi-Alkyl.
7
.74–8.00 m (1H); 7.71–7.79 m (2H); 7.45–7.49 m
8.33 s (1H); 7.53–7.55 d (J = 8.43 Hz, 2H); 7.42–7.45
m (2H); 6.96–6.98 d (J = 8.04 Hz, 1H); 6.82–6.85 d
(J = 8.58 Hz, 2H); 4.30 s (4H). MS: m/z: 298.1 [M +
(
4H); 6.98–7.01 d (J = 8.58 Hz, 1H); 4.31 s (4H); 3.17
+
s (1H). MS: m/z: 310.1 [M + H] . Found, %: C 65.85 H
4
4
+
.51; N 9.34. C H N O . Calculated, %: C 65.80 H
H] . Found, %: C 64.46; H 4.73; N 9.35. C H N O .
1
7
14
2
4
16 14
2
4
.55; N 9.30.
Calculated, %: C 64.42; H 4.78; N 9.39.
(
E)-N'-(4-Hydroxybenzylidene)-2,3-dihydro-
(E)-N'-(4-Methoxybenzylidene)-2,3-dihydro-
benzo[b][1,4]-6-carbohydrazide (4i). mp 185–189°C.
H NMR spectrum, δ, ppm: 11.5496 s (1H). 8.74 s
benzo[b][1,4]-6-carbohydrazide (4h). mp 247–250°C.
H NMR spectrum, δ, ppm: 11.47 s (1H); 9.89 s (1H);
1
1
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

SYNTHESIS, BIOLOGICAL EVALUATION, AND MOLECULAR DOCKING
2607
Table 4. Molecular docking values for compounds 4a–4s
CDOCKER_INTERACTION_ENERGY, kcal/mol
-
Comp. no.
1
VBM
1KZE
19.0786
19.9851
20.818
1PFY
26.0215
31.4072
33.2328
35.7799
25.46
2VVT
31.9964
30.9021
30.8796
35.5791
35.6387
33.5681
32.1584
32.8772
34.7772
32.3345
36.1728
38.2088
33.0106
33.2413
30.8815
40.087
3FY8
3SLY
4
4
a
39.3609
42.9604
43.1962
47.1486
42.4443
40.1377
44.8369
43.1038
42.6011
37.896
34.9746
36.069
35.6504
37.957
b
4
c
39.0212
39.5175
38.6448
36.7413
32.5522
34.9377
31.6437
33.3973
42.296
36.1243
37.6954
34.221
4
d
24.2729
20.6997
21.5187
20.3402
22.6902
20.228
4
e
4
f
29.1245
29.394
35.0902
35.4947
34.7404
39.2301
34.4477
37.6678
38.5191
41.0415
31.2961
38.8345
38.4059
32.7445
34.5612
28.605
4
4
g
h
36.752
4
i
38.8938
29.3292
39.5657
35.8983
29.2344
27.0826
27.9109
30.7128
32.4531
32.856
4
j
20.2057
23.9406
26.8925
19.3733
22.626
4
k
43.8237
41.4125
47.3776
40.2734
45.8463
43.0021
39.9589
43.0277
37.6805
4ALM
4
l
42.4505
36.2841
37.7435
41.2824
43.1369
37.5451
35.2899
32.7496
1HNJ
4
m
4
n
o
p
q
4
22.2428
21.4705
19.774
4
4
31.2672
35.4361
30.6372
3G75
4
r
21.1262
21.7116
2VAM
4
s
30.4133
4HEJ
Comp. no.
1JIJ
4
4
a
20.3747
28.8793
32.9551
30.0192
29.7274
24.2476
26.9871
37.3166
36.4327
31.5603
33.3979
31.9442
37.0251
25.6653
28.0438
35.0272
22.5643
28.4941
25.026
31.9594
36.0918
30.658
32.5264
35.8462
35.1048
35.9255
34.9509
36.8656
37.2149
35.7176
34.1819
34.251
37.6327
37.2929
36.8286
39.7354
39.8847
40.1922
35.5737
37.5847
38.6838
37.8953
40.6257
40.5534
44.7868
38.5031
37.364
28.1742
34.1572
31.7989
34.8809
34.2174
31.2649
32.8235
33.7495
37.7495
31.2935
36.1148
35.89
37.1694
38.5207
37.6191
41.89
b
4
c
4
d
29.9581
33.9133
34.4743
35.1196
29.9219
32.105
4
e
40.1967
39.5337
37.6679
38.8959
38.3272
31.804
4
f
4
4
g
h
4
i
4
j
31.9174
34.6051
37.5439
34.8603
34.6221
27.3347
32.3559
28.0774
34.2285
27.408
4
k
36.685
38.9517
40.554
4
l
39.2061
36.1478
31
4
m
37.5197
30.8043
35.5181
32.4042
31.8476
32.8022
29.8731
43.2117
34.7123
37.3882
41.6013
37.4253
39.1652
21.7116
4
n
o
p
q
4
38.1462
39.5794
35.1469
34.3075
32.5096
4
4
38.9022
36.9761
38.8953
34.0752
4
r
4
s
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

2
608
LIU et al.
(
(
1H); 7.64–7.67 d (J = 11.4 Hz, 2H); 7.43–7.46 m
7.46–7.49 m (2H); 6.99–7.02 d (J = 8.96 Hz, 1H); 4.30–
4.34 m (4H). MS: m/z: 327.09 [M + H] . Found, %: C
+
2H); 6.96–7.03 m (3H); 3.81 s (3H); 4.31 s (4H). MS:
+
m/z: 312.11 [M + H] . Found, %: C 65.43; H 5.12; N
58.76; H 3.93; N 12.80. C H N O . Calculated, %: C
16
13
3
5
8
.93. C H N O . Calculated, %: C 65.38; H 5.16; N 8.97.
58.72; H 4.00; N 12.84.
17
16
2
4
(
E)-2,3-Dihydro-N'-pentylidenebenzo[b][1,4]-
(E)-2,3-Dihydro-N'-[(naphthalen-1-yl)methlene]-
benzo[b][1,4]dioxine-6-carbohydrazide (4p). mp 262–
265°C. H NMR spectrum, δ, ppm: 11.77 s (1H); 9.09
1
dioxine-6-carbohydrazide (4j). mp 147–149°C. H
NMR spectrum, δ, ppm: 7.71 s (1H); 7.36–7.39 m
1
(
2H); 6.93–6.95 m (1H); 4.27–4.31 m (4H); 2.21–2.28
s (1H); 8.84–8.87 d (J = 11.4 Hz, 1H); 8.01–8.04 d
(J = 8.04 Hz, 2H); 7.91–7.93 d (J = 6.93 Hz, 1H); 7.59–
7.67 m (3H); 7.50–7.53 d (J = 11.4 Hz, 2H); 7.01–7.03
d (J = 8.04 Hz, 1H); 4.33 s (4H). MS: m/z: 332.12
m (2H); 1.40–1.52 m (2H); 1.29–1.38 m (2H); 0.88–
+
0
6
6
.93 m (3H). MS: m/z: 262.13 [M + H] . Found, %: C
4.15; H 6.88; N 10.63. C H N O . Calculated, %: C
14
18
2
3
+
4.10; H 6.92; N 10.68.
[M + H] . Found, %: C 72.33; H 4.81; N 8.46.
C H N O . Calculated, %: C 72.28; H 4.85; N 8.43.
2
0
16
2
3
(
E)-N'-(2-Nitrobenzylidene)-2,3-dihydrobenzo[b]-
1
(
E)-N'-(4-Chlorobenzylidene)-2,3-dihydrobenzo-
[
1,4]-6-carbohydrazide (4k). mp 221–223°C.
NMR spectrum, δ, ppm: 12.03 s (1H); 8.85 s (1H);
.06–8.13 m (2H); 7.70–7.70 m (1H); 7.65–7.67 m
1H); 7.47–7.50 d (J = 8.4 Hz, 2H); 6.98–7.01 d (J =
.22 Hz, 1H); 4.31–4.32 m (4H). MS: m/z: 327.09
H
1
[
b][1,4]-6-carbohydrazide (4q). mp 234–236°C. H
NMR spectrum, δ, ppm: 11.69 s (1H); 8.43 s (1H);
.75–7.79 m (2H); 7.43–7.47 m (2H); 7.27–7.33 m
2H); 6.97–7.00 d (J = 8.4 Hz, 1H); 4.31–4.33 m (4H).
MS: m/z: 316.06 [M + H] . Found, %: C 60.74; H 4.08;
Cl 11.14; N 8.80. C H ClN O . Calculated, %: C
8
(
8
[
7
(
+
+
M + H] . Found, %: C 58.76; H 3.97; N 12.81.
C H N O . Calculated, %: C 58.77; H 4.04; N 12.80.
16 13
2
3
1
6
13
3
5
6
0.67; H 4.14; Cl 11.19; N 8.84.
E)-N'-(2-Chlorobenzylidene)-2,3-dihydrobenzo-
(
E)-N'-(5-Chloro-2-hydroxybenzylidene)-2,3-di-
(
hydrobenzo[b][1,4]-6-carbohydrazide (4l). mp 194–
1
1
[b][1,4]-6-carbohydrazide (4r). mp 185–186°C. H
NMR spectrum, δ, ppm: 11.91 s (1H); 8.85 s (1H);
1
96°C. H NMR spectrum, δ, ppm: 12.04 s (1H). 8.59
s (1H); 7.64 s (1H); 7.47–7.50 d (J = 8.43 Hz, 2H);
.28–7.32 m (1H); 6.93–7.01 m (2H); 4.31–4.31 m
5H). MS: m/z: 332.06 [M + H] . Found, %: C 57.79;
H 3.90; Cl 10.61; N 8.48. C H ClN O . Calculated,
8
8
.01 s (1H); 7.43–7.55 m (5H); 6.98–7.01 d (J =
7
(
+
.22 Hz, 1H); 4.31–4.33 m (4H). MS: m/z: 316.06
+
[
M + H] . Found, %: C 60.72; H 4.09; Cl 11.15; N
1
6
13
2
4
8
.87. C H ClN O . Calculated, %: C 60.67; H 4.14;
16 13 2 3
%
: C 57.75; H 3.94; Cl 10.65; N 8.42.
E)-N'-(4-(Methoxymethyl)benzylidene)-2,3-di-
hydrobenzo[b][1,4]-6-carbohydrazide (4m). mp 201–
Cl 11.19; N 8.84.
E)-2,3-Dihydro-N'-[(thiophen-2-yl)methylene]-
benzo[b][1,4]dioxine-6-carbohydrazide (4s). mp 183–
(
(
1
2
04°C. H NMR spectrum, δ, ppm: 11.55 s (1H), 8.38
s (1H); 7.64–7.67 d (J = 8.86 Hz, 2H); 7.43–7.48 m
2H); 7.08–7.12 d (J = 10.41 Hz, 2H); 6.96–6.99 d (J =
.43 Hz, 1H); 4.31 s (4H); 3.32 s (3H). MS: m/z:
26.13 [M + H] . Found, %: C 66.31; H 5.52; N 8.63.
1
1
87°C. H NMR spectrum, δ, ppm: 11.63 s (1H); 8.65
s (1H); 7.65–7.67 d (J = 5.02 Hz, 1H); 7.41–7.45 m
3H); 7.12–7.15 m (1H); 6.96–6.99 d (J = 8.04 Hz,
(
8
3
(
+
+
1H); 4.30 s (4H). MS: m/z: 288.06 [M + H] . Found
(
%): C 58.38; H 4.14; N 9.76. C H N O S.
14 12 2 3
C H N O . Calculated, %: C 66.25; H 5.58; N 8.58.
1
8
18
2
4
Calculated, %: C 58.32; H 4.20; N 9.72.
(
E)-2,3-Dihydro-N'-(-3-methylbutylidene)benzo-
X-Ray crystallography. Single crystal X-ray dif-
fraction data were collected on a Bruker D-8 venture
diffractometer at 293 K. The X-ray generator was
[
b][1,4]dioxine-6-carbohydrazide (4n). mp 148–151°C.
H NMR spectrum, δ, ppm: 11.19 s (1H). 7.65–7.66 d
J = 5.13 Hz, 1H); 7.36–7.39 m (2H); 6.92–6.95 d (J =
1
(
8
2
operated at 50 KV and 35 mA using MoK radiation
α
.07 Hz, 1H); 4.26–4.31 m (4H); 3.32 s (1H); 2.49–
(
λ = 0.71,073 Å). The data were collected using
.51 m (2H); 1.01–1.07 m (6H). MS: m/z: 262.13 [M +
SMART software package and reduced by SAINT-
PLUS. The packages SADABS and XPREP were used
for empirical absorption correction and determination
of the space group. The crystal structure was resolved
by direct methods using SIR92 and refined by full-
matrix least-squares method using SHELXL97
[11, 12]. All non-hydrogen atoms were refined
+
H] . Found, %: C 64.16; H 6.88; N 10.63. C H N O .
1
4
18
2
3
Calculated, %: C 64.10; H 6.92; N 10.68.
(E)-N'-(4-Nitrobenzylidene)-2,3-dihydrobenzo[b]-
1
[
1,4]-6-carbohydrazide (4o). mp 264–269°C. H NMR
spectrum, δ, ppm: 11.98 s (1H), 8.53 s (1H); 8.29–8.32
d (J = 8.79 Hz, 2H); 7.96–7.99 d (J = 8.58 Hz, 2H);
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

SYNTHESIS, BIOLOGICAL EVALUATION, AND MOLECULAR DOCKING
2609
anisotropically and hydrogen atoms have been refined
in the riding mode on their carrier atoms wherever
applicable.
protein, and the polar hydrogens and the Kollman-
united charges were added to the proteins.
The molecular docking procedure was performed
by using CDocker protocol for receptor–ligand
interactions section of Discovery Studio 4.5 (Accelrys
Software Inc, San Diego, CA). Initially both a ligand
and a receptor were pretreated. For ligand preparation,
the 3D structures of all synthesized compounds were
generated with ChemBioOffice 2010 and optimized
with MMFF94 method. For enzyme preparation,
hydrogen atoms were added, pH of the protein was in
the range of 7.25–7.65.
Antibacterial assay. Antibacterial activity of the
synthesized compounds was tested against Bacillus
subtilis, Escherichia coli, Pseudomonas aeruginosa,
and Staphylococcus aureus using LB medium (Luria-
Bertani medium: yeast extract 5.0 g, peptone 10.0 g,
sodium chloride 5.0 g, distilled water 1000 mL).
Minimum inhibitory concentration of the tested
compounds was determined by the colorimetric
method using the dye MTT. Activity of the reference
compound penicillin was determined under identical
conditions. A stock solution of synthesized compounds
The binding poses of active compounds were selected
through CDocker interaction energy. Docking algorithm
utilized: CDocker algorithm; all protein SDB Radius:
(
1000 µmol/mL) in DMSO were prepared, and graded
quantities of the test compounds were incorporated in
the specified quantity of sterilized liquid LB medium.
Drug stocks were formulated in DMSO and then the
compounds were diluted in media to final working
concentrations of 25, 12.5, 6.25, 3.125, 1.5625 μg/mL.
A specified amount of the medium containing the
compound was added to a 96-well plate. Then, a
1
0; scoring function: CDOC-KER interaction energy;
rigid receptor: PDB code 4ALM, 3SIY, 3FY8, 2VVT,
PFY, 4HEJ, 3G75, 1HNJ, 2VAM, 1JIJ, 1VBM;
1
flexible ligand docking: YES; cluster analysis of
docking poses: ten optimal poses were retained.
CONCLUSIONS
bacterial suspension containing the concentration of ca
5
1
0 cfu/mL was added to a 96-well plate and incubated
New 1,4-benzodioxane derivatives containing
Schiff base are synthesized and tested for their
antimicrobial activity. The preliminary results indicate
that most of the compounds demonstrate higher
antibacterial activity against gram-negative than gram-
positive bacteria strains. Molecular docking with
eleven common antibacterial activity targets and the
sites of action of the target compounds are screened.
These indicate that the target compounds have the
strongest binding ability to Tyrosine-tRNA synthetase.
The binding energy of compounds 4d and compound
at 37°C for 24 h. Afterwards, PBS (10 μL) containing
MTT (4 mg/mL) was added to each well. Incubation
was continued at 37°C for 4 h. The content of each
well was removed, and 150 μL of DMSO was added to
extract the dye. The optical density was measured with
an ELISA plate reader at 492 nm.
Molecular docking study. Automated docking
studies were carried out using Discovery Studio
(
version 2.5) as implemented through the graphical
user interface DS-CDocker protocal [13]. Three-
dimensional structures of the studied compounds were
constructed using Chem. 3D ultra 11.0 software
4
m to E. coli Tyrosine-tRNA synthetase is the highest.
According to the docking simulation, the target
compounds can be completely embedded in the active
site with the phenyl ring located inside the active
pocket, and 1,4-benzodioxane is located at the opening
of the active pocket.
[Chemical Structure Drawing Standard; Cambridge
Soft corporation, USA (2009)]. The crystal structure
complexes of FabI (PDB code: 4ALM), β-Lactamase
(
PDB code: 3SIY), Dihydrofolate reductas (PDB code:
3
2
FY8), Glutamate recemase (MurI) (PDB code:
VVT), Methionyl-tRNA synthetase (1PFY), Bacterial
ACKNOWLEDGMENTS
thymidylate kinase (PDB code: 4HEJ), Bacterial DNA
gyrase (PDB code: 3G75), the ATP binding site of
FabH (PDB code:1HNJ), FtsZ (PDB code: 2VAM ), S.
aureus Tyrosyl-tRNA synthetase (PDB code: 1JIJ),
and E.coil Tyrosyl-tRNA synthetase (PDB code:
This work was financed by Natural Science Founda-
tion of Shandong Province (grant no. ZR2018BH040
and Natural Science Foundation of Shandong Province,
(
grant no. ZR2016BL03).
CONFLICT OF INTEREST
No conflict of interest was declared by the authors.
1
VBM) were retrieved from the RCSB Protein Data
Bank (http://www.rcsb.org/pdb/home/home.do). The
bound water and ligands were eliminated from the
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018

2
610
LIU et al.
7. Desai, S.B., Desai, P.B., and Desai, K.R., Heterocycl.
REFERENCES
Commun., 2001, vol. 7, p. 83. doi 10.1515/HC
1
. Fischbach, M.A. and Walsh, C.T. Science, 2009,
vol. 325, p. 1089. doi 10.1126/science.1176667
8
9
. Samadhiya, S. and Halve, A., Orient J. Chem., 2001,
vol. 17, p. 119.
. Kabeer, A.S., Baseer, M.A., and Mote, N.A., Asian. J.
Chem., 2001, vol. 13, p. 496.
2
3
4
5
6
. Khalilullah, H., Ahsan, M.J., Hedaitullah, M., Khan, S.,
and Ahmed, B., Mini Rev. Med. Chem., 2012, vol. 12,
p. 789. doi 10.2174/138955712801264800
. Ahmed, B., Ahsan, M.J., Khan, S., Khalilullah, H., Anti-
Infective Agents, 2012, vol. 10, p. 142. doi
1
0. El-Masry, A.H., Fahmy, H.H., and Abdelwahed, S.H.A.,
Molecules, 2000, vol. 5, p. 1429. doi 10.3390/51201429
1
0.2174/2211362611208020142
11. Oliva, M.A., Trambaiolo, D., and Löwe, J., J. Mol.
Biol., 2007, vol. 373, p. 1229. doi 10.1016/
j.jmb.2007.08.056
. Song, X., Yang, Y., Zhao, J., and Chen, Y., Chem.
Pharm. Bull., 2014, vol. 62, p. 1110. doi 10.1248/
cpb.c14-00485
. Yang, F., Han, J., Wang, Y., Chen, F., Chinese J. Appl.
Chemi., 2015, vol. 32, p. 392. doi 10.11944/j.issn.1000-
12. Sheldrick, G.M., SHELXS 97. Program for Crystal
Structure Determinations, University of Göttingen,
Germany, 1997.
0
518.2015.04.140286
13. Wu, G., Robertson, D.H., Brooks, C.L. III, and Vieth, M.,
J. Comput. Chem., 2003, vol. 24, p. 1549. doi 10.1002/
jcc.10306
. More, P.G., Bhalvankar, R.B., and Patter, S.C.J., Indian
Chem. Soc., 2001, vol. 78, p. 474.
RUSSIAN JOURNAL OF GENERAL CHEMISTRY Vol. 88 No. 12 2018