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Polycyclic Aromatic Compounds
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Synthesis, Molecular Docking, and DFT Studies
of Some New 2,5-Disubstituted Benzoxazoles as
Potential Antimicrobial and Cytotoxic Agents
Meryem Erol , Ismail Celik , Ebru Uzunhisarcikli & Gulcan Kuyucuklu
To cite this article: Meryem Erol , Ismail Celik , Ebru Uzunhisarcikli & Gulcan Kuyucuklu (2020):
Synthesis, Molecular Docking, and DFT Studies of Some New 2,5-Disubstituted Benzoxazoles
as Potential Antimicrobial and Cytotoxic Agents, Polycyclic Aromatic Compounds, DOI:
10.1080/10406638.2020.1802305
To link to this article: https://doi.org/10.1080/10406638.2020.1802305
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Published online: 06 Aug 2020.
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Synthesis, Molecular Docking, and DFT Studies of Some New
2,5-Disubstituted Benzoxazoles as Potential Antimicrobial
and Cytotoxic Agents
Meryem Erol
a
, Ismail Celik
a,b
, Ebru Uzunhisarcikli
c
, and Gulcan Kuyucuklu
d
a
Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey;
b
Faculty of
Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey;
c
Faculty of Pharmacy,
Department of Pharmacology, Erciyes University, Kayseri, Turkey;
d
Faculty of Medicine, Department of
Medical Microbiology, Trakya University, Edirne, Turkey
ABSTRACT
In this study, a total of 17 piece 2,5-disubstituted benzoxazole derivatives
were synthesized, 2 of which were not original, their antimicrobial activities
were determined using microdilution method and their in vitro cytotoxic
activities were investigated on MCF-7 and A549 cells by MTT test. When
the activity results are examined, although the antibacterial effects of ben-
zoxazole derivatives are weaker than standard drugs; 3N13 and 3N19
against Candida albicans isolate showed the closest activity to fluconazole
with MIC: 16 mg/ml. The cytotoxicity test was measured at a concentration
of 100 mM and a 24-h incubation period. The results showed that the com-
pounds had weak activities against two cell lines. Molecular docking stud-
ies of synthesized compounds were performed on sterol 14a-demethylase
protein (CYP51) and protein-ligand interactions of 3N13, the most effective
derivative against C. albicans isolate, were showed (PDB: 5TZ1). Estimated
ADME profiles of compounds were calculated and also 3N13’s were calcu-
lated HUMO-LUMO energies, molecular electrostatic potential analysis, and
geometric optimization parameters with 6-311 Gþ(d,p) base set using
DFT/B3LYP theory, and the results were displayed.
ARTICLE HISTORY
Received 9 June 2020
Accepted 7 July 2020
KEYWORDS
ADME prediction;
antimicrobial activity;
benzoxazole; cytotoxicity;
molecular docking
Introduction
Infectious diseases caused by bacteria and fungi are still one of the most important threats to
public health, despite huge advances in pharmaceutical and medicinal chemistry. Conditions such
as the use of medicines in the wrong dose or irrelevant indication, misdiagnosis and the wrong
treatment methods followed, prescriptions written only to eliminate the symptoms or the patients
abandoning their treatment make it difficult to fight infectious disease.
1–3
In fact, recent studies
showing mortality and morbidity rates increase the anxiety for infection cases, and microbial
resistance developed by bacteria and fungi is added to this concern.
4,5
Antimicrobial resistance is
currently responsible for more than 700,000 deaths annually worldwide, and by 2050 it is esti-
mated that it will exceed an estimated economic cost of $100 million annually and over 10 mil-
lion deaths.
6
CONTACT Meryem Erol eczacimeryem@gmail.com Faculty of Pharmacy, Department of Pharmaceutical Chemistry,
Erciyes University, Kayseri 38039, Turkey.
Supplemental data for this article is available online at https://doi.org/10.1080/10406638.2020.1802305.
ß2020 Taylor & Francis Group, LLC
POLYCYCLIC AROMATIC COMPOUNDS
https://doi.org/10.1080/10406638.2020.1802305
Widespread drug resistance, especially fluconazole-resistant Candida albicans are among the
most important problems of our age.
7–9
C. albicans is the most common type of Candida that
causes bloodstream infections and has a frequency of 37–70% worldwide.
10
Prevention and treat-
ment of Candida infections generally requires long-term drug use, fluconazole is an antifungal
the most commonly used triazole class for this purpose. It has been reported that both long and
repeated use of fluconazole and exposure to other antifungals cause resistance problems in C.
albicans isolates.
11
It is stated that many mechanisms responsible for azole resistance play a role
in C. albicans strains. These mechanisms decrease in the accumulation of the drug in the cell can
be listed as a change in lanosterol demethylase and ergosterol biosynthesis, which is the target of
the drug.
12–14
Another important disease, cancer is a complex disease that manifests itself as a result of
uncontrolled proliferation of cells as a result of environmental and/or genetic factors, showing
spread to surrounding organs and tissues and thus causing secondary tumors by metastasis.
15,16
It
is considered the first leading cause of death in economically developed countries and the second
leading cause of death in developing countries.
17
It is estimated that in 2018, 18.1 million new
cancer cases and 9.6 million deaths worldwide.
18
It is predicted that by 2030, 21.7 million new
cases will occur and 13 million people will die due to cancer due to the increase in the world
population and average life expectancy.
19
It has become one of the most important health prob-
lems of our age due to the increase in the number of people who are caught and dying of cancer,
the length of the treatment period and the many side effects of the drugs used.
Benzoxazole ring system is an analogue of adenine and guanine bases in the structure of
nucleic acids and is considered as an important ring system for easy interaction especially in anti-
microbial activities.
20
Some natural/semi-synthetic antibiotics carrying benzoxazole ring in the
structure have been found to exhibit good activity against various microorganisms.
21,22
In add-
ition, UK-1 and L-697.661 containing benzoxazole ring system show anticancer activity
(Figure 1).
23–25
In recent studies, besides the antimicrobial
26
and anticancer
27
activities of benzoxazole ring
system; it has been reported to have many effects such as antiviral,
25
antiparkinsonian,
28
Figure 1. Benzoxazole derivatives exhibiting antimicrobial and anticancer activity.
2 M. EROL ET AL.
antihistamine,
29
antihypertensive,
30
antioxidant,
31
anticonvulsant,
32
anti-inflammatory,
33
herbici-
dal,
34
and antialzheimer.
35
Researches on the benzoxazole ring system focus on derivatives of the ring substituted from
the second and fifth positions. In previous studies, some derivatives containing p-(substituted)-
phenyl/benzyl) at position 2- and 6-membered rings attached to the amide side chain at position
5 were synthesized, and promising results were obtained by examining their antimicrobial and
anticancer effects.
36–38
Based on this data, within the scope of this study, some new compounds
whose general structure is 2-(p-(substituted)phenyl/benzyl)-5-(2-substituted acetamido)benzoxa-
zole were synthesized (Figure 2) and their structures were illuminated by
1
H-NMR and
13
C-NMR
spectroscopy and HRMS. In addition, antimicrobial activities of all compounds against various
Gram (þ), Gram (-) bacteria and fungi and in vitro cytotoxic activities on MCF-7 and A549 cell
line were determined. Estimation of ADME profiles were calculated and molecular docking stud-
ies were performed with Schr€
odinger software. In addition, molecular electrostatic potential
(MEP) analysis, geometric optimization, and molecular reactivity analysis (HOMO-LUMO) of
3N13, which one of the compounds with the highest antifungal activity, were performed.
Experimental details
Chemistry
Chemicals and solvents were purchased from Sigma Aldrich, Merck, Riedel de Haen, and Fluka
and used without further purification. For the TLC, 60 F
254
coated aluminum plates (Merck) were
used and the UV light at 254 and 366 nm wavelength was used for the detection of stains. The
TLC mobile phase composition used in each step was demonstrated in the respective method.
Silica gel 60 (Merck) with a particle size of 230–400 mesh was used in column chromatography.
Soluble compounds in the small mobile phase (3–5 ml) were applied by dissolving in the mobile
phase of the column. The resulting compounds, which were insoluble in the mobile phase, were
applied solidly by adsorption of silica gel. Melting points were determined by Electrothermal
9100 (Varian, Palo Alto, CA) instrument and the results were given without correction.
1
H and
13
C NMR spectra were analyzed on a Varian Mercury 400 MHz High Performance Digital FT-
NMR spectrometer (Palo Alto, CA, USA). Tetramethylsilane was used as an internal standard
substance, and dimethylsulfoxide-d
6
(DMSO-d
6
) was used as a solvent. M þ1 peaks were deter-
mined by Shimadzu LC/MS ITTOF system (Shimadzu, Tokyo, Japan). The mass spectra (high-
resolution mass spectrometry [HRMS]) of all of the synthesized compounds showed molecular
ion [M þH]
þ
peaks in agreement with their molecular formula.
For biological activity experiments, dimethyl sulfoxide (DMSO, Cat. A36720100) was pur-
chased from Applichem. Ham’s F-12 Medium (Cat. N4888), Dulbecco’s Modified Eagle’s Medium
(DMEM, cat. D5796), fetal bovine serum (FBS, Cat. F2442), L-glutamine solution (Cat. G7513),
penicillin-streptomycin (Cat. P4333), and trypsin-EDTA (Cat. T3924) were purchased from
Figure 2. Designed 2,5-disubstituted benzoxazoles derivatives.
POLYCYCLIC AROMATIC COMPOUNDS 3
Sigma-Aldrich. MTT was purchased from RPI. A549 (American Type Culture Collection
[ATCC], CCL-185
TM
) cell line and MCF-7 (ATCC, HTB-22
TM
) cell line purchased from ATCC.
General procedure for the synthesis of 5-amino-2-(p-(substituted)phenyl/benzyl)benzoxa-
zole (M1 series)
One millimoles of 2,4-diaminophenol dihydrochloride and 1 mmol of p-substituted phenyl acetic
acid or p-substituted benzoic acid were stirred at 160 to 190 C for about 2 h at 25 g of polyphos-
phoric acid (PPA) catalyst. At the end of the reaction, the reaction contents were poured over
ice, and the solution was neutralized with 10% NaOH. The resulting precipitate was filtered,
washed with distilled water, dissolved in boiling ethanol with 0.2 g charcoal, and filtered off.
Crystallization was achieved by dissolving the precipitate in ethanol and adding distilled water.
The crude compound was obtained by filtration and drying the filtrate at room temperature.
During the synthesis studies, ethyl acetate: n-hexane (1:1) TLC mobile phase was used to monitor
the reaction end and to check the purity of the compound.
General procedure for the synthesis 5-(2-chloroacetamido)-2-(p-(substituted)phenyl/benzyl)
benzoxazole (M2 series)
One millimoles of 2-(p-(substituted)phenyl/benzyl)-5-aminobenzoxazole were dissolved in 20 ml
of diethyl ether and 2 mmol of NaHCO
3
in 10 ml of distilled water. One millimoles of chloroace-
tyl chloride was slowly added while the ether and water phase were stirred in the ice bath in the
magnetic stirrer. Continue mixing overnight. At the end of the reaction, the reaction medium
was filtered, the distilled was washed with water, dissolved in ethanol by heating. The solution
was precipitated slowly by the addition of distilled water. The crude compounds were filtered off
and dried at room temperature. During the synthesis studies, ethyl acetate: n-hexane (1:1) TLC
mobile phase was used to monitor the reaction end and to check the purity of the compound.
General procedure for the synthesis 2-(p-(substituted)phenyl/benzyl)-5-(2-substituted acet-
amido)benzoxazole (3N1–3N19)
One millimoles of 2-(p-(substituted)phenyl/benzyl)-5-(2-chloroacetamido)benzoxazole was reacted
with 1 mmol of p-substituted piperazine/piperidine derivatives in the presence of dimethylforma-
mide and triethylamine for 1 day at room temperature. The mixture was stirred at room tempera-
ture for 24 h. At the end of the reaction time, the mixture was poured over ice, the same volume
of 10% NaOH solution was added. Extraction was carried out twice with chloroform. The chloro-
formed phases were collected, and the solvent was evaporated, and the residue was purified by
column chromatography. The solvent of the resultant compound fractions collected after column
chromatography was evaporated, the residue was dissolved in chloroform and precipitated with
petroleum ether. The precipitate was filtered off and the resulting compounds are dried at room
temperature. During the synthesis studies, TLC/column mobile phase of ethyl acetate: n-hexane
(1:3) was used to monitor the end of the reaction, purify the resulting compound and purify the
resulting compound by column chromatography. All compounds are original except for 3M14
and 3M17. The structures of them were supported by spectral data. The
1
H-NMR,
13
C-NMR, and
HRMS spectrometry results agree with those of the proposed structures.
2-(p-chlorophenyl)-5-(2-(4-phenylpiperidine-1-yl)acetamido)benzoxazole (3N1): Yield 45%,
Mp: 180–182 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.89 (s, H, -NH), 8.24 8.15 (m, 3H,
Ar-H), 7.70 (dd, J¼20.9, 8.3 Hz, 4H, Ar-H), 7.29 (d, J¼6.5 Hz, 4H, Ar-H), 7.18 (t, J¼6.8 Hz,
1H, Ar-H), 3.19 (s, 2H, -CH
2
), 3.01 (d, J¼11.1 Hz, 2H, -CH
2
), 2.30 (t, J¼11.2 Hz, 2H, -CH
2
),
1.85 1.73 (m, 5H,
2
CH
2
and -CH).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 169.13, 162.45,
146.94, 146.71, 142.01, 137.15, 136.46, 129.96, 129.43, 128.79, 127.21, 126.48, 125.73, 118.69,
4 M. EROL ET AL.
111.17, 110.83, 62.68, 54.36, 41.84, 33.39. HRMS (m/z): [M þH]
þ
Calcd for C
26
H
24
ClN
3
O
2
:
446.15570; found: 446.16533.
2-(p-chlorophenyl)-5-(2-(4-bromopiperidine-1-yl)acetamido)benzoxazole (3N2): Yield 40%,
Mp: 200–202 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.89 (s, 1H, NH), 8.22 8.11 (m, 3H,
Ar-H), 7.73 (d, J¼8.8 Hz, 1H, Ar-H), 7.72 7.63 (m, 2H, Ar-H), 7.63 (dd, J¼8.8, 2.1 Hz, 1H,
Ar-H), 4.42 (s, 1H, -CH-Br), 3.16 (s, 2H, -CH
2
), 2.76 (dd, J¼11.2, 5.7 Hz, 2H, -CH
2
), 2.44 (d,
J¼10.8 Hz, 2H, -CH
2
), 2.17 (dq, J¼8.1, 4.0, 3.6 Hz, 2H, -CH
2
), 2.04 (tt, J¼8.3, 3.7 Hz, 2H,
-CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 168.88, 162.44, 146.95, 141.98, 137.14, 136.40,
129.94, 129.43, 125.72, 118.75, 111.13, 110.92, 61.99, 52.23, 51.83, 36.30. HRMS (m/z): [M þH]
þ
Calcd for C
20
H
19
ClBrN
3
O
2
: 448.03492; found: 448.04424.
2-(p-fluorophenyl)-5-(2-(4-benzoylpiperazine-1-yl)acetamido)benzoxazole (3N3): Yield 65%,
Mp: 185–187 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.99 (s, 1H, -NH), 8.26 8.21 (m, 3H,
Ar-H), 8.17 (d, J¼2.1 Hz, 1H, Ar-H), 7.73 (d, J¼8.8 Hz, 1H, Ar-H), 7.62 7.57 (m, 1H, Ar-H),
7.47 7.43 (m, 4H, Ar-H), 7.41 7.37 (m, 2H, Ar-H), 3.72 (s, 4H,
2
-CH
2
), 3.22 (s, 2H, -CH
2
),
2.62 (s, 6H,
3
-CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 169.42, 168.62, 165.93, 163.44,
162.58, 146.96, 142.04, 136.36, 130.39, 130.30, 129.97, 128.90, 127.36, 123.54, 123.51, 118.47,
117.14, 116.91, 111.10, 110.86, 61.83, 53.81, 46.50. HRMS (m/z): [M þH]
þ
Calcd for
C
26
H
23
FN
4
O
3
: 459.17542; found: 459.18541.
2-(p-fluorophenyl)-5-(2-(4-(p-nitrophenylpiperazine-1-yl)acetamido)benzoxazole (3N4):
Yield 75%, Mp: 218–220 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 10.01 (s, 1H, -NH),
8.24 8.19 (m, 4H, Ar-H), 8.05 (d, J¼7.3 Hz, 2H, Ar-H), 7.73 (d, J¼8.8 Hz, 1H, Ar-H),
7.63 7.60 (m, 1H, Ar-H), 7.46 (d, J¼6.9 Hz, 2H, Ar-H), 7.03 (d, J¼2.3 Hz, 1H, Ar-H), 3.54 (d,
J¼4.9 Hz, 3H, -CH
2
and -CH), 3.36 (s, 2H, -CH
2
), 2.68 (d, J¼5.0 Hz, 5H,
2
-CH
2
and -CH).
13
C-
NMR dppm (100 MHz, DMSO-d
6
): 168.61, 165.91, 163.42, 162.56, 155.15, 146.95, 142.05, 137.29,
136.35, 130.35, 130.26, 126.17, 123.51, 123.48, 118.41, 117.08, 116.86, 113.06, 111.08, 110.82,
61.83, 52.66, 46.70. HRMS (m/z): [M þH]
þ
Calcd for C
25
H
22
FN
5
O
4
: 476.16558;
found: 476.17435.
2-(p-fluorophenyl)-5-(2-(4-(p-methoxyphenylpiperazine-1-yl)acetamido)benzoxazole (3N6):
Yield 60%, Mp: 188–190 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.97 (s, 1H, -NH), 8.24 (dd,
J¼8.7, 5.5 Hz, 2H, Ar-H), 8.19 (d, J¼2.0 Hz, 1H, Ar-H), 7.73 (d, J¼8.8 Hz, 1H, Ar-H), 7.61 (dd,
J¼8.8, 2.1 Hz, 1H, Ar-H), 7.46 (t, J¼8.8 Hz, 2H, Ar-H), 6.90 (d, J¼9.1 Hz, 2H, Ar-H), 6.81 (d,
J¼9.1 Hz, 2H, Ar-H), 3.68 (s, 3H, -CH
3
), 3.22 (s, 2H, -CH
2
), 3.09 (t, J¼4.9 Hz, 4H,
2
-CH
2
), 2.68
(t, J¼4.8 Hz, 4H,
2
-CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 168.77, 162.59, 153.34, 146.96,
145.87, 142.06, 136.39, 130.41, 130.31, 118.43, 117.85, 117.15, 116.93, 114.69, 111.12, 110.79,
62.24, 55.62, 53.33, 49.93. HRMS (m/z): [M þH]
þ
Calcd for C
26
H
25
FN
4
O
3
: 461.19107;
found: 461.19892.
2-(p-fluorophenyl)-5-(2-(4-bromopiperidine-1-yl)acetamido)benzoxazole (3N7): Yield 45%,
Mp: 175–177 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.90 (s, 1H, -NH), 8.24 (ddd, J¼8.8,
5.5, 2.6 Hz, 2H, Ar-H), 8.18 (d, J¼2.1 Hz, 1H, Ar-H), 7.72 (d, J¼8.8 Hz, 1H, Ar-H), 7.61 (dd,
J¼8.8, 2.1 Hz, 1H, Ar-H), 7.46 (dd, J¼10.0, 7.7Hz, 2H, Ar-H), 4.42 (s, 1H, -CH-Br), 3.16 (s,
2H, -CH
2
), 2.75 (dd, J¼11.7, 5.9 Hz, 2H, -CH
2
), 2.44 (s, 2H, -CH
2
), 2.23 2.12 (m, 2H, -CH
2
),
2.02 (dtd, J¼12.7, 8.5, 3.4 Hz, 2H, -CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 168.79,
165.91, 163.42, 162.56, 146.95, 142.03, 136.31, 130.37, 130.28, 123.53, 123.50, 118.49, 117.11,
116.89, 111.06, 110.87, 61.92, 52.21, 51.75, 36.23. HRMS (m/z): [M þH]
þ
Calcd for
C
20
H
19
FBrN
3
O
2
: 432.06447; found: 432.07381.
2-(p-fluorophenyl)-5-(2-(4-phenylpiperidine-1-il)acetamido)benzoxazole (3N8): Yield 40%,
Mp: 173–175 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.94 (s, 1H, -NH), 8.29 8.19 (m, 3H,
Ar-H), 7.73 (d, J¼8.8 Hz, 1H, Ar-H), 7.64 (dd, J¼8.9, 2.0 Hz, 1H, Ar-H), 7.46 (t, J¼8.8 Hz, 2H,
Ar-H), 7.29 (d, J¼6.6 Hz, 4H, Ar-H), 7.19 (ddd, J¼8.5, 5.6, 2.2 Hz, 1H, Ar-H), 3.36 (s, 1H,
-CH), 3.19 (s, 2H, -CH
2
), 3.00 (dd, J¼11.4, 3.9 Hz, 2H, -CH
2
), 2.28 (td, J¼11.5, 2.7 Hz, 2H,
POLYCYCLIC AROMATIC COMPOUNDS 5
-CH
2
), 1.89 1.74 (m, 3H, -CH
2
and -CH), 1.77 1.70 (m, 1H, -CH).
13
C-NMR dppm
(100 MHz, DMSO-d
6
): 169.09, 165.92, 163.43, 162.57, 146.95, 146.70, 142.06, 136.38, 130.38,
130.29, 128.78, 127.21, 126.48, 123.55, 123.52, 118.44, 117.13, 116.91, 111.09, 110.80, 62.66, 54.36,
41.83, 33.38. HRMS (m/z): [M þH]
þ
Calcd for C
26
H
24
FN
3
O
2
: 430.18526; found: 430.19385.
2-(p-chlorobenzyl)-5-(2-(4-(p-nitrophenylpiperazine-1-yl)acetamido)benzoxazole (3N9):
Yield 75%, Mp: 214–216 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.94 (s, 1H, -NH), 8.06 (d,
J¼9.1 Hz, 3H, Ar-H), 7.63 7.50 (m, 2H, Ar-H), 7.46 7.41 (m, 1H, Ar-H), 7.41 (s, 3H, Ar-H),
7.04 (d, J¼9.2 Hz, 2H, Ar-H), 4.34 (s, 2H, -CH
2
), 3.57 3.51 (m, 4H,
2
-CH
2
), 3.23 (s, 2H, -CH
2
),
2.66 (t, J¼5.0 Hz, 4H,
2
-CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 168.55, 166.18, 155.17,
147.06, 141.39, 137.29, 135.89, 134.63, 132.27, 131.47, 129.07, 126.20, 117.82, 113.11, 110.78,
110.74, 61.80, 52.65, 46.71, 33.84. HRMS (m/z): [M þH]
þ
Calcd for C
26
H
24
ClN
5
O
4
: 506.15168;
found: 506.16164.
2-(p-chlorobenzyl)-5-(2-(4-(p-methoxyphenylpiperazine-1-yl)acetamido)benzoxazole (3N10):
Yield 65%, Mp:192–194 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.90 (s, 1H, -NH), 8.07 (d,
J¼2.0 Hz, 1H, Ar-H), 7.59 (d, J¼8.8 Hz, 1H, Ar-H), 7.53 (dd, J¼8.8, 2.1 Hz, 1H, Ar-H), 7.41 (d,
J¼1.2 Hz, 4H, Ar-H), 6.88 (d, J¼2.7 Hz, 2H, Ar-H), 6.81 (d, J¼9.0 Hz, 2H, Ar-H), 4.34 (s, 2H,
-CH
2
), 3.67 (s, 3H, -CH
3
), 3.20 (s, 2H, -CH
2
), 3.08 (s, 3H, -CH
2
and -CH), 2.66 (t, J¼4.9 Hz,
5H,
2
-CH
2
and -CH).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 168.67, 166.17, 153.33, 147.04,
145.85, 141.39, 135.92, 134.63, 132.26, 131.47, 129.07, 117.84, 117.78, 114.68, 110.76, 110.69,
62.21, 55.61, 53.31, 49.91, 33.84. HRMS (m/z): [M þH]
þ
Calcd for C
27
H
27
ClN
4
O
3
: 491.17717;
found: 491.18699.
2-(p-chlorobenzyl)-5-(2-(4-bromopiperidine-1-yl)acetamido)benzoxazole (3N11): Yield 50%,
Mp: 210–212 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.84 (s, 1H, -NH), 8.05 (d, J¼2.0 Hz,
1H, Ar-H), 7.59 (d, J¼8.8 Hz, 1H, Ar-H), 7.53 (dd, J¼8.8, 2.0 Hz, 1H, Ar-H), 7.41 (d, J¼1.7 Hz,
4H, Ar-H), 4.33 (s, 2H, -CH
2
), 3.13 (s, 2H, -CH
2
), 2.73 (d, J¼5.7 Hz, 1H, -CH), 2.42 (s, 2H,
-CH
2
), 2.19 2.13 (m, 3H, -CH
2
and -CH), 2.01 (dd, J¼8.7, 4.1 Hz, 2H, -CH
2
).
13
C-NMR dppm
(100 MHz, DMSO-d
6
): 168.77, 166.15, 147.06, 141.37, 135.85, 134.63, 132.27, 131.45, 129.06,
117.89, 110.79, 110.72, 61.94, 52.22, 51.81, 40.42, 36.26, 33.85. HRMS (m/z): [M þH]
þ
Calcd for
C
21
H
21
ClBrN
3
O
2
: 462.05057; found: 462.06008.
2-(p-fluorobenzyl)-5-(2-(4-(p-methoxyphenylpiperazine-1-yl)acetamido)benzoxazole (3N13):
Yield 55%, Mp: 183–185 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.89 (s, 1H, -NH), 8.07 (s,
1H, Ar-H), 7.59 (d, J¼8.7 Hz, 1H, Ar-H), 7.53 (d, J¼8.9 Hz, 1H, Ar-H), 7.46 7.39 (m, 2H, Ar-
H), 7.18 (t, J¼8.7 Hz, 2H, Ar-H), 6.89 (d, J¼8.4 Hz, 2H, Ar-H), 6.81 (d, J¼8.7 Hz, 2H, Ar-H),
4.32 (s, 2H, -CH
2
), 3.68 (s, 3H, -CH
3
), 3.20 (s, 2H, -CH
2
), 3.08 (t, J¼5.0 Hz, 4H,
2
-CH
2
), 2.66 (s,
2H, -CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 168.66, 166.43, 162.98, 160.57, 153.33,
147.04, 145.86, 141.42, 135.90, 131.80, 131.77, 131.54, 131.46, 117.84, 117.75, 115.98, 115.77,
114.68, 110.75, 110.69, 62.21, 55.61, 53.32, 49.91, 33.73. HRMS (m/z): [M þH]
þ
Calcd for
C
27
H
27
FN
4
O
3
: 475.20672; found: 475.21304.
2-(p-fluorobenzyl)-5-(2-(4-bromopiperidine-1-yl)acetamido)benzoxazole (3N14): Yield 55%,
Mp: 210–212 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.81 (s, 1H, -NH), 8.05 (d, J¼2.1 Hz,
1H, Ar-H), 7.62 7.49 (m, 2H, Ar-H), 7.46 7.37 (m, 2H, Ar-H), 7.23 7.12 (m, 2H, Ar-H),
4.41 (s, 1H, -CH-Br), 3.13 (s, 2H, -CH
2
), 2.79 2.71 (m, 2H, -CH
2
), 2.48 2.38 (m, 2H, -CH
2
),
2.21 2.12 (m, 2H, -CH
2
), 2.01 (dtd, J¼12.9, 8.9, 3.7 Hz, 2H, -CH
2
).
13
C-NMR dppm
(100 MHz, DMSO-d
6
): 168.73, 166.41, 162.98, 160.57, 147.07, 141.40, 135.83, 131.79, 131.76,
131.53, 131.45, 117.85, 117.74, 115.98, 115.77, 110.80, 110.71, 61.91, 52.21, 51.79, 36.24, 33.73.
HRMS (m/z): [M þH]
þ
Calcd for C
21
H
21
FBrN
3
O
2
: 446.08012; found: 446.08756.
2-(p-methylbenzyl)-5-(2-(4-(p-nitrophenylpiperazine-1-yl)acetamido)benzoxazole (3N15):
Yield 65%, Mp: 212–214 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.91 (s, 1H, -NH),
8.07 8.03 (m, 3H, Ar-H), 7.57 7.51 (m, 2H, Ar-H), 7.24 (d, J¼7.8 Hz, 2H, Ar-H), 7.15 (d,
J¼7.8 Hz, 2H, Ar-H), 7.05 7.02 (m, 2H, Ar-H), 4.25 (s, 2H, -CH
2
), 3.53 (d, J¼5.1 Hz, 4H,
6 M. EROL ET AL.
-CH
2
), 3.32 (s, 1H, -CH), 2.67 (d, J¼4.8 Hz, 4H,
2
-CH
2
), 2.27 (s, 3H, -CH
3
).
13
C-NMR dppm
(100 MHz, DMSO-d
6
): 168.82, 164.15, 157.21, 148.85, 143.78, 141.14, 136.19, 136.26, 130.38,
128.69, 127.71, 123.35, 118.23, 115.78, 113.52, 110.47, 61.83, 56.82, 52.67, 46.72, 21.63. HRMS (m/
z): [M þH]
þ
Calcd for C
27
H
27
N
5
O
4
: 486.20630; found: 486.21560.
2-(p-methylbenzyl)-5-(2-(4-bromopiperidine-1-yl)acetamido)benzoxazole (3N17): Yield 40%,
Mp: 224–226 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): d9.82 (s, 1H, -NH), 8.05 (t, J ¼2.1 Hz,
1H, Ar-H), 7.60 7.48 (m, 2H, Ar-H), 7.24 (d, J ¼8.0 Hz, 2H, Ar-H), 7.15 (d, J ¼7.8 Hz, 2H, Ar-
H), 4.41 (s, 1H, -CH-Br), 4.25 (s, 2H, -CH
2
), 3.35 3.28 (m, 1H, -CH), 2.74 (d, J ¼11.7 Hz, 2H,
-CH
2
), 2.43 (q, J ¼9.4 Hz, 2H, -CH
2
), 2.27 (s, 3H, -CH
3
), 2.17 (dt, J ¼15.2, 4.0 Hz, 2H, -CH
2
),
2.10 1.94 (m, 2H, -CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 167.82, 164.15, 148.58,
143.51, 143.47, 132.21, 130.63, 128.95, 123.33, 117.67, 112.48, 110.79, 62.31, 52.83, 50.87, 42.52,
36.26, 21.69. HRMS (m/z): [M þH]
þ
Calcd for C
22
H
24
BrN
3
O
2
: 442.10519; found: 442.11418.
2-(p-bromobenzyl)-5-(2-(4-(p-nitrophenylpiperazine-1-yl)acetamido)benzoxazole (3N18):
Yield 55%, Mp: 220–222 C.
1
H-NMR dppm (400 MHz, DMSO-d
6
): 9.94 (s, 1H, -NH), 8.07 (s,
3H, Ar-H), 7.63 7.49 (m, 4H, Ar-H), 7.34 (dd, J¼8.5, 2.2 Hz, 2H, Ar-H), 7.07 7.00 (m, 2H,
Ar-H), 4.32 (s, 2H, -CH
2
), 3.56 3.52 (m, 4H,
2
-CH
2
), 3.22 (s, 2H, -CH
2
), 2.70 2.63 (m, 4H,
2
-CH
2
).
13
C-NMR dppm (100 MHz, DMSO-d
6
): 167.25, 162.82, 156.91, 147.85, 143.11, 138.45,
136.71, 134.37, 129.98, 128.45, 126.17, 125.71, 118.15, 112.12, 110.95, 110.51, 61.93, 56.85, 52.67,
46.73. HRMS (m/z): [M þH]
þ
Calcd for C
26
H
24
BrN
5
O
4
: 550.10117; found: 550.10965.
Biological part
Antimicrobial evaluation
Antimicrobial activity determinations of benzoxazole derivatives were determined by in vitro
microdilution technique. Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC
29213, Escherichia coli ATCC 25922, Enterococcus faecalis ATCC 29212, C. albicans ATCC 10231
standard strains and clinical isolates of these microorganisms known to be resistant to various
antimicrobial drugs were used. Antimicrobial susceptibility testing was performed through
Clinical and Laboratory Standards Institute (CLSI) M100-S25 and CLSI M27-A3 directions.
39,40
The synthesized result was prepared by DMSO for the stock solutions of the compounds. First,
microorganisms were passaged by single colony cultivation method for purity and viability con-
trol. Bacteria were incubated on SDA plates at 24 C for 24 h and fungus at 35 C for 24–48 h at
37 C. The resulting synthesized compounds were diluted in 96-well microplates in liquid
medium (Mueller Hinton Broth [MHB] or RPMI-1640) to give concentrations of 1024, 512, 256,
128, 64, 32, 16, and 8 lg/ml. Reference antimicrobial drugs were diluted in liquid media (MHB
or RPMI-1640) in 96-well microplates to achieve concentrations of 16, 8, 4, 2, 1, 0.5, 0.25, and
0.125 lg/ml. A bacterial susceptibility test was performed at the MHB feeder. Bacterial suspen-
sions to be used in the susceptibility test were prepared at a density of 10
6
cfu/ml, diluted with
fresh broth from overnight culture at a density of 0.5 McFarland (10
8
cfu/ml). The bacterial sus-
pension at a concentration of 10
6
cfu/ml was inoculated in 10 ll of wells containing 0.1 ml of
diluted compounds. After inoculation, there are 10
5
cfu/ml bacteria in the wells. The microplates
were incubated at 35 C for 24 h. Fungal susceptibility testing was performed in RPMI-1640
medium buffered with pH 7 MOPS containing L-glutamine. For inoculation, the yeast suspension
adjusted to a McFarland 0.5 concentration (10
6
cfu/ml) was diluted 1/100, followed by 1/20 dilu-
tion and inoculated to 0.9 ml in wells containing 1 ml of diluted compounds. After inoculation,
there are 5 10
2
cfu/ml yeast in the wells. Microplates were incubated at 35 C for 24–48 h. Each
stage of the experiment was repeated thrice. The amount of substance in the previous well from
the first well with reproduction after incubation was determined as the minimum inhibitory con-
centration (MIC) value.
POLYCYCLIC AROMATIC COMPOUNDS 7
Cell culture and cell proliferation assay
The effects of 3N1–3N19 on the proliferation of A549 and MCF-7 cells were determined by
MTT assay. A549 and MCF-7 cells cultured with Ham’s F-12 and DMEM respectively which are
contain with FBS 10%, L-glutamine 1%, 100 U/ml penicillin and 100 lg/ml streptomycin. The cells
were grown to 80% confluence at 37 C and humidified atmosphere with CO
2
5%. When
cells reached approximately 80% confluence, we detached cells with 0.25% trypsin-EDTA. The
cells were centrifuged with the Universal 320 R (Hettich, Zentrifugen, 1406 Germany) at
1000 rpm for 5 min at 24 C. A549 cells (12,500 cells/well) and MCF-7 cells (10,000 cells/well)
were planted in 96-well plates in a final volume of 100 mL medium. When cells reached log
growth phase 24 h later from seeding to plate, cells were treated with 3N1–3N19 at 100 mM con-
centrations. The cells were incubated with MTT solution (5 mg/ml) in medium for 4 h at 37 C.
Viable cells convert the MTT to formazan, which generates a blue-purple color after dissolving in
100 mL DMSO. The absorbance at 570 nm was the measured by microplate reader.
41–44
Computational and theoretical details
Molecular docking
Molecular docking studies of compounds Maestro 11.5. program was carried out using.
45
Crystal
structure of sterol 14-alpha demethylase (CYP51) from C. albicans in complex with the tetrazole-
based antifungal drug candidate VT1161 (PDB ID: 5TZ1 at 2.00 Å resolution) were imported
from protein data bank (https://www.rcsb.org/). Protein preparation was done using the Protein
Preparation Wizard, the water molecules in the protein were deleted during preparation, and
hydrogen atoms were added. The energy of the compound was minimized using the OPLS3 force
field. Ligands were prepared with LigPrep using the OPLS3 force field. Receptor Grid Generation
creation program was run by clicking any atom of the ligand and the default grid box was pre-
pared. Ligand was attached to the grid box made of protein using standard precision. The results
were given as Docking score, Glide gscore, and Glide emodel values.
DFT/B3LYP calculations
All theoretical calculations were made using the Gaussian 09 package program.
46
Using the DFT/
B3LYP method and 6-311 Gþ(d,p) base set; HOMO-LUMO energies of 3N13 and other elec-
tronic parameters obtained from these energies (ionization potential [IP], electronegativity, elec-
trophilic index, nucleophilic index, chemical potential obtained from these energies etc. electronic
parameters), MEP analysis, and geometry optimization were obtained. The results were shown
using the GaussView 6 program.
47
Theoretical ADME predictions
To evaluate ADME profiles of compounds, some physicochemical parameters such as logP, TPSA,
nrotb, molecular weight, and hydrogen bond donor-acceptor number were calculated using the
Molinspiration software program.
48
Drug-likeness scores were calculated using the Molsoft program.
49
Results and discussion
Chemistry
In this study, a new sequence of 2-(p-(substituted)phenyl/benzyl)-5-(2-substituted acetamido)ben-
zoxazole (3N1–3N19) was synthesized using the three-step procedure given in the literature as
8 M. EROL ET AL.
shown in Scheme 1.
26,50–53
The compounds were obtained by introducing various substituents to
the para position of the phenyl/benzyl group at position 2 and to the fourth position of the
piperazine and piperidine ring at the end of the amide side chain at position 5. For the M1 series,
p-substituted benzoic acid or p-substituted phenyl acetic acid was heated with PPA and 2,4-dia-
minophenol and cyclization of the benzoxazole ring was achieved. Then, the benzoxazole ring
with the amine group at its fifth position was treated with 2-chloroacetyl chloride to form the
amide side chain (M2 series). In the last step, the final compounds were prepared by treating
them with piperazine or piperidine derivatives (3N1–3N19). During the synthesis processes, the
reaction medium was checked by TLC and the compounds were purified by column chromatog-
raphy as specified in the synthesis methods. All compounds are original except for 3N16 and
3N19. Their structures were confirmed by HRMS and
1
H-NMR and
13
C-NMR spectroscopy.
Melting points of the synthesized structures were determined and uncorrected. The list of synthe-
sized compounds (Supporting Information Table S1) and their physical and spectral data were
reported in the experimental section (see also Supplementary Information).
According to the spectroscopic data of the final compounds, in the
1
H-NMR spectra of the com-
pounds 3N1–3N19, the signal of the NH protons appeared at 10.01–9.82 ppm as singlet bands.
Also, aromatic protons were between 6.81 and 8.29ppm and aliphatic protons were between 0.98
and 4.42 ppm. Besides
13
C-NMR spectra of the compounds were appropriate with their structures
and HRMS of the compounds showed a [M þH]
þ
peak, in agreement with their formula.
Biological assay
Antimicrobial evaluation
Antimicrobial activities of all newly synthesized benzoxazole derivates (3N1–3N19) were tested
against S. aureus ATCC 29213, E. faecalis ATCC 29212, P. aeruginosa ATCC 27853, E. coli
ATCC 25922, C. albicans ATCC 10231, and their isolates. As reference drug, ampicillin, vanco-
mycin, gentamicin, ciprofloxacin, cefotaxime, fluconazole, and amphotericin B were used. The
MIC values were determined by microdilution method according to the guidelines of CLSI. The
data on the antimicrobial activity of the compounds and the reference drugs as MIC (mg/ml)
Scheme 1. Synthesis of target benzoxazole compounds (3N1–3N19)
POLYCYCLIC AROMATIC COMPOUNDS 9
values were given in Table 1.3N16 and 3N19 were previously synthesized in another publication
and their antimycobacterial effects were evaluated.
53
In this study, when the antimicrobial effects of the synthesized compounds were analyzed as
MIC values, they were found in the range of 16–256 mg/ml. Compounds showed weak effect
against S. aureus,E. coli, MRSA, and E. coli isolate with 256 mg/ml and it was determined that the
difference in the structure of the compounds did not make any difference in the effect. While it
shows effect against E. faecalis and P. aeruginosa with 128 mg/ml; it was found effective against
VREF between 128 and 256 mg/ml and against P. aeruginosa isolate between 64 and 128 mg/ml.
When the general structure of the compounds was examined, it was observed that those with a
phenyl group at the second position of the benzoxazole ring against VREF were more effective
than those with the benzyl group, while 3N9 was more effective against the P. aeruginosa isolate
than other derivatives. Derivatives, while C. albicans showed activity between 64 and 128 mg/ml,
against C. albicans isolate showed promising activity with 16–128 mg/ml. While 3N13 shows an
activity very close to fluconazole, when the general structure of the compounds is examined, it
was observed that those carrying benzyl group at the second position of the benzoxazole ring are
much more antifungal effective than the derivatives carrying the phenyl group. These promising
results showed that drug-resistant C. albicans could be the leading compounds to find new anti-
fungal candidates.
Effects of the molecules (3N1–3N19) on the cell viability by MTT assay
MTT method, which is a cytotoxicity method based on the measurement of metabolic activity, is
frequently used in the evaluation of cell viability, multiply of living cells and cytotoxic effects of
chemicals. It primarily measures the activity of dehydrogenases found in mitochondria and deter-
mines macrophage mediated cytotoxicity by evaluating the ratio of living/growing cells. Since the
tetrazolium ring is opened only in metabolically active cells as a result of the activity of mito-
chondrial dehydrogenases, only living cells can be identified by this method. MTT is actively
taken into the cell and converted to formazan products by a mitochondria-dependent reaction.
Since these substances cannot pass through the intact cell membrane, they accumulate inside the
cells. When a suitable solvent such as DMSO is added, these substances are released from the cell
and can be easily measured colorimetrically. Since only living cells can reduce MTT, the severity
of the reduced MTT is proportional to the blue-purple color formed and is an indicator of cell
viability. This method is suitable for use in cell culture systems with relatively high levels of mito-
chondrial activity.
54
All synthesized derivates were tested for cytotoxic activity against MCF-7 (human breast
adenocarcinoma) and A549 (human alveolar basal epithelium) cell lines by MTT analysis.
Cytotoxicity was measured at a dose of 100 mM and 24 h incubation time. Cytotoxicity results
against these two cell lines are given in Table 2. The results showed that the compounds had
weak activities against two cell lines. As a result of the best activity, 3N16 reduced viability to
80.13% in A549 cells, while 3N15 MCF-7 reduced viability to 81.9%. Compounds generally
showed higher activity against the MCF-7 cell line. In both cell lines, those with benzyl group at
position 2 of the benzoxazole ring showed higher activity than those with the phenyl group.
However, those carrying bromine at the fourth position of the benzyl group showed
lower activity.
Molecular docking study
The benzoxazole derivatives especially 3N13 and 3N19 were showed very close activity to the ref-
erence drug fluconazole. As mentioned in the introduction, resistance mechanism against flucon-
azole in C. albicans; the decrease in the accumulation of the drug in the cell can be listed as a
10 M. EROL ET AL.
Table 1. In vitro antimicrobial MIC values (lg/ml) of synthesized compounds (3N1–3N19) and reference drugs.
Compound
S. aureus
ATCC 29213
S. aureus
isolate
E. faecalis
ATCC 29212
E. faecalis
isolate
E. coli
ATCC 25922
E. coli
isolate
P. aeruginosa
ATCC 27853
P. aeruginosa
isolate
C. albicans
ATCC 10231
C. albicans
isolate
3N1 256 256 128 128 256 256 128 128 128 128
3N2 256 128 128 128 256 256 128 128 128 128
3N3 256 256 128 128 256 256 128 128 64 128
3N4 256 256 128 128 256 256 128 128 128 128
3N6 256 256 128 128 256 256 128 128 128 64
3N7 256 256 128 128 256 256 128 128 128 64
3N8 256 256 128 256 256 256 128 128 128 32
3N9 256 256 128 256 256 256 128 64 128 32
3N10 256 256 128 256 256 256 128 128 128 64
3N11 256 256 128 128 256 256 128 128 64 64
3N13 256 256 128 256 256 256 128 128 128 16
3N14 256 256 128 128 256 256 128 128 64 64
3N15 256 256 128 256 256 256 128 128 128 64
3N16 256 256 128 256 256 256 128 128 128 64
3N17 256 256 128 128 256 256 128 128 128 64
3N18 256 256 128 256 256 256 128 128 128 64
3N19 256 256 128 256 256 256 128 128 128 16
Ampicillin 2 >16 2 >16 8 >16 ––––
Vancomycin 2 2 1 8 –– – – – –
Gentamycin 0.25 >16 ––0.5 >8 0.5 >8––
Ciprofloxacin 0.5 >16 2 >4 0.0156 >2 0.125 >2––
Cefotaxime 1 >16 ––0.125 >88 –––
Fluconazole ––– – ––– –0.125 >4
Amphotericin B ––– – ––– – 0.5 0.5
Bold value signifies MIC value closest to the reference drug.
E. coli isolate is resistant to ciprofloxacin. It contains a Broad Spectrum b-Lactamase Enzyme (ESBL) and is resistant to oxyiminobetalactam antibiotics. P. aeruginosa isolate is resistant to
ciprofloxacin and ampicillin. E. faecalis isolate is resistant to vancomycin (VREF). Also, it is resistant to ampicillin and ciprofloxacin. S. aureus isolate is MRSA (resistant to all beta lactam
antibiotics). It is also sensitive to vancomycin, resistant to gentamycin, and resistant to ciprofloxacin.
POLYCYCLIC AROMATIC COMPOUNDS 11
change in lanosterol demethylase (Erg11p) and ergosterol biosynthesis, which is the target of the
drug. That is why we focused on sterol 14a-demethylase (CYP51) protein (PDB: 5TZ1). The cal-
culated Docking score of all compounds was given in Table 3 with Glide gscore and Glide emo-
del. Accordingly, a moderate relationship emerged between the scores was obtained and the
antifungal effect.
Based on the antifungal activity results, 2D and 3D interactions of 3N13, one of the most
effective compounds against C. albicans isolate, were shown in Figure 3. While 3N13 did not
form any hydrogen bond in active site; it formed hydrophobic bonds with amino acids such as
LEU121, PHE380, ILE379, SER378, HIE377, PHE233, PHE228, PHE126, and PRO230.
In silico ADME prediction
In the process of drug discovery and development, molecules are asked to show high biological
activity with low toxicity. Early prediction of ADME parameters has been shown to greatly reduce
the rate of pharmacokinetic failure in clinical phases during the design phase. ADME parameters
can be estimated by in silico methods using the molecular structure. Therefore, in silico studies
allow us to learn about the possibility of a compound being a potentially good drug. It is increas-
ingly accepted to predict ADME parameters in cases where numerous compounds are screened
for ADME or access to physical samples is limited.
Calculated for 3N1–3N19; some physicochemical parameters such as log P, TPSA, nrotb,
molecular weight, volume, number of hydrogen bond transceivers are given in Table 4. According
Table 2. Percent live cell presence values from 100 mM concentration.
Comp.
MCF-7 A549
Comp.
MCF-7 A549
% Vitality % Vitality % Vitality % Vitality
3N1 92.3 100.95 3N13 90.8 82.33
3N2 93.8 109.15 3N14 83.1 94.32
3N3 89.9 106.31 3N15 81.9 85.49
3N4 94.4 123.66 3N16 86.9 80.13
3N6 87.2 105.36 3N17 88.4 87.38
3N7 93.2 90.54 3N18 95.0 99.37
3N8 91.7 89.59 3N19 96.7 93.38
3N9 89.3 90.85 Control 100.0 100.00
3N10 83.4 100.00 DMSO control 85.2 93.38
3N11 90.8 99.05
Table 3. Calculated Docking score, Glide gscore, and Glide emodel values of 3N1–3N19.
Compound Docking score Glide gscore Glide emodel
3N1 –9.597 –9.712 –96.881
3N2 –7.922 –8.275 –82.741
3N3 –9.765 –10.064 –91.856
3N4 –8.488 –8.700 –81.037
3N6 –9.160 –9.449 –86.115
3N7 –8.715 –9.068 –82.983
3N8 –9.571 –9.686 –88.161
3N9 –8.710 –8.921 –90.655
3N10 –9.263 –9.552 –87.586
3N11 –8.873 –9.226 –92.731
3N13 –8.147 –8.436 –83.711
3N14 –8.776 –9.129 –88.754
3N15 –8.325 –8.537 –89.312
3N16 –8.808 –8.932 –90.522
3N17 –9.039 –9.392 –89.706
3N18 –8.867 –9.078 –96.523
3N19 –9.210 –9.344 –91.557
12 M. EROL ET AL.
to the five rules of Lipinski, the molecule should be logP 5, molecular weight 500, the number
of hydrogen bond receptors 10, and the number of hydrogen bond donors 5. According to
this rule, an orally active drug should either comply with all or violate at most one. All compounds
except 3N9,3N18,and3N19 comply with Lipinski rule. The absorption percentage (%ABS) was
calculated using the formula %ABS ¼109 –(0.345 TPSA) and the compounds show a good
absorption profile in the range of 71.73–88.86%.
55
Compounds with zero or negative values are not
considered drug-like candidates, but 3N1–3N19 generally showed a good drug-likeness score. But
compounds bearing the p-nitrophenylpiperazine in the amide side chain of the benzoxazole ring
and the p-substituted benzyl group at position 2 showed a low drug similarity score.
Molecular reactivity analyses
All molecules have the highest occupied molecular orbital HOMO filled with electrons and the
lowest unoccupied molecular orbital LUMO unfilled with electrons. HOMO and LUMO molecu-
lar orbitals play a role in determining the molecular properties of the molecule such as optical
and electronic properties, chemical reactivity and stability, biological activity resulting from inter-
molecular charge transfer, chemical hardness, and chemical softness. HOMO energy is defined as
the ability of the molecule to give electrons, LUMO energy is the ability of the molecule to
Figure 3. Two-dimensional and 3D interaction between 3N13 with CYP51 (5TZ1) active site.
Table 4. Calculated ADME parameters (3N1–3N19).
Comp.
LogP
5 TPSA –%ABS –
MW
500
nON
10
nOHNH
5
nviolations
1 nrotb –Volume –
Drug-likeness
score
3N1 6.35 58.37 88.86 445.95 5 1 1 5 395.96 1.41
3N2 5.00 58.37 88.86 448.75 5 1 1 4 342.44 1.13
3N3 3.82 78.68 81.85 458.49 7 1 0 5 402.30 1.26
3N4 4.91 107.43 71.93 475.48 9 1 0 6 406.65 0.67
3N6 5.01 70.84 84.56 460.51 7 1 1 6 408.86 0.86
3N7 4.49 58.37 88.86 432.29 5 1 0 4 333.84 1.03
3N8 5.83 58.37 88.86 429.50 5 1 1 5 387.36 1.32
3N9 5.71 107.43 71.93 505.93 9 1 2 7 432.06 0.92
3N10 5.80 70.84 84.56 490.99 7 1 1 7 434.27 1.16
3N11 5.29 58.37 88.86 462.77 5 1 1 5 359.24 1.28
3N13 5.29 70.84 84.56 474.54 7 1 1 7 425.66 1.05
3N14 4.77 58.37 88.86 446.32 5 1 0 5 350.64 1.18
3N15 5.48 107.43 71.93 485.54 9 1 1 7 435.08 0.52
3N16 5.68 61.61 87.74 458.54 6 1 1 6 416.68 0.86
3N17 5.06 58.37 88.86 442.36 5 1 1 5 362.27 0.80
3N18 5.84 107.43 71.93 550.41 9 1 2 7 436.41 0.65
3N19 6.56 61.61 87.74 539.86 6 1 2 6 426.61 0.81
Bold values signifies compounds that do not comply with the Lipinski rule.
MW: molecular weight; TPSA: topological polar surface area; %ABS: percentage absorption; NROTB: number of rotatable bonds;
nON: number of hydrogen acceptors; nOHNH: number of hydrogen donors; LogP: log octanol/water partition coefficient.
POLYCYCLIC AROMATIC COMPOUNDS 13
receive electrons, and the energy difference between HOMO and LUMO gives information about
the stability of the molecule.
56
If the energy difference between HOMO and LUMO is large, it
can be said that the reaction ability is low, i.e., the molecule is stable. 3N13’s HOMO-LUMO
energies and other electronic properties (IP, electron affinity [EA], electronegativity [X], chemical
hardness [g], chemical softness [S], chemical potential [l], and electrophilic index [x]) were
given in Table 5 and the pictorial drawing of HOMO-LUMO energies was shown in Figure 4.
MEP analysis
The MEP map of a molecule describes the interaction of the charges dispersed on the atoms in
the molecule with a positive point charge. While the regions indicated in red in these maps repre-
sent the negative region of the electrostatic potential, they also represent the region that is prone
to chemical reaction, where the electron density is higher than the nucleus over the entire mol-
ecule. The blue regions on the potential surface are the regions where there are partial positive
charges and are unstable in terms of reaction.
57
Regions containing less electrons are shown in
yellow, while almost neutral regions are shown in green. Looking at the MEP map of 3N13
(Figure 5), while the red zones were particularly concentrated on oxygen atoms (more negative),
the perimeter of the carbon and hydrogen atoms looked more positive.
Geometry optimization
Geometric optimization is expressed as the process of finding the most stable geometric structure
of a molecule, i.e., the minimum energy conformation of the molecule. First of all, energy is
Table 5. Calculated electronic parameters of 3N13.
3N13
Energy (Hartree) –1589.908070
Dipole moment (Debye) 5.132549
HOMO (eV) –0.04764
LUMO (eV) –0.17828
DE(eV) 0.13064
ӀP¼–HOMO 0.04764
EA ¼–LUMO 0.17828
X¼(IP þEA)/2 0.11296
ἠ¼(IP EA)/2 –0.06532
(S¼1/2ἠ)–7.65462
m¼(IP þEA)/2 –0.11296
x¼m2/2g0.09767
Figure 4. (a) HOMO and (b) LUMO plots of 3N13.
14 M. EROL ET AL.
calculated in an initial geometry. By moving the atoms in the molecule, a little, the molecular
geometry is changed a bit and the energy is calculated again. This process is continued until you
find the lowest energy. Thus, the lowest energy molecular structure, that is, the equilibrium
geometry of the molecule is obtained. The experimental geometric structure of the compounds is
unknown. In some recent studies, experimental and computational studies of the molecular
geometry of compounds have been reported as comparisons.
58,59
The numbered optimized geo-
metrical structure of 3N13 were given in Figure 6, the bond lengths (Å), bond angles (), and
dihedral angles were given in the Supplementary Information section.
Conclusion
In this study, a series of 2,5-disubstituted benzoxazole derivative compounds were designed, syn-
thesized, and their antimicrobial activities by microdilution method and cytotoxic activities by
MTT test were determined. Compounds exhibited weak antibacterial action against the examined
Figure 5. MEP map of 3N13.
Figure 6. Optimized molecular structure of 3N13.
POLYCYCLIC AROMATIC COMPOUNDS 15
structures compared to reference drugs, while 3N13 and 3N19 against C. albicans isolate showed
very close activity to fluconazole. In addition, all compounds exhibited a weak cytotoxic effect on
A549 and MCF-7 cells. Molecular docking studies of all compounds were conducted against sterol
14a-demethylase protein (CYP51) and a moderate correlation was found between Docking score,
Glide gscore, and Glide emodel values and antimicrobial activity (PDB: 5TZ1). Two-dimensional/
3D interactions of 3N13, one of the most effective antifungal compounds against C. albicans iso-
late, were showed and DFT calculations were performed to estimate its geometric structure and
electronic properties. The compounds also showed a good ADME profile in general. According
to all these results, the synthesized compounds can be promising antifungal agent.
Acknowledgment
NMR analysis of the compounds were performed by Erciyes University Technology and Research Center (TAUM)
and HRMS analysis were performed by Bilkent University National Nanotechnology Research Center (UNAM).
Disclosure statement
No potential conflict of interest was reported by the authors.
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