New oxadiazole derivatives: Synthesis and appraisal of their potential as antimicrobial agents

Article abstract of DOI:10.2174/1570180814666170425160545

Introduction: The escalating threat due to dwindling effect of antibiotics and challenge of tackling rising drug-resistant infections has gathered high focus in current medicinal research. Methods: In an attempt to find new molecules that can defeat microbial resistance, two new series of 2-[2-substituted ethenyl]-5-(substituted methoxy)-1,3,4-oxadiazole derivatives were synthesized. Various aromatic hydrazides were allowed to undergo cyclization to substituted oxadiazole-2- amines in the presence of cyanogen bromide and further condensed with different heterocyclic aldehydes to give new oxadiazole derivatives. The synthesized molecules were fully characterized by various spectral techniques and tested for antimicrobial activity. Results: Almost all the newly synthesized compounds especially (5g-5l) displayed remarkable growth inhibition against three bacterial strains: M. smegmatis, S. aureus, E. coli and fungi C. albicans. The antimicrobial activity was further confirmed by MIC assay against the same microorganisms. Oxadiazole 5g displayed promising activity with a MIC value of 0.025 mM for two bacteria and fungi, whereas MIC of this compound for E. coli was 0.1 mM. Other active compounds (5h-5l) also exhibited good MIC ranging between 0.313 to 5.0 mM against the selected microorganisms. Docking simulations were generated to explore the potential binding approaches of ligand 5g at the D-alanine:d-alanine ligase (Ddl) protein of E. coli and S. aureus. Conclusion: Molecule 5g was active even at a lower concentration and could probably act as a prospective lead molecule for targeting the drug resistant microorganisms.

Full text of DOI:10.2174/1570180814666170425160545

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21
Letters in Drug Design & Discovery, 2018, 15, 21-30
RESEARCH ARTICLE
ISSN: 1570-1808
eISSN: 1875-628X
Impact
Factor:
1.17
New Oxadiazole Derivatives: Synthesis and Appraisal of Their Potential as
Antimicrobial Agents
BENTHAM
S
CIENCE
Deboleena Dharaa, Dhanya Sunilb,*, Pooja R. Kamathb, K. Anandac, S. Shrilakshmic and S. Balajid
aDepartment of Chemical Engineering, Manipal Institute of Technology, Manipal University, Manipal-576104, India;
c
bDepartment of Chemistry, Manipal Institute of Technology, Manipal University, Manipal, India; Biological Sciences
d
Division, Poornaprajna Institute of Scientific Research, Devanahalli, Bangalore, India; Department of Biotechnology,
Manipal Institute of Technology, Manipal University, Manipal-576104, India
Abstract: Introduction: The escalating threat due to dwindling effect of antibiotics and challenge
of tackling rising drug-resistant infections has gathered high focus in current medicinal research.
Methods: In an attempt to find new molecules that can defeat microbial resistance, two new series
of 2-[2-substituted ethenyl]-5-(substituted methoxy)-1,3,4-oxadiazole derivatives were synthesized.
Various aromatic hydrazides were allowed to undergo cyclization to substituted oxadiazole-2-
amines in the presence of cyanogen bromide and further condensed with different heterocyclic al-
dehydes to give new oxadiazole derivatives. The synthesized molecules were fully characterized by
A R T I C L E H I S T O R Yꢀ
various spectral techniques and tested for antimicrobial activity.
Received: January 30, 2017
Results: Almost all the newly synthesized compounds especially (5g-5l) displayed remarkable
Revised: April 26, 2017
Accepted: April 30, 2017
growth inhibition against three bacterial strains: M. smegmatis, S. aureus, E. coli and fungi C. albi-
DOI:
cans. The antimicrobial activity was further confirmed by MIC assay against the same microorgan-
10.2174/1570180814666170425160545
isms. Oxadiazole 5g displayed promising activity with a MIC value of 0.025 mM for two bacteria
and fungi, whereas MIC of this compound for E. coli was 0.1 mM. Other active compounds (5h-5l)
also exhibited good MIC ranging between 0.313 to 5.0 mM against the selected microorganisms.
Docking simulations were generated to explore the potential binding approaches of ligand 5g at the
D-alanine:d-alanine ligase (Ddl) protein of E. coli and S. aureus.
Conclusion: Molecule 5g was active even at a lower concentration and could probably act as a
prospective lead molecule for targeting the drug resistant microorganisms.
Keywords: Oxadiazole, antimicrobial, D-alanine:d-alanine ligase docking, drug resistance, schiff bases, agents.
1. INTRODUCTION
infections all over the world [6]. Resistance to tetracyclines
and fluoroquinolones which is one among the most exten-
sively used oral antibacterial drug for the treatment of uri-
nary tract infections caused by Escherichia coli is very
common [7]. Despite the use of antifungal therapies, Can-
dida albicans evolves better and develops azole resistance to
exploit the host environment during infection [8, 9]. Patients
infected by resistant strains of microorganisms thus fail to
respond to marketed standard antimicrobial agents and are
generally at an increased threat of poorer clinical outcomes
that may ultimately lead to death. The world is now moving
towards a dangerous era where the common infections which
were once treatable, are posing a risk to humans. Hence,
there is an exigent need for newer antibiotics that can fight
against the emerging resistant microbes.
Antimicrobial resistance is a serious threat to community
health worldwide that demands effective treatment of an
ever-increasing array of infections instigated by micro-
organisms such as bacteria, viruses, fungi and other parasites
[1, 2]. The resistant strains naturally evolve either when mi-
croorganisms reproduce themselves erroneously or when
resistant traits are exchanged among them. The mismanage-
ment of currently marketed antimicrobials has accelerated
the emergence of new resistance mechanisms and a gradual
rise in resistance in microbes, which spreads globally [3, 4].
Multidrug-resistant tuberculosis (MDR-TB) requires much
longer treatment courses than those for non-resistant TB [5].
The increasing magnitudes of antibiotic resistance in Staphy-
lococcus aureus (MRSA) strains cause hospital-acquired
There are a plethora of medically important molecules
that incorporate the heterocyclic biologically privileged
1,3,4-oxadiazole ring [10-15]. A few marked formulations
that contain oxadiazole scaffold are antiretroviral drug Ral-
*Address correspondence to this author at the Department of Chemistry,
Manipal Institute of Technology, Manipal-576104, India; Tel: +91 820
2924412; E-mail: dhanyadss3@gmail.com
1875-628X/18 $58.00+.00
©2018 Bentham Science Publishers

22 Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1
Dhara et al.
tegravir®, anticancer agent Zibotentan®, antihypertensives
such as Tiodazosin and Nesapidil and antibiotic Furamizole.
During the past few years, there are considerable literature
evidence to validate the efficiency of the highly privileged
1,3,4-oxadiazole derivatives as antimicrobial agents [16, 17].
As resistance to existing antimicrobial drugs to a variety of
clinically relevant species of bacteria is becoming a crucial
global problem, this study is focussed on the synthesis of
twelve new oxadiazole derivatives that exhibit novel modes
of action against multidrug resistant micro-organisms to
overcome the existing microbial resistance of currently mar-
keted antimicrobial drugs.
hexane and spots were visualized under UV light. Infrared
and mass spectra were recorded in the region of 4000–400
cm-1, on a Schimadzu 8400S spectrometer using KBr disc as
background and Shimadzu GCMS-QP5050 mass spectrome-
1
ter respectively. The H and 13C NMR were recorded in a
Bruker 400 MHz instrument in DMSO using tetramethylsi-
lane as internal standard. Melting points were found out us-
ing the open capillary method and are uncorrected. Flash
thermo 1112 series CHN analyser was used for carrying out
elemental analysis.
2.1. Chemistry
The cell wall of a bacteria is critical for its survival.
Hence it is a privileged target for several antibiotics. The
main constituent of the bacterial cell wall is peptidoglycan.
It is synthesized in four sequential stages: i) formation
of a glycopepentapeptidic monomer unit (UDP-MurNAc-
pentapeptide) in the cytoplasm, ii) integration of the Mur-
NAc-pentapeptide to undecapenoylphosphate, a lipid carrier
at the inner surface of the cell membrane, iii) the attachment
of an N-acetylglucosamine, and the translocation of the re-
sulting disaccharide-(peptide)-pyrophosphate undecaprenyl-
carrier to the outer face of the membrane and iv) addition of
new monomer units in the mature peptidoglycan by
transpeptidation and transglycosylation reactions at the ex-
ternal side of the cytoplasmic membrane [18]. Acquisition of
bacterial resistance to two major current therapeutic classes
of antibiotics, namely glycopeptides and β-lactams, which
hinder the late phases of its biosynthetic pathway [19], has
revealed the need to exploit the possibility of targeting other
enzymes that act on the initial steps of peptidoglycan synthe-
sis. D-alanine:D-alanine ligase (Ddl), is an indispensable
ATP-dependent enzyme involved in peptidoglycan biosyn-
thesis [20], which is present in both gram positive and gram
negative bacteria. They catalyze the formation of D-alanyl –
D-alanine that will occupy the terminal end of the cytosolic
UDP-MurNAc-pentapeptide precursor units in the bacterial
growth phase. In the stationary phase, D-alanyl – D-alanine
is reincorporated into the new cell wall precursors or con-
verted back to D-alanine that can be used as an energy
source during bacterial starvation. This enzyme can act as an
attractive target for developing newer antibiotic drugs as it
does not have a human ortholog [21]. Inhibitors acting on the
DD-ligase would thus represent a clinically significant ad-
vancement in the current antibiotic collection, as alternates
are rare to act upon superbugs like methicillin-resistant
Staphylococci, vancomycin- resistant strains. The present
study is focussed on the synthesis of nine new oxadiazole
derivatives and investigation of their antimicrobial potential
against various microbial strains. Interaction studies have
been carried out with the most promising molecule with Ddl,
thereby establishing their effectiveness as potential inhibitors
against microorganisms.
2-Naphthol and 8-quinolinol (1a-b) were allowed to un-
dergo esterification in the presence of ethyl chloroacetate
[22]. The corresponding esters (2a-b) obtained were treated
with 80% hydrazine hydrate to produce respective hydraz-
ides (3a-b) [23], which on further refluxing with cyanogen
bromide lead to oxidative cyclisation of hydrazide resulting
in respective 2-amino-1,3,4-oxadiazoles (4a-b) [24]. The
amino-condensation of compounds (4a-b) with various alde-
hydes yielded the final oxadiazole ring incorporated schiff
bases (5a-l). The synthetic pathway and reaction mechanism
for the new oxadiazoles (5a-l) is presented in Scheme 1.
2.2. Antibacterial and Antifungal Studies
2.2.1. Disc Diffusion Method
Antibacterial activities of the compounds were assessed
by diffusion method in nutrient agar media plates. The in
vitro antibacterial potency of the synthesized compounds
were evaluated by measuring the zone of inhibition against
the following species; Mycobacterium smegmatis (MTCC
943) which is a variant of tuberculosis bacteria that has an
unusual cell wall structure and shares more than 2000 ho-
mologs, Staphylococcus aureus (MTCC 3160) - a gram posi-
tive bacteria, and Escherichia coli (MTCC 1687) - a gram-
negative bacteria. Antifungal activity studies of all the com-
pounds were performed using pathogenic fungi Candida
albicans (MTCC 7253). The bacterial and fungal cultures
were purchased from the microbial type culture collection,
Institute of Microbial Technology, Chandigarh, India and
maintained as per the standard protocol. About 15-20 mL of
the nutrient agar media was poured into petri-plates kept in
aseptic conditions and solidified inside a laminar air flow
chamber. About 100 µL of the 0.5 McFarland standard of the
microbial suspension was spread across the whole surface of
the agar plate using a sterile cotton bud. Test compounds
were dissolved in DMSO to obtain 10 mM concentration.
Different volumes (0.5, 1 and 2 µL) of these compounds in
triplicates were transferred to the inoculated plates and incu-
bated at 37 °C for 4 h and eventually, the zone of inhibition
was measured. All the experiments were performed in tripli-
cates, and the average value was taken. Streptomycin (10
mM) was used both as antibacterial and antifungal standard
[25].
2. MATERIALS AND METHODS
All chemicals used were purchased from Sigma-Aldrich,
Himedia, E. Merck India Ltd. and Spectrochem Chemicals
Pvt. Ltd. Reaction progress was monitored by pre aluminium
coated thin layer chromatographic sheets with Aluchrosep
silica Gel 60/ UV254 using 2:1 mixture of ethyl acetate and
2.2.2. Minimum Inhibitory Concentration (MIC)
Standard pathogenic bacterial strains of M. smegmatis, S.
aureus, E. coli and fungi C. albicans were used in the MIC
determination. The compounds were dissolved in DMSO at

New Oxadiazole Derivatives
Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1 23
O
ClCH2COOC2H5
KOH
O
H2N
NH2
R
OH
O
C2H5
O
NH2
R
O
R
N
H
EtOH
(1a-b)
(2a-b)
(3a-b)
CNBr
MeOH
O
H
R
R1
R
O
O
Conc. H2SO4
EtOH
O
N
NH2
R1
CHO
+
N
N
N
N
(5a-l)
(4a-b)
R
R
H
O
O
O
H
O
H
H
H+
C+
R1
H
O
O
O
H
R1
N+
H
H
R1
N
N
N
N
N
H
R
H
R1
O
O+
H
O
H
N
N
H
N
R
O
H
N
R1
O
N
N
Scheme 1. Synthetic pathway and mechanism for the preparation of oxadiazole derivatives.
an initial concentration of 10 mM and serially diluted 8 times
in microwell plates. MIC assay was performed as per the
protocol explained elsewhere with some modifications [14-
16]. About 100 μL of 10 mM stock solution was transferred
to the first lane of the microplate and 50 µL from this well
was taken out and serially diluted. The samples were serially
diluted using DMSO to obtain 10, 5, 2.5, 1.25, 0.625, 0.313,
0.156 and 0.078 mM sample concentration. All the microbial
cultures were grown in nutrient broth to reach 0.5 McFarland
concentrations. About 25 µL of the cultures and 125 µL of
nutrient broth were added to each well. The contents of mi-
cro-well plate were mixed well and incubated at room tem-
perature for 12 h [26].
eight serially diluted samples of each compound, the lowest
concentrated one which showed no microbial growth on agar
media was taken as MIC of that compound [27].
2.2.4. Resazurin Reduction Assay Method
Minimum inhibitory concentration obtained via plating
method was confirmed by resazurin reduction assay. Resazu-
rin cell viability test checks the viability of the cells and re-
lies on the ability of metabolically active viable cells to re-
duce resazurin (blue) to resorufin (pink). About 20 μL of
0.02% resazurin solution was added to the incubated sample
in the micro-well plate and further incubated for 4 h at room
temperature. The serially diluted samples for each compound
in the micro-well plate were observed for a change in color
from blue to pink. The last well in the series where no mi-
crobial growth had occurred retained blue color, and that
concentration was considered as MIC of that compound [16,
17]. The MIC values obtained from both plating and resazu-
rin assay methods were compared, and the most accurate
values were considered [28, 29].
2.2.3. Agar Plating Method
Minimum inhibitory concentration of synthesized com-
pound was measured based on viable micro-organisms in the
microplate wells. About 1µL of incubated sample was trans-
ferred from each microplate well to an agar plate, and the
growth of microorganisms was observed for 12 h. Out of

24 Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1
Dhara et al.
2.3. Docking Studies
(methylene C-H sym. str.), 1601 (C=N str.), 1581, 1398 (Ar.
C=C str.), 1275 (C-O-C asym. str.), 1090 (C-O-C sym. str.);
1H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.20 (s, 2H,
OCH2), δ 6.97 (s, 1H, naphthalene 1-H), δ 7.04-7.06 (m, 2H,
naphthalene 7-H & 8-H), δ 7.21-7.25 (d, 2H, naphthalene 5-
H & 4-H), δ 7.35- 7.41 (m, 3H, phenyl 3-H, 4-H & 5-H), δ
7.56-7.58 (m, 2H, naphthalene 3-H & 6-H), δ 7.60-7.62 (d,
2H, phenyl 2-H & 6-H), δ 8.73 (s, 1H, CH=N); 13C NMR
(100 MHz, DMSO-d6) δ = 72.25, 120.13, 120.03, 121.23,
121.68, 123.44, 127.41, 128.30, 129.37, 130.23, 131.43,
133.58, 134.10, 135.00, 137.67, 151.60, 164.70, 165.88; MS
(m/z): 330 (M+1); Anal. Calcd. for C20H15N3O2: C, 72.94; H,
4.56; N, 12.76; found: C, 73.15; H, 4.58; N, 12.79.
The ATP-driven ligation of two d-alanine (d-Ala) mole-
cules that results in the formation of d-alanyl:d-alanine
dipeptide is catalyzed by D-Alanine:d-alanine ligase (Ddl).
As inhibition of Ddl prevents bacterial growth, this enzyme
forms a viable and attractive target for probing effective an-
timicrobial drugs [30]. The crystal structure of Ddl in E. coli
and S. aureus were retrieved from the PDB database with the
corresponding entry codes 1IOV (resolution of 2.2 Å) and
2I80 (resolution of 2.19 Å), respectively. The former was
complexed with a transition state inhibitor, D-Ala-D-alpha
hydroxyl butyrate phosphonate [31], whereas the latter was
complexed with 3-chloro-2,2-dimethyl-N-[4(trifluoromethyl)
phenyl] propanamide inhibitor [32]. Both the crystal structures
were co-crystallized with ADP.
3.1.1.2.
5-((naphthalen-2-yloxy)methyl)-N-(pyridin-4-
ylmethylene)-1,3,4-oxadiazol-2-amine (5b)
The proteins were prepared by adding all hydrogen at-
oms, and all the water molecules were kept invariable for
docking studies. Electrostatic point charges on the ligand
atoms were calculated, and energy minimization was done.
This calculation was based on the number of free valences of
each type of atom and the number of bonds attributed to the
individual atoms [33]. Charges were added to the ligand and
twenty conformations were generated. The heteroatoms and
substructures were removed from the protein structure, and
the addition of hydrogens and side chain amide fixation was
done using the options available in Surflex 7.3 [34]. Proto-
mol was generated for binding of the ligand to the specific
site of the protein. The ligand was then subjected to the in-
teraction studies with the target Ddl of E. coli and S. aureus
using Surflex Dock module of Sybyl 7.3. The interaction
(docking) score was computed using ChemScore, a scoring
function that is obtained from regression against ligand-
receptor binding free energies. The docked complexes were
visualized using DS Visualizer v 16.1.0.15350 (Dassault
Systèmes Biovia group).
Pale brown solid; (79%); m.p. 176-178°C; IR (KBr)
[cm-1]: 3118 (Ar. C-H str.), 2955 (methylene C-H asym.
str.), 2852 (methylene C-H sym. str.), 1607 (C=N str.), 1552,
1401 (Ar. C=C str.), 1327 (C-O-C asym. str.), 1068 (C-O-C
1
sym. str.); H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.20 (s,
2H, OCH2), δ 6.96 (s, 1H, naphthalene 1-H), δ 7.03-7.05 (m,
2H, naphthalene 7-H & 8-H), δ 7.20-7.24 (d, 2H, naphtha-
lene 5-H & 4-H), δ 7.36-7.38 (d, 2H, pyridine 3-H & 5-H), δ
7.57-7.59 (m, 2H, naphthalene 3-H & 6-H), δ 7.63-7.65 (d,
2H, pyridine 2-H & 6-H), δ 8.74 (s, 1H, CH=N); 13C NMR
(100 MHz, DMSO-d6) δ = 72.13, 105.96, 118.77, 124.13,
124.19, 124.29, 126.71, 126.94, 127.80, 129.57, 129.64, 134.
81, 144.30, 149.57, 149.70, 157.30, 160.13, 176.37, 178.70;
MS (m/z): 331 (M+1); Anal. Calcd. for C19H14N4O2: C,
69.09; H, 4.24; N, 16.97; found: C, 69.29; H, 4.26; N, 17.00.
3.1.1.3. 1-(furan-2-yl)-N-{5-[(naphthalen-2-yloxy)methyl]-
1,3,4-oxadiazol-2-yl}methanimine (5c)
Pale yellow solid; (77%); m.p. 164-166°C; IR (KBr)
[cm-1]: 3112 (Ar. C-H str.), 2957 (methylene C-H asym.
str.), 2855 (methylene C-H sym. str.), 1618 (C=N str.), 1559,
1423 (Ar. C=C str.), 1323 (C-O-C asym. str.), 1062 (C-O-C
3. RESULTS AND DISCUSSION
3.1. Chemistry
1
sym. str.); H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.23 (s,
2H, OCH2), δ 6.56-6.58 (m, 2H, furan 3-H & 4-H), δ 6.98 (s,
1H, naphthalene 1-H), δ 7.05-7.07 (m, 2H, naphthalene 7-H
& 8-H), δ 7.20-7.24 (d, 2H, naphthalene 5-H & 4-H), δ 7.56-
7.58 (m, 2H, naphthalene 3-H & 6-H), δ 7.60 (d, 1H, furan
5-H), δ 8.73 (s, 1H, CH=N); 13C NMR (100 MHz, DMSO-
d6) δ = 72.13, 105.91, 109.59, 111.13, 118.86, 124.14, 126.
70, 126.94, 127.86, 129.51, 129.67, 134.83, 143.90, 146.52,
149.19, 157.30, 176.35, 178.79; MS (m/z): 320 (M+1); Anal.
Calcd. for C18H13N3O3: C, 67.71; H, 4.10; N, 13.16; found:
C, 67.93; H, 4.11; N, 13.18.
The FT-IR spectra of the molecules showed absorption
band in the range of 1601-1678 cm−1 attributed to the azome-
thine group stretching confirming the product formation. In
1
the HNMR spectra of compounds 5a-l, the O-CH2 protons
appeared as a singlet around 5.2 ppm, all aromatic protons at
6.9-8 ppm and the characteristic azomethine proton at 8.70-
8.77 ppm. The absence of characteristic singlet due to alde-
hydic and amino protons at 11 and 4.3 ppm respectively was
indicative of the formation of schiff bases from aldehyde and
oxadiazole-2-amine. In the 13C NMR spectra of the com-
pounds, the carbon of the azomethine group resonated at
178-179 ppm. The mass spectra of all the molecules were in
agreement with their corresponding molecular mass.
3.1.1.4. 1-(4-methyl-1H-imidazol-5-yl)-N-{5-[(naphthalen-
2-yloxy)methyl]-1,3,4-oxadiazol-2-yl}methanimine (5d)
Yellow solid; (76%); m.p. 168-170°C; IR (KBr) [cm-1]:
3099 (Ar. C-H str.), 2920 (methyl C-H asym. str.), 2850
(methyl C-H sym. str.), 1668 (C=N str.), 1610, 1555 (Ar.
C=C str.), 1319 (C-O-C asym. str.), 1058 (C-O-C sym. str.);
1H NMR (400 MHz, DMSO-d6) [ppm]: δ 2.12 (s, 3H, CH3),
δ 5.10 (s, 2H, OCH2), δ 6.94 (s, 1H, naphthalene 1-H), δ
7.00-7.02 (m, 2H, naphthalene 7-H & 8-H), δ 7.20-7.24 (d,
2H, naphthalene 5-H & 4-H), δ 7.40 (s, 1H, imidazole 2-H),
δ 7.56-7.58 (m, 2H, naphthalene 3-H & 6-H), δ 8.73 (s, 1H,
3.1.1. Experimental
3.1.1.1. N-{5-[(naphthalen-2-yloxy)methyl]-1,3,4-oxadiazol-
2-yl}-1-phenylmethanimine (5a)
Yellow solid; (91%); m.p. 186-188°C; IR (KBr) [cm-1]:
3173 (Ar. C-H str.), 2952 (methylene C-H asym. str.), 2855

New Oxadiazole Derivatives
Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1 25
CH=N), δ 12.78 (s, 1H, imidazole N-H); 13C NMR (100
MHz, DMSO-d6) δ = 11.20, 72.11, 105.91, 118.56, 123.71,
124.63, 126.70, 126.93, 127.80, 129.34, 129.60, 134.82,
135.54, 144.90, 151.81, 157.33, 176.39, 178.70; MS (m/z):
334 (M+1); Anal. Calcd. for C18H15N5O2: C, 64.86; H, 4.54;
N, 21.01; found: C, 67.99; H, 4.55; N, 21.05.
331 (M+1); Anal. Calcd. for C19H14N4O2: C, 69.08; H, 4.24;
N, 16.96 ; found: C, 69.13; H, 4.26; N, 16.98.
3.1.1.8.
N-(pyridin-4-ylmethylene)-5-((quinolin-8-yloxy)
methyl)-1,3,4-oxadiazol-2-amine (5h)
Brown solid; (82%); m.p. 195-197°C; IR (KBr) [cm-1]:
3109 (Ar. C-H str.), 2963 (methylene C-H asym. str.), 2855
(methylene C-H sym. str.), 1602 (C=N str.), 1551, 1473 (Ar.
C=C str.), 1320 (C-O-C asym. str.), 1065 (C-O-C sym. str.);
1H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.26 (s, 2H,
OCH2), δ 7.28-7.30 (d, 2H, pyridine 3-H & 5-H), δ 7.55-7.57
(d, 2H, pyridine 2-H & 6-H), δ 7.68 - 7.77 (d, 2H, quinoline
4-H & 7-H), δ 7.78 - 7.80 (m, 2H, quinoline 3-H & 6-H), δ
7.98 - 8.00 (d, 1H, quinoline 5-H), δ 8.53-8.55 (d, 1H, quino-
line 2-H), δ 8.97 (s, 1H, CH=N); 13C NMR (100 MHz,
DMSO-d6) δ = 72.15, 105.98, 124.15, 124.29, 125.32,
126.73, 126.95, 127.82, 129.58, 129.67, 134.84, 144.31,
149.58, 149.72, 157.31, 160.17, 176.38, 178.71; MS (m/z):
332 (M+1); Anal. Calcd. for C18H13N5O2: C, 65.25; H, 3.95;
N, 21.14; found: C, 65.32; H, 3.97; N, 21.15.
3.1.1.5. N-{5-[(naphthalen-2-yloxy)methyl]-1,3,4-oxadiazol-
2-yl}-1-(3-phenyl-1H-pyrazol-4-yl)methanimine (5e)
Straw yellow solid; (87 %); m.p. 190-192°C; IR (KBr)
[cm-1]: 3109 (Ar. C-H str.), 2920 (methylene C-H asym. s-
tr.), 2853 (methylene C-H sym. str.), 1672 (C=N str.), 1611,
1557 (Ar. C=C str.), 1323 (C-O-C asym. str.), 1060 (C-O-C
1
sym. str.); H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.22 (s,
2H, OCH2), δ 7.00 (s, 1H, naphthalene 1-H), δ 7.08-7.10 (m,
2H, naphthalene 7-H & 8-H), δ 7.25-7.30 (d, 2H, naphtha-
lene 5-H & 4-H), δ 7.45-7.50 (m, 3H, phenyl 3-H, 4-H & 5-
H), δ 7.59-7.61 (m, 2H, naphthalene 3-H & 6-H), δ 7.75-7.77
(d, 2H, phenyl 2-H & 6-H), δ 7.92 (s, 1H, pyrazole 5-H), δ
8.77 (s, 1H, CH=N), δ 12.16 (s, 1H, pyrazole N-H); 13C
NMR (100 MHz, DMSO-d6) δ = 72.76, 102.43, 105.90,
118.83, 124.56, 126.72, 126.91, 127.53, 127.56, 127.82,
128.89, 129.30, 129.39, 129.58, 129.60, 133.15, 134.00,
134.88, 147.73, 151.89, 157.37, 176.38, 178.76; MS (m/z):
396 (M+1); Anal. Calcd. for C23H17N5O2: C, 69.87; H, 4.30;
N, 17.72; found: C, 70.02; H, 4.32; N, 17.75
3.1.1.9. 1-(furan-2-yl)-N-{5-[(quinolin-8-yloxy)methyl]-1,3,
4-oxadiazol-2-yl}methanimine (5i)
Yellow solid; (81%); m.p. 160-162°C; IR (KBr) [cm-1]:
3098 (Ar. C-H str.), 2961 (methylene C-H asym. str.), 2860
(methylene C-H sym. str.), 1607 (C=N str.), 1562, 1456 (Ar.
C=C str.), 1328 (C-O-C asym. str.), 1069 (C-O-C sym. str.);
1H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.20 (s, 2H,
OCH2), δ 6.58-6.60 (m, 2H, furan 3-H & 4-H), δ 6.92-6.94
(d, 1H, quinoline 7-H), δ 7.16-7.18 (m, 2H, quinoline 6-H &
3-H), δ 7.20-7.22 (d, 1H, quinoline 5-H), δ 7.56-7.58 (d, 1H,
quinoline 4-H), δ 7.68 (d, 1H, furan 5-H), δ 8.06-8.08 (d, 1H,
quinoline 2-H), δ 8.83 (s, 1H, CH=N); 13C NMR (100 MHz,
DMSO-d6) δ = 72.17, 105.93, 109.60, 111.15, 124.18,
126.74, 126.97, 127.87, 129.50, 129.68, 134.86, 143.91,
146.55, 149.20, 157.31, 176.36, 178.80; MS (m/z): 321
(M+1); Anal. Calcd. for C17H12N4O3: C, 63.75; H, 3.78; N,
17.50 ; found: C, 63.96; H, 3.79; N, 17.51.
3.1.1.6. 1-[3-(4-methylphenyl)-1H-pyrazol-4-yl]-N-{5-[(nap-
hthalen-2-yloxy)methyl]-1,3,4-oxadiazol-2-yl}methanimine (5f)
Cream solid; (86%); m.p. 212-214°C; IR (KBr) [cm-1]:
3088 (Ar. C-H str.), 2926 (methyl C-H asym. str.), 2855
(methyl C-H sym. str.), 1673 (C=N str.), 1606, 1551 (Ar.
C=C str.), 1311 (C-O-C asym. str.), 1059 (C-O-C sym. str.);
1H NMR (400 MHz, DMSO-d6) [ppm]: δ 3.24 (s, 3H, CH3),
δ 5.20 (s, 2H, OCH2), δ 6.99 (s, 1H, naphthalene 1-H), δ
7.06-7.08 (m, 2H, naphthalene 7-H & 8-H), δ 7.23-7.27 (d,
2H, naphthalene 5-H & 4-H), δ 7.43-7.45 (d, 2H, phenyl 3-H
& 5-H), δ 7.57-7.59 (m, 2H, naphthalene 3-H & 6-H), δ
7.73-7.75 (d, 2H, phenyl 2-H & 6-H), δ 7.93 (s, 1H, pyrazole
5-H), δ 8.73 (s, 1H, CH=N), δ 12.13 (s, 1H, pyrazole N-H);
13C NMR (100 MHz, DMSO-d6) δ = 24.32, 72.73, 102.42,
105.88, 118.80, 124.55, 126.73, 126.89, 127.51, 127.55,
127.81, 128.86, 129.26, 129.38, 129.56, 129.59, 133.14,
134.02, 134.89, 147.70, 151.86, 157.35, 176.34, 178.79; MS
(m/z): 410 (M+1); Anal. Calcd. for C24H19N5O2: C, 70.41; H,
4.64; N, 17.07; found: C, 70.59; H, 4.66; N, 17.10.
3.1.1.10. 1-(4-methyl-1H-imidazol-5-yl)-N-{5-[(quinolin-8-
yloxy)methyl]-1,3,4-oxadiazol-2-yl}methanimine (5j)
Straw yellow solid; (75%); m.p. 180-182°C; IR (KBr)
[cm-1]: 3090 (Ar. C-H str.), 2930 (methyl C-H asym. str.),
2858 (methyl C-H sym. str.), 1608 (C=N str.), 1526, 1454
(Ar. C=C str.), 1318 (C-O-C asym. str.), 1058 (C-O-C sym.
1
str.); H NMR (400 MHz, DMSO-d6) [ppm]: δ 2.18 (s, 3H,
CH3), δ 5.09 (s, 2H, OCH2), δ 6.92-6.94 (d, 1H, quinoline 7-
H), δ 7.11-7.13 (m, 2H, quinoline 6-H & 3-H), δ 7.15-7.17
(d, 1H, quinoline 5-H), δ 7.45 (s, 1H, imidazole 2-H), δ 7.58-
7.60 (d, 1H, quinoline 4-H), δ 8.33-8.35 (d, 1H, quinoline 2-
H), δ 8.94 (s, 1H, CH=N), δ 12.70 (s, 1H, imidazole N-H);
13C NMR (100 MHz, DMSO-d6) δ = 11.34, 72.15, 105.93,
124.72, 125.65, 126.70, 126.97, 127.81, 129.32, 129.69,
134.88, 135.55, 144.95, 151.80, 157.35, 176.40, 178.77; MS
(m/z): 335 (M+1); Anal. Calcd. for C17H14N6O2: C, 61.08; H,
4.22; N, 25.15 ; found: C, 61.21; H, 4.24; N, 25.17.
3.1.1.7. N-benzylidene-5-((quinolin-8-yloxy)methyl)-1,3,4-
oxadiazol-2-amine (5g)
Pale yellow solid; (85%); m.p. 220-222°C; IR (KBr)
[cm-1]: 3180 (Ar. C-H str.), 2958 (methylene C-H asym.
str.), 2858 (methylene C-H sym. str.), 1608 (C=N str.), 1580,
1400 (Ar. C=C str.), 1278 (C-O-C asym. str.), 1095 (C-O-C
1
sym. str.); H NMR (400 MHz, DMSO-d6) [ppm]: δ 5.25 (s,
2H, OCH2), δ 7.39-7.48 (m, 5H, phenyl ring), δ 7.55 - 7.67
(d, 2H, quinoline 4-H & 7-H), δ 7.78 - 7.80 (m, 2H, quino-
line 3-H & 6-H), δ 7.98 - 8.00 (d, 1H, quinoline 5-H), δ 8.53-
8.55 (d, 1H, quinoline 2-H), δ 9.02 (s, 1H, CH=N); 13C NMR
(100 MHz, DMSO-d6) δ = 72.31, 120.15, 120.23, 121.25,
121.70, 123.49, 127.49, 128.35, 129.43, 130.48, 131.63,
133.63, 134.11, 135.03, 151.68, 164.73, 166.00; MS (m/z):
3.1.1.11.
N-((3-phenyl-1H-pyrazol-4-yl)methylene)-5-
((quinolin-8-yloxy)methyl)-1,3,4-oxadiazol-2-amine (5k)
Yellow solid (79%); m.p. 182-184°C; IR (KBr) [cm-1]:
3113 (Ar. C-H str.), 2923 (methylene C-H asym. str.), 2854

26 Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1
Dhara et al.
(methylene C-H sym. str.), 1601 (C=N str.), 1510, 1459 (Ar.
C=C str.), 1320 (C-O-C asym. str.), 1060 (C-O-C sym. str.);
1H NMR (400 MHz, DMSO-d6): δ 5.23 (s, 2H, OCH2), δ
6.97-6.99 (d, 1H, quinoline 7-H), δ 7.03-7.05 (m, 1H, phenyl
4-H), δ 7.17-7.19 (m, 2H, quinoline 3-H & 6-H), δ 7.21-7.23
(d, 1H, quinoline 5-H), δ 7.33- 7.35 (m, 2H, phenyl 3-H & 5-
H), δ 7.55-7.57 (d, 1H, quinoline 4-H), δ 7.73-7.75 (d, 2H,
phenyl 2-H & 6-H), δ 7.89 (s, 1H, pyrazole 5-H), δ 8.09-8.11
(d, 1H, quinoline 2-H), δ 8.75 (s, 1H, CH=N), δ 12.10 (s, 1H,
pyrazole N-H); 13C NMR (100 MHz, DMSO-d6) δ = 72.73,
102.42, 105.92, 118.86, 125.74, 126.81, 127.54, 127.58,
127.82, 128.90, 129.31, 129.36, 129.51, 129.62, 133.20,
134.10, 134.94, 147.74, 151.89, 157.36, 176.33, 178.91; MS
(m/z): 397 (M+1); Anal. Calcd. for C22H16N6O2: C, 66.66; H,
4.04; N, 21.21; found: C, 66.81; H, 4.05; N, 21.24.
72.70, 102.41, 105.89, 123.55, 125.73, 126.80, 127.50, 127.
54, 127.81, 128.89, 129.29, 129.30, 129.57, 129.60, 133.19,
134.09, 134.93, 147.72, 151.88, 157.35, 176.31, 178.90; MS
(m/z): 411 (M+1); Anal. Calcd. for C23H18N6O2: C, 67.32; H,
4.39; N, 20.49; found: C, 67.58; H, 4.42; N, 20.53.
3.2. Antimicrobial Activity
All the synthesized compounds displayed moderate to
good antimicrobial action when subjected to the microbial
zone of inhibition assay. Oxadiazoles with naphthalene sub-
stituent 5a-f did not display much microbial growth inhibi-
tion, whereas compounds with quinoline moiety exhibited
good inhibition activity against all the microorganisms stud-
ied. Interestingly, among all the oxadiazoles screened, com-
pound 5g revealed the highest zone of inhibition against all
the microorganisms. Compounds 5h and 5k displayed good
inhibition against few microorganisms, and moderate activ-
ity was observed in the case of other oxadiazoles. The zone
of inhibition values for all synthesized compounds on re-
spective microbes are presented in Table 1.
3.1.1.12.
1-[3-(4-methylphenyl)-1H-pyrazol-4-yl]-N-{5-
[(quinolin-8-yloxy)methyl]-1,3,4-oxadiazol-2-yl}methanimine
(5l)
Dark yellow solid; (81%); m.p. 176-178°C; IR (KBr)
[cm-1]: 3103 (Ar. C-H str.), 2932 (methyl C-H asym. str.),,
2852 (methyl C-H sym. str.), 1605 (C=N str.), 1508, 1456
(Ar. C=C str.), 1319 (C-O-C asym. str.), 1058 (C-O-C sym.
str.); 1H NMR (400 MHz, DMSO-d6): δ 3.22 (s, 3H, CH3), δ
5.20 (s, 2H, OCH2), δ 6.95-6.97 (d, 1H, quinoline 7-H), δ
7.13-7.17 (m, 2H, quinoline 3-H & 6-H), δ 7.20-7.22 (d, 1H,
quinoline 5-H), δ 7.30- 7.35 (d, 2H, phenyl 3-H & 5-H), δ
7.53-7.55 (d, 1H, quinoline 4-H), δ 7.70-7.72 (d, 2H, phenyl
2-H & 6-H), δ 7.96 (s, 1H, pyrazole 5-H), δ 8.04-8.06 (d,
1H, quinoline 2-H), δ 8.70 (s, 1H, CH=N), δ 12.08 (s, 1H,
pyrazole N-H); 13C NMR (100 MHz, DMSO-d6) δ = 24.36,
All the compounds were subjected to MIC studies against
M. smegmatis, S. aureus, and C. albicans, and E. coli and the
results are depicted in Table 2. Oxadiazoles 5g-l with quino-
line scaffolds displayed better activity compared to 5a-f that
incorporated a naphthalene moiety. Compound 5g was found
to be the best among all the molecules screened with MIC
value less than 0.078 mM (lowest concentration studied for
MIC). To arrive at the exact MIC value of 5g, MIC assay
was repeated by serially diluting 100 µM stock solution up to
0.78 µM concentration. The potent oxadiazole 5g exhibited a
MIC value of 0.025 mM (25 µM) in two bacterial strains M.
Table 1. Results of antimicrobial inhibition assay for compounds 5a-l.
Inhibition of bacteria and fungi with 10 mM concentration of Synthesized compounds: zone of inhibition in mm (Mean SD) n=3
MS
1.0
SA
1.0
EC
1.0
CA
1.0
Samp Vol.(µL)
0.5
2.0
0.2
0.5
2.0
0.2
0.5
2.0
0.2
5.1 0.3
0.5
2.0
5a
4.1 0.7
0
5.1 0.3
0
6
3.1 0.5
0
5.1 0.4
6
6
2.1 0.4
2.5 0.5
2.6 0.5
2.6 0.3
2.5 0.4
0
4.2 0.5
3.2 0.3
4.2 0.4
4.1 0.3
3.2 0.4
0
6
3.1 0.4
0.0
5.1 0.7
0.0
8.2 0.3
0.0
5b
0
0
0
5c
5
0.3
6.1 0.3
7.2 0.4
6.9 0.4
7.1 0.4
2.6 0.5
0
4.2 0.4
0
0.3
6
6
0.3
0.4
0.5
0.7
2.5 0.3
0.0
4.2 0.4
0.0
6.1 0.4
0.0
5d
5.9 0.4
5
4
0.5
0.2
0
0
0
5e
3
3
0.5
0.2
0
0
4
0.0
0.0
0.0
5f
5.1 0.3
7.5 0.5
7
0.3
0
0
4
0.0
0.0
0.0
5g
6.5 0.5
0.6
5.2 0.5
9.7 0.3
8.1 0.4
7.5 0.3
7.3 0.4
7.2 0.3
6.1 0.3
5.8 0.7
6.5 0.4
7.2 0.5
5.0 0.4
-
8.3 0.6
8.6 0.3
9.1 0.2
9.0 1.0
10.2 0.9
10.2 0.4
9.5 0.4
11 0.6
6.0 0.5
8.7 0.6
6.6 0.3
10.7
0
7.7 0.6
8.1 0.3
7.1 0.4
8.0
0
10.5 0.5
11.1 0.7
9.5 0.6
7.9 0.3
10.1 0.3
8.5 0.4
27.3 2.5
5h
5
6
6
7
7
6
0.5
0.2
0.3
0.3
0.4
5
0.3
7.5 0.3
7.6 0.5
8.5 0.4
7.5 0.5
8.1 0.4
9.1 0.3
7.6 0.4
6.9 0.4
7.6 0.4
7.5 0.4
-
5i
5.5 0.8
5.9 0.4
5.5 0.6
6.1 0.4
-
7
0.4
5j
5
6
0.2
0.3
8
0.4
6.9 0.4
6.5 0.4
7.1 0.3
-
6
0.4
5k
5l
8
8
0.5
0.5
8.1 0.5
7.5 0.4
-
6.2 0.4
6.5 0.4
-
5.5 0.4
-
8.9 0.6
32 3.6
Streptomycin
-
30.3 2.5
24
2
MS: Mycobacterium smegmatis; SA: Staphylococcus aureus; EC: Escherichia coli; CA: Candida albicans.

New Oxadiazole Derivatives
Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1 27
Table 2. Minimum Inhibition concentration assay (plate
method) for compounds 5a-l serially diluted from 10
mM concentration.
5l with a methyl substituted phenyl ring attached to pyrazole
displayed good antimicrobial activity, whereas molecule 5g
with phenyl ring directly attached to imine group revealed
excellent growth inhibitory properties. The replacement of
naphthalene moiety in 5a by a quinoline unit as in 5g en-
hanced the activity of molecule significantly. Thus it was
inferred that the nature of the substituent and the heterocyclic
skeleton attached to the oxadiazole unit has a strong influ-
ence on the extent of antimicrobial activity. The presence of
quinoline moiety and a phenyl ring directly attached to the
imine group was found to be crucial for antimicrobial action
of the synthesized oxadiazole derivatives.
MIC (mM)
Synthesized Sample
MS
SA
EC
CA
5a
> 10
> 10
> 10
> 10
> 10
> 10
> 10
> 10
> 10
> 10
0.1
> 10
> 10
> 10
> 10
> 10
> 10
0.025
2.5
5b
5c
> 10
> 10
5d
> 10
> 10
3.3. Interaction Studies of Ligand 5g with Ddl
5e
> 10
> 10
As molecule 5g aided in arresting the growth of the se-
lected microbes effectively, it was of interest to study the
interaction with the protein target (ATP-dependent Ddl) that
is involved in cell wall synthesis. Ddl is a highly conserved
protein for both gram-negative (E. coli) and gram-positive
(S. aureus and M. smegmatis) organisms, as well as in other
prokaryotes Moreover the enzyme is absent in humans, and
hence is a perfect target for novel antibiotics. Ddl enzymes
derived from different microbial sources carry multiple
ligand binding domains related to their catalytic activity: d-
Ala1 binds the first monomer of d-Ala with high affinity,
whereas d-Ala2 binds the second d-Ala with lower affinity.
Moreover, there is a separate ATP binding domain [35],
which serves as a favourable target for the design of ATP-
competitive ligands. The mechanism for the synthesis of
peptidoglycan of bacterial cell wall involves the following
steps: binding of d-Ala to the d-Ala1 site, phosphorylation of
the amino acid’s carboxylate by the γ-phosphate of ATP, and
subsequent binding to the d-Ala2 site. The nucleophilic at-
tack of the amine at the d-Ala2 site on the phosphorylated d-
Ala at the d-Ala1 site completes the ligation to yield d-Ala:d-
Ala. Inhibitors mimicking d-Ala or d-Ala:d-Ala have been
discovered, which include cis- and trans-dl-cyclothreonine,
d-cycloserine (DCS), and reaction transition state intermedi-
ates related compounds, such as phosphinate and phospho-
nate derivatives [36]. However, there are no studies to block
the ATP binding site of Ddl.
5f
> 10
> 10
5g
0.025
1.25
0.025
1.25
5h
1.25
1.25
5
5i
1.25
1.25
0.625
2.5
5j
5k
1.25
1.25
1.25
0.625
<0.07
< 0.024
5
2.5
5l
0.625
< 0.024
0.625
< 0.024
1.25
< 0.024
ABS/ AFS
ABS: antibacterial standard (Ciprofloxacin); AFS: anti-fungal standard (Fluconazole);
>:more than; <: lesser than; control: dimethylsulfoxide had no inhibition; MS: Myco-
bacterium smegmatis; SA: Staphylococcus aureus; EC: Escherichia coli; CA: Candida
albicans.
smegmatis, S. aureus and the fungal strain C. albicans,
whereas 0.1 mM (100 µM ) against E. coli. Compound 5l
was also found to be active with MIC ranging from 1.25 to
0.313 mM against all the microbial strains. The MIC values
of the standard antibacterial agent Ciprofloxacin and anti-
fungal standard Fluconazole were found to be less than 0.24
mM against respective microorganisms. The resazurin reduc-
tion assay was employed to confirm the exceptionally sig-
nificant activity of 5g. The MIC values obtained by the re-
duction assay confirmed the MIC results generated in the
plate method. The study thus reveals the potent antimicrobial
activity of 5g which is very much comparable to that of the
standard drugs and there is a greater possibility that this
compound can be a potent antibiotic against MDR strains.
The molecule 5g interacted well with the ATP biding site
of Ddl of both S. aureus and E. coli, analogous to ATP. The
docked conformers of 5g into the binding domains of Ddl of
both the microbes and its interactions with the amino acids in
the respective binding pockets are presented in Fig. (1). Mo-
lecular interactions of 5g with Ddl of E. coli and S. aureus
were compared with that of the complexed crystal structures
retrieved from PDB. The ligand 5g associated with the Ddl
of S aureus and revealed similar interaction pattern as that of
the co-crystallized inhibitor 3-chloro-2,2-dimethyl-N-[4-
(trifluoromethyl) phenyl]propanamide) (PDB ID: 1IOV).
The interactions between 5g and S. aureus Ddl were mainly
aided by electrostatic and hydrophobic forces. The following
amino acids: Leu94, Met310, Pro311 and Gly312 (HA1)
were found to have hydrophobic interactions with the S.
aureus Ddl. Two more amino acids were observed to take
part in an H-bonded electrostatic engagement: an oxygen
atom of Pro93 with H5 and another oxygen atom of Met310
with H32 of the ligand 5g. The Ddl inhibitor, 3-chloro-2,2-
dimethyl-N-4-trifluoromethyl)phenyl-propan-amide did not
In brief, oxadiazole analogs with modification in 2 and 5-
positions were synthesized and assessed for their growth
inhibition capabilities in the microbes. The effects of phenyl,
heterocyclic rings like pyridine, furan, imidazole and pyra-
zole rings were investigated in oxadiazole derivatives 5a-f.
Compound 5a with phenyl ring attached to imine group ex-
hibited the maximum zone of inhibition, while in contrary,
the phenyl ring when attached to pyrazole ring connected to
the imine group did not show any appreciable inhibition
zone. The presence of heterocyclic substituents did not create
any noticeable impact on the growth inhibition activity. The
inhibitory potency was considerably improved in the com-
pounds 5g-h when the naphthalene unit was replaced by qui-
noline scaffold. All the six compounds exhibited growth
inhibitory effect on all the four microbes studied. Compound

28 Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1
Dhara et al.
Fig. (1). A) Molecular interactions of ligand 5g with S. aureus Ddl: H-bonded interactions are showed in green, whereas electrostatic and
hydrophobic interactions are represented in pink. B) In E. coli Ddl, only polar amino acids (Lys 97 and Ser 150 and 151) interact with the
ligand. (The color version of the figure is available in the electronic copy of the article).
Fig. (2). Multiple sequence alignment generated using Clustal X 1.83 [37]. Sequence conservations (*) and substitutions {both conserved (:)
and semi-conserved (.)} are highlighted for amino acids with positions involved in ATP/ADP binding.
interfere with direct binding of ATP or D-Ala, but it bind to
a hydrophobic pocket near the first D-Ala binding site. Con-
trarily, though hydrophobic interactions were not observed
between ligand 5g and E. coli Ddl, electrostatic engagements
were seen with the following amino acids: Lys 97 and Lys
144: HZ1 with N1 and N20 of the ligand, Ser150 and 151:
HN with N24 and N21 of the ligand, respectively. Moreover,
the ligand 5g was able to block the binding site of the co-
crystallized ADP in 1IOV (-58.4434 Kcal/mol). Although
there are no crystal structures available for M. smegmatis and
C. albicans in PDB, the sequence comparison of M. smeg-
matis with E.coli and S. aureus revealed similar ATP/ADP
binding site as highlighted in the Fig. (2). Thus the results of
the docking simulations suggested that oxadiazole 5g can
block ATP binding in microbial Ddl enzymes and thereby
provide novel approach for the design of antibiotics.
CONCLUSION
Two series of new 2-[2-substituted ethenyl]-5-(substituted
methoxy)-1,3,4-oxadiazole derivatives (5a-f and 5g-l) were
synthesized in reasonably good yields. The compounds were
1
characterized by IR, H NMR, 13C NMR spectroscopy, mass
spectrometry and elemental analyses techniques. All the

New Oxadiazole Derivatives
Letters in Drug Design & Discovery, 2018, Vol. 15, No. 1 29
new trifluoromethyl quinoline-3-carbohydrazide and 1, 3, 4-
oxadiazoles. RSC Adv., 2014, 4(58), 30864-30875.
Chandrakantha, B.; Shetty, P.; Nambiyar, V.; Isloor, N.; Isloor, A.
M. Synthesis, characterization and biological activity of some new
1,3,4-oxadiazole bearing 2-flouro-4-methoxy phenyl moiety. Eur.
J. Med. Chem., 2010, 45(3), 1206-1210.
Rane, R.A.; Bangalore, P.; Borhade, S.D.; Khandare, P.K. Synthe-
sis and evaluation of novel 4-nitropyrrole-based 1,3,4-oxadiazole
derivatives as antimicrobial and anti-tubercular agents. Eur. J. Med.
Chem., 2013, 70, 49-58.
Khalilullah, H.; Khan, S.; Nomani, M.S.; Ahmed, B. Synthesis,
characterization and antimicrobial activity of benzodioxane ring
containing 1, 3, 4-oxadiazole derivatives. Arabian. J. Chem., 2016,
9(2), 1029-1035.
newly synthesized compounds were screened for in vitro
antimicrobial activity by the zone of inhibition assay and
MIC. Among all the twelve samples, 5g showed highest
growth inhibition in all the four microbes studied with MIC
very near to the standard antibiotics, which was further con-
firmed by resazurin assay. The docking interaction studies of
5g revealed its potential to act as an ATP-competitive inhibi-
tor of microbial Ddl enzyme. Oxadiazole 5g can be taken up
as a lead molecule and further explored for its application in
controlling multidrug-resistant microorganisms.
[11]
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D.; Legnani, L.; Toma, L.; Kwon, B. M.; Nakano, S.; Asai, A. Bio-
logical and computational evaluation of an oxadiazole derivative
(MD77) as a new lead for direct STAT3 inhibitors. Med. Chem.
Comm., 2012, 3, 592-599.
CONSENT FOR PUBLICATION
Not applicable.
CONFLICT OF INTEREST
[15]
Shin, D.S.; Masciocchi, D.; Gelain, A.; Villa, S.; Barlocco, D.;
Meneghetti, F.; Pedretti, A.; Han, Y.M.; Han, D.C.; Kwon, B.M.
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disubstituted-1, 2, 5-oxadiazoles and evaluation of their ability to
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The authors declare no conflict of interest, financial or
otherwise.
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ACKNOWLEDGEMENTS
Declared none.
SUPPLEMENTARY MATERIAL
Supplementary material is available on the publisher’s
web site along with the published article.
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