Bhaumik et al Journal of Drug Delivery & Therapeutics.

2019; 9(4):438-453

Available online on 15.07.2019 at http://jddtonline.info

Journal of Drug Delivery and Therapeutics

Open Access to Pharmaceutical and Medical Research
© 2011-18, publisher and licensee JDDT, This is an Open Access article which permits unrestricted
non-commercial use, provided the original work is properly cited

Open Access Research Article

Evaluation of Antimicrobial Profile of Some Novel 1, 3, 4-Oxadiazole
Derivatives Followed by Molecular Docking Against 3G7E Bacterial DNA
Gyrase
Asish Bhaumik*1; M. Chinna Eswaraiah2; Raja Chakraborty3
1* Research Scholar, Faculty of Pharmaceutical Science, Assam down town University, Gandhi Nagar, Panikhaiti, Guwahati - 781026, Assam,

India.
2 Professor, Department of Pharmacognosy, Anurag Pharmacy College, Ananthagiri, Kodad-508206, Suryapet (Dist.), Telangana, India.
3 Professor, Faculty of Pharmaceutical Science, Assam down town University, Gandhi Nagar, Panikhaiti, Guwahati- 781026, Assam, India.

ABSTRACT
The main aim and objective of the present research work was the design, synthesis, spectral characterization and evaluation o f in vitro
antimicrobial profile of some novel oxadiazole derivatives followed by molecular docking studies against bacterial DNA gyrase. The molecular
structures of the synthesized compounds were assigned by IR, NMR and Mass spectral analysis. Molecular docking studies were c arried out by
AUTO DOCK programme. The in vitro antibacterial and antifungal activities were done by paper disk diffusion and agar streak dilution
technique. In silico molecular docking studies the binding energy of synthesized compounds (AB1-AB8) were found to be -7.66, -7.67, -7.12, -
7.12, -6.59, -6.46, -7.35, -5.09 which indicated that the compound had the high binding affinity towards the bacterial DNA gyrase with PDB id
3G7E and inhibit the function topoisomerase in comparison with standard drug ciprofloxacin (-7.44). The preliminary antimicrobial screening
displayed that most of the synthesized compounds were executed moderate to good antimicrobial activity against following bacteria: S. aureus
(ATCC 9144), B. subtilis (ATCC 6633), S. epidermidis (ATCC 12228), P. Aeruginosa (ATCC27853), E.coli (ATCC25922), V. cholerrae (ATCC14035) and
fungi: A. Niger (ATCC 9029), A.flavus (ATCC204304), C. albicans (ATCC10231) and B. dermatitis (ATCC 26199) etc. All the synthesized compounds
exhibited moderate to good antibacterial and antifungal activity with an MIC range of 12-37µg/ml. Among these eight synthesized oxadiazole
derivatives, compound AB1; AB2 and AB7 were found to be very good antibacterial as well as antifungal potentiality with an MIC range of 13-12
µg/ml; 7-10 µg/ml and 15-18 µg/ml.
Keywords: Molecular docking; NMR; disk diffusion; antibacterial; antifungal and MIC etc.

Article Info: Received 14 May 2019; Review Completed 27 June 2019; Accepted 04 July 2019; Available online 15 July 2019
Cite this article as:
Bhaumik A, Chinna Eswaraiah M; Chakraborty R, Evaluation of Antimicrobial Profile of Some Novel 1, 3, 4-Oxadiazole
Derivatives Followed by Molecular Docking Against 3G7E Bacterial DNA Gyrase, Journal of Drug Delivery and
Therapeutics. 2019; 9(4):438-453 http://dx.doi.org/10.22270/jddt.v9i4.3081

*Address for Correspondence:

Asish Bhaumik, Research Scholar, Faculty of Pharmaceutical Science, Assam down town University, Gandhi Nagar, Panikhaiti, Guwahati-
781026, Assam, India.

1. INTRODUCTION methyne or methene; its IUPAC systematic name is

methylylidene or methanylylidene. Oxadiazole is derived
1. 1. Structural features of Oxadiazole from furan by replacement of two methine (-CH=) group by
Oxadiazoles are a class of heterocyclic aromatic chemical two pyridine type nitrogen (-N=) [2]. 1, 3, 4-oxadiazole is a
compound of the azoles family; with the molecular formula five member heterocyclic aromatic compound containing
C2H2N2O. There are four isomers of oxadiazole depending on two nitrogen atom at position three and four and one oxygen
the position of nitrogen atom in the ring [1]. In chemistry, atom present at position one. 1, 3, 4 oxadiazole is thermally
methine is a trivalent functional group =C(−, derived stable than other oxadiazoles, these oxadiazole are very
formally from methane. It consists of a carbon atom bound important compound in medicinal chemistry due to their
by two single bonds and one double bond, where one of the potential therapeutic efficacy.
single bonds is to hydrogen. The group is also called

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Table-1: Structure of different isomers of Oxadiazole 1. 3. Chemical properties of 1, 3, 4-Oxadiazole

1, 3, 4-oxadiazole is a five member heterocyclic aromatic
compound containing two nitrogen atom at position three
and four and one oxygen atom present at position one. 1, 3,
4-oxadiazole is thermally stable than other oxadiazoles,
these oxadiazoles are very important compound in medicinal
chemistry due to their potential biological activities.
Oxadiazole, a very weak base due to inductive effect of the
extra heteroatom. The replace of two -CH= groups in furan
by two pyridine type (-N=) lowers aromaticity of resulting
oxadiazole ring to an extent that the oxadiazole ring exhibit
character of conjugated diene. The electrophillic
substitutions in oxadiazole ring are extremely difficult at the
carbon atom because, the relatively low electron density on
the carbon atom which can be attributed to electron
withdrawal effect of the pyridine type nitrogen atom. If
1. 2. Physico-chemical properties of 1, 3, 4-Oxadiazole oxadiazole ring is substituted with electron-releasing groups,
the attack of electrophiles occurs at nitrogen. The ring is
1, 3, 4-oxadiazole is a liquid having boiling point 150ºC. 2, 5- generally resistant to nucleophiles attack [4].
disubstituted-1, 3, 4-oxadiazole derivatives are colourless
substances. The lower alkyl derivatives are liquids which 1. 4. Biological activity
distil without decomposition. Replacement of an alkyl The extensive literature survey revealed that 1, 3, 4-
residue by an aryl radical considerably raises the melting oxadiazoles were reported to possess a wide range of
and boiling points. Usually the asymmetrical 1, 3, 4- biological activities such as anti inflammatory, anticancer,
oxadiazole derivatives melt and boil at lower temperature antibacterial, antifungal, anti tubercular, anti-HIV,
than the symmetrical compounds. The solubility of anthelmentic (antimicrobial), anti oxidant, analgesic and
oxadiazoles in water varies with the substituent’s present: , anticonvulsant [5-8].
5-dimethyl-1, 3, 4-oxadiazole is miscible with water in all
proportions whereas the solubility of 2, 5-diphenyl-1, 3, 4- 2. EXPERIMENTAL CHEMISTRY
oxadiazole in water is less. Electrophilic introduction of
2. 1. Materials and method
functional groups (for example nitro or sulphuric acid
groups) into the nucleus is unusual. Electrophilic 2. 1. 1. Chemicals
substitution occurs in aryl substituent. Halogenations are
also difficult, but 2, 5-diaryl-1, 3, 4-oxadiazoles, afford The solvents and other chemicals which were used for the
complexes with halogens. A range of acylation and alkylation synthesis and purification of target compounds provided by
reactions of hydroxyl, thio and amino-1, 3, 4-oxadiazoles institutional store and were of LR and AR grade.
occur at the ring nitrogen [3]. 2. 1. 2. Synthetic scheme

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Steps involved in the synthesis of target compounds [9- Percentage yield (%): The theoretical yield is an organic
10] reaction is the weight of the product which would be
obtained if the reaction had proceeded to completion
Step 1: Ethyl-4-acetamido phenoxy acetate: A mixture of according to the chemical equation. The yield is the weight
p-acetamido phenol (0.01 mol) and ethyl chloroacetate (0.01 of pure product which is isolated from the reaction. The
mol) was refluxed by using dry acetone in presence of
percentage yield may be expressed as:
anhydrous potassium carbonate (K2CO3) for 6hrs. The
reaction mixture was cooled and then poured in to crushed
ice. The solid product obtained, these product was filtered,
dried and recrystallized using ethanol.
2. 1. 4. Spectral analysis
Step 2: 4-Acetamido phenoxy acetyl hydrazide: A mixture
of ethyl-4-acetamido phenoxy acetate (0.01 mol), hydrazine Functional group determination
hydrate (0.01 mol) in ethanol (15 ml) was refluxed for 5-8 The IR spectra of the synthesized compounds were recorded
hrs. The reaction mixture was cooled and then poured in to on ABB Bomen FT-IR spectrometer MB 104 IR spectra with
crushed ice. The solid product was obtained; this product potassium bromide pellets.
was filtered, dried and recrystallized from ethanol.
Determination of number of protons
Step 3: 2-(4-Acetamidophenoxy methyl) -5-aryl
substituted - 1, 3, 4-oxadiazole: A mixture of 4-Acetamido The number of protons present in each synthesized
phenoxy acetyl hydrazide (0.01 mol) and various aromatic compounds were determined by BRUKER NMR
acids (0.01 mol) in phosphorus oxychloride (10 ml) was spectrometer (1H-NMR) in DMSO. TMS was used as an
refluxed for 6-8 hours. The completion of the reaction internal standard.
process was monitored by TLC plates. The contents were Determination of molecular weight
cooled and poured into the crushed ice and then neutralized
the reaction mixture with sodium bicarbonate solution and The Mass spectra of synthesized compounds were recorded
the solid product was obtained, the product was filtered, by JEOL GCmate. Mass spectroscopy mainly used to
dried and recrystallized from ethanol . determine the molecular weight of the synthesized
compounds. The IR, 1H-NMR and MASS spectra are used to
2. 1. 3. Determination of Physicochemical properties assign the structure of synthesized compounds.
Melting point: The melting point (or, rarely, liquefaction 3. COMPUTATIONAL CHEMISTRY
point) of a substance is the temperature at which it changes
state from solid to liquid. At the melting point the solid and 3. 1. Molecular docking [11]
liquid phase exists in equilibrium. The melting points of the
Computational chemistry is a branch of chemistry that uses
synthesized compounds were determined by open capillary
computer simulation to assist in solving chemical problems.
tube method.
It uses methods of theoretical chemistry, incorporated into
Rf value: The retardation factor, Rf is commonly used in efficient computer programs, to calculate the structures and
paper chromatography and thin layer chromatography for properties of molecules and solids. Molecular docking is
analyzing and comparing different substances. It can be defined as an optimization problem, which would describe
mathematically described by the following ratio. TLC the best-fit orientation of a ligand that binds to a particular
method was used to determine the progress of the reaction. protein of interest. During the course of the process, the
TLC plates were pre-coated Silica gel (HF254-200 mesh) ligand and the protein adjust their conformation to achieve
aluminium plates using ethyl acetate: n-hexane are used as an overall best-fit and this kind of conformational
solvent and visualized under UV- chamber. adjustment resulting in the overall binding is referred to as
induced fit. The aim of the molecular docking to achieve an
optimized conformation for both the protein and the ligand
and to achieve relative orientation between protein and
Solubility profile: Solubility is the property of a solid, liquid ligand such that free energy of overall system is minimized.
or gaseous chemical substance called solute to dissolve in a The application of docking are the hit identification docking
solid, liquid or gaseous solvent. The solubility of a substance combined with a scoring function can be used to quickly
fundamentally depends on the physical and chemical screen large databases of potential drugs in silico to identify
properties of the solute and solvent as well as on molecules that are likely to bind to protein target of interest
temperature, pressure and presence of other chemicals and the lead optimization docking can be used to predict in
(including changes to the pH) of the solution. where and in which relative orientation a ligand binds to a
protein. This information may in turn be used to design
more potent and selective analogues.

Fig-1-A: Elements in molecular docking

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3. 2. Posing and scoring function of docking [12] usually involves simple energy calculations (Vdw + H-bond +
dE = Vender walls + Hydrogen bond + Dessolve energy. EE=
Posing the process of determining whether a given
Electrostatic Energy. TIME = Total Intermolecular Energy).
conformation and orientation of a ligand fits the active site.
One early general-purposed empirical scoring function to
This is usually a fuzzy procedure that returns many
describe the binding energy of ligands to receptors was
alternative results. pose score is a measure of the fit of a
developed by Böhm. This empirical scoring function took the
ligand into the active site. Scoring during the posing phase
form:

∑ ∑ | |

A more general thermodynamic "master" equation is as follows:

[ ][ ]
[ ]

3. 3. Requirements protein data bank and protein clean-up process was done
and essential missing hydrogen atom were been added.
Purpose: Computational Analysis. Job Id:
Different orientation of the lead molecules AB1 to AB8 along
NRS/008/10/2016. PDB Code: 3G7E. Soft ware used: Auto with standard drug ciprofloxacin with respect to the target
Dock 4. protein was evaluated by Auto dock program and the best
Structure of bacterial DNA gyrase (E. coli gyrase B) dock pose was selected based on the interaction study
analysis.
Crystalline structure of the target protein Topoisomerase
bacterial DNA gyrase with PDB id 3G7E was retrieved from

Fig-1-B: Structure of bacterial DNA gyrase

4. EXPERIMENTAL MICROBIOLOGY B. Fungi: A. Niger (ATCC 9029), A. flavus (ATCC204304), C.

albicans (ATCC10231) and B. dermatitis (ATCC 26199) etc.
4. 1. Microorganisms
4. 2. Chemicals and drugs
The standard strains (American type culture collection,
ATCC, USA, Rockville) and the pathological strains were DMF was used as solvent and Ciprofloxacin (antibacterial
supplied from the department of Pharmaceutical and Ketaconazole (antifungal) were used as standard
Microbiology & Biotechnology, Anurag Pharmacy College, antimicrobial drugs.
Kodad, Nalgonda, T. S, India. The antimicrobial activity of the
4. 3. Procedure
synthesized compounds was screened by using against the
following bacteria and fungi. Preparation of nutrient agar medium [13-14]
A. Bacteria: Gram positive: S. aureus (ATCC 9144), B. subtilis Nutrient agar medium is one of the most commonly used
(ATCC 6633), S. epidermidis (ATCC 12228). Gram negative: P. medium for several routine bacteriological purposes:
Aeruginosa (ATCC27853), E.coli (ATCC25922), V. cholerrae
(ATCC14035)

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Table-2-A: Composition of Nutrient agar medium for bacterial growth

S. l No. Ingredients Grams/Litter
1. Peptone 10 gm
2. Beef extract 10 gm
3. Agar 20 gm
4. Sodium chloride 5.0 gm
5. Distilled water 1000 ml
6. PH 7.0

Table-2-B: Composition of Sabouraud dextrose agar medium for fungal growth

S. l No. Ingredients Grams/Litter
1. Glucose 20 gm
2. Peptone 10 gm
3. Agar 20 gm
4. Distilled water 1000 ml
5. PH 5.4

All the ingredients were added to distilled water and boiled a standard. The observed zone of inhibition was compared
to dissolve all the ingredients in medium completely. The with standard drug.
medium sterilized by autoclaving at 15 lbs pressure.
Temperature was maintained at 1210C for 15 minutes. Determination of MIC [14 and 16]

Preliminary screening of anti-bacterial activity by paper MIC of the synthesized compounds was determined by agar
disc diffusion method [15] streak dilution method. A stock solution of the synthesized
compounds (100 µg/ml) in dimethyl formamide was
The sterilized (autoclaved at 120o C for 30 min) medium prepared and graded quantities of the test compounds were
was inoculated (1mL/100 ml of medium) with the incorporated in specified quantities of molten nutrient agar
suspension [105 cfu m/l (colony forming unit per millilitre)] medium. A specified quantity of the medium containing the
of the microorganism (matched to McFarland barium compounds was poured into a Petri dish to give a depth of 3-
sulphate standard) and poured in Petri dish to give a depth 4mm and allowed to solidify. Suspension of the
of 3-4mm. The paper impregnated with the test compounds microorganism were prepared to contain approximately105
(50, 100,150 µg/ml in dimethyl formamide) was placed on cfu m/l and applied or spread on surface of agar medium. All
the solidified medium. The plates were pre-incubated for plates were incubated at 37o C 2 to 3 days for bacterial and
1hour at RT and incubated at 37 oC for 24 hours for anti- fungal growth. The MIC was considered to be the lowest
bacterial and antifungal activities respectively. Ciprofloxacin concentration of the test substance exhibiting no visible
(100 µg/disc) and ketoconazoloe (100 µg/disc) was used as growth of bacteria on the plate.

5. RESULTS
Table-3: Represents the list of synthesized oxadiazole derivatives
Sl. No. Compound codes.

R
1. AB1 4-NH
2
2. AB2 2, 4-di-Cl
3. AB3 4-F
4. AB4 2-Br
5. AB5 2-Br, 4-NO2
6. AB6 4-NO2
7. AB7 3, 5-di-NO2
8. AB8 2-OH, 3, 5-di-NO2

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Table 4: Physicochemical properties of synthesized compounds

Sl. No. Compounds code M. F M. Wt Rf value m. p Yield
1. AB1 C17H16N4O3 324.33 0.77 116-119 0C 74.5 %.
2. AB2 C17H13Cl2N3O3 378.209 0.74 180-183 0C 69.9%
3. AB3 C17H14FN3O3 327.309 0.75 189-193 0C 74%
4. AB4 C17H14BrN3O3 388.215 0.65 183-186 0C 69%
5. AB5 C17H13BrN4O5 433.213 0.64 166-163 0C 60%
6. AB6 C17H14N4O5 354.31 0.72 171-175 0C 64%
7. AB7 C17H13N5O7 399.31 0.68 199-204 0C 78%
8. AB8 C17H13N5O8 415.31 0.72 212-2150C 68%

Spectral data of synthesized compounds Compound AB5

Compound AB1 N-(4-{[5-(2-bromo,4-nitrophenyl)-1,3,4-oxadiazol-2-
yl]methoxy}phenyl acetamide. )R KBr cm -1): 3381.95
N-(4-{[5-(4-aminophenyl)-1, 3, 4-oxadiazol-2- cm-1 (Ar-NH), 1684.44 cm-1 (C=N), 1586.2 cm-1 (C=C),
yl]methoxy}phenyl acetamide. )R KBr cm -1): 3393.16 1064.25 cm-1 (-C-O-C-), 1365.57 cm-1(N=O), 619.89 cm-1 (C-
cm-1 (Ar-NH), 1633.67 cm-1 (C=N), 1575.88 cm-1 (C=C), Br), 3130.43 cm-1 (Ar-CH), 1H-NMR δ ppm : . -8.36(m,
1069.05 cm-1 (-C-O-C-), 3132.54 cm-1 (Ar-CH), 1249.43 cm- 7H, Ar-CH) ,5.31(s, 2H, -CH2),2.31 (s, 1H, -CH3), 8.16(s, 1H, -
1(Ar-NH2), 1H-NMR δ ppm : . -7.4 (s, 8H, Ar-H), 5.17 (s, NH), Mass (m/e value) % relative abundance: 432.00 (M +)
2H,-CH2), 4.1(s, 2H, -NH2), 2.05 (s,1H, -CH3), 8.05 (s, 1H, -NH), (4), 388.71 (8.1), 362.27 (4.2), 233.28 (5), 217.31 (8.9),
Mass (m/e value) % relative abundance: 324.12 (M+) (5.1), 182.52 (5), 96.79 (7), 78.82(B).
310.87 (4) , 296.22 (8.25), 282.76 (2.2), 272.38(2.32),
262.6432 (7.3), 248.34 (11), 217.12 (15), 207.14 (7), 116.67 Compound AB6
(18), 58.33(B).
N-(4-{[5-(4-nitrophenyl)-1,3,4-oxadiazol-2-
Compound AB2 yl]methoxy}phenyl acetamide. )R KBr cm -1): 3382.43
cm-1 (Ar-NH), 1703.01 cm-1 (C=N), 1592.32 cm-1 (C=C),
N-(4-{[5-(2,4-dichlorophenyl)-1,3,4-oxadiazol-2- 1088.54 cm-1 (-C-O-C-), 1378.11 cm-1 (N=O), 3112.69 cm-1
yl]methoxy}phenyl acetamide.. )R KBr cm -1): 3381.92 (Ar-CH), 1H-NMR δ ppm : . -7.8(m, 8H, Ar-CH), 2.42 (s,
cm-1 (Ar-NH), 1673.42 cm-1 (C=N), 1545.03 cm-1 (C=C), 3H, -CH3), 8.13(s, 1H, -NH), 5.21(s, 2H, CH2), Mass (m/e
1085.04 cm-1 (-C-O-C-), 687.47 cm-1 (C-Cl), 3115.62 cm-1 (Ar- value) % relative abundance: 354.09 (M+) (3.8), 335.16 (4.8),
CH), 1H-NMR δ ppm : . -7.82(s, 8H, Ar-CH), 2.5 (s, 3H, - 302.39 (3.1), 287.43 (3.7), 249.58 (7.1), 226.00 (5.8), 204.96
CH3), 8.03(s, 1H, -NH), 5.22(s, 2H, -CH2), Mass (m/e value) % (6.7), 127.56 (13.1), 103.69 (9), 89.93 (B).
relative abundance: 377.03 (M+) (2.8), 333.16 (1.5), 325.42
(2.7), 286.43 (2.6), 183.26 (6), 160.62 (7), 140.65 (16), Compound AB7
115.64 (33), 95.53 (B).
N-(4-{[5-(3,5-dinitrophenyl)-1,3,4-oxadiazol-2-
Compound AB3 yl]methoxy}phenyl) acetamide. )R KBr cm-1): 3382.02
cm-1 (Ar-NH), 1677.79 cm-1 (C=N), 1530.6 cm-1 (C=C),
N-(4-{[5-(4-flurophenyl)-1,3,4-oxadiazol-2- 1089.68 cm-1 (-C-O-C-), 1372.45 cm-1 (N=O), 1523.12 asym
yl]methoxy}phenyl acetamide. )R KBr cm -1): 3392.09 cm-1 (N=O), 3117.5 cm-1 (Ar-CH), 1H-NMR δ ppm : . -
cm-1 (Ar-NH), 1617.53 cm-1 (C=N), 1528.16 cm-1 (C=C), 8.42(m, 8H, Ar-CH), 5.35(s, 2H,-CH2), 2.07 (s, 1H,- CH3), 8.24
1093.52 cm-1 (-C-O-C-), 1371.78 cm-1 (C-F), 3114.61 cm-1 (s, 1H, -NH), Mass (m/e value) % relative abundance: 399.08
(Ar-CH), 1H-NMR δ ppm : . s, (, -CH3), 8.09 (s, 1H, - (M+) (5), 388.76 (13), 380.25 (8), 261.63 (8), 182.52 (5),
NH), 5.21(s, 1H, -CH2), 6.7-8.01(m, 8H, Ar-CH), Mass (m/e 167.62 (17), 156.56 (19), 81.97(B).
value) % relative abundance: 327.10 (M+) (6.3), 310.37 (2.3),
299.57 (3), 282.87 (3.9), 266.22 (5), 249.61 (1.2), 232.72 (4), Compound AB8
104.86 (8.1), 75.50 (B).
N-(4-{[5-(2-hydroxy-3,5-dinitrophenyl)-1,3,4-oxadiazol-2-
Compound AB4 yl]methoxy}phenyl) acetamide. )R KBr cm-1): 3118.84
cm (Ar-NH), 1654.42 cm (C=N), 1541.89. cm-1 (C=C),
-1 -1
N-(4-{[5-(2-bromophenyl)-1,3,4-oxadiazol-2- 1368.45 cm-1 (N=O), 1528.45 asym. cm-1 (N=O),1090.01 cm-
yl]methoxy}phenyl acetamide. )R KBr cm -1): 3286.82 1 (-C-O-C-), 3118.84 cm-1 (Ar-CH), 3382.83 cm-1(Ar-OH), 1H-
cm-1 (Ar-NH), 1617.53 cm-1 (C=N), 1528.16 cm-1 (C=C), NMR δ ppm : . -7.6(s, 6H, Ar-CH), 2.11 (s, H, -CH3), 8.00(s,
1093.52 cm-1 (-C-O-C-), 687.47 cm-1 (C-Br), 3114.61 cm-1 1H, -NH), 5.12(s, 1H, -CH2), Mass (m/e value) % relative
(Ar-CH), 1H-NMR δ ppm : . s, (, -CH3), 8.09(s, 1H, - abundance: 415.07(M) (11.1), 318.68 (16), 292.76 (7),
NH), 5.21(s, 1H, -CH2), 6.7-8.01(m, 8H, Ar-CH), Mass (m/e 276.89 (20), 249.99 (8.2), 236.0277 (28.1), 203.2266 (76),
value) % relative abundance: 387.02(M+) (6.3), 310.37 (2.3), 182.2587 (8), 134.4966 (32), 116.55 (B)
299.57 (3), 282.87 (3.9), 266.22 (5), 249.61 (1.2), 232.72 (4),
104.86 (8.1), 75.60 (B).

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Table-5: Docking results analysis

C. C EFEB EIC (Ki) vdw+H-bond+de EE TIME Fr (%) IS
(k.cal/mol) uM (k.cal/mol) (k.cal/mlo) (k.cal /mol)
AB1 -7.66 2.43 -9.16 -0.22 -9.37 50 859.57
AB2 -7.67 2.40 -9.08 +0.05 -9.04 50 937.679
AB3 -7.12 6.03 -8.71 -0.20 -8.91 100 907.998
AB4 -7.12 6.00 -8.54 +0.13 -8.41 50 824.232
AB5 -6.59 14.77 -8.70 +0.10 -8.60 50 920.18
AB6 -6.46 18.24 -7.89 -0.21 -8.10 50 917.303
AB7 -7.35 4.10 9.70 -0.04 -9.74 50 928.775
AB8 -5.09 187.23 -7.79 +0.46 -7.32 100 909.889
Ciprofl -7.44 -3.51 7.26 -1.21 -8.47 50 850.017
oxacin
C. C = Compounds code. EFEB = Est. Free Energy of Binding. EIC = Est. Inhibition Constant. Vdw + H-bond + dE = Vender walls + Hydrogen bond
+ Dessolve energy. EE = Electrostatic Energy. TIME = Total Intermolecular Energy. Fr = Frequency. IS = Interaction Surface.

AB1 WITH 3G7E BACTERIAL DNA GYRASE AB2 WITH 3G7E -BACTERIAL DNA GYRASE

INTERACTION STUDY INTERACTION STUDY

RECEPTOR LIGAND COMPLEX RECEPTOR LIGAND COMPLEX

Fig-2-A: MD of Compound AB1 and AB2 against bacterial DNA gyrase.

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AB3 WITH 3G7E BACTERIAL DNA GYRASE AB4 WITH 3G7E BACTERIAL DNA GYRASE

INTERACTION STUDY INTERACTION STUDY

RECEPTOR LIGAND COMPLEX RECEPTOR LIGAND COMPLEX

Fig-2-B: MD of Compound AB3 and AB4 against bacterial DNA gyrase.

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AB5 WITH 3G7E BACTERIAL DNA GYRASE AB6 WITH 3G7E BACTERIAL DNA GYRASE

INTERACTION STUDY INTERACTION STUDY

RECEPTOR LIGAND COMPLEX RECEPTOR LIGAND COMPLEX

Fig-2-C: MD of Compound AB5 and AB6 against bacterial DNA gyrase.

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AB7 WITH 3G7E BACTERIAL DNA GYRASE AB8 WITH 3G7E BACTERIAL DNA GYRASE

INTERACTION STUDY INTERACTION STUDY

RECEPTOR LIGAND COMPLEX RECEPTOR LIGAND COMPLEX

Fig-2-D: MD of Compound AB7 and AB8 against bacterial DNA gyrase.

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Bhaumik et al Journal of Drug Delivery & Therapeutics. 2019; 9(4):438-453

Table-6-A: Zone of inhibition of synthesized compounds (AB1-AB8) against Gram positive bacteria
C. C BACTERIA
S. aureus B. subtilis S. epidermidis
Concentration μg/ml
50 100 150 50 100 150 50 100 150
Zone of inhibition in mm
AB1 7.4 12.3 10.1 9.1 10.9 9.1 7.5 11.6 8.7
AB2 7.6 12.8 8.4 7.1 11.4 9.4 7.9 13.1 10.4
AB3 6.7 11.2 8.1 6.5 10.4 8.1 6.3 10.4 7.9
AB4 6.2 10.2 6.9 5.0 9.5 6.9 6.1 8.8 7.1
AB5 5.6 8.6 6.5 5.2 8.2 6.7 5.2 8.0 6.3
AB6 5.4 7.8 9.5 5.2 8.0 6.3 5.0 7.1 6.3
AB7 7.2 11.9 6.4 6.5 10.6 8.4 7.0 11.0 8.3
AB8 5.3 7.8 7.1 5.2 7.5 6.2 5.0 8.1 6.1
Ciprofloxac Concentration μgm/ml
in 28.9 24.4 26.8

Table-6-B: Zone of inhibition of synthesized compounds (AB1-AB8) against Gram negative bacteria
C. C BACTERIA
E. coli P. aeruginosa V. cholerae
Concentration μg/ml
50 100 150 50 100 150 50 100 150
Zone of inhibition in mm
AB1 7.2 11.4 10.4 6.4 10.7 8.8 7.3 11.3 8.4
AB2 7.3 11.6 10.8 6.9 11.0 9.0 7.5 12.8 10.0
AB3 6.5 10.9 10.2 6.0 10.0 7.8 6.3 10.4 7.5
AB4 6.2 10.5 9.2 5.0 9.5 6.9 6.1 8.8 7.1
AB5 5.5 7.5 6.9 5.3 8.3 6.8 5.3 8.2 6.4
AB6 5.3 7.6 6.2 5.2 7.9 6.1 5.1 7.2 5.7
AB7 7.0 11.0 10.9 6.1 10.3 8.1 6.9 11 8.0
AB8 5.1 7.4 6.0 5.0 7.5 6.0 5.0 8.0 6.0
Ciprofloxac Concentration μgm/ml
in 28.5 24 26.4

Fig 3-A(1): Zone of inhibition of bacteria by test compounds.

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Fig 3-A(2): Zone of inhibition of bacteria by test compounds.

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Bhaumik et al Journal of Drug Delivery & Therapeutics. 2019; 9(4):438-453

Table-6-C: Zone of inhibition of synthesized compounds (AB1-AB8) against fungi.

C. C FUNGI
A. niger C. albicans B. dermatitis
Concentration μg/ml
50 100 150 50 100 150 50 100 150
Zone of inhibition in mm
AB1 7.1 11.4 9.4 6.3 9.9 8.2 6.9 11.3 8.7
AB2 7.3 11.9 9.7 6.8 10.2 8.4 7.1 11.9 9.2
AB3 6.5 10.0 8.2 5.6 9.0 7.2 5.5 9.3 7.5
AB4 6.0 9.6 7.8 5.0 8.8 6.4 5.2 8.7 7.2
AB5 5.5 8.7 6.9 5.3 8.3 6.3 5.3 8.2 6.8
AB6 5.3 7.6 6.2 5.2 7.9 6.1 5.1 7.2 5.9
AB7 6.9 10.6 8.8 5.8 9.3 7.5 5.8 9.8 7.9
AB8 5.1 7.4 6.4 5.0 7.5 6.2 5.0 8.3 6.4
Ketoconazo Concentration μgm/ml
le 28 29 27

Fig 3-B: Zone of inhibition of fungi by test compounds

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Table-7-A Minimum inhibitory Concentration (MIC) of Synthesized compounds against Gram positive bacteria
C.C BACTERIA
S. aureus B. subtilis S. epidermidis
Concentration μgm/ml
AB1 12 13 12
AB2 7 8 10
AB3 22 23 20
AB4 25 26 22
AB5 27 28 30
AB6 30 32 33
AB7 17 18 17
AB8 33 37 37
Ciprofloxacin 0.2 0.2 0.2

Table-7-B: Minimum inhibitory Concentration (MIC) of Synthesized Compounds against Gram negative bacteria
C.C BACTERIA
E. coli P. aeruginosa V. cholerae
Concentration μg/ml
AB1 13 12 12
AB2 8 7 10
AB3 23 22 20
AB4 22 26 22

AB5 28 27 30
AB6 30 32 33
AB7 15 18 17
AB8 37 33 37
Ciprofloxacin 0.3 0.3 0.3

Table-7-C: Minimum Inhibitory Concentration (MIC) of Synthesized Compounds against fungi

C.C FUNGI
A. niger C. albicans B. dermatitis
Concentration μgm/ml
AB1 12 12 13
AB2 10 7 8
AB3 20 22 23
AB4 25 26 26
AB5 30 27 28
AB6 33 32 35
AB7 17 18 18
AB8 35 33 37
Ketoconazole 5 5 5

Fig-4A: MIC of synthesized compounds against different bacteria.

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Fig-4-B: MIC of synthesized compounds against different fungi

6. DISCUSSION  When compared to standard drug ciprofloxacin,

compounds AB2, AB1, AB7, AB3, AB4 were found to
6. 1. Experimental chemistry exhibit good Antibacterial activity.
An Rf value was characteristic for any given compound  When compared to standard drug ketoconazole,
(provided that the same stationary and mobile phases are compounds AB2, AB1, AB7, AB3, AB4 and AB8 were
used). It provided corroborative evidence as to the identity found to exhibit good antifungal activity.
of the new synthetic compound. Rf values of synthesized
compounds indicated the reaction was proceeded in right (ii) The MIC of synthesized compounds was screened by agar
direction and purity of new synthetic derivatives (AB1-AB8). streak dilution method and from the experimental data the
The synthetic procedure of oxadiazole derivatives was found following observation was made:

to have satisfactory yield. All the synthesized compounds
All the synthesized compounds exhibited moderate to
were found to be insoluble in water, slightly soluble in
good antibacterial and antifungal activity with an MIC
Chloroform, ethanol and freely soluble in DMF, DMSO. The
range of 12-37µg/ml.
spectral analysis confirmed the successful synthesis of
desired compounds.  Among these eight synthesized oxadiazole derivatives,
compound AB1; AB2 and AB7 were found to be very
6. 2. Computational chemistry
good antibacterial as well as antifungal potentiality
Most of the scoring functions in molecular docking are with an MIC range of 13-12 µg/ml; 7-10 µg/ml and 15-
physics based molecular mechanics force fields that estimate 18 µg/ml.
the energy of the binding pose; a low (negative) energy
indicates a stable system and thus a likely binding
7. CONCLUSION
interaction. Molecular docking is performed to find out the Here we concluded that the compound AB2, AB1, AB7, AB3,
binding affinity or molecular interaction energy (kcal/mol) AB4 and AB8 possessed potential antimicrobial activity
of docked compounds. Lowest (negative value) energy of against following bacteria: S. aureus (ATCC 9144), B. subtilis
docked molecule indicates high binding affinity with the (ATCC 6633), S. epidermidis (ATCC 12228), P. Aeruginosa
target protein/compound. In silico molecular docking (ATCC27853), E.coli (ATCC25922), V. cholerrae (ATCC14035)
studies the binding energy of synthesized compounds (AB1- and fungi: A. Niger (ATCC 9029), A.flavus (ATCC204304), C.
AB8) were found to be -7.66, -7.67, -7.12, -7.12, -6.59, -6.46, albicans (ATCC10231) and B. dermatitis (ATCC 26199) etc.
-7.35, -5.09 which indicated that the compound had high The antibacterial potentiality of synthesized compounds
binding affinity towards the bacterial DNA gyrase were correlated with in silico molecular docking studies
(topoisomerase) with PDB id 3G7E and inhibit the function which was also proved molecular interaction of the
topoisomerase in comparison with standard drug compounds with the target protein bacterial DNA gyrase for
ciprofloxacin (-7.44). their binding affinity and known to be inhibitors for bacterial
6. 3. Experimental microbiology DNA gyrase.

(i) Synthesized compounds were (50, 100 and 150 g/ml) ACKNOWLEDGEMENT
screened for antimicrobial activity by paper disc diffusion We would like to thank the Department of Pharmaceutical
method. From the data shown in table the observations Microbiology and Biotechnology, Anurag Pharmacy College,
were made as followed: Suryapet, Kodad, Telangana. We would like to express our
 Most of the synthesized compounds executed moderate heartful thank to Indian Nobel Research Solution, Chennai,
to good antimicrobial activity against the tested Tamil Nadu.
microorganisms. CONFLICT OF INTEREST
We declare that we have no conflict of interest.
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Bhaumik et al Journal of Drug Delivery & Therapeutics. 2019; 9(4):438-453

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