Advances in Biological Chemistry, 2011, 1, 7-14 ABC
doi:10.4236/abc.2011.12002 Published Online August 2011 (http://www.SciRP.org/journal/abc/).
Published Online August 2011 in SciRes. http://www.scirp.org/journal/ABC
Novel 1,3,4-(thiadiazol-2-ylamino)
methyl-5-(pyridin-4-yl)-1,3,4-oxadiazol-2-thiones:
synthesis, docking and antimycobacterial testing
Trupti S. Chitre, Santosh Panda, Shital M. Patil, Aparna S. Chothe, G. Vignesh,
Amol B. Salake, Muthu K. Kathiravan*
Department of Pharmaceutical Chemistry, (PGwing), AISSMS College of Pharmacy, Maharashtra, India.
Received 17 May 2011; revised 2 June 2011; accepted 2 July 2011.
ABSTRACT
In the present study, a novel series of Mannich
bases of 3-substituted 5-(pyridin-4-yl)-1,3, 4-oxadi-
azol-2-thione derivatives were synthesized. Docking
study was performed to rationalize the possible in-
teractions between the synthesized compounds and
active site of 14DM. The test compounds were
screened for antimycobacterial activity using Mid-
dlebrook 7H9 medium against M. tuberculosis H37Rv
(ATCC 27294) as well as Isoniazid (INH) resistant
clinical strain. Among the series 5c and 5a are found
to be most potent (susceptible) while the compound
5f did not show activity against M. tuberculosis
H37Rv (resistant). The SAR study reveals the im-
portance of substitutions at para position for good
activity.
Keywords: Mannich Base; Oxadiazole; Thiadiazole;
Antimycobacterial; Docking
1. INTRODUCTION
Tuberculosis (TB) is a pandemic disease and its causa-
tive agent Mycobacterium tuberculosis is one of the
most prolific infectious agents affecting humans. The
196 countries reporting to WHO in 2008 notified 5.6
million new and relapse cases in 2007, of which 2.6 mil-
lion (46%) were new smear-positive cases [1]. Further-
more, treatment of tuberculosis with human immuno
deficiency virus infected patients (HIV) is difficult and
results as the leading cause of death among HIV positive
patients worldwide. Another factor which contributes to
more number of deaths is the emergence of multiple
drug resistance (MDR) [2-5].
1,3,4-Oxadiazoles and thiadiazoles have been reported
as potent heterocyclic ring system with wide spectrum of
biological activities [6-10]. Recently, 1,3,4-oxadiazole
derivatives has been reported as antimycobacterial
agents also [11]. The conversion of Isoniazid (INH) to
Oxadiazoles produces the corresponding 5- substituted
3H-1,3,4-oxadiazol-2-thione, 3H-1,3,4,-oxadiazol-2-one
and their 3-alkyl or aralkyl derivatives and is responsible
for potent activity against M. tuberculosis strain H37Rv
[12,13]. Foroumadi et al have reported a series of alkyl
(5-(nitroaryl)-1,3,4-thiadiazole-2-ylthio) propionates as
antimycobacterial agents [14]. The biologically active
derivatives synthesized as mannich bases are reported to
be physiologically important because of the altered solu-
bility in aqueous solvents and has been used as antitu-
bercular, antimalarial, vasorelaxing, anticancer and an-
algesic drugs [15-18].
Till now, no new drug has been introduced since the
discovery of Rifampin in spite of major advances that
have been made in the drug discovery process. Hence,
there is an overwhelming need to develop novel anti-
mycobacterial agents. Literature survey revealed that
genomic DNA from the M. tuberculosis (MT) H37
Rvstrain, CYP 51-like gene encodes a bacterial sterol
14α-demethylase (MT P450 14DM), which acts on 14 α
-methyl sterols. Recently we have reported a series of
novel 4-(morpholin-4-yl)-N’-(arylidene) benzohy-dra-
zides as antimycobacterial agent [19]. In continuation of
our project in development of new antimycobacterial
agents, we thought of hybridizing the two potential
pharmacophores i.e., 1,3,4-oxadiazole and thiadiazole
which as such has been reported as antimycobacterial
agents. Furthermore, solubility plays an important role
for the development of drug in tuberculosis. Thus our
aim was further refined to synthesize mannich base of
these two pharmacophores and evaluate them for anti
antimycobacterial activity. Herein we report the synthe-
sis, docking and in vitro antimycobacterial activity of a

T. S. Chitre et al. / Advances in Biological Chemistry, 2011, 1, 7-14 8
series of mannich bases belonging to
5-(pyridine-4-yl)-1,3,4-oxadiazo l-2-thiones. The dock-
ing study was performed to rationalize the possible in-
teractions between the synthesized compounds and the
active site of 14DM.
2. EXPERIMENTAL
2.1. Chemistry
The synthetic route used for the title compounds is out-
lined in Scheme 1. The thiosemicarbazones 2 were pre-
pared by refluxing thiosemicarbazide and appropriate
aromatic aldehydes 1 at 80˚C for 4 hr. 2-amino –
5-substituted 1,3,4-thiadiazole 3 were obtained by re-
fluxing thiosemicarbazones 2 with ammonium ferric
sulphate in water for 5 hrs. Oxadiazole-2-thione 4 was
prepared according to the method reported in the litera-
ture using Isoniazid as starting material [13]. Mannich
bases 5a-f were obtained by reacting 2-amino-5-substi-
tuted 1,3,4-thiadiazole and oxadiazole-2-thione in DMF
with formamide for 2-3 hr [20-22].
2.2. Modeling Studies
2.2.1. Molecul ar Docki n g Protoc ol
All computations were carried out on a Wipro Intel Pen-
tium processor with Windows XP Operating System. All
the compounds were constructed using standard frag-
ment library of Maestro 8.0 and geometry optimization
was done by Macromodel program Schrödinger, LLC)
using Optimized Potentials for Liquid Simulations-all
atom (OPLS-AA) force field [23]. The molecular dock-
ing tool, GLIDE (Schrodinger Inc., USA) was used for
ligand docking studies into the X-ray crystal structure of
cytochrome P450 14α-sterol Demethylase (14DM) from
Mycobacterium in complex with 4-phenylimidazole
(PDB entry code 1E9X) [24] were downloaded from the
RCSB Protein Data Bank (PDB). The protein structure
was prepared for docking using ‘protein preparation
wizard’ in Maestro wizard 8.0. The protein preparation
uses the OPLS force field 23 for this purpose. Grids
were defined by centering them on the ligand in the
crystal structure using the 10 Å box size. Ligprep 2.2
module utilized to produce the low energy conformer of
ligands using MMFF94 force field [25]. The lower en-
ergy conformations of the ligands were selected and
were docked into the grid generated from protein struc-
tures using standard precision (SP) docking mode [26].
2.2.2. Docking and Scoring Functions
The docking studies were performed for the designed
compounds with 14DM enzyme and the results were
compared with the natural ligand phenyl imidazole pre-
sent within the receptor. The docked complexes of the
designed compounds along with the ligand receptor poses
have been shown in the Figure 1. The final evaluation is
done with glide score (docking score) and single best
pose is generated as the output for particular ligand.
**
Gscore=avdwbcow+Lipo+H bond
+Metal+BuryP+Rot B+Site

where, vdW: Van der Waal energy; Coul: Coulomb en-
ergy; Lipo: lipophilic contact term; HBond: hydro-
gen-bonding term; Metal: metal-binding term; BuryP:
penalty for buried polar groups; RotB: penalty for freez-
ing rotatable bonds; Site: polar interactions at the active
site; and the Coefficients of vdW and Coul are: a = 0.065,
b = 0.130. If GScore was selected as the scoring function,
a composite Emodel score is then used to rank the poses
of each ligand and to select the poses to be reported to
the user. Emodel combines GlideScore, the nonbonded
interaction energy, and, for flexible docking, the excess
internal energy of the generated ligand conformation.
2.2.3. Antimycobacterial Acti vity
All the newly synthesized mannich bases were assayed
in vitro for antitubercular activity against M. tuberculosis
H37Rv (ATCC 27294) and Isoniazid resistant strain. The
anti-TB screening was carried out by using Middlebrook
7H9 medium [27,28].
3. RESULTS
3.1. Modeling
The docked complex of the designed compounds is
shown in Figure 1. The designed compounds were
found to display good binding affinity to the receptor.
G-score, H-Bond Interaction and Contacts The more
negative value of G-score indicates that the compound is
more potent and good binding affinity (Table 1). The
Standard (CoCrystalisedLigand) and Isoniazid have
shown G-Score of –4.73 and –5.02. The G-score of the
designed compounds were found to be 5c > 5a > Isoni
azid > 5b > 5e > standard co-crystallized ligand > 5d.
Besides the G-score, other parameters like energy and
the E-model were also taken into consideration for the
evaluation of the docking results; the values of the en-
ergy and E-model were found to be significantly more
than that of the values of the standard co-crystallized
ligand and Isoniazid. The designed compounds, 5a and
5d found to display 1 and 2 H- bonds with HIS 259 re-
spectively. Standard (CoCrystalised Ligand) showed 1
H-Bond with HIS 259. It is well established and ac-
cepted fact that number of good van der Waals interac-
tions decides the binding affinity for any ligand with
receptor enzyme protein and bad, ugly contacts indicate
steric clashes after docking which should be less for
good activity. Therefore we have analyzed the binding

T. S. Chitre et al. / Advances in Biological Chemistry, 2011, 1, 7-14 9
Scheme 1. Synthesis of 1,3,4-(thiadiazol-2-ylamino)methyl-5-(pyridine-4-yl)-1,3,4- oxadia-
zol-2-thione. Reagents and conditions (a) Ethanol, HCl, Reflux (b) Ammonium ferric sul-
phate, H2O, Reflux, (c) CS2, KOH, (d) CH2O, 37%.
Figure 1. (a) Binding mode of 5c inside the pocket of crystal structure 14 demethylase; (b) Binding of 5a in
14 demethylase.
modes and abilities, considering the number of good,
bad and ugly van der Waals (vdW) interactions of the
standard and designed compounds with 14-DM active
binding site.
3.2. ADME Properties
We have analyzed 44 physical descriptors and pharma-
ceutically relevant properties of mannich bases of

T. S. Chitre et al. / Advances in Biological Chemistry, 2011, 1, 7-14 10
3-substituted 5-(pyridine-4-yl)-1,3,4-oxadiazol-2-thione
derivatives using Qikprop, among which significant de-
scriptors are reported (Table 2) and are important for
predicting the drug-like properties of molecules. These
properties were:
1) Molecular weight (Mol_MW) (130 - 460)
2) Octanol/water partition coefficient (Log Po/w) (–2 -
3.6)
3) Aqueous solubility (QPlogS) (–5.5 - 1)
4) Apparent MDCK cell permeability (QPPMDCK)
(<25 poor, >500 great)
5) Brain/blood partition coefficient (QPlogBB)
(<–1.7)
6) Percent human oral absorption (C80% is high,
B25% is poor)
3.3. Antimycobacterial Activity
Amongst the compound tested 5c and 5a have shown
good antimycobacterial activity (susceptible) against M.
tuberculosis H37Rv (ATCC 27294) among the series.
The effect of other test compounds on H37Rv and
Isoniazid resistant strain is given in Table 3.
4. DISCUSSION
The results obtained reveals that the nature of substitu-
ents on the aromatic ring have a considerable impact on
the antitubercular activities of the test compounds. Litera-
ture survey indicates that electrons-withdrawing groups
amend lipophilicity of the test compounds, which in turn
alters permeability across the mycobacterial cell mem-
brane. Furthermore, the presence of electronegative atom
such as fluoro in 5c has shown better activity than
5e and 5b which have nitro at ortho and meta position
respectively, clearly indicating the importance of para
positions for substitutions. Also 5a bearing a methoxy
group at para position have shown good activity. Nitro
group in spite of being electron withdrawing does not
show significant biological response, revealing the im-
portance of para substitution than ortho and meta. Com-
plete lose of activity in 5d and 5f observed may be due to
bulky less and steric factors. This is well supported by the
docking studies performed, as more the G score of the
test compounds better the activity and binding ability of
molecule into the active site. Our docking indicates good
van der Waals interaction than the standard with 14DM.
Unlike antifungal azoles, it had shown just a stacking
effect with Fe of 14DM and not binding with Fe.
5. CONCLUSIONS
In conclusion a series of mannich bases containing two
pharmacophores were synthesized and characterized.
Molecular docking studies were performed in 14 DM
protein docked with ligand to identify the possible inter-
action. However two test compounds have shown better
G score than Isoniazid. The test compounds were sub-
jected to antimycobacterial study against H37Rv and
INH Resistant Clinical Strain. Larger G score better the
binding affinity of test molecules and is reflected in an-
timycobacterial activity indicating a direct correlation
between observed activity and energy score. This indi-
cates that the designed series of mannich bases possess-
ing electron withdrawing group at para position have
shown antimycobacterial activity. So, these factors col-
lectively indicate the importance, simplicity and wide
applicability of designed series as antimycobacterial
activity.
6. SUPPLEMENTARY INFORMATION
(SI)
Synthesis of 5-(pyridine-4-yl)-1,3,4-oxadiazole-2(3H)-
thione 4.
The compound, 5-(pyridine-4-yl)-1,3,4-oxadiazole-
2(3H)-thione were prepared as per the reported proce-
dure [13].
Synthesis of Thiosemicarbazones 2.
A mixture of appropriate aromatic aldehyde 1 (1 g,
8.06 mmol), thiosemicarbazide (0.73g, 8.06 mmol) and
catalytic amount of HCl in 10 ml ethanol were refluxed
at 80˚C. The progress of the reaction was monitored by
TLC. On completion, solvent were removed under vac-
uum. The solid obtained was recrystallized from 50%
aqueous ethanol.
Synthesis of 2-Amino thiadiazoles 3.
A mixture of thiosemicarbazone 2 (1g, 5.07 mmol)
and ammonium ferric sulfate dodecahydrate (0.1 g) in
H2O (5 ml) were refluxed for 1 h. Then 1 g ammonium
ferric sulfate in H2O (10 ml) were added and further
continued for 5 hr. On completion of reaction, the mix-
ture was chilled; the solid separated was filtered off,
washed and crystallized from EtOH-H2O.
Synthesis of Mannich bases 5a-f
General procedure for the synthesis of
1,3,4-thiadiazol-2-ylamino)methyl)-5-(pyridine-4-yl)-1,3
,4-oxadiazole-2(3H)-thione.
Oxadiazole-2-thione 4 (0.5 g, 2.79 mmol) and substi-
tuted 2-amino thiadiazoles 3 (0.54 g, 2.79 mmol) were
mixed in 15 ml absolute ethanol and stirred. To the
stirred suspension (2.79 mmol, 37%) formaldehyde was
added drop wise and heated to reflux for 10 - 12 hrs. The
progress of the reaction was monitored by TLC. On
completion, reaction mixture was concentrated under
reduced pressure and the residue obtained were re-
crysatllised from appropriate solvent.
Representative data from the series
3-((5-(4-methoxyphenyl)-1,3,4-thiadiazol-2-ylamino)
methyl)-5-(pyridin-4-yl)-1,3,4-oxadiazole-2(3H)-thione

T. S. Chitre et al. / Advances in Biological Chemistry, 2011, 1, 7-14 11
Table 1. Results of molecular docking studies using standard precision mode of Glide.
Sr. No Title G-score E-Model Energy H-Bond Good VDW Bad VDW Ugly
VDW
1 5c –5.70 –59.7 -46.3 0 167 5 0
2 5a –5.66 –52.3 -40.7 1 193 5 1
3 Isoniazid –5.02 –32.4 -21.8 2 82 1 1
4 5b –4.91 –55.9 -43.3 0 168 1 0
5 5e –4.73 –57.3 -44.3 0 157 0 0
6
Standard
(CoCrystalised
Ligand)
–4.73 –34.3 -21.6 1 119 1 0
7 5d –4.60 –55.0 -42.7 2 170 0 0
8 5f –4.57 –52.0 -41.3 0 160 0 0
Table 2. Prediction of ADME properties of designed derivatives using qikprop.
Compd. no. Mol_MW Log Po/wLog SLog BBPMDCKHuman oral absorption (%)
5a 398.45 3.025 –5.076–0.6521191.7696.55
5b 413.42 2.397 –4.856–1.379209.62 80.46
5d 458.50 2.226 –5.253–0.8021193.20100
5e 413.42 3.663 –5.007–1.671120.54 75.37
5f 394.46 –1.592 –5.564–0.8221266.35100
5c 386.42 3.195 –5.342–0.4772127.74100
Isoniazid 137.14 –0.646 –0.052–0.843123.74 66.89
Higher the value of MDCK cell, higher the cell permeability. All designed compounds have shown the ADME properties in acceptable range.
(5a)
83%, mp 243-245. 1H NMR (CDCl3) δ (ppm): 3.73 (s,
3H, OCH3), 4.0 (s, 1H, NH), 4.81(s, 2H, CH2), 7.21-7.65
(m, 4H, phenyl), 7.73-7.85 (d, 2H, pyridyl), 8.12-8.31(d,
2H, pyridyl). MS (m/z %) 398 (M+), 399 (M+1). Anal.
Calcd for C17H14N6O2S2: C, 51.24; H, 3.54; N, 21.09;
Found C, 51.41; H, 3.44; N, 21.11
3-((5-(4-fluorophenyl)-1,3,4-thiadiazol-2-ylamino)met
hyl)-5-(pyridin-4-yl)-1,3,4-oxadiazole-2(3H)-thione ( 5c)
79.2%, mp 257-259. 1H NMR (CDCl3) δ (ppm): 4.32 (s,
1H, NH), 4.61 (s, 2H, CH2), 7.17 - 7.44 (m, 4H, phenyl),
7.53 - 7.72 (d, 2H, pyridyn), 7.98 - 8.21(d, 2H, pyridyn).
MS (m/z %) 386 (M+), 387 (M+1). Anal. Calcd for
C16H11FN6OS 2: C, 49.73; H, 2.87; F,4.92; N, 21.75; O,
4.14; S, 16.60; Found C, 49.63; H, 2.76; N, 21.69
3-((5-(3-nitr ophenyl)- 1,3,4-thiadiazol-2 -ylamino) methyl
)-5-(pyridin-4-yl)-1,3,4-oxadiazole-2(3H)-thione (5e)
82.8%, mp 272-273˚C. 1H NMR (CDCl3) δ (ppm):
4.35 (s, 1H, NH), 4.58 (s, 2H, CH2), 7.61-7.91 (m, 4H,
phenyl), 7.96-8.12 (d, 2H, pyridin), 8.23-8.48 (d, 2H,
pyridyn). MS (m/z%) 413 (M+), 414 (M+1). Anal. Calcd
for C16H11N7O3S2: C, 46.48; H, 2.68; N, 23.72; Found C,
46.53; H, 2.84; N, 23.79
Anti-TB sensitivity test by Middlebrook 7H-9 broth
(Macro)
The anti-TB screening was carried out by using
Mid dlebrook 7H9 medium [25,26] against M. tuberculosis
H37Rv (ATCC 27294). The basal medium was prepared,
sterilized and to 4.5 ml of this broth, 0.5 ml of ADC
(al-bumin-dextrose-catalase) supplement was added.
Then a stock solution (10 mg/ml) of the test compounds
was prepared and the final concentrations of 10, 25 and
50 µg/ml were transferred to media bottles. Finally, 10
µg suspension of M. tuberculosis H37Rv strain (100,000
organisms/ml adjusted by McFarland’s turbidity stan-
dard) was transferred to each of the tubes and incubated
at 37˚C along with one growth control without com-
pound and drug control was also set up. The bottles were
observed for growth twice a week for a period of three
weeks.The appearance of turbidity was considered as
growth and indicates resistance to the compound. The
growth was confirmed by making a smear from each bottle
and performing a Zeil-Nelson stain at the end of 4
weeks.

T. S. Chitre et al. / Advances in Biological Chemistry, 2011, 1, 7-14 12
Table 3. Results of H37Rv and INH Resistant clinical strain testing.
N
NN
OS
NH
S
N
N
Ar
Compound Code Ar MIC in μg ml–1 (H37Rv) MIC in μg ml–1 (INH Resis-
tant Clinical Strain)
5a
OCH
3
12.5 >25
5b
O
2
N
>50 >100
5c
F
6.25 25
5d
OCH
3
OCH
3
OCH
3
>100 nd
5e
NO
2
>25 >100
5f >100 nd
Std Isoniazid 0.25 --
nd = not determined
7. ACKNOWLEDGMENTS
We are grateful to Dr. Mrs. A. R. Madgulkar, Principal, AISSMS Col-
lege of Pharmacy, Pune, for providing us with the necessary financial
support and infrastructure for carrying out this work.
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