Synthesis, spectroscopic analyses, chemical reactivity and molecular docking study and anti-tubercular activity of pyrazine and condensed oxadiazole derivatives

Article abstract of DOI:10.1016/j.molstruc.2018.03.085

The FT-IR spectral analysis and theoretical calculations of the wavenumbers of three oxadiazole derivatives, 2-(5-(2-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (ORTHOPHPZ), 2-(5-(3-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (METAPHPZ) and 2-(5-(4-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (PARAPHPZ) were reported in the present work. The theoretically predicted values of polarizability give the nonlinear behaviour of the compounds. The frontier molecular orbital analysis show the chemical stability of the title compounds and the NBO analysis gives the interactions in the molecular systems. Understanding of reactivity of newly synthetiszed oxadiazole derivatives in this study has been achieved thanks to combination of density functional theory (DFT) calculations, molecular dynamics (MD) simulations and molecular docking procedures. New oxadiazole derivatives have also been characterized experimentally through FT-IR and NMR approaches, thanks to which detailed structural properties have been understood. Both global and local reactivity properties have been investigated by calculations of quantum molecular descriptors such as molecular electrostatic potential (MEP), local average ionization energy (ALIE), Fukui functions, bond dissociation energies for hydrogen abstraction (H-BDE), radial distribution functions and binding energies of ligand against selected protein. The first hyperpolarizabilities of ORTHOPHPZ, METAPHPZ and PARAPHPZ are respectively, 84.62, 94.71 and 184.10 times that of urea. The docked ligands form stable complexes with the receptor 1-phosphatidylinositol phosphodiesterase and the results suggest that these compounds can be developed as new anti-cancer drugs. The anti-TB activity of PM series against M. tuberculosis H37RV strain was performed by Middlebrooke 7H-9 method. The compounds, ORTHOPHPZ, METAPHPZ and PARAPHPZ were moderately active between 25 and 50 μg/ml concentration as compared with the standard anti-TB agents and the –log MIC activity was found in the range of 1.011–1.274 as compared with isoniazid (INH) (1.137) and pyrazinamide (PZA) (1.115) standard anti-TB agents.

Full text of DOI:10.1016/j.molstruc.2018.03.085

Accepted Manuscript
Synthesis, spectroscopic analyses, chemical reactivity and molecular docking study
and anti-tubercular activity of pyrazine and condensed oxadiazole derivatives
Abdul-Malek S. Al-Tamimi, Y. Sheena Mary, Pankaj B. Miniyar, Lamya H. Al-Wahaibi,
Ali A. El-Emam, Stevan Armaković, Sanja J. Armaković
PII:
S0022-2860(18)30373-9
10.1016/j.molstruc.2018.03.085
MOLSTR 25024
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 15 February 2018
Revised Date: 21 March 2018
Accepted Date: 21 March 2018
Please cite this article as: A.-M.S. Al-Tamimi, Y.S. Mary, P.B. Miniyar, L.H. Al-Wahaibi, A.A. El-Emam,
S. Armaković, S.J. Armaković, Synthesis, spectroscopic analyses, chemical reactivity and molecular
docking study and anti-tubercular activity of pyrazine and condensed oxadiazole derivatives, Journal of
Molecular Structure (2018), doi: 10.1016/j.molstruc.2018.03.085.
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to
our customers we are providing this early version of the manuscript. The manuscript will undergo
copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please
note that during the production process errors may be discovered which could affect the content, and all
legal disclaimers that apply to the journal pertain.

ACCEPTED MANUSCRIPT

ACCEPTED MANUSCRIPT
Synthesis, spectroscopic analyses, chemical reactivity and molecular docking study and
anti-tubercular activity of pyrazine and condensed oxadiazole derivatives
Abdul-Malek S. Al-Tamimia, Y.Sheena Maryb*, Pankaj B.Miniyarc, Lamya H. Al-
Wahaibid, Ali A. El-Emame, Stevan Armakovićf, Sanja J. Armakovićg
a Department of Pharmaceutical Chemistry, College of Pharmacy, Sattam bin Abdulaziz
University, Alkharj 11942, Saudi Arabia
b Department of Physics, Fatima Mata National College, Kollam, Kerala, India
cDepartment of Pharmaceutical Chemistry, Sinhgad Institute of Pharmacy, Narhe, Pune,
University of Pune, Ganeshkhind, India
d Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman
University, Riyadh 11671, Saudi Arabia
e Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura,
Mansoura 35516, Egypt
f University of Novi Sad, Faculty of Sciences, Department of Physics,
Trg D. Obradovića 4, 21000 Novi Sad, Serbia
g University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry
and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia
*author for correspondence:email:sypanicker@rediffmail.com
Abstract
The FT-IR spectral analysis and theoretical calculations of the wavenumbers of three
oxadiazole
derivatives,
2-(5-(2-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine
(ORTHOPHPZ), 2-(5-(3-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (METAPHPZ) and
2-(5-(4-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (PARAPHPZ) were reported in the
present work. The theoretically predicted values of polarizability give the nonlinear
behaviour of the compounds. The frontier molecular orbital analysis show the chemical
1

ACCEPTED MANUSCRIPT
stability of the title compounds and the NBO analysis gives the interactions in the
molecular systems. Understanding of reactivity of newly synthetiszed oxadiazole
derivatives in this study has been achieved thanks to combination of density functional
theory (DFT) calculations, molecular dynamics (MD) simulations and molecular docking
procedures. New oxadiazole derivatives have also been characterized experimentally
through FT-IR and NMR approaches, thanks to which detailed structural properties have
been understood. Both global and local reactivity properties have been investigated by
calculations of quantum molecular descriptors such as molecular electrostatic potential
(MEP), local average ionization energy (ALIE), Fukui functions, bond dissociation
energies for hydrogen abstraction (H-BDE), radial distribution functions and binding
energies of ligand against selected protein. The first hyperpolarizabilities of
ORTHOPHPZ, METAPHPZ and PARAPHPZ are respectively, 84.62, 94.71 and 184.10
times that of urea. The docked ligands form stable complexes with the receptor 1-
phosphatidylinositol phosphodiesterase and the results suggest that these compounds can
be developed as new anti-cancer drugs. The anti-TB activity of PM series against M.
tuberculosis H37RV strain was performed by Middlebrooke 7H-9 method. The
compounds, ORTHOPHPZ, METAPHPZ and PARAPHPZ were moderately active
between 25 to 50 µg/mL concentration as compared with the standard anti-TB agents and
the –log MIC activity was found in the range of 1.011 to 1.274 as compared with isoniazid
(INH) (1.137) and pyrazinamide (PZA) (1.115) standard anti-TB agents.
Keywords: DFT; ALIE; RDF; BDE; NLO; Molecular docking.
1.
Introduction
Pyrazine nucleus constitutes the essential pharmacophore of various
chemotherapeutic agents. Pyrazinamide and morinamide are currently used as effective
therapy for the treatment of tuberculosis [1-3]. After the discovery of pyrazinamide,
several pyrazine derivatives were proved to possess potent activity against pyrazinamide-
resistant TB strains [4-8]. The pyrazine-based drugs Oltipraz [9] and Bortezomib [10]
were developed as potent anticancer agents. In addition, pyrazine derivatives were
reported to display marked antifungal [11], antibacterial [8, 12], anti-malarial [13] and
herbicidal [14] activities. On the other hand, 1,3,4-oxadiazole derivatives were early
2

ACCEPTED MANUSCRIPT
recognized as a structural motif of particular value as efficient chemotherapeutic agents
possessing significant antibacterial [15-17], antifungal [18], anti-tubercular [19], antiviral
[20,21] and anticancer [22,23] activities. Various global and local quantum-molecular
descriptors have been employed in order to understand in details reactive properties of
newly synthetized oxadiazole derivatives. Spectroscopic characterization via FT-IR and
NMR approaches has been performed as well, and confirmed computationally at adequate
levels of theory. The principles of molecular modeling have been widely accepted as
important and inexpensive computational tools for understanding of fundamental reactive
properties [24-28]. Locating molecular sites of high reactivity are important for
understanding of degradation properties of organic pollutants [29-32]. Beside DFT
calculations, MD simulations are particularly important for the investigation of solvent
effects by explicit consideration of the influence of solvating molecules [33-35].
2.
Experimental details
Synthesis of the compounds:
General procedure for synthesis of pyrazine-2-carbohydrazide [36]
A mixture of pyrazinoic acid hydrazide (1mmol), substituted aromatic aldehyde
(1mmol) in ethanol (5mL) was heated under reflux with stirring for 30 min. Water (5mL)
was added and the precipitated product was filtered and re-crystallized from ethanol.
General procedure for synthesis of 2,5-disubstituted-1,3,4-oxadiazole [36]
Pyrazine-2-carbohydrazide (0.75mmol) and ammonium cerium(IV) nitrate
(1mmol) were ground in a mortar and pestle at room temperature without any solvent for
20 min. Dichloromethane (5mL) was added followed by addition of water (5mL). The
organic phase was separated and dried over MgSO4. The mixture was concentrated and
the solid residue was re-crystallized from dichloromethane.
Organic synthesis
Pyrazinoic acid was prepared from pyrazinamide by alkaline hydrolysis. The core
intermediate pyrazinoic acid hydrazide was prepared from pyrazinoic acid by
esterification followed by hydrazinolysis. The hydrazones were prepared by condensation
of hydrazide with different substituted aromatic aldehyde in ethanol. The final compounds
ORTHOPHPZ, METAPHPZ and PARAPHPZ were prepared according to procedure
3

ACCEPTED MANUSCRIPT
described in literature (scheme 1-supporting material). The structure of the final
compounds was fully characterized on the basis of melting points. FT-IR spectra (Fig.S1-
supporting information) were recorded by JASCO FTIR 4100 series in the range of 4000-
1
400 cm-1 using the standard KBr pellet technique. HNMR spectra were recorded by
Varian-NMR-Mercury 300 using DMSO as a solvent and their chemical shifts are
recorded in δ (parts per million) units with respect to tetramethylsilane (TMS) as an
internal standard. Mass spectra were recorded using time of flight detector
ORTHOPHPZ(2-(5-(2-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine): Yield 62%; m.p.
1
218-221°C; H NMR (300 MHz, CDCl3) (δ ppm): 8.741-8.848 (m, 3H, pyrazine), 7.312-
7.393 (m, 4H, aromatic); MS (m/z) : 259.3 (M+1)+; METAPHPZ(2-(5-(3-chlorophenyl)-
1,3,4-oxadiazol-2-yl)pyrazine): Yield 50%; m.p. 184-187°C.;PARAPHPZ(2-(5-(4-
chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine): Yield 58%; m.p. 148-150°C;.
3.
Computational details
Optimizations (Fig.1) and wavenumber calculations of the title compounds were
done at B3LYP/6-31G(d,p) level of theory using Gaussian09 software package [37]. The
vibrational assignments of the theoretical wavenumbers were done using Gaussview [38]
and GAR2PED program [39] and a scaling factor of 0.9613 is used to scale the
theoretically obtained wavenumbers [40]. Using NBO 3.1 program as implemented in the
Gaussian09 package, natural bond orbitals (NBO) calculations were performed [41, 42].
Schrödinger Materials Science Suite 2017-4(SMSS) for molecular modelling has been
primarily used for computational studies of newly synthetized oxadiazole derivatives. This
state-of-the-art software package consists of several powerful and highly efficient
programs, including MacroModel [43] for calculations based on classical potentials,
Jaguar [44-46] for DFT calculations and Desmond [47-50] for MD simulations. All
possible conformers of ORTHOPHPZ, METAPHPZ and PARAPHPZ molecules have
been generated with MacroModel program using OPLS3 [47, 51-53] force field. All
conformations have been geometrically optimized using B3LYP exchange-correlation
functional [54] and 6-31G(d,p) basis set using Jaguar program. Lowest energy conformers
have been chosen for further calculations, while their true ground states had been checked
by vibrational analysis which yielded only positive frequencies. MEP and ALIE
4

ACCEPTED MANUSCRIPT
descriptors have been calculated by single point energy calculations at B3LYP/6-
311++G(d,p) level of theory, while Fukui functions and H-BDE have been obtained also
with B3LYP functional and 6-31+G(d,p) and 6-311G(d,p) basis sets. OPLS3 force field
was used for MD simulations. Simulation time was set to 10 ns, temperature to 300 K,
pressure to 1.0325 bar and cut-off radius to 12 Å. The whole system was modelled by
placing of one corresponding molecule to the simulation box with ~3000 water molecules
and was considered as isothermal–isobaric (NPT) ensemble. Simple point charge (SPC)
model [55] was used for the description of solvent. Whenever SMSS software package
was used, manipulation of structures, preparation of input files and visualization of results
had been done with Maestro GUI [56]. All molecular docking calculations were
performed on AutoDock-Vina software and as reported in literature [57-59].
4.
Results and discussion
4.1
Biological study
From the MIC determination, it was found that compound ORTHOPHPZ (o-chloro
derivative) and METAPHPZ (m-chloro derivative) were more active than PZA which
exerts their activity at concentration of 0.8µg/ml while the PZA exerts its activity at
3.125µg/ml. At 1.6µg/ml conc., MTb H37Rv was found to be sensitive to compound
PARAPHPZ. The streptomycin was also used as another standard. All the compounds,
were found to be more active than streptomycin (MIC = 6.25 µg/ml). The synthesized
derivatives were tested in vitro for its antibacterial activity against two gram positive
bacteria viz., S. aureus and B. Subtilis; two gram negative bacteria viz. E. coli and S. typhi
at 250µg/ml. But all the tested derivatives show no activity against B. subtilis and E. coli.
In case of S. aureus, derivative METAPHPZ was found to be equipotent with the standard
while compound ORTHOPHPZ and PARAPHPZ showed activity less active than
standard. In case of S. typhi, only ORTHOPHPZ was found to be active. MIC for active
compound METAPHPZ against S. aureus was found at 250 µg/ml conc., but it is not
comparable with the standard Ciprofloxacin (table 1).
4.2
IR and VCD spectra
The observed IR bands, calculated scaled wavenumbers and assignments of
ORTHOPHPZ, METAPHPZ and PARAPHPZ are presented in table S1 (supporting
5

ACCEPTED MANUSCRIPT
material). In the following discussion, phenyl, pyrazine and oxadiazole rings are
designated as Ph, Pz and Ring, respectively.
C-Cl modes
For the title compounds, CCl stretching modes are assigned at 749 cm-1 (ORTHOPHPZ),
740 cm-1 (METAPHPZ), and at 722 cm-1 (PARAPHPZ) theoretically and bands are
observed in the IR spectrum at 750 cm-1 (ORTHOPHPZ), and at 725 cm-1 (PARAPHPZ)
and the reported values are at 656, 684 cm-1 in the IR spectrum and theoretically at 654,
688 cm-1 which is expected in the region 850-550 cm-1 [60].
Oxadiazole ring modes
The C=N stretching modes are assigned at 1434, 1428 cm-1 for ORTHOPHPZ, 1466, 1429
cm-1 for METAPHPZ and at 1464, 1429 cm-1 for PARAPHPZ theoretically and these
values are in agreement with literature [61]. The N-N stretching of oxadiazole ring is
expected in the range 1100-950 cm-1 [62]. DFT computation gives mode arising from the
N-N stretching at 944 cm-1 for ORTHOPHPZ, 895 cm-1 for METAPHPZ and at 921 cm-1
for PARAPHPZ [61]. For the title compound, the C-O stretching modes are assigned at
1060, 928 cm-1 for ORTHOPHPZ, 1034, 923 cm-1 for METAPHPZ and at 1034, 934 cm-1
for PARAPHPZ theoretically and these are in agreement with literature [61].
Pyrazine ring modes
The pyrazine CH stretching modes of the title compound are assigned 3119, 3112,
3094 cm-1 for ORTHOPHPZ, 3120, 3113, 3095 cm-1 for METAPHPZ and at 3120, 3113,
3094 cm-1 for PARAPHPZ theoretically which are expected in the range 3100-3000 cm-1
[63]. The pyrazine CH stretching modes of the title compounds were observed at 3075,
3050 cm-1 for METAPHPZ and at 3099 cm-1 for PARAPHPZ in the IR spectrum. In the
present case, the pyrazine ring stretching modes were assigned at 1531, 1125 1026 cm-1
for ORTHOPHPZ, 1550, 1103 cm-1 for METAPHPZ and 1550, 1151, 1002 cm-1 for
PARAPHPZ in the IR spectrum and the PED analysis gives these modes in the ranges,
1548-1025 cm-1 for ORTHOPHPZ, 1548-1007 cm-1 for METAPHPZ and 1548-1000 cm-1
for PARAPHPZ [63, 64]. The reported values of pyrazine ring stretching modes are at
1525, 1120 cm-1 in the IR spectrum and at 1551, 1524, 1182, 1117, 1009 cm-1 (DFT) [64].
For the title compounds, the ring breathing mode of the pyrazine ring were assigned at 985
6

ACCEPTED MANUSCRIPT
cm-1 theoretically which is agreement with reported values [64]. For the title compounds,
the in-plane and out-of-plane CH bending modes of the pyrazine ring were assigned at
1323, 1285, 1181 cm-1 and at 974, 956, 859 cm-1 for ORTHOPHPZ, 1323, 1299, 1155 cm-
1 and 975, 956, 859 cm-1 for METAPHPZ and at 1306, 1232, 1082 cm-1 and 975, 956, 859
cm-1 for PARAPHPZ, theoretically. The experimentally observed values are at 954, 855
cm-1 for ORTHOPHPZ, 975, 954, 856 cm-1 for METAPHPZ and at 1078, 977, 954, 857
cm-1 for PARAPHPZ in the IR spectrum are in agreement with the literature [63, 64].
Phenyl ring modes
The phenyl ring stretching modes are assigned at 1588, 1508, 1303 cm-1 (IR),
1595-1306 cm-1 (DFT) for ORTHOPHPZ, 1567, 1470, 1402 cm-1 (IR), 1598-1321 cm-1
(DFT) for METAPHPZ and 1600, 1579, 1470, 1403 cm-1 (IR), 1593-1325 cm-1 (DFT) for
PARAPHPZ as expected [65]. In the present case, the ring breathing mode of
ORTHOPHPZ is assigned at 1026 cm-1 in the IR spectrum and at 1027 cm-1 theoretically
[66]. For the 1,3-disubstituted benzene ring of METAPHPZ, the ring breathing mode is
assigned at 990 cm-1 (DFT) and for 1,4-disubstituted phenyl ring of PARAPHPZ, the ring
breathing mode is assigned at 1020 cm-1 in the IR spectrum and at 1011 cm-1 theoretically
as expected [65, 66]. The in-plane CH deformation modes of the phenyl rings are
assigned at 1125 cm-1 (IR), 1263, 1155, 1125, 1092 cm-1 (DFT) for ORTHOPHPZ, 1274,
1075 cm-1 (IR), 1271, 1182, 1078, 1070 cm-1 (DFT) for METAPHPZ and at 1108, 1020
cm-1 (IR), 1312, 1187, 1113, 1011 cm-1 (DFT) for PARAPHPZ as expected [65]. The out-
of-plane phenyl CH bending modes are assigned theoretically in the ranges, 1004-751 cm-
1
for ORTHOPHPZ, 993-765 cm-1 for METAPHPZ and 985-849 cm-1 for PARAPHPZ
[65]. According to Roeges [65] in the case of 1,2-disubstituion only one strong band due
to γCH is observed in the region 755 ± 35 cm-1. This is confirmed by the appearance of a
strong γCH at 752 cm-1 in the IR spectrum and the computational value is at 751 cm-1 for
ORTHOPHPZ. The 1,3-substituted benzene resembles that of mono substitution, with out
of plane γCH vibration near 765 cm-1 and out of plane ring deformation in the
neighbourhood of 685 cm-1. These bands are observed at 765, 680 cm-1 in the IR spectrum
and finds support from computational results at 765, 685 cm-1 for the phenyl ring of
METAPHPZ [65, 67]. The strong γCH deformation occurring at 840 ± 50 cm-1 it typical
7

ACCEPTED MANUSCRIPT
for para substituted benzene derivatives [65] and this band is observed at 857 cm-1 in the
IR spectrum and at 859 cm-1 theoretically for PARAPHPZ [82].
VCD spectra
Vibrational circular dichroism (VCD) is an electro-magneto-optic effect which
gives differences in left and right circularly polarized light passing through the molecules
which is an extension of circular dichroism spectroscopy into the IR and near infrared
region [69]. The C-C stretching modes of the aromatic rings, C-H and C=O stretching
modes at stereogenic centers produce generate VCD signals and these are efficient
identifiers of configuration identification of molecular systems. The ring stretching modes
show right polarization at 1229, 1011 cm-1 (ORTHOPHPZ), 1546, 1523, 1463, 1105 cm-1
(METAPHPZ), 1500, 1464, 1409, 1320, 1010 cm-1 (PARAPHPZ) while ring stretching
modes show left polarization at 1560, 1507, 1028 cm-1 (ORTHOPHPZ), 1412 cm-1
(METAPHPZ), 1568, 1545 cm-1 (PARAPHPZ). The CH stretching mode shows right
polarization at 3105 cm-1 (ORTHOPHPZ), 3114 cm-1 (METAPHPZ), 3117 cm-1
(PARAPHPZ) while for METAPHPZ, CH stretching modes at 3090 cm-1 in the VCD
spectrum (Fig.S2-supporting material) show left polarization. The VCD spectra of show
left polarization at 1389 cm-1 (ORTHOPHPZ), 1268, 1077 cm-1 (METAPHPZ), 1390,
1239 cm-1 (PARAPHPZ) and right polarization at 1391, 1236, 1069 cm-1 (METAPHPZ),
1080 cm-1 (PARAPHPZ) for the CH in-plane deformation modes.
4.3
Nonlinear optical properties
Due to an external electric field, the energy of molecular system is a function of
the electric field and polarizability and hyperpolarizability values will gives the NLO
properties [70]. The computed values of dipole moment, polarizability, first order
hyperpolarizability and second order hyperpolarizability values are: 2.877 Debye, 2.514 ×
10-23 esu, 11.000× 10-30 esu, -12.634 × 10-37 esu for ORTHOPHPZ, 1.386 Debye,
2.532× 10-23 esu, 12.312× 10-30 , -15.613× 10-37 esu for METAPHPZ and 3.0257 Debye,
2.602× 10-23 esu, 23.933× 10-30 esu, -18.0205× 10-37 esu for PARAPHPZ. The energy
gaps for 2.799, 2.942 and 2.809 eV for ORTHOPHPZ, METAPHPZ and PARAPHPZ
respectively which are lower than that of urea (6.706eV) [71] and the first
hyperpolarizabilities of ORTHOPHPZ, METAPHPZ and PARAPHPZ are respectively,
8

ACCEPTED MANUSCRIPT
84.62, 94.71 and 184.10 times that of urea [71]. The reported first order
hyperpolarizability of oxadiazole derivative is 2.414× 10-30 esu [57].
4.4
Frontier molecular orbital analysis
The HOMO-LUMO plots of the title compounds are presented in Fig.2 and
HOMO is delocalized over the entire molecule, except pyrazine ring and LUMO is
delocalized over the entire molecule except phenyl ring for all the molecules. From the
HOMO and LUMO energies, the ionization potential I=-EHOMO and electron affinity A=-
E
LUMO [72]. The ionization potential, electron affinity and HOMO-LUMO energy gap are
respectively, 7.938, 5.139, 1.400 for ORTHOPHPZ, 8.128, 5.186, 2.942 for METAPHPZ
and 7.878, 5.069, 2.809 for PARAPHPZ. The chemical descriptors are given by hardness
η= (I-A)/2; chemical potential µ = -(I+A)/2 and electrophilicity index ω = µ2/2η [73].The
values of chemical descriptors vary in the order: η : METAPHPZ (1.471) > PARAPHPZ
(1.405) > ORTHOPHPZ (1.400); µ are nearly same for all derivatives; ORTHOPHPZ (-
6.539), METAPHPZ (-6.657), PARAPHPZ (-6.474) and ω are also nearly same for all
derivatives; ORTHOPHPZ (15.271), METAPHPZ (15.663), PARAPHPZ (14.916). Molar
refractivity (MR) is a term used in quantitative structure property relationship, given as,
MR= 1.333παN, where α is the polarizability and N is the Avogadro number [74]. For the
title compounds, MR values are also same for all derivatives, ORTHOPHPZ (63.38),
METAPHPZ (63.83), PARAPHPZ (65.60) and this is responsible for the binding nature of
the molecular assembly and can be used for the cure of different diseases [75].
4.5
Natural Bond Orbital Analysis
The perturbation energies of significant donor-acceptor interactions and occupancy
of electrons and p-character in significant NBO natural atomic hybrid orbitals of
ORTHOPHPZ, METAPHPZ and PARAPHPZ compounds are presented in Tables S2 and
S3 (supporting material). The three compounds have the same stronger interactions are
n2O8→π*(C7-N11) and n2O8→π*(C9-N10) have the higher E(2) value 33.05, 34.08
kcal/mol for ORTHOPHPZ, 32.73, 32.74 kcal/mol for METAPHPZ and 32.64, 32.64
kcal/mol for PARAPHPZ. The strong interactions π(C12-C17)→π*(C9-N10), π(C15-
C16)→π*(C12-C17), are observed in ORTHOPHPZ and METAPHPZ having the energy
values 21.31 and 21.41 kcal/mol. The larger the E(2) value, the greatest delocalization
9

ACCEPTED MANUSCRIPT
interaction between electron donors and electron acceptors. For the three compounds,
100% p-character was observed in lone pair of chlorine atom, O8 and π bonding of C7-C11
and C9-N10. Similarly, 100% p-character was also observed π bonding of (C12-C17), (C15-
C16), (C14-C15) in ORTHOPHPZ, METAPHPZ and PARAPHPZ respectively.
4.6
Local reactivity descriptors: MEP, ALIE surfaces and Fukui functions
A combination of MEP and ALIE descriptors has been employed in this work in order
to identify the molecular sites possibly prone to electrophilic attacks. MEP descriptor
nicely indicates molecule sites with abundance or excess of electrons however ALIE
descriptor might be better solution when it comes to the identification of molecule sites
prone to electrophilic attacks. In general, these descriptors are widely used for
identification of prospective reactive areas of molecules of interest [29, 76-84]. Both MEP
and ALIE descriptors have been visualized by mapping of their values to the electron
density surface, Fig.3. MEP surfaces indicate very similar topological and quantitative
picture between investigated derivatives. This descriptor indicates the abundance of
electrons, and therefore the sensitivity towards electrophilic attacks, in the near vicinities
of nitrogen atoms N10 and N11, belonging to oxadiazole unit, and in the near vicinities of
nitrogen atoms N1 and N4 of pyrazine ring. ALIE surface also recognizes these molecule
sites as possible sensitive towards the electrophilic attacks, however the red color is more
intensive in the near vicinities of nitrogen atoms of pyrazine ring. While maximal and
minimal MEP values are practically the same for all three derivatives, the lowest minimal
value of ALIE is the lowest in the case of ORTHOPHPZ derivative. Beside MEP and
ALIE surfaces, reactive molecular sites of investigated derivatives have been identified
with Fukui functions as well. This quantum-molecular descriptor tracks the changes in
electron density due to the addition or removal of overall charge. The values of Fukui f+
and f– functions in finite difference approximation using Jaguar software are calculated
according to the following equations:
δ
(
ρ N+
(
r
)
−
ρ N
(
r
)
)
f + =
f − =
,
(1)
(2)
δ
δ
(
ρ N−
(
r
)
δ
−
ρ N
(
r
)
)
,
10

ACCEPTED MANUSCRIPT
where N stands for the number of electrons in reference state of the molecule and
δ is the
fraction of electron which default value is set to be 0.01 [85]. The values of Fukui
functions have been mapped to the electron density surface and the corresponding
maximal and minimal values have been presented in Fig.4. Maximal positive values of
Fukui f+ functions, indicated with purple colour in Fig.4, are located only within pyrazine
ring. This indicates that electron density increased within pyrazine ring after the addition
of overall charge. More interested situation happened in the case of Fukui f– function.
Namely, the minimal values of Fukui f– function, marked with red colour, are delocalized
over the whole METAPHPZ and PARAPHPZ derivatives, while in the case of
ORTHOPHPZ derivative minimal values of Fukui f– function are localized in the near
vicinity of chlorine atom. These results, together with the fact that the lowest ALIE values
have been calculated for this derivative, indicate that ORTHOPHPZ has the highest
reactivity.
4.7
Selectivity towards autoxidation and influence of water
As demonstrated in several important papers [24, 86] the concept of H-BDE can be
used for the prediction of molecule sites sensitive towards the autoxidation. Identifying the
molecule sites prone to autoxidation is of great importance due to the fact that oxidative
reactions are one of the most important pathways for the removal of organic molecules by
their degradation [87]. Bonds between molecule and hydrogen atom for which H-BDE
takes values between 70 and 85 kcal/mol [88, 89] are considered to be highly sensitive
towards the autoxidation mechanism. H-BDE which are taking values between 85 and 90
kcal/mol are also of importance for autoxidation mechanism, but they should be taken
with caution [89]. While it might be logical that H-BDE values lower than 70 kcal/mol
reflect great sensitivity towards autoxidation, this is not the case [24, 86, 88]. H-BDE and
BDE values for the remaining single acyclic bonds of oxadiazole derivatives investigated
in this work are summarized in Fig.5. Very high H-BDE values calculated for all three
oxadiazole derivatives clearly indicate that studied molecules are very stable towards the
autoxidation mechanism. Namely, all of the calculated H-BDE values are higher than 110
kcal/mol, which is much higher than the desired range of values. Concerning the rest of
the single acyclic bonds, it is worth of mentioning that BDE for the chlorine atom in case
11

ACCEPTED MANUSCRIPT
of the ORTHOPHPZ derivative is lower for ca. 5 kcal/mol, comparing to derivatives
METAPHPZ and PARAPHPZ. Taking into account the presence of pharmaceutical
molecules in water resources, in this work we were also interested to study the stability of
title compounds in water, applying MD simulations. After obtaining trajectories in MD
simulations, the radial distribution functions were calculated in order to identify atoms of
investigated molecules with the most pronounced interactions with water molecules. The
results are presented in Fig.S3 (supporting material). According to presented RDFs,
investigated oxadiazole derivatives don’t possess significant interactions with water
molecules, which indicate their stability in water. This indicates that hydrolysis and
spontaneous degradation is hard to be expected. Stability in water is indicated by the
absence of atoms for which the RDF have sharp profile whose maximal g(r) values are
located at distances below 2Å. Of all atoms, maximal g(r) values are located at the
shortest distances for nitrogen atoms N1 and N10. In the same time, chlorine atoms are
characterized by the high maximal g(r) values, but unfortunately their peaks are located at
distances higher than 3.5 Å.
4.8
Molecular docking
PASS (Prediction of Activity Spectra) [90] is an online tool which predicts
different types of activities. PASS analysis of the compounds (ORTHOPHPZ,
METAPHPZ and PARAPHPZ) predicts activities given in the table 2,
Glycosylphosphatidylinositol phospholipase D inhibitor with probability to be active (Pa)
value of 0.806 for ORTHOPHPZ, 0.820 for METAPHPZ and 0.844 for PARAPHPZ.
Glycosylphosphatidylinositol (GPI)-anchored proteins are numerous on the surface of
eukaryotic cells and are involved in a wide variety of physiological functions. In the
mammalian immune system, they are involved in the complement cascade, the pro- and
anti-inflammatory responses of macrophages, and tumour invasion [91, 92]. To explore
the possible utility of acute and chronic Phospholipase D (PLD) inhibition in vivo and
such inhibitors have recently been described and demonstrated to block neutrophil
chemotaxis and invasion by breast cancer cells in culture, increasing the prospects for a
new class of therapeutics for autoimmune disorders and several types of metastatic cancer
[93]. The pyrazine derivatives are clinically used drugs worldwide and some of them are
12

ACCEPTED MANUSCRIPT
active against cancer cell [4, 94, 95]. High resolution crystal structure of 1-
phosphatidylinositol phosphodiesterase was downloaded from the protein data bank
website with PDB ID is4SG. The ligands bind at the active site of the substrate by weak
non-covalent interactions. The residue Arg 69, Ser 71, Ser 77 and His 79 forms H-bond
with oxadiazole ring. Tyr 84 shows π-π stacked interaction with phenyl and oxadiazole
ring. Amino acids, Arg 69, Ser77 and His79 forms H-bond with oxadiazole ring but Ser71
and ser77 forms H-bond with pyrazine ring. Tyr 84 form π-π stacked interaction with
pyrazine and oxadiazole ring while Glu 88 forms π-anion interaction with pyrazine ring.
Amino acids Ser 251 shows H-bond but Ala248 forms π-sigma interaction with pyrazine
ring of PARAPHPZ. Tyr 282 and Tyr 25 gives π-π stacked interaction with oxadiazole
and phenyl ring. The interactive plot of ORTHOPHPZ, METAPHPZ and PARAPHPZ
with the amino acids of the receptor is shown in Fig.S4 (supporting material). The docked
ligands form stable complexes with the receptor 1-phosphatidylinositol phosphodiesterase
which gives binding affinity value of -6.6kcal/mol for ORTHOPHPZ and PARAPHPZ
while -6.4 kcal/mol for METAPHPZ. These binding affinity values of different poses of
ligands with same protein are tabulated in table 3. The highest negative value reflects the
affinity between ligand and receptor and vice-versa. The view of ligands bound at their
active site of same receptor as depicted in Fig.S5 (supporting material). These preliminary
results suggest that these compounds can be developed as new anti-cancer drugs.
Conclusion
The FT-IR and VCD spectra of three oxadiazole derivatives are discussed and the
experimental IR bands are in good agreement with the theoretical wavenumbers. In terms
of electrophilic attacks, both MEP and ALIE descriptors indicated reactivity of nitrogen
atoms, while red colour of ALIE descriptor was the most intensive in the near vicinity of
nitrogen atoms of pyrazine ring. The lowest minimal ALIE value was calculated in the
case of ORTHOPHPZ oxadiazole derivative, just around 2 kcal/mol lower in comparison
with METAPHPZ and PARAPHPZ. Fukui f+ function indicated that electron density
increased within the pyrazine ring for all three derivatives after the charge addition. On the
other side, the lowest values of Fukui f– function were localized around chlorine atoms
only in case of the ORTHOPHPZ derivative, while for other two derivatives these values
13

ACCEPTED MANUSCRIPT
were delocalized over the whole molecule. All H-BDE values are too high, therefore all
investigated derivatives are stable towards the autoxidation mechanism. However, the
BDE of chlorine atom in case of the ORTHOPHPZ derivative is 5 kcal/mol lower
comparing to the other two derivatives. Although all three derivatives have similar
reactive properties according to computational results, BDE values for bond containing
chlorine atom, ALIE surfaces and Fukui functions indicate slightly higher reactivity of
ORTHOPHPZ in comparison with METAPHPZ and PARAPHPZ. Finally, the results of
MD simulations and RDFs indicate high stability in water thanks to which it is highly
unlikely to expect spontaneous degradation of investigated molecules under natural
conditions. PASS analysis of the title compounds predicts Glycosylphosphatidylinositol
phospholipase D inhibitor activity and the results suggest that these compounds can be
developed as new anti-cancer drugs. From the anti-tubercular activity, it was found that
ortho, meta and para chloro substitution helps to enhance the anti-TB activity. The results
obtained from anti-TB activity are more promising as the compounds were found to be
more potent than reference standard, INH and PZA.
Acknowledgements
This work was funded by the Deanship of Scientific Research at Princess Nourah bint
Abdulrahman University through the Research Group Program (Grant No. RGP-1438-
0010).
References
[1]
Y. Zhang, D. Mitchison, The curious characteristics of pyrazinamide: a review, Int.
J. Tuberc. Lung Dis. 7 (2003) 6-21.
[2]
S.P. Klemens, C.A. Sharpe, M.H. Cynamon, Activity of pyrazinamide in a murine
model against Mycobacterium tuberculosis isolates with various levels of in vitro
susceptibility, Antimicrob. Agents Chemother. 40 (1996) 14-16.
G. Bonanni, M. Ciccariello, P. Mancini, V. Pace, G. Sagliaschi, Concomitant ceco-
appendicular and urinary tuberculosis. Description of two rare cases:
physiopathological and diagnostic remarks, Riv. Eur. Sci. Med. Farmacol. 15
(1993) 171-174.
[3]
14

ACCEPTED MANUSCRIPT
[4]
[5]
M. Doležal, J. Zitko, D. Kešetovičová, J. Kuneš, M. Svobodová, Substituted N-
phenylpyrazine-2-carboxamides: Synthesis and antimycobacterial evaluation,
Molecules 14 (2009) 4180-4189.
S. Zhou, S. Yang, G. Huang, Design, synthesis and biological activity of
pyrazinamide derivatives for anti-Mycobacterium tuberculosis, J. Enz. Inhib. Med.
Chem. 32 (2017) 1183-1186.
[6]
[7]
[8]
H. Cynamon, S.P. Klemens, T.S. Chou, R.H. Gimi, J.T. Welch, Antimycobacterial
activity of a series of pyrazinoic acid esters, J. Med. Chem. 35 (1992) 1212-1215.
S. Yamamoto, I. Toida, N.Watanabe, T. Ura, In vitro antimycobacterial activities
of pyrazinamide analogs, Antimicrob. Agents Chemother. 39 (1995) 2088-2091.
K. Gobis, H. Foks, A. Kędzia, M. Wierzchowska, E. Kwapisz, Z. Zwolska, E.
Augustynowicz-Kopeć, Studies on pyrazine derivatives. XLVII. Synthesis and
antibacterial activity of novel pyrazine derivatives with amidoxime moiety, Acta
Pol. Pharm. Drug Res. 63 (2006) 39-46.
[9]
K. Iida, K. Itoh, Y. Kumagai, R. Oyasu, K. Hattori, K. Kawai, T. Shimazui, H.
Akaza, M. Yamamoto, Nrf2 is essential for the chemopreventive efficacy of
oltipraz against urinary bladder carcinogenesis, Cancer Res. 64 (2004) 6424-6431.
[10] J. Adams, M. Kauffman, Development of the proteasome inhibitor Velcade
(Bortezomib), Cancer Invest. 22 (2004) 304-311.
[11] M. Mitsuo, Total syntheses of racemic aspergillic acid and neoaspergillic acid, J.
Org. Chem. 31 (1966) 4143-4146.
[12] O.O. Odebiyi, Antibacterial property of tetramethyl-pyrazine from the stem of
Jatropha podagrica, Planta Med. 38 (1980) 144-146.
[13] Y. Younis, F. Douelle, D.G. Cabrera, C. Le Manach, A.T. Nchinda, T. Paquet,
L.J. Street, K.L. White, K.M. Zabiulla, J.T. Joseph, S. Bashyam, D. Waterson,
M.J. Witty, S. Wittlin, S.A. Charman, K. Chibale, Structure-activity-relationship
studies around the 2-amino group and pyridine core of antimalarial 3,5-
diarylaminopyridines lead to a novel series of pyrazine analogues with oral in vivo
activity, J. Med. Chem. 56 (2013) 8860-8871.
15

ACCEPTED MANUSCRIPT
[14] A. Nakamura, T. Ataka, H. Segawa, Y. Takeuchi, T. Takematsu, Studies on
herbicidal 2,3-dicyanopyrazines. 1. Structure-activity relationship of herbicidal
2,3-dicyano-5-substituted pyrazines, Agric. Biol. Chem. Vol. 47 (1883) 1555-
1560.
[15] A.A. Kadi, N.R. El-Brollosy, O.A. Al-Deeb, E.E. Habib, T.M. Ibrahim, A.A. El-
Emam, Synthesis, antimicrobial, and anti-inflammatory activities of novel 2-(1-
adamantyl)-5-substituted-1,3,4-oxadiazoles
and
2-(1-adamantylamino)-5-
substituted-1,3,4-thiadiazoles, Eur. J. Med. Chem. 42 (2007) 235-242.
[16] S.L. Gaonkar, K.M.L. Rai, B. Prabhuswamy, Synthesis and antimicrobial studies
of a new series of 2-{4-[2-(5-ethylpyridin-2-yl)ethoxy]phenyl}-5-substituted-1,3,4-
oxadiazoles, Eur. J. Med. Chem. 41 (2006) 841-846.
[17] R.Y. Morgan, A.M. Mkadmah, I. Beedham, A.A Elmanama, M.R. Mattar, J.
Raftery, R.G. Pritchard, A.M. Awadallah, J.M. Grandier, Antibacterial activities of
novel nicotinic acid hydrazides and their conversion into N-acetyl-1,3,4-
oxadiazoles. Bioorg. Med. Chem. Lett. 24 (2014) 5796-5800.
[18] X.J. Zou, L.H. Lai, G.Y. Jin, Z.X. Zhang, Syntheis, fungicidal acivity, and 3D-
QSAR of pyridazinone-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazoles, J.
Agric. Food Chem. 50 (2002) 3757-3760.
[19] D. Zampieri, M.G. Mamolo, E. Laurini, M. Fermeglia, P. Paola, S. Pricl, E. Banfi,
G. Scialino, L. Vio, Antimycobacterial activity of new 3,5-disubstituted 1,3,4-
oxadiazole-2(3H)-one derivatives: Molecular modelling investigations, Bioorg.
Med. Chem. 17 (2009) 4693-4707.
[20] A. Savarino, A historical sketch of the discovery and development of HIV-1
integrase inhibitors, Expert Opin. Investig. Drugs, 15 (2006) 1507-1522.
[21] A.A. El-Emam, O.A. Al-Deeb, M. Al-Omar, J. Lehmann, Synthesis, antimicrobial,
and anti-HIV-1 activity of certain 5-(1-adamantyl)-2-substituted thio-1,3,4-
oxadiazoles and 5-(1-adamantyl)-3-substituted aminomethyl-1,3,4-oxadiazoline-2-
thiones, Bioorg. Med. Chem. 12 (2004) 107-113.
[22] N.D. James, J.W. Growcott, Zibotentan, Drugs Future, 34 (2009) 624-633.
16

ACCEPTED MANUSCRIPT
[23] Y. Luo, Z.-J. Liu, G. Chen, J. Shi, J.-R. Li, H.-L. Zhu, 1,3,4-Oxadiazole
derivatives as potential antitumor agents: discovery, optimization and biological
activity evaluation, Med. Chem. Commun. 7 (2016) 263-2771.
[24] P. Lienard, J. Gavartin, G. Boccardi, M. Meunier, Predicting drug substances
autoxidation, Pharm. Res. 32(1) (2015) p. 300-310.
[25] G.L. de Souza, L.M. de Oliveira, R.G. Vicari, A. Brown, A DFT investigation on
the structural and antioxidant properties of new isolated interglycosidic O-(1→ 3)
linkage flavonols, J. Mol. Model. 22(4) (2016) 1-9.
[26] Z. Sroka, B. Żbikowska, J. Hładyszowski, The antiradical activity of some selected
flavones and flavonols, Experimental and quantum mechanical study, J. Mol.
Model. 21 (2015) 1-11.
[27] H. Djeradi, A. Rahmouni, A. Cheriti, Antioxidant activity of flavonoids: a QSAR
modeling using Fukui indices descriptors, J. Mol. Model. 20 (2014) 1-9.
[28] S. Armaković, S.J. Armaković, S. Koziel, Optoelectronic properties of curved
carbon systems, Carbon 111 (2017) 371-379.
[29] S. Armaković, S.J. Armaković, J.P. Šetrajčić, I.J. Šetrajčić, Active components of
frequently used β-blockers from the aspect of computational study, J. Mol. Model.
18(9) (2012) 4491-4501.
[30] S.J. Armaković, S. Armaković, N.L. Finčur, F. Šibul, D. Vione, J.P. Šetrajčić, B.
Abramović, Influence of electron acceptors on the kinetics of metoprolol
photocatalytic degradation in TiO 2 suspension. A combined experimental and
theoretical study, RSC Adv. 5 (2015) 54589-54604.
[31] M. Blessy, R.D. Patel, P.N. Prajapati, Y. Agrawal, Development of forced
degradation and stability indicating studies of drugs-A review, J. Pharm. Anal. 4
(2014) 159-165.
[32] S. Armaković, S.J. Armaković, B.F. Abramović, Theoretical investigation of
loratadine reactivity in order to understand its degradation properties: DFT and
MD study, J. Mol. Model. 22 (2016) 240.
[33] B. Sureshkumar, Y.S. Mary, C.Y. Panicker, S. Suma, S. Armaković, S.J.
Armaković, C. Van Alsenoy, B. Narayana, Quinoline derivatives as possible lead
17

ACCEPTED MANUSCRIPT
compounds for anti-malarial drugs: Spectroscopic, DFT and MD study, Arab. J.
Chem. In Press, DOI.org/10.1016/j.arabjc.2017.07.006.
[34] S.J. Armaković, M. Grujić-Brojčin, M. Šćepanović, S. Armaković, A. Golubović,
B. Babić, B.F. Abramović, Efficiency of La-doped TiO 2 calcined at different
temperatures in photocatalytic degradation of β-blockers, Arab. J. Chem. In Press,
DOI: org/10.1016/j.arabjc.2017.01.001.
[35] Y.S. Mary, V. Aswathy, C.Y. Panicker, A. Bielenica, P. Brzózka, O. Savczenko, S.
Armaković, S.J. Armaković, C. Van Alsenoy, Spectroscopic, single crystal XRD
structure, DFT and molecular dynamics investigation of 1-(3-chloro-4-
fluorophenyl)-3-[3-(trifluoromethyl) phenyl] thiourea, RSC Adv. 6 (2016) 111997-
112015.
[36] M. Dabiri, P. Salehi, M. Baghbanzadeha, M.A. Bahramnejad, A facile procedure
for the one-pot synthesis of unsymmetrical 2,5-disubstituted 1,3,4-oxadiazoles,
Tetrahedron Lett. 47 (2006) 6983-6986.
[37] Gaussian 09, Revision B.01, M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E.
Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci,
G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov,
J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda,
J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven,
J.A. Montgomery, Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers,
K.N. Kudin, V.N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K.
Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega,
J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo,
R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W.
Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador,
J.J. Dannenberg, S. Dapprich, A.D. Daniels, O. Farkas, J.B. Foresman, J.V. Ortiz,
J. Cioslowski, D.J. Fox, Gaussian, Inc., Wallingford CT, 2010.
[38] R. Dennington, T. Keith, J. Millam, Gaussview, Version 5, Semichem. Inc.,
Shawnee Mission, KS, 2009.
18

ACCEPTED MANUSCRIPT
[39] J.M.L. Martin, C. Van Alsenoy, GAR2PED, a Program to Obtain a Potential
Energy Distribution from a Gaussian Archive Record, University of Antwerp,
Belgium, 2007.
[40] J.B. Foresman, in: E. Frisch (Ed.), Exploring Chemistry with Electronic Structure
Methods: a Guide to Using Gaussian, Gaussian Inc., Pittsburg, PA, 1996.
[41] E.D. Glendening, A.E. Reed, J.E. Carpenter, F. Weinhold, NBO Version 3.1,
Gaussian Inc., Pittsburgh, PA, 2003.
[42] A.E. Reed, L.A. Curtiss, F. Weinhold, Intermolecular interactions from a natural
bond orbital, donor-acceptor viewpoint, Chem. Rev. 88 (1988) 899–926.
[43] Schrödinger Release 2017-4: MacroModel, Schrödinger, LLC, New York, NY,
2017. 2017.
[44] A.D. Bochevarov, A.D., E. Harder, T.F. Hughes, J.R. Greenwood, D.A. Braden,
D.M. Philipp, D. Rinaldo, M.D. Halls, J. Zhang, R.A. Friesner, Jaguar: A
high‐performance quantum chemistry software program with strengths in life and
materials sciences, Int. J. Quantum Chem. 113 (2013) 2110-2142.
[45] Schrödinger Release 2017-4: Jaguar, Schrödinger, LLC, New York, NY, 2017.
2017.
[46] L.D. Jacobson, A.D. Bochevarov, M.A. Watson, T.F. Hughes, D. Rinaldo, S.
Ehrlich, T.B. Steinbrecher, S. Vaitheeswaran, D.M. Philipp, M.D. Halls,
Automated Transition State Search and Its Application to Diverse Types of
Organic Reactions, J. Chem. Theor. Comput. 13 (2017) 5780-5797.
[47] D. Shivakumar, J. Williams, Y. Wu, W. Damm, J. Shelley, W. Sherman,
Prediction of absolute solvation free energies using molecular dynamics free
energy perturbation and the OPLS force field, J. Chem. Theor. Comput. 6 (2010)
1509-1519.
[48] Z. Guo, U. Mohanty, J. Noehre, T.K. Sawyer, W. Sherman, G. Krilov, Probing the
α‐Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics
Simulations and Analysis, Chem. Biol. Drug Des. 75 (2010) 348-359.
[49] K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L.
Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti. Scalable algorithms for
19

ACCEPTED MANUSCRIPT
molecular dynamics simulations on commodity clusters. in Proceedings of the
2006 ACM/IEEE conference on Supercomputing. 2006. ACM.
[50] P. Sjoberg, J.S. Murray, T. Brinck, P. Politzer, Average local ionization energies
on the molecular surfaces of aromatic systems as guides to chemical reactivity,
Canadian J. Chem. 68 (1990) 1440-1443.
[51] E. Harder, W. Damm, J. Maple, C. Wu, M. Reboul, J.Y. Xiang, L. Wang, D.
Lupyan, M.K. Dahlgren, J.L. Knight, OPLS3: a force field providing broad
coverage of drug-like small molecules and proteins, J. Chem. Theor. Comput. 12
(2015) 281-296.
[52] W.L. Jorgensen, D.S. Maxwell, J. Tirado-Rives, Development and testing of the
OPLS all-atom force field on conformational energetics and properties of organic
liquids, J. Am. Chem. Soc. 118 (1996) 11225-11236.
[53] W.L. Jorgensen, J. Tirado-Rives, The OPLS [optimized potentials for liquid
simulations] potential functions for proteins, energy minimizations for crystals of
cyclic peptides and crambin, J. Am. Chem. Soc. 110(6) (1988) 1657-1666.
[54] A.D. Becke, Density‐functional thermochemistry. III. The role of exact exchange,
J. Chem. Phys. 98 (1993) 5648-5652.
[55] H.J. Berendsen, J.P. Postma, W.F. van Gunsteren, J. Hermans, Interaction models
for water in relation to protein hydration, in Intermolecular forces. 1981, Springer.
p. 331-342.
[56] Schrödinger Release 2017-4: Maestro, Schrödinger, LLC, New York, NY, 2017.
2017.
[57] F.A.M. Al-Omary, Y.S. Mary, C.Y. Panicker, A.A. El-Emam, I.A. Al-Swaidan,
A.A. Al-Saadi, C. Van Alsenoy, Spectroscopic investigations, NBO, HOMO-
LUMO and molecular docking of 5-(adamantan-1-yl)-3-anilinomethyl-2,3-
dihydro-1,3,4-oxadiazole-2-thione, a potential bioactive agent, J. Mol. Struct. 1096
(2015) 1-14.
[58] O. Trott, A. J. Olson, AutoDock Vina: Improving the speed and accuracy of
docking with a new scoring fuction, efficient optimization and multithreading, J.
Comput. Chem. 31 (2010) 455-461.
20

ACCEPTED MANUSCRIPT
[59] B. Kramer, M. Rarey, T. Lengauer, Evaluation of the FlexX incremental
construction algorithm for protein ligand docking, Proteins: Struct. Funct. Genet.
37 (1999) 228-241.
[60] S. Parveen, M.A. Al-Alshaikh, C.Y. Panicker, A.A. El-Emam, B. Narayana, V.V.
Saliyan, B.K. Sarojini, C. Van Alsenoy, Vibrational and structural observations
and molecular docking study on 1-(3-(4-chlorphenyl)-5-[4-(propan-2-yl)phenyl]-
4,5-dihydro-1H-pyrazol-1-yl-ethanone, J. Mol. Struct. 1112 (2016) 136-146.
[61] N.G. Haress, F. Al-Omary, A.A. El-Emam, Y.S. Mary, C.Y. Panicker, A.A. Al-
Saadi, J.A. War, C.V an Alsenoy, Spectroscopic investigation (FT-IR and FT-
Raman), vibrational assignments, HOMO-LUMO analysis and molecular docking
of 2-(adamantan-1-yl)-5-(4-nitrophenyl)-1,3,4-oxadiazole, Spectrochim. Acta 135
(2015) 973-983.
[62] D. LinVien, N.B. Colthup,W.G. Fately, J.G. Grasselli, The Handbook of Infrared
and Raman Characteristic frequencies of organic molecules, Academic Press
Limited, London, 1991.
[63] P.K. Ranjith, E.S. Al-Abdullah, F.A.M.
Al-Omary, A.A. El-Emam, P.L. Anto,
Y.S. Mary, S. Armaković, S.J. Armaković, J. Zitko, D. Dolezal, C. Van Alsenoy,
FT-IR and FT-Raman characterization and investigation of reactive properties of
N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide by molecular dynamics
simulations and DFT calculations, J. Mol. Struct. 1136 (2017) 14-24.
[64] J. Lukose, C.Y. Panicker, P.S. Nayak, B. Narayana, B.K. Sarojini, C. Van
Alsenoy, A.A. Al-Saadi, Synthesis, structural and vibrational investigation on 2-
phenyl-N-(pyrazine-2-yl)acetamide combining XRD diffraction, FT-IR and NMR
spectroscopies with DFT calculations, Spectrochim. Acta 135 (2015) 608-616.
[65] N.P.G. Roeges, A Guide to the Complete Interpretation of Infrared Spectra of
Organic Structures, John Wiley and Sons Inc., New York, 1994.
[66] G. Varsanyi, Assignments of Vibrational Spectra of Seven Hundred Benzene
Derivatives, Wiley, New York, 1974.
[67] C.S.C. Kumar, C.Y. Panicker, H.K. Fun, Y.S. Mary, B. Harikumar, S. Chandraju,
21

ACCEPTED MANUSCRIPT
C.K. Quah, C.W. Ooi, Molecular structure, FT-IR, first order hyperpolarizability,
NBO analysis, HOMO and LUMO analysis of 2-(4-chlorophenyl)-2-oxoethyl-3-
methylbenzoate by HF and density functional methods, Spectrochim. Acta 128
(2014) 327-336.
[68] C.Y. Panicker, H.T. Varghese, K.R. Ambujakshan, S. Mathew, S. Ganguli, A.K.
Nanda, C. Van Alsenoy, Y.S. Mary, Ab initio and density functional theory studies
on
vibrational
spectra
of
3-{[(4-methoxyphenyl)methylene]amino}-2-
phenylquinazolin-4(3H)-one, Eur. J. Chem. 1 (2010) 37-43.
[69] T.A. Keiderling, I.C. Baianu, H. Pessen, T. Kumosinski, Physical Chemistry of
Food Processes, Advanced techniques, Structures and Applications, New York,
Van Norstrand Reinhold (1993), 307-337.
[70] D.A. Kleinman, Nonlinear dielectric polarization in optical media, J. Phys. Rev.
126 (1962) 640-646.
[71] C. Adant, M. Dupuis, J.L. Bredas, Ab initio study of the nonlinear optical
properties of urea: Electron correlation and dispersion effects, Int. J. Quantum
Chem. 56 (1995) 497-507.
[72] Y.S. Mary, H.T. Varghese, C.Y. Panicker, M. Girisha, B.K. Sagar, H.S.
Yathirajan, A.A. Al-Saadi, C. Van Alsenoy, Vibrational spectra, HOMO, LUMO,
NBO, MEP analysis and molecular docking study of 2,2-diphenyl-4-(piperidin-1-
yl)butanamide, Spectrochim. Acta 150 (2015) 543-556.
[73] R.G. Parr, R.G. Pearson, Absolute hardness: companion parameter to absolute
electronegativity, J. Am. Chem. Soc. 105 (1983) 7512-7516.
[74] B. Sureshkumar, Y.S. Mary, C.Y. Panicker, K.S. Resmi, S. Suma, S. Armakovic,
S.J. Armakovic, C. Van Alsenoy, Spectroscopic analysis of 8-hydroxyquinoline-5-
sulphonic acid and investigation of its reactive properties by DFT and molecular
dynamics simulations, J. Mol. Struct. 1150 (2017) 540-552.
[75] R.P. Verma, C. Hansch, A comparison between two polarizability parameters in
chemical biological interactions, Bioorg.Med. Chem. 13 (2005) 2355-2372.
22

ACCEPTED MANUSCRIPT
[76] N. Okulik, A.H. Jubert, Theoretical study on the structure and reactive sites of
three non-steroidal anti-inflammatory drugs: Ibuprofen, Naproxen and Tolmetin
acids, J. Mol. Sruct. THEOCHEM, 769 (2006) 135-141.
[77] J.S. Murray, J.M. Seminario, P. Politzer, P. Sjoberg, Average local ionization
energies computed on the surfaces of some strained molecules, Int. J. Quantum
Chem. 38 (1990) 645-653.
[78] P. Politzer, F. Abu‐Awwad, J.S. Murray, Comparison of density functional and
Hartree–Fock average local ionization energies on molecular surfaces, Int. J.
Quantum Chem. 69 (1998) 607-613.
[79] F.A. Bulat, A. Toro-Labbé, T. Brinck, J.S. Murray, P. Politzer, Quantitative
analysis of molecular surfaces: areas, volumes, electrostatic potentials and average
local ionization energies, J. Mol. Model. 16 (2010) 1679-1691.
[80] P. Politzer, J.S. Murray, F.A. Bulat, Average local ionization energy: a review, J.
Mol. Model. 16 (2010) 1731-1742.
[81] J.A. War, K. Jalaja, Y.S. Mary, C.Y. Panicker, S. Armaković, S.J. Armaković,
S.K. Srivastava, C. Van Alsenoy, Spectroscopic characterization of 1-[3-(1H-
imidazol-1-yl) propyl]-3-phenylthiourea and assessment of reactive and
optoelectronic properties employing DFT calculations and molecular dynamics
simulations, J. Mol. Struct. 1129 (2017) 72-85.
[82] D.A. Zainuri, S. Arshad, N.C. Khalib, I.A. Razak, R.R. Pillai, S.F. Sulaiman, N.S.
Hashim, K.L. Ooi, S. Armaković, S.J. Armaković, C.Y. Panicker, C. Van Alsenoy,
Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and
13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies
using molecular dynamics simulations and evaluation of antimicrobial and
antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-
iodophenyl)prop-2-en-1-one, J. Mol. Struct. 1128 (2017) 520-533.
[83] V.V. Menon, E. Fazal, Y.S. Mary, C.Y. Panicker, S. Armaković, S.J. Armaković,
S. Nagarajan, C. Van Alsenoy, FT-IR, FT-Raman and NMR characterization of 2-
isopropyl-5-methylcyclohexyl quinoline-2-carboxylate and investigation of its
23

ACCEPTED MANUSCRIPT
reactive and optoelectronic properties by molecular dynamics simulations and DFT
calculations, J. Mol. Struct. 1127 (2017) 124-137.
[84] S. Armaković, S.J. Armaković, S. Pelemiš, D. Mirjanić, Influence of sumanene
modifications with boron and nitrogen atoms to its hydrogen adsorption properties,
Phys. Chem. Chem. Phys. 18(4) (2016) 2859-2870.
[85] A. Michalak, F. De Proft, P. Geerlings, R. Nalewajski, Fukui functions from the
relaxed Kohn-Sham orbitals, J. Phys. Chem. A 103 (1999) 762-771.
[86] T. Andersson, A. Broo, E. Evertsson, Prediction of Drug Candidates' Sensitivity
Toward Autoxidation: Computational Estimation of C-H Dissociation Energies of
Carbon‐Centered Radicals, J. Pharm. Sci. 103 (2014) 1949-1955.
[87] S.W. Hovorka, C. Schöneich, Oxidative degradation of pharmaceuticals: Theory,
mechanisms and inhibition, J. Pharm. Sci. 90 (2001) 253-269.
[88] J.S. Wright, H. Shadnia, L.L. Chepelev, Stability of carbon‐centered radicals:
Effect of functional groups on the energetics of addition of molecular oxygen, J.
Comput. Chem. 30 (2009) 1016-1026.
[89] G. Gryn'ova, J.L. Hodgson, M.L. Coote, Revising the mechanism of polymer
autooxidation, Org. Biomol. Chem. 9 (2011) 480-490.
[90] A. Lagunin, A. Stepanchikova, D. Filimonov, V. Poroikov, PASS: prediction of
activity spectra for biologically active substances, Bioinformatics 16 (2000) 747-
748.
[91] P. Antal-Szalmás, Evaluation of CD14 in host defence, Eur. J. Clin. Investig. 30
(2000) 167-179.
[92] X. Du, M. G. Low, Down-Regulation of Glycosylphosphatidylinositol-Specific
Phospholipase D Induced by Lipopolysaccharide and Oxidative Stress in the
Murine Monocyte- Macrophage Cell Line RAW 264, Infect. Immun. 69 (2001)
3214-3223.
[93] W. Su, Q. Chen, M.A. Forman, Targeting phospholipase D with small-molecule
inhibitors as a potential therapeutic approach for cancer metastasis, Future
Oncology 5 (2009) 1477-1486.
24

ACCEPTED MANUSCRIPT
[94] M. Dolezal, J. Zitko, Pyrazine derivatives: a patent review (June 2012 – present)
Expert Opinion on Therapeutic Patents 25 (2015) 33-47.
[95] F.A.R. Rodrigues, I. D. S. Bomfim, B. C. Cavalcanti, C.Ó Pessoa, A.C. Pinheiro,
C. H. S. Lima, M.V. N. de Souza, Biological evaluation of pyrazinamide
Derivatives as an anticancer class, Eur. Chem. Bull., 3 (2014) 358-361.
Figure captions
Fig.1 Optimized geometries of a) ORTHOPHPZ, b) METAPHPZ and c) PARAPHPZ
Fig.2 HOMO-LUMO plots of a) ORTHOPHPZ, b) METAPHPZ and c) PARAPHPZ
Fig.3. MEP and ALIE surfaces with their corresponding minimal and maximal values of
oxadiazole derivatives: a) ORTHOPHPZ, b) METAPHPZ and c) PARAPHPZ
Fig.4 Fukui functions and their minimal and maximal values of investigated oxadiazole
derivatives a) ORTHOPHPZ, b) METAPHPZ and c) PARAPHPZ
Fig.5 H-BDE (red colour) and BDE (blue colour) values for a) ORTHOPHPZ, b)
METAPHPZ and c) PARAPHPZ molecules
25

ACCEPTED MANUSCRIPT
Table 1
Determination of MIC against MTb H37RV of compounds
Compound code
ORTHOPHPZ
METAPHPZ
PARAPHPZ
MIC (µg/ml)
0.8
0.8
1.6
Pyrazinamide
Streptomycin
3.125
6.25
Anti-bacterial activity against S. aureus
Zone of Inhibition of PP-5 to PP-7 at 250µg/ml
Compound code
ORTHOPHPZ
METAPHPZ
PARAPHPZ
Zone of inhibition (mm)
05
13
05
14
Ciprofloxacin
Anti-bacterial Activity against S. typhi
Zone of Inhibition of PP-5 at 250µg/ml
Compound code
ORTHOPHPZ
Ciprofloxacin
Zone of inhibition (mm)
6
13
1

ACCEPTED MANUSCRIPT
Table 2
PASS prediction for the activity spectrum of title compounds
Pa represents probability to be active and Pi represents probability to be inactive
Table 2.1- 2-(5-(2-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (ORTHOPHPZ)
Pa
Pi
Activity
0.806 0.012 Glycosylphosphatidylinositol phospholipase D inhibitor
0.774 0.004 CYP2A8 substrate
0.694 0.016 Phthalate 4.5-dioxygenase inhibitor
0.689 0.039 Antiseborrheic
0.618 0.022 Chloride peroxidase inhibitor
0.612 0.024 27-Hydroxycholesterol 7alpha-monooxygenase inhibitor
0.618 0.042 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase inhibitor
0.567 0.014 Antiobesity
0.613 0.065 Nicotinic alpha6beta3beta4alpha5 receptor antagonist
0.575 0.045 Complement factor D inhibitor
0.633 0.107 Phobic disorders treatment
0.583 0.061 Taurine dehydrogenase inhibitor
0.550 0.030 Fructose 5-dehydrogenase inhibitor
0.521 0.025 Amine dehydrogenase inhibitor
0.515 0.027 Creatininase inhibitor
Table 2.2 - 2-(5-(3-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (METAPHPZ)
Pa
Pi
Activity
0.820 0.010 Glycosylphosphatidylinositol phospholipase D inhibitor
0.796 0.004 CYP2A8 substrate
0.735 0.060 Phobic disorders treatment
0.665 0.021 Phthalate 4.5-dioxygenase inhibitor
0.642 0.036 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase inhibitor
0.586 0.028 Chloride peroxidase inhibitor
0.566 0.026 Fructose 5-dehydrogenase inhibitor
0.595 0.057 Taurine dehydrogenase inhibitor
0.582 0.058 Antiseborrheic
0.551 0.036 27-Hydroxycholesterol 7alpha-monooxygenase inhibitor
1

ACCEPTED MANUSCRIPT
0.543 0.041 2-Hydroxyquinoline 8-monooxygenase inhibitor
0.525 0.024 Amine dehydrogenase inhibitor
0.522 0.022 Nicotine dehydrogenase inhibitor
Table 2.3- 2-(5-(4-chlorophenyl)-1,3,4-oxadiazol-2-yl)pyrazine (PARAPHPZ)
Pa
Pi
Activity
0.844 0.007 Glycosylphosphatidylinositol phospholipase D inhibitor
0.769 0.004 CYP2A8 substrate
0.722 0.012 Phthalate 4.5-dioxygenase inhibitor
0.703 0.022 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase inhibitor
0.712 0.071 Phobic disorders treatment
0.650 0.017 Chloride peroxidase inhibitor
0.634 0.014 Fructose 5-dehydrogenase inhibitor
0.636 0.023 2-Hydroxyquinoline 8-monooxygenase inhibitor
0.652 0.046 Antiseborrheic
0.647 0.044 Taurine dehydrogenase inhibitor
0.594 0.020 Creatininase inhibitor
0.587 0.017 Amine dehydrogenase inhibitor
0.586 0.028 27-Hydroxycholesterol 7alpha-monooxygenase inhibitor
0.617 0.063 Nicotinic alpha6beta3beta4alpha5 receptor antagonist
0.554 0.016 Nicotine dehydrogenase inhibitor
0.570 0.032 Pterindeaminase inhibitor
0.571 0.046 Complement factor D inhibitor
2