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Theoretical studies of structure/activity relationships applied to flavone derivates for drug discovery View project
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Abdou Boucekkine
Univ Rennes, CNRS, ISCR – UMR 6226
F-35000 Rennes, France
abdou.boucekkine@univ-rennes1.fr
**aichachimie1@gmail.com
†Corresponding author.
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using natural bond orbital analyses NBO. Then, the structure-activity properties of a large
series of derivatives were investigated using the HyperChem 8.0.6 software considering the
Lipinski's \rule of ¯ve". The results of QSAR analyses showed that the most promising com-
pound among others, named f1 (a thiophen ring being attached to the nitrogen atom 3 of 1)
should be a good candidate for experimental testing.
1. Introduction
Oxazinones are important heterocyclic compounds because of their broad biological
activities. Considerable attention has been given to these compounds since the dis-
covery of efavirenz, a tri°uoromethyl-1, 3-oxazin-2-one compound which is a non-
nucleoside reverse transcriptase inhibitor and a selective anti-HIV drug. Several
benzoxazinones exhibit various pharmacological properties, such as progesterone
receptor antagonist, with antitumor, antiviral, antithrombotic, antimycobacterial,
anti-in°ammatory, antidiabetic and hypolipidemic activities. Indeed, recently,
some synthesized oxazinones have shown good antibacterial and antifungal ac-
tivities.1 For our part, we synthesized several pyrazolooxazines derivatives; the
evaluation of their pharmacological properties showed that some of these com-
pounds exhibit an interesting anti-in°ammatory activity.2,3 In the continuation
of this work, we plan to investigate theoretically pyrazolooxazines derivatives, using
Density Functional Theory (DFT) as well as QSAR calculations, in order to bring to
light for these derivatives structure-reactivity relationships, and ¯nally help to the
design of molecules with the best anti-in°ammatory activity (a weak IC50).The syn-
thesis reactions of oxazin-2-ones 1 and oxazin-2-thiones 2 are given in Fig. 1.
The theoretical prediction of various properties among them biological ones often
needs accurate ab initio and DFT computations.4–7 Understanding of fundamental
processes and phenomena in medicinal chemistry and drug design is based on the
calculation of relevant descriptors able to bring to light quantitative structure-ac-
tivity relationships.8 Basic molecular descriptors, such as log P (partition coe±-
cient), molecular weight (MW), acceptors and hydrogen-bonding donors in a
molecule, may characterize the molecular properties such as membrane permeability
and oral bioavailability. By using these molecular properties, Lipinski et al. intro-
duced a well-known rule for drug design.9 Lipinski's \rule of ¯ve" with parameters
such as Lipophilic E±cacy (LipE) has been demonstrated to be a useful tool in the
process of drug selection for oral medications.10,11
In the present work, large series of pyrazolooxazine derivatives are investigated
for their physico-chemical properties related to their biological activity. For this aim,
DFT computations have been carried out to estimate HOMO-LUMO energy gaps,
ionization potential (I), electron a±nity (A), electrophilicity index (!), nucleophi-
licity index (N), chemical potential (), hardness () and softness (S) of the con-
sidered pyrazolooxazine derivatives. The determination of their optimized molecular
1950001-2
DFT and QSAR investigations of substituent e®ects
2. Computational Details
The Gaussian 09 program, HyperChem8.0.6 software and the Mol inspiration online
database have been used for all calculations presented in this work.12–14 In a ¯rst
step, the geometries of the considered pyrazolooxazines derivatives were fully opti-
mized at the B3LYP/6-311þþG (d, p) level using the Gaussian 09 program package.
In the literature, the largely used B3LYP DFT functional is presented to give reliable
results regarding the ground state properties of organic molecules.7 The normal
modes of vibration calculations which have been carried out using the optimized
geometries, led to real frequencies indicating that these geometries are minima on the
potential energy surfaces. NBO15,16 calculations have then been done as well as the
computation of di®erent indexes of chemical reactivity at the same level of theory.
In the case of NBO computations, the stabilization energy E2 associated with a pair
of a donor (i) and acceptor (j) natural orbitals is given by:
E 2 ¼ Eij ¼ qi F ði; jÞ2 =ð"j "i Þ; ð1Þ
where F (i; j) is the corresponding Fock matrix element, qi is the donor
orbital occupancy and "i;j are the orbital energy. Finally, in order to select optimal
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Z. Haddadi et al.
compounds, the module QSAR Properties (version 8.0.6) has been used with
HyperChem, allowing to evaluate several properties commonly used in QSAR
studies.
EHOMO ELUMO E S ! N A I
Compounds (eV) (eV) (eV) (eV) (eV) (eV) (eV) (eV) (eV) (eV)
1 5:929 2:717 3.211 0.311 1.606 4:323 5.819 4.323 2.717 5.929
2 5:533 2:572 2.961 0.338 1.480 4:053 5.547 4.053 2.572 5.533
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DFT and QSAR investigations of substituent e®ects
Fig. 2. HOMO and LUMO of pyrazolooxazin-2-one (1, left) andpyrazolooxazin-2-thione (2, right). The atom
colors are gray for carbon, blue for nitrogen, red for oxygen, yellow for sulfur and white for hydrogen atoms.
negative phase with the green one). As expected, they are very similar, especially the
HOMOs; these frontier MOs exhibit a character, the HOMO being mainly localized
on the donating part of the molecule including the phenyl group and the LUMO on
the electron with drawing moiety of the molecules. The electrostatic potential sur-
faces considered below will indicate more precisely the electron rich or poor sites of
the molecules.
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Z. Haddadi et al.
1 2
Donor (i) Acceptor (j) E2 (kcal/mol) Donor (i) Acceptor (j) E2 (kcal/mol)
(C4 –C5 ) (C6 –C4 ) 21.6 (C4 –C5 ) (C6 –C4 ) 21.4
(C6 –C4 ) (C3 –C2 ) 19.7 (C6 –C4 ) (C3 –C2 ) 19. 6
(C6 –C4 Þ (C5 –O4 Þ 22.0 (C6 –C4 ) (C5 –O4 ) 21.8
n (LP2 N1 ) (N2 –C3 ) 22.5 n (LP2 N1 ) (N2 – C3 ) 22.5
n (LP2 N1 ) (C5 –O6 ) 62.8 n (LP2 N1 ) (C5 –O6 ) 62.7
n (LP2 O7 ) (C2 –O1 ) 36.7 n (LP2 S7 ) (C2 –O1 ) 17.5
n (LP2 O7 ) (O1 –N3 ) 25.3 n (LP2 S7 ) (O1 –N3 ) 11.5
n (LP1 O1 ) (C2 –O7 ) 40.4 n (LP1 O1 ) (C2 –S7 ) 45.9
n (LP1 O1 ) (C6 –C4 ) 29.0 n (LP1 O1 ) (C6 –C4 ) 27.1
n (LP1 N3 ) (C2 –O7 ) 57.3 n (LP1 N3 ) (C2 –S7 ) 70.0
n (LP1 N3 ) (C4 –C5 ) 37.6 n (LP1 N3 ) (C4 –C5 ) 36.1
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DFT and QSAR investigations of substituent e®ects
Fig. 3. Molecular electrostatic potential and electron density ED contour maps of pyrazolooxazin-2-one
(1) and pyrazolooxazin-2-thione (2). The atom colors are gray for carbon, blue for nitrogen, red for oxygen,
yellow for sulfur and white for hydrogen atoms.
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DFT and QSAR investigations of substituent e®ects
Fig. 5. 3D Conformation of a2 . The atom colors are green for carbon, cyan for nitrogen, red for oxygen,
yellow for sulfur and white for hydrogen atoms.
properties is based on total polar surface area (TPSA).26 The latter descriptor is
de¯ned as the sum of the surfaces of the polar atoms (usually oxygen, nitrogen and
bound hydrogen) in a molecule. It is a parameter that has a good correlation with
human intestinal absorption, the single-layer permeability of Caco-2 and the pene-
tration of the blood–brain barrier.27 Molecules with TPSA values of 140 A2 or more
28
should exhibit poor intestinal absorption. The number of rotating bonds (nrotb) is
a descriptor of the oral bioavailability of the drugs; it measures the molecular °ex-
ibility.29 The rotator links are de¯ned as a single non-ring bond, bound to the non-
hydrogen charges. Amide C–N bonds are not considered due to their high energy
barrier in the rotation. The computed QSAR descriptors are given in Table 3.
In Table 3, the decreasing order of the polarizability magnitude of the studied
derivatives of 1: h > e > f > g > b > a > c whereas for the 2 derivatives, it is:
h > c ¼ e > g > b > a. The polarizability order is approximately the same for the
volume and surface for the two series of derivatives. In the derivatives of 1, the
surfaces vary from 560.890 A2 to 634.794 A2. The derivatives of 1 exhibit a large
1 Derivatives
a1 325.367 560.890 943.667 34.967 92.510 3:2 70.04 2
b1 339.394 585.903 990.414 36.802 96.982 2:8 70.04 3
c1 339.394 585.903 585.903 36.802 96.982 2:8 70.04 3
e1 373.411 620.575 1056.315 40.957 116.798 5:5 70.04 3
f1 379.433 608.15 1025.246 40.479 114.094 6:0 70.04 3
g1 359.384 605.139 1017.873 39.122 112.634 5:8 70.04 2
h1 373.411 634.794 1070.789 40.957 116.916 4:7 70.04 2
2 Derivatives
a2 341.428 574.020 968.144 38.127 100.797 4:2 70.04 2
b2 355.454 599.146 1019.433 39.962 105.268 3:7 52.97 2
c2 378.468 617.577 1050.370 40.636 107.113 4:2 52.97 3
d2 378.468 611.646 1045.480 40.636 107.113 5:6 52.97 3
e2 372.421 608.729 1027.783 40.060 106.701 7:2 70.04 2
g2 389.472 647.978 1100.222 44.117 117.166 5:3 52.97 2
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Z. Haddadi et al.
variation of the volume distribution, the h1 and e1 species showing the highest
volumes, respectively 1070.789 A3 and 1056. 315 A3 (Table 3). In the case of the
derivatives of 2, g2 and c2 exhibit the highest volumes; respectively 1100.222 A3 and
3
1050.370 A (Table 3).
The highest absolute hydration energy for the derivatives of 1 is that of f 1
(6.0 kcal/mol) and the lowest is that of b1 (2.8 kcal/mol) (Table 3). In the case of the
derivatives of 2, the most important energy of hydration is that of e2 (7.2 kcal/mol)
and the lowest absolute hydration energy is that of b2 (3.7 kcal/mol) (Table 3).
In the biological environment, polar molecules are surrounded by water molecules;
thus, hydrogen bonds could occur between the water molecules and the solute. The
proton donor sites interact with the oxygen atom of the water and the proton ac-
ceptor sites interact with the hydrogen atom of the water molecule. The ¯rst ones
lead to complexes with a strong hydrogen bond. These hydrated molecules are
dehydrated at least partially before and during the biological interaction. Low energy
interactions are reversible.30 The same TPSA value for the derivatives of 1 (70.04 A 2)
2
is observed and it is well below 140
A ; we also observe for the derivatives of 2 that
the TPSA is in the range of 52.97–70.04 A2. The entire screened compounds are
weakly °exible. Attack sites [acceptors H (HBA)] are shown in Fig. 6.
1950001-10
DFT and QSAR investigations of substituent e®ects
Table 4. Lipophilic e±ciency and Lipinski's rule of ¯ve for drug likeness of pyrazolooxazine
derivatives.
1 Derivatives
a1 3.699 1.819 1.880 325.367 6 0 0
b1 3.699 1.416 2.283 339.394 6 0 0
c1 3.699 1.416 2.283 339.394 6 0 0
e1 4.602 3.710 0.892 373.411 6 0 0
f1 3.699 4.196 -0.497 379.433 6 0 0
g1 4.100 3.729 0.371 359.384 6 0 0
h1 4.040 3.516 0.524 373.411 6 0 0
2 Derivatives
a2 3.699 0.698 3.001 341.428 5 0 0
b2 3.699 0.295 3.404 355.454 5 0 0
c2 3.699 -0.123 3.822 378.468 5 0 0
e2 4.602 0.780 3.822 378.468 6 0 0
g2 4.750 0.383 4.367 372.421 5 0 0
h2 4.670 -0.117 4.787 389.472 5 0 0
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Z. Haddadi et al.
lipophilic properties of the chemical compounds evaluated on the basis of the concept
of Lipophilic E±cacy (LipE). Ryckmans et al. reported that high quality compounds
have higher LipE values.39 The results of calculations relative to these properties are
given in Table 4.
Our calculations show that the Log P values are found to be in the range
(0.497)–(2.283) for the derivatives of 1 and (3.001)–(4.787), for derivatives of 2.
The compounds c1 , b1 derivatives of 1 and h2 derivative of 2 have the greatest
hydrophilicity based on their signi¯cant log P values, while f 1 and a2 are the most
lipophilic. This implies that these compounds will have low permeability across the
cell membrane. For a good improvement in their absorption, bioavailability and oral
permeability, some structural changes should be done. The result of the calculations
shows that all the compounds meet the Lipinski's \rule of ¯ve", suggesting that these
compounds theoretically should not have problems with oral bioavailability. The
results reported in Table 4 show that f 1 exhibits the highest LipE value (4.196) in the
dataset; therefore, it can be considered to be one of the most interesting species
regarding the biological activity.
4. Conclusion
The theoretical study of the molecular properties of pyrazolooxazine derivatives
likely to exhibit anti-in°ammatory activities have been carried out. DFT compu-
tations indicate that Pyrazolooxazine-2-thione 2 has a smaller HOMO-LUMO en-
ergy gap than pyrazolooxazin-2-one 1. NBO analysis showed that strong
intramolecular interactions taking place in pyrazolooxazin-2-one 1 and pyrazoloox-
azin-2-thione 2 contribute to their stabilities. Compound 2 is more reactive and more
electron-donating than 1 since its ionization energy (5.533 eV) is lower than that of 1
(5.929 eV). The electrophilic character of 1 is higher than that of 2, since its electron
a±nity A is slightly higher, (2.717 versus 2.572 eV); moreover, its electrophilicity
index is also higher.
A series of di®erently substituted pyrazolooxazine has been considered in order to
check their potential biological activity. It has been found that these compounds
should exhibit good cell plasma membrane permeability. Furthermore, they satisfy
the Lipinski's \rule of ¯ve", indicating that these compounds theoretically would not
have oral bioavailability problems. In particular, f 1 (a thiophen ring attached to the
nitrogen atom 3 of 1) which has the highest LipE value of the dataset could be
considered as a good candidate for biological testing.
Acknowledgment
This work was supported by the University of Sciences and Technology Houari
Boumediene of the Ministry of Higher Education and Scienti¯c Research, ALGERIA
(research project number CNEPRU : E00220120042).
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DFT and QSAR investigations of substituent e®ects
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