Molecular docking studies on novel phenyl hydrazine derivatives of piperidones for anticancer efficiency

Article abstract of DOI:10.14233/ajchem.2015.19011

Phenyl hydrazine derivatives of some 2, 6-diphenyl-4-piperidones (3-4) were synthesized by the reaction of piperidone derivatives with phenyl hydrazine. The synthesized compounds (3-4) were characterized using IR, 1H NMR and 13C NMR techniques. ADME-Tox properties of the two compounds showed the drug likeliness property and found to obey Lipinski's rule of five. Molecular docking study for both the synthesized compounds (3-4) exhibited significant binding potency to the target protein structures. The glide score (G.Score) was least observed with dihydrofolate reductase protein which was -7.88 and -5.44 for compounds (3) and (4) respectively. The hydrogen bonds were formed with the residues THR56, SER59 of 2.1 ?, 2.4 ? bond. The Glide score was observed nearly equal to the quinazolinone derivative against dihydrofolate reductase. Therefore further studies could be carried out for the synthesized compounds as lead molecule for cancer drug development.

Full text of DOI:10.14233/ajchem.2015.19011

Asian Journal of Chemistry; Vol. 27, No. 11 (2015), 3969-3974
A
SIAN
J
OURNAL OF HEMISTRY
C
http://dx.doi.org/10.14233/ajchem.2015.19011
Molecular Docking Studies on Novel Phenyl Hydrazine
Derivatives of Piperidones for Anticancer Efficiency
1,*
1
1
2
P. RAJESH , M. DINESH KUMAR , R. JAMUNARANI and J. MANIKANDAN
1
2
Department of Chemistry, Government Arts College (Autonomous), Coimbatore-641 018, India
Department of Chemistry, PSG College of Arts and Science (Autonomous), Civil Aerodrome, Coimbatore-641 014, India
*
Corresponding author: E-mail: gacchemistryrajesh@gmail.com
Received: 12 January 2015; Accepted: 16 February 2015;
Published online: 16 July 2015;
AJC-17384
Phenyl hydrazine derivatives of some 2, 6-diphenyl-4-piperidones (3-4) were synthesized by the reaction of piperidone derivatives with
1
13
phenyl hydrazine. The synthesized compounds (3-4) were characterized using IR, H NMR and C NMR techniques.ADME-Tox properties
of the two compounds showed the drug likeliness property and found to obey Lipinski’s rule of five. Molecular docking study for both the
synthesized compounds (3-4) exhibited significant binding potency to the target protein structures. The glide score (G.Score) was least
observed with dihydrofolate reductase protein which was -7.88 and -5.44 for compounds (3) and (4) respectively. The hydrogen bonds
were formed with the residues THR56, SER59 of 2.1 Å, 2.4 Å bond. The Glide score was observed nearly equal to the quinazolinone
derivative against dihydrofolate reductase. Therefore further studies could be carried out for the synthesized compounds as lead molecule
for cancer drug development.
Keywords: Cancer, Piperidones, Molecular docking, Glide score, Dihydrofolate reductase protein.
Bcl-2, targeting Bcl-2 may provide therapeutic benefit where the
Bcl-2 inhibitors like navitoclax, BH3 are under investigation .
INTRODUCTION
5
Cancer is considered to be a heterogeneous disease both
Cyclooxygenase (COX), officially known as prostaglandin-
endoperoxide synthase (PTGS) is an enzyme responsible for the
formation of important biological mediators called prostanoids,
also known as prostaglandins, prostacyclin and thromboxane.
Normal growth of cell involves the metabolites of arachidonic
acid where the conversion to prostaglandins is catalyzed by
the cyclooxygenase. Cyclooxygenase enzymes exist in two
forms COX-1 and COX-2 where COX-2 is found overexpre-
morphologically and genetically. In general tumor develop-
ment occurs when the environment enhances its growth. This
may be due to the defect in nascent neoplastic cells thereby
arresting the cell proliferation which lead the cell to be insen-
1
sitive for signaling . The androgen receptor (AR) also known
as NR3C4 (nuclear receptor subfamily 3, group C, member 4)
is a transcription factor which comes under the type of nuclear
receptor. In normal condition the expression of the genes
maintains the function and development of male sexual
6
ssed in cancerous growth . COX-2 is also found to mediate
the inflammatory effect of cyclooxygenase activity. COX-2
selective inhibitors are potent suppressor of colon polyps in
colorectal cancer and even the treatment with celecoxib has
shown promising results in cancer prevention. Harris and his
2
organs . Therefore defects may develop prostate cancer.
The discovery of Bcl-2 gene is believed to be one of the
milestones achieved in tumor biology. The name is derived
from B-cell lymphoma 2 and found regulating major types of
cell death, including apoptosis, necrosis and autophagy, thus
operating as nodal points at the convergence of multiple path-
7
colleagues had reported COX-2 inhibitors also provide the
same magnitude of protection for prostate and lung cancer.
Dihydrofolate reductase (DHFR) is an enzyme which
catalyzes the reduction of dihydrofolic acid to tetrahydrofolic
acid using NADPH as electron donor. It plays an essential
role in cell metabolism, cellular growth and in regulating the
amount of tetrahydrofolate in the cell. Tetrahydrofolate and
its derivatives are essential for purine and thymidylate
3
ways with broad relevance to oncology . In majority of the
cancer types, the expression of proapoptotic members of Bcl-2
was found in defected state; therefore the cell loses its tumor
suppressor function. mRNA expression of Bcl-2 subfamily
members were found highest in many cancer types such as lung,
4
8
prostate, breast, ovarian, renal and glioma cancer cell lines .
synthesis . Therefore DHFR is considered to play a central
Since the multiple tumor types shows the over- expression of
role in the synthesis of nucleic acid precursors and has been

3
970 Rajesh et al.
Asian J. Chem.
O
shown that a mutant cell completely lacks DHFR therefore it
has to be supplied with glycine, purine and thymidine to grow.
Estrogen receptor is activated by the hormone 17β-estradiol
R
R'
C HO
O
(estrogen) and it exists in two forms, one as a member of nuclear
C HO
hormone family of intracellular receptors.Also as an estrogen
G protein-coupled receptor GPR30 (GPER) belongs to G
protein-coupled receptor. ERs are widely expressed in different
tissue types however exhibits some notable diffe-rences in their
expression patterns in which ERα found in breast cancer cells
R
Ethanol
2H
+
–
2
O
C
6
H
5
N
H
6 5
C H
NH COOCH3
4
(
1-2)
R = –CH , –CH (CH )
3 2
9
are one such example . The expression of ER is the main
3
2
indicator of potential responses to endocrine therapy (ET) and
approximately 70 % of human breast cancers are hormone-
R = CH3
R' = –C H , –CH (CH )
2
5
2
3
2
CH COONa
3
10
dependent and ER-positive .
6 5 2
C H NHNH
6 5
NNHC H
The glucocorticoid receptor (GR or GCR) also known as
NR3C1 (nuclear receptor subfamily 3, group C, member 1) is
expressed in almost every cell regulating the genes to control
the development, metabolism and immune response . Gluco-
corticoid receptor is found involved in the prostate cancer,
breast cancer, solid tumors and acute lymphoblastic leukemias
R
11
N
H
(
3-4)
(
ALL). Mechanism of cancer cell resistance in acute lympho-
blastic leukemias may due to the glucocorticoid receptor-
mediated apoptosis .
The mammalian target of rapamycin (mTOR) also known
as mechanistic target of rapamycin or FK506 binding protein
3 2 3 2
R = –CH , –CH (CH )
12
Fig. 1. Synthetic scheme for phenyl hydrazine derivatives of 2,6-diphenyl-
piperidin-4-ones (3-4)
The conversion of active compounds into qualified clinical
candidates has proved to be a challenge. In silicoADME-Tox
analysis focuses mainly on predicting the absorption, distri-
bution, metabolism, excretion and toxicity properties of
chemical compounds, therefore assist in modifying the small
molecules accordingly to develop into a potent drug. Bioavail-
ability depends mainly on absorption and liver first-pass
metabolism. The volume of its distribution, together with its
clearance rate, determines the half-life of a drug and therefore
its dosage is a key point. This information is valuable for the
refinement of the in silico ADME-Tox models. Both the
compounds were studied for its mode of interaction with cancer
targets like androgen receptor, Bcl2 protein, cyclooxygenase
II, dihydrofolate reductase, estrogen receptor, glucocorticoid
receptor and mammalian target for rapamycin through
molecular docking analysis.
The 3D structures of the synthesized molecules were drawn
using Chemsketch 11.0. TheADME toxicity was analyzed for
both the compounds using the QikProp module of Schrodinger
suite. The protein structures were retrieved from PDB (Protein
Data Bank). Molecular docking was carried out using Glide
module of Schrodinger suite. Small molecules were prepared
with LigPrep which produces a single, low-energy, 3D structure
with correct chirality for eachsuccessfully processed input
structure. The ligand structures were prepared adding hydrogen
atoms and minimized with OPLS 2005 force field. The salts
and water molecules which did not show interaction with the
protein was removed. The resulting energy minimized prepared
structures were used for further docking studies. The proteins
were prepared by removing the water molecules which do not
have the particular role in ligand binding.
1
2-rapamycin associated protein 1 (FRAP1) is a protein which
in humans is encoded by the FRAP1 gene. Mammalian target
of rapamycin is a serine/threonine protein kinase that regulates
cell growth, cell proliferation, cell motility, cell survival, protein
synthesis and transcription. Mammalian target of rapamycin
inhibition clinically showed promising activity against particular
cancers including cell lymphoma, endometrial cancer and renal
cell carcinoma.
EXPERIMENTAL
The compounds (3) and (4) were synthesized by mixture
of corresponding ketone (0.1 mol), benzaldehyde (0.2 mol)
and dried ammonium acetate (0.1 mol) were dissolved in
13
ethanol (50 mL) . These contents were heated until the yellow
colour turns into orange and were kept in room temperature
for 14 h. Concentrated ammonia (30 mL) was added followed
by conc. HCl (30 mL) and then cooled in ice water. Then the
precipitate was neutralized with dry ether (30 mL). Finally,
the neutralized product 3-methyl-2, 6-diphenyl-piperidin-4-
one (1-2) was filtered and recrystallized from absolute ethanol.
Phenyl hydrazine derivative of 2,6-diphenyl-piperidin-4-ones
(
3-4) were synthesized by the reaction of corresponding 2, 6-
diphenyl-piperidin-4-ones (0.01 mol) with phenyl hydrazine
0.01 mol) and sodium acetate (0.01 mol) in ethanol (30 mL)
(
with continuous stirring and heating for 3 h. The contents were
kept undisturbed for 24 h. The precipitate was filtered, washed
with ether and recrystallized from absolute ethanol. All the
compounds (3-4) having very good yield. The synthetic scheme
of the preparation of compounds 3 and 4 is given in Fig. 1.
Purity test for the compounds were performed by TLC using
glass plates coated with silica gel of 0.25 mm thickness. Spots
were visualized using iodine chamber and characterized by
The receptor grid can be set up and generated from the
Receptor Grid Generation panel.Glide ligand docking requires
a set of previously calculated receptor grids and one or more
ligand structures.The Settings tab defines the basic options
1
H NMR and IR spectroscopy analysis.

Vol. 27, No. 11 (2015)
Molecular Docking Studies on Novel Phenyl Hydrazine Derivatives of Piperidones 3971
TABLE-1
ADME-Tox PROPERTIES OF THE SYNTHESIZED COMPOUND (3) and (4)
Properties
Normal Range
Compound (3)
Compound (4)
Molecular weight
130.00-725.00
355.482
383.535
Solute as donor- hydrogen bond
Solute as acceptor- hydrogen bond
Octanol-water partition coefficient
0-10
0-5
<5
2
3.5
5.1
2
3.5
5.8
for docking ligands specifying the grid, selectingthe precision
and setting flexibility options.Docking was carried out to
perform XP ligand docking with the receptor Grid generated.
visualize and the glide score, interacting residues along with
their bond length are given in Table-2.
TABLE-2
RESULTS AND DISCUSSION
INTERACTION PROFILE OF CANCER SPECIFIC
PROTEIN WITH THE SYNTHESIZED COMPOUNDS
1
13
The IR, H NMR, C NMR spectra of compounds 3 and 4
have been studied and reported in this study.
Compd. No.
G.Score
Interacting residues
Bond length (Å)
Androgen receptor
PRO682 (O-H)
GLY683 (O-H)
ASN705 (O-H)
BCL-2 Protein
ALA4 (O-H)
ASP103 (O-H)
COX-2 Protein
GLY225 (O-H)
ASN375 (O-H)
GLN374 (O-H)
GLY225 (O-H)
N-(3-Methyl-2,6-diphenyl-piperidin-4-ylidine)-N’-
phenyl-hydrazine (3): Brown solid; Yield: 68 % m.p.: 115
3
4
-3.45
-2.68
2.8
2.1
2.1
-1
°
(
C; IR (KBr) λmax (cm ): 3339, 3309 (NH) 2253 (C=N) 1369
1
C-N) 1113 (N-N); H NMR (300 MHz, CDCl
3
) 3.54-3.57 (d,
1
2
2
7
4
1
H, J 10.2 Hz), 2.92-2.98 (m, 1H, J 16.8 Hz), 2.57-2.65 (dd,
H, J 23.4 Hz), 3.89-3.94 (m, 1H, J 14.7 Hz), 1.01-1.03 (d,
H, J 6.6 Hz), 2.09-2.25 (dd, 1H, J 45.9 Hz), 8.45 (s, 1H),
3
4
-3.92
-2.53
1.9
2.5
13
-2.97
1.8
2.1
2.1
1.8
3
4
.05-7.51 (m, 15H); C NMR (75 MHz, CDCl ) 12.32, 34.55,
3
4.83, 60.83, 69.43, 112.76-129.15, 143.00, 143.66, 146.01,
48.59.
-2.93
N-(3-Isopropyl-2,6-diphenyl-piperidin-4-ylidine)-N’-
Dihydrofolate reductase protein
phenyl-hydrazine (4): Brown solid; Yield: 45 % m.p.: 138
3
4
-7.88
-5.44
THR56 (O-H)
SER59 (O-H)
2.1
2.4
-1
°
(
1
2
6
C; IR (KBr) λmax, (cm ): 3228, 3427 (NH) 2238 (C=N) 1352
1
C-N) 1116 (N-N); H NMR (300 MHz, CDCl
3
) 3.98-4.04 (t,
Estrogen receptor
TRP393 (N-H)
GLU323(O-H)
PRO324 (O-H)
GLU323 (O-H)
H, J 19.8 Hz), 2.64-2.72 (m, 1H, J 24.6 Hz), 2.58-2.59 (dd,
H, J 16.8 Hz), 4.07-4.12 (d, 1H, J 14.4 Hz), 1.03-1.26 (m,
H, J 68.1 Hz), 2.53-2.54 (m, 1H, J 3.3Hz) 1.62-1.70 (m, 1H,
J 25.5 Hz), 8.79 (s, 1H), 7.05-7.51 (m, 15H); C NMR (75
MHz, CDCl ) 17.52-20.85, 25.76, 37.81, 51.74, 60.99, 64.53,
15.75-128.44, 136.66, 141.98, 142.67, 148.59.
ADME-Tox refers to absorption, distribution, metabolism,
3
4
-5.34
-5.15
2.3
2.0
1.9
1.9
13
Glucocorticoid receptor
3
3
4
-2.47
-2.41
ASN491 (O-H)
ASN491 (O-H)
Mammalian target of rapamycin
2.6
2.3
1
excretion and toxicity properties which should be considered
to develop a new drug, because they are the main cause of
failures for candidate molecules in drug design. The synthe-
sized compounds were subjected for analyzing the ADME-
Tox properties and the results are given in Table-1. Compound
3
4
-2.89
ARG 2043 (O-H)
GLU 2053 (O-H)
GLU2060 (O-H)
1.9
2.0
2.1
-2.47
The glide score (G.Score) was least observed with
dihydrofolate reductase protein and therefore the interaction
of compound (3) and compound (4) were shown in the Fig. 2.
Compound (3) has scored -7.88 and compound (4) has scored
-5.44 of G.score which was found nearly equal to the quinazoli-
3
has obeyed the Lipinski’s rule of five rather compound 4
has violated the octanol-water partition co-efficient showing
.8.The rule has following criteria: no more than 5 hydrogen
5
bond donors, not more than 10 hydrogen bond acceptors, a
molecular mass less than 500 daltons, an octanol-water parti-
1
5
none derivative against DHFR . The hydrogen bond was
formed with the residues THR56, SER59 of 2.1 Å, 2.4 Å bond
length for compound (3) and compound (4), respectively.
The interaction of the compound (3) and (4) with the rest of
the proteins were shown in the Fig. 3. With androgen receptor
the glide score was observed to be -3.45 and -2.1. Compound
(3) forms two hydrogen bonds whereas one bond is formed in
the case of compound (4). Both shared the electrons from the
atom “O” (representing oxygen) of protein to “H” (representing
hydrogen) atom of the ligand. The amino acids proline and
glycine located at the position 682 and 683 forms hydrogen
bond of length 2.8 Å and 2.1 Å. Compound (4) forms bond
with ASN705 showing bond length of 2.1 Å. Likewise, the
14
tion coefficient log P not greater than 5 . Both the compounds
were found with molecular weight of about 355 and 383 KDa
respectively which were less than 500 KDa. The number of
donor and acceptor are below the normal range, is about 2
and 3.5 for both the compounds.
The proteins androgen receptor (2AM9), Bcl2 protein
(
(
(
1GJH), cyclooxygenase II (4OTY), dihydrofolate reductase
1DRF), estrogen receptor (3ERD), glucocorticoid receptor
1R4O) and mammalian target for rapamycin (1AUE) were
retrieved from PDB with respective to PDB ID. The active sites
were predicted using the online tool LigSite.The interaction
of the molecules with each protein was observed using XP

3
972 Rajesh et al.
Asian J. Chem.
DHFR vs. compound (3)
DHFR vs. compound (4)
Fig. 2. Interaction of DHFR with compounds (3) and (4)
Androgen receptor vs. compound (3)
Androgen receptor vs. compound (4)
Bcl-2 vs. compound (3)
Bcl-2 vs. compound (4)
COX2 vs. compound (3)
COX2 vs. compound (4)

Vol. 27, No. 11 (2015)
Molecular Docking Studies on Novel Phenyl Hydrazine Derivatives of Piperidones 3973
Estrogen receptor vs. compound (3)
Estrogen receptor vs. compound (4)
Glucocorticoid receptor vs. compound (3)
Glucocorticoid receptor vs. compound (4)
Mammalian target of rapamycin vs. compound (3)
Mammalian target of rapamycin vs. compound (4)
Fig. 3. Interaction of compounds (3) and (4) with respective proteins
synthesized compounds were observed to show interactions
with the active site residues of each protein. Next to DHFR,
the compounds show least score with estrogen receptor of
about -5.34 and -5.15. Both the compounds interacted with
the GLU323 of bond length 2.0 Å for compound 1 and 1.9 Å
for compound (4). Compound (3) also formed hydrogen bond
with TRP393 residue, where the bond is shared between the
N and H atom is of 2.3 Å length. Compound (3) interacts with
the residue PRO324 of bond length 1.9 Å.
for the present study. The synthesized compounds were subjected
for analyzing the ADME-Tox properties and the compound
(3) has not shown any violation in the Lipinski rule of five.
The compound (3) and compound (4) were docked and the
interaction with each protein was analyzed and it was found
that both the compounds exhibited the glide score was least
observed with dihydrofolate reductase protein which was -7.88
and -5.44 respectively. Therefore, the current study would be
a foundation for developing the compound (3) in the treating
cancer.
Conclusion
A series of phenyl hydrazine derivatives of some 2,6-
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