New PPARγ ligands based on 2-hydroxy-1,4-naphthoquinone: Computer-aided design, synthesis, and receptor-binding studies

Article abstract of DOI:10.1016/j.bmcl.2008.04.072

FlexX-based molecular docking study was employed to identify 2-hydroxy-1,4-naphthoquinone as a new 'acidic head group' for the design of a novel series of PPARγ ligands. To provide the proof of concept, designed molecules were synthesized and evaluated in a standard radioligand-binding assay. Out of eight molecules, four were found to bind to the murine PPARγ with IC₅₀ ranging from 0.2 to 56.2 μM as compared to standard pioglitazone, with IC₅₀ of 0.7 μM.

Full text of DOI:10.1016/j.bmcl.2008.04.072

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 18 (2008) 3192–3195
New PPARc ligands based on 2-hydroxy-1,4-naphthoquinone:
Computer-aided design, synthesis, and receptor-binding studies
Sandeep Sundriyal,a Bhoomi Viswanad,b Elumalai Bharathy,a Poduri Ramarao,b
Asit K. Chakrabortia and Prasad V. Bharatama,*
aDepartment of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar, Punjab 160 062, India
bDepartment of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar, Punjab 160 062, India
Received 15 January 2008; revised 22 April 2008; accepted 26 April 2008
Available online 1 May 2008
Abstract—FlexX-based molecular docking study was employed to identify 2-hydroxy-1,4-naphthoquinone as a new ‘acidic head
group’ for the design of a novel series of PPARc ligands. To provide the proof of concept, designed molecules were synthesized
and evaluated in a standard radioligand-binding assay. Out of eight molecules, four were found to bind to the murine PPARc with
IC50 ranging from 0.2 to 56.2 lM as compared to standard pioglitazone, with IC50 of 0.7 lM.
Ó 2008 Elsevier Ltd. All rights reserved.
Peroxisome proliferator-activated receptor (PPAR) be-
longs to the nuclear hormone receptor (NHR) super-
family.1 Three subtypes, PPARa, PPARc, and PPARd
for this receptor have been discovered and identified as
important targets for the treatment of metabolic disor-
ders such as type 2 diabetes, dyslipidemia, atherosclero-
sis, etc.2 PPARc first came into the picture when it was
established as the target for the thiazolidinediones
(TZD) class of insulin sensitizers,3 synthesized in the
early 1980s.4 The molecules belonging to the fibrate class
of drugs, such as clofibrate (1) and fenofibrate (2), are
known to act as PPARa agonists. Recently, PPARd is
also being studied as the target for the treatment of
obesity.5 Out of the three isoforms, PPARc and its ago-
nists have been studied extensively. Recently, the role of
PPARc has been established in the treatment of inflam-
matory conditions and cancer, thus, providing more
therapeutic value to this target.6 Currently, rosiglitazone
(3) and pioglitazone (4) are being used clinically (Fig. 1).
However, in a recent study, rosiglitazone has been found
to increase the incidences of heart attack among pa-
tients.7 Thus, there is scope to discover novel and safer
molecules as PPARc agonists. In continuation of our
previous work on PPAR ligands,8 we hereby report
the computer-aided design (CAD) and synthesis of a no-
vel series of PPARc ligands.
The crystal structure of PPARc with co-crystallized
rosiglitazone molecule showed that the TZD ring makes
H-bonds with His323, Tyr473, Ser289 and His449 which
are important for the activity.9 This is in accordance
with structure–activity relationship studies, which show
that the acidic hydrogen of TZD is vital for the biolog-
ical activity. Hence, a variety of ‘acidic head groups’
such as free carboxyl group, oxazolidinedione, tetra-
zoles, etc., were successfully used to replace the TZD
ring to obtain a new class of such agents.10 However,
most of the PPARc agonists described in the literature
belong to either the ‘glitazone’ class (possessing a TZD
ring) or to the ‘glitazar’ class (possessing free carboxylic
acid). Many of these ligands are associated with adverse
effects such as weight gain, edema, carcinogenicity,
etc.7,11 Thus, we recognized the importance of designing
new series of PPAR ligands by exploring new ‘acidic
head groups’. We employed molecular docking as a
computational tool for this purpose.
To start with, a few molecules were designed by replac-
ing the ‘acidic head group’ of farglitazar (5), a PPARa/c
dual agonist, with a number of acidic moieties.
However, the lipophilic group was kept same as that
Keywords: PPARc; Glitazones; Docking; Computer-aided drug design;
Rosiglitazone; Farglitazar; 2-Hydroxy-1,4-naphthoquinone.
*
Corresponding author. Tel.: +91 172 2214684; fax: +91 172
2214692; e-mail: pvbharatam@niper.ac.in
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.04.072

S. Sundriyal et al. / Bioorg. Med. Chem. Lett. 18 (2008) 3192–3195
3193
O
the design of novel series. One of such moieties was
2-hydroxy-1,4-naphthoquinone (HNQ) ring (Fig. 1),
which was preferred for further studies over others
on the basis of its commercial availability, low cost,
and easy derivatization. Thus, different derivatives of
HNQ ring with a variety of lipophilic groups were de-
signed as potential PPARc agonists. One of the de-
signed molecules docked in the active site of PPARc
(1FM9) is shown in Figure 2 which was found to main-
tain the H-bonding interactions with His323, Tyr327,
and Ser289 in the PPARc active site, important for
the receptor-binding and activation.
O
O
O
Cl
O
O
Cl
Clofibrate, 1
Fenofibrate, 2
O
O
O
NH
NH
N
S
S
O
N
O
N
O
O
3
Pioglitazone, 4
Rosiglitazone,
Lipophilic group
Acidic head group
OH
O
N
O
HN
O
O
It was decided to synthesize a few molecules in order to
verify the docking results. The first step in the synthetic
strategy was the O-alkylation of p-hydroxy benzalde-
hyde (6) with 1,2-dibromoethane (7) to yield the mono-
bromo derivative (8) and also with benzyl bromide and
2-fluoro benzyl bromide to yield aldehydes 9a and 9b
(Scheme 1). The monobromo aldehyde (8) was further
used to alkylate different phenols to yield aldehydes
9c–h. These were then reduced to benzyl alcohols, and
further converted to the corresponding benzyl bromide
derivatives using well-known procedures. In the final
step, the benzyl bromide derivatives were used to alkyl-
ate the 2-hydroxy-1,4-naphthoquinone with a reported
procedure13 to yield the final products 11a–h. In all
cases, the isomeric O-alkylated product was also
formed, which was separated from the desired C-alkyl-
ated product by column chromatography. All the final
products were characterized using 1H NMR, 13C
NMR, and mass spectrometry.14
Farglitazar, 5
OH
O
R
O
O
O
Designed
molecules
Figure 1. Structures of a few PPAR ligands and the design of new
series of PPARc ligands based on 2-hyroxy-1,4-naphthoquinone
(HNQ).
of farglitazar in these molecules. These virtual mole-
cules were then docked in the active site of PPARc
(PDB code 1FM9) using the FlexX algorithm imple-
mented in Sybyl 6.9 and analyzed for binding interac-
tions.12 This study showed that a number of acidic
moieties can maintain the important H-bonding inter-
actions with the PPARc active site as exhibited by
the TZD ring and can act as ‘acidic head group’ for
Finally, molecules 11a–h were evaluated for their ability
to bind to the murine PPARc using a standard receptor-
Figure 2. Predicted binding mode of the most potent compound (11b, ball and stick model) in the active site of PPARc (PDB code 1FM9). The
cocrystallized ligand (5, farglitazar) is shown in green color for comparison. The interacting amino acids (Tyr327, His323, and Ser289) are shown in
magenta color and H-bonds are represented with yellow dashed lines.

3194
S. Sundriyal et al. / Bioorg. Med. Chem. Lett. 18 (2008) 3192–3195
Table 1. Structures of final molecules with corresponding IC50 values
CHO
OH
CHO
Br
a
O
Br
O
+
3 eq.
8
6
7
Br
OH
O
R
O
Br
b
c
Compound
R
IC50 (lM)
X
11aa
3.6
CHO
CHO
O
O
X
9a
11b
11c
0.2
i.a.
, X= H
O
9c-9h
9b, X = F
Ar
F
d
O
H3C
OH
e
Br
11d
11e
11f
11g
11h
i.a.
i.a.
i.a.
56.2
1.9
O
O
R
O
R
O
f
OH
O
O
Cl
R
O
O
11a-11h
O
MeO
NC
Scheme 1. Reagents and conditions: (a) K2CO3, DMF, 50 °C, 5 h,
50%; (b) ArOH, K2CO3, DMF, reflux, 2–4 h, 84–93%; (c) K2CO3,
DMF, reflux, 2–4h, 64–85%; (d) NaBH4, MeOH–THF, 0 °C–RT, 0.5–
1 h, 90–95%; (e) SOBr2, Toluene, 0 °C–RT; (f) 2-hydroxy-1,4-naphtho-
quinone (HNQ), Li2CO3, DMF, 80 °C, 15–25%.
O
Pioglitazone (reference standard) IC50 = 0.7 lM. i.a., inactive (less
than 20% inhibition at 10À7 M).
a Inhibited nearly 100% binding of [3H]-rosiglitazone.
binding assay, with pioglitazone as a reference stan-
dard.15 Interestingly, out of the eight molecules, four
were found to be active in this assay and one molecule
(11b) was found to possess IC50 value of 0.2 lM (Table 1),
comparable to the reference molecule. However, only one
molecule (11a) inhibited nearly 100% binding of the
radioligand [3H]-rosiglitazone, while others were found
to be partial inhibitors (Fig. 3). Addition of a ‘F’ atom
in the lipophilic group of 11a improved the binding
strength tremendously in 11b. Molecules with bulky lipo-
philic group (11d and 11e) were found to be inactive, pos-
sibly due to unfavorable steric clashes with the amino acid
residues in the active site. Nonetheless, these experimental
results verify the molecular docking studies and demon-
strate that the HNQ ring can actually be employed as
the ‘acidic head group’ for the design of novel class of
PPAR ligands.
11g
11h
11a
11b
120
100
80
60
40
20
0
Pioglitazone
-10
-9
-8
-7
-6
-5
-4
In summary, using docking studies we have identified a
novel series of PPAR ligands based on 2-hydroxy-1,4-
naphthoquinone, as a ‘acidic head group’. The designed
molecules were predicted to retain the H-bonding interac-
tions important for the receptor activation. Preliminary
synthetic and receptor binding studies were undertaken
to provide the experimental evidence. The synthesized
molecules were indeed found to bind to the receptor with
IC50 comparable to the reference standard, pioglitazone.
Further structure–activity relationship studies for this
series are in progress.
- Log [M]
Figure 3. Plot of specific binding versus concentration of the active
PPARc ligands.
Acknowledgment
Authors thank the Department of Science and Technol-
ogy (DST), New Delhi, for providing financial
assistance.

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3195
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