Identification of novel PPARα ligands by the structural modification of a PPARγ ligand

Article abstract of DOI:10.1016/j.bmcl.2006.03.031

To develop novel PPARα ligands, we designed and synthesized several 3-{3-[2-(nonylpyridin-2-ylamino)ethoxy]phenyl}propanoic acid derivatives. Compound 10, the meta isomer of a PPARγ agonist 1, has been identified as a PPARα ligand. The introduction of methyl and ethyl groups at the C-2 position of the propanoic acid of 10 further improved the PPARα-binding potency.

Full text of DOI:10.1016/j.bmcl.2006.03.031

Bioorganic & Medicinal Chemistry Letters 16 (2006) 3249–3254
Identification of novel PPARa ligands by the structural
modification of a PPARc ligand
Shinya Usui, Hiroki Fujieda, Takayoshi Suzuki, Naoaki Yoshida,
Hidehiko Nakagawa and Naoki Miyata*
Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
Received 2 February 2006; revised 1 March 2006; accepted 13 March 2006
Available online 18 April 2006
Abstract—To develop novel PPARa ligands, we designed and synthesized several 3-{3-[2-(nonylpyridin-2-ylamino)ethoxy]phenyl}-
propanoic acid derivatives. Compound 10, the meta isomer of a PPARc agonist 1, has been identified as a PPARa ligand. The
introduction of methyl and ethyl groups at the C-2 position of the propanoic acid of 10 further improved the PPARa-binding
potency.
Ó 2006 Elsevier Ltd. All rights reserved.
Peroxisome proliferator-activated receptors (PPARs)
belong to the nuclear receptor superfamily1 and the
PPAR subfamily consists of three members, PPARa,
PPARc, and PPARd. These receptors act as ligand-acti-
vated transcription factors with other members of the
nuclear receptor family,2–4 and play a central role in
the storage and catabolism of dietary fats by regulating
the expression of a large number of genes involved in
lipid metabolism and the energy balance.5 PPARa is
highly expressed in metabolically active tissues such as
liver, heart, and muscle, and activation of PPARa
decreases the serum triglyceride level and increases the
HDL-c level.6 Therefore, PPARa agonists such as clofi-
brate (Fig. 1) are being utilized as hypolipidemic agents.
Meanwhile, PPARc is expressed predominantly in adi-
pose tissues and functions as a regulator of glucose
and lipid homeostasis. The clinically useful thiazolidin-
edione (TZD) class of insulin sensitizers such as rosiglit-
azone7 and pioglitazone8 (Fig. 1) are potent PPARc
agonists used in the treatment of Type 2 diabetes. In
addition, recent studies revealed that dual agonists of
PPARa/c decreased the free triglyceride plasma
concentration and increased the plasma HDL
concentration in an insulin resistant animal model.9–11
Thus, many groups have ongoing research programs
to find more potent and less toxic PPARa agonists
and PPARa/c dual agonists.
We previously reported compound 1, which was de-
signed based on the structure of rosiglitazone and 15d-
PGJ2,12,13 as a potent PPARc ligand.14 To find novel
PPARa agonists, we chose compound 1 as a lead struc-
ture, because recent reports on selective PPAR ligands
indicated that minor structural modifications can affect
selectivity.15–17 In this letter, we report the design, syn-
thesis, and binding affinity of PPAR ligands based on
the structure of compound 1.
In the course of our computational studies on com-
pound 1 and its derivatives using Glide 3.5 software,
we found that compound 10 (Fig. 2), the meta isomer
of 1, likely fits PPARa protein more tightly than 1.18
An inspection of the simulated PPARa/1 complex
showed that one of the two oxygen atoms of the carbox-
ylate group forms hydrogen bonds with His 440 and Tyr
464, and that the nonyl group is located in the hydro-
phobic region formed by Ile 241, Leu 247, Ala 250,
Leu 254, Ile 272, Val 332, and Ala 333 (Fig. 3, left). In
the simulated PPARa/10 complex, as well as the hydro-
gen bonds and the hydrophobic interaction found in the
PPARa/1 complex, the existence of added hydrogen
bonds was expected between the other oxygen atom of
the carboxylate and Ser 280, and between the tertiary
nitrogen and Thr 279 (Fig. 3, right). These results
prompted us to evaluate the affinity for PPAR of 10
and its derivatives 2–9 and 11–20 (Fig. 2).
Keywords: Peroxisome proliferator-activated receptor; PPARa ligand;
PPARc ligand; Nuclear receptor.
*
Corresponding author. Tel./fax: +81 52 836 3407; e-mail: miyata-n@
phar.nagoya-cu.ac.jp
0960-894X/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.03.031

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S. Usui et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3249–3254
O
O
Et
Me
N
NH
S
NH
O
N
S
O
N
O
O
Pioglitazone
Rosiglitazone
O
COOEt
COOH
Cl
O
Clofibrate
15d-PGJ2
O
Me
O
S
O
OH
O
OH
N
H
N
S
F3C
S
N
Me
GW501516
GW7647
O
Nonyl
N
OH
N
O
1
Figure 1. Structures of rosiglitazone, pioglitazone, 15d-PGJ2, clofibrate, GW7647, GW501516, and compound 1.
was applied to the conversion of 24a, b into acrylic acid
derivatives 25a–g. The double bond of 25a–g was hydroge-
nated to yield compounds 26a–g. Coupling between 2-
alkylaminopyridine 22a–k and propanoic acid ethyl esters
26a afforded N-(2-pyridinyl)-N-alkylpropanoic acids 27a–
k. Propanoicacidethylesters26b–gwerealsoallowedtore-
act with 2-nonylaminopyridine 22i to afford N-(2-pyridi-
nyl)-N-nonylpropanoic acids 27l–q. The subsequent
hydrolysis of 27a–q gave the desired carboxylic acids
2–16, 18, and 19.
2 : n = 0
3 : n = 1
4 : n = 2
5 : n = 3
6 : n = 4
7 : n = 5
8 : n = 6
9 : n = 7
10 : n = 8
11 : n = 9
12 : n = 10
O
O
N
N
OH
(CH2)nCH3
13 : R1 = Me, R2 = H, R3 = H
14 : R1 = Et, R2 = H, R3 = H
15 : R1 = OEt, R2 = H, R3 = H
16 : R1 = H, R2 = H, R3 = OMe
17 : R1 = Me, R2 = H, R3 = OMe
18 : R1 = Et, R2 = H, R3 = OMe
19 : R1 = OEt, R2 = H, R3 = OMe
20 : R1 = Me, R2 = Me, R3 = OMe
The preparation of 3-{4-methoxy-3-[2-(nonylpyridin-2-
ylamino)ethoxy]phenyl}propanoic acids 17 and 20, which
have one or two methyl groups at the C-2 position of the
propanoic acid, is outlined in Scheme 2. The aldehyde 24b
was reduced by NaBH4 and allowed to react with acetic
anhydride to give acetic acid 3-(2-bromoethoxy)benzyl
ester 29. Compound 29 was treated with 1-methoxy-1-
trimethylsilyloxypropene or dimethylketene methyltrim-
ethylsilyl acetal in the presence of magnesium perchlorate
in anhydrous CH2Cl2 to give esters 30a,b.21 Coupling
between 2-nonylaminopyridine 22i and propanoic acid
methyl esters 30a,b afforded N-(2-pyridinyl)-N-nonyl
compounds 31a,b and subsequent hydrolysis gave
carboxylic acids 17 and 20.
O
O
N
N
OH
R1 R2
Nonyl
R3
Figure 2. Structures of compounds 2–20.
The compounds prepared for this study are shown in
Figure 2, and the routes used for their synthesis are
illustrated in Schemes 1 and 2. Scheme 1 shows the
preparation of the 3-{3-[2-(alkylpyridin-2-ylamino)eth-
oxy]phenyl}propanoic acid derivatives 2–16, 18, and 19.
The yield of 2-alkylaminopyridine 22a–k was 69–86%,
using the method of Buchwald:19 treatment of 2-bromo-
pyridine 21 with n-nonylamine (4 equiv), Pd2(DBA)3,
BINAP, and t-BuONa in toluene under reflux.
m-Hydroxybenzaldehyde 23a and isovaniline 23b were
allowed to react with 1,2-dibromoethane to give ethers
24a and 24b. The Horner–Wadsworth–Emmons reaction20
The binding affinity of the compounds for PPARs was
evaluated with a CoA-BAP System (Microsystems).22
In this system, the alkaline phosphatase (AP) activity
is directly proportional to the affinity of the ligands
for PPARs.

S. Usui et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3249–3254
3251
Figure 3. View of the lowest energy conformations of 1 (left) and 10 (right) docked in PPARa. Residues around compounds and hydrogen bonds are
displayed as wires and dotted lines, respectively. Figures represent distances in angstrom.
H3C
22a : n = 0
22b : n = 1
22c : n = 2
22d : n = 3
22e : n = 4
22f : n = 5
( )n
NH
22g : n = 6
22h : n = 7
22i : n = 8
22j : n = 9
22k : n = 10
N
Br
N
a
21
22a-k
O
O
O
b
c
HO
R1
O
H
O
Br
H
Br
OEt
R2
R1
R1
23a : R1= H
24a : R1= H
24b : R1 = OMe
25a : R1 = H, R2 = H
23b : R1 = OMe
25b : R1 = H, R2 = Me
25c : R1 = H, R2 = Et
25d : R1 = H, R2 = OEt
25e : R1 = OMe, R2 = H
25f : R1 = OMe, R2 = Et
25g : R1 = OMe, R2 = OEt
O
O
d
O
e
Br
OEt
O
R2
N
N
( )n
OEt
R1
R2
H3C
R1
26a : R1 = H, R2 = H
26b : R1 = H, R2 = Me
26c : R1 = H, R2 = Et
26d : R1 = H, R2 = OEt
26e : R1 = OMe, R2 = H
26f : R1 = OMe, R2 = Et
27a : R1 = H, R2 = H, n = 0 27j : R1 = H, R2 = H, n = 9
27b: R1 = H, R2 = H, n = 1 27k : R1 = H, R2 = H, n = 10
27c : R1 = H, R2 = H, n = 2 27l : R1 = H, R2 = Me, n = 9
27d : R1 = H, R2 = H, n = 3 27m : R1 = H, R2 = Et, n = 9
27e : R1 = H, R2 = H, n = 4 27n : R1 = H, R2 = OEt, n = 9
27f : R1 = H, R2 = H, n = 5 27o : R1 = OMe, R2 = H, n = 9
27g : R1 = H, R2 = H, n = 6 27p : R1 = OMe, R2 = Et, n = 9
27h : R1 = H, R2 = H, n = 7 27q : R1 = OMe, R2 = OEt, n = 9
27i : R1 = H, R2 = H, n = 8
26g : R1 = OMe, R2 = OEt
2 : R1 = H, R2 = H, n = 0
3 : R1 = H, R2 = H, n = 1
4 : R1 = H, R2 = H, n = 2
5 : R1 = H, R2 = H, n = 3
6 : R1 = H, R2 = H, n = 4
7 : R1 = H, R2 = H, n = 5
8 : R1 = H, R2 = H, n = 6
9 : R1 = H, R2 = H, n = 7
10 : R1 = H, R2 = H, n = 8
11 : R1 = H, R2 = H, n = 9
12 : R1 = H, R2 = H, n = 10
13 : R1 = H, R2 = Me, n = 9
14 : R1 = H, R2 = Et, n = 9
15 : R1 = H, R2 = OEt, n = 9
16 : R1 = OMe, R2 = H, n = 9
18 : R1 = OMe, R2 = Et, n = 9
19 : R1 = OMe, R2 = OEt, n = 9
O
f
O
R1
N
N
( )n
OH
R2
H3C
Scheme 1. Reagents and conditions: (a) CH3 (CH2)nNH2, Pd2(DBA)3, BINAP, t-BuOH, toluene, 80 °C, 69–86%; (b) 1,2-dibromoethane, Cs2CO3,
THF, 65 °C, 40–57%; (c) (EtO)2P(O)CH(R2)CO2Et, NaH, anhydrous THF, 0 °C to rt, 47–95%; (d) H2, Pd/C, EtOH, 79–97%; (e) 22a–k, Et3N, KI,
105 °C, 7–14%; (f) aq NaOH, EtOH–THF, rt, 89–95%.

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S. Usui et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3249–3254
O
O
O
Br
OH
a
Br
H
MeO
MeO
28
24b
O
O
c
b
Br
O
Me
MeO
O
29
O
Br
OMe
OMe
d
Me
R
MeO
30a: R = H
30b: R = Me
O
O
N
N
e
Me
R
Nonyl
MeO
31a : R = H
31b : R = Me
O
O
N
H
Me
R
Nonyl
MeO
17 : R = H
20 : R = Me
Scheme 2. Reagents and conditions: (a) NaBH4, EtOH, rt, 97%; (b) Ac2O, DMAP, rt, 96%; (c) 1-methoxy-1-trimethylsilyloxypropene or
dimethylketene methyltrimethyl silyl acetal, Mg(ClO4)2, rt, 94–95%; (d) 22i, Et3N, KI, 105 °C, 5–13%; (e) aq NaOH, EtOH, rt, 75–76%.
The ability of compounds 2–20 to bind PPARa, PPARc,
and PPARd was evaluated and the results are shown in
Tables 1–3, respectively. GW764723 (PPARa), rosiglit-
azone7 (PPARc), and GW50151624 (PPARd) were used
as reference compounds (Fig. 1). The lead compound 1
showed high affinity for PPARc and little affinity for
PPARa and PPARd (Tables 1–3, line 1). As we had
expected from the computational study described above,
Table 2. Binding affinity for PPARc of compounds 1–20 at 0.1, 1.0,
and 10 lM
Table 1. Binding affinity for PPARa of compounds 1–20 at 0.1, 1.0,
and 10 lM
0.7
0.3
0.1 μM 1 μM 10 μM
0.1 μM 1 μM 10 μM
0.6
0.5
0.4
0.3
0.2
0.1
0
0.25
0.2
0.15
0.1
0.05
0
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
1 2
3
4 5
6
7 8 9 10 11 12 13 14 15 16 17 18 19 20
compounds
compounds
Values are means of at least three experiments.
Values are means of at least three experiments.

S. Usui et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3249–3254
3253
Table 3. Binding affinity for PPARd of compounds 1–20 at 0.1, 1.0,
and 10 lM
ture of the PPARc agonist 1. Compound 10, the meta
isomer of 1, was found to be a PPARa ligand. The intro-
duction of methyl (13) and ethyl (14) groups at the C-2
position of the propanoic acid of 10 further improved
the PPARa-binding potency. The findings of this study
will help provide an effective agent for hyperlipidemia.
Currently, further detailed studies pertaining to com-
pounds 13 and 14 are under way.
0.25
0.1 μM 1 μM 10 μM
0.2
0.15
0.1
0.05
0
References and notes
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much higher affinity for PPARa than did 1 (Table 1, line 1
vs 10). Furthermore, the affinity for PPARc of 10 is lower
than that of 1 (Table 2, line 1 vs 10), and compound 10
exhibited no affinity for PPARd (Table 3, line 10).
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Bank (PDB code 1K7L). The protein was prepared for
docking, using the protein preparation and refinement
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To study the structure–activity relationship of 3-{3-[2-
(alkylpyridin-2-ylamino)ethoxy]phenyl}propanoic acid
derivatives and to find more potent PPARa ligands,
we initially evaluated the PPAR-binding affinity of com-
pounds 2–12 which have alkyl chains of various lengths
on their nitrogen atom. It was found that the affinity of
these compounds was closely related to chain length.
Among compounds 2–12, nonyl 10 showed the greatest
affinity for PPARa, while decyl 11 and undecyl 12 were
most active toward PPARc, and heptyl 8 and octyl 9
showed little affinity for PPARd (Tables 1–3, lines 2–12).
We next examined the effect of substituents at the C-2 po-
sition of the propanoic acid of 10, because it has been
reported that the introduction of an alkyl or alkoxy group
at this position increases activity for PPARa.15,25–27
Methyl 13, ethyl 14, and ethoxy 15 were tested, and much
to our satisfaction, 13 and 14 showed strong affinity for
PPARa and slightly weak affinity for PPARc as com-
pared with the parent compound 10. In addition, com-
pounds 13–15 had no affinity for PPARd (Tables 1–3,
lines 13–15).
To examine the effect of the introduction of a methoxy
group at the C-4 position of the benzene ring,
compounds 16–20 were investigated. However, these
compounds did not show
a pronounced affinity
for PPARa compared to compounds 10, 13, and 14
(Tables 1, lines 16–20).
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acid derivatives which were designed based on the struc-
22. Kanayama, T.; Mamiya, S.; Nishihara, T.; Nishikawa, J.
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