Design of a partial PPARδ agonist

Article abstract of DOI:10.1016/j.bmcl.2007.05.079

Structure based ligand design was used in order to design a partial agonist for the PPARδ receptor. The maximum activation in the transactivation assay was reduced from 87% to 39%. The crystal structure of the ligand binding domain of the PPARδ receptor in complex with compound 2 was determined in order to understand the structural changes which gave rise to the decrease in maximum activation.

Full text of DOI:10.1016/j.bmcl.2007.05.079

Bioorganic & Medicinal Chemistry Letters 17 (2007) 4625–4629
Design of a partial PPARd agonist
a
b
b
b
Ingrid Pettersson,a, Søren Ebdrup, Miroslav Havranek, Pavel Pihera, Marek Korˇınek,
*
´
John P. Mogensen,a Claus B. Jeppesen,a Eva Johanssona and Per Sauerberga
a
˚
Novo Nordisk A/S, Novo Nordisk Park, 2760 Maløv, Denmark
b
´
RE&D VUFB, s.r.o., Podeˇbradska´ 56/186, 180 66 Praha 9, Czech Republic
Received 19 April 2007; revised 22 May 2007; accepted 24 May 2007
Available online 27 May 2007
Abstract—Structure based ligand design was used in order to design a partial agonist for the PPARd receptor. The maximum acti-
vation in the transactivation assay was reduced from 87% to 39%. The crystal structure of the ligand binding domain of the PPARd
receptor in complex with compound 2 was determined in order to understand the structural changes which gave rise to the decrease
in maximum activation.
ꢀ 2007 Elsevier Ltd. All rights reserved.
The peroxisome proliferator-activated receptors (PPARs)
are transcription factors belonging to the nuclear recep-
tor super-family. There are three PPAR subtypes,
PPARa, PPARc and PPARd.1 The use of PPARc acti-
vators, for example, rosiglitazone and pioglitazone (glit-
azones), in the treatment of type 2 diabetes has been
established due to their abilities to lower blood glucose
and insulin levels and improve insulin sensitivity.2,3 Sim-
ilarly, PPARa activators, for example, fenofibrate and
clofibrate (fibrates), have been used clinically for more
than three decades for their ability to lower plasma tri-
glycerides (TG) and moderately raise HDL-cholesterol.4
There is no drug available targeting the third PPARd
receptor, but there is evidence that PPARd is involved
in lipid homeostasis.5–7 The ligand binding domains of
the PPARs consist of 13 a-helices and four b-strands.
One of the a-helices is the C-terminal helix that contains
the AF-2 transcriptional activation domain which is in-
volved in recruitment of co-activators. The use of partial
PPARc agonists has been suggested in order to avoid ad-
verse effects, such as oedema and body weight gain.8 In
this work, the partiality was obtained by design of com-
pounds without direct interactions with the AF-2 helix.
structure was 1 with 87% maximum activation compared
to GW501516 on the hPPARd receptor, Figure 1,
Table 1.5 Compound 1 came out of our PPAR pro-
gramme, where it was derived from GW501516 utilizing
the Y-shaped PPAR receptor binding pocket to design a
more rigid molecule. Compound 1 was a partial agonist
on the PPARa and PPARc receptor subtypes and close
to a full agonist on the PPARd receptor subtype (Table 1).
Compound 1 was docked into the crystal structure of
the ligand binding domain of the PPARd receptor crys-
tallized with GW2433 (1GWX).10,11 In the predicted
docking pose, the ortho-methyl group was positioned
in a rather narrow binding pocket close to the AF-2 he-
lix. The carboxylic acid in 1 was predicted to make
hydrogen bond interactions with H323 on helix 5,
H449 on helix 10 and Y473 on the AF-2 helix, Figure
2. The hypothesis was that introduction of a group lar-
ger than the ortho-methyl in this part of the molecule
would prevent or weaken interactions between the car-
boxylic acid in the molecule and the AF-2 helix.
Compound 2, containing a cyclopentyl ring instead of
the methyl, was therefore synthesized9 and tested in
the transactivation assay, Figure 1, Scheme 1 and Table
1 and Figure 3.
The aim of this investigation was to identify partial
PPARd agonists by design of compounds with weaker
or none interactions with the AF-2 helix. Our starting
Reduction of the commercially available 4-hydroxy-1-
indanone gave the core structure of the acid half of
the molecule (top line Scheme 1). The sulfur ether linker
was introduced using sodium thiocyanate and bromine
to give the thiocyanate adduct, which after alkylation
Keywords: PPARd; Agonist; Partial; Docking; Design.
*
Corresponding author. Fax: +45 44663450; e-mail: inpe@novonordisk.
com
0960-894X/$ - see front matter ꢀ 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2007.05.079

4626
I. Pettersson et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4625–4629
F
HO2C
O
S
Cl
O
N
N
CO2H
O
N
S
CF3
Cl
Cl
GW2433
GW501516
O
HO2C
O
HO2C
O
S
O
S
N
N
N
N
CF3
CF3
1
2
Figure 1. Graphical illustration of the structures discussed.
of the phenol was reduced to the thioether with dithio-
erythritol. Arylation of the thioether with tribromopyri-
dine gave the desired 4-pyridyl product in good yield.
Sonogashira cross-coupling with 4-trifluorophenylacety-
lene and then with N-propargylmorpholine gave the ester
of the desired product. Basic hydrolysis of the ester gave
compound 2.
between the carboxylic acid in 2 and H449 in the recep-
tor, Figure 4. However, no hydrogen bonds are ob-
served between the ligand and H323 or Y473, Figure
4. In addition, a water molecule, Wat21, which makes
a hydrogen bond both with the nitrogen atom in the
pyridine ring in 2 and the backbone carbonyl in L340
in the receptor, is observed in the hydrophobic part of
the binding pocket.
In the transactivation assay, 2 had similar potency as 1
but the maximum activation was reduced from 87% to
39%, Table 1 and Figure 3. In order to investigate if this
was due to a reduced interaction between the carboxylic
acid and the AF-2 helix, the ligand binding domain of
the hPPARd receptor was co-crystallized with 2.14 In
the crystal structure a hydrogen bond is observed
The crystal structures of PPARd crystallized with
GW2433 (1GWX) and PPARd co-crystallized with 2
(2Q5G) have the same overall structure except for the
AF-2 helix, Figure 5. The AF-2 helix in 2Q5G adopts
Table 2. Diffraction data and refinement statistics for the PPARd-
compound 2 complex
Table 1. In vitro human PPAR transactivation data for 1 and 2 and
standard compounds
˚
Diffraction data statistics (53.73–2.70 A)
No. of measured reflections
No. of unique reflections
R-mergea
41117
16233
a
a
a
Compound
hPPARa EC50 hPPARc EC50 hPPARd EC50
c
(lM)/% maxb
(lM)/% max
(lM)/% maxd
0.099 (0.373)
95.7 (98.6)
6.3 (2.1)
2.53 (2.47)
Completeness (%)
Mean I/r(I)
Average redundancy
1
2
0.1/50
–/<10
5.5/28
–/<10
0.05/87
0.13/39
6.4/57
NNC61-4655 0.01/100
Rosiglitazone >10 / >24
2.6/96
0.3/100
>10/>22
˚
–/<10
0.008/100
Refinement statistics (83.92–2.70 A)
R-factorb (%)
GW501516
3.9/68
22.5 (31.2)
30.5 (47.0)
3904
R-freec (%)
No. of atoms (total)
If a plateau was not reached at the highest concentration then the
maximal effect was indicted to be greater than this value and the EC50
was assigned to be >10 lM.
˚
Bond length rmsd from ideal (A)
Bond angle rmsd from ideal (deg)
0.014
1.625
41.6
a Compounds were tested in at least three separate experiments in at
least five concentrations ranging from 0.001 to 30 lM. EC50 is the
concentration giving 50% of the maximal activity observed for a
given compound. EC50 was not calculated for compounds producing
transactivation lower than 10% at 30 lM. The results are expressed
as means and SEM was less than 15%.
2
Average B-factor (A )
˚
Values in parentheses refer to the highest resolution shell.
a R-merge = RjIꢀ<I>j/RI, where the sums are overall symmetry rela-
ted reflections of intensity I.
b R-factor = RworkjjFobsjꢀkjFcalcjj/RworkFobs
.
, where Fobs and Fcalc are
b Fold activation relative to maximum activation (100%) obtained with
NNC 61-4655.18
c Rosiglitazone.
d GW501516.
c R-free = RtestjjFobsjꢀkjFcalcjj/RtestFobs
observed and calculated structure factors, respectively, k is the scale
factor, and the sums are overall reflections in the working set and the
test set (5.1% of the data), respectively.

I. Pettersson et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4625–4629
4627
GW501516
100
75
50
25
0
Compound 1
Compound 2
10-11 10-10 10-9 10-8 10-7 10-6 10-5 10-4
[Compound], M
Figure 3. In vitro human PPARd transactivation data for 1, 2 and
GW501516.
Figure 2. Compound 1 (yellow) docked into the crystal structure of the
ligand binding domain of the PPARd receptor crystallized with
GW2433 (magenta). H323, H449 and Y473 are shown in ball-and-stick
˚
representation. The white surface shows the binding pocket 5 A from
GW2433.
a position in which interactions between Y473 and the
ligand are absent. H323 and H449 are more or less in
the same position as in 1GWX, Figure 6. The distance be-
˚
tween the Ca carbons in H323 and H449 is 9.7 A in
˚
1GWX and 9.5 A in 2Q5G. In GWX the distances be-
tween the Ca carbons in H323 and Y473 and between
˚
H449 and Y473 are 9.7 and 10.4 A, respectively. In
˚
2Q5G the same were longer, 14.4 and 20.9 A, respec-
tively. When the positions of the two ligands were
compared, compound 2 in 2Q5G was moved away from
the AF-2 helix compared to GW2433 in 1GWX, Figure
6. As a consequence of this a hydrogen bond interaction
could still be formed between 2 and H449 but not to
H323 and Y473. Compound 2 was also docked into the
crystal structure of 2Q5G. The rmsd between the crystal
Figure 4. The crystal structure of the ligand binding domain of the
PPARd receptor (green) co-crystallized with 2 (yellow). H323, L340
and H449 are shown in ball-and-stick representation. The water
molecule Wat21 makes a hydrogen bond to the nitrogen atom in the
pyridine ring in 2 and to the backbone oxygen in L340. A hydrogen
bond is observed between the carboxylic acid in 2 and H449.
˚
structure and the predicted docking pose was 1.2 A.
CN
SH
CN
S
S
NaSCN
NaBr
NaCNBH3
ZnI2
BrCH2CO2Et
O
Dithio-
Cs2CO3
MeCN
erythriol
MeCN
Br2
ethylene chloride
O
O
OH
MeOH
OH
OH
CO2Me
96%
CO2Me
80%
50%
42%
O
N
O
CF
3
N
Br
N
Br
Br
Br
NaOH
EtOH
(PPh3)2PdCl2
(PPh3)2PdCl2
Br
Br
N
N
N
2
CuI
S
S
S
Na2CO3
MeCN
TEA
CuI
DMF
CF3
TEA
CF3
DMF
O
O
O
CO2Me
70%
CO2Me
33%
CO2Me
Scheme 1. Synthesis of compound 2.9

4628
I. Pettersson et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4625–4629
Acknowledgments
The technical assistance of Otto Larsson, Per Klifforth
and Dorthe D. Andersen is highly appreciated. We also
thank ActiveSight, San Diego, for solving the crystal
structure.
References and notes
1. Issemann, I.; Green, S. Nature 1990, 347, 645.
2. Chilcott, J.; Tappenden, P.; Jones, M. L.; Wright, J. P. A.
Clin. Ther. 2001, 23, 1792.
3. Boyle, P. J.; King, A. B.; Olansky, L.; Marchetti, A.; Lau,
H.; Magar, R.; Martin, J. Clin. Ther. 2002, 24, 378.
4. Staels, B.; Dallongeville, J.; Auwerx, J.; Schoonjans, K.;
Leitersdorf, E.; Fruchart, J.-C. Circulation 1998, 98, 2088.
5. Oliver, W., Jr.; Shenk, J. L.; Snaith, M. R.; Russell, C. S.;
Plunket, K. D.; Bodkin, N. L.; Lewis, M. C.; Winegar, D.
A.; Sznaidman, M. L.; Lambert, M. H.; Xu, H. E.;
Sternbach, D. D.; Kliewer, S. A.; Hansen, B. C.; Willson,
T. M. Proc. Natl. Acad. Sci. 2001, 98, 5306.
6. Tanaka, T.; Yamamoto, J.; Iwasaki, S.; Asaba, H.;
Hamura, H.; Ikeda, Y.; Watanabe, M.; Magoori, K.;
Ioka, R. X.; Tachibana, K.; Watanabe, Y.; Uchiyama, Y.;
Sumi, K.; Iguchi, H.; Ito, S.; Dio, T.; Hamakubo, T.;
Naito, M.; Auwerx, J.; Yanagisawa, M.; Kodama, T.;
Sakai, J. PNAS 2003, 100, 15924.
7. Sauerberg, P.; Olsen, G. O.; Jeppesen, L.; Mogensen, J. P.;
Pettersson, I.; Christensen, S. M.; Rasmussen, K. G.;
Jeppesen, C. B.; Daugaard, J. R.; Galsgaard, E. D.;
Ynddal, L.; Fleckner, J.; Din, N.; Panajotova, V.; Polivka,
Z.; Pihera, P.; Havranek, M.; Wulff, E. M. J. Med. Chem.
2007, 50, 1495.
Figure 5. The crystal structure between PPARd and GW2433 (1GWX,
magenta) superimposed with the crystal structure of the ligand binding
domain of the PPARd receptor (green) co-crystallized with 2 (yellow).
To demonstrate the relative position of the AF-2 helix, the ribbon from
P467 to K474 in PPARd co-crystallized with 2 is coloured yellow.
8. Burgermeister, E.; Schnoebelen, A.; Flament, A.; Benz, J.;
Stihle, M.; Gsell, B.; Rufer, A.; Ruf, A.; Kuhn, B.; Ma¨rki,
H. P.; Mizrahi, J.; Sebokova, E.; Niesor, E.; Meyer, M.
Mol. Endocrinol. 2006, 20, 809.
9. Experimental procedure for the synthesis of 2: A solution
of
4-hydroxy-1-indanone
(10.74 g,
72.46 mmol),
NaCNBH3 (13.66 g, 217.4 mmol) and zinc(II)iodide
(69.1 g, 217.4 mmol) in ethylenechloride (200 mL) was
stirred at reflux for 2 h. The cooled reaction mixture was
filtered through silica gel and the filtrate was evaporated.
The residue was purified by column chromatography using
methylene chloride as eluent to give 4-hydroxyindane in
4.1 g (42%) yield. 1H NMR (CDCl3, 300 MHz): d 7.04
(t, 2H), 6.83 (d, 1H), 6.61 (d, 1H), 4.58 (br. s, 1H), 2.93
(t, 2H), 2.85 (t, 2H), 2.1 (m, 2H).
To a solution of 4-hydroxyindane (5.2 g, 38.8 mmol) in
dry methanol (50 ml) were added sodium thiocyanate
(10.0 g, 124 mmol) and sodium bromide (4.0 g,
38.8 mmol). Bromine (2.2 mL, 43 mmol) was added to
the reaction mixture over 15 min and the reaction mixture
was stirred overnight at room temperature. Brine (50 mL)
and ethyl acetate (100 mL) were added to the mixture, the
mixture was shaken and the organic phase was isolated.
The aqueous phase was extracted with additional ethyl
acetate (2· 100 mL), and the combined organic phases
were washed with brine (50 mL). The combined organic
phases were dried and evaporated. The residue was
suspended in methylene chloride (100 mL) and filtered.
The filtrate was evaporated and the residue was purified by
column chromatography using methylene chloride as
eluent to give 7-thiocyanato-indan-4-ol in 3.7 g (50%)
yield. 1H NMR (CDCl3, 300 MHz): d 7.27 (d, 1H), 6.66 (d,
1H), 5.52 (br.s, 1H), 3.09 (t, 2H), 2.91 (t, 2H), 2.17 (m,
2H).
Figure 6. GW2433 in the crystal structures of PPARd crystallized with
GW2433 (1GWX, magenta) superimposed with the crystal structure of
the ligand binding domain of the PPARd receptor (green) co-
crystallized with 2 (yellow). H323, L340 and H449 are shown in ball-
and-stick representation.
In conclusion, a selective, partial PPARd agonist was de-
signed by introducing a bulky substituent close to the car-
boxylic acid. X-ray crystallographic data confirmed the
impaired interaction to the AF-2 domain explaining the
partial PPARd efficacy. The data therefore give guidance
to the design of other partial PPARd agonists.

I. Pettersson et al. / Bioorg. Med. Chem. Lett. 17 (2007) 4625–4629
4629
To a solution of 7-thiocyanato-indan-4-ol (3.7 g, 19.5 mmol)
and caesium carbonate (19 g, 58 mmol) in dry acetonitrile
was added methyl bromoacetate (2.0 mL, 21 mmol). The
reaction mixture was stirred for 1 h at room temperature,
filtered and the filtrate was evaporated. The residue was
purified by column chromatography using methylene chlo-
ride as eluent to give (7-thiocyanato-indan-4-yloxy)-acetic
acid methyl ester in 4.1 g (80%) yield. H NMR (CDCl3,
300 MHz): d 7.33 (d, 1H), 6.57 (d, 1H), 4.67 (s, 2H), 3.79 (s,
3H), 3.08 (t, 2H), 3.01 (t, 2H), 2.16 (m, 2H).
(7-Thiocyanato-indan-4-yloxy)-acetic acid methyl ester
(4.1 g, 15.6 mmol) and 1,4-dithioerythritol (3.1 g, 20 mmol)
were refluxed for 3 h in a mixture of water (10 mL) and
acetonitrile (75 mL). The reaction mixture was evaporated
and the residue was purified by column chromatography
using methylene chloride as eluent to give (7-mercapto-
indan-4-yloxy)-acetic acid methyl ester in 3.55 g (96%) yield.
1H NMR (CDCl3, 300 MHz): d 7.05 (d, 1H), 6.47 (d, 1H),
4.62 (s, 2H), 3.79 (s, 3H), 3.16 (s, 1H), 2.98 (t, 2H), 2.89 (t,
2H), 2.11 (m, 2H).
A mixture of (7-mercapto-indan-4-yloxy)-acetic acid methyl
ester (5.0 g, 21 mmol), tribromopyridine (6.6 g, 21 mmol)
and sodium carbonate (2.7 g, 25 mmol) in acetonitrile
(100 mL) was stirred at 80 ꢁC for 5 h. The reaction mixture
was evaporated and the residue was extracted with meth-
ylene chloride (3· 50 mL). Ethyl acetate (30 mL) was added
and the mixture was heated to reflux. After cooling to room
temperature crystals of [7-(2,6-dibromo-pyridin-4-ylsulfa-
nyl)-indan-4-yloxy]-acetic acid methyl ester were collected
by filtration in 7 g (70%) yield. 1H NMR (CDCl3,
400 MHz): d 7.29 (d, 1H), 6.94 (s, 2H), 6.63 (d, 1H),
4.73 (s, 2H), 3.83 (s, 3H), 3.05 (t, 2H), 2.86 (t, 2H), 2.10
(m, 2H), 1.54 (br. s, 1H).
A solution of {7-[2-(3-morpholin-4-yl-prop-1-ynyl)-6-(4-
trifluoromethyl-phenylethynyl)-pyridin-4-ylsulfanyl]-
indan-4-yloxy}-acetic acid methyl ester (40 mg,
0.066 mmol) in ethanol (10 mL) and 1N NaOH (5 mL)
were stirred at room temperature for 30 min. To the
reaction mixture was added 1N HCl(5 mL) and the mixture
was extracted with ethyl acetate (3· 20 mL). The organic
phase was washed with water, dried and evaporated to give
{7-[2-(3-morpholin-4-yl-prop-1-ynyl)-6-(4-trifluoromethyl-
phenylethynyl)-pyridin-4-ylsulfanyl]-indan-4-yloxy}-acetic
acid (2) in 35 mg yield. 1H NMR (CDCl3, 400 MHz): d 7.66
(d, 2H), 7.60 (d, 2H), 7.26 (m, 4H), 6.69 (d, 1H), 6.57 (s,
1H), 4.70 (s, 2H), 3.82 (m, 4H), 3.65 (s, 2H), 3.6 (br.s, 2H),
3.05 (t, 2H), 2.87 (t, 2H), 2.82 (m, 4H), 2.08 (m, 2H).
10. Glide docking. The structure manipulations were per-
formed in Maestro version 7.5 (Maestro 7.0, Schro¨dinger,
LLC, New York, NY, 1999–2005). Glide calculations were
performed with Impact version 4.0.12,13 1 was built in
Maestro version 7.5, a formal charge of ꢀ1 was assigned
and the molecule was minimized with the OPLS_2005
force field. Compound 1 was docked with Glide version
4.0 using the SP mode and the van der Waals radii of the
ligand atoms were scaled by 0.8.
11. Xu, H. E.; Lambert, M. H.; Montana, V. G.; Parks, D. J.;
Blanchard, S. G.; Brown, P. J.; Sternbach, D. D.;
Lehmann, J. M.; Wisly, G. B.; Willson, T. M.; Kliever,
S. A.; Milburn, M. V. Mol. Cell 1999, 3, 397.
12. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T.
A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E.
H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.;
Shenkin, P. S. J. Med. Chem. 2004, 47, 1739.
13. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H.
S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. J. Med. Chem.
2004, 47, 1750.
14. The crystal structure was determined by ActiveSight, San
Diego.
1
Triethylamine (10 mL) and DMF (10 mL) were added
under nitrogen to a mixture of [7-(2,6-dibromo-pyridin-4-
ylsulfanyl)-indan-4-yloxy]-acetic acid methyl ester (3.0 g,
6.3 mmol), 4-trifluorophenylacetylene (0.8 g, 4.8 mmol),
CuI (72 mg, 0.38 mmol) and bis(triphenylphosphine)palla-
dium chloride (356 mg, 0.5 mmol). The reaction mixture
was heated in a microwave oven at 110 ꢁC for 1 h. The
reaction mixture was evaporated and the residue was
extracted with citric acid solution (5%, 50 mL) and meth-
ylene chloride (50 mL). The aqueous layer was further
extracted with methylene chloride (2· 15 mL). The com-
binedorganic phasesweredriedandevaporated. Theresidue
was purified by HPLC to give {7-[2-bromo-6-(4-trifluoro-
methyl-phenylethynyl)-pyridin-4-ylsulfanyl]-indan-4-yloxy}-
Crystals were grown at 277 K using the hanging drop
vapour diffusion technique mixing 1 ll of 6 mg/ml
PPARd, 1mM 2, 0.5% (w/v) heptyl-b-D-glucopyranoside,
20 mM Hepes, pH 7.5, 40 mM imidazole, 40 mM NaCl,
2 mM Tris(2-carboxyethyl)phosphine hydrochloride, and
500 mM ammonium acetate with 1 ll mother liquor
(2 M NaCl, 10% (w/v) PEG6000) leaving it to equilibrate
over 300 ll mother liquor. Diffraction data were col-
lected at 95 K on crystals cryocooled in mother liquor
containing 15% (w/v) xylitol at ALS, beamline 5.0.3,
using an ADSC Quantum 4R detector. The crystals
1
˚
˚
acetic acid methyl ester in 900 mg (33%) yield. H NMR
belong to space group C2 (a = 112.6 A, b = 65.6A,
˚
(CDCl3, 400 MHz): d 7.47 (d, 2H), 7.41 (d, 2H), 7.12 (d, 1H),
6.85 (s, 1H), 6.75 (s, 1H), 6.45 (d, 1H), 4.54 (s, 2H), 6.63 (s,
3H), 2.86 (t, 2H), 2.68 (t, 2H), 1.90 (m, 2H).
Triethylamine (5 mL) and DMF (5 mL) were added under
nitrogen to a mixture of {7-[2-bromo-6-(4-trifluoromethyl-
phenylethynyl)-pyridin-4-ylsulfanyl]-indan-4-yloxy}-acetic
acid methyl ester (150 mg, 0.27 mmol), N-propargylmorph-
oline (66 mg, 0.53 mmol), CuI (3 mg, 0.016 mmol) and
c = 101.2 A, b = 124.1ꢁ). Auto indexing, data reduction
and scaling of the data were performed with d TREK.15
*
The structure was determined using the molecular
replacement technique implemented in the program
Phaser16 with PDB entry 2GWX[11] as search model.
Introduction of the ligand and alternating cycles of
manual rebuilding and positional refinement using
REFMAC517 gave a final model with R-factor = 22.5%
(R-free = 30.5%). The statistics for diffraction data and
refinement are summarized in Table 2. Coordinates and
structure factors have been deposited in the PDB
(Accession code 2Q5G).
bis(triphenylphosphine)palladium
chloride
(14 mg,
0.02 mmol). The reaction mixture was heated in a micro-
wave oven at 110 ꢁC for 1 h. The reaction mixture was
evaporated and the residue was purified by HPLC to give
{7-[2-(3-morpholin-4-yl-prop-1-ynyl)-6-(4-trifluoromethyl-
phenylethynyl)-pyridin-4-ylsulfanyl]-indan-4-yloxy}-acetic
acid methyl ester in 40 mg yield. 1H NMR (CDCl3,
400 MHz): d 7.66 (d, 2H), 7.60 (d, 2H), 7.33 (d, 1H), 7.02
(s, 1H), 6.94 (s, 1H), 6.64 (d, 1H), 4.73 (s, 2H), 3.83 (s, 3H),
3.75 (m, 4H), 3.50 (s, 2H), 3.05 (t,2H), 2.87 (t, 2H), 2.62 (m,
4H), 2.10 (m, 2H), 1.62 (br.s, 1H).
15. Pflugrath, J. Acta Crystallogr. 1999, D55, 1718.
16. Read, R. J. Acta Crystallogr. 2001, D57, 1373.
17. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta
Crystallogr. 1997, D53, 240.
18. Deussen, H.-J.; Jeppesen, L.; Scha¨rer, N.; Junager, F.;
Betzen, B.; Weber, B.; Weil, V.; Mozer, S. J.; Sauerberg, P.
Org. Process Res. Dev. 2004, 8, 363.