Design, synthesis and structure-activity relationship of novel RXR-selective modulators

Article abstract of DOI:10.1016/j.bmcl.2003.12.089

The synthesis and in vitro characterization of novel RXR-selective ligands possessing various substituted 1-benzofuran or 1-benzothiophene moieties are described.

Full text of DOI:10.1016/j.bmcl.2003.12.089

Bioorganic & Medicinal Chemistry Letters 14 (2004) 1593–1598
Design, synthesis and structure–activity relationship of novel
RXR-selective modulators
Pierre-Yves Michellys,*,k Jennifer D’Arrigo,y Timothy A. Grese,x Donald S. Karanewsky,k
Mark D. Leibowitz,** Dale A. Mais,y Christopher M. Mapes,yy Anne Reifel-Miller,{
Deepa Rungtay and Marcus F. Boehm{
Department of Medicinal Chemistry, Ligand Pharmaceuticals Incorporated, 10275 Science Center Drive, San Diego, CA 92121, USA
Received 3 April 2003; accepted 11 December 2003
Abstract—The synthesis and in vitro characterization of novel RXR-selective ligands possessing various substituted 1-benzofuran
or 1-benzothiophene moieties are described.
# 2004 Elsevier Ltd. All rights reserved.
Retinoids play a major role in a wide variety of biolo-
gical functions, such as cell differentiation, proliferation
and embryonic development in vertebrates.1 All-trans-
retinoid acid (ATRA, Fig. 1), 13-cis-retinoid acid (13-cis-
RA, Fig. 1), 9-cis-retinoid acid (9-cis-RA, Panretin1,
Fig. 1) and more recently the RXR selective LGD1069
(Targretin1, Fig. 1), have been administered for treatment
of numerous skin diseases like psoriasis, acne, Karposi’s
sarcoma and CTCL.2 Moreover, there is evidence that
retinoids may be useful in the treatment and prevention
of various other cancers.3 The retinoid receptors belong
to the superfamily of intracellular nuclear receptors,
which function to regulate gene transcription.4 They are
divided into two families of homologous receptors, the
retinoic acid receptors (RARs) and the retinoid x receptors
(RXRs), each divided into three sub-types a, b and g
encoded by a single gene.5 RXR has long been recognized
to both form homodimers and to heterodimerize with
various other nuclear receptors, such as RAR, TR,
VDR, NGFIB, LXR, FXR and PPARs.1,5 Because of
this unique profile, RXR is a very interesting drug target
and new synthetic RXR-selective ligands may have new
and interesting applications.
Previously, we published the synthesis and biological
evaluation of novel trienoic acids (LG101506, Fig. 1) and
6,7-locked-trienoic acid RXR-selective modulators.6ꢀ9
Here, we describe the design and synthesis of novel
RXR-selective ligands possessing a 4,5- and 6,7-‘double-
locked’ trienoic acid moiety as shown in Figure 2.
The boronate 3 was synthesized in 74% yield from
the known 2-acetyl-4-iodo-1-benzothiophene10 using the
method described by Murata and Al.11
2-Acetyl-7-iodo-1-benzothiophene
5
was synthesized
according to the same scheme described for 2 from 2-
fluoroiodobenzene. The triflate derivative 7 was easily pre-
pared from the commercially available 2-acetyl-7-hydroxy-
benzofuran 6 in excellent yield (>90%) (Scheme 1).
*
Corresponding author. E-mail: pmichellys@gnf.org
Department of New Leads Discovery, Ligand Pharmaceuticals,
Incorporated, San Diego, CA, USA.
Current address: Conforma Therapeutics, San Diego, CA, USA.
Discovery Chemistry Research, Lilly Research Laboratories,
Indianapolis, IN, USA.
Current address: Genomic Institute of the Novartis Research
Foundation, San Diego, CA, USA.
Division of Endocrine Research, Lilly Research Laboratories,
Indianapolis, IN, USA.
y
{
The synthesis of the acids 32–39 possessing a 2,7-di-
substituted-1-benzothiophene was realized according to
Scheme 2. Suzuki coupling of 3 with the iodides 8–15 in
the presence of PdCl2(dppf) and 2M Na2CO3 in refluxing
DME afforded the corresponding adducts 16–23 in good
yields (>75%). The esters 24–31 were synthesized by
condensation of the anion of the triethylphosphono-
acetate (generated from slow addition of triethylphospho-
x
k
{
** Department of Pharmacology, Ligand Pharmaceuticals, Incorpo-
rated, San Diego, CA, USA.
yy
Current Address: Johnson and Johnson, San Diego, CA, USA.
0960-894X/$ - see front matter # 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2003.12.089

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P.-Y. Michellys et al. / Bioorg. Med. Chem. Lett. 14 (2004) 1593–1598
Figure 1.
Figure 2. Design of novel RXR ligands possessing a benzo[b]thiophene or benzo[b]furan core.
Scheme 1. 2,4 and 2,7-disubstituted 1-benzothiophene and 1-benzofuran synthesis. Reagents: (a) LDA, DMF, ꢀ78 ꢁC to rt; (b) 3-mercaptopropanone,
Et3N, DMSO, 60 ꢁC; (c) PdCl2(dppf), pinacol borane, dioxane, Et3N, 80 ꢁC; (d) Tf2O, Hunig’s base, CH2Cl2.

P.-Y. Michellys et al. / Bioorg. Med. Chem. Lett. 14 (2004) 1593–1598
1595
Scheme 2. 2,4-Disubstituted 1-benzothiophene RXR modulators synthetic scheme. Reagents: (a) PdCl2(dppf), 3, DME, 2M Na2CO3, reflux; (b)
Triethylphosphonoacetate, NaH, DMF, 0–60 ꢁC; (c) LiOH, THF/MeOH then HCl followed by recrystallization from CH3CN.
noacetate in a suspension of NaH in DMF at 0 ꢁC) at
60 ꢁC. Hydrolysis (LiOH/MeOH/THF, reflux) followed
by recystallization from CH3CN released the desired
acids 32–39 in excellent yields (>80%).
for RXRs over RARs. In fact, except 32 and 59 (Table 1,
entries 3 and 14), all the compounds are more selective for
RXR than our standard, LG101506 (Table 1, entry 2).
LG101506 shows weak affinity for RARa and RARb of
2745 and 3515 nM, respectively (Table 1, entry 2), 32
has a weak Ki of 1786 nM for RARa (Table 1, entry 3)
and 59 has a weak Ki of 2700 nM for RARb (Table 1,
entry 14). Otherwise, no RARa,b or g binding is generally
observed (Ki>5000 nM). All the compounds show a
good affinity for RXRa, except compounds 59, 61, 63 or
67 (Table 1, entries 14, 16, 17 and 19) which have a Ki
for RXRa>100 nM. All the compounds possessing a 7-
disubstituted-1-benzothiophene scaffold (compounds 32
to 39) bind to RXRa with high affinity (Ki<15 nM).
This particular scaffold appears to be better for RXR
activity than its 2,4-disubstituted analogues or the 2,4-
disubstituted-1-benzofuran. More interestingly, the RXR
binding of each compound possessing the 2,7-disub-
stituted-1-benzothiophene moiety remains in the same
potency range independent of R1 while both other scaffolds
tested show a dramatic change in RXR binding when
R1 gets bulkier.
The derivatives 56–61 and 63 possessing a 2,4-di-
substituted-1-benzofuran and a 2,4-disubstituted-1-benzo-
thiophene moieties were synthesized according to
Scheme 3. The sequence follows the same general route
described in Scheme 2 from the boronic acids 40 and
41 and the intermediates 5 and 7. Alkylation of the
corresponding adducts with various alkyl bromides in the
presence of Cs2CO3 affords the derivatives 44–49 and 62
in excellent yields (>90%). The last steps of the
sequence are identical to Scheme 2. The acids 56–61 and
63 were isolated after recrystalization from CH3CN.
In previous communications, we demonstrated that the
introduction of a fluorine on the trienoic acid moiety
has a dramatic effect on the metabolic properties of such
molecules.8,9 Scheme 4 describes the introduction of a
fluorine at the a-position of the acidic moiety. This was
easily realized by condensation of the anion of ethyl-2-
fluorophosphonoacetate (generated by addition of ethyl-
2-fluorophosphonoacetate to a suspension of NaH in
DMF at 0 ꢁC) on the ketones 46 and 49. The corresponding
esters 64 and 65 were isolated in good yield (>80%) as
a mixture of isomers. Hydrolysis of these esters followed
by acidic work up and HPLC purification released the
acids 66 and 67 in moderate yield (<50%).12
Table 2 describes the co-transfection activity of com-
pounds 32–39, 56–61, 63, 66 and 67. Previous SAR
studies have shown that the alkoxy side chain plays a
critical role in modulating the RXR activity of such
compounds.6,14 As a general rule, a short alkoxy side
chain (methoxy or ethoxy) usually produces agonist
activity; while a longer one (propoxy and longer) pro-
duces antagonist activity. The same trend is observed
here with compounds 32–39, 56–61, 63, 66 and 67
except no compound shows a full agonist profile against
LG100268 (Table 2, entry 1). Compounds 32, 57 and 63
Tables 1 and 2 describe the binding affinity and the in
vitro profiling of compounds 32–39, 56–61, 63, 66, and
67.13 All the compounds show a remarkable selectivity

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P.-Y. Michellys et al. / Bioorg. Med. Chem. Lett. 14 (2004) 1593–1598
Scheme 3. 2,7-Disubstituted 1-benzofuran and 1-benzothiophene RXR modulators synthetic scheme. Reagents: (a) Pd(PPh3)4, 6 or 7, toluene/EtOH,
2 M Na2CO3, reflux. (b) R-Br, Cs2CO3, DMF, rt. Steps (c) and (d) identical of these described in Scheme 2 (b,c).
Scheme 4. Fluorinated 2,7-disubstituted-1-benzofuran RXR modulators synthetic scheme. Reagents: (a) Ethyl-2-fluorophonoacetate, NaH, DMF,
0 ꢁC to rt; (b) 2 N aqueous LiOH, THF/MeOH, reflux then 2 N aqueous HCl and recrystallization from CH3CN.
are RXR agonists but show only modest efficacy
(Efficacy <45%) in our co-transfection assay (Table 2,
entries 3, 12, and 17). Moreover, compound 63 has a
weak EC50 (390 nM) in addition to its low efficacy.
Compounds 33 and 56 are partial RXR agonists and
also have some RXR antagonist activity (Table 2 entries
4 and 11). All the other compounds (34–39, 58–61 and
66–67) are RXR antagonists in our co-tranfection assay,
however, compounds 39, 58, 59, 60 and 61 have weak
potency (83<IC50<347 nM). Compounds like 36, 37
and 66 are full RXR antagonists (Efficacy >90%,
IC50<11 nM).
As a result, we have described novel molecules acting as
RXR agonists (32, 57, and 63), RXR partial agonists (33
and 56) and RXR antagonists (34–39, 58–61 and 66–67).
Compounds 32–39 and 66 possess roughly the same
binding affinity for RXR (low nanomolar). Compounds
32–39 possess a 7-disubstituted-1-benzothiophene scaffold
while 66 possess a fluorinated 2,4-disubstituted-1-benzo-
furan scaffold. The introduction of a fluorine in the 2-
position of the crotonic acid moiety (compounds 66 and
67) increases the binding affinity and co-transfection
activity for RXR of these compound compared to their
respective non-fluorinated analogues (58 and 61).

P.-Y. Michellys et al. / Bioorg. Med. Chem. Lett. 14 (2004) 1593–1598
1597
Table 1. Binding data for RXRa, RXRb, RXRg, RARa, RARb and RARg. All data shown in nM
Entries
Compd
RXRa
Ki (nM)
RXRb
Ki (nM)
RXRg
Ki (nM)
RARa
Ki (nM)
RARb
Ki (nM)
RARg
Ki (nM)
1
2
3
4
5
6
7
8
LG100268
LG101506
18ꢂ1
3ꢂ2
18ꢂ12
7.5ꢂ2.5
33ꢂ11
11ꢂ2
15ꢂ4
55ꢂ12
10ꢂ2
10ꢂ3
12ꢂ4
12ꢂ3
12ꢂ3
NT
39ꢂ21
12ꢂ2
54ꢂ12
12ꢂ3
20ꢂ3
20ꢂ14
20ꢂ9
21ꢂ6
37ꢂ12
28ꢂ5
29ꢂ5
NT
>1000
2745
1786
>10,000
6910
8360
>1000
3515
>10,000
5940
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
9200
>1000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
>10,000
32
33
34
35
36
37
38
39
56
57
58
59
60
61
63
66
67
7ꢂ2
6ꢂ1
14ꢂ2
12ꢂ4
3ꢂ2
>10,000
7280
3ꢂ2
9
7ꢂ3
>10,000
>10,000
>10,000
>10,000
8500
10
11
12
13
14
15
16
17
18
19
5ꢂ1
19ꢂ11
22ꢂ11
44ꢂ1
198ꢂ80
47ꢂ10
161ꢂ62
271ꢂ95
16ꢂ8
101ꢂ50
NT
142ꢂ64
NT
334ꢂ53
NT
2700
NT
261ꢂ45
NT
NT
500ꢂ96
NT
>10,000
>10,000
6024
>10,000
>10,000
>10,000
>10,000
5736
>10,000
>10,000
64.5ꢂ15
28ꢂ12
4ꢂ2
49ꢂ16
NT: Not tested.
Table 2. In vitro profiling of RXR modulators in CV1 cells. Ki calculated using [3H]-9-cis-RA for RXR and [3H]-ATRA for RAR. All data shown
is in nM
Entries
Compd
RXRa
Agonist Efficacy
RXRa
Agonist EC50
RXRa
Antagonist Efficacy
RXRa
Antagonist IC50
1
2
3
4
5
6
7
8
LG100268
LG101506
70ꢂ21
11ꢂ10
NC
39ꢂ8
20ꢂ10
NC
NC
NC
NC
NC
12
0
4ꢂ2
84ꢂ10
8ꢂ11
26ꢂ6
81ꢂ8
79ꢂ13
93ꢂ1
94ꢂ0
94ꢂ1
96ꢂ0
64ꢂ0
10ꢂ2
74ꢂ5
76ꢂ6
84ꢂ0
67ꢂ6
5
8ꢂ4
32
33
34
35
36
37
38
39
56
57
58
59
60
61
63
66
67
43ꢂ15
NC
NC
21ꢂ13
4
16ꢂ12
24ꢂ14
14ꢂ5
8ꢂ1
1
1
0
0
9
16ꢂ7
83ꢂ63
20ꢂ13
NC
10
11
12
13
14
15
16
17
18
19
2
NC
19ꢂ67
86ꢂ43
74ꢂ23
NC
NC
NC
31ꢂ27
4
129ꢂ68
347ꢂ101
194ꢂ13
300ꢂ74
NC
4
1
7
NC
390ꢂ110
35ꢂ1
1
16
NC
NC
93ꢂ1
11ꢂ6
62ꢂ22
22ꢂ2
In conclusion, we have described a new series of RXR-
selective compounds. Both a 1-benzothiophene and a
1-benzofuran moiety have been used to successfully
replace the trienoic acid moiety present in our lead
compound LG101506. We have demonstrated that a
2,7-disubstituted-1-benzothiophene is a better replace-
ment of the parent trienoic acid. Using this new mole-
cular template, we have synthesized compounds that
cover a wide spectrum of activity for the RXR receptor
(agonist, partial agonist and antagonist) without alter-
ing the binding affinity for RXR of such molecules.
None of the compounds described bind to RAR. These
new RXR-selective ligands were synthesized in only five
steps from commercially available phenols or bromides.
References and notes
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