Systematic evaluation of amide bioisosteres leading to the discovery of novel and potent thiazolylimidazolidinone inhibitors of SCD1 for the treatment of metabolic diseases

Article abstract of DOI:10.1016/j.bmcl.2013.12.036

Several five- and six-membered heterocycles were introduced to replace the C2-position amide bond of the original 2-aminothiazole-based hit compound 5. Specifically, replacement of the amide bond with an imidazolidinone moiety yielded a novel and potent thiazolylimidazolidinone series of SCD1 inhibitors. XEN723 (compound 22) was identified after optimization of the thiazolylimidazolidinone series. This compound demonstrated a 560-fold improvement in in vitro potency and reduced plasma desaturation indices in a dose dependent manner, with an EC₅₀ of 4.5 mg/kg.

Full text of DOI:10.1016/j.bmcl.2013.12.036

Bioorganic & Medicinal Chemistry Letters 24 (2014) 520–525
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Systematic evaluation of amide bioisosteres leading to the discovery
of novel and potent thiazolylimidazolidinone inhibitors of SCD1
for the treatment of metabolic diseases
a
a
a
a
a
Shaoyi Sun a, , Zaihui Zhang , Vishnumurthy Kodumuru , Natalia Pokrovskaia , Julia Fonarev , Qi Jia ,
⇑
Po-Yee Leung b, Jennifer Tran b, Leslie G. Ratkay a, David G. McLaren a, Chris Radomski a,
Sultan Chowdhury a, Jianmin Fu a, Brian Hubbard b, Michael D. Winther a, Natalie A. Dales b,
⇑
a Xenon Pharmaceuticals Inc., 200-3650 Gilmore Way, Burnaby, BC V5G 4W8, Canada
b Novartis Institute for Biomedical Research, 100 Technology Square, Cambridge, MA 02139, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Several five- and six-membered heterocycles were introduced to replace the C2-position amide bond of
the original 2-aminothiazole-based hit compound 5. Specifically, replacement of the amide bond with an
imidazolidinone moiety yielded a novel and potent thiazolylimidazolidinone series of SCD1 inhibitors.
XEN723 (compound 22) was identified after optimization of the thiazolylimidazolidinone series. This
compound demonstrated a 560-fold improvement in in vitro potency and reduced plasma desaturation
indices in a dose dependent manner, with an EC50 of 4.5 mg/kg.
Received 8 October 2013
Revised 3 December 2013
Accepted 9 December 2013
Available online 16 December 2013
Keywords:
Stearoyl-CoA desaturase-1
SCD1 inhibitors
Ó 2013 Elsevier Ltd. All rights reserved.
Amide bioisosteres
Thiazolylimidazolidinone
Desaturation index
Stearoyl-CoA desaturase-1 (SCD1, also known as delta-9 desat-
urase, D9D) is a microsomal enzyme that catalyzes the de novo
synthesis of monounsaturated fatty acids (MUFA) from saturated
fatty acids by introducing a cis-double bond between carbons 9
and 10. The products, mainly oleate and palmitoleate, are sub-
strates for synthesis of triglycerides, wax esters, cholesterol esters
and phospholipids.1 To date, four SCD isoforms (SCD1-4) have been
characterized in rodents,2–5 and two SCD isoforms (SCD1 and
SCD5) in humans, with SCD1 identified as the predominant isoform
expressed in the liver.6,7 SCD1 knockout mice display a beneficial
metabolic phenotype characterized by increased energy expendi-
ture, reduced adiposity, improved insulin sensitivity and resistance
to high fat diet-induced obesity.8–10 These beneficial phenotypes
are also observed in high fat diet-induced obese (DIO) mice treated
with SCD1 antisense oligonucleotides.11,12 In humans, elevated
SCD1 activity is positively correlated with high triglyceride levels
in familial hypertriglyceridemia subjects,13 increased body mass
index (BMI) and high plasma insulin levels.14 Cross species studies
provide solid evidence to support the view that SCD1 is a critical
player in the regulation of skeletal muscle fat metabolism.15 Even
though the detailed mechanism by which SCD1 deficiency affects
body weight, adiposity and glucose regulation is not completely
understood, it is widely accepted that SCD1 plays an important role
in lipid metabolism;16 and further that inhibition of SCD1 repre-
sents a novel approach for the treatment of metabolic disorders.
Since we disclosed a series of small molecule SCD1 inhibitors,
such as compound 1, in 200517,18 (Fig. 1), many small-molecule
SCD1 inhibitors have been reported.19–25 Several reported SCD1
inhibitors have strikingly similar structural features to the scaffolds
identified in our first high throughput screen (HTS). To identify
additional novel, potent and structurally distinct SCD1 inhibitors,
we conducted a second high throughput screen which identified a
class of 2-aminothiazole-based SCD1 inhibitors with moderate
activity against mouse SCD1 (5, Fig. 2). Initial modification of 5 led
to the discovery of compound 6 with a more than 6-fold increase
in activity against mouse SCD1; however, compound 6 had poor
activity against human SCD1 as measured by a HepG2 cell assay
(Fig. 2). The poor cell activity may be attributed to poor permeability
and/or poor stability in the HepG2 cells due to the amide moieties at
the 2- and 4-position of the thiadizole hit compounds. Therefore, we
investigated the replacement of the 2-position amide moiety with
other, more metabolically stable functionalities,. In this paper, we
report the bioisostere replacements of the amide moiety at the
C2-position in compound 6 with different heterocycles.
⇑
Corresponding authors. Tel.: +1 604 484 3300 (S.S.), +1 617 871 7796 (N.A.D.).
E-mail addresses: ssun@xenon-pharma.com (S. Sun), natalie.dales@novartis.com
The application of heterocycles as amide bioisosteres is a
well-known practice in medicinal chemistry.26,27 These surrogates
(N.A. Dales).
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.12.036

S. Sun et al. / Bioorg. Med. Chem. Lett. 24 (2014) 520–525
521
Table 1
SAR of heterocyclic amide bond bioisosteres
O
O
O
O
N
N
CF3
N
N
N
NH N N
N
NH N N
H
N
W
S
OH
1 (Xenon)
2 (Daiichi Sankyo)
O
Br
N
N
N
O
O
a
a
N
O
F
Compound
W
Mouse SCD1 IC50
(nM)
HepG2 SCD1 IC50
(nM)
N
N
NH N N
O
N
HO
F
O
F
3 (Abbott)
4 (Merck)
N
N
N
7
28
53
Figure 1. Selected reported SCD1 inhibitors.
O
8
NH
154
2175
O
O
H
N
N
N
O
O
NH
N
H
S
NH
S
6
O
O
9
>10,000
601
nd
5
N
Mouse SCD1 IC50: 512 nM
HepG2 SCD1 IC50: 2677 nM
Mouse SCD1 IC50: 3400 nM
10
11
nd
O
N
N
Figure 2. 2-Aminohiazole-based SCD1 inhibitors discovered at Xenon.
75
1925
N
O
often introduce structural rigidity, which may lead to improved
selectivity, metabolic stability and enhanced pharmacokinetic
properties. We first examined the effect of several 5- or 6-mem-
bered heterocycles on potency (Table 1). The syntheses of these
compounds are illustrated in Schemes 1–6.
As described in Scheme 1, imidazolidinone analogues 7 and 8
were prepared in a straightforward manner from ethyl 2-amino-
4-methylthiazole-5-carboxylate (7a). Treatment of 7a with 2-chlo-
roethyl isocyanate, followed by in situ cyclization in the presence
of potassium carbonate provided compound 7b. Alkylation of 7b
with benzyl bromide afforded compound 7c. Subsequent hydroly-
sis to generate the acid 7d, followed by amide formation yielded
compound 7. Alternatively, treatment of compound 7a with CDI,
followed by reaction with (R)-(+)-2-amino-3-phenyl-1-propanol
generated intermediate 8a. Cyclization via the mesylate intermedi-
ate provided compound 8b. Ester hydrolysis, followed by amide
formation, then afforded compound 8.
N
N
12
33
9983
N
N
13
14
15
55
675
236
nd
N
N
N
27
N
NH
N
N
1007
N
N
16
200
618
a
IC50s are an average of at least two independent determinations; nd: not
determined.
Synthesis of the oxazole isostere 9 (Scheme 2) began by treating
4-methylthiazole-5-carboxylic acid (9a) with benzylamine under
standard EDCI–HOBt conditions. The resulting amide 9b was trea-
ted with lithium bis(trimethylsilyl)-amide, followed by quenching
with DMF to afford aldehyde 9c. Subsequent treatment of 9c with
p-tosylmethyl isocyanide in the presence of potassium carbonate
generated the oxazole intermediate 9d. The oxazole intermediate
9d was first converted to its corresponding 2-iodide by treating
with n-butyllithium, followed by quenching with I2 and in one
pot, the iodide was then coupled with benzylzinc bromide under
Negishi cross-coupling conditions to yield compound 9.
As outlined in Scheme 3, isoxazole 10 and 1,2,3-triazole 12 were
synthesized from intermediate 10b, which was in turn prepared
from 2-bromo-4-methylthiazole-5-carboxylic acid (10a) and
benzylamine under standard amide formation conditions. Interme-
diate 10b was further converted to compound 10c under Sonogash-
ira coupling conditions followed by a CuI-mediated cyclization of
10c with benzyl azide to afford 1,2,3-triazole 12. Similarly, treat-
ment of 10c with nitrile oxide 10d28 under CuI catalysis yielded
isoxazole 10.
ate the corresponding N-hydroxyamidine followed by cyclization
with the mixed anhydride of phenylacetic acid afforded oxadiazole
11. The nitrile intermediate 11c was also converted to the
corresponding 1,2,4-triazole 14 by treatment with phenylacetic
hydrazide under microwave irradiation conditions. The regioiso-
meric 1,2,3-triazole 13 was obtained by treatment of 11b with
tosyl azide under phase transfer conditions, followed by a CuI-
mediated cyclization with phenylacetylene.
The pyrazole analogue 15 was prepared starting from a palla-
dium-mediated cross coupling reaction of intermediate 10b with
1H-pyrazol-4-boronic acid, followed by reaction with benzyl
bromide in the presence of K2CO3 (Scheme 5).
The pyrazine compound 16 was obtained following the
synthetic procedure outlined in Scheme 6. 2,6-Dichloropyrazine
16a was converted to the corresponding diiodo compound 16b
by reaction with NaI in the presence of p-toluenesulfonic acid
and 15-crown-5. Bromo intermediate 10b was converted to its
corresponding zinc intermediate by treatment with Rieke zinc
under microwave irridation. Negishi cross-coupling between the
resulting zinc intermediate and the diiodo intermediate 16b affor-
ded compound 16c. The final pyrazine compound 16 was obtained
via Suzuki cross-coupling methodology.
Compounds 11, 13 and 14 were prepared from intermediate
11b (Scheme 4), which was synthesized from 2-amino-4-methyl-
thiazole-5-carboxylic acid (11a) and benzylamine as described
above. Treatment of 11b with isoamyl nitrite and copper cyanide
generated nitrile 11c. Addition of hydroxylamine to 11c to gener-
The inhibitory activity of these compounds against SCD1 was
assessed by two assay systems: a mouse liver microsomal assay29
and a human HepG2 cell-based assay.30 Compounds with good po-

522
S. Sun et al. / Bioorg. Med. Chem. Lett. 24 (2014) 520–525
N
a, b
c
N
N
N
N
NH
N
S
NH2
EtO2C
EtO2C
S
S
O
RO2C
O
7c R = Et
7d R = H
7a
7b
d
f
e
OH
NH
N
S
N
H
N
N
NH
S
N
EtO2C
O
O
O
8a
7
g
N
S
N
e
H
N
O
N
N
NH
RO2C
NH
S
O
O
8b R = Et
8c R = H
d
8
Scheme 1. Reagents and conditions: (a) 2-chloroethyl isocyanate, THF, reflux; (b) K2CO3, THF, reflux; (c) K2CO3, benzyl bromide, acetone, reflux; (d) LiOH, THF, H2O, reflux; (e)
EDCI, HOBt, iPr2NEt, DMF, benzylamine; (f) CDI, THF; (R)-(+)-2-amino-3-phenyl-1-propanol; (g) MsCl, iPr2NEt, THF; K2CO3, reflux.
a
b
N
N
N
lidinone analogue 7 was the most potent compound in both the
mouse SCD1 assay and in the HepG2 SCD1 assay; however, its
metabolic stability was poor (10% remaining after a 30 min
incubation with 0.5 mg/mL rat liver microsomes). Shifting the
benzyl group from the nitrogen to the neighboring carbon, as in
compound 8, resulted in decreased activity in both assays.
Although oxadiazole 11 and triazoles 12, 13 and 14 exhibited
comparable inhibitory activity against the mouse SCD1 enzyme,
their cellular potencies were significantly decreased. This de-
creased potency in HepG2 cells may be attributed to differences
in mouse versus human isoform selectivity or poor permeability.
Oxazole 9, isoxazole 10, pyrazole 15 and pyrazine 16 were the
least potent against SCD1 in mouse liver microsomal assay
among all of the amide replacements reported herein. These
results suggest that in our case, a desirable and effective hetero-
cyclic amide bond bioisostere requires a hydrogen bond acceptor
functionality to mimic the carbonyl group present in the original
amide moiety.
Given the good in vitro potencies observed in both SCD assays
with the imidazolidinone bioisostere, we focused our efforts on
this particular replacement moiety and further optimization was
conducted with the thiazolylimidazolidinone as the central core
structure. As outlined in Scheme 1 for compound 7, a similar syn-
thetic procedure was utilized to synthesize R1 and R2 analogues of
the parent compound 7. The activity of these analogues against
SCD1 was assessed using the same methods as outlined above
and the results are summarized in Table 2. In general, analogues
H
N
H
N
CHO
HO
S
S
S
O
O
O
9b
9a
9c
c
N
N
d
O
O
H
N
H
N
S
N
S
N
O
O
9d
9
Scheme 2. Reagents and conditions: (a) EDCI, HOBt, iPr2NEt, benzylamine, DMF; (b)
LiHMDS, THF, À78 °C; then DMF, À78 °C to RT; (c) p-tosylmethyl isocyanide, K2CO3,
MeOH; (d) n-BuLi, THF, À78 °C; then I2, À78 °C to RT; BnZnBr, Pd(PPh3)4, 50 °C.
tency on SCD1 were also screened against delta-5 desaturase (D5D)
and delta-6 desaturase (D6D) to determine the selectivity against
these desaturases. In humans, these two desaturases are involved
in the synthesis of highly unsaturated fatty acids which play cru-
cial roles in maintaining membrane fluidity; therefore, achieving
selectivity against D5D and D6D is essential to avoid undesirable
toxicities.31 None of the compounds evaluated (cell-based IC50
<100 nM on SCD1) demonstrate any D5D and D6D activity at
10
l
M.
As shown in Table 1, SCD1 potency was highly dependent on
the nature of the heterocyclic bioisosteric replacements. Imidazo-
N
N
a
N
b
H
N
H
N
Br
Br
HO
S
S
S
O
O
10b
O
10a
10c
O
c
N
Ph
d
10d
N
N
H
H
N
N
N
N
S
N
S
O
N
O
O
12
10
Scheme 3. Reagents and conditions: (a) benzylamine, EDCI, HOBt, iPr2NEt, DMF; (b) trimethylsilyacetylene, Pd(PPh3)2Cl2, CuI, iPr2NEt, toluene, 60 °C; LiOH, MeOH, H2O; (c)
BnN3, CuI, iPr2NEt, THF; (d) 10d, CuI, tBuOH, H2O.

S. Sun et al. / Bioorg. Med. Chem. Lett. 24 (2014) 520–525
523
N
N
N
N
H
N
H
N
S
NH
S
O
N
N
O
O
14
11
e
c, d
N
N
a
b
N
H
N
H
N
NH2
NH2
CN
HO
S
S
S
O
O
11b
O
11a
11c
f
N
N
g
H
N
H
N
N
N
N3
S
N
S
O
O
13a
13
Scheme 4. Reagents and conditions: (a) benzylamine, EDCI, HOBt, iPr2NEt, DMF; (b) isoamyl nitrite, CuCN, CH3CN, reflux; (c) NH2OH.HCl, Et3N, ethanol, reflux; (d)
PhCH2CO2H, CDI, DMF, then N-hydroxyamidine; (e) phenylacetic hydrazide, K2CO3, n-BuOH, 150 °C (microwave); (f) TsN3, BnMe3N hydrochloride, NaOH, CH2Cl2, H2O; (g)
phenylacetylene, iPr2NEt, CuI, THF.
N
assay (compounds 24, 26 and 27). However, installation of a
tetrahydropyran (compound 25) was not tolerated and resulted
in a significant decrease in potency.
a
N
H
N
Br
H
N
N
NH
S
S
O
10b
O
Based on the in vitro potencies in both SCD1 assays, we evalu-
ated the in vivo effect of compounds 19, 22, and 23 on the plasma
C16:1/C16:0 and C18:1/C18:0 triglycerides (TG) desaturation
indices (DI)33 in an acute Lewis rat model.34 C16 and C18 DI have
been well-documented as biomarkers for SCD1 target engage-
ment.12,36 The results of the C16:1/C16:0 plasma DI are illustrated
in Figure 3. 22 was the most efficacious among the three com-
pounds tested in this in vivo model as it reduced C16:1/C16:0 plas-
ma DI by 59%. Compounds 19 and 23 did not have a significant
effect on plasma DI reduction even though the in vitro potencies
were similar to that of 22. This discrepancy in PD effects may be
attributed to poor metabolic stability of Compounds 19 and 23.
Compound 22 was further evaluated in the acute DI model in a
dose-responsive manner at doses ranging from 0.5 mg/kg to
10 mg/kg. The results are illustrated in Figure 4 and indicated a
clear dose-related reduction of plasma TG DI with the ED50 esti-
mated to be 4.5 mg/kg.
In order to provide an initial assessment of the therapeutic in-
dex of 22 with respect to the adverse effects associated with
SCD1 deficiency,35,36 a tolerability study was carried out. In this
study, female Sprague–Dawley rats were dosed orally at 100 mg/
kg once daily for ten days and the clinical signs, such as red eyes,
hair loss and dry skin were assessed daily. Animals treated with
22 started to show mild eye symptoms on Day 3 and a dry skin
phenotype on Day 4 of dosing. These clinical signs related to
SCD1 inhibition in harderian and sebaceous glands slowly pro-
gressed to greater severity throughout the study, indicating that
prolonged systemic exposure and SCD1 inhibition in tissues, such
as in skin and eye glands, led to severe side effects. PK analysis
at the end of this study indicated a relatively high exposure in plas-
15a
N
b
H
N
N
N
S
O
15
Scheme 5. Reagents and conditions: (a) 1H-pyrazol-4-boronic acid, K2CO3,
Pd(PPh3)4, toluene, 100 °C; (b) K2CO3, DMSO.
I
N
R
N
N
R
N
b
H
N
S
N
O
16a R = Cl
16b R = I
16c
a
N
N
c
H
N
S
N
O
16
Scheme 6. Reagents and conditions: (a) NaI, p-toluenesulfonic acid, 15-crown-5,
sulfolane, 150 °C, 2 h; (b) 10b, Rieke zinc, THF, 100 °C, 15 min (microwave) under
nitrogen atmosphere; then 16b, Pd(PPh3)4, THF/DMF, 160 °C for 16 h under
nitrogen atmosphere; (c) 16c, Na2CO3, benzyl boronic acid pinacol ester, PdCl2(-
dppf), DME, 100 °C, 4 h.
with an aryl or a heteroaryl group at R1 displayed good potency in
both assays. Compounds 19 and 2232 were the most potent in the
mouse liver microsomal assay and by HepG2 cell-based assay.
Moreover, 22 demonstrated better metabolic stability than
compound 19. While analogue of oxazole (31) displayed compara-
ble potency, and most surprisingly the unsubstituted primary
amide (32) was potent in both SCD assays. Extension of the chain
length even by one carbon at R1 led to decreased activity as illus-
trated by compound 30, At R2, a longer chain length such as the
phenylpropyl group in compound 23 was well tolerated with
regards to SCD1 inhibition but was much less metabolically stable
in rat liver microsomes. Introduction of an alkyl or a cycloalkyl
group at R2 maintained potency by mouse liver microsomal SCD1
ma of the 22 (Cmax = 6 lM and AUC0–24 h = 78 lM h).
In conclusion, we discovered a number of heterocyclic amide
bond replacements capable of retaining good activity and im-
proved properties relative to the original 2-aminothiazole-based
HTS hit. Furthermore, we discovered novel and potent thiazolylim-
idazolidinone SCD1 inhibitors, including 22 (XEN723), which
demonstrates an improvement in SCD1 in vitro potency of more
than 560-fold compared to the original HTS hit, and exhibits robust
in vivo PD effects. Clinical observation studies with XEN723
revealed adverse effects related to SCD1 inhibition. Therefore,

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S. Sun et al. / Bioorg. Med. Chem. Lett. 24 (2014) 520–525
Table 2
SAR of thiazolylimidazolidinones
O
N
H
N
R1
R2
N
N
S
O
R1
R2
Mouse SCD1 IC50 (nM)
HepG2 SCD1 IC50 (nM)
Rat liver microsome stabilityb
a
a
Compound
17
18
19
20
3-Fluorobenzyl
4-Fluorobenzyl
Benzyl
Benzyl
Benzyl
Benzyl
63
91
5
145
45
6
16
45
>1000
47
46
87
13
3473
11
219
194
14
656
524
10
8
135
nd
16
40
27
nd
46
67
4
43
nd
55
67
57
54
nd
88
82
5-Methylfuranylmethyl
Pyridin-4-ylmethyl
Pyridin-3-ylmethyl
Pyridin-3-ylmethyl
Pyridin-3-ylmethyl
Pyridin-3-ylmethyl
Pyridin-3-ylmethyl
Pyridin-3-ylmethyl
Pyridin-3-ylmethyl
Pyridin-2-ylmethyl
Pyridin-2-ylmethyl
Pyridin-2-ylethyl
Oxazol-2-ylmethyl
H
21
Benzyl
22 (XEN723)
4-Fluorobenzyl
3-Phenylpropyl
Cyclohexylmethyl
Tetrahydro-2H-pyran-2-yl
Cyclopropylmethyl
n-Butyl
23
24
25
26
27
28
29
30
31
32
63
748
158
40
nd
95
Benzyl
4-Fluorobenzyl
4-Fluorobenzyl
4-Fluorobenzyl
4-Fluorobenzyl
15
55
a
IC50s are an average of at least two independent determinations; nd: not determined.
Expressed as% of compound remaining after a 30 min incubation with 0.5 mg/mL rat liver microsomes.
b
the therapeutic indices and thereby be more suitable for clinical
development for metabolic diseases.
Acknowledgments
We thank Kuldip Khakh, Elaine Chang, Wendy Young, Joseph
Sangara, Pritpaul Samra, Monica Mork, Caroline Hall, Rainbow
Kwan and Jing Zhong for their technical assistance.
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Figure 4. Dose response of 22 (XEN723) on plasma C16:1/C16:0 TG desaturation
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and/or reduced systemic exposure would be desirable to improve

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6.97 (m, 2H), 6.23 (t, J = 5.7 Hz, 1H), 4.57 (d, J = 5.7 Hz, 2H), 4.42 (s, 2H), 4.04 (t,
J = 8.1 Hz, 2H), 3.43 (t, J = 8.1 Hz, 2H), 2.58 (s, 3H). 13C NMR (75 MHz, CDCl3): d
164.1, 162.6, 160.8, 157.3, 155.3, 153.6, 148.5, 136.0, 134.1, 131.3, 129.9, 123.7,
116.9, 115.9, 115.6, 47.2, 42.0, 41.6, 41.3, 17.2. MS (ES+) m/z 475.0 (M+1). HPLC
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samples were collected 4 h after dosing. The plasma lipid profiles were
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chromatography and lipid analyses by gas chromatography.
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