SAR studies of C2 ethers of 2H-pyrano[2,3-d]pyrimidine-2,4,7(1H,3H)-triones as nicotinic acid receptor (NAR) agonist

Article abstract of DOI:10.1016/j.bmcl.2011.12.041

Based on in house screening lead compound 1 for the NAR project, SAR studies have been focused on the modification of the C2 ethers of the pyrimidinedione core structure. In this effort, an unpredictable SAR trend was overcome in the alkyl ether and arylalkyl ether series to identify compound 24 with improved in vitro activity compared to nicotinic acid. More consistent and predictable SAR was achieved in the propargyl ether series. Lead compound 41 was identified with good in vitro and in vivo activity in rat, and much improved rat PK profile.

Full text of DOI:10.1016/j.bmcl.2011.12.041

Bioorganic & Medicinal Chemistry Letters 22 (2012) 854–858
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
SAR studies of C2 ethers of 2H-pyrano[2,3-d]pyrimidine-2,4,7(1H,3H)-triones
as nicotinic acid receptor (NAR) agonist
Xianhai Huang a, , Jing Su a, Ashwin U. Rao a, Haiqun Tang a, Wei Zhou a, Xiaohong Zhu a, Xiao Chen a,
⇑
Zhidan Liu a, Ying Huang a, Sylvia Degrado a, Dong Xiao a, Jun Qin a, Robert Aslanian a, Brian A. McKittrick a,
Scott Greenfeder b, Margaret van Heek b, Madhu Chintala b, Anandan Palani a
a Department of Chemical Research, Merck Research Laboratory, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
b Department of In vitro and In vivo Biology, Merck Research Laboratory, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Based on in house screening lead compound 1 for the NAR project, SAR studies have been focused on the
modification of the C2 ethers of the pyrimidinedione core structure. In this effort, an unpredictable SAR
trend was overcome in the alkyl ether and arylalkyl ether series to identify compound 24 with improved
in vitro activity compared to nicotinic acid. More consistent and predictable SAR was achieved in the
propargyl ether series. Lead compound 41 was identified with good in vitro and in vivo activity in rat,
and much improved rat PK profile.
Received 16 November 2011
Revised 6 December 2011
Accepted 8 December 2011
Available online 13 December 2011
Keywords:
Nicotinic acid
HDI
Ó 2011 Elsevier Ltd. All rights reserved.
TG
FFA
HM74A
Agonist
Dyslipidemia
Flushing
Heart Disease is the number one cause of death in the USA. High
levels of cholesterol, has long been known to be a risk factor for
heart attack and stroke.1–3 LDL-C was well documented as being
an independent risk factor for increased cardiovascular risk.4
HDL-C was recently thought as independent factor for reduction
of CVD mortality and emerges as new therapeutic target.5–7 Niacin
as a nicotinic acid receptor agonist was proved to be safe and effi-
cacious which has been used as a lipid lowering drug for over 30
years8,9 and helped to decrease VLDL-C, LDL-C, triglyceride, and in-
creases HDL-C.10–13 It can be used alone or in combination with
other lipid lowering agents to promote coronary artery disease
(CAD) regression, and reduces cardiovascular disease (CVD) mor-
tality. However, the patients needed to take gram amounts of the
drug multiple times per day with food due to poor human PK pro-
file (low exposure and short half life). High percentage of patients
had intense flushing of the face and upper body and severe itching,
some of them quitted the therapy after initial treatment due to this
reason.14 GI side effects including nausea, gastrointestinal discom-
fort and diarrhea were observed in some patients as well.15,16 Some
might display hepatotoxicity and hyperuricemia and gout.15,16
Although extended release formulation of NA (niaspan) is available
by prescription to alleviate the flushing side effect,16,17 this comes
with compromised efficacy and can not totally eliminate side ef-
fects such as potential hepatotoxicity.18–20 Due to these consider-
ations, the discovery of new NAR agonist without or minimized
side effect liability is highly desirable.
Nicotinic acid receptor (NAR), which enables rational drug
discovery for NAR agonist with improved profile, was identified
in the beginning of 21st century.21–23 NAR is a G-protein coupled
receptor which includes the high affinity agonist known as
HM74A (GPR109A) and the low affinity agonist known as HM74
(GPR109B) with 95% homology. Studies suggested that activation
of HM74A by nicotinic acid could result in downstream effect to
reduce intracellular triglyceride (TG) and free fatty acids (FFA)
secretion which eventually lead to the increase of HDL level.24–28
Thus HM74A as a potential novel therapeutic target has attracted
much attention from the pharmaceutical industry. Recently, we
started our effort in the NAR agonist area and have identified
two pyrimidinedione derived leads (Fig. 1, 1 and 2) with moderate
HM74A agonist activity from in house screening. The goal of our
NAR project was to identify a NAR agonist that, compared to NA,
had (1) decreased flushing liability; (2) similar or improved
⇑
Corresponding author. Tel.: +1 908 740 3487; fax: +1 908 740 7664.
E-mail addresses: xianhai.huang@merck.com, xianhai.huang@spcorp.com
(X. Huang).
0960-894X/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2011.12.041

X. Huang et al. / Bioorg. Med. Chem. Lett. 22 (2012) 854–858
855
groups gave comparable activity (Table 2, 13 and 16). Biarylalkyl
ethers were tolerated, and the ortho-substitution gave better activ-
ity (Table 2, 19 and 20). Heterobiaryl (21) was acceptable as well.
Since all these modifications did not lead to better binding activity
than NA (100 nM), we next introduced heteroaryl alkyl ethers. Pyr-
idazine substitution (22) gave better activity than the pyridine
(23). Isooxazole derivative (24) gave the best activity. SAR was very
sensitive to substitution modifications (25) and simple relocation
of the isooxazole heteroatom position resulted in much reduced
activity (26).
O
S
H
N
1
N
OH
O
O
S
O
O
2
N
O
NH
5
6
3NH
4
O
O
1
2
Nicotinic Acid
EC50 = 100 nM
EC50 = 1388 nM
EC50 = 470 nM
Figure 1. Structures of NAR screening leads and nicotinic acid.
Encouraged by the improved in vitro activity of compound 24,
and based on SAR information from the alkyl and arylalkyl ether
series, we felt that the properties especially electronic nature of
the ether side chain might play important role in affecting the activ-
ity profile. We thought that an alkyne group could be used to mimic
the electronic effect of the aryl group and at the same time to mimic
the size of simple alkyl groups. Based on this hypothesis, we pre-
pared a series of alkynylalkyl ethers. It turned out that the propar-
gyl ether series had the most consistent SAR as summarized in
Table 3. With a simple propargyl ether, the compound showed
moderate in vitro activity (Table 3 and 27). Introduction of
substitutions on the propargyl group resulted in improved activity
(28–31). The activity increased with the increased size of the sub-
stitutions. However, when the size was getting too big such as
cyclohexanyl group (Table 3 and 32), the activity started to drop.
Polar groups such as hydroxyl was tolerated in this series as well,
and again it showed consistent improvement of activity with the in-
creased length of the spacer between the alkyne and hydroxyl
group (Table 3 and 33–35) with the three carbon spacer most active
(35, 26 nM). Encouraged by these results, we then fixed the C2
substitution as ethyl substituted propargyl ether and modified C5
substitutions. As summarized in Table 3, aryl substitution (36),
longer chain and bulky substitution (37, 38) were tolerated and
resulted in compounds with good activity. Cyclopropyl and cyclo-
butyl alkyl substitutions at C5 provided compounds with very good
in vitro activity (39–41). This may be resulted from the subtle elec-
tronic effect brought by these groups. To determine the importance
of the propargyl group, compounds 42–44 were prepared. The
location of the alkyne was important for activity. When the ether
oxygen atom was linked by two carbons to the alkyne, decreased
potency and in vivo efficacy; (3) similar or improved pharmacoki-
netic profile. SAR studies following lead 2 and C2 carbon series
have been reported.29,30 Herein we report our SAR study effort on
the C2 substitution modifications of the screening lead 1 focusing
on the ether side chain to improve PK/PD profile.
We initially prepared a series of alkylethers at C2 positions and
the SAR is summarized in Table 1. When we introduced the
methoxy group, the compound showed good binding activity
(3, 125 nM). However, the SAR of the alkylethers seemed rather
narrow and did not follow a rational trend. When an ethyl group
was introduced (Table 1 and 4), the activity decreased significantly.
Interestingly cyclopropyl methyl group (5) brought back activity.
To mimic the electronic effect of a cyclopropyl group, a phenyl
group (6) was introduced and it gave good activity. Again, one car-
bon elongation of the linker between phenyl group and the core (7)
resulted in much reduced activity. Introduction of heteroatoms
such as oxygen within the ether side chain helped to maintain ago-
nist activity, but SAR did not follow a predictable trend either
(Table 1 and 8 vs 9). We also modified C5 substitutions to see
whether this would help to improve the activity profile. However,
longer (10) and bulkier chain (11, 12) at C5 seemed not helpful to
improve the activity.
We next looked into the SAR of substituted benzyl ether series
based on compound 6 to see whether we could improve the
in vitro activity.31 As summarized in Table 2, SAR in this series
was a little more consistent. Ortho-substitution showed better
activity than the meta- and para-substituted compounds with
meta- and para-compounds having similar activity (Table 2,
13–15 and 16–18). Both electron withdrawing and donating
Table 1
SAR summary of C2 alkyl ethersa
R3
NH
O
O
N
R1
O
Compound number
R1
R3
Ec50
Compound number
R1
R3
Ec50
138
O
O
O
O
3
4
125
8
9
O
O
O
O
10000
2060
5
6
7
285
190
10
11
12
417
319
260
O
Ph
Ph
O
O
O
10000
a
Data is in nM for human HM74A receptor and represents an average of multiple determinations (3 or more).

856
X. Huang et al. / Bioorg. Med. Chem. Lett. 22 (2012) 854–858
Table 2
SAR Summary of C2 aryl–alkyl ethersa
O
O
N
O
O
R2
NH
Compound number
R2
Ec50
Compound number
R1
Ec50
238
Compound number
R1
Ec50
N
13
113
19
22
738
OMe
CN
N
N
OMe
OMe
14
860
20
21
723
291
23
24
93
63
CN
N
O
O
N
N
15
16
1061
133
F
25
26
588
N
CF3
17
18
290
270
10000
O
CF3
CF3
N
a
Data is in nM for human HM74A receptor and represents an average of multiple determinations (3 or more).
Table 3
SAR summary of C2 propargyl ethersa
O
O
N
O
O
R2
NH
R1
Compound number
R1
R2
Ec50
Compound number
R1
R2
Ec50
137
27
911
425
36
28
29
37
38
66
96
53
172
30
39
22

X. Huang et al. / Bioorg. Med. Chem. Lett. 22 (2012) 854–858
857
Table 3 (continued)
Compound number
R1
R2
Ec50
34
Compound number
R1
R2
Ec50
90
31
40
32
33
34
177
312
179
41
42
43
67
OH
424
OH
>1000
>1000
OH
35
26
44
a
Data is in nM for human HM74A receptor and represents an average of multiple determinations (3 or more).
activity was observed (Table 3 and 42). The alkyne group was cru-
cial for activity, when the alkyne was reduced to an alkene (43) or
simple alkyl group (44), these compounds lost activity dramati-
cally. With improved in vitro activity, compounds 39 and 41 were
selected for further profiling in in vivo studies. Compound 39 had
a binding activity of 28 nM in rats, however, it did not show robust
TG decrease (2.6% reduction at 0.3 mpk at 6 h time point) in rats. On
the other hand, compound 41 had 83 nM binding activity in rat and
showed very good in vivo activity in rat TG assay (34% reduction at
0.3 mpk at 6 h time point). This compound had very good PK profile
and the product (48) was crashed out with DMF and water. The
methyl thioether (48) was oxidized with m-CPBA in diclorome-
thane (DCM) and provided key intermediate sulfone 49 after sol-
vent removal and washing with ethyl acetate and hexane
mixture. Different nucleophiles were introduced at this stage in
the presence of base in a mixture of THF and DMF to give the final
compounds 50. The overall synthesis was straight forward and re-
quired no column chromatography of the intermediates. Consider-
ing the difficulties to handle these compounds which had very
poor solubility in organic solvents, this process offered the oppor-
tunity to carry out the SAR studies quickly and provided key com-
pounds in sufficient quantity.
In summary, based on in house screening lead compound 1 for
the NAR project, SAR studies have been focused on the modifica-
tion of the C2 ethers. In this effort, we overcame an unpredictable
SAR trend in the alkyl ether and arylalkyl ether series to identify
compound 24 with improved in vitro activity compared to nico-
tinic acid. More consistent and predictable SAR was achieved in
the propargyl ether series. Lead compound 41 was identified with
good in vitro and in vivo activity in rat, and much improved rat PK
profile.
in rat (42.5
l
M h AUC at 10 mpk oral dosing in rapid rat studies,32
M, and Tmax = 4 h). On the other hand, the rat PK of
M h
M, and Tmax = 1 h) which
Cmax = 29.2
l
compound 39 was moderate with much shorter Tmax (21.8
l
AUC at 10 mpk oral dosing, Cmax = 15.7
l
might explain the lack of in vivo activity of this compound at 6 h
time point.
The synthesis of the C2 substituted compounds is summarized
in Scheme 1. Thiobarbituric acid (45) was first condensed with
the ketoester (46) as a neat mixture at 165 °C to give thiopyrimid-
inedione 47 after washing the crude with water. Methylation of
compound 47 was achieved using MeI in DMF without any base
H
H
O
O
N
O
SMe
NH
O
N
S
O
O
N
S
O
O
MeI/DMF
98%
heat
84%
+
NH
NH
O
O
O
48
45
46
47
O
O
N
O
Nu
mCPBA
DCM
O
O
N
O
SO2Me
HNu, NaH
30-80%
NH
NH
95%
50
Nu = nucleophile
49
Scheme 1. The synthetic route of C2 ethers

858
X. Huang et al. / Bioorg. Med. Chem. Lett. 22 (2012) 854–858
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