Piperazinyl pyrimidine derivatives as potent γ-secretase modulators

Article abstract of DOI:10.1016/j.bmcl.2009.11.101

The development of a novel series of piperazinyl pyrimidines as γ-secretase modulators for potential use in the treatment of Alzheimer's disease is disclosed herein. Optimization of a screening hit provided a series of potent γ-secretase modulators with >

Full text of DOI:10.1016/j.bmcl.2009.11.101

Bioorganic & Medicinal Chemistry Letters 20 (2010) 1269–1271
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Piperazinyl pyrimidine derivatives as potent c-secretase modulators
a
a
a
a
a
Alexey Rivkin a, , Sean P. Ahearn , Stephanie M. Chichetti , Yoona R. Kim , Chaomin Li , Andrew Rosenau ,
Sam D. Kattar a, Joon Jung a, Sanjiv Shah b, Bethany L. Hughes a, Jamie L. Crispino a, Richard E. Middleton a,
Alexander A. Szewczak a, Benito Munoz a, Mark S. Shearman b
*
a Department of Drug Design and Optimization, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
b Department of Neuroscience Drug Discovery, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The development of a novel series of piperazinyl pyrimidines as c-secretase modulators for potential use
in the treatment of Alzheimer’s disease is disclosed herein. Optimization of a screening hit provided a ser-
Received 21 September 2009
Revised 18 November 2009
Accepted 19 November 2009
Available online 23 November 2009
ies of potent
c-secretase modulators with >180-fold in vitro selectivity over inhibition of Notch cleavage.
Ó 2009 Elsevier Ltd. All rights reserved.
Keywords:
Alzheimer’s disease
c
-Secretase modulators
Alzheimer’s disease (AD) is a debilitating illness that represents a
selectively inhibited the production of Fb42 over Fb40
(IC50 À Fb42 = 1912 nM and IC50 À Fb40 = 3736 nM; Figure 1).10
Preliminary SAR studies led to the discovery of 2, a more selective
significant unmet medical need.1 The number of people afflicted
with the disease worldwide is expected to triple by the year 2050.2
Whiletherearesymptomatictreatmentsavailable, thereiscurrently
no treatment that is considered disease-modifying.3 The primary
pathological event in sporadic and familial AD is the extracellular
accumulation of amyloid-b (Fb) peptides and formation of amyloid
plaques.4 One strategy for developing a disease-modifying AD ther-
apy has been to reduce or eliminate the production of Fb peptides
c
-secretase modulator (IC50 À Fb42 = 169 nM and IC50 À Fb40 =
2953 nM), which was identified as a lead candidate. Encouraged by
the structural simplicity and degree of selectivity of this lead candi-
date, we initiated a lead optimization campaign.
The general synthetic approach employed to prepare analogs of
1 is outlined in Scheme 1. Regioselective nucleophilic addition of
anilines and aminopyrazoles to 2,4-dichloropyrimidines 3 in the
through inhibition of
the amyloid precursor protein (APP).
Several
-secretase inhibitors are currently in clinical trials.5
The major side effects observed with -secretase inhibitors are
thought to be associated with blocking the processing of Notch, a
transmembrane receptor which is also a substrate of
-secretase.6
c-secretase, which generates Fb peptides from
c
c
N
c
N
To avoid Notch-related toxicity we pursued a strategy that focused
on the discovery of a small molecule that modulates the processing
of c-secretase substrates, specifically targeting reductions in Ab42.
N
N
N
H
N
The pathogenic Ab42 peptide fragment is thought to play a more
significant role in AD pathology.4 This approach was supported
by recent reports that non-steroidal anti-inflammatory drugs re-
duce Ab42 generation and spare Notch processing and Ab40
production.7,8
1 (IC50(nM) Aβ42/40 = 1912/ 3736)
O
O
N
N
We describeherein the synthesisand biological activity of a novel
series of piperazinyl pyrimidine based
c-secretase modulators,
N
N
N
H
which have been the subject of a recent patent application by our
N
group.9 As part of our screening campaign, we identified 1 which
2 ( IC50(nM) Aβ42/40 = 169/ 2953)
* Corresponding author.
E-mail address: alexey_rivkin@merck.com (A. Rivkin).
Figure 1. Novel class of piperazinyl pyrimidine c-secretase modulators.
0960-894X/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2009.11.101

1270
A. Rivkin et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1269–1271
Table 1
R1
R1
In vitro activity of 2,4-disubstituted pyrimidines against Ab42 and Ab40
H2N
R2
N
N
N
R2
Hunig's base,
ethanol, 80 oC
Cl
N
N
H
Cl
N
3
Cl
N
N
R
4
N
R1
NH
O
N
N
R3 R4
R2
O
Compound
R1
Ab42
IC50 (nM)
Ab40
IC50 (nM)
N
N
N
10
10
H
Hunig's base,
N
isopropanol, 175 oC
R3 R4
O
1, 2, 5-28
5
1004
4579
N
H
Scheme 1. Synthetic strategy for the preparation of 2,4-disubstituted and 2,4,6-
trisubstituted pyrimidines.
O
O
6
7
534
6303
presence of base afforded the corresponding 4-aminopyrimidines.
A second addition of 4-methoxyphenyl piperazines to 4 using
microwave irradiation gave the corresponding pyrimidines 1, 2,
5–28.11
N
H
3444
10,000
Initial SAR studies focused on improving potency, selectivity of
Ab42 against Ab40, and the replacement of the electron rich
anilines which are potential metabolic liabilities. SAR of the 4-
methoxyphenyl piperazine of 1 showed this region to be very
sensitive to modification. For example, attempts to migrate or re-
place the 4-methoxy group led to complete loss in potency. The
piperazine ring proved to tolerate substitution, with minor
changes often leading to very little change in potency; however,
there was one important exception. Introduction of a gem-di-
methyl group into the piperazine ring improved potency of Ab42
inhibition but had very little effect on Ab40 inhibition ( Fig. 1 ,
1?2). The conformation of the 4-methoxyphenyl piperazine of 1
and 2 sample different conformational spaces as shown in Figure
2.12 This subtle difference in the conformational space, especially
the orientation of the 4-methoxyphenyl group with respect to
the aniline group, may contribute to the observed 17-fold Ab42
selectivity of 2. Given the improvement in selectivity, future SAR
continued with 2 as the lead candidate.
N
H
O
8
35.6
737
N
H
9
255
410
5565
2282
N
H
Ph
10
N
H
We then turned our attention toward exploring the SAR profile
of the 1,4-benzenediamine moiety (Table 1). Removal of the
4-diethylamino group led to a loss in potency that could be
partially recovered via introduction of a 4-ethoxy group (5, 6).
Interestingly, removal of the 5-methyl group led to a 10-fold loss
in potency, whereas introduction of an isopropyl group in the same
position resulted in a 10-fold improvement in potency (7, 8). Using
this observation to our advantage, we were able to remove the 4-
ethoxy group while maintaining potency by introduction of a
tert-butyl group at the 5-position (9). The introduction of a phenyl
11
12
695
150
1000
1938
N
H
Cl
N
N
N
N
H
N
13
272
5087
N
H
F3C
ring at the 5-position led to a loss of potency (10). The methyl
group in the 2-position proved to be important for both potency
and selectivity (11). The importance of the 5-tert-butyl and 2-
methyl groups for potency and selectivity is further supported by
the fact that the 3-tert-butyl-1-methyl-1H-pyrazol-5-amine is a
good isostere for the 5-tert-butyl-2-methylaniline (9 vs 12). We
Figure 2. Two most diverse representative conformers of 1 (left) and 2 (right) are
shown above.12

A. Rivkin et al. / Bioorg. Med. Chem. Lett. 20 (2010) 1269–1271
1271
Table 3
continued our SAR studies with 9 since 5-tert-butyl-2-methylani-
In vitro activity of 2,4,6-trisubstituted pyrimidines against Notch cleavage
line was potentially less prone to metabolism than 4-ethoxyaniline
or 1,4-benzenediamine moieties.
13
Compound
Notch IC50 (nM)
Notch IC50/Ab42 IC50
Preliminary SAR studies showed that the 6-position of the
pyrimidine ring of 9 was a permissive region for polar groups. With
this in mind, we focused our SAR efforts in this area with the goal
of concurrently improving potency and the physical parameters of
9 (Table 2). In our survey we found that polar groups were well tol-
erated in this region with potency retained and physical parame-
ters improved. Of all the polar substitutions examined,
19
22
23
24
25
26
27
29
6140
180
>50,000
>50,000
28,840
>50,000
>50,000
>50,000
34,430
>250
>190
270
>230
>210
>190
390
Table 2
In vitro activity of 2,4,6-trisubstituted pyrimidines against Ab42 and Ab40
hydroxymethyl 19 was the most potent which may be due to the
gain of a hydrogen bond interaction.
R
N
Several lead compounds were profiled in a Notch cleavage as-
say13 and found to have at least a 180-fold selectivity ratio be-
tween inhibition of Ab42 and Notch cleavage (Table 3).
In summary, a novel class of piperazinyl pyrimidines was dis-
covered which demonstrates potent and selective in vitro inhibi-
tion of Fb42 over Ab40 production and at least 180-fold
selectivity over inhibition of Notch cleavage. The SAR studies are
highlighted by the significant improvement in Fb42/Ab40 selectiv-
ity via introduction of the gem-dimethyl group. These results sup-
N
N
N
H
N
O
Compound
R1
Ab42
Ab40
IC50 (nM)
10
10
IC50 (nM)
port that modulating the cleavage site of
c-secretase substrates
with small molecules may prove to be an effective anti-amyloid
therapeutic strategy while avoiding Notch-related toxicities.
O
S
14
348
6461
O
References and notes
O O
S
15
16
400
234
5780
1927
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572
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18
19
85
34
2289
823
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OH
O
O
O
20
21
22
307
112
194
2985
1712
8120
N
H
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O
N
H
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N
H
the profiles of c-secretase modulators, total Ab peptide levels were constant (a)
O
O
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23
24
262
108
5682
1586
N
O
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25
26
216
235
5452
5598
OH
N
12. Conformational analysis was performed with the implicit Generalized–Born
solvent model with 8 kcal/mol energy cutoff. Clustering of conformers based
on the atomic RMS dissimilarity was used to generate the 10 most diverse
representative conformers. Two of the most diverse conformers for 1 and 2 are
shown in Figure 2.
O
O
13. HeLa cells were made to co-express nonfunctional halves of luciferase, one
N
27
263
6151
fused to Notch
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O
D
j
N
a
28
29
213
88
1970
830
N
complementation system is used to detect NICD levels by measuring total
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NH2