Discovery and SAR of novel pyrazole-based thioethers as cathepsin S inhibitors. Part 2: Modification of P3, P4, and P5 regions

Article abstract of DOI:10.1016/j.bmcl.2010.01.104

A novel class of tetrahydropyrido-pyrazole thioether amines that display potency against human Cathepsin S have been previously reported. Here, further SAR investigations of the P3, P4, and P5 regions are described. In particular, 4-fluoropiperidine is identified as a competent P3 binding element when utilized in conjunction with a (S)-2-hydroxypropyl linker-containing P5 moiety and oxamide or sulfonamide P4 substitution.

Full text of DOI:10.1016/j.bmcl.2010.01.104

Bioorganic & Medicinal Chemistry Letters 20 (2010) 2375–2378
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Discovery and SAR of novel pyrazole-based thioethers as cathepsin S
inhibitors. Part 2: Modification of P3, P4, and P5 regions
*
John J. M. Wiener , Alvah T. Wickboldt Jr., Danielle K. Wiener, Alice Lee-Dutra, James P. Edwards,
Lars Karlsson, Steven Nguyen, Siquan Sun, Todd K. Jones, Cheryl A. Grice
Johnson & Johnson Pharmaceutical Research & Development L.L.C., 3210 Merryfield Row, San Diego, CA 92121, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
A novel class of tetrahydropyrido-pyrazole thioether amines that display potency against human Cathep-
sin S have been previously reported. Here, further SAR investigations of the P3, P4, and P5 regions are
described. In particular, 4-fluoropiperidine is identified as a competent P3 binding element when utilized
in conjunction with a (S)-2-hydroxypropyl linker-containing P5 moiety and oxamide or sulfonamide P4
substitution.
Received 30 October 2009
Revised 15 January 2010
Accepted 20 January 2010
Available online 1 February 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Cathepsin S
Pyrazole
Inhibitor
P3
Cathepsin S (CatS) is a cysteine protease that mediates cleavage
of major histocompatibility class II (MHC II)-associated invariant
chain (Ii), crucial in the initiation of MHC II-related immune re-
sponse to an antigen.1 The invariant chain blocks the MHC II bind-
ing groove and prevents loading of the antigen into the groove for
subsequent presentation on the cell surface to CD4+ T-cells. Inhibi-
tion of the CatS enzyme slows the degradation of the invariant
chain, thereby reducing antigen presentation. For this reason, CatS
inhibitors have been proposed for treatment of various autoim-
mune disorders, as well as other diseases. Inhibitors of CatS are of-
ten covalent-binding active site-modifiers, though recently
noncovalent inhibitors have been disclosed.2,3
linker
CF
S
3
N
N
N
N
P5
N
hCatS IC = 0.38 µM
P4
50
SO CH
2
3
JY Ii IC = 0.38 µM
50
1
Figure 1.
In the preceding paper,4 the synthesis and biological evaluation
of a novel class of noncovalent thioether amine- and amide-con-
taining tetrahydropyrido-pyrazoles led to the identification of a
series of molecules (e.g., 1, Fig. 1) with good in vitro potency
against human CatS, as measured in an enzymatic assay (hCatS
IC50) and in an invariant chain degradation cellular assay in human
JY cells (Ii IC50); these compounds are hypothesized to access the
S3 binding pocket of the enzyme, based on computational studies
and preliminary X-ray crystal structure analysis. In an effort to im-
prove potency and further elucidate the binding mode, additional
investigations into the SAR of this template were undertaken, seek-
ing to optimize the P3, P4, and P5 regions of this thioether amine
series.
S
a
CF
3
CF
3
N
N
N
2
HN
HN
HS
S
N
NO
2
K2CO3, DMF, 70 °C
N
N
4
SO Me
2
3
SO Me
2
CF
3
N
b, c
R R N
N
2
1
OH
S
N
N
SO Me
5
2
* Corresponding author. Tel.: +1 858 450 2054; fax: +1 858 450 2089.
E-mail address: Jwiener1@its.jnj.com (J.J.M. Wiener).
Scheme 1. Reagents and conditions: (a) piperidine, toluene, 110 °C; (b) epichloro-
hydrin, Cs2CO3, DMF, rt; (c) NR1R2, EtOH, 80 °C.
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.01.104

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J. J. M. Wiener et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2375–2378
Variation of the P5 amine architecture was explored in conjunc-
and morpholine (7 and 8) as well as acyclic amine substituents
(9). Notably, the presence of a second basic amine in the six-mem-
bered ring is deleterious (10), though decreasing the basicity of
that second basic amine can restore potency (11), as can exocyclic
placement of the second basic amine (12 and 13). Significant
improvement in enzymatic potency is realized only for analogs
with aromatic substituents at the 4-position of the piperidine (14
and 15), though these compounds are significant inhibitors of the
hERG K+ channel as measured by an astemizole binding assay (data
not shown). Given the reasonable potency and suitable secondary
properties of the simple, relatively low molecular weight com-
pound 6 (in contrast to potent but also larger analogs such as
14–17), further optimization focused on this structure.
tion with a 2-hydroxypropyl linker found in other pyrazole-based
CatS inhibitor series reported previously.3 The desired analogs
were prepared according to the revised synthetic route shown in
Scheme 1, which allowed for both introduction of the hydroxyl
substituent as well as rapid variation of the P5 substituent. Treat-
ment of thiirane with a secondary amine afforded the amino thiol
2. This thiol was added in nucleophilic fashion to the unsubstituted
tetrahydropyrido-pyrazole core 3, prepared in an analogous fash-
ion to similar cores previously described,3 to afford pyrazole 4.
Alkylation with epichlorohydrin affords an epoxide intermediate,
which is readily derivatized to the desired analogs 5 by simple
treatment with various amines. The desired analogs can be pre-
pared in enantiopure form by replacing epichlorohydrin with (R)-
or (S)-glycidyl nosylate.
Table 2
Aminothioethers with 2-hydroxypropyl linker: variation of right-hand side amine
(P3)
Generally, analogs with the 2-hydroxypropyl linker-containing
a variety of amines as P5 elements display good potency in the
enzymatic and cellular assays, comparable to the piperidine P5
parent 6 (Table 1). Tolerated P5 substituents include pyrrolidine
CF3
N
R
S
N
N
OH
(rac)
Table 1
Aminothioethers with 2-hydroxypropyl linker: variation of left-hand side amine (P5)
N
SO2CH3
CF3
N
N
a
a,b
Compound
R
hCatS IC50
1.13
(lM)
JY Ii IC50
nd
(lM)
S
R
N
OH
18
NH2
(rac)
19
20
O
N
N
0.420
0.712
2.517
N
SO2CH3
N
0.458
a
a,b
Compound
R
hCatS IC50
(lM)
JY Ii IC50
(lM)
O
N
21
1.035
nd
6
7
8
N
N
0.204
0.335
Me
HO
22
N
0.565
0.149
0.395
0.058
nd
0.335
0.401
23
F
F
F
0.493
N
N
N
0.325
0.889
O
N
24c
25d
0.810
0.120
H
9
0.595
nd
N
Me
Me
10
11
12
1.15
nd
N
N
N
a
CatS IC50 and JY Ii degradation IC50 values are the mean of n P 2 runs and
determined as described previously.3a,c All IC50s were within a twofold range.
N
0.290
0.218
0.220
0.081
b
‘nd’ denotes data not determined.
(R)-Enantiomer.
(S)-Enantiomer.
c
N
N
d
Me
Me
N
N
13
0.710
nd
S
a
N
F
14
15
0.010
0.010
0.160
0.062
CF3
CF3
N
N
N
HN
CN
HN
HS
F
S
N
NO2
N
K2CO3, DMF, 70 °C
N
N
N
Boc
27
Boc
26
N
16
17
0.090
0.040
0.096
0.152
CF3
(S)
N
N
b, c, d, e
N
N
O
O
F
OH
S
N
N
N
N
R4
28
a
CatS IC50 and JY Ii degradation IC50 values are the mean of n P 2 runs and
Scheme 2. Reagents and conditions: (a) 4-fluoropiperidine, toluene, 110 °C; (b) (S)-
glycidyl nosylate, Cs2CO3, DMF, rt; (c) piperidine, EtOH, 80 °C; (d) 4 N HCl/dioxane,
rt; (e) R4-Cl, CH2Cl2; or R4-OH, HATU, HOAt, i-Pr2EtN, DMF; or R-NCO, CH2Cl2.
determined as described previously.3a,c All IC50s were within a twofold range.
b
‘nd’ denotes data not determined.

J. J. M. Wiener et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2375–2378
2377
A variety of analogs (Table 2) exploring changes to the P3 sub-
stituent in conjunction with the 2-hydroxypropyl linker and the
piperidine P5 moiety were prepared using the methods of Scheme
1 or methods similar to those reported previously.4 Replacement
of piperidine with a simple primary amine (18) decreases enzy-
matic inhibition, as does inclusion of rings such as morpholine,
pyrrolidine, and substituted piperazine (19–21). Substitution of
the piperidine at the 4-position with a hydroxyl was not benefi-
cial (22). Though fluorine substitution on the piperidine, as in
racemate 23, does not appreciably affect potency, the stereo-
chemical orientation of the hydroxyl moiety has a marked effect.
Comparison of compounds 24 and 25 reveals that the (S) orienta-
tion is preferred to the (R) orientation. Indeed, the (S)-2-hydroxy-
propyl linker analog 25 offers the best combination of increased
potency and low molecular weight, and, as such, was selected
for further optimization through variation of the P4 binding
element.
Table 3
Aminothioethers with (S)-2-hydroxypropyl linker: variation of P4 region
Following a sequence similar to that shown in Scheme 1,
replacement of the sulfonamide moiety to modify the P4 region
of these molecules was accomplished as shown in Scheme 2. The
sequence started from the Boc substituted pyrazole intermediate
26, prepared analogously to the sulfonamide material. Following
introduction of the P3 and P5 amino fragments, removal of the
Boc group was accomplished using HCl, and this secondary amine
intermediate was treated with a variety of acid chlorides, sulfonyl
chlorides, carboxylic acids, or alkyl halides under the appropriate
conditions to afford the desired analogs.
As shown in Table 3, removal of the P4 substituent altogether
leads to a molecule without appreciable potency (29), as does
replacement of the methyl sulfonamide with a simple methyl sub-
stituent (30). Other sulfonamides such as 31 and 32 are slightly
less potent than the methyl sulfonamide parent 25, as are ureas
and aromatic amides (33–36). Simple acetamide and propiona-
mide substituents (37 and 38), as well as substituted acetamides
(39–42), are somewhat deleterious to potency. Basic amine sub-
stituents on the acetamide are not beneficial (43), though, impor-
tantly, preserving the overall length of the amino-acetamide
substituent while also reducing the basicity in the context of an
oxamide substituent as in analog 44 reproduces the enzymatic
and cellular potency of sulfonamide analog 25. Though none of
these P4 variations successfully improved potency relative to the
sulfonamide P4 element, the ability to retain potency with a
non-sulfonamide entity offers opportunities for further exploration
of other P4 substituents.
CF3
F
N
(S)
N
S
N
N
OH
N
R4
a
Compound
R4
hCatS IC50 (lM)
0.058 (0.120)c
25
SO2Me
H
Me
SO2iPr
SO2Pr
29b
30b
31
9.6
9.0
0.35
0.30
32
O
33
34
0.235
1.19
NH2
O
N
O
O
S
35
36
0.355
N
0.205 (0.32)c
N
NH
O
These studies with pyrazole-based CatS inhibitors have pro-
vided an expanded understanding of SAR within several relevant
enzyme binding regions. The fluoro-piperidine P3 substituent, an
enantiomerically-pure (S)-2-hydroxypropyl linker, and a variety
of non-sulfonamide P4 substituents have been identified as bene-
ficial, offering favorable enzymatic and cellular potency. Further
investigations with these and other, related structures will be re-
ported in due course.
37
38
39
0.385
0.690
0.235
Me
O
O
O
Me
OH
OH
40
0.245
References and notes
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