Design and synthesis of tetracyclic nonpeptidic biaryl nitrile inhibitors of cathepsin K

Article abstract of DOI:10.1016/j.bmcl.2006.05.061

The synthesis and biological profile of a novel series of potent and selective inhibitors of cysteine protease cathepsin K (Cat K) are described. Pharmacokinetic evaluation of 12 indicated that some members of this series could be suitable candidates to develop new orally active therapeutic agents for the treatment of osteoporosis.

Full text of DOI:10.1016/j.bmcl.2006.05.061

Bioorganic & Medicinal Chemistry Letters 16 (2006) 4296–4299
Design and synthesis of tetracyclic nonpeptidic biaryl nitrile
inhibitors of cathepsin K
Eduardo L. Setti,a,* Shankar Venkatraman,a James T. Palmer,a Xiaoming Xie,a
Harry Cheung,a Walter Yu,a Gregg Wesolowskib and Joel Robichaudb
aCelera Genomics, 180 Kimball Way, South San Francisco, CA 94080, USA
bMerck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Que., Canada H9H 3L1
Received 6 March 2006; revised 17 May 2006; accepted 18 May 2006
Available online 5 June 2006
Abstract—The synthesis and biological profile of a novel series of potent and selective inhibitors of cysteine protease cathepsin K
(Cat K) are described. Pharmacokinetic evaluation of 12 indicated that some members of this series could be suitable candidates to
develop new orally active therapeutic agents for the treatment of osteoporosis.
ꢀ 2006 Elsevier Ltd. All rights reserved.
P2
Osteoporosis, defined as a systemic skeletal disease char-
acterized by low bone mass and microarchitectural dete-
rioration of bone tissue, occurs as an imbalance between
bone degradation and bone reconstruction. Cathepsin K
(Cat K) is a cysteine protease of the papain superfamily
that is highly and selectively expressed in osteoclasts.
Osteoclasts are specialized multinuclear cells that pro-
mote bone degradation. Cat K is the proteolytic enzyme
released by the osteoclasts that hydrolyzes type I colla-
gen, the major component of bone matrix.1 Thus,
recently the use of selective Cat K inhibitors has been
considered as a promising approach to treat diseases
characterized by excessive bone loss such as
osteoporosis.
P3
H
N
N
H
P1
N
N
O
1
Figure 1.
tested against human cathepsins K, L, B, and S. They
were also tested in an in vitro bone resorption assay that
evaluates degradation of bovine bone by isolated rabbit
osteoclasts.4
Recently, we showed that compound 1 (Fig. 1) displayed
excellent in vivo efficacy in the rhesus monkey model for
inhibition of urinary collagen breakdown products asso-
ciated with bone resorption.2 This compound displayed
a good PK profile in rhesus monkey and an acceptable
potency in enzyme (Ki: 8 nM)3 as well as in cellular assay
(bone res. IC50: 95 nM).
From our previous work in the nonpeptidic biaryl
series,2 as well as from the tricyclic P3 benzamide con-
taining aminoacetonitriles5 and 3,4-disubstituted azetid-
inone series,6 we have shown that the S3 subsite of
cathepsin K can accommodate fairly large moieties
without adversely affecting potency and selectivity. This
fact led us to conduct further SAR studies on the termi-
nal P3 portion of the molecule.
In this report, we describe the synthesis and biological
activity of a novel series of nonpeptidic biaryl inhibitors
with enhanced potency against Cat K. Compounds were
The terminal portions of compounds 11–13 and 16 were
obtained by following the general synthetic procedure
depicted in Scheme 1. Assembly of the tri-ring system
Keywords: Cathepsin K inhibitors; Nonpeptidic biaryl nitriles.
*
Corresponding author. Tel.: +1 650 579 2718; e-mail:
eduardo.setti@sbcglobal.net
0960-894X/$ - see front matter ꢀ 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.05.061

E. L. Setti et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4296–4299
4297
Br
S
H
a, b
N
N
c
N
NH2
N
N
R
N
S
R
N
R
2 a (R: CH3)
b (R: Boc)
3 a (R;CH3)
b (R: Boc)
4 a (R;CH3)
b (R: Boc)
Scheme 1. Reagents and conditions: (a) CSCl2, Et3N, THF, 0 ꢁC to rt; (b) NH3/EtOH (2.0 M), rt, 16 h; (c) 2,30-dibromoacetophenone, EtOH, 75 ꢁC,
4 h.
H
NH2
N
N
N
CN
a
b
O
N
O
N
S
O
N
O
O
O
2b
6
5
O
c
N
O
N
N
S
Br
7
Scheme 2. Reagents and conditions: (a) BrCH2CN, K2CO3, CH3CN, rt, 16 h; (b) H2S, Et3N–pyridine (3:1), rt, 16 h; (c) 2,30-dibromoacetophenone,
EtOH, 75 ꢁC, 4 h.
O
B
H
H
N
N
a
N
N
N
S
O
N
N
O
O
11
8
Scheme 3. Reagents and conditions: (a) compound 4a, PdCl2(dppf), 2.0 M aq Na2CO3, DMF, 85 ꢁC, 4 h.
Boc
N
b
a
O
B
H
N
H
N
N
N
N
N
S
O
O
O
10
9
HN
H
N
N
N
N
S
O
15
Scheme 4. Reagents and conditions: (a) compound 7, PdCl2(dppf), 2.0 M aq Na2CO3, DMF, 85 ꢁC, 4 h; (b) CH3SO3H, THF, rt, 16 h.
(4a/b–7) was accomplished by heating the corresponding
thiourea or thiamide (3a,b or 6) with 2,30-dibromoace-
tophenone (Schemes 1 and 2) in ethanol for 4 h
(Schemes 3 and 4). The syntheses of the key intermedi-
ates 8 and 9 were performed using the procedures de-
scribed by Robichaud et al.2 Suzuki cross-coupling

4298
E. L. Setti et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4296–4299
between the pinacoldiborane 8 and 9 with the corre-
sponding aryl bromide intermediate (4a/b–7) afforded
the tetracyclic final product, or a boc-protected interme-
diate (10) which was subsequently deprotected with
methanesulfonic acid in THF at room temperature
(Scheme 4).
present in other series5,6 (Fig. 2). This binding mode
was found to be comparable to the binding mode of
compound 17 to Cat K established by X-ray structure
(Fig. 3).5
The enantiomeric mixture 12 also displayed, overall, a
better PK profile in rat than compound 1, when dosed
intravenously (Table 2). Unfortunately, the increase in
Cat K potency did not translate well in cell since the
bone resorption assay value (IC50: 349 nM) showed a
more than 400-fold shift as compared to 12-fold for
the lead compound. Low solubility of compounds 12
and 16 in the cellular assay medium was thought to be
in part responsible for the shift between enzyme and
cellular assay potencies. Other factors, such as cellular
permeability and nonspecific protein binding, may also
play a role, although we did not specifically quantify
these in the context of the assays. When this mixture
of compounds was administered orally in rat at a dose
of 10 mg/kg, it had a very good bioavailability
(F: 85%) and a terminal t1/2 of 3.9 h (Table 3). Capping
Knowing that the introduction of a thiazole moiety
boosted potency in the benzamide series,5 we decided
to insert this group between the distal phenyl group
and the piperazine of our lead structure 1. As shown
in Table 1, the introduction of a thiazole ring clearly in-
creased the selectivity against Cat B and S. When the
thiazole–piperazine group was placed at the meta-posi-
tion of the distal phenyl, the modification yielded a more
potent Cat K inhibitor (12, Ki: 0.8 nM) despite the fact
that it was an enantiomeric mixture. Docked structure
of compound (R)-12 into in-house Cat K protein
showed that the proximal meta-substituted phenyl ring
orients the P3 residue deep into the S3 pocket of the en-
zyme, acting as a proper surrogate for the amide bond
Table 1. Inhibition of human cathepsins K, L, S and B by tetracyclic analogues
H
N
R
N
O
R
Stereo chem.
Cat K Ki (nM)
Cat L Ki (nM)
Cat B Ki (nM)
Cat S Ki (nM)
Bone res. IC50 (nM)
N
R
8.0
1.3
4641 (·580)
390 (·300)
3843 (·481)
1695 (·212)
1800 (·1384)
95
59
N
1
N
S
R,S
22,000 (·16,923)
N
N
11
N
R,S
R,S
R
0.8
3.5
1.3
190 (·237)
2500 (·714)
360 (·276)
18,000 (·22,500)
12,000 (·3428)
37,000 (·28,461)
5600 (·7000)
9500 (·2714)
5600 (·4307)
349
12
HN
N
S
12
N
S
HN
N
13
N
S
28
N
N
14
H
N
N
N
R
R
4.8
3.0
680 (·141)
540 (·180)
51,000 (·10,625)
51,000 (·17,000)
7400 (·1541)
3600 (·1200)
43
S
15
N
172
N
S
N
16
Selectivities over Cat K are shown in brackets.8

E. L. Setti et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4296–4299
4299
only a 3.4-fold shift between enzyme and cellular assay
values.
In order to explore how far away the basic nitrogen9
could be placed without affecting potency, we synthe-
sized compound 15. We have found that this one carbon
homologation rendered the molecule slightly less potent
against Cat K (4.8 nM), possibly due to a combination
of the size and a certain loss of rigidity of the terminal
portion at which the basic nitrogen is attached.
In summary, we have shown that the insertion of a thi-
azole moiety between the piperazine and the distal phen-
yl ring of the biaryl structure 1 enabled us to synthesize a
series of more potent and selective Cat K inhibitors in
enzyme and, many instances, more potent in bone
resorption assay as well. Preliminary pharmacokinetic
evaluation of the enantiomeric mixture 12 in rat demon-
strated that members of this series could be suitable can-
didates to develop new orally active therapeutic agents
for the treatment of osteoporosis.
Figure 2. Modeled structure of compound (R)-12 bound to Cat K.7
O
N
N
N
Acknowledgments
N
H
O
N
N
The authors thank Dr. Paul Grothaus, Dr. Cameron
Black and Mr. Leland Burrill for their critical reviews
of this manuscript.
S
17
Figure 3.
References and notes
Table 2. Rat PK parameters after iv administration at 0.5 mg/kg
1. Garnero, P.; Borel, O.; Borel, O.; Byrjalsen, I.; Ferreras,
M.; Drake, F. H.; McQueney, M. S.; Foged, N. T.; Delmas,
P. D.; Delaisse, J.-M. J. Biol. Chem. 1998, 273, 2347.
2. Robichaud, J.; Oballa, R.; Prasit, P.; Falgueyret, J.-P.;
Percival, M. D.; Wesolowski, G.; Rodan, S. B.; Kimmel,
D.; Johnson, C.; Bryant, C.; Venkatraman, S.; Setti, E.;
Mendonca, R.; Palmer, J. T. J. Med. Chem. 2003, 46,
3709.
Compound
Vss (l/kg)
MRT (min)
CL (ml/kg/min)
1
11
12
13
14
15
14.8
1.7
155
54
98
32
4.3
176
106
109
140
25
12.0
6.6
114
60
9.1
65
3. The reported Cat K IC50 of compound 1 in Ref. 2 is 3 nM.
4. Falgueyret, J. P.; Oballa, R. M.; Okamoto, O.; Wesolowski,
G.; Aubin, Y.; Rydzewski, R. M.; Prasit, P.; Riendeau, D.;
Rodan, S. B.; Percival, M. D. J. Med. Chem. 2001, 44, 94.
5. Palmer, J. T.; Bryant, C.; Wang, D. –X.; Davis, D. E.; Setti,
E. L.; Rydzewski, R. M.; Venkatraman, S.; Tian, Z.-Q.;
Burrill, L. C.; Mendonca, R. V.; Springman, E.; McCarter,
J.; Chung, T.; Cheung, H.; Janc, J. W.; McGrath, M.;
Somoza, J.; Enriquez, P.; Yu, Z. W.; Strickley, R. M.; Liu,
L.; Venuti, M. C.; Percival, M. C.; Falgueyret, J.-P.; Prasit,
P.; Oballa, R.; Riendeau, D.; Young, R. N.; Wesolowski,
G.; Rodan, S. V.; Johnson, C.; Kimmel, D. B.; Rodan, G.
J. Med. Chem. 2005, 48, 7520.
Table 3. Rat PK data for compound 14
Compound Dose Cmax Tmax
(mg/kg) (mM) (min) (uM min) (h) (%)
10 1.1 200 560 3.9 85
AUC
t1/2
F
12
the nitrogen with a methyl (11, Ki: 1.3 nM) yielded an
enantiomeric mixture with similar potency against Cat
K and higher potency in cell (bone res. IC50: 59 nM),
a finding that is in agreement with results found in other
series.5
6. Setti, E. L.; Davis, D.; Janc, J.; Jeffery, D. A.; Cheung, H.;
Yu, W. Bioorg. Med. Chem. Lett. 2005, 15, 1529.
7. Docking experiment was done by using GOLD 3.0 software
from Cambridge Crystallography Data Center. Water
molecules were removed from the protein and hydrogen
Interestingly, when the thiazole–piperazine pair was at-
tached to the para-position of the distal phenyl, the
resulting mixture of compounds (13, Ki: 3.5 nM against
Cat K) turned out to be about 4-fold less potent than the
meta-substituted analogue with a poorer overall PK
profile, illustrated by its higher clearance (114 ml/kg/
min, Table 2). To our surprise, the mixture 13 showed
bond constrain was added between ligand and Asn158
8. Same enzyme assay conditions as described in Ref. 5.
.
9. The presence of a basic nitrogen at the distal position of the
molecule was shown to be essential for potency and
selectivity in other series. See Refs. 4–6.