Potent and selective P2-P3 ketoamide inhibitors of cathepsin K with good pharmacokinetic properties via favorable P 1′, P1, and/or P3 substitutions

Article abstract of DOI:10.1016/j.bmcl.2004.07.031

A series of ketoamides were synthesized and evaluated for inhibitory activity against cathepsin K. Exploration of the interactions between achiral P² substituents and the cysteine protease based on molecular modeling suggestions resulted in potent cathepsin K inhibitors that demonstrated high selectivity versus cathepsins B, H, and L. Subsequent modifications of the P³, P¹, and P^1′ moieties afforded orally bioavailable inhibitors. A series of ketoamides were synthesized and evaluated for inhibitory activity against cathepsin K. Exploration of the interactions between achiral P² substituents and the cysteine protease based on molecular modelling suggestions resulted in potent cathepsin K inhibitors that demonstrated high selectivity versus cathepsins B, H, and L. Subsequent modifications of the P³, P¹, and P^1′ moieties afforded orally bioavailable inhibitors.

Full text of DOI:10.1016/j.bmcl.2004.07.031

Bioorganic & Medicinal Chemistry Letters 14 (2004) 4897–4902
Potent and selective P2–P3 ketoamide inhibitors of cathepsin K
with good pharmacokinetic properties via favorable
0
P1 , P1, and/or P3 substitutions
a
b
David G. Barrett,a,ꢀ John G. Catalano,a, David N. Deaton, Anne M. Hassell,
Stacey T. Long,c Aaron B. Miller,b Larry R. Miller,d Lisa M. Shewchuk,b
Kevin J. Wells-Knecht,e Derril H. Willard, Jr.f,z and Lois L. Wrightg
*
aDepartment of Medicinal Chemistry, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
bDiscovery Research Computational, Analytic, and Structural Sciences, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
cDepartment of World Wide Physical Properties, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
dDepartment of Molecular Pharmacology, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
eDepartment of Research Bioanalysis and Drug Metabolism, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
fDepartment of Gene Expression and Protein Purification, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
gDiscovery Research Biology, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
Received 18 May 2004; revised 13 July 2004; accepted 17 July 2004
Available online 4 August 2004
Abstract—A series of ketoamides were synthesized and evaluated for inhibitory activity against cathepsin K. Exploration of the
interactions between achiral P2 substituents and the cysteine protease based on molecular modelling suggestions resulted in potent
cathepsin K inhibitors that demonstrated high selectivity versus cathepsins B, H, and L. Subsequent modifications of the P3, P1, and
0
P1 moieties afforded orally bioavailable inhibitors.
Ó 2004 Elsevier Ltd. All rights reserved.
Healthy bone tissue is maintained by specialized cells
called osteoclasts and osteoblasts.1 These cells operate
in concert by continuously remodelling bone tissue in
a process of bone resorption by osteoclasts and bone
formation by osteoblasts. Osteoclasts affect resorption
by secreting acid and proteolytic enzymes to degrade
the mineral and matrix components of bone, respec-
tively. Healthy bone maintains equilibrium between
the bone resorption and bone formation processes. Bone
becomes susceptible to osteoporosis and fracture when
bone degradation significantly outpaces bone formation.
A potentially promising strategy to correct such an
imbalance is to slow bone degradation by inhibiting
cathepsin K, the main proteolytic enzyme secreted by
osteoclasts to break down type I collagen, the primary
component of bone matrix.2 Small molecule inhibitors
of cathepsin K, a cysteine protease, have shown promise
in attenuating bone resorption in osteoporosis animal
models.3
This group has previously reported potent small mole-
cule cathepsin K inhibitors based on aldehyde and a-ke-
toamide electrophiles.4–8 Inhibitors such as a-ketoamide
1 (IC50 = 1.1nM) bind directly to the active site of cath-
epsin K. Binding modes for these molecules were clearly
defined through molecular modelling constructs de-
signed directly from inhibitor-bound enzyme crystal
structures.4,5,8 The reactive cysteine thiol of the enzyme
forms a reversible covalent bond with the a-ketoamide
moiety and the bulky t-butyl group at P2 effectively fills
the hydrophobic S2 enzyme subsite. The S2 subsite of
cathepsin K is the deepest, most pronounced hydropho-
bic binding pocket of the cathepsin K active site and
contains key structural variances over other human cys-
teine cathepsin family members.9 The P3 phenyl group
Keywords: Cathepsin K; Ketoamide; Cysteine protease inhibitor.
*
Corresponding author. Tel.: +1-919-483-6264; fax: +1-919-483-
6053; e-mail: john.g.catalano@gsk.com
ꢀ Present address: Lilly Forschung GmbH, Essener Street 93, 22419
Hamburg, Germany.
z Deceased.
0960-894X/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2004.07.031

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D. G. Barrett et al. / Bioorg. Med. Chem. Lett. 14 (2004) 4897–4902
of 1 adds an additional interaction for binding. These
significant binding sites warranted further SAR explora-
tion of the P2–P3 substituents. Modelling studies sug-
gested that achiral P2–P3 groups such as in 2 had
potential to bind favorably at the S2–S3 subsites of cath-
epsin K.10 To circumvent the need for asymmetric syn-
theses or efficient chiral separations required for the
preparation of inhibitors such as 1, analogs with achiral
groups were studied.
ylethylamine or 3-aminopyrazole to give the desired
a-ketoamides 2a–e, and 2l.
The P2–P3 alcohols used for the synthesis of 2h–k (Table
1) and 2l–p (Table 2) were prepared as in Scheme 2. The
enolates of ethyl cyclobutane carboxylate or methyl
cyclopentane carboxylate 7 were formed by treatment
with LDA. The enolates thus formed were coupled with
preferred P3 bromomethyl arenes to give esters 8.
Lithium aluminum hydride reductions of 8 provided
desired P2–P3 alcohols 9.
O
O
H
H
N
H
H
N
O
N
O
N
Ketoamides 2f–k were synthesized as in Scheme 3.
Treatment of P2–P3 alcohols with phosgene yielded
chloroformates that were coupled with the previous
described amino alcohols 10.6 Subsequent oxidation
provided the a-ketoamides 2f–k.
()m
P1'
Ph
O
nBu
O
Ph P3
P2O
P1
O
()n
P2
1
2
Additionally, it was desired to incorporate hydrophilic
groups into the inhibitors to promote greater water sol-
ubility and a more favorable pharmacokinetic profile.
Although hydrophilic substituents are not well tolerated
at S2, molecular modelling and previous SAR studies
suggested that heteroatom substitution would likely be
Table 1. Inhibition of human cathepsin K by P2–P3 analogs
O
H
H
R
N
N
10
tolerated at P3, P1, and P .4,8,10 The n-butyl P1 substit-
O
nBu
O
Ph
uent in 1 runs the length of a shallow hydrophobic
groove that extends roughly four carbon–carbon bond
lengths and then gives way to solvent, thereby allowing
an opportunity to introduce hydrophilic groups. The
S3 site is hydrophobic in nature, but more solvent
exposed than S2. The P3 position was therefore also con-
#
R
IC50 (nM)a
630
O
O
2a
Ph
Ph
2b
2c
710
25
sidered for incorporating water-solubilizing groups. Pre-
vious SAR studies showed that S1 would also accept
hydrophilic substitution.
0
O
O
O
Ph
Ph
Ph
As shown in Scheme 1, the first process to synthesize
ketoamides applied the acyl cyanophosphorane oxida-
tive cleavage and amine coupling procedure of Wasser-
man and Petersen.11 Coupling of the known
isocyanate 36 with commercially available alcohols 4a
and 4d–e or known alcohols 4b–c12 afforded carbamate
esters that were hydrolyzed to the acids 5a–e. Coupling
the acids 5a–e with cyanomethyltriphenylphosphonium
ylide yielded phosphoranes 6a–e. Oxidative cleavage of
the carbon–phosphorous bond generated reactive acyl
cyanophosphoranes that were coupled with (R)-1-phen-
2d
2e
150
210
2f
65
13
O
Ph
Ph
2g
O
2h
2i
8.5
26
Ph
O
O
O
O
C
N
O
H
a,b
d
O
N
c
OH
Ph
Ph
R
OH
R
O
+
O
nBu
nBu
3
4a-4e
5a-5e
2j
24
O
O
O
H
H
N
H
Ph
O
N
CN
O
N
R
R
R1
2k
17
O
O
nBu PPh3
6a-6e
O
nBu
2a-2e, 2l
O
a Inhibition of recombinant human cathepsin K activity in a fluores-
cence assay using 10lM Cbz-Phe-Arg-AMC as substrate in 100mM
NaOAc, 10mM DTT, 120mM NaCl, pH = 5.5. The IC50 values are
the mean of two or three inhibition assays, individual data points in
each experiment were within a 3-fold range of each other.
Scheme 1. Reagents and conditions: (a) ROH, PhMe, 85°C, sealed
tube, 89–99%; (b) LiOHÆH2O, THF, H2O; 1N HCl; (c) Ph3P@CCN,
DMAP, EDC, CH2Cl2, 46–79% over two reactions; (d) O3, CH2Cl2,
ꢀ78°C; N2; R1NH2, ꢀ78°C to rt; AgNO3, THF, H2O, 19–45%.

D. G. Barrett et al. / Bioorg. Med. Chem. Lett. 14 (2004) 4897–4902
Table 2. Inhibition of human cathepsin K by combination analogs
4899
Ph
#
R
IC50 (nM)a
C-
O
O
O
N+
H
N
H
R1
O
O
N
O
F
H
+
O
O
H
N
H
N
H
O
Ph
O
HN
a
R1
O
O
N
H
H
2l
0.83
N
N
O
N
O
O
O
11
12
13
O
O
OH
Ph
OH
F
H
N
H
H
N
O
N
H2N
H
N
H
N
R1
R1
O
N
O
O
O
b, c
d, e
2m
2n
2o
40
24
13
O
S
H
N
NH2
R2
14
15
H
N
N
R3
O
OH
R3
O
O
H
H
N
H
N
H
O O
N
N
F
R1
R1
O
g
f
H
N
H
O
O
O
O
O
N
H
H
N
N
R2
R2
F
O
O
O
16
2m-2p
H
N
H
N
Scheme 4. Reagents and conditions: (a) R1NC, PhCOOH, CH2Cl2,
60–65%; (b) LiOHÆH2O, dioxane, H2O, 100°C, 86–95%; (c) 10% Pd/C,
EtOH, 40psi H2, 99% (d) MeN@C@O or Me2NSO2Cl or 4-morpho-
linecarbonyl chloride, NEt3, THF, 48–80%; (e) HCl(g), EtOAc, 0°C,
99%; (f) R3OH, 1.93M COCl2 in PhMe, THF, ꢀ20°C to rt; 17, Et3N,
THF, 30–59%; (g) (COCl)2, CH2Cl2, DMSO, Et3N, ꢀ60°C to rt, 42–
77%.
F
O
H
H
N
O
N
O
O
O
O
H
N
N
Another route exploited the Passerini reaction to synthe-
size inhibitors 2m–p as shown in Scheme 4.13 P isocya-
10
N
O
nides 12 were synthesized from amines under known
conditions14 and reacted with aldehyde 11 using Passe-
rini conditions to yield 13. Acyloxyamides 13 were
hydrolyzed with aqueous lithium hydroxide, and the
benzyl carbamate protecting group was removed under
hydrogenolysis conditions to give amines 14. Amines
14 were coupled with dimethylsulfamoyl chloride,
methyl isocyanate, or 4-morpholinecarbonyl chloride
to introduce the P1 substituent before Boc removal with
hydrogen chloride in ethyl acetate yielded amino alco-
hols 15. P2–P3 chloroformates were coupled with 15 to
provide alcohols 16. Subsequent Swern oxidation pro-
vided a-ketoamides 2m–p.
H
N
H
O
N
O
O
O
2p
7.6
O
H
N
N
a Inhibition of recombinant human cathepsin K activity in a fluores-
cence assay using 10lM Cbz-Phe-Arg-AMC as substrate in 100mM
NaOAc, 10mM DTT, 120mM NaCl, pH = 5.5. The IC50 values are
the mean of two or three inhibition assays, individual data points in
each experiment were within a 3-fold range of each other.
O
Ar
()n
O
Ar OH
()n
As shown in Table 1, compounds 2a–e incorporated
achiral P2 tertiary carbamates to occupy the S2 pocket,
and included a fixed benzyl group extending out towards
S3. Dimethyl and cyclobutyl P2 analogs, 2a
(IC50 = 630nM) and 2b (IC50 = 710nM) respectively,
were only moderately active against cathepsin K. The
relative geometry and smaller size of these P2 groups
seemingly prevent an optimal binding interaction at
S2. The increased P2 bulk of cyclopentyl analog 2c
(IC50 = 25nM), however, translated into a significant
potency boost over 2a and 2b. The P2 diethyl group of
2d (IC50 = 150nM) presumably may only use a single
ethyl group to interact with S2 as it is significantly less
potent than 2c. Potency was also reduced by increasing
the size of the P2 substituent as in cyclohexyl analog 2e
(IC50 = 210nM).
a
b
O
R
O
R
()m
()m
()m
7
8
9
Scheme 2. Reagents and conditions: (a) Di-iso-propylamine, 1.6M
n-BuLi, ꢀ78 to 0°C, THF; ArCH2Br, 75–90%; (b) LiAlH4, THF, 0°C,
25–90%.
OH
O
H
H
H
H2N
N
O
N
N
a, b
R
nBu
10
O
Ph
O
nBu
2f-2k
O
Ph
Scheme 3. Reagents and conditions: (a) ROH, 1.93M COCl2 in PhMe,
pyridine, CH2Cl2, ꢀ20°C to rt; 10, i-Pr2NEt, dioxane, 22–91%; (b)
Dess–Martin periodinane, CH2Cl2, 55–78%.
Further molecular modelling suggested that the P2 moi-
eties of 2a–e did not extend far enough to fully access

4900
D. G. Barrett et al. / Bioorg. Med. Chem. Lett. 14 (2004) 4897–4902
the S2 pocket. Inhibitor 2f (IC50 = 65nM) was synthe-
sized for direct comparison to 2a and included a one
atom shift of P2 substituent. The ꢁ10-fold increase in
potency observed for 2f over 2a reinforced the molecular
modelling studies. Modelling also suggested that
extending the P3 linker would enhance S3 subsite inter-
actions. Increasing the linker between P2 and P3 by
one atom as in 2g (IC50 = 13nM) resulted in an addi-
tional 5-fold increase in potency. The cyclobutyl analog
2h (IC50 = 8.5nM) was equally active, but additional
increases in the size of P2 as in 2i (IC50 = 26nM) did
not increase potency. Extending the phenyl group
further towards S3, as with 2j (IC50 = 24nM) and 2k
(IC50 = 17nM), gave equivalent activity versus cathepsin
K. These last two inhibitors must pay a higher entropic
cost upon binding to the cathepsin K active site.
Although conformational constraints to the P2–P3 linker
could reduce this cost and might enhance activity, those
changes would increase size and reduce solubility and
were not pursued.
inhibitors such as 2f (L/K = 46) and 2o (L/K = 28) were
less selective versus this enzyme. Furthermore, these
inhibitors showed little selectivity versus cathepsin S,
with the cyclopentyl analog 2i being an apparently more
potent cathepsin S inhibitor. These results were not too
surprising since cathepsin K is structurally more similar
to the endopeptidases cathepsin L and cathepsin S than
the exopeptidases cathepsin B and cathepsin H.15
Cell permeability, solubility, and pharmacokinetic
parameters for analogs 2l–p are depicted in Table 4.
With the exception of 2p (PAPP = 14nm/sec), all of these
analogs exhibited good permeability in Madin–Darby
canine kidney cell monolayer assays (PAPP = 69–
470nm/sec).16 Inhibitors 2m (FS-SIF Sol. = 0.032mg/
mL, F = 18%) and 2n (FS-SIF Sol. = 0.027mg/mL,
F = 15%) were poorly soluble in fasted state-simulated
intestinal fluid,17 and this probably contributes to their
moderate oral bioavailability in male Han–Wistar rats.
Analogs 2l (FS-SIF Sol. = 0.15mg/mL, F = 31%) and
2o (FS-SIF Sol. = 0.098 mg/mL, F = 38%) exhibited 3-
to 5-fold increases in solubility compared to 2m and
2n and resulted in a doubling of oral bioavailability.
Although 2p (FS-SIF Sol. = 0.30mg/mL) was the most
soluble analog, its moderate membrane permeability
(PAPP = 14nm/sec) presumably limits oral bioavailabili-
ty (F = 8.1%). The total clearance of analog 2m was low
(Cl = 9.6mL/min/kg), leading to a long terminal half-life
(t1/2 = 270min) despite a moderate volume of distribu-
tion (VSS = 420mL/kg). The other inhibitors were more
rapidly eliminated (Cl = 27–45mL/min/kg) resulting in
shorter half-lifes (t1/2 = 74–120min) even though the
volumes were enhanced (VSS = 660–4200mL/kg). Of
particular notice, analog 2l was an extremely potent
cathepsin K inhibitor that demonstrated good oral bio-
availability in rats.
Having achieved reasonable inhibitory activity against
cathepsin K, focus shifted towards improving the phar-
macokinetic profile of these molecules. With highly lipo-
philic molecules such as 2a–k, aqueous solubility and
oral bioavailability were obvious concerns. Utilizing
SAR from previous ketoamide inhibitors,6,8 hydrophilic
moieties were substituted, singly or in combination, at
0
P1 , P1, and P3 to enhance solubility. Furthermore,
potential metabolic sites were also altered. The resulting
0
analogs 2l–p are shown in Table 2. The P1 pyrazole-con-
taining analog 2l (IC50 = 0.83nM) exhibited enhanced
10
potency versus 2h,8 whereas the P pyridine-containing
analog 2m (IC50 = 40nM) showed decreased activity rel-
ative to 2h.7 P1 lysine derivatives 2n–o and the P3 pyr-
idine 2p did not significantly alter inhibitory activity.
As shown in Table 3, all inhibitors in this series dis-
played excellent selectivity for cathepsin K versus cath-
epsin B and cathepsin H. Although reasonable
selectivity was also achieved against cathepsin L, several
Subsequent to the above work, an X-ray co-crystal
structure of cathepsin K with inhibitor 2l was solved
and the active site is shown in Figure 1. A covalent hemi-
thioketal intermediate is formed by the a-keto moiety of
Table 3. Selectivity of cathepsin K inhibitor analogs
#
Cat B IC50 (nM)a
Cat H IC50 (nM)b
Cat L IC50 (nM)c
Cat S IC50 (nM)d
B/K
H/K
L/K
120
S/K
2c
2f
>12,000
>5000
>5000
3600
>12,000
>5000
>5000
>5000
>5000
>2000
>2000
>500
3000
3000
1200
1300
2200
1600
1300
330
430
270
20
>480
>77
>480
>77
17
46
92
4.2
1.5
2.4
0.4
1.4
1.0
6.3
3.2
2.1
2g
2h
2i
>380
420
>380
>580
>190
>83
20
11
150
85
>5000
>2000
>2000
>500
>190
>83
2j
34
17
67
76
2k
2l
>120
>600
>120
>200
>120
>600
>120
>200
5.2
130
27
390
>120
28
2m
2o
>5000
>5000
>5000
>5000
>5000
680
a Inhibition of recombinant human cathepsin B activity in a fluorescence assay using 10lM Cbz-Phe-Arg-AMC as substrate in 100mM NaOAc,
10mM DTT, 120mM NaCl, pH = 5.5.
b Inhibition of recombinant human cathepsin H activity in a fluorescence assay using 50lM L-Arg-b-naphthalamide as substrate in 100mM NaOAc,
10mM DTT, 120mM NaCl, pH = 5.5.
c Inhibition of recombinant human cathepsin L activity in a fluorescence assay using 5lM Cbz-Phe-Arg-AMC as substrate in 100mM NaOAc,
10mM DTT, 120mM NaCl, pH = 5.5.
d Inhibition of recombinant human cathepsin S activity in a fluorescence assay using 10lM Cbz-Val-Val-Arg-AMC as substrate in 100mM NaOAc,
10mM DTT, 120mM NaCl, pH = 5.5.

D. G. Barrett et al. / Bioorg. Med. Chem. Lett. 14 (2004) 4897–4902
Table 4. Pharmacokinetics of combination analogs
4901
MDCKa PAPP (nm/sec)
Sol. FS-SIFc (mg/mL)
Clh (mL/min/kg)
F j (%)
b
d
t1/2 (min)
i
VSS (mL/kg)
#
2l
150
69
0.15
120e
270f
94e
110g
74g
45
9.6
33
43
27
––
31
18
15
38
2m
2n
2o
2p
0.032
0.027
0.098
0.30
420
1600
4200
660
140
470
14
8.1
a Madin–Darby canine kidney cell monolayer transport assay.
b PAPP is the apparent permeability coefficient for apical to basoplateral flux in nanometers per second.
c FS-SIF is the equilibrium solubility in fasted state-simulated intestinal fluid.
d t1/2 is the iv terminal half-life dosed as a solution.
e Dosed as a solution in 30% hydroxypropyl-b-cyclodextrin, pH = 5.1.
f Dosed as a solution in 30% sulfobutylether-b-cyclodextrin, pH = 3.5.
g Dosed as a solution in 40% hydroxypropyl-b-cyclodextrin, pH = 5.1.
h Cl is the total clearance.
i VSS is the steady state volume of distribution.
j F is the oral bioavailability.
the inhibitor and the active site 25Cys of the enzyme.
This is consistent with the reversible nature of these
time-dependent, tight binding inhibitors. As in other ke-
toamide co-crystal structures from this group, the hem-
ithioketal hydroxyl is stabilized by hydrogen bonds to
the catalytic histidine (162His) and the backbone
carbonyl of 161Asn, but does not occupy the oxy-anion
hole.8 Thus, the active site thiol attacks the carbonyl
with opposite stereochemistry from published aldehyde
and ketone cathepsin K structures.5,18 Instead, the car-
bonyl of the amide rests in the oxyanion hole where it
is stabilized by hydrogen bonds to the side chain NH
of 19Gln and the backbone NH of 25Cys. The carbamate
also forms two hydrogen bonds with the peptide back-
bone recognition site of the enzyme. Thus, the carba-
mate NH donates a hydrogen bond to 161Asn, while
the carbamate carbonyl accepts a hydrogen bond from
the backbone NH of 66Gly. Furthermore, the P1 pyraz-
ole forms a final hydrogen bond to the 184Trp indole NH.
0
Besides these hydrogen bond stabilizing interactions
with the protein, the norleucine-derived P1 group of
the inhibitor faces the S1 wall formed from 23Gly,
24Ser, 64Gly, and 65Gly, with one side of the n-butyl
group forming van der Waals interactions with the pro-
tease while its terminal carbon is exposed to solvent.
Moreover, the P2 cyclobutyl group forms hydrophobic
interactions with the S2 pocket composed of 67Tyr,
68Met, 134Ala, 163Ala, and 209Leu. The cyclobutyl P2
moiety occupation of the only deep pocket in the pro-
tease is not as favorable as in the case of the asymmet-
rically directed P2 substituents exemplified by 1. This
discrepancy, arising from the P2 cyclobutyl projecting
one atom further down the inhibitor backbone than
the asymmetric P2 t-butyl and at a different angle, may
account for the slight decrease in potency between 1
(IC50 = 1.1nM) and 2h (IC50 = 8.5nM). Finally, the P3
phenyl extends toward the S3 groove framed by 60Asn,
61Asp, 66Gly, and 67Tyr, making hydrophobic contacts
with this trough.
The original modeled structure of analog 2h docked into
the cathepsin K structure with the MVP modelling pro-
gram is also depicted.10 The inhibitor was docked into
the active site by growing the ligand in a covalently at-
tached state, starting at the b-carbon of 25Cys. There
is excellent agreement between the modeled structure
of 2h and the solved structure of 2l. This modelling
was undertaken to assist in designing achiral P2–P3 moi-
eties. The bound and modeled P3 phenyl groups occupy
virtually identical space, while the distal part of the
modeled P2 cyclobutyl substituent is only slightly ske-
wed from the bound cyclobutyl. The difference may re-
flect movement of the protein to best accommodate
the inhibitor, since the modelling uses a constrained en-
zyme. The exceptional harmony between the modeled
and bound structures and the usefulness of docking
potential inhibitors to identify novel and potent P2–P3
moieties further attests to the utility of this approach
in lead development.
Figure. 1. Active site of the X-ray co-crystal structure of compound 2l
complexed with cathepsin K. The cathepsin K carbons are colored
magenta with inhibitor 2l carbons colored green. The semi-transparent
white surface represents the molecular surface, while hydrogen bonds
are depicted as yellow dashed lines. The original modeled structure of
inhibitor 2h, with its carbons colored cyan, is also shown in the figure.
The coordinates have been deposited in the Brookhaven Protein Data
Bank, accession number 1TU6. This figure was generated using PY-
MOL version 0.93 (Delano Scientific, www.pymol.org).

4902
D. G. Barrett et al. / Bioorg. Med. Chem. Lett. 14 (2004) 4897–4902
7. Barrett, D. G.; Catalano, J. G.; Deaton, D. N.; Long, S.
T.; Miller, L. R.; Tavares, F. X.; Wells-Knecht, K. J.;
Wright, L. L.; Zhou, H.-Q. Q. Bioorg. Med. Chem. Lett.
2004, 14, 2543.
8. Tavares, F. X.; Boncek, V.; Deaton, D. N.; Hassell, A. M.;
Long, S. T.; Miller, A. B.; Payne, A. A.; Miller, L. R.;
Shewchuk, L. M.; Wells-Knecht, K.; Willard, D. H., Jr.;
Wright, L. L.; Zhou, H.-Q. J. Med. Chem. 2004, 47, 588.
9. Turk, D.; Guncar, G.; Podobnik, M.; Turk, B. Biol. Chem.
1998, 379, 137.
10. Lambert, M. H. In Practical Application of Computer-
Aided Drug Design; Charifson, P. S., Ed.; Marcel Dekker:
New York, 1997; p 243.
11. Wasserman, H. H.; Petersen, A. K. J. Org. Chem. 1997,
62, 8972.
In summary, this article describes SAR studies for a po-
tent series of cathepsin K inhibitors. Incorporation of
achiral P2–P3 substituents, based on molecular model-
ling suggestions, afforded good inhibitory activity versus
0
cathepsin K. Furthermore, modifications to P1 , P1, and
P3 groups, designed to enhance solubility and permea-
bility, and to block potential sites of metabolism, im-
proved pharmacokinetic properties. The resulting
inhibitors exhibited good to excellent selectivity versus
cathepsins B, H, and L. These studies resulted in the dis-
covery of potent and selective inhibitors like 2l that
demonstrated good oral bioavailability.
12. Finkelꢁshtein, E. S.; Mikaya, A. I.; Zaikin, V. G.; Vdovin,
V. M. Neftekhimiya 1980, 20, 75.
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