Exploration of cathepsin S inhibitors characterized by a triazole P1-P2 amide replacement

Article abstract of DOI:10.1016/j.bmcl.2012.09.054

This paper details exploration of a class of triazole-based cathepsin S inhibitors originally reported by Ellman and co-workers. SAR studies involving modifications across the whole inhibitor provide a perspective on the strengths and weaknesses of this class of inhibitors. In addition, we put the unique characteristics of this class of compounds into perspective with other classes of cathepsin S inhibitors.

Full text of DOI:10.1016/j.bmcl.2012.09.054

Bioorganic & Medicinal Chemistry Letters 22 (2012) 7189–7193
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Exploration of cathepsin S inhibitors characterized by a triazole P1–P2
amide replacement
⇑
⇑
Neil Moss , Zhaoming Xiong , Mike Burke, Derek Cogan, Donghong A. Gao, Kathleen Haverty,
Alexander Heim-Riether, Eugene R. Hickey, Raj Nagaraja, Matthew Netherton, Kathy O’Shea,
Philip Ramsden, Racheline Schwartz, Daw-Tsun Shih, Yancey Ward, Erick Young, Qing Zhang
Departments of Medicinal Chemistry, Immunology and Inflammation, Boehringer Ingelheim Pharmaceutical, Inc., 900 Ridgebury Road, Ridgefield, CT 06877, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 22 July 2012
Revised 2 September 2012
Accepted 17 September 2012
Available online 2 October 2012
This paper details exploration of a class of triazole-based cathepsin S inhibitors originally reported by
Ellman and co-workers. SAR studies involving modifications across the whole inhibitor provide a
perspective on the strengths and weaknesses of this class of inhibitors. In addition, we put the unique
characteristics of this class of compounds into perspective with other classes of cathepsin S inhibitors.
Ó 2012 Elsevier Ltd. All rights reserved.
Keywords:
Cathepsin S
Reversible covalent inhibitors
Triazole
SAR
Metabolic stability
Antigen presentation is an important process in normal immune
responses and autoimmunity. In humans, there exists a clear associ-
ation betweencertainMHC II polymorphisms andincreased autoim-
munityrisk.1 MHCII isresponsibleforpresentingantigenpeptidesto
CD4+ T cells, a key cell type in the pathogenesis of autoimmunity.
Cathepsin (Cat) S plays a critical role in antigen possessing and
presentation.2 Gene deletion and pharmacological inhibition exper-
iments in rodents demonstrate that Cat S is essential for MHC II med-
iated antigen presentation and its inhibition leads to reduced
immune response of CD4+ T cells.3 In addition, increased expression
of extracellular Cat S is detected in tissues, suggesting direct involve-
ment in tissue destruction.4,5 Cat S deficiency has been shown to
lower mobility of dendritic cells and B cells.6 These three mecha-
nisms support Cat S as an attractive therapeutic target for autoim-
mune diseases like multiple sclerosis and rheumatoid arthritis.
Despite numerous reports of Cat S inhibitors over the past dec-
ade,7 the therapeutic benefit of Cat S inhibition in clinical trials has
not yet been reported. However, Merck have advanced a Cat K
inhibitor, odanacatib, into Phase III clinical trials for osteoporosis.8
They have also disclosed factors they investigated and addressed in
designing a Cat K inhibitor. These include warhead reactivity,
lysosomotropism, and the pharmacokinetics (PK) of peptide de-
rived inhibitors. The majority of low molecular weight cathepsin
inhibitors rely on an electrophilic nitrile (warhead) to achieve
low nanomolar potency. The nitrile forms a reversible covalent
bond with the cathepsin active site cysteine. More electrophilic ni-
triles (e.g. cyanopyrimidines)9 have a higher risk of non specific
reactivity to biological thio-nucleophiles.10 Less electrophilic ni-
triles (e.g. a-amido-nitriles) have limited reactivity to thio-nucleo-
philes but can achieve excellent potency against their targeted
cathepsin. The presence of amine functionality in cathepsin inhib-
itors often results in greater potency in cell-based assays compared
to the corresponding non-amine containing analogues of equiva-
lent molecular potency. This is believed to be due to accumulation
of basic inhibitors in acidic lysosomes (lysosomotropism), the cel-
lular compartment where most cathepsins are typically located. In
vivo, this accumulation of basic cathepsin inhibitor in the lysosome
can lead to inhibition of off-target cathepsins despite reasonable
selectivity in molecular assays.11 This accumulation phenomenon
was shown to enhance Cat L and B selectivity issues with early
basic Cat K inhibitors and was postulated to be a reason why these
compounds had toxicity issues in clinical trials.8 The Merck publi-
cations also highlighted that good pharmacokinetics was possible
with these peptide derived inhibitors by incorporating polar func-
tionality and blocking sites of metabolism.
The above led us to conclude that key criteria for a successful
Cat
S inhibitor should include a mildly electrophilic nitrile
warhead, high selectivity over other cathepsins, especially Cat L,
no basic amine, and functionality that reduces the potential for
metabolism. Our past Cat S inhibitors exemplified by compounds
⇑
Corresponding author. Tel.: +1 203 431 1272 (N.M.), +1 203 798 4854 (Z.X).
E-mail addresses: Neil.Moss@comcast.com (N. Moss), zhaoming.xiong@
boehringer-ingelheim.com (Z. Xiong).
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2012.09.054

7190
N. Moss et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7189–7193
Table 1
Data for known Cat S inhibitors
O
O
O
H
N
H
N
H
N
CN
CN
CN
N
N
H
N
N
H
N
N
H
O
O
O
O
O
O
N
N
1
2
3
O
O
S
O
S O
CF3
CF3
H
N
H
N
CN
CN
N
H
N
H
O
O
F
F
4
5
S
N
S
N
N
N
H
N
H
N
N
N
CN
CN
H
O
O
6
7
Compound
Cat S IC50 (nM)
Cat L IC50 (nM)
Antigen Challenge IC50 (nM)
1
2
3
4
5
6
7
1.5
17
1.6
2.5
0.4
9
990
>20,000
200
230
62
0.9
2.8
10
5
33
30
76
>20,000
>20,000
10
IC50 values are means of 2–4 experiments. IC50s for n > 2 experiments typically fall within a range defined by multiplying or dividing the reported value by 1.5.
1–3, Table 1, did not meet all these criteria.12 For example, the
most potent molecules in our antigen challenge cell assay13 typi-
cally required the presence of amine functionality (cf. 1 and 2).
Analogue 3 was the best neutral inhibitor to confer nanomolar cell
potency in this series. The branched heptyl group in compound 2
provided a better balance of selectivity and cell potency than com-
pound 1. However, this class of compounds generally displayed
poor PK. Subsequent to our initial work, a set of Cat S inhibitors
represented by compounds 4 and 5, was reported that came closer
to meeting the key criteria.14 In our assays, these neutral inhibitors
possessed good molecular potency and reasonable cell potency for
a neutral inhibitor. Their selectivity over Cat L was modest, but
they had superior rodent PK properties relative to our initial series.
Also subsequent to our initial work, Ellman and co-workers pub-
lished a series of Cat S inhibitors represented by compounds 6
and 7.15 These neutral non-peptidic inhibitors contained a new
variation of a mildly electrophilic nitrile warhead, they were rela-
tively potent against Cat S, and they appeared to be highly selective
against Cat L. We became intrigued by the potential of this series to
meet the criteria discussed above. We prepared compounds 6 and
7 and discovered they possessed quite good potency in the antigen
challenge cell assay despite their relatively modest molecular po-
tency and lack of basic amine. We also confirmed their lack of po-
tency against Cat L. A key weakness however was PK. Compound 7
was rapidly metabolized in human liver microsomes (half-life
<5 min). This high rate of metabolism translated into poor i.v. PK
for an analogue of compound 6 (compound 13) with a clearance
of 90% of hepatic blood flow (63 mL/min/kg) and a half-life of
0.7 h observed in Sprague Dawley rats. Nevertheless, the desirable
combination of structural features, potency and selectivity encour-
aged us to investigate this triazole-based series more thoroughly.
All the triazole-based Cat S inhibitors in the Ellman publication
contained an S-butyl group adjacent to the nitrile (P1 position).
Table 2 summarizes some key findings from a further investigation
of SAR at this position. Interestingly the S-stereochemistry, which
corresponds to the natural configuration of the corresponding
amino acid, proved not to be the preferred configuration. The
R-diastereomer for both the butyl (8) and methyl (10) compounds
was more potent than the corresponding S analogues 6 and 9.
However, the potency of the unsubstituted derivative 11 highlights
that a P1 substituent is not necessary for good potency. In most
cases an increase in molecular potency translated into an increase
in cell assay potency, especially for compounds 10 and 13. The
increase in Cat S potency appears in some cases to coincide with
an increase in Cat L potency, although from this limited set ofexam-
ples, it is unclear whether the differences observed in Cat L potency
are due to true differential SAR. The high Cat S potency of these
inhibitors complicates a precise potency ranking due to limitations
in assay sensitivity for compounds in the sub-nanomolar range.
Table 3 highlights the contribution of the two central methyl
groups to Cat L selectivity, with compounds 10 and 13 chosen as
frames of reference. Together, the two central methyl groups ap-
pear to decrease Cat L potency by an order of magnitude while
trending to increase Cat S potency. The central region of the inhib-
itor (P2) binds to the S2 pocket of Cat S and Cat L. The S2 pocket of
Cat L differs from that of Cat S primarily by the presence of two ala-
nines instead of glycines. The sterically smaller alanine containing
S2 pocket of Cat L would be predicted to disfavor binding of certain
larger P2 substituents. The three sets of comparisons in Table 3
also show compounds with a cyclopropyl adjacent to the nitrile
to have about 10-fold less Cat L potency than the corresponding
R-methyl analogue. The corresponding impact on Cat S potency

N. Moss et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7189–7193
7191
Table 2
Table 4
Effect of substitutions adjacent to nitrile (P1 position)
P2 SAR–impact on potency and stability in human liver microsomes
S
N
S
N
N
N
H
N
H
N
H
N
R
N
CN
H
O
O
R
Compound
R
Cat S IC50 (nM)
Half-life human liver
microsomes (min)
Compound
R
Cat S IC50
(nM)
Cat L IC50
(nM)
Antigen Challenge
IC50 (nM)
15
2.3
19
6
9
>20,000
30
18
19
27
40
81
CN
760
8
9
0.3
0.5
600
24
13
CN
CN
20
13
26
18,000
F
F
10
11
12
0.1
0.1
1
400
3
21
22
72
10
52
CN
CN
1000
11
20
1500
>20,000
CN
13
0.7
9300
6
23
93
68
CN
See note from Table 1.
Cl
24
25
3200
93
13
Table 3
Impact of P2 methyls on selectivity
O
>90
S
N
N
H
N
R1
R2
N
R
26
27
310
400
>90
>90
H
O
O
O
S
Compound
R
R1
R2
Cat S IC50 (nM)
0.7
Cat L IC50 (nM)
9000
13
CH3
CH3
28
4000
78
CN
CN
O
O
14
CH3
H
1.1
1300
O
O
29
30
>20,000
8000
>90
60
S
15
10
16
17
H
H
2.3
0.1
0.6
0.6
500
400
130
50
O
O
S
CN
CN
CN
CN
See note from Table 1.
CH3
CH3
H
CH3
H
15 with lipophilic analogues 18–24 shows the cyclohexyl group of
15 to provide the best potency. Of particular note, the cyclo-
hexylmethyl group in 21 is 30-fold less potent than the cyclohexyl.
This is in contrast to the peptidic Cat S inhibitors represented by
compounds 1–3 where a cyclohexylmethyl group is 15-fold more
potent than the a cyclohexyl.17 Although the cyclohexyl group ap-
pears to be the best for Cat S inhibition, compound 15 and related
analogues in Tables 1–3 all have relatively short half-lives in
human liver microsomes. Consequently, in an effort to reduce lipo-
philicity, we probed the tolerance of polar functionality in the P2
pocket, as previously demonstrated by the sulfone functionality
in compounds 4 and 5.14,18 Unfortunately, both ether (25–27)
and sulfone modifications (28–30) resulted in inhibitors with
H
See note from Table 1.
appears to be less, but this could be influenced by the Cat S assay
sensitivity.
We further probed the structural requirements for potency at
the P2 position using compound 15 as a frame of reference
(selected R groups shown in Table 4).16 A comparison of compound

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N. Moss et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7189–7193
Table 5
Table 6
P3 SAR–examples with Cat S potency 610 nM and greater stability in human liver
microsomes versus compounds 15 or 34
Effect of P3 carbonyl on molecular and cell potency
N
N
H
N
R1
N
N
N
R
H
N
H
N
X
CN
R
CN
O
Compound
R
X
R1
Cat S IC50
(nM)
Antigen Challenge
IC50 (nM)
Compound
R
Cat S IC50
(nM)
Half-life human liver
microsomes (min)
S
14
42
43
15
44
45
CH3 1.1
CH3 28
CH3 34
23
2
S
O
15
31
2.3
4.2
19
S
O
N
H
H
H
54
4
H
32
33
4.6
1.0
>90
S
S
O
H
H
H
2.3
17
39
110
S
O
60
107
206
H
H
H
H
34
35
1.8
8.8
20
>90
N
See note from Table 1.
N
36
2.2
48
to have greater stability in human liver microsomes. One intriguing
exception is compound 33 which has one of the most potent P3
substituents and has reasonable microsomal stability despite
greater lipophilicity. All the top examples contain a five membered
aromatic heterocycle, a substituted phenyl20 or a morpholine.
These groups are all precedented favored P3 substituents in pep-
tide based Cat S inhibitors. Thus unlike the SAR at the P2 position,
the SAR at the P3 position seems more consistent across the three
inhibitor classes mentioned in this paper.
H
N
37
38
39
0.5
3.1
3.5
>90
82
O
H
N
O
H
N
S
>90
Our original intention at the start of this work was to focus on
non-basic cathepsin S inhibitors. Nevertheless removing the P2
amide carbonyl to provide analogues with a weakly basic amine
provided an interesting example of how a basic amine can impact
potency in a Cat S dependent cell assay (Table 6). A comparison of
compound 14 and 42 revealed that while replacing the carbonyl in
14 with a methylene lowered molecular potency approximately
25-fold, it increased cell potency 10-fold. Similar data was gener-
ated for the phenyl analog 43. Interestingly, the impact of remov-
ing the carbonyl of amide 15 to amine 44 was more muted; a trend
also consistent with the corresponding phenyl analogue 45. We
speculate that the relative cell potency of the amine analogues
compared to their amide counterparts is a consequence of lyso-
O
O
O
40
41
10
>90
69
H2N
O
5.2
N
See note from Table 1.
substantially reduced Cat S potency, though molecular modeling
overlap of compounds 4 and 5 with triazoles 28–30 placed the sul-
fone in a similar region of the P2 pocket. Evidently, the subtle dif-
ferences in binding conformations between the peptidic, Merck
and triazole series result in distinct SAR in the P2 pocket for each
series. Nevertheless, the change in physicochemical properties
from compound 15 to compounds 25–27 did result in better stabil-
ity in human liver microsomes.19 This increased stability translated
into better rat pharmacokinetics for compound 27 compared to
compound 15 (27: clearance 36% QH (25 mL/min/kg), BA 62%, oral
Cmax 5200 nM (10 mg/kg dose): 15: clearance 69% QH (48 mL/
min/kg), BA 11%, and oral Cmax 200 nM).
somal accumulation. However, it is unclear why the
compounds 42 and 43 provide a disproportionately greater in-
crease in cell potency than the -hydrogen analogues 44 and 45.
a-methyl
a
Synthesis of most of the compounds in Tables 2–6 was accom-
plished via the following schemes (Scheme 1 and 2) based on
chemistry previously published by Ellman.16 Synthetic schemes
for compounds 11, 22, 23, 29 and 30 are provided as Supplemen-
tary data. Compound 28 was prepared by oxidation of the corre-
sponding sulfide (same as for 29), which was prepared according
synthetic route outlined in Scheme 1.
Compound 15 was also selected as a convenient frame of refer-
ence for SAR at the left hand side (P3 position, Table 5). We hoped
that this position would be more fruitful than the P2 position in
identifying modifications that improved microsomal stability
while at least maintaining Cat S potency. The compounds shown
in Table 5 returned Cat S IC50s at or below 10 nM (a full range of
substituents is provided as supplementary data). Consistent with
the results from Table 4, modifications that introduce polarity tend
The SAR presented in Tables 2–6 expand the understanding of
triazole-based Cat S inhibitors, and show they have the potential
to fulfill a defined set of criteria for cathepsin inhibitors. These
compounds contain a mildly electrophilic nitrile warhead, they
achieve good cell potency without the need for a basic amine, they
can achieve good selectivity over cathepsin L, and they can provide
adequate PK through the addition of appropriately positioned polar
functionality. Our investigation of this class of Cat S inhibitors

N. Moss et al. / Bioorg. Med. Chem. Lett. 22 (2012) 7189–7193
7193
Supplementary data
O
O
R
O
S
S
Si
S
N
O
R'
b
a
R'
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.bmcl.2012.09.
054.
+
HN
R'
NH2
R
R
c
O
S
S
References and notes
H
N
R'
R'
R'
e
d
H2N
HN
1. Gregersen, P. K. Lab. Invest. 1989, 61, 5.
2. Sercarz, E.; Marerakis, E. Nat. Rev. Immunol. 2003, 3, 621.
O
R
R
R
3. For a general review of Cat S as a therapeutic taget see Gupta, S.; Singh, RK;
Dastidar, S.; Ray, A. Exp. Opin. Ther. Targets 2008, 12, 291.
4. Hou, W.-S.; Li, W.; Keyszer, G.; Weber, E.; Levy, R.; Klein, M. J.; Gravallese, E. M.;
Goldring, S. R.; Bromme, D. Arthritis Rheum. 2002, 46, 663.
5. Sukhova, G. K.; Zhang, Y.; Pan, J.-H.; Wada, Y.; Yamamoto, T.; Naito, M.;
Kodama, T.; Tsimikas, S.; Witztum, J. L.; Lu, M. L.; Sakara, Y.; Chin, M. T.; Libby,
P.; Shi, G.-P. J. Clin. Invest. 2003, 111, 897.
6. Faure-André, G.; Vargas, P.; Yuseff, M.-I.; Heuzé, M.; Diaz, J.; Lankar, D.; Steri,
V.; Manry, J.; Hugues, S.; Vascotto, F.; Boulanger, J.; Raposo, G.; Bono, M.-R.;
Rosemblatt, M.; Piel, M.; Lennon-Duménil, A.-M. Science 2008, 322, 1705.
7. For reviews on cathepsin inhibitor classes see: (a) Lee-Dutra, A.; Wiener, D. K.;
Sun, S. Expert Opin. Ther. Patents 2011, 21, 311; (b) Wiener, J. M.; Sun, S.;
Thurmond, R. L. Curr. Top. Med. Chem. 2010, 10, 717; (c) Link, J. O.; Zipfel, S. Curr.
Opin. Drug Discov. Dev. 2006, 9, 471; (d) Thurmond, R. L.; Sun, S.; Karlsson, L.;
Edwards, J. P. Curr. Opin. Invest. Drugs 2005, 6, 473; (e) Leroy, V.; Thurairatnam,
S. Expert Opin. Ther. Patents 2004, 14, 301.
8. Gauthier, J. Y.; Chauret, N.; Cromlish, W.; Desmarais, S.; Duong, L. T.;
Falgueyret, J. P.; Kimmel, D. B.; Lamontagne, S.; Léger, S.; LeRiche, T.; Li, C. S.;
Massé, F.; McKay, D. J.; Nicoll-Griffith, D. A.; Oballa, R. M.; Palmer, J. T.; Percival,
M. D.; Riendeau, D.; Robichaud, J.; Rodan, G. A.; Rodan, S. B.; Seto, C.; Thérien,
M.; Truong, V. L.; Venuti, M. C.; Wesolowski, G.; Young, R. N.; Zamboni, R.;
Black, W. C. Bioorg. Med. Chem. Lett. 2008, 18, 923.
X
f, g, h
Y
f, d
or Y f, h
R'"
N
R'"
N
R"
N
for A: e, h
for B: i-l
N
R"
m, h
H
N
R'
R
N
R'
R
N
Ar
41
H2N
CN
O
O
H2N
A: Ar = 3-thiophenyl
B: Ar = aryl groups in Table 5
R'" R"
N3
R'" R"
H2N
R'" R"
H2N
R'" R"
N3
g
n
j
n
OH
OH
NH2
NH2
O
O
O
O
Y
X
Scheme 1. General synthetic scheme for compounds in Tables 2–5.Reagents and
conditions: (a) Ti(OEt)4 or Ti(O-i-Pr)4, THF, reflux; (b) AlMe3, trimethylsilylacetylene
BuLi or i-PrMgCl, ꢀ78 °C to rt; (c) TBAF, THF, rt; or 4 N NaOH, MeOH, rt; (d) HCl,
MeOH, rt; (e) 3-thiophenecarboxylic acid, HATU, Et3N, rt; or 3-thiophenecarbonyl
chloride, Et3N, THF, rt; (f) Cu2SO4, sodium ascorbate, BuOH/water (1:1), rt,
overnight; or CuI, i-Pr2NEt, THF, rt; (g) Boc2O, pyridine, (NH4)HCO3, MeCN, rt; (h)
cyanuric chloride, DMF, 0 °C to rt; or TFAA, pyridine, rt; (i) Boc2O, TEA, DCM, rt; (j)
cyanuric chloride, DMF, 0 °C to rt; (k) 4 N HCl, dioxane, rt; (l) ArCOOH, HATU, Et3N,
rt; (m) triphosgene, i-Pr2NEt, CH2Cl2, then morpholine, rt; (n) Tf2O, NaN3, CuSO4,
K2CO3, H2O, MeOH, CH2Cl2.
9. Cai, J.; Baugh, M.; Black, D.; Long, C.; Bennett, J.; Dempster, M.; Fradera, X.;
Gillespie, J.; Andrews, F.; Boucharens, S.; Bruin, J.; Cameron, K. S.; Cumming, I.;
Hamilton, W.; Jones, P. S.; Kaptein, A.; Kinghorn, E.; Maidment, M.; Martin, I.;
Mitchell, A.; Rankovic, Z.; Robinson, J.; Scullion, P.; Uitdehaag, J. C. M.; Vink, P.;
Westwood, P.; Van Zeeland, M.; Van Berkom, L.; Bastiani, M.; Meulemans, T.
Bioorg. Med. Chem. Lett. 2010, 20, 4350.
10. Oballa, R. M.; Truchon, J.-F.; Bayly, C. I.; Chauet, N.; Day, S.; Crane, S.;
Berthelette, C. Bioorg. Med. Chem. Lett. 2007, 17, 998.
R'
N
N
11. (a) Falgueyret, J.-P.; Desmarais, S.; Oballa, R.; Black, W. C.; Cromlish, W.;
Khougaz, K.; Lamontagne, S.; Masse, F.; Riendeau, D.; Toulmond, S.; Percival, M.
D. J. Med. Chem. 2005, 48, 7535; For a discussion of basic nitrogen pKa,
lysosomotropism, and undesired tissue accumulation, see (b) Arbuckle, W.;
Baugh, M.; Belshaw, S.; Bennett, D. J.; Bruin, J.; Cai, J.; Cameron, K. S.; Claxton,
C.; Dempster, M.; Everett, K.; Fradera, X.; Hamilton, W.; Jones, P. S.; Kinghorn,
E.; Long, C.; Martin, I.; Robinson, J.; Westwood, P. Bioorg. Med. Chem. Lett. 2011,
21, 932.
12. Unpublished results. Related compounds found in Bekkali, Y.; Thomson, D. S.;
Betageri, R.; Emmanuel, M. J.; Hao, M.-H.; Hickey, E.; Liu, W.; Patel, U.; Ward, Y.
D.; Young, E. R. R.; Nelson, R.; Kukulka, A.; Brown, M. L.; Crane, K.; White, D.;
Freeman, D. M.; Labadia, M. E.; Wildeson, J.; Spero, D. M. Bioorg. Med. Chem.
Lett. 2007, 17, 2465.
H2N
H
N
HN
N
R'
c, d
a, b
N
NH2
R'
N3
O
Y
N
N
N
N
H
N
H
N
H
N
e, f, d, g
H2N
NH2
O
N
13. Assay protocols are provided in Supplementary data.
14. Gauthier, J. Y.; Black, W. C.; Courchesne, I.; Cromlish, W.; Desmarais, S.; Houle,
R.; Lamontagne, S.; Li, C. S.; Masse, F.; McKay, D. J.; Ouellet, M.; Robichaud, J.;
Truchon, J.-F.; Truong, V.-L.; Wang, Q.; Percival, M. D. Bioorg. Med. Chem. Lett.
2007, 17, 4929.
15. Patterson, A. W.; Wood, W. J. L.; Hornsby, M.; Lesley, S.; Spraggon, G.; Ellman, J.
A. J. Med. Chem. 2006, 49, 6298.
16. Though Compound 15 was not the most selective frame of reference, its
relative ease of synthesis allowed a more rapid assessment of SAR at the P2
position.
Scheme 2. General synthetic scheme for compounds in Table 6.Reagents and
conditions: (a) 1 N NaOH (1 equiv), R0CHO, toluene, rt, 16 h; (b) NaBH4, MeOH, 0 °C,
2 h; (c) Y, Cu2SO4, sodium ascorbate, t-BuOH/water (1:1), rt, overnight; (d) cyanuric
chloride, DMF, 0 °C to rt; (e) R0CHO, NaOAc, HOAc, then NaB(OAc)3H, ClCH2CH2Cl, rt;
(f) Boc2O, TEA, DCM, rt; (g) 4 N HCl in dioxane, DCM, rt.
17. Ward, Y. D.; Thomson, D. S.; Frye, L. L.; Cywin, C. L.; Morwick, T.; Emmanuel, M.
J.; Zindell, R.; McNeil, D.; Bekkali, Y.; Girardot, M.; Hrapchak, M.; DeTuri, M.;
Crane, K.; White, D.; Pav, S.; Wang, Y.; Hao, M.-H.; Grygon, C. A.; Labadia, M. E.;
Freeman, D. M.; Davidson, W.; Hopkins, J. L.; Brown, M. L.; Spero, D. M. J. Med.
Chem. 2002, 45, 5471.
18. The importance of a sulfone for good PK is also shown for Cat K inhibitors: Li, C.
S.; Deschenes, D.; Desmarais, S.; Falgueyret, J.-P.; Gauthier, J. Y.; Kimmel, D. B.;
Leger, S.; Masse, F.; McGrath, M. E.; McKay, D. J.; Percival, M. D.; Riendeau, D.;
Rodan, S. B.; Therien, M.; Truong, V. L.; Wesolowski, G.; Zamboni, R.; Black, W.
C. Bioorg. Med. Chem. Lett. 1985, 2006, 16.
19. These modifications also could impact the rate of metabolism by directly
blocking a metabolic site. However, the relatively fast rate of metabolism of
compound 20 compared to 27 did not support this.
20. Ayesa, S.; Lindquist, C.; Agback, T.; Benkenstock, K.; Classon, B.; Henderson, I.;
Hewitt, E.; Jansson, K.; Kallin, A.; Sheppard, D.; Samuelsson, B. Bioorg. Med.
Chem. 2009, 17, 1307.
revealed that (1) Cat S and antigen challenge cell assay potency can
be improved by modifications adjacent to the nitrile (can impact
selectivity), (2) the two methyl groups at the P2 position contrib-
ute significantly to Cat L selectivity, (3) SAR at the P2 position is
distinct from structurally related classes of Cat S inhibitors, (4)
the introduction of polar functionality into the inhibitor is neces-
sary to achieve good stability in human liver microsomes and con-
sequently useful rat PK, and 5) removal of the P2 carbonyl can have
a dramatic effect on cell potency especially in the presence of an
adjacent P2 a-methyl. It remains to investigate what combinations
of the above findings lead to the best balance of cell potency,
selectivity and PK.