Novel thiol-based TACE inhibitors: Rational design, synthesis, and SAR of thiol-containing aryl sulfonamides

Article abstract of DOI:10.1016/j.bmcl.2007.01.064

A series of potent thiol-containing aryl sulfonamide TACE inhibitors was designed and synthesized. The SAR and MMP selectivity of the series were investigated. In particular, compound 4b has shown excellent in vitro potency against the isolated TACE enzym

Full text of DOI:10.1016/j.bmcl.2007.01.064

Bioorganic & Medicinal Chemistry Letters 17 (2007) 2250–2253
Novel thiol-based TACE inhibitors: Rational design, synthesis,
and SAR of thiol-containing aryl sulfonamides
B. Govinda Rao,* Upul K. Bandarage,* Tiansheng Wang, Jon H. Come,
Emanuele Perola, Yunyi Wei, Shi-Kai Tian and Jeffrey O. Saunders
Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, MA 02139, USA
Received 4 December 2006; revised 18 January 2007; accepted 19 January 2007
Available online 26 January 2007
Abstract—A series of potent thiol-containing aryl sulfonamide TACE inhibitors was designed and synthesized. The SAR and MMP
selectivity of the series were investigated. In particular, compound 4b has shown excellent in vitro potency against the isolated TACE
enzyme and good selectivity over MMP-2, -7, -8, -9, and -13. The X-ray structure of 4b bound to TACE was obtained.
Ó 2007 Elsevier Ltd. All rights reserved.
Inhibition of TACE (TNF-a converting enzyme) is con-
sidered an attractive mechanism to control the release of
TNF-a (tumor necrosis factor-a) and a viable therapy
for the treatment of rheumatoid arthritis and Crohn’s
disease, as these illnesses are caused by overexpression
of TNF-a, a pro-inflammatory cytokine.1 The active site
domain of TACE is homologous to matrix metallopro-
teinases (MMPs).2 A large number of MMP inhibitors
have been reported over the years and some were tested
in clinical trials.3 Not surprisingly, many of these MMP
inhibitors are also found to be good inhibitors of TACE.
The structural similarity between the active sites of var-
ious MMPs and TACE offered a big challenge for the
design of specific inhibitors. One major approach used
to overcome this challenge was to exploit the differences
in the primary and secondary structures of the active site
loops of MMPs and TACE that form the S10 pocket. In
particular, the narrow channel between the S10 and S30
pockets offers an avenue to build selectivity over other
MMPs.4,5 Another approach used successfully for
designing selective MMP inhibitors,3 but seldom applied
to design specific TACE inhibitors, is to use non-
hydroxamate zinc-binding groups (ZBGs) such as a thi-
ol.6 In this investigation, we have applied a combination
of these two approaches to design specific TACE inhib-
itors with novel scaffolds designed using the TACE crys-
tal structure.
Compound 1 (Ki = 10 nM) is a potent and modestly spe-
cific inhibitor of TACE.4 It has a hydroxamate as the
zinc-binding group and a sulfonamide scaffold that
directs the phenyl ring into the S10 pocket. The specificity
of the inhibitor is imparted by the butynyloxy tail of the
inhibitor that reaches into the S30 pocket from the S10
pocket via a narrow channel observed only in the crystal
structure of TACE (PDB code: 1BKC2) (Fig. 1). We were
interested in exploring non-hydroxamates as ZBGs for
our initial studies because hydroxamic acids are often
poorly absorbed in vivo and hence carry metabolic
liabilities.7 It is also known that inhibitors with thiol as
the ZBG group (e.g., compound 2) offer an advantage in
imparting specificity in inhibition of MMPs.6,8 Hybrids
of compounds 1 and 2 led to the synthesis of compound
3. Modeling of these compounds in the active site of
TACE suggested that the two methyl substituents of
compound 3 might be connected to form a ring to produce
compound 4b without losing the potency. A crystal
structure of compound 4b bound to the active site of the
TACE enzyme was obtained to guide structure-based
optimization of these novel thiol-based inhibitors.
The general synthesis of sulfonamide-thiols is shown in
Scheme 1. Sulfonylation of various cyclic 3-hydroxy sec-
ondary amines 5 (n = 1, 2, and 3) with 4-buty-
6 in THF gave
sulfonamides 7 in good yield. These sulfonamides 7 were
then subjected to standard Mitsunobu conditions to
Keywords: TACE inhibitors; MMP selectivity; Rheumatoid arthritis;
Hydroxamates; Thiols.
nyloxybenzenesulfonyl chloride9
*
Corresponding authors. Tel.: +1 617 444 6334 (B.G.R); tel.: +1 617
444 6882; fax: +1 617 444 7827 (U.K.B); e-mail addresses:
govinda_rao@vrtx.com; upul_bandarage@vrtx.com
0960-894X/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2007.01.064

B. Govinda Rao et al. / Bioorg. Med. Chem. Lett. 17 (2007) 2250–2253
2251
O
O
O
O
H
N
S
HS
S
HO
N
N
O
O
O
2 (
Ki= 56 nm)
1 (Ki= 10 nm)
O O
S
N
O
O
HS
S
N
HS
O
O
4b (Ki = 28 nm)
3 (Ki = 27 nm)
Figure 1. TACE inhibitors bearing butynyloxy group.
OH
Mannich condensation of 10 with a mixture of parafor-
maldehyde and piperidine or N-methyl piperazine in the
presence of CuSO4 afforded 11a or 11b in good to mod-
erate yield. Compound 11a or 11b was then converted to
target thiol 12a or 12b as described in Scheme 1.
Cl
S
OH
(C)n
O
O
N
S
a
+
(C)n
O
O
N
H
O
Syntheses of the butynylamine tail containing sulfon-
amide-thiols 16 are shown in Scheme 3. Sulfonylation
of 5 with commercially available sulfonyl chloride 13
followed by protection of hydroxyl group with TBSCl
afforded 14 in good yield. Alkylation of 14 with 1-bro-
mo-2-butyne gave 15 in moderate yield. Removal of
the TBS group of 15 followed by Mitsunobu reaction
and subsequent hydrolysis afforded desired thiols 16.
5
n= 1,2,3
O
6
7
O
S
SH
As shown in Table 1, the azetidine thiols 4a, 16a turned
out to be very potent TACE inhibitors (entries 1 and 7),
while solubilizing group containing thiols 12a and 12b
were the least potent compounds in this set (entries 5
and 6). Changing the stereochemistry from R to S did
not improve TACE potency in the five-membered-series
(entries 2 and 3). Replacement of the ether oxygen of the
butynyloxy tail with NH did not produce a significant
change in TACE potency in the four-membered-series
(azetidine series) (entries 1 and 7). On the other hand,
similar changes in the five-membered-series (pyrrolidine
series) increased the TACE potency by 5-fold (entries 2
and 8). Increasing the ring size from five to six did not
improve the TACE affinity (entry 4). Introduction of
basic amine-containing tails diminished the TACE
potency. The compound with a piperidine-containing
tail 12a was approximately 20-fold less potent than 4b,
while the N-methylpiperazine-containing compound
12b was approximately 120-fold less potent than 4b
(entries 2, 5, and 6). This observation suggests that the
large cyclic basic amine moieties are not well tolerated
in the S30 pocket despite the fact these analogs were
designed based on the X-ray crystal structure of 4b.
(C)n
O
(C)n
b
c
N
S
N
S
O
O
O
O
O
4
8
Scheme 1. Reagents: (a) Et3N, THF/H2O, 88–92%; (b) Ph3P, DEAD,
CH3COSH, THF 76–82%; (c) i—10% NaOCH3, MeOH, ii—10% HCl
95–98%.
obtain thioacetates 8 in good yield. Hydrolysis of thi-
oacetates 8 with aqueous sodium methoxide followed
by acidification afforded the desired thiols 4 in high
yields.
Synthesis of thiols containing solubilizing groups is
shown in Scheme 2. The reaction of 4-benzyloxyben-
zene-1-sulfonyl chloride10 with (R)-pyrrolidin-3-ol fol-
lowed by debenzylation of the resulting benzyloxy
intermediate gave compound 9 in high yield. Compound
9 was alkylated with propargyl bromide in the presence
of K2CO3 in DMF at 60 °C to give 10 also in high yield.
An X-ray crystal structure has been obtained for 4b
bound to the active site of TACE (Fig. 2).11 In this struc-
ture, the thiol group of the inhibitor makes a strong
interaction with the active site Zn2+ ion providing the

2252
B. Govinda Rao et al. / Bioorg. Med. Chem. Lett. 17 (2007) 2250–2253
HO
HO
HO
N
S
N
S
c
a, b
O
O
O
O
N
H
(R) -pyrrolidin-3-ol
H
O
OH
9
10
HS
HO
N
N
S
e,f
d
S
O
O
O
O
N
N
O
O
X
X
11a X = C
11b X = NMe
12a X = C
12b X = NMe
Scheme 2. Reagents and conditions: (a) 4-benzyloxybenzene-1-sulfonyl chloride, Et3N, THF/H2O, 91%; (b) 10% Pd/C, H2, MeOH /EtOAC, 99%; (c)
K2CO3, 3-bromoprop-1-yne, DMF, 60 °C, 82%; (d) HCHO, CuSO4, piperidine, 85 °C, 11a 78%, 11b 62%; (e) Ph3P, DEAD, CH3COSH, THF 88%
and 36%; (f) i—10% NaOCH3, MeOH, ii—10% HCl, 12a 94%, 12b 92%.
Table 1. In vitro potency of thiol–arylsulfonamide series
OTBS
Cl
O O
S
OH
(C)n
N
H
5
(C)n
O
O
O
R
N
S
Y
S N
SH
a, b
+
(C)n
O
O
Entry Compound
n
Y
R
TACE Ki (nM)
NH
1
2
3
4
4a
1
2
2
3
O
O
O
O
CH3
CH3
CH3
CH3
13
28
33
55
O
13
4b (3R)
4c (3S)
4d (racemic)
NH
n = 1, 2
14
5
6
12a (3R)
12b (3R)
2
2
O
O
530
OTBS
SH
3400
(C)n
N
(C)n
O
7
8
16a
16b (3R)
1
2
NH CH3
NH CH3
11
5
N
S
c
S
d,e,f
O
O
O
O
stacks against the His-405 side chain and is surrounded
by other hydrophobic side chains of the S10 pocket. The
butynyloxy tail bends into a narrow channel connecting
the S10 and S30 pockets. A similar binding mode was ob-
served recently for a different class of TACE inhibi-
tors.12 The crystal structure suggests that the tail can
be extended with bigger groups to fill the S30 pocket,
and gain potency.
N
HN
16
15
Scheme 3. Reagents: (a) Et3N, THF/H2O, 88–92%; (b) TBSCI,
imidazole, CH2Cl2, 93%; (c) NAH, CH3CH„CHCH2Br, DMF, 76–
83%; (d) TBAF, THF, 100%; (e) Ph3P, DEAD, CH3COSH, THF, 76–
88%; (f) 4 N HCl in dioxane, 90–96%.
We tested a few of the potent TACE inhibitors against a
set of closely related MMPs (MMP-2, -7, -8, -9, and -13)
and found them to be selective (Table 2). Compounds 2,
4b, and 4d are more selective than compound 1 (with
hydroxamate as ZBG). To understand this selectivity,
we overlaid the crystal structure of TACE:4b complex
with the crystal structures of the five MMPs. As stated
fourth ligand of the tetrahedral coordination in addition
to the three histidine side chains (His-405, His-409, and
His-415). The only other observed specific interaction is
the hydrogen bond between the sulfonamide oxygen of
the inhibitor and the NH of Gly-349. The phenyl ring

B. Govinda Rao et al. / Bioorg. Med. Chem. Lett. 17 (2007) 2250–2253
2253
enzyme. One of the potent TACE compounds, 4b pos-
sesses 200-fold selectivity over MMP-2 and MMP-7 as
well as 40-fold selectivity over MMP-8 and MMP-13.
Discovery of this novel class of TACE inhibitors offers
a therapeutic potential for the treatment of rheumatoid
arthritis and Crohn’s disease.
Acknowledgments
We thank Joe Drumm and Dr. Robert Davies at Vertex
Pharmaceuticals for useful comments and suggestions.
References and notes
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March, C. J.; Paxton, R. J.; Black, R. A.; Bode, W. Proc.
Natl. Acad. Sci. U.S.A 1998, 95, 3408.
Figure 2. Crystal structure of compound 4b bound to TACE. The Zn
atom is shown as a light blue sphere. The three His side chains
coordinating the Zn shown as sticks along with the inhibitor (color
coded: C, purple; O, red; N, blue; and S, yellow). The thiol sulfur is at a
2+
˚
distance of 2.2 A from the Zn ion.
Table 2. Selectivity profile of selected compounds
3. Rao, B. G. Curr. Pharm. Des. 2005, 11, 295.
4. Levin, J. I.; Chen, J. M.; Cheung, K.; Cole, D.; Crago, C.;
Santos, E. D.; Du, X.; Khafizova, G.; MacEwan, G.; Niu,
C.; Salaski, E. J.; Zask, A.; Cummons, T.; Sung, A.; Xu,
J.; Zhang, Y.; Xu, W.; Ayral-Kaloustian, S.; Jin, G.;
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Skotnicki, J. S. Bioorg. Med. Chem. Lett. 2003, 13, 2799.
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Compound
Ki (nM)
TACE MMP-2 MMP-7 MMP-8 MMP-9 MMP-13
1
10
52
28
55
27
3400
43
800
200
200
90
17
2000
1200
700
2
5700 33000 1300
5000 >6000 1900
4b
4d
>3000 >3000
800
earlier, the butynyloxy group of 4b occupies a channel-
like space between the S10 and S30 subsites in TACE.
This channel is blocked in these MMPs by a conserved
Tyr (Tyr-423 in MMP-9) present in all MMPs at the
beginning of the S10 specificity loop.3 The same residue
in TACE is Ala-439. Therefore, it is not surprising that
compound 4b is less potent against these MMPs. It is
very likely that the butynyloxy group swings away to
occupy a different part of the S10 subsite in MMPs as
observed by NMR for a similar inhibitor with butynyl-
oxy tail.13 The differences in the shape and size of this
part of the pocket may be responsible for reduced selec-
tivity of 4b against MMP-9.
9. Levin, J. I.; Chen, J. M.; Cheung, K.; Cole, D.; Crago, C.;
Santos, E. D.; Du, X.; Khafizova, G.; MacEwan, G.; Niu,
C. Bioorg. Med. Chem. Lett. 2003, 13, 2799.
10. Brinner, K. M.; Kim, J. M.; Habashita, H.; Gluzman, I.
Y.; Goldberg, D. E.; Ellman, J. A. Bioorg. Med. Chem.
2002, 10, 3649.
11. PDB Deposition No: 2OI0.
12. Niu, X.; Umland, S.; Ingram, R.; Beyer, B. M.; Liu, Y.-H.;
Sun, J.; Lundell, D.; Orth, P. Arch. Biochem. Biophys.
2006, 451, 43.
13. Moy, F. J.; Chanda, P. K.; Chen, J.; Cosmi, S.; Edris, W.;
Levin, J. I.; Rush, T. S.; Wilhelm, J.; Powers, R. J. Am.
Chem. Soc. 2002, 124, 12658.
In summary, we have designed and synthesized a novel
series of thiol-containing aryl sulfonamides as inhibitors
of TACE. Most of these compounds show very potent
inhibition in an enzyme assay using the isolated TACE