Novel, sulfonamide linked inhibitors of the hepatitis C virus NS3 protease

Article abstract of DOI:10.1016/j.bmcl.2013.12.060

A sulfonamide replacement of the P2-P3 amide bond in the context of macrocyclic HCV NS3 protease inhibitors was investigated. These analogs displayed good inhibitory potency in the absence of any P3 capping group. The synthesis and preliminary SAR are des

Full text of DOI:10.1016/j.bmcl.2013.12.060

Bioorganic & Medicinal Chemistry Letters 24 (2014) 969–972
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Novel, sulfonamide linked inhibitors of the hepatitis C virus NS3
protease
a
b
b
b
Thorsten A. Kirschberg a, , Neil H. Squires , Huiling Yang , Amoreena C. Corsa , Yang Tian ,
⇑
Neeraj Tirunagari b, X. Christopher Sheng a, Choung U. Kim a,c
a Gilead Sciences, Inc., Department of Medicinal Chemistry, 333 Lakeside Dr, Foster City, CA 94404, USA
b Gilead Sciences, Inc., Department of Biology, 333 Lakeside Dr, Foster City, CA 94404, USA
c Kainos Medicine, Inc., 88, Olympic-ro 43-gil, Seoul 138-736, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history:
A sulfonamide replacement of the P2–P3 amide bond in the context of macrocyclic HCV NS3 protease
inhibitors was investigated. These analogs displayed good inhibitory potency in the absence of any P3
capping group. The synthesis and preliminary SAR are described.
Received 2 October 2013
Revised 13 December 2013
Accepted 16 December 2013
Available online 21 December 2013
Ó 2014 Elsevier Ltd. All rights reserved.
Keywords:
HCV
NS3 protease
Sulfonamide
The discovery and successful development of hepatitis C prote-
ase NS3/4a inhibitors has had major impact on the prospect of
achieving sustained virological responses in patients infected with
hepatitis C.1 Two alpha ketoamides, teleprevir and boceprevir, are
FDA approved and their clinical use has increased SVR rates to
approximately 70% in the genotype 1 infected patients when opti-
mally combined with pegylated interferon alpha and ribavirin.2
The class of non-covalent HCV-protease inhibitors is still an area
of active research and clinical development. Originally described
in 2003, it yielded the first clinical candidate ciluprevir (BI-
2061).3 Many variations of this highly valuable structure have
since been disclosed with improvements in potency, safety pro-
files, pharmacokinetic profiles, resistance profiles, and, most re-
180°. The introduction of a bulky P3-amide substituent further
selects one conformer over the other. When omitting the hydro-
phobic P3 capping group and hence the conformational bias to-
wards the bioactive conformation compounds are distinctly less
potent.8 It has been established that an acylsulfonamide modifica-
tion of the P1 carboxylate can effectively remedy this drop in po-
tency (Fig. 1).9
In an attempt to introduce alternative bioisosteric replacements
for the proline amide bond the sulfonamide group was investi-
gated and initial results are presented here. The geometry observed
around the nitrogen to sulfur bond in sulfonamides differs signifi-
cantly from that of carboxylic acid amides. In the Newman projec-
tion of the most commonly encountered rotamer, the free electron
cently, the targeting of genotype
3
more extensively.4 The
sustained interest in this inhibitor class can be attributed to the
dual mode of action of the NS3 protease; beyond viral polypeptide
processing it is also a key component of the virus’ ability to avoid
an interferon based innate immune response to infection.5
One area of these peptide derived molecules that has been
probed often is the connection from the proline nitrogen to a large
variety of structural elements (the P3 moieties). Amides, ureas, and
reverse amides from a cyclopentane dicarboxylic acid core have
successfully been explored.7 In addition, all macrocycles use this
site as the attachment point.6 For amides, there exists a strong con-
formational bias towards two rotamer structures separated by
⇑
Corresponding author. Tel.: +1 650 522 5133.
E-mail address: tkirschberg@gilead.com (T.A. Kirschberg).
Figure 1. HCV NS3/4a protease inhibitors. First clinical compound and analog with
P3 cap deletion and P1 acylsulfonamide.
0960-894X/$ - see front matter Ó 2014 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.12.060

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T. A. Kirschberg et al. / Bioorg. Med. Chem. Lett. 24 (2014) 969–972
S
O
N
O
N
BsO
O
BsO
O
a, b, c
H
N
H
N
d
O
O
O
N
H
N
S
O
N
S
O
O
O
O
O
O
3
4
5
S
S
O
N
O
O
N
N
N
O
O
g, h
O
e, f
O
O
S
H
H
N
N
H
N
OH
N
N
S
O
O
O
S
O
O
O
6
7
Scheme 1. Reagents and conditions: (a) Octenyl-SO2Cl, DIEA, THF, rt, 50%; (b) LiOH, THF, MeOH, H2O, rt, 93%; (c) vinyl cyclopropyl aminoacid methyl ester, HATU, DIEA, DCM/
DMF, 54%; (d) 2-isopropylthiazolyl-7-methoxy-8-methylquinolin-4-ol, Cs2CO3, NMP, 75 °C, 74%; (e) Hoveyda–Grubb’s catalyst G1, DCE, 70 °C, 60%; (f) = (b), 90%; (g) CDI, THF
70 °C, then cyclopropylsulfonamide, DBU, 65%; (h) TsNHNH2, NaOAc, DME/H2O, 95 °C, 62%.
TBSO
TBSO
TBSO
O
O
a, b, c
O
d, e
N
S
N
Boc
N
Boc
O
O
O
O
O
O
H
9
8
10
S
O
N
O
N
HO
O
O
OH
j, k
O
f, g, h, i
S
N
H
N
O
N
O
S
H
N
S
O
O
O
O
11
12
Scheme 2. Reagents and conditions: (a) DIBALH, THF, À78 °C, 78%; (b) (i) o-NO2PhSeCN, THF, (ii) P(nBu)3; (c) m-CPBA, DCM,À78 °C to rt, 96% over 2 steps; (d) ZnCl2, DCM, rt,
83%; (e) allyl-SO2Cl, DIEA, THF, rt, 36%; (f) Grubb’s catalyst G1, DCM, 45 °C, 57%; (g) H2, Pd/C, MeOH, 90%; (h) HCl, MeOH, rt, 98%; (i) LiOH, THF, MeOH, H2O, rt, 79%; (j)
4-chloro-2-isopropylthiazolyl-7-methoxy-8-methylquinoline, tBuOK, DMSO, 95 °C, 97%; (k) acylsulfonamido vinyl cyclopropyl aminoacid, HATU, DIEA, DCM/DMF, 47%.
pair on nitrogen bisects the two oxygen atoms displaying two
gauche interactions.10 A second, less frequently observed confor-
mation places one oxygen in the anti conformation with respect
to the nitrogen lone pair. The effect of the conformational bias on
the activity for a small set of HCV protease inhibitors was investi-
gated in this study. This change was assessed in the absence of P3
substituents that could introduce secondary binding events poten-
tially masking the primary effect of the replacement. In this con-
membered macrocyclic inhibitors (6, 7, 20). The required sulfonyl
chloride was prepared in high yield from -bromo-1-octene with
x
sodium sulfite and treatment of the resultant acid with phospho-
rylchloride. Reaction with proline derivative 3 gave sulfonamide
4 as the starting point for the synthesis of the macrocycle. Elabora-
tion used standard peptide chemistry and the well established bro-
sylate displacement under cesium carbonate conditions. The
crucial macrocyclization was achieved at 70 °C in DCE in good yield
following the procedure of Raboisson et al.6,8 Final installation of
the acyl-sulfonamide relied on CDI/DBU activated coupling to
cyclopropyl sulfonamide. An optional reduction of the double bond
was achieved cleanly using tosyl hydrazide at elevated tempera-
tures. The 14 membered macrocyclic structures (16, 17, 18) were
synthesized according to the same procedures with very compara-
ble chemical yields.
text
a study from Raboisson et al. was consulted, where
macrocyclic inhibitors without a P3 cap were discussed.8 Further-
more, the indolizidinone-based inhibitor core described recently
offered a second opportunity to investigate the replacement of
the amide group with a sulfonamide.11
The synthesis of the sulfonamide containing inhibitors is de-
picted in Schemes 1–3. Scheme 1 describes the synthesis of 15

T. A. Kirschberg et al. / Bioorg. Med. Chem. Lett. 24 (2014) 969–972
971
S
O
N
O
N
O
O
O
O
O
BsO
BsO
O
S
S
H
N
H
N
e, f, g
N
a, b, c, d
O
N
H
H
N
Boc
N
S
N
Boc
O
O
O
O
O
13
14
15
Scheme 3. Reagents and conditions: (a) LiOH, THF, MeOH, H2O, rt, 97%; (b) vinyl cyclopropyl aminoacid methyl ester, HATU, DIEA, DCM/DMF, 84%; (c) LiOH, THF, MeOH, H2O,
rt, 79%; (d) CDI, THF, 70 °C, then cyclopropylsulfonamide, DBU, 61%; (e) 2-isopropylthiazolyl-7-methoxy-8-methylquinolin-4-ol, Cs2CO3, NMP, 75 °C, 45%; (f) HCl dioxane, rt;
(g) allyl-SO2Cl, DIEA, THF, rt, 31%.
The synthesis of a second class of bicyclic inhibitors is depicted
in scheme 2 starting from known aldehyde 8.12 Conversion to the
vinyl group was achieved via reduction to the alcohol and intro-
duction of the phenyl seleno group. Oxidation at À78 °C and ther-
mal elimination upon warming to room temperature gave the
olefin in good and reproducible yield. Standard chemistry intro-
duced the allylsulfonamide and the ring closure was performed
using Grubb’s catalyst. Reduction of the double bond can be
achieved at this stage with hydrogen gas and Pd/C. The TBS and
methyl ester were removed and KOtBu mediated nucleophilic aro-
matic substitution installed the proline substituent. A HATU cou-
pling to the acyclsulfonamide containing vinyl cyclopropane
amino acid derivative concluded the synthesis.
The simple allyl-sulfonamides were prepared according to
scheme 3. The reaction with the allyl sulfonyl chloride in the final
step allowed for the straight-forward synthesis of the P1 reduced
analog of 15.
The compounds were tested for their inhibitory activity in bio-
chemical assays with the HCV protease NS3/4a as well as in the
replicon system. The results obtained with known proline amide
analogs are included for comparison and are shown in Table 1. Re-
sults for compounds 6 and 16 indicate that in this structural class
the lack of a P3 capping group is detrimental for potency. The
incorporation of an acylsulfonamide replacing the terminal carbox-
ylate at the P1 site is required to achieve meaningful potency. The
macrocyclic compounds 17 and 18 are the most potent inhibitors
with the sulfonamide linkage. In biochemical assays, all 4 analogs
inhibit the enzyme in the low nanomolar range. The proline amide
control compounds (19, 21) are slightly more potent. When tested
in the replicon system the differential activity became more pro-
nounced. While the amide analogs 19 and 21 are reported to have
an EC50 of 3.6 and 5.8 nM, respectively, all sulfonamide analogs
were at least 10 times less potent.8 Unexpectedly, the reduction
of the double bond had little effect on the potency of the com-
pound. This is different from the literature report for the respective
amides where activity decreased significantly.8 It is worth pointing
out that the current level of potency was achieved without any P3
capping group.
The cyclization of the sulfonamide substituent towards the C5
position of the proline ring yielded compound 12 with consider-
ably reduced biochemical inhibitory activity and consequently this
analog lacked useful replicon activity. No change was observed
when releasing the conformational restriction and testing a simpli-
fied allyl sulfonamide 15 (IC50: 438 nM). In line with the current
view of the P1 vinyl group, all residual activity is lost upon reduc-
tion of the vinyl group to an ethyl substituent in structures 12 and
15.
Table 1
IC50/EC50 results of different HCV protease inhibitors
The microsomally predicted clearance numbers for 17 and 19
were <0.17/<0.7 and <0.17/0.82 L/h/kg (h/r), respectively. Hence,
the sulfonamide linkage affected the metabolic profile of this
inhibitor pair only minimally.
Replacing the proline amide linkage with a sulfonamide is pos-
sible. Depending on the residual molecular architecture, moder-
ately potent inhibitors can be synthesized. This particular set of
analogs was also less sensitive to a reduction of the endocyclic
double bond as replicon activity was essentially not affected by
this modification.
S
S
O
N
O
O
N
O
N
N
O
O
H
N
H
N
R
R
N
X
N
X
O
O
A
A
n
a
b
Compd
X
n, A
R
IC50
(
lM)
EC50
>2.0
(
lM)
Acknowledgment
16
17
18
19
6
20
7
21
12
22
SO2
SO2
SO2
CO
SO2
SO2
SO2
CO
1, CH
1, CH
OH
0.747
NHSO2cPr
NHSO2cPr
NHSO2cPr
OH
NHSO2cPr
NHSO2cPr
NHSO2cPr
NHSO2cPr
NHSO2cPr
0.0029
0.0047
0.0004
0.712
0.079
0.089
0.004
>2.0
The authors thank Michael O. Clarke for insightful discussions.
References and notes
1, CH2
1, CH
2, CH
2, CH
2, CH2
2, CH
na
0.013
0.44
0.0074
0.0003
0.639
0.257
0.0058
>2.0
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