3-Hydroxyisoquinolines as inhibitors of HCV NS5b RNA-dependent RNA polymerase

Article abstract of DOI:10.1016/j.bmcl.2008.11.060

Isoquinoline-based non-nucleoside inhibitors of HCV NS5b RNA-dependent RNA-polymerase are described. The synthesis and structure-activity relationships are detailed, along with enzyme and cellular activity.

Full text of DOI:10.1016/j.bmcl.2008.11.060

Bioorganic & Medicinal Chemistry Letters 19 (2009) 410–414
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
3-Hydroxyisoquinolines as inhibitors of HCV NS5b RNA-dependent
RNA polymerase
a
a
a
a
a
Robert T. Hendricks b, , Stacey R. Spencer , James F. Blake , Jay B. Fell , John P. Fischer , Peter J. Stengel ,
Vincent J. P. Leveque b, Sophie LePogam b, Sonal Rajyaguru b, Isabel Najera b,
John A. Josey a, Steven Swallow b,
*
a Array BioPharma, Inc, 3200 Walnut Street, Boulder, CO 80301, USA
b Roche Palo Alto LLC, Medicinal Chemistry, 3431 Hillview Avenue, MS: R6E-3 (R6W-120B), Palo Alto, CA 94304, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Isoquinoline-based non-nucleoside inhibitors of HCV NS5b RNA-dependent RNA-polymerase are
Received 28 October 2008
Revised 13 November 2008
Accepted 17 November 2008
Available online 20 November 2008
described. The synthesis and structure–activity relationships are detailed, along with enzyme and cellular
activity.
Ó 2008 Elsevier Ltd. All rights reserved.
Keywords:
HCV
NS5b
rdrp
Gamess
Polymerase
Hepatitis
Inhibitor
Non-nucleoside
Palm
Isoquinoline
3-Hydroxyisoquinoline
Replicon
Dioxo-benzoisothiazole
Negishi
Suzuki
2-Aminobenzenesulfonamide
N-tert-Butyl-2-chlorobenzene-sulfonamide
3-Carbomethoxy-1,2,3,4-
tetrahydroisoquinoline-1,4-dione
Computational
Model
Conformation
Hepatitis C Virus (HCV) has become a major epidemic, infecting
nearly 200 million people worldwide. Infection with HCV can lead
to more serious liver diseases such as cirrhosis and hepatocellular
carcinoma.1 No vaccine is currently available for HCV and therapies
are limited. The current best treatment option consists of a combi-
The HCV genome encodes for a polypeptide which is processed
to produce both structural (C, E1, E2, and p7) and non-structural
(NS2, NS3, NS4a, NS4b, NS5a, and NS5b) proteins. The non-struc-
tural proteins are considered excellent targets for new, much-
needed HCV therapies. NS3 protease inhibitors have shown
efficacy in human HCV patients,2 and it is known that the NS5b
RNA-dependent RNA-polymerase (RdRp) plays a central role in
HCV virus replication.1 For that reason, an investigation into devel-
oping small molecule NS5b inhibitors was undertaken in our labs.
Hydroxyquinolone-thiadiazines 1 (Fig. 1) have been reported as
inhibitors of the NS5b polymerase and a crystal structure of 1a
bound to NS5b has been published.3 Docking comparisons made
nation of pegylated interferon-a-2a and ribavirin, however, this
therapy is only effective in about 50% of patients infected with
the most prevalent genotype of the virus, genotype 1.1
* Corresponding author. Tel.: +1 650 855 6486.
E-mail address: Than.Hendricks@Roche.com (R.T. Hendricks).
AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.11.060

R. T. Hendricks et al. / Bioorg. Med. Chem. Lett. 19 (2009) 410–414
411
Figure 1. Hydroxyquinolone compounds 1 and the isoquinoline compounds 2 and 3.
by placing the alternative 3-hydroxyisoquinoline scaffold 2 into
the NS5b binding site of 1 suggest that the isoquinoline ring sys-
tem should make similar favorable interactions in the binding site.
The synthesis of isoquinoline-thiadiazine 2a began with commer-
cially available 3-carbomethoxy-1,2,3,4-tetrahydroisoquinoline-1,4-
dione (Scheme 1). The dione was selectively mono-chlorinated
using phosphorous oxychloride4 and methylated to give 5 in good
yield. A Negishi coupling5 with isoamyl zinc bromide, followed by
hydrolysis, afforded acid 7. Coupling with 2-aminobenzenesulfona-
mide, removal of the methyl protecting group, and cyclization under
basic conditions (sealed tube) provided the desired compound 2a.
The corresponding benzyl analog 2b was prepared similarly.
The NS5b (GT-1b) inhibitory potency6 of the isoquinoline-thi-
scaffold was not ideal when compared with 1a (1.1
l
M). However,
we were encouraged that our first attempts at least showed mea-
surable activity. We hypothesized that the reduced NS5b potency
was likely due to a mismatch between the required binding confor-
mation and the ground-state conformation of the isoquinoline-thi-
adiazine combination. This was verified by computing the ‘bound’
and ‘unbound’ (i.e., lowest energy) structures of methyl-prototypes
1b and 2c via ab initio molecular orbital calculations at the
6-311++G(d,p)//6-311++G(d,p) level of theory with the GAMESS
program.7 The enolic anion form of each prototype was examined.
Compound 1b requires ca 1.56 kcal/mol to adopt the proper bound
conformation, while compound 2c requires ca 9.49 kcal/mol. The
favored thiadiazine ring tautomer is as shown in Figure 1. Delocal-
ization of the anion in 2c is less favored, leading to significant lone
adiazine analogs (2a: 51 lM, 2b: 47 lM) indicated this particular
Scheme 1. Synthesis of isoquinoline thiadiazine 2a.

412
R. T. Hendricks et al. / Bioorg. Med. Chem. Lett. 19 (2009) 410–414
Scheme 2. Synthesis of isoquinoline-dioxo-benzoisothiazole 3b.
pair repulsion in the bound conformation. The observed low en-
ergy conformation for 2c in the ‘unbound’ state results from a
180 degr rotation about the isoquinoline-thiadiazine linking bond.
Based on these observations the 5-membered dioxo-benzoiso-
thiazole ring was investigated in the isoquinoline series
(3; Fig. 1). The ab initio calculations for the prototype 3a found that
the predicted bound conformation was only ca. 0.57 kcal/mol
higher in energy relative to the lowest energy conformation.
Synthesis of dioxo-benzoisothiazole isoquinoline 3b is shown in
Scheme 2. Using the same acid intermediate 7 from Scheme 1,
Weinreb amide 10 was prepared and treated with the dianion8 of
N-tert-butylbenzenesulfonamide. This gave ketone 11 which
underwent a one-step deprotection/cyclization upon treatment
with boron trichloride to generate the dioxo-benzoisothiazole ring
system. Compounds 3c and 3d (Table 1) were prepared in an anal-
ogous fashion.
The initial dioxo-benzoisothiazole analogue 3b showed an NS5b
IC50 of 4.5 M, only 4-fold less potent than 1a (1.1 M). The cyclo-
propyl-ethyl side chain provided a modest improvement in the
enzyme potency (3c: 1.0 M) and was active in a cellular HCV
GT-1b replicon assay (2.7
M).6 The 4-fluorobenzyl substituent
showed similar enzyme potency (3d: 2.2 M), but more impor-
tantly showed improved cellular activity (0.44 M).
l
l
l
l
l
l
A model based on the X-ray structure9 of the NS5b polymerase
palm site region was used to further refine this series of inhibitors.
Examination of 3d in this model (Fig. 2) revealed a large pocket
containing several water molecules directly off the 7-position of
the dioxo-benzoisothiazole ring. Based on this observation a num-
ber of analogues substituted at C-7 were designed to probe this
area with the goal of either interacting with or displacing one or
more of the bound water molecules.
The synthesis of the C-7 substituted compounds is outlined in
Scheme 3. This route utilized the ortho-substituted analogs 12a
Scheme 3. Synthesis of 7-substituted dioxo-benzoisothiazoles 15a–j.

R. T. Hendricks et al. / Bioorg. Med. Chem. Lett. 19 (2009) 410–414
413
Table 1
Enzyme and replicon (GT-1b) inhibitory potency, and aqueous solubility for compounds 3b–d and 15a–j
Compound
R
R0
NS5B IC50,
lM
Replicon IC50,
nd
lM
Solubility
nd
lg/mL
3b
4.5
3c
1.0
2.2
2.7
10
16
3d
0.44
15a
15b
15c
0.58
0.61
3.9
0.43
0.76
0.8
2
40
41
15d
15e
0.53
0.35
0.94
1.1
17
3
15f
15g
15h
0.72
1.8
0.78
0.38
0.15
nd
9
0.55
3
15i
15j
0.73
0.41
0.40
6
7
0.075
and 12b prepared by coupling N-tert-butyl-2-chlorobenzene-sul-
fonamide and N-tert-butyl-2-methoxybenzene-sulfonamide with
10 in a similar manner as described previously for 11. Treatment
of 12a and 12b directly with BCl3 gave 15a and 15b. Cyclization
of 12a using a modified procedure employing sulfuric acid in EtOH
in place of BCl3 gave the O-protected 7-chloro-dioxo-benzoiso-
thiazole compound 13. Aryl chloride 13 underwent Suzuki cou-
plings10 with a variety of boronic acids/esters. Deprotection of
methyl ethers 14 gave analogs 15c–15j (Table 1).
Small substituents (15a, 15b) at the 7 position of the dioxo-ben-
zoisothiazole ring were well-tolerated, but did not show any
improvement in cellular potency over the 7-H compound 3d. Phe-
nyl (15c), substituted phenyl (15d, 15e) and heterocycles (15f–j)
were all tolerated, but only the 6-membered heterocycles 15h
and 15j showed any noticeable improvement in cellular activity.
The smaller 7-H and 7-OMe substituents, along with the unsubsti-
tuted 7-phenyl analog showed the best aqueous solubilities within
the series examined.
In summary, a series of new isoquinoline-based HCV NS5b poly-
merase inhibitors have been efficiently synthesized in 7–9 steps
from 3-carbomethoxy-1,2,3,4-tetrahydroisoquinoline-1,4-dione. A
structure–activity relationship was generated around the 7-posi-
tion of the dioxo-benzoisothiazole series, and the pyridone ana-
logue 15j was identified as the most potent HCV replicon
Figure 2. Model of isoquinoline 3d in the NS5b active site binding region. Connolly
surface is depicted.

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R. T. Hendricks et al. / Bioorg. Med. Chem. Lett. 19 (2009) 410–414
7. GAMESS Version 27 June 2005 (R2). Schmidt, M. W.; Baldridge, K. K.; Boatz, J.
inhibitor in this investigation (0.075 l
M).11,12 These isoquinolines
represent a promising new series of HCV NS5b inhibitors and
efforts to further enhance their properties are ongoing.
A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. J.; Koseki, S.; Matsunaga, N.; Nguyen, K.
A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993,
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8. (a) Lombardino, J. G. J. Org. Chem. 1971, 36, 1843; (b) Dauban, P.; Dodd, R. H.
Org. Lett. 2000, 2, 2327.
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