Aryl uracil inhibitors of hepatitis C virus NS5B polymerase: Synthesis and characterization of analogs with a fused 5,6-bicyclic ring motif

Article abstract of DOI:10.1016/j.bmcl.2013.04.057

The synthesis and structure-activity relationships of a novel aryl uracil series which contains a fused 5,6-bicyclic ring unit for HCV NS5B inhibition is described. Several analogs display replicon cell culture potencies in the low nanomolar range along with excellent rat pharmacokinetic values.

Full text of DOI:10.1016/j.bmcl.2013.04.057

Bioorganic & Medicinal Chemistry Letters 23 (2013) 3487–3490
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Aryl uracil inhibitors of hepatitis C virus NS5B polymerase: Synthesis
and characterization of analogs with a fused 5,6-bicyclic ring motif
a
a
a
b
A. Chris Krueger a, , John T. Randolph , David A. DeGoey , Pamela L. Donner , Charles A. Flentge ,
Douglas K. Hutchinson c, Dachun Liu a, Christopher E. Motter d, Todd W. Rockway e, Rolf Wagner a,
David W. A. Beno f, Gennadiy Koev a, Hock B. Lim a, Jill M. Beyer a, Rubina Mondal g, Yaya Liu a,
Warren M. Kati a, Kenton L. Longenecker a, Akhteruzzaman Molla a, Kent D. Stewart a, Clarence J. Maring a
⇑
a AbbVie Inc., 1 North Waukegan Road, North Chicago, IL 60064, USA
b Knopp Biosciences LLC, 2100 Wharton Street, Suite 615, Pittsburg, PA 15203, USA
c Bedoukian Research Inc., 21 Finance Dr., Danbury, CT 06810-4133, USA
d Univ. of Illinois at Urbana-Champaign, 101 S. Gregory St., Urbana, IL 61801, USA
e McHenry County College, Crystal Lake, IL 60012-2761, USA
f Abbott Nutrition Research and Development, 3300 Stelzer Road, Columbus, OH 43219, USA
g Abbott, Global Pharmaceutical Regulatory Affairs, 200 Abbott Park Road, Abbott Park, IL 60064-6216, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The synthesis and structure–activity relationships of a novel aryl uracil series which contains a fused 5,6-
bicyclic ring unit for HCV NS5B inhibition is described. Several analogs display replicon cell culture
potencies in the low nanomolar range along with excellent rat pharmacokinetic values.
Ó 2013 Elsevier Ltd. All rights reserved.
Received 8 February 2013
Revised 12 April 2013
Accepted 22 April 2013
Available online 1 May 2013
Keywords:
Hepatitis C
NS5B polymerase inhibitors
Aryl uracil
Hepatitis C virus (HCV) is a (+)-strand RNA virus of the Flavivi-
ridae family that was first identified in 1989.1 HCV is a common
pathogen that can lead to cirrhosis, hepatocellular carcinoma
(HCC) and liver failure. It is estimated that 170 million people were
infected worldwide in the year 2000, and that the virus is respon-
sible for at least 10,000 deaths annually in the United States alone.2
HCV has six major genotype classes, with genotypes 1 and 2 being
the most prevalent in the United States, Europe, and Japan.3 Re-
cently two new protease inhibitor drugs, boceprevir and telaprevir,
were approved by the FDA. However these drugs still must be used
in combination with the standard of care which imparts several
drug-related toxicities. Thus there is still an urgent need for new
HCV drugs with diverse modes of action.4
a dose of 5 mg/kg, the bioavailability was only 1.4%. Discovery ef-
forts led to the discovery of a series of substituted aryl uracil ana-
logs that showed improved antiviral potency while also improving
upon the poor pharmacokinetic properties (Scheme 1).
This series of substituted aryl uracil analogs were constructed
by employing the general sequence as shown in Scheme 2.6 Key
intermediate 3 was generated from a three step sequence employ-
ing 2-tert-butylphenol as the starting material. Iodide 3 could then
be reacted in a Suzuki coupling protocol with boronate 5 to gener-
ate inhibitor 6 after subsequent removal of the para-methoxyben-
zyl (PMB) group. The corresponding benzofuran (10) and
H
Me
O
Our research team has been pursuing inhibition of the Hepatitis
C virus by targeting the HCV polymerase enzyme. Our initial at-
tempts at optimizing a lead series resulted in the generation of a
highly potent arylsulfonamide amide (1).5 Unfortunately, the phar-
macokinetics of this amide series were poor. For instance when
compound 1 was administered as a solution in vehicle in rats at
H
N
H
N
H
N
N
S
O
O
O
Me
O
O
Y
X
O
S
L
O
O
N
N
N
H
OMe
OMe
1
X,Y = C,N,S, or O,L = linker
⇑
Corresponding author. Tel.: +1 847 938 2944; fax: +1 847 938 2756.
E-mail address: a.chris.krueger@abbvie.com (A.C. Krueger).
Scheme 1.
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.04.057

3488
A. C. Krueger et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3487–3490
O
N
benzothiophene (13) inhibitors were also constructed using iodide
O
S
N
O
3, utilizing the same Suzuki coupling procedure, as shown in
Scheme 3. The 3-bromobenzo[b]thiophene (11) employed was ob-
tained by following a literature procedure for its preparation.7
Two heterocyclic inhibitors, benzothiazole 17 and benzothio-
phene 21, both of which have the sulfonamide functionality in a
different orientation than the previous analogs, were constructed
according to the synthetic sequence shown in Scheme 4. Again, a
Suzuki reaction was utilized as one of the key reactions in the over-
all synthetic sequence. Finally, several all carbon bicyclic sulfon-
amide inhibitors were also generated as shown in Schemes 5 and 6.
Commercially available 5-bromo-2,3-dihydro-1H-indene-1-one
(22) was utilized as the starting material for six analogs. The first,
racemic sulfonamide indane 25, was synthesized by homologating
the ketone group in 22 to an aldehyde, then performing a reductive
amination followed by the key Suzuki coupling once again as
shown in Scheme 5. An additional methyl group could be incorpo-
rated onto the indane unit of inhibitor 25 by employing a longer
synthetic route. A different set of reagents transformed the starting
material 22 to the homologated ester 26, which was then alkylated
with methyl iodide and the subsequent racemic ester was hydro-
lyzed, made into an amide, then the amide was reduced with bor-
ane to give the primary amine. Protection of the amine, then
formation of the boronate provided 27, which was carried on to
analog 28, as shown in Scheme 5. Starting material indanone 22
could also be transformed into indeneamine 29, which after con-
version to the sulfonamide boronate 30, is subjected to another Su-
zuki reaction. In this instance, the Suzuki coupling between
boronate 30 and aryl iodide 3 was observed to be very sensitive
to the amount of unwanted oxygen present in the reaction mixture
and thus the yield of inhibitor 31 was much improved upon the
utilization of an argon gas inert atmosphere for the desired trans-
formation. Boronate 30 was also methylated on the nitrogen of the
sulfonamide and then converted to the corresponding inhibitor 32.
Additionally the dimethylated indene sulfonamide linker analog
(33) was generated by yet a different set of reagents also shown
in Scheme 6. Finally, the methanesulfonylhydrazone analog 34,
and the corresponding hydrazine analog 35 were constructed
employing the short synthetic sequence as shown in Scheme 7.
Benzoxazole inhibitor 6 was initially synthesized. This analog
(6) displays roughly a 20–50 fold loss in in vitro potency versus
the starting amide (1) comparator as shown in Table 1. Even more
disappointing was the poor replicon potency results with benzox-
azole 6 against both genotypes 1a and 1b. Undeterred by these
NH
a,b,c
H
O
H
N
O
O
N
OH
2
N
O
I
g,h
O
O
3
O
S
N
O
+
6
PMB
d,e,f
N
N
O
O
O
B
O
Br
4
5
Scheme 2. Reagents and conditions: (a) NaOH, MeOH, NaI, then NaOCl, 93%; (b)
MeI, acetone, NaOH, 25 °C, 48 h, 99%; (c) uracil, N-(2-cyanophenyl)picolinamide,
K3PO4, CuI, DMSO, 60 °C, 18 h, 61%; (d) 1-bromopyrrolidine-2,5-dione, dibenzoyl
peroxide, CCl4, reflux, 6 h, 43%; (e) N-(4-methoxybenzyl)methanesulfonamide,
EtOH, aq NaOH, 80 °C, 1.5 h, 22%; (f) bis(pinacolato)diboron, KOAc, Pd(dppf)2Cl2–
CH2Cl2, dioxane, 80 °C, 16 h, 79%; (g) Pd(dppf)2Cl2–CH2Cl2, EtOH, toluene, 1 M aq
Na2CO3, 100 °C, microwave, 1 h, 83%; (h) TFA, 40 °C, 6 h, 41%.
O
Br
OH
a,b,c
O
S
7
O
O
S
N
O
N
H
PMB
H
N
O
O
O
d,e,f
g,h,f
O
B
N
X
O
i, j
O
9
Br
O
O
S
8
or
O
N
PMB
10, X = O
13, X = S
O
S
B
O
S
Br
12
11
Scheme 3. Reagents and conditions: (a) NaH, DMF, 0.5 h, then methyl bromoace-
tate, 25 °C, 18 h, 82%; (b) NaOH, H2O, THF, 25 °C, 3 h, 97%; (c) Ac2O, NaOAc, reflux,
18 h, 82%; (d) NBS, dibenzoyl peroxide, PhCl, reflux, 2 h, 32%; (e) N-(4-methoxy-
benzyl)methanesulfonamide, K2CO3, DMF, 70 °C, 3 h, 35%; (f) bis(pinacolato)dibo-
ron, KOAc, Pd(dppf)2Cl2–CH2Cl2, dioxane, 80 °C, 16 h, 75–86%; (g) 37% aq
formaldehyde, concd HCl, HCl gas, 70 °C, 1 h, 82%; (h) N-(4-methoxybenzyl)meth-
anesulfonamide, K2CO3, DMA, 25 °C, 3 h, 64%; (i) compound 3, Pd(dppf)2Cl2–CH2Cl2,
EtOH, toluene, 1 M aq Na2CO3, 100 °C, microwave, 1 h, 43–87%; (j) TFA, DCM, 25 °C,
18 h, 75–84%.
O
O
NH
NH
O
O
N
N
N
S
c
d,e
N
S
N
a,b
O
NH2
B
O
Br
N
N
O
S
O
O
15
S
O
S
14
N
H
N
17
16
O
OMe
NH
O
O
F
N
OH
f,g
c,j
h,i,b
O
S O
S
N
Br
Br
O
19
O
H
N
18
S
B
S
21
S
O
O
20
O
Scheme 4. Reagents and conditions: (a) hexane-2,5-dione, PPTS, benzene, Dean–tark trap, reflux, 16 h, 84%; (b) bis(pinacolato)diboron, KOAc, bis(di-tert-
butyl(hydroxyl)phosphino)palladium(II) dichloride, toluene, reflux, 72 h, 73–74%; (c) compound 3, Pd(dppf)2Cl2–CH2Cl2, EtOH, toluene, 1 M aq Na2CO3, 100 °C, microwave,
1 h, 65–68%; (d) TFA, water, 80 °C, 2.5 h, 98%; (e) MeSO2Cl, pyridine, CH2Cl2, 25 °C, 16 h, 4%; (f) methyl mercaptoacetate, Et3N, DMSO, 75 °C, 2 h, 100%; (g) LiAlH4, diethyl ether,
5 °C, 1 h, 83%; (h) NBS, TPP, CH2Cl2, 25 °C, 2 h, 89%; (i) N-(4-methoxybenzyl)methanesulfonamide, 1.0 M aq NaOH, EtOH, reflux, 1 hr, 33%; (j) TFA, CH2Cl2, 25 °C, 4 h, 44%.

A. C. Krueger et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3487–3490
3489
O
NH
O
O
S
N
O
N
O
O
PMB
f,g
a,b
O
O
S
c,d,e
O
N
Br
B
O
Br
O
H
22
23
25
24
O
NH
Boc
NH
O
N
O
O
O
f,q,d
l,m,n,o,p,e
h,i,j,k
O
O
S
O
N
H
Br
B
O
Br
O
22
26
27
28
Scheme 5. Reagents and conditions: (a) MeOCH2PPh3+Clꢀ, THF, KOtBu, ꢀ20 to 25 °C, 3 h, 93%; (b) BBr3, ꢀ78 °C, 4 h, 45%; (c) 4-methoxybenzylamine, decaborane, MeOH,
25 °C, 1 h, 57%; (d) MeSO2Cl, pyridine, 25 °C, 1 h, 46–51%; (e) bis(pinacolato)diboron, KOAc, Pd(dppf)2Cl2–CH2Cl2, dioxane, 95 °C, 8 h, 66–83%; (f) Pd(dppf)2Cl2–CH2Cl2, EtOH,
toluene, 1 M aq Na2CO3, 100 °C, microwave, 1 h, 47–85%; (g) TFA, 25 °C, 1 h, 95%; (h) 1,3-dithiane, THF, ꢀ30 to ꢀ15 °C, nBuLi, then 22, 0 °C, 18 h; (i) pTSA, reflux, benzene, 1 h;
(j) concd HCl, AcOH, reflux, 3 h, 58% for three-steps; (k) MeOH, 4 N HCl in dioxane, reflux, 8 h, 77%; (l) LiHMDS, THF, MeI, ꢀ78 to 25 °C, 96%; (m) Me3SiOK, THF, reflux, 3 h, 99%;
(n) oxalyl chloride, DMF, hexanes, 25 °C, 1 h, then concd NH4OH, acetone, 0–25 °C, 1 h, 100%; (o) BH3–Me2S, THF, reflux, 2 h, 68%; (p) (Boc)2O, THF, Na2CO3, H2O, 25 °C, 18 h,
94%; (q) 4 N HCl in dioxane, 25 °C, 18 h, 96%.
O
O
S
NH
O
N
NH2
O
O
H
N
f
a,b,c
d,e
O
O
O
S
Br
B
O
Br
22
29
N
O
30
H
31
h,i,d
O
g,f
O
NH
NH
O
O
O
O
S
N
N
N
e,f
H
O
O
S
O
O
S
N
H
N
Me
O
Br
O
33
32
Scheme 6. Reagents and conditions: (a) N-methyl-morpholine N-oxide, TMSCN, CH2Cl2, 25 °C, 72 h, 86%; (b) LiAlH4, Et2O, 0–25 °C, 3 h, then NH4OH, 70%; (c) 6 N aq HCl,
MeOH, 70 °C, 3 h, 92%; (d) MeSO2Cl, (iPr)2NEt, CH2Cl2, 25 °C, 10 h, 56–83%; (e) bis(pinacolato)diboron, KOAc, Pd(dppf)2Cl2–CH2Cl2, dioxane, 95 °C, 8 h, 65–87%; (f) compound
3, Pd2(dba)3, 1,3,5,7-tetramethyl-2,4,8-trioxa-6-phospha-6-phenyl-adamantane (Cytec [97739-46-3]), THF, H2O, 1 M aq K3PO4, 50 °C, 2.5 h, 24–84%; (g) LiHMDS, THF, then
MeI, 25 °C, 2 h, 57%; (h) LDA, THF, diethylcyanophosphonate, ꢀ10 to 25 °C, 3 h, then BF3–OEt2, ꢀ78 °C to rt, 16 h, 69%; (i) anhydrous CeCl3, THF, MeLi–LiBr, ꢀ78 to ꢀ20 °C,
24 h, 20%.
hepatocytes (containing 5% fetal calf serum). Unfortunately, 13 dis-
O
S
O
S
O
O
played greater affinity for plasma proteins than 1, consequently
reducing its potency when 40% human plasma was added to the
replicon assay. Surprisingly the effect of moving the sulfonamide
functionality to a different attachment point on the heterobicyclic
ring (2 vs 3 position) as demonstrated in comparing analogs 13
versus 21 was dramatic. The latter, 2-substituted methylsulfona-
mide (21), was much weaker in the cell culture replicon assay, as
was the 2-substituted thiazole (17). We also explored the possibil-
ity of removing all of the heteroatoms from the bicyclic unit. Thus
indane inhibitor 25 was synthesized and ultimately demonstrated
a very favorable HCV inhibition profile. Inhibitor 25 is slightly more
potent than amide 1, and turned out to be one of the most potent
analogs in this series against genotype 1b, even in the replicon
experiment containing 40% human plasma. With this success, we
constructed a number of closely related analogs to indane inhibitor
25. This synthetic activity resulted in the methyl substituted in-
dane analog 28, and the three related indenes (31, 32 and 33). Of
these analogs the indene inhibitor 31 is the best, displaying favor-
able potency profile similar to the potencies of indane inhibitor 25.
H
N
H
N
NH
H
N
N
H
N
O
O
O
O
O
N
a,b,c
N
d
Br
O
O
22
34
35
Scheme 7. Reagents and conditions: (a) bis(pinacolato)diboron, KOAc,
Pd(dppf)2Cl2–CH2Cl2, dioxane, 80 °C, 8 hrs, 65%; (b) compound 3, Pd(dppf)2Cl2–
CH2Cl2, EtOH, toluene, 1 M aq Na2CO3, 100 °C, microwave, 1 h, 61%; (c) metha-
nesulfonylhydrazide, THF, MeOH, 60 °C, 24 hrs, 66%; (d) NaBH3CN, aq HCl, MeOH,
THF, 25 °C, 1 hr, 58%.
poor initial results we forged ahead to construct the related benzo-
furan (10) and benzothiophene (13) inhibitors. These two analogs
displayed improved HCV inhibition results, with the benzothio-
phene (13) analog being better than the amide 1 in the enzyme
inhibition assay as well as inhibiting the HCV replicon in Huh7

3490
A. C. Krueger et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3487–3490
Table 1
Potency of aryl uracil analogs
Compd #
HCV polymerase IC50 (nM)a
HCV replication EC50 (nM)a,b
PAMPA Effective Permeability
Genotype 1a
Genotype 1b
Genotype 1a
Genotype 1b
Genotype 1b with 40% HP
Pe (ꢁ 10ꢀ6) cm/s
1
6
11
540
9
22
510
21
10
45
245
18
41
11
20
51
>1000
240
27
>1000
>1000
20
480
14
4
27
>1000
22
18
—
0.22
—
—
0.81
1.40
0.81
8.93
—
5.43
—
4.06
0.47
0.24
10
13
17
21
25
28
31
32
33
34
35
260
46
5
3
19
180
8
16
6
7
185
3
>1000
>1000
3
89
3
100
>1000
1
—
>10000
13
560
22
50
>1000
1
950
215
3
47
1000
2
140
33
>100
a
IC50 and EC50 values are means of at least two independent determinations, with a maximum twofold value variation.
Assay run with 5% fetal calf serum except for last column, in which 40% human plasma was added.
b
Table 2
Single IV and oral dose pharmacokinetics of select aryl uracil analogs in rat
Compd IV dose (mg/kg) IV t1/2 (h) IV CLp (L/h/kg) Oral dosea (mg/kg) Oral t1/2 (h) Oral Cmax
(l
g/mL) Oral Tmax (h) Oral AUC0–1
(
lgꢂh/mL) F (%)
1
5
5
5
5
5
5
1.1
3.6
1.8
2.3
1.9
2.8
1.53
0.27
0.45
0.61
0.77
1.19
5
5
5
5
5
5
1.0
3.2
2.3
2.4
3.0
3.0
0.03
1.41
2.36
1.01
0.66
0.12
0.33
0.50
0.33
0.25
6.17
2.50
0.5
9.3
13.5
5.1
7.2
0.88
1.4
13
25
28
31
34
41
119
62
86
18
a
Compounds dosed as a solution.
The related hydrazone inhibitor 34 also shows outstanding po-
tency against both genotypes. Unfortunately this analog (34) was
subsequently found to be unstable in vivo, resulting in cleavage
of the hydrazone functionality. In an effort to stabilize this hydra-
zone analog (34) from hydrolysis, the hydrazine analog 35 was
made from 34. Even though 35 is isosterically matched with 25,
the potencies of both analogs were surprisingly different, with 35
suffering a dramatic loss in the replicon experiments. Finally, we
examined the pharmacokinetic characteristic of the most potent
analogs in rats. As shown in Table 2, we were surprised to see that
the potent HCV inhibitors 13, 25, 28, 31 and 34 all demonstrated
much improved oral pharmacokinetic parameters in rat when
compared to amide 1.
In summary, we discovered a number of aryl uracil bicyclic HCV
NS5B polymerase inhibitors that have both excellent in vitro and
cell culture replicon potencies. We also discovered that the inter-
vening scaffolding between the tert-butyl aryl uracil and the meth-
ane sulfonamide seemed to play an important role in the
improvement of PK parameters in the rat upon oral dosing.
A.C.K., J.T.R., D.A.D., P.L.D., D.L., R.W., G.K., H.B.L., J.M.B., Y.L.,
W.M.K., K.L.L., A.M., K.D.S. and C.J.M. are all employees of Abbvie.
References and notes
1. Choo, Q. L.; Kuo, G.; Weiner, A. J.; Overby, L. R.; Bradley, D. W.; Houghton, M.
Science 1989, 244, 359.
2. (a) Alter, M. J.; Kruszon-Moran, D.; Nainan, O. V.; McQuillan, G. M.; Gao, F.;
Moyer, L. A.; Kaslow, R. A.; Margolis, H. S. N. Engl. J. Med. 1999, 341, 556; (b)
Hepatology, 1997, 26, 2S–10S.
3. Simmonds, P. J. Hepatol. 1999, 31, 54.
4. Rice, C. Nature 2011, 474, S8.
5. (a) Donner, P.; Randolph, J. T.; Huang, P.; Hutchinson, D.; Xie, Q.; Wagner, R.;
Lim, H.; Colletti, L.; Koev, G.; Liu, Y.; Mondal, R.; Beyer, J.; Marsh, K.; Beno, D.;
Longenecker, K.; Pilot-Matias, T.; Kati, W.; Molla, A.; Maring, C. Presented at the
244th National Meeting of the American Chemical Society, Philadelphia, PA,
August 2012; paper MEDI 147.; (b) Liu, Y.; Lim, B. H.; Jiang, W. W.; Flentge, C. A.;
Hutchinson, D. K.; Madigan, D. L.; Randolph, J. T.; Wagner, R.; Maring, C. J.; Kati,
W. M.; Molla, A. Bioorg. Med. Chem. Lett. 2012, 22, 3747.
6. Wagner, R.; Tufano, M. D.; Stewart, K. D.; Rockway, T. W.; Randolph, J. T.; Pratt, J.
K.; Motter, C. E.; Maring, C. J.; Longenecker, K. L.; Liu, Y.; Liu, D.; Krueger, A. C.;
Kati, W. M.; Hutchinson, D. K.; Huang, P. P.; Flentge, C. A.; Donner, P. L.; DeGoey,
D. A.; Betebenner, D. A.; Barnes, D. M.; Chen, S.; Franczyk II, T. S.; Gao, Y.; Haight,
A. R.; Hengeveld, J. E.; Henery, R. F.; Kotecki, B. J.; Lou, X.; Sarris, K.; Zhang, G. G.
Z. Patent Application WO 2009/039127, 26 March 2009.
7. (a) Allen, D.; Callaghan, O.; Cordier, F. L.; Dobson, D. R.; Harris, J. R.; Hotten, T.
M.; Owton, W. M.; Rathmell, R. E.; Wood, V. A. Tetrahedron Lett. 2004, 45, 9645;
(b) Diaz, C. J.; Haffner, C. D.; Speake, J. D.; Zhang, C.; Mills, W. Y.; Spearing, P. K.;
Cowan, D. J.; Green, G. M. Patent Application WO 2008/021851, 21 February
2008.
Disclosures
This research was sponsored by Abbvie. Abbvie contributed to
the research, interpretation of data, writing, reviewing, and
approving the publication.