Inhibitors of HCV NS5B polymerase: Synthesis and structure-activity relationships of N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides

Article abstract of DOI:10.1016/j.bmcl.2006.04.015

Substituted N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides were investigated as inhibitors of genotype 1 HCV polymerase. Structure-activity relationship patterns for this class of compounds are discussed.

Full text of DOI:10.1016/j.bmcl.2006.04.015

Bioorganic & Medicinal Chemistry Letters 16 (2006) 3367–3370
Inhibitors of HCV NS5B polymerase: Synthesis and structure–
activity relationships of N-alkyl-4-hydroxyquinolon-3-yl-
benzothiadiazine sulfamides
A. Chris Krueger,* Darold L. Madigan, Wen W. Jiang, Warren M. Kati, Dachun Liu,
Yaya Liu, Clarence J. Maring, Sherie Masse, Keith F. McDaniel, Tim Middleton,
Hongmei Mo, Akhteruaman Molla, Debra Montgomery, John K. Pratt,
Todd W. Rockway, Rong Zhang and Dale J. Kempf
Infectious Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, IL 60064, USA
Received 10 March 2006; accepted 6 April 2006
Available online 2 May 2006
Abstract—Substituted N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides were investigated as inhibitors of genotype 1
HCV polymerase. Structure–activity relationship patterns for this class of compounds are discussed.
Ó 2006 Elsevier Ltd. All rights reserved.
Hepatitis C virus (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 by the year 2000, and that the virus
is responsible for at least 10,000 deaths annually in the
United States alone.1 HCV has six major genotype clas-
ses, with genotypes 1 and 2 being most prevalent in the
United States, Europe, and Japan.2 Currently combina-
tion drug treatment of genotype 2 or 3 is more successful
than treatment of genotype 1 infection.3,4 Moreover,
existing therapies are hampered by drug-related toxici-
ties. Therefore, there is a particular need for new thera-
pies directed toward genotype 1 HCV infection. Our
group has been pursuing inhibition of the HCV NS5B
RNA-dependent RNA polymerase (RdRp) enzyme by
hydroxyquinolon-3-yl-benzothiadiazines.5 Other groups
have reported nucleoside as well as other non-nucleoside
inhibitors of this viral enzyme.6
possibly obtain even greater potency against the RdRp,
we sought to extend more functionality away from the
methyl sulfonamide. An attractive strategy for accom-
plishing this endeavor was to synthesize a number of di-
verse thiadiazine sulfamide derivatives (Fig. 1).
A variety of sulfamide carbamates were synthesized
according to the protocol shown in Scheme 1. Chloro-
O
O
S
C
OH
N
O
O
H
D
S
N
N
S
N
H
A
N
B
N
O O
N
H
O
1
We have recently shown that the addition of a methyl
sulfonamide group to the 7-position of the D-ring of
the benzothiadiazine core (compound 1, IC50 = 2.4 nM)
dramatically improved the potency of the series.7 In an
effort to further probe the thiadiazine binding site and
O
O
R1
H
S
N
N
R2
OH
N
N
S
O O
N
H
N
O
substituted sulfamides
Keyword: HCV polymerase antiviral.
*
Corresponding author. Tel.: +1 847 938 2944; fax: +1 847 938
2756; e-mail: a.chris.krueger@abbott.com
Figure 1. Substituted sulfamide analog strategy.
0960-894X/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.04.015

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A. Chris Krueger et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3367–3370
O O
S
X
O O
S
X
a
H
Y
Z
NH2
Y
Z
N
Cl
a
Cl
NCO
Cl
NH
3
S
2
O O
RO
O
16
17
O
O
S
NH2
b
N
b
N
H
4
X
O
O
H
H
S
N
N
Y
Z
OH
N
N
S
O O
18, 22, 26
or d,e
R
O
O
O
H
N
H
N
S
N
H
OH
N
S
O O
N
O
O
N
H
c
N
N
O
5-15
X
H
N
H
c : 21, 24
d : 19, 23
e : 20, 25
N
Y
Z
S
Scheme 1. Reagents and conditions: (a) primary alcohol, CH2Cl2, 1 h,
100%; (b) compound 4, Et3N, CH2Cl2, 22 h, rt, 40–80%.
O O
Scheme 2. Reagents and conditions: (a) chlorosulfonic acid, CH2Cl2,
0 °C, then rt, 1 h, then PCl5, reflux, 3.5 h; (b) compound 4, Et3N, rt,
3 h, 5–48%; (c) NH4OH, rt, 72 h, 100%; (d) LiOH, THF, H2O, rt, 20 h,
90–95%; (e) HOBT, EDAC, DMF, rt, 18 h, 64–97%.
sulfonyl isocyanate was treated with a wide variety of
primary alcohols to provide the requisite intermediate
sulfonyl chlorides (3), which were allowed to react with
thiadiazine aniline 47 to provide the desired sulfamide
carbamate analogs 5–15. The biochemical activities of
these compounds measured against the genotype 1a
HCV polymerase are shown in Table 1.8 For the most
part the analogs displayed similar potencies regardless
of the hydrophobic or hydrophilic functionality append-
ed to the sulfamide group. The primary amine 11 was
the most potent analog in this initial series
(IC50 = 21 nM).
compounds were converted to the corresponding
primary amides and substituted amide analogs. The
para-substituted analogs (18–21) as
a class were
generally more potent than the corresponding
ortho- (26) and meta- (22–25) substituted analogs, as
shown in Table 2. However, there were few discernable
structure–activity relationships among the para-
substituted analogs 18–21, and all displayed roughly
equivalent potencies.
A series of phenyl-substituted sulfamides were also con-
structed according to the conditions shown in Scheme 2.
Substituted anilines (16) were treated sequentially with
chlorosulfonic acid and phosphorus pentachloride to
provide phenyl-substituted chlorosulfonamides (17).
Subsequent reaction with thiadiazine aniline 4 provided
the desired ester analogs 18, 22, and 26. These
Several other substituted benzothiadiazine sulfamides
(compounds 28–40) were prepared by primary amine
displacement of the oxazolidinone ring from compound
2 as shown in Scheme 3.9 This method was less efficient
for cyclic secondary amines, thus sulfamides 41–43 were
prepared by reaction of the corresponding sulfamyl
chlorides with thiadiazine aniline 4 (Scheme 4). Most
of these sulfamide analogs (Table 3) demonstrated sim-
ilar potencies when compared to the sulfamide carba-
mates (Table 1) and phenyl sulfamides (Table 2). The
exception was benzyl derivative 29, with an IC50 of
5.5 nM.
Table 1. Biochemical potency of sulfamide carbamate derivatives 5–15
a
1a IC50 (nM)
Compound
R
5
6
CH3
63
189
88
72
35
58
21
61
87
96
50
CH2CH2Cl
CH2CHCH2
CH2CCH
7
8
Table 2. Biochemical potency of phenyl sulfamide derivatives 18–26
9
CH2CH2CN
CH2Ph
Compound
X
Y
Z
1a IC50
(nM)
10
11b
12
13
14
15c
CH2CH2NH2
CH2CO2CH2CH3
CH2CH2OCH3
CH2CH2OCH2Ph
CH2CO2H
18
19
20
21
22
23
24
25
26
H
H
CO2Me
CO2H
48
20
H
H
H
H
CONHMe 43
H
H
CO2Et
CONH2
18
132
115
43
a IC50 values in all tables are means of at least two independent
determinations, standard deviation 10%. Detailed protocols can be
found in Supplementary data.
b Prepared from the cleavage of the Boc-protected primary amine.
c Prepared from the hydrolysis of compound 12.
H
H
H
H
H
H
H
CO2H
CONH2
H
H
CO2Me
CONHCH2CONH2
H
43
129

A. Chris Krueger et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3367–3370
Table 3. Biochemical potency of sulfamide derivatives 28–43
3369
O
O
H
H
S
N
N
O
OH
N
N
S
Compound
R1
R2
1a IC50 (nM)
18
5.5
O O
O
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
H
H
H
H
H
H
H
H
H
H
H
H
H
CH2CH2Ph
CH2Ph
Ph
N
H
41
107
67
39
10
32
20
10
15
57
13
51
27
24
N
O
Cl
6
CH2CH2OH
Cyclohexane
Cyclopentane
CH2CH2NH2
4-Piperidine
CH2CH2CONH2
CH2(4-OMe–Ph)
CH2(3-OMe–Ph)
CH2(2-OMe–Ph)
CH2(3-NO2–Ph)
Piperidine
a
O
N
O
O
O
H
S
N
N
S
O O
N
H
27
b
Pyrrolidine
Azetidine
R1
N
O
O
H
S
N
OH
N
S
O O
R2
N
O
O
H
H
H
S
N
N
O
N
N
O
OH
N
S
O O
28-40
O
N
H
10
N
N
O
Scheme 3. Reagents and conditions: (a) excess Et3N, CH2Cl2, rt, 6 h,
82%; (b) primary amines, CH2Cl2, CH3CN, 70 °C, 24 h, 25–50%.
a
b
O
N S
Cl
a
( )n
O
NH
( )n
Me
H
N
H
NH2
N
N
O
S
S
b
O O
O O
O
45
b
O
O
H
N
( )n
S
N
OH
N
N
S
H
H
N
N
O O
S
Me
44
N
H
O O
N
O
46
41-43
Scheme 5. Reagents and conditions: (a) TMS–diazomethane, THF, rt,
16 h, 15%; (b) MeOH, 10% Pd/C, H2 gas, 1 atm, rt, 3 h, 70–80%.
Scheme 4. Reagents and conditions: (a) sulfuryl chloride, CH2Cl2,
À20 °C, then 0 °C for 2 h, 20–35%; (b) compound 4, Et3N, CH2Cl2, rt,
18 h, 25–45%.
Table 4. Biochemical and cell culture potency of selected compounds
a,b
a,c
1b EC50 (nM)
Compound
IC50 (nM)
1a 1b
2.4 6.0
35 6.7
18 37
5.5
1b EC50
(nM)
(40% serum)
Simple unencumbered sulfamides 45 and 46 were
prepared from the benzyl carbamate 10 (Scheme 5).
These two analogs were nearly as potent as the methyl
sulfonamide (1) against genotype 1a HCV polymerase
(Table 4). In addition, two unencumbered sulfamides
from a different thiadiazine series5 were prepared and
tested (Scheme 6).
1
9
3.0
98
1310
—
28
29
41
44
45
46
48
49
1266
398
940
—
—
—
44
45
—
51
121
—
—
9.0
14
5.2
8.7
2.8
17
—
—
—
—
In general, the SAR in Tables 1–4 suggest that larger
sulfamide derivatives do not offer any extra binding
interactions with the polymerase binding site over the
unsubstituted sulfamide 45. Rather, it is likely that the
sulfamide substituents in many cases either project into
solvent or undergo hydrophobic collapse to produce flat
SAR trends.
0.4
3.0
81
420
—
11
a EC50 values in this table are means of at least two independent
determinations, standard deviation 10%. Detailed protocols can be
found in Supplementary data.
b Assay run with 5% fetal calf serum.
c Assay run with 40% human serum.

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A. Chris Krueger et al. / Bioorg. Med. Chem. Lett. 16 (2006) 3367–3370
O
O
Supplementary data
S
NH2
OH
N
Supplementary data associated with this article can be
found in the online version at doi:10.1016/j.bmcl.2006.
04.015.
N
H
N
O
47
NH
a,c or a,b,c
References and notes
1. (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. Eng. J. Med. 1999, 341, 556; (b).
Hepatology 1997, 26(Suppl. 1), 2S.
O
O
H
H
S
N
N
OH
N
S
R
O O
2. Simmonds, P. J. Hepatology 1999, 31(Suppl. 1), 54.
3. Manns, M. P.; McHutchison, J. G.; Gordon, S. C.; Rustgi,
V. K.; Shiffman, M.; Reindollar, R.; Goodman, Z. D.;
Koury, K.; Ling, M.; Albrecht, J. K. Lancet 2001, 358, 958.
4. Freid, M. W.; Shiffman, M. L.; Reddy, K. R.; Smith, C.;
Marinos, G.; Goncales, F. L., Jr.; Haussinger, D.; Diago,
M.; Carosi, G.; Dhumeaux, D.; Craxi, A.; Lin, A.;
Hoffman, J.; Yu, J. N. Engl. J. Med. 2002, 347, 975.
5. Pratt, J. K.; Donner, P.; McDaniel, K. F.; Maring, C. J.;
Kati, W. K.; Mo, H.; Middleton, T.; Liu, Y.; Ng, T.; Xie,
Q.; Zhang, R.; Montgomery, D.; Molla, A.; Kempf, D. J.;
Kohlbrenner, W. Bioorg. Med. Chem. Lett. 2005, 15, 1577.
6. (a) Powers, J. P.; Piper, D. E.; Li, Y.; Mayorga, V.; Anzola,
J.; Chen, J. M.; Jaen, J. C.; Lee, G.; Liu, J.; Peterson, M. G.;
Tonn, G. R.; Ye, Q.; Walker, N. P. C.; Wang, Z. J. Med.
Chem. 2006, 49, 1034; (b) Tedesco, R.; Shaw, A. N.;
Bambal, R.; Chai, D.; Concha, N. O.; Darcy, M. G.;
Dhanak, D.; Fitch, D. M.; Gates, A.; Gerhardt, W. G.;
Halegoua, D. L.; Han, C.; Hofmann, G. A.; Johnston, V.
K.; Kaura, A. C.; Liu, N.; Keenan, R. M.; Lin-Goerke, J.;
Sarisky, R. T.; Wiggall, K. J.; Zimmerman, M. N.; Duffy, K.
J. J. Med. Chem. 2006, 49, 971; (c) Fitch, D. M.; Evans, K.
A.; Chai, D.; Duffy, K. J. Org. Lett. 2005, 7, 5521; (d)
Gordon, C. P.; Keller, P. A. J. Med. Chem. 2005, 48, 1.
7. Rockway, T. W.; Zhang, R.; Liu, D.; Betebenner, D. A.;
McDaniel, K. F.; Beno, D.; Montgomery, D.; Jiang, W.
W.; Masse, S.; Kati, W. M.; Middleton, T.; Molla, A.;
Maring, C. J.; Kempf, D. J. Bioorg. Med. Chem. Lett.,
accepted for publication, doi:10.1016/j.bmcl.2006.04.022.
8. All compound structures were consistent by 1H NMR and
LC–MS analysis (>95% purity).
N
H
N
O
NH
48 : R = H
49 : R = Me
Scheme 6. Reagents and conditions: (a) chlorosulfonylisocyanate,
benzyl alcohol, CH2Cl2, 1 h, then compound 47, CH2Cl2, Et3N, 2 h,
66%; (b) TMS–diazomethane, THF, MeOH, 70 °C, 16 h, 98%; (c)
MeOH, THF, 10% Pd/C, H2 gas, 1 atm, rt, 24 h, 17–83%.
The biochemical activities of several analogs were
measured against the genotype 1b HCV polymerase
as shown in Table 4. The analogs displayed similar
activities against the 1a and 1b virus strains. Many
of these analogs were also tested in a replicon cell
culture assay based on the 1b virus genotype (Table
4).10 Consistent with the biochemical results, larger
substituted sulfamide analogs displayed weaker
activities. The primary sulfamide (48) and methyl sul-
famide (49) derivatives potently inhibited HCV repli-
cation, with EC50 values in the single digit nanomolar
range. In addition, the activity of compound 48 was
attenuated to a lesser extent than that of compound
1 (81 vs 1310 nm) when the cell culture assay was
run using 40% human serum versus 5% fetal calf
serum.
9. (a) Montero, J.-L.; Dewynter, G.; Agoh, B.; Delaunay, B.;
Imbach, J.-L. Tetrahedron Lett. 1983, 24, 3091; (b) Agoh,
B.; Dewynter, G.; Montero, J-L.; Leydet, A.; Imbach, J.-
L. Bull. Soc. Chim. Fr. 1987, 5, 867; (c) Dewynter, G.;
Abdaoui, M.; Regainia, Z.; Montero, J.-L. Tetrahedron
1996, 52, 14217; (d) Ducry, L.; Reinelt, S.; Seiler, P.;
Diederich, F.; Bolin, D. R.; Campbell, R. M.; Olson, G. L.
Helv. Chim. Acta 1999, 82, 2432.
In summary, we synthesized a number of substituted
benzothiadiazine sulfamide analogs and assessed their
inhibitory potency against genotype 1 HCV polymerase.
Overall we observed that the simple methyl and unsub-
stituted benzothiadiazine sulfamides displayed the most
potent biochemical and cell culture activities.
Detailed biological protocols for biochemical IC50
determinations and cell culture replicon assay EC50
determinations are available in Supplementary data.
10. (a) Ikeda, M.; Yi, M.; Li, K.; Lemon, S. M. J. Virol. 2002,
76, 2997; (b) Blight, K. J.; Kolykhalov, A.; Rice, C. M.
Science 2000, 290, 1972.