Novel indole-3-sulfonamides as potent HIV non-nucleoside reverse transcriptase inhibitors (NNRTIs)

Article abstract of DOI:10.1016/j.bmcl.2007.11.085

This Letter describes the design, synthesis, and biological evaluation of novel 3-indole sulfonamides as potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) with balanced profiles against common HIV RT mutants K103N and Y181C.

Full text of DOI:10.1016/j.bmcl.2007.11.085

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 18 (2008) 554–559
Novel indole-3-sulfonamides as potent HIV non-nucleoside
reverse transcriptase inhibitors (NNRTIs)
Zhijian Zhao,a,* Scott E. Wolkenberg,a Meiqing Lu,b Vandna Munshi,b Gregory Moyer,b
Meizhen Feng,b Anthony V. Carella,b Linda T. Ecto,b Lori J. Gabryelski,b Ming-Tain Lai,b
Sridar G. Prasad,a Youwei Yan,a Georgia B. McGaughey,c Michael D. Miller,b
Craig W. Lindsley,a, George D. Hartman,a Joseph P. Vaccaa and Theresa M. Williamsa
aDepartment of Medicinal Chemistry, Merck & Co., Inc., PO Box 4, West Point, PA 19486, USA
bDepartment of Antiviral Research, Merck & Co., Inc., PO Box 4, West Point, PA 19486, USA
cDepartment of Molecular Systems, Merck & Co., Inc., PO Box 4, West Point, PA 19486, USA
Received 10 October 2007; revised 20 November 2007; accepted 20 November 2007
Available online 28 November 2007
Abstract—This Letter describes the design, synthesis, and biological evaluation of novel 3-indole sulfonamides as potent non-nucle-
oside reverse transcriptase inhibitors (NNRTIs) with balanced profiles against common HIV RT mutants K103N and Y181C.
Ó 2007 Published by Elsevier Ltd.
HIV reverse transcriptase (HIV-RT) plays an essential
role in the life cycle of HIV replication. Three non-
O
WT RT IC50 3 nM
nucleoside reverse transcriptase inhibitors (NNRTIs)
have been introduced as a key class of drugs for the
treatment of HIV infection (ViramuneÒ, RescriptorÒ,
and SustivaÒ) in highly active antiretroviral therapy
(HAART).1 However, the emergence of drug-resistant
mutations in HIV-RT from NNRTI treatment raises
an urgent need to discover and develop new agents with
improved resistance profiles.2 In this letter, we wish to
report our efforts in the discovery of novel NNRTIs
based on an indole core through an iterative analogue
library approach.
S
O
K103N RT IC50 116 nM
Y181C RT IC50 71 nM
Cl
O
N
NH2
H
1
Figure 1. Structure and HIV-RT inhibitory activity of 1.
activity of 1. In recent years, other groups have reported
the discovery of indole derivatives as NNRTIs.4,5 In
light of these encouraging results, we undertook an ef-
fort to identify NNRTIs from this series with an im-
proved mutant profile.
In 1993, Williams and co-workers reported that 5-
chloro-3-(phenylsulfonyl)indole-2-carboxamide (1, Fig. 1)
was a potent NNRTI against wild-type enzyme.3 Com-
pound 1 also displays sub-micromolar activity against
K103N and Y181C, two HIV-RT mutants observed
clinically with high frequency. It has been demonstrated
that the two oxygen atoms on the sulfone moiety are
critical to maintain both the enzymatic and cellular
Our initial attempt was to replace the sulfone group in 1
with a sulfonamide group to generate compounds of
general structure 7. This change was motivated by dock-
ing studies of 1 and HIV-RT in which the indole 3-phen-
ylsulfonyl group occupies a hydrophobic pocket formed
by Y181, Y188, and W229;5 we hypothesized that due to
its close contact with Y181, the indole 3-substituent may
affect activity versus the Y181C mutant. Earlier results
demonstrated the necessity for substitution at the indole
5-position for optimal potency;3 because of this require-
ment, and to provide a handle for further derivatization,
5-bromoindole analogues 7 were prepared in parallel.
Keywords: HIV; Antiviral; Indole; Sulfonamide.
*
Corresponding author. E-mail: zhijian_zhao@merck.com
Present address: VICB Program in Drug Discovery, Department of
Pharmacology, Vanderbilt Medical Center, Nashville, TN 37232,
USA.
0960-894X/$ - see front matter Ó 2007 Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2007.11.085

Z. Zhao et al. / Bioorg. Med. Chem. Lett. 18 (2008) 554–559
555
Table 1. Anti-HIV activities of indole sulfonamide amide library 7
Br
O
Br
O
b
a
c
O
NR1R2
N
H
3
OEt
S
N
Ts
OEt
O
Br
NH2
4
N
O
SO2NR1R2
O
SO2Cl
H
Br
O
Br
d
7
N
Ts
OEt
Compound
–NR1R2
WT RT IC50
(nM)
SPREAD
b
CIC95 (nM)
N
Ts
a
OEt
6
5
H
N
SO2NR1R2
NH2
7a
7b
7c
7d
7e
7f
19
160
Br
N
O
HN
0.5
18
125
125
125
<7.8
16
H
7
H
N
Scheme 1. Synthesis of indole-sulfonamide-amide 7 series. Reagents
and conditions: (a) i—NaH, THF, rt, ii—TsCl, 70–80%; (b) SO2Cl2,
DCM, rt, 90%; (c) NHR1R2, DIEA, DCM; (d) NH3, MeOH, 110 °C,
overnight, 60–90%. All compounds were purified by mass-directed
HPLC.7
HN
N
14
3.6
5.7
0.2
4.5
The synthesis of library 7 is illustrated in Scheme 1.
Commercially available indole 3 was N-protected and
converted smoothly to sulfonyl chloride 5 via treatment
with SO2Cl2. Sulfonyl chloride 5 was then reacted with
48 amines in a parallel fashion to generate 48 sulfona-
mides represented by general structure 6. Finally, con-
comitant deprotection of indole N1 and aminolysis of
2-carbonyl ester were executed in one pot to provide
the sulfonamide library 7. Selected compounds and their
HIV-RT inhibition data are presented in Table 1.6
N
H
N
F
F
7g
7h
140
410
F
N
F
a IC50 values versus isolated RT enzyme.
b The values of CIC95 are defined as those which inhibited by 95% the
spread of HIV infection in susceptible cell cultures in the presence of
10% FBS (fetal bovine serum).
As shown in Table 1, both secondary and tertiary indole
sulfonamides exhibit potent inhibition of wild-type
HIV-RT (IC50 < 55 nM). Greater variation was ob-
served for activity in a cell-based assay versus wild-type
HIV (SPREAD) where cell culture inhibitor concentra-
tions (CIC95) are defined as those which inhibited 95%
of the spread of HIV infection in susceptible cell cul-
tures. Only the tertiary cyclic sulfonamides 7e and 7f dis-
played a small shift (<3) between enzyme inhibition
activity (WT RT) and cell based activity (SPREAD,
10% FBS). Indeed, sulfonamide 7e exhibited antiviral
activity versus wild-type HIV equivalent to sulfone 1
indicating that the 3-pyrrolidine sulfonamide is an
acceptable isosteric replacement for the 3-phenylsulfo-
nyl group in 1.
Despite potent activity versus wild-type enzyme and
virus compounds 7e, 8a, and 8b displayed only weak
inhibition against the mutant RT K103N (>2000 nM)
regardless of variation at the sulfonamide moiety or in-
dole 5-position. Analogues 7e and 8b suffer from com-
paratively weak Y181C RT activity as well. As a
result, attention was turned to the indole 2-carboxamide
to improve the mutant profile; simple secondary amide
replacements have been reported to improve activity
versus the Y181C and the Y181C/K103N double mu-
tant.4,5 Again the optimized indole-3-pyrrolidine sulfon-
amide 7e was selected for further modification, and the
synthesis of these analogues is illustrated in Scheme 2.
Sulfonyl chloride 5 was converted to pyrrolidine sulfon-
amide 9, before being subjected to parallel aminolysis of
the ester and tosyl groups in 9 with 48 primary amines
generating a secondary amide library 10. Consistent
with prior observations,4,5 balanced inhibition of wild-
type and mutant K103N and Y181C RT could be
achieved by extending the 2-carboxamide substituent
(Table 3). In particular, benzamide analogues bearing
ortho substituents (e.g., 10b and10c) exhibit <5-fold
shifts in their wild-type and mutant enzyme potencies.
Keeping the indole-3-pyrrolidinosulfonamide constant,
investigation of the indole 5-substituent revealed that
Br, Cl, and CN were the preferred groups (Table 2);
compounds in Table 2 were prepared via the route de-
scribed in Scheme 1 (comparable yields were obtained)
or via cross-coupling reactions of 7e. Consistent with
previous work,3 5-Cl (8a) is well tolerated and provides
potent enzymatic and cellular activity versus wild type
RT and virus. The nitrile analogue 8b also exhibits high
activity versus wild type RT; however, other substitu-
tions are less well tolerated (e.g., 8c–8g) including small
non-polar groups (see 8c and 8d).

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Z. Zhao et al. / Bioorg. Med. Chem. Lett. 18 (2008) 554–559
Table 2. Anti-HIV activities of pyrrolidine sulfonamides 8
O
N
O
S
R
NH2
O
N
H
8
a
WT RT IC50 (nM)
b
SPREAD CIC95 (nM)
a
K103N RT IC50 (nM)
a
Y181C RT IC50 (nM)
Compound
R
8a
Cl
3.9
<7.8
1963
2300
nd
48
8b
8c
8d
8e
8f
CN
9.1
16
>10000
nd
940
430
550
2200
59
160
630
1300
310
nd
nd
nd
Ph
nd
nd
nd
nd
N
Cl
8g
8200
>10000
N
a IC50 values versus isolated RT enzyme.
b The values of CIC95 are defined as those which inhibited by 95% the spread of HIV infection in susceptible cell cultures in the presence of 10% FBS
(fetal bovine serum).
these properties, the 2-carboxamide moiety in library 10
N
O
SO2Cl
was replaced with an amide surrogate, an approach pre-
viously reported by Young and co-workers within the
indole sulfone series.8 This work demonstrated that
replacing the carboxamide in 1 with an imidazole ring
could not only improve physical properties but also
boost inhibition of K103N RT (Fig. 2). Synthesis of a
library of 2-(imidazol-2-yl)-indoles 13 is shown in
Scheme 3.
S
O
Br
O
Br
O
a
b
N
OEt
N
Ts
OEt
Ts
5
9
N
O
S
O
Br
O
Deprotection of 9 generated the free indole ester 11
which was reduced (LiAlH4) and reoxidized (MnO2) to
provide indole-2-carboxaldehyde 12. Conversion of 12
to imidazoles 13 was achieved under microwave heating
conditions in the presence of NH4OH and various 2-
ketoaldehydes or phenyldiamines. Imidazoles bearing
various substituents were prepared and in general mini-
mal effect on wild-type RT enzyme inhibition was ob-
served (Table 4). However, significant effects on
mutant enzyme inhibition were found. In accord with re-
sults in the indole sulfone series, >20-fold improvement
in K103N enzyme inhibition was observed (7e versus
13a). A more modest 5-fold improvement was observed
in Y181C RT potency (7e versus 13a), although Y181C
potency was strongly dependent on substitution on the
imidazole ring with a trend toward decreasing activity
with increasing steric bulk of the substituent (compare
N
H
NHR
10
Scheme 2. Synthesis of indole-sulfonamide-amide 10 series. Reagents
and conditions: (a) pyrrolidine, DCM, (b) RNH2, i-PrOH, 110 °C,
overnight, 60–90%. All compounds were purified by mass-directed
HPLC.7
As they retain potent cellular activity, 10b and 10c rep-
resent the best balance among cellular, wild-type, and
mutant activity within the amide series.
Despite this balanced profile, 10b and 10c exhibit less
than optimal physical properties and high clearance in
animal pharmacokinetic studies. In an effort to improve

Z. Zhao et al. / Bioorg. Med. Chem. Lett. 18 (2008) 554–559
557
Table 3. Antiviral activities of indole sulfonamide amide library 10
O
N
O
S
Br
NHR
O
N
H
10
a
WT RT IC50 (nM)
b
SPREAD CIC95 (nM)
a
K103N RT IC50 (nM)
a
Y181C RT IC50 (nM)
Compound
–NHR
NH2
7e
3.6
<7.8
10000
2800
120
H
N
10a
10b
15
625
25
6.9
16
OH
Cl
3.8
20
N
H
F
N
H
10c
10d
10e
10f
10g
2.4
14
23
31
9.4
6.3
829
200
6.0
HO
N
H
<7.8
<7.8
<7.8
16
170
260
280
93
N
N
H
2.5
2.8
6.2
HN
N
N
N
H
S
N
H
N
S
HN
10h
3.1
82
25
63
N
a IC50 values versus isolated RT enzyme.
b The values of CIC95 are defined as those which inhibited by 95% the spread of HIV infection in susceptible cell cultures in the presence of 10% FBS
(fetal bovine serum).
N
O
N
O
O
O
S
S
S
O
S
O
O
O
Br
Br
H
N
O
Br
b,c
a
Cl
O
Cl
O
N
Ts
OEt
N
OEt
N
NH2
N
N
H
H
H
1
2
9
11
Compound
WT RT IC50 (nM)
SPREAD CIC95 (nM)
3
5
N
N
O
O
3
12
S
S
d
O
R1
R2
O
Br
O
H
N
K103N RT IC50 (nM)
116
9
N
H
N
N
H
Figure 2. Structure and antiviral activity of 1 and 2.
H
12
13
13a with 13b and 13d). Comparison of 13f and 13h sug-
gests there may be an electronic component to this sub-
stituent effect as well.
Scheme 3. Synthesis of imidazole library 13. Reagents and conditions:
(a) PS-trisamine, DCM, 45 °C 70–80%; (b) LiAlH4, THF, 0 °C, 80%;
(c) MnO2, THF, rt, 70–85%; (d) RCOCHO or phenyldiamine,
NH4OH, EtOH, microwave, 70 °C, 20–65%. All compounds were
purified by mass-directed HPLC.7
An X-ray co-crystal structure of wild type RT-bound 7e
˚
was obtained at 2.4 A resolution which provides insight

558
Z. Zhao et al. / Bioorg. Med. Chem. Lett. 18 (2008) 554–559
Table 4. Antiviral activities of indole sulfonamideimidazole 13
O
N
O
S
Br
R
N
H
13
a
WT RT IC50 (nM)
b
SPREAD CIC95 (nM)
a
K103N RT IC50 (nM)
a
Y181C RT IC50 (nM)
Compound
R
H
N
13a
3.1
8.8
<7.8
42
62
25
N
OH
H
N
13b
13c
50
2600
N
OMe
H
N
16
100
110
240
N
H
N
Ph
13d
13e
11
10
67
82
150
48
>9100
810
N
OH
H
N
N
H
N
13f
6.9
45
78
280
150
38
N
H
N
OMe
F
13g
400
5100
N
H
N
13h
13i
15
40
280
82
220
370
5300
5000
N
H
N
N
N
a IC50 values versus isolated RT enzyme.
b The values of CIC95 are defined as those which inhibited by 95% the spread of HIV infection in susceptible cell cultures in the presence of 10% FBS
(fetal bovine serum).
into the binding interactions of the inhibitor (Fig. 3).9
The overall structure of the enzyme is consistent with
previously described NNRTI/HIV-RT complexes,
where a conformational change results in the formation
of the characteristic NNRTI binding pocket occupied by
7e. The newly formed binding pocket consists of aro-
matic residues (Y181, Y188, F227, Y318), aliphatic res-
idues (L100, L234), and two polar interactions between
1) the indole nitrogen and the carbonyl of K101 and 2)
the amide carbonyl oxygen and the nitrogen backbone
of K101. An intramolecular H-bond is also observed be-
tween the indole 2-carboxamide NH and an oxygen of
the sulfonamide in 7e. This arrangement provides a
structural basis for the necessity for a sulfone in inhibi-
tors within this series: in addition to stabilizing a butter-
fly-like conformation characteristic of NNRTIs,10 the
sulfone increases the acidity of the indole NH permitting
the formation of a hydrogen bond with K101. Addition-
ally, a hydrogen bond between K101 and E138 is ob-
served. X-ray crystal structures of related inhibitors (1
and 2) reveal a nearly identical binding pocket, position
of inhibitor, and orientation of binding site side chains.

Z. Zhao et al. / Bioorg. Med. Chem. Lett. 18 (2008) 554–559
559
2. (a) Richman, D.; Havlir, D.; Corbeil, J.; Lonney, D.;
Ignacio, C.; Spector, S.; Sullivan, J.; Cheeseman, S.;
Barringer, K.; Pauletti, D. J. Virol. 1994, 68, 1660; (b)
Wei, X.; Ghosh, S.; Taylor, M.; Johnson, V.; Emini, E.;
Deutsch, P.; Lifson, J.; Bonhoeffer, S.; Nowak, M.; Hahn,
B.; Saag, M.; Shaw, G. Nature 1995, 373, 117.
3. Williams, T. M.; Ciccarone, T. M.; MacTough, S. C.;
Rooney, C. S.; Balani, S. K.; Condra, J. H.; Emini, E. A.;
Goldman, M. E.; Greenlee, W. J.; Kauffman, L. R.;
O’Brien, J. A.; Sardana, V. V.; Schleif, W. A.; Theoharides,
A. D.; Anderson, P. S. J. Med. Chem. 1993, 36, 1291.
4. (a) Silvestri, R.; De Martino, G.; La Regina, G.; Artico,
M.; Massa, S.; Vargiu, L.; Mura, M.; Loi, A. G.;
Marceddu, T.; La Colla, P. J. Med. Chem. 2003, 46,
2482; (b) Silvestri, R.; Artico, M.; De Martino, G.; La
Regina, G.; Loddo, R.; La Colla, M.; La Colla, P. J. Med.
Chem. 2004, 47, 3892.
5. (a) Silvestri, R.; Artico, M.; Bruno, B.; Massa, S.;
Novellino, E.; Greco, G.; Marongiu, M. E.; Pani, A.; De
Montis, A.; La Colla, P. Antiviral Chem. Chemother. 1998,
9, 139; (b) Ragno, R.; Artico, M.; De Martino, G.; La
Regina, G.; Coluccia, A.; Di Pasquali, A.; Silvestri, R.
J. Med. Chem. 2005, 48, 213; (c) Ragno, R.; Coluccia, A.;
La Regina, G.; De Martino, G.; Piscitelli, F.; Lavecchia,
A.; Novellino, E.; Bergamini, A.; Ciaprini, C.; Sinistro, A.;
Maga, G.; Crespan, E.; Artico, M.; Silvestri, R. J. Med.
Chem. 2006, 49, 3172.
Figure 3. X-ray co-crystal structure of 7e bound to wild-type RT.
These insights notwithstanding, the highly flexible nat-
ure of the NNRTI binding site11 makes rationalization
of inhibitor activity versus mutant RTs challenging. As
such, optimization of mutant RT inhibitors (e.g., in
the cases of 10b, 10c, and 13a versus 7e) was empirically
driven.
6. Isolated RT enzyme SPA assay: The polymerase activity
of reverse transcriptase was measured using a 500 nt
heteropolymeric RNA template and a biotinylated DNA
primer. 3HdNTP incorporation by purified recombinant
In summary, a new series of NNRTIs bearing an indole-
3-sulfonamide has been described. Introduction of a
pyrrolidine sulfonamide at the 3-position of the indole
ring generated analogues with excellent wild-type HIV-
RT potency and comparatively weak K103N and
Y181C RT activities. Variation in the indole 2-substitu-
ent (to provide analogues 10b, 10c, and 13a) improved
mutant activities and resulted in optimized inhibitors
with balanced wild-type, K103N, and Y181C RT inhibi-
tion which retain potent cellular activity. Further results
in this series will be reported in due course.
RT
[wild-type
(NL_43),
K103N(NL_43),
or
Y181C(HXB2), was measured by scintillation proximity
assay (SPA) on a Topcount instrument. Data represent
means and standard deviations of P2 experiments.
Antiviral activity: (a) The antiviral potency of compounds
against wild-type (H9IIIB) virus was measured in a
multiple-cycle replication assay in MT4 cells in the
presence of 10% FBS. Cells were infected overnight
(moi’’ 0.01) in the absence of compound, washed, and
cultured for 3 days in varying compound concentrations.
Viral replication was assessed by measuring p24 in culture
supernatants. The CIC95 is the lowest concentration of
compound inhibiting replication by P95%. (b) The
antiviral potency of compounds against wild-type (ABI
R8) virus or ABI R8 with K103N or Y181C mutations
was measured as described above. The CIC95 is the lowest
concentration of compound inhibiting replication by
P95%.
Acknowledgments
The authors thank Sandor Varga for extensive NMR
work to confirm the structural assignments of several
analogues, and Joan S. Murphy and Dr. Charles W.
Ross, III for obtaining HRMS data.
7. Leister, W.; Strauss, K.; Wisnoski, D.; Zhao, Z.; Lindsley,
C. J. Comb. Chem. 2003, 5, 322.
8. Young, S. D.; Amblard, M. C.; Britcher, S. F.; Grey, V.
E.; Tran, L. O.; Lumma, W. C.; Huff, J. R.; Schleif, W. A.;
Emini, E. E.; O’Brien, J. A.; Pettibone, D. J. Bioorg. Med.
Chem. Lett. 1995, 5, 491.
References and notes
1. (a) Yeni, P. G.; Hammer, S. M.; Carpenter, C. C. J.;
Cooper, D. A.; Fischl, M. A.; Gatell, J. M.; Gazzard, B.
G.; Hirsch, M. S.; Jacobsen, D. M.; Katzenstein, D. A.;
Montaner, J. S. G.; Richman, D. D.; Saag, M. S.;
Schechter, M.; Schooley, R. T.; Thompson, M. A.; Vella,
S.; Volberding, P. A. J. Am. Med. Assoc. 2002, 288, 222;
(b) Palella, F. J.; Delaney, K. M.; Moorman, A. C.;
Loveless, M. O.; Fuhrer, J.; Satten, G. A.; Aschman, D. J.;
Holmberg, S. D. N. Engl. J. Med. 1998, 338, 853; (c)
Tarby, C. M. Curr. Top. Med. Chem. 2004, 4, 1045; (d)
Fortin, C.; Joly, V.; Yeni, P. Expert Opin. Emerging Drugs
2006, 11, 217.
9. Compounds were soaked into a pre-existing crystal of
HXB2 RT containing a weakly bound efavirenz analogue.
˚
Electron density was mapped at a resolution of 2.4 A and
the structure solved by molecular replacement. PDB
deposition number 2RF2.
10. Mager, P. P. Drug Design Disc. 1996, 14, 241.
11. Himmel, D. M.; Das, K.; Clark, A. D.; Hughes, S. H.;
Benjahad, A.; Oumouch, S.; Guillemont, J.; Coupa, S.;
Poncelet, A.; Csoka, I.; Meyer, C.; Andries, K.; Nguyen,
C. H.; Grierson, D. S.; Arnold, E. J. Med. Chem. 2005, 48,
7582.