Synthesis and biological activity of novel nonnucleoside inhibitors of HIV-1 reverse transcriptase. 2-Aryl-substituted benzimidazoles

Article abstract of DOI:10.1021/jm970096g

The development of new nonnucleoside inhibitors of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) active against the drug-induced mutations in RT continues to be a very important goal of AIDS research. We used a known inhibitor of HIV-1 RT, 1-(2,6- difluorophenyl)-1H,3H-thiazolo[3,4-a]benzimidazole (TZB), as the lead structure for drug design with the objective of making more potent inhibitors against both wild-type (WT) and variant RTs. A series of structurally related 1,2-substituted benzimidazoles was synthesized and evaluated for their ability to inhibit in vitro polymerization by HIV-1 WT RT. A structure- activity study was carried out for the series of compounds to determine the optimum groups for substitution of the benzimidazole ring at the N1 and C2 positions. The best inhibitor, 1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)- 4-methylbenzimidazole (35), has an IC₅₀ = 200 nM against HIV-1 WT RT in an in vitro enzyme assay. Cytoprotection assays utilizing HIV-infected MT-4 cells revealed that 35 had strong antiviral activity (EC₅₀ = 440 nM) against wild-type virus while retaining broad activity against many clinically observed HIV-1 strains resistant to nonnucleoside inhibitors. Overall, the activity of 35 against wild-type and resistant strains with amino acid substitution in RT is 4-fold or greater than that of TZB and is comparable to that of other nonnucleoside inhibitors currently undergoing clinical trials, most of which do not have the capacity to inhibit the variant forms of the enzyme.

Full text of DOI:10.1021/jm970096g

J . Med. Chem. 1997, 40, 4199-4207
4199
Articles
Syn th esis a n d Biologica l Activity of Novel Non n u cleosid e In h ibitor s of HIV-1
Rever se Tr a n scr ip ta se. 2-Ar yl-Su bstitu ted Ben zim id a zoles
Thomas Roth,†,‡ Marshall L. Morningstar,† Paul L. Boyer,§ Stephen H. Hughes,§ Robert W. Buckheit, J r.,| and
Christopher J . Michejda*,†
Molecular Aspects of Drug Design Section and Gene Expression in Eukaryotes Section, ABL-Basic Research and
Development Program, National Cancer Institute-Frederick Cancer Research and Development Center, P.O. Box B,
Frederick, Maryland 21702, and Southern Research Institute-Frederick Research Center, 431 Aviation Way,
Frederick, Maryland 21701
Received February 14, 1997X
The development of new nonnucleoside inhibitors of human immunodeficiency virus type-1
(HIV-1) reverse transcriptase (RT) active against the drug-induced mutations in RT continues
to be a very important goal of AIDS research. We used a known inhibitor of HIV-1 RT, 1-(2,6-
difluorophenyl)-1H,3H-thiazolo[3,4-a]benzimidazole (TZB), as the lead structure for drug design
with the objective of making more potent inhibitors against both wild-type (WT) and variant
RTs. A series of structurally related 1,2-substituted benzimidazoles was synthesized and
evaluated for their ability to inhibit in vitro polymerization by HIV-1 WT RT. A structure-
activity study was carried out for the series of compounds to determine the optimum groups
for substitution of the benzimidazole ring at the N1 and C2 positions. The best inhibitor, 1-(2,6-
difluorobenzyl)-2-(2,6-difluorophenyl)-4-methylbenzimidazole (35), has an IC50 ) 200 nM against
HIV-1 WT RT in an in vitro enzyme assay. Cytoprotection assays utilizing HIV-infected MT-4
cells revealed that 35 had strong antiviral activity (EC50 ) 440 nM) against wild-type virus
while retaining broad activity against many clinically observed HIV-1 strains resistant to
nonnucleoside inhibitors. Overall, the activity of 35 against wild-type and resistant strains
with amino acid substitution in RT is 4-fold or greater than that of TZB and is comparable to
that of other nonnucleoside inhibitors currently undergoing clinical trials, most of which do
not have the capacity to inhibit the variant forms of the enzyme.
In tr od u ction
8-chloro-4,5,6,7-tetrahydro-5-methylimidazo[4,5,1-jk]-
[1,4]benzodiazepin-2(1H)-one (8-Cl TIBO) and nevir-
apine. As opposed to the nucleoside drugs, the NNRTIs
do not function as chain terminators and do not bind at
the dNTP binding site. The results of mutational,
modeling, and crystallographic studies suggest that
most of these compounds share a common binding site
located proximal to the RT polymerase active site.7-10
However, in the absence of the NNRTI, the nonnucleo-
side binding pocket does not exist. It is only during the
binding of an inhibitor that the aromatic residues
Tyr181, Tyr188, and Trp229 reorient to create a hydro-
phobic pocket of sufficient volume to accommodate the
inhibitor.8 By binding to this allosteric site, the NNRTI
increases the distance between the nucleic acid primer
grip and the dNTP binding site in RT, suggesting this
as a possible mechanism for the inhibition of polymerase
activity.8 The structural features that seem important
for NNRTI binding include the presence of planar
π-electron systems and the ability of those systems to
adopt a conformation designated the “butterfly-like”
orientation.9,10 Despite these general features, the
structures of different NNRTIs bound to RT vary
considerably.7,9,10 This complexity arises from the abil-
ity of the side-chain residues surrounding the pocket
to adapt to each bound NNRTI in a highly specific
manner, closing down around the surface of the drug
to make tight van der Waals contacts. Because of this
unique binding, NNRTIs do not inhibit other poly-
The acquired immunodeficiency syndrome (AIDS) was
first recognized in 1981 and has since become a major
worldwide epidemic. A key target in the search for
effective drugs useful for AIDS therapy is the viral
enzymes that have critical roles in the life cycle of the
human immunodeficiency virus type 1 (HIV-1), the
causative agent of AIDS. One such essential enzyme
is reverse transcriptase (RT), an enzyme that contains
both a DNA polymerase activity that can use either
RNA or DNA as a template and a ribonuclease H
activity.1,2 These activities are essential for the conver-
sion of retroviral genomic RNA into the double-stranded
linear viral DNA that subsequently integrates into the
genome of the infected host cell. Inhibition of RT should
therefore provide an effective means of blocking HIV-1
replication.3,4
A number of inhibitors of HIV RT have been devel-
oped.5,6 These inhibitors can be generally divided into
two classes: (i) nucleoside analogues such as 3′-azido-
3′-deoxythymidine (AZT) and 2′,3′-dideoxycytidine (ddC)
and (ii) nonnucleoside RT inhibitors (NNRTI) such as
* To whom correspondence should be addressed.
† Molecular Aspects of Drug Design Section.
‡ Current address, Oncotest GmbH, Am Flughafen 8, 79110 Freiburg,
Germany.
§ Gene Expression in Eukaryotes Section.
| Southern Research Institute-Frederick Research Center.
X Abstract published in Advance ACS Abstracts, December 1, 1997.
S0022-2623(97)00096-4 CCC: $14.00 © 1997 American Chemical Society

4200 J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26
Roth et al.
Sch em e 1a
F igu r e 1. Retrosynthetic analysis.
merases (not even HIV-2 RT) and are thus potentially
highly effective and nontoxic drugs. The goal of our
work was to determine the structural features of
NNRTIs that enhance the binding to RT with a special
emphasis on the structural features least affected by
mutations surrounding the NNRTI binding pocket.
Although 1-(2,6-difluorophenyl)-1H,3H-thiazolo[3,4-
a]benzimidazole (TZB) was shown to be an inhibitor of
HIV-1 RT, its potential therapeutic utility is hampered
by a number of liabilities.11-13 One problem is the
metabolic oxidation of the thiazolo ring of TZB leading
to the formation of less potent sulfoxide and sulfone
metabolites.14 A second problem with TZB is the
complete loss of antiviral activity against HIV-1 variants
containing amino acid substitutions in RT that arise
following NNRTI treatment.15,16 As a means to improve
the RT inhibitory activity of TZB, removal of the thiazolo
ring appeared to be an ideal starting point for the
development of a more effective NNRTI. Retrosynthetic
analysis of TZB suggested that opening of the thiazolo
ring leads to N-benzyl-2-alkylbenzimidazoles (Figure 1).
Similar to TZB, N-benzyl-2-alkylbenzimidazoles contain
two aromatic rings that can form a butterfly-like
conformation critical for binding to the NNRTI binding
pocket. As indicated in Figure 1, synthesis of N-benzyl-
2-alkylbenzimidazoles would readily be accomplished by
the alkylation of 2-substituted benzimidazoles. The goal
of this study was to determine substituents of N-
benzylbenzimidazole, particularly at the C2 position,
that would enhance the inhibition of HIV-1 wild-type
(WT) and NNRTI resistant HIV-1 variants. The second
part of this goal was especially important because the
emergence of mutant forms of the virus renders most
of the known NNRTIs ineffective.17 This paper details
our synthetic efforts toward achieving this goal leading
to the discovery of 1-(2,6-difluorobenzyl)-2-(2,6-difluoro-
phenyl)-4-methylbenzimidazole (35). This compound is
a better inhibitor of WT RT than TZB and appears to
retain its inhibitory activity against a broad range of
HIV-1 RT variants that engender resistance to many
NNRTIs.
a
Reagents: (a) glycolic or isobutyric acid, 4 N HCl, reflux; (b)
2,6-F2BnBr (27); (c) t-BDMSCl, pyridine; (d) Bu4NF, THF; (e)
KMnO4, H2SO4; (f) CrO3.
butyldimethylsilyl (TBDMS) before N-alkylation with
2,6-difluorobenzyl bromide (27). Removal of TBDMS
from 33 gave the desired 1-(2,6-difluorobenzyl)-2-(hy-
droxymethyl)-4-methylbenzimidazole (51).
Oxidation of the hydroxymethyl to the carboxylic acid,
however, turned out to be problematic. When a strong
oxidant (KMnO4) was used, the isolated product 52
indicated that decarboxylation occurred under the acidic
reaction conditions. Oxidation under basic conditions
with chromium oxide also yielded 52 along with the
formyl product (53). The carboxylic acid was never
isolated in this study. The bis(2,6-difluorobenzyl) de-
rivative (34) was prepared by bis-alkylation of 2-(hy-
droxymethyl)benzimidazole (2).
The ability to inhibit HIV-1 WT RT by the hydrogen
(52), methyl (38), hydroxymethyl (51), isopropyl (37),
formyl (53), phenyl (42), and bis(2,6-difluorobenzyl) (34)
compounds was determined by measuring the relative
nucleotide incorporation using a poly(rC)-oligo(dG) tem-
plate primer at 10 mmol drug concentration to the
amount of incorporation with no inhibitor present.18 As
seen in Table 1, most of the C2 alkyl compounds failed
to appreciably inhibit HIV-1 RT. Only in the case of
compound 42, where C2 was phenyl, was significant RT
inhibition determined. To understand the structural
variation introduced by the C2 phenyl, we compared the
geometry of TZB and 1-(2,6-difluorobenzyl)-2-phenyl-
benzimidazole (42) by semiempirical quantum mechan-
ical minimization at the AM1 level.
As seen in Figure 2, considerable similarity exists
between the energy minimized butterfly-like shape of
TZB and 42. For TZB, the butterfly-like shape has been
proven by crystallographic analysis.19 In contrast to
TZB, 42 has more than one butterfly-like conformation
that arises by rotation of the benzyl side chain. Whereas
the C2 phenyl of the AM1 energy-minimized 42 does
not overlap the thiazolo ring of TZB, at least two higher
energy rotational isomers result in almost complete
overlap. Without an X-ray structure of 42 in a complex
with HIV-1 RT, the correct butterfly-like orientation of
this compound in the NNRTI binding pocket cannot be
predicted. Nevertheless, since some predominant con-
tributions to binding of NNRTI to RT involve π stacking
and hydrophobic interactions, this extra aromatic ring
Resu lts a n d Discu ssion
The first 2-substituted derivatives of N-(2,6-difluoro-
benzyl)benzimidazole that we examined were the meth-
yl, hydroxymethyl, isopropyl, carboxylic, formyl, and
phenyl derivatives. In the case of the methyl and
phenyl compounds, commercially available benzimid-
azoles were allowed to react with 2,6-difluorobenzyl
bromide (27) to give compounds 38 and 42. Preparation
of hydroxymethyl analogues was achieved by acid-
catalyzed condensation-cyclization of glycolic acid with
either o-phenylenediamine (1) or 2,3-diaminotoluene (3)
via an approach similar to the one used by Chimirri et
al. for the synthesis of TZB11,12 (Scheme 1). The
hydroxymethyl group was then protected with tert-

2-Aryl-Substituted Benzimidazoles
J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26 4201
Ta ble 1. Structural, Physical, and Enzyme Inhibition Data for 1-(2,6-Difluorobenzyl)-2-substituted-benzimidazoles
no.
X
R′
formula
mp, °C
anal.
% inhibn (10 µM)a
42
53
37
52
38
51
34
H
Ph
C20H14F2N2
C16H12F2N2O
C18H18F2N2
C15H12F2N2
C15H12F2N2
C16H14F2N2O
C22H16F4N2O
127-129
144-146
151-153
98-100
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
77
59
53
40
22
12
7
CH3
CH3
CH3
H
CH3
H
CHO
i-Pr
H
CH3
CH2OH
99-100
203-205
107-109
CH2O(2,6-F2Bn)
a
Enzyme assay done with WT RT.
inhibitory activity. These results suggest that the size
of the inhibitor that the NNRTI binding pocket can
accommodate is limited.
We synthesized a second series of compounds to ask
whether the position and nature of the substitutents on
the benzyl ring at N1 were analogous to those in the
TZB series. In the TZB series, the optimal anti-HIV
activity was achieved when the phenyl ring was sub-
stituted at the 2 and 6 positions with fluorine. Treat-
ment of benzimidazole 19 or 20 with benzyl bromide
analogues (benzyl bromide; 2,6-dichloro-R-bromo tolu-
ene; 2,3,4,5,6-pentafluoro-R-bromo toluene) allowed us
to test whether compounds with hydrogen, chlorine, or
multiple fluorines on the N1 benzyl ring were better
inhibitors. Since a number of NNRTIs, such as 2-nitro-
phenyl phenyl sulfone21 and 5-chloro-3-(phenylsulfonyl)-
indole-2-carboxamide,22 contain sulfonyl links, we also
assessed whether a sulfonyl group could replace the
methylene linker in compound 35. By allowing 19 or
20 to react with benzenesulfonyl chloride, compounds
48 and 49 were obtained in good yields. Similarly,
treatment of compound 19 with 2,6-difluorobenzoyl
chloride provided the N-(2,6-difluorobenzoate) (50) al-
lowing us to examine the carbonyl group as the linker.
We also tested the effect of introducing nitrogen into
the N1-benzyl ring by synthesizing the 3-pyridyl deriva-
tive (46) via alkylation with R-(bromomethyl)pyridine.23
As seen in Table 3, the benzenesulfonyl and benzoate
derivatives (48, 49, 50) did not appreciably inhibit HIV-1
RT. Substitution of the phenyl ring by a pyridine ring
(46) similarly led to lower inhibition. Removal of the
fluorines at the 2 and 6 positions (30 or 31) or replace-
ment with chlorine (32) also resulted in decreased
inhibition. Likewise, increasing the number of fluorines
on the benzyl ring (45) yielded a compound showing
greatly decreased inhibition. These findings are similar
to those reported for the TZB series.12-14
F igu r e 2. AM1 minimized structures of 42 and TZB.
present in 42 could significantly influence these interac-
tions. The ability of HIV-1 RT to accommodate the extra
phenyl ring led us to examine additional aromatic
moieties that might further enhance binding.
The general approach used for the synthesis of
2-arylbenzimidazoles is outlined in Scheme 2. As is
evident from this scheme, a variety of 2-arylbenzimid-
azoles can be prepared by using an appropriate acylat-
ing reagent. In most cases, high yields of the desired
N-acylnitroaniline could be obtained from either 2-nitro-
aniline (8) or 2-methyl-6-nitroaniline (9). Only in the
case of the 1-naphthyl derivative (14) was a mixture of
mono- and bisacylated products formed. Subsequent
reductive cyclization of compounds 10-17 with iron in
acetic acid yielded the desired 2-arylbenzimidazoles 19-
26. Following coupling with 2,6-difluorobenzyl bromide
(27), the desired 2-aryl-1-(2,6-difluorobenzyl)benzimid-
azoles [R2 ) 2,6-difluorophenyl (28 and 35); 4-cyano-
phenyl (36); 2-methylphenyl (39); naphthyl (40 and 41);
pyridyl (43 and 44)] were obtained.
Biochemical activity of the various compounds was
initially determined by examining their ability to inhibit
HIV-1 WT RT at 10 mM drug concentration (Table 2).
In the cases where the percent inhibition was greater
than 75%, the IC50 (the drug quantity required to inhibit
50% of RT activity) and EC50 (the drug quantity
required to inhibit 50% of virus-induced cell killing of
CEM-SS cells in vitro by HIV-1)20 were determined.
Substitution of the phenyl group with fluorine at the 2
Biological evaluation of the RT inhibitory properties
of the most active difluorophenyl compounds, 28 and
35, was carried out in vitro with CEM-SS cells infected
with WT or HIV-1 variants containing amino acid
substitutions in RT.24 Comparison of the methyl 35 and
its desmethyl analogue 28 revealed that the methylated
compound 35 was consistently 3-4-fold better at inhib-
iting the various viral isolates examined (Table 4). For
most of the NNRTIs, π-stacking and van der Waals
interactions between the inhibitor and the NNRTI
binding pocket are very important. The enhanced
inhibitory activity for 35 suggests that additional hy-
and 6 positions yielded the best inhibitor, 35 (IC50
)
200 nM and EC50 ) 440 nM). Conservative changes,
such as the addition of an o-methyl or a heteroatom to
the 2-phenyl ring, resulted in only a small decrease in
the percent inhibition (e.g. 39 and 44 vs 42). Surpris-
ingly, the 3-pyridyl compound (43) showed much less
activity (over 10× lower EC50 as compared to the
4-pyridyl, 44). Larger or longer aromatic moieties at
C2, such as naphthyl or 4-cyanophenyl, led to loss of

4202 J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26
Roth et al.
Sch em e 2a
a
Reagents: (a) aroyl chloride, pyridine/THF (1:1); (b) Fe (18), AcOH; (c) 2,6-F2BnBr (27), NaH, THF; (d) BnBr (29) or PhSO2Cl (47) or
2,6-F2BzCl (7), NaH, THF.
Ta ble 2. Structural, Physical, and Enzyme Inhibition Data for 1-(2,6-Difluorobenzyl)-2-arylbenzimidazoles
no.
42
X
R′
formula
mp, °C
anal.
% inhibn (10 µM)
IC50 (µM)a
EC50 (mM)b
H
H
CH3
H
CH3
CH3
CH3
CH3
CH3
Ph
C20H14F2N2
C20H12F4N2
C21H14F4N2
C21H16F2N2
C20H15F2N3
C20H15F2N3
C22H15F2N3
C25H18F4N3
C25H18F4N3
127-129
138-140
182-186
138-140
171-172
186-188
207-208
121-123
175-176
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
77
93
92
71
70
35
26
2
16
0.11
0.20
6.06c
1.70d
0.44d
28
35
39
44
43
36
40
41
TZB
2,6-F2Ph
2,6-F2Ph
2-CH3-Ph
4-Py
3-Py
4-CN-Ph
1-Nap
3.5
31.6
2-Nap
8
84
C
15H10F2N2S
0.5e
0.52f
a
b
The quantity of drug required to reduce WT RT enzyme activity by 50% (IC50). 50% cellular protection of CEM-SS cells from HIV-1
induced cytopathicity. c Average of two independent experiments. Average of three independent experiments. e For ribosomal RNA by
d
Buckheit et al.13 f Yang et al.25
drophobic substitutents on the benzimidazole ring can
significantly improve binding of this class of drugs to
the NNRTI binding pocket residues.
Y181C) which have shown resistance to combination
nucleoside/nonnucleoside treatment. Equally impor-
tant, 35 is not cytotoxic at <10 mM inhibitor concentra-
tion in cell culture, resulting in an antiviral index
(AI50%) >70.
In comparing 35 against TZB, the starting point in
our drug design effort, a 3-fold increase in inhibition
against WT RT has been achieved (Table 4). The EC50
for 35 against WT HIV-1 RT (NL4-3 isolate) in a
cytopathic cell killing assay is in fact similar to the EC50
of TIBO. However, the real advantage of 35 over TZB
involves its ability to inhibit many of the mutant HIV-1
isolates which are resistant to TZB. Likewise, 35
inhibits mutant HIV-1 RTs (i.e., A98G, L100I, V179D
and Y188C isolates) which are resistant to TIBO.
Additionally, our data suggest that 35 may be useful in
combination drug therapy with nucleoside inhibitors
since it is effective against nucleoside resistant strains
(L74V and 4xAZT, an AZT drug resistant isolate). In
fact, 35 inhibits strains (4xAZT/L100I and 4xAZT/
In summary, this paper presents our initial studies
in the development of a novel series of nonnucleoside
HIV-1 RT inhibitors. By using standard medicinal
chemistry techniques, a series of 2-substituted benz-
imidazoles was synthesized and tested as NNRTIs.
Substitution of the C2 of benzimidazole with a 2,6-
difluorophenyl ring was found to give the best HIV-1
WT RT inhibition. Biological testing using a cytopathic
cell killing assay found that compound 35 yielded the
best overall biological profile of this series. The sub-
stitution of an aryl group in place of the thiazolo ring
of TZB produced a novel nonnucleoside HIV-1 RT
inhibitor, while eliminating the metabolically labile

2-Aryl-Substituted Benzimidazoles
J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26 4203
Ta ble 3. Structural, Physical, and Enzyme Inhibition Data for 1-Aryl-2-(2,6-difluorophenyl)benzimidazoles
no.
X
R′′
formula
mp, °C
anal.
% inhibn (10 mM)
IC50 (mM)
EC50 (mM)
28
35
30
31
32
45
46
48
49
50
H
CH3
H
CH3
CH3
CH3
CH3
H
2,6-F2Bn
2,6-F2Bn
Bn
C20H12F4N2
C21H14F4N2
138-140
182-186
122-125
112-117
202-203
155-156
131-132
104-106
134-135
144-146
C,H,N
C,H,N
C,H,N
C,H,Na
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
C,H,N
93
92
71
87
58
36
43
52
39
8
0.11
0.20
18.6
1.6
1.70
0.44
toxic >32
0.75
C
20H14F2N2
Bn
C21H16F2N2
C21H14Cl2F2N2
C21H11F7N2
2,6-Cl2Bn
2,3,4,5,6-F5Bn
CH2(3-Py)
PhSO2
PhSO2
2,6-F2Bz
3.16
C20H15F4N3
C19H12F2N2SO2
C20H14F2N2SO2
C20H10F4N2O
CH3
H
a
Anal. (C21H16F2N2‚1/4H2O) Calcd C, 74.43; H, 4.91; N, 8.27. Found C, 74.81; H, 4.90; N, 7.85.
Ta ble 4. Cross-Resistance Profile with NNRTI Resistant HIV
for 4 h. After cooling to room temperature, the pH was
adjusted to 7 with NaOH(solid). The resulting brown precipi-
tate was filtered, washed with water, and dried in vacuo (0.71
g, 4.8 mmol, 40%): 1H NMR (300 MHz, DMSO-d6) δ 7.48 (m,
2H, H4,7), 7.13 (m, 2H, H5,6), 5.67 (t, J ) 5.5 Hz, 1H, OH), 4.68
(d, J ) 5.5 Hz, 2H, CH2).
2-(Hyd r oxym eth yl)-4-m eth ylben zim id a zole (4). 2,3-
Diaminotoluene (3) (2.65 g, 21.7 mmol) and 85% glycolic acid
(8.20 g, 107.8 mmol, 500 M%) were stirred in 4 N HCl (80 mL)
under reflux for 2 h. After cooling to room temperature, the
pH was adjusted to 7 with NaOH(solid). The resulting brown
precipitate was filtered, washed with water, and dried in vacuo
(2.97 g, 18.3 mmol, 84% yield): 1H NMR (200 MHz, DMSO-
d6) δ 7.28 (br d, 1H, H7), 6.98 (dd, J ) 8.0, 7.3 Hz, 1H, H6),
6.90 (m, 1H, H5), 4.67 (s, 2H, CH2), 2.49 (s, 3H, CH3).
Isolates from Cytopathic Cell Killing Assaya
isolate
35
28
TZB
1.7
0.7
17.7
12.2
>20
>20
>20
TIBO
NL4-3 (WT)
L74V
A98G
L100I
K101E
K103N
V106A
V108I
V179D
0.5
0.1
1.4
0.3
16.7
8.1
20
2.8
0.5
6
1.85
0.46
4.75
1.36
0.3
0.2
11
17.4
17.4
17.4
12.5
2.4
>20
12.9
>20
10.4
2.3
15.2
11.7
0.27
0.84
>20
9.7
3.1
16.3
6.2
4.2
Y181C
Y188C
2.3
0.1
0.2
3.5
>20
>17.4
4xAZTb
4xAZT/L100I
4xAZT/Y181C
1.5
1.7
0.3
>17.4
2.0
2-[[(t er t -Bu t yld im e t h ylsilyl)oxy]m e t h yl]-4-m e t h yl-
ben zim id a zole (5). To 4 (1.50 g, 9.24 mmol) dissolved in
pyridine (30 mL) was added t-BDMSCl (2.35 g, 15.6 mmol, 170
M%). After 4 h at room temperature, the reaction was
concentrated to dryness. The residue was redissolved in
CH2Cl2 and washed with NaHCO3(sat aq) and NaCl(sat aq),
dried (Na2SO4), filtered, and concentrated. The product was
purified by flash chromatography, eluting with 4% MeOH/
CH2Cl2, and then recrystallized from hexane (2.15 g, 7.78
mmol, 84% yield of white powder): 1H NMR (300 MHz,
CD3OD) δ 7.36 (br d, J ) 11.1 Hz, 1H, H7), 7.11 (dd, J ) 11.1,
10.4 Hz, 1H, H6), 7.01 (br d, J ) 10.4 Hz, 1H, H5), 4.94 (s, 2H,
CH2O), 2.55 (s, 3H, CH3), 0.95 (s, 9H, t-BuSi), 0.14 (s, 6H,
Si(CH3)2).
14.5
a
Antiviral data is reported as the average from three determi-
nations of the quantity of drug in micromolar required to reduce
b
cell killing or virus production by 50% (EC50). 4xAZT is an AZT
resistant virus isolate containing four specific amino acid changes.
sulfur. In addition, our studies indicate that 35 should
have broad inhibitory effects against both WT and a
number of clinically important variant HIV-1 RTs. It
is interesting to note that compound 35 resembles
another important RT inhibitor, R-anilinophenylaceta-
mide (R-APA),24 that also exhibits broad spectrum
inhibitory activity against variant RTs. The good activ-
ity against variant forms of RT exhibited by both
compounds may reflect on their flexibility that allows
them to assume a number of butterfly-like conforma-
tions in response to the spacial demands imposed by
the various RT mutations.
2-Isop r op yl-4-m eth ylben zim id a zole (6). 3 (1.00 g, 8.19
mmol) and isobutyric acid (4.0 mL, 43.1 mmol, 525 M%) were
dissolved in 4 N HCl (90 mL). After 2 h at reflux, the reaction
was cooled in an ice bath and the pH adjusted to 7 with NaOH
(solid). The resulting precipitate was filtered and washed with
water (0.63 g, 3.62 mmol, 44% yield): 1H NMR (200 MHz,
DMSO-d6) δ 12.02 (br, 1H, NH), 7.26 (br, 1H, H7), 6.99 (dd, J
) 7.4, 7.7 Hz, 1H, H6), 6.87 (ddt, J ) 0.8, 1.1, 7.4 Hz, 1H, H5),
3.14 (sep, J ) 7.0, 1H, i-Pr), 2.48 (s, 3H, CH3), 1.34 (d, J ) 7.0
Hz, 6H, i-Pr).
Exp er im en ta l Section
Gen er a l. Where analyses are indicated by symbols of the
elements, results were within 0.4% of the theoretical values.
Elemental analyses were determined by Atlantic Microlab, Inc.
Norcross, GA. Melting points were determined on an electro-
thermal apparatus using the supplied, stem-corrected ther-
mometer and are as read. 1H NMR spectra were recorded on
a Varian 200 or 300 MHz spectrometer with Me4Si as the
internal standard. Yields were not optimized. Merck silica
gel, 70-230 and 230-400 mesh, was used for gravity and flash
chromatography, respectively. Primes used in NMR assign-
ments are defined by R′ and R′′ in the structures shown in
Tables 1 and 3.
Meth od A: N-(2,6-Diflu or oben zoyl)-2-n itr oa n ilid e (10).
To 2-nitroaniline (8) (1.1 g, 8.0 mmol) dissolved in THF (10
mL) and pyridine (2 mL) was added 2,6-difluorobenzoyl
chloride (7) (1.11 mL, 8.8 mmol, 110 M%) dissolved in THF
(15 mL). After stirring for 5 h at room temperature, the
reaction was concentrated to dryness. The residue was
redissolved in ethyl acetate and washed with NaHSO4(5%
solution), NaHCO3(sat. aq) and NaCl(sat. aq). The organic
layer was dried (Na2SO4), filtered, and concentrated under
reduced pressure. The residue was recrystallized from ethyl
acetate/hexane resulting in slightly yellow crystals (1.7 g, 6.1
mmol, 76%): mp 139 °C; 1H NMR (300 MHz, CD2Cl2) δ 10.77
(s, 1H, NH), 8.89 (dd, J ) 1.2, 8.5 Hz, 1H, H3), 8.26 (dd, J )
1.5, 8.5 Hz, 1H, H6), 7.75 (ddd, J ) 1.2, 7.9, 8.5 Hz, 1H, H5),
2-(Hyd r oxym eth yl)ben zim id a zole (2). o-Phenylenedi-
amine (1) (1.3 g, 12 mmol) and 85% glycolic acid (2.74 g, 36
mmol, 300 M%) were stirred in 4 N HCl (40 mL) under reflux

4204 J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26
Roth et al.
7.50 (m, 1H, H3′), 7.29 (ddd, J )1.5, 7.9, 8.5 Hz, 1H, H4), 7.07
(m, 2H, H3′,5′).
mmol, 85% yield of white powder): 1H NMR (300 MHz, CD2Cl2)
δ 9.92 (br, 1H, NH), 7.69 (br, 1H, H4,7), 7.45 (m, 1H, H4′), 7.31
(ddd, J ) 3.2, 4.0, 6.0 Hz, 2H, H5,6), 7.11 (m, 2H, H3′,5′).
The following compounds were prepared by method B.
2-(2,6-Diflu or op h en yl)-4-m eth ylben zim id a zole (20). 11
(1.35 g, 4.62 mmol) and 18 (1.3 g) gave, after recrystallization
from diethyl ether:hexane (3:1), 1.1 g (4.48 mmol, 97%) of
colorless crystals: mp 148 °C; 1H NMR (300 MHz, DMSO-d6)
δ 12.86 (s, 1H, NH), 7.66 (m, 1H, H4′), 7.33 (m, 2H, H3′,5′), 7.27-
7.18 (m, 1H, H7), 7.15 (dd, J ) 8.0, 7.2 Hz, 1H, H6), 7.05 (d, J
) 7.2 Hz, 1H, H5), 2.55 (s, 3H, CH3).
2-(4-Cyan oph en yl)-4-m eth ylben zim idazole (21). 17 (3.15
g, 11.2 mmol) and 18 (2.15 g) gave, after recrystallization from
methanol, 1.69 g (7.57 mmol, 68%) of colorless crystals: 1H
NMR (300 MHz, DMSO-d6) δ 8.18 (m, 2H, H2′,6′), 7.79 (m, 2H,
H3′,5′), 7.46 (m, 1H, H7), 7.21 (dd, J ) 7.4, 8.1 Hz, 1H, H6), 7.05
(m, 1H, H5), 2.62 (s, 3H, CH3).
The following compounds were prepared by method A.
N-(2,6-Diflu or oben zoyl)-2-m eth yl-6-n itr oa n ilid e (11).
2-Methyl-6-nitroaniline (9) (2.25 g, 14.8 mmol) and 7 (1.9 mL,
15 mmol, 100 M%) after stirring overnight and purification
by gravity chromatography eluting with CH2Cl2/hexane/diethyl
ether (380 + 120 + 10) gave 2.36 g (8.1 mmol, 55%) of slightly
yellow crystals: 1H NMR (300 MHz, CD2Cl2) δ 8.55 (s, 1H, NH),
7.87 (dd, J ) 8.2, 0.92 Hz, 1H, H5), 7.61 (d, J ) 7.4 Hz, 1H,
H3), 7.48 (m, 1H, H4′), 7.38 (dd, J ) 7.4, 8.2 Hz, 1H, H4), 7.05
(m, 2H, H3′,5′), 2.43 (s, 3H, CH3).
N-Ison icotin oyl-2-m eth yl-6-n itr oa n ilid e (12). 9 (1.52 g,
10.0 mmol) and isonicotinoyl chloride hydrochloride (2.95 g,
19.7 mmol, 200 M%) and a second addition of isonicotinoyl
chloride hydrochloride (1.05 g, 5.90 mmol, 60 M%) at 4 h after
stirring overnight and recrystallization from diethyl ether:
hexane (3:1) gave 1.61 g (6.26 mmol, 63% yield) of white
powder: 1H NMR (300 MHz, CD2Cl2) δ 9.06 (br, 1H, NH), 8.82
(m, 2H, H2′,6′), 7.93 (br d, J ) 7.9 Hz, H6), 7.77 (m, 2H, H3′,5′),
7.63 (br d, J ) 8.0 Hz, 1H, H3), 7.40 (dd, J ) 7.9, 8.0 Hz, H4),
2.38 (s, 3H, CH3).
N-(2-Meth ylben zoyl)-2-n itr oa n ilid e (13). 8 (1.28 g, 9.3
mmol) and o-toluoyl chloride (1.52 mL, 11.6 mmol, 125 M%)
gave 2.2 g (8.6 mmol, 92% yield) of yellow crystals after
recrystallization from diethyl ether:hexane (1:1): 1H NMR (300
MHz, CDCl3) δ 10.75 (s, 1H, NH), 8.98 (d, J ) 8.5 Hz, 1H,
H3), 8.27 (d, J ) 8.5 Hz, 1H, H6), 7.72 (dd, J ) 8.5, 7.4 Hz, 1H,
H5), 7.61 (d, J ) 8.4 Hz, 1H, H6′), 7.41 (dd, J ) 8.5, 7.4 Hz,
1H, H4), 7.32 (t, J ) 7.4 Hz, 1H, H4′), 7.31 (d, J ) 7.4 Hz, 1H,
H3′), 7.23 (dd, J ) 8.4, 7.4 Hz, 1H, H5′), 2.56 (s, 3H, CH3).
N-(1-Na p h th oyl)-2-m eth yl-6-n itr oa n ilid e (14). 9 (1.52
g, 10.0 mmol) and 1-naphthoyl chloride (2.00 mL, 13.3 mmol,
130 M%) and a second addition of 1-naphthoyl chloride (1.00
mL, 6.65 mmol, 66 M%) at 1 h after stirring for 6 h and
recrystallization from ethyl acetate gave 2.79 g (9.11 mmol,
91% yield) of white powder: 1H NMR (200 MHz, CD2Cl2) δ
8.09-7.99 (m, 2H), 7.77 (m, 1H), 7.66-7.41 (m, 5H), 7.23 (d,
J ) 8.3 Hz, 1H), 7.24 (dd, J ) 7.3, 8.3 Hz, 1H), 2.77 (s, 3H,
CH3).
N-(2-Na p h th oyl)-2-m eth yl-6-n itr oa n ilid e (15): 9 (1.52 g,
10.0 mmol) and 2-naphthoyl chloride (2.00 mL, 13.3 mmol, 130
M%) and a second addition of 2-naphthoyl chloride (1.00 mL,
6.65 mmol, 66 M%) at 1 h yielded, after 6 h and recrystalli-
zation from ethyl acetate, 2.29 g (7.48 mmol, 75% yield) of
white powder: 1H NMR (300 MHz, CD2Cl2) δ 9.15 (br s, 1H,
NH), 8.49 (s, 1H, H1′), 8.06-7.86 (m, 5H, nap and H5), 7.72-
7.45 (m, 3H, nap and H3), 7.37 (dd, J ) 7.3 Hz, 1H, H4), 2.43
(s, 3H, CH3).
N-Nicotin oyl-2-m eth yl-6-n itr oa n ilid e (16). 9 (1.52 g,
10.0 mmol) and nicotinoyl chloride hydrochloride (2.67 g, 15.0
mmol, 150 M%) after stirring overnight and recrystallization
from diethyl ether:hexane (3:1) gave 1.41 g (5.49 mmol, 55%
yield) of white powder: 1H NMR (300 MHz, CD2Cl2) δ 9.16
(dd, J ) 0.8, 2.2 Hz, 1H, H2′), 9.01 (br, 1H, NH), 8.80 (dd, J )
1.7, 4.8 Hz, 1H, H6′), 8.23 (ddd, J ) 1.7, 2.2, 8.0 Hz, 1H, H4′),
7.92 (m, 1H, H5), 7.62 (br d, J ) 7.5 Hz, 1H, H3), 7.48 (ddd, J
) 0.8, 4.8, 8.0 Hz, 1H, H5′), 7.39 (dd, J ) 7.5, 8.5 Hz, 1H, H4),
2.39 (s, 3H, CH3).
N-(4-Cyan oben zoyl)-2-m eth yl-6-n itr oan ilide (17): 9 (2.60
g, 17.1 mmol) and 4-cyanobenzoyl chloride (3.70 g, 22.3 mmol,
130 M%) after stirring overnight and recrystallization from
diethyl ether:hexane (3:1) gave 3.69 g (13.1 mmol, 77% yield)
of white powder: 1H NMR (300 MHz, CD2Cl2) δ 9.00 (br, 1H,
NH), 8.04 (cm, 2H, H2′,6′), 7.93 (m, 1H, H5), 7.84 (cm, 2H, H3′,5′),
7.63 (m, 1H, H3), 7.39 (dd, J ) 7.8, 8.2 Hz, 1H, H4), 2.60 (s,
3H, CH3).
Meth od B: 2-(2,6-Diflu or op h en yl)ben zim id a zole (19).
To 10 (9.31 g, 31.9 mmol) dissolved in glacial acetic acid (100
mL) was added iron powder (18) (4.95 g). After 30 min at
reflux, the reaction was concentrated to dryness, diluted with
ethyl acetate, and washed with NaHCO3. The aqueous layer
was back-extracted with ethyl acetate, and the combined
organic solution was washed with NaHCO3(sat. aq) and
NaCl(sat. aq), dried (Na2SO4), filtered, and concentrated. The
product was recrystallized from ethyl acetate (6.24 g, 27.1
2-(2-Met h ylp h en yl)ben zim id a zole (22). 13 (1.9 g, 7.4
mmol) and 18 (1.2 g) gave, after recrystallization from diethyl
ether:hexane (3:1) 1.2 g (5.76 mmol, 78%) of colorless crys-
1
tals: mp 215 °C; H NMR (300 MHz, CD2Cl2) δ 7.63 (m, 1H,
H6′), 7.58 (dd, J ) 6.1, 3.2 Hz, 2H, H4,7), 7.39-7.21 (m, 3H,
H3′,4′,5′), 7.25 (dd, J ) 6.1, 3.2 Hz, 2H, H5,6), 2.58 (s, 3H, CH3).
2-(1-Na p h th yl)-4-m eth ylben zim id a zole (23). 14 (2.60 g,
11.7 mmol) and 18 (2.00 g) gave, after purification by flash
chromatography eluting with 4% MeOH/CH2Cl2 and recrys-
tallization from diethyl ether:hexane (3:1) 1.63 g (6.31 mmol,
54% yield) of white powder: 1H NMR (200 MHz, CD2Cl2) δ
9.71 (br, 1H, NH), 8.80 (m, 1H), 8.01-7.89 (m, 2H), 7.81 (dd,
J ) 1.3, 7.3 Hz, 1H), 7.61-7.47 (m, 4H), 7.21 (dd, J ) 7.3, 7.6
Hz, 1H), 7.11 (m, 1H), 2.66 (s, 3H, CH3).
2-(2-Na p h th yl)-4-m eth ylben zim id a zole (24). 15 (2.25 g,
7.34 mmol) and 18 (1.60 g) gave, after purification by flash
chromatography eluting with 4% MeOH/CH2Cl2 and recrys-
tallization from diethyl ether:hexane (3:1) 1.00 g (3.88 mmol,
53% yield) of white powder: 1H NMR (300 MHz, CD2Cl2) δ
8.70 (br, 1H, NH), 8.34 (dd, J ) 1.7, 8.6 Hz, 1H), 7.99-7.87
(m, 3H), 7.57-7.51 (m, 2H), 7.50-7.43 (m, 1H), 7.15 (dd, J )
7.3, 7.5 Hz, 1H, H6), 7.04 (m, 1H, H5), 2.67 (s, 3H, CH3).
2-(3-P yr id yl)-4-m eth ylben zim id a zole (25): 16 (1.00 g,
3.89 mmol) and 18 (0.75 g) and a second addition of 18 (0.75
g) at 30 min gave, after recrystallization from ethyl acetate,
0.72 g (3.44 mmol, 88% yield) of white powder: 1H NMR (300
MHz, DMSO-d6) δ 9.38 (dd, J ) 2.3, 0.9 Hz, 1H, H2′), 8.67 (dd,
J ) 1.7, 4.8 Hz, 1H, H6′), 8.53 (ddd, J ) 1.7, 2.3, 8.0 Hz, 1H,
H4′), 7.58 (ddd, J ) 0.9, 4.8, 8.0 Hz, 1H, H5′), 7.44 (dd, J ) 0.9,
8.1 Hz, 1H, H7), 7.12 (dd, J ) 7.3, 8.1 Hz, 1H, H6), 7.02 (ddt,
J ) 0.8, 0.9, 7.3 Hz, 1H, H5), 2.59 (s, 3H, CH3).
2-(4-P yr id yl)-4-m eth ylben zim id a zole (26). 12 (1.02 g,
3.97 mmol) and 18 (1.10 g) gave, after recrystallization from
ethyl acetate, 0.70 g (3.34 mmol, 84% yield) of white powder:
1H NMR (300 MHz, DMSO-d6) δ 8.75 (m, 2H, H2′,6′), 8.14 (m,
2H, H3′,5′), 7.46 (dd, J ) 0.9, 8.1 Hz, 1H, H7), 7.15 (dd, J ) 7.3,
8.1 Hz, 1H, H6), 7.05 (ddt, J ) 0.8, 0.9, 7.3 Hz, 1H, H5), 2.59
(s, 3H, CH3).
Met h od C:
1-(2,6-Diflu or ob en zyl)-2-(2,6-d iflu or o-
p h en yl)ben zim id a zole (28). To 19 (2.00 g, 8.70 mmol) and
2,6-difluorobenzyl bromide (27) (2.85 g, 160 M%) dissolved in
THF (20 mL) was added NaH (60% dispersion in mineral oil)
(0.75 g, 215 M%). After 2 h, the reaction was quenched with
MeOH and concentrated. The residue was redissolved in ethyl
acetate, washed with NaHCO3(sat. aq) and NaCl(sat. aq), dried
(Na2SO4), filtered, and concentrated. The product was recrys-
tallized from ethyl acetate:hexane (1:1) (2.62 g, 0.35 mmol, 85%
yield of white powder): mp 145 °C; 1H NMR (300 MHz, CD2Cl2)
δ 7.77 (m, 1H, H4), 7.54 (m, 1H, H4′), 7.49 (m, 1H, H7), 7.29
(m, 2H, H5,6), 7.24 (m, 1H, H4′′), 7.08 (m, 2H, H3′,5′), 6.82 (m,
2H, H3′′,5′′), 5.36 (s, 2H, CH2PhF2). Anal. (C20H12F4N2) C, H,
N.
The following compounds were prepared by method C.
1-Ben zyl-2-(2,6-d iflu or op h en yl)ben zim id a zole (30). 19
(0.50 g, 2.17 mmol) and benzyl bromide 29 (0.40 mL, 3.36
mmol, 155 M%) and a second addition of 29 (0.20 mL, 1.68
mmol, 80 M%) after 5 h gave, after stirring overnight at room
temperature, aqueous workup, flash chromatography eluting
with 2% methanol/CH2Cl2, and recrystallization from diethyl

2-Aryl-Substituted Benzimidazoles
J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26 4205
ether, 0.57 g (1.78 mmol, 82% yield) of colorless crystals: mp
124 °C; H NMR (200 MHz, CD2Cl2) δ 7.81 (m, 1H, H4), 7.51
1.70 mmol) gave, after recrystallization from diethyl ether:
hexane (3:1), 290 mg (1.12 mmol, 73%) of colorless crystals:
mp 99 °C; 1H NMR (300 MHz, CDCl3) δ 7.66 (m, J ) 8.0, 1.1,
0.6 Hz, 1H, H4), 7.37 (m, J ) 0.6, 1.1, 8.2 Hz, 1H, H7), 7.30
(m, 1H, H4′′), 7.20 (m, J ) 8.0, 1.1, 7.3, 1H, H5), 7.19 (m, J )
8.2, 7.3, 1.1 Hz, 1H, H6), 6.92 (m, 2H, H3′′,5′′) 5.35 (s, 2H, CH2),
2.71 (s, 3H, CH3). Anal. (C15H12F2N2) C, H, N.
1
(m, 1H, H4′), 7.34-7.19 (m, 6H, H5,6,7,2′′,4′′,6′′), 7.06 (m, 2H, H3′,5′
)
6.99 (m, 2H, H3′′,5′′), 5.27 (s, 2H, CH2). Anal. (C20H14F2N2‚1/
8H2O) C, H, N.
1-Be n zyl-2-(2,6-d iflu or op h e n yl)-4-m e t h ylb e n zim id -
a zole (31). 20 (0.50 g, 2.05 mmol) and 29 (0.35 mL, 2.94
mmol, 140 M%) gave, after 2 h and flash chromatography
eluting with 2% methanol/CH2Cl2 and recrystallization from
hexane, 0.41 g (1.23 mmol, 60% yield) of colorless crystals: mp
1-(2,6-Diflu or ob en zyl)-2-(2-m et h ylp h en yl)b en zim id -
a zole (39). 22 (0.10 g, 0.48 mmol) and 27 (0.15 g, 0.73 mmol,
150 M%) gave 109 mg (0.33 mmol, 68%) of colorless crystals
after flash chromatography eluting with 2% MeOH/CH2Cl2 and
recrystallization from diethyl ether:hexane (3:1): mp 139 °C;
1H NMR (300 MHz, CDCl3) δ 7.80 (m, 1H, H4), 7.43-7.23 (m,
7H, H5,6,7,3′,4′,5′,6′), 7.21 (m, 1H, H4′′), 6.79 (m, 2H, H3′′,5′′), 5.31
(s, 2H, CH2), 2.23 (s, 3H, CH3). Anal. (C21H16F2N2) C, H, N.
1-(2,6-Diflu or ob en zyl)-2-(1-n a p h t h yl)-4-m et h ylb en z-
im id a zole (40). 23 (0.30 g, 1.16 mmol) and 27 (0.54 g, 2.60
mmol, 225 M%) gave, after stirring overnight and purification
by flash chromatography eluting with ethyl acetate:hexane (1:
4) and recrystallization from diethyl ether:hexane (3:1), 0.32
g (0.83 mmol, 72% yield) of white powder: mp 121-123 °C;
1H NMR (300 MHz, CD2Cl2) δ 8.00 (d, J ) 8.1 Hz, 1H), 7.96
(d, J ) 8.1 Hz, 1H), 7.66 (d, J ) 6.3 Hz, 1H), 7.60 (t, J ) 7.5
Hz, 1H), 7.53 (dt, J ) 1.3, 7.5 Hz, 1H), 7.43 (dt, J ) 1.3, 7.6
Hz, 1H), 7.28 (d, J ) 8.1 Hz, 1H), 7.19 (t, J ) 7.5 Hz, 1H),
1
112-118 °C; H NMR (300 MHz, CDCl3) δ 7.46 (m, 1H, H4′),
7.26-7.22 (m, 3H, H7,3′′,5′′), 7.18-6.98 (m, 7H, H5,6,3′,5′,2′′,4′′,6′′),
5.25 (s, 2H, CH2), 2.74 (s, 3H, CH3); HRMS 334.1281 (calcd),
334.1266 (found) δ 4.6. Anal. (C21H16F2N2‚1/4H2O) Calcd C,
74.43; H, 4.91; N, 8.27. Found: C, 74.81; H, 4.90; N, 7.85.
1-(2,6-Dich lor oben zyl)-2-(2,6-d iflu or op h en yl)-4-m eth -
ylben zim id a zole (32). 20 (0.50 g, 2.05 mmol) and 2,6-
dichlorobenzyl bromide (0.74 g, 3.08 mmol, 150 M%) gave, after
2 h and purification by flash chromatography eluting with 4%
MeOH/CH2Cl2 and recrystallization from diethyl ether:hexane
(3:1), 0.70 g (1.74 mmol, 85% yield) of white powder: mp 202-
1
203 °C; H NMR (300 MHz, CD2Cl2) δ 7.48 (m, 1H, H4′), 7.26
(m, 2H, H5,7), 7.19 (dd, J ) 8.0, 8.2 Hz, 1H, H6), 7.14-6.98 (m,
5H, H3′,5′,3′′,4′′,5′′), 5.56 (s, 2H, CH2PhCl2), 2.64 (s, 3H, CH3). Anal.
(C21H14Cl2F2N2‚1/4H2O) C, H, N.
7.11 (m, 2H), 6.67 (m, 2H), 5.28 (s, 2H, CH2
CH3). Anal. (C25H18F2N2) C, H, N.
PhF2), 2.68 (s, 3H,
1-(2,6-Diflu or oben zyl)-2-[[(ter t-bu tyldim eth ylsilyl)oxy]-
m eth yl]-4-m eth ylben zim id a zole (33). 5 (3.25 g, 11.76
mmol) and 27 (3.65 g, 150 M%) gave, after 4 h and purification
by flash chromatography with ethyl acetate:hexane (1:4), 4.41
g (10.96 mmol, 93% yield) of white powder: 1H NMR (300
MHz, CD2Cl2) δ 7.32 (m, 1H, H4′′), 7.17 (br d, J ) 8.2 Hz, 1H,
H7), 7.08 (dd, J ) 7.3, 8.2 Hz, 1H, H6), 7.00 (br d, J ) 7.3 Hz,
1H, H5), 6.95 (m, 2H, H3′′,5′′), 5.63 (s, 2H, CH2PhF2), 5.13 (s,
2H, CH2O), 2.59 (s, 3H, CH3), 0.94 (s, 9H, Si-t-Bu), 0.14 (s,
6H, Si(CH3)2).
1-(2,6-Diflu or ob en zyl)-2-(2-n a p h t h yl)-4-m et h ylb en z-
im id a zole (41). 24 (0.30 g, 1.16 mmol) and 27 (0.36 g, 1.74
mmol, 150 M%) and a second addition of 27 (0.18 g, 0.87 mmol,
75 M%) at 2 h gave, after stirring overnight and purification
by flash chromatography eluting with ethyl acetate:hexane (1:
4) and recrystallization from diethyl ether:hexane (3:1), 0.35
g (0.91 mmol, 78% yield) of white powder: mp 175-176 °C;
1H NMR (300 MHz, CD2Cl2) δ 8.20 (d, J ) 1.6 Hz, 1H), 8.02
(d, J ) 8.5 Hz, 1H), 7.96 (m, 2H), 7.83 (dd, J ) 1.7, 8.5 Hz,
1H), 7.59 (m, 2H), 7.20 (m, 2H), 7.12 (m, 1H), 7.06 (m, 1H),
6.80 (m, 2H), 5.60 (s, 2H, CH2PhF2), 2.66 (s, 3H, CH3). Anal.
(C25H18F2N2) C, H, N.
1-(2,6-Diflu or ob e n zyl)-2-[[(2,6-d iflu or ob e n zyl)oxy]-
m eth yl]ben zim id a zole (34). 2 (92 mg, 0.62 mmol) and 27
(334 mg, 1.61 mmol, 260 M%) gave, after recrystallization from
diethyl ether:hexane (3:1), 66 mg (0.165 mmol, 27%) of
1
colorless crystals: mp 109 °C; H NMR (300 MHz, CDCl3) δ
1-(2,6-Diflu or ob en zyl)-2-p h en ylb en zim id a zole (42).
2-Phenylbenzimidazole (300 mg, 1.54 mmol) and 27 (1.70
mmol, 110 M%) gave, after recrystallization from diethyl ether:
hexane (3:1), 300 mg (0.94 mmol, 63% yield) of colorless
7.73 (m, 1H, H4), 7.38 (m, 1H, H7), 7.36-7.18 (m, 4H, H5,6,4′,4′′),
6.98-6.82 (m, 4H, H3′,5′,3′′,5′′), 5.58 (s, 2H, NCH2PhF2), 5.07 (s,
2H, OCH2), 4.70 (s, 2H, OCH2PhF2). Anal. (C22H16F4N2O‚1/
2H2O) C, H, N.
1
crystals: mp 163 °C; H NMR (300 MHz, CDCl3) δ 7.82 (d, J
1-(2,6-Diflu or ob en zyl)-2-(2,6-d iflu or op h en yl)-4-m et h -
ylben zim id a zole (35). 20 (400 mg, 1.63 mmol) and 27 (388
mg, 1.87 mmol) gave, after stirring overnight and recrystal-
lization with diethyl ether:hexane (3:1), 453 mg (1.22 mmol,
) 8.3 Hz, 1H, H4), 7.75 (m, 2H, H3′,5′), 7.53 (m, 3H, H2′,4′,6′),
7.33 (d, J ) 8.3 Hz, 1H, H7), 7.25 (m, 3H, H5,6,4′′), 6.81 (m, 2H,
H3′′,5′′), 5.55 (s, 2H, CH2). Anal. (C20H14F2N2‚1/4H2O) C, H, N.
1-(2,6-Diflu or ob e n zyl)-2-(3-p yr id yl)-4-m e t h ylb e n z-
im id a zole (43). 25 (0.30 g, 1.43 mmol) and 27 (0.49 g, 2.37
mmol, 165 M%) gave, after stirring overnight and purification
by flash chromatography eluting with 4% methanol:CH2Cl2
and recrystallization from diethyl ether/hexane (3:1), 0.34 g
1
75% yield) of white powder: mp 182-186 °C; H NMR (300
MHz, CDCl3) δ 7.48 (m, 1H, H4′), 7.32 (d, J ) 8.1 Hz, 1H, H7),
7.20 (m, 1H, H4′′), 7.19 (dd, J ) 8.1, 7.2 Hz, 1H, H6), 7.09 (d,
J ) 7.2 Hz, 1H, H5), 7.04 (m, 2H, H3′,5′), 6.79 (m, 2H, H3′′,5′′),
5.33 (s, 2H, CH2), 2.70 (s, 3H, CH3). Anal. (C21H14F4N2) C,
H, N.
1
(1.02 mmol, 71% yield) of white powder: mp 186-188 °C; H
NMR (300 MHz, CD2Cl2) δ 8.92 (dd, J ) 0.9, 2.3 Hz, 1H, H2′),
8.74 (dd, J ) 1.7, 4.9 Hz, 1H, H6′), 8.05 (dt, J ) 2.0, 7.8 Hz,
1H, H4′), 7.48 (ddd, J ) 0.9, 4.9, 7.8, 1H, H5′), 7.24 (m, 1H,
H4′′), 7.22 (br d, J ) 7.7 Hz, 1H, H7), 7.15 (dd, J ) 7.7, 7.2, 1H,
H6), 7.07 (dt, J ) 1.0, 7.2 Hz, 1H, H5), 6.83 (m, 2H, H3′′,5′′),
5.51 (s, 2H, CH2PhF2), 2.64 (s, 3H, CH3). Anal. (C20H15F2N3)
C, H, N.
1-(2,6-Diflu or ob e n zyl)-2-(4-cya n op h e n yl)-4-m e t h yl-
ben zim id a zole (36). 21 (0.26 g, 1.11 mmol) and 27 (0.31 g,
1.50 mmol, 135 M%) gave, after stirring overnight, flash
chromatography with 2% methanol/CH2Cl2, and recrystalli-
zation with diethyl ether:hexane (3:1), 0.19 g (1.22 mmol, 48%
1
yield) of white powder: mp 207-208 °C; H NMR (300 MHz,
CDCl3) δ 7.84 (cm, 4H, H2′,3′,5′,6′), 7.32-7.03 (cm, 4H, H4′,5,6,7),
6.82 (m, 2H, H3′′,5′′), 5.51 (s, 2H, CH2), 2.62 (s, 3H, CH3). Anal.
(C22H15F2N3‚1/2H2O) C, H, N.
1-(2,6-Diflu or ob e n zyl)-2-(4-p yr id yl)-4-m e t h ylb e n z-
im id a zole (44). 26 (0.30 g, 1.43 mmol) and 27 (0.45 g, 2.17
mmol, 150 M%) gave, after stirring overnight and purification
by flash chromatography eluting with 4% methanol:CH2Cl2
and recrystallization from diethyl ether:hexane (3:1), 0.29 g
1-(2,6-D iflu o r o b e n zy l)-2-is o p r o p y l-4-m e t h y lb e n z-
im id a zole (37). 6 (0.20 g, 1.15 mmol) and 27 (0.36 g, 1.74
mmol, 150 M%) gave, after stirring for 5 h and purification by
flash chromatography eluting with 4% methanol:CH2Cl2 and
recrystallization from diethyl ether:hexane (3:1), 0.20 g (0.67
mmol, 58% yield) of white powder: mp 151-153 °C; 1H NMR
(200 MHz, CD2Cl2) δ 7.30 (m, 1H, H4′′), 7.15 (br d, J ) 7.7 Hz,
1H, H7), 7.04 (dd, J ) 7.3, 7.7 Hz, 1H, H6), 6.96 (br d, J ) 7.3
Hz, 1H, H5), 6.82 (m, 2H, H3′′,5′′), 5.38 (s, 2H, CH2PhF2), 3.40
(sep, J ) 6.8 Hz, 1H, i-Pr), 2.57 (s, 3H, CH3), 1.38 (d, J ) 6.8
Hz, 6H, i-Pr). Anal. (Cl8H18F2N2) C, H, N.
1
(0.86 mmol, 60% yield) of white powder: mp 171-172 °C; H
NMR (300 MHz, CD2Cl2) δ 8.77 (dd, J ) 1.6, 4.4 Hz, 2H, H2′,6′),
7.66 (dt, J ) 1.4, 4.4 Hz, 2H, H3′,5′), 7.24 (m, 1H, H4′′), 7.22
(dd, J ) 0.8, 8.1 Hz, 1H, H7), 7.15 (dd, J ) 7.5, 8.1 Hz, 1H,
H6), 7.07 (ddq, J ) 0.4, 0.8, 7.5 Hz, 1H, H5), 6.82 (m, 2H, H3′′,5′′),
5.54 (s, 2H, CH2PhF2), 2.63 (s, 3H, CH3). Anal. (C20H15F2N3)
C, H, N.
1-(2,3,4,5,6-P en ta flu or oben zyl)-2-(2,6-d iflu or op h en yl)-
4-m eth ylben zim id a zole (45). 20 (0.31 g, 1.27 mmol) and
2,3,4,5,6-pentafluoro-R-bromotoluene (0.30 mL, 1.99 mmol, 155
M%) gave, after 4 h and purification by flash chromatography
1-(2,6-Diflu or oben zyl)-2-m eth ylben zim id a zole (38). 2-
Methylbenzimidazole (204 mg, 1.54 mmol) and 27 (351 mg,

4206 J ournal of Medicinal Chemistry, 1997, Vol. 40, No. 26
Roth et al.
eluting with 4% methanol:CH2Cl2 and recrystallization from
diethyl ether:hexane (3:1), 0.33 g (0.77 mmol, 61% yield) of
white powder: mp 155-156 °C; H NMR (200 MHz, CD2Cl2)
δ 7.57 (m, 1H, H4′), 7.29-7.23 (m, 2H, H6,7), 7.19-7.05 (m, 3H,
H5,3′,5′), 5.35 (s, 2H, CH2PhF5), 2.64 (s, 3H, CH3). Anal.
(C21H11F7N2) C, H, N.
(m, 2H, H3′′,5′′,), 5.40 (s, 2H, CH2PhF2), 2.59 (s, 3H, CH3). Anal.
(C15H12F2N2‚1/4H2O) C, H, N.
1
1-(2,6-Diflu or ob e n zyl)-2-for m yl-4-m e t h ylb e n zim id -
a zole (53). To pyridine (3.4 mL) dissolved in CH2Cl2 (50 mL)
was added CrO3 (2.20 g). After 15 min, 51 dissolved in DMF
(10 mL) was added. After 20 min, the organic solution was
decanted from a tarry black deposit. The organic solution was
washed with 5% NaOH, 5% HCl, NaHCO3, and NaCl, dried
(Na2SO4), filtered, and concentrated. Purification by flash
chromatography eluting with 2% methanol/CH2Cl2 gave 0.55
g (1.92 mmol, 44% yield) of 53 and 0.17 g (0.66 mmol, 15%
yield) of 52: 1H NMR (200 MHz, CD3OD) δ 10.13 (s, 1H, CHO),
7.36-7.10 (cm, 4H, H5,6,7,4′′), 6.90 (m, 2H, H3′′,5′′), 6.05 (s, 7H,
CH2PhF2), 2.66 (s, 3H, CH3). Anal. (C16H12F2N2O‚1/5H2O) C,
H, N.
1-(3-P yr id ylm et h yl)-2-(2,6-d iflu or op h en yl)-4-m et h yl-
ben zim id a zole (46). 20 (0.21 g, 0.86 mmol) and R-(bromo-
methyl)pyridine (0.22 g, 1.28 mmol, 150 M%) gave, after 1 h
and purification by flash chromatography eluting with ethyl
acetate:hexane (1:1) increasing to ethyl acetate (100%) and
recrystallization from diethyl ether:hexane (3:1), 0.24 g (0.73
mmol, 85% yield) of white powder: mp 131-132 °C; 1H NMR
(300 MHz, CD2Cl2) δ 8.45 (d, J ) 3.4 Hz, 1H, H6′′), 8.32 (s, 1H,
H2′′), 7.53 (m, 1H, H4′), 7.25-7.03 (m, 7H, H5,6,7,3′,5′,4′′,5′′), 5.26
(s, 2H, CH2Py), 2.67 (s, 3H, CH3Ar). Anal. (C20H15F2N3‚1/
2H2O) C, H, N.
Meth od D: 1-(P h en ylsu lfon yl)-2-(2,6-d iflu or op h en yl)-
ben zim id a zole (48). To 19 (0.31 g, 1.34 mmol) dissolved in
THF (5 mL) was added NaH (60% dispersion in mineral oil)
(0.10 g, 190 M%). After 5 min, benzenesulfonyl chloride (47)
(0.25 mL, 0.35 g, 2.00 mmol, 150 M%) was added. After 2 h
of stirring the reaction mixture was dissolved in ethyl acetate,
washed with NaHCO3(sat. aq) and NaCl(sat. aq), dried
(Na2SO4), filtered, and concentrated. The product was purified
by flash chromatography eluting with 2% methanol:CH2Cl2
and then recrystallized from diethyl ether:hexane (3:1) (0.41
g, 1.10 mmol, 83% yield of white powder): mp 104-106 °C;
1H NMR (300 MHz, CD2Cl2) δ 8.09 (m, 1H, PhSO2), 7.77 (m,
1H, PhSO2), 7.69 (m, 2H, PhSO2), 7.66-7.53 (m, 2H, H4,7),
7.51-7.39 (m, 4H, H3,5 and PhSO2), 7.07 (m, 2H, H3′,5′). Anal.
(C19H12F2N2SO2) C, H, N.
1-(P h en ylsu lfon yl)-2-(2,6-d iflu or op h en yl)-4-m et h yl-
ben zim id a zole (49). 20 (0.20 g, 0.82 mmol) and 47 (0.20 mL,
0.28 g, 1.58 mmol, 190 M%) gave, after purification by flash
chromatography eluting with 2% methanol:CH2Cl2 and re-
crystallization from diethyl ether:hexane (3:1), 0.24 g (0.62
mmol, 76% yield) of white powder: mp 134-135 °C; 1H NMR
(200 MHz, CD2Cl2) δ 7.89 (br d, J ) 8.2 Hz, 1H), 7.73-7.38
(m, 6H), 7.34 (dd, J ) 7.4, 8.1 Hz, 1H, H6), 7.22 (br d, J ) 7.4
Hz, 1H, H5), 7.07 (m, 2H, H3′,5′), 2.59 (s, 3H, CH3). Anal.
(C20H14F2N2SO2) C, H, N.
1-(2,6-Diflu or ob en zoyl)-2-(2,6-d iflu or op h en yl)b en z-
im id a zole (50). To 19 (30 mg, 0.13 mmol) dissolved in
pyridine (0.5 mL) and chloroform (1.2 mL) was added 7 (20
µL, 0.16 mmol, 120 M%). After 5 h at room temperature, the
mixture was diluted with chloroform and washed with NaH-
SO4(2% solution). The organic layer was dried (Na2SO4),
filtered, and evaporated. The solid was recrystallized from
diethyl ether:hexane (19 mg of colorless crystals, 40% yield):
mp 145 °C; 1H NMR (300 MHz, CDCl3) δ 8.14 (m, 1H, H4),
7.89 (m, 1H, H7), 7.48 (m, 2H, H5,6), 7.31-7.18 (m, 2H, H4′,4′′),
6.77 (m, 4H, H3′,5′,3′′,5′′). Anal. (C20H10F4N2O) C, H, N.
1-(2,6-Diflu or ob en zyl)-2-(h yd r oxym et h yl)-4-m et h yl-
ben zim id a zole (51). To 33 (1.82 g, 4.52 mmol) dissolved in
THF (20 mL) was added tetrabutylammonium fluoride (1.45
g, 4.60 mmol, 100 M%). After 30 min at room temperature,
the reaction mixture was concentrated to dryness. The residue
was suspended in water, filtered, and washed with water (1.28
g, 4.44 mmol, 98% yield of white powder): 1H NMR (300 MHz,
CD3OD) δ 7.39 (m, 1H, H4′′), 7.18 (br d, J ) 8.3 Hz, 1H, H7),
7.09 (dd, J ) 7.4, 8.3 Hz, 1H, H6), 7.05-6.97 (m, 3H, H3′′,5′′,5),
5.68 (s, 2H, CH2PhF2), 4.99 (s, 2H, CH2O), 2.57 (s, 3H, CH3).
Anal. (C16H14F2N2O) C, H, N.
1-(2,6-Diflu or oben zyl)-4-m eth ylben zim id a zole (52). To
51 (1.82 g, 4.52 mmol) dissolved in 1.5 M H2SO4 (40 mL) was
added KMnO4 (1.50 g, 9.49 mmol, 160 M%). After 1 h at room
temperature, the reaction was filtered and washed with water.
The brown solid was collected, suspended in acetone:methanol,
and filtered. The filtrate was collected and purified by flash
chromatography, eluting with 10% methanol/CH2Cl2 increas-
ing to 50% methanol/CH2Cl2 (1.42 g, 4.70 mmol, 80% yield of
white powder): 1H NMR (200 MHz, CD2Cl2) δ 7.99 (br s, 1H,
H2), 7.37 (br d, J ) 7.9 Hz, 1H, H7), 7.32 (m, 1H, H4′′), 7.17
(dd, J ) 7.3, 7.9 Hz, 1H, H6), 7.03 (d, J ) 7.3 Hz, 1H, H5), 6.96
R T Assa y. The RNA-dependent DNA polymerase assay
has been described previously.18 Briefly, purified heterodimer
RT protein (0.015 mg/mL) was incubated in the presence and
absence of inhibitor at various concentrations in a 100 µL
reaction mixture [25 mM Tris (pH 8.0), 75 mM KCl, 8 mM
MgCl2, 2 mM dithiothreitol, 0.1 units poly(rC)-oligo(dG), 0.01
mM dGTP, 0.1 mg/mL BSA, 10 mM CHAPS, 0.025 mCi [R-35S]-
dGTP (specific activity, 1000 Ci/mmol)] for 30 min at 37 °C.
The assays were stopped by adding 1 mL of 10% trichloroacetic
acid and 10 µL of denatured and sheared salmon sperm DNA
(10 mg/mL) as a carrier. The labeled polymer was collected
on Whatman glass GF/C filters by suction filtration. After
washing sequentially with 10% trichloroacetic acid and 95%
ethanol, the filter was collected and counted. The reported
inhibitory values were determined as the average of three
determinations.
Abbr evia tion s: AIDS, acquired immunodeficiency syn-
drome; HIV-1, humans immunodeficiency virus type 1; RT,
reverse transcriptase; TZB, 1-(2,6-difluorophenyl)-1H,3H-
thiazolo[3,4-a]benzimidazole; NNRTI, nonnucleoside reverse
transcriptase inhibitor; WT, wild-type; AZT, 3′-azido-3′-deoxy-
thymidine; ddC, 2′,3′-dideoxycytidine; 8-Cl TIBO, 8-chloro-
4,5,6,7-tetrahydro-5-methylimidazo[4,5,1-jk][1,4]benzodiazepin-
2(1H)-one.
Ack n ow led gm en t. We thank Dr. Marilyn Kroeger
Smith for computational modeling and critical reading
of the manuscript. The authors acknowledge the techni-
cal efforts of Valerie Fliakas-Boltz for the cytopathic cell
killing assays. We are grateful for the support of the
Developmental Therapeutics Program, National Cancer
Institute, and to Drs. Edward Sausville and J ohn Bader
for their help and advice. Research was sponsored in
part by the National Cancer Institute, DHHS, under
contract with ABL. The contents of this publication do
not necessarily reflect the views or policies of the
Department of Health and Human Services, nor does
mention of trade names, commercial products, or orga-
nizations imply endorsements by the U.S. Government.
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