Novel 1-[2-(diarylmethoxy)ethyl]-2-methyl-5-nitroimidazoles as HIV-1 non-nucleoside reverse transcriptase inhibitors. A structure-activity relationship investigation

Article abstract of DOI:10.1021/jm050273a

1-[2-(Diarylmethoxy)ethyl]-2-methyl-5-nitroimidazoles (DAMNIs) is a novel family of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) active at submicromolar concentration. Replacement of one phenyl ring of 1-[2-(diphenylmethoxy)ethyl]-2-methyl-5-nitroimidazole (4) with heterocyclic rings, such as 2-thienyl or 3-pyridinyl, led to novel DAMNIs with increased activity. In HIV-1 WT cell-based assay the racemic 1-{2-[α-(thiophen-2-yl) phenylmethoxy]ethyl}-2-methyl-5-nitroimidazole (7) (EC₅₀ = 0.03 μM) proved 5 times more active than compound 4. Docking experiments showed that the introduction of a chiral center would not affect the binding of both (R)-7 and (S)-7. The internal scoring function of the Autodock program calculated the same inhibition constant (K_i = 7.9 nM) for the two enantiomers. Compounds 7 (ID₅₀ = 8.25 μM) were found more active than efavirenz (ID₅₀ = 25 μM) against the viral RT carrying the K103N mutation, suggesting for these compounds a potential use in efavirenz based anti-AIDS regimens.

Full text of DOI:10.1021/jm050273a

4378
J. Med. Chem. 2005, 48, 4378-4388
Novel 1-[2-(Diarylmethoxy)ethyl]-2-methyl-5-nitroimidazoles as HIV-1
Non-Nucleoside Reverse Transcriptase Inhibitors. A Structure-Activity
Relationship Investigation
Gabriella De Martino,† Giuseppe La Regina,† Alessandra Di Pasquali,† Rino Ragno,# Alberto Bergamini,‡
Chiara Ciaprini,‡ Anna Sinistro,‡ Giovanni Maga,| Emmanuele Crespan,| Marino Artico,† and
Romano Silvestri*,†
Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Studi Farmaceutici, Universita` di Roma “La Sapienza”,
Piazzale Aldo Moro 5, I-00185 Roma, Italy, Dipartimento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente
Attive, Universita` di Roma “La Sapienza”, Piazzale Aldo Moro 5, I-00185 Roma, Italy, Dipartimento di Sanita` Pubblica e
Biologia Cellulare, Universita` di Roma “Tor Vergata”, Via Tor Vergata 135, I-00133 Roma, Italy, and Istituto di Genetica
Molecolare - CNR, via Abbiategrasso 207, I-27100 Pavia, Italy
Received March 25, 2005
1-[2-(Diarylmethoxy)ethyl]-2-methyl-5-nitroimidazoles (DAMNIs) is a novel family of HIV-1
non-nucleoside reverse transcriptase inhibitors (NNRTIs) active at submicromolar concentra-
tion. Replacement of one phenyl ring of 1-[2-(diphenylmethoxy)ethyl]-2-methyl-5-nitroimidazole
(4) with heterocyclic rings, such as 2-thienyl or 3-pyridinyl, led to novel DAMNIs with increased
activity. In HIV-1 WT cell-based assay the racemic 1-{2-[R-(thiophen-2-yl)phenylmethoxy]ethyl}-
2-methyl-5-nitroimidazole (7) (EC50 ) 0.03 µM) proved 5 times more active than compound 4.
Docking experiments showed that the introduction of a chiral center would not affect the binding
of both (R)-7 and (S)-7. The internal scoring function of the Autodock program calculated the
same inhibition constant (Ki ) 7.9 nM) for the two enantiomers. Compounds 7 (ID50 ) 8.25
µM) were found more active than efavirenz (ID50 ) 25 µM) against the viral RT carrying the
K103N mutation, suggesting for these compounds a potential use in efavirenz based anti-
AIDS regimens.
Chart 1. Approved NNRTIs
Introduction
Acquired immune deficiency syndrome (AIDS)/
infection caused by human immunodeficiency virus
(HIV) is unceasingly widespreading. According to WHO/
UNAIDS estimates 45 million people will become HIV
infected between 2002 and 2010.1
Anti-AIDS drugs fall into three main categories,
the nucleoside reverse transcriptase inhibitors
(NRTIs), the non-nucleoside reverse transcriptase in-
hibitors (NNRTIs), and the protease inhibitors (PIs).
Recently the viral entry inhibitor enfuvirtide has been
licensed for the treatment of HIV infection.2 Effective
anti-AIDS treatments are usually obtained combining
the drugs in highly active anti-retroviral therapies
(HAARTs), which are able to reduce the incidence of
AIDS-infections and deaths. Despite their efficacy,
HAARTs cannot suppress completely the viral infec-
tion,3 thus forcing to long-term or permanent treat-
ments. These conditions clearly promote the emergence
of drug resistant variants, cross-resistance inside the
same category and unwanted metabolic side effects.3
The NNRTIs act through the allosteric inhibition of
the viral reverse transcriptase (RT) and then are
endowed with low cytotoxity.4 Nevertheless this real
advantage is vanished by the broad cross-resistance
displayed by all approved NNRTIs nevirapine (1),
delavirdine (2), and efavirenz (3) (Chart 1).5,6
To overcome these difficulties novel anti-HIV agents
are searched with obstinacy either by improvements of
the existing drug classes (NRTIs, NNRTIs, and PIs) or
by discovery of agents targeting new mechanism of
action (integrase inhibitors, Rnase-H inhibitors, and
viral entry inhibitors).7-9
Our decennial commitment in the field of anti-AIDS
* Corresponding author: phone +390649913800, fax +3906491491,
e-mail: romano.silvestri@uniroma1.it
agents10 led to the discovery of 1-[2-(diarylmethoxy)-
† Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di
Studi Farmaceutici, Universita` di Roma “La Sapienza”.
# Dipartimento di Studi di Chimica e Tecnologia delle Sostanze
Biologicamente Attive, Universita` di Roma “La Sapienza”.
‡ Dipartimento di Sanita` Pubblica e Biologia Cellulare, Universita`
di Roma “Tor Vergata”.
ethyl]-2-methyl-5-nitroimidazoles (DAMNIs, e.g.
4
(RS1478)) (Chart 2), a novel family of NNRTIs active
at submicromolar concentration.11 SAR studies showed
that the diarylmethane moiety strongly influenced the
antiviral activity of DAMNIs, leading to different results
| Istituto di Genetica Molecolare-CNR.
10.1021/jm050273a CCC: $30.25 © 2005 American Chemical Society
Published on Web 05/27/2005

Novel DAMNIs as HIV NNRTIs
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13 4379
Chart 2. Reference and Novel Derivativesa
a X ) S, O; Y ) H, phenyl, 1-naphthyl, cyclohexyl; Z ) S, SO2, NH, N-benzyl, O; R1-R3 ) H, CH3, Cl, F; R4 ) H, Cl; R5,R6 ) H, NO2;
R7 ) H, CH3.
Scheme 1a
a Reagents. a: NaBH4; b: 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole, PTSA, Dean-Stark trap.
depending on nature and position of atoms/groups
introduced.11b Inside the RT non-nucleoside binding site
(NNBS), DAMNIs assume a typical “butterfly-like”
conformation, the diphenylmethane moiety mimicking
the wings of the Scha¨fer’s 3D model,12 and the 1-(2-
methyl-5-nitroimidazolyl)ethane portion the indolyl ring
of BHAPs.
38-44 were also synthesized to complete the SAR
evaluation.
Chemistry
Aryl-(thiophen-2-yl)-methanones15 45-55 were pre-
pared by reacting proper aroyl chlorides with thiophene
or 2-chlorothiophene in the presence of anydrous alu-
minum chloride in dichloromethane at room tempera-
ture. Sodium borohydride reduction of ketones 45-55
furnished the corresponding aryl-(thiophen-2-yl)-metha-
nols16 56-66. These compounds were reacted with 1-(2-
hydroxyethyl)-2-methyl-5-nitroimidazole in the presence
of para-toluenesulfonic acid in boiling benzene using a
Dean-Stark trap to afford 1-{2-[aryl-(R-thiophen-2-yl)-
methoxy]ethyl}-2-methyl-5-nitroimidazoles (7-17). Simi-
larly was prepared 1-{2-[phenyl-(R-furan-2-yl)methoxy]-
ethyl}-2-methyl-5-nitroimidazole (18) using (furan-2-yl)-
phenylmethanol (Scheme 1). Phenyl-(pyridin-3-yl)meth-
anone17a (67) was prepared following the method of
Bochis et al.17b by reacting pyridin-3-carbonyl chloride
with benzene in the presence of anhydrous aluminum
chloride. Sodium borohydride reduction of 67 gave
phenyl-(pyridin-3-yl)methanol (68) which was trans-
formed into R-(pyridin-3-yl)phenylmethyl chloride hy-
drochloride (69) with thionyl chloride. Reaction of 69
with 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole in
the presence of triethylamine led to 1-{2-[R-(pyridin-3-
yl)phenylmethoxy]ethyl}-2-methyl-5-nitroimidazole (19)
(Scheme 2).
Since the introduction of different substituents on the
phenyl ring of DAMNIs did not increase strongly the
antiviral potency,11b we planned to replace one of the
phenyl rings with a thiophene nucleus. Docking experi-
ments on a thiophene DAMNI analogue indeed sup-
ported the design of novel derivatives. Autodock internal
scoring functions predicted the inhibition constant (Ki)
of the thiophene DAMNI in the low nanomolar range.
Our project was also encouraged by some reports.
Sowell13 et al. synthesized a series of 3-arylsulfonyl-
thiophenes as novel antiviral/antitumor agents, with
3-(2-nitrophenylsulfonyl)-2-aminothiophene (5) as the
most active compound within the series (CC50 ) >351
µM and EC50 ) 13.3 µM). Uckun14 et al. prepared N-[2-
(5-bromopyridyl)]-N′-[2-(2-thiophene)ethyl]-thiourea (HI-
443, 6) by replacing the pyridyl ring of trovirdine with
a 2-thiophenyl nucleus. This compound showed high
selectivity index and low cytotoxicity.
The above findings prompted us to synthesize the
1-{2-[aryl-(R-thiophen-2-yl)methoxy]ethyl}-2-methyl-5-
nitroimidazoles (7-17) here reported. To further eluci-
date SAR analysis, some DAMNI derivatives were also
prepared by replacing one aryl with furan (18) or
pyridine (19) or by substituting the oxygen of the side
chain with NH, S or SO2 (20-37). Finally derivatives
Reaction of proper arylphenylbromomethanes11b or
benzyl chloride with 2-(2-methyl-5-nitroimidazol-1-yl)-
ethanethiol in the presence of potassium carbonate in

4380 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13
De Martino et al.
Scheme 2a
Scheme 4a
a Reagents. a: thionyl chloride; b: benzene, anydrous aluminum
chloride; c: NaBH4; d: thionyl chloride; e: 1-(2-hydroxyethyl)-2-
methyl-5-nitroimidazole, triethylamine.
a Reagents. a: 2-methyl-4(5)-nitroimidazole, diethyl azodicar-
boxylate, triphenylphosphine; b: 4(5)-nitroimidazole, diethyl azodi-
carboxylate, triphenylphosphine.
Scheme 3a
Table 1. Cytotoxicity, Anti-HIV-1 Activity, and Selectivity
Index of Compounds 7-19
a Reagents. a: 2-(2-methyl-5-nitroimidazol-1-yl)ethanethiol,
K2CO3; b: 2-(2-methyl-5-nitroimidazol-yl)ethylamine dihydro-
chloride, K2CO3.
a
b
compd
X
R1
R2
R3
R4 CC50
EC50
SIc
boiling acetone furnished derivatives 20-25 and 27
(Scheme 3). Sulfur derivative 20 was oxidized to the
corresponding sulfone 26 with MCPBA. Derivatives 28-
36 were obtained by reacting the arylphenylbromo-
methanes or benzyl chloride with 2-(2-methyl-5-nitro-
imidazol-yl)ethylamine dihydrochloride18 in the pres-
ence of potassium carbonate in DMF at 100 °C.
7
S
S
S
S
S
S
S
S
S
S
S
O
-
H
H
H
H
H
Cl
H
H
F
H
F
H
H
-
H
H
H
H
H
H
H
H
H
H
H
>100
92
>100
>100
72
0.03 >3333
8
CH3
H
Cl
H
H
F
H
CH3
H
H
Cl
H
H
F
0.45
0.3
204
9
>333
10
11
12
13
14
15
16
17
18
19
4d
1.9
52.6
0.08
900
>100 58
>1.7
>100
>100
>100
>100
0.12
0.14
3.1
>833
H
H
F
H
H
-
>714
Reaction of 2-(diphenylmethoxy)ethanol19 with 2-meth-
yl-4(5)-nitroimidazole in the presence of diethyl azodi-
carboxylate and triphenylphosphine according to the
Mitsunobu reaction20 afforded a mixture of 1-[2-(di-
phenylmethoxy)ethyl]-2-methyl-5-nitroimidazole (4)11a
and the related isomer 1-[2-(diphenylmethoxy)ethyl]-2-
methyl-4-nitroimidazole (38). In a similar way were
>32.3
H
H
H
-
0.06 >1667
Cl >100
1.2
0.1
8.33
840
H
-
84
>100
>100
0.08 >1250
0.2 >500
a Data are mean values of two experiments performed in
triplicate. b Compound dose (µM) required to reduce the viability
of mock-infected cells by 50%, as determined by MTT method.
c Compound dose (µM) required to achieve 50% protection of MT-4
cells from HIV-1 induced cytopathogenicity, as determined by MTT
method. d Selectivity Index, CC50:EC50 ratio. d Literature11a
prepared
1-[2-(diphenylmethoxy)ethyl]-5-nitroimid-
azole (41), 1-[2-(diphenylmethoxy)ethyl]-4-nitroimid-
azole (42), 1-[2-(phenylmethoxy)ethyl]-2-methyl-5-nitro-
imidazole (43), and 1-[2-(phenylmethoxy)ethyl]-2-meth-
yl-4-nitroimidazole (44), using 4(5)-nitroimidazole and
2-(diphenylmethoxy)ethanol or 2-(phenylmethoxy)etha-
nol, respectively (Scheme 4).
17), seven derivatives (7-9, 11, 13, 14, and 16) were
endowed with antiviral activities at submicromolar
concentrations, three compounds (10, 15, and 17) were
active at micromolar concentration, and only one (12)
was poorly active (Table 1). With the only exception of
compound 12, the inhibitory activities ranged from 0.03
µM (compound 7) to 3.1 µM (compound 15). 1-{2-[R-
(Furan-2-yl)arylmethoxy]ethyl}-2-methyl-5-nitroimid-
azole (18) and 1-{2-[R-(pyridin-3-yl)arylmethoxy]ethyl}-
2-methyl-5-nitroimidazole (19) were also active at sub-
micromolar concentrations, showing EC50s ) 0.1 and
0.08 µM, respectively. Among compounds 7-19, 10
derivatives (7, 9, 10, 12-17, and 19) were found poor
cytotoxic showing CC50 greater or equal to 100 µM. The
SAR Evaluation
Test derivatives were evaluated for cytotoxicity and
anti-retroviral activity against HIV-1 WT strain. The
efficacy of test compounds against HIV-1 WT was
evaluated in MT-4 cells by means of an MTT assay
(EC50 values). Selected compounds were tested in vitro
against RT WT and a panel of RTs containing the single
amino acid mutation L100I, K103N, Y181I, V179D, and
Y188L (ID50 values).
Among eleven newly synthesized 1-{2-[R-(thiophen-
2-yl)arylmethoxy]ethyl}-2-methyl-5-nitroimidazoles (7-

Novel DAMNIs as HIV NNRTIs
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13 4381
Table 2. Cytotoxicity, Anti-HIV-1 Activity, and Selectivity Index of Compounds 20-44
a
b
compd
Y
Z
R1
R2
R3
R4
R5
R6
CC50
EC50
1.2
12
5
3
64
80
SIc
20
21
22
23
24
25
26
27
28d
29
30
31d
32
33d
34d
35d
36d
37
38
39e
40
41
42
43
44
4d
phenyl
phenyl
phenyl
phenyl
phenyl
phenyl
phenyl
H
phenyl
phenyl
phenyl
phenyl
phenyl
phenyl
phenyl
phenyl
H
S
H
Cl
F
H
H
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
NO2
H
H
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
H
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>83.5
>8.3
>20
S
H
H
CH3
Cl
F
H
H
H
H
H
H
H
H
H
H
H
H
H
CH3
F
H
S
H
S
H
H
H
H
H
H
Cl
F
H
H
H
H
H
H
H
H
H
H
H
H
H
H
-
H
>33.3
>1.6
>1.2
>19.2
>1.7
>8.3
>1.1
>2
>1.5
>47.6
>55.6
>2.3
>1.1
-
>1.2
>1.5
-
>333.3
-
>1.3
>2.38
>4.5
>500
S
H
S
H
SO2
S
H
H
H
H
H
CH3
Cl
F
H
H
H
H
H
H
H
H
H
H
H
-
H
5.2
H
60
12
90
50
65
NH
NH
NH
NH
NH
NH
NH
NH
NH
H
H
H
H
H
2.1
1.8
44
H
H
H
92
>100
84
67
>100
H
H
H
H
H
H
H
H
H
-
H
H
N-benzyl
H
phenyl
2-naphthyl
cyclohexyl
phenyl
phenyl
H
O
O
O
O
O
O
O
-
NO2
H
NO2
NO2
NO2
H
NO2
H
H
H
NO2
H
NO2
-
0.3
>100
H
78
CH3
CH3
-
4.2
22
0.2
H
-
-
a Data are mean values of two experiments performed in triplicate. b Compound dose (µM) required to reduce the viability of mock-
infected cells by 50%, as determined by MTT method. c Compound dose (µM) required to achieve 50% protection of MT-4 cells from HIV-1
induced cytopathogenicity, as determined by MTT method. d Selectivity Index: CC50:EC50 ratio. d Tested as dihydrochloride. e Literature10a,b
selectivity indexes of derivatives 7-19 ranged from 2275
>3333 (7) to >1.7 (12).
(Table 2). Replacement of the ethereal oxygen of 4 with
a sulfur atom or an amino group resulted in 6 and 60
times abatement of the inhibitory activity, respectively
(compare 4 with 20, EC50 ) 1.2 µM, and 28, EC50 ) 12
µM). Oxidation of sulfur to sulfone further reduced 4.3
times the activity of 20 (compare 20 with 26). Introduc-
tion of substituents on the phenyl ring did not affect
remarkably the antiviral activity of derivatives 21-25
and 29-35. In the sulfur series, only the meta-methyl
derivative 23 (EC50 ) 3 µM) retained partially the
antiviral activity of 20, being 2.5 times less potent. In
the amino series, the meta-chloro- and the meta-fluoro-
derivatives (32 and 33) were about 5.7 and 6.7 times
more potent than 28.
Finally we confirmed the essential role of the second
(hetero)aryl group for the antiviral activity of DAMNIs
(compare 27 with 20, 36, 37 with 28, and 39, 40, 43, 44
with 4). Morover the presence of the methyl and nitro
groups at position 2 and 5 of the imidazole ring,
respectively, were also crucial for inhibition the RT of
HIV-1. In fact, 1-[2-(diphenylmethoxy)ethyl]-2-methyl-
4-nitroimidazole (38), 1-[2-(diphenylmethoxy)ethyl]-5-
nitroimidazole (41), and 1-[2-(diphenylmethoxy)ethyl]-
4-nitroimidazole (42) were drammatically less active
than the 4. The SAR evaluations of the DAMNI family
are summarized in Chart 3.
1-{2-[R-(Thiophen-2-yl)phenymethoxy]ethyl}-2-meth-
yl-5-nitroimidazole (7, EC50 ) 0.03 µM for the racemic
compound) was 6.7 times more potent than the parent
compound 4 (EC50 ) 0.2 µM), and it was also the most
potent derivative within the series. In general the
introduction of chlorine or fluorine atoms or a methyl
group on the phenyl ring of 7 decreased the antiviral
activity in the order ortho > meta > para (compare 8,
10, and 13 with 11, 14, and with 9, 12, and 15). With
the exception of derivatives 8 and 11, the cytotoxitity
>100 µM.
Among ortho-substituted derivatives, the fluoro com-
pound 13 (EC50 ) 0.12 µM) was found 3.7 and 15.8 times
more potent than 8 (EC50 ) 0.45 µM) and 10 (EC50
)
1.9 µM), respectively. Interestingly, the introduction of
a fluorine atom at meta position of 13 did not decrease
the antiviral activity as it did for the monosubstituted
derivatives (compare 13 with 16). Introduction of a
chlorine atom at position 2 of the thiophene ring of 7
led to a 40 times abatement of the antiviral activity
(compare 7 with 17). Replacement of the 2-thiophenyl
nucleus for a 2-furanyl or a 3-pyridinyl ring led to
derivatives 18 and 19 endowed with 2- or 2.5-fold
superior activity than 4, but 3.3 and 2.7 times less active
than 7, respectively.
Derivatives 7 and 11 were tested against RT WT and
a panel RTs containing the single amino acid mutation
(L100I, K103N, Y181I, V179D, and Y188L) responsible
Although scarcely cytotoxic, sulfur and amino deriva-
tives 20-39 weakly inhibited the HIV multiplication

4382 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13
Chart 3. SARs on the DAMNI Family
De Martino et al.
Molecular Docking of Compound 7
Because of the very well-known isosteric interchange
between benzene ring and thiophene nucleus, the bind-
ing mode of designed compound 7 was investigated as
possible new DAMNI lead compound. Either the R or S
absolute configurations were modeled starting from the
available model structure of 411b and optimized using a
standard molecular dynamics protocol. Autodock pro-
gram was used to dock (R)-7 and (S)-7 into the RT non-
nucleoside binding pocket (NNBS). Analogously as
previously reported the NNBS was obtained using the
coordinates of HIV-1 RT/TNK-651 (70)21 taken from the
Protein Brookheaven database (PDB entry code 1rt2).
The docking experiments were carried out employing
the Lamarckian genetic algorithm with local search
(GA-LS) hybrid formalism of the docking program
Autodock 3.0.522 that predicts the bound conformations
of flexible ligands to macromolecular targets. Primarily,
the docking of 70 into the RT was performed to test the
reliability of the docking formalism for our purposes.
Second similar docking experiment was conducted on
lead compound 4 as test for our previous findings11b and
for comparison purposes.
Autodock was able to reproduce the experimental
binding conformation of 70 within a minimal root-mean-
square deviation (RMSD ) 0.99 Å) and confirmed our
previous findings about the binding mode of compound
4 (see Experimental Section). About the docking experi-
ments on the designed derivative 7, interestingly it
seems that the introduction of a chiral center would not
affect the binding of both (R)-7 and (S)-7. Either R or S
absolute configurations of 7 seems to bind into the
NNBS in similar way, in fact autodock internal scoring
function calculated the same inhibition constant for the
two enantiomers (Ki ) 7.9 nM). A closer investigation
of the (R)-7 and (S)-7 binding mode reveals that the
thiophene rings are not overlapped each other, but are
cross superimposed with the phenyl rings confirming
the full benzene - thiophene interchange (Figure 1).
Table 3. HIV-1 RT Inhibitory Activity of Compounds 7, 11, 20,
and 28 against Wild-Type and Mutant Enzymes Carrying
Single Amino Acid Substitutionsa
wt
wt L100I K103N Y181I V179D Y188L
b
compd EC50 ID50
ID50
ID50
ID50
ID50
ID50
7
0.04
0.1
2.3
8
0.37 5.5
1.17 3.2
8.25 >50
1.9
30.2
15.1
n.t.
n.t.
18
11
20
28
5.1
n.t.
n.t.
7
6.25 10.8
10.64 n.t.c
n.t.
n.t.
36
0.4
n.t.
n.t.
0.3
16.5
0.4
n.t.
9
NVP (1)d 0.25
EFV (3)e 0.004 0.08 0.2
25
0.09
0.1
a Data represent mean values of at least three separate experi-
ments. b Compound dose (Ki, µM) required to inhibit by 50% the
RT activity of the indicated strain. c n.t., not tested. d Literature.10e
e Literature.10k
for resistance to NNRTIs. The esperimental results are
shown in Table 3. Compound 7 showed a profile of
inhibition comparable or slightly less potent to that of
nevirapine (1) against all the tested RTs. Compound 11
was found more potent than 1 against the L100I,
K103N, and Y181I RTs, but less potent than 3 against
all the tested RTs. Both compounds 7 and 11 were
generally less active than efavirenz (3), with the notable
exception of the K103N mutation for which 7 and 11
were 3- and 5-times more potent.
Figure 1. Superimposition of compound 7 as found from Autodock. In yellow is reported the (R) absolute configuration and in
magenta the (S) configuration. A 3 Å core of NNBS is also displayed.

Novel DAMNIs as HIV NNRTIs
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13 4383
indicator at 254 nm) and silica gel TLC cards from Fluka (silica
gel-precoated aluminum cards with fluorescent indicator at
254 nm) were used for thin-layer chromatography (TLC).
Developed plates were visualized by a Spectroline ENF 260C/F
UV apparatus. Organic solutions were dried over anhydrous
sodium sulfate. Concentration and evaporation of the solvent
after reaction or extraction were carried out on a rotary
evaporator (Bu¨chi Rotavapor) operating at reduced pressure.
Elemental analyses were found to be within (0.4% of the
theoretical values. (Furan-2-yl)-phenylmethanol, (cyclohexyl)-
phenylmethanone, phenylmethoxyethanol, and 1-(2-hydroxy-
ethyl)-2-methyl-5-nitroimidazole were obtained from commer-
cial sources.
General Procedure for the Synthesis of DAMNIs 7-18.
Example. 1-{2-[R-(Thiophen-2-yl)phenylmethoxy]ethyl}-
2-methyl-5-nitroimidazole (7). A solution phenyl-(thiophen-
2-yl)-methanol (56, 1.9 g, 0.01 mol), 1-(2-hydroxyethyl)-2-
methyl-5-nitroimidazole (0.51 g, 0.003 mol), and para-toluene-
sulfonic acid (0.10 g,) in benzene (80 mL) was refluxed under
nitrogen atmosphere with azeotropic removal of the water
using a Dean-Stark trap. After evaporation of the solvent,
the crude residue was treated with sodium hydrogen carbonate
solution and extracted with ethyl acetate. The organic solution
was shaken with brine, dried, and evaporated in vacuo to leave
a dark oil which was purified through a silica gel column
chromatography (chloroform as eluent) to give 7 (0.55 g, 53%),
mp 90-92 °C (from cyclohexane). Anal. (C17H17N3O3S (343.41))
C, H, N, S.
1-{2-[R-(Thiophen-2-yl)-(2-methylphenyl)methoxy]eth-
yl}-2-methyl-5-nitroimidazole (8). Was prepared as 7 using
alcohol 57. Yield 82%, oily material. 1H NMR (CDCl3): δ 2.18
(s, 3H), 2.56 (s, 3H), 3.77 (m, 2H), 4.53 (t, J ) 4.8 Hz, 2H),
5.63 (s, 1H), 6.61 (m, 1H), 6.85 (dd, J ) 1.9 and 5.0 Hz, 1H),
7.08-7.25 (m, 5H), 7.95 ppm (s, 1H). Anal. (C18H19N3O3S
(357.43)) C, H, N, S.
1-{2-[R-(Thiophen-2-yl)-(4-methylphenyl)methoxy]eth-
yl}-2-methyl-5-nitroimidazole (9). Was prepared as 7 using
alcohol 58. Yield 50%, oily material. Anal. (C18H19N3O3S
(357.43)) C, H, N, S.
1-{2-[R-(Thiophen-2-yl)-(2-chlorophenyl)methoxy]ethyl}-
2-methyl-5-nitroimidazole (10). Was prepared as 7 using
alcohol 59. yield 80%, mp 45-47 °C (from cyclohexane). Anal.
(C17H16ClN3O3S (377.84)) C, H, Cl, N, S.
1-{2-[R-(Thiophen-2-yl)-(3-chlorophenyl)methoxy]ethyl}-
2-methyl-5-nitroimidazole (11). Was prepared as 7 using
alcohol 60. Yield 60%, oily material. Anal. (C17H16ClN3O3S
(377.84)) C, H, N, Cl, S.
1-{2-[R-(Thiophen-2-yl)-(4-chlorophenyl)methoxy]ethyl}-
2-methyl-5-nitroimidazole (12). Was prepared as 7 using
alcohol 61. Yield 66%, mp 75-77 °C (from cyclohexane). Anal.
(C17H16ClN3O3S (377.84)) C, H, N, Cl, S.
1-{2-[R-(Thiophen-2-yl)-(2-fluorophenyl)methoxy]ethyl}-
2-methyl-5-nitroimidazole (13). Was prepared as 7 using
alcohol 62. Yield 74%, oily material. Anal. (C17H16FN3O3S
(361.39)) C, H, N, F, S.
1-{2-[R-(Thiophen-2-yl)-(3-fluorophenyl)methoxy]ethyl}-
2-methyl-5-nitroimidazole (14). Was prepared as 7 using
alcohol 63. Yield 42%, oily material. Anal. (C17H16FN3O3S
(361.39)) C, H, N, F, S.
1-{2-[R-(Thiophen-2-yl)-(4-fluorophenyl)methoxy]ethyl}-
2-methyl-5-nitroimidazole (15). Was prepared as 7 using
alcohol 64. Yield 78.4%, mp 81-85 °C (from cyclohexane).
Anal. (C17H16FN3O3S (361.39)) C, H, N, F, S.
1-{2-[R-(Thiophen-2-yl)-(2,3-difluorophenyl)methoxy]-
ethyl}-2-methyl-5-nitroimidazole (16). Was prepared as 7
using alcohol 65. Yield 71%, oily material. Anal. (C17H15F2N3O3S
(379.38)) C, H, N, F, S.
1-{2-[R-(5-Chlorothiophen-2-yl)phenylmethoxy]ethyl}-
2-methyl-5-nitroimidazole (17). Was prepared as 7 using
alcohol 66. Yield 82%, mp 109-112 °C (from cyclohexane).
Anal. (C17H16ClN3O3S (377.84)) C, H, N, Cl, S.
Moreover as a consequence of the thiophene ring inver-
sion a positional switch between the nitro and the
methyl groups of the imidazole moiety occurs. This is
in agreement with the dual binding mode observed for
compound 4.10b Ligand/receptors interactions also re-
semble those already described for 4, the phenyl ring
of (R)-7 (thiophene for (S)-7) makes favorable interac-
tions with a mild hydrophobic pocket formed by the side
chain of Val106, the R-CH2 of Gly190, and â-CH2 of
Tyr181; the thiophene ring of (R)-7 (benzene for (S)-7)
makes favorable interactions with a bigger hydrophobic
and aromatic rich pocket formed by the side chains of
Tyr181, Tyr188, Phe227, Trp229, and Leu234. On the
other side of the molecule the basic nitrogen of imidazole
ring of (R)-7 makes an hydrogen bond with the NH of
Lys103 (distance Nimidazole‚‚‚NHLys103 ) 2.5 Å) while the
same interaction occurs for (S)-7 by the mean of the
nitro group (average distance NO2‚‚‚NHLys103 ) 2.9 Å).
Conclusions
DAMNIs are a novel family of NNRT agents initially
designed taking account the “butterfly-like” conforma-
tion as a determinant requisite for antiretroviral activ-
ity. Although not very potent, DAMNIs were found
active with compound 4 showing EC50 ) 0.2 µM, CC50
> 100 µM, and SI > 500.
Replacement of one phenyl group with heterocyclic
rings led to novel DAMNIs with increased activity.
Compounds 7 and 19, with 2-thienyl and 3-pyridinyl
rings, were found 6.7 and 2.5 times more active than
compound 4. Introduction of halogens, chlorine, and
fluorine in the phenyl ring of 7 did not improve the
antiviral activity, thus proving that sterical impedi-
ments produced by substituents are deleterious for
binding of DAMNIs at the NNBS of the RT.
Efavirenz is the a first line NNRTI which was found
highly effective when used in combination with two
NRTIs in protease-sparing regimen. However the ma-
jority of patients (>90%) treated with efavirenz, whose
viral loads rebounded after an initial response to the
drug, selected the K103N mutation. Furthermore, after
the emergence of the K103N mutation, additional
double mutations (K103N-V108N, K103N-P225H)
slowly appear in many patients.24 These observations
highlighted the dramatic need of novel NNRTI effective
against HIV-1 RT containing either single or double
K103N mutations, when used in combination with other
antiretroviral agents. Compounds 7 and 11 were found
more active than efavirenz against the viral RT carrying
the K103N mutation, suggesting for these compounds
a potential use in efavirenz based anti-AIDS regimens.
These findings are of great stimulus to develop novel
DAMNI derivatives.
Experimental Section
Chemistry. Melting points were determined on a Bu¨chi 510
apparatus and are uncorrected. Infrared spectra were run on
Perkin-Elmer 1310 and SpectrumOne spectrophotometers.
Band position and absorption ranges are given in cm-1. Proton
nuclear magnetic resonance spectra were recorded on Bruker
A300 (200 MHz) Fourier transform spectrometer in the
indicated solvent. Chemical shifts are expressed in δ units
(ppm) from tetramethylsilane. Chromatographic columns were
packed with alumina (Merck, 70-230 mesh) and silica gel
(Merck, 70-230 mesh). Aluminum oxide TLC cards from Fluka
(aluminum oxide-precoated aluminum cards with fluorescent
1-{2-[R-(Furan-2-yl)phenylmethoxy]ethyl}-2-methyl-5-
nitroimidazole (18). Was prepared as 7 using the (furan-2-

4384 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13
De Martino et al.
yl)-phenylmethanol. Yield 7.5%, yellow oil. Anal. (C17H17N3O4
(327.38)) C, H, N.
1-{2-[R-(Cyclohexyl)phenylmethoxy]ethyl}-2-methyl-5-
nitroimidazole (40). Was prepared as 7 using the (cyclo-
hexyl)-phenylmethanol. Yield 46%, yellow oil. Anal. (C19H25N3O3
(343.43)) C, H, N.
acetone (28 mL) was refluxed for 48 h. Benzyl chloride (0.33
g, 0.36 mL, 0.0026 mol) and potassium carbonate (1.00 g,
0.0074 mol) were added at half time. After cooling, the reaction
was diluted with water and extracted with ethyl acetate. The
organic layer was washed with brine, dried, and evaporated.
The remaining oil was purified through a silica gel column
chromatography (ethyl acetate as eluent) to furnish 27 (0.19
g, yield 42%) as a yellow oil. Anal. (C13H15N3O2S (277.34)) C,
H, N, S.
1-{2-[R-(Pyridin-3-yl)phenylmethoxy]ethyl}-2-methyl-
5-nitroimidazole (19). A solution of thionyl chloride (1.27 g,
0.78 mL, 0.011 mol) in chloroform (5 mL) was added dropwise
to a an ice-cooled mixture of phenyl-(pyridin-3-yl)methanol (68)
(1.65 g, 0.0089 mol) in the same solvent (18.1 mL). The reaction
was heated at 50 °C for 5 h. The R-(pyridin-3-yl)phenylmethyl
chloride hydrochloride (70) was precipitated with anhydrous
dry diethyl ether, filtered, and used without purification. A
mixture of 69, triethylamine (0.63 g, 0.88 mL, 0.0075 mol),
and 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole (0.33 g, 0.0019
mol) in anhydrous N,N-dimethylformamide was stirred under
dry nitrogen atmosphere at 50 °C overnight. After cooling, the
reaction mixture was diluted with water and extracted with
ethyl acetate. The organic layer was separated, washed with
brine, and dried. Evaporation of the solvent gave a residue
which was purified by passing through an alumina column
(chloroform as eluent) to afford 19, (0.06 g, 9.3%) as a yellow
oil. Anal. (C18H18N4O3 (338.36)) C, H, N.
1-[2-(Diphenylmethylthio]ethyl]-2-methyl-5-nitroimid-
azole (20). A mixture of dipheylbromomethane (0.13 g, 0.0005
mol), 2-(2-methyl-5-nitroimidazol-1-yl)ethanethiol (0.10 g, 0.0005
mol), and potassium carbonate (0.22 g, 0.0016 mol) in acetone
(6 mL) was stirred at reflux for 4 days. After 24, 48, and 72 h,
diphenylbromomethane (0.13 g, 0.0005 mol) and potassium
carbonate (0.218 g, 0.0016 mol) were added. After cooling, the
reaction was poured on ice-water, stirred for 15 min, and
extracted with ethyl acetate. The organic layer was washed
with brine, dried, and evaporated in vacuo to give a the crude
product which was purified through a silica gel column
cromatography (chloroform as eluent) to afford 20 (0.042 g,
yield 24%), mp 124-126 °C (from cyclohexane). Anal.
(C19H19N3O2S (353.44)) C, H, N, S.
1-[2-(Diphenylmethylamino]ethyl]-2-methyl-5-nitro-
imidazole (28). To a suspension of 2-(2-methyl-5-nitroimid-
azol-yl)ethylamine dihydrochloride23 (0.64 g, 0.003 mol) and
triethylamine (0.76 g, 1.045 mL, 0.0075 mol) in dry DMF (10
mL) was added a solution of diphenylbromomethane (0.62 g,
0.0025 mol) in the same solvent (2 mL). Reaction was stirred
at 100 °C overnight under dry nitrogen atmosphere. After
cooling, the mixture was diluted with water and extracted with
ethyl acetate. The organic layer was washed with brine, dried,
and evaporated in vacuo. The residue was purified by passing
at first through a silica gel column chromatography (ethyl
acetate as eluent) and then through an alumina column
chromatography (chloroform as eluent) to afford 28 (0.11 g,
yield 13%), mp 145 °C (dihydrochloride, triturated with diethyl
ether). Anal. (C19H20N4O2‚2HCl (409.31)) C, H, Cl, N.
1-{2-[R-(2-Chlorophenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (29). Was prepared as 28 using (2-
chlorophenyl)phenylbromomethane. Yield 18%, mp 96-98 °C
(from n-hexane). Anal. (C19H19ClN4O2 (370.83)) C, H, Cl, N.
1-{2-[R-(2-Fluorophenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (30). Was prepared as 28 using (2-
fluorophenyl)phenylbromomethane. Yield 23%, mp 72-73 °C
(from n-hexane). Anal. (C19H19FN4O2 (354.38)) C, H, F, N.
1-{2-[R-(3-Methylphenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (31). Was prepared as 28 using (3-
methylphenyl)phenylbromomethane. Yield 10%, mp 147 °C
(dihydrochloride, from triturated with diethyl ether). Anal.
(C20H22N4O2‚2HCl (423.34)) C, H, Cl, N.
1-{2-[R-(3-Chlorophenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (32). Was prepared as 28 using (3-
chlorophenyl)phenylbromomethane. Yield 36%, mp 106-110
°C (from n-hexane). Anal. (C19H19ClN4O2 (370.83)) C, H, Cl,
N.
1-{2-[R-(2-Chlorophenyl)phenylmethylthio]ethyl}-2-
methyl-5-nitroimidazole (21). Was prepared as 20 using (2-
chlorophenyl)phenylbromomethane. Yield 56%, oily material.
Anal. (C19H18ClN3O2S (387.88)) C, H, Cl, N, S.
1-{2-[R-(2-Fluorophenyl)phenylmethylthio]ethyl}-2-
methyl-5-nitroimidazole (22). Was prepared as 20 using (2-
fluorophenyl)phenylbromomethane. Yield 30%, mp 93-95 °C
(from n-hexane). Anal. Calcd. (C19H18FN3O2S (371.43)) C, H,
F, N, S.
1-{2-[R-(3-Fluorophenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (33). Was prepared as 28 using (3-
fluorophenyl)phenylbromomethane. Yield 23%, mp 226-228
°C (dihydrochloride, triturated with diethyl ether). Anal.
(C19H19FN4O2‚2HCl (427.30)) C, H, Cl, F, N.
1-{2-[R-(3-Methylphenyl)phenylmethylthio]ethyl}-2-
methyl-5-nitroimidazole (23). Was prepared as 20 using (3-
methylphenyl)phenylbromomethane. Yield 30%, mp 113-115
°C (from n-hexane). Anal. (C20H21N3O2S (367.46)) C, H, N, S.
1-{2-[R-(3-Chlorophenyl)phenylmethylthio]ethyl}-2-
methyl-5-nitroimidazole (24). Was prepared as 20 using (3-
chlorophenyl)phenylbromomethane. Yield 58%, mp 81-83 °C
(from ligroin). Anal. (C19H18ClN3O2S (387.88)) C, H, Cl, N, S.
1-{2-[R-(3-Fluorophenyl)phenylmethylthio]ethyl}-2-
methyl-5-nitroimidazole (25). Was prepared as 20 using (3-
fluorophenyl)phenylbromomethane. Yield 57%, mp 92-93 °C
(from n-hexane). Anal. (C19H18FN3O2S (371.43)) C, H, F, N, S.
1-[2-(Diphenylmethylsulfonyl]ethyl]-2-methyl-5-nitro-
imidazole (26). 3-Chloroperbenzoic acid (0.048 g, 0.00028 mol)
was added while stirring to an ice-cooled solution of 1-[2-
(diphenylmethylthio]ethyl]-2-methyl-5-nitroimidazole (20, 0.10
g, 0.00028 mol). The reaction was stirred at 25 °C for 30 min
and then was poured on ice-water and extracted with ethyl
acetate. The organic layer was washed with brine and dried.
Evaporation of the solvent gave a residue which was purified
through a silica gel column chromatography (ethyl acetate as
eluent) to afford 26, (0.11 g, yield 100%), mp 189-191 °C (from
benzene). Anal. (C19H19N3O4S (385.88)) C, H, N, S.
1-{2-[R-(4-Methylphenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (34). Was prepared as 28 using (4-
methylphenyl)phenylbromomethane. Yield 3%, mp 162-163
°C (dihydrochloride, triturated with diethyl ether). Anal.
(C20H22N4O2‚2HCl (423.34)) C, H, Cl, N.
1-{2-[R-(4-Fluorophenyl)phenylmethylamino]ethyl}-2-
methyl-5-nitroimidazole (35). Was prepared as 28 using (4-
fluorophenyl)phenylbromomethane. Yield 10%, mp 220-222
°C (dihydrochloride, triturated with diethyl ether). Anal.
(C19H19FN4O2‚2HCl (427.30)) C, H, Cl, F, N.
1-[2-(Phenylmethylamino)ethyl]-2-methyl-5-nitroimid-
azole (36). To a solution of 2-(2-methyl-5-nitroimidazol-yl)-
ethylamine dihydrochloride (0.5 g, 0.002 mol), and triethyl-
amine (0.21 g, 1.045 mL, 0.0075 mol) in dry DMF (8 mL) was
added a solution of benzyl chloride in the same solvent (1.6
mL). The reaction was stirred overnight at room temperature
under nitrogen atmosphere and then diluted with water and
extracted with ethyl acetate. The organic layer was washed
with brine, dried, and evaporated in vacuo. The crude product
was purified through a silica gel column chromatography
(chloroform-ethanol 95:5 as eluent) to afford 36, (0.14 g, yield
29%), mp 107-110 °C (dihydrochloride, triturated with diethyl
ether). Anal. (C13H16N4O2‚2HCl (333.21)) C, H, Cl, N.
1-{2-[(Diphenylmethyl)amino]ethyl}-2-methyl-5-nitro-
imidazole (37). To a suspension of 36 (0.5 g, 0.002 mol) and
triethylamine (0.22 g, 0.3 mL, 0.002 mol) in dry DMF (8 mL)
was added a solution of benzyl chloride (0.25 g, 0.23 mL, 0.002
1-[2-(Phenylmethylthio]ethyl]-2-methyl-5-nitroimid-
azole (27). A mixture of benzyl chloride (0.33 g, 0.36 mL,
0.0026 mol), 2-(2-methyl-5-nitroimidazol-1-yl)etanethiol (0.45
g, 0.0026 mol), potassium carbonate (1.02 g, 0.0074 mol), and

Novel DAMNIs as HIV NNRTIs
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13 4385
mol) in the same solvent (1.6 mL). The mixture was stirred
for 12 h at room temperature. Benzyl chloride (0.25 g, 0.23
mL, 0.002 mol) and triethylamine (0.212 g, 0.3 mL, 0.002 mol)
were added, and the reaction was kept for additional 2 h. After
dilution with water, the reaction mixture extracted with ethyl
acetate. Organic extracts were combined, washed with brine,
and dried. Removal of the solvent gave a residue which was
purified through a silica gel column chromatography (chloro-
form as eluent) to afford 37 (0.06 g, yield 9%), mp 198-200
°C (dihydrochloride, triturated with diethyl ether). Anal.
(C20H22N4O2‚2HCl (423.34)) C, H, N.
1-[2-(Diphenylmethoxy)ethyl]-2-methyl-4-nitroimid-
azole (38). A solution of diethyl azodicarboxylate (0.63 g, 0.56
mL, 0.0036 mol) in dry THF (10 mL) was added dropwise to a
mixture of 2-(diphenylmethoxy)ethanol19 (0.75 g, 0.0033 mol),
2-methyl-5-nitroimidazole (0.46 g, 0.0036 mol), and anhydrous
triphenylphosphine (0.95 g, 0.0036 mol) in the same solvent
(20 mL). The reaction was stirred under dry nitrogen at room-
temperature overnight. Evaporation of the solvent gave a
residue which was diluted with water and extracted with ethyl
acetate. The organic layer was washed with brine, dried, and
evaporated in vacuo. The crude residue was purified at first
through a silica gel column chromatography (chloroform-
ethanol 95:5 as eluent) and then through an alumina column
(chloroform as eluent). First eluates gave to give 1-[2-(di-
phenylmethoxy)ethyl]-2-methyl-5-nitroimidazole (4)10a (0.33 g,
34%). Further elution with the same solvent afforded 38 (0.20
g, yield 20%), mp 112-114 °C (from cyclohexane). Anal.
(C19H19N3O3 (337.38)) C, H, N.
1-[2-(Diphenylmethoxy)ethyl]-5-nitroimidazole (41) and
1-[2-(Diphenylmethoxy)ethyl]-4-nitroimidazole (42). Were
prepared as 4 and 38 using 4(5)-nitroimidazole. The mixture
of isomers was separated through a silica gel column chroma-
tography (two repeated passages, chloroform-ethanol 95:5 and
ethyl acetate-petroleum ether 1:1). First eluates gave 42, yield
33%, mp 126-127 °C (from toluene-cyclohexane). Further
elution with the same solvent afforded 41, yield 22%, mp 110-
112 °C (from toluene-cyclohexane). Anal. (C18H17N3O3 (323.35))
C, H, N.
1-[2-(Phenylmethoxy)ethyl]-5-nitroimidazole (43) and
1-[2-(Phenylmethoxy)ethyl]-4-nitroimidazole (44). Were
prepared as 4 and 38 using 2-(phenylmethoxy)ethanol. The
mixture of isomers was separated through a silica gel column
chromatography (chloroform-ethanol 95:5 as eluent). First
eluates gave 43, yield 22%, mp 60-62 °C (from cyclohexane).
Anal. (C13H15N3O3 (261.28)) C, H, N. Further elution with the
same solvent afforded 44, yield 30%, mp 88-90 °C. Anal.
(C13H15N3O3 (261.28)) C, H, N.
(3-Fluorophenyl)-(thiophen-2-yl)methanone (52). Was
prepared as 45 using 2-fluorobenzoyl chloride. Yield 97%,
yellow oil. Anal. (C11H7FOS (206,23)) C, H, F, S.
(4-Fluorophenyl)-(thiophen-2-yl)methanone (53). Was
prepared as 45 in yield 84% using 4-fluorobenzoyl chloride.15f
(2,3-Difluorophenyl)-(thiophen-2-yl)methanone (54).
Was prepared as 45 using 2,3-difluorobenzoyl chloride. Yield
26%, brown oil. Anal. (C11H6F2OS (224.22)) C, H, F, S.
Phenyl-(5-chlorothiophen-2-yl)methanone (55). Was
prepared as 45 in yield 86% using 2-chlorothiophene.15g
General Procedure for the Synthesis of Methanols
56-66. Example. Phenyl-(thiophen-2-yl)methanol (56).
Sodium borohydride (3.80 g, 0.01 mol) was added to a solution
of phenyl-(thiophen-2-yl)methanone (45) (1.50 g, 0.008 mol)
in THF (16 mL) containing 0.5 mL of water. The mixture was
refluxed for 2 h. After cooling, the mixture was carefully
diluted with water, concentrated to a small volume, and
extracted with ethyl acetate. The organic layer was washed
with brine, dried, and evaporated to afford 56, (1.46 g, yield
96%), mp 49-51 °C (from cyclohexane).16a
(2-Methylphenyl)-(thiophen-2-yl)methanol (57). Was pre-
pared as 56 by reduction of the methanone 46. Yield 90%,
yellow oil. Anal. (C12H12OS (204.28)) C, H, S.
(4-Mehylphenyl)-(thiophen-2-yl)methanol (58). Was pre-
pared as 56 in yield 94% by reduction of the methanone 47.16b
(2-Chlorophenyl)-(thiophen-2-yl)methanol (59). Was
prepared as 56 in yield 92% by reduction of the methanone
48.16c
(3-Chlorophenyl)-(thiophen-2-yl)methanol (60). Was
prepared as 56 by reduction of the methanone 49. Yield 94%,
brown oil. Anal. (C11H9ClOS (224.70)) C, H, Cl, O, S.
(4-Chlorophenyl)-(thiophen-2-yl)methanol (61). Was
prepared as 56 in yield 92% by reduction of the methanone
50.16c
(2-Fluorophenyl)-(thiophen-2-yl)methanol (62). Was
prepared as 56 by reduction of the methanone 51. Yield 88%,
yellow oily material. Anal. (C11H9FOS (208.25)) C, H, F, S.
(3-Fluorophenyl)-(thiophen-2-yl)methanol (63). Was
prepared as 56 by reduction of the methanone 52. Yield 92%,
yellow oily material. Anal. (C11H8F2OS (226.24)) C, H, F, S.
(4-Fluorophenyl)-(thiophen-2-yl)methanol (64). Was
prepared as 56 by reduction of the methanone 53.16d
(2,3-Difluorophenyl)-(thiophen-2-yl)methanol (65). Was
prepared as 56 by reduction of the methanone 54. Yield 89%,
brown oil. Anal. (C11H8F2OS (226.24)) C, H, F, O, S.
Phenyl-(5-chlorothiophen-2-yl)methanol (66). Was pre-
pared as 56 by reduction of the methanone 55, yield 100%.
Phenyl-(pyridin-3-yl)methanone (67). A suspension of
nicotinic acid (3.00 g, 0.024 mol) in thionyl chloride (17 mL)
was heated at 85 °C under stirring for 90 min. The excess of
thionyl chloride was evaporated in vacuo, and the crude
residue was treated with benzene (21 mL) and portionwise
while stirring with anhydrous aluminum chloride (12.11 g,
0.091 mol) at 0 °C. The mixture was heated at reflux for 6 h,
cooled, poured on ice containing 37% HCl (5 mL), and extracted
with chloroform. The organic solution was washed with 1 N
NaOH (50 mL) and with water (50 mL) and then dried and
evaporated in vacuo. The residue was passed through a silica
gel column chromatography (chloroform as eluent) to give 67
(1.75 g, yield 40%) as oily material.17a
General Procedure for the Synthesis of Methanones
45-55. Example. Phenyl-(thiophen-2-yl)methanone (45).
A solution of benzoyl chloride (1.84 g, 0.013 mol) in dichloro-
methane (18 mL) was added dropwise to an ice-cooled suspen-
sion of anhydrous aluminum chloride (1.9 g, 0.013 mol) and
thiophene (1.09 g, 0.013 mol) in the same solvent (18 mL). The
reaction was sirred at room temperature for 2 h. After
quenching on crushed ice the mixture was made acid with 37%
HCl (1.3 mL) extracted with chloroform. The organic layer was
washed with brine, dried, and evaporated to dryness. The
crude product was purified through a silica gel column
chromatography (dichloromethane petroleum ether 1:1 as
eluent) to afford pure 45 (2.4 g, 90%) as yellow oil.15a
Phenyl-(pyridin-3-yl)methanol (68). Was prepared as 56
(2-Methylphenyl)-(thiophen-2-yl)methanone (46). Was
in yield 43% by reduction of the methanone 67.17c
prepared as 45 in yield 80% using 2-methylbenzoyl chloride.15b
2-(2-Methyl-5-nitroimidazol-1-yl)ethanthiol. A solution
of 1-(2-hydroxyethyl)-2-methyl-5-nitroimidazole mesylate (2.00
g, 0.008 mol) and NaHS (0.58 g, 0.008 mol) in dry DMF was
stirred under nitrogen stream at room temperature for 48 h.
The reaction was poured on ice-water, stirred for additional
15 min, and extracted with ethyl acetate. The organic layer
was washed with brine and dried. After removing of the
solvent, the crude product was purified through a silica gel
column chromatography (ethyl acetate-ethanol 1:1 as eluent)
to give 2-(2-methyl-5-nitro-imidazol-1-yl)ethanthiol, (0.41 g,
yield 30%), mp 115-118 °C (from ethanol).25
(4-Methylphenyl)-(thiophen-2-yl)methanone (47). Was
prepared as 45 in yield 90% using 4-methylbenzoyl chloride.15c
(2-Chlorophenyl)-(thiophen-2-yl)methanone (48). Was
prepared as 45 in yield 90% using 2-chlorobenzoyl chloride.15e
(3-Chlorophenyl)-(thiophen-2-yl)methanone (49). Was
prepared as 45 in yield 90% using 3-chlorobenzoyl chloride.15c
(4-Chlorophenyl)-(thiophen-2-yl)methanone (50). Was
prepared as 45 in yield 86% using 4-chlorobenzoyl chloride.15e
(2-Fluorophenyl)-(thiophen-2-yl)methanone (51). Was
prepared as 45 in yield 82% using 2-fluorobenzoyl chloride.15e

4386 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13
De Martino et al.
Figure 2. A: Superimposition of experimental bound conformation of 70 (black) and that predicted by Autodock (grey). B: Previous
model for 4 (black) compared to that found by Autodock (grey).
Computational Studies. All molecular modeling calcula-
tions and manipulations were performed using the software
packages Macromodel 7.1,26 Autodock 3.0.5,27 running on
Silicon Graphics O2 R10000 and Octane R10000, IBM-compat-
ible AMD Athlon XP 3.0 GHz workstations. For any minimiza-
tion the all-atom Amber force field27 was adopted as imple-
mented in the Macromodel package.
The geometry of the NNBS of the wt RT strain was taken
from the structure of HIV-1 RT/70 complex filed in the
Brookhaven Protein Data Bank28 (entry code 1rt2). All the
residues within 20 Å from any ligand’s atom (70) were used
to define the NNBS.
square deviation (RMSD) of atom coordinates in either (RMSD
) 1.01 Å) and confirmed our previous findings about 4. In
Figure 2A is reported the superimposition of experimental
bound conformation of 70 and that predicted by Autodock; in
Figure 2B our previous model for 4 compared to that found
by Autodock (RMSD ) 1.2 Å).
Cell Based Antiviral Assay Procedures. Viruses. A
laboratory lymphocyte-tropic strain of HIV (HTLV-IIIB also
called HIV-IIIB) was used to infect MT-4 cells. The strain is
available through the AIDS Research and Reference Reagent
Program (NIH, Bethesda, MD).
HIV Titration. Titration to determine the infectivity of
laboratory viral strains was performed in C8166 cells (HIV-
IIIB)31 The titer of virus stocks, expressed as 50% tissue
culture infectious dose (TCID50) was determined as previously
described.32
Anti-HIV Assays. The activity of test compounds against
multiplication of HIV-1 in MT-4 cells was based on inhibition
of virus-induced cytopathogenicity. Briefly, 150 µL of culture
medium containing 2 × 104 cells were added to each well flat-
bottom microtiter trays containing 50 µL of culture medium
with or without various concentrations of test compounds.
Then 50 µL of HIV suspension (100 TCID50) was added. After
5 days incubation at 37 °C, the viral activity of compounds
was evaluated by quantifying the HIV induced cytopatho-
genicity by means of the 3-(4,5-dimethylthiazol-1-yl)-2,5-
diphenyltetrazolium bromide (MTT) method.33 Protection (%)
from the viral induced cytopathogenicity in HIV-infected cells
as mesured by the MTT assay was calculated as follows:
(ODT)HIV - (ODC)HIV: (ODC)mock - (ODC)HIV, whereby (ODT)HIV
is the optical density measured with a given concentration
of cysteamine in HIV infected cells, (ODC)HIV is the optical
density measured for the control untreated HIV-infected cells,
(ODC)mock is the optical density measured for the control
untreated mock-infected cells. The optical density at 540/690
nm was measured using a plate reader.
The reference compound 4 modeled as previously reported11b
was used to build the two enantiomeric configurations of 7.
The starting conformations for docking studies were obtained
using molecular dynamics with simulated annealing as imple-
mented in Macromodel version 7.1 and conducted as follow-
ing: either (R)-7 or (S)-7 was energy minimized to a low
gradient. The nonbonded cutoff distances were set to 20 Å for
both van der Waals and electrostatic interactions. An initial
random velocity to all atoms corresponding to 300 K was
applied. Three subsequent molecular dynamic runs were then
performed. The first was carried out for 10 ps with a 1.5 fs
time-step at a constant temperature of 300 K for equilibration
purposes. The next molecular dynamic was carried out for 20
ps, during which the system is coupled to a 150 deg thermal
bath with a time constant of 5 ps. The time constant represents
approximately the half-life for equilibration with the bath;
consequently the second molecular dynamic command caused
the molecule to slowly cool to approximately 150 K. The third
and last dynamic cooled the molecule to 50 K over 20 ps. A
final energy minimization was then carried out for 250
iterations using conjugate gradient. The minimizations and
the molecular dynamics were in all cases performed in aqueous
solution. The atom charges automatically assigned by the
batchmin module were retained for the docking calculations.29
For the docking procedure the program Autodock was used
to explore the binding conformation of either (R)-7 or (S)-7.
For the docking a grid spacing of 0.375 Å and 60 × 80 × 60
number of points was used. The grid was centered on the mass
center of the experimental bound 70 coordinates. The GA-LS
method was adopted using the default settings. Amber united
atom charges were assigned to the protein using the program
ADT (AutoDock Tools).30 Autodock generated 250 possible
binding conformations for each docking.
Cytotoxicity. The cytotoxicity of test compounds was
evaluated in parallel with their antiviral activity and was
based on the viability of mock-infected cells, as monitored by
the MTT method. The 50% effective dose (ED50) and 50%
cytotoxic dose (TD50) values were calculated from pooled values
in the effective dynamic range of the antiviral activity and
cytotoxicity assays (5-95%) using the median effect equation
as previously described.34 The selectivity index (SI) was
calculated ad TD50:ED50 ratio.
To validate the use of the Autodock program, the docking
studies were performed on the reference compound 70 and for
comparison purposes also on the previously reported 4. Auto-
dock successfully reproduced the experimental binding con-
formations of the reference drug 70 with acceptable root-mean-
Enzymatic Assay Procedures. Chemicals. [3H]dTTP (40
Ci/mmol) was from Amersham and unlabeled dNTP's from
Boehringer. Whatman was the supplier of the GF/C filters.
All other reagents were of analytical grade and purchased from
Merck or Fluka.

Novel DAMNIs as HIV NNRTIs
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13 4387
P. Synthesis of pyrryl aryl sulfones targeted at the HIV-1 reverse
transcriptase. Arch. Pharm. (Weinheim) 1995, 328, 223-229. (c)
Silvestri, R.; Pagnozzi, E.; Artico, M.; Stefancich, G.; Massa, S.;
La Colla, P. Synthesis of 9H-pyrrolo[2,1-b][1,3,6]benzothiadiazocin-
10(11H)-one 4,4-dioxide, potential anti-HIV agent. J. Heterocycl.
Chem. 1995, 32, 683-685. (d) Artico, M.; Silvestri, R.; Massa,
S.; Loi, A. G.; Corrias, S.; Piras, G.; La Colla, P. 2-Sulfonyl-4-
chloroanilino moiety: a potent pharmacophore for the anti-
human immunodeficiency virus type 1 activity of pyrrolyl aryl
sulfones. J. Med. Chem. 1996, 39, 522-530. (e) Artico, M.;
Silvestri, R.; Pagnozzi, E.; Stefancich, G.; Massa, S.; Loi, A. G.;
Scano, P.; Corrias, S.; Spiga, M. G.; P.; La Colla, P. Pyrrolo[1,2-
b][1,2,5]benzothiadiazepines (PBTDs): a novel class of HIV-1-
specific non-nucleoside reverse transcriptase inhibitors. Bioorg.,
Med. Chem. 1996, 4, 837-850. (f) Artico, M.; Silvestri, R.;
Pagnozzi, E.; Stefancich, G.; Massa, S.; La Colla, P. Synthesis
and anti-HIV activity of 10,11-dihydropyrrolo[1,2-b][1,2,5]benzo-
thiadiazepine-11-acetic acid 5,5-dioxide derivatives and related
compounds. Farmaco 1996, 51, 425-430. (g) Silvestri, R.; Artico,
M.; Massa, S.; Stefancich, G.; Congeddu, E.; Putzolu, M.; La
Colla, P. Sulfone derivatives with anti-HIV activity. Farmaco
1997, 52, 323-329. (h) Silvestri, R.; Artico, M.; Bruno, B.; Massa,
S.; Novellino, E.; Greco, G.; Marongiu, M. E.; Pani, A.; De Montis,
A.; La Colla, P. Synthesis and biological evaluation of 5H-indolo-
[3,2-b][1,5]benzothiazepine derivatives, designed as conforma-
tionally constrained analogues of the human immunodeficiency
virus type 1 reverse transcriptase inhibitor L-737, 126. Antiviral
Chem., Chemoth. 1998, 9, 139-148. (i) Artico, M.; Silvestri, R.;
Pagnozzi, E.; Bruno, B.; Novellino, E.; Greco, G.; Massa, S.;
Ettorre, A.; Loi, A. G.; Scintu, F.; La Colla. P. Structure-based
design, synthesis and biological evaluation of novel pyrrolyl aryl
sulfones (PASs), HIV-1 non-nucleoside reverse transcriptase
inhibitors active at nanomolar concentrations. J. Med. Chem.
2000, 43, 1886-1891. (j) Silvestri, R.; De Martino, G.; Artico,
M.; La Regina G.; Ragno, R.; Loddo, R.; La Colla, P.; Marongiu,
M. E.; La Colla, M.; Pani. A. Anti-HIV-1 NNRT Agents: Acyl-
amino Pyrryl Aryl Sulfones (APASs) as Truncated Analogues
of Tricyclic PBTDs. Med. Chem. Res. 2002, 11, 195-218. (k)
Silvestri, R.; De Martino, G.; La Regina, G.; Artico, M.; Massa,
S.; Vargiu, L.; Mura, M.; Loi, A. G.; Marceddu, T.; La Colla, P.
Novel Indolyl Aryl Sulfones Active against HIV-1 Carrying
NNRTI Resistance Mutations: Synthesis and SAR Studies. J.
Med. Chem. 2003, 46, 2482-2493.
Nucleic Acid Substrates. The homopolymer poly(rA)
(Pharmacia) was mixed at weight ratios in nucleotides of 10:
1, to the oligomer oligo(dT)12-18 (Pharmacia) in 20 mM Tris-
HCl (pH 8.0), containing 20 mM KCl and 1 mM EDTA, heated
at 65 °C for 5 min and then slowly cooled at room temperature.
Expression and Purification of Recombinant HIV-1
RT Forms. The coexpression vectors pUC12N/p66(His)/
p51with the wild-type or the mutant forms of HIV-1 RT p66
(Boyer et al., 1994a) were kindly provided by Dr. S. H. Hughes
(NCI-Frederick Cancer Research and Development Center).
Proteins were expressed in E. coli and purified as described.35
HIV-1 RT RNA-Dependent DNA Polymerase Activity
Assay. RNA-dependent DNA polymerase activity was assayed
as follows: a final volume of 25 µL contained reaction buffer
(50 mM Tris-HCl pH 7.5, 1 mM DTT, 0.2 mg/mL BSA, 4%
glycerol), 10 mM MgCl2, 0.5 µg of poly(rA)/oligo(dT)10:1 (0.3 µM
3′-OH ends), 10 µM [3H]-dTTP (1Ci/mmol) and 2-4 nM RT.
Reactions were incubated at 37 °C for the indicated time.
Aliquots (20 µL) were then spotted on glass fiber filters GF/C
which were immediately immersed in 5% ice-cold TCA. Filters
were washed twice in 5% ice-cold TCA and once in ethanol for
5 min, dried, and acid-precipitable radioactivity was quanti-
tated by scintillation counting.
Inhibition Assays. Reactions were performed under the
conditions described for the HIV-1 RT RNA-dependent DNA
polymerase activity assay. Incorporation of radioactive dTTP
into poly(rA)/oligo(dT) at different substrate (nucleic acid or
dTTP) concentrations was monitored in the presence of
increasing fixed amounts of inhibitor. Data were then plotted
according to Lineweaver-Burke and Dixon. For Ki determi-
nation, an interval of inhibitor concentrations between 0.2 Ki
and 5 Ki was used.
Acknowledgment. We thank the Universita` degli
Studi di Roma “La Sapienza”, Finanziamento progetti
di ricerca di Ateneo (ex quota 60%) - Anno 2002. We
also acknowledge the finacial support of the Italian
MIUR (cofin 2000) and the Italian Ministero della
Salute - Istituto Superiore di Sanita` - Fourth National
Research Program on AIDS (grants no. 40C.8 and no.
40D.46).
(11) (a) Silvestri, R.; Artico, M.; Massa, S.; Marceddu, T.; De Montis,
F.; La Colla, P. 1-[2-(Diphenylmethoxy)ethyl]-2-methyl-5-nitro-
imidazole: a potent lead for the design of novel NNRTIs. Bioorg.,
Med. Chem. Lett. 2000, 10, 253-256. (b) Silvestri, R.; Artico,
M.; De Martino, G.; Ragno, R.; Massa, S.; Loddo, R.; Murgioni,
C.; Loi, A. G.; Pani, A.; La Colla, P.. Synthesis, biological
evaluation and binding mode of novel 1-[2-(diarylmethoxy)ethyl]-
2-methyl-5-nitroimidazoles targeted at the HIV-1 reverse tran-
scriptase. J. Med. Chem. 2002, 45, 1567-1576.
Supporting Information Available: Spectroscopic data
of new compounds 7-38, 40-44, 52, 54, 57, 60, 62, 63, and
65 and elemental analyses data of 7-38 and 40-44 are
available free of charge via the Internet at http://pubs.acs.org.
(12) (a) Scha¨fer, W.; Friebe, W.-G.; Leinert, H.; Mertens, H.; Poll,
T.; von del Saal, W.; Zilch, H.; Nuber, B.; Zigler, M. L. Non
nucleoside inhibitors of HIV-1 reverse transcriptase: molecular
modeling and X-ray structure investigations. J. Med. Chem.
1993, 36, 726-732. (b) Scha¨fer, W. Rational design of inhibitors
of HIV-1 reverse transcriptase. In Methods and priciples in
medicinal chemistry. Structure-based ligand design; Guberbator,
K., Bo¨hm, H.-J., Eds.; Wiley-VCH: Weinheim, Germany, 1998.
(13) Stephens, C. E.; Felder, T. M.; Sowell, J. W., Sr.; Andrei, G.;
Balzarini, J.; Snoeck, R.; De Clercq, E. Synthesis and antiviral/
antitumor evaluation of 2-amino- and 2-carboxamide-3-aryl-
sulfonylthiophenes and related compounds as a new class of
diarylsulfones. Bioorg., Med. Chem. 2001, 9, 1123-1132.
(14) (a) Uckun, F. M.; Pendergrass, S.; Mahere, D.; Zhu, D.; Tuel-
Ahlgren, L.; Mao, C.; Ventkatachalam, T. K. N′-[2-(2-thiophene)-
ethyl]-N-[2-(5-bromopyridyl)]thiourea as a potent inhibitor of
NNI-resitant and multidrug-resistant human immunodeficiency
virus-1. Bioorg., Med. Chem. Lett. 1999, 9, 3411-3416. (b)
Venkatachalam, T. K.; Sudbeck, E. A.; Mao, C.; Uckun, F. M.
Anti-HIV activity of aromatic and heterocyclic thazolyl thiourea
compounds. Bioorg., Med. Chem. Lett. 2001, 11, 523-528.
(15) Literature related to methanones. (a) Curran, D. P.; Nakamura,
H.; Ryu, I.; Matsubara, H. Fluorous triphase and other multi-
phase systems. U.S. Patent 877,944, 2003. (b) Wittenberg, R.;
Srogl, J.; Egi, M.; Liebeskind, L. S. Ketone synthesis under
neutral conditions. Cu(I) diphenylphosphinate-mediated, pal-
ladium-catalyzed coupling of thiol esters and organostannanes.
Org. Lett. 2003, 5, 3033-3035. (c) Keumi, T.; Y.; Kiichiro; S.,
Masakazu; K., H. 2-(Trifluoromethylsulfonyloxy)pyridine as a
reagent for ketone synthesis from carboxylic acids and aromatic
hydrocarbons. Bull. Chem. Soc. Jpn. 1988, 61, 455-459. (d)
Andrieu, C.; Mollier, Y.; Lozac′h, N. Heterocyclic sulfur com-
pounds. XXXII. 2-Thienyl ketones and thioketones. Bull. Soc.
Chim. Fr. 1969, 3, 827-830. (e) Haddach, M.; McCarthy, J. R.
A new method for the synthesis of ketones: the palladium-
catalyzed cross-coupling of acid chlorides with arylboronic acids.
References
(1) WHO/UNAIDS. AIDS Epidemic Update: December 2003.
(2) Williams, I. G. Enfuvirtide (Fuzeon): the first fusion inhibitor.
Int. J. Clin. Pract. 2003, 57, 890-897.
(3) Vandamme, A.-M.; Van Vaerenbergh, K.; De Clercq, E. Anti-
human immunodeficiency virus drug combination strategies.
Antiviral Chem., Chemother. 1998, 9, 187-203.
(4) Spence, R. A.; Kati, W. M.; Anderson, K. S.; Johnson, K. A.
Mechanism of inhibition of HIV-1 reverse transcriptase by non-
nucleoside inhibitors. Science 1995, 267, 988-993.
(5) Artico, M. Non-nucleoside anti-HIV-1 reverse transcriptase
inhibitors (NNRTIs): a chemical survey from lead compounds
to selected drugs for clinical trials. Farmaco 1996, 51, 305-331.
(6) Buckheit, R. W. Non-nucleoside reverse transcriptase inhibi-
tors: perspectives on novel therapeutic compounds and strate-
gies for the treatment of HIV infection. Exp. Op. Invest. Drugs
2001, 10, 1423-42.
(7) Condra, J. H.; Miller, M. D.; Hazuda, D. J.; Emini, E. A. Potential
new therapies for the treatment of HIV-1 infection. Annu. Rev.
Med. 2002, 53, 541-555.
(8) Young, S. D. Recent advances in the chemotherapy of HIV. Annu.
Rep. Med. Chem. 2003, 38, 173-182.
(9) Flynn, D. L. Presented at the 226th American Chemical Society
National Meeting, New York, Sept 7-11, 2003; Abstracts 127-
130.
(10) (a) Artico, M.; Stefancich, G.; Silvestri, R.; Massa, S.; Pagnozzi,
E.; Loi, A. G.; Musu, D.; Doa, M.; Scano, P.; La Colla, P.
Pyrrolobenzothiazepines: a new class of non-nucleoside HIV-1
reverse transcriptase inhibitors. Med. Chem. Res. 1994, 4, 283-
290. (b) Artico, M.; Silvestri, R.; Stefancich, G.; Massa, S.;
Pagnozzi, E.; Musu, D.; Scintu, F.; Pinna, E.; Tinti, E.; La Colla,

4388 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 13
De Martino et al.
Tetrahedron Lett. 1999, 40, 3109-3112. (f) Stoner, E. J.; Co-
thron, D. A.; Balmer, M. K.; Roden, B. A. Benzylation via tandem
Grignard reaction - Iodotrimethylsilane (TMSI) mediated re-
duction. Tetrahedron 1995, 51, 11043-11062. (g) Puschmann,
I.; Erker, T. Chemistry of thienoannelated O, N- and S, N-
containing heterocycles. X. Synthesis of 2-substituted thieno-
diltiazem derivatives. Monat. Chem. 1995, 126, 569-78.
(16) Literature related to methanols. (a) Barker, M.; Huddleston, P.
R.; Clephane, J.; Wood, M. L.; Holmes, D. Dehalogenation of
1-halothienyldi- and-tetrahydroisoquinolines by sodium meth-
oxide in dimethyl sulfoxide. J. Chem. Soc., Perkin Trans. 1 1985,
275-281. (b) Cho, W.-S.; Kim, H.-J.; Littler, B. J.; Miller, M. A.;
Lee, C.-H.; Lindsey, J. S. Rational synthesis of trans-substituted
porphyrin building blocks containing one sulfur or oxygen atom
in place of nitrogen at a designated site. J. Org. Chem. 1999,
64, 7890-7901. (c) Krishnaswamy, N. R.; Kumar, C. S. S. R.;
Prasanna, S. R. Photochemical reactions of thienyl-, bithienyl-,
terthienyl- and thienylaroylmethanols. J. Chem. Res., Synop.
1991, 7, 166-169. (d) Stoner, E. J.; Cothron, D. A.; Balmer, M.
K.; Roden, B. A. Benzylation via tandem Grignard reaction -
Iodotrimethylsilane (TMSI) mediated reduction. Tetrahedron
1995, 51, 11043-11062.
(17) (a) Ohba, S.; Sakamoto, T.; Yamanaka, H. Reactions of â-bromo-
N-heteroaromatics with phenylacetonitrile. Heterocycles 1990,
31, 1301-1308. (b) Bochis, R. J.; Olen, L. E.; Waksmunski, F.
S.; Mrozik, H.; Eskola, P.; Kulsa, P.; Wilks, G.; Taylor, J. E.;
Egerton, J. R.; Ostlind, D. A.; Olson, G. Substituted imidazo-
[1,2-a]pyridine-2-carbamate anthelmintics. J. Med. Chem. 1981,
24, 1518-1521. (c) Stoner, E. J.; Cothron, D. A.; Balmer, M. K.;
Roden, B. A. Benzylation via tandem Grignard reaction -
Iodotrimethylsilane (TMSI) mediated reduction. Tetrahedron
1995, 51, 11043-11062.
(18) Hay, M. P.; Wilson, W. R.; Moselen, J. W.; Palmer, B. D.; Denny,
W. A. Hypoxia-selective antitumor agents. 8. Bis(nitroimid-
azolyl)alkane-carboxamides: a new class of hypoxia-selective
cytotoxins and hypoxic cell radiosensitizers. J. Med. Chem. 1994,
37, 381-391.
(19) Coderc, E.; Martin-Fardon, R.; Vignon, J.; Kamenka, J. M. New
compounds resulting from structural and biochemical similari-
ties between GBR 12783 and BTCP, two potent inhibitors of
dopamine uptake. Eur. J. Med. Chem. 1993, 28, 893-898.
(20) Mitsunobu, O.; Yamada, M. Preparation of esters of carboxylic
and phosphoric acid via quaternary phosphonium salts. Bull.
Chem. Soc. Jpn. 1967, 40, 2380-2382.
(21) Hopkins, A. L.; Ren, J.; Esnouf, R. M.; Willcox, B. E.; Jones, E.
Y.; Ross, C.; Miyasaka, T.; Walker, R. T.; Tanaka, H.; Stammers,
D. K.; Stuart, D. I. Complexes of HIV-1 reverse transcriptase
inhibitors of the HEPT series reveal conformational changes to
the design of potent non-nucleoside inhibitors. J. Med. Chem.
1996, 39, 1589-1600.
alkanecarboxamides: a new class of hypoxia-selective cytotoxins
and hypoxic cell radiosensitizers. J. Med. Chem. 1994, 37, 381-
391.
(24) Corbett, J. W.; Rodgers, J. D. Discovery of second generation of
quinazoline non-nucleoside reverse transcriptase inhibitors of
HIV-1. Prog. Med. Chem. 2002, 40, 63-105.
(25) Caplar, V.; Sunjic, V.; Kafjez, F. N′-Substitution in 2-methyl-
4(5)niroimidazole. III. New syntheses of 1-(2′-(ethylsulfonyl)-
ethyl)-2-methyl-5-nitroimidazole. J. Heterocycl. Chem. 1974, 11,
1055-60
(26) Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.;
Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W.
C. MacroModel - An Integrated Software System for Modeling
Organic and Bioorganic Molecules Using Molecular Mechanics.
J. Comput. Chem. 1990, 11, 440-467.
(27) Goodsell, D. S.; Morris, G. M.; Olson, A. J. Automated docking
of flexible ligands: applications of AutoDock. J. Mol. Recognit.
1995, 9, 1-5.
(28) Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.;
Cheatham T. E.; I.; Debolt, S.; Ferguson, D. M.; Seibel, G. L.;
Kollman, P. A. AMBER, a Package of Computer Programs for
Applying Molecular Mechanics, Normal-Mode Analysis, Molec-
ular Dynamics and Free Energy Calculations to Simulate the
Structural and Energetic Properties of Molecules. Comput. Phys.
Commun. 1995, 91, 1-41.
(29) Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.
N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data
Bank. Nucleic Acids Res. 2000, 28, 235-242.
(30) Michel F. Sanner. Python: A Programming Language for
Software Integration and Development. J. Mol. Graphics Mod.
1999, 17, 57-61.
(31) (a) Andreoni, M.; Sarmati, L.; Parisi, S. G.; Ercoli, L.; Rocchi,
G. Efficient and reproducible new semimicromethod for the
detection and tritation of HIV in human plasma. J. Med. Virol.
1992, 38, 207-213. (b) Bergamini, A.; Capozzi, M.; Ghibelli, L.;
Dini, L.; Salanitro, A.; Milanese, G.; Wagner, T.; beninati, S.;
Pesce, C. D.; amici, C.; Rocchi, G. Cystamine potently suppresses
in vitro HIV replication in acutely and chronically infected
human cells. J. Clin. Invest. 1994, 93, 2251-2257.
(32) Karber, G. Beitrag zur kollectiven Behandlung Pharmakolo-
gisher Reihenversuche. Arch. Exp. Pharmakol. 1931, 162, 480-
483.
(33) Pauwels, R.; Balzarini, J.; Baba, M.; Snoeck, R.; Schols, D.;
Hederwijn, P.; Desmyster, J.; De Clercq, E.
A rapid and
automated tetrazolium-based colorimetric assay for the detection
of anti HIV compounds. J. Virol. Methods 1988, 20, 309-321.
(34) Chou, T. C. Derivation and properties of Micaelis-Menten type
and Hill type equation for reference ligands. J. Theor. Biol. 1976,
59, 253-276.
(35) Maga, G.; Amacker, M.; Ruel, N.; Hubsher, U.; Spadari, S.;
Resistance to nevirapine of HIV-1 reverse transcriptase mu-
tants: loss of stabilizing interactions and thermodynamic or
steric barriers are induced by different single amino acid
substitutions. J. Mol. Biol. 1997, 274, 738-747.
(22) Goodsell, D. S.; Morris, G. M.; Olson, A. J. J Mol. Recognit. 1996,
9, 1-5.
(23) Hay, M. P.; Wilson, W. R.; Moselen, J. W.; Palmer, B. D.; Denny,
W. A. Hypoxia-selective antitumor agents. 8. Bis(nitroimidazolyl)
JM050273A