Synthesis and antiviral evaluation of 6-(trifluoromethylbenzyl) and 6-(fluorobenzyl) analogues of HIV drugs emivirine and GCA-186

Article abstract of DOI:10.1002/ardp.200700113

The present study describes the synthesis and antiviral evaluation of a series of novel 6-(3-trifluoromethylbenzyl) and 6-(fluorobenzyl) analogues of the HIV drugs emivirine and GCA-186. The objective was to investigate whether the fluoro or trifluoromethyl substituents could lead to an improved antiviral activity against HIV-1 wild type and mutants resistant to non-nucleoside RT inhibitors. The biological test results showed that the most of theses compounds showed good activity against wild type HIV-1. Among them, compound 1-(ethoxymethyl)-6-(3-fluorobenzyl)-5-isopropyluracil (9i) showed the largest inhibitory potency (EC₅₀ = 0.02 μM), resulting equally potent than emivirine against wild type HIV-1. Furthermore, compound 9i showed marginal better activity against resistant mutants than emivirine. The key steps in the synthesis of the target compounds were either reaction of an appropriate β-keto ester with thiourea or a cross-coupling reaction of 6-chloro-2,4-dimethoxypyrimidines with benzylic Grignard reagents.

Full text of DOI:10.1002/ardp.200700113

Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
N. R. El-Brollosy et al.
9
Full Paper
Synthesis and Antiviral Evaluation of 6-(Trifluoromethylbenzyl)
and 6-(Fluorobenzyl) Analogues of HIV Drugs Emivirine and
GCA-186
Nasser R. El-Brollosy1, 2, Esben R. Sørensen1, Erik B. Pedersen1, Giuseppina Sanna3,
Paolo La Colla3, and Roberta Loddo3
1 Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense M,
Denmark
2
Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi
Arabia
3 Dipartimento di Scienze e Tecnologie Biomediche, Sezione di Microbiologia e Virologia Generale e
Biotecnologie Microbiche, Universita di Cagliari, Monserrato, Italy
The present study describes the synthesis and antiviral evaluation of a series of novel 6-(3-tri-
fluoromethylbenzyl) and 6-(fluorobenzyl) analogues of the HIV drugs emivirine and GCA-186.
The objective was to investigate whether the fluoro or trifluoromethyl substituents could lead
to an improved antiviral activity against HIV-1 wild type and mutants resistant to non-nucleo-
side RT inhibitors. The biological test results showed that the most of theses compounds showed
good activity against wild type HIV-1. Among them, compound 1-(ethoxymethyl)-6-(3-fluoroben-
zyl)-5-isopropyluracil (9i) showed the largest inhibitory potency (EC50 = 0.02 lM), resulting
equally potent than emivirine against wild type HIV-1. Furthermore, compound 9i showed mar-
ginal better activity against resistant mutants than emivirine. The key steps in the synthesis of
the target compounds were either reaction of an appropriate b-keto ester with thiourea or a
cross-coupling reaction of 6-chloro-2,4-dimethoxypyrimidines with benzylic Grignard reagents.
Keywords: Alkenyloxymethyluracils / Grignard reaction / HIV-1 / Non-nucleoside reverse transcriptase inhibitors /
Received: May 30, 2007; accepted: August 24, 2007
DOI 10.1002/ardp.200700113
quently is incorporated into the DNA of the infected host
cell [1, 2]. In recent years, much effort has been put into
the design and synthesis of HIV-1 non-nucleoside RT
inhibitors (NNRTIs) [3]. The NNRTIs are highly specific as
their binding site is a hydrophobic pocket located
approximately 10 ꢀ from the polymerease active site [4]
forcing the RT subunit into an inactive conformation [5].
One of the first NNRTIs was 1-[(2-hydroxyethoxy)methyl]-
6-(phenylthio)thymine (HEPT) [6, 7]. Although HEPT did
not show very high activity against HIV-1, it was consid-
ered an interesting lead compound for the synthesis of
new analogues. Among them 6-benzyl-1-(ethoxymethyl)-
5-isopropyluracil (Emivirine, formerly MKC-442) [8], 6-
(3,5-dimethylbenzyl)-5-isopropyluracil (GCA-186) [9], and
the corresponding N-1 allyloxymethyl analogues [10]
(BED-60 and AMB-A10) showed high potent activity
against HIV-1 (Fig. 1).
Introduction
The reverse transcriptase (RT) enzyme of the human
immunodeficiency virus type 1 (HIV-1) is an important
target for development of anti-AIDS drugs. It is responsi-
ble for the conversion of a single-stranded RNA viral
genome into a double-stranded DNA chain that subse-
Correspondence: Erik B. Pedersen, Nucleic Acid Center, Department of
Physics and Chemistry, University of Southern Denmark, Campusvej 55,
DK-5230 Odense M, Denmark.
E-mail: ebp@ifk.sdu.dk
Fax: +45 6615 8780
Abbreviations: reverse transcriptase (RT); human immunodeficiency vi-
rus type 1 (HIV-1); non-nucleoside RT inhibitors (NNRTIs); 1-[(2-hydrox-
yethoxy)methyl]-6-(phenylthio)thymine (HEPT); N,O-bis(trimethylsilyl)a-
cetamide (BSA); trimethylsilyl trifluoro-methanesulfonate (TMS triflate); 3-
(4,5-dimethylthiazol-1-yl)-2,5-diphenyltetrazolium bromide (MTT)
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

10
N. R. El-Brollosy et al.
Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
wildtype and mutants resistant to non-nucleoside RT
inhibitors (NNRTIs).
Results and discussion
Chemistry
The required key intermediate – the 5,6-disubstituted
uracil derivatives 4a–i were synthesized via two inde-
pendent routes based on the commercial availability of
the starting materials (Scheme 1).
With the nitriles commercially available for com-
pound 1a, b, we choose the b-keto ester strategy, devel-
oped by one of us [22], for the synthesis of the correspond-
ing uracil derivatives 4a–d (Scheme 2). However, with
the fluoro-substituted benzylic bromide commercially
available for compounds 7a–d, we choose another strat-
egy based on a Grignard reaction followed by a cross-cou-
pling reaction for the synthesis of the uracil derivatives
4e–i (Scheme 3). This method was chosen despite the fact
that it is known that benzylic-type Grignard reagents can
be difficult to prepare via the classical method with the
treatment of magnesium powder.
Figure 1. Structures of the lead molecules HEPT, MKC-442,
GCA-186, BED-60, and AMB-A10.
During NNRTI mono therapy for HIV-1 infected
patients [11] and in-vitro culture [12], rapid emergence of
highly drug-resistant viruses is often observed. The pri-
mary cause of drug resistance is the substitution of tyro-
sine by cysteine at position 181 in the HIV-1 RT (Y181C).
Furthermore, the RT mutation of the lysine at position
103 to asparagine (K103N) is frequently observed on treat-
ment with retroviral regimens containing many NNRTIs
[13] including the FDA-(U.S. Food and Drug Administra-
tion) approved drugs (nevirapine [14], delavirdine [15],
and efavirenz [16]). Therefore, it is of importance to find
novel NNRTIs that may be able to overcome such resist-
ance issue.
GCA-186 (Fig. 1) differs structurally from emivirine
only in the introduction of two methyl substituents in 3-
and 5-position at the C-6 benzyl group. It performed bet-
ter in tolerating the presence of the Y181C and K103N
mutations than did emivirine itself. The increase of
potency of GCA-186 over emivirine against the wildtype
HIV and mutants has been correlated with an overall
tighter and/or more complete fit in the hydrophobic
pocket due to the presence of 3,5-dimethyl groups [9]. On
the other hand, the two methyl substituents on GCA-186
were thought to undergo metabolism, e.g. by the cyto-
chrome P 450 family in the liver.
(Trifluoromethylphenyl)acetonitriles 1a,
b
were
reacted with the zinc organometallic reagent from ethyl
2-bromobutyrate or methyl 2-bromoisovalerate in anhy-
drous THF [22] to give the corresponding b-keto esters 2a-
d which were condensed with thiourea in the presence of
sodium ethoxide to afford the 2-thiouracils 3a–d. The
NMR spectra of the crude compounds 2a, c showed an
impurity identified as another b-keto ester resulting
from self-condensation of ethyl 2-bromobutyrate. On
reaction with thiourea, the b-keto ester impurity also
formed a pyrimidine compound as an impurity in the
raw materials of 3a, c which were easily purified accord-
Recently, we synthesized a series of 6-(3,5-dichloroben-
zyl) derivatives as isosteric analogues of GCA-186 [17] on a
trial to avoid rapid metabolism in the liver. In an effort to
improve the activity against HIV-1 wild type and resistant
mutants, and as a part of our continuing interest in the
chemistry of NNRTIs [10, 17–21], the present study
describes the synthesis and antiviral evaluation of 6-(tri-
fluoromethylbenzyl) and 6-(fluorobenzyl) analogues of
emivirine and GCA-186. The objective was to investigate
whether the fluoro- or trifluoromethyl substituents
could lead to an improved antiviral activity against HIV-1
Scheme 1. Synthetic route for uracils 4a–i.
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
New Emivirine and GCA-186 Analogues
11
(a) R9CH(Br) CO2R2, Zn, THF; (b) K2CO3; (c) HCl, 90 – 94% (one-pot synthesis);
(d) (H2N)2CS, NaOEt, 19 – 60%; (e) aq ClCH2CO2H 61 – 72%.
Scheme 2. Synthetic route of compounds 1–4.
ing to usual work-up procedures [23]. De-sulfurization of
compounds 3a–d with boiling aqueous chloroacetic acid
gave the corresponding uracils 4a–d (Scheme 2).
The fluoro-substituted uracil analogues 4e–i were syn-
thesized in analogy to literature procedures [24, 25]. The
appropriate Grignard reagents synthesized in situ in a
standard way from the corresponding bromide as
described by Wakefield [24] for benzyl bromide, were
added to the methoxy-protected uracil derivatives 6a [26]
or 6b [25] in the presence of an appropriate catalyst. A sys-
tematic investigation (including use of different cata-
lysts, solvents, reaction time, and temperature) showed
that the best results were obtained when Fe(acac)3 was
used as a catalyst in the cross-coupling reaction and the
subsequent hydrolysis for the compounds with the fol-
lowing aromatic substitution pattern: 3-F (8a/4e, 61%),
2,5-F (8b/4f, 24%), and 2,3,5,6-F (8d/4h, 18%). The signifi-
cant drop in yields, corresponding to the number and
positions, was occupied by the fluoro group on the aro-
mat with the highest yield for the mono-substituted aro-
mat. Surprisingly, it was not possible to synthesize com-
pound 8c using Fe(acac)3 as a catalyst. However, we suc-
ceeded to synthesize compound 8c in 10% yield using
commercially available catalyst NiCl2(dppe). It is note-
worthy that the catalyst used by Adriane et al. [25] –
NiCl2(tpp) [27] was not successful in our hands.
(a) Ref. [25, 26]; (b) 4 equiv. Mg powder, dry Et2O; (c) 6a or 6b, cat., dry Et2O; (d) aq.
HCl (4M).
Scheme 3. Synthetic route of compounds 5–8.
It was not possible to isolate the pure compounds 8a–e
due to a complex mixture. Nevertheless, compounds 4e–
i were easily obtained as solid compounds after hydroly-
sis of the corresponding methoxy-protected compounds
8a–e in boiling aqueous HCl following evaporation and
adition of water with overall yields of 8–61% (Scheme 3).
The low yield for the synthesis of 4i (8%) compared to the
corresponding 5-ethyl derivative 4e obtained in 61% yield
is presumably due to steric hindrance of the larger iso-
propyl at the 5-position of the uracil ring. However, the
(a) BSA, H3CCH2OCH2Cl, CsI, CHCl3, 19 – 95%; (b) BSA, TMS-triflate, R2CH2O-
CH2OCH2R2, H3CCN, 38 – 89%.
Scheme 4. Synthetic route of compounds 9–12.
cross-coupling reaction was responsible for the overall
low yield as the Grignard reagents were obtained in
quantitative yield according to TLC analysis showing dis-
appearance of the benzyl bromide.
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

12
N. R. El-Brollosy et al.
Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
Table 1. Antiviral activity and cytotoxicity of compounds 9–12 against HIV-1 in MT-4 cells.a)
Compound
Wild type
CC50c) (lM)
N119 (Y181C)
A17 (K103N +
Y181C)
EFVR (K103R +
V179D + P225H)
EC50b) (lM)
SId)
EC50b) (lM)
EC50b) (lM)
EC50b) (lM)
9a
9b
9c
9d
9e
9f
9g
9h
9i
10a
10b
10c
10d
10e
10f
10h
11a
11b
11c
11e
0.4 l 0.1
0.1 l 0.08
1.9 l 0.7
0.9 l 0.5
0.05 l 0.01
0.05 l 0.001
0.08 l 0.02
0.09 l 0.005
0.02 l 0.005
0.2 l 0.1
0.05 l 0.03
1.7 l 0.7
1.3 l 0.1
0.03 l 0.005
0.04 l 0.02
0.07 l 0.01
0.2 l 0.1
0.05 l 0.03
3 l 1
0.05 l 0.01
0.05 l 0.005
0.09 l 0.005
0.1 l 0.01
0.2 l 0.05
0.4 l 0.05
0.03 l 0.005
0.004 l 0.005
0.009 l 0.001
0.0006 [8]
0.002 l 0.0005
A100
54 l 3
A100
A100
A100
A100
A100
A100
A100
77 l 5
39 l 0.5
A100
A100
A100
A100
A100
68 l 5
46 l 4
A100
A100
A100
5 l 1
A250
240
A52
A111
A2000
A2000
A1250
A1111
A5000
385
780
A59
A77
A3333
A2500
A1428
340
920
33
A2000
A2000
56
A1000
280
95
A3333
21250
6111
72000
15000
4.5 l 0.3
1.5 l 0.5
80
17 l 3
18 l 2
11 l 0.5
35
45 l 15
12 l 2
A100
A100
68
50
87
54
42
A100
A54
A100
A100
A100
A100
A100
A100
56
23
14 l 3
3.2 l 0.5
1.3 l 0.2
A100
13 l 1
10 l 1
14 l 6
40
5.5 l 0.5
2.6 l 0.8
100 l 3
A20
17 l 3
A5
24
19 l 9
12 l 4
A100
A100
42
14 l 6
44
A68
A77
A39
A100
A100
60
70
A100
A68
10 l 0.5
A100
56
A46
A100
A100
A100
A5
11f
11h
12e
53
A5
A100
56 l 2
38 l 1
A100
85
55
43 [8]
30 l 1
A100
A56
A100
A56
A38
A100
6.2 l 0.3
6.1 l 0.7
12f
25 l 5
A38
12h
MKC-442
BED-60
AMB-A10
GCA-186
Efavirenz
A38
A20
56
0.3 l 0.01
0.4 l 0.06
2.0 l 0.3
6.3 l 1.4
0.008 l 0.0009
0.3 l 0.05
3.0 l 1
a)
Data represent mean values of at least two separate experiments.
Compound dose required to achieve 50% protection of MT-4 cells from HIV-1 induced cytopathogenicity, as determined by the
MTT method.
Compound dose required to reduce the viability of mock-infected cells by 50%, as determined by the MTT method.
Selectivity index: ratio CC50/ED50. The symbol (>) indicates that CC50 was not reached at the highest concentration tested. For
description of assay see Experimental, section 4.
b)
c)
d)
The 1-ethoxymethyluracils 9a–i were prepared from Lewis acid catalyst to give the target molecules; 1-(ally-
4a–i via silylation in situ with N,O-bis(trimethylsilyl)ace- oxymethyl)uracils 10a–f, and 10h, 1-(propargyloxyme-
tamide (BSA) in anhydrous chloroform followed by treat- thyl)uracils 11a–c, 11e, f, and 11h and 1-(2-methylally-
ment with chloromethyl ethyl ether in the presence of oxymethyl)uracils 12e, f, and 12h, respectively
cesium iodide to give the MKC-442 analogues 9a-i in 19–
(Scheme 4). The yield for the alkylation reactions varied
95% yields (Scheme 4). For the synthesis of compounds in a range from 38 to 89%. Especially, the propynyloxy-
10–12, the method was modified. The appropriate ura- methyl alkylation proceeded badly, even though the reac-
cils 4a–f or 4h were silylated in situ with BSA in anhy- tion time was extended to three days. However, we suc-
drous acetonitrile and alkylated at the N-1 position with ceeded to increase the yield up to 81% by using four
bis(allyloxy)methane [10, 28] (for compounds 4a–f, and equivalents of TMS triflate, and the reaction was finished
4h) or bis(propargyloxy)methane [10] (for compounds after about 4 h.
4a–c, 4e, f, and 4h) or bis(2-methylallyoxy)methane [10]
The compounds were identified by comparison of simi-
(for compounds 4e, f and 4h) in the presence of trimethyl- lar NMR data [10, 18–23]. MS and elemental analysis are
silyl trifluoro-methanesulfonate (TMS triflate) [29] as a in full agreement with the proposed structures.
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
New Emivirine and GCA-186 Analogues
13
Biological screening
Conclusion
Compounds 9a–i and 10–12 were tested for biological
activity against wildtype HIV-1 strain IIIB in MT-4 cells.
Results were compared with the antiviral activity of emi-
virine, a well examined HEPT analogues and efavirenz,
the most active anti-HIV drug used in therapy today.
Compounds were also tested against NNRTI-resistant
mutants [Y181C, K103N + Y181C, and triple mutant
(K103R + V179D + P225H), highly resistant to efavirenz].
Results are listed in Table 1.
In summary, we have described the synthesis and anti-
HIV activity of novel 6-(3-trifluoromethylbenzyl) and 6-
(fluoromethylbenzyl) analogues of emivirine, GCA-186,
and BED-60. The most active compounds 9i and 10e
showed activity against wildtype HIV-1 in the nanomolar
range with a selective index of greater than 3333.
This work received funding from the European Community's
Sixth Framework Programme under contract number LSHP-
CT-2004-503162 (Selection and development of microbicides for
mucosal use to prevent sexual HIV transmission/acquisition)
[30].
As seen from the results listed in Tabel 1, most of the
tested compounds showed good activity against wildtype
HIV-1 with a wide range of EC50 values from 3–0.02 lM.
Generally, the majority of the novel compounds were not
cytotoxic for MT-4 cells at the maximum concentration
tested (100 lM). The only exception is compound 11h,
which was surprisingly cytotoxic (5 lM). In general, the
3-fluoro-substituted uracil series (9e, 10e, and 11e) were
10-times more potent than the corresponding CF3-series
(9a, 10a, and 11a). Compound 9i, the most active com-
pound tested against HIV-1, substituted at R by a fluorine
atom was in our study marginally more potent than
MKC-442 (20 nM versus 30 nM). Increasing the electrone-
gativity by the replacements of hydrogen atoms with up
to four fluorine atoms on the benzyl ring, is well toler-
ated (9f–h, 10h, and 11f, h). However, replacement of the
3,5-dimethyl groups in BED-60, with the strong with-
drawing group CF3 (9c, 10c, and 11c) resulted in the least
active among the synthesized compounds. In fact, the
activity was about 100-times lower when compared with
the corresponding 3,5-dichloro derivatives which have
previously been synthesized in our laboratory as isosteric
analogues of GCA-186 and BED-60. Furthermore, the
introduction of different unsaturated N-1 substituents
had no effect on the anti-HIV-1 activity, except, when
increasing the bulkiness around the double bond of 9e
with methyl moieties (12e–h), leads to a significant drop
in activity compared to 9e (2-, 4-, and 8-fold, respectively)
which is in in accordance with our previous observations
[10]. It is well known that introduction of an isopropyl
group instead of an ethyl group at C-5 leads to a rise in
biologic activity. Surprisingly, only the emivirine ana-
logues having an allyloxymethyl or a propynyloxymethyl
at the N-1 position, and substitution with one CF3 group
on the aromatic ring leads to an up to 4-fold increase in
activity (11a vs. 11b and 10a vs. 10b).
The authors have declared no conflict of interest.
Experimental
Chemistry
NMR spectra were recorded on a Varian Gemini 2000 NMR spec-
trometer (Varian Inc., Palo Alto, CA, USA ) at 300 MHz for 1H and
75 MHz for13C with TMS as internal standard. Due to complexity
of 13C-NMR spectra for polyfluorinated benzylic groups, only
strong peaks are reported for the benzylic group. MALDI spectra
were recorded on a Fourier Transform (FT) Ion Cyclotron Reso-
nance Mass Spectrometer (IonSpec Corporation, Lake Forest, CA,
USA). Melting points were determined on a Bꢁchi melting point
apparatus (Bꢁchi Labortechnik, Flawil, Switzerland). Elementary
analyses were performed at H.C. Ørsted Institute, University of
Copenhagen. Silica gel (0.040-0.063 mm) used for column chro-
matography and analytical silica gel TLC plates 60 F254 were pur-
chased from Merck (Darmstadt, Germany). Solvents used for col-
umn chromatography were distilled prior to use. The fluoro-ben-
zyl bromides were purchased from Fluorochem,8 Old Glossop,
Derbyshire, UK) Mg powder was purchased from Riedel-De Haꢂn
(Seelze, Germany). Reagents were used as purchased.
General procedure for synthesis of 2-alkyl-4-aryl-3-
oxobutyrates 2a–d
Zn dust 25–30 g was activated by stirring with 4 M HCl (100 mL)
for 5 min. The zinc dust was filtered and washed sequentially
with water, ethyl alcohol, and ether. Dried by evaporation under
reduced pressure at 808C for five hours, and kept in vacuo over-
night. The activated Zn was suspended in anhydrous THF
(35 mL) and heated to reflux. A few drops of ethyl 2-bromobuty-
rate or methyl 2-bromoisovalerate were added and the mixture
was refluxed for 10 min. The appropriate nitrile; (3-trifluorome-
thylphenyl)acetonitrile 1a or [3,5-bis(trifluoromethyl)phenyl]a-
cetonitrile 1b (0.015 mol) was added in one portion and ethyl 2-
bromobutyrate or methyl 2-bromoisovalerate (0.03 mol) was
added dropwise. After the addition was completed, the mixture
was refluxed for 30 min. The reaction mixture was diluted with
THF (100 mL) and saturated aqueous K2CO3 (30 mL) was added.
The mixture was stirred for 1 h and the THF layer was decanted
Unfortunately, only a marginally improvement in
activity compared to the clinically important mutants
(N119, A17 or EFVR) was observed for compounds 9a, b,
10a, b and 11a, b when compared with MKC-442.
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

14
N. R. El-Brollosy et al.
Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
off. The residue was washed with THF (3620 mL) and the com-
bined THF fractions were stirred with 10% aqueous HCl (20 mL)
for 30 min. The solution was concentrated under reduced pres-
sure and diluted with CH2Cl2 (75 mL). The organic phase was
washed with saturated aqueous NaHCO3 (2650 mL), dried
(Na2SO4), and evaporated under reduced pressure to give 2a–d
as pale yellow oils.
cipitate thus formed was filtered off, washed with H2O, then
with Et2O, and dried to give 3a–d as white solids.
5-Ethyl-6-(3-trifluoromethylbenzyl)-2-thiouracil 3a
Yield 1.88 g (60%); mp. 182–1848C. 1H-NMR (DMSO-d6): d (ppm) =
0.80 (t, 3H, J = 7.2 Hz, CH3), 2.28 (q, 2H, J = 7.2 Hz, CH2), 3.97 (s, 2H,
CH2), 7.53–7.67 (m, 4H, Harom), 12.29, 12.41 (26s, 2H, 26NH).13C-
NMR (DMSO-d6): d (ppm) = 12.77 (CH3), 17.69 (CH2), 34.13 (CH2),
117.41 (C-5), 123.47, 123.52, 124.95, 125.00, 129.71, 132.09,
138.21 (CF3, Carom), 148.27 (C-6), 161.35 (C-4), 174.24 (C-2). MS-EI:
m/z (%) = 314 [M+] (100).
Ethyl-2-ethyl-3-oxo-4-(3-trifluoromethylphenyl)butyrate
2a
Yield 4.1 g (91%). 1H-NMR (CDCl3): d (ppm) = 0.80 (t, 3H, J = 7.2 Hz,
CH3), 1.16 (t, 3H, J = 7.1 Hz, CH3), 1.78 (m, 2H, CH2), 3.37 (t, 1H, J =
7.3 Hz, CH), 3.81 (s, 2H, CH2), 4.07 (q, 2H, J = 7.2 Hz, CH2), 7.30–
7.47 (m, 4H, Harom). 13C-NMR (CDCl3): d (ppm) = 11.77 (CH3), 14.01
(CH3), 21.51 (CH2), 48.21 (CH2), 60.06 (CH), 61.45 (CH2), 123.98,
124.03, 126.32, 126.37, 128.99, 133.07, 134.25 (CF3, Carom), 169.43
(CO), 201.80 (CO). HRMS – MALDI: m/z = 325.1022 [M+Na+]
(C15H17F3O3Na+); requires 325.1030.
5-Isopropyl-6-(3-trifluoromethylbenzyl)-2-thiouracil 3b
1
Yield 1.9 g (58%); mp. 189-1918C. H-NMR (DMSO-d6): d (ppm) =
0.85 (d, 6H, J = 6.6 Hz, 26CH3), 2.85 (hept. 1H, J = 6.6 Hz, CH), 4.01
(s, 2H, CH2), 7.50–7.64 (m, 4H, Harom), 12.23, 12.36 (26s, 2H,
26NH). 13C-NMR (DMSO-d6): d (ppm) = 19.45 (26CH3), 26.57 (CH),
34.25 (CH2), 119.85 (C-5), 123.34, 123.48, 124.68, 124.73, 129.73,
132.09, 138.31 (CF3, Carom), 148.02 (C-6), 160.61 (C-4), 174.20 (C-2).
MS-EI: m/z (%) = 328 [M+] (100).
Methyl-2-isopropyl-3-oxo-4-(3-trifluoromethyl-
phenyl)butyrate 2b
Yield 4.3 g (94%). 1H-NMR (CDCl3): d (ppm) = 0.89, 0.96 (26d, 6H, J
= 6.9 Hz, 26CH3), 2.43–2.49 (m, 1H, CH), 3.31 (d, 1H, J = 7.3 Hz,
CH), 3.69 (s, 3H, OCH3), 3.87 (s, 2H, CH2), 7.36–7.54 (m, 4H, Harom).
13C-NMR (CDCl3): d (ppm) = 20.35 (CH3), 20.53 (CH3), 28.70 (CH),
48.61 (CH2), 52.24 (OCH3), 66.15 (CH), 124.02, 124.07, 126.37,
126.42, 128.99, 133.13, 134.09 (CF3, Carom), 169.27 (CO), 201.44
(CO). HRMS – MALDI: m/z = 325.1022 [M+Na+] (C15H17F3O3Na+);
requires 325.1025.
6-[3,5-Bis(trifluoromethyl)benzyl]-5-ethyl-2-thiouracil 3c
Yield 1.75 g (46%); mp. 223–2258C. 1H-NMR (DMSO-d6): d (ppm) =
0.80 (t, 3H, J = 7.4 Hz, CH3), 2.14 (q, 2H, J = 7.4 Hz, CH2), 4.08 (s, 2H,
CH2), 8.01 (s, 2H, Harom), 8.03 (s, 1H, Harom), 12.28, 12.47 (26s, 2H,
26NH). 13C-NMR (DMSO-d6): d (ppm) = 12.76 (CH3), 17.68 (CH2),
33.90 (CH2), 117.83 (C-5), 120.68, 124.99, 129.20, 130.12, 140.21
(CF3, Carom), 147.23 (C-6), 161.33 (C-4), 174.33 (C-2). MS-EI: m/z (%) =
382 [M+] (29).
Ethyl-4-[3,5-bis(trifluoromethyl)phenyl]-2-ethyl-3-
oxobutyrate 2c
6-[3,5-Bis(trifluoromethyl)benzyl]-5-isopropyl-2-thiouracil
3d
Yield 5.1 g (92%). 1H-NMR (CDCl3): d (ppm) = 0.92 (t, 3H, J = 7.4 Hz,
CH3), 1.25 (t, 3H, J = 7.1 Hz, CH3), 1.90 (m, 2H, CH2), 3.46 (t, 1H, J =
7.4 Hz, CH), 3.96 (s, 2H, CH2), 4.18 (q, 2H, J = 7.1 Hz, CH2), 7.64 (s,
2H, Harom), 7.79 (s, 1H, Harom). 13C-NMR (CDCl3): d (ppm) = 11.82
(CH3), 14.03 (CH3), 21.55 (CH2), 47.54 (CH2), 60.45 (CH), 61.65
(CH2), 121.20, 129.95, 131.52, 131.97, 135.79 (CF3, Carom), 169.35
(CO), 201.01 (CO).
Yield 0.75 g (19%); mp. 210–2128C. 1H-NMR (DMSO-d6): d (ppm) =
1.09 (d, 6H, J = 6.6 Hz, CH3), 2.94 (hept. 1H, J = 6.6 Hz, CH), 4.10 (s,
2H, CH2), 7.99 (s, 2H, Harom), 8.02 (s, 1H, Harom), 12.22, 12.37 (26s,
2H, 26NH). 13C-NMR (DMSO-d6): d (ppm) = 19.43 (CH3), 26.56 (CH),
34.01 (CH2), 120.57 (C-5), 120.66, 125.03, 129.09, 130.61, 140.32
(CF3, Carom), 147.05 (C-6), 160.58 (C-4), 174.29 (C-2). MS-EI: m/z (%) =
396 [M+] (58).
Methyl-4-[3,5-bis(trifluoromethyl)phenyl]-2-isopropyl-3-
oxobutyrate 2d
General procedure for synthesis of 5-alkyl-6-
(trifluoromethylbenzyl)uracils 4a–d
A suspension of 2-thiouracils (3a–d, 0.01 mol) in 10% aqueous
ClCH2CO2H (200 mL) was refluxed overnight. After cooling, the
precipitate was filtered off, washed with cold EtOH, then Et2O,
and dried to give 4a–d as white solids.
Yield 5.0 g (90%). 1H-NMR (CDCl3): d (ppm) = 0.94, 0.99 (26d, 6H, J
= 6.9 Hz, 26CH3), 1.97 (m, 1H, CH), 3.33 (d, 1H, J = 7.3 Hz, CH),
3.73 (s, 3H, OCH3), 3.97 (s, 2H, CH2), 7.63 (s, 2H, Harom), 7.79 (s, 1H,
Harom). 13C-NMR (CDCl3): d (ppm) = 20.38 (CH3), 20.56 (CH3), 28.87
(CH), 47.79 (CH2), 52.37 (OCH3), 66.52 (CH), 121.22, 129.97,
131.52, 131.96, 135.65 (CF3, Harom), 169.24 (CO), 200.73 (CO).
General procedure for synthesis of 5-alkyl-6-
(trifluoromethyl)benzyl-2-thiouracils 3a–d
5-Ethyl-6-(3-trifluoromethylbenzyl)uracil 4a
1
Yield 2.1 g (70%); mp. 218-2198C. H-NMR (DMSO-d6): d (ppm) =
Na (4.92 g, 0.217 mol) was dissolved in absolute ethanol
(100 mL). Thiourea (11.42 g, 0.15 mol) was added and the reac-
tion mixture was heated to reflux. The b-keto ester 2a–d
(0.01 mol) was added dropwise and the mixture was refluxed for
two hours. The mixture was evaporated to dryness under
reduced pressure and the residue was redissolved in H2O
(100 mL). The solution was acidified with HCl to pH 4. The pre-
0.91 (t, 3H, J = 6.5 Hz, CH3), 2.46 (q, 2H, J = 6.5 Hz, CH2), 3.87 (s, 2H,
CH2), 7.36–7.54 (m, 4H, Harom), 10.79, 11.12 (26s, 2H, 26NH). 13C-
NMR (DMSO-d6): d (ppm) = 13.39 (CH3), 17.55 (CH2), 34.54 (CH2),
111.63 (C-5), 123.41, 123.46, 124.89, 124.94, 129.64, 132.14,
138.35 (CF3, Carom), 147.73 (C-6), 150.86 (C-2), 164.38 (C-4). MS-EI:
m/z (%) = 298 [M+] (66). Anal. Calcd. for C14H13F3N2O260.25 H2O: C,
55.54; H, 4.49; N, 9.25. Found: C, 55.76; H, 4.24; N, 9.24.
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
New Emivirine and GCA-186 Analogues
15
26NH). 13C-NMR (DMSO-d6): d (ppm) = 13.43 (CH3), 17.53 (CH2),
34.55 (CH2), 111,49 (C-5), 113.37 (d, J = 20.3 Hz, Carom), 115.00 (d, J
= 21.8 Hz, Carom), 124.14 (d, J = 3.0 Hz, Carom), 130.46 (d, J = 9.0 Hz,
5-Isopropyl-6-(3-trifluoromethylbenzyl)uracil 4b
Yield 2.27 g (73%); mp. 206–2088C. 1H-NMR (DMSO-d6): d (ppm) =
1.07 (d, 6H, J = 6.7 Hz, 26CH3), 2.83 (hept, 1H, J = 6.7 Hz, CH),
3.89 (s, 2H, CH2), 7.58–7.64 (m, 4H, Harom), 10.85 (br s, 2H, 26NH).
13C-NMR (DMSO-d6): d (ppm) = 19.99 (CH3), 26.36 (CH), 34.78 (CH2),
114.20 (C-5), 123.37, 123.43, 124.62, 124.68, 129.69, 132.11,
138.49 (CF3, Carom), 147.47 (C-6), 150.87 (C-2), 163.74 (C-4). MS-EI:
m/z (%) = 312 [M+] (47). Anal. calcd for C15H15F3N2O260.25 H2O: C,
56.87; H, 4.93; N, 8.84. Found: C, 56.94; H, 4.67; N, 8.82.
Carom), 139.67 (d, J = 10.0 Hz, Carom), 147,91 (C-6), 150,85 (C-2),
162.13 (d, J = 242.20 Hz, Carom), 164,40 (C-4). HRMS – MALDI: m/z =
+
249.1034 [M + H+] (C13H13FN2O2 ); requires 249.1037.
5-Ethyl-6-(2,5-difluorobenzyl)uracil 4f
Yield 308 mg (24%); mp. 223–2258C. 1H-NMR (DMSO-d6): d (ppm)
= 0.80 (t, 3H, J = 7.2 Hz, CH3), 2.19 (q, 2H, J = 7.3 Hz, CH2), 3.79 (s,
2H, CH2), 7.09–7.31 (m, 3H, Harom), 10.71, 11.06 (26s, 2H,
26NH). 13C-NMR (DMSO-d6): d (ppm) = 13.29 (CH3), 17.44 (CH2),
28.25 (CH2), 112.17 (C-5), 114.91–116.91, 125.54–125.65 (Carom),
146.42 (C-6), 150.82 (C-2), 156.34 (d, J = 239.3 Hz, Carom), 158.11 (d,
J = 241.5 Hz, Carom), 164.31 (C-4). HRMS – MALDI: m/z = 267.0940
6-[3,5-Bis(trifluoromethyl)benzyl]-5-ethyluracil 4c
Yield 2.3 g (63%), mp. 250–2528C. 1H-NMR (DMSO-d6): d (ppm) =
0.81 (t, 3H, J = 7.2 Hz, CH3), 2.29 (q, 2H, J = 7.2 Hz, CH2), 3.99 (s, 2H,
CH2), 8.02–8.03 (m, 3H, Harom), 10.79, 11.08 (26s, 2H, 26NH).13C-
NMR (DMSO-d6): d (ppm) = 13.39 (CH3), 17.52 (CH2), 34.28 (CH2),
112.01 (C-5), 120.62, 125.01, 129.19, 130.54, 140.37 (CF3, Carom),
146.78 (C-6), 150.84 (C-2), 164.32 (C-4). MS- EI: m/z (%) = 366 [M+]
(49). Anal. calcd for C15H12F6N2O2: C, 49.19; H, 3.30; N, 7.65.
Found: C, 49.23; H, 3.16; N, 7.55.
[M+H+] (C13H12F2N2O2 ); requires 267.0940.
+
5-Ethyl-6-(2,3,6-trifluorobenzyl)uracil 4g
Yield 333 mg (10%); mp 215–2208C.1H-NMR (DMSO-d6): d (ppm) =
0.68 (t, 3H, J = 7.2 Hz, CH3), 2.17 (q, 2H, J = 7.3 Hz, CH2), 3.88 (s, 2H,
CH2), 7.12–7.52 (m, 2H, Harom), 10.75, 11.05 (26s, 2H, 26NH).13C-
NMR (DMSO-d6): d (ppm) = 12.66 (CH3), 17.33 (CH2), 23.95 (CH2),
111.48 (C-5), 111.16–116.47 (Carom), 146.68 (C-6), 150.69 (C-2),
6-[3,5-Bis(trifluoromethyl)benzyl]-5-isopropyluracil 4d
Yield 2.3 g (61%); mp. 231–2338C. 1H-NMR (DMSO-d6): d (ppm) =
1.10 (d, 6H, J = 6.8 Hz, 26CH3), 2.91 (hept, 1H, J = 6.8 Hz, CH),
4.01 (s, 2H, CH2), 8.01 (s, 2H, Harom), 8.04 (s, 1H, Harom), 10.77, 10.98
(26s, 2H, 26NH). 13C-NMR (DMSO-d6): d (ppm) = 19.92 (CH3),
26.33 (CH), 34.47 (CH2), 114.49 (C-5), 120.55, 125.03, 129.01,
130.59, 140.51 (CF3, Carom), 146.55 (C-6), 150.84 (C-2), 163.67 (C-4).
MS-EI: m/z (%) = 380 [M+] (58). Anal. calcd for C16H14F6N2O2: C,
50.53; H, 3.71; N, 7.37. Found: C, 50.92; H, 3.59; N, 7.35.
164.18 (C-4). HRMS
(C13H11F3N2O2 ); requires 285.0848.
–
MALDI: m/z
=
285.0845 [M+H+]
+
5-Ethyl-6-(2,3,5,6-tetrafluorobenzyl)uracil 4h
Yield 690 mg (18%); mp. 205–2108C. 1H-NMR (DMSO-d6): d (ppm)
= 0.76 (t, 3H, J = 7.3 Hz, CH3), 2.19 (q, 2H, J = 7.3 Hz, CH2), 3.95 (s,
2H, CH2), 7.86 (m, 1H, Harom), 10.73, 11.09 (26s, 2H, 26NH). 13C-
NMR (DMSO-d6): d (ppm) = 12.79 (CH3), 17.36 (CH2), 23.98 (CH2),
102.96–106.00 (Carom), 111.75 (C-5), 145.89 (C-6), 150.68 (C-2),
General procedure for synthesis of 5-alkyl-6-
(fluoromethylbenzyl)uracils 4e-i
MALDI: m/z =
303.0751 [M+H+]
In-vacuo dried magnesium powder (4 equiv.) and anhydrous Et2O
was stirred under a dry nitrogen atmosphere. A crystal of I2 was
added. Immediately after addition of the first few drops of the
appropriate fluorobenzyl bromide (1 equiv in Et2O), the color
turned from red/brown to white/green and the rest of the bro-
mide was added dropwise during 10 min. The reaction mixture
was stirred for one hour at room temperature and used in the
next step without further purification.
A mixture of the methoxy protected uracil chloride 6a or 6b (1
equiv.), Fe(acac)3 (0.1 equiv.) or NiCl2(dppe) (30 mol% based on 6b)
and Et2O was stirred under a dry nitrogen atmosphere. A solu-
tion of the appropriate fluorobenzylmagnesium bromide (1.33
equiv.) in anhydrous Et2O was added via a syringe. During the
addition, the reaction mixture started to reflux and a color shift
from red to brown was observed. The stirring was continued
overnight at room temperature. The reaction mixture was
quenched with saturated NH4Cl, and extracted with H2O. The
aqueous layer was extracted with Et2O, and the combined ether
phases were dried (MgSO4) and evaporated in vacuo to give a yel-
low/brown oil. The crude products were deprotected in refluxed
4 M HCl overnight. Upon cooling to room temperature, white
crystals precipitated. These were filtered off, washed with Et2O,
and dried in vacuo to give 4e–i.
164.10 (C-4). HRMS
(C13H10F4N2O2 ); requires 303.0758.
–
+
6-(3-Fluorobenzyl)-5-isopropyluracil 4i
Yield 198 mg (8%). 1H-NMR (DMSO-d6): d (ppm) = 1.06, 1.08 (d, 6H,
J = 6 Hz, 26CH3), 3.05 (sep, 1H, CH), 3.80 (s, 2H, CH2), 7.08–7.39
(m, 4H, Harom), 10.71, 10.90 (26s, 2H, 26NH). 13C-NMR (DMSO-d6):
d (ppm) = 19.32 (26CH3), 20.02 (CH), 31.49 (CH2), 113.41 (d, J =
20.2 Hz, Carom), 114.86 (d, J = 21.0 Hz, Carom), 124.00 (d, J = 3.0 Hz,
Carom), 130.47 (d, J = 8.2 Hz, Carom), 139.84 (d, J = 7.5 Hz, Carom),
162.13 (d, J = 204.9 Hz, Carom), 114.10 (C-5), 147.64 (C-6), 150.84 (C-
2), 162.19 (C-4).
General procedure for N-1 alkylation of 4a–i
Method A: To a suspension of compound 4a–i (1 equiv.), in anhy-
drous CHCl3 (20 mL), was added N,O-bis(trimethylsilyl)acetamide
(BSA) (3.5 equiv.) and the mixture was stirred under a nitrogen
atmosphere at room temperature. After a clear solution was
obtained (10 min), chloromethyl ethyl ether (1.5 equiv.) and CsI
(1 equiv.) were added. The reaction mixture was stirred at room
temperature under a nitrogen atmosphere for three hours (for
the synthesis of compounds 9a–d) or overnight (for the synthe-
sis of compounds 9e–i). The reaction mixture was quenched
with saturated aqueous NaHCO3 (20 mL). The mixture was
extracted with CH2Cl2 (3650 mL). The organic phases were col-
lected, dried (MgSO4), and evaporated under reduced pressure.
The products were purified by silica gel column chromatogra-
5-Ethyl-6-(3-fluorobenzyl)uracil 4e
Yield 798 mg (61%); mp. 224–2268C. 1H-NMR (DMSO-d6): d (ppm)
= 0.84 (t, 3H, J = 7.3 Hz, CH3), 2.25 (q, 2H, J = 7.3 Hz, CH2), 3.79 (s,
2H, CH2), 7.07–7.43 (m, 4H, Harom), 10.73, 11.04 (26s, 2H,
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

16
N. R. El-Brollosy et al.
Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
phy using 0-1% MeOH/CHCl3 (9a–d) or 42% EtOH/petroleum
ether (9e–i) as eluents.
7.2 Hz, CH3), 2.44 (q, 2H, J = 7.5 Hz, CH2), 3.59 (q, 2H, J = 7.2 Hz,
CH2), 4.14 (s, 2H, CH2), 5.10 (s, 2H, CH2), 6.81–7.33 (m, 4H, Harom),
9.59 (s, H, NH).13C-NMR (CDCl3): d (ppm) = 13.71 (CH3), 14.98 (CH3),
19.14 (CH2), 33.11 (CH2), 65.04 (CH2), 72.73 (CH2), 114.33 (d, J =
21.0 Hz, Carom), 114.41 (d, J = 22.5 Hz, Carom), 122.93 (d, J = 3.0 Hz,
Carom), 130.74 (d, J = 8.3 Hz, Carom), 137.80 (d, J = 7.5 Hz, Carom),
163.24 (d, J = 246.0 Hz, Carom), 117.16 (C-5), 148.32 (C-6), 151.86
(C-2), 164.24 (C-4). HRMS – MALDI: m/z = 329.1272 [M+Na+]
(C16H19FN2O3Na+); requires 329,1273. Anal. calcd for C16H19FN2O3:
C, 62,73; H, 6,25; N, 9,14. Found: C, 62,85; H, 6,31; N, 9,12.
1-(Ethoxymethyl)-5-ethyl-6-(3-
trifluoromethylbenzyl)uracil 9a
Yield 256 mg (72%) as white solid; mp. 131–1328C. 1H-NMR
(CDCl3): d (ppm) = 1.04 (t, 3H, J = 7.4 Hz, CH3), 1.13 (t, 3H, J =
7.0 Hz, CH3), 2.42 (q, 2H, J = 7.4 Hz, CH2), 3.57 (q, 2H, J = 7.0 Hz,
CH3), 4.22 (s, 2H, CH2), 5.11 (s, 2H, CH2), 7.23–7.56 (m, 4H, Harom).
13C-NMR (CDCl3): d (ppm) = 13.67 (CH3), 14.94 (CH3), 19.21 (CH2),
33.23 (CH2), 65.08 (CH2), 72.82 (CH2), 117.36 (C-5), 124.10, 124.18,
124.23, 124.29, 129.73, 130.44, 136.47 (CF3, Carom), 147.93 (C-6),
151.89 (C-2), 163.25 (C-4). MS-EI: m/z (%) = 356 [M+] (25). Anal. calcd
for C17H19F3N2O3: C, 57.30; H, 5.37; N, 7.86. Found: C, 57.16; H,
5.32; H, 7.76.
6-(2,5-Difluorobenzyl)-1-(ethoxymethyl)-5-ethyluracil 9f
Yield 206 mg (85%) as white solid; mp. 117–1208C. 1H-NMR
(CDCl3): d (ppm) = 1.05 (t, 3H, J = 7.2 Hz, CH3), 1.15 (t, 3H, J =
7.2 Hz, CH3), 2.44 (q, 2H, J = 7.2 Hz, CH2), 3.58 (q, 2H, J = 7.2 Hz,
CH2), 4.12 (s, 2H, CH2), 5.14 (s, 2H, CH2), 6.62–7.12 (m, 3H, Harom),
9.54 (s, H, NH). 13C-NMR (CDCl3): d (ppm) = 13.57 (CH3), 14.87
(CH3), 19.12 (CH2), 29.71 (d, J = 4.5 Hz, CH2), 64.96 (CH2), 72.87
(CH2), 114.45–116.94, 124.35–124,69, 156.36 (d, J = 220.8 Hz,
1-(Ethoxymethyl)-5-isopropyl-6-(3-
trifluoromethylbenzyl)uracil 9b
Yield 288 mg (78%) as white solid; mp. 138–1398C. 1H-NMR
(CDCl3): d (ppm) = 1.14 (t, 3H, J = 7.1 Hz, CH3), 1.28 (d, 6H, J =
6.9 Hz, 26CH3), 2.75 (hept, 1H, J = 6.9 Hz, CH), 3.59 (q, 2H, J =
7.1 Hz, CH2), 4.25 (s, 2H, CH2), 5.14 (s, 2H, CH2), 7.31–7.57 (m, 4H,
Harom), 9.41 (s, 1H, NH). 13C-NMR (CDCl3): d (ppm) = 14.93 (CH3),
20.27 (CH3), 28.47 (CH), 33.31 (CH2), 65.09 (CH2), 72.98 (CH2),
120.14 (C-5), 124.06, 124.11, 124.14, 124.19, 129.67, 130.54,
136.61 (CF3, Carom), 147.36 (C-6), 151.84 (C-2), 162.23 (C-4). HRMS –
MALDI: m/z = 393.1396 [M+Na+] (C18H21F3N2O3Na+); requires
393.1404. Anal. calcd for C18H21F3N2O3: C, 58.37; H, 5.72; N, 7.56.
Found: C, 58.33; H, 5.66; N, 7.53.
C
arom), 158.95 (d, J = 242.3 Hz, Carom), 117.63 (C-5), 147.31 (C-6),
151.71 (C-2), 162.99 (C-4). HRMS – MALDI: m/z = 347.1178 [M+Na+]
(C16H18F2N2O3Na+); requires 347.1171. Anal. calcd for
C16H18F2N2O3: C, 59.25; H, 5.59; N, 8.64. Found: C, 59.25; H, 5.50;
N, 8.60.
1-(Ethoxymethyl)-5-ethyl-6-(2,3,6-trifluorobenzyl)uracil
9g
Yield 5 mg (11%) as white solid. 1H-NMR (CDCl3): d (ppm) = 0.89 (t,
3H, J = 7.4 Hz, CH3), 1.17 (t, 3H, J = 7.1 Hz, CH3), 2.37 (q, 2H, J =
7.5 Hz, CH2), 3.60 (q, 2H, J = 7.1 Hz, CH2), 4.15 (s, 2H, CH2), 5.35 (s,
2H, CH2), 6.82–7.15 (m, 2H, Harom), 8.53 (s, H, NH). 13C-NMR
(CDCl3): d (ppm) = 12.78 (CH3), 14.94 (CH3), 19.21 (CH2), 23.27
(CH2), 64.88 (CH2), 73.20 (CH2), 110.87–111.34, 115.79–117.10
(Carom), 117.05 (C-5), 147.54 (C-6), 151.54 (C-2), 162.86 (C-4). HRMS
– MALDI: m/z = 365.1084 [M+Na+] (C16H17F3N2O3Na+); requires
365.1078.
6-[3,5-Bis(trifluoromethyl)benzyl]-1-(ethoxymethyl)-5-
ethyluracil 9c
Yield 300 mg (71%) as white solid; mp. 139–1408C. 1H-NMR
(CDCl3): d (ppm) = 1.04 (t, 3H, J = 7.4 Hz, CH3), 1.10 (t, 3H, J =
7.1 Hz, CH3), 2.41 (q, 2H, J = 7.4 Hz, CH2), 3.56 (q, 2H, J = 7.1 Hz,
CH2), 4.29 (s, 2H, CH2), 5.14 (s, 2H, CH2), 7.58 (s, 2H, Harom), 7.82 (s,
1H, Harom), 9.53 (s, 1H, NH). 13C-NMR (CDCl3): d (ppm) = 13.57
(CH3), 14.82 (CH3), 19.27 (CH2), 33.24 (CH2), 65.19 (CH2), 72.96
(CH2), 117.81 (C-5), 121.15, 127.42, 127.46, 132.82, 138.31 (CF3,
Carom), 146.75 (C-6), 151.67 (C-2), 162.92 (C-4). HRMS – MALDI: m/z
= 447.1114 [M+Na+] (C18H18F6N2O3Na+); requires 447.1124. Anal.
calcd for C18H18F6N2O3: C, 50.95; H, 4.28; N, 6.60. Found: C, 51.25;
H, 4.28; N, 6.54.
1-(Ethoxymethyl)-5-ethyl-6-(2,3,5,6-
tetrafluorobenzyl)uracil 9h
1
Yield 84 mg (36%). H-NMR (CDCl3): d (ppm) = 0.92 (t, 3H, J =
7.5 Hz, CH3), 1.15 (t, 3H, J = 7.2 Hz, CH3), 2.38 (q, 2H, J = 7.5 Hz,
CH2), 3.60 (q, 2H, J = 7.2 Hz, CH2), 4.20 (s, 2H, CH2), 5.35 (s, 2H,
CH2), 6.82–7.15 (m, 1H, Harom), 9.40 (s, H, NH). 13C-NMR (CDCl3): d
(ppm) = 12.81 (CH3), 14.89 (CH3), 19.19 (CH2), 23.47 (CH2), 64.95
(CH2), 73.19 (CH2), 104.96–106.01 (Carom), 117.37 (C-5), 146.68 (C-
6), 151.59 (C-2), 162.89 (C-4). HRMS – MALDI: m/z = 383.0989
[M+Na+] (C16H16F4N2O3Na+); requires 383.0989.
6-[3,5-Bis(trifluoromethyl)benzyl]-1-(ethoxymethyl)-5-
isopropyluracil 9d
Yield 306 mg (70%) as white solid; mp. 160–1618C. 1H-NMR
(CDCl3): d (ppm) = 1.09 (t, 3H, J = 7.1 Hz, CH3), 1.28 (d, 6H, J =
6.8 Hz, 26CH3), 2.67 (hept, 1H, J = 6.8 Hz, CH), 3.58 (q, 2H, J =
7.1 Hz, CH2), 4.31 (s, 2H, CH2), 5.18 (s, 2H, CH2), 7.60 (s, 2H, Harom),
7.82 (s, 1H, Harom), 9.40 (s, 1H, NH). 13C-NMR (CDCl3): d (ppm) =
14.81 (CH3), 20.16 (CH3), 28.66 (CH), 33.22 (CH2), 65.18 (CH2),
73.12 (CH2), 120.56 (C-5), 121.33, 124.81, 127.45, 132.75, 138.39
(CF3, Carom), 146.17 (C-6), 151.70 (C-2), 161.99 (C-4). HRMS –
MALDI: m/z = 461.1270 [M+Na+] (C19H20F6N2O3Na+); requires
461.1280.
1-(Ethoxymethyl)-6-(3-fluorobenzyl)-5-isopropyluracil 9i
1
Yield 23 mg (19%). H-NMR (CDCl3): d (ppm) = 1.18 (t, 3H, J =
7.2 Hz, CH3), 1.28 (d, 6H, J = 6.9 Hz, 26CH3), 2.83 (sep, 1H, CH),
3.61 (q, 2H, J = 7.2 Hz, CH2), 4.18 (s, 2H, CH2), 5.13 (s, 2H, CH2),
6.82–7.35 (m, 4H, Harom), 9.45 (s, H, NH). 13C-NMR (CDCl3): d (ppm)
= 14.97 (CH3), 19.53 (CH), 20.33 (26CH3), 33.19 (CH2), 65.02 (CH2),
72.88 (CH2), 114.33 (d, J = 21.0 Hz, Carom), 114.24 (d, J = 21.0 Hz,
Carom), 114.37 (d, J = 21.8 Hz, Carom), 122.86 (d, J = 3.0 Hz, Carom),
130.69 (d, J = 8.3 Hz, Carom), 137.99 (d, J = 7.5 Hz, Carom), 163.22 (d, J
= 246.0 Hz, Carom), 119.90 (C-5), 147.77 (C-6), 151.81 (C-2), 162.36
(C-4). HRMS – MALDI: m/z = 343.1428 [M+Na+] (C17H21FN2O3Na+);
1-(Ethoxymethyl)-5-ethyl-6-(3-fluorobenzyl)uracil 9e
Yield 117 mg (95%) as white solid; mp. 114–1168C. 1H-NMR
(CDCl3): d (ppm) = 1.05 (t, 3H, J = 7.5 Hz, CH3), 1.16 (t, 3H, J =
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
New Emivirine and GCA-186 Analogues
17
requires 343.1427. Anal. calcd for C17H21FN2O360.5 H2O: C,
61.99; H, 6.73; N, 8.59. Found: C, 61.58; H, 6.97; N, 8.86.
(C-4). HRMS – MALDI: m/z = 459.1114 [M+Na+] (C19H18F6N2O3Na+);
requires 459.1129. Anal. calcd for C19H18F6N2O3: C, 52.30; H, 4.16;
N, 6.42. Found: C, 52.53; H, 4.13; N, 6.33.
General procedure for N-1 alkylation of 4a-f, h
1-(Allyloxymethyl)-6-[3,5-bis(trifluoromethyl)benzyl]-5-
Method B: The pyrimidine 4a–f (1 equiv.) was stirred in anhy-
drous CH3CN (15 mL) under a nitrogen atmosphere and BSA (3.5
equiv.) was added. After a clear solution was obtained (10 min),
the mixture was cooled to -508C, and TMS triflate (one equiv. for
preparation of 10a–f, 10h, and 12e, f, h; four equiv. for prepara-
tion of 11a–c, 11e, f, and 11h) was added followed by dropwise
addition of the appropriate acetal (2 equiv.). The reaction mix-
ture was stirred at room temperature for 3–4 hours (for the syn-
thesis of compounds 10a–d and 11a–c) or overnight (for the syn-
thesis of compounds 10e, f, g, 11e, f, h, and 12e, f, h). The reac-
tion was quenched with cold, satutated, aqueous NaHCO3 solu-
tion (5 mL), and the solvent was evaporated under reduced pres-
sure at room temperature. The residue was extracted with
CH2Cl2 (3650 mL). The organic phases were collected, dried
(MgSO4), and evaporated under reduced pressure. The products
were purified by silica gel column chromatography using 0–1%
MeOH/CHCl3 (10a–d and 11a–c) or 42% EtOH/petroleum ether
(10e, f, g, 11e, f, h, and 12e, f, h) as eluents.
isopropyluracil 10d
Yield 298 mg (66%) as white solid; mp. 166–1678C. 1H-NMR
(CDCl3): d (ppm) = 1.28 (d, 6H, J = 6.9 Hz, 26CH3), 2.70 (hept, 1H, J
= 6.9 Hz, CH), 4.11 (d, 2H, J = 5.6 Hz, CH2), 4.31 (s, 2H, CH2), 5.16–
5.26 (m, 2H, CH2=), 5.18 (s, 2H, CH2), 5.74–5.84 (m, 1H, =CH), 7.59
(s, 2H, Harom), 7.82 (s, 1H, Harom), 9.29 (s, 1H, NH). 13C-NMR (CDCl3):
d (ppm) = 20.18 (CH3), 28.68 (CH), 33.35 (CH2), 70.56 (CH2), 72.82
(CH2), 118.16 (C-5), 120.66 (CH2=), 121.41, 124.79, 127.43, 132.81,
138.21 (CF3, Carom), 133.06 (=CH), 146.06 (C-6), 151.61 (C-2), 161.91
(C-4). HRMS – MALDI: m/z = 473.1270 [M+Na+] (C20H20F6N2O3Na+);
requires 473.1283.
1-(Allyloxymethyl)-5-ethyl-6-(3-fluorobenzyl)uracil 10e
Yield 227 mg (89%) as white solid; mp. 60–628C. 1H-NMR (CDCl3):
d (ppm) = 1.07 (t, 3H, J = 7.4 Hz, CH3), 2.45 (q, 2H, J = 7.2 Hz, CH2),
4.10 (dt, 2H, J = 5.7, 1.5 Hz, CH2), 4.16 (s, 2H, CH2), 5.13 (s, 2H,
CH2), 5.17–5.32 (m, 2H, =CH2), 5.79–5.90 (m, 1H, CH=), 6.82–
7.35 (m, 4H, Harom), 9.42 (s, H, NH). 13C-NMR (CDCl3): d (ppm) =
13.72 (CH3), 19.16 (CH2), 33.16 (CH2), 70.56 (CH2), 72.54 (CH2),
117.87 (=CH2), 133.45 (CH=), 114.40 (d, J = 21.0 Hz, Carom), 122.94
(d, J = 3.0 Hz, Carom), 130.75 (d, J = 8.3 Hz, Carom), 137.64 (d, J =
6.8 Hz, Carom), 163.26 (d, J = 246.0 Hz, Carom), 117.24 (C-5), 148.23
(C-6), 151.77 (C-2), 163.12 (C-4). HRMS – MALDI: m/z = 341,1277
[M+Na+] (C17H19FN2O3Na+); requires 341,1310. Anal. calcd for
C17H19FN2O3: C, 64.14; H, 6.02; N, 8.80. Found: C, 64.22; H, 6.05; N,
8.75.
1-(Allyloxymethyl)-5-ethyl-6-(3-
trifluoromethylbenzyl)uracil 10a
1
Yield 253 mg (69%) as white foams. H-NMR (CDCl3): d (ppm) =
1.04 (t, 3H, J = 7.5 Hz, CH3), 2.43 (q, 2H, J = 7.5 Hz, CH2), 4.11 (dd,
2H, J = 1.3, 5.7 Hz, CH2), 4.23 (s, 2H, CH2), 5.13 (s, 2H, CH2), 5.17–
5.31 (m, 2H, CH2=), 5.77–5.90 (m, 1H, =CH), 7.26–7.57 (m, 4H,
Harom), 9.47 (s, 1H, NH). 13C-NMR (CDCl3): d (ppm) = 13.68 (CH3),
19.21 (CH2), 33.28 (CH2), 70.59 (CH2), 72.57 (CH2), 117.45 (C-5),
117.99 (CH2=), 124.20, 124.25, 124.31, 124.36, 129.79, 130.45,
136.33 (CF3, Carom), 133.35 (=CH), 147.84 (C-6), 151.76 (C-2), 163.08
(C-4). HRMS – MALDI: m/z = 391.1240 [M+Na+] (C18H19F3N2O3Na+);
requires 391.1235.
1-(Allyloxymethyl)-6-(2,5-difluorobenzyl)-5-ethyluracil 10f
Yield 165 mg (84%) as white solid; mp. 93–968C. 1H-NMR (CDCl3):
d (ppm) = 1.05 (t, 3H, J = 7.5 Hz, CH3), 2.41 (q, 2H, J = 7.5 Hz, CH2),
4.09 (dt, 2H, J = 5.4, 1.2 Hz, CH2), 4.13 (s, 2H, CH2), 5.15 (s, 2H,
CH2), 5.17–5.30 (m, 2H, =CH2), 5.78–5.90 (m, 1H, CH=), 6.62–
7.12 (m, 3H, Harom), 9.42 (s, H, NH). 13C-NMR (CDCl3): d (ppm) =
13.59 (CH3), 19.15 (CH2), 26.77 (d, J = 3.8 Hz, CH2), 70.48 (CH2),
72.66 (CH2), 117.89 (=CH2), 133.29 (CH=), 114.52–117.00,
124.31–124.55, 156.37 (d, J = 243.8 Hz, Carom), 159.00 (d, J =
243.0 Hz, Carom), 117.71 (C-5), 147.23 (C-6), 151.61 (C-2), 162.85 (C-
4). HRMS – MALDI: m/z = 359,1178 [M+Na+] (C17H18F2N2O3Na+);
requires 359,1180. Anal. calcd for C17H18F2N2O3: C, 60.71; H, 5.39;
N, 8.33. Found: C, 60.73; H, 5.27; N, 8.25.
1-(Allyloxymethyl)-5-isopropyl-6-(3-
trifluoromethylbenzyl)uracil 10b
Yield 290 mg (76%) as white solid; mp. 112–1138C. 1H-NMR
(CDCl3): d (ppm) = 1.28 (d, 6H, J = 6.9 Hz, CH3), 2.77 (hept, 1H, J =
6.9 Hz, CH), 4.11 (dd, 2H, J = 1.2, 4.4 Hz, CH2), 4.25 (s, 2H, CH2),
5.16 (s, 2H, CH2), 5.17–5.31 (m, 2H, CH2=), 5.79–5.86 (m, 1H,
=CH), 7.30–7.57 (m, 4H, Harom), 9.41 (s, 1H, NH). 13C-NMR (CDCl3):
d (ppm) = 20.29 (CH3), 28.49 (CH), 33.36 (CH2), 70.57 (CH2), 72.74
(CH2), 117.96 (C-5), 120.26 (CH2=), 124.08, 124.13, 124.21, 124.26,
129.73, 130.53, 136.48 (CF3, Carom), 133.36 (=CH), 147.25 (C-6),
151.83 (C-2), 162.20 (C-4). MS-EI: m/z (%) = 382 [M+] (5). Anal. calcd
for C19H21F3N2O3: C, 59.68; H, 5.54; N, 7.33. Found: C, 59.68; H,
5.48; N, 7.34.
1-(Allyloxymethyl)-5-ethyl-6-(2,3,5,6-
tetrafluorobenzyl)uracil 10h
Yield 115 mg (48%). 1H-NMR (CDCl3): d (ppm) = 1.04 (t, 3H, J =
7.5 Hz, CH3), 2.49 (q, 2H, J = 7.5 Hz, CH2), 4.15 (dt, 2H, J = 5.4,
1.2 Hz, CH2), 4.20 (s, 2H, CH2), 5.41 (s, 2H, CH2), 5.14–5.34 (m, 2H,
=CH2), 5.76–5.95 (m, 1H, CH=), 7.00–7.15 (m, 1H, Harom), 9.00 (s,
H, NH). 13C-NMR (CDCl3): d (ppm) = 13.22 (CH3), 18.77 (CH2), 24.03
(CH2), 69.92 (CH2), 71.31 (CH2), 117.85 (=CH2), 133.25 (CH=),
105.02-106.09, 117.21–117.45 (Carom), 114.14 (C-5), 146.56 (C-6),
151.45 (C-2), 162.75 (C-4). HRMS – MALDI: m/z = 395,0989 [M+Na+]
(C17H16F4N2O3Na+); requires 395,0971.
1-(Allyloxymethyl)-6-[3,5-bis(trifluoromethyl)benzyl]-5-
ethyluracil 10c
Yield 296 mg (68%) as white solid; mp. 131–1328C. 1H-NMR
(CDCl3): d (ppm) = 1.05 (t, 3H, J = 7.4 Hz, CH3), 2.46 (q, 2H, J =
7.4 Hz, CH2), 4.08 (d, 2H, J = 5.9 Hz, CH2), 4.30 (s, 2H, CH2), 5.16 (s,
2H, CH2), 5.20–5.28 (m, 2H, CH2=), 5.74–5.87 (m, 1H, =CH), 7.58
(s, 2H, Harom), 7.82 (s, 1H, Harom), 9.66 (s, 1H, NH). 13C-NMR (CDCl3):
d (ppm) = 13.59 (CH3), 19.28 (CH2), 33.27 (CH2), 70.59 (CH2), 72.66
(CH2), 117.93 (C-5), 118.17 (CH2=), 121.56, 124.74, 127.41, 132.86,
138.15 (CF3, Carom), 133.06 (=CH), 146.63 (C-6), 151.68 (C-2), 162.94
5-Ethyl-1-(prop-2-ynyloxymethyl)-6-(3-
trifluoromethylbenzyl)uracil 11a
Yield 297 mg (81%) as white solid; mp. 129–1308C. 1H-NMR
(CDCl3): d (ppm) = 1.05 (t, 3H, J = 7.5 Hz, CH3), 2.44 (t, 1H, J =
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

18
N. R. El-Brollosy et al.
Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
2.4 Hz, CH:), 2.45 (q, 2H, J = 7.5 Hz, CH2), 4.22 (s, 2H, CH2), 4.28
(d, 2H, J = 2.4 Hz, CH2), 5.18 (s, 2H, CH2), 7.27–7.58 (m, 4H, Harom),
9.64 (s, 1H, NH). 13C-NMR (CDCl3): d (ppm) = 13.72 (CH3), 19.19
(CH2), 33.21 (CH2), 57.16 (CH2), 72.51(CH:), 74.92 (CH2), 78.85
(:C), 117.59 (C-5), 124.25, 124.29, 124.35, 124.41, 129.82,
130.40, 136.16 (CF3, Carom), 147.66 (C-6), 151.84 (C-2), 163.09 (C-4).
MS-EI: m/z (%) = 366 [M+] (56). Anal. calcd for C18H17F3N2O3: C,
59.02; H, 4.68; N, 7.65. Found: C, 59.10; H, 4.66; N, 7.64.
5-Ethyl-1-(prop-2-ynyloxymethyl)-6-(2,3,5,6-
tetrafluorobenzyl)uracil 11h
1
Yield 93 mg (38%). H-NMR (CDCl3): d (ppm) = 0.94 (t, 3H, J =
7.2 Hz, CH3), 2.41 (s, 1H, :CH), 2.39 (q, 2H, J = 7.2 Hz, CH2), 4.18
(s, 2H, CH2), 4.27 (s, 2H, CH2C:), 5.43 (s, 2H, CH2), 6.99-7.15 (m,
1H, Harom), 9.11 (s, H, NH). 13C-NMR (CDCl3): d (ppm) = 12.89 (CH3),
19.18 (CH2), 23.49 (CH2), 57.17 (CH2), 72.98 (:CH), 74.83 (CH2),
78.66 (C:), 105.13–115.75 (Carom), 117.63 (C-5), 146.39 (C-6),
151.55 (C-2), 162.66 (C-4). HRMS – MALDI: m/z = 393.0833 [M+Na+]
(C17H14F4N2O3Na+); requires 393.0837.
5-Isopropyl-1-(prop-2-ynyloxymethyl)-6-(3-
trifluoromethylbenzyl)uracil 11b
Yield 308 mg (81%) as white solid; mp. 141–1428C. 1H-NMR
(CDCl3): d (ppm) = 1.30 (d, 6H, J = 6.9 Hz, 26CH3), 2.45 (t, 1H, J =
2.4 Hz, CH:), 2.81 (hept, 1H, J = 6.9 Hz, CH), 4.25 (s, 2H, CH2),
4.29 (d, 2H, J = 2.4 Hz, CH2), 5.20 (s, 2H, CH2), 7.27–7.58 (m, 4H,
Harom), 9.57 (s, 1H, NH). 13C-NMR (CDCl3): d (ppm) = 20.31 (CH3),
28.48 (CH), 33.29 (CH2), 57.15 (CH2), 72.63 (CH:), 74.90 (CH2),
78.88 (:C), 120.44 (C-5), 124.19, 124.23, 124.26, 124.31, 129.76,
130.48, 136.31 (CF3, Carom), 147.06 (C-6), 151.90 (C-2), 162.23 (C-4).
MS-EI: m/z (%) = 380 [M+] (34). Anal. calcd for C19H19F3N2O3: C,
60.00; H, 5.03; N, 7.36. Found: C, 59.95; H, 4.97; N, 7.25.
5-Ethyl-6-(3-fluorobenzyl)-1-(2-
methylallyloxymethyl)uracil 12e
Yield 219 mg (82%) as white solid; mp. 105–1078C. 1H-NMR
(CDCl3): d (ppm) = 1.07 (t, 3H, J = 7.5 Hz, CH3), 1.71 (s, 3H, CH3),
2.45 (q, 2H, J = 7.5 Hz, CH2), 4.02 (s, 2H, CH2), 4.18 (s, 2H, CH2),
4.89, 4.95 (26s, 2H, =CH2), 5.14 (s, 2H, CH2), 6.82–7.35 (m, 4H,
H
arom), 9.53 (s, H, NH). 13C-NMR (CDCl3): d (ppm) = 13.73 (CH3),
19.14 (CH2), 19.44 (CH3), 33.10 (CH2), 72.71 (CH2), 73.59 (CH2),
112.65 (=CH2), 141.12 (C=), 114.27-114.55 (m, 26Carom), 122.95 (d,
J = 3.0 Hz, Carom), 130.80 (d, J = 8.3 Hz, Carom), 137.69 (d, J = 7.5 Hz,
Carom), 163.27 (d, J = 246.0 Hz, Carom), 117.22 (C-5), 148.25 (C-6),
151.79 (C-2), 163.20 (C-4). HRMS – MALDI: m/z = 355.1434 [M+Na+]
(C18H21FN2O3Na+); requires 355.1400. Anal. calcd for C18H21FN2O3:
C, 65.05; H, 6.37; N, 8.43. Found: C, 65.22; H, 6.37; N, 8.32.
6-[3,5-Bis(trifluoromethyl)benzyl]-5-ethyl-1-(prop-2-
ynyloxymethyl)uracil 11c
Yield 342 mg (79%); mp. 155–1568C. 1H-NMR (CDCl3): d (ppm) =
1.05 (t, 3H, J = 7.4 Hz, CH3), 2.42 (q, 2H, J = 7.4 Hz, CH2), 2.43 (t, 1H,
J = 2.3 Hz, CH:), 4.27 (d, 2H, J = 2.3 Hz, CH2), 4.29 (s, 2H, CH2),
7.60 (s, 2H, Harom), 7.83 (s, 1H, Harom), 9.57 (s, 1H, NH). 13C-NMR
(CDCl3): d (ppm) = 13.63 (CH3), 19.29 (CH2), 33.19 (CH2), 57.17
(CH2), 72.59 (CH:), 75.08 (CH2), 78.67 (:C), 118.04 (C-5), 121.61,
124.74, 127.48, 132.91, 137.93 (CF3, Carom), 146.48 (C-6), 151.62
(C-2), 162.86 (C-4). HRMS – MALDI: m/z = 457.0957 [M+Na+]
(C19H16F6N2O3Na+); requires 457.0954. Anal. calcd for
C19H16F6N2O3: C, 52.54; H, 3.71; N, 6.45. Found: C, 52.60; H, 3.68;
N, 6.38.
6-(2,5-Difluorobenzyl)-5-ethyl-1-(2-
methylallyloxymethyl)uracil 12f
Yield 190 mg (72%) as white solid; mp. 96–998C. 1H-NMR (CDCl3):
d (ppm) = 1.05 (t, 3H, J = 7.5 Hz, CH3), 1.70 (s, 3H, CH3), 2.41 (q, 2H,
J = 7,5 Hz, CH2), 4.00 (s, 2H, CH2C=), 4.14 (s, 2H, CH2), 4.87, 4.94
(26s, 2H, =CH2), 5.15 (s, 2H, CH2), 6.62–7,12 (m, 3H, Harom), 9.44 (s,
H, NH). 13C-NMR (CDCl3): d (ppm) = 13.60 (CH3), 19.12 (CH3), 19.38
(CH2), 26.70 (d, J = 3.0 Hz, CH2), 72.83 (CH2), 73.54 (CH2), 112.67
(=CH2), 140.99 (C=), 114.48–117.01, 124.19–124.52, 156.37 (d, J =
243.8 Hz, Carom), 158.98 (d, J = 243.00 Hz, Carom), 117.69 (C-5),
147.25 (C-6), 151.63 (C-2), 162.95 (C-4). HRMS – MALDI: m/z =
373.1334 [M+Na+] (C18H20F2N2O3Na+); requires 373.1331. Anal.
calcd for C18H20F2N2O3: C, 61.71; H, 5.75; N, 8.00. Found: C, 61.77;
H, 5.62; N, 7.92.
5-Ethyl-6-(3-fluorobenzyl)-1-(prop-2-ynyloxymethyl)uracil
11e
Yield 168 mg (66%) as white solid; mp. 109–1118C. 1H-NMR
(CDCl3): d (ppm) = 1.08 (t, 3H, J = 7.5 Hz, CH3), 2.46 (s, 1H, :CH),
2.47 (q, 2H, J = 7.5 Hz, CH2), 4.16 (s, 2H, CH2), 4.29 (s, 2H, CH2C:),
5.19 (s, 2H, CH2), 6.84–7.36 (m, 4H, Harom), 9.50 (s, H, NH).13C-NMR
(CDCl3): d (ppm) = 13.76 (CH3), 19.15 (CH2), 33.11 (CH2), 57.21
(CH2), 72.52 (:CH), 74.82 (CH2), 78.95 (C:), 114.47 (d, J = 21.0 Hz,
5-Ethyl-1-(2-methylallyloxymethyl)-6-(2,3,5,6-
tetrafluorobenzyl)uracil 12h
Yield 144 mg (56%).1H-NMR (CDCl3): d (ppm) = 1.04 (t, 3H, J =
7.5 Hz, CH3), 2.49 (q, 2H, J = 7.5 Hz, CH2), 4.15 (m, 2H, CH2), 4.20 (s,
2H, CH2), 5.41 (s, 2H, CH2), 5.14–5.34 (m, 2H, =CH2), 5.76–5.95
(m, 1H, CH=), 7.00–7.15 (m, 1H, Harom), 9.00 (s, H, NH). 13C-NMR
(CDCl3): d (ppm) = 13.22 (CH3), 18.77 (CH2), 24.03 (CH2), 69.92
(CH2), 71.31 (CH2), 117.85 (=CH2), 133.25 (CH=), 105.02–106.09,
117.21–117.45 (Carom), 114.14 (C-5), 146.56 (C-6), 151.45 (C-2),
162.75 (C-4).
Carom), 122.94 (d, J = 3.0 Hz, Carom), 130.83 (d, J = 8.3 Hz, Carom),
137.53 (d, J = 7.5 Hz, Carom), 163.26 (d, J = 246.0 Hz, Carom), 117.38
(C-5), 148.08 (C-6), 151.85 (C-2), 163.09 (C-4).
6-(2,5-Difluorobenzyl)-5-ethyl-1-(prop-2-
ynyloxymethyl)uracil 11f
Yield 183 mg (73%) as white solid; mp. 108–1108C. 1H-NMR
(CDCl3): d (ppm) = 1.06 (t, 3H, J = 7.5 Hz, CH3), 2.45 (s, 1H, :CH),
2.42 (q, 2H, J = 7.5 Hz, CH2), 4.13 (s, 2H, CH2), 4.27 (s, 2H, CH2C:),
5.22 (s, 2H, CH2), 6.64–7.13 (m, 3H, Harom), 9.51 (s, H, NH). 13C-
NMR (CDCl3): d (ppm) 13.62 (CH3), 19.12 (CH2), 26.80 (d, J = 3.0 Hz,
CH2), 57.15 (CH2), 72.61 (:CH), 74.90 (CH2), 78.69 (C:), 114.47–
117.03, 124.06, 124.16, 124.30, 124.41, 156.38 (d, J = 243.8 Hz,
Carom), 158.99 (d, J = 240.00 Hz, Carom), 117.89 (C-5), 147.04 (C-6),
151.76 (C-2), 162.89 (C-4). HRMS – MALDI: m/z = 357.1021 [M+Na+]
(C17H16F2N2O3Na+); requires 357.1016.
HRMS – MALDI: m/z = 395.0989 [M+Na+] (C18H18F4N2O3Na+);
requires 395.0971.
Antiviral assay procedures
Compounds were solubilized in DMSO at 100 mM and then
diluted in culture medium. Cells and viruses: MT-4, C8166, and
H9/IIIB cells were grown at 378C in a 5% CO2 atmosphere in RPMI
1640 medium supplemented with 10% fetal calf serum (FCS),
100 IU/mL penicillin G, and 100 lg/mL streptomycin. Cell cul-
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com

Arch. Pharm. Chem. Life Sci. 2008, 341, 9–19
New Emivirine and GCA-186 Analogues
19
tures were checked periodically for the absence of mycoplasma
contamination with a MycoTect Kit (Gibco). Human immunode-
ficiency viruses type 1 (HIV-1, IIIB strain) was obtained from
supernatants of persistently infected H9/IIIB cells. The HIV-1
stock solutions had titers of 4.56106, 50% cell culture infectious
dose (CCID50)/mL. The K103R + V179D + P225H mutant (EFVR) was
derived from an IIIB strain passaged in MT-4 cells in the presence
of efavirenz (up to 2 lM). The Y181C mutant (NIH N119) was
derived from an AZT-sensitive clinical isolate passaged initially
in CEM and then in MT-4 cells in the presence of nevirapine
(10 lM). The double mutant K103N + Y181C (NIH A17) was
derived from the IIIB strain passaged in H9 cells in the presence
of BI-RG 587 (1 lM). EFVR, N119, and N117 stock solutions had
titers of 4.06105, 1.26108, and 2.16107 CCID50/mL, respectively.
HIV titration: Titration of HIV was performed in C8166 cells by
the standard limiting dilution method (dilution 1 : 2, four rep-
lica wells per dilution) in 96-well plates. The infectious virus titer
was determined by light microscope scoring of syncytia after
4 days of incubation. Virus titers were expressed as CCID50/mL.
[8] H. Tanaka, H. Takashima, M. Ubasawa, K. Sekiya, et al., J.
Med. Chem. 1995, 38, 2860–2865.
[9] A. L. Hopkins, J. Ren, H. Tanaka, M. Baba, et al., J. Med.
Chem. 1999, 42, 4500–4505.
[10] N. R. El–Brollosy, P. T. Jørgensen, B. Dahan, A. M. Boel, et
al., J. Med. Chem. 2002, 45, 5721–5726.
[11] D. V. Havlir, S. Eastmen, A. Garnst, A. D. D. Richman, J.
Virol. 1996, 70, 7894–7899.
[12] J. P. Kleim, I. Winkler, M. Rosner, R. Kirsch, et al., Virology
1997, 231, 112–18.
[13] L. T. Bacheler, Drug Resist. Updat 1999, 2, 56–67.
[14] V. J. Merluzzi, K. D. Hargrave, M. Labadia, K. Grozinger, et
al., Science 1990, 250, 1411–1413.
[15] D. L. Romero, R. A. Morge, M. J. Genin, C. Biles, et al., J.
Med. Chem. 1993, 36, 1505–1508.
[16] S. D. Young, S. F. Britcher, L. O. Tran, L. S. Payne, et al.,
Antimicrob. Agents Chemother. 1995, 39, 2602–2605.
Anti-HIV assays
[17] E. R. Sørensen, N. R. El-Brollosy, P. T. Jørgensen, E. B. Pe-
dersen, C. Nielse, Arch. Pharm. Chem. Life Sci. 2005, 338,
299–304.
The activity of test compounds against multiplication of wild
type HIV-1, EFVR, N119, and N117 in acutely infected cells was
based on inhibition of virus-induced cytopathicity in MT-4 cells.
Briefly, an amount of 50 lL of culture medium containing
26104 cells was added to each well of flat-bottom microtiter
trays containing 50 lL of culture medium with or without vari-
ous concentrations of test compounds. Then, an amount of
20 lL of HIV suspensions (containing the appropriate amount of
CCID50 to cause complete cytopathicity at day 4) was added. After
incubation at 378C, cell viability was determined by the 3-(4,5-
dimethylthiazol-1-yl)-2,5-diphenyltetrazolium bromide (MTT)
method [31]. The cytotoxicity of test compounds was evaluated
in parallel with their antiviral activity and was based on the via-
bility of mock-infected cells, as monitored by the MTT method.
[18] N. R. El–Brollosy, E. B. Pedersen, C. Nielsen, Arch. Pharm.
Pharm. Med. Chem. 2003, 336, 236–241.
[19] F. A. El-Essawy, N. R. El-Brollosy, E. B. Pedersen, C. Niel-
sen, J. Heterocycl Chem. 2003, 40, 213–217.
[20] M. Wamberg, E. B. Pedersen, N. R. El-Brollosy, C. Nielsen,
Bioorg. Med. Chem. 2004, 12, 1141–1149.
[21] N. R. El-Brollosy, C. Nielsen, E. B. Pedersen, Monatsh.
Chem. 2005, 136, 1247–1254.
[22] K. Danel, E. Larsen, E. B. Pedersen, Synthesis 1995, 8, 934–
936.
[23] K. Danel, C. Nielsen, E. B. Pedersen, Acta Chem. Scand.
1997, 51, 426–430.
[24] B. J. Wakefield Methods in Organic Synthesis, Academic
Press, London, 1995, pp. 32, 36.
References
[25] G. Adrian, F. Lecoutteux, S. Mignonac, US 6,452,006,
[1] H. Mitsuya, R. Yarchoan, S. Broder, Science 1990, 249,
2002.
1533–1544.
[26] A. V. Merkatz, Ber. Dtsch. Chem. Ges. 1919, 52, 869–880.
[27] L. M. Venaz, J. Chem. Soc. 1958, 719–724.
[2] E. De Clercq, Trends Pharmacol. Sci. 1990, 11, 198–202.
[3] O. S. Pedersen, E. B. Pedersen, Antiviral Chem. Chemother.
1999, 10, 285–314; O. S. Pedersen, E. B. Pedersen, Synthe-
sis 2000, 4, 479–495.
[28] A. Kh. Nazaretyan, G. O. Torosyan, A. T. Babayan, J. Appl.
Chem. USSR 1985, 58, 2396–2400.
[4] A. L. Hopkins, J. Ren, R. M. Esnouf, B. E. Willcox, et al., J.
Med. Chem. 1996, 39, 1589–1600.
[29] H. Vorbrꢁggen, K. Krolikiewiecz, B. Bennua, Chem. Ber.
1981, 114, 1234–1255.
[5] R. Esnouf, J. Ren, C. Ross, Y. Jones, et al., Nat. Struct. Biol.
1995, 2, 303–308.
[30] The information in this document is provided as is and
no guarantee or warranty is given that the information
is fit for any particular purpose. The user thereof uses
the information at his/her sole risk and liability.
[6] M. Baba, H. Tanaka, E. De Clercq, R. Pauwels, et al., Bio-
chem. Biophys. Res. Commun. 1989, 165, 1375–1381.
[7] T. Miyasaka, H. Tanaka, M. Baba, H. Hayakawa, et al., J.
Med. Chem. 1989, 32, 2507–2509.
[31] R. Pauwels, J. Balzarini, M. Baba, R. Snoeck, et al., J. Virol.
Methods 1988, 20, 309–321.
i 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
www.archpharm.com