Synthesis and antiviral activity of 1-{[2-(phenoxy)ethoxy]methyl}uracil derivatives

Article abstract of DOI:10.1007/s10593-005-0193-5

The synthesis of novel 1-{[2-(phenoxy)ethoxy]methyl}uracil derivatives with different substituents in positions and 6 of the pyrimidine ring has been carried out. It has been shown that the alkylation of trimethylsilyl derivatives of uracil with 2-(4-chlo

Full text of DOI:10.1007/s10593-005-0193-5

Chemistry of Heterocyclic Compounds, Vol. 41, No. 5, 2005
SYNTHESIS AND ANTIVIRAL
ACTIVITY OF 1-{[2-(PHENOXY)ETHOXY]-
METHYL}URACIL DERIVATIVES
M. S. Novikov1, A. A. Ozerov1, Yu. A. Orlova1, and R. W. Buckheit2
The synthesis of novel 1-{[2-(phenoxy)ethoxy]methyl}uracil derivatives with different substituents in
positions and 6 of the pyrimidine ring has been carried out. It has been shown that the alkylation of
trimethylsilyl derivatives of uracil with 2-(4-chlorophenoxy)- and 2-(4-methylphenoxy)ethoxymethyl
chloride under Hilbert–Johnson reaction conditions gives N(1)-substitution products. It was found that
the 1-{[2-(phenoxy)ethoxy]methyl}uracil derivatives show viral inhibition properties relative to human
immunodeficiency type 1 virus in vitro. The most active compounds are 5-bromo-6-methyluracil
derivatives which suppress viral reproduction by 50% at 7.2 and 7.8 micromolar concentrations.
Keywords: 1-{[2-(phenoxy)ethoxy]methyl}uracil derivatives, synthesis, anti HIV-1 activity.
From the time of the discovery of the human immunodeficiency virus (HIV) as the etiological agent of
acquired immunodeficiency syndrome (AIDS) [1, 2] up to the present time the HIV infection has been a serious
clinical problem [3]. Preparations used in the clinic can be divided into two main classes viz., inhibitors of viral
protease and of reverse transcriptase. Their use is accompanied by serious side effects and the creation of
resistant strains of HIV [4]. Hence the search for novel HIV inhibitors is an extremely urgent problem.
The majority of non-nucleoside inhibitors of reverse transcriptase, as used in combination HIV infection
and AIDS therapy, have a butterfly like shape according to X-ray data (Figure 1). In "wing 1" they have nitrogen
atoms as part of a heterocycle in direct proximity to the catalytic site of the viral enzyme. In "wing 2" an
aromatic fragment is located in a hydrophobic pocket of the enzyme and the lower "body" of the butterfly fits a
lipophilic area of the reverse transcriptase [5-8]. Hence the derivatives of HEPT (1-[(2-hydroxyethoxy)methyl]-
6-(phenylthio)thymine 1) and their 6-benzyl analogs 2 show high anti-HIV-1 activity and the aromatic fragment
forming "wing 2" is bonded to the uracil position 6 either via a sulphur atom or via a methylene group [9].
O
O
R
X
R
HN
HN
N
N
O
O
O
O
Me
1 Х = S, СН2; 1, 2 R = alkyl C1-C3
O
2
1
__________________________________________________________________________________________
1
Research Institute of Pharmacology, Volgograd State Medicinal University, Volgograd 400131,
2
Russia; e-mail: ozerov@vlink.ru.
TherImmune Research Corporation, Maryland USA. Translated from
Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 726-731, May, 2005. Original article submitted September
24, 2003.
0009-3122/05/4105-0625©2005 Springer Science+Business Media, Inc.
625

Fig. 1. Butterfly form of the non-nucleoside
inhibitors of HIV-1 reverse transcriptase:
1: "wing 1" (pyrimidine base);
1
2
2: "wing 2" (aromatic nucleus);
3
3) "body" of the butterfly (substituent at
position N(1))
We have proposed that the aromatic fragment might be bonded with the uracil residue through the N(1)
atom rather than at position 6 and the overall butterfly structure of the HIV-1 reverse transcriptase inhibitor
retained. Further, the optimum length of connecting chain should be a five to six carbon and oxygen fragment. In
this case, "geometrical" analogs of 6-(phenylthio)- and 6-benzyluracils might be formed.
The closest structures corresponding to this criterion are 1-{[2-(phenoxy)ethoxy]methyl} uracils, in the
chains of which there occur three methylene groups and two oxygen atoms. Their synthesis was carried out as
shown in the scheme below.
OSiMe3
R1
R3
O
N
R1
O
Me3SiO
N
R2
O
CH2O/HCl
HN
OH
O
Cl
R2
3
R
3
R
N
O
3, 4
5, 6
O
O
7–19
7, 10, 13, 16 R1 = H; 8, 11, 14, 17 R 1 = Br; 9, 12, 15, 18 R1 = Me; 19 R1 = Et;
7-9, 13-15 R2 = H; 10-12, 16-19 R2 = Me; 3, 5, 7-12 R3 = Cl; 4, 6, 13-19 R3 = Me
In the presence of paraformaldehyde and gaseous hydrogen chloride the starting
2-(4-chlorophenoxy)ethanol (3) or 2-(4-methylphenoxy)ethanol (4) were converted to the corresponding
2-(4-chlorophenoxy)- (5) or 2-(4-methylphenoxy)ethoxymethyl (6) chlorides in 92 and 90% yields respectively.
The subsequent step in the synthesis is condensation of the α-chloro ethers 5 and 6 with
2,4-bis(trimethylsilyloxy)pyrimidines in aqueous methylene chloride solution at room temperature. The target
1-{[2-(phenoxy)ethoxy]methyl}uracils 7-19 were obtained in 56-71% yields after preparative chromatography.
The basic strategy in the synthesis has been reported by us previously [10].
The purity of the compounds 7-19 obtained was monitored using TLC, their composition proved by
1
elemental analysis, and their structure by H NMR spectroscopy and mass spectrometry. The physicochemical
properties of compounds 7-19 are given in Table 1.
The in vitro antiviral activities of the synthesized compounds towards HIV-1 were measured at the
TherImmune Research Corporation (Maryland, USA) using the CEM-SS cell culture. The screening results
showed that several of the uracil derivatives 7-19 show marked antiviral activity. The most active compounds of
this series proved to be the 1-{[2-(4-chlorophenoxy)ethoxy]methyl}- (11) and 1-{[2-(4-methylphenoxy)-
ethoxy]methyl}- (17) derivatives of 5-bromo-6-methyluracil which showed a 50% inhibition of the reproduction
of HIV-1 at 7.2 and 7.8 micromolar concentrations, respectively. However, due to their relatively high toxicity,
their selectivity indices were equal to 4.3 and 7.7. The uracil derivatives 1-{[2-(4-chlorophenoxy)ethoxy]-
methyl- (7) and 1-{[2-(4-methylphenoxy)ethoxy]methyl} (13) uracils had EC50 values of 23.7 and
16.1 micromolar and were an order less active but had lower toxicity and their selectivity indices were
comparable with the indices for compounds 11 and 17. The remaining compounds proved to be either inactive
towards HIV-1 or showed weak viral inhibiting activity (Table 2).
626

TABLE 1. Parameters for the Compounds Synthesized
Found, %
——————
Calculated, %
Com-
pound
Empirical
formula
mp, °С
Rf
Yield, %
С
Н
N
7
C13H13ClN2O4
C13H12BrClN2O4
C14H15ClN2O4
C14H15ClN2O4
C14H14BrClN2O4
C15H17ClN2O4
C14H16N2O4
52.45
52.62
41.88
41.57
53.97
54.11
54.03
54.11
43.34
43.16
55.21
55.48
60.95
60.86
47.50
47.34
61.91
62.06
62.18
62.06
48.97
48.80
62.95
63.14
4.57
4.42
3.61
3.22
5.04
4.87
5.06
4.87
3.88
3.62
5.07
5.28
5.63
5.84
4.41
4.26
6.12
6.25
6.13
6.25
4.79
4.64
6.51
6.62
9.53
9.44
7.70
7.46
8.72
9.02
9.24
9.02
7.05
7.19
8.39
8.63
9.99
10.14
7.78
7.89
9.44
9.65
9.46
9.65
7.40
7.59
9.03
9.20
9.23
8.80
126-127
155-156
121-123
146-148
157-159
167-168
139-140
70-73
0.16
0.38
0.22
0.20
0.39
0.31
0.28
0.49
0.34
0.32
0.51
0.43
0.48
60
56
71
64
63
57
63
70
64
59
58
56
71
8
9
10
11
12
13
14
15
16
17
18
19
C14H15BrN2O4
C15H18N2O4
143-144
140-143
149-150
141-143
120-121
C15H18N2O4
C15H17BrN2O4
C16H20N2O4
C17H22N2O4
62.96
63.13
6.82
6.97
TABLE 2. In vitro anti-HIV-1-Activity of the Synthesized Compounds
Selectivity index,
TC50 / EC50
TC50, micromolar*2
Compound
EC50, micromolar*
7
23.7
>100.0
50.9
>100.0
48.2
> 4.2
—
8
9
>100.0
>100.0
31.1
> 2.0
—
10
11
12
13
14
15
16
17
18
19
>100.0
7.2
4.3
>100.0
16.1
69.1
96.3
—
>100.0
>100.0
>100.0
>100.0
60.0
> 6.2
> 1.5
—
>100.0
>100.0
7.8
—
7.7
76.8
>100.0
19.8
> 1.3
—
>100.0
_______
* EC50. The effective concentration giving a 50% protection of the cell from
the cytopathic effect of the virus
*2 TC50. The cytotoxic concentration decreasing the survival of uninfected
cells by 50%.
627

EXPERIMENTAL
1H NMR spectra were recorded on a Bruker DRX-500 instrument (500 MHz) using CCl4 (compounds 5
and 6) or DMSO-d6 (compounds 7-19) and with TMS as internal standard. The interpretation of the spectra was
carried out using the ACD/HNMR Predictor Pro 3.0 licensed program from Advanced Chemistry of Canada.
Mass spectra were recorded on a Varian MAT-11 spectrometer (direct introduction, EI ionization method,
70 eV). TLC was performed on Silufol UV-254 plates in the system ethyl acetate-chloroform (1:1) and revealed
using iodine vapour. Melting points were measured in glass capillaries on a Mel-Temp 3.0 instrument
(Laboratory Devices Inc., USA).
2-(4-Chlorophenoxy)ethoxymethyl Chloride (5). A stream of dry hydrogen chloride was passed
through a stirred mixture of 2-(4-chlorophenoxy)ethanol (3) (19.1 g, 0.111 mol) and paraformaldehyde (3.5 g,
0.117 mol) in anhydrous methylene chloride (100 ml) at 0-5°C for 2 h. The organic layer was separated, dried
over CaCl2, filtered, and the filtrate was evaporated in a vacuum to give compound 5 (22.6 g, 92%) as a viscous
liquid which was used subsequently without further purification. 1H NMR spectrum, δ, ppm (J, Hz): 3.66 (2H, t,
J = 7, CH2O); 3.96 (2H, t, J = 7, CH2OAr); 5.41 (2H, s, CH2Cl); 6.96-7.31 (4H, m, arom. H).
1
2-(4-Methylphenoxy)ethoxymethyl chloride (6) was prepared similarly in 90% yield. H NMR
spectrum, δ, ppm (J, Hz): 2.11 (3H, s, 4-CH3); 3.72 (2H, t, J = 7, CH2O); 4.10 (2H, t, J = 7, CH2OAr); 5.51 (2H,
s, CH2Cl); 6.66-6.98 (4H, m, arom. H).
1-{[2-(4-Chlorophenoxy)ethoxy]methyl}uracil (7). A solution of the chloroether 5 (2.4 g, 10.86 mmol)
in methylene chloride (20 ml) was added to a solution of 2,4-bis(trimethylsilyloxy)pyrimidine (2.75 g, 10.72
mmol) in anhydrous methylene chloride (30 ml) and stirred for 1 day at about 20°C. Ethanol (95%, 10 ml) was
added and the product was stirred for 30 min, filtered, and the filtrated was evaporated to dryness in vacuo. The
solid residue obtained was chromatographed on a silica gel column (2 × 35 cm) and eluted with a mixture of
chloroform and methanol (10: 1). The fractions containing the target compound were combined, evaporated in
vacuo, and the residue was recrystallized from ethyl acetate to give compound 7 (1.9 g, 60%) as a white, finely
crystalline material with mp 126-127°C and Rf 0.16 (ethyl acetate–chloroform, 1: 1). 1H NMR spectrum, δ, ppm
(J, Hz): 3.81 (2H, t, J = 6, CH2CH2OAr); 4.08 (2H, t, J = 6, CH2OAr); 5.14 (2H, s, NCH2); 5.60 (1H, d, J = 8,
H-5); 6.92-7.32 (4H, m, arom. H); 7.66 (1H, d, J = 8, H-6); 11.06 (1H, br. s, NH). Mass spectrum, m/z: 296
[M]+.
Compounds 8-19 were prepared similarly
5-Bromo-1-{[2-(4-chlorophenoxy)ethoxy]methyl}uracil (8). H NMR spectrum, δ, ppm (J, Hz): 3.82
1
(2H, t, J = 6, CH2CH2OAr; 4.09 (2H, t, J = 6, CH2OAr); 5.14 (2H, s, NCH2); 6.91-7.32 (4H, m, arom. H); 8.20
(1H, s, H-6); 11.64 (1H, br. s, NH). Mass spectrum, m/z: 375 [M].
1-{[2-(4-Chlorophenoxy)ethoxy]methyl}thiamine (9). 1H NMR spectrum, δ, ppm (J, Hz): 1.78 (3H, s,
CH3); 3.81 (2H, t, J = 6, CH2CH2OAr); 4.08 (2H, t, J = 6, CH2OAr); 5.12 (2H, s, NCH2); 6.90-7.31 (4H, m,
arom. H); 7.56 (1H, s, H-6); 11.26 (1H, br. s, NH). Mass spectrum, m/z: 310 [M]+.
1-{[2-(4-Chlorophenoxy)ethoxy]methyl}-6-methyluracil (10). 1H NMR spectrum, δ, ppm (J, Hz): 2.27
(3H, s, 6-CH3); 3.81 (2H, t, J = 6, CH2CH2OAr); 4.09 (2H, t, J = 6, CH2OAr); 5.30 (2H, s, NCH2); 5.3 (1H, s,
H-5); 6.91-7.33 (4H, m, C6H4);11.18 (1H, br. s, 3-NH). Mass spectrum, m/z: 310 [M]+.
1
5-Bromo-1-{[2-(4-chlorophenoxy)ethoxy]methyl}-6-methyluracil (11). H NMR spectrum, δ, ppm
(J, Hz): 2.36 (3H, s, CH3); 3.82 (2H, t, J = 6, CH2CH2OAr); 4.10 (2H, t, J = 6, CH2OAr); 5.31 (2H, s, NCH2);
6.90-7.32 (4H, m, arom. H); 11.49 (1H, br. s, NH). Mass spectrum, m/z: 389 [M]+.
1
1-{[2-(4-Chlorophenoxy)ethoxy]methyl}-5,6-dimethyluracil (12). H NMR spectrum, δ, ppm (J, Hz):
1.81 (3H, s, 5-CH3); 2.26 (3H, s, 6-CH3); 3.81 (2H, t, J = 6, CH2CH2OAr); 4.09 (2H, t, J = 6, CH2OAr); 5.32
(2H, s, NCH2); 6.90-7.32 (4H, m, C6H4); 11.21 (1H, br. s, 3-NH). Mass spectrum, m/z: 324 [M]+.
1
1-{[2-(4-Methylphenoxy)ethoxy]methyl}uracil (13). H NMR spectrum, δ, ppm (J, Hz): 2.22 (3H, s,
CH3); 3.81 (2H, t, J = 6, CH2CH2OAr); 4.04 (2H, t, J = 6, CH2OAr); 5.12 (2H, s, NCH2); 5.58 (1H, d, J = 8,
H-5); 6.77-7.05 (4H, m, arom. H); 7.68 (1H, s, H-6); 11.14 (1H, br. s, NH). Mass spectrum, m/z: 276 [M]+.
628

5-Bromo-1-{[2-(4-methylphenoxy)ethoxy]methyl}uracil (14). 1H NMR spectrum, δ, ppm (J, Hz): 2.21
(3H, s, 4-CH3); 3.84 (2H, t, J = 6, CH2CH2OAr); 4.04 (2H, t, J = 6, CH2OAr); 5.15 (2H, s, NCH2); 6.78-7.09
(4H, m, C6H4); 8.25 (1H, s, H-6); 11.76 (1H, br. s, 3-NH). Mass spectrum, m/z: 354 [M]+.
1
1-{[2-(4-Methylphenoxy)ethoxy]methyl}thiamine (15). H NMR spectrum, δ, ppm (J, Hz): 1.77 (3H,
s, 5-CH3); 2.22 (3H, s, 4-CH3); 3.81 (2H, t, J = 6, CH2CH2OAr); 4.04 (2H, t, J = 6, CH2OAr); 511 (2H, s,
NCH2); 6.78-7.07 (4H, m, arom. H); 7.54 (1H, s, H-6); 11.22 (1H, br. s, 3-NH). Mass spectrum, m/z: 290 [M]+.
1
6-Methyl-1-{[2-(4-methylphenoxy)ethoxy]methyl}uracil (16). H NMR spectrum, δ, ppm (J, Hz):
2.22 (3H, s, 4-CH3); 2.28 (3H, s, 6-CH3); 3.80 (2H, t, J = 6, CH2CH2OAr); 4.05 (2H, t, J = 6, CH2OAr); 5.30
(2H, s, NCH2); 5.52 (1H, s, H-5); 6.80-7.06 (4H, m, arom. H); 11.15 (1H, br. s, NH). Mass spectrum, m/z: 290
[M]+.
5-Bromo-6-methyl-1-{[2-(4-methylphenoxy)ethoxy]methyl}uracil (17). 1H NMR spectrum, δ, ppm (J,
Hz): 2.21 (3H, s, CH3); 2.35 (3H, s, 6-CH3); 3.81 (2H, t, J = 6, CH2CH2OAr); 4.07 (2H, t, J = 6, CH2OAr); 5.30
(2H, s, NCH2); 6.81-7.07 (4H, m, arom. H); 11.29 (1H, br. s, NH). Mass spectrum, m/z: 369 [M]+.
5,6-Dimethyl-1-{[2-(4-methylphenoxy)ethoxy]methyl}uracil (18). 1H NMR spectrum, δ, ppm (J, Hz):
1.82 (3H, s, 5-CH3); 2.22 (3H, s, 4-CH3); 2.28 (3H, s, 6-CH3); 3.79 (2H, t, J = 6, CH2CH2OAr); 4.03 (2H, t,
J = 6, CH2OAr); 5.32 (2H, s, NCH2); 6.75-7.06 (4H, m, arom. H); 11.21 (1H, br. s, 3-NH). Mass spectrum, m/z:
304 [M]+.
1
6-Methyl-1-{[2-(4-methylphenoxy)ethoxy]methyl}uracil (19). H NMR spectrum, δ, ppm (J, Hz):
1.09 (3H, t, J = 7, CH3); 2.34 (3H, s, CH3); 2.50 (3H, s, 6-CH3); 2.58 (2H, q, J = 7, CH2); 3.81 (2H, t, J = 6,
CH2CH2OAr); 3.94 (2H, t, J = 6, CH2OAr); 5.31 (2H, s, NCH2); 6.80-7.05 (4H, m, arom. H); 11.27 (1H, br. s,
NH). Mass spectrum, m/z: 318 [M]+.
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