Synthesis and Antiviral Activity of Novel Fluorinated 2′,3′ -Dideoxynucleosides

Article abstract of DOI:10.1081/NCN-120027814

A series of 5-(trifluoroethoxymethyl)-2′,3′-dideoxyuridines and 5-[bis(trifluormethoxy)-methyl]-2′,3′-dideoxyuridines have been prepared and screened for antiviral activity. The conformations of these compounds are discussed on the bases of NOE studies and the MO calculations. Modelling and NOE studies suggest both syn- and anti conformations for these 5-(2,2,2-trifluoroethoxymethyl)- and 5-[bis(2,2,2-trifluoroethoxy)-methyl]-derivatives. The NOE parameters are also suggested to be more attributable to the nature of the fluorine atom than to structural or conformational changes. Compounds 17, 26 and 30 showed some activity in anti-HIV-1 and anti-HIV-2 assays, but the compounds were devoid of activity against HSV and human rhinovirus. The compounds tested exhibited low cytotoxicity and were inactive against a bank of cancer cells in vitro.

Full text of DOI:10.1081/NCN-120027814

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Synthesis and Antiviral Activity of Novel Fluorinated
2′,3′‐Dideoxynucleosides
Piyush Kumar a , Kazue Ohkura b , Jan Balzarini c , Erik De Clercq c , Koh‐ichi Seki d
&
Leonard I. Wiebe a
a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton,
Alberta, Canada , T6G 2N8
b Faculty of Pharmaceutical Sciences , Health Sciences University of Hokkaido ,
Ishikari‐Tobestsu, Hokkaido, 061‐0293, Japan
c Rega Institute of Medical Research , Katholieke Universiteit Leuven , B‐3000, Leuven,
Belgium
d Central Institute of Isotope Science , Hokkaido University , Kita‐ku, Kita 15, Nishi 7,
Sapporo, 060‐0815, Japan
Published online: 01 Jun 2007.
To cite this article: Piyush Kumar , Kazue Ohkura , Jan Balzarini , Erik De Clercq , Koh‐ichi Seki & Leonard I. Wiebe (2004)
Synthesis and Antiviral Activity of Novel Fluorinated 2′,3′‐Dideoxynucleosides , Nucleosides, Nucleotides and Nucleic
Acids, 23:1-2, 7-29, DOI: 10.1081/NCN-120027814
To link to this article: http://dx.doi.org/10.1081/NCN-120027814
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 23, Nos. 1 & 2, pp. 7–29, 2004
Synthesis and Antiviral Activity of Novel Fluorinated
2’,3’-Dideoxynucleosidesy
Piyush Kumar,1 Kazue Ohkura,2 Jan Balzarini,3 Erik De Clercq,3
Koh-ichi Seki,4 and Leonard I. Wiebe1,
*
1Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton,
Alberta, Canada
2Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido,
Ishikari-Tobestsu, Hokkaido, Japan
3Rega Institute of Medical Research, Katholieke Universiteit Leuven,
Leuven, Belgium
4Central Institute of Isotope Science, Hokkaido University, Kita-ku, Sapporo, Japan
ABSTRACT
A series of 5-(trifluoroethoxymethyl)-2’,3’-dideoxyuridines and 5-[bis(trifluor-
roethoxy)-methyl]-2’,3’-dideoxyuridines have been prepared and screened for antiviral
activity. The conformations of these compounds are discussed on the bases of NOE
studies and the MO calculations. Modelling and NOE studies suggest both syn- and
anti conformations for these 5-(2,2,2-trifluoroethoxymethyl)- and 5-[bis(2,2,2-
trifluoroethoxy)-methyl]- derivatives. The NOE parameters are also suggested to be
more attributable to the nature of the fluorine atom than to structural or
conformational changes. Compounds 17, 26 and 30 showed some activity in anti-
HIV-1 and anti-HIV-2 assays, but the compounds were devoid of activity against HSV
yIn honor and celebration of the 70th birthday of Professor Leroy B. Townsend.
*
Correspondence: Leonard I. Wiebe, Faculty of Pharmacy and Pharmaceutical Sciences,
University of Alberta, Edmonton, Alberta, Canada, T6G 2N8; E-mail: leonard.wiebe@
ualberta.ca.
7
DOI: 10.1081/NCN-120027814
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com
Copyright D 2004 by Marcel Dekker, Inc.

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Kumar et al.
and human rhinovirus. The compounds tested exhibited low cytotoxicity and were
inactive against a bank of cancer cells in vitro.
Key Words: Fluorinated 2’,3’-dideoxynucleosides; Syntheses; NOE; Antiviral
nucleosides.
INTRODUCTION
Viral diseases have long been intractable to chemotherapy because of the intimate
association of viruses with normal cellular biochemistry. However, chemical
modification of physiological nucleosides can impart therapeutic activity against
viruses. The antiviral potential of appropriately modified nucleosides depends on their
selective interaction with both host- and virus-encoded enzymes in infected cells.
Particularly for the herpesvirus family, many important structure-activity relationships
for antiviral activity have been elucidated over the past several decades. It is known,
for example, that many derivatives of 2’,3’-dideoxyribopyrimidine nucleosides having a
C-5 substituent no longer than a four carbon chain and starting with a carbon atom
have antiviral properties.[1–3] These properties extend to C-5 ether substituents,
5-methoxymethyl-2’-deoxyuridine (MMdU) and its 2’-deoxycytidine analogs,[4] which
are active against various strains of herpes simplex virus type 1 (HSV-1).[5]
Incorporation of fluorine and fluoro-alkyl substituents at C-5 similarly establishes
Figure 1. C-5-Elaborated 2’,3’-dideoxynucleosides.

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9
antiviral activity. Of the fluoropyrimidine nucleosides, 5-fluoro-2’-deoxyuridine (FUdR)
was developed for the treatment of cancer, whereas 5-trifluoromethyl-2’-deoxyuridine
(trifluridine; TFT), has clinical efficacy in the treatment of herpetic eye infection.[6]
5-(2-Fluoroethyl)-2’-deoxyuridine (FEDU) inhibits HSV-1 replication.[7,8] Introduction
of fluorine into the sugar moiety creates antiviral selectivity, especially in the C-2’-
arabino configuration, as in the case of 2’-fluoroarabinothymidine, which is a selective
inhibitor of HSV-1 and HSV-2.[9] Several dideoxy- and didehydrodideoxynucleosides
are useful in the chemotherapy of human immunodeficiency virus (HIV) infections.[10,11]
3’-Azido-3’-deoxythymidine (zidovudine, AZT)[12,13] and stavudine (3’-deoxy-2’,3’-
didehydrothymidine, D4T)[14,15] are active as inhibitors of reverse transcriptase, and
5-chloro-3’-fluoro-2’,3’-dideoxyuridine (FddClUrd) has a selectivity index similar to that
of AZT.[16] Finally, ring-opening of the sugar moiety imparts selective antiviral activity
among a range of nucleosides including 1-(2-hydroxyethoxymethyl)-6-(phenylthio)thy-
mine (HEPT),[17] which also demonstrates selective inhibition of HIV-1. Several
excellent reviews of antiviral nucleosides have been published.[18,19]
The syntheses of several novel pyrimidine nucleosides that feature selected
chemical modifications described above are now reported. Specifically, a series of 5-
(trifluoroethoxymethyl)-2’,3’-dideoxyuridines and 5-[bis(trifluoroethoxy)methyl]-2’,3’-
dideoxyuridines (Figure 1) have been prepared and screened for antiviral activity.
Antiviral activities of previously reported but un-tested pyrimidine nucleosides are also
presented.[20,21]
RESULTS AND DISCUSSION
Chemistry
The synthesis of compounds 1–8 (Figure 1) has been described in previous
communications.[20,21] 3’-Substituted-5’-O-protected-3’-deoxythymidines, the synthons
for the corresponding 5-(2,2,2-trifluoroethoxymethyl)- and 5-[bis(2,2,2-trifluoroethoxy)
methyl]- derivatives now reported, were prepared by sequential bromination and then
trifluoroethoxylation at C-5 methyl of thymidine. The C-5 halomethyluracils are very
labile in protic solvents or moisture and undergo nucleophilic displacement of the
halogen via a 1,4-conjugate addition–elimination mechanism.[22 – 24] However,
appropriately protected 5-a-bromomethyl pyrimidine nucleosides resist solvolysis and
yet undergo facile nucleophilic substitution in the presence of strong nucleophiles such
as trifluoroethoxide-copper complex, to afford the corresponding 5-trifluoroethoxy-
methyl derivatives (Scheme 1).
Reported approaches to the synthesis of AZT and FLT include a variety of
protecting groups[25–27] depending on the demands of subsequent chemical reaction.
We now report the synthesis of 5-(2,2,2-trifluoroethoxymethyl)- and 5-[bis(2,2,2-
trifluoroethoxy)-methyl]- derivatives from 3’-substituted-5’-O-protected-3’-deoxythymi-
dines (11, 14). 5’-O-tert-Butyldiphenylsilyl protection of thymidine was selected to
withstand the acidic conditions generated during bromination, and resist the strongly
alkaline conditions of nucleophilic substitution by the trifluoroethoxy group.[28] Thus,
thymidine was converted to 9 (86%), and hydrolysis of 9 with ethanolic sodium
afforded the anhydrothymidine 10 (80%), which, in turn formed the 5’-O-TBDPS-3’-
azido-3’-deoxythymidine 11 (46%) upon treatment with NaN3. Insertion of the azide
1
group was confirmed by H NMR and by IR (absorbance at 2125 cmꢀ 1). FLT 13 was

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Kumar et al.
Scheme 1. Preparation of the synthons 5’-O-tert-butyl-AZT (11) and -FLT (14).
prepared by basic hydrolysis of 9 to afford threothymidine 12 (70%), which, after C-5’
triphenylmethyl protection, was fluorinated with diethylaminosulfurtrifluoride (DAST)
and sequential acidic deprotection to afford FLT 13 (65%) (Scheme 1). The
1
incorporation of fluorine at 3’- was confirmed by H NMR, 19F NMR and 13C NMR
spectroscopy of 14. 5’-O-TBDPS-3’-azido-3’-deoxythymidine (11) and 5’-O-TBDPS-3’-
fluoro-3’-deoxythymidine (14) were the key precursors for preparing substituted 5-
fluoroalkoxy products.
For C-5 methyl bromination, a solution of bromine and 11 was irradiated under a
75 W UV lamp to afford 15 or 18, depending on the amount of bromine used (Scheme 2).
These brominated intermediates are unstable, and were therefore used immediately. Upon
reaction with potassium trifluoroethoxide alone, most of the bromomethylthymidine was
hydrolyzed to the corresponding 5-hydroxymethyl-3’azido-5’-O-TBDPS-3’-deoxythymi-
dine, but reaction of 2,2,2-trifluoroethoxide-copper complexa with 15 gave 16, and
reaction with 18 afforded the bis-substituted 19, both in moderate yields. Introduction of
aIn the absence of cuprous iodide, most of the bromomethylthymidine was hydrolyzed to the
corresponding 5-hydroxymethyl-3’azido-5’-O-TBDPS-thymidine.

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11
Scheme 2. Synthesis of 5-(2,2,2-trifluoroethoxymethyl)- and 5-[bis-(2,2,2-trifluoroethoxy)-
methyl]- dideoxynucleosides 17, 20, 23, and 26.
trifluoroethoxymethyl moieties at C-5 of 16 and 19 was confirmed by 19F NMR.
Fluorine–carbon couplings (quartets) were observed in 13C NMR spectra, at the expected
chemical shifts. Desilylation of 16 and 19, gave 17 (71%) and 20 (57%), respectively
(Scheme 2). Removal of the silyl protecting groups was confirmed by the characteristic
downfield shifts of the fluorine signals of 17 and 20 in their 19F NMR spectra.
The synthesis (Scheme 2) of 22 and 25 started from 14 and followed similar
reaction pathways as described for the synthesis of 16 and 19. A characteristic CH2CF3
proton quartet in 22 reflected the coupling of these methylenic protons with fluorine

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Kumar et al.
Scheme 3. Synthesis of the gem-difluorodideoxynucleoside 30.
atoms at CF3. In the case of 25, similar observations confirmed formation of the 5-[bis-
(2,2,2-trifluoroethoxy)methyl]- group.
The gem-difluoro nucleoside 30 was prepared from 1[29] via the 3’-keto
dideoxynucleoside 28 (Scheme 3). The 19F NMR spectrum of 30 exhibited signals at
d 51.43 and d 65.44, corresponding to two fluorine atoms with strong geminal fluorine
coupling (Jgem = 238.8 Hz) at C-3’. In addition, a triplet at d127.75 ppm in the 13C
NMR spectrum of 30 was ascribed to the coupling of C-3’ with geminal fluorine atoms
at this position.
In addition, protection of the 5’-OH group and trifluoroethoxylation at C-5 methyl
also had significant electronic impact on various substituents of these molecules. For
example, desilylation of 22, 25, 16 and 19 induced not only the expected upfield shifts
of the C-5’-protons in the respective deblocked compounds 23, 26, 17 and 20, and
deshielded H-6, C-6, and the methylene protons and fluorine in CH2CF3. The impact of
silylation on fluorine chemical shifts of the trifluoroethoxy group at C-5 (compare 1
to 1a, 2 to 2a, 22 to 23 and 25 to 26) and the fluorine present at C-3’ is also
evident, with CF3 fluorines appearing at higher chemical shift after desilylation. The
effect of desilylation on C-3’ fluorines was inconsistent, shifting 3’-fluorine downfield
in 23 and upfield in 26. These results (Table 1) indicate that these 5-(2,2,2-
trifluoroethoxymethyl)- and 5-[bis-(2,2,2-trifluoroethoxy)methyl]- derivatives may
adopt the anti-conformation.
The contribution of the anti-conformation to the stereochemistry of these
molecules (1, 2, 22, 25 and 26, Figure 2) were further demonstrated by NOE ex-
periments. As seen in Table 2, significant NOE correlation between H-5’ (or tert-butyl

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13
1
Table 1. Perturbation of H, 13C and 19F-NMR chemical shifts for H-6, C-6 and the 5-(2,2,2-
trifluoroethoxymethyl)- substituents, by the 3’-substituent (-OH, -F or N3).
1H NMR
CH2CF3
19F NMR
13C NMR
Compound
H-6
CF3
C-6
CH2CF3
CF3
1
8.16
7.74
8.24
7.68
7.6
4.00
3.75
4.09
3.92
3.70
3.96
3.82
4.07
89.44
87.65
89.56
87.29
87.64
89.52
87.32
89.70
141.38
138.66
139.15
139.12
138.48
142.27
138.98
140.36
134.48
138.55
138.55
138.68
141.36
68.63
68.37
64.36
64.12
68.49
69.14
64.18
68.20
125.75
123.91
125.36
123.47
*
1a
2
2a
16
17
19
20
14
22
23
25
26
8.08
7.25
8.22
7.60
7.73
8.11
7.83
8.28
126.22
133.92
125.22
3.77
4.00
4.22
4.08
87.24
89.34
87.32
89.45
68.39
68.62
64.11
64.32
123.85
123.85
123.42
125.38
*embedded.
or phenyl protons) and H-6 was observed for 1, 2, and 25, supporting the importance of
the anti-conformation, wherein H-6 stands towards the C-5’ substituents. Compound 22
and 26 showed weak NOE at H-6 upon irradiation at H-5’, while no NOE was observed
at H-5’ when H-6 was irradiated. These findings may suggest that contribution of the
syn-conformation increased for compounds 22 and 26, while the anti-conformation is
still involved as an important conformation though the contribution is reduced. NOE
correlation between 6-H and 3’-H which was observed for 1, and 2, disappeared for
compounds substituted by a fluorine atom at C-3’ (22, 25 and 26), suggesting that the
fluorine atom is aligned in such a way that these proton interactions are reduced or the
introduced fluorine atom served to diminish the NOE interaction between 6-H and 3’-H,
Similarly NOE correlation between 3’-H and 4’-H observed for compounds 1 and 2
disappeared for the compounds 22, 25, and 26.
In order to investigate changes occurring upon introducing fluorine at C-3’,
conformational analysis (MM2 method) was applied to the structures of 2 and 26.
Structures were optimized by the PM3 method using MOPAC (Cache ver. 94, release
3.7, CaChe Scientific Inc.). As shown in Figure 3, no remarkable changes were found
either in the structure or in the energy curves of the conformational analysis. Similar
energy curves are seen for 2 and 26 with the lowest points at the dihedral angles of 64°
and 60°, corresponding to the anti-conformation. The energy curves for 2 and 26 show
three local minimum points at ꢀ 110°/ ꢀ 116° (corresponding to syn-conformation),
0°/0° (staggered conformation), and 170°/170° (staggered conformation) (2/26)
suggesting that both conformations can be involved as the rotational isomers.
No significant differences were observed from the computational analysis to
explain the changes in the NOE due to the introduction of the C-3’ fluorine atom,
suggesting that the above findings are more attributable to the nature of the fluorine
atom than the structural or conformational changes.

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Kumar et al.

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15

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Kumar et al.
Figure 3. Optimized structures for 2 and 26. Conformational analysis was made by rotating the
pyrimidine moiety on the axis of N-1 and C-1’.
It was also observed that C-4’ and C-5’ protons showed significant electronic
deshielding in the 3’-fluorine in compounds 23 and 26, while substitution by an azido
function at the same position made little difference in the chemical shifts of these
protons. The effect on carbon chemical shifts by replacing the 3’-OH group in
compounds 1 and 2 with fluorine or azido groups is anticipated within the sugar
moiety, but these effects are surprisingly extended to the carbon atoms of pyrimidine
base at C-6 and its C-5 substituent. It is apparent from the data in Table 1 that both C-6
and CF3 carbons have shifted upfield in 3’-fluoro-5-trifluoroethoxymethyl analogue 23,
whereas they appeared at higher chemical shifts in the corresponding 3’-fluoro-5-
[bis(trifluoroethoxy)methyl]- and 3’azido analogues (compare 1 with 17, and 23 and 2
with 20 and 26, respectively).
Antiviral Activity
Compounds 17, 26 and 30 showed significant potency in the HIV-1 and HIV-2 assays
(Table 3). Activity of 1, 2, 7 and 8 against rhinovirus type 1A and rhinovirus type 39 in

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17
Table 3. Anti-HIV-1 and -HIV-2 activity of the compounds 1, 2, 6, 17,
26 and 30 in human T-lymphocyte (CEM cells).
EC50 (Mg/mL)*
Compound
HIV-I
> 100
>100
HIV-2
100
>100
1
2
6
>100
>100
17
26
30
1.50 0.87
15.0 7.1
53.3 41.6
3.1 1.6
35.0 7.1
ꢁ100
*50% Effective concentration or concentration required to protect
CEM cells against the cytopathogenicity of HIV by 50%; the AZT EC50
is 10 nM (2.5 ng/mL) in this system.
W138 cells was minimal, with IC50 and CC50 concentrations of > 50 mg/mL in each case.
In this assay, the positive reference compound WIN (2,6-dimethyl-1-(3-[3-methyl-5-
isoxazolyl]-propanyl)-4-[4-methyl-2h-tetrazol-2-yl]-phenol) was active against rhinovirus
1A (25 mg/mL) and rhinovirus 39 (5 mg/mL), with a CC50 of > 25 mg/mL. Similar low
potencies (IC50 and CC50 were > 50 mg/mL) were observed against TK+ VZV (YS and
OKA strains), TKꢀVZV (07/1 and YS/R strains) and CMV (AD-169 and Davis strains) in
human embryonic cells (HEL). VZV was similarly insensitive to 1, 2, 6, 17, 26 and 30,
in comparison to positive controls ACV (IC50: 0.9, 0.96, 6 and 8 mg/mL,
respectively; MCC50 > 50 and CC50 > 200 mg/mL) and BVDU (IC50: 0.0047, 0.0043,
> 50 and > 50 mg/mL, respectively; MCC50 > 50 and CC50> 200 mg/mL). CMV-active
compounds ganciclovir and cidofovir had IC50 values of 2 and 3 mg/mL and 0.35 and
0.85 mg/mL for the respective strains, respectively (Table 3). In the CMV assay,
ganciclovir and cidofovir had MCC50 and CC50 > 50, with cidofovir being slightly
more toxic to the host (HEL) cells in the CC50 (35 mg/mL) determination.
Cytotoxicity
Growth of L1210/0, FM3A/0 and CEM/0 cells was inhibited by 1 IC50: 7.2, 53 and
8.3 mg/mL. Inhibitory concentrations of 2 were 35.5, > 100 and 35.5 mg/mL for these
cell lines. These compounds (1, 2, 6, 17, 26 and 30) were not toxic to Molt4/C8 cells in
this study. All compounds were rated inactive in the NCI in vitro antitumor screen
(data not shown).
CONCLUSION
A series of 5-(trifluoroethoxymethyl)-2’,3’-dideoxyuridines and 5-[bis(trifluoro-
ethoxy)methyl]-2’,3’-dideoxyuridines were prepared. The structural assignments for 1,
2, 22, 25, and 26 are based on NOE experiments and MO calculations. Compounds 1,
2, and 25 are suggested to adopt anti-conformation more favourably in solution, while

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Kumar et al.
compound 22 and 26 may take the syn-conformation more preferably than the anti-
conformation. As anticipated on the basis of the bulky C-5 substituents, these
compounds were devoid of anti-HSV activity. This structural feature reduced, but did
not totally eliminate anti-HIV activity. The compounds were not active against a bank
of cancer cell lines in vitro.
EXPERIMENTAL SECTION
Abbreviations. AZT, 3’azido-3’-deoxythymidine; D4T, didehydrodeoxythymi-
dine; (FddClUrd), 5-chloro-3’-fluoro-2’,3’-dideoxyuridine; (FEDU), 5-(2-fluoroethyl)-
2’-deoxyuridine; (HEPT), 1-(2-hydroxyethoxymethyl)-6-(phenylthio)thymine; (MMdU),
5-methoxymethyl-2’-deoxyuridine; HSV-1, herpes simplex virus type 1; HSV-2, herpes
simplex virus type 2; CMV, cytomegalovirus; VZV, varicella zoster virus; AIDS, ac-
quired-immune deficiency syndrome; HeLa (human epithelial carcinoma cells); HIV-1,
human immunodeficiency virus type 1; HIV-2. Human immunodeficiency virus type-2;
s, singlet; d, doublet; dd, doublet of doublet; dddd, doublet of doublet of doublet of
doublet, q, quartet, t, triplet; m, multiplet; br, broad; tlc, thin layer chromatography;
TBDPS, tert-butyldiphenylsilyl; THF, tetrahydrofuran; DME, 1,2-dimethoxyethane;
DAST, diethylaminosulfurtrifluoride; DMAP, N,N-dimethylaminopyridine; CCl4, car-
bon tetrachloride; DMF, dimethylformamide; EtOH, ethanol.
Cytotoxicity and Antiviral Activity Assays. The methodology used to assess the
activity against varicella-zoster virus in human embryonic lung (HEL) cells,
cytomegalovirus in human embryonic lung (HEL) cells, proliferation of murine
leukemia cells (L1210/0), murine mammary carcinoma cells (FM3A) and human
T-lymphocyte cells (Molt4/C8, CEM/0), HIV-1 and HIV-2 proliferation has been
described by De Clercq.[30]
In vitro KB cell cytotoxicity assay. Test compounds (0.05, 0.1, 0.5, 1.0, 5, and
10 mg/mL) were added to wells of a 96-well plates. Each well was seeded with KB
cells (ATCC-CCL17; 104 cells in 100 mL). The plates were incubated for 3 days at
37°C in a CO2 incubator. The toxicity was determined using the neutral red dye uptake
assay: neutral red solution (25 mL) was added to each well, followed by incubation at
37°C for 2.5 h. The cells were then washed with PBS. Washing buffer (50 mL) was
added to each well, followed by a two-hour incubation, when the plates were optically
read at 540 nm on a spectrophotometer. The concentration of compound required to
reduce cell viability by 50% was determined to be the TD50.
In vitro Human Rhinovirus (HRV-1A, HRV-39) Antiviral Assay. Test
compounds (50 mL; 0.2, 1.0, 5, 10, 25 and 50 mg/mL) were added to wells of a 96
well plate. Each well was seeded with W138 cells (ATCC-CCL75; 104 cells in 100 mL)
and 50 mL of rhinovirus type 1A (nasopharyngeal washing/ATCC-VR1110) or rhi-
novirus type 39 (nasal washing/ATCC-VR340) was added to the appropriate plate. The
plates were incubated at 37°C in a CO2 incubator. The cytopathic effect caused by the
virus was scored and the concentration of compound required to reduce this effect by
50% was determined.

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19
Chemistry. The reagents used in the chemical reactions were of reagent grade,
purchased from Aldrich Chemical Co. Anhydrous solvents were dried over appropriate
drying agents and freshly distilled at the time of use. The progress of reactions was
monitored by tlc on Whatman MK6F silica gel micro slides (250 mm thickness) and the
products were purified by silica gel (Merck 7734; particle size 100–200 mesh) column
chromatography using the eluent of choice. Melting points were determined on a Bu¨chi
capillary apparatus and are uncorrected. The compounds were characterized by their
elemental analyses for C, H and N. In some cases, exact ionization high resolution
mass spectral analyses (HRMS-EI) were obtained in lieu of elemental analyses. Nuclear
magnetic resonance spectra (1H, 13C and 19F NMR) were recorded on a Bruker AM
300 spectrometer. Chemical shifts are reported in d ppm downfield from tetra-
1
methylsilane (1H) and hexafluorobenzene (19F) that were used as internal standards. H
NMR assignments were confirmed by double irradiation experiments. 13C NMR res-
onances were assigned using the J modulation spin echo technique (Jmod) where methyl
and methine carbon resonances appear as positive peaks, and methylene and quaternary
carbons appear as negative peaks.
5’ -O-tert-Butyldiphenylsilyl-3’ -O-methanesulfonylthymidine (9). tert-Butyl-
chloro diphenylsilane (5.76 mL, 21.79 mmol) was added to a solution of thymidine (5
g, 20.7 mmol) in anhydrous pyridine (20 mL) and the mixture was stirred overnight at
25°C under an atmosphere of argon. Tlc at this point showed complete disappearance
of thymidine. The contents were cooled to 0°C and methanesulfonyl chloride (2.45 mL,
21.79 mmol) was added drop-wise. Stirring was continued for 2 h and then the mixture
was allowed to warm up to 25°C. After stirring the reaction for an additional 30 min.,
the contents were poured into crushed ice/water and then the solvent was evaporated in
vacuo. The viscous mass so obtained was taken in chloroform (100 mL) and washed
with water (20 mL ꢂ 2). The organic phase was dried over anhydrous sodium sulfate,
filtered and evaporated on a rotary evaporator to obtain impure product. Silica gel
column purification, eluting with a linear gradient beginning with toluene and ending
with 10% ethyl acetate, afforded pure 9 (9.65 g, 86%) as a foam: mp 76°C; Rf 0.41
1
(CHCl3:MeOH, 9:1); H NMR (CDCl3)- d 1.13 (s, 9H, t-butyl), 1.62 (s, 3H, CH3), 2.34
(d, J1’,2@ = 8.6 Hz, of d, J3’,2@ = 6.3 Hz, of d, Jgem = 13.7 Hz), 2.64 (d, J1’,2@ = 5.1 Hz,
of d, Jgem = 13.7 Hz, 1H, H-2’), 3.07 (s, 3H, SO2CH3), 3.96 and 4.02 (two d,
J4’,5@ = 2.3 Hz, of d, Jgem = 11.4 Hz, 2H, H-5’ and H-5@), 4.37 (d, J5’,4’ = J5@,4’ = 2.3
Hz, 1H, H-4’), 5.41 (d, J2@,3’ = 6.3 Hz, 1H, H-3’), 6.43 (d, J2’,1’ = 5.1 Hz of d,
J2@,1’ = 8.6 Hz, 1H, H-1’), 7.38–7.54 (m, 7H, 1H of H-6 and 6H aromatic), 7.62–7.72
(m, 4H, aromatic) and 9.24 (s, br, 1H, NH) ppm; 13C NMR (CDCl3)- d11.97
(SO2CH3), 19.34 (tert-C of butyl), 26.98 (5-CH3), 38.44 (C-2’), 38.66 (CH3’s of tert-
butyl group), 63.47 (C-5’), 79.42 (C-3’), 84.21 (C-4’), 84.72 (C-1’), 111.69 (C-5),
128.05–132.59 (aromatic carbons), 134.66 (C-6), 135.22 and 135.49 (remaining
aromatic carbons), 150.23 (C-2) and 163.39 (C-4); anal. for SiC27H34N2O7 calc. C
58.05, H 6.13, N 5.01; found C 58.62, H 5.97 and N 4.89.
2,3’ -Anhydro-5’ -O-tert-butyldiphenylsilyl-3’ -deoxythymidine (10). An aqueous
solution of 1N NaOH (0.4 g, 10 mmol) was added to a refluxing solution of 9 (5.58 g,
10 mmol) in absolute EtOH (35 mL) drop-wise. Stirring was continued at this
temperature for 2 h. At that time, the tlc showed complete conversion of starting

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20
Kumar et al.
material to the product. The content was cooled to 25°C and neutralized with acetic
acid to pH 7.0. The solution was evaporated to dryness and the residue purified on a
silica gel column by elution first with chloroform and ending with 3% methanol to
1
yield 4.33 g (80%) of pure 10 as a semisolid: H NMR (CDCl3)- d 1.06 (s, 9H of tert-
butyl group), 1.90 (s, 3H, 5-CH3), 2.41 (d, J3’,2 = 3.0 Hz of d, J1’,2@ = 4.0 Hz of d,
Jgem = 13.0 Hz, 1H, H-2@), 2.72 (d, Jgem = 13.0 Hz, 1H, H-2’), 3.78 (d, J4’,5@ = 7.0 Hz
of d, Jgem = 15 Hz, 1H, H-5@), 3.84 (d, J4’,5’ = 7.0 Hz of d, Jgem = 15 Hz, 1H, H-5’),
4.31 (d, J5’,4’ = 7.0 Hz of d, J3’,4’ = 2.0 Hz, 1H, H-4’), 5.20 (br, 1H, H-3’), 5.48 (d,
J2@,1’ = 4.0 Hz, 1H, H-1’), 6.9 (s, 1H, H-6), and 6 7.30–7.70 (m, 10H of two phenyl
groups) ppm; anal. calc. for SiC26H31N2O4 (463.66), C 67.38, H 6.69, N 6.04; found, C
67.28, H 6.51, N 5.89.
3’ -Azido-5’ -O-tert-butyldiphenylsilyl-3’ -deoxythymidine (11). A mixture of
sodium azide (1.95 g, 30 mmol) and 2,3’-anhydro-5’-O-tert-butyldiphenylsilyl
thymidine 10 (2.77 g, 6.0 mmol) in anhydrous DMF (10 mL) was heated at 110°C
under stirring for 24 h. The progress of the reaction was monitored by tlc. After the
reaction was complete, the solvent was evaporated in vacuo, and the crude mass
extracted with chloroform/cold water (20 mL ꢂ 2). The chloroform phase was dried
over anhydrous magnesium sulfate, filtered and evaporated to collect a solid that was
purified on a silica gel column, eluting with toluene and finally with 20% ethyl acetate,
1
to give 1.4 g (46%) of pure 11: mp 55°C (softened); H NMR (CDCl3)- d 1.14 (s, 9H,
tert-butyl group), 1.66 (s, 3H, CH3), 2.33 (d,
= 6.2 Hz of d, J3’,2@ = 6.2 Hz of d,
1’,2@
Jgem = 13.8 Hz, 1H, H-2@), 2.48 (d, J1’,2’ = 6.2 Hz of d, J3’,2’ = 3.75 Hz of d,
Jgem = 13.8 Hz, 1H, H-2’), 3.85 (d, J4’,5@ = 3.8 Hz of d, Jgem = 12.5Hz, 1H, H-5@),
3.99 (d, J3’,4’ = 7.5 Hz of d, J5’,4’ = 3.8 Hz, 1H, H-4’), 4.04 (d, J4’,5’ = 3.8 Hz of d,
Jgem = 12.5 Hz, 1H, H-5’), 4.34 (quintet, J4’,3’ = 7.5 Hz, J2’,3’ = 3.8 Hz, J2@,3’ = 6.2 Hz,
1H, H-3’), 6.28 (t, J2’,1’ = 6.2 Hz, H-1’), 7.56–7.36 (m, 7H, 6H of phenyls and 1H of H-
6), 7.76–7.64 (m, 4H of two phenyls) and 9.24 (s, br, D2O exchangeable, 1H, NH)
ppm; anal. calc. for SiC26H31N5O4 (505.646); C, 61.76; H, 6.17; N, 13.85; found; C,
62.86; H, 6.36; N, 12.85.
5-(2,2,2-Trifluoroethoxy)methyl-3’ -azido-5’ -O-tert-butyldiphenylsilyl-2’ ,3’ -
dideoxyuridine (16). Bromine (0.14 mL, 2.48 mmol) was dissolved in anhydrous
carbon tetrachloride (10 mL) and added drop-wise to a stirred refluxing solution of 11
(1.0 g, 1.99 mmol) in CCl4 (30 mL) under irradiation with a 75 W UV lamp.[31] Strict
anhydrous reaction atmosphere was maintained by circulating argon through the
reaction vessel. After the addition of bromine was complete and showed no 11, argon
was bubbled through the reaction mixture to remove residual bromine and HBr
generated during the reaction. The solvent was evaporated under complete exclusion of
moisture to give 5-(bromomethyl)-3’-azido-2’,3’-dideoxyuridine 15. This bromo
intermediate was used without further purification. It was re-dissolved in anhydrous
1,2-dimethoxyethane (DME) (15 mL) and added to a solution of trifluoroethoxide-
copper complex[20,21] (2.5 mmol) in DME (15 mL). The mixture was stirred overnight
at 25°C under argon, and then diluted with diethyl ether (150 mL). The organic layer
was washed with ammonium hydroxide solution (28%, 15 mL ꢂ 2) followed by cold
water until the pH of the mixture was neutral, then dried over anhydrous MgSO4,
filtered and the solvent evaporated in vacuo. Purification of this impure product on a

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Fluorinated 2’ ,3’ -Dideoxynucleosides
21
silica gel column using toluene/ethyl acetate (20%) afforded 0.21 g (17%) of pure 16 as
a foam: mp 76°C (softening); Rf 0.61 (CHCl3:MeOH, 9.5:0.5); IR (neat)- 2110 cmꢀ 1
(N3 stretch);1H NMR (CDCl3)- d 1.04 (s, 9H of tert-butyl group), 2.21 (quintet,
Jgem = 14.0 Hz, J1’,2@ = 6.75 Hz, J3’,2@ = 6.75 Hz, 1H, H-2@), 2.44 (d, Jgem = 14.0 Hz of
d, J1’,2’ = 6.75 Hz of d, J3’,2’ = 3.9 Hz, 1H, H-2’), 3.70 (q, JF,H = 8.3 Hz, 2H of
OCH2CF3), 3.78 (d, J4’,5’ = 3.9 Hz of d, Jgem = 12.4 Hz, 1H, H-5’), 3.90 (m, 2H, 1H,
H-4’ and 1H, H-5’), 4.02 (d, Jgem = 11.3 Hz, 1H of CH2OCH2CF3), 4.06 (d,
Jgem = 11.3Hz, 1H of CH2OCH2CF3), 4.20 (quintet, J4’,3’ = 3.9 Hz, J2’,3’ = 3.9 Hz,
J2@,3’ = 8.5 Hz, 1H, H-3), 6.12 (t, J2’,1’ = J2@,1’ = 6.8 Hz, 1H, H-1’), 7.28–7.44 (m, 6H of
phenyls), 7.53–7.64 (m, 5H, 4H of phenyls and 1H of H-6), and 9.25 (s, broad, D2O
exchangeable, 1H, NH) ppm; 19FMR (CDCl3+ C6F6)- d 87.64 (t, JF,H = 8.3 Hz) ppm;
13C NMR (CDCl3)- d 19.31 (tert-carbon of tert-butyl group), 26.98 (methyl carbons of
tert-butyl group), 37.92 (C-2’), 60.59 (C-4’), 63.52 (C-5’), 66.55 (CH2OCH2CF3), 68.49
(q, JF,C = 33.9 Hz, CH2CF3), 84.57 (C-3’), 85.09 (C-1’), 111.12 (C-5), CF3 embedded in
the basal line, 135.53–130.26 (phenyl carbons), 138.48 (C-6), 149.67 (C-2), and 162.10
(C-4) ppm; anal. calc. for SiC28H27F3N5O5 (603.66); C, 55.70; H, 5.34; N, 11.60; found;
C, 55.68; H, 5.46; N, 11.21.
5-(2,2,2-Trifluoroethoxy)methyl-3’ -azido-2’ ,3’ -dideoxyuridine (17). Tetrabutyl
ammonium fluoride (0.19 mL, 0.19 mmol) solution was added to a solution of 16 (0.1
g, 0.18 mmol) in anhydrous THF under argon, and the reaction mixture was stirred
overnight at 25°C. Evaporation of the solvent in vacuo, followed by the purification of
impure material on a silica gel column by eluting with 5% methanol in chloroform
gave 40 mg (71%) of pure 17 as a semisolid: Rf 0.48 (CHCl3:MeOH, 9:1,v/v); IR
1
(neat)- 2110 cmꢀ 1 (N3 stretch); H NMR (CD3OD)- d 2.4 (t, J3’,2’ = J1’,2’ = 6.2 Hz,
2H, H-2’), 3.71 (d, J4’,5@ = 2.3 Hz of d, Jgem = 12.4 Hz, 1H, H-5@), 3.81 (d, J4’,5’ = 2.3
Hz of d, Jgem = 12.4 Hz IH, H-5’), 3.90 (d, J5’,4’ = 2.3 Hz of d, J3’,4’ = 7.9 Hz, 1H,
H-4’), 3.96 (q, JF,H = 8.9 Hz, 2H, OCH2CF3), 4.34 (m, 3H, 2H of CH2OCH2CF3 and
1H of H-3’), 6.12 (t, J2’,1’ = 6.2 Hz, 1H, H-1’) and 8.08 (s, 1H, H-6) ppm; 19FMR
(CD3OD + C6F6)- d 89.52 (t, JH,F = 8.9 Hz) ppm; 13C NMR (CD3OD)- d 39.08 (C-
2’), 61.99 (C-4’), 62.79 (C-5’), 68.34 (CH2OCH2CF3), 69.14 (q, JF,C = 34.2 Hz,
OCH2CF3), 86.87 (C-3’), 87.12 (C-1’), 112.01 (C-5), 126.22 (q, JF–C = 278 Hz, CF3),
142.27 (C-6), 152.51 (C-2) and 165.60 (C-4) ppm; LRMS- M+ (relative abundance
0.8%); anal. calc. for C12H14F3N5O5 (365.27); C:, 39.46; H, 3.86; N, 19.17; found; C,
39.44; H, 3.95; N, 17.56.
5-[bis(2,2,2-Trifluoroethoxy)methyl]-3’ -azido-5’ -O-tert-butyldiphenylsilyl-2’ ,3’ -
dideoxyuridine (19). Bromine (0.14 mL, 2.48 mmol) solution in carbon tetrachloride
(10 mL) was added drop-wise to a refluxing solution of 11 (0.5g, 0.99 mmol) in anhydrous
carbon tetrachloride (25 mL), under argon atmosphere. This reaction mixture was con-
tinuously irradiated through a 75 W UV lamp. When the reaction mixture showed no
evidence of 11 on tlc, excess bromine and HBr were removed from the reaction mixture.
The work up was done as described in the synthesis of 16. The bromide intermediate 18, so
obtained, was dissolved in anhydrous DME (15 mL) and transferred to the flask containing
2,2,2-trifluoroethoxide-copper complex (2.5 mmol) in anhydrous ethylene glycol di-
methyl ether (DME, 10 mL). The contents were stirred under argon overnight and then
extracted sequentially with chloroform/ ammonium hydroxide (5:1; 60 mL ꢂ 2) followed

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Kumar et al.
by cold water until the pH was neutral. The organic phase was dried over anhydrous
magnesium sulfate, filtered and evaporated, in vacuo, to afford impure 19. It was purified
on a silica gel column using toluene:ethyl acetate (80:20, v/v) to give (0.4g, 57%) of
a viscous product 19: Rf 0.56 (CHCl3:MeOH, 9.5:0.5, v/v); IR (neat)- 2110 cmꢀ 1
;
1H NMR (CDCl3)- d 1.06 (s, 9H, tert-butyl), 2.17 (d, J1’,2@ = 7.5 Hz of d, J3’,2@ = 7.0 Hz
of d, Jgem = 14.5 Hz, 1H, H-2@), 2.44 (d, J1’,2’ = 6.5 Hz of d, J3’,2’ = 3.5 Hz of d,
Jgem = 14.5 Hz, 1H, H-2’), 3.82 (two q, JF,H = 8.5 Hz, 4H for 2 ꢂ OCH2CF3), 3.88 (d,
J4’,5’ = 3.5 Hz of d, Jgem = 11.0 Hz, 1H of H-5’), 4.0 (d, J4’,5@ = 3.5 Hz of d, Jgem = 11.0
Hz, 1H, H-5@), 4.0 (quintet, J3’,4’ = J5’,4’ = J5@,4’ = 3.5 Hz, 1H, H-4’), 4.20 (d, J2@,3’ = 7.0 Hz
of d, J4’,3’ = 3.5 Hz, 1H, H-3’), 5.61 (s, 1H, 5-CH), 6.01 (d, J2’,1’ = 7.5 Hz of d, J2@,1’ = 6.5
Hz, 1H, H-1’), 7.25 (s, 1H, H-6), 7.30–7.60 (m, 10H, phenyls) and 8.24 (s, br, 1H, NH,
exchanges with deuterium) ppm; 19F NMR (CDCl3)- d 87.32 (t, JH,F = 8.0 Hz, for one
CH2CF3 moiety) and 87.35 (t, JH,F = 8.5 Hz, for other CH2CF3 moiety); 13C NMR
(CDCl3)- d 26.56 (CH3s of tert-butyl group), 29.67 (tertiary carbon of tert-butyl), 39.53
(C-2’), 61.20 (C-4’), 63.52 (C-5’), 64.18 (two q, merged, two OCH2CF3s, JF,C = 34.0 Hz),
84.72 (5-CH), 86.05 (C-3’), 97.49 (C-1’), 110.16 (C-5), 127.71–135.51 (aromatic carbons),
133.92 (q, JF,C = 278.0 Hz, two CF3), 138.98 (C-6), C-4 and C-2 were buried in the basal
line due to dilution of the sample; EI for SiC30H33F6N5O6 (701.60) found, M+ (1.5%).
5-[bis(2,2,2-Trifluoroethoxy)methyl]-3’ -azido-2’ ,3’ -dideoxyuridine (20). Tetra-
butyl ammonium fluoride solution in THF (0.22 mL, 0.22 mmol) was added to a solution
of 19 (95 mg, 0.135 mmol) in anhydrous tetrahydrofuran (5 mL) under nitrogen. The
contents were stirred at 25°C overnight, and then the solvent was removed in vacuo.
Chromatography of the crude residue on silica gel with 2% methanol in chloroform
afforded 20 as a semisolid: yield, 20 mg (32%); Rf 0.53 (CHCl3:MeOH, 9:1, v/v); IR
1
(neat)- 2120 cmꢀ 1 (N3 stretch); H NMR (CD3OD)-d 2.45 (t, J3’,2’–J1’,2@ = 6.2 Hz, 2H,
H-2@), 3.73 (d, J4’,5@ = 3.4 Hz of d, Jgem = 11.3 Hz, 1H, H-5@), 3.80 (d, J4’,5’ = 3.4 Hz of
d, Jgem = 11.3 Hz, 1H, H-5’), 3.98 (d, J5’,4’ = 3.4 Hz of d, J3’,4’ = 8.4 Hz, 1H, H-4’), 4.07
(two q, merged together, JF,H = 9.0 Hz, 4H of two OCH2CF3 groups), 4.32 (d,
J2@,3’ = 6.2 Hz of , J4’,3’ = 8.4 Hz, 1H, H-3’), 5.73 (s, 1H, CH(OCH2CF3)2), 6.14 (t,
d
J2’,1’ = J2@,1’ = 6.2 Hz, 1H, H-1’), and 8.22 (s, 1H, H-6) ppm; 19F NMR (CD3OD + C6F6)-
d 89.70 (t, JF,H = 9.0 Hz, for one OCH2CF3 group) and 89.65 (t, JF,H = 8.6 Hz, for
the other OCH2CF3 group) ppm; 13C NMR (CDCl3)- d30.72 (C-2’), 61.19 (C-4’), 62.12
(C-5’), 68.20 (two q, merged, two OCH2CF3, JF,C = 34.0 Hz), 86.53 (5-CH), 87.48 (C-3’),
98.20 (C-1’), 110.60 (C-5), 125.22 (q, JF,C = 272.0 Hz, two CF3), 140.36 (C-6), 151.53
(C-2) and 163.51 (C-4) ppm; LRMS- M+ (relative abundance 0.4%); HRMS-EI for
C14H15F6N5O6, calc. 463.0926 ; found, 463.0926, M+ 1.21%.
Threothymidine (12). 5’-O-tert-Butyldiphenylsilyl-3’-O-methanesulphonyl thymi-
dine 9 (4.45 g, 7.94 mmol) was dissolved in 98% EtOH (25 mL) and warmed to reflux.
A 10N aqueous solution of sodium hydroxide (1.27 g, 31.8 mmol in 32 mL water) was
added to this solution and the refluxing was continued for 4 h. A tlc examination at this
time showed complete disappearance of 5’-O-tert-butyldiphenylsilyl-3’-O-methanesul-
phonylthymidine. The mixture was cooled down to 25°C and acidified with 1N HCl to
pH 7.0, filtered, evaporated and purified on a silica gel column. The elution started
with chloroform and ended with 5% methanol to afford 1.29 g of pure 12 (70%): mp

ORDER
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Fluorinated 2’ ,3’ -Dideoxynucleosides
23
172–173°C (reported 170–171°C);[32] 1H NMR (D2O)- d 1.73 (s, 3H, 5-CH3), 1.91
(d, J1’,2@ = 2.5 Hz of d, Jgem = 15.0 Hz, 1H, H-2@), 2.57 (d, Jgem = 15.0 Hz of d
J1’,2’ = 8.5 Hz of d, J3’,2’ = 5.5 Hz, 1H, H-2’), 3.74 (d, J4’,5@ = 7.0 Hz of d,
Jgem = 13.5 Hz, 1H, H-5@), 3.90 (d, J4’,5’ = 4.5 Hz of d, Jgem = 13.5 Hz, 1H, H-5’),
3.95 (d, J5’,4’ = 4.5 Hz of d, J3’,4’ = 3.2 Hz of d, J5@,4’ = 7.0 Hz, 1H, H-4’), 4.33 (d,
J2’,3’ = 5.5 Hz of d, J4’,3’ = 3.0 Hz, 1H, H-3’), 6.00 (d, J2@,1’ = 2.5 Hz of d, J2’,1’ = 8.2 Hz,
1H, H-1’) and 7.73 (s, 1H, H-6) ppm.
3’ -Fluoro-3’ -deoxythymidine (13). Threothymidine (2.3 g, 9.5 mmol) was
dissolved in anhydrous dimethylformamide (10 mL) and triphenylmethyl chloride
(2.91 g, 10.45 mmol) was added to this solution under stirring at 25°C. This was followed
by the addition of N,N-dimethylaminopyridine (DMAP, 58 mg, 0.48 mmol) and heating
of the reaction mixture at 50°C for 4 h. Threothymidine was completely changed to its 5’-
trityl analog at this time. The solvent was evaporated on a rotary evaporator and ice/water
was poured into the resulting viscous mixture. A white solid precipitated (3.9 g, 85%) that
was filtered and washed thoroughly with cold water, dried over P2O5, re-dissolved in
anhydrous dichloromethane (150 mL) and then cooled to 0°C. Diethylaminosulfurtri-
fluoride (2.46 mL, 16.9 mmol) was added to this solution under stirring while the
temperature was maintained at 0°C.[33] The mixture was allowed to warm to 25°C once
the addition of DAST was over and stirred for further 4 h. The contents were poured into
a saturated solution of sodium bicarbonate (200 mL), and the organic phase was washed
with cold water and dried over anhydrous sodium sulfate. Evaporation of the solvent led
to a brown semi-crystalline mass that was treated with 80% acetic acid at 25°C.
Detritylation was complete after 3 h of acid treatment. The viscous mass, obtained after
evaporation of acetic acid, was purified on the silica gel column using 5% methanol in
chloroform as eluent to afford 1.28 g (65%) of pure 13; mp 178–179°C. Spectroscopic
data for this compound corresponded to literature data.[34]
3’ -Fluoro-5’ -O-tert-butyldiphenylsilyl-3’ -deoxythymidine (14). 3’-Fluoro-3’-
deoxythymidine 13 (0.4 g, 1.64 mmol) was dissolved in anhydrous pyridine (5 mL) and
tert-butyldiphenylchlorosilane (0.59 g, 2.13 mmol) was added to it while stirring. The
reaction was allowed to proceed overnight at 25°C and then quenched by adding ice/water
to the reaction mixture. The solvent was removed in vacuo and the impure product was
purified on a silica gel column. Elution with 20% ethyl acetate in toluene afforded 0.71 g
(90%) of 14: mp 72°C (softened); 1H NMR (CDCl3)- d 1.29 (s, 9H, tert-butyl group), 1.35
(s, 3H, CH3), 2.18 (d,
= 9.0 Hz of d, J3’,2@ = 5.0 Hz of d, Jgem = 14.5 Hz of d,
1’,2@
JF,H = 39.0 Hz, 1H, H-2@), 2.64 (d, J1’,2’ = 5.5 Hz of d, Hz of d, Jgem = 14.5 Hz,
JF,H = 20.9 Hz, 1H, H-2’), 3.87 (d, J4’,5@ = 2.0 Hz of d, Jgem = 11.5Hz, 1H, H-5@), 4.02 (d,
J4’,5’ = 1.5 Hz of d, Jgem = 11.5 Hz, 1H, H-5’), 4.29 (d, J5@,4’ = 2.0 Hz of d, J5’,4’ = 1.5 Hz
of d, JF,4’ = 28.0 Hz,1H, H-4’), 5.29 (d, J2@,3’ = 5.0 Hz of d, JF,3’ = 54.0 Hz, 1H, H-3’), 6.43
(d, J2’,1’ = 5.5 Hz of d, J2@,1’ = 9.5 Hz, 1H, H-1’), 7.38–7.72 (m, 11H, 10H of phenyls and
1H of H-6) and 8.08 (s, br, D2O exchangeable, 1H, NH) ppm; 19F NMR (CDCl3)- d -14.26
(d, J3’,F = 53.7 of d, J2@,F = 39.3 Hz of d, J2’,F = 20.9 Hz of d, J4’,F = 28.1 Hz) ppm; 13C
NMR (CDCl3)- d 11.99 (CH3 at C-5), 19.39 (tert-carbon of t-butyl group), 27.60 (methyl
carbons of tert-butyl group), 38.83 (d, JF,C = 21.3 Hz, C-2’), 63.92 (d, JF,C = 11.1 Hz,
C-5’), 84.57 (C-1’), 84.98 (d, JF,C = 25 Hz, C-4’), 94.64 (d, JF,C = 177.8 Hz, C-3’), 111.41

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Kumar et al.
(C-5), 134.84 (C-6), 135.50–128.07 (phenyl carbons), 147.60 (C-2) and 163.15 (C-4)
ppm; anal. calc. for SiC26H31FN2O4.1/4H2O (487.116); C, 64.02; H, 6.52; N, 5.75; found;
C,63.86; H, 6.65; N, 5.42.
5-(2,2,2-Trifluoroethoxymethyl)-3’ -fluoro-5’ -O-tert-butyldiphenylsilyl-2’ ,3’ -
dideoxyuridine (22). A solution of 14 (0.53 g, 1.08 mmol) in anhydrous CCl4 (25 mL)
was irradiated with a 75 W UV lamp and bromine (0.082 mL, 1.6 mmol) was added to it
slowly under reflux. This precursor completely changed to its 5-bromomethyl derivative
21 in 1 h. After the removal of excess bromine, HBr and the solvent, as described earlier,
this intermediate product was re-dissolved in anhydrous DME (25 mL) and added to
trifluoroethoxide-copper complex (3.24 mmol). The reaction was allowed to stir for 16 h at
25°C under argon. Work-up of the reaction was performed as described for the synthesis of
16. Purification of the impure product on a silica gel column with toluene:ethyl acetate
(80:20, v/v) gave 380 mg (60%) of pure 22: mp 55°C (softened); Rf 0.13 (toluene:ethyl
acetate; 80:20, v/v); 1HNMR (CDCl3)- d 1.08 (s, 9H, t-butyl group), 2.18 (d, J1’,2@ = 8.5
Hz of d, J3’,2@ = 5.0 Hz of d, Jgem = 14.0 Hz of d, JF,H = 39.0 Hz, 1H, H-2@), 2.77 (d,
J1’,2’ = 5.2 Hz of d, Jgem = 14.0 Hz of d, JF,H = 20.0 Hz, 1H, H-2’), 3.77 (q, JF,H = 8.5 Hz,
2H, CH2CF3), 3.87 (d, J4’,5@ = 3.0 Hz of d, Jgem = 11.5Hz, 1H, H-5@), 3.95 (d, J4’,5’ = 3.0
Hz of d, Jgem = 11.5 Hz, 1H, H-5’), 4.06 (d, Jgem = 12.0 Hz, 1H, CH2OCH2), 4.13 (d,
Jgem = 12.0 Hz, 1H, CH2OCH2), 4.31 (dd, J5@,4’ = J5’,4’ = 3.0 Hz of d, JF,4’ = 26.5 Hz,1H,
H-4’), 5.26 (d, J2@,3’ = 5.0 Hz, JF,3’ = 53.5 Hz, 1H, H-3’), 6.38 (d, J2’,1’ = 5.2 Hz of d,
J2@,1’ = 8.5 Hz, 1H, H-1’), 7.30–7.70 (m, 10H, phenyls), 7.73 (s, 1H, H-6) and 9.78 (s,
broad, D2O exchangeable, 1H, NH) ppm; 19F NMR (CDCl3)- d 87.24 (t, JH,F = 8.9 Hz,
CH2CF3), ꢀ 13.68 (d, J3’,F = 53.7 of d, J2@,F = 39.3 Hz of d, J2’,F = 20.3 Hz of d,
J4’,F = 27.0 Hz, 3’-F) ppm; 13C NMR (CDCl3)- d 26.92 (methyl carbons of t-butyl group),
29.64 (tert-carbon of tert-butyl group), 39.02 (d, JF,C = 20.7 Hz, C-2’), 63.67 (d,
JF,C = 10.2 Hz, C-5’), 66.51 (CH2OCH2), 68.39 (q, JF,C = 34.3 Hz, CH2CF3), 85.20 (d,
JF,C = 24.8 Hz, C-4’), 85.24 (C-1’), 93.93 (d, JF,C = 178.4 Hz, C-3’), 111.24 (C-5), 123.85
(q, JF,C = 280.1 Hz, CF3), 128.01–135.50 (phenyl carbons), 138.55 (C-6), 150.09 (C-2),
and 162.73 (C-4) ppm; anal. calc. for SiC28H32F4N2O5.1/2H2O (589.696); C, 57.03; H,
5.64; N, 4.75; found; C, 57.02; H, 5.64; N, 5.27.
5-(2,2,2-Trifluoroethoxymethyl)-3’ -fluoro-2’ ,3’ -dideoxyuridine (23). Com-
pound 22 (300 mg, 0.50 mmol) was desilylated by treating it with ammonium fluoride
(188 mg, 5.0 mmol, 10 equivalents) in refluxing ethanol (25 mL). The reaction was
complete in 45 min. The contents were cooled and the solvent was removed. The
mixture was purified on a silica gel column using CHCl3:MeOH (95:5, v/v) as elution
solvent to afford 130 mg (73%) of 23 as a semisolid: Rf 0.52 (CHCl3: MeOH, 9:1,
v/v); 1H NMR (CD3OD)- d 2.29 (d, J1’,2@ = 9.5 Hz of d, J3’,2@ = 5.5 Hz of d, Jgem = 14.0
Hz of d, JF,H = 39.0 Hz, 1H, H-2@), 2.57 (d, J1’,2’ = 5.5 Hz of d, Jgem = 14.0 Hz of d,
JF,H = 21.5 Hz, 1H, H-2’), 3.86 (d, J4’,5@ = 3.0 Hz of d, Jgem = 11.0Hz, 1H, H-5@), 3.91
(d, J4’,5’ = 3.0 Hz of d, Jgem = 11.0 Hz, 1H, H-5’), 4.00 (q, JF,H = 8.5 Hz, 2H,
CH2CF3), 4.27 (dd, J5’,4’ = J5’,4’ = 3.0 Hz of d, JF,4’ = 26.5 Hz,1H, H-4’), 4.38 (s, 2H,
CH2OCH2), 5.27 (d, J2@,3’ = 5.5 Hz, JF,3’ = 53.0 Hz, 1H, H-3’), 6.32 (d, J2’,1’ = 9.5 Hz of
d, J2@,1’ = 5.5 Hz, 1H, H-1’) and 8.11 (s, 1H, H-6) ppm; 19F NMR (CDCl3)- d 89.34 (t,
JH,F = 8.6 Hz, CH2CF3), ꢀ 11.36 (d, J3’,F = 53.6 of d, J2@,F = 38.9 Hz of d, J2’,F = 21.7
Hz of d, J4’,F = 27.3 Hz, 3’-F) ppm; 13C NMR (CDCl3)- d 39.43 (d, JF,C = 20.9 Hz, C-2’),

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Fluorinated 2’ ,3’ -Dideoxynucleosides
25
62.65 (d, JF,C = 11.0 Hz, C-5’), 67.80 (CH2OCH2), 68.62 (q, JF,C = 34.0 Hz, CH2CF3),
86.80 (C-1’), 87.16 (d, JF,C = 23.8 Hz, C-4’), 93.93 (d, JF,C = 178.4 Hz, C-3’), 111.24 (C-
5), 123.85 (q, JF,C = 280.1 Hz, CF3), 128.01–135.50 (phenyl carbons), 138.55 (C-6),
150.09 (C-2), and 162.73 (C-4) ppm; HRMS-EI for C12H14F4N2O5 calc. 342.0840; found;
342.0840; M+ present (1.76%).
5-[bis(2,2,2-Trifluoroethoxy)methyl]-3’ -fluoro-5’ -O-tert-butyldiphenylsilyl-2’ ,3’ -
dideoxyuridine (25). This product was prepared by reacting 14 (400 mg, 0.82 mmol)
with excess bromine (0.16 mL, 3.2 mmol) under UV irradiation using a similar procedure
as described above for synthesis of 22. Treatment of the 5-dibromomethyl intermediate
24 with trifluoroethoxide-copper complex (6.4 mmol) led to the formation of 25. This
impure product was purified on a silica gel column using toluene:ethyl acetate (80:20, v/
v) as elution solvent to give 290 mg (52%) of pure 25: Rf 0.23 (toluene:ethyl acetate,
80:20, v/v); mp 54°C (softened); 1H NMR (CDCl3)- d 1.04 (s, 9H, tert-butyl group), 2.20
(d, J1’,2@ = 10.0 Hz of d, J3’,2@ = 5.0 Hz of d, Jgem = 14.5 Hz of d, JF,H = 39.0 Hz, 1H, H-
2@), 2.71 (d, J1’,2’ = 5.2 Hz of d, Jgem = 14.5 Hz of d, JF,H = 20.5 Hz, 1H, H-2’), 3.86 (m,
2H, H-5’ and H-5@), 4.22 (q, JF,H = 8.5 Hz, 4H, two CH2CF3), 4.33 (dd,
J5@,4’ = J5’,4’ = 5.0 Hz of d, J3’,4’ = 4.5 Hz of d JF,4’ = 27.0 Hz,1H, H-4’), 5.13 (d,
J2@,3’ = 5.0 Hz, JF,3’ = 54.0 Hz, 1H, H-3’), 5.66 (s, 1H, CH(OCH2CF3)2), 6.10 (d,
J2’,1’ = 5.2 Hz of d, J2@,1’ = 10.0 Hz, 1H, H-1’), 7.35–7.76 (m, 10H, phenyls), 7.83 (s, 1H,
H-6) and 9.64 (s, broad, D2O exchangeable, 1H, NH) ppm; 19F NMR (CDCl3)- d 87.32
(t, JH,F = 10.9 Hz, CH2CF3), ꢀ 14.46 (d, J3’,F = 54.0 of d, J2@,F = 39.9 Hz of d,
J2’,F = 21.1 Hz of d, J4’,F = 25,8 Hz, 3’-F) ppm; 13C NMR (CDCl3)- d 26.77 (methyl
carbons of tert-butyl group), 29.61 (tert-carbon of tert-butyl), 38.39 (d, JF,C = 20.7 Hz,
C-2’), 63.10 (d, JF,C = 9.9 Hz, C-5’), 64.11 (two q, merged JF,C = 34.4 Hz, CH2CF3),
85.25 (d, JF,C = 24.6 Hz, C-4’), 86.07 (C-1’), 93.61 (d, JF,C = 178.4 Hz, C-3’), 97.52
(CH), 110.19 (C-5), 123.42 (q, JF,C = 278.3 Hz, CF3), 128.73–135.42 (phenyl carbons),
138.68 (C-6), 149.49 (C-2), and 161.42 (C-4) ppm; anal. calc. for SiC30H34F7N2O6
(679.66); C, 53.09; H, 4.90; N, 4.13; found; C, 53.27; H, 5.16; N, 4.22.
5-[bis(2,2,2-Trifluoroethoxy)methyl]-3’ -fluoro-2’ ,3’ -dideoxyuridine (26). The
silylated precursor 25 (250 mg, 0.37 mmol) was dissolved in methanol and ammonium
fluoride (136 mg, 3.7 mmol) was added under reflux. The reaction was allowed to
proceed for 45 min and then worked up as described in the synthesis of 23. Purification
of the reaction mixture, after evaporation of methanol, on a silica gel column using 5%
methanol in chloroform afforded 100 mg (62%) of pure 26: mp 55°C (softened); Rf
1
0.57 (CHCl3:MeOH, 9:1, v/v); H NMR (CDCl3)- d 2.31 (d, J1’,2@ = 10.0 Hz of d,
J2@,3’ = 4.5 Hz of d, Jgem = 14.0 Hz of d, JF,H = 39.5 Hz, 1H, H-2@), 2.63 (d, J1’,2’ = 5.2
Hz of d, Jgem = 14.0 Hz of d, JF,H = 20.5 Hz, 1H, H-2’), 3.73 (d, J4’,5’ = 3.0 Hz of d,
Jgem = 11.5 Hz of d JF,5’ = 1.5 Hz, 1H, H-5’), 3.80 (d, J4’,5’ = 3.0 Hz of d, Jgem = 11.5
Hz, 1H, H-5@), 4.08 (two q, merged, JF,H = 9.0 Hz, 4H, two CH2CF3), 4.32 (d,
JF,4’ = 26.0 Hz of t, J5@,4’ = J5’,4’ = 3.0 Hz,1H, H-4’), 5.26 (d, J2@,3’ = 4.5 Hz, JF,3’ = 53.0
Hz, 1H, H-3’), 5.74 (s, 1H, CH(OCH2CF3)2), 6.28 (d, J2’,1’ = 5.2 Hz of d, J2@,1’ = 10.0
Hz, 1H, H-1’) and 8.28 (s, 1H, H-6) ppm; 19F NMR (CDCl3)- d 89.45 (two t, merged
JH,F = 9.6 Hz, CH2CF3), ꢀ 11.31 (d, J3’,F = 53.0 of d, J2@,F = 39.5 Hz of d, J2’,F = 21.0
Hz of d, J4’,F = 25,8 Hz, 3’-F) ppm; 13C NMR (CDCl3)- d 39.81 (d, JF,C = 20.9 Hz, C-
2’), 62.64 (d, JF,C = 11.0 Hz, C-5’), 64.32 (two q, merged JF,C = 34.4 Hz and

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26
Kumar et al.
JF,C = 35.7, two CH2CF3), 87.43 (C-1’), 87.52 (d, JF,C = 22.6 Hz, C-4’), 96.68 (d,
JF,C = 178.4 Hz, C-3’), 98.52 (CH), 110.62 (C-5), 125.38 (q, JF,C = 277.4 Hz, CF3),
141.36 (C-6), 151.27 (C-2), and 163.70 (C-4) ppm; HRMS-EI for C14H15F7N2O6 calc.
440.0823; found; 440.0821; M+ present (0.51%).
5-(2,2,2-Trifluoroethoxymethyl)-5’ -O-trityl-3’ -keto-2’ ,3’ -dideoxyuridine (28).
Compound 1 (0.4 g; 1.18 mmol) was dissolved in anhydrous pyridine (20 mL) and
triphenylmethylchloride (0.334 mg, 1.2 mmol) was added to it under an atmosphere of
argon. N,N-Dimethylamino pyridine (15 mg) was also added to this mixture and the
reaction was allowed to stir at 25°C. Pyridine was evaporated in vacuo and the viscous
mass was triturated with ice/water. This resulted in the precipitation of corresponding
5’-trityl product 27 as a white solid that was filtered, washed with water, dried and then
oxidized without any further purification. A solution of 27 (0.33 g, 0.57 mmol) in
dichloromethane (20 mL) was pulverized and pre-dried molecular sieves (812 mg) were
added. Pyridinium dichromate (812 mg) was then added slowly and the mixture was
stirred vigorously. The oxidation was complete in 3 h (tlc). The solvent was evaporated
and the product was extracted with ethyl acetate/water (30:10 mL ꢂ 2). The organic
phase was dried over anhydrous sodium sulfate, filtered and the solvent was removed
to get a foamy material which was purified on a silica gel column. The elution started
with toluene and ended with 20% ethyl acetate to give 0.25 g, 37%) of pure 28: mp
1
202°C (dec.); Rf 0.54 (toluene:ethyl acetate, 8:2, v/v); H NMR (CD3OD) d 2.76 (d,
J1’,2@ = 8.0 Hz of d, Jgem = 18.5 Hz 1H, H-2@), 3.12 (d, J1’,2’ = 6.8 Hz of d,
Jgem = 18.5 Hz, 1H, H-2’), 3.38 (d, J4’,5@ = 2.5 Hz of d, Jgem = 11.0Hz, 1H, H-5@),
3.48 (d, Jgem = 11.5 Hz, 1H, CH2OCH2), 3.58 (q, JF,H = 8.5 Hz, 2H, CH2CF3), 3.68
(d, J4’,5’ = 2.5 Hz of d, Jgem = 11.0 Hz, 1H, H-5’), 3.89 (d, Jgem = 11.5 Hz, 1H,
CH2OCH2), 4.19 (t, J5@,4’ = J5’,4’ = 2.5 Hz,1H, H-4’), 6.52 (d, J2’,1’ = 6.8 Hz of d,
J2@,1’ = 8.5 Hz, 1H, H-1’), 7.14–7.54 (m, 15H, phenyls), 7.92 (s, 1H, H-6) and 8.04 (s,
br, 1H, NH) ppm; 19F NMR (CDCl3)- d 86.58 (t, JH,F = 8.6 Hz, CH2CF3) ppm; 13C
NMR (CDCl3)- d 42.04 (C-2’), 63.01 (C-5’), 66.07 (CH2OCH2), 68.43 (q, JF,C = 35.0
Hz, CH2CF3), 81.53 (C-1’ and C-4’), 87.66 (tertiary-C of trityl), 111.20 (C-5), 123.65
(q, JF,C = 286.8 Hz, CF3), 127.23–128.55 (phenyl), 139.05 (C-6), 149.95 (C-2), 162.40
(C-4) and 208.79 (C-3’) ppm; anal. for C31H27F3N2O6.3/4 H2O (609.81) calc. C 61.05,
H 4.46, N 4.61; found C 60.91, H 4.61 and N 4.30%.
5-(2,2,2-Trifluoroethoxymethyl)-5’ -O-trityl-3’ ,3’ -difluoro-2’ ,3’ -dideoxyuridine
(29). A solution of 28 (0.20 g, 0.33 mmol) in anhydrous dichloromethane (20 mL)
was cooled to 0°C. DAST (0.11 g, 0. 70 mmol) was slowly added under an argon
atmosphere. The contents were stirred at low temperature for 30 min and then allowed
to warm to 25°C. Stirring was continued for an additional 4 h. The reaction was
quenched by saturated solution of sodium bicarbonate (25 mL) and the product was
extracted in dichloromethane. The organic phase was dried over anhydrous sodium
sulfate, filtered and evaporated in vacuo. The viscous mass was purified on a silica gel
column. The elution started with toluene and ended with 20% ethyl acetate to give
0.11 g, 52%) of pure 29: mp 55°C (softened); Rf 0.16 (toluene:ethyl acetate, 8:2, v/v);
1H NMR (CD3OD)- d 2.56 (d, J1’,2@ = 8.0 Hz of d, Jgem = 18.5 Hz 1H, H-2@), 2.96 (d,
J1’,2’ = 6.8 Hz of d, Jgem = 18.5 Hz, 1H, H-2’), 3.46 (m, 2H, H-5’ and H-5@), 3.67 (q,
JF,H = 8.5 Hz, 2H, CH2CF3), 3.78 (d, Jgem = 12.5 Hz, 1H, CH2OCH2), 4.00 (d,

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Fluorinated 2’ ,3’ -Dideoxynucleosides
27
Jgem = 12.5 Hz, 1H, CH2OCH2), 4.20 (m, 1H, H-4’), 6.35 (d, J2’,1’ = 6.8 Hz of d,
J2@,1’ = 8.5 Hz, 1H, H-1’), 7.14–7.54 (m, 15H, phenyls), 7.70 (s, 1H, H-6) and 8.25 (s,
br, 1H, NH) ppm; 19F NMR (CDCl3)- d d 49.86 (m, J gem = 238.0 Hz, 3-F@), 63.59
(d, Jgem = 238.0 Hz of d, J2’,F’ = 15.0 Hz of d, J4’,F’ = 34.0 Hz, 3-F’), 86.61(t,
JH,F = 8.6 Hz, CH2CF3) ppm.
5-(2,2,2-Trifluoroethoxymethyl)-3’ ,3’ -difluoro-2’ ,3’ -dideoxyuridine (30). Acetic
acid (80%, 3 mL) was added to 29 (0.10 g, 0.16 mmol) and the contents were stirred at
25°C for 4 h. The solvent was evaporated in vacuo and the viscous mass was purified
on a silica gel column. Elution with 5% methanol in chloroform gave 50 mg (87%) of
pure 30: mp 55°C (softened); 1H NMR (CD3OD)- d 2.65 (d, J1’,2@ = 7.0 Hz of d,
Jgem = 14.0 Hz of d, J3F’,2@ = 14 Hz of d J3F@,2@ = 7.5 Hz, 1H, H-2@), 2.88 (d,
J1’,2’ = 7.0 Hz of d, Jgem = 14.0 Hz of d, J3F@,2’ = 15.0 Hz of d, J3F’,2’ = 7.0 Hz, 1H, H-
2’), 3.85 (m, br, 2H, H-5’ and H-5@), 4.01 (q, JF,H = 8.5 Hz, 2H, CH2CF3), 4.18 (d,
J5’,4’ = 3.8 Hz of d, J5@,4’ = 3.6 Hz of d, J3F’,4’ = 14.5 Hz of d, J3F@,4’ = 7.8 Hz, 1H, H-
4’), 4.40 (s, 2H, CH2OCH2), 6.30 (t, J2’,1’ = J2@,1’ = 7.0 Hz, 1H, H-1’) and 8.10 (s, 1H,
H-6) ppm; 19F NMR (CD3OD)- d 51.43 (m, J gem = 238.7 Hz, 3-F@), 65.44 (d,
Jgem = 238.8 Hz of d, J2’,F’ = 15.2 Hz of d, J4’,F’ = 33.4 Hz, 3-F’) and 89.31 (t,
JH,F = 8.8 Hz, CH2CF3) ppm; 13C NMR (CD3OD)- d 40.97 (t, JF,2’ = 23.8 Hz, C-2’),
60.19 (C-5’), 67.74 (CH2OCH2), 68.65 (q, JF,C = 34.0 Hz, CH2CF3), 83.26 (C-1’), 83.32
(t, JF,C = 25.1 Hz, C-4’), 112.17 (C-5), 127.51 (q, JF,C = 278.3 Hz, CF3), 127.75 (t,
JF,C = 247.9 Hz, C-3’), 140.75 (C-6), 151.90 (C-2), 164.80 (C-4) ppm; HRMS-EI for
C12H13F5N2O5 calc. 360.0759; found 360.0752, M+ 3.02%.
ACKNOWLEDGMENTS
The authors gratefully acknowledge the financial support from the Medical
Research Council of Canada (now Canadian Institutes for Health Research). We thank
Dr. V.V. Somayaji for his assistance in recording and interpreting the NMR spectra, Dr.
M. Daneshtalab, Mark Tempest and Cathy Koski (Synphar, Inc, Edmonton) for anti-
rhinovirus testing, Dr. Chris Tseng (NIH/NCI, Bethesda) for HSV-1 and HSV-2 tests,
and Dr. Michael Grever (NIH/NCI, Bethesda) for antitumor screening.
REFERENCES
1. Shugar, D. Virus-Cell Interactions and Viral Antimetabolites; Shugar, D., Ed.;
Academic Press: New York, 1972; 193.
2. Shugar, D. Progress with antiviral agents. FEBS Lett. 1974, 40, S48.
3. Prusoff, W.H.; Goz, B. Antineoplastic and Immunosuppressive Agents; Sartorelli,
A.C., Johns, D.G., Eds.; Springer-Verlag: West Berlin, 1975; Vol. 2, 272.
4. Gupta, S.V.; Tourigny, G.; Stuart, A.L.; De Clercq, E.; Quail, J.W.; Ekiel, I.; El-
Kabbani, O.A.L.; Delbaere, L.T.J. Relationship between structure and antiviral
activity of 5-methoxymethyl-2’-deoxyuridine and 5-methoxymethyl-1-(2’-deoxy-
beta-D-lyxofuranosyl) uracil. Antivir. Res. 1987, 7, 69–77.
5. Zoghaib, W.M.; Mannala, S.; Gupta, S.; Tourigny, G.; Reid, R.S. Synthesis,

ORDER
REPRINTS
28
Kumar et al.
conformation and anti-viral activity of 5-methoxymethyl-2’-deoxycitidine analogs.
Nucleosides Nucleotides Nucleic Acids 2003, 22, 223, 268.
6. Kaufman, H.E.; Warnel, E.D.; Thompson, H.W. Trifluridine, cidofovir and
penciclovir in the treatment of experimental herpetic keratitis. Arch. Ophthalmol.
1998, 116, 777–780.
7. Griengl, H.; Bodenteich, M.; Hayden, W.; Wanek, E.; Streicher, W.; Stutz, P.;
Bachmayer, H.; Ghazzauli, I.; Rosenwirth, B. 5-(Haloethyl)-2’-deoxyuridines: a
novel type of potent anti-viral nucleoside analogue. J. Med. Chem. 1985, 28, 1679–
1684.
8. Bergstrom, D.E.; Ruth, J.L.; Reddy, P.A.; De Clercq, E. Synthesis of (E)-5-(3,3,3-
trifluoro-1-propenyl)-2’,deoxyuridine and related analogues: potent and unusually
selective anti-viral activity of (E)-5-(3,3,3-trifluoro-1-propenyl)-2’deoxyuridine
against herpes simplex virus type-1. J. Med. Chem. 1984, 27, 274–284.
9. Sidwell, R.W.; Huffaman, J.H. Use of disposable micro tissue culture plates for
anti-viral and interferon induction studies. Appl. Microbiol. 1971, 22, 780–797.
10. De Clercq, E. Antiviral therapy for human immunodeficiency virus infections. Clin.
Microbiol. Rev. 1995, 8, 200–230.
11. De Clercq, E. Toward improved anti-HIV chemotherapy: therapeutic strategies for
intervention with HIV infections. J. Med. Chem. 1995, 38, 1517–2491.
12. Mitsuya, H.; Border, S. Inhibition of the in vitro infectivity and the cytopathic effect
of human T-lymphotropic virus type III/lymphoadenopathy-associated virus
(HTLV-III/LA V0 by 2’,3’-dideoxynucleosides). Proc. Natl. Acad. Sci. U. S. A.
1986, 83, 1911–1915.
13. Mitsuya, H.; Weinhold, K.J.; Furman, P.A.; St. Clair, M.; Lehrman, S.N.; Gallo,
R.C.; Bolognesi, D.; Barry, D.W.; Border, S. 3’-Azido-3’-deoxythymidine (BW
A509U): an antiviral agent that inhibits the infectivity and cytopathic effect of
human T-lymphotropic virus type III/lymphoadenopathy-associated virus in vitro.
Proc. Natl. Acad. Sci. U. S. A. 1985, 82, 7096–7100.
14. Baba, M.; Pauwels, P.; Herdewijn, P.; De Clercq, E.; Desmyter, J.; Vandeputte, M.
Both 2’,3’-dideoxythymidine and its 2’,3’-unsaturated derivative (2’,3’-dideoxy-
thymidinene) are potent and selective inhibitors of human immuno deficiency virus
replication in vitro. Biochem. Biophys. Res. Commun. 1987, 142, 128–134.
15. Hamamoto, Y.; Nakashima, T.; Matsui, T.; Matsuda, A.; Ueda, T.; Yamamoto, N.
Inhibotory effect of 2’,3’-didehydro-2’,3’-dideoxynucleosides on infectivity, cyto-
pathic effects and replication of immunodeficiency virus. Antimicrob. Agents.
Chemother. 1987, 31, 907–910.
16. Daluge, S.M.; Purifoy, D.J.M.; Savina, P.M.; St. Clair, M.H.; Parry, N.R.; Dev,
I.K.; Novak, P.; Ayers, K.M.; Reardon, J.E.; Roberts, G.B.; Fyfe, J.A.; Blum, M.R.;
Averett, D.R.; Dornsife, R.E.; Domin, B.A.; Ferone, R.; Lewis, D.A.; Krenitsky,
T.A. 5-Chloro-2’,3’-dideoxy-3’-fluorouridine (935U83), a selective anti-human
immunodeficiency virus agent with an improved metabolic and toxicological
profile. Antimicrob. Agents Chemother. 1994, 38, 1590–1603.
17. Baba, M.; Tanaka, E.; De Clercq, E.; Pauwels, R.; Balzarini, J.; Schols, D;
Nakashima, H.; Perno, C.-F.; Walker, R.T.; Miyasaka, T. Highly specific inhibition
of human immunodeficiency virus type 1 by a novel 6-substituted acyclouridine
derivative. Biochem. Biophys. Res. Commun. 1989, 165, 1375–1381.
18. De Clercq, E. Strategies in the design of antiviral drugs. Drug Discovery 2002, 11,
13–25.

ORDER
REPRINTS
Fluorinated 2’ ,3’ -Dideoxynucleosides
29
19. Pathak, T. Azidonucleosides: synthesis, reactions and biological properties. Chem.
Rev. 2002, 102, 1623–1667.
20. a. Kumar, P.; Wiebe, L.I. The synthesis of novel 5-trifluoroethyl ethers of
thymidine. Nucleosides Nucleotides 1990, 9 (6), 847–859. b. Kumar, P.; Wiebe,
L.I. The synthesis of novel trifluoroethoxy pyrimidine nucleosides. Nucleosides
Nucleotides 1990, 9 (6), 861–873.
21. Kumar, P.; Wiebe, L.I. Synthesis of novel fluorinated 2’,3’-dideoxynucleosides.
Nucleosides Nucleotides 1992, 11, 401–416.
22. Wardman, P.W.; Sarrif, A.M.; Heidelberger, C. Inhibition of nucleoside
phosphorylase cleavage of 5-fluoro-2’-deoxyuridine by 2,4-pyrimidinedione
derivatives. Biochem. Pharmacol. 1980, 29, 1059–1063.
23. Carmine, A.A.; Brogden, R.N.; Heel, R.C.; Speight, T.M.; Avery, G.S. Antiviral
2’,3’-dideoxynucleosides. Trifluridine: a review of its anti-viral activity and
therapeutic use in the treatment of viral eye infection 1982, 23, 329–353.
24. Cristol, S.J. meso-Dihydroanthracene chemistry: synthesis and mechanistic
information, 1,4-conjugate elimination. Acc. Chem. Res. 1971, 4, 393–400.
25. Rao, T.S.; Reese, C.B. A novel one step-procedure for conversion of thymidine into
2,3’-anhydrothymidine. J. Chem. Soc. Chem. Commun. 1989, 997.
26. Horowitz, J.P.; Chua, J. Nucleosides V. The monomesylates of 1-(2’-Deoxy-b-D-
lyxofuranosyl)thymine. J. Org. Chem. 1964, 29, 2076.
27. Vanheusden, V.; Munier-Lehmann, H.; Pochet, S.; Herdewijn, P.; Calenbergh, S.V.
Synthesis and evaluation of thymidine 5’-O-monophosphate analogues as inhibitors
of mycobacterium tuberculosis thymidylate kinase. Bioorg. Med. Chem. Lett. 2002,
12, 2695–2698.
28. Hanessian, S.; Lavalee, P. The preparation and synthetic utility of tert-
butyldiphenylsilyl ethers. Can. J. Chem. 1975, 53, 2975–2977.
29. Vander Kelen, G.P.; Eeckhaut, Z. C13 splitting in protein and fluorine nuclear
magnetic resonance spectra by halogenated aliphatic compounds. J. Mol. Spectrosc.
1963, 10, 141–151.
30. De Clercq, E. Minutes of European Symposium; Crommelin, D., Couvreur, P.,
Duchene, D., Eds.; France, 1994; 108–125.
31. Inoue, H.; Saito, N.; Ueda, T. Reaction of 5-brominated derivatives with
dimethylmalonate carbanion. A novel entry to the synthesis of uridine-5-acetic
acids. Chem. Pharm. Bull. 1986, 34, 4585–4589.
32. Horton, D.; Sakata, M. Synthesis of purine and pyramidine 2’-deoxynucleosides
from a 1,2-dithio sugar precursors. Carbohydrate Res. 1976, 48, 41–63.
33. Herdewijn, P.; Balzarini, J.; De Clercq, E.; Pauwels, R.; Baba, M.; Border, S.;
Vanderhaeghe, H. 3’-Substituted 2’,3’-dideoxynucleoside analogs as potential anti-
HIV (HTLV-III/LAV) agents. J. Med. Chem. 1987, 30, 1270–1278.
34. Fleet, G.W.J.; Son, J.C.; Derome, A.E. Methyl 5-O-tert-butyldiphenylsilyl-2-deoxy
a, b-D-threo pentofuranosides as a divergent intermediate for the synthesis of 3’-
substituted-2’3’-dideoxynucleosides: synthesis of 3’-azido-3’-deoxythymidine, 3’-
deoxy-3’-fluorothymidine and 3’-cyano-3’-deoxythymidine. Tetrahedron 1988, 44,
625–636.
Received August 6, 2003
Accepted September 13, 2003

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