β-Selective synthesis of 2′-deoxy-5,6-dihydro-4-thiouridine, a precursor of the unstable nucleoside product of ionising radiation damage 2′-deoxy-5,6-dihydrocytidine

Article abstract of DOI:10.1039/b502302e

4-Thio oxathiaphosphepane nucleosides 2-4 undergo a rearrangement in pyridine that leads selectively to the β anomer of the 2′-deoxy-5,6- dihydro-4-thiouridine derivative 5. This diastereoselective reaction proceeds through a multistep mechanism initiated

Full text of DOI:10.1039/b502302e

View Article Online / Journal Homepage / Table of Contents for this issue
A R T I C L E
b-Selective synthesis of 2ꢀ-deoxy-5,6-dihydro-4-thiouridine, a
precursor of the unstable nucleoside product of ionising radiation
damage 2ꢀ-deoxy-5,6-dihydrocytidine
Fre´de´ric Peyrane and Pascale Clivio*
Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91190,
Gif-sur-Yvette, France
Received 15th February 2005, Accepted 10th March 2005
First published as an Advance Article on the web 24th March 2005
4-Thio oxathiaphosphepane nucleosides 2–4 undergo a rearrangement in pyridine that leads selectively to the b
anomer of the 2ꢀ-deoxy-5,6-dihydro-4-thiouridine derivative 5. This diastereoselective reaction proceeds through a
multistep mechanism initiated by the addition of pyridine at the C1ꢀ position of 2–4 and concomitant opening of the
oxathiaphosphepane. This was confirmed by the trapping of the corresponding intermediate in the closely related
DMAP series. In contrast, LR thiation of 1 in pyridine leads to a new class of modified nucleosides 12 containing an
oxathiaphospholane moiety. The quantitative conversion of 5 into the corresponding 5,6-dihydrocytosine derivative
with NH3–MeOH is also reported.
Introduction
Results and discussion
Exposure of DNA to ionising radiation induces the formation of
5,6-dihydrocytosine (DHC).1 Under biological conditions, this
primary base damage undergoes hydrolytic deamination to give
rise to 5,6-dihydrouracil (DHU) which is currently considered
to be the species responsible for the mutagenic properties of
DHC.2,3 However, the lifespan of DHC in DNA is unknown, nor
are its intrinsic mutagenic properties and its repair. To address
these points, DHC-containing oligodeoxynucleotides (ODNs)
and, therefore, DHC derivatives are highly desirable. Synthesis
of DHC by catalytic hydrogenation of cytosine derivatives
is frequently accompanied by concomitant deamination and
overhydrogenation.4 Consequently, alternative strategies have
been developed and 5,6-dihydro-4-thiouracil has been proved
to be a useful synthetic intermediate in the nucleobase and
ribose series.5 The deoxyribose series is known to be more
labile towards thiation reagents than the base or ribonucleoside
series.6 In this series, our first attempts at thiation of the disilyl
derivative of 2ꢀ-deoxy-5,6-dihydrouridine (1) have revealed that
the use of P4S10 leads exclusively to degradative material whereas
the use of one molar equivalent of Lawesson’s reagent (LR)
gives rise to the corresponding thiated compound 5, though
in poor yield.7 However, the use of two molar equivalents
of LR leads to oxathiaphosphepanes 2–4 (93%◦yield) whose
subsequent thermal rearrangement (dioxane, 85 C, 2 h) gives
rise to 5 and its a anomer 6 (75 : 25 ratio, 58% yield).7 We now
report a modified procedure that allows the diastereoselective
synthesis of the 2ꢀ-deoxy-5,6-dihydro-4-thiouridine derivative in
the b anomeric form (5) from oxathiaphosphepanes 2–4. The
subsequent quantitative conversion of 5 into the 2ꢀ-deoxy-5,6-
dihydrocytidine derivative 15 is also reported.
1
b-Selective synthesis of 5 from oxathiaphosphepanes 2–4
Access to the mixture of oxathiaphosphepanes 2–4 in high
yield and its possible thermal transformation into 2ꢀ-deoxy-
5,6-dihydro-4-thiouridine compounds 5 and 67 prompted us to
examine this transformation more closely. Though no reaction
occurred when the 2–4 mixture was allowed to stand at rt for
24 h in dioxane, to our delight we observed that stirring the 2–4
mixture in pyridine at rt for 24 h led exclusively to 5 in 57% yield
after column chromatography.8 Interestingly, when 2 (b anomer)
was treated in pyridine at rt for 1 h, a mixture composed of 2–5
(50, 31, 7 and 12%, respectively) was obtained; after 3 h, the
respective yields were 35, 34, 9 and 21%. This clearly indicated
that during the process leading to the b-selective formation of
5, oxathiaphosphepane 2 partially epimerized, leading to its
phosphorus diastereomer 3. Epimerization at the C1ꢀ position
led to a anomer 4, elimination of AnPS2/cyclization led to 5.
2
Proposed mechanisms
Reactivity in dioxane.
Formation of oxathiaphosphepanes 2–4 in the thiation reaction.
We have previously proposed that reaction between LR and
1 proceeds through a cyclic oxonium intermediate that opens
to give Schiff base 77 whose cyclization yields 2 and 3, or 4
after rotation of the C1ꢀ-C2ꢀ bond. However, so far, we have
not considered the stereochemical parameters governing the
observed yield of each oxathiaphosphepane during the thiation
of 1 conducted with two eq. of LR. Since 2 and 3 (both
b oxathiaphosphepane anomers) are the major compounds
obtained, their favoured formation is likely to be induced by
the neighbouring non-participating a-oriented silyl substituant
at the C3ꢀ position of 7 and/or consecutively to the stabilisation
(by p-stacking and/or ionic bonds) of a conformation in
which the base moiety is b-configurated. Additionally, that
compound 2 (Rp) is the major isomer formed reflects the
preferred anti orientation adopted by the An group, with respect
to the dihydropyrimidine, in order to avoid steric constraints.
Accordingly, in the minor a series, only 4 (dihydropyrimidine
and An anti) is observed, diastereomer 8 being unfavoured.
Thermal transformation of oxathiaphosphepanes 2–4. The
thermal conversion of the 2–4 mixture (50 : 35 : 15) into 5 and 6
(58%, 75 : 25, respectively) also involves the participation of the
T h i s j o u r n a l i s
T h e R o y a l S o c i e t y o f C h e m i s t r y 2 0 0 5
O r g . B i o m o l . C h e m . , 2 0 0 5 , 3 , 1 6 8 5 – 1 6 8 9
1 6 8 5
©

View Article Online
Schiff base intermediate 7.7 It is likely that thermal conditions
increase the yield of the less favoured a anomer 6 by allowing or
easing the C1ꢀ-C2ꢀ bond rotation of 7.
cyclization and concomitant elimination of AnPS2 leads to 5
(path c, Scheme 1), and pyridine elimination leads to 7 (path d,
Scheme 1).
However, 9 could not be isolated. To ascertain the C1ꢀ addition
of the pyridine, we investigated the reactivity of the 2–4 mixture
in the presence of DMAP. Treatment of a dichloromethane
solution of the 2–4 mixture with DMAP (1 eq.) led to a
mixture of two separable isomers (10a and b) in 6 and 19%
yield, respectively, for which dimethylaminopyridinyl insertion
was supported by HRMS (10a: calcd 877.3448, found 877.3423;
10b: calcd 877.3448, found 877.3478). Addition of DMAP onto
Reactivity in pyridine. Whereas heating (100 ◦C) of 2–4 in
dioxane or pyridine led to 5 and 6, treatment with pyridine
for 24 h at rt led exclusively to 5. It is likely that in this latter
case, the precursor of 5 is 9 (Scheme 1) which results from the
nucleophilic attack of pyridine on 2 or 3 C1ꢀ-position.9 From
9, oxathiaphosphepanes 2 and 3 can be obtained consecutively
to a S-directed cyclization (path a or b, Scheme 1); O-directed
Scheme 1
1 6 8 6
O r g . B i o m o l . C h e m . , 2 0 0 5 , 3 , 1 6 8 5 – 1 6 8 9

View Article Online
the oxathiaphosphepane skeleton C1ꢀ position was evidenced
by its downfield 13C chemical shift (10a d 75.5; 10b d 74.7 vs.
d 57.1–58.6 for 2–4).10 Observation of a correlation between
C1ꢀ and o-protons of DMAP on the1H-13C HMBC spectrum
further confirmed the DMAP substitution location. Therefore,
compounds 10a and 10b are diastereomers at their C1ꢀ position
and their isolation fully supports the hypothesis of a C1ꢀ addition
of pyridine.
Thus, we believe that 12a–d are isomers at their C3ꢀ and
P position. A formation mechanism involving an oxonium
intermediate at the C3ꢀ position to assist the elimination of
the silyloxy group is proposed (Scheme 2). Pyridine-initiated
abstraction of an acidic proton at the C2ꢀ position of 13 could
lead to olefinic compounds 13a (path a) or 13b (path b), both
affording 14. Subsequent cyclisation of 14 would then lead to 12.
4
Synthesis of the 2ꢀ-deoxy-5,6-dihydrocytidine derivative 15
from 5
Displacement of the thiocarbonyl function by NH3 is known
to be very efficient in the 5,6-dihydropyrimidine series.5 Indeed,
when 5 was treated with NH3–MeOH at rt, its conversion to
the 5,6-dihydrocytosine derivative occurred smoothly and 15
[HRMS (calcd 514.3496, found 514.3489); 13C NMR (d 165.0
(C4), 28.6 (C5))] was obtained in quantitative yield (Scheme 3).
Alternatively, if 9 undergoes pyridine elimination, Schiff base
7 is obtained (path d, Scheme 1). Following the mechanism
depicted for the reactivity in dioxane, 7 can afford 2, 3 or 4.
Addition of pyridine on the C1ꢀ position of 4 leads to 11. The
exclusive isolation of 5 in pyridine, whereas 6 is also obtained in
dioxane, suggests that the kinetics of the pyridinium elimination
or of the S-oriented cyclisation are faster than the O-oriented
cyclisation (the lack of formation of 8 has been previously
explained; vide supra).
3
Thiation in pyridine
As the treatment of oxathiaphosphepane nucleosides 2–4 with
pyridine at rt selectively afforded 5, we investigated the thiation
reaction of 1 in this solvent. When treated with 2 eq. of LR at
85 ◦C in pyridine, 1 remained unaltered. Only the use of 10 eq.
◦
of LR at 100 C allowed the consumption of 1 in 30 min, but
Scheme 3
instead of 5, we obtained, as major compounds, a mixture of
four isomers 12a–d. The main isomer was isolated in 20% yield.
Its NMR data were in good agreement with the presence of a
5,6-dihydro-4-thiouracil moiety (13C: d 201.6 (C4), 40.2 (C6),
Conclusion
The b-selective synthesis of the delicate 5,6-dihydrocytosine de-
oxynucleoside derivative using the thiation/amination pathway
can be achieved in three steps and an overall yield of 53%.
Further work to prepare ODNs containing site specifically DHC
using a suitably protected DHC, or a 4-thio-DHU, derivative is
currently in progress in our laboratory.
1
38.4 (C5); H: d 9.10 (NH), 3.18 (H5)), confirming thiation at
the C4 position. The HRMS spectrum revealed the occurrence
of only one thexyldimethylsilyl group (calcd 595.1320, found
595.1358, C24H37N2O4PS3Si) and confirmed the presence of an
1
AnPS2 unit by the signals on the H NMR spectrum (d 7.98,
6.95, 3.88) along with the signal at d 99.4 on the 31P NMR
spectrum. In addition, the presence of an ethylenic moiety in
the vicinity of the dihydropyrimidine (1H NMR: d H1ꢀ 7.36,
H2ꢀ 5.04; 13C NMR: d C1ꢀ 128.3, C2ꢀ 105.0)10 suggested the
oxathiaphospholane nature of 12.
Experimental
LR was purchased from Acros (Noisy Le Grand, France).
Dioxane was freshly distilled under argon over sodium–
benzophenone. Pyridine and dichloromethane were dried over
Scheme 2
O r g . B i o m o l . C h e m . , 2 0 0 5 , 3 , 1 6 8 5 – 1 6 8 9
1 6 8 7

View Article Online
˚
CaH2, distilled and stored on 4 A molecular sieves. Methanol
Analytical samples were obtained by HPLC using an Hypersil
HS (250 × 10 mm) column and an isocratic eluent consisting of
isopropanol–heptane 0.3% at a flow rate of 5 mL min−1. 230 nm
detection: 2 rt, 13 min; 3 rt, 29 min; 4 rt, 25 min
was distilled over magnesium methoxide. Chromatography was
performed on Chromagel 60 silica (35–70 lm) from SDS
(Peypin, France) and preparative TLC were home-made using
Kieselgel 60 PF254 silica from Merck. NMR experiments were
performed on Bruker AC-250, AM-300, AMX-400 spectrome-
ters. Chemical shifts (d) are reported in ppm relative to residual
solvent peak (CHCl3 dH 7.26, dC 77.4; CH3CN dH 1.96, dC
1.79.) 31P Chemical shifts are reported relative to an external
capillary standard of 85% phosphoric acid. High resolution
mass spectra were recorded on Micromass LCT (ESI, CH3OH)
and PerSeptive Biosystems Voyager-DE STR (MALDI, 2,5-
dihydroxybenzoic acid).
For convenience, the numbering system of the nucleoside
series has been used for compounds 2–4, 10, and 12. Ho,
Hm and Ci, Co, Cm, Cp in 2–4, 10, and 12 refer to the
An group signals, in ortho, meta and ipso, ortho, meta and
para, respectively with respect to the phosphorus substitution.
Prime index in 10 refers to the DMAP signals with respect
to the C1ꢀ substitution. Superscript (a) and (b) labels indicate
interchangeable assignments within a compound.
Oxathiaphosphepane 2. dH (250 MHz; CDCl3) 8.85 (1H, s,
NH), 7.93 (2H, dd, Jo,m 8.8 Hz, JP,o 14.3 Hz, Ho), 6.93 (2H,
dd, Jo,m 8.8 Hz, JP,m 3.4 Hz, Hm), 6.43 (1H, m, H1ꢀ), 4.90 (1H,
m, H4ꢀ), 4.18 (1H, m, H6a), 4.13 (1H, m, H3ꢀ), 3.95 (2H, m,
H5ꢀH5ꢀꢀ), 3.85 (3H, s, OCH3), 3.74 (1H, m, H2ꢀ(a)), 3.70 (1H, m,
H6b), 3.14 (2H, m, H5aH5b), 1.96 (1H, m, H2ꢀꢀ(a)), 1.65 (2H, m,
H-Tex), 0.93–0.83 (8 × 3H, m, CH3-Tex), 0.14–0.08 (4 × 3H,
m, CH3–Si); dC (75 MHz; CDCl3)203.2 (C4), 163.4 (JP,p 3.0 Hz,
Cp), 148.5 (C2), 133.3 (JP,o 13.9 Hz, Co), 126.9 (JP,i 121.4 Hz,
Ci), 114.0 (JP,m 16.2 Hz, Cm), 85.4 (JP,4 12.0 Hz, C4ꢀ), 67.9 (C3ꢀ),
ꢀ
63.7 (JP,5 10.4 Hz, C5ꢀ), 57.1 (JP,1 3,5 Hz, C1ꢀ), 55.6 (OCH3),
ꢀ
ꢀ
39.7 (C6), 39.5 (C5), 37.2 (JP,2 5.3 Hz, C2ꢀ), 34.1 (CH-Tex),
ꢀ
25.4/24.9 (C-Tex), 20.4/18.6 (CH3-Tex), −3.0/−3.2 (CH3–Si);
dP (121.5 MHz; CDCl3) 89.9; HRMS (MALDI) (M + Na)+
Calcd for C32H57N2O5PS3Si2Na 755.26035, found 755.26206.
Oxathiaphosphepane 3. dH (250 MHz; CDCl3)8.80 (1H, s,
NH), 7.91 (2H, dd, Jo,m 8.8 Hz, JP,o 13.8 Hz, Ho), 7.00 (2H,
2ꢀ-Deoxy-5,6-dihydro-3ꢀ,5ꢀ-di-O,Oꢀ-thexyldimethylsilyluridine (1)
dd, Jo,m 8.8 Hz, JP,m 3.6 Hz, Hm), 6.16 (1H, td, J4 ,5 = JP,4
ꢀ
ꢀ
ꢀ
12.1 Hz, J4 ,5 3.0 Hz, H1ꢀ), 4.92 (1H, m, H4ꢀ), 4.56 (1H, m, H3ꢀ),
3.98 (2H, m, H5ꢀH5ꢀꢀ), 3.89 (3H, s, OCH3), 2.80–2.64 (4H, m,
H5aH5b, H6aH6b), 2.56 (1H, m, H2ꢀ(a)), 1.89 (1H, m, H2ꢀꢀ(a)),
1.67 (2H, m, H-Tex), 0.94–0.89 (24H, m, CH3-Tex), 0.16–0.10
(12H, m, CH3–Si); dC (75 MHz; CDCl3)202.4 (C4), 162.9 (JP,p
3.3 Hz, Cp), 148.0 (C2), 132.5 (JP,o 13.2 Hz, Co), 128.9 (JP,i
ꢀ
ꢀꢀ
A suspension of 2ꢀ-deoxyuridine (2.0 g, 8.77 mmol) in MeOH
(100 mL) containing rhodium on alumina (5%, 500 mg) was
hydrogenated at 35 psi for 4 h in a Parr apparatus. Then, the
reaction mixture was filtered on celite. The filtrate was concen-
trated to give a residue, which was repeatedly co-evaporated with
diethyl ether to afford 2ꢀ-deoxy-5,6-dihydrouridine as a white
solid in quantitative yield. dH (250 MHz; CD3OD) 6.26(1H,
129.5 Hz, Ci), 114.4 (JP,m 16.5 Hz, Cm), 78.5 (JP,4 7.1 Hz, C4ꢀ),
ꢀ
66.3 (C3ꢀ), 62.3 (JP,5 7.7 Hz, C5ꢀ), 58.6 (JP,1 6.6 Hz, C1ꢀ), 55.7
ꢀ
ꢀ
dd, J1 ,2 7.9 Hz, J1 ,2 6.4 Hz, H1ꢀ), 4.28 (1H, dt, J3 ,2 6.5 Hz,
ꢀ
ꢀ
ꢀ
ꢀꢀ
ꢀ ꢀ
(OCH3), 39.3/38.1 (C6,C5), 37.2 (JP,2 2.2 Hz, C2ꢀ), 34.4/34.2
ꢀ
J3 ,2 = J3 ,4 3.3 Hz, H3ꢀ), 3.76 (1H, m, H4ꢀ), 3.65 (2H, m,
ꢀ
ꢀꢀ
ꢀ ꢀ
(CH-Tex), 25.3/25.0 (C-Tex), 20.6/20.4 (CH3-Tex), 18.8/18.6
(CH3-Tex), −2.2/−3.3 (CH3–Si); dP (121.5 MHz; CDCl3)89.6;
HRMS (MALDI) (M + Na)+ Calcd for C32H57N2O5PS3Si2Na
755.26035, found 755.26576.
H5ꢀH5ꢀꢀ), 3.57 (1H, m, H6a), 3.42 (1H, m, H6b), 2.62 (2H, m,
ꢀ
ꢀꢀ
ꢀ
ꢀ
ꢀ ꢀ
H5aH5b), 2.20 (1H, ddd, J2 ,2 13.5 Hz, J1 ,2 7.9 Hz, J3 ,2 6.5 Hz,
H2ꢀ(a)), 1.98 (1H, ddd, J1 ,2 6.4 Hz, J3 ,2 3.3 Hz, J2 ,2 13.5 Hz,
H2ꢀꢀ(a)); dC (75 MHz; CD3OD) 173.0 (C4), 154.9 (C2), 87.4 (C4ꢀ),
85.3 (C1ꢀ), 72.4 (C3ꢀ), 63.3 (C5ꢀ), 37.5 (C2ꢀ), 36.9 (C6), 31.9 (C5);
HRMS (ESI) (M + Na)+ Calcd for C9H14N2O5Na 253.0800,
found 253.0791.
ꢀ
ꢀꢀ
ꢀ
ꢀꢀ
ꢀ ꢀꢀ
Oxathiaphosphepane 4. dH (300 MHz; CDCl3) 8.75 (1H, s,
NH), 8.05 (2H, dd, Jo,m 8.9 Hz, JP,o 14.5 Hz, Ho), 7.00 (2H, dd,
ꢀ
ꢀ
ꢀ
Jo,m 8.9 Hz, JP,m 3.7 Hz, Hm), 5.88 (1H, dd, J4 ,5 10.3 Hz, JP,4
Dry 2ꢀ-deoxy-5,6-dihydrouridine (1.0 g, 4.35 mmol) obtained
by repeated coevaporation with anhydrous pyridine was dis-
solved in anhydrous pyridine (3 mL). To this solution imidazole
(1.2 g, 17.4 mmol) and thexyldimethylsilyl chloride (2.52 mL,
13.0 mmol) were added. The mixture was stirred at rt for
16 h. The solvent was then evaporated and the crude material
partitioned between dichloromethane and brine. The organic
phase was dried with Na2SO4 and evaporated to give a residue
purified by column chromatography on silica gel using a gradient
of EtAc in heptane (10–30%) as the eluent to afford 1 (2.23 g,
99%) as a colourless oil, which solidified after several days at rt.
7.4 Hz, H4ꢀ), 4.77 (1H, m, H1ꢀ), 4.19 (1H, m, H4ꢀ), 4.04 (1H,
m, H5ꢀ(a)), 3.87 (3H, s, OCH3), 3.86 (1H, m, H5ꢀꢀ(a)), 3.46 (2H,
m, H6aH6b), 3.06 (2H, m, H5aH5b), 2.69 (1H, m, H2ꢀꢀ(b)), 2.35
(1H, m, H2ꢀ(b)), 1.61 (2H, m, H-Tex), 0.90–0.83 (24H, m, CH3-
Tex), 0.18–0.10 (12H, m, CH3–Si); dC (75 MHz; CDCl3)202.1
(C4), 163.3 (JP,p 3.0 Hz, Cp), 148.0 (C2), 133.0 (JP,o 14.2 Hz,
Co), 127.0 (JP,i 133.2 Hz, Ci), 114.0 (JP,m 16.9 Hz, Cm), 79.1
(JP,4 6.8 Hz, C4ꢀ), 67.3 (JP,3 2.2 Hz, C3ꢀ), 62.7 (C5ꢀ), 57.3 (JP,1
ꢀ
ꢀ
ꢀ
5.2 Hz, C1ꢀ), 55.5 (OCH3), 46.6 (C2ꢀ), 39.3 (C5), 38.8 (C6), 34.1
(CH-Tex), 25.4/25.0 (C-Tex), 20.5/20.3 (CH3-Tex), 18.7/18.6
(CH3-Tex), −2.16-(-3.1) (CH3–Si); dP (121.5 MHz; CDCl3) 88.3;
HRMS (MALDI) (M + Na)+ Calcd for C32H57N2O5PS3Si2Na
755.26035, found 755.26357.
ꢀ
ꢀ
ꢀ ꢀꢀ
dH (250 MHz; CDCl3) 7.96 (1H, s, NH), 6.28 (1H, t, J1 ,2 = J1 ,2
7.0 Hz, H1ꢀ), 4.35 (1H, m, H3ꢀ), 3.78 (1H, m, H4ꢀ), 3.70 (2H, m,
H5ꢀH5ꢀꢀ), 3.65 (1H, m, H6a), 3.29 (1H, ddd, J6b,6a 12.4 Hz, J6b,5a
9.1 Hz, J6b,5b 5.6 Hz, H6b), 2.59 (2H, m, H5aH5b), 1.97 (2H,
m, H2ꢀH2ꢀꢀ), 1.62 (2H, m, H-Tex), 0.87 (4 × 3H, d, J = 7.0 Hz,
CH3-Tex), 0.84 (4 × 3H, s, CH3-Tex); 0.10 (4 × 3H, m, CH3–Si);
dC (62.5 MHz; CDCl3)·169.9 (C4), 152.2 (C2), 86.3 (C4ꢀ), 83.9
(C1ꢀ), 71.8 (C3ꢀ), 62.8 (C5ꢀ), 37.6 (C2ꢀ), 35.4 (C6), 34.2 (CH-
Tex), 31.2 (C5), 25.4 and 24.9 (C-Tex), 20.4 and 18.6 (CH3-Tex),
−2.5 and −2.7 (CH3–Si), −3.4 and −3.5 (CH3–Si); HRMS (ESI)
(M + Na)+ Calcd for C25H50N2O5Na 537.3156, found 537.3177.
Reaction of 2–4 in pyridine: 2ꢀ-deoxy-5,6-dihydro-3ꢀ,5ꢀ-di-O,Oꢀ-
thexyldimethylsilyl-4-thiouridine (5)
Compounds 2–4 (133 mg, 0.18 mmol) were dissolved in pyridine
(10 mL), and the solution was stirred at rt for 24 h. The
solvent was evaporated and the residue was purified by column
chromatography using a gradient of EtAc in heptane (10–20%)
as the eluent yielding 5 (55 mg, 57%) as a yellowish glassy film.
ꢀ
ꢀ
ꢀ ꢀꢀ
dH (250 MHz; CDCl3) 8.99 (1H, s, NH), 6.25 (1H, t, J1 ,2 = J1 ,2
7.1 Hz, H1ꢀ), 4.34 (1H, m, H3ꢀ), 3.79 (1H, m, H4ꢀ), 3.70 (2H, m,
H5ꢀH5ꢀꢀ), 3.62 (1H, m, H6a), 3.29 (1H, ddd, J6b,6a 12.4 Hz, J6b,5a
9.0 Hz, J6b,5b 5.1 Hz, H6b), 3.02 (2H, m, H5aH5b), 1.97 (2H, m,
H2ꢀH2ꢀꢀ), 1.62 (2H, m, H-Tex), 0.89 and 0.86 (4 × 3H, 2s, CH3-
Tex), 0.83 (4 × 3H, d, J = 7 Hz, CH3-Tex), 0.11, 0.10, 0.09, 0.08
(4 × 3H, 4s, CH3–Si); dC (75 MHz; CDCl3) 203.6 (C4), 148.8
(C2), 86.6 (C4ꢀ), 84.1 (C1ꢀ), 71.9 (C3ꢀ), 62.8 (C5ꢀ), 39.6 (C5), 37.7
(C2ꢀ), 36.1 (C6), 34.2/34.1 (CH-Tex), 25.4/24.9 (C-Tex), 20.4
Preparation of oxathiaphosphepanes 2–4
To a solution of 1 (100 mg, 0.19 mmol) in dioxane (1 mL) was
added LR (157 mg, 0.39 mmol). The reaction was stirred at 85 ◦C
for 20 min. After filtration on cotton, the filtrate was concen-
trated to give a residue, which was briefly chromatographed on
silica gel, using EtAc–heptane 10% as the eluent, affording 2–4
(133 mg, 93%, 60 : 31 : 9 estimated by 1H NMR) as a yellow foam.
1 6 8 8
O r g . B i o m o l . C h e m . , 2 0 0 5 , 3 , 1 6 8 5 – 1 6 8 9

View Article Online
ꢀꢀ
ꢀ
ꢀ ꢀ
and 20.3 (CH3-Tex), 18.6 and 18.5 (CH3-Tex), −2.5 and −2.7
(CH3–Si), −3.4 and −3.5 (CH3–Si); HRMS (MALDI) (M +
Na)+ Calcd for C25H50N2O4SSi2Na 553.29276, found 553.29278.
Reaction of 2–4 with DMAP (10a and b): To a solution of
compounds 2–4 (133 mg, 0.19 mmol) in CH2Cl2 (3 mL) was
added DMAP (23 mg, 0.18 mmol). The mixture was stirred at rt
for 40 h, the solvent was evaporated and the crude material was
purified on silica gel column chromatography using a gradient
of MeOH in CH2Cl2 (3–5%) as the eluent. Compounds 10a and
10b were separated by preparative TLC (MeOH–CH2Cl2 3%,
4 times elution) yielding 10a (10 mg, 6%) and 10b (29 mg, 19%)
as pale yellow solids.
H4ꢀ), 4.08 (dd, 1H, J5 11.7 Hz, J5 ,4 2.3 Hz, H5ꢀ(a)), 3.88 (3H, s,
,5
OCH3), 3.83 (1H, m, H5ꢀꢀ(a)), 3.62 (2H, t, J6,5 6.5 Hz, H6aH6b),
3.18 (2H, t, J6,5 6.5 Hz, H5aH5b), 1.63 (1H, m, H-Tex), 0.90
(2 × 3H, d, J 7 Hz, CH3-Tex), 0.89 (2 × 3H, s, CH3-Tex),
0.11 and 0.09 (2 × 3H, 2s, CH3–Si); dC (75 MHz; CDCl3) 201.6
(C4), 163.3 (JP,p 3.3 Hz, Cp), 146.8 (C2), 133.7 (JP,o 14.8 Hz,
Co), 128.3 (C1ꢀ), 127.5 (JP,i 122.4 Hz, Ci), 113.9 (JP,m 16.5 Hz,
Cm), 105.0 (JP,2 7.7 Hz, C2ꢀ), 85.5 (JP,4 4.9 Hz, C4ꢀ), 60.5 (JP,5
ꢀ
ꢀ
ꢀ
13.2 Hz, C5ꢀ), 56.3 (C3ꢀ), 55.6 (OCH3), 40.2 (C6), 38.4 (C5), 34.2
(CH-Tex), 25.4 (C-Tex), 20.4 and 20.3 (CH3-Tex), 18.7 and 18.6
(CH3-Tex), −3.3 and −3.5 (CH3–Si), dP (121.5 MHz; CDCl3)
99.4; HRMS (ESI) (M + Na)+ Calcd for C24H37N2O4PS3SiNa
595.1320, found 595.1358.
Compound 10a. dH (400 MHz; CD3CN) 9.81 (1H, s, NH),
8.34 (2H, d, Jo ,m 7.9 Hz, Hoꢀ), 8.07 (2H, dd, JP,o 13.2 Hz, Jo,m
ꢀ
ꢀ
2ꢀ-Deoxy-5,6-dihydro-3ꢀ,5ꢀ-di-O,Oꢀ-thexyldimethylsilylcytidine
8.8 Hz, Ho), 6.86 (2H, dd, Jo,m 8.8 Hz, JP,m 2.5 Hz, Hm), 6.77
(15)
ꢀ
ꢀ
ꢀ
ꢀ
ꢀꢀ
ꢀ ꢀ
(2H, d, Jo ,m 7.9 Hz, Hm ), 6.58 (1H, dd, J1 ,2 9.6 Hz, J1 ,2 6.2 Hz,
H1ꢀ), 4.49 (1H, m, H4ꢀ), 3.99 (1H, m, H3ꢀ), 3.79 (3H, s, OCH3),
Compound 5 (35 mg, 0.06 mmol) was treated with a saturated
solution of methanolic ammonia (3 mL) for 20 min at rt. The
volatile materials were then evaporated to yield 15 (34 mg,
quantitative) as a colourless film. dH (300 MHz; CDCl3) 6.31
3.75–3.48 (4H, m, H5ꢀH5ꢀꢀ, H6aH6b), 3.25–3.17 (7H, m, H2ꢀ(a)
,
N(CH3)2), 3.02 (2H, t, J5,6 6.5 Hz, H5aH5b), 2.53 (1H, m, H2ꢀꢀ(a)),
1.68–1.49 (2H, m, H-Tex), 0.91–0.75 (24H, m, CH3-Tex), 0.08-(-
0.03) (12H, m, CH3–Si); dC (75 MHz; CD3CN) 206.1 (C4), 161.6
(1H, t, J1 ,2 = J1 ,2 7.1 Hz, H1ꢀ), 4.30 (1H, m, H3ꢀ), 3.74 (1H,
m, H4ꢀ), 3.66 (2H, m, H5ꢀH5ꢀꢀ), 3.54 (1H, m, H6a), 3.18 (1H,
m, H6b), 2.60 (2H, m, H5aH5b), 1.93 (2H, m, H2ꢀH2ꢀꢀ), 1.60
(2H, m, H-Tex), 0.86 (4 × 3H, d, J 7 Hz, CH3-Tex), 0.83
and 0.82 (2 × (2 × 3H), 2s, CH3-Tex), 0.08 (12H, m, CH3–
Si); dC (75 MHz; CDCl3) 165.0 (C4), 156.3 (C2), 86.0 (C4ꢀ), 84.0
(C1ꢀ), 71.9 (C3ꢀ), 62.8 (C5ꢀ), 37.3 (C2ꢀ), 35.7 (C6), 34.2 (CH-Tex),
28.6 (C5), 25.4/24.9 (C-Tex), 20.3/18.6 (CH3-Tex), −2.5/−2.7
(CH3–Si), −3.4/−3.5 (CH3–Si); HRMS (ESI) (M + H)+ Calcd
for C25H52N3O4Si2 514.3496, found 514.3489.
ꢀ
ꢀ
ꢀ ꢀꢀ
(Cp), 157.9 (Cpꢀ), 150.9 (C2), 141.9 (Coꢀ), 132.9 (JP,o 13.1 Hz,
Co), 113.2 (JP,m 14.2 Hz, Cm), 108.5(Cmꢀ), 77.6 (JP,4 7.6Hz, C4 ),
ꢀ
ꢀ
75.5 (C1ꢀ), 69.6 (JP,3 4.3 Hz, C3ꢀ), 62.7 (C5ꢀ), 56.0 (CH3O), 41.6
ꢀ
(C6), 40.8 (CH3N), 40.7 (C5), 37.1 (C2ꢀ), 34.9 (CH-Tex), 25.9
(C-Tex), 20.9/20.7 (CH3-Tex), 18.9/18.8 (CH3-Tex), −2.9/−3.0
(CH3–Si); dP (121.5 MHz; CD3CN) 109.5; HRMS (ESI) (M +
Na)+ Calcd for C39H67N4O5PS3Si2Na 877.3448, found 877.3423.
Compound 10b. dH (300 MHz; CD3CN) 9.86 (1H, s, NH),
8.20 (2H, d, Jo ,m 7.9 Hz, Hoꢀ), 8.07 (2H, dd, JP,o 13.4 Hz, Jo,m
ꢀ
ꢀ
8.8 Hz, Ho), 6.87–6.83 (4H, m, Hmꢀ, Hm), 6.43 (1H, dd, J1 ,2
ꢀ
ꢀ
5.3 Hz, J1 ,2 10.2 Hz, H1ꢀ), 4.58 (1H, ddt, JP,4 17.3 Hz, J4 ,3
Acknowledgements
ꢀ
ꢀꢀ
ꢀ
ꢀ
ꢀ
7.2 Hz, J4 ,5 = J4 ,5 3.6 Hz, H4ꢀ), 4.16 (1H, m, H3ꢀ), 3.94–
ꢀ
ꢀ
ꢀ ꢀꢀ
We thank the Ligue Nationale Contre le Cancer for a doctoral
fellowship to F.P.
3.79 (5H, m, H6a, H5ꢀ(a), OCH3), 3.66 (1H, dd, J5 ,4 3.6 Hz,
ꢀ
ꢀ
J5 ,5 10.0 Hz, H5ꢀꢀ(a)), 3.47 (1H, m, H6b), 3.24–3.13 (8H, m,
ꢀ
ꢀꢀ
H5a, N(CH3)2, H2ꢀ(b)), 3.00 (1H, m, H5b), 2.36 (1H, ddd, J2 ,2
ꢀ
ꢀꢀ
14.0 Hz, J1 ,2 10.2 Hz, J3 ,2 7.8 Hz, H2ꢀꢀ(b)), 1.68–1.48 (2H,
m, H-Tex); 0.91–0.75 (8 × 3H, m, CH3-Tex); 0.08-(−0.03)
(4 × 3H, m, CH3–Si); dC (100 MHz; CD3CN) 206.2 (C4),
161.5 (JP,p 3.5 Hz, Cp), 157.9 (Cpꢀ), 151.5 (C2), 141.5 (Coꢀ),
138.1 (JP,i 115.0 Hz, Ci), 132.4 (JP,o 13.2 Hz, Co), 113.1 (JP,m
14.6 Hz, Cm), 108.5 (Cmꢀ), 77.0 (C4ꢀ), 74.7 (C1ꢀ), 70.6 (C3ꢀ),
References
ꢀ
ꢀꢀ
ꢀ ꢀꢀ
1 M. Dizdaroglu, J. Laval and S. Boiteux, Biochemistry, 1993, 32,
12105–12111.
2 J. Liu, W. Zhou and P. W. Doetsch, Mol. Cell. Biol., 1995, 15, 6729–
6735.
3 J. Liu and P. W. Doetsch, Nucleic Acids Res., 1998, 26, 1707–1712.
4 (a) C. Janion and D. Shugar, Acta Biochim. Pol., 1960, 7, 309–329
and references cited; (b) A. R. Hanze, J. Am. Chem. Soc, 1967, 89,
6720–6725.
5 (a) D. M. Brown and M. J. E. Hewlins, J. Chem. Soc. C, 1968, 2050–
2055; (b) V. Skaric, B. Gaspert, M. Hohnjec and G. Lacan, J. Chem.
Soc., Perkin Trans. 1, 1974, 267–271.
6 K. Felczak, M. Bretner, T. Kulikowski and D. Shugar, Nucleosides
Nucleotides, 1993, 12, 245–261.
7 F. Peyrane, J.-L. Fourrey and P. Clivio, Chem. Commun., 2003, 736–
62,6 (JP,5 3.5 Hz, C5ꢀ), 55.9 (OCH3), 41.1 (C5), 40.8 (CH3N),
ꢀ
39.8 (C6), 37.2 (C2ꢀ), 34.9/34.8 (CH-Tex), 25.9/25.7 (C-Tex),
20.7/20.6 (CH3-Tex), 18.9/18.7 (CH3-Tex), −3.0/−3.1 (CH3–
Si); dP (121.5 MHz; CD3CN) 110.8; HRMS (ESI) (M + Na)+
Calcd for C39H67N4O5PS3Si2Na 877.3448, found 877.3478.
Compound 12. To a solution of 1 (50 mg, 0.01 mmol) in
pyridine (0.8 mL) was added LR (393 mg, 0.97 mmol). The
◦
737.
mixture was stirred at 100 C for 30 min. Chromatography on
8 The b-configuration of the anomeric center of 5 was deduced from a
NOE between H1ꢀ and H4ꢀ.
silica gel using CH2Cl2 provided a mixture of isomers from which
the major one was isolated by preparative TLC (CH2Cl2, 3 times
elution) yielding 12 (11.5 mg, 20%) as a pale yellow film. dH
(250 MHz; CDCl3) 9.10 (1H, s, NH), 7.98 (dd, 2H, JP,o 15.0 Hz,
9 Since we did not observed any epimerisation in dioxane at rt, it is
unlikely that 9 results from the addition of pyridine to 7. However,
this possibility cannot be totally discarded.
Jo,m 8.7 Hz, Ho), 7.36 (1H, d, J1 ,2 13.8 Hz, H1ꢀ), 6.95 (2H, dd,
10 Assignments were performed by 2D 1H-1H and 1H-13C NMR
experiments.
ꢀ
ꢀ
J
o,m 8.7 Hz, JP,m 3.4 Hz, Hm), 5.04 (2H, m, H2ꢀ,H3ꢀ), 4.54 (1H, m,
O r g . B i o m o l . C h e m . , 2 0 0 5 , 3 , 1 6 8 5 – 1 6 8 9
1 6 8 9