Study on disulfur-backboned nucleic acid: Part 1, efficient synthesis of 3′,5′-dithio-2′-deoxyadenosine

Article abstract of DOI:10.1055/s-2004-834809

An efficient procedure is established to synthesize 3′,5′- dithio-2′-deoxyadenosine starting from 2′-deoxyadenosine in five steps in 33% overall yield. In this procedure, the key intermediate 9 was synthesized by twice S_N2 reactions with twice

Full text of DOI:10.1055/s-2004-834809

LETTER
2585
Study on Disulfur-Backboned Nucleic Acid: Part 1, Efficient Synthesis of
3¢,5¢-Dithio-2¢-Deoxyadenosine
S
tudyonDisulfur-
o
BackbonedN
n
ucleic
A
cidgchao Zheng, Changmei Cheng,* Hua Wang, Shanshan Xu, Yufen Zhao
Key Laboratory for Bioorganic Phosphorus Chemistry of Education Ministry, Department of Chemistry, School of Life Sciences and
Engineering, Tsinghua University, 100084 Beijing, P. R. China
Fax +86(10)62781695; E-mail: chengcm@mail.tsinghua.edu.cn
Received 17 July 2004
DNu
DNu
S
M
S
DNu
DNu
DNu
DNu
S
S
DNu
Abstract: An efficient procedure is established to synthesize 3¢,5¢-
dithio-2¢-deoxyadenosine starting from 2¢-deoxyadenosine in five
steps in 33% overall yield. In this procedure, the key intermediate 9
was synthesized by twice SN2 reactions with twice 3¢-configuration
inversions and then it was deprotected to title compound by remov-
ing three acyl groups in one pot.
R
O
S
C
R
S
S
P
S
DNu
O
Key words: 3¢,5¢-dithio-2¢-deoxynucleoside, 3¢,5¢-dithio-2¢-deoxy-
adenosine, disulfur-backboned nucleic acid, configuration inver-
sions, synthesis
DNu=2′-deoxynucleoside
R=H, Me; M=Hg2+, Cd2+, etc.
Figure 1 Disulfur-backbones of novel nucleic acid.
3¢-Thio-2¢-deoxynucleoside and 5¢-thio-2¢-deoxynucleo-
side are important monomers1a,b that can be used in anti- ture to selectively remove the ester-benzoyl group and get
sense and RNAi fields. But little work has been devoted compound 5 in 70% yield. If the reaction time was longer
to studying 3¢,5¢-dithio-2¢-deoxynucleoside. Recently, we than 30 minutes, further debenzoylation of the 6-amide
started a project to synthesize a series of disulfur- would occur.
backbones2a,b (Figure 1) of novel nucleic acids and to ap-
ply them to the study of antisense, RNAi, nucleic acids
probe and the origin of nucleic acid. However, the synthe-
sis of 3¢,5¢-dithio-2¢-deoxy-nucleoside tends to be cum-
bersome and low-yielding. This is mainly due to the
following two reasons. One is the difficult 3¢-configura-
tion inversion, which will cause many side reactions. The
other is that 3¢,5¢-dithio-2¢-deoxynucleoside is too easily
oxided to disulfides.3 Recently, two approaches to synthe-
size 3¢,5¢-dithio-2¢-deoxynucleoside have been described.
The first one is to synthesize 3¢,5¢-dithiothymidine start-
ing from thymidine.2a Although the method is good, it is
not suitable for the synthesis of purine analogues. The sec-
ond one is to prepare 3¢,5¢-dithio-2¢-deoxyadenosine from
3¢,5¢-dithiothymidine by nucleobase exchange with ade-
nine.2b This procedure took six steps and produced both a-
and b-nucleosides which is not easy to be separated.
NHBz
NH2
N
N
N
N
N
N
N
N
BzO
HO
a
O
O
OH
OH
2
1
b (1)
NHBz
NHBz
NHBz
N
N
N
N
N
N
N
N
N
N
N
N
HO
BzO
b (2)
HO
OH
OH
OBz
O
+
O
O
3
5
4
In this paper, we would like to report an efficient synthesis
Scheme 1 Reaction conditions: (a) (1) BzCl, C5H5N; (2) Me3SiCl,
of 3¢,5¢-dithio-2¢-deoxyadenosine starting from 2¢-deoxy- BzCl, MeOH, NH3, 80%; (b) (1) (CF3SO2)2O, C5H5N, CH2Cl2, H2O;
(2) MeOH, MeONa, 70%.
adenosine. Firstly, we use TfO- as leaving group and H2O
as nucleophile to realize the first 3¢-configuration inver-
sion by a modified procedure (Scheme 1) of Ishido4 and
Secondly, compound 9 was synthesized as shown in
Scheme 2. In this procedure, we employed MsO- as a
Herdewijn.5 Thus, 2¢-deoxyadenosine (1) was smoothly
benzoylated to afford 2 and subsequently 2 was converted
into 3 and 4 (3:7 by NMR determination) according to the
literature procedure. Then the mixture of 3 and 4 was
treated with NaOMe–MeOH 5 minutes at room tempera-
leaving group and AcSK as a nucleophile to realize the
second 3¢-configuration inversion (from 6 to 9). Thus,
compound 5 was converted into compound 6 by treatment
with MsCl in pyridine. Then, compound 6 and AcSK were
mixed in dioxane and the suspensions were heated to a
certain temperature. We found that even though the sus-
pension was heated at 40 °C for more than 4 days, no
change occurred. When compound 6 was heated at 50 °C
SYNLETT 2004, No. 14, pp 2585–2587
2
2
.1
1
.2
0
0
4
Advanced online publication: 20.10.2004
DOI: 10.1055/s-2004-834809; Art ID: U20504ST
© Georg Thieme Verlag Stuttgart · New York

2586
H. Zheng et al.
LETTER
for 3 days, only 5¢-MsO- had been replaced by -SAc,
while 3¢-MsO- still kept unchanged. As a result, com-
pound 8 was isolated in 81% yield. When the heating tem-
perature reached 60 °C, we found that both 3¢-MsO- and
5¢-MsO- were replaced by -SAc after 36 hours. But if the
heating temperature increased to 70 °C or more, com-
pound 4 underwent elimination to form compound 7 and
the compound 9 could not be generated. The side products
7 and 8 had been identified by mass spectra and the 3¢-
configuration of 10 was determined by nuclear Overhaus-
er effects (1H NOE). Irradiation of the 3¢-proton of the
deoxyribose moiety gave a significant nuclear Overhauser
enhancement of 5.1% at the 2¢Hb-proton, and nearly gave
no enhancement at the 4¢-proton (0.1%) and at the 2¢Ha-
proton (0.3%, Figure 2).
NHBz
NHBz
NHBz
N
N
N
N
N
N
N
N
N
N
N
N
b
HO
AcS
MsO
OH
OMs
a
O
O
O
SAc
9
6
5
c
e or f
d
NH2
N
NHBz
NHBz
N
N
N
N
N
N
N
N
N
N
N
HS
AcS
AcS
OMs
O
O
O
SH
10
7
8
NH2
Scheme 2 Reaction conditions: (a) MsCl, C5H5N, 91%; (b) AcSK,
Dioxane, N2, 60 °C, 36 h, 77%; (c) AcSK, Dioxane, N2, 70 °C or
more; (b) AcSK, Dioxane, N2, 50 °C, 3 days, 81%; (e) LiAlH4, THF,
HCl, N2, 71%; (f) EtSH, EtSNa, N2, 85%.
5.1%
N
N
HS
N
H
H
N
O
0.1%
ture and distilled; 1,4-dioxane was dried by sodium and distilled;
THF was freshly distilled under nitrogen after sodium treatment.
Thin layer chromatography (TLC) was performed on silica gel F254
and the spots were examined with UV light and sulfuric acid–etha-
nol spray. All experiments were carried out in dried glassware. The
–30 °C and 0 °C external bath temperatures designated are approxi-
mate as achieved by a dry ice-acetone or ice baths. Column chroma-
tography was carried out using silica gel (100–200 mesh).
H
H
HS
H
0.3%
Figure 2 Illustration of nuclear Overhauser enhancements for 10.
Finally, we synthesized the target compound 10 by two
ways (Scheme 2). Initially, we successfully used LiAlH4
as reducing agent to deprotect compound 9 in 4 hours, but
the work up was time consume. In another procedure, we
treated compound 9 with EtSNa–EtSH under nitrogen at-
mosphere. The reaction completed in five minutes and all
three acyl groups were removed at the same time. Then
the mixture was neutralized with acetic acid and exacted
with chloroform. After the solution was dried and evapo-
rated, the residual oil was saturated with diethyl ether to
precipitate compound 10 in 85% yields. This procedure
not only had a good yield, but also avoided the formation
N6,5¢-Dibenzoyl-2¢-deoxyadenosine (2)
To a stirred solution of 2¢-deoxyadenosine (2.0 g, 8.0 mmol) in py-
ridine (30 mL) was added dropwise a solution of benzoyl chloride
(1.0 mL, 8.8 mol) in pyridine (20 mL) at room temperature in 30
min. To this solution were added in turn chlorotrimethylsilane (5.1
mL, 40 mmol) and benzoyl chloride (2.8 mL, 24 mmol) dropwise.
After further stirring for 1.5 h, the resulting mixture was quenched
with MeOH (10 mL), and treated with ammoniacal MeOH (sat. at 0
°C, 60 mL) dropwise at 0 °C. The resulting solution was, after stir-
ring for 30 min at r.t., evaporated and the residue was distributed be-
tween CHCl3 and H2O. The syrup obtained by evaporating the
organic solution after drying over anhyd MgSO4, was purified by
of disulfide bonds. We also used EtONa–EtOH instead of column chromatography (CH2Cl2–MeOH 20:1), yielding 2.94 g
(6.4 mmol, 80%) of compound 2. 1H NMR (DMSO-d6): d = 11.15
EtSNa–EtSH to treat compound 9 and as a result, the com-
pound 9 was converted to some side products that may be
a series of disulfide-linked oligonucleosides.
(1 H, s, NH), 8.67 (1 H, s, adenine), 8.61 (1 H, s, adenine), 7.40–
8.10 (10 H, m, phenyl), 6.48 (1 H, dd, J = 6.5, 6.5 Hz, 1¢-H), 5.56 (1
H, d, J = 4.1 Hz, 3¢-OH), 4.69 (1 H, ddd, J = 4.1, 4.1, 6.2 Hz, 4¢-H),
In summary, we have developed an efficient route for the
preparation of 3¢,5¢-dithio-2¢-deoxyadenosine (10) start-
ing from 2¢-deoxyadenosin in five steps in 33% overall
yield. Furthermore, this method is also suitable for the
preparation of other 3¢,5¢-dithio-2¢-deoxynucleosides. The
further work to develop antisense drug and to study the
origin of nucleic acid is on progress.
4.57 (1 H, dd, J = 4.1, 12.0 Hz, 5¢-H), 4.46 (1 H, dd, J = 6.2, 12.0
Hz, 5¢¢-H), 4.19 (1 H, dddd, J = 3.3, 4.1, 4.1, 4.7 Hz, 3¢-H), 3.01 (1
H, ddd, J = 3.4, 6.5, 12.4 Hz, 2¢-H), 2.47 (1 H, ddd, J = 4.8, 6.5, 12.4
Hz, 2¢¢-H). ESI-MS: m/e = 460 [M + H]+, 240 [adenine + H]+.
N6-Benzoyl-9-(2¢-deoxy-b-D-threo-pentofuranosyl) Adenine (5)
A suspension of 1.84 g (4.0 mmol) of 2 in anhyd CH2Cl2 (100 mL)
and pyridine (4 mL) was cooled to –30 °C and 10 mL of trifluo-
romethanesulfonic anhydride (10% vol. in CH2Cl2) was added
dropwise. The reaction mixture was stirred in air for 30 min till it
became complete clear. After addition of H2O (2 mL), the emulsion
was further stirred for 3 h at r.t. Then 10 mL H2O was added, and
the organic layer was separated, dried, evaporated and co-evaporat-
ed with toluene to remove pyridine. The residual oil was diluted
with 100 mL of anhyd MeOH and 100 mg sodium in MeOH was
added. The suspension was stirred for 5 min at r.t., neutralized with
HOAc, evaporated, and purified by column chromatography
1H NMR spectra were obtained on JOEL JNM-ECA600 and JOEL
JNM-ECA300 spectrometers. Mass spectra were recorded with a
Bruker ESQUIRE-LC ion trap spectrometer equipped with a gas
nebulizer probe, capable of analyzing ions up to m/e 6000. Dichlo-
romethane was treated for 16 hours with P2O5 and distilled; pyridine
was refluxed overnight over potassium hydroxide and distilled;
methanol was dried by magnesium overnight at refluxing tempera-
Synlett 2004, No. 14, 2585–2587 © Thieme Stuttgart · New York

LETTER
Study on Disulfur-Backboned Nucleic Acid
2587
(CH2Cl2–MeOH 9:1),yielding 1.00 g (2.8 mmol, 70%) of com-
pound 5. 1H NMR (DMSO-d6): d = 11.19 (1 H, s, NH), 8.75 (1 H,
s, adenine), 8.67 (1 H, s, adenine), 7.50–8.10 (5 H, m, phenyl), 6.45
(1 H, dd, J = 7.9, 7.9 Hz, 1¢-H), 5.53 (1 H, d, J = 4.1 Hz, 3¢-OH),
4.71 (1 H, dd, J = 5.7, 5.7 Hz, 5¢-OH), 4.40 (1 H, ddd, J = 2.3, 7.0,
7.0 Hz, 4¢-H), 3.99 (1 H, dddd, J = 2.3, 4.1, 8.4, 8.4 Hz, 3¢-H), 3.75
(1 H, ddd, J = 5.7, 7.0, 11.7 Hz, 5¢-H), 3.64 (1 H, ddd, J = 5.7, 7.0,
11.7 Hz, 5¢¢-H), 2.81 (1 H, ddd, J = 7.9, 8.4, 14.4 Hz, 2¢-H), 2.37 (1
H, ddd, J = 7.9, 8.4, 14.4 Hz, 2¢¢-H). ESI-MS: m/e = 356 [M + H]+,
378 [M + Na]+, 240 [base + H]+.
3¢,5¢-Dithio-2¢-deoxyadenosine (10)
Method A: A suspension of 30.4 mg (0.800 mmol) of LiAlH4 in an-
hyd THF (5 mL) was cooled to 0 °C and a solution of 47.1 mg
(0.100 mmol) compound 9 in 5 mL THF was added dropwise under
nitrogen. After the reaction mixture was stirred for 4 h at 0 °C, the
resulting solution was treated with 1 N HCl to adjust the pH value
of the solution to 4.0. Then 20 mL CHCl3 was added, and the organ-
ic layer was separated, dried, and evaporated. The residual oil was
purified by column chromatography (CH2Cl2–MeOH 20:1) and 20
mg (0.071 mmol, 71%) of compound 10 was yielded.
Method B: To a solution of compound 9 (47.1 mg, 0.100 mmol) in
5 mL EtSH, was added 10 mg (0.120 mmol) EtSNa under nitrogen.
The suspension was stirred for 5 min at r.t. and neutralized with
HOAc. Then 20 mL EtOAc was added and the organic layer was
separated, dried, and evaporated. The residual oil was saturated
with 5 mL Et2O and the precipitate was collected by filtration and
washed with cold Et2O (4 × 1 mL) to give the title compound 10 (24
mg, 0.085 mmol, 85%).1H NMR (DMSO-d6 containing one drop of
D2O): d = 8.37 (1 H, s, adenine), 8.21 (1 H, s, adenine), 6.40 (1 H,
dd, J = 6.5, 6.5 Hz, 1¢-H), 4.52 (1 H, ddd, J = 3.4, 3.4, 3.4 Hz, 4¢-H),
4.04 (1 H, ddd, J = 2.8, 3.0, 5.8 Hz, 3¢-H), 3.74 (1 H, dd, J = 4.1,
12.4 Hz, 5¢-H), 3.64 (1 H, dd, J = 4.1, 12.4 Hz, 5¢¢-H), 2.73 (1 H,
ddd, J = 2.8, 6.2, 13.5 Hz, 2¢-H), 2.44 (1 H, ddd, J = 6.2, 7.5, 13.8
Hz, 2¢¢-H). ESI-MS: m/e = 284 [M + H]+, 306 [M + Na]+.
N6-Benzoyl-9-(3¢,5¢-di-O-methylsulfonyl-2¢-deoxy-b-D-threo-
pentofuranosyl) Adenine (6)
To a solution of compound 5 (532.5 mg, 1.50 mmol) in 10 mL py-
ridine was added dropwise a solution of 0.3 mL (3.90 mmol) MsCl
in 2.0 mL pyridine at 0 °C. After removal of the cooling bath, the
reaction mixture was further stirred for 12 h at r.t. Then 5 mL ice
water and 20 mL CHCl3 were added, and the organic layer was sep-
arated, dried, evaporated and co-evaporated with toluene to remove
pyridine. The residual oil was purified by column chromatography,
eluted with EtOAc, yielding 697.5 mg (1.37 mmol, 91%) of com-
pound 6. 1H NMR (DMSO-d6): d = 11.23 (1 H, s, NH), 8.78 (1 H,
s, adenine), 8.53 (1 H, s, adenine), 7.50–8.10 (5 H, m, phenyl), 6.58
(1 H, dd, J = 3.0, 7.7 Hz, 1¢-H), 4.53–4.70 (2 H, m, 3¢-H and 4¢-H),
4.51 (1 H, dd, J = 4.5, 11.3 Hz, 5¢-H), 3.80 (1 H, dd, J = 5.9, 11.3
Hz, 5¢¢-H), 3.35 (3 H, s, 3¢-Me), 3.24 (3 H, s, 5¢-Me), 3.14 (1 H, ddd,
J = 3.0, 7.5, 15.5 Hz, 2¢-H), 2.91 (1 H, ddd, J = 7.4, 7.8, 15.5 Hz, 2¢¢-
H). ESI-MS: m/e = 512 [M + H]+, 534 [M + Na]+, 550 [M + K]+,
240 [base + H]+, 262 [base + Na]+.
Acknowledgment
This work was supported by the National Natural Science Founda-
tion of China (No. 20272031) and the Basic Science Research
Foundation of Tsinghua University (JC 2001046).
N6-Benzoyl–S,S¢-diacetyl-3¢,5¢-dithio-2¢-deoxyadenosine (9)
To a solution of compound 6 (511 mg, 1.00 mmol) in 20 mL 1,4-
dioxane was added 456 mg (4.00 mmol) AcSK. Then the suspen-
sion was stirred and heated at 60 °C for 36 h under nitrogen. The re-
sulting solution was evaporated and the residue was distributed
between CHCl3 and H2O. The syrup obtained by evaporating the or-
ganic solution after drying over anhyd MgSO4, was purified by col-
umn chromatography (eluted with EtOAc), yielded 362.7 mg (0.77
mmol, 77%) of compound 9. 1H NMR (CDCl3): d = 11.23 (1 H, s,
NH), 8.78 (1 H, s, adenine), 8.28 (1 H, s, adenine), 7.50–8.10 (5 H,
m, phenyl), 6.36 (1 H, dd, J = 3.9, 7.0 Hz, 1¢-H), 4.08–4.23 (2 H, m,
3¢-H and 4¢-H), 3.44 (1 H, dd, J = 3.1, 14.0 Hz, 5¢-H), 3.27 (1 H, dd,
J = 6.0, 14.0 Hz, 5¢¢-H), 3.15 (1 H, ddd, J = 4.0, 7.3, 14.0 Hz, 2¢-H),
2.62 (1 H, ddd, J = 7.0, 7.3, 14.0 Hz, 2¢¢-H), 2.40 (3 H, s, 3¢-Me),
2.34 (3 H, s, 5¢-Me). ESI-MS: m/e = 472 [M + H]+, 494 [M + Na]+,
510 [M + K]+, 240 [base + H]+, 262 [base + Na]+.
References
(1) (a) El-Barbary, A. A.; Khodair, A. I.; Pedersen, E. B.;
Nielsen, C. Monatsh. Chem. 1994, 125, 1017. (b) Reist, E.
J.; Benitez, A.; Goodman, L. J. Org. Chem. 1964, 29, 554.
(2) (a) Eleuteri, A.; Reese, C. B.; Song, Q. J. Chem. Soc., Perkin
Trans. 1 1996, 2237. (b) Chiba, J.; Tanaka, K.; Ohshiro, Y.;
Miyake, R.; Hiraoka, S.; Shiro, M.; Shionoya, M. J. Org.
Chem. 2003, 68, 331.
(3) Oae, S.; Okuyama, T. Organic Sulfur Chemistry:
Biochemical Aspects; CRC Press: Boca Raton, FL, 1992,
217–222.
(4) Nishino, S.; Yamamoto, H.; Nagato, Y.; Ishido, Y.
Nucleosides, Nucleotides Nucleic Acids 1986, 5, 159.
(5) Herdewijn, P. A. J. Org. Chem. 1988, 53, 5050.
Synlett 2004, No. 14, 2585–2587 © Thieme Stuttgart · New York