Convenient and efficient approach to di- and trideoxyribonucleotide N3′→P5′ phosphoramidates

Article abstract of DOI:10.1055/s-2005-871580

Arbuzov reaction of phenyl phosphorodichloridite with an equivalent of allyl alcohol and tert-butyl alcohol produced phenyl allyl H-phosphonate and the subsequent ester-exchange with various nucleosides produced nucleoside allyl H-phosphonates. Antherton-Todd reaction of the nucleoside allyl H-phosphonates with 3′-amino-3′-deoxythymidine yielded dideoxyribonucleotide N3′→P5′ phosphoramidates, and the repetition of this procedure provided trideoxyribonucleotide N3′→P5′ phosphoramidates. The method can be used for the synthesis of oligodeoxyribonucleotide N3′→P5′ phosphoramidates without any protection for all nucleosides. Georg Thieme Verlag Stuttgart.

Full text of DOI:10.1055/s-2005-871580

1930
LETTER
Convenient and Efficient Approach to Di- and Trideoxyribonucleotide
N3¢→P5¢ Phosphoramidates
A
pproach to Di- an
u
d
Trideoxyribonuc
T
leotide N3
¢
→
P
5
¢
Phosphon
ramidates g,a,b Cheng Huang,a Hua Fu,*a Yufen Zhaoa,b
a
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry,
Tsinghua University, Beijing 100084, P. R. China
b
Department of Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
Fax +86(10)62781695; E-mail: fuhua@mail.tsinghua.edu.cn
Received 22 April 2005
mediates in chemistry, and to find the new synthetic
routes to these compounds constitutes a valuable target. In
the past two decades, studies on H-phosphonate deriva-
tives have greatly progressed.16–22 Advances on the devel-
Abstract: Arbuzov reaction of phenyl phosphorodichloridite with
an equivalent of allyl alcohol and tert-butyl alcohol produced
phenyl allyl H-phosphonate and the subsequent ester-exchange with
various nucleosides produced nucleoside allyl H-phosphonates.
Antherton–Todd reaction of the nucleoside allyl H-phosphonates opment of a comprehensive H-phosphonate methodology
with 3¢-amino-3¢-deoxythymidine yielded dideoxyribonucleotide
N3¢→P5¢ phosphoramidates, and the repetition of this procedure
provided trideoxyribonucleotide N3¢→P5¢ phosphoramidates. The
have been discussed by Stawinski and Kraszewski.20
method can be used for the synthesis of oligodeoxyribonucleotide
N3¢→P5¢ phosphoramidates without any protection for all nucleo-
and the underlying chemistry for the preparation of bio-
logically important phosphate esters and their analogues
Stawinski and co-workers have developed H-phosphonate
methods to synthesize dideoxynucleotide N3¢→P5¢ phos-
phoramidates through reaction of nucleoside H-phos-
phonate monoester with aminonucleoside in the presence
sides.
Key words: nucleotide N3¢→P5¢ phosphoramidate, H-phospho-
nate, ester-exchange, Antherton–Todd reaction
21
of Me3SiCl and I2 or exchange of aryl H-phosphonates
with aminonucleoside and the following oxidation.22
However, all these methods required the protection of
functional groups in nucleosides. Here we would like to
report a convenient and efficient synthesis of dideoxy-
ribonucleotide N3¢→P5¢ phosphoramidates without any
protection for nucleosides.
Oligonucleotide N3¢→P5¢ phosphoramidates have been
attracted considerable attention as a class of compounds
of potential therapeutic value,1–6 since these oligonucle-
otide analogues are resistant towards various nucleases2,7
and hybridize to complementary DNA or RNA targets
with much higher affinity than their natural congeners
do.2 Some synthetic methods of these phosphoramidates
have been developed using phosphotriester chemistry,8
via the Staudinger type of reaction,9 or by the phosphora-
midite method.4 Gryaznov and co-workers have prepared
oligonucleotide N3¢→P5¢ phosphoramidates via oxidative
coupling of aminonucleosides with H-phosphonate di-
esters under Antherton–Todd oxidation conditions.4,10–13
Stec and co-workers synthesized a kind of compounds by
using 2-alkylamino-2-thio-1,3,2-oxathiaphospholanes14
as the starting material.15 H-phosphonates are useful inter-
Reaction of phenyl phosphorodichloridite (1) with one
equivalent of allyl alcohol and one equivalent of tert-butyl
alcohol in CH2Cl2 at room temperature under nitrogen
atmosphere provided phenyl allyl H-phosphonate diester
(2) in 90% yield with minor diallyl H-phosphonate diester
appearing (determined by 31P NMR). The reaction could
undergo the formation of the corresponding major tert-
butyl phenyl allyl phosphite triester (1¢) and phenyl diallyl
phosphate triester (2¢) intermediates, followed by
Arbuzov rearrangement by the reaction of HCl
(Scheme 1).
O
OH
P
OPh
O
O
OH (1:1)
1'
(major)
Cl
Cl
HCl
P
H
OPh
O
P
OPh
–
Cl
Cl
O
1
P
OPh
2
O
or
2'
(minor)
Scheme 1 Synthesis of phenyl allyl H-phosphonate
SYNLETT 2005, No. 12, pp 1930–1932
0
1
.0
8
.2
0
0
5
Advanced online publication: 07.07.2005
DOI: 10.1055/s-2005-871580; Art ID: U12005ST
© Georg Thieme Verlag Stuttgart · New York

LETTER
Approach to Di- and Trideoxyribonucleotide N3¢→P5¢ Phosphoramidates
1931
Scheme 2 shows the synthetic route of di- and trideoxyri- i.e. ester exchange reaction of 2 with 6 yielded 7, and
bonucleotide N3¢→P5¢ phosphoramidates. The displace- Atherton–Todd reaction of 7 with 3¢-amino-3¢-deoxy-
ment reaction of 2 with nucleoside in dry pyridine at room thymidine (5) produced trinucleotide N3¢→P5¢ phos-
temperature provided nucleoside allyl H-phosphonate di- phoramidate 8 in 58–70% yield after silica gel
ester (4) in 73–89% yield (determined by 31P NMR). The chromatography using CHCl3–MeOH (3:1) as eluent.
chemoselectivity observed for 5¢-hydroxyl in non-protect-
ed nucleosides 2, leading to nucleoside allyl 5¢-phospho-
nate diesters, is different from reactivity and steric
In conclusion, we have developed a new convenient and
efficient synthetic method that provides a facile access to
di- and trideoxyribonucleotide N3¢→P5¢ phosphorami-
dates. In these reactions, phenyl allyl H-phosphonate is a
good phosphonylating agent of nucleosides. The method
is simple and efficient, and makes use of readily available
nucleosides H-phosphonates without any protection for
nucleosides. It is also suitable to the preparation of oli-
godeoxyribonucleotide N3¢→P5¢ phosphoramidates.
hindrance among 5¢-OH, 3¢-OH and amino group of base.
3
1
The JP–H coupling between 5¢-CH2 and P in H NMR
spectra of compounds 4 was observed.
Table 1 Isolated Yields of Synthesized Di- and Trideoxyribonucle-
otide N3¢→P5¢ Phosphoramidates (6 and 8)23
Compound
Yield of 6 (%)a
Yield of 8 (%)b
a
b
c
70
78
64
60
76
64
70
61
58
69
General Procedure for Preparation of Di- and Trideoxyribo-
nucleotide N3¢→P5¢ Phosphoramidates
To a flask containing phenyl phosphorodichloridite (195 mg, 1
mmol) in 2 mL of CH2Cl2, mixture of allyl alcohol (1 mmol) and
tert-butanol (1 mmol) in 3 mL of CH2Cl2 was added dropwise at r.t.,
and the solution was stirred at that temperature for 20 min. After
evaporation of the solvent in vacuo, the residue was dissolved in 2
mL of pyridine and added to 3¢-deoxynucleoside (1 mmol) in 2 mL
of pyridine, and the mixture was stirred at r.t. for 2 h. Then, the
solvent was removed by evaporation, the residue was dissolved in 2
mL of THF, and the solution was added dropwise to the mixture of
3¢-amino-3¢-deoxythymidine (241 mg, 1 mmol), carbon tetra-
chloride (308 mg, 2 mmol), Et3N (202 mg, 2 mmol), small amount
of H2O (1 mL) and THF (4 mL). The resulting solution was stirred
at r.t. for 30 min. Then, the solvent was removed in vacuo, and
dideoxyribonucleotide N3¢→P5¢ phosphoramidates (6a–e) are puri-
fied over silica gel chromatography using CHCl3–MeOH (3:1) as
eluent. Repeating the above procedure, ester exchange reaction of 2
with 6 yielded 7, and Atherton–Todd reaction of 7 with 3¢-amino-
3¢-deoxythymidine produced 8, and trinucleotide N3¢→P5¢ phos-
phoramidate was obtained in 58–70% yield after silica gel chroma-
tography using CHCl3–MeOH (3:1) as eluent.
d
e
a Overall yield from 1 to 6.
b Overall yield from 6 to 8.
Antherton–Todd reaction of 4 with 3¢-amino-3¢-deoxy-
thymidine 5 in THF, in the presence of carbon tetra-
chloride, trimethylamine and small amount of H2O
(almost quantitatively) yielded dinucleotide N3¢→P5¢
phosphoramidates (6a–e, Scheme 2) at room temperature,
and purification by silica gel column chromatography us-
ing CHCl3–MeOH (3:1) as eluent provided 6a–e in 60–
78% yields (see Table 1). The repetition of the above
procedure gave trinucleotide N3¢→P5¢ phosphoramidate,
T
HO
B
HO
O
O
O
P
NH2
O
OH
3a-e
B
5
O
O
O
O
P
H
OPh
H
CCl4/Et3N
THF/H2O
Py
OH
4a–e
2
T
HO
O
O
T
O
O
O
P
H
T
HO
O
O
O
HN
5
O
O
P
HN
P
HN
P
2
CCl4/Et3N
THF/H2O
T
O
O
O
O
O
B
O
B
8
O
7
O
HN
P
O
O
OH
6a–e
OH
O
B
O
B = A (adenine) (a) , T (thymine) (b), C (cytosine) (c),
G (guanine) (d), U (uracil) (e),
OH
Scheme 2 Synthetic route of di- and trideoxyribonucleotide N3¢→P5¢ phosphoramidates
Synlett 2005, No. 12, 1930–1932 © Thieme Stuttgart · New York

1932
X. Tang et al.
LETTER
(18) Froehler, B. C.; Matteucci, M. D. Tetrahedron Lett. 1986,
27, 469.
(19) Froehler, B. C.; Ng, P. G.; Matteucci, M. D. Nucleic Acids
Res. 1986, 14, 5399.
Acknowledgment
This work was supported by the Excellent Dissertation Foundation
of the Chinese Ministry of Education (No. 200222), the Excellent
Young Teacher Program of MOE, P. R. C., and the National Natural
Science Foundation of China (Grant No. 20472042).
(20) Stawinski, J.; Kraszewski, A. Acc. Chem. Res. 2002, 35, 952.
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(23) Spectral data for the representative products 6b and 8b.
Compound 6b: 31P NMR (121.5 MHz, DMSO-d6): d =
10.37, 10.26 ppm. 1H NMR (300 MHz, DMSO-d6): d = 1.76
(s, 3 H, 5-CH3 of 3¢-amino-3¢-deoxythymidine), 1.78 (s, 3 H,
5-CH3 of 3¢-deoxythymidine), 2.11–2.17 (m, 5 H, 2¢-H of 3¢-
amino-3¢-deoxythymidine and 3¢-deoxythymidine and 4¢-H
of 3¢-amino-3¢-deoxythymidine), 3.50–3.65 (m, 2 H, 3¢-H of
3¢-amino-3¢-deoxythymidine and 3¢-H of 3¢-
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(s, 3 H, 5-CH3 of 3¢-amino-3¢-deoxythymidine), 1.78 (s, 6 H,
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Synlett 2005, No. 12, 1930–1932 © Thieme Stuttgart · New York