A convenient way to N-allyloxycarbonyl protected adenosine and cytidine derivatives

Article abstract of DOI:10.1055/s-1998-1822

A convenient method for the introduction of an allyloxycarbonyl protector to adenyl and cytosyl bases using commercially available allyloxycarbonyl chloride as the protecting reagent has been developed.

Full text of DOI:10.1055/s-1998-1822

August 1998
SYNLETT
853
A Convenient Way to N-Allyloxycarbonyl Protected Adenosine and Cytidine Derivatives
Sophie B. Heidenhain and Yoshihiro Hayakawa*
Laboratory of Bioorganic Chemistry, Graduate School of Human Informatics
Nagoya University, Chikusa, Nagoya 464-01, Japan
Fax +81-52-789-4848; E-mail yoshi@info.human.nagoya-u.ac.jp
Received 26 May 1998
Abstract:
A convenient method for the introduction of an
allyloxycarbonyl protector to adenyl and cytosyl bases using
commercially available allyloxycarbonyl chloride as the protecting
reagent has been developed.
In oligonucleotide synthesis, the development of good protecting groups
for amino functions of nucleoside bases is an important subject. The
protector should be easily introduced and removed under mild
conditions, because the internucleotide bond is sensitive to strong acids
or bases. As a protector fulfilling such requirements, we developed the
allyloxycarbonyl (AOC) group removable by a Pd(0)-catalyzed reaction
1-3
under almost neutral conditions. The AOC protection is useful for the
synthesis of DNA and RNA oligomers, particularly, base-labile
derivatives with artificial modifications. Actually, its utility has been
demonstrated in the preparation of oligoDNAs containing alkaline-
labile (5R)-5,6-dihydro-5-hydroxythymidine, known as a mutagenic
4
and/or cytotoxic modification of RNA. Further, AOC protection was
effectively employed in the synthesis of oligoDNAs with modified
5
5
backbones such as phosphonodiesters, phosphotriesters, and
6
phosphorothiodiesters,
2’-deoxy-3-isoadenosine-incorporated
7
oligoDNAs,
cytidine-5’-monophosphono-N-acetylneuraminic acid
8
9
4
(CMP-Neu5Ac), branched-type RNAs, and N -acetylcytidine-
10
incorporated oligoRNAs.
However, the existing strategy has a
drawback in the preparation of N-AOC adenosine and cytosine
compounds: the protection needs rather expensive reagents and time-
consuming multi-operations. For instance, the allyloxycarbonylation of
these two bases requires allyl 1-benzotriazolyl carbonate
2,3,9
3,9
(AOCOBT)
or 1-(allyloxycarbonyl)tetrazole (AOCTet)
as
reagents, which are not commercially available but have to be prepared
from allyloxycarbonyl chloride (AOCCl) using expensive 1-
(hydroxy)benzotriazole or 1H-tetrazole. Further, in the preparation of
2
the N-AOC-adenosines, moisture-sensitive tert-butyllithium or tert-
9
butylmagnesium chloride is employed for the activation of the amino
function of the nucleobase. These reagents require special care, like
working under an argon atmosphere. This paper describes a simple
access to the N-AOC-protected adenosine and cytidine derivatives using
commercially available, less expensive AOCCl in the presence of N-
methylimidazole.
6
Introduction of the AOC group to the N -position of 2’-deoxyadenosine
was achieved in one pot via the following process. Initially, 2’-
yield), (2) silylation with t-C H (CH ) SiCl and imidazole in DMF,
4
9
3 2
deoxyadenosine was treated with an excess of hexamethyldisilazane and
19
producing 8 (33% yield) together with the 3'-O-silylated derivative 9
(45% yield), and (3) the condensation of 8 and (CH =CHCH O)P[N(i-
11
a catalytic amount of (NH ) SO in refluxing dioxane to give the bis-
4 2
4
2
2
silylated compound 1. Subsequently, 1 was allyloxycarbonylated with
AOCCl and N-methylimidazole, giving 2, and finally the transient silyl
protector was removed by triethylamine in methanol to afford 3 in 70 %
C H ) ] in the presence of diisopropylammonium tetrazolide (81%
3
7 2 2
20
yield).
In conclusion, the present allyloxycarbonylation is superior in the
respect of operational simplicity and cost-performance to previous
methods.
12
6
13
4
isolated yield. In a similar manner, N -AOC-adenosine 4, N -AOC-
14
4
15
2’-deoxycytidine 5, and N -AOC-cytidine 6 were prepared from the
parent nucleosides in 89–99% overall yields. This method could not be
16
applied to the amino group of the guanyl base. According to literature
methods or their modifications, the AOC-protected compounds, 3–6,
Acknowledgment. This work was financially supported by a Grant-in-
Aid for Scientific Research (Nos. 08454200, 10169225, and 10554042)
from the Ministry of Education, Science, Sports and Culture, and the
Asahi Glass Foundation.
3
17-20
3
10,17
can be converted to the phosphoramidites, 10, 11,
12, and 13,
requisite as monomer units for oligonucleotide synthesis. For example,
11 was obtained from 4 via (1) tritylation of the 5’-hydroxyl group by
18
C H (p-CH OC H ) CCl in a pyridine–DMF mixture, giving 7 (77%
6
5
3
6 4 2

854
LETTERS
SYNLETT
References and Notes
1H), 4.17 (m, 1H), 4.61–4.66 (m, 3H), 5.14–5.44 (m, 4H), 5.53 (s,
1H), 5.90–6.04 (m, 2H), 8.63 (s, 1H), 8.68 (s, 1H), 10.66 (s, 1H).
(1) Kunz, H.; Unverzagt, C.; Angew. Chem. Int. Ed. Engl., 1984, 23,
(14) 5: A foam; 95% yield; R 0.4 (a 1:9 methanol–dichloromethane
436.
f
1
mixture); H-NMR (270 MHz, DMSO-d ) δ 1.89–2.04 (m, 1H),
6
(2) Hayakawa, Y.; Kato, H.; Uchiyama, M.; Noyori, R. J. Org. Chem.
1986, 51, 2400.
2.22–2.28 (m, 1H), 3.52–3.58 (m, 2H), 3.83–3.84 (m, 1H), 4.21
(m, 1H), 4.60–4.62 (m, 2H), 5.09–5.38 (m, 4H), 5.86–5.99 (m,
1H), 6.06–6.11 (m, 1H), 7.00–7.03 (d, 1H, J = 7.4 Hz), 8.30–8.32
(d, 1H, J = 7.4 Hz), 10.78 (s, 1H).
(3) Hayakawa, Y.; Wakabayashi, S.; Kato, H.; Noyori, R. J. Am.
Chem. Soc. 1990, 112, 1691.
(4) Matray, T. J.; Greenberg, M. M. J. Am. Chem. Soc. 1994, 116,
(15) 6: Mp 103–107 °C (recrystallization from a methanol–ethyl
6931.
acetate mixture); 99
dichloromethane mixture); H-NMR (400 MHz, DMSO-d ) δ
%
yield;
R
0.3 (a 1:9 methanol–
f
1
(5) Hayakawa, Y.; Hirose, M.; Hayakawa, M.; Noyori, R. J. Org.
Chem. 1995, 60, 925.
6
3.57–3.97 (m, 5H), 4.62–4.64 (m, 2H), 5.03 (d, 1H, J = 5.4 Hz),
5.15 (t, 1H, J = 4.9 Hz), 5.22–5.38 (m, 2H), 4.47 (d, 1H, J = 4.4
Hz), 5.77 (d, 1H, J = 2.4 Hz), 5.91–5.98 (m, 1H), 7.00 (d, 1H, J =
7.3 Hz), 8.40 (d, 1H, J = 7.3 Hz), 10.80 (s, 1H).
(6) Hayakawa, Y.; Hirose, M.; Noyori, R. Nucleosides Nucleotides
1994, 13, 1337.
(7) Leonard, N. J.; Neelima Nucleosides Nucleotides 1996, 15, 1369.
(16) A similar result was reported in Watkins, B. E.; Rapoport, H. J.
Org. Chem. 1982, 47, 447.
(8) Makino, S.; Ueno, Y.; Ishikawa, M.; Hayakawa, Y.; Hata, T.
Tetrahedron Lett. 1993, 34, 2775.
(17) (a) Hakimelahi, G. H.; Proba, Z. A.; Oglivie, K. K. Can. J. Chem.
1982, 60, 1106. (b) Lyttle, M. H.; Wright, P. B.; Sinha, N. D.;
Bain, J. D.; Chamberlin, A. R. J. Org. Chem. 1991, 56, 4608.
(9) Hayakawa, Y.; Hirose, M.; Noyori, R. Tetrahedron 1995, 51,
9899.
(10) Bogdan, F. M.; Chow, C. S. Tetrahedron Lett. 1998, 39, 1897.
(18) 7: A yellow foam; 77% yield from 4; R 0.76 (a 1:9 methanol–
f
1
dichloromethane mixture); H-NMR (270 MHz, DMSO-d ) δ
(11) Schirmeister, H.; Himmelsbach, F.; Pfleiderer, W. Helv. Chim.
Acta 1993, 76, 385.
6
3.22–3.24 (m, 2H), 3.71 (s, 6H); 4.06–4.11 (m, 1H), 4.30–4.34
(m, 1H), 4.64–4.66 (m, 2H), 4.73–4.78 (m, 1H), 5.25–5.44 (m,
3H), 5.59–5.61 (m, 1H), 5.90–6.04 (m, 2H), 6.79–6.84 and 7.18–
7.36 (2 m's, 13H), 8.56 (s, 2H), 10.65 (s, 1H).
6
(12) The experimental procedure for the preparation of N -
(allyloxycarbonyl)-2’-deoxyadenosine (3): A mixture of pre-dried
2'-deoxyadenosine (1.50 g, 5.97 mmol), hexamethyldisilazane (20
mL), and a catalytic amount of (NH ) SO in dioxane (20 mL)
(19) 8: A colorless foam; 33 % yield from 7; R 0.64 (a 3:2 ethyl
f
4 2
4
1
acetate–hexane mixture); H-NMR (270 MHz, DMSO-d ) δ –0.15
was heated under reflux for 2.5 h. The reaction mixture was
concentrated and coevaporated twice with dry toluene, giving an
oily residue, which was dissolved in dichloromethane (50 mL). To
this solution were added N-methylimidazole (1.40 mL, 1.44 g,
17.8 mmol) and AOCCl (1.90 mL, 2.16 g, 17.8 mmol) and the
resulting mixture was stirred at room temperature for 36 h.
Concentration of the reaction mixture gave a viscous oil, which
was dissolved in methanol (50 mL) containing triethylamine (13
mL). The resulting solution was stirred at room temperature for 12
h and then was evaporated to afford an oil. This crude material
was subjected to silica gel column chromatography with a 1:25
mixture of methanol and dichloromethane as eluent to give 3
6
(s, 3H), –0.05 (s, 3H), 0.73 (s, 9H), 3.27–3.68 (m, 2H), 3.71 (s,
6H), 4.11–4.28 (m, 2H), 4.63–4.65 (m, 2H), 4.86 (t, J = 4.78 Hz,
1H), 5.47–5.92 (m, 3H), 5.86–6.04 (m, 2H), 6.80–6.84 and 7.19–
7.47 (2 m's, 13H), 8.54 (s, 1H), 8.62 (s, 1H), 10.65 (s, 1H). 9: A
colorless foam; 45 % yield from 7; R 0.4 (a 3:2 ethyl acetate–
f
1
hexane mixture); H-NMR (270 MHz, DMSO-d ) δ 0.04 (s, 3H),
6
0.08 (s, 3H), 0.84 (s, 9H), 3.11–3.16 (m, 1H), 3.33–3.39 (m, 1H),
3.71 (s, 6H), 4.00–4.06 (m, 1H), 4.48–4.51 (m, 1H), 4.64–4.66 (m,
2H), 4.86–4.90 (m, 1H), 5.18–5.43 (m, 3H), 5.89–6.05 (m, 2H),
6.82–6.85 and 7.19–7.39 (2 m's, 13H), 8.54 (s, 1H), 8.57 (s, 1H),
10.67 (s, 1H).
(1.40g, 70% yield) as a colorless foam; R 0.3 (a 1:9 methanol–
(20) 11: A colorless foam; 81% yield from 8; R 0.42 (a 3:7 ethyl
f
f
1
1
dichloromethane mixture); H-NMR (270 MHz, DMSO-d ) δ
acetate–hexane mixture); H-NMR (400 MHz, CDCl ) δ –0.21 (s,
6
3
2.30–2.36 (m, 1H), 2.72–2.79 (m, 1H), 3.49–3.64 (m, 2H), 3.86–
3.89 (m, 1H), 4.42–4.44 (m, 1H), 4.64–4.65 (m, 2H), 4.98–5.00
(m, 1H), 5.22–5.43 (m, 3H), 5.92–6.00 (m, 1H), 6.42–6.45 (m,
1H), 8.62 (s, 1H), 8.68 (s, 1H), 10.60 (s, 1H).
3H), –0.02 (s, 3H), 0.75 and 0.77 (2 s's, 9H), 1.15–1.28 (m, 12 H),
3.44–3.62 (m, 2H), 3.78 (s, 3H), 3.79 (s, 3H), 3.96–4.26 (m, 2H),
4.41-4–49 (m, 3H), 4.76–4.78 (m, 2H), 4.97–5.44 (m, 6H), 5.89–
6.09 (m, 3H), 6.77–6.85 and 7.20–7.73 (2 m's, 13 H), 8.16–8.19
31
(m, 2H), 8.64 and 8.66 (2 s's, 1H); P-NMR (400 MHz, CDCl ,
(13) 4: Mp 164–166 °C (crystallization from the reaction mixture); 89
3
1
H PO standard) δ 148.8, 151.0.
% yield; R 0.3 (a 1:9 methanol–dichloromethane mixture); H-
3
4
f
NMR (270 MHz, DMSO-d ) δ 3.55–3.71 (m, 2H), 3.95–3.97 (m,
6