Synthesis of a novel nucleoside based on a spiroacetal framework

Article abstract of DOI:10.1071/CH04021

The first synthesis of a nucleoside analogue 1 is reported wherein the nucleobase 5-fluorocytosine is attached to a 1,6-dioxaspiro[5,5]undecane spiroacetal ring system. The spiroacetal system acts as a substitute for the sugar unit of natural nucleosides

Full text of DOI:10.1071/CH04021

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Aust. J. Chem. 2004, 57, 665–668
Synthesis of a Novel Nucleoside Based on a Spiroacetal Framework∗
Margaret A. Brimble,A,B James E. Robinson,A Ka Wai Choi,A and Paul D. WoodgateA
A
Department of Chemistry, University of Auckland, Auckland, New Zealand.
B Author to whom correspondence should be addressed (e-mail: m.brimble@auckland.ac.nz).
The first synthesis of a nucleoside analogue 1 is reported wherein the nucleobase 5-fluorocytosine is attached to a
1,6-dioxaspiro[5.5]undecane spiroacetal ring system. The spiroacetal system acts as a substitute for the sugar unit
of natural nucleosides and provides a conformationally restricted framework upon which to append nucleobases
in a well defined geometry. Trimethylsilyl triflate promoted Vorbrüggen-type coupling of bis(trimethylsilyl)-5-
fluorocytosine 3 with spiroacetal acetate 2 provided spiroacetal nucleoside 1 in which the nucleobase occupied
an equatorial position together with the ring opened (Z)-alkene 10. Spiroacetal acetate 2 serves as the spiroacetal
donor and was prepared from the readily available starting materials δ-valerolactone and but-3-yn-1-ol 4.
Manuscript received: 3 February 2004.
Final version: 26 March 2004.
The synthesis of nucleosides (the formation of N-glycosides
of the sugars d-ribose and 2-deoxyribose with heterocyclic
bases)hasreceivedconsiderableattention[1−3] fromsynthetic
chemists largely stimulated by the prospect of developing
therapeutic analogues of naturally occurring nucleosides and
nucleic acids. Analogues of the natural substrates for nucleic
acid processing enzymes are a good source of antiviral agents
which target the enzymes specific to the disease state.[4−6]
Modified oligonucleotides have been synthesized with the
aim of creating analogues able to bind complementary single-
stranded RNA with high affinity and specificity enabling
use of an antisense strategy to inhibit the biosynthesis of a
disease-related protein.[7,8]
The two main sources of variation in the structure of
nucleoside analogues, namely the sugar component and
the heterocyclic base, have provided medicinal chemists
with enormous scope for exploitation. Considerable inter-
est has been focussed on the synthesis of nucleoside ana-
logues wherein the sugar ring oxygen has been replaced by
carbon,[9−15] nitrogen,[16] or sulfur.[17−22] Other modifica-
tions made in an effort to improve the chemotherapeutic
potential include the introduction of a double bond into
the 2ꢀ,3ꢀ-position of the ribose unit,[4] incorporation of this
double bond into an aromatic structure,[23] and the prepa-
ration of bicyclic compounds[24,25] including cyclopropano
homologues.[26]
spirocyclic restriction was developed by Paquette[30] and
others[31] whereby the synthesis of 4ꢀ-spirocyclic nucleoside
mimics provided a new direction in the design of antisense
molecules.
Given the widespread occurrence of spiroacetals in nature
and their ease of availability through synthesis,[32] we were
attracted to the possibility of preparing nucleoside mim-
ics using a spiroacetal framework as a pseudosugar. The
1,6-dioxaspiro[5.5]undecane ring system was particularly
attractive due to its thermodynamic preference to adopt a
trans-diaxial conformation in which there is a lone pair of
electrons antiperiplanar to each C O bond, thus gaining
maximum stability from the anomeric effect[33] and provid-
ing a scaffold to which nucleobases can be attached in a
precisely configured arrangement. Our initial work in this
area focussed on the construction of nucleosides based on a
spiroacetal framework (see Scheme 1), and we herein report
the first synthesis of nucleoside mimic 1 using a spiroacetal
framework as a pseudosugar.
A retrosynthetic analysis for a prototype spiroacetal
nucleoside in which 5-fluorocytosine was chosen as the
nucleobase is shown in Scheme 2. The synthetic strategy
hinges on the Lewis acid mediated addition of a silyl-
activated nucleobase 3 to an oxocarbenium ion generated
from a spiroacetal 2 that bears an acetate leaving group at the
anomeric position. Precedent for the successful generation
of oxocarbenium ions from spiroacetal acetates, followed by
trapping with allylstannanes, has been demonstrated by this
research group[34] and Mead.[35]
The design of nucleosides to study the role of sugar con-
formation in the processes of recognition and binding of
nucleosides, nucleotides, and oligonucleotides to their target
enzymes has also prompted the synthesis of conformationally
restricted nucleoside analogues mainly based on a furanose
or a cyclopentane moiety.[27−29] Recently, the concept of
The spiroacetal acetate 2 intermediate was prepared from
but-3-yn-1-ol 4 and δ-valerolactone as outlined in Scheme 3.
After standard protection of the alcohol as a benzyl ether 5,
∗ Dedicated to Professor Lew Mander on the occasion of his 65th birthday.
© CSIRO 2004
10.1071/CH04021
0004-9425/04/070665

666
M. A. Brimble et al.
O
Base
O
NH2
NH2
O
N
O
N
R
R
N
N
NH
N
NH
N
Base ϭ
N
N
N
O
O
N
NH2
adenine
cytosine; R ϭ H
5-fluorocytosine; R ϭ F
uracil; R ϭ H
thymine; R ϭ Me
Scheme 1.
NH2
F
N
NHSiMe3
N
O
O
OAc
N
F
O
ϩ
O
O
N
OSiMe3
1
2
3
Scheme 2.
O
BuLi, THF, Ϫ78ºC
NaH, BnBr
97%
HO
OH
OBn
O
87%
O
OBn
4
5
6
O
H
O
O
O
NaClO2, But OH, pH 7
92%
TEMPO (cat.), PhI(OAc)2,
HO
MeCN, pH 7
92%
OBn
OBn
7
9
8
1. 10% Pd/C,
THF, HOAc (cat.)
1. DIBALH, toluene
O
O
OAc
O
2. HOAc, 30–35ºC
94%
2. Ac2O, DMAP, Et3N
25% for 2 steps
O
O
2
Scheme 3.
generation of the lithium acetylide followed by addition of
δ-valerolactone afforded keto alcohol 6 in good yield. After
much experimentation, TEMPO-catalyzed oxidation of alco-
hol 6 using iodobenzene diacetate afforded aldehyde 7 in 92%
yield which underwent further oxidation to acid 8 also in 92%
yield. One-pot hydrogenation of the acetylene and debenzy-
lation of the benzyl ether proceeded using 10% palladium on
charcoal as catalyst. The resultant keto acid then underwent
smooth spirocyclization to oxaspirolactone 9 in 94% yield
upon gentle heating in acetic acid.
of the ester and cyclization. However, this procedure was
undesirable due to the necessity to use HMPA in order to
achieve a successful outcome in the initial Wittig olefina-
tion step. Conversion of lactone 9 into spiroacetal acetate 2
by reduction using diisobutylaluminium hydride followed by
acetylation afforded spiroacetal acetate 2 as a 1 : 1 mixture
of anomers in low yield due to the capricious nature of the
product upon purification by chromatography.
With spiroacetal acetates 2 in hand, the final crucial
Vorbrüggen coupling with bis(silylated)-5-fluorocytosine
(Scheme 4) was investigated using a procedure adapted from
those reported by Mann et al.[37] and Paquette et al.[38−40]
Thus, treatment of the acetates 2 with trimethylsilyl triflate
Oxaspirolactone 9 has previously been prepared[36] by
Wittig reaction of a tetrahydropyranyl triphenylphosphonium
ylide with methyl 3-formylpropionate followed by hydrolysis

Synthesis of a Novel Nucleoside
667
NH2
N
NHSiMe3
N
F
F
F
NH2
O
N
O
O
OAc
O
N
OSiMe3
N
OH
O
3
O
N
ϩ
Me3SiOTf, CH2Cl2
O
2
1
10
41%
24%
Scheme 4.
NH2
NH2
NH2
N
F
F
F
N
N
N
O
N
O
O
O
N
O
Me3SiOTf
O
ϩ
O
OH
O
H
SiMe3
10
Scheme 5.
generated an oxocarbenium ion that underwent reaction with
the silylated 5-fluorocytosine∗ at the less hindered N1 posi-
tion to give a mixture of the 5-fluorocytidine spiroacetal 1† in
41% yield together with (Z)-enamide 10‡ in 24% yield after
purification by flash chromatography.
Assignment of the heterocyclic base to an equatorial posi-
tion on the spiroacetal ring in 1 was determined by the
observation that the pseudo-anomeric proton H2ꢀ resonated
as a doublet of doublets at δH 5.96 with coupling constants
To conclude, the synthesis of the first nucleoside ana-
logue based on a spiroacetal framework has been reported.
Spiroacetal-based nucleosides such as 1 represent promising
building blocks for the synthesis of artificial oligonucleotides
and other complex molecules. This novel class of molecule
also provides an interesting structural scaffold to probe for
antiviral activity. Further work on the incorporation of addi-
tional nucleobases onto the 1,6-dioxaspiro[5.5]undecane ring
system and efforts to improve the stereocontrol in the critical
N-pseudoglycosylation step are currently underway in our
laboratory.
ꢀ
ꢀ
ꢀ
ꢀ
J2 ax,3 eq 2.2 Hz and J2 ax,3 ax 11.2 Hz. The magnitude of this
latter coupling constant clearly established that the proton
at the pseudo-anomeric position occupied an axial position
placing the heterocyclic base in an equatorial position. The
‘anti-orientation’ of the nucleobase and the oxygen atom of
the second ring is determined by the adoption of the more sta-
ble trans-diaxial conformation of the spiroacetal ring system.
The magnitude of the vinylic coupling constant,
J 8.4 Hz, observed for alkene 10 clearly established the
(Z)-stereochemistry of the double bond. The formation of
(Z)-alkene 10 as a by-product in the Vorbrüggen coupling
step is thought to arise from the corresponding nucleo-
side spiroacetal in which the heterocyclic base occupies
the more sterically hindered axial position. In this case the
unstable spiroacetal undergoes an elimination–ring opening
sequence to the (Z)-alkene in the presence of the electrophilic
trimethylsilyl triflate (Scheme 5). If the elimination were
stereospecific, one would expect the (Z)-alkene to be formed
from the spiroacetal nucleoside in which the heterocycle is
axial, as observed.
References
[1] H. Vorbrüggen, C. Ruh-Pohlenz, Org. React. 2000, 55, 1.
[2] L. J. Wilson, M. W. Hager, Y. A. El-Kattan, D. C. Liotta,
Synthesis 1995, 1465.
[3] E. Lukevics, A. Zablocka, Nucleoside Synthesis: Organosilicon
Methods 1991 (Ellis Horwood: New York, NY).
[4] R. Challand, R. J. Young, Antiviral Chemotherapy 1996
(Spectrum Academic: Oxford).
[5] D. W. Norbeck, Ann. Rep. Med. Chem. 1990, 25, 149.
[6] C. K. Chu, D. C. Baker, Nucleosides and Nucleotides as
Antitumour and Antiviral Agents 1993 (Plenum Press: New
York, NY).
[7] A. De Mesmaeker, R. Haner, P. Martin, H. E. Moser, Acc.
Chem. Res. 1995, 28, 366.
[8] E. Uhlmann, A. Peyman, Chem. Rev. 1990, 990, 543.
[9] J. Velcicky, J. Lex, H.-G. Schmalz, Org. Lett. 2002, 4, 565.
doi:10.1021/OL017181+
[10] A. D. Borthwick, K. Biggadike, Tetrahedron 1992, 48, 571.
doi:10.1016/S0040-4020(01)88122-9
∗ Silylation of 5-fluorocytosine was achieved by heating with N,O-bis(trimethylsilyl)acetamide.
† Data for 1: δH (400 MHz, CDCl3) 7.55 (1 H, d, 3JH,F 6.0, H6), 5.96 (1 H, dd, J 11.2, 2.2, H2ꢀ), 5.55 (2 H, br s, NH2), 3.75–3.62 (2 H, m, H8ꢀ), 2.05–1.98
(1 H, m, H3ꢀA), 1.80–1.20 (11 H, m, H3ꢀB, H4ꢀ, H5ꢀ, H9ꢀ, H10ꢀ, H11ꢀ). δC (100 MHz, CDCl3) 156.5 (CF, d, 1JC,F 223, C5), 155.1 (quat., C2), 153.6 (quat.,
C4), 125.5 (CH, d, 2JC,F 31.4, C6), 98.5 (quat., C6ꢀ), 77.5 (CH, C2ꢀ), 61.0 (CH2, C8ꢀ), 35.2 (CH2, C5ꢀ or C11ꢀ), 34.9 (CH2, C11ꢀ or C5ꢀ), 30.8 (CH2, C3ꢀ),
24.8 (CH2, C9ꢀ), 18.3 (CH2, C4ꢀ or C10ꢀ), 18.0 (CH2, C10ꢀ or C4ꢀ). m/z (EI+) 283 (M+•, 0.4%), 155 (14), 136 (100), 129 (65), 108 (38), 98 (27), 86 (20),
79 (34), 66 (14), 51 (21), 41 (23), 39 (17). m/z (FAB+) Found: 284.1433. Calc. for C13H19FN3O+3 [M + H+]: 284.1410.
‡ Data for 10: δH (300 MHz, CDCl3) 7.38 (1 H, d, 3JH,F 5.4, H6), 5.27 (1 H, d, J8.4, H2ꢀ), 4.81 (1 H, m, H3ꢀ), 4.02 (2 H, m, H8ꢀ), 2.13–1.20 (12 H, m, H3ꢀ,
H4ꢀ, H5ꢀ, H9ꢀ, H10ꢀ, H11ꢀ).

668
M. A. Brimble et al.
[11] L. Agrofolio, E. Suhas, A. Farese, R. Condom, S. R. Challand,
R. Earl, R. Guedj, Tetrahedron 1994, 50, 10611. doi:10.1016/
S0040-4020(01)89258-9
[12] M. T. Crimmins, Tetrahedron 1998, 54, 9229. doi:10.1016/
S0040-4020(98)00320-2
[13] M. Ferrero, V. Gotor, Chem. Rev. 2000, 100, 4319. doi:10.1021/
CR000446Y
[14] V. E. Marquez, M.-U. Lim, Med. Res. Rev. 1996, 6, 1.
[15] R. Vince, L. B. Akella, Tetrahedron 1996, 52, 2789. doi:10.1016/
0040-4020(96)00015-4
[16] M. Yokoyama, A. Momotake, Synthesis (Mass.) 1999, 9, 1541.
doi:10.1055/S-1999-3559
[17] M. R. Dyson, P. L. Coe, R. T. Walker, J. Med. Chem. 1991,
34, 2782.
[18] D. F. Ewing, G. MacKenzie, Nucleosides Nucleotides 1996,
15, 809.
[26] C. Lescop, F. Huet, Tetrahedron 2000, 56, 2995. doi:10.1016/
S0040-4020(00)00174-5
[27] M. Meldgaard, J. Wengel, J. Chem. Soc., Perkin Trans. 1 2000,
3539. doi:10.1039/B000114G
[28] Y. Choi, C. George, P. Strazewski, V. E. Marquez, Org. Lett.
2002, 4, 589. doi:10.1021/OL010288C
[29] H. O. Kim, K.A. Jacobson, Org. Lett. 2003, 5, 1665. doi:10.1021/
OL034326Z
[30] L. A. Paquette, Aust. J. Chem. 2004, 57, 7. doi:10.1071/CH03267
[31] (a) S. Wendeborn, G. Binot, M. Nina, T. Winkler, Synlett 2002,
1683. doi:10.1055/S-2002-34242
(b) B. R. Babu, L. Keinicke, M. Petersen, C. Nielsen, J. Wengel,
Org. Biomol. Chem. 2003, 1, 3514. doi:10.1039/B306354B
[32] K. T. Mead, B. N. Brewer, Curr. Org. Chem. 2002, 6, 1.
[33] E. Juaristi, G. Cuevas, The Anomeric Effect 1995 (CRC Press:
Boca Raton, FL).
[19] J. A. Secrist III, K. N. Tiwari, J. M. Riordan, J. A. Montgomery,
J. Med. Chem. 1991, 34, 2361.
[34] M. A. Brimble, F. Fares, P. Turner, J. Chem. Soc., Perkin Trans.
1 1998, 677. doi:10.1039/A707607J
[20] N. A. Van Draanen, G. A. Freeman, S. A. Short, R. Harvey,
R. Jansen, G. Szczech, G. W. Koszalka, J. Med. Chem. 1996,
39, 538. doi:10.1021/JM950701K
[21] S. G. Rahim, N. Trivedi, M. V. Bogunovic-Batchelor,
G. W. Hardy, G. Mills, J. W. T. Selway, W. Snowden, E. Littler,
et al., J. Med. Chem. 1996, 39, 789. doi:10.1021/JM950029R
[22] M. Yokoyama, Synthesis (Mass.) 2000, 12, 1637. doi:10.1055/S-
2000-8194
[23] D. F. Ewing, N.-E. Fahmi, C. Len, G. Mackenzie, A. Pranzo, J.
Chem. Soc., Perkin Trans. 1 2000, 3561. doi:10.1039/B006417N
[24] H. R. Moon, H. O. Kim, M. W. Chun, L. S. Jeong, V. E. Marquez,
J. Org. Chem. 1999, 64, 4733. doi:10.1021/JO990010M
[25] M. Bolli, P. Lubini, C. Leumann, Helv. Chim. Acta 1995,
78, 2077.
[35] K. T. Mead, R. Zemribo, Synlett 1996, 11, 1063. doi:10.1055/S-
1996-5687
[36] J. B. Ousset, C. Mioshowski, Y.-L. Tang, J. R. Falck, Tetrahedron
Lett. 1984, 25, 5903. doi:10.1016/S0040-4039(01)81716-0
[37] J. Mann, M. G. B. Drew, S. Gorsuch, J. H. M. Gould, J. Chem.
Soc., Perkin Trans. 1 1999, 969.
[38] L. A. Paquette, R. T. Bilart, C. K. Seekamp, A. L. Kahane,
Org. Lett. 2001, 3, 4039. doi:10.1021/OL010209X
[39] L. A. Paquette, D. R. Owen, R. T. Bilart, C. K. Seekamp, Org.
Lett. 2001, 3, 4043. doi:10.1021/OL010212G
[40] L. A. Paquette, C. K. Seekamp, A. L. Kahane, J. Org. Chem.
2003, 68, 8614. doi:10.1021/JO0301954