Synthesis and chemoselective activation of phenyl 3,5-di-O-benzyl-2-O,4-C-methylene-1-thio-β-D-ribofuranoside: A key synthon towards α-LNA

Article abstract of DOI:10.1039/a806817h

A bicyclic thiofuranoside (phenyl 3,5-di-O-benzyl-2-O,4-C-methylene-β-D-ribofuranoside) was efficiently synthesized and introduced as the key synthon in a method for convergent synthesis of α- and β-LNA nucleosides; acid-induced ring-opening reactions of

Full text of DOI:10.1039/a806817h

Synthesis and chemoselective activation of phenyl
3,5-di-O-benzyl-2-O,4-C-methylene-1-thio-b-
towards a-LNA
D-ribofuranoside: a key synthon
Poul Nielsena and Jesper Wengel*b
a Department of Chemistry, Odense University, DK-5230 Odense M, Denmark
b Center for Synthetic Bioorganic Chemistry, Department of Chemistry, University of Copenhagen,
Universitetsparken 5, DK-2100 Copenhagen, Denmark. E-mail: wengel@kiku.dk
Received (in Cambridge, UK) 2nd September 1998, Accepted 27th October 1998
A bicyclic thiofuranoside (phenyl 3,5-di-O-benzyl-2-O,4-C-
-ribofuranoside) was efficiently synthesized
and introduced as the key synthon in a method for
convergent synthesis of a- and b-LNA nucleosides; acid-
induced ring-opening reactions of the corresponding bicyclic
methyl furanoside are also described.
to give a deprotected intermediate, which was subsequently
methylene-b-
D
acetylated. The latter reaction was slow and problematic giving
a major product in only 23% yield, which was assigned as the
pure b-anomer 7. NMR spectra of the deprotected intermediate
showed distinctive aldehyde signals suggesting ring strain and
the predominance of the monocyclic intermediate 4a to be
responsible for the slow and low-yielding conversion to
furanose 7. Summarizing, the strategies depicted in Scheme 1
are not convenient for synthesis of the bicyclic nucleosides.
Thioglycosides have been intensively investigated for glyco-
sylation reactions due to their ability to react with sulfur-
specific electrophiles, thereby creating sulfonium cations
readily displaced as leaving groups.13,14 In the case of phenyl
thioglycosides, there have been reports of nucleobase coupling
reactions yielding natural as well as modified nucleosides.15,16
In the search for an ideal nucleic acid mimic, intensive research
towards conformationally restricted oligonucleotide analogues
has been carried out during the last years.1 We have recently
introduced LNA (Locked Nucleic Acid) as a novel class of
preorganized oligonucleotide analogues showing very inter-
esting properties.2–4† In our initial synthetic approaches,
monomeric b-configurated LNA nucleosides (e.g. the thymine
derivative 13, 5-methyl-2A-O,4A-C-methyleneuridine or
(1S,3R,4R,7S)-7-hydroxy-1-hydroxymethyl-3-(thymin-1-yl)-
2,5-dioxabicyclo[2.2.1]heptane, Scheme 2) were synthesized
by stereoselective condensation of appropriately protected 4-C-
hydroxymethyl-1,2-di-O-acetyl furanoses with silylated nucle-
obases and subsequent base-induced ring-closure and deprotec-
tion;2,3 linear syntheses of LNA nucleosides have also been
accomplished.5–7 Here, a novel synthetic strategy is introduced,
involving the use of a bicyclic carbohydrate precursor for
nucleobase coupling reactions thus revealing the first synthesis
of a-configurated LNA nucleosides. Our interest in these a-
anomers, and in a-LNA, was stimulated by reports that a-DNA,
in comparison with b-DNA, forms a more stable duplex with
complementary RNA.8,9
BnO
BnO
O
O
ii
OCH3
RO
MsO
O
BnO
O
BnO
OH
1 R = H
2 R = Ms
3
i
iii
BnO
OCH3
BnO
O
O
+
OCH3
O
4
O
BnO
BnO
The protected 4-C-hydroxymethyl furanose 1 was synthe-
sized according to the known method3,10 and converted to the
methanesulfonate 2 in 99% yield (Scheme 1). This compound
was treated with HCl in MeOH–H2O (7:1 v/v) to give the
anomeric mixture of methyl furanosides 3 in 95% yield.
Treatment with NaH gave the two isomeric bicyclic methyl
furanosides 4 and 5 in 60 and 30% yield, respectively. The
structures of the two products were verified using NMR
experiments. Thus, mutual NOE contacts between H-1, H-2 and
H-3 verified the a-configuration of 5 and the absence of NOE
contacts between H-1 and H-3 verified the b-configuration of 4.
5
OBn
BnO
TMSO
O
H
N
iv
4
O
O
N
H3CO
6
3
3
BnO
OAc
The coupling constants JH1,H2 and JH2,H3 were in both cases
extremely small ( ~ 0 Hz) confirming the bicyclo[2.2.1]heptane
structures. An attempt to use these bicyclic methyl furanosides
as precursors for synthesis of LNA nucleosides failed. Thus,
coupling of thymine to furanoside 4 using a modified Vor-
brüggen methodology11 [N,O-bis(trimethylsilyl)acetamide
(BSA) and Me3SiOTf in MeCN] afforded in 59% yield one
major product which was assigned as the ring-opened derivative
6 existing as a mixture of diastereoisomers.12 The considerable
ring strain in the bicyclic structure is a plausible explanation for
the favouring of the Lewis acid mediated ring-opening reaction
over the cleavage of the anomeric bond.
OBn
O
O
BnO
v
vi
4
HO
CHO
O
BnO
7
4a
OBn
BnO
vii
4
HO
O
SPh
PhS
As an attempt to overcome this problem, better leaving
groups were introduced at the anomeric position (Scheme 1 and
2). In order to obtain a mixture of 1A-O-acetyl derivatives,
methyl furanoside 4 (and/or 5) was treated with 80% aq. AcOH
8
Scheme 1 Reagents and conditions: i, MsCl, pyridine; ii, 20% HCl in
MeOH, H2O; iii, NaH, DMF; iv, thymine, BSA, Me3SiOTf, MeCN; v, 80%
AcOH; vi, Ac2O, pyridine; vii, Me3SiSPh, Me3SiOTf, CH2Cl2.
Chem. Commun., 1998, 2645–2646
2645

BnO
MsO
BnO
MsO
SPh
O
O
useful for convergent syntheses of other constrained bicyclic
nucleoside derivatives. The general use of 11 as a precursor for
synthesis of a- and b-LNA nucleosides is currently under
investigation.
ii
OCH3
BnO
OR
BnO
OAc
The Danish Natural Science Research Council, The Danish
Technical Research Council and Exiqon A/S, Denmark, are
thanked for financial support.
3 R = H
10
i
9 R = Ac
iii
O
N
H
N
BnO
BnO
SPh
O
O
iv
O
Notes and references
O
O
BnO
BnO
† LNA is defined as an oligonucleotide (analogue) containing one or more
monomeric LNA nucleosides. These LNA monomers are preorganized in a
3A-endo conformation as shown by X-ray crystallography (see ref. 5) and
NMR studies (see ref. 2 and 3).
‡ Selected data for 11: dH(CDCl3) 7.46–7.26 (15 H, m, Bn, SPh), 5.35 (1 H,
s, H-1), 4.68–4.56 (4 H, m, Bn), 4.31 (1 H, s, H-2), 4.10 (1 H, s, H-3), 4.09
(1 H, d, J 7.3, H-5A), 3.93 (1 H, d, J 7.8, H-5A), 3.79 (2 H, m, H-5); dC(CDCl3)
138.03, 137.45, 133.42, 132.36, 129.19, 128.55, 128.46, 128.05, 127.84,
127.83, 127.76 (Bn, SPh), 89.96 (C-1), 87.18 (C-4), 79.71 (C-2), 79.40 (C-
3), 73.64 (Bn), 73.23 (C-5A), 72.30 (Bn), 66.31 (C-5); m/z (FAB) 435 (M +
H), 457 (M + Na) (Found: C, 71.76; H, 6.18; C26H26O4S requires C, 71.86;
H, 6.03%).
§ Selected data for 14: dH(CD3OD) 7.78 (1 H, d, J 1.3, H-6), 5.88 (1 H, s,
H-1A), 4.38 (1 H, s, H-2A), 4.34 (1 H, s, H-3A), 4.08–3.69 (4 H, m, H-5A, H-
5AA), 1.92 (3 H, d, J 1.2, CH3); dC(CD3OD) 138.00 (C-6), 110.08 (C-5),
92.49, 89.01 (C-4A, C-1A), 80.89, 74.27, 73.33 (C-2A, C-3A, C-5A), 59.29 (C-
5AA), 12.53 (CH3); m/z (EI) 270 (M+, 100%).
12
11
v
O
N
NH
HO
O
O
HO
O
+
O
HO
N
O
O
O
HO
NH
13
14
Scheme 2 Reagents and conditions: i, Ac2O, pyridine; ii, Me3SiSPh,
Me3SiOTf, CH2Cl2; iii, NH3, MeOH, then NaH, DMF; iv, thymine, HMDS,
then NBS, 11, 4 Å molecular sieves, CH2Cl2; v, H2, Pd(OH)2/C, EtOH,
CH2Cl2.
1 P. Herdewijn, Liebigs Ann., 1996, 1337.
2 S. K. Singh, P. Nielsen, A. A. Koshkin and J. Wengel, Chem. Commun.,
1998, 455.
Furthermore, oxidized phenylsulfenyl glycosides have been
used in glycosylations17 and in nucleobase coupling reac-
tions.18,19 Thioglycosides have been obtained from O-glyco-
sides,13 but treatment of the bicyclic methyl furanoside 4 with
Me3SiSPh and Me3SiOTf13 gave the ring-opened dithioacetal
derivative 8 in 61% yield (Scheme 1). However, after protection
of the methyl furanoside 3 to give 2A-O-acetyl derivative 9 in
97% yield (Scheme 2), the b-thiofuranoside 10 was obtained in
66% yield using Me3SiSPh and Me3SiOTf (25% of starting
material 9 was recovered). Only trace of the a-anomer of 10 was
detected due to the expected anchimeric assistance from the 2A-
O-acetyl group. The acetyl group was removed with methanolic
ammonia and direct ring-closure was very efficiently performed
using NaH affording phenyl 3,5-di-O-benzyl-2-O,4-C-methyl-
3 A. A. Koshkin, S. K. Singh, P. Nielsen, V. K. Rajwanshi, R. Kumar, M.
Meldgaard, C. E. Olsen and J. Wengel, Tetrahedron, 1998, 54, 3607.
4 S. K. Singh and J. Wengel, Chem. Commun., 1998, 1247.
5 S. Obika, D. Nanbu, Y. Hari, K. Morio, Y. In, T. Ishida and T. Imanishi,
Tetrahedron Lett., 1997, 38, 8735.
6 A. A. Koshkin, V. K. Rajwanshi and J. Wengel, Tetrahedron Lett.,
1998, 39, 4381.
7 S. Obika, D. Nanbu, Y. Hari, J. Andoh, K. Morio, T. Doi and T.
Imanishi, Tetrahedron Lett., 1998, 39, 5401.
8 N. T. Thuong, U. Asseline, V. Roig, M. Takasugi and C. Hélène, Proc.
Natl. Acad. Sci. U.S.A., 1987, 84, 5129.
9 C. Gagnor, J.-R. Bertrand, S. Thenet, M. Lemaitre, F. Morvan, B.
Rayner, C. Malvy, B. Lebleu, J.-L. Imbach and C. Paoletti, Nucleic
Acids Res., 1987, 15, 10419.
10 T. Waga, T. Nishizaki, I. Miyakawa, H. Ohrui and H. Meguro, Biosci.
Biotechnol. Biochem., 1993, 57, 1433.
11 H. Vorbrüggen, K. Krolikiewicz and B. Bennua, Chem. Ber., 1981, 114,
1234.
12 A similar ring-opening has been observed when coupling monocyclic
methyl furanosides: P. T. Jørgensen, E. B. Pedersen and C. Nielsen,
Synthesis, 1992, 1299.
13 K. C. Nicolaou, S. P. Seitz and D. P. Papahatjis, J. Am. Chem. Soc.,
1983, 105, 2430.
14 P. Fügedi, P. J. Garegg, H. Lönn and T. Norberg, Glycoconjugate J.,
1987, 4, 97.
15 L. J. Wilson, M. W. Hager, Y. A. El-Kattan and D. C. Liotta, Synthesis,
1995, 1465.
16 H. Sugimura, K. Osumi, T. Yamazaki and T. Yamaya, Tetrahedron
Lett., 1991, 32, 1813.
17 D. Kahne, S. Walker, Y. Cheng and D. J. Van Engen, J. Am. Chem. Soc.,
1989, 111, 6881.
18 L. Chanteloup and J.-M. Beau, Tetrahedron Lett., 1992, 33, 5347.
19 A. De Mesmaeker, C. Lesueur, M.-O. Bévièrre, A. Waldner, V. Fritsch
and R. M. Wolf, Angew. Chem., Int. Ed. Engl., 1996, 35, 2790.
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ene-b- -ribofuranoside 11‡ in 95% yield.
D
Condensation of the bicyclic phenyl thiofuranoside 11 with
silylated thymine20 using NBS as a thiophilic activator13,16 gave
an inseparable mixture of anomeric nucleosides 12 (a:b ~ 2:1)
in 61% yield (or 100% yield based on the recovery of 39%
starting material). This mixture was directly deprotected by
hydrogenation to give the known b-LNA nucleoside 13 and its
a-LNA nucleoside analogue 14§ (in preliminary yields of 12
and 25%, respectively). The expected bicyclic structure of 14
was verified by mass spectrometry and NMR spectroscopy
3
3
which revealed, as for 13,2,3,5 negligible JH1A,H2A and JH2A,H3A
coupling constants ( ~ 0 Hz). Importantly, no ring-opening
reactions were detected using this nucleobase coupling method
taking advantage of the chemoselective cleavage of the
anomeric bond by NBS.
A general bicyclic thioglycoside synthon 11 for nucleobase
coupling reactions has been efficiently synthesized. The
applicability of thiofuranoside 11 has been demonstrated by the
synthesis of the known b-LNA nucleoside 13 and the first a-
LNA nucleoside 14, and analogous thioglycosides may prove
Communication 8/06817H
2646
Chem. Commun., 1998, 2645–2646