Facile synthesis and conformation of 3'-O,4'-C-methyleneribonucleosides

Article abstract of DOI:10.1039/a907218g

Bicyclic nucleoside analogues, 3'-O,4'-C-methyleneribonucleosides 1, including thymine, cytosine, adenine and guanine nucleobases, were conveniently synthesized from D-glucose, and the ribofuranose ring of I was found to exist predominantly in a S-conform

Full text of DOI:10.1039/a907218g

Facile synthesis and conformation of 3A-O,4A-C-methyleneribonucleosides
Satoshi Obika, Ken-ichiro Morio, Yoshiyuki Hari and Takeshi Imanishi*
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
E-mail: imanishi@phs.osaka-u.ac.jp
Received (in Cambridge, UK) 7th September 1999, Accepted 26th October 1999
Bicyclic nucleoside analogues, 3A-O,4A-C-methyleneribonu-
cleosides 1, including thymine, cytosine, adenine and
guanine nucleobases, were conveniently synthesized from d-
glucose, and the ribofuranose ring of 1 was found to exist
with AcOH and Ac2O in the presence of a catalytic amount of
H2SO4. Debenzylation and subsequant acetylation of the
3-hydroxy group in 5 gave the triacetate 6 (91%). The reaction
of 6 with O,OA-bis(trimethylsilyl)thymine (T·2TMS) under
Vorbrüggen’s conditions11 afforded only the b-anomer of
1
predominantly in a S-conformation by means of H NMR
and X-ray analysis.
In recent studies aimed at developing an effective antisense
molecule, numerous oligonucleotide analogues have been
synthesized with various chemical modifications of the phos-
phodiester backbone, sugar moiety and/or nucleobase region.1
In these attempts, the oligonucleotide analogues containing
‘non-genetic’ 2A,5A-phosphodiester linkages (2A,5A-linked oligo-
nucleotides) were found to be favorable as antisense molecules
because of their RNA selective hybridization ability and
enzymatic stability.2 Furthermore, 2-5A (2A,5A-linked oligoade-
nylate 5A-triphosphate) is well-known to have an important role
in the interferon-mediated antiviral system in living cells,3 and
intensive studies on various 2-5A analogues have been
reported.4 However, there is only limited information available
on the relationship between the sugar conformation in 2A,5A-
linked oligonucleotides and their attractive properties, such as
hybridization ability and antiviral activity.5
From the consideration that the restriction of sugar puckering
in nucleosides to a proper conformation would serve as an
advantageous strategy to develop a desired antisense (antigene)
molecule,6,7 we have recently accomplished the synthesis of
conformationally restricted nucleoside analogues, 3A-O,4A-C-
methylene-uridine and -cytidine 1 (B = U and C) by using
uridine as a starting material,8 and also demonstrated interesting
properties of the 2A,5A-linked oligonucleotide analogues contain-
ing 1 (B = U and T), e.g. RNA selective hybridization
abilities.9
Scheme 1 Reagents and conditions: i, TBDPSCl, Et3N, CH2Cl2, room
temp., 14 h; ii, TsCl, Et3N, DMAP, CH2Cl2, room temp., 16 h; iii, AcOH,
Ac2O, conc. H2SO4, room temp., 30 min; iv, 10% Pd-C/H2, Et-OAc–
CHCl3, room temp., 17 h; v, Ac2O, Py, room temp., 20 h; vi, sililated base,
TMSOTf, CH2CH2Cl2, reflux, 8–18 h; vii, K2CO3, room temp., 15 min; viii,
NaHMDS, THF, room temp., 1h; ix, TBAF, THF, room temp., 15 min.
Unfortunately, the synthetic route of 1 was not practical for
purine analogues. We now report a novel and practical synthetic
route to 1 bearing various nucleobases, exemplfied by synthesis
of all four nucleoside analogues 1 (B = T, CBz, ABz and GiBu),
and also discuss their conformation.
After several attempts,† the synthesis of the target com-
pounds 1 was performed by a coupling reaction of a 1-O-
acetylribofuranose derivative with silylated nucleobases and a
subsequent oxetane ring formation, as shown in Scheme 1. A
stereoselective silylation of the diastereotopic hydroxy groups
in
3-O-benzyl-4-hydroxymethyl-1,2-O-isopropylidene-a-d-
ribofuranose 210 gave the desired compound 3 (67%). The
stereochemistry at C4 in 3 was confirmed by means of NOE
measurements. A p-tolylsulfonylation of 3 afforded the tosylate
4 (97%), which was converted to diacetate 5 (86%) by treatment
Fig. 1 ORTEP drawing of 1a.
Chem. Commun., 1999, 2423–2424
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for C11H14N2O6·H2O: C, 45.83; H, 5.59; N, 9.72. Found: C, 45.81; H, 5.51;
N, 9.71%).
¶ The percentage of S-conformation (S%) is calculated from the equation:
S% = 100(J1A2A 2 1)/6.9. See ref. 8 and 14.
∑ Crystal data for 1a: C11H14N2O6·H2O, M = 288.26, colourless plate, 0.30
thymidine derivative 7a (77%). The triacetate 6 was also
coupled with silylated N4-benzoylcytosine (CBz·2TMS), N6-
benzoyladenine (ABz·2TMS) and N2-isobutyrylguanine (G
iBu·3TMS) to give the corresponding b-nucleoside derivatives
7b (82%), 7c (70%) and 7d (72%),‡ respectively. Methanolysis
of 7 gave diols 8 (63–90%) and then oxetane ring formation
from 8 was accomplished on treatment with sodium hexame-
thyldisilazide in THF at room temperature, yielding only the
corresponding 3A-O,4A-C-methyleneribonucleoside derivatives
9 (78–100%). The desired products 1 were obtained (65–71%)
by removal of a TBDPS group in 9. We have, thus, achieved a
facile synthesis of 3A-O,4A-C-methyleneribonucleosides 1 in
good yield.§
3 0.20 3 0.10 mm, orthorhombic, P212121, a
= 8.6242(10), b =
20.6008(8), c = 7.2767(11) Å, V = 1292.8(3) Å3, T = 283 K, Z = 4, m
(Cu–Ka) = 1.54 mm21, 1177 reflections measured, 1155 independent
reflections, 1037 reflections observed, R = 0.0397, Rw = 0.0984. CCDC
182/1463. See http://www.rsc.org/suppdata/cc/1999/2423/ for crystallo-
graphic data in .cif format.
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The conformational analysis of the obtained 3A-O,4A-C-
1
methyleneribonucleosides 1 was carried out by means of H
NMR and X-ray crystallographic data. Namely, all of the
bicyclic nucleoside analogues 1 show a relatively large J1A2A
value (7.3–7.6 Hz in CD3OD), which means that these
nucleoside analogues have predominantly the S-conformation
(S% = 91–96%),¶ regardless of the type of the nucleobase.
Furthermore, an X-ray crystallographic analysis of 1a shows
that the sugar pucker pseudorotation phase angle (P) is 136.2°
and the maximum out-of-plane pucker (nmax) is 32.3°, charac-
teristic of the C1A-exo-C2A-endo form (S-conformation) of sugar
puckering.∑
It is noteworthy and very interesting that the expressed S-
preference of the nucleoside analogues 1 is vastly different from
conformational analysis of other nucleosides possessing a 2A-
OH group, e.g. uridine (S% = 52%),8 cytidine (S% = 26%),8
3A-deoxyuridine (S% = 3%)8,12 and 3A-deoxycytidine (S% =
0%).8,13
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Further studies on these bicyclic nucleosides are now in
progress.
A part of this work was supported by a Grant-in-Aid for
Scientific Research (B), No. 09557201, from the Japan Society
for the Promotion of Science. We are also grateful to the Takeda
Science Foundation for financial support.
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Notes and references
† As an altanative route for the synthesis of 1, we briefly tried a coupling
reaction of the oxetane derivative 10 with silylated thymine, resulting in
exclusive C–O bond fission of the oxetane ring to afford only 11.
8 S. Obika, K. Morio, D. Nanbu and T. Imanishi, Chem. Commun., 1997,
1643.
9 S. Obika, K. Morio, Y. Hari and T. Imanishi, Bioorg. Med. Chem. Lett.,
1999, 9, 515.
10 R. D. Youssefyeh, J. P. H. Verheyden and J. G. Moffatt, J. Org. Chem.,
1979, 44, 1301.
11 H. Vorbrüggen, K. Krolikiewiczz and B. Bennua, Chem. Ber., 1981,
114, 1234; H. Vorbrüggen and G. Höfle, Chem. Ber., 1981, 114,
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12 Measured in (CD3)2SO: T.-S. Lin, J.-H. Yang, M.-C. Liu, Z.-Y. Shen,
Y.-C. Cheng, W. H. Prusoff, G. I. Birnbaum, J. Giziewicz, I. Ghazzouli,
V. Brankovan, J.-S. Feng and G.-D. Hsiung, J. Med. Chem., 1991, 34,
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‡ Guanosine derivative 7d was obtained as a mixture of N9 and N7
regioisomers (72%, N9/N7 = ca. 1/3) which was directly converted to 8d
without separation. The N9 and N7 isomers of 8d were obtained in 63 and
18% yield, respectively, after silica gel chromatography. The ster-
eochemistry of each isomer 8d was determined by comparison of their 1H
and 13C NMR data.
§ Selected data for 1a: mp 119–120 °C (AcOEt); [a]2D5 263.1 (c 0.44,
MeOH); nmax(KBr)/cm21 4016, 3451, 1723; dH(CD3OD) 1.89 (3H, s),
3.75, 3.83 (2H, AB, J 12), 4.14 (1H, d, J 8), 4.51, 4.83 (2H, AB, J 8), 5.05
(1H, d, J 5), 6.42 (1H, d, J 8), 7.52 (1H, s); m/z (FAB) 277 (M+Li+) (calc.
Communication 9/07218G
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