3′,4′-trans-Linked bicyclic nucleosides locked in S-type conformations

Article abstract of DOI:10.1039/b205031e

A novel class of 3′,4′-trans-linked bicyclic nucleosides with locked S-type furanose conformations is introduced by synthesis of two model derivatives; one was obtained by cyclic ether formation and the other by ring-closing metathesis methodology.

Full text of DOI:10.1039/b205031e

3A,4A-trans-Linked bicyclic nucleosides locked in S-type conformations
Helena Thomasen,a Michael Meldgaard,b Morten Freitag,a Michael Petersen,a Jesper Wengela and
Poul Nielsen*a
a Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230, Odense M,
Denmark. E-mail: pon@chem.sdu.dk
b Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen,
Denmark
Received (in Cambridge, UK) 24th May 2002, Accepted 4th July 2002
First published as an Advance Article on the web 12th August 2002
A novel class of 3A,4A-trans-linked bicyclic nucleosides with
locked S-type furanose conformations is introduced by
synthesis of two model derivatives; one was obtained by
cyclic ether formation and the other by ring-closing met-
athesis methodology.
Conformationally restricted oligonucleotides have enabled high
affinity recognition of DNA and RNA.1,2 Thus, LNA (locked
nucleic acid) is a prime example with the monomers (e.g. 1)
locked in an N-type conformation (Fig. 1).3–5 We have earlier
presented oligonucleotides containing the bicyclic nucleosides
26 and 37 modeling natural nucleosides locked in S-type
conformations,6,7 and S-type mimics without the natural
ribofuranose skeleton have also been presented, e.g. 4.8
However, oligomers containing 2, 3 or 4 display decreased
affinities towards natural nucleic acid complements, probably
due to steric problems or unfavorable duplex hydration.
Additional structurally related analogues include arabino-
configured 2A-ethynyl,9 2A-methoxy10 and 2A-fluoro11 oligonu-
cleotides, none of which, however, is an ideal S-type mimic.9–11
Recently, we introduced a tricyclic nucleoside derivative also
being strongly restricted in an S-type conformation.12 However,
for this nucleoside, and the bi- and tricyclic nucleoside
analogues of Leumann and coworkers,13,14 the C4A–C5A bond is
involved in the conformational restricted skeleton imposing
unfavorable positioning of the 5A-oxygen atom for formation of
native Watson–Crick type double helices.12–14 Herein we report
the synthesis of two new bicyclic nucleoside derivatives in
which the furanose rings are locked in typical S-type conforma-
tions and the C4A–C5A bonds retain their natural flexibility. In
addition, the introduction of C3A–C4A trans-fused six-membered
rings is expected to be sterically well tolerated in the major
groove of B-type nucleic acid duplexes.
Diacetone- -glucose was converted in three steps to the 3A-C-
D
allyl derivative 5 (Scheme 1).15 In situ regioselective cleavage
of the primary acetonide and subsequent diol cleavage16 was
followed by an aldol condensation of the resulting aldehyde
with formaldehyde and a Cannizzarro reaction affording the
diol 6. Acetylation to give 7 and subsequent acetolysis followed
by another acetylation afforded the glycosyl donor 8. Coupling
with silylated thymine in a modified Vorbrüggen coupling
reaction gave exclusively the b-nucleoside 9 due to anchimeric
assistance from the 2-O-acetyl group.17,18 The b-configuration
of nucleoside 9 and of nucleosides 10–15 was confirmed by the
large values of 3JH1A,H2A (between 7.1 and 8.3 Hz). Deacetylation
of 9 to give nucleoside 10 was followed by regioselective
monotosylation at the 4A-C-hydroxymethyl functionality afford-
ing 11. The site of tosylation was confirmed chemically, as it
would be possible to cyclize 11 to give a 3A-C-branched-2A-O,4A-
C-methylene linked LNA-type nucleoside if the tosylation had
Scheme 1 Reagents and conditions: i) a, H5IO6, EtOAc; b, H2CO, NaOH,
THF, H2O then NaBH4 (82%); ii) Ac2O, DMAP, pyridine (85%); iii) a, 80%
aq. AcOH, 90 °C; b, Ac2O, DMAP, pyridine (88%); iv) thymine, N,O-
bis(trimethylsilyl)acetamide, TMS-triflate, MeCN, 60 °C (67%); v)
NaOMe, MeOH (81%); vi) TsCl, pyridine (70%); vii) a, DMTCl, pyridine;
b, NaH, CH3I, THF, 0°C (65%); viii) a, OsO4, NaIO4, H2O, dioxane; b,
NaBH4, H2O, dioxane (48%); ix) NaH, DMF (89%); x) H2, Pd/C, EtOH
(67%); xi) NaH, BnBr, DMF (55%); xii) a, PCC, CH2Cl2; b, vinylMgBr,
THF (63%); xiii) BzCl, pyridine (98%); xiv) a, 80% aq. AcOH, 90 °C; b,
Ac2O, pyridine (92%); xv) thymine, N,O-bis(trimethylsilyl)acetamide,
TMS-OTf, MeCN (93%); xvi) 2 mol-% Grubbs‘ catalyst,21 ClCH2CH2Cl
(90%); xvi) NaOMe, MeOH, reflux (69%); xviii) BCl3, hexane, CH2Cl2
(69%). Thy = thymin-1-yl.
occurred at the assigned position (11, R3 = Ts).3,4,6 Actually,
derivative 11 upon treatment with NaH in DMF was efficiently
Fig. 1 Structures of bicylic nucleosides; Thy = thymin-1-yl.
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CHEM. COMMUN., 2002, 1888–1889
This journal is © The Royal Society of Chemistry 2002

converted into a compound for which the 1H NMR spectral data
were in accordance with data expected for an LNA-type
nucleoside (data not shown). As the next step selective
protection of the 5A-OH group as its DMT ether was accom-
plished followed by chemoselective 2A-O-methylation. In order
to limit the competing methylation at N3, we applied conditions
which have earlier been used for chemoselective O-methylation
of nucleosides,19 and obtained 12 in reasonable yield.†
Oxidative cleavage of the C3A-allyl moiety of 12 followed by
reduction afforded the 2-hydroxyethyl substituted nucleoside
13. Subsequent efficient cyclization to give 14 and hydro-
genolysis furnished the conformationally locked bicyclic nu-
cleoside 15.‡§
The Danish National Research Foundation, Danish National
Science Research Council and the Danish Technical Research
Council are thanked for financial support.
Note added in proof. After submission of this manuscript, a
slightly different preparation of 15 was published: S. Obika, M.
Sekiguchi, T. Osaki, N. Shibata, M. Masaki, Y. Hari and T.
Imanishi, Tetrahedron Lett., 2002, 43, 4365.
Notes and references
† Methylation at O2A and not N3 was verified by NMR spectroscopy. The
N3-proton of 12 appeared at 8.5 ppm together with a signal at 3.5 ppm
diagnostic of an OCH3 substituent (corresponding to a signal at 60 ppm in
the 13C NMR spectrum).
‡ Synthesis of compound 15 was included in the Ph.D. thesis of Dr M.
Meldgaard, Dept. of Chemistry, University of Copenhagen, June 2000.
§ Selected data for (1S,6R,8R,9R)-1-hydroxy-6-hydroxymethyl-9-me-
thoxy-8-(thymin-1-yl)-4,7-dioxabicyclo[4.3.0]nonane (15); 1H NMR
(CD3OD) d 8.11 (d, J 1.4 Hz, 1H, 6-H), 6.17 (d, J 7.1 Hz, 1H, 1A-H), 4.63
(d, J 7.1 Hz, 1H, 2A-H), 4.02 (m, 4H, CH2), 3.75 (dd, J 5.0, 11.0 Hz, 1H,
CH2), 3.48 (d, J 9.6 Hz, 1H, CH2), 3.42 (s, 1H, OCH3), 2.08 (m, 1H, CH2),
1.90 (d, J 1.4 Hz, 3H, CH3), 1.84 (dd, J 3.0, 13.2 Hz, 1H, CH2); selected data
for (1S,5S,6S,8R,9R)-1,5,9-trihydroxy-6-hydroxymethyl-8-(thymin-1-yl)-
7-oxabicyclo[4.3.0]non-3-ene (23); 1H NMR (DMSO-d6) d 11.31 (br s, 1H,
N-H), 8.17 (br s, 1H, 6-H), 6.10 (d, J 7.4 Hz, 1H, 1A-H), 5.81–5.71 (m, 3H,
2B-H, 3B-H, 3A-OH), 5.48 (br s, 1H, 5A-OH), 5.29 (d, J 6.3 Hz, 1H, 2A-OH),
5.10 (d, J 8.9 Hz, 1H, 1B-OH), 4.64 (dd, J 6.3, 7.4 Hz, 1H, 2A-H), 3.76 (m,
1H, 1B-H), 3.56–3.35 (m, 2H, 5A-H), 2.32-2.26 (m, 2H, 4B-H), 1.79 (s, 3H,
CH3).
In order to obtain the related bicyclic nucleoside 23 likewise
conformationally locked in an S-type conformation due to the
additional C3A–C4A-trans-fused six-membered ring, a ring-
closing metathesis-based synthesis starting from the diol 6 was
accomplished. Differentiation between the two primary alco-
hols of 6 was possible probably because of steric shielding of
the a-face of the bicyclic system, and benzylation afforded a
4+1 ratio of bisbenzylic ethers of which 16 was obtained in 55%
yield as the major isomer after chromatographic separation. The
full assignments of 16 and its 4-epimer were performed by 1H
NMR spectroscopy. A similar ratio between 4-epimers has
earlier been obtained on a similar substrate without the 3A-C-
1
allyl group.¶ When exploring the H NMR data given for that
case,20 the H1A signals∑ of both isomers were seen to be shifted
downfield compared to the H5 signals.¶20 We ascribe this
phenomenon to deshielding by the electronegative 3-O atom.
For 16, the highest chemical shifts were observed for the signal
coupling to an OH-signal hereby confirming the 5-O-benzyla-
tion, whereas in the 4-epimer the situation is opposite.
Subsequently, 16 was oxidized to an aldehyde followed by
another Grignard addition to give two epimers in a 1+3 ratio
from which 17 was isolated as the major isomer after
chromatographic separation.** Protection as the benzoic ester
18 was followed by hydrolysis and acetylation to give the
anomeric mixture 19. A Vorbrüggen-type coupling gave
exclusively the b-nucleoside 20. The RCM reaction was
performed using Grubbs’ commercially available carbene
precatalyst21 affording smoothly the bicyclic nucleoside 21 in a
high yield. The structure of this compound was confirmed by
NMR and MS verifying the loss of ethylene, and by the large
coupling constant 3JH1AH2A = 7.4 Hz confirming this nucleoside
to be b-configured and locked in an S-type conformation (vide
infra). A basic treatment of 21 afforded cleavage of both the
ester moieties to give 22 and finally, a Lewis acid mediated
cleavage of the benzylic ethers gave the target bicyclic
nucleoside 23.§
The furanose conformations of nucleosides 15 and 23 were
analyzed using the theory of Altona and coworkers.22,23 The
possible H1AH2A torsion angles derived from the vicinal 3JH1AH2A
coupling constants were 148 and 152° for 15 and 23,
respectively. The exocyclic H1AH2A torsion angle is a function
of the pseudorotation angle, P, and the puckering amplitude,
Fmax, and considering Fmax in the range from 32 to 46°, we
found possible ranges of P of 190–205° for 15 and 180–200° for
23. This corresponds perfectly with 15 and 23 being the first
nucleosides (despite 3) with a natural ribofuranose skeleton
locked in S-type conformations and with preserved flexibility of
the C4A–C5A bond.
¶ The O-benzylation of 4A-C-hydroxymethyl-3-O-benzyl-1,2-O-isopropyli-
dene-a-D-ribofuranose with NMR assignments of the products given from
NOE-difference spectra; ref. 20.
∑ We define the first carbon of the C4 substituent as C1A i.e. defined as C1B
in corresponding nucleosides.
** Determination of the C1B-configuration was accomplished by NMR
spectroscopy on the tricyclic RCM products of 17 and its C1B-epimer;
manuscript in preparation.
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In summary, the bicyclic nucleosides 15 and 23 have been
synthesized in 11 steps from 5 in overall yields of 4.5 and 10%,
respectively. In a very satisfying 22% overall yield from 5, the
RCM strategy afforded smoothly a highly constrained bicyclic
nucleoside derivative 21 as a key intermediate towards the
construction of other bicyclic nucleosides, e.g., saturated,
hydroxylated or 2A-deoxygenated derivatives. In short, 3A,4A-
trans-linked bicyclic nucleosides have been introduced herein
as a novel class of locked S-type nucleoside mimics exemplified
by the synthesis of ribonucleoside analogues.
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