Synthesis and NMR-analysis of tricyclic nucleosides

Article abstract of DOI:10.1081/NCN-100002543

Two anomeric tricyclic nucleosides have been synthesised from diacetone-D-glucose using oxidation, stereoselective Grignard-addition of a vinyl-group, a stereoselective dihydroxylation followed by a tandem ring closing reaction, and finally a nucleobase coupling. The main β-configured product was examined and its configuration confirmed using NMR-spectroscopy in connection to ab initio calculations. The preferred conformation of this tricyclic nucleoside was described.

Full text of DOI:10.1081/NCN-100002543

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SYNTHESIS AND NMR-ANALYSIS OF TRICYCLIC
NUCLEOSIDES
Poul Nielsen a , Michael Petersen a & Jens Peter Jacobsen a
a Department of Chemistry , University of Southern Denmark , Odense M, 5230, Denmark
Published online: 07 Feb 2007.
To cite this article: Poul Nielsen , Michael Petersen & Jens Peter Jacobsen (2001) SYNTHESIS AND NMR-ANALYSIS OF
TRICYCLIC NUCLEOSIDES, Nucleosides, Nucleotides and Nucleic Acids, 20:4-7, 1309-1312, DOI: 10.1081/NCN-100002543
To link to this article: http://dx.doi.org/10.1081/NCN-100002543
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS, 20(4–7), 1309–1312 (2001)
SYNTHESIS AND NMR-ANALYSIS OF
TRICYCLIC NUCLEOSIDES
Poul Nielsen,∗ Michael Petersen, and Jens Peter Jacobsen
Department of Chemistry, University of Southern Denmark,
5230 Odense M, Denmark
ABSTRACT
Two anomeric tricyclic nucleosides have been synthesised from diacetone-D-
glucose using oxidation, stereoselective Grignard-addition of a vinyl-group, a
stereoselective dihydroxylation followed by a tandem ring closing reaction, and
finally a nucleobase coupling. The main β-configured product was examined
and its configuration confirmed using NMR-spectroscopy in connection to ab
initio calculations. The preferred conformation of this tricyclic nucleoside was
described.
Conformationally restricted nucleosides have been intensively investigated
as potential antiviral agents and in oligonucleotide analogues (1). Thus, bi- and
tricyclic nucleosides have been constructed and further developed into nucleic acid
analogues with very promising abilities in the recognition of complementary nu-
cleic acid sequences (2–6). As an example, the bicyclic nucleoside 1 (Scheme 1) has
been synthesised and incorporated into oligodeoxynucleotides (2). A fully modi-
fied sequence demonstrated moderately enhanced affinity towards complementary
RNA. The furanose ring in 1 has been shown to prefer an O4ꢀ-endo conformation
as demonstrated by an X-ray crystallographic study of 1 incorporated in a DNA
dodecamer duplex (7) as well as by a corresponding NMR-study (8).
In order to improve the properties of 1, we decided to introduce further
conformational restriction into this bicyclic structure by the synthesis of
tricyclic nucleosides (Scheme 1). As a convenient and cheap starting material,
∗Corresponding author.
1309
ꢁ
C
Copyright 2001 by Marcel Dekker, Inc.
www.dekker.com

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NIELSEN, PETERSEN, AND JACOBSEN
Scheme 1. a) i. CrO3, Ac2O, Pyridine, CH2Cl2, ii. VinylMgBr, Ether, THF, iii. 80% AcOH (75%);
b) i. TrCl, Pyridine, ii. BnBr, NaH, DMF (63%); c) i. 20% HCl in MeOH, H2O (76%), ii. MsCl,
Pyridine (95%); d) i. OsO4, NMO, H2O, Pyridine, t-BuOH, ii. NaH, DMF (48/42%); e) i. Thymine,
BSA, TMS-Tf, CH3CN (52%), ii. H2, Pd(OH)2-C, EtOH (73%). T = thymin-1-yl.
diacetone-D-glucose was chosen and stereoselectively converted to the 3ꢀ-C-
vinyl compound 2 using a slightly changed literature method (9). Reprotection
to give 3, acidic treatment and mesylation gave the separable anomers 4a and 4b.
Dihydroxylation of 4a followed by a base-induced tandem ring closure afforded
only one major product 5a. The exact configuration of 5a was not elucidated at this
stage. However, MS-data and NMR strongly suggested the formation of a tricyclic
structure. In a similar sequence, 4b afforded the other anomer 5b. A nucleobase
coupling of either of the two anomers gave the same inseparable anomeric mixture
of nucleosides which after deprotection were separated to give the two tricyclic
nucleoside products 6 and 7 in a 1:3 ratio.
The exact configurations of 6 and 7 could only partly be confirmed by NOE-
spectroscopy due to spectral overlap. Thus, an NOE-contact between H1ꢀ and H4ꢀ
was only seen for the major product (7) confirming its β-configuration. However,
the exact 3JHH coupling constants were measured for both compounds as shown for
7 in Table 1. Subsequently, ab initio calculations were performed for 7 as well as
for three alternative tricyclic structures A, B and C, which from a synthetic point of
view had to be considered (Fig. 1). The torsional angles were calculated as shown
ꢀ
ꢀ
in Table 1. Furthermore, the Karplus relationships (10) between JH1 H2 and the
pseudorotation angle P of the furanose ring (11) as well as between the other 3JHH
coupling constants listed in Table 1 and the corresponding dihedral angles were
derived. From these Karplus curves (not shown), the dihedral angles allowed by
the experimental coupling constants could be found. In none of the calculations
performed on A–C, a geometry was obtained in which all torsional angles could fit
all the measured coupling constants simultaneously. Even though calculations were

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TRICYCLIC NUCLEOSIDES
1311
Table1. Exp.1H-NMRDataa for7andCalc. Datab fortheTheoreticallyPossibleβ-Nucleosidesc
δ/ppm
3JHH/Hz
7
A
B
C
H1ꢀ 6.11
H2ꢀ 4.39
H4ꢀ 4.04
H5ꢀ 4.22
H6ꢀ 4.02
H6ꢀꢀ 3.72
H7ꢀꢀ 3.90
H8 4.01
H8ꢀꢀ 3.95
P
ꢀmax
85◦
37◦
39◦
22◦
175◦
23◦
85◦
38◦
H1ꢀH2ꢀ 4.7
H4ꢀH5ꢀ 3.1
H5ꢀH6ꢀ 7.7
H5ꢀH6ꢀꢀ 8.0
H7ꢀH8ꢀ 3.2
H7ꢀH8ꢀꢀ <1.5
55◦
−26◦
−42◦
−23◦
ꢀ
θH4 H5
ꢀ
−23◦
−141◦
38◦
54◦
84◦
−39◦
−55◦
62◦
83◦
ꢀ
θH5 H6
ꢀ
−65◦
44◦
−39◦
−69◦
165◦
95◦
ꢀ
θH5 H6
ꢀꢀ
ꢀ
θH7 H8
ꢀ
−85◦
172◦
92◦
ꢀ
θH7 H8
ꢀꢀ
γ
178◦
81◦
aCD3OD at 500 MHz.
bPerformed at the 3–21G level.
cFor definitions on P, ꢀmax and γ see ref. 11.
performed in which some of the angles were constrained in allowed angles (not
shown), other angles did not fit the experimental data. Thus, we conclude that 7 is
the only possible structure fitting our experimental NMR-data and the configuration
of 7 is hereby confirmed.
Since no change in the coupling constants of 7 was observed in the tem-
perature range from −50 to 50◦C, the nucleoside is believed to exist in only one
conformation. This conformation is described by the torsional angles obtained from
the unconstrained geometry optimisation (Table 1) and is shown in Figure 1. The
furanose ring of this tricyclic nucleoside prefers the O4ꢀ-endo conformation as
in the bicyclic nucleoside 1. This is an unusual and high-energy conformation in
unmodified nucleosides (11). However, this conformation might be favourable for
nucleic acid recognition as found for oligodeoxynucleotides containing 1 (2), its
smalleranaloguewithafour-memberedring(3), orthe2ꢀF-arabinodeoxynucleoside
analogues (7,12). On the other hand, the C4ꢀ-C5ꢀ torsional angel γ of 7 is found to
be in the +ap range which is probably unfavourable for Watson-Crick type duplex
formation (6).
In conclusion, the alternative epimer A seems to be restricted in a more
favourable conformation than 7 and the synthesis of this nucleoside as well as the
Figure 1. The determined conformation of 7, and the possible alternative structures.

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NIELSEN, PETERSEN, AND JACOBSEN
incorporation of both epimers into oligonucleotide sequences will be performed in
due course.
ACKNOWLEDGMENTS
The Danish Natural Science Research Council is thanked for financial support.
REFERENCES
1. Herdewijn, P. Liebigs Ann. 1996, 1337–1348.
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3. Christensen, N. K.; Petersen, M.; Nielsen, P.; Jacobsen, J. P.; Olsen C. E. Wengel J.
J. Am. Chem. Soc. 1998, 120, 5458–4562.
4. S. K. Singh, P. Nielsen, A. A. KoshkinandJ. Wengel, Chem. Commun., 1998, 455–456.
5. Tarko¨y, M.; Leumann, C. Angew. Chem. Int. Ed. Engl. 1993, 32, 1432–1434.
6. Steffens, R.; Leumann, C. J. J. Am. Chem. Soc. 1997, 119, 11548–11549.
7. Minasov, G.; Teplova, M.; Nielsen, P.; Wengel, J.; Egli, M. Biochemistry, 2000, 39,
3525–3532.
8. Jørgensen, L. B.; Nielsen, P.; Wengel, J.; Jacobsen, J. P. J. Biomol. Struc. Dyn., 2000,
in Press.
9. Marco-Contelles, J.; Ruiz, P.; Mart´ınez, L.; Mart´ınez-Grau, A. Tetrahedron 1993, 49,
6669–6694.
10. Donders, L. A.; de Leeuw, F. A. A. M.; Altona, C. Magn. Res. Chem., 1989, 27,
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11. Saenger, W. Principles of Nucleic Acid Structure, Springer, New York, 1984.
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Parniak, M. A. J. Am. Chem. Soc., 1998, 120, 12976–12977.

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