Synthesis of bicyclo-DNA nucleosides with additional functionalization in the carbocyclic ring

Article abstract of DOI:10.2533/chimia.2008.270

Two novel bicyclo nucleoside isomers carrying the base thymine in the furanose ring and an ester substituent in the carbocyclic ring were synthesized from a common bicyclic sugar precursor via a cyclopropanation/ fragmentation pathway in nine steps. The relative configuration of the ester substituent in both isomers as well as the anomeric configuration in one nucleoside was determined by ¹H-NMR difference NOE spectroscopy. Schweizerische Chemische Gesellschaft.

Full text of DOI:10.2533/chimia.2008.270

LAUREATES: AWARDS AND HONORS SCS FALL MEETING 2007
270
doi:10.2533/chimia.2008.270
CHIMIA 2008, 62, No. 4
Chimia 62 (2008) 270–272
Schweizerische Chemische Gesellschaft
ISSN 0009–4293
©
Synthesis of Bicyclo-DNA Nucleosides
with Additional Functionalization in the
Carbocyclic Ring
§
Samuel Luisier and Christian J. Leumann*
§SCS Poster Prize Winner
Abstract: Two novel bicyclo nucleoside isomers carrying the base thymine in the furanose ring and an ester sub-
stituent in the carbocyclic ring were synthesized from a common bicyclic sugar precursor via a cyclopropanation/
fragmentation pathway in nine steps. The relative configuration of the ester substituent in both isomers as well as
1
the anomeric configuration in one nucleoside was determined by H-NMR difference NOE spectroscopy.
Keywords: Antisense oligonucleotides · Bicyclo-DNA · Nucleosides · Thymine · Tricyclo-DNA
Introduction
also proven to increase siRNA efficacy.[5]
While chemistry has provided solutions to tricyclo-DNA is ideally suited to accommo-
increase duplex stability with target RNA date further functional groups. Such groups
Th e molecular scaffold of bicyclo- and
[1]
Th e concept of conformational restriction
has been successfully applied in the past in and to enhance resistance towards nuclease can for example prove useful in cellular tar-
nucleic acid chemistry and has produced induced degradation, there are still a series geting and cellular uptake when modified
analogues such as the family of the locked of largely unsolved problems on the way to with appropriate molecular entities. With
[2]
nucleic acids (LNA) or tricyclo-DNA effective oligonucleotide drugs, the most thisbackgroundwebecameinterestedinthe
tc-DNA)[ (Fig. 1) which show strongly prominent ones being cellular uptake and bicyclo-DNA derivatives containing an ad-
3]
(
increased affinity to complementary RNA distribution,[ as well as, depending on the ditional carboxyl substituent, such as 1 and
6]
without compromising base-recognition se- mechanism of action, off target effects.[
7]
2 (bc -DNA, Fig. 1). From model building
alk
lectivity. Th ese analogues are currently con-
sidered as advanced generation antisense
agents and are expected to replace the phos-
phorothioate DNA and some of the simpler
DNA
O
DNA
O
[4]
2
’-O-alkyl-RNA analogues in therapy.
H
Besides this, some of these analogues have
O
Base
O
Base
O
O
O
DNA
DNA
LNA
tc-DNA
DNA
DNA
O
H
O
H
O
O
6
'
Base
Base
ROOC
O
O
*
Correspondence: Prof. Dr. C. J. Leumann
DNA
University of Bern
Department of Chemistry and Biochemistry
Freiestrasse 3
DNA
bcalk-DNA
bc-DNA
CH-3012 Bern
Tel.: +41 31 631 4355
Fax: + 41 31 631 3422
E-mail: leumann@ioc.unibe.ch
Fig. 1. Structures of selected examples of conformationally restricted DNA
analogues as well as of bc -DNA described in this paper
alk

LAUREATES: AWARDS AND HONORS SCS FALL MEETING 2007
271
CHIMIA 2008, 62, No. 4
O
TESO
OCH3 a, b
OTES
O
H
H
EtO C
H
2
O
O
O
EtO2C
O
OCH3 c, d
OCH3
OCH3
OH
3
OTMS
4
OTMS
5
OH
6
(
mixture of 3 isomers,
(
mixture of 2 isomers
ratio:2:1:1)
ratio 1:1)
e
HO
TMSO
EtO C
HO
H
H
H
EtO C
O
O
EtO C
O
2
2
2
f
N
O
O
g, h, i
OCH3
NH
OH
OTMS
OH
7
+
1
9
only ꢀ-anomer
HO
H
TMSO
EtO C
HO
H
H
EtO C
O
2
O
EtO C
2
O
2
N
O
O
g, h, i
f
OCH3
NH
OH
OTMS
OH
2
10
8
1
:1 ratio of anomers
Scheme. Reagents and conditions: a) Li-DIPA, Et SiCl, THF, −78 °C, 2 h, 54%; b) BSA, pyridine, 17 h, rt, 86%; c) N CHCOOEt, ClCH CH Cl, Cu(acac) ,
3
2
2
2
2
9
0 °C, 9 h, 80%; d) HF-pyridine, pyridine, r.t. 1h, 81%; e) CeCl , NaBH , 15 min, 0 °C, 57%; f), 2,6-lutidine, TMSOTf, CH Cl , 1h, rt, quant.; g) thymine,
3
4
2
2
BSA, NIS, rt, 3h, h) AIBN, Bu SnH, toluene, refl ux, 2h; i) HF.pyridine, pyridine, rt, 4h, 20−30% over the last three steps.
3
it appears that these functional groups are
located on the rim of the backbone point-
7
.5%
6
.6%
5
.2%
2
.2%
ing away from the helical axis. Th us only
OH
OH
H
little or no interference with duplex forma-
tion as a consequence of a molecular entity
attached in this position can be expected.
In this preliminary communication we de-
scribe a convenient synthetic access to the
corresponding nucleosides carrying the
base thymine.
H
H
H
H
O
EtO C
O
2
H
EtO C
2
OCH3
OCH3
OH
7
OH
8
1
0.3%
4
.9%
3
.1%
OH
H
Results and Discussion
H
O
H
H
EtO C
2
In our synthetic strategy we envisaged
the introduction of the functional group into
C(6’) of the sugar unit via a cyclopropana-
tion/fragmentation pathway on enol ether
N
O
OH
NH
O
1
4
. Th is pathway also provides an entry into
1
Fig. 2. Intensities of observed (mutual) H-NMR difference NOE effects of
functionalizedtricyclo-DNAbuildingblocks
the relevant protons used for assigning the cis- and trans-relationship of
and was therefore considered to be more ap- substituents in the carbocyclic ring in 7 and 8 as well as the β-anomeric
propriate than direct alkylation strategies. configuration in 1
Th e synthesis started with ketone 3 which
is a known key intermediate in the synthe-
sis of tricyclo-DNA.[ (Scheme). Ketone standard column chromatography. We as-
8]
In the light of previous results in the syn-
was converted into the silyl enol ether 4 sume that this isomeric mixture reflects ther- thesis of tricyclo-nucleosides[ we planned
by standard reactions. Cyclopropanation of modynamic equilibrium although we did not the introduction of the nucleobase in a two-
with ethyldiazoacetate in the presence of investigate this fact in detail. Th is mixture step procedure via NIS induced nucleosida-
9]
3
4
[10]
Cu(acac) yielded 5 as a mixture of three iso- of ketones 6 was subsequently reduced with tion of enol ether 9 and 10, followed by
2
mers in a ratio of roughly 2:1:1 in a combined NaBH /CeCl to the hydroxyesters 7 and 8 radical dehalogenation, as this promised to
4
3
yield of 80%. Desilylation with HF·pyridine that could be isolated as pure isomers. Th e
afforded under concomitant cleavage of the relative configuration of 7 and 8 was unam- and thus seemed superior to the standardVor-
yieldstereoselectivelyonlytheβ-nucleosides
1
[11]
cyclopropane ring a mixture of ketoesters 6 biguously assigned by H-NMR NOE spec- brüggen procedure, in which a mixture of
81%) in a 1:1 ratio that was inseparable by troscopy (Fig. 2). anomers had to be expected. To this end the
(

LAUREATES: AWARDS AND HONORS SCS FALL MEETING 2007
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CHIMIA 2008, 62, No. 4
isomers 7 and 8 were separately converted
into enol ethers 9 and 10 by treatment with
Acta 1999, 1489, 167; d) J. Wengel, Acc.
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2] a) S. K. Singh, P. Nielsen,A.A. Koshkin, J.
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Obika, D. Nanbu,Y. Hari, J.-I.Andoh, K.-I.
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3
Morio, T. Doi, T. Imanishi, Tetrahedron
AIBN gave the corresponding nucleoside 1
as a single β-isomer while nucleoside 2 was
obtained as a 1:1 mixture of anomers. We ra-
tionalized the mixture of anomers in the NIS
mediated addition to 9 as the consequence of
the ester substituent at C(6’). In the concave-
shaped intermediate after iodine addition,
this substituent protects the β-face at the
anomeric center from nucleophilic attack by
the nucleobase, thus leading to partial syn
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[
3] a) R. Steffens, C. J. Leumann, J. Am.
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1
the basis of H-NMR NOE spectroscopy
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[
[
Conclusions
2
Biol. 2007, 3, 8; c) A. Grünweller, R. K.
Hartmann, BioDrugs 2007, 21, 235.
We have successfully synthesized two
novel bicyclo-nucleoside modifications
with an additional ester function on the car-
5] a) D. A. Braasch, S. Jensen, Y. Liu, K.
Kaur, K. Arar, M. A. White, D.R. Corey,
bocyclic ring. Th ese nucleosides will now
Biochemistry 2003, 42, 7967; b) J. Elmen,
be converted into the corresponding build-
ing blocks for automated DNA synthesis.
H. Th onberg, K. Ljungberg, M. Frieden,
M. Westergaard, Y. Xu, B. Wahren, Z.
Th e next set of experiments will then be
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Moulton, P. Clair, M. J. Gait J.-J., Vasseur,
B. Lebleu, Curr Top. Med. Chem. 2007, 7,
devoted to the incorporation of these units
into oligodeoxynucleotides and the study
of the effect of the substituent at C(6’) on
the hybridization behavior towards comple-
mentary DNA and RNA.
[
7
27.
7] O. Snøve, Jr, J. J. Rossi, ACS Chem. Biol.
006, 1, 274.
[
[
[
2
Acknowledgements:
8] R. Steffens, C. J. Leumann, Helv. Chim.
Acta 1997, 80, 2426.
9] D. Ittig, D. Renneberg, D. Vonlanthen, S.
Luisier, C. J. Leumann, in Coll. Symp.
Series, Ed. M. Hocec, Academy of
Sciences of the Czech Republic, Prague,
We thank the Swiss National Science
Foundation(grant-No.:3152A0-105968)andthe
Association Monégasque contre les myopathies
for fi nancial support of this project.
Received: February 25, 2008
2
005, Vol. 7, pp 21.
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10] C. U. Kim, P. F. Misco, Tetrahedron Lett.
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[
1
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