An efficient synthetic approach to 6,5′-(S)- and 6,5′-(R)- cyclouridine

Article abstract of DOI:10.1039/c2cc31597a

Here we present new routes for the efficient syntheses of 6,5′-(S)- and 6,5′-(R)-cyclouridine. The syntheses utilize readily accessible uridine as a starting material. This route to the R diastereomer is significantly more efficient than previous synthetic efforts, allowing us to obtain large amounts of pure material for future biological testing.

Full text of DOI:10.1039/c2cc31597a

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An efficient synthetic approach to 6,5 -(S)- and 6,5 -(R)-cyclouridinew
Christopher S. Theile and Larry W. McLaughlin
Received 2nd March 2012, Accepted 3rd April 2012
DOI: 10.1039/c2cc31597a
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Here we present new routes for the efficient syntheses of 6,5 -(S)-
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and 6,5 -(R)-cyclouridine. The syntheses utilize readily accessible
uridine as a starting material. This route to the R diastereomer
is significantly more efficient than previous synthetic efforts,
allowing us to obtain large amounts of pure material for future
biological testing.
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Fig. 1 6,5 -(S)- and 6,5 -(R)-cyclouridine.
Cyclonucleosides have been interesting targets of the nucleo-
side community due to their rigid geometry. A second linkage
Our synthesis is a modification of the path established by
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Ueda et al. to obtain the protected 6,5 -cyclo-5 -deoxyuridine
compound, 7. We have been able to achieve higher yields with
fewer steps while synthesizing compound 7. Our synthesis
between the 5 -carbon of the sugar and the nucleobase fixes the
base in the anti conformation. Such a linkage results in two
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unique diastereomers at the 5 -position in regards to the 5 -OH
(
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begins by protecting the 2 , 3 , and 5 OH positions on uridine
with acetate groups (Scheme 1). The 5 position on the uridine
base is then chlorinated with CAN and LiCl using Asakura’s
Fig. 1).
0
6
,5 -cyclouridine (1S and 1R) and similar compounds are
unable to bind uridine phosphorylase (UrdPase), an enzyme
involved in the anabolism and catabolism of pyrimidines, that
has been shown to be upregulated in multiple human cancer
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2
method.
acetonide protection of the 2 and 3 hydroxyls yields 5. At
Deprotection of the acetates and subsequent
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1
–3
this point we perform a one-step iodination of the 5 position
cell lines.
known to be potent inhibitors of UrdPase. Cyclouridine has
Nucleosides locked in a syn conformation are
using Moffatt’s chemistry, instead of the two-step procedure
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0,13
5
previously utilized.
Radical cyclization with AIBN and
been shown to reduce the rate of hydrolysis in Ribonuclease A.
Ribonucleases degrade unprotected single stranded RNA and
some homologs, most notably Ranpirnase, have been shown
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to have cytotoxic effects on cancer cells. To date, information
Bu SnH and dehydrohalogenation with NaOMe produces 7 in
3
very good yield.
Compound 7 can be directly oxidized to ketone, 8, via an
allylic oxidation with SeO
NaBH yields exclusively the S diastereomer at the 5 position.
2
(Scheme 2). Reduction with
0
relating to the specific binding events of cyclouridine is sparse,
due to low amounts of pure, stereometrically defined, samples.
An efficient synthesis of the S and R diastereomers of
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Acidic removal of the acetonide gives 6,5 -(S)-cyclouridine,
1S. This represents the most efficient pathway that has been
reported to obtain the S diastereomer.
0
6
,5 -cyclouridine will allow for further investigation of the
interactions that these enzymes have with cyclouridine, and
allow for stability studies to be performed with oligonucleotide
strands. Cyclonucleosides also provide unique opportunities
for template studies, where the cyclonucleoside could be used
in the template strand or as a substrate to test the promiscuity
of polymerases.
Meanwhile the acetonide of 7 can be replaced with acetates
to give 10. Oxidation with SeO and t-BuOOH, using methods
2
established by Sharpless, affords a mixture of the R and S
products, with the R diastereomer being the dominant product
1
4
in a better than 3/1 ratio. The two diastereomers can be
separated with purification by column chromatography. A
justification for this reactivity is that when t-BuOOH is added
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Several syntheses of 6,5 -cyclo-5 -deoxyuridine have been under-
7–11
taken, but access to the 5 -OH derivative has been problematic.
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suring SeO oxidation of 7, it results in a mixture of the S
2
The R 5 -OH derivative has been particularly difficult to make,
with only one previously reported synthesis, which relied on
the epimerization of the S diastereomer and resulted in an
diastereomer and starting material. Likely, the rigid nature of
the acetonide protected sugar prevents the R diastereomer
from forming, while the acetates allow the sugar to be more
flexible during the oxidation and the R diastereomer can be
obtained. The acetates on 11S and 11R were removed with 7N
7
unfavorable 2 : 1 ratio of S to R after a 24 h reaction.
Merkert Chemistry Center, 2609 Beacon Street, Chestnut Hill, MA,
USA. E-mail: larry.mclaughlin@bc.edu; Fax: +01 617 552 2705;
Tel: +01 617 552 3622
w Electronic supplementary information (ESI) available. CCDC
870187 and 870188. For ESI and crystallographic data in CIF or
other electronic format see DOI: 10.1039/c2cc31597a
3
NH in MeOH to yield the cyclonucleosides.
Crystal structures of compounds 9 and 11R were obtained
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to confirm the stereochemistry at the 5 position (Fig. 2 and
ESIw). Attempts to crystallize the fully deprotected products,
1R and 1S, yielded poor quality crystals, however, the crystal
This journal is c The Royal Society of Chemistry 2012
Chem. Commun., 2012, 48, 5587–5589 5587

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Scheme 1 The synthesis of 2 , 3 -isopropylidine 6-5 -cyclo-5 -deoxyuridine.
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Scheme 2 Synthesis of R and S diastereomers of 6,5 -cyclouridine.
detrimental to interstrand base pairing. Studies relating to the
strength of base pairing interactions are ongoing in the lab.
One beneficial characteristic of the compounds was seen
with regards to the glycosidic torsion angle, w, of 11R.
The angle is ꢀ148.801, very close to ribonucleosides, which
have a w value near ꢀ1601. Cyclouridine provides an effective
substrate for studies requiring a nucleoside in the anti
conformation.
The sugar pucker of the cyclouridine resides in the envelope
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Fig. 2 A front and overhead view of the crystal structure of 11R with
configuration rather than the C -endo half chair adopted by
3
the acetates removed overlaid with a crystal of uridine, excised from an
4
RNA strand.
the native nucleoside. This change in the sugar conformation
has implications for the structure of an oligomer of cyclo-
0
nucleotides, as the 3 OH is shifted further down from the endo
of 11R is a good approximation of 1R when the acetate groups
are hidden. When overlaying the crystal of 11R and a uridine
nucleotide whose structural parameter were obtained from a
crystal of an RNA dodecamer, several differences are observed
position. Further investigation is needed to understand if this
is the preferred sugar pucker that is adopted when cyclouridine
is inserted into an oligonucleotide strand.
0
The 5 OH in 11R is in a gauche, trans position in relation to
0
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0
between the cyclo and native nucleosides. The additional
0
the O4 and the C , while the S diastereomer is locked in a
3
bond between the 5 carbon and the 6 carbon causes the
trans, gauche position. Native nucleosides usually adopt the
0
U base to be ‘‘pulled’’ back quite dramatically. This may explain
why the rate of hydroysis in RNase A is slowed, since the
shape and conformation of the nucleoside is distorted. Pulling
the base away from the Watson–Crick interactions could be
gauche, gauche position, where the 5 OH points back towards
the furanose ring, as seen in the crystal structure overlay. The
implication of the sugar pucker will be taken into considera-
tion in our continued investigations.
5
588 Chem. Commun., 2012, 48, 5587–5589
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In summary a new and improved route to the S and R
0
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diastereomers of 6,5 -cyclouridine is presented. A key oxida-
tion step with SeO and t-BuOOH affords the R diastereomer
2
in a 3 : 1 ratio compared with the S diastereomer, greatly
increasing the yield and lowering the reaction time previously
reported. These syntheses will allow for the production of
large quantities of each diastereomer of cyclouridine to be
obtained for further biological studies. Additionally, the
crystal structures of cyclouridine have helped to elucidate
the unique structural features caused by the introduction of
3
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6
7
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the C6–C5 bond.
The authors would like to acknowledge Bo Li and Marek
Domin for their guidance in the analytical techniques used in
this manuscript. We would also like to thank Carl Christianson
for the critical reading of this manuscript and for helpful
discussion regarding the science herein.
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Notes and references
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This journal is c The Royal Society of Chemistry 2012
Chem. Commun., 2012, 48, 5587–5589 5589