Practical silyl protection of ribonucleosides

Article abstract of DOI:10.1021/ol402023c

Herein we report the site-selective silylation of the ribonucelosides. The method enables a simple and efficient procedure for accessing suitably protected monomers for automated RNA synthesis. Switching to the opposite enantiomer of the catalyst allows f

Full text of DOI:10.1021/ol402023c

ORGANIC
LETTERS
2013
Vol. 15, No. 18
4710–4713
Practical Silyl Protection
of Ribonucleosides
Thomas P. Blaisdell,† Sunggi Lee,† Pinar Kasaplar,‡ Xixi Sun,† and Kian L. Tan*,†
Institute of Chemical Research of Catalonia, Av. Paisos Catalans 16,
43007 Tarragona, Spain, and Boston College, 2609 Beacon Street,
Chestnut Hill, Massachusetts 02467-3860, United States
kian.tan@novartis.com
Received July 18, 2013
ABSTRACT
Herein we report the site-selective silylation of the ribonucelosides. The method enables a simple and efficient procedure for accessing suitably
protected monomers for automated RNA synthesis. Switching to the opposite enantiomer of the catalyst allows for the selective silylation of the
30-hydroxyl, which could be used in the synthesis of unnatural RNA or for the analoging of ribonucelosides. Lastly, the procedure was extended to
ribavirin a potent antiviral therapeutic.
Site-selective catalysis1 is the ability to differentiate a
functional group, when multiple similar groups are present
in the molecule. Over the past several years site-selective
catalysis has emerged as a powerful and efficient means of
derivatizing and analoging natural products.2,3 To achieve
site selectivity in the absence of a catalyst, synthetic
chemists rely on either a significant bias in innate reactivity
within the substrate (e.g., functionalizing a primary over a
tertiary hydroxyl) or protecting group strategies, which
mask other potential reactive sites. Beyond late stage
functionalization, site-selective catalysis can also be em-
ployed in more traditional synthetic streamlining; in parti-
cular, it has been employed in the selective functionalization
of monosaccharides.4,5
A significant challenge for site-selective catalysis is the
manipulation of sites that are less or similarly reactive to
other positions within the molecule. To this end, we have
been pursuing catalysts that react with specific functional
group motifs within complex molecules. To achieve this
goal we have synthesized catalysts that have a catalytic
residue appended to a substrate-binding site (Figure 1).
The substrate-binding event occurs through a reversible
covalent bond,6 minimizing the molecular interactions
necessary for substrate localization. Through this design,
† Boston College.
‡ Institute of Chemical Research of Catalonia.
(1) Mahatthananchai, J.; Dumas, A. M.; Bode, J. W. Angew. Chem.,
Int. Ed. 2012, 51, 10954–10990.
(2) (a) Lewis, C. A.; Miller, S. J. Angew. Chem., Int. Ed. 2006, 45,
5616–5619. (b) Chen, M. S.; White, M. C. Science 2007, 318, 783–787. (c)
Lewis, C. A.; Longcore, K. E.; Miller, S. J.; Wender, P. A. J. Nat. Prod.
2009, 72, 1864–1869. (d) Yoshida, K.; Furuta, T.; Kawabata, T. Tetra-
hedron Lett. 2010, 51, 4830–4832. (e) Fowler, B. S.; Laemmerhold,
K. M.; Miller, S. J. J. Am. Chem. Soc. 2012, 134, 9755–9761. (f) Pathak,
T. P.; Miller, S. J. J. Am. Chem. Soc. 2012, 134, 6120–6123. (g) Bruckl,
T.; Baxter, R. D.; Ishihara, Y.; Baran, P. S. Acc. Chem. Res. 2012, 45,
826–839. (h) Beale, T. M.; Taylor, M. S. Org. Lett. 2013, 15, 1358–1361.
(i) Pathak, T. P.; Miller, S. J. J. Am. Chem. Soc. 2013, 135, 8415–8422.
(3) For examples of directed and reagent controlled functionalization
of natural products, see: (a) Breslow, R.; Baldwin, S.; Flechtne, T.;
Kalicky, P.; Liu, S.; Washburn, W. J. Am. Chem. Soc. 1973, 95, 3251–
3262. (b) Breslow, R.; Corcoran, R. J.; Snider, B. B.; Doll, R. J.; Khanna,
P. L.; Kaleya, R. J. Am. Chem. Soc. 1977, 99, 905–915. (c) Breslow, R.;
Heyer, D. J. Am. Chem. Soc. 1982, 104, 2045–2046. (d) Wilcock, B. C.;
Uno, B. E.; Bromann, G. L.; Clark, M. J.; Anderson, T. M.; Burke,
M. D. Nat. Chem. 2012, 4, 996–1003.
(4) For a review on sugar functionalization, see: Lee, D.; Taylor,
M. S. Synthesis 2012, 44, 3421–3431.
(5) (a) Griswold, K. S.; Miller, S. J. Tetrahedron 2003, 59, 8869–8875.
(b) Kawabata, T.; Muramatsu, W.; Nishio, T.; Shibata, T.; Schedel, H.
J. Am. Chem. Soc. 2007, 129, 12890–12895. (c) Kawabata, T.; Furuta, T.
Chem. Lett. 2009, 38, 640–647. (d) Chan, L.; Taylor, M. S. Org. Lett.
2011, 13, 3090–3093. (e) Gouliaras, C.; Lee, D.; Chan, L.; Taylor, M. S.
J. Am. Chem. Soc. 2011, 133, 13926–13929. (f) Lee, D.; Taylor, M. S.
J. Am. Chem. Soc. 2011, 133, 3724–3727. (g) Lee, D.; Williamson, C. L.;
Chan, L.; Taylor, M. S. J. Am. Chem. Soc. 2012, 134, 8260–8267.
(6) (a) Park, Y. J.; Park, J. W.; Jun, C. H. Acc. Chem. Res. 2008, 41,
222–234. (b) Rousseau, G.; Breit, B. Angew. Chem., Int. Ed. 2011, 50,
2450–2494. (c) Tan, K. L. ACS Catal. 2011, 1, 877–886.
r
10.1021/ol402023c
Published on Web 09/03/2013
2013 American Chemical Society

selectivity and rate acceleration are achieved through
proximity effects.7 This is an ideal mechanism for site-
selective catalysis, because acceleration is directly linked to
the structural arrangement of the functional groups. Be-
cause proximity effects can result in orders of magnitude of
rate acceleration, differentiation of groups that have simi-
lar reactivity and even the functionalization of inherently
less reactive sites is possible.8
Table 1. Optimization of D-Uridine Silylationa
equiv
conversion
(%)c
entry
catalyst
TBSCl/DIPEA
2a:3ad
1
20% NMI
1.5/2.0
1.5/2.0
1.5/2.0
1.5/2.0
2.0/1.5
2.0/1.5
2.0/1.5
71:29
98:2
98:2
45:55
98:2
98:2
98:2
100
2
20% (ꢀ)-4a
20% (ꢀ)-4b
20% (ꢀ)-5
20% (ꢀ)-4b
10% (ꢀ)-4b
5% (ꢀ)-4b
70
3
72
4
45
5b
6b
7b
100
Figure 1. Design of scaffolding catalysts.
100 (93)e
88 (84)e
Most recently we applied scaffolding catalysts to the
derivatization of monosaccharides and natural products.9
In this manuscript we apply the catalyst to the selective
functionalization of ribonucleosides.10 Ribonucleosides
are the core building blocks for RNA and also serve as
templates for the development of therapeutics, in particu-
lar antiviral agents.11 Beyond RNA’s traditional role in
protein expression (i.e., tRNA and mRNA), RNA has
been found to be critical in gene regulation through
riboswitches12 and RNAi.13 These discoveries have led to
an explosion in the use of synthetic RNA as potential
therapeutics14 as well as tools for the biological sciences.
Although the expectation would be that RNA and DNA
synthesis would be similar, the additional 20-hydroxyl adds
a layer of complexity to the synthesis of RNA and deriva-
tives, because this hydroxyl has to be differentiated from
the 30-position. Current automated methods for RNA
synthesis require that the 20-hydroxyl be protected. One
of the most popular protecting groups used with the RNA
monomers is a tert-butyldimethylsilyl (TBS) group due to
its chemical orthogonality. The current synthesis of these
a Reactions performed at 0.2 M of 1a with 3 mol % DIPEAꢀHCl.
using trimethoxybenzene as an internal standard. d Ratio was deter-
mined by 1H NMR. e Isolated yield.
1
b Reactions run at 1.0 M of 1a. c Conversion determined by H NMR
monomers requires either an unselective silylation of the 20
and 30 positions followed by separation of the isomers15 or
a multistep protecting group sequence.16 Given the in-
creasing importance of RNA synthesis, we have devised a
simple one-step procedure that provides the desired mono-
mers in high yield and selectivity for all the natural
ribonucleosides. Moreover, switching to the opposite en-
antiomer of the catalyst enables the selective protection of
the 30-hydroxyl, which can be potentially used in the
synthesis of unnatural ribonucleosides.
We initially investigated site-selective functionalization
of uridine using TBSCl as the electrophile.17 As a control
reaction, we employed N-methylimidazole (NMI) as the
catalyst, and similar to previous reports15c the product
forms in a 71:29 ratio of the silylated C20ꢀOH:C30ꢀOH
(2a:3a, Table 1 entry 1). Using scaffolding catalyst (ꢀ)-4a
or (ꢀ)-4b18 results in a dramatic improvement in selectivity
to 98:2 with more moderate conversion (∼70%, Table 1,
entries 2 and 3). To test for the necessity of covalent
bonding to (ꢀ)-4b, an additional control reaction was
(7) (a) Page, M. I.; Jencks, W. P. Proc. Natl. Acad. Sci. U.S.A. 1971,
68, 1678–1683. (b) Pascal, R. Eur. J. Org. Chem. 2003, 1813–1824.
(8) Worthy, A. D.; Sun, X.; Tan, K. L. J. Am. Chem. Soc. 2012, 134,
7321–7324.
(9) Sun, X.; Lee, H.; Lee, S.; Tan, K. L. Nat. Chem. 2013, 5, 790–795.
(10) (a) Somoza, A. Chem. Soc. Rev. 2008, 37, 2668–2675. (b) Zewge,
D.; Gosselin, F.; Sidler, R.; DiMichele, L.; Cvetovich, R. J. J. Org.
Chem. 2010, 75, 5305–5307.
(16) Erlacher, M. D.; Lang, K.; Wotzel, B.; Rieder, R.; Micura, R.;
Polacek, N. J. Am. Chem. Soc. 2006, 128, 4453–4459.
(11) (a) Butler, M. S. Nat. Prod. Rep. 2008, 25, 475–516. (b) Leyssen,
P.; De Clercq, E.; Neyts, J. Antivir. Res. 2008, 78, 9–25.
(12) Serganov, A.; Nudler, E. Cell 2013, 152, 17–24.
(13) Kurreck, J. Angew. Chem., Int. Ed. 2009, 48, 1378–1398.
(14) (a) Kim, D. H.; Rossi, J. J. Nat. Rev. Genet. 2007, 8, 173–184. (b)
Keefe, A. D.; Pai, S.; Ellington, A. Nat. Rev. Drug Discovery 2010, 9,
537–550. (c) Davidson, B. L.; McCray, P. B. Nat. Rev. Genet. 2011, 12,
329–340.
(15) (a) Hakimelahi, G. H.; Proba, Z. A.; Ogilvie, K. K. Tetrahedron
Lett. 1981, 22, 4775–4778. (b) Hakimelahi, G. H.; Proba, Z. A.; Ogilvie,
K. K. Tetrahedron Lett. 1981, 22, 5243–5246. (c) Hakimelahi, G. H.;
Proba, Z. A.; Ogilvie, K. K. Can. J. Chem. 1982, 60, 1106–1113. (d)
MatulicAdamic, J.; Beigelman, L.; Portmann, S.; Egli, R.; Usman, N.
J. Org. Chem. 1996, 61, 3909–3911. (e) Song, Q.; Wang, W.; Fischer, A.;
Zhang, X.; Gaffney, B. L.; Jones, R. A. Tetrahedron Lett. 1999, 40,
4153–4156.
(17) For examples of catalyzed silyl transfer, see: (a) Isobe, T.;
Fukuda, K.; Araki, Y.; Ishikawa, T. Chem. Commun. 2001, 243–244.
(b) Rendler, S.; Auer, G.; Oestreich, M. Angew. Chem., Int. Ed. 2005, 44,
7620–7624. (c) Zhao, Y.; Rodrigo, J.; Hoveyda, A. H.; Snapper, M. L.
Nature 2006, 443, 67–70. (d) Zhao, Y.; Mitra, A. W.; Hoveyda, A. H.;
Snapper, M. L. Angew. Chem., Int. Ed. 2007, 46, 8471–8474. (e) You, Z.;
Hoveyda, A. H.; Snapper, M. L. Angew. Chem., Int. Ed. 2009, 48, 547–
550. (f) Weickgenannt, A.; Mewald, M.; Muesmann, T. W. T.; Oestreich,
M. Angew. Chem., Int. Ed. 2010, 49, 2223–2226. (g) Weickgenannt, A.;
Mewald, M.; Oestreich, M. Org. Biomol. Chem. 2010, 8, 1497–1504.
(h) Rodrigo, J. M.; Zhao, Y.; Hoveyda, A. H.; Snapper, M. L. Org. Lett.
2011, 13, 3778–3781. (i) Sheppard, C. I.; Taylor, J. L.; Wiskur, S. L. Org.
Lett. 2011, 13, 3794–3797. (j) Sun, X.; Worthy, A. D.; Tan, K. L. Angew.
Chem., Int. Ed. 2011, 50, 8167–8171. (k) Giustra, Z. X.; Tan, K. L. Chem.
Commun. 2013, 49, 4370–4372.
(18) Catalysts 4a and 4b are available at Strem Chemicals.
Org. Lett., Vol. 15, No. 18, 2013
4711

Table 2. Silylation of Natural Ribonucleosides
Table 3. Protection of the C3-Hydroxyl of Ribonucleosides
nucleobase
entry
catalyst
5:6a
7:93
yield (%)b
U (1a)
1
(þ)-4a
(ꢀ)-4b
(þ)-4a
(ꢀ)-4b
(þ)-4b
(ꢀ)-4b
(þ)-4a
(ꢀ)-4b
80
86
85
88
86
86
78
71
2
>98:<2
4:96
ABz(1b)
CBz(1c)
GIb(1d)
3
4
98:2
5
2:98
6
98:2
7c
8d
14:86
92:8
a Ratio was determined by 1H NMR. b Isolated yield. c 20 mol % (þ)-
4a. d 10 mol % (ꢀ)-4b.
a Reaction conditions: 0.5 M concentration in substrate. b Reaction
conditions: 1.0 M concentration in substrate. c Reaction conditions: 20
mol % (ꢀ)-4b, 0.5 M concentration in substrate. d Ratio was determined
by 1H NMR. e Isolated yield
performed with (ꢀ)-5, which lacks a substrate binding site;
both the reactivity and selectivity (2a:3a = 45:55, Table 1,
entry 4) decreased as expected. By both increasing the
number of equivalents of TBSCl and the concentration of
the reaction (1.0 M in substrate), complete conversion was
achieved without loss of selectivity (Table 1, entry 5).
Moreover, the catalyst loading could be lowered to 10%
4b affording an isolated yield of 93% and a site selectivity
of 98:2 (2a:3a, Table 1, entry 6). Lowering the catalyst
loading to 5% results in a modest decrease in yield (84%)
with no change in selectivity (98:2, Table 1, entry 7).
With the optimal conditions in hand, we surveyed the
remaining naturally occurring ribonucleosides. To our de-
light all the ribonucleosides yielded the desired TBS protected
product in excellent selectivity and yield (Table 2). The most
problematic substrate was guanosine which required an
increase in the catalyst loading (20 mol %) and a decrease
in substrate concentration (0.5 M) to obtain the optimal
selectivity (2d:3d = 97:3) and yield (75%, Table 2, entry 3).
A way to view the current silylation reaction is as
a pseudodesymmetrization of a cis-1,2-diol. This would
Figure 2. Functionalization of ribavirin.
imply that switching to the opposite enantiomer of catalyst
would result in silylation of the C30-hydroxyl. Initial efforts
to TBS protect the 30 position resulted in poor yield and
low selectivity in the reaction. We have previously reported
that for inherently less reactive positions within molecules
it is often necessary to use more reactive electrophiles.
Using chlorotriethylsilane (TESCl) in place of TBSCl
allowed for the highly selective protection of the 30-hydro-
xyl ofuridine (20:30 = 7:93, Table3, entry1). Withthemore
reactive electrophile the catalyst loading can be reduced to
5 mol % with a reaction time of 4 h. Moreover, switching
to (ꢀ)-4b affords the 20-protected product in excellent
4712
Org. Lett., Vol. 15, No. 18, 2013

yield and selectivity (Table 3, entry 2). Application of the
scaffolding catalysts to the other natural ribonucleosides
allows for switching of the site selectivity through simply
changing the enantiomer of the catalyst. In general either
isomer of product can be isolated in >95:5 selectivity and
>80% yield using 5% catalyst (Table 3). Guanosine proved
to be the most challenging substrate, but by increasing the
catalyst loading to 20 mol % the desired product was isolated
in 78% yield (5:6 = 14:86, Table 3, entry 7).
Using a scaffolding catalyst, site-selective functionaliza-
tion of ribonucleosides was achieved enabling an efficient
synthesis of appropirately protected monomers for auto-
mated RNA synthesis. Moreover, simply switching the
antipode of the catalyst allows for toggling of the site
selectivity to favor protection of the 30-hydroxyl. We believe
that developing catalysts that recognize specific functional
group motifs will provide a practical and predictable meth-
od for manipulating polyfunctional molecules.
Unnatural ribonucleosides have been found to be effec-
tive antiviral agents, and so the selective modification of
these compounds is critical to the development of novel
therapeutics. We investigated whether the scaffolding cat-
alysts would also be effective in the selective protection of
ribavirin, which is currently used to treat Hepatitis C virus
(HCV). Using unprotected ribavirin, catalyst (ꢀ)-4b sily-
lates the 50 and 20 positions with high selectivity (7:8 =
94:6, Figure 2), leaving the 30 hydroxyl available for further
manipulation. Switching to catalyst (þ)-4a affords the
product with the 50 and 30 hydroxyls protected, allowing
access to the 20-hydroxyl (Figure 2).
Acknowledgment. We thank the Alfred P. Sloan foun-
dation (K.L.T.), NSF (CHE-1150393), and NIGMS
(RO1GM087581) for funding of this project. Mass spec-
trometry instrumentation at Boston College is supported
by funding from the NSF (DBI-0619576).
Supporting Information Available. Experimental proce-
dures, characterization data, and spectra. This material is
available free of charge via the Internet at http://pubs.acs.org.
The authors declare no competing financial interest.
Org. Lett., Vol. 15, No. 18, 2013
4713