Facile deprotection of O-Cbz-protected nucleosides by hydrogenolysis: An alternative to O-benzyl ether-protected nucleosides

Article abstract of DOI:10.1021/ol048426w

(Chemical Equation Presented) Because of side-reactions encountered during hydrogenolysis, benzyl ethers are usually not an effective protecting group for nucleosides. Benzyloxycarbamates provide an alternative to traditional benzyl ethers for protection of nucleoside hydroxyl groups, as they are much more labile to hydrogenolysis. Deprotection conditions using transfer hydrogenolysis are described that avoid the reduction of the pyrimidine nucleobase during deblocking of O-Cbz-protected nucleosides. Additionally, an experiment is described that suggests the nucleobase component of a nucleoside is responsible for the sluggish hydrogenolysis of nucleosides.

Full text of DOI:10.1021/ol048426w

ORGANIC
LETTERS
2004
Vol. 6, No. 25
4643-4646
Facile Deprotection of O-Cbz-Protected
Nucleosides by Hydrogenolysis: An
Alternative to O-Benzyl Ether-Protected
Nucleosides
David C. Johnson II and Theodore S. Widlanski*
Department of Chemistry, Indiana UniVersity, Bloomington, Indiana 47405
twidlans@indiana.edu
Received August 9, 2004
ABSTRACT
Because of side-reactions encountered during hydrogenolysis, benzyl ethers are usually not an effective protecting group for nucleosides.
Benzyloxycarbamates provide an alternative to traditional benzyl ethers for protection of nucleoside hydroxyl groups, as they are much more
labile to hydrogenolysis. Deprotection conditions using transfer hydrogenolysis are described that avoid the reduction of the pyrimidine
nucleobase during deblocking of O-Cbz-protected nucleosides. Additionally, an experiment is described that suggests the nucleobase component
of a nucleoside is responsible for the sluggish hydrogenolysis of nucleosides.
The benzyl moiety is widely used as a hydroxyl protecting
group, in part, because its removal (via hydrogenolysis) is
effected under conditions orthogonal to many other func-
tionalities and protecting groups. Yet, in the field of
nucleoside chemistry, the benzyl moiety is primarily used
as a monophosphate protecting group,1 receiving limited
attention as a hydroxyl protecting group. This may be, in
part, because difficulties often arise during hydrogenolysis
of O-benzyl-protected nucleosides. An often observed side-
reaction is the reduction of the nucleobase, particularly with
the pyrimidines: uridine,2 cytosine,3 and to a lesser extent,
thymidine.4 Thus, hydrogenolysis is often eschewed in favor
of other means to deblock benzyl-protected nucleosides
(BCl3,5 BBr3,6 or dissolving metal reduction7) and/or through
modification of the benzyl moiety (e.g., use of the F-meth-
oxybenzyl ether, which is acid-labile8). However, there are
situations when hydrogenolysis is a highly desirable method
for deprotection of benzyl-protected nucleosides. Hydro-
genolysis, which can be conducted under neutral conditions,
is advantageous when working with nucleosides containing
phosphoanhydride bonds. Nucleoside diphosphates, and
especially nucleoside triphosphates, degrade under acidic
conditions. Therefore, we explored ways to facilitate hydro-
genolysis of O-benzyl groups from nucleosides and found
that the benzyloxycarbonyl (Cbz) moiety functions as a
versatile alternative to the traditional O-benzyl ether protect-
ing group for use in nucleoside chemistry.
While determining optimum reaction conditions for hy-
drogenolysis of a benzyl-protected uridine (1), we observed
that hydrogenolysis of the O-benzyl moieties did not occur
(1) Freel Meyers, C. L.; Borch, R. F. Org. Lett. 2001, 3 (23), 3765-
3768.
(2) Reitz, G.; Pfleiderer, W., Chem. Ber. 1975, 108, 2878-2894.
(3) Christensen, L. F.; Broom, A. D., J. Org. Chem. 1972, 37 (22), 3398-
3401.
(4) Pedersen, D. S.; Koch, T., Synthesis 2004, 4, 578-582.
(5) Meade, E. A.; Wotring, L. L.; Drach, J. C.; Townsend, L. B. J. Med.
Chem. 1992, 35 (3), 526-533.
(6) Greene, T. W.; Wuts, P. G. M. ProtectiVe Groups in Organic
Sytnthesis, 3rd ed.; John Wiley & Sons: New York, 1999.
(7) Philips, K. D.; Horwitz, J. P., J. Org. Chem. 1975, 40 (12), 1856-
1858.
(8) Luzzio, F. A.; Menes, M. E., J. Org. Chem. 1994, 59 (24), 7167-
7272.
10.1021/ol048426w CCC: $27.50
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when using palladium on charcoal catalyst.9 However, the
simple expedient of Pearlman’s catalyst10 [Pd(OH)2] led to
facile hydrogenolysis of the O-benzyl moieties in excellent
yield (92%), although the N-benzyl group of the imide moiety
did not hydrogenolyze (Scheme 1). N-Benzyl imides are a
the hydrogenolysis of benzyl-protected moieties is unknown,
data in the literature supports that ester groups undergo
hydrogenolysis with greater facility than ether groups.14
Therefore, we reasoned that the hydroxyl groups of nucleo-
sides functionalized as benzyloxycarbamates (Cbz) may be
more labile toward hydrogenolysis than their benzyl ether
counterparts. Indeed, hydrogenolysis of Cbz-protected uridine
5 was complete in less than 90 min using palladium on
carbon catalyst in ethanol. Given that palladium on charcoal
catalysts promoted the reduction of the nucleobase for the
benzylidene-protected uridine, we carefully examined the
products from the hydrogenolysis of Cbz-protected uridine
5 using NMR spectroscopy. We observed evidence consistent
with minor reduction (0.2%) of the nucleobase (Scheme 3).
Scheme 1. Pearlman’s Catalyst Is More Effective for
Hydrogenolysis of Nucleoside O-Bn Groups than Pd/C
particularly difficult functionality to hydrogenolyze,4,11 and
previous reports12,13 attest to the difficulty associated with
the hydrogenolysis of N-benzyl pyrimidine nucleosides. Thus,
the per-benzyl-protected nucleoside (1) was deemed to be
incompatible with our future plans.
Scheme 3. Minor Reduction (0.2%) of the Nucleobase Can
Occur with Pyrimidine Nucleosides
The benzylidene moiety has been used with purine
nucleosides as a diol protecting group that is labile to
hydrogenolysis. Therefore, we explored whether the ben-
zylidene acetal of a pyrimidine nucleoside (i.e., uridine 3)
is also labile to hydrogenolysis. Deprotection of the ben-
zylidene-protected pyrimidine requires 2 days to reach
complete reaction. Upon isolating the product (4), we find
that reduction of the nucleobase C5-C6 alkene occurs
(Scheme 2).
The separation of uridine 6 from its reduced side-product 4
is nontrivial. Therefore, we explored other conditions to
affect hydrogenolysis of the Cbz moieties that would avoid
even this small amount of reduction of the nucleobase. To
that end, transfer hydrogenolysis has been reported by
Rapoport et al.15 as a method to avoid reduction of the
pyrimidine C5-C6 alkene.
Scheme 2. Reduction of the Nucleobase-alkene Occurs during
Prolonged Hydrogenolysis
Transfer hydrogenolysis of Cbz-protected uridine 5 (Scheme
4) gives no appreciable reduction of the nucleobase in the
Scheme 4. Transfer Hydrogenolysis Avoids Minor Reduction
of Pyrimidine Nucleobase
The long reaction times and concomitant reduction of the
nucleobase, as well as the resistance of the N-benzyl imide
toward hydrogenolysis, prompted us to investigate alternate
means to use hydrogenolysis for deblocking pyrimidine-
containing nucleosides. Although a detailed mechanism for
product (6), within the limits detectable by NMR spectros-
copy (see Supporting Information for spectra).
(9) A variety of reaction conditions were explored using 10% Pd/C
catalyst (1 mg of catalyst/5 mg of nucleoside). Solvents (EtOH, EtOAc,
THF), additives (AcOH/ heat), and reaction times (up to 48 h) were also
investigated but were not observed to promote hydrogenolysis.
(10) Pearlman, W. M. Tetrahedron Lett. 1967, 17, 1663-1664.
(11) Johnson, D. C., II; Widlanski, T. S. Tetrahedron Lett. 2004, 45 (46),
8483-8487.
The Cbz-protecting group is easily installed in high yield
for various pyrimidines and purine nucleosides using ben-
zylchloroformate (1.5 equiv/OH group) and DMAP (2 equiv/
OH group) in dichloromethane. Under these conditions, the
(12) Luzzio, F. A.; Menes, M. E. J. Org. Chem. 1994, 59 (24), 7167-
7272.
(14) Kieboom, A. P. G.; De Kreuk, J. F.; Van Bekkum, H. J. Catal.
1971, 20, 58-66.
(15) Watkins, B. E.; Kiely, J. S.; Rapoport, H., J. Am. Chem. Soc. 1982,
104 (21), 5702-5708.
(13) Bar, N. C.; Patra, R.; Achari, B.; Mandal, S. B. Tetrahedron 1997,
53 (13), 4727-4738.
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Org. Lett., Vol. 6, No. 25, 2004

Table 1. Carbonylation/Carbamoylation of Representative Purine and Pyrimidine Nucleosides in Ribo- and Deoxyribonucleic Acid
Forms
a Yield for the two-step procedure: 5′-silyation followed by carbonylation.
amino functionality of cytosine is carbamoylated along with
carbonylation of the nucleoside hydroxyl groups. However,
the aromatic amino functionality of adenosine is not car-
bamoylated. A particularly salient feature about the instal-
lation of the Cbz-protecting group is that the imide nitrogens
of uridine and thymidine are not carbamoylated (Table 1).
Silyl-ethers are easily removed in high-yield from the Cbz-
protected nucleosides using a buffered fluoride source such
as triethylamine trihydrofluoride (Table 1).
As found in other published reports, we observe that
hydrogenolysis of benzyl-protected nucleosides (both purine
and pyrimidine) sometimes requires long reaction times.
There are a number of possible reasons for this. The amino
functionalities of nucleosides may inhibit hydrogenolysis.
Table 2. Hydrogenolysisa of O-Benzyl Menthol Is Inhibited in the Presence of Nucleoside Additivesb
a Hydrogenolysis reaction was performed for 22 min, as monitored by a stopwatch. The “start” of the reaction was considered to be the moment the H2
balloon pierced the septum. At completion, the reaction was promptly filtered through Celite 545. b Additives were present prior to introduction of H2.
c Percent of 18 recovered is representative of the inhibitory influence additives have upon hydrogenolysis of O-benzyl menthol.
Org. Lett., Vol. 6, No. 25, 2004
4645

Free amines have been shown to inhibit the hydrogenolysis
of O-benzyl ethers,16 presumably by formation of a complex17
between the amine and the palladium catalyst, thereby
deactivating the catalyst. Another possibility is that the
nucleoside adsorbs to the catalyst in some fashion, thereby
hindering hydrogenolysis. To better understand the hydro-
genolysis of benzyl-protected nucleosides, we examined the
effect nucleosides have upon the hydrogenolysis of a model
compound, O-benzyl menthol.
The hydrogenolysis of O-benzyl menthol is complete in
28 min using 10% Pd/C in ethyl acetate under an atmosphere
of hydrogen. Menthol is a volatile compound, whereas
O-benzyl menthol is not volatile. One can examine the effect
nucleosides have upon the hydrogenolysis of O-benzyl
menthol by quenching the reaction at 80% completion,
separating the catalyst by filtration, and removing of all
volatile components under reduced pressure. The remaining
O-benzyl menthol is easily separated from the nucleoside
additive. The isolated O-benzyl menthol is representative of
the effect a nucleoside has upon the hydrogenolysis process.
Under these experimental conditions we find that repre-
sentative purine and pyrimidine nucleosides inhibit the
hydrogenolysis process (Table 2). The amino functionality
of adenosine does not appear to be responsible for the
inhibition, as both amino-adenosine 19 and amido-adenosine
20 show similar inhibitory effects upon the hydrogenolysis
of O-benzyl menthol. The representative pyrimidine (uridine
21) also inhibits hydrogenolysis, but much less effectively
than the purines (adenosines 19 or 20). To rule out the
possibility that the silyl-ethers interfered with the hydro-
genolysis process, we examined the effect an isolated
nucleobase (i.e., uracil) had upon the hydrogenolysis process.
Uracil (22) also inhibits the hydrogenolysis of O-benzyl
menthol. Interestingly, uracil inhibits hydrogenolysis with
the same general efficacy as uridine 21. These data suggest
that the nucleobase component of a nucleoside is responsible
for the sluggish hydrogenolysis of O-benzyl-protected nu-
cleosides.
In this communication we have demonstrated the prob-
lematic nature of deblocking benzyl-ether protecting groups
from nucleosides. The long reaction times and accompanying
reduction of pyrimidine nucleobases are easily avoided by
use of carbobenzyloxy protecting groups and deprotection
under transfer hydrogenolysis conditions. Further, we have
shown experimental evidence that the sluggish deprotection
of O-benzyl-protected nucleosides may be a result of
inhibition due to the presence of the nucleobase.
Supporting Information Available: Experimental pro-
cedures and spectral data (1H, 13C, MS, IR) for all compounds
synthesized in this study. This material is available free of
charge via the Internet at http://pubs.acs.org.
(16) Sajiki, H., Tetrahedron Lett. 1995, 36 (20), 3465-3468.
(17) Sajiki, H.; Hattori, K.; Hirota, K., J. Org. Chem. 1998, 63, (22),
7990-7992.
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