Regioselective 2′-O-debenzoylation of 2',3'-di-O-benzoyl threose nucleosides

Article abstract of DOI:10.1016/j.tetlet.2013.08.117

A simple and convenient procedure for the regioselective 2′-O-debenzoylation of 2',3'-di-O-benzoyl threose nucleosides has been achieved successfully affording 3′-O-benzoyl threose nucleosides, which are useful starting material synthons for the synthesis

Full text of DOI:10.1016/j.tetlet.2013.08.117

Tetrahedron Letters 54 (2013) 6084–6086
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Regioselective 20-O-debenzoylation of 2’,3’-di-O-benzoyl threose
nucleosides
⇑
Mi-Yeon Jang, Matheus Froeyen, Piet Herdewijn
Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
a r t i c l e i n f o
a b s t r a c t
A simple and convenient procedure for the regioselective 20-O-debenzoylation of 2’,3’-di-O-benzoyl thre-
ose nucleosides has been achieved successfully affording 30-O-benzoyl threose nucleosides, which are
useful starting material synthons for the synthesis of modified threose nucleosides for different purposes.
Ó 2013 Published by Elsevier Ltd.
Article history:
Received 11 June 2013
Revised 29 July 2013
Accepted 28 August 2013
Available online 5 September 2013
Keywords:
Threose
Regioselective debenzoylation
Potassium tert-butoxide
TNA
20-Modified threose nucleosides
(30–20)
a-L
-Threose nucleic acid (TNA) is an artificial genetic
mixture of regioisomers and required tedious chromatographic
separations.
polymer in which the five-carbon ribose sugar of RNA and DNA
is replaced by the four-carbon threose sugar and linked together
through their 30- and 20-hydroxyls in a diaxial orientation.1–4 A sys-
tematic study of alternative carbohydrate-based nucleic acids has
revealed that TNA can form stable Watson–Crick base-pairing du-
plexes with DNA, RNA, and TNA. As a possible RNA progenitor, TNA
In the case of ribonucleosides, several procedures for the regio-
selective deacylation have been developed. For example, the reac-
tion of fully acylated ribonucleosides (1) with small alkoxide such
as sodium methoxide resulted in 20 and 30-O-deacylated compound
(2)12 while bulkier alkoxide such as potassium tert-butoxide affor-
ded 20-O-deacylated compound (3a)13 as a major product. The
hydroxylaminolysis (treatment with hydroxylaminium acetate)
also resulted in 20-O-deacylated compound (4a) as a major prod-
uct14 (Fig. 2(a)). It seems that the 2’-O-acyl group of nucleosides
is the most active ester function toward an appropriate nucleo-
phile, due to the electronic effect of the aglycone moiety. More-
over, in the case of xylonucleoside (5), hydroxylaminolysis gave 6
as a sole product14 (Fig. 2(b)). The high selectivity of xylonucleo-
side may reflect steric hindrance as 30-ester function is sterically
less accessible by the adenyl moiety. As 2’,3’-di-O-acyl threose
nucleosides have N-type conformation,2 they may also have differ-
ent accessibility toward nucleophilic attack on 20 and 30-ester func-
tions. The central C atom in the ester function in the top (30) is
sterically less accessible by the presence of the nucleobase (t-BuOꢀ
needs to attack from the front, next to the plane of the nucleobase)
(Fig. 3(a)). The central carbon of the ester in the bottom (20) is
completely accessible (Fig. 3(b)). Therefore, we envisioned to
explore a procedure for the regioselective mono-deprotection of
2’,3’-di-O-acyl threose nucleosides with potassium tert-butoxide.
Herein, we describe a simple and convenient procedure for the
regioselective 20-O-debenzoylation of 2’,3’-di-O-benzoyl threose
has received considerable attention and numerous
a-L-threose
nucleoside analogues have been synthesized and assembled chem-
ically to TNA analogues.5,6 It was also demonstrated that threose
nucleoside triphosphates (tNTPs, substrates) are incorporated well
into DNA or RNA primers by selected DNA polymerases.7–10 Re-
cently, we have demonstrated that L
-20-deoxythreose nucleoside
phosphonates PMDTA and PMDTT selectively inhibit HIV without
affecting normal cell proliferation.11
As part of a research program to discover new threose-nucleo-
side analogues as anti-viral agents, we were interested in develop-
ing efficient synthetic routes for the introduction of various
functionalities at the 20- and/or 30- position of threose nucleosides.
One of the current strategies for the synthesis of sugar pro-
tected threose nucleosides, developed by Eschenmoser and co-
workers, includes a full-deprotection of the dibenzoyl threose moi-
ety followed by mono-protection of the 20- and 30-hydroxyl
groups2 (Fig. 1). However, this reaction typically resulted in a
⇑
Corresponding author. Tel.: +32 16 337367; fax: +32 16 337340.
E-mail address: piet.herdewijn@rega.kuleuven.be (P. Herdewijn).
0040-4039/$ - see front matter Ó 2013 Published by Elsevier Ltd.
http://dx.doi.org/10.1016/j.tetlet.2013.08.117

M.-Y. Jang et al. / Tetrahedron Letters 54 (2013) 6084–6086
6085
Figure 1. Current strategy for the synthesis of threose nucleosides.
Table 1
Regioselective 20-O-debenzoylation of 2’,3’-di-O-benzoyl threose nucleosides with
potassium tert-butoxide
Entry Reactant
B
t-BuOK (equiv) Product Yield (%)
NHBz
N
N
1
2
7a
7b
2.5
2.5
8a
8b
70a
91
N
N
O
N
NH
O
NHBz
N
3
7c
2.5
8c
90
N
O
OCONPh2
N
N
N
b
4
5
7d
7e
2.5
4.5
8d
8e
—
N
O
NHAc
67a
N
N
NH
NHAc
N
a
Starting material was recovered in 10% yield.
Products: 50% yield (3:1 mixture of 7e and 10), starting material was recovered
Figure 2. Regioselective O-deacylation of fully acylated ribonucleosides (a) and
xylonucleoside (b).
b
in 15% yield.
nucleosides affording 30-O-benzoyl threose nucleosides, which are
useful starting material synthons for the synthesis of modified
threose nucleosides for different purposes.
2’,3’-di-O-benzoyl threose nucleosides (7a–d, Table 1) were
prepared by the procedure described by Eschenmoser and
co-workers.2 Treatment of nucleosides 7a, 7b, and 7c with
2.5 equivalents of freshly prepared 0.1 M solution of potassium
tert-butoxide in THF at room temperature gave mono-20-O-deben-
zoylated products in good to moderate yields (Table 1). Their struc-
ture was confirmed by HMBC analysis. A clear HMBC cross-peak
between H30 and carbonyl carbon of the O-benzoyl group was
observed.
However, reaction of compound 7d, under the same conditions,
resulted in the formation of 2 products. The O6-diphenylcarbamoyl
group of guanine-base proved to be labile under the reaction
conditions and it was deprotected releasing 9 and tert-butyl
diphenylcarbamate as a by-product (Scheme 1). The remaining
potassium tert-butoxide deprotected 20-O-benzoyl group and the
resulting alkoxide reacted with tert-butyl diphenylcarbamate
affording compound 10. The structure of compound 10 was
Figure 3. Isodensity surfaces of
1 L
0a-(uridin-1-yl)-2’,3’-di-O-benzoyl- -threose15
and t-BuOꢀ at contour value 0.02 color coded by the electrostatic potential from
negative to positive colored red, yellow, green, light blue, dark blue.16,17 The
C-atoms of the ester groups susceptible for reaction are in a dark blue area (more
positive potential). The t-BuO- oxygen potential is colored red (negative electro-
static potential). (a) the approach of t-BuOꢀ to the 30 ester carbon; (b) the approach
of t-BuOꢀ to the 20 ester carbon.

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M.-Y. Jang et al. / Tetrahedron Letters 54 (2013) 6084–6086
10. Kempeneers, V.; Vastmans, K.; Rozenski, J.; Herdewijn, P. Nucleic Acids Res.
2003, 31, 6221.
11. Wu, T.; Froeyen, M.; Kempeneers, V.; Pannecouque, C.; Wang, J.; Busson, R.; De
Clercq, E.; Herdewijn, P. J. Am. Chem. Soc. 2005, 127, 5056.
12. Nishino, S.; Rahman, M. D. A.; Takamura, H.; Iahido, Y. Tetrahedron 1985, 41,
5503.
13. Nishino, S.; Takamura, H.; Iahido, Y. Tetrahedron 1986, 42, 1995.
14. Ishido, Y.; Sakairi, N.; Okazaki, K.; Nakazaki, N. J. Chem. Soc., Perkin Trans. 1
1980, 563.
´
1
15.
a-(Uridin-1-yl)-2’,3’-O-dibenzoyl-L-threose (CCDC 183997) was downloaded
from the CCDC database. http://www.ccdc.cam.ac.uk/.
16. The molecular structure was energy optimized and electron densities were
calculated at the 6-31G⁄ level using gamess. Schmidt, M. W.; Baldridge, K. K.;
Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.;
Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput.
Chem. 1993, 14, 1347.
17. The isodensity surface at 0.02 color coded by the electrostatic potential was
calculated by Modern. Schaftenaar, G.; Noordik, J. H. J. Comput.-Aided Mol. Des.
2000, 14, 123.
Scheme 1. Proposed mechanism of synthesis of compound 10.
18. Upadhayaya, R.; Deshpande, S. G.; Li, Q.; Kardile, R. A.; Sayyed, A. Y.; Kshirsagar,
E. K.; Salunke, R. V.; Dixit, S. S.; Zhou, C.; Földesi, A.; Chattopadhyaya, J. J. Org.
Chem. 2011, 76, 4408.
19. General procedure of mono-2’-O-debenzoylation of 2’,3’-dibenzoyl threose
nucleosides: to a solution of 10a-(thymin-1-yl)-2’,3’-di-O-benzoyl-
L-threose 7b
(1.0 g, 2.35 mmol) in dry THF (100 ml) was added fresh prepared 0.1 M KOtBu
in THF (58.6 ml, 5.86 mmol). After stirring for 5 min, the mixture was
quenched by addition of 1 N HCl (5.86 ml, 5.86 mmol). After removing
volatiles, the residue was dissolved with DCM and washed with water, brine,
dried over Na2SO4 and evaporated under reduced pressure. The crude residue
was purified by silica gel chromatography (CH2Cl2/MeOH 30/1) to afford 10a
-
Scheme 2. Selective deprotection of O6-diphenylcarbamoyl group of compound 7d.
(thymin-1-yl)-30-O-benzoyl-
L
-threose (0.71 g, 91%) as white foam.
1
0a-(N6-Benzoyladenin-9-yl)-30-O-benzoyl-
L
-threose (8a): 1H NMR (300 MHz,
confirmed by HMBC and mass analysis. An attempt to obtain only
one product (compound 10) in the reaction mixture by adding
more potassium tert-butoxide was not successful. Even with
10 equiv of potassium tert-butoxide, a considerable amount of
starting material remained and a complex mixture of products
was obtained. To avoid this side reaction, the diphenylcarbamoyl
group of 7d was selectively removed by a treatment with glacial
acetic acid18 (Scheme 2). Compound 7e could be successfully mono
20-O-debenzoylated with 4.5 equivalents of potassium tert-butox-
ide (Table 1).
Purine threose nucleosides showed lower yield compared to
pyrimidine threose nucleosides as a certain amount of starting
material (ꢁ10%) remained. Adding more base or longer reaction
time did not improve the yield because it caused 30-O-
debenzoylation.
CDCl3): d 9.44 (br s, 1H, NH), 8.65 (s, 1H, H8), 8.34 (s, 1H, H2), 7.99 (d,
J = 7.2 Hz, 2H, Bz), 7.70 (d, J = 7.1 Hz, 2H, Bz), 7.55 (t, J = 7.4 Hz, 1H, Bz), 7.45 (t,
J = 7.6 Hz, 3H, Bz), 7.32 (t, J = 7.8 Hz, 2H, Bz), 6.23 (d, J = 1.7 Hz, 1H, H10), 5.48–
5.49 (m, 1H, H3’), 5.03 (s, 1H, H20), 4.59 (dd, J = 4.5, 10.8 Hz, 1H, H4’), 4.47(dd,
J = 1.4, 10.6 Hz, 1H, H40) ppm. 13C NMR (75 MHz, DMSO): d 165.56, 164.93,
151.76, 151.57, 150.31, 142.41, 133.53, 133.39, 132.38, 129.17, 128.89, 128.69,
128.47, 128.42, 125.88, 90.47, 78.25, 77.21, 72.59 ppm. HRMS (ESI+) calcd for
C
23H20N5O5 [M+H]+ 446.1459, found 446.1460.
0a-(Thymin-1-yl)-30-O-benzoyl- -threose (8b): 1H NMR (300 MHz, CDCl3): d
1
L
10.30 (br s, 1H, NH), 7.83 (d, J = 7.1 Hz, 2H, Bz), 7.58 (t, J = 7.4 Hz, 1H, Bz), 7.44
(s, 1H, H6), 7.41 (t, J = 7.5 Hz, 2H, Bz), 5.87 (s, 1H, H10), 5.45 (d, J = 3.4 Hz, 1H,
H3’), 4.60 (dd, J = 3.6, 11.1 Hz, 1H, H40), 4.58 (s, 1H, H20), 4.46 (d, J = 10.8 Hz, 1H,
H40), 1.84 (d, J = 0.9 Hz, 3H, CH3) ppm. 13C NMR (75 MHz, CDCl3): d 165.21,
164.77, 151.01, 135.89, 133.94, 129.61, 128.98, 128.78, 110.27, 93.98, 79.38,
77.63, 75.10 ppm. HRMS (ESI+) calcd for C16H17N2O6 [M+H]+ 333.1081, found
333.1077.
1
0a-(N4-Benzoylcytosin-1-yl)-30-O-benzoyl- -threose (8c): 1H NMR (300 MHz,
L
CDCl3): d 8.09 (d, J = 7.5 Hz, 1H, H6), 7.95 (d, J = 7.2 Hz, 2H, Bz), 7.72 (d,
J = 7.2 Hz, 2H, Bz), 7.61 (d, J = 7.5 Hz, 1H, H5), 7.57 (t, J = 7.3 Hz, 1H, Bz), 7.43–
7.50 (m, 3H, Bz), 7.30 (t, J = 7.8 Hz, 2H, Bz), 6.00 (s, 1H, H10), 5.55 (d, J = 3.3 Hz,
1H, H30), 4.72 (s, 1H, H20), 4.66 (dd, J = 3.7, 10.9 Hz, 1H, H40), 4.46 (d, J = 10.8 Hz,
1H, H40) ppm. 13C NMR (75 MHz, CDCl3): d 166.85, 165.31, 162.89, 155.94,
144.40, 133.63, 133.13, 133.10, 129.65, 128.93, 128.89, 128.49, 127.94, 94.60,
94.88, 79.18, 78.09, 74.95 ppm. HRMS (ESI+) calcd for C22H20N3O6 [M+H]+
422.1347, found 422.1351.
In summary, we have developed a simple and efficient regiose-
lective 20-O-debenzoylation method of 2’,3’-di-O-benzoyl threose
nucleosides.19 The resulting products are valuable intermediates
for the synthesis of new 20-modified threose nucleosides.
1
0a-(N2-Acetylguanin-9-yl)-30-O-benzoyl- -threose (8e): 1H NMR (300 MHz,
L
MeOD): d 8.11 (s, 1H, H8), 7.66 (d, J = 8.5 Hz, 2H, Bz), 7.55 (t, J = 7.44 Hz, 1H,
Bz), 7.38 (t, J = 7.8 Hz, 2H, Bz), 5.99 (d, J = 0.72 Hz, 1H, H10), 5.39–5.54 (m, 1H,
H30), 4.93 (s, 1H, H20), 4.57 (dd, J = 4.5, 10.8 Hz, 1H, H40), 4.48 (dd, J = 1.1,
10.7 Hz, 1H, H40), 2.18 (s, 3H, CH3) ppm. 13C NMR (75 MHz, MeOD): d 174.85,
166.70, 157.29, 149.70, 149.32, 139.09, 134.63, 130.36, 130.27, 129.62, 92.77,
79.70, 79.34, 74.52, 23.84 ppm. HRMS (ESI+) calcd for C18H18N5O6 [M+H]+
400.1251, found 400.1248.
References and notes
1. Schöning, K.; Scholz, P.; Guntha, S.; Wu, X.; Krishnamurthy, R.; Eschenmoser, A.
Science 2000, 290, 1347.
2. Schöning, K.; Scholz, P.; Wu, X.; Guntha, S.; Delgado, G.; Krishnamurthy, R.;
Eschenmoser, A. Helv. Chim. Acta 2002, 85, 4111.
3. Wilds, C. J.; Wawrzak, Z.; Krishnamurthy, R.; Eschenmoser, A.; Egli, M. J. Am.
Chem. Soc. 2002, 124, 13716.
4. Pallan, P. S.; Wilds, C. J.; Wawrzak, Z.; Krishnamurthy, R.; Eschenmoser, A.; Egli,
M. Angew. Chem., Int. Ed. 2003, 42, 5893.
5. Wu, X.; Gunta, S.; Ferencic, M.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett.
2002, 4, 1279.
6. Wu, X.; Delgado, G.; Krishnamurthy, R.; Eschenmoser, A. Org. Lett. 2002, 4,
1283.
7. Ichida, J. K.; Horhota, A.; Zou, K.; McLaughlin, L. W.; Szostak, J. W. Nucleic Acids
Res. 2005, 33, 5219.
1
0a-(N2-Acetylguanin-9-yl)-30-O-benzoyl-20-O-diphenylcarbamoyl-L-threose
(10): 1H NMR (300 MHz, CDCl3): d 11.93 (s, 1H, NH), 9.89 (s, 1H, NH), 7.95 (s,
1H, H8), 7.66 (d, J = 7.2 Hz, 2H, Bz), 7.52 (t, J = 7.4 Hz, 1H, Bz), 7.21–7.36 (m,
12H, Bz, Ph), 6.15 (s, 1H, H20), 5.99 (s, 1H, H10), 5.43 (br s, 1H, H30), 4.30 (dd,
J = 1.8, 10.8 Hz, 1H, H40), 4.21 (dd, J = 4.8, 10.8 Hz, 1H, H40) ppm. 13C NMR
(75 MHz, CDCl3): d 172.38, 165.43, 155.63, 152.99, 147.91, 147.65, 141.74,
137.29, 134.09, 129.47, 128.76, 128.37, 126.99, 121.72, 89.01, 79.89, 75.79,
73.50, 24.26 ppm. HRMS (ESI+) calcd for C31H27N6O7 [M+H]+ 595.1936, found
595.1938.
8. Yu, H. Y.; Zhang, S.; Chaput, J. C. Nat. Chem. 2012, 4, 183.
9. Chaput, J. C.; Ichida, J. K.; Szostak, J. W. J. Am. Chem. Soc. 2003, 125, 856.