Synthesis of a novel 1,2-dithianenucleoside via Pummerer-like reaction, followed by Vorbruggen glycosylation between a 1,2-dithiane derivative and uracil

Article abstract of DOI:10.1039/c3cc44848g

The novel 1,2-dithianenucleoside was designed as a hybrid type of modification between 4′-thioribonucleoside and altritol nucleoside. The desired compound, i.e., 1-[(3R,4R,5S,6R)-4,5-dihydroxy-6-hydroxymethyl-1,2- dithianyl]uracil (20), was prepared via the Pummerer-like reaction, followed by Vorbruggen glycosylation between an appropriately protected 1,2-dithiane derivative and silylated uracil.

Full text of DOI:10.1039/c3cc44848g

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Synthesis of a novel 1,2-dithianenucleoside via
Pummerer-like reaction, followed by Vorbruggen
glycosylation between a 1,2-dithiane derivative
and uracil†
Cite this: Chem. Commun., 2013,
49, 7851
Received 28th June 2013,
Accepted 5th July 2013
DOI: 10.1039/c3cc44848g
Tadashi Miyazawa, Kouhei Umezaki, Noriko Tarashima, Kazuhiro Furukawa,
Takashi Ooi and Noriaki Minakawa*
www.rsc.org/chemcomm
The novel 1,2-dithianenucleoside was designed as a hybrid type of
modification between 40-thioribonucleoside and altritol nucleoside.
The desired compound, i.e., 1-[(3R,4R,5S,6R)-4,5-dihydroxy-6-hydroxy-
methyl-1,2-dithianyl]uracil (20), was prepared via the Pummerer-like
reaction, followed by Vorbruggen glycosylation between an appro-
priately protected 1,2-dithiane derivative and silylated uracil.
Fig. 1 Design concept of the 1,2-dithianenucleoside.
In a synthetic study of chemically-modified nucleoside units that can
be applicable to nucleic acid-based therapeutics, we have reported a
With these individual successful results in mind, we planned
practical synthesis of 40-thioribonucleosides1 and their incorporation to develop a novel nucleoside unit, that is, 1,2-dithianenucleoside.
into oligonucleotides (ONs) to develop short-interfering RNA (siRNA) As shown in Fig. 1, this unit has sulfur atoms and a six-
and aptamers.2–6 Since the resulting ONs, i.e., 40-thioRNA and its membered sugar mimic, which can be considered as a hybrid
analogs, showed high thermal stability in duplex formation and type of modification, in its structure. In this communication,
nuclease resistance in biological fluids,7,8 substitution of sugar ring we report the experimental details for the synthesis of a novel
oxygen with a sulfur atom appears to be one of the ideal approaches 1,2-dithianenucleoside (20).
to develop versatile chemically-modified ONs.
Thus far, we have reported a practical synthesis of 40-thioribo-
As an alternative approach to chemical modification, sub- nucleosides via the Pummerer reaction between an appropriately
stitution of five-membered sugar rings into six-membered sugars protected sulfoxide and a silylated nucleobase.1 Accordingly, we
or their mimics has intensely been studied by the group of planned to achieve the synthesis of the desired compound using
Herdewijn. Thus far, hexitol, altritol, and cyclohexenyl nucleo- the Pummerer-like reaction of a thiolsulfinate derivative obtained
sides and their derivatives have been prepared, and incorpora- from oxidation of a 1,2-dithiane derivative. To the best of our
tion of these units into ONs has been attempted. Accordingly, knowledge, however, no example of such a kind of reaction has
ONs consisting of these modified nucleoside units, i.e., hexitol been reported. Thus, we started our synthetic study using model
nucleic acid (HNA; consisting of hexitol nucleosides), altritol nucleic compounds as shown in Scheme 1. Starting with 1,2-dithio-
acid (ANA; consisting of altritol nucleosides), and cyclohexenyl erythritol (1), 1,2-dithiane derivative 2 was prepared according to
nucleic acid (CeNA; consisting of cyclohexenyl nucleosides), the literature.14 The hydroxyl groups of 2 were then protected by
showed high thermal stability and nuclease resistance.9–11 In acetyl groups to give 315 for neighboring group assistance in the
addition, HNA, ANA, and CeNA have been attempted to develop subsequent Pummerer-like reaction with a nucleobase. After
antisense and siRNA molecules due to their preferable proper- the requisite protection, the resulting 3 was converted into the
ties as chemically-modified ONs.12,13
thiolsulfinate derivative 4 (as a 7 : 1 mixture of diastereomers)16
by mCPBA oxidation. In a similar manner as for the Pummerer
reaction with the sulfoxide derivative,1 a solution of the silylated
uracil in a mixture of toluene–CH2Cl2 containing excess amount
of triethylamine and trimethylsilyl trifluoromethanesulfonate
(TMSOTf) was added to a solution of 4 in CH2Cl2 at 0 1C. However,
no coupling product with uracil was observed. Further attempts
with other solvents and reaction temperatures also did not
afford the desired 5. As an alternative tactic, we changed acetyl
Graduate School of Pharmaceutical Sciences, The University of Tokushima,
Shomachi 1-78-1, Tokushima 770-8505, Japan.
E-mail: minakawa@tokushima-u.ac.jp; Fax: +81 (0)88-633-7288;
Tel: +81 (0)88-633-7288
† Electronic supplementary information (ESI) available: Experimental procedures
and characterization data of all new compounds. CCDC 931650. For ESI and
crystallographic data in CIF or other electronic format see DOI: 10.1039/
c3cc44848g
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Scheme 1 Reagents and conditions: (a) Ac2O, Et3N, DMAP in CH3CN; (b) 2,2-
dimethoxypropane, p-TsOH in acetone; (c) mCPBA in CH2Cl2, ꢀ78 1C; (d) uracil,
Et3N, TMSOTf in toluene–CH2Cl2 or toluene–CH3CN, 0 1C.
groups of 3 into the isopropylidene group, since this protecting
group is often used in the Pummerer reaction with sulfoxide
derivatives. In addition, preferable formation of the b-product
is reported in spite of the absence of an acyl protecting group.17
Thus, treatment of 2 with 2,2-dimethoxypropane in acetone in
the presence of p-TsOH afforded 6. Then, mCPBA oxidation of 6
gave thiolsulfinate derivative 7 as a 5 : 1 mixture of diastereo-
mers.16 To our delight, the desired Pummerer-like reaction
proceeded to give the desired b-product 8 in 25% yield along
with a-product 9 in 16% yield, when 7 was treated with silylated
uracil in the presence of triethylamine and TMSOTf. The
chemical yields of coupling products were somewhat improved
to give 8 and 9 in yields of 32% and 17%, respectively, when the
reaction solvent was changed to a mixture of toluene–CH3CN.
Scheme 2 Reagents and conditions: (a) KSAc in DMF, 100 1C; (b) 10% aq. KOH–
MeOH (1 : 5), O2 atmosphere; (c) 20% TFA in CH2Cl2; (d) TIPSCl, imidazole in DMF;
(e) 2,2-dimethoxypropane, p-TsOH in acetone; (f) mCPBA in CH2Cl2, ꢀ78 1C; (g) uracil,
Et3N, TMSOTf in toluene–CH3CN, 0 1C; (h) Ac2O, reflux; (i) uracil, N,O-bis(trimethyl-
silyl)acetamide, TMSOTf in CH3CN, reflux; (j) TFA in CH2Cl2 (1 : 1).
The structure of 8 was confirmed by X-ray analysis. As can be seen in give 12. Since a model study revealed that the isopropylidene
Fig. 2, a uracil base is introduced at the a-position of the sulfur group was suitable for the cis-diol protection, the PMB groups of
atom in the 1,2-dithiane skeleton. In addition, the b-configuration 12 were first removed by treatment with trifluoroacetic acid in
of glycosidic linkage is obviously proved. As mentioned above, CH2Cl2. Subsequent treatment of the resulting 13 by triiso-
this was the first example of introduction of a heteroatom at the propylsilyl chloride in DMF, followed by 2,2-dimethoxypropane
a-position of the 1,2-dithiane skeleton via Pummerer-like reaction. afforded the fully-protected 15. To carry out the Pummerer-like
With these successful results in hand, we examined the reaction, 15 was converted into thiolsulfinate derivative 16 as a
synthesis of desired 20 (Scheme 2). Following our previous method, 4 : 1 mixture of diastereomers by mCPBA oxidation.16,19 In a
D-ribose was converted into the dibromide 10 in 6 steps.18 The similar manner as described for 8, 16 was treated with silylated
resulting 10 was then treated with KSAc in DMF at 100 1C to give uracil in the presence of triethylamine and TMSOTf. However,
bisthioacetate 11. To construct the 1,2-dithiane skeleton, 11 was no desired 18 was observed under these reaction conditions.
treated with 10% aq. KOH–MeOH (1 : 5) under O2 atmosphere to Accordingly, 16 was converted into the acetate 17 by treatment
with acetic anhydride under reflux. Although the Pummerer-like
reaction was very slow and the chemical yield of 17 was rather
low (19%) compared with those of the corresponding sulfoxide
derivative,1 the desired 17 was obtained by treatment with acetic
anhydride. The resulting 17 was then subjected to the Vorbruggen
glycosylation conditions. As a result, the b-product 18 was
obtained along with the a-product 19 in yields of 37% and 15%,
respectively. The b configuration of 18 and a configuration of 19
1
were estimated by comparison with H-NMR spectra of 8 and 9.
Thus, H-30 of 8, which corresponds to the anomeric proton in
natural nucleosides, appeared at 5.60 ppm in CDCl3. The larger
coupling constant with H-40 (J3 ,4 = 9.8 Hz) suggested a diaxial
relationship, which can be seen in the X-ray structure of 8 (Fig. 2).
0
0
Fig. 2 X-Ray crystal structure of 8.
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the Pummerer-like reaction, followed by Vorbruggen glycosyl-
ation between an appropriately protected 1,2-dithiane deriva-
tive and silylated uracil. To the best of our knowledge, this is
the first example of introduction of a heteroatom at the
a-position of the 1,2-dithiane skeleton via Pummerer-like reac-
tion. Accordingly, our study reported in this manuscript has
novelty in not only the nucleoside derivative, but also organic
chemistry. Further studies including ON synthesis containing
the novel nucleoside unit(s) are in progress and will be reported
elsewhere.
Fig. 3 Selective NOE correlations of 18.
The H-30 of 18 appeared at 5.78 ppm (J3 ,4 = 7.6 Hz) in CDCl3,
which was close to that of 8. On the other hand, the H-30 of 19
0
0
Notes and references
0
0
was observed at 6.25 ppm (J3 ,4 = 2.7 Hz), which was very close to
1 T. Naka, N. Minakawa, H. Abe, D. Kaga and A. Matsuda, J. Am. Chem.
Soc., 2000, 122, 7233.
2 S. Hoshika, N. Minakawa, H. Kamiya, H. Harashima and
A. Matsuda, FEBS Lett., 2005, 579, 3115.
3 S. Hoshika, N. Minakawa, A. Shionoya, K. Imada, N. Ogawa and
A. Matsuda, ChemBioChem, 2007, 8, 2133.
0
0
that of 9 (6.29 ppm with J3 ,4 = 2.5 Hz). This good agreement of
chemical shifts and coupling constants seems to support structures
of 18 and 19. Finally, treatment of 18 with TFA in CH2Cl2 afforded
the desire 1,2-dithiane nucleoside 20 in 91% yield.
To confirm the structure of newly synthesized 1,2-dithiane-
nucleoside, NOESY experiment of 18 was carried out. As can be
seen in Fig. 3, the H-6 of uracil gave correlations with H-40 and
H-50, suggesting that these protons were located on the same face.
In addition, one of the acetonide methyl protons at 1.57 ppm gave
correlations with H-30 and H-60, indicating that these protons
were in a-orientation. On the other hand, the other acetonide
methyl protons that appeared at 1.37 ppm were found to
correlate with H-40 and H-50. Other correlations including
H-30/H-40 and H-50/H-60 suggested that 18 was in the equilibrium
with two chair conformers and all correlations strongly supported
structure of 18.
4 M. Takahashi, C. Nagai, H. Hatakeyama, N. Minakawa,
H. Harashima and A. Matsuda, Nucleic Acids Res., 2012, 40, 5787.
5 Y. Kato, N. Minakawa, Y. Komatsu, H. Kamiya, H. Harashima and
A. Matsuda, Nucleic Acids Res., 2005, 33, 2942.
6 N. Minakawa, M. Sanji, Y. Kato and A. Matsuda, Bioorg. Med. Chem.,
2008, 16, 9450.
7 S. Hoshika, N. Minakawa and A. Matsuda, Nucleic Acids Res., 2004,
32, 3815.
8 M. Takahashi, N. Minakawa and A. Matsuda, Nucleic Acids Res.,
2009, 37, 1353.
9 P. Herdewijn, Chem. Biodiversity, 2010, 7, 1.
10 B. Allart, K. Khan, H. Rosemeyer, G. Schepers, C. Hendrix,
K. Rothenbacher, F. Seela, A. V. Aerscot and P. Herdewijn,
Chem.–Eur. J., 1999, 5, 2424.
11 J. Wang, B. Verbeure, I. Luyten, E. Lescrinier, M. Froeyen, C. Hendrix,
H. Rosemeyer, F. Seela, A. V. Aerscot and P. Herdewijn, J. Am. Chem.
Soc., 2000, 122, 8595.
12 H. Kang, M. H. Fisher, D. Xu, Y. J. Miyamoto, A. Marchand,
A. V. Aerschot, P. Herdewijn and R. L. Juliano, Nucleic Acids Res.,
2004, 32, 4411.
Recently, Baba et al. reported the synthesis of a bridged
nucleoside derivative possessing disulfide linkage (disulfide-type
BNA monomer).20 The authors demonstrated that this monomer
is conformationally changeable in its sugar structure using a 13 M. Fisher, M. Abramov, A. V. Aerschot, D. Xu, R. L. Juliano and
P. Herdewijn, Nucleic Acids Res., 2007, 35, 1064.
14 S. H. Lee and H. Kohn, Heterocycles, 2003, 60, 47.
15 L. Field and Y. H. Khim, J. Org. Chem., 1972, 37, 2710.
reductant or oxidant. Since the compounds prepared in this study
also have disulfide linkage, we investigated conformational changes
resulting from treatment of 18 with a reductant. When 18 was 16 The configurations of each diastereomer were not determined.
17 L. S. Jeong, D. Z. Jin, H. O. Kim, D. H. Shin, H. R. Moon, P. Gunaga,
treated with dithiothreitol in CH2Cl2 in the presence of Et3N,
formation of uracil along with a certain sugar was observed on
M. W. Chun, Y.-C. Kim, N. Melman, Z.-G. Gao and K. A. Jacobson,
J. Med. Chem., 2003, 46, 3775.
TLC analysis. The structure of the resulting sugar was suggested 18 N. Minakawa, Y. Kato, K. Uetake, D. Kaga and A. Matsuda, Tetra-
as a 1,4-dithio-D-ribofuranoside derivative from 1H NMR and MS
hedron, 2003, 59, 1699.
19 In this oxidation, it was difficult to determine which sulfur was
spectra.21 Unlike the disulfide-type BNA monomer, compound
oxidized. In order to determine the regiochemistry, the diastereo-
20 would be utilized as a nucleoside monomer which is subject
to a reductant-triggered structural change.
mers were separated, and each compound was subjected to the
Pummerer-like reaction with acetic ahhydride. As a result, both
reactions afforded 17, and thus, the structures of oxidized products
were decided as a diastereomeric mixture of 16.
In conclusion, we designed the novel 1,2-dithianenucleoside
possessing sulfur atoms and a six-membered sugar mimic, which 20 T. Baba, T. Kodama, K. Mori, T. Imanishi and S. Obika, Chem.
can be considered a hybrid type of modification between 40-thioribo-
nucleoside and altritol nucleoside. The desired 1-[(3R,4R,5S,6R)-4,5-
Commun., 2010, 46, 8058.
21 Experimental details and the possible mechanism of uracil and
1,4-dithio-D-ribofuranoside derivative formation are given in the
dihydroxy-6-hydroxymethyl-1,2-dithianyl]uracil (20) was prepared via
ESI† (Scheme S3).
c
This journal is The Royal Society of Chemistry 2013
Chem. Commun., 2013, 49, 7851--7853 7853