Synthesis of nonionic ether-backbone analogues of RNA from pseudooligosaccharides

Article abstract of DOI:10.1016/j.tetlet.2011.09.139

Uracil nucleosides with internucleosidic ether linkage as nonionic analogues of RNA were synthesized by glycosylation of ether-backbone pseudooligosaccharides.

Full text of DOI:10.1016/j.tetlet.2011.09.139

Tetrahedron Letters 52 (2011) 6610–6612
Contents lists available at SciVerse ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Synthesis of nonionic ether-backbone analogues of RNA
from pseudooligosaccharides
⇑
⇑
Prithwish Kumar Jana, Soumendra Nath Das, Sukhendu B. Mandal , Anup Bhattacharjya
Chemistry Division, Indian Institute of Chemical Biology (a unit of CSIR), 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
a r t i c l e i n f o
a b s t r a c t
Article history:
Uracil nucleosides with internucleosidic ether linkage as nonionic analogues of RNA were synthesized by
glycosylation of ether-backbone pseudooligosaccharides.
Received 29 August 2011
Revised 27 September 2011
Accepted 29 September 2011
Available online 8 October 2011
Ó 2011 Elsevier Ltd. All rights reserved.
Keywords:
Synthesis
Non-ionic
Ether-backbone
RNA analogue
Pseudooligosaccharide
Structural modification of nucleic acids has remained a topic of
great importance, because alterations in the structure may lead to
improvement in stability, bioavailability and hybridization proper-
ties. So synthesis of nucleic acid analogues is a worthwhile engage-
ment with synthetic chemists. The potential of RNA interference as
a new therapeutic strategy calls for the synthesis of short stretches
of RNA analogues, in which chemical modifications optimize the
pharmacological properties of short interfering RNAs.1–3 Chemical
modifications, particularly backbone and 20-O-modifications, have
been demonstrated to provide the resistance towards chemical
and enzymatic hydrolysis.4 One way to alter the backbone struc-
ture is to replace the anionic phosphate groups by nonionic linkers.
This modification might retain some of the interstrand recognition
properties of natural oligonucleotides, and the resulting nucleo-
sides might possess solubility in organic solvents besides water.
Formacetal-linked polynucleotides,2–5 thioether-linked oligonucle-
osides and their dimethylene sulfone analogues6–10 are some of the
well-studied examples of oligonucleotide analogues featuring neu-
tral backbone. Formacetal modifications have been shown to give
rise to nucleosides, which have increased affinities to their comple-
mentary RNA fragments relative to the unmodified oligoribonu-
cleotides, at the same time virtually retaining the native
conformation.2 Extensively studied dimethylene sulfone analogues
exhibited properties, which revealed, apart from their significant
bioavailability, notable similarity in the duplex structure with that
in native RNA.6,8 Figure 1 shows a structural comparison between
native RNA and the aforementioned analogues. It is apparent that a
new analogue may be derived by replacement of the linkers in
O
O
B
O
B
O
OH
O
P
OH
O
O
O
O
O
B
O
B
O
OH
O
OH
O
Formacetal-linked
RNA analogue
RNA
O
X
B
O
B
O
OH
OH
O
O
X
B
O
B
OH
OH
O
X
X = S or SO2
Dimethylene sulfide or
dimethylene sulfone-linked
RNA analogue
ether-backbone
RNA analogue
⇑
Corresponding authors. Tel.: +91 33 24995758; fax: +91 33 24735197.
E-mail addresses: sbmandal@iicb.res.in (S.B. Mandal), anupbh@hotmail.com,
Figure 1. Structural comparison between RNA and its analogues.
anupbhattacharjya@iicb.res.in (A. Bhattacharjya).
0040-4039/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2011.09.139

P. K. Jana et al. / Tetrahedron Letters 52 (2011) 6610–6612
6611
MeO
these analogues with an ether-linkage as shown, resulting in the
MeO
O
O
development of an ether-backbone RNA analogue. Recently we re-
ported the synthesis of ether-linked oligoribonucleosides from
3,50-ether-linked pseudosaccharides, with the linkage consisting
of two atoms.11 We envisaged that increasing the length of the
ether linker would lead to nucleosides, which would more closely
resemble the ribonucleotide structure as depicted in Figure 1. The
synthesis of these ether-backbone RNA analogues from pseudooli-
gosaccharides is reported herein.
O
O
Pd-C (10%), H2,
EtOAc, 25 oC,
15 h, 96%
O
O
O
O
O
O
O
O
O
O
OH
OBn
MeO
8
9
O
In order to synthesize the ether-backbone RNA analogues, we
required suitable ether-backbone pseudooligosaccharides, which
could be later converted to nucleosides. Scheme 1 outlines the syn-
thesis of a pseudodisaccharide with an ether linkage. The known
alcohol 312,13 was alkylated with the mesyl derivative 2 obtained
from the sugar alcohol 112 in the presence of tetrabutyl ammonium
bromide in aqueous NaOH according to the alkylation protocol re-
ported by us.11,14 The pseudodisaccharide derivative 4 obtained in
77% yield was selectively deprotected by aqueous 75% acetic acid
to furnish the diol 5, which was converted to the corresponding
dimesylate and then treated with NaI to give the alkene 6 in 57%
yield. Hydroboration of 6 led to the alcohol 7 in 61% yield. For
the purpose of facile characterization of the future nucleosides,
the hydroxyl group in 7 was capped by methylation using NaH
and MeI to give rise to the pseudodisaccharide derivative 8 in
89% yield. The pseudotrisaccharide 10 was prepared according to
Scheme 2. Debenzylation of 8 by hydrogenolysis in the presence
of 10% Pd-C resulted in the formation of the alcohol 9. Alkylation
of 9 with 2 as previously described gave rise to the capped pseudo-
trisaccharide 10 in 69% yield.
O
MsO
O
O
O
O
O
O
OBn
O
2
O
14% aq. NaOH, TBAB,
60 oC, 30 h, 69%
O
O
O
O
OBn
10
Scheme 2. Synthesis of the pseudotrisaccharide 10.
MeO
MeO
O
O
OAc
OAc
O
1. 90% AcOH, reflux,
7 h
O
2. Py, Ac2O, DMAP,
0-25 oC, 12 h,
67% from 8
O
O
With the precursor pseudosaccharides in hand, they were next
converted to the corresponding uracil nucleosides using the Vor-
brüggen method of glycosylation.15 Removal of the 1,2-O-isopro-
O
O
OAc
O
O
OAc
11
OBn
O
OBn
8
NH
MeO
HO
MsO
O
O
N
O
O
O
MsCl, Et3N, CH2Cl2,
0-20 oC, 4 h, 95%
O
O
O
Uracil, BSA,
O
OAc
OBn
OBn
TMSOTf, MeCN,
1
2
O
55 oC, 17 h, 62%
NH
N
O
O
O
O
HO
HO
O
O
O
O
O
O
O
O
OAc
12
H
H
H
O
O
O
OBn
3
OH
75% aq. AcOH,
O
O
25 oC, 12 h, 90%
Scheme 3. Conversion of 8 to ether-backbone uracil nucleoside 12.
12% aq. NaOH,
Bu4NBr, 70 oC,
40 h, 77%
O
O
O
O
O
O
OBn
OBn
pylidene groups in 8 by treatment with 90% acetic acid under re-
flux followed by acetylation gave the pseudosaccharide tetraace-
tate derivative 11 as an anomeric mixture (Scheme 3). The
glycosylation of 11 by the Vorbrüggen procedure in the presence
of uracil, N,O-bis(trimethylsilyl)acetamide (BSA) and TMSOTf gave
rise to the uracil nucleoside 12 in 62% yield. The nucleoside 12 rep-
resents an example of an ether-backbone RNA analogue, in which
the phosphodiester group of RNA has been replaced by a four-atom
ether moiety. Similarly, the pseudotrisaccharide 10 was converted
to the uracil nucleoside 14 via the hexaacetate 13 by applying the
same reactions described above (Scheme 4). The structures of 12
and 14 were established on the basis of IR, NMR and high resolu-
tion mass spectral analyses.16 The 1H NMR spectra of 12 and 14
exhibited signals due to –CH3 and uracil 5-H and 6-H having inte-
grations expected for indicated structures.
4
5
HO
O
O
O
O
O
O
1. BH3.SMe2, THF,
1. MsCl, Et3N, CH2Cl2
0
oC, 20 h
O
O
2. H2O2-NaOH, 25 oC,
3 h, 61%
2. NaI, DME,
57% (from 5)
O
O
O
O
O
O
OBn
OBn
7
6
MeO
O
O
NaH, THF, MeI,
0-25 oC, 12 h,
89%
O
O
O
O
In conclusion, examples of ether-backbone RNA analogues with
uracil as the nucleobase were synthesized from pseudooligosac-
charides. Synthesis of analogues bearing other nucleobases, and
incorporation of these nucleosides in native RNA in order to study
their ability to form duplexes will be reported in due course.
O
OBn
8
Scheme 1. Synthesis of the pseuododisaccharide 8.

6612
P. K. Jana et al. / Tetrahedron Letters 52 (2011) 6610–6612
15. Niedballa, U.; Vorbrüggen, H. J. Org. Chem. 1974, 39, 3660–3663.
MeO
MeO
16. Spectral data 4. Colourless liquid; ½a D25
ꢀ
+21.7 (c 0.15, CHCl3); IR (neat): 1376,
O
O
OAc
OAc
1217, 1099, 874, 747 cmꢁ1 1H NMR (600 MHz, CDCl3): d 1.31 (s, 3H), 1.32 (s,
;
O
3H), 1.34 (s, 3H), 1.39 (s, 3H), 1.48 (s, 3H), 1.50 (s, 3H), 1.70–1.74 (m, 1H), 2.02–
2.10 (m, 2H), 2.17 (br s, 1H), 3.50 (dd, 1H, J = 6.6, 10.2 Hz), 3.60 (t, 2H,
J = 6.6 Hz), 3.66–3.68 (m, 2H), 3.75–3.78 (m, 2H), 3.90 (dd, 1H, J = 9.6, 12.6 Hz),
3.96–3.99 (m, 1H), 4.04 (d, 1H, J = 7.2 Hz), 4.06 (d, 1H, J = 6.6 Hz), 4.52 (d, 1H,
J = 12.0 Hz), 4.56 (d, 1H, J = 12.0 Hz), 4.71 (d, 1H, J = 3.6 Hz), 4.72 (d, 1H,
J = 4.2 Hz), 5.74 (d, 1H, J = 3.6 Hz), 5.79 (d, 1H, J = 3.6 Hz), 7.26–7.35 (m, 5H);
13C NMR (150 MHz, CDCl3): d 25.3 (CH3), 26.3 (CH3), 26.5 (CH3), 26.6 (CH3),
26.7 (CH3), 26.9 (CH3), 33.8 (CH2), 48.4 (CH), 49.5 (CH), 66.3 (CH2), 66.4 (CH2),
67.0 (CH2), 67.8 (CH2), 73.3 (CH), 77.2 (CH2), 77.5 (CH), 79.5 (CH), 81.0 (CH),
81.2 (CH), 104.8 (CH), 105.1 (CH), 109.5 (C), 111.5 (C), 112.0 (C), 127.5 (2 ꢂ CH),
127.6 (CH), 128.4 (2 ꢂ CH), 138.2 (C); HRMS (ESI) m/z calcd for C30H44O10Na,
O
O
O
1.90% aq. AcOH,
reflux, 7 h
2. Py, Ac O, DMAP,
2
O
O
OAc
OAc
O
O
o
0-25 C, 14 h, 65%
O
O
from 10
O
O
OAc
OAc
O
O
587.2832; found, 587.2812. Compound 6: colourless liquid; ½a D25
ꢀ
+52.1 (c 0.27,
OBn
10
CHCl3); IR (neat): 1460, 1375, 1215, 1101, 743 cmꢁ1 1H NMR (600 MHz,
;
OBn
13
CDCl3): d 1.31 (s, 3H), 1.32 (s, 3H), 1.48 (s, 3H), 1.51 (s, 3H), 1.68–1.72 (m, 1H),
2.01–2.09 (m, 3H), 3.35 (dd, 1H, J = 5.4, 9.6 Hz), 3.50 (dd, 1H, J = 6.0, 9.0 Hz),
3.53–3.60 (m, 2H), 3.71 (t, 1H, J = 9.0 Hz), 3.76 (dd, 1H, J = 7.8, 9.6 Hz), 3.97 (dt,
1H, J = 2.4, 10.2 Hz), 4.18 (dd, 1H, J = 7.2, 10.2 Hz), 4.52 (d, 1H, J = 12.0 Hz), 4.56
(d, 1H, J = 12.0 Hz), 4.70 (d, 1H, J = 4.2 Hz), 4.71 (d, 1H, J = 4.8 Hz), 5.19 (d, 1H,
J = 10.2 Hz), 5.30 (td, 1H, J = 1.2, 16.8 Hz), 5.77–5.83 (m, 1H), 5.79 (d, 1H,
J = 4.2 Hz), 5.81 (d, 1H, J = 3.6 Hz), 7.28–7.35 (m, 5H); 13C NMR (150 MHz,
CDCl3): d 26.3 (CH3), 26.4 (CH3), 26.6 (CH3), 26.7 (CH3), 33.8 (CH2), 49.5 (CH),
49.8 (CH), 66.0 (CH2), 66.4 (CH2), 67.8 (CH2), 73.3 (CH2), 76.9 (CH), 80.4 (CH),
80.5 (CH), 81.0 (CH), 104.8 (CH), 105.0 (CH), 111.5 (C), 111.7 (C), 118.1 (CH2),
127.5 (2 ꢂ CH), 127.6 (CH), 128.3 (2 ꢂ CH), 136.0 (CH), 138.2 (C); HRMS (ESI)
m/z calcd for C27H38O8Na, 513.2464; found, 513.2490. Compound 8: colourless
O
NH
MeO
O
N
O
O
OAc
O
O
NH
Uracil, BSA,
TMSOTf, MeCN,
55 C, 19 h, 51%
N
O
o
OAc
O
liquid; ½a 2D5
ꢀ
+70.8 (c 0.24, CHCl3); IR (neat): 1456, 1375, 1215, 1106, 1017,
O
873 cmꢁ1 1H NMR (600 MHz, CDCl3): d 1.30 (s, 3H), 1.32 (s, 3H), 1.49 (s, 6H),
;
NH
O
N
1.66–1.73 (m, 2H), 1.96–2.08 (m, 4H), 3.32 (s, 3H), 3.40 (dd, 1H, J = 6.0, 9.6 Hz),
3.46–3.53 (m, 3H), 3.54–3.59 (m, 2H), 3.70 (dd, 1H, J = 8.4, 9.6 Hz), 3.77 (dd, 1H,
J = 7.8, 9.6 Hz), 3.91–3.98 (m, 2H), 4.52 (d, 1H, J = 12.0 Hz), 4.56 (d, 1H,
J = 12.0 Hz), 4.66 (t, 1H, J = 4.2 Hz), 4.71 (t, 1H, J = 4.2 Hz), 5.77 (d, 1H,
J = 3.6 Hz), 5.79 (d, 1H, J = 3.6 Hz), 7.28–7.31 (m, 1H), 7.33–7.36 (m, 4H); 13C
NMR (150 MHz, CDCl3): d 26.3 (CH3), 26.4 (CH3), 26.64 (CH3), 26.65 (CH3), 33.8
(CH2), 34.0 (CH2), 49.5 (CH), 49.6 (CH), 58.7 (CH3), 66.4 (CH2), 66.8 (CH2), 67.9
(CH2), 69.6 (CH2), 73.3 (CH2), 76.9 (2 ꢂ CH), 81.01 (CH), 81.04 (CH), 104.8
(2 ꢂ CH), 111.5 (2 ꢂ C), 127.5 (2 ꢂ CH), 127.6 (CH), 128.4 (2 ꢂ CH), 138.2 (C);
HRMS (ESI) m/z calcd for C28H42O9Na, 545.2727; found, 545.2738. Compound
O
OAc
14
Scheme 4. Conversion of 10 to ether-backbone uracil nucleoside 14.
OBn
Acknowledgments
10: colourless liquid; ½a D25
ꢀ
+66.2 (c 0.15, CHCl3); IR (neat): 1376, 1216, 1108,
1020, 875 cmꢁ1 1H NMR (600 MHz, CDCl3): d 1.30 (s, 3H), 1.31 (s, 3H), 1.32 (s,
;
3H), 1.47(s, 3H), 1.48 (s, 3H), 1.49 (s, 3H), 1.60–1.74 (m, 4H), 1.95–2.09 (m, 5H),
3.32 (s, 3H), 3.40 (dt, 2H, J = 5.4, 9.0 Hz), 3.47–3.52 (m, 3H), 3.53–3.61 (m, 4H),
3.68–3.73 (m, 2H), 3.77 (dd, 1H, J = 7.8, 9.0 Hz), 3.90–3.98 (m, 3H), 4.52 (d, 1H,
J = 12.0 Hz), 4.56 (d, 1H, J = 12.0 Hz), 4.66 (q-like, 2H, J = 4.2 Hz), 4.71 (t, 1H,
J = 4.2 Hz), 5.76 (d, 1H, J = 3.6 Hz), 5.78 (d, 1H, J = 3.6 Hz), 5.79 (d, 1H,
J = 3.6 Hz), 7.28–7.31 (m, 1H), 7.34–7.35 (m, 4H); 13C NMR (150 MHz, CDCl3):
d 26.3 (2 ꢂ CH3), 26.4 (2 ꢂ CH3), 26.7 (2 ꢂ CH3), 33.7 (CH2), 33.8 (CH2), 34.0
(CH2), 49.3 (CH), 49.4 (CH), 49.5 (CH), 58.6 (CH3), 66.4 (CH2), 66.6 (CH2), 66.8
(CH2), 67.87 (CH2), 67.89 (CH2), 69.6 (CH2), 73.3 (CH2), 76.6 (CH), 76.9 (CH),
77.0 (CH), 80.9 (CH), 80.96 (CH), 81.02 (CH), 104.8 (3 ꢂ CH), 111.4 (C), 111.46
(C), 111.48 (C), 127.5 (2 ꢂ CH), 127.6 (CH), 128.4 (2 ꢂ CH), 138.2 (C); HRMS
(ESI) m/z calcd for C38H58O13Na, 745.3775; found, 745.3820. Compound 12:
AB is grateful to CSIR, India for Emeritus Scientist Fellowship.
The award of Senior Research Fellowship to PKJ by CSIR, India is
gratefully acknowledged. SBM and SND thank CSIR for financial
support and Project Assistantship respectively from Network Pro-
ject (No. NWP0036).
Supplementary data
Supplementary data (1H and 13C spectra of 4, 6, 8, 10, 12 and
14.) associated with this article can be found, in the online version,
at doi:10.1016/j.tetlet.2011.09.139.
colourless viscous liquid; ½a D25
ꢀ
+31.7 (c 0.10, CHCl3); IR (neat): 3468, 3222,
1736,1689, 1459, 1377, 1233, 1109, 753 cmꢁ1
;
1H NMR (600 MHz, CDCl3): d
1.80–1.86 (m, 3H), 2.04 (s, 3H), 2.09 (s, 3H), 2.10–2.11 (m, 1H), 2.47–2.51 (m,
2H), 3.34 (s, 3H), 3.43 (dd, 1H, J = 6.6, 9.6 Hz), 3.48 (dd, 1H, J = 6.6, 9.6 Hz),
3.52–3.57 (m, 5H), 3.61 (dd, 1H, J = 6.6, 9.6 Hz), 4.12–4.18 (m, 2H), 4.46 (d, 1H,
J = 12.0 Hz), 4.50 (d, 1H, J = 12.0 Hz), 5.41 (dt, 2H, J = 2.4, 6.6 Hz), 5.71 (s, 2H),
5.74 (br t, 2H, J = 6.6 Hz), 7.24–7.30 (m, 5H, overlapped with solvent), 7.34 (br
d, 2H, J = 7.2 Hz), 8.43 (br s, 2H); 13C NMR (150 MHz, CDCl3): d 20.6 (CH3), 20.7
(CH3), 34.5 (2 ꢂ CH2), 45.6 (CH), 46.0 (CH), 58.8 (CH3), 65.9 (CH2), 66.7 (CH2),
67.6 (CH2), 69.0 (CH2), 73.5 (CH2), 76.86 (CH), 76.9 (CH), 79.4 (CH), 79.7 (CH),
90.87 (CH), 90.94 (CH), 102.56 (CH), 102.64 (CH), 127.6 (2 ꢂ CH), 127.8 (CH),
128.5 (2 ꢂ CH), 137.7 (C), 140.1 (CH), 140.2 (CH), 149.7 (2 ꢂ C), 162.7 (2 ꢂ C),
169.8 (C), 169.9 (C); HRMS (ESI) m/z calcd for C34H42O13NaN4, 737.2646; found,
References and notes
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737.2675. Compound 14: colourless viscous liquid; ½a D25
ꢀ
+25.5 (c 0.11, MeOH);
;
IR (neat): 3195, 1689, 1459, 1378, 1231, 1108, 756 cmꢁ1
1H NMR (600 MHz,
CDCl3): d 1.80–1.92 (m, 6H), 2.08 (s, 3H), 2.09 (s, 3H), 2.11 (s, 3H), 2.46 (m, 1H),
2.54 (m, 1H), 2.66 (m, 1H), 3.35 (s, 3H), 3.43 (dd, 2H, J = 5.4, 9.0 Hz), 3.47–3.63
(m, 10H), 4.09–4.18 (m, 3H), 4.46 (d, 1H, J = 12.0 Hz), 4.52 (d, 1H, J = 12.0 Hz),
5.40–5.46 (m, 4H), 5.68 (s, 2H), 5.75 (d, 3H, J = 6.0 Hz), 7.23–7.30 (m, 5H,
overlapped with solvent), 7.34 (t-like, 2H, J = 6.6, 7.2 Hz), 8.61 (br s, 1H, NH),
9.14 (br s, 1H, NH), 9.18 (br s, 1H, NH); 13C NMR (150 MHz, CDCl3): d 20.7
(3 ꢂ CH3), 34.1 (CH2), 34.7 (2 ꢂ CH2), 45.4 (CH), 45.5 (CH), 45.7 (CH), 58.8
(CH3), 60.4 (CH2), 66.0 (CH2), 66.4 (CH2), 66.8 (CH2), 67.6 (CH2), 69.0 (CH2), 73.4
(CH2), 76.9 (3 ꢂ CH, overlapped with solvent), 79.2 (CH), 79.4 (CH), 79.7 (CH),
91.0 (3 ꢂ CH), 102.6 and 102.7 (3 ꢂ CH), 127.6 (2 ꢂ CH), 127.8 (CH), 128.5
(2 ꢂ CH), 137.9 (C), 140.4 (2 ꢂ CH), 140.5 (CH), 150.0 (3 ꢂ C), 161.5 (C), 163.2
(2 ꢂ C), 169.8 and 170.5 (3 ꢂ C); HRMS (ESI) m/z calcd for C47H58O19NaN6,
1033.3654; found, 1033.3654.