Synthesis of pyrimidine 1′,3′-anhydro-β-D-psico- and -sorbo-furanosyl nucleosides

Article abstract of DOI:10.1055/s-2005-871547

A novel approach for the synthesis of pyrimidine 1′,3′-anhydro- β-D-psico- and -sorbo-furanosyl nucleosides 2 and 3, respectively, has been developed. The approach described here employs a readily available O ²,3′-anhydro-β-D-fructofuranosyl-ur

Full text of DOI:10.1055/s-2005-871547

LETTER
1683
Synthesis of Pyrimidine 1¢,3¢-Anhydro-b-D-psico- and -sorbo-furanosyl
Nucleosides
S
ynthesisof Py
a
1
¢
m
¢
-Anhydro-
b
-
D
-
psi
a
co
-
a
nd-so
r
rbo-fura
a
nosyl Nucleoside
I
. Kulak,a Olga V. Tkachenko,a Svetlana L. Sentjureva,a Jouko Vepsäläinen,b Igor A. Mikhailopulo*a,c
a
b
c
Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5, 220141 Minsk, Belarus
Department of Chemistry, University of Kuopio, PO Box 1627, 70211 Kuopio, Finland
Department of Pharmaceutical Chemistry, University of Kuopio, PO Box 1627, 70211 Kuopio, Finland
Fax +358(17)162456; E-mail: Igor.Mikhailopulo@uku.fi
Received 18 April 2005
chromatographic separation gave the desired compound 8
(48%), its derivative 9 (25%), as well as two minor prod-
ucts, the epoxide 10 (6%) and fructoside 11 (10%). The
formation of the epoxide 10 likely results from an in-
tramolecular nucleophilic attack of a 4¢-alkoxide at the 3¢-
carbon atom leading to the O2,3¢-anhydro ring-opening.
The transient existence of similar pyrimidine ribo-ep-
oxides under alkaline conditions has been previously
postulated11 and 2¢,3¢-anhydrouridine was recently syn-
thesized from O2,2¢-anhydro-1-(b-D-arabinofurano-
syl)uracil on treatment with NaH in anhydrous DMSO.12
It was shown that 2¢,3¢-anhydrouridine is readily convert-
ed back into O2,2¢-anhydro-1-(b-D-arabinofurano-
syl)uracil by heating or by treating it with Et3N–MeOH at
room temperature.12 Note that standard detritylation of the
epoxide 10 afforded the anhydro nucleoside 1 in high
yield pointing to the 3¢,4¢-psico-epoxide structure of com-
pound 10. The formation of the fructosides 9 and 11 may
be accounted for an acidic neutralization of the reaction
mixture before chromatography (Scheme 1).
Abstract: A novel approach for the synthesis of pyrimidine 1¢,3¢-
anhydro-b-D-psico- and -sorbo-furanosyl nucleosides 2 and 3,
respectively, has been developed. The approach described here
employs a readily available O2,3¢-anhydro-b-D-fructofuranosyl-
uracil (1) as a key starting compound.
Key words: pyrimidine nucleosides, hexofuranosides, anhydro
derivatives
Oligonucleotides containing rigid nucleosides display a
number of exciting biological properties, which are of im-
portance for possible biomedical applications.1 The fura-
nose ring of natural nucleosides is flexible and exists in an
equilibrium of the N- and S-type conformations.2 The in-
troduction of a bridge between diverse carbon atoms of
the pentofuranose moieties results in the fixation of the
furanose ring in one of the possible conformations.
Among such rigid nucleosides, the 1¢,3¢-anhydro nucleo-
sides of D-psicofuranose have been recently independent-
ly synthesized by Chattopadhyaya and co-workers3 and
by us4,5 employing a convergent approach.6–8 In the
present communication, we report on the synthesis of py-
rimidine 1¢,3¢-anhydro-b-D-psico- and -sorbo-furanosyl
nucleosides 2–4 (Figure 1) employing O2,3¢-anhydro-b-
D-fructofuranosyluracil (1)9,10 as a key starting com-
pound.
Cleavage of the anhydro ring of 8 was achieved under al-
kaline hydrolysis to afford the 1¢,4¢,6¢-O-protected fructo-
side 9 in 88% yield. Its conventional mesylation followed
by detritylation gave the fructoside 12 in 77% combined
yield. Treatment of the latter with MeONa–MeOH under
reflux resulted in the 1¢,3¢-anhydro ring-closure (13;
46%). Catalytic debenzylation of the psicoside 13 gave
the desired 1-(1,3-anhydro-b-D-psicofuranosyl)uracil (2;
67%).
HO
HO
B
U
O
O
HO
Compound 7 was alternatively transformed into the anhy-
dro psicoside 2 in five steps: (i) cleavage of the O2,3¢-an-
hydro ring (0.5 M NaOH in a mixture of EtOH–dioxane–
H2O, 2:1:1; 95%); (ii) selective 1¢-O-benzoylation (BzCl/
anhyd pyridine; 0 °C, 16 h) followed by (iii) conventional
mesylation (59%, combined); (iv) the 1¢,3¢-anhydro ring-
closure on treatment with 0.5 M MeONa/MeOH under
reflux (46%), and (v) detritylation (75%).
O
O
HO
2, B = U (uracil-1-yl)
3, B = C (cytosin-1-yl)
4
Figure 1
Treatment of the anhydro nucleoside 1 with (4-
monomethoxy)trityl (MMTr) chloride in pyridine afford-
ed, after silica gel column chromatography, mainly 1¢,6¢-
di-O-MMTr (5; 42%) and 6¢-O-MMTr (6; 22%) deriva-
tives, along with the isomeric 4¢,6¢-di-O-MMTr nucleo-
side 7 (7%). Benzylation of the former followed by
Uracil nucleoside 13 was transformed to 1-(1,3-anhydro-
b-D-psicofuranosyl)cytosine (3; 68%)13,3b through inter-
mediary formation of cytosine derivative 1414 by consec-
utive treatments with (i) Ac2O/DMAP/pyridine, (ii)
tris(triazolyl)-phosphate in MeCN, (iii) aqueous ammo-
nia, (iv) NH3/MeOH, and (v) H2/Pd/C in MeOH.
SYNLETT 2005, No. 11, pp 1683–1686
0
7
.0
7
.2
0
0
5
Advanced online publication: 14.06.2005
DOI: 10.1055/s-2005-871547; Art ID: G14005ST
© Georg Thieme Verlag Stuttgart · New York
Treatment of compound 5 with 0.5 M NaOH in dioxane–
H2O (1:1, v/v) gave the 1,6-di-O-MMTr fructo-nucleoside

1684
T. I. Kulak et al.
LETTER
O
N
O
N
N
N
RO
HO
a
O
O
O
O
OR1
OH
R2O
HO
5, R = R1 = MMTr; R2 = H
6, R = MMTr; R1 = R2 = H
7, R = R2 = MMTr; R1 = H
1
b
O
N
O
N
O
O
N
N
NH
NH
NH
RO
RO
RO
RO
O
N
O
O
O
O
O
H
O
O
H
O
O
+
+
+
OR
OR
OR
OR
O
BzlO
BzlO
d,e
HO
8
9
10
11
c
HO
HO
HO
U
U
C
O
Ms
O
O
f
O
h,i
OH
O
O
BzlO
BzlO
BzlO
12
13
14
g
g
U - uracil-1-yl
C - cytosin-1-yl
2
3
Scheme 1 Reagents and conditions: (a) (1) MMTrCl/anhyd pyridine, r.t., 20 h; (2) SiO2, elution with a MeOH gradient (0–10%, v/v) in CHCl3
5 (42%), 6 (22%), 7 (7%); (b) (1) NaH/THF, 0–4 °C, 5 min; + BzlBr, 4 °C to 20 °C, 20 h; (2) SiO2, elution with a MeOH gradient (0–1%, v/v)
in CHCl3: 8 (48%), 9 (25%), 10 (6%), 11 (10%); (c) 1 M NaOH/dioxane–H2O, 1:1 (v/v), r.t., 1 h (88%); (d) MsCl/anhyd pyridine, 0 °C to 20 °C
20 h (87%); (e) 2% p-TsOH/CHCl3–MeOH (7:3, v/v), r.t. 10 min (89%); (f) 1 M MeONa/MeOH, reflux, 5 h (46%); (g) H2/5% Pd/C/MeOH
r.t., 24 h: 2 (67%); 3 (62%); (h) Ac2O/DMAP/pyridine, r.t., 30 min (96%); (i) (1) tris(triazolyl)phosphate/MeCN; (2) 25% aq ammonia/dioxane
1:5 (v/v), r.t., 16 h; (3) NH3/MeOH, r.t., 6 h (70%).
(11) in 97% yield. Its careful mesylation in anhydrous 1H and 13C resonances was made by 2D [1H,1H] and
pyridine gave the mesylate 15 (89%), treatment of which [1H,13C] correlation spectra and in some cases by homo-
with MeONa/MeOH led to the 3¢,4¢-anhydro derivative 16 decoupling experiments. The values of the H3¢/H4¢ and
(80%). Detritylation of the latter gave 1-(3,4-anhydro-b-
O
D-tagatofuranosyl)uracil (17; 84%). Finally, the tagato-
side 17 was isomerized into 1-(1,3-anhydro-b-D-sorbo-
NH
furanosyl)uracil (4) upon treatment either with NaH in
RO
RO
N
O
U
anhydrous DMF at 75–80 °C for seven minutes [48%;
uracil (20%) and the starting 17 (28%) have been also iso-
lated] or with MeONa/MeOH at reflux for 40 minutes
[61%; uracil: 14%; 17: 20%; Scheme 2].
O
H
O
O
a
b
c
11
O
OR
OR
MsO
16
15
No formation of isomeric 1-(1,4-anhydro-b-D-fructofura-
nosyl)uracil was detected. In the case of a rather rigid
furanose ring of the epoxide 17, such a regioselectivity of
an intramolecular attack of the O1¢-oxygen at C3¢-carbon
atom maybe explained by a greater spatial proximity of
these atoms vs. the O1¢–C4¢. Indeed, a geometry optimi-
zation of compound 17 using the HyperChem® program
(Hypercube, Inc., 2002; release 7.1; AMBER force field)
furnished the 2.9 Å and 3.3 Å distances between the O1¢–
C3¢ and O1¢–C4¢ atoms, respectively (Figure 2).
HO
HO
U
U
O
O
O
d
HO
OH
O
17
4
U - uracil-1-yl
R = MMTr
Scheme 2 Reagents and conditions: (a) MsCl/anhyd pyridine, 0–
20 °C, 16 h (89%); (b) 0.5 M MeONa/MeOH, r.t., 3 h (80%); (c) 60%
aq CF3COOH, 45–50 °C, 4 h (84%); (d) (1) NaH/anhyd DMF, 75–
80 °C, 7 min (48%); (2) MeONa/MeOH, reflux, 40 min (61%).
The structure of the synthesized compounds was proved
by 1H NMR and 13C NMR data. The assignment of all the
Synlett 2005, No. 11, 1683–1686 © Thieme Stuttgart · New York

LETTER
Synthesis of Pyrimidine 1¢,3¢-Anhydro-b-D-psico- and -sorbo-furanosyl Nucleosides
1685
Figure 2 Computer-generated (molecular mechanics; AMBER) re-
presentation of 1-(3,4-anhydro-b-D-tagatofuranosyl)uracil (17).
Figure 3 The CD spectra of 1-(1,3-anhydro-b-D-psicofuranosyl)-
uracil (2, ···), its sorbo-isomer 4 (---), and 1-(3,4-anhydro-b-D-tagato-
furanosyl)uracil (17, –––) in MeOH.
H4¢/H5¢ proton–proton coupling constants for the psico-
sides 2 and 3 are similar to those for the relevant thymine
and cytosine nucleosides3 as well as adenine4 counterpart.
Moreover, the aforementioned couplings are in a fair cor-
respondence with the respective torsion angles of 45° and
168° deduced from the energy minimized structures of
1,3-anhydro-b-D-psico nucleosides.
the glycosyl bond. These data gave further support to the
C4¢-OH···O=C2 hydrogen bond. It is noteworthy that the
CD curve of the tagatoside 17 exhibits, like that of uridine,
a positive B2u CD band, whereas is anomalous in the B1u
and E1ua spectral regions.
By going from the psicoside 215 to the sorboside 4,16 rather
remarkable changes in the coupling constants and chemi-
cal shifts have been observed. Thus, the vicinal J3¢,4¢ < 0.5
Hz and J4¢,5¢ = 3.35 Hz couplings are again in a fair corre-
spondence with the respective torsion angles of 85° and
38°, which are found in the energy-minimized structure of
the sorboside 4. As might be expected, an inversion of a
hydroxyl group configuration at C4¢ resulted in displace-
ments of the H5¢ resonance to a lower field (Dd = –0.35
ppm). The most striking observation consists in the con-
siderable displacement to a lower field of the C3¢ reso-
nance (Dd = –4.56 ppm) on passing from the psicoside 2
to the sorboside 4. The most probable explanation may be
the anisotropic effect of the C2=O carbonyl group of the
aglycon on the C3¢ atom resulting from the formation of
an intramolecular hydrogen bond between the 4¢-OH
group and the oxygen of the C2=O carbonyl. A downfield
shift of the 4¢-OH resonance by 0.39 ppm in the 1H NMR
spectrum of the sorboside 4 vs. the psicoside 2 agrees with
the C4¢-OH···O=C2 hydrogen bond.
In conclusion, a novel approach for the synthesis of pyri-
midine 1¢,3¢-anhydro-b-D-psico- and -sorbo-furanosyl
nucleosides has been developed. The approach described
here employs a readily available O2,3¢-anhydro-b-D-
fructofuranosyluracil (1) as a key starting compound that
may be transformed into a number of pyrimidine anhydro
hexofuranosyl nucleosides.
Acknowledgment
This work was supported by a grant from the Byelorussian Republi-
can Foundation for Fundamental Researches (No. Ch03IC-012).
References
(1) (a) Jepsen, J. S.; Sorensen, M. D.; Wengel, J.
Oligonucleotides 2004, 14, 130. (b) Petersen, M.; Wengel,
J. Trends Biotechnol. 2003, 21, 74. (c) Imanishi, T.; Obika,
S. Chem. Commun. 2002, 1653. (d) Leumann, C. J. Bioorg.
Med. Chem. 2002, 10, 841.
(2) Thibaudeau, C.; Chattopadhyaya, J. Stereoelectronic Effects
in Nucleosides and Nucleotides and their Structural
Implications; Uppsala University Press: Sweden, 1999,
jyoti@boc.uu.se; ISBN 91-506-1351-0.
The NMR data for the psicoside 1017 correlate well with
those published for 2¢,3¢-anhydrouridine;12 the most char-
acteristic are the high-field resonances at d = 57.37 ppm
(C3¢), 56.12 ppm (C4¢).
The formation of the C4¢-OH···O=C2 hydrogen bond leads
to a syn-conformation about the glycosyl bond. In this re-
spect, the CD spectra of nucleosides 2 and 4 feature inter-
esting changes in the Cotton effects (Figure 3). No clear
CD maxima are observed in the spectrum of the psicoside
2. On the contrary, the CD curve of the sorboside 4 exhib-
its a large negative CD band in the B2u spectral region, and
a positive B1u and E1ua CD bands. Thus, the sorboside 4
displays approximately mirror-image CD curve vs. uri-
dine and closely related uracil nucleosides18,19 and essen-
tially identical CD spectrum with that of 6,1¢-
propanouridine,20 which is the pure syn-conformer about
(3) (a) Pradeepkumar, P. I.; Zamaratski, E.; Földesi, A.;
Chattopadhyaya, J. J. Chem. Soc., Perkin Trans. 2 2001,
402. (b) Pradeepkumar, P. I.; Amirkhanov, N. V.;
Chattopadhyaya, J. Org. Biomol. Chem. 2003, 1, 81.
(c) Pradeepkumar, P. I.; Cheruku, P.; Plashkevych, O.;
Acharya, P.; Gohil, S.; Chattopadhyaya, J. J. Am. Chem. Soc.
2004, 126, 11484.
(4) Roivainen, J.; Vepsäläinen, J.; Azhayev, A.; Mikhailopulo,
I. A. Tetrahedron Lett. 2002, 43, 6553.
(5) Note that the structure of compound 16 in ref. 4 was
erroneously described to 1-(1,3-anhydro-b-D-psicofura-
nosyl)thymine. Single-crystal X-ray analysis showed that
compound 16 actually is methyl 1-deoxy-1-(N1-thyminyl)-
b-D-psicofuranoside: (Roivainen, J.; Reuter, H.;
Synlett 2005, No. 11, 1683–1686 © Thieme Stuttgart · New York

1686
T. I. Kulak et al.
LETTER
Mikhailopulo, I. A., unpublished). The structures of the
anhydro nucleosides 9, 12, and 13 have been proved by X-
ray analyses (Roivainen, J. A.; Reuter, H.; Mikhailopulo, I.
A., unpublished).
(16) 1-(1,3-Anhydro-b-D-sorbofuranosyl)uracil (4): amorphous
powder; UV (MeOH): lmax = 256 nm (e 9900), lmin = 227 nm
(e 2800). 1H NMR (500.13 MHz, (DMSO-d6): dTMS = 11.39
(br s, 1 H, N3H), 7.40 (d, 1 H, J5,6 = 8.05 Hz, H6), 5.73 (d, 1
H, H5), 5.60 (d, 1 H, J = 4.42 Hz, 4¢-OH), 5.17 (s, 1 H, J3¢,4¢
< 0.5 Hz, H3¢), 5.04 (d, 1 H, J1¢,1¢¢ = 8.28 Hz, H1¢), 4.80 (t, 1
H, J = 5.70 Hz, 6¢-OH), 4.57 (d, 1 H, H1¢¢), 4.42 (m, 1 H,
J4¢,5¢ = 3.35 Hz, J5¢,6¢ = 5.54 Hz, J5¢,6¢¢ = 5.88 Hz, H5¢), 4.10
(br t, 1 H, H4¢), 3.74 (ddd, 1 H, J6¢,6¢¢ = 11.60 Hz, H6¢), 3.63
(ddd, 1 H, H6¢¢) ppm. 13C NMR (125.77 MHz, DMSO-d6):
dTMS = 163.23 (C4), 149.65 (C2), 141.68 (C6), 102.45 (C5),
92.96 (C2¢), 91.40 (C3¢), 84.92 (C5¢), 78.61 (C1¢), 70.91
(C4¢), 58.79 (C6¢). Anal. Calcd for C10H12N2O6: C, 46.88; H,
4.72; N, 10.93. Found: C, 46.75; H, 4.61; N, 10.88.
(6) (a) Hrebabecky, H.; Farkas, J.; Sorm, F. Coll. Czech. Chem.
Commun. 1972, 37, 2059. (b) Hrebabecky, H.; Farkas, J.;
Sorm, F. Coll. Czech. Chem. Commun. 1974, 39, 1098.
(7) Elliott, R. D.; Niwas, S.; Riordan, J. M.; Montgomery, J. A.;
Secrist, J. A. III Nucleosides Nucleotides 1992, 11, 97.
(8) Sarma, M. S. P.; Megati, S.; Klein, R. S.; Otter, B. A.
Nucleosides Nucleotides 1995, 14, 393.
(9) (a) Sanchez, R. A.; Orgel, L. E. J. Mol. Biol. 1970, 47, 531.
(b) Shannahoff, D. H.; Sanchez, R. A. J. Org. Chem. 1973,
38, 593.
(10) Holy, A. Nucleic Acids Res. 1974, 1, 289.
(11) Codington, J. F.; Doerr, I. L.; Fox, J. J. J. Org. Chem. 1964,
29, 564; and references therein..
(17) 1-[3,4-Anhydro-1,6-di-O-(4-monomethoxy)-trityl-b-D-
psicofuranosyl]uracil (10): amorphous powder; UV
(MeOH): lmax = 231.5 nm (e 26900), lmax = 263 nm (e
9000), lmin = 225 nm (e 23500), lmin = 255 nm (e 8800). 1H
NMR (500.13 MHz, DMSO-d6): dTMS = 11.35 (s, 1 H, N3H),
7.71 (d, 1 H, J5,6 = 8.14 Hz, H6), 5.47 (d, 1 H, H5), 4.92 (d,
1 H, J3¢,4¢ = 2.54 Hz, H3¢), 4.56 (t, 1 H, J5¢,6¢ = J5¢,6¢¢ = 4.26 Hz,
H5¢), 3.92 (d, 1 H, J4¢,5¢ < 0.5 Hz, H4¢), 3.61 (d, 1 H,
(12) Miah, A.; Reese, C. B.; Song, Q.; Sturdy, Z.; Neidle, S.;
Simpson, I. J.; Read, M.; Rayner, E. J. Chem. Soc., Perkin
Trans. 1 1998, 3277.
(13) The 1H NMR and 13C MNR data for the psicoside 3 are in
agreement with those previously published.3b
(14) Divakar, K. J.; Reese, C. B. J. Chem. Soc., Perkin Trans. 1
1982, 1171.
J1¢,1¢¢ = 9.29 Hz, H1¢), 3.16 (d, 1 H, H-1¢¢), 3.19 (d, H6¢ and
H6¢¢) ppm. 13C NMR (125.77 MHz, DMSO-d6): dTMS
=
(15) 1-(1,3-Anhydro-b-D-psicofuranosyl)uracil (2): amorphous
powder; UV (MeOH): lmax = 257 nm (e 9500), lmin = 227 (e
2700) nm. 1H NMR (500.13 MHz, DMSO-d6): dTMS = 7.44
(d, 1 H, J5,6 = 7.99 Hz, H6), 5.63 (d, 1 H, H5), 5.25 (d, 1 H,
J3¢,4¢ = 3.91 Hz, H3¢), 5.21 (br s, 1 H, 4¢-OH), 5.00 (d, 1 H,
J1¢,1¢¢ = 8.13 Hz, H1¢), 4.82 (br t, 1 H, J = 4.10 Hz, 6¢-OH),
4.57 (d, 1 H, H1¢¢), 4.07 (ddd, 1 H, J4¢,5¢ = 8.59 Hz, J5¢,6¢ = 2.0
Hz, J5¢,6¢¢ = 5.68 Hz, H5¢), 4.03 (br m, 1 H, H4¢), 3.75 (br d, 1
163.14 (C4), 150.47 (C2), 141.64 (C6), 100.63 (C5), 63.21
(C1¢), 95.92 (C2¢), 57.37 (C3¢), 56.12 (C4¢), 79.83 (C5¢),
62.65 (C6¢) ppm. Anal. Calcd for C50H44N2O8: C, 74.98; H,
5.54; N, 3.50. Found: C, 74.83; H, 5.50; N, 3.42.
(18) Miles, D. W.; Robins, R. K.; Eyring, H. Proc. Natl. Acad.
Sci. U.S.A. 1967, 57, 1138.
(19) (a) Miles, D. W.; Robins, M. J.; Robins, R. K.; Winkley, M.
W.; Eyring, H. J. Am. Chem. Soc. 1969, 91, 824. (b) Miles,
D. W.; Robins, M. J.; Robins, R. K.; Winkley, M. W.;
Eyring, H. J. Am. Chem. Soc. 1969, 91, 831. (c) Miles, D.
W.; Inskeep, W. H.; Robins, M. J.; Winkley, M. W.; Robins,
R. K.; Eyring, H. J. Am. Chem. Soc. 1970, 92, 3872.
(20) Yoshimura, Y.; Ueda, T.; Matsuda, A. Tetrahedron Lett.
1991, 32, 4549.
H, J6¢,6¢¢ = 12.9 Hz, H6¢), 3.50 (br m, 1 H, H6¢¢) ppm. 13
C
NMR (125.77 MHz, DMSO-d6): dTMS = 163.22 (C4), 149.24
(C2), 141.60 (C6), 101.96 (C5), 90.85 (C2¢), 86.84 (C3¢),
83.30 (C5¢), 77.83 (C1¢), 69.65 (C4¢), 60.57 (C6¢) ppm. Anal.
Calcd for C10H12N2O6: C, 46.88; H, 4.72; N, 10.93. Found:
C, 46.77; H, 4.63; N, 10.90.
Synlett 2005, No. 11, 1683–1686 © Thieme Stuttgart · New York