Synthesis of 2',3'-dideoxy-2'-fluoro-3'-thioarabinothymidine and its 3'-phosphoramidite derivative.

Article abstract of DOI:10.1081/NCN-120022961

An efficient method for the synthesis of 5'-O-monomethoxytrityl-2',3'-dideoxy-2'-fluoro-3'-thioarabinothymidine [(5'MMT)araF-T(3'SH), (5)] and its 3'-phosphoramidite derivative (6) suitable for automated incorporation into oligonucleotides, is demonstrated. A key step in the synthesis involves reaction of 5'-O-MMT-2,3'-O-anhydrothymidine (4) (Eleuteri, A.; Reese, C.B.; Song, Q. J. Chem. Soc. Perkin Trans. 1 1996, 2237 pp.) with sodium thioacetate to give (5'-MMT)araF-T(3'SAc) (5) (Elzagheid, M.I.; Mattila, K.; Oivanen, M.; Jones, B.C.N.M.; Cosstick, Loennberg, H. Eur. J. Org. Chem. 2000, 1987-1991). This nucleoside was then converted to its corresponding phosphoramidite derivative, 6, as described previously ((a) Sun, S.; Yoshida, A.; Piccirilli, J.A. RNA, 1997, 3, 1352-1363; (b) Matulic-Adamic, J.; Beigelman, L. Helvetica Chemica Acta 1999, 82, 2141-2150: (c) Fettes, K.J.; O'Neil, I.; Roberts, S.M.; Cosstick, R. Nucleosides, Nucleotides and Nucl. Acids 2001, 20, 1351-1354).

Full text of DOI:10.1081/NCN-120022961

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Synthesis of 2′,3′-Dideoxy-2′-fluoro-3′-
thioarabinothymidine and Its 3′-Phosphoramidite
Derivative
Mohamed I. Elzagheid a , Anna Lisa Tedeschi a & Masad J. Damha a b
a Department of Chemistry , McGill University , Montreal, Quebec, Canada
b McGill University , Otto Maass Chemistry Building 801 Sherbrooke Street W, H3A 2K6,
Montreal, QC, Canada
Published online: 31 Aug 2006.
To cite this article: Mohamed I. Elzagheid , Anna Lisa Tedeschi & Masad J. Damha (2003) Synthesis of 2′,3′-Dideoxy-2′-
fluoro-3′-thioarabinothymidine and Its 3′-Phosphoramidite Derivative, Nucleosides, Nucleotides and Nucleic Acids, 22:5-8,
1343-1346, DOI: 10.1081/NCN-120022961
To link to this article: http://dx.doi.org/10.1081/NCN-120022961
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 22, Nos. 5–8, pp. 1343–1346, 2003
Synthesis of 20,30-Dideoxy-20-fluoro-30-thioarabinothymidine
and Its 30-Phosphoramidite Derivative
*
Mohamed I. Elzagheid, Anna Lisa Tedeschi, and Masad J. Damha
Department of Chemistry, McGill University, Montreal,
Quebec, Canada
ABSTRACT
An efficient method for the synthesis of 50-O-monomethoxytrityl-20,30-dideoxy-20-
0
fluoro-30-thioarabinothymidine [5 -MMTaraF-T3 SH, (5)] and its 30-phosphorami-
dite derivative (6) suitable for automated incorporation into oligonucleotides, is
0
demonstrated. A key step in the synthesis involves reaction of 50-O-MMT-2,30-
O-anhydrothymidine (4) (Eleuteri, A.; Reese, C.B.; Song, Q., J. Chem. Soc.
Perkin Trans. 1 1996, 2237 pp.) with sodium thioacetate to give 5 -MMTaraF-T3 SAc
0
0
(5) (Elzagheid, M.I.; Mattila, K.; Oivanen, M.; Jones, B.C.N.M.; Cosstick,
Lo¨nnberg, H. Eur. J. Org. Chem. 2000, 1987–1991). This nucleoside was then
converted to its corresponding phosphoramidite derivative, 6, as described pre-
viously ((a) Sun, S.; Yoshida, A.; Piccirilli, J.A. RNA, 1997, 3, 1352–1363; (b)
Matulic-Adamic, J.; Beigelman, L. Helvetica Chemica Acta 1999, 82, 2141–
2150; (c) Fettes, K.J.; O’Neil, I.; Roberts, S.M.; Cosstick, R. Nucleosides,
Nucleotides and Nucl. Acids 2001, 20, 1351–1354).
Key Words: Thionucleosides; Arabinonucleic acids; Antisense.
*Correspondence: Masad J. Damha, McGill University, Otto Maass Chemistry Building
801 Sherbrooke Street W, H3A 2K6 Montreal, QC, Canada; Fax: þ514 398 3797; E-mail:
masad.damha@mcgill.ca.
1343
DOI: 10.1081/NCN-120022961
Copyright # 2003 by Marcel Dekker, Inc.
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com

1344
Elzagheid, Tedeschi, and Damha
Synthetic oligonucleotides are of considerable importance because of their abi-
lity to inhibit gene expression through antisense effects.[4] The most efficacious anti-
sense oligonucleotides (AON) are those that possess stabilities against nucleases, and
adequate lipophilicity to ensure efficient cell permeation. Ideally, they should also
suppress gene activity with the assistance of intracellular ribonuclease H (RNase
H), an enzyme that degrades the RNA strand of the AON=RNA hybrid (see
Ref.[5], and references therein). However, most AONs lack the appropriate structural
attributes for RNase H elicitation and typically display less than optimal cellular
potencies. Our laboratory has recently demonstrated that arabinonucleic acids
Figure 1. Structure of modified oligonucleotides.
ꢀ
Scheme 1. i) [Bis(2-methoxyethyl)amino]sulfur trifluoride, CH2Cl2, 50 C, 83%; ii) HBr,
CH2Cl2, rt, 24h, 90%; iii) silylated thymine, CCl4, 3d, 77 ꢀC, 75%; iv) NH4OH, MeOH, rt,
24h, 90%; v) MMTr-Cl, pyridine, 87%; vi) MsCl, pyridine= Et3N, EtOH, reflux, 16h, 92%;
vii) NaSAc, dioxane, reflux, 12h, 84%; viii) 1M NaOMe, MeOH, 1h; ix) 2-cyanoethyl-N,N-dii-
sopropylchlorophosphoramidite,1-methylimidazole, diisopropyl- ethylamine, CH2Cl2, 80%.

20,30-Dideoxy-20-fluoro-30-thioarabinothymidine
1345
(e.g., 20F-ANA), like DNA phosphorothioates (S-DNA), possess the ability to elicit
RNase H-mediated hydrolysis of target RNA.[6]
The antisense activity of phosphorothioate linked 20-deoxy-20-fluoro-arabinonu-
cleic acids (S-20F-ANA, Fig. 1) has been evaluated,[5] however, nothing is known
about the isomeric analogue in which a sulfur atom replaces one of the two bridging
oxygen atoms, i.e., 20,30-dideoxy-20-fluoro-30-thioarabinonucleic acids (20F-30S-ANA;
Fig. 1). Here we report preparation of one of the four nucleoside monomers required
for the solid-phase synthesis of 20F-30S-ANA.
The synthesis is depicted in Sch. 1. Sugar precursor 1 (from Pfanstiehl) was con-
verted into the a-1-bromoarabinose 2 with retention of sugar C-1 configuration.[7]
Compound 2 was then used, without isolation, for SN2-type glycosylation reaction
with silylated thymine base according to literature procedure[7] which resulted, after
removal of 50- and 30-O-benzoyl groups, in the formation of nucleoside 3. The latter
nucleoside then 50-monomethoxytritylated and 30-mesylated before being converted
to 2,30-anhydronucleoside 4.[2] Direct ring opening of the 2,30-anhydro linkage,
in nucleoside 4, with thioacetate gave nucleoside 5a that was then converted to the
phosphoroamidothioite derivative 6b following literature protocols.[3] The synthesis
of 20F-30S-ANA oligonucleotides is in progress.
ACKNOWLEDGMENT
We wish to thank CIHR (Canada) for financial support.
REFERENCES
1. Eleuteri, A.; Reese, C.B.; Song, Q. J. Chem. Soc. Perkin Trans. 1 1996, 2237 pp.
2. Elzagheid, M.I.; Mattila, K.; Oivanen, M.; Jones, B.C.N.M.; Cosstick, R.;
Lo¨nnberg, H. Eur. J. Org. Chem. 2000, 1987–1991.
3. (a) Sun, S.; Yoshida, A.; Piccirilli, J.A. RNA, 1997, 3, 1352–1363; (b) Matulic-
Adamic, J.; Beigelman, L. Helvetica Chemica Acta 1999, 82, 2141–2150; (c)
Fettes, K.J.; O’Neil, I.; Roberts, S.M.; Cosstick, R. Nucleosides, Nucleotides
and Nucleic Acids 2001, 20, 1351–1354.
4. De Mesmaeker, A.; Ha¨ner, R.; Martin, P.; Moser, H.E. Acc. Chem. Res. 1995,
28, 366–374.
aNucleoside 5: TLC (20:1 [v=v] chloroform=methanol)0.49;1H-NMR (400 MHz acetone-d6,
tetramethylsilane as internal reference): 10.15 (1H, s, N-H), 7.60–6.90 (16H, m, trityl and
0
0
0
0
0
0
0
H-6), 6.33 (1H, dd, J1 ,F ¼ 15.6Hz J1 ,2 ¼ 4.4Hz H-1 ), 5.3 ( 1H, dt, J2 ,F ¼ 54.8Hz, J2 ,3 ¼ 5.2Hz
5.2Hz H-20) 4.3 (1H, dm or ddd, J3 ,F ¼ 16.8Hz J3 ,F ¼ 3.6Hz H-30), 4.1 (1H, m, H-40), 3.79
(3H, s, CH3O), 3.36 (2H, dd, H-50,500), 2.37 (3H, s, CH3CO-S), 1.64 (3H, CH3-C5); 19F-
NMR (283MHz, acetone-d6, 99% trifluoroacetic acid as external reference): –106,63 (ddd);
ESI-MS: 589.1 (M-1), 590.1 (Mþ), 613.1 (M þ Naþ).
0
0
bPhosphoroamidothioite. 6: 31P-NMR (200 MHz, DMSO-d6, 85%H3PO4 as external refe-
rence): 162.2, 158.7.

1346
Elzagheid, Tedeschi, and Damha
5. Lok, C.-N.; Viazovkina, E.; Min, K.-L.; Nagy, E.; Wilds, C.J.; Damha, M.J.;
Parniak, M.A. Biochemistry 2002, 41, 3457–3467.
6. (a) Damha, M.J.; Wilds, C.J.; Noronha, A.; Brukner, I.; Borkow, G.; Arion, D.;
Parniak, M.A., J. Am. Chem. Soc. 1998, 120, 12,976–12,977; (b) Noronha,
A.M.; Wilds, C.J.; Lok, C-N.; Viazovkina, K.; Arion, D.; Parniak, M.A.;
Damha, M. J. Biochemistry 2000, 39, 7050–7062.
7. Elzagheid, M.I.; Viazovkina, E.; Masad, M.J. Current Protocols in Nucleic Acid
Chemistry 2002, 1.7.1–1.7.19.