A new synthesis of 9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)guanine (araF-G)

Article abstract of DOI:10.1081/NCN-120022960

Interesting and very promising antisense properties of 2′ -deoxy-2′-fluoroarabinonucleic acids ((a) Wilds, C.J.; Damha, M.J. 2′-Deoxy-2′-fluoroarabinonucleosides and oligonucleotides (2′F-ANA): synthesis and physicochemical studies. Nucl. Acids Res. 2000, 28, 3625-3635; (b) Viazovkina, E.; Mangos, M.; Elzagheid, M.I.; Damha, M.J. Current Protocols in Nucleic Acid Chemistry 2002, 4.15.1-4.15.21) (2′F-ANA) has encouraged our research group to optimize the synthetic procedures for 2′-deoxy-2′-fluoro-β-D-arabinonucleosides (araF-N). The synthesis of araF-U, araF-T, araF-A and araF-C is straightforward, (Tann, C.H.; Brodfuehrer, P.R.; Brundidge, S.P.; Sapino, C., Jr. Howell H.G. Fluorocarbohydrates in synthesis. An efficient synthesis of 1-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)-5-iodouracil (β-FIAU) and 1-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)thymine (β-FMAU). J. Org. Chem. 1985, 50, 3644-3647; Howell, H.G.; Brodfuehrer, P.R.; Brundidge, S.P.; Benigni, D.A.; Sapino, C., Jr. Antiviral nucleosides. A stereo-specific, total synthesis of 2′-fluoro-2′-deoxy-β-D-arabinofuranosyl nucleosides. J. Org. Chem. 1988, 53, 85-88; Maruyama, T.; Takamatsu, S.; Kozai, S.; Satoh, Y.; Izana, K. Synthesis of 9-(2-deoxy-2-fluoro-β -D-arabinofuranosyl)adenine bearing a selectively removable protecting group. Chem. Pharm. Bull. 1999, 47, 966-970) however, the synthesis of the guanine analogue is more complicated and affords poor to moderate yields of araF-G (4) ((a) Elzagheid, M.I.; Viazovkina, E.; Masad, M.J. Synthesis of protected 2′-deoxy-2′-fluoro-β-D-arabinonucleosides. Synthesis of 2′-fluoroarabino nucleoside phosphoramidites and their use in the synthesis of 2′F-ANA. Current Protocols in Nucleic Acid Chemistry 2002, 1.7.1-1.7.19; (b) Tennila, T.; Azhayeva, E.; Vepsalainen, J.; Laatikainen, R.; Azhayev, A.; Mikhailopulo, I. Oligonucleotides containing 9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)-adenine and -guanine: synthesis, hybridization and antisense properties. Nucleosides, Nucleotides and Nucl. Acids 2000, 19, 1861-1884). Here we describe an efficient synthesis of araF-G (4) that involves coupling of 2-deoxy-2-fluoro-3,5-di-O-benzoyl-α -D-arabinofuranosyl bromide (1) with 2-chlorohypoxanthine (2) to afford 2-chloro-β-araF-I (3) in 52% yield. Nucleoside (3) was transformed into araF-G (4) by treatment with methanolic ammonia (150°C, 6h) in 67% yield.

Full text of DOI:10.1081/NCN-120022960

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A New Synthesis of 9-(2-Deoxy-2-fluoro-β-D-
arabinofuranosyl)guanine (araF-G)
Mohamed I. Elzagheid a , Ekaterina Viazovkina a & Masad J. Damha a b
a Department of Chemistry, McGill University, Montreal, QC, Canada
b Otto Maass Chemistry Building, McGill University, 801 Sherbrooke Street W., H3A 2K6,
Montreal, Quebec, Canada
Available online: 31 Aug 2006
To cite this article: Mohamed I. Elzagheid, Ekaterina Viazovkina & Masad J. Damha (2003): A New Synthesis of 9-(2-Deoxy-2-
fluoro-β-D-arabinofuranosyl)guanine (araF-G), Nucleosides, Nucleotides and Nucleic Acids, 22:5-8, 1339-1342
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 22, Nos. 5–8, pp. 1339–1342, 2003
A New Synthesis of 9-(2-Deoxy-2-fluoro-b-d-
arabinofuranosyl)guanine (araF-G)
Mohamed I. Elzagheid, Ekaterina Viazovkina,
*
and Masad J. Damha
Department of Chemistry, McGill University,
Montreal, QC, Canada
ABSTRACT
Interesting and very promising antisense properties of 20-deoxy-20-fluoroarabino-
nucleic acids ((a) Wilds, C.J.; Damha, M.J. 20-Deoxy-20-fluoroarabinonucleosides
and oligonucleotides (20F-ANA): synthesis and physicochemical studies. Nucl.
Acids Res. 2000, 28, 3625–3635; (b) Viazovkina, E.; Mangos, M.; Elzagheid,
M.I.; Damha, M.J. Current Protocols in Nucleic Acid Chemistry 2002, 4.15.1–
4.15.21) (20F-ANA) has encouraged our research group to optimize the synthetic
procedures for 20-deoxy-20-fluoro-b-d-arabinonucleosides (araF-N). The synthesis
of araF-U, araF-T, araF-A and araF-C is straightforward, (Tann, C.H.; Brod-
fuehrer, P.R.; Brundidge, S.P.; Sapino, C., Jr. Howell H.G. Fluorocarbohydrates
in synthesis. An efficient synthesis of 1-(2-deoxy-2-fluoro-b-d-arabinofuranosyl)-
5-iodouracil (b-FIAU) and 1-(2-deoxy-2-fluoro-b-d-arabinofuranosyl)thymine
(b-FMAU). J. Org. Chem. 1985, 50, 3644–3647; Howell, H.G.; Brodfuehrer,
P.R.; Brundidge, S.P.; Benigni, D.A.; Sapino, C., Jr. Antiviral nucleosides. A stereo-
specific, total synthesis of 20-fluoro-20-deoxy-b-d-arabinofuranosyl nucleosides.
J. Org. Chem. 1988, 53, 85–88; Maruyama, T.; Takamatsu, S.; Kozai, S.; Satoh,
Y.; Izana, K. Synthesis of 9-(2-deoxy-2-fluoro-b-d-arabinofuranosyl)adenine
*Correspondence: Masad J. Damha, Otto Maass Chemistry Building, McGill University, 801
Sherbrooke Street W., H3A 2K6 Montreal, Quebec, Canada; Fax: þ1 514 398 3797; E-mail:
masad.damha@mcgill.ca.
1339
DOI: 10.1081/NCN-120022960
Copyright # 2003 by Marcel Dekker, Inc.
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com

1340
Elzagheid, Viazovkina, and Damha
bearing a selectively removable protecting group. Chem. Pharm. Bull. 1999, 47,
966–970) however, the synthesis of the guanine analogue is more complicated
and affords poor to moderate yields of araF-G (4) ((a) Elzagheid, M.I.;
Viazovkina, E.; Masad, M.J. Synthesis of protected 20-deoxy-20-fluoro-b-d-ara-
binonucleosides. Synthesis of 20-fluoroarabino nucleoside phosphoramidites and
their use in the synthesis of 20F-ANA. Current Protocols in Nucleic Acid
Chemistry 2002, 1.7.1–1.7.19; (b) Tennila, T.; Azhayeva, E.; Vepsalainen, J.;
Laatikainen, R.; Azhayev, A.; Mikhailopulo, I. Oligonucleotides containing
9-(2-deoxy-2-fluoro-b-d-arabinofuranosyl)-adenine and -guanine: synthesis,
hybridization and antisense properties. Nucleosides, Nucleotides and Nucl.
Acids 2000, 19, 1861–1884). Here we describe an efficient synthesis of araF-G (4)
that involves coupling of 2-deoxy-2-fluoro-3,5-di-O-benzoyl-a-d-arabinofurano-
syl bromide (1) with 2-chlorohypoxanthine (2) to afford 2-chloro-b-araF-I (3)
in 52% yield. Nucleoside (3) was transformed into araF-G (4) by treatment
with methanolic ammonia (150ꢀC, 6 h) in 67% yield.
Key Words: Nucleoside synthesis; Guanine arabinonucleoside.
A very convenient method for the synthesis of araF-nucleosides (e.g., araF-T and
C) involves direct coupling of 3,5-di-O-benzoyl-2-deoxy-2-fluoro-a-d-arabinofurano-
syl bromide with a silylated base.[1,3] This produces primarily the desired
b-anomer with < 5% of the a-stereoisomer which is removed by chromatography
and=or crystallization. AraF-A can be prepared by the same procedure, except that
a pre-silylation step is not required.[1b] A recently reported synthesis of araF-G
required coupling of 2,6-dichloropurine to arabinoside 1.[5b] This method produces
a mixture of isomers (N7- and N9-regioisomers, as well as a and b anomers) that
can be separated by silica gel chromatography to afford the desired N9-b–anomer in
38% yield.[5a] Displacement of the chlorine atoms at positions 2 and 6 with lithium
azide, followed by reduction with tin dichloride affords the araF-(2,6-diaminopurine)
nucleoside. Removal of the sugar O-benzoyl protecting groups followed by regio-
selective deamination by treatment with adenosine deaminase affords araF-G in
20% overall yield (from 1).[5a] To minimize the number of steps, we attempted
coupling of arabinoside 1 with a variety of ‘masked’ guanines. Among these were
2-chloro-6-hydroxypurine (2-chlorohypoxanthine), 2-amino-6-chloropurine, 2,6-di-
aminopurine, 2-amino-6-(1,2,4-triazol-4-yl)-9-H-purine, guanine, N2-acetyl-O6-di-
phenylcarbamoylguanine and O6-diphenylcarbamoyl-N2-isobutyryl guanine. While
Scheme 1. i) CCl4, 77ꢀC, 3 days, 52%; ii) saturated methanolic ammonia, steel bomb, 150ꢀC,
6 h, 67%.

9-(2-Deoxy-2-fluoro-b-d-arabinofuranosyl)guanine
1341
coupling of guanine (and its derivatives) and 2,6-diaminopurine (and its derivatives)
to arabinoside 1 were not successful and gave non nucleosidic products, coupling of
2-chloro-6-hydroxypurine and 2-amino-6-chloro-purine to the same arabinoside gave
the anticipated N9-b-anomers in 50–60% yield. Displacement of the chloro function
in 9-(2-deoxy-2-b-d-fluoroarabinofuranosyl)-2-amino-6-chloropurine with 0.1–2 M
hydrochloric acid[6,7] or 2 N sodium hydroxide in dioxane[8] or a mixture of sodium
methoxide= mercaptoethanol= water[9,10] were not successful and gave only modified
starting material (not isolated). Treatment of the same nucleoside, 9-(2-deoxy-2-b-d-
fluoroarabinofuranosyl)-2-amino-6-chloropurine, with trimethylamine gave the
trimethylammonium salt of the nucleoside.[11,12] When the latter intermediate was
treated with 1 N sodium hydroxide, at room temperature, it resulted in the
formation of araF-G in less than 5% yield. In contrast, the treatment of
N9-glycoside 3a with methanolic ammonia (150ꢀC, 6 h) afforded araF-G (4)b in 67%
yield (35% overall, from 1) (Sch. 1).
ACKNOWLEDGMENTS
We wish to thank CIHR (Canada) and Anagenis, Inc. for financial support.
REFERENCES
1. (a) Wilds, C.J.; Damha, M.J. 20-Deoxy-20-fluoroarabinonucleosides and oligo-
nucleotides (20F-ANA): synthesis and physicochemical studies. Nucl. Acids
Res. 2000, 28, 3625–3635; (b) Viazovkina, E.; Mangos, M.; Elzagheid, M.I.;
Damha, M.J. Current Protocols in Nucleic Acid Chemistry 2002, 4.15.1–
4.15.21.
2. Tann, C.H.; Brodfuehrer, P.R.; Brundidge, S.P.; Sapino, C., Jr.; Howell, H.G.
Fluorocarbohydrates in synthesis. An efficient synthesis of 1-(2-deoxy-2-fluoro-
aN9-b-isomer 3: TLC (9:1 [v=v] methylene chloride=methanol) 0.42; 1H-NMR (400 MHz
DMSO-d6): 8.10–7.46 (10H, m, Bz), 8.15 (1H, d, J8,F ¼ 2.8 Hz, H-8), 6.50 (1H, dd
J1 ,2 ¼ 4.4 Hz, J1 ,F ¼ 18 Hz, H-10), 5.85 (1H, 2 dd, J3 ,F ¼ 19.2 Hz, H-30), 5.70 (1H, 2dd,
0
0
0
0
J2 ,F ¼ 50 Hz, H-20), 4.80–4.65 (3H, m, H-40, H-50,500); 13C-NMR (100.61 MHZ, DMSO-d6):
0
166 (C-6), 165 (C-4), 148.49 (C-2), 139.92 (d, JC8,F ¼ 5.3 Hz, C-8), 134.54–129.14 (Bz),
123.09 (C-5), 92.70 (d, JC2 ,F ¼ 189.7 Hz, C-20), 83.19 (d, JC1 ,F ¼ 16.7 Hz, C-10), 79.26
0
0
þ
(d, JC4 ,F ¼ 3 Hz, C-40), 77.21 (d, JC3 ,F ¼ 29 Hz, C-30), 64.48 (C-50); APCI-MS: 512.9 (M þ H ),
0
0
535 (M þ Naþ).
bAraF-G 4: 1H-NMR (400 MHz, DMSO-d6): 10.62 (1H, s, N-H), 7.77 (1H, d, J8,F ¼ 2.8, H-8),
6.51 (2H, br, s, NH2), 6.11 (1H, dd, J1 ,2 ¼ 4.4 Hz, J1 ,F ¼ 15.80 Hz, H-10), 5.91 (1H, d,
0
0
0
0
0
0
0
0
JOH,2 ¼ 4.8 Hz, HO-C2 ), 5.00 and 5.15 (1H, dt or ddd, J2 ,F ¼ 32.80 Hz, J2 ,3 ¼ 3.60 Hz, H-
20), 5.05 (1H, t, HO-C50), 4.32 (1H, m, J3 ,F ¼ 14 Hz, H-30), 3.77 (1H, m, H-40), 3.57 (2H, m,
0
H-50 and H-500); 19F-NMR (300 MHz, DMSO-d6, 99% [v=v] trifluoroacetic acid as
external reference): ꢁ120.14 (ddd): FAB-MS (NBA-matrix): 286 [M þ Hþ].

1342
Elzagheid, Viazovkina, and Damha
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