Fluorinated 7-deazapurine 2′-deoxyribonucleosides: Modification at the nucleobase and the sugar moiety

Article abstract of DOI:10.1080/15257770701490357

7-Deaza-7-fluoro-purine 2′-deoxynucleosides as well as 2′-deoxy-2′-fluoroarabinofuranosyl nucleosides 1-8 were synthesized. The fluorine atom was introduced on the base level with Selectfluor. Nucleobase-anion glycosylation was then employed to form the n

Full text of DOI:10.1080/15257770701490357

Nucleosides, Nucleotides, and Nucleic Acids, 26:607–610, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701490357
FLUORINATED 7-DEAZAPURINE 2ꢀ-DEOXYRIBONUCLEOSIDES:
MODIFICATION AT THE NUCLEOBASE AND THE SUGAR MOIETY
Frank Seela, Kuiying Xu, Padmaja Chittepu, and Xin Ming
Laboratory of
2
Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Mu¨nster, germany,
and Laboratorium fu¨r Organische und Bioorganische Chemie, Universita¨t Osnabru¨ck,
Osnabru¨ck, Germany
7-Deaza-7-fluoro-purine 2ꢁ-deoxynucleosides as well as 2ꢁ-deoxy-2ꢁ-fluoroarabinofuranosyl nu-
2
cleosides 1–8 were synthesized. The fluorine atom was introduced on the base level with Selectfluor.
Nucleobase-anion glycosylation was then employed to form the nucleosides. Properties of the fluo-
rine compounds were studied in solution and in solid state. Compound 4a was incorporated into
oligonucleotides where the stabilizing effect was observed.
Keywords fluorination; pyrrolo[2,3-d]pyrimidine; glycosylation; sugar conformation;
base pairing
INTRODUCTION
Replacement of hydrogen atoms or functional groups in an organic
compound by fluorine atoms may cause a dramatic change in physical prop-
erties and biological activities, which is one of the reasons for the interest in
the synthesis of fluoro compounds. Our group has expended effort to intro-
duce the fluorine atom to nucleosides. We are interested in combining the
favorable properties of pyrrolo[2,3-d]pyrimidine nucleosides with the well
documented pharmaceutical behavior of fluorine substitution. Apart from
the properties of monomeric nucleosides, 7-halogenated 7-deazapurine nu-
cleosides can stabilize the DNA duplexes.[1−4] Herein, we report on the syn-
thesis of nucleosides 1–3 and 6–8, as well as the phosphoramidite 9 and
10. The nucleosides 4a, b and 5 were described recently[5] (Scheme 1).
Oligonucleotides containing compound 4a were prepared and their stability
in DNA duplexes was determined.
We gratefully acknowledge financial support by Idenix Pharmaceuticals, Cambridge, USA.
Address correspondence to Frank Seela, Laboratory of Bioorganic Chemistry and Chemical Bi-
ology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Mu¨nster, Germany, and Laboratorium
fu¨r Organische und Bioorganische Chemie, Universita¨t Osnabru¨ck, Barbarastraße 7, 49069 Osnabru¨ck,
Germany. E-mail: frank.seela@uni-osnabrueck.de
607

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F. Seela et al.
SCHEME 1
RESULTS AND DISCUSSION
Earlier, a 7-fluoro residue was introduced in the nucleobase 11 em-
ploying Selectfluor.[6] The same strategy was used to synthesize the fluori-
nated pyrrolo[2,3-d]pyrimidine derivatives 12 and 13 by utilizing lower tem-
perature conditions than used for 11. The nucleobase-anion glycosylation
reaction[7,8] of the base (11-13) afforded the 7-fluorinated inosine deriva-
tives 4a,b, as well as the 7-deaza-7-fluoro-2ꢁ-deoxyguanosine (5), 7-deaza-
7-fluoro-2ꢁ-deoxyisoguanosine (7), and 7-deaza-7-fluoro-2ꢁ-deoxyxanthosine
(8). Glycosylation of 11 with the halogenose 14a,b gave the nucleo-
sides 15a,b, which were deprotected in NaOCH3 to afford the 6-methoxy
derivatives 1a,b. Compounds 4a,b were obtained by heating 1a,b in aqueous
NaOH (Scheme 2). Conformational analysis of the nucleosides 4a,b showed
that the fluorine substitution in the 2ꢁ-arabino position biased the confor-
mation toward N (from 30% N for 4a to 40% N for 4b).[5]
In a similar way, compounds 12 and 13 were glycosylated with 14a to
form the nucleosides 16 and 17, which were deprotected in NaOMe/MeOH
to give the intermediate methoxy derivatives 2 and 3. Consequently, 2 and
3 were converted to 7-deaza-7-fluoro-2ꢁ-deoxyguanosine (5) and 7-deaza-7-
fluoro-2ꢁ-deoxyxanthosine (8) in aqueous NaOH or with Me3SiCl/NaI in
MeCN. The isodG derivative 7 was obtained from 6 by photochemically in-
duced displacement reaction performed in water (30% yield) (Scheme 3).

Fluorinated 7-Deazapurine 2ꢁ-Deoxyribonucleosides
609
SCHEME 2
The 7-deazapurine 2ꢁ-deoxyribonucleosides 4a and 5 were converted
into the corresponding phosphoramidites 9 and 10 by standard proce-
dures. Oligonucleotides containing compound 4a were synthesized em-
ploying compound 9 in solid-phase oligonucleotide synthesis. As supposed
to be an analog of the universal nucleoside 7-deaza-2ꢁ-deoxyinosine, com-
pound 4a was incorporated in the duplexes opposite to the canonical 2ꢁ-
deoxynucleosides dA, dG, dC, and dT. According to Table 1, compound 4a
shows base pairing with duplex stabilities similar to 7-deaza-2ꢁ-deoxyinosine
(c7Id).[9] Thus, the 7-fluoro substituent has only a minor influence when
only one 7-deaza-2ꢁ-deoxyinosine residue was replaced by the fluoro analog
4a. However, a strong stabilizing effect was observed when twelve 4a residues
were incorporated in a self-complementary alternating 12-mer duplex 2323
(Table 1).
SCHEME 3

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F. Seela et al.
TABLE 1 Tm values and thermodynamic data of oligonucleotides containing 4a and
7-deaza-2ꢁ-deoxyinosine (c7I)a,b
Duplex
Tm
Duplex
Tm
5ꢁ-d(GGAAAA4aAAAAGG)-3ꢁ(18)
3ꢁ-d(CCTTTT A TTTTCC)-5ꢁ (19)
43
5ꢁ-d(GGAAAAc7IAAAAGG)-3ꢁ
43[9]
3ꢁ-d(CCTTTT A TTTTCC)-5ꢁ
5ꢁ-d(GGAAAA4aAAAAGG)-3ꢁ(18)
35
46
5ꢁ-d(GGAAAAc7IAAAAGG)-3
37[9]
45[9]
40[9]
13c
3ꢁ-d(CCTTTT G TTTTCC)-5ꢁ (20)
3ꢁ-d(CCTTTT G TTTTCC)-5ꢁ
5ꢁ-d(GGAAAA4aAAAAGG)-3ꢁ(18)
3ꢁ-d(CCTTTT C TTTTCC)-5ꢁ (21)
5ꢁ-d(GGAAAAc7IAAAAGG)-3ꢁ
3ꢁ-d(CCTTTT C TTTTCC)-5ꢁ
5ꢁ-d(GGAAAA4aAAAAGG)-3ꢁ(18)
39
5ꢁ-d(GGAAAAc7IAAAAGG)-3ꢁ
3ꢁ-d(CCTTTT T TTTTCC)-5ꢁ (22)
3ꢁ-d(CCTTTT T TTTTCC)-5ꢁ
5ꢁ-d(4aC4aC4aC4aC4aC4aC)-3ꢁ (23)
3ꢁ-d(C4aC4aC4aC4aC4aC4a)-5ꢁ (23)
29c
5ꢁ-d(c7ICc7ICc7ICc7ICc7ICc7IC)-3ꢁ (24)
3ꢁ-d(Cc7ICc7ICc7ICc7ICc7ICc7I)-5ꢁ (24)
aThermodynamic parameters are derived from the fitting of melting curves measured at 260 nm in
1 M NaCl, 100 mM MgCl2, and 60 mM Na-cacodylate buffer, pH 7.0, with 5 µM + 5 µM single-strand
concentration. b Tm values are given in ◦C. c Measured in 100 mM NaCl, 10 mM MgCl2, and 10 mM
Na-cacodylate buffer, pH 7.0, with 10 µM single-strand concentration.
CONCLUSION
7-deaza-7-fluoro-2ꢁ-deoxynucleosides were synthesized by nucleobase-
anion glycosylation stereoselectively. A fluorine atom introduced in the 2ꢁ-
arabino position biases the conformation of the sugar toward N . oligonu-
cleotides containing 7-fluoro nucleosides increase the Tm value of duplex
melting compared to the non-functionalized compounds (see duplex 23.23
versus 24.24).
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