Synthesis of 2'-deuterio and 3'-deuterio cytidine 5'-diphosphate.

Article abstract of DOI:10.1081/NCN-120023106

2'-2H- and 3'-2H-CDP were synthesized from 5'-MMT-3'-O-TBDMS and 2',5'-O-diTBDMS cytidine derivatives, respectively, by oxidation followed by acidic removal of 5'-protection, reduction with [NaBD(OAc)3] and finally displacement of a tosyl group by pyropho

Full text of DOI:10.1081/NCN-120023106

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Synthesis of 2′-Deuterio and 3′-Deuterio Cytidine 5′-
Diphosphate
Jessica Sandbrink a & Roger Strömberg a b
a Division of Organic and Bioorganic Chemistry , MBB Scheele Laboratory , Karolinska
Institute , Stockholm, Sweden
b Karolinska Institutet, MBB–Division of Organic and Bioorganic Chemistry , Scheele Vag 2,
Stockholm, S-17177, Sweden
Published online: 31 Aug 2006.
To cite this article: Jessica Sandbrink & Roger Strömberg (2003) Synthesis of 2′-Deuterio and 3′-Deuterio Cytidine 5′-
Diphosphate, Nucleosides, Nucleotides and Nucleic Acids, 22:5-8, 1657-1659, DOI: 10.1081/NCN-120023106
To link to this article: http://dx.doi.org/10.1081/NCN-120023106
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 22, Nos. 5–8, pp. 1657–1659, 2003
Synthesis of 20-Deuterio and 30-Deuterio Cytidine
50-Diphosphate
*
¨
Jessica Sandbrink and Roger Stromberg
Division of Organic and Bioorganic Chemistry, MBB Scheele Laboratory,
Karolinska Institute, Stockholm, Sweden
ABSTRACT
20-2H- and 30-2H-CDP were synthesized from 50-MMT-30-O-TBDMS and 20,50-
O-diTBDMS cytidine derivatives, respectively, by oxidation followed by acidic
removal of 50-protection, reduction with [NaBD(OAc)3] and finally displacement
of a tosyl group by pyrophosphate.
Key Words: CDP; Deuteriumlabelled; Stereoselectivity; Nucleotides.
Monodeuterated nucleoside diphosphates can be valuable tools in mechanistic
studies on the enzyme ribonucleotide reductase[1] (e.g., through EPR analysis
where the deuteron gives a unique coupling pattern). Thus, we considered it most
significant to devise syntheses of the deuterated cytidine 50-diphosphates 4 and 8.
Ketonucleosides of adenosine have earlier been employed to synthesize
deuterium labelled analogues from the parent ribonucleoside via an oxidation-
reduction sequence, using sodium triacetoxyborodeuteride [NaBD(OAc)3][2] which
gives excellent stereoselectivity when the 50-OH is left unprotected during the
reduction step. Hence, this methodology was an obvious choice for introduction
*Correspondence: Roger Stro¨mberg, Karolinska Institutet, MBB–Division of Organic and
Bioorganic Chemistry, Scheele Vag 2, Stockholm S-17177, Sweden; Fax: þ46 8 311 052; E-mail:
Roger.Stromberg@mbb.ki.se.
1657
DOI: 10.1081/NCN-120023106
Copyright # 2003 by Marcel Dekker, Inc.
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com

¨
Sandbrink and Stromberg
1658
of the deuterium label. The diphosphate moiety was introduced by the known
procedure of substituting a tosyl group by pyrophosphate.[3]
The synthesis of the 30-deuterio cytidine 50-diphosphate 4 was performed as
outlined in Sch. 1a. Oxidation of 1 by CrO3=acetic anhydride=pyridine gave 2,
72%. Selective acidic cleavage of the 50-O-TBDMS by TFA-water 9 : 1[4a] at ꢀ15ꢁC
prior to reduction afforded 3 in 92% yield (ribo-xylo ratio = 97.5 : 2.5). For incor-
poration of the diphosphate functionality the 50-hydroxy group was first converted
to the tosylate by treatment with tosyl chloride in MeCN-pyridine (2 : 1). The
20-O-TBDMS was then cleaved off by means of 0.1 M TBAF in THF. Substitution
of the tosyl moiety by tris(tetra-n-butylammonium) pyrophosphate followed by
ammonia-ethanol (3 : 1) treatment resulted in the desired product 4, in 25% yield
after HPLC purification.
For the synthesis of the 20-deuterio cytidine 50-diphosphate 8 a slightly different
protection strategy had to be used. This was due to difficulties in removal of the 50-O-
TBDMS without cleaving off the 30-O-TBDMS to a large extent, when attempting to
synthesize the 20-deuterio isomer by the same route as the 30-deuterio isomer.
Several different acidic conditions were tested for selective removal of the 50-O-
TBDMS without much success. Various TFA treatments cleaved off both the 50 and
the 30-silyls while the cleavage attempts with acetic acid[4b] resulted in very slow
reactions where several byproducts were formed. The above problem was, however,
circumvented by changing the strategy, i.e., to the use of the more acid labile mono-
methoxytrityl group as protection for the 50-hydroxyl function. The 20-deuteriocyti-
dine 50-diphosphate was then synthesised by the sequence shown in Sch. 1b.
Compound 5 was oxidized to ketonucleoside 6, in 81% yield. Selective removal of
the 50-O-MMT from 6 by p-toluenesulfonic acid in CH2Cl2-MeOH and subsequent
Scheme 1. i) CrO3=acetic anhydride=pyridine, CH2Cl2, rt., 2 h; ii) TFA-water 9 : 1–15ꢁC,
0.5 h; iii) NaBD(OAc)3=acetic acid (generated in situ by NaBD4=AcOH), rt. 2 h; iv) TsCl,
MeCN-pyridine (2 : 1), rt., 24 h; v) 0.1 M TBAF, THF, rt., 15 min.; vi) 2M ((BuN4)3)
H2P2O7, MeCN, rt, 4 days; vii) NH3-EtOH (3 : 1), rt, 12 h; iix) TsOH 1%, CH2Cl2-MeOH
7 : 3 15 min; ix) NH3-EtOH (3 : 1), rt, 2 h.

20-Deuterio and 30-Deuterio Cytidine 50-Diphosphate
1659
reduction gave the 20-deuterio isomer 7, in 90% yield (ribo-arabino ratio = 93.5 : 6.5).
Introduction of the diphosphate and removal of the base protection gave the 20-deu-
teriocytidine 50-diphosphate 8 in a yield of 23% after HPLC purification.
Both 20-deuterio- and 30-deuteriocytidine 50-diphosphate could be made success-
fully and should be useful in future mechanistic studies. In addition it is worth noting
that the selective cleavage of 50-O-TBDMS relative to the secondary O-TBDMS
under acidic conditions[4] worked well with the 30-ketocytidine derivative 2 but the
corresponding 20-ketoderivative is an exception to this selectivity.
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TIBS 2001, 26 (2), 93–99.
2. Robins, M.J.; Sarker, S.; Samano, V.; Wnuk, S.F. Nucleic acid related com-
pounds. 94. Remarkably high stereoselective reductions of 20- and 30-keto
nucleosides to give arabino, ribo, and xylofuranosyl nucleosides with hydrogen
isotopes at C20 and C30. Tetrahedron 1997, 53, 447.
3. Davisson, V.J.; Davis, D.R.; Dixit, V.M.; Poulter, C.D. Synthesis of nucleotide
50-diphosphates from 50-O-tosyl nucleosides. J. Org. Chem. 1987, 52, 1794.
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Synthesis of 9-(b-d-xylofuranosyl)adenine or 30-deuterioadenosine from adeno-
sine. J. Org. Chem. 1990, 55, 410; (b) Ogilvie, K.K.; Beaucage, S.L.; Schifman,
A.L.; Theriault, N.Y.; Sadana, K.L.; The synthesis of oligoribonucleotides. II.
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