An Oxazaphospholidine Approach for the Stereocontrolled Synthesis of Oligonucleoside Phosphorothioates

Abstract

The stereocontrolled synthesis of oligodeoxyribonucleoside phosphorothioates (PS-ODNs) using nucleoside 3'-O-oxazaphospholidine derivatives as monomer units is described. 2-Chloro-1,3,2-oxazaphospholidine derivatives were prepared from six kinds of enantiopure 1,2-amino alcohols and used for the phosphitylation reactions of 5'-O-protected nucleosides. A detailed study of these reactions revealed that the diastereoselectivity of the reaction depended on the structure of the enantiopure 1,2-amino alcohol, the reaction temperature, and the amine used as a scavenger of HCl. In addition, ab initio molecular orbital calculations for the 2-chlorooxazaphospholidine derivatives were carried out to elucidate the mechanism of these diastereoselective phosphitylation reactions. The LUMO of the 2-chloro-5-phenyloxazaphospholidine derivatives on the phosphorus atom was found to be almost orthogonal to the P-Cl bond. This LUMO may be involved in the phosphitylation reactions with predominant retention of the P-configuration. A series of dialkyl(cyanomethyl)ammonium salts were developed and used as activators for the condensation reactions of the diastereopure nucleoside 3'-O-oxazaphospholidines with 3'-O-protected nucleosides. In the presence of the new activators, the reactions proceeded rapidly to give the corresponding dinucleoside phosphite triesters. The diastereoselectivity of the condensation reaction did not depend on the counteranion but on the structure of the dialkyl(cyanomethyl)amine. In the presence of the activator, which consists of a relatively small dialkyl(cyanomethyl)amine, the condensation proceeded with excellent diastereoselectivity. After sulfurization and deprotection, diastereopure (R(p))- and (S(p))-dinucleoside phosphorothioates were obtained in excellent yields. The present methodology was also applied to the solid-phase synthesis of stereoregulated PS-ODNs. all-(R(p))-[T(PS)](3)T, all-(S(p))-[T(PS)](3)T, all-(R(p))-d[G(PS)A(PS)C(PS)]T, and all-(R(p))-[T(PS)](9)T were synthesized on a highly cross-linked polystyrene resin.

Selective Phosphoramidite Cleavage as a Route to Novel Chiral and Achiral Pentacoordinated Nickel(II) PNP Pincer Complexes

“…The solvents were purified according to standard procedures. The starting materials (4S,5S)-2-chloro-4,5-diphenyl-1,3,2-dioxaphospholane, [27] (4S,5R)-2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidine, [28] PNP-BIPOL (1e), PNP-TAR Me (1g), PNP-TAR Pr (1h), and [Pd(PNP-BIPOL)Cl]Cl (3) were prepared according to literature procedures. [11] The deuterated solvents were purchased from Aldrich and dried with molecular sieves (4 Å).…”

A Strategy for the Stereoselective Preparation of Thymidine Phosphorothioates with the (R) or the (S) Configuration at the Stereogenic Phosphorus Atom and Their Application to the Synthesis of Oligodeoxyribonucleotides with Stereochemically Pure Phosphate/Phosphorothioate Chimeric Backbones

“…These involve: 1) 1H-tetrazolepromoted condensation of thymidine and (allyloxy)[bis(diisopropylamino)]phosphane followed by thermal equilibration of the resulting product, affording an (Sp)-thymidine 3Ј,5Ј-cyclic phosphate [23] as the major component, 2) stereospecific sulfurization of this major product, giving an allyl (Rp)-thymidine 3Ј,5Ј-cyclic phosphorothioate, 3) regioselective and stereoselective methanolysis of the allyl (Rp)-thymidine 3Ј,5Ј-cyclic phosphorothioate, producing an allyl methyl (Rp)-thymidine 3Ј-phosphorothioate as the major product, 4) after dimethoxytritylation of the free 5Ј-hydroxy group in the allyl methyl (Rp)-thymidine 3Ј-phosphorothioate, stereospecific removal of the methyl group from the phosphorothioate triester moiety by treatment with tert-butylamine, giving an allyl (Rp)-5Ј-O-dimethoxytritylthymidine 3Ј-phosphorothioate diester, or stereospecific removal of the allyl group from the phosphate moiety in an organopalladium-catalyzed reaction, producing a methyl (Sp)-5Ј-O-dimethoxytritylthymidine 3Ј-phosphorothioate, and 5) stereospecific condensation of the allyl (Rp)-thymidine 3Ј-phosphorothioate or the methyl (Sp)-thymidine 3Ј-phosphorothioate with a 5Ј-O-free thymidine derivative in Mitsunobu reactions, which results in retention of the stereochemistry of the phosphorothioate function to provide an allyl (3Ј-5Ј)-linked (Sp)-dithymidine phosphorothioate or a methyl (3Ј-5Ј)-linked (Rp)-dithymidine phosphorothioate, respectively. This preparation of 7 and 10 has remarkable advantages not found in existing methods for the stereodefined preparation of related dinucleoside phosphorothioates, including those developed by Stec,[8b,10,24] Beaucage, [25] Agrawal, [26] Just, [27] Wada, [28] and Stawinski. [29] The…”

Utilization of selected biorenewable resources: solubilization of lignocellulosics and conjugation of soybean oil

“…Phosphitylation has been developed in recent years as a technique for derivatizing carbohydrates, nucleosides and nucleotides Michalski, 2004, 2005;Laneman, 2005;Ahmadibeni and Parang, 2005;Oka et al, 2003;Parang et al, 2001), although this technique has been known longer for simple alcohols Watanabe et al, 1990). In our efforts to solubilize cellulosic materials with phosphite esters, we have taken advantage of this well known reaction which is an equilibrium transesterification process in which a new phosphite ester is formed with the release of a new alcohol.…”