Study of asymmetrically substituted myo-inositols. XXXIX. The synthesis of conjugate of 2',3'-didehydro-3'-dehydroxythymidine with phosphatidylinositol: a new nucleoside phospholipid with potential anti-HIV activity

A partially protected phosphatidylinositol with a free hydroxyl group in the cyclitol moiety was synthesized by phosphorylation of a tetrasubstituted myo-inositol using the H-phosphonate and phosphoamidite methods. The H-phosphonate method was advantageous for the synthesis of selectively protected monophosphoinositide due to a lesser number of stages. Two schemes for the conjugation of 2',3'-didehydro-3'-dehydroxythymidine with phosphatidylinositol using succinic acid as a linker were tested in the synthesis of the target nucleoside phospholipid.     

Some aspects of oligoribonucleotides synthesis via the H-phosphonate approach.

This review gives a short account of selected aspects of oligoribonucleotide synthesis via the H-phosphonate method. It includes: (i) recent methods for the preparation of suitably protected ribonucleoside 3'-H-phosphonates (the phosphonylation step), (ii) some chemical and stereochemical features of the formation of H-phosphonate internucleosidic linkages, and (iii) stereoselective synthesis of oligoribonucleoside phosphorothioates using chemo-enzymatic approach.     

Use of a temporary protective group during the synthesis of oligonucleotides with an unnatural bond

Methoxygroup has been used for transient P-protection on H-phosphonate oligonucleotide synthesis. Whereas other H-phosphonate linkages can be irreversibly transformed into phosphoramidates by treatment with alkylamines, the protected phosphoralkoxyl groups generate natural phosphodiester linkages after the final deprotection. The method allows for synthesis of oligonucleotides with addressed position of internucleotide phosphoralkylamidate groups.     

N-phosphonate synthesis of oligodeoxyribonucleotides with the use of a p-nitrophenylethyl blocking group

p-Nitrophenylethyl blocking group was used to protect the endocyclic imido groups of guanine and thymine nucleoside 3'-H-phosphonates employed in the H-phosphonate synthesis of a large number of oligodeoxyribonucleotides varying in length from 8 to 45 units. A combination of the fully protected monomers with a condensing agent, pivaloyl chloride or mesitylenesulphonyl-3-nitro-1,2,4-triazole, provides a rapid and effective synthesis of long oligonucleotides.     

Building Blocks for Synthesis of Oligoarabinonucleotides: Preparation of Arabinonucleoside H-Phosphonates from Protected Ribonucleosides

Abstract

A straightforward and inexpensive synthesis of arabinonucleoside H-phosphonates has been developed. Arabinonucleosides were synthesised from protected ribonucleosides via 2′-keto derivatives. Reaction conditions have been optimised for compounds bearing labile N-protections. Further protecting group manipulation and phosphonylation gave the required H-phosphonate monomers.     

Synthesis of 3',5'-cyclic diguanylic acid (cdiGMP) using 1-(4-chlorophenyl)-4-ethoxypiperidin-4-yl as a protecting group for 2'-hydroxy functions of ribonucleosides

We herein report a convenient synthesis of 3',5'-cyclic diguanylic acid via the modified H-phosphonate approach. The 1-(4-chlorophenyl)-4-ethoxypiperidin-4-yl (Cpep) group was used as protecting group for the 2'-hydroxy functions of ribonucleosides. Complete unblocking of the fully protected 3',5'-cyclic diguanylic acid gave cdiGMP as a homogeneous compound in an excellent yield.     

Synthesis and separation of diastereomers of uridine 2',3'-cyclic boranophosphate

The first boron-containing 2',3'-cyclic phosphate-modified analogue, uridine 2',3'-cyclic boranophosphate (2',3'-cyclic-UMPB), was synthesized. 5'-O-Protected uridine was cyclophosphorylated by diphenyl H-phosphonate to yield uridine 2',3'-cyclic H-phosphonate, which upon silylation followed by boronation and subsequent acid treatment gave 2',3'-cyclic-UMPB in high yield. The two diastereomers of 2',3'-cyclic-UMPB were separated by HPLC. An alternative method for synthesis of uridine 2',3'-cyclic phosphorothioate (2',3'-cyclic-UMPS) via H-phosphonate was also described.     

Synthesis of phosphodiesters of 2-acetamido-2-deoxy-D-glucose--fragments of polymers of capsules from Escherichia coli K51 and Neisseria meningitidis X

Hydrogenphosphonate method was used for synthesis of 4-nitrophenyl 2-acetamido-3- and 4-nitrophenyl 2-acetamido-4-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl phosphate)-2-deoxy-beta-D-glucopyranosides. The glycosides, phosphate diester fragments of the title bacteria capsular antigens, were obtained by H-phosphorylation of the suitably protected 2-acetamido-2-deoxy-beta-D-glucopyranosides with 2-acetamido-3,4,6-tri-O-benzoyl-2-deoxy-alpha-D-glucopyranosyl H-phosphonate in the presence of trimethylacetyl chloride followed by oxidation and deprotection.     

Gel-phase P-NMR. A new analytical tool to evaluate solid phase oligonucleoside synthesis.

This paper shows Gel-phase ³¹P-NMR spectra of synthetic intermediates obtained during solid-phase oligonucleotide synthesis on polystyrene for the first time. We have demonstrated the application of this technique using the phosphotriester, H-phosphonate and phosphite triester approaches. The use of Gel-phase ³¹P-NMR for monitoring solid phase oligonucleotide synthesis is discussed.     

A CAUTIONARY NOTE ON THE USE OF THE 31P NMR SPECTROSCOPY IN STEREOCHEMICAL CORRELATION ANALYSIS

Stereoselectivity in condensation of protected ribonucleoside 3′-H-phosphonates with hydroxylic components was investigated using ³¹P NMR spectroscopy. The correlation between absolute configuration at the phosphorus center and the chemical shifts of the produced H-phosphonate diesters and the corresponding phosphorothioates, was studied.     

Use of new phosphonylating and coupling agents in the synthesis of oligodeoxyribonucleotides via the H-phosphonate approach.

New phosphonylating and coupling agents for the synthesis of oligodeoxyribonucleotides via H-phosphonate approach have been developed. Tris(1,1,1,3,3,3-hexafluoro-2-propyl) phosphite, prepared by the reaction of lithium salt of 1,1,1,3,3,3-hexafluoro-2-propoxide with PCl3, reacts with deoxyribonucleosides in the presence of a catalytic amount of triethylamine to produce in the high yield the corresponding deoxyribonucleoside 3'-H-phosphonate units. The use of a new coupling reagent, 1,3-dimethyl-2-chloro-imidazolinium chloride (DMCI) for the internucleotidic H-phosphonate bond formation via the H-phosphonate approach is also discussed in detail.     

Stereochemistry of internucleotide bond formation by the H-phosphonate method. 1. Synthesis and 31P NMR analysis of 16 diribonulceoside (3'-5')-H-phosphonates and the corresponding phosphorothioates

Sixteen diribonucleoside (3'-5')-H-phosphonates were synthesized via condensation of the protected ribonucleoside 3'-H-phosphonates with nucleosides, and the influence of a nucleoside sequence on the observed stereoselectivity was analyzed. 31P NMR spectroscopy was used to evaluate a relationship between chemical shift and absolute configuration at the phosphorous center of the H-phosphonate diesters as well as of the corresponding phosphorothioate diesters. Although for the most cases such correlation was found, there was however several exceptions to the rule where the relative positions of resonances arisingfrom Rp and Sp diastereomers were reversed.     

Synthesis and hybridization properties of inverse oligonucleotides.

The synthesis of adenine and thymine cyclopentylethyl nucleosides is presented. This novel constrained monomeric building block is very difficult to incorporate into oligonucleotides. It was introduced in 13mer oligodeoxynucleotide sequences at a single position using H-phosphonate chemistry. Phosphoramidite chemistry completely failed in this particular case. The H-phosphonate building blocks were obtained starting from the corresponding phosphoramidites. Stability of duplexes with RNA and DNA is significantly reduced.     

A cautionary note on the use of the 31P NMR spectroscopy in stereochemical correlation analysis

Stereoselectivity in condensation of protected ribonucleoside 3'-H-phosphonates with hydroxylic components was investigated using 31P NMR spectroscopy. The correlation between absolute configuration at the phosphorus center and the chemical shifts of the produced H-phosphonate diesters and the corresponding phosphorothioates, was studied.     

Boranophosphate Oligonucleotides: New Synthetic Approaches

Abstract

Recently our laboratory reported a new backbone-modified class of oligonucleotides, with a borane (B₃3?) group replacing one of the non-bridging oxygen atoms. Here we present two new approaches to synthesize the boranophosphate oligonucleotides. All-stereoregular boranophosphate oligonucleotides can be prepared by enzymatic template extension reactions using nucleoside a-boranotriphosphates, which are good substrates for a number of polymerases. Larger scale synthesis of boranophosphate oligonucleotides can be carried out by effective chemical synthesis using the H-phosphonate approach, instead of previously used phosphoramidite methodology. The main advantage of H-phosphonate methodology is the ability to carry out one boronation reaction, after oligonucleotide chain elongation has been completed, using mild conditions without base damage and producing the desired boranophosphate oligonucleotides in high yield.     

A synthesis of dolichyl fluorophosphate

An improved method for the synthesis of dolichyl H-phosphonate was developed using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one (salicyl chlorophosphite) as a reagent. Dolichyl phosphorofluoridate was for the first time synthesized from dolichyl H-phosphonate by its treatment with chlorotrimethylsilane, oxidation with iodine, and subsequent interaction with fluoride ion in pyridine.     

Evaluation of 2'-hydroxyl protection in RNA-synthesis using the H-phosphonate approach.

A number of different protecting groups were compared with respect to their usefulness for protection of 2'-hydroxyl functions during synthesis of oligoribonucleotides using the H-phosphonate approach. The comparison was between the t-butyldimethylsilyl (t-BDMSi), the o-chlorobenzoyl (o-CIBz), the tetrahydropyranyl (THP), the 1-(2-fluorophenyl)-4-methoxypiperidin-4-yl (Fpmp), the 1-(2-chloro-4-methylphenyl)-4-methoxypiperidin-4-yl (Ctmp), and the 1-(2-chloroethoxy)ethyl (Cee) protecting groups. All these groups were tested in synthesis of dodecamers, (Up)11U and (Up)11A, using 5'-O-(4-monomethoxytrityl) or (4,4'-dimethoxytrityl) uridine H-phosphonate building blocks carrying the respective 2'-protection. The performance of the t-BDMSi and o-CIBz derivatives were also compared in synthesis of (Up)19U. The most successful syntheses were clearly those where the t-butyldimethylsilyl group was used. The o-chlorobenzoyl group also gave satisfactory results but seems somewhat limited with respect to synthesis of longer oligomers. The results with all tested acetal derivatives (Fpmp, Ctmp, Cee, THP) were much less successful due to some accompanying cleavage of internucleotidic H-phosphonate functions during removal of 5'-O-protection (DMT).     

Synthesis of phosphopeptides via global phosphorylation on the solid phase: Resolution of H-phosphonate formation

Summary The formation of the H-phosphonate by-products from the ‘global’ phosphorylation of a Thr-containing peptide resin using both di-t-butyl and dibenzylN,N-diethylphosphoramidite was identified to result from 1H-tetrazolemediated cleavage of thet-butyl or benzyl from the intermediate dialkyl phosphite triester and re-arrangement of the resultant hydroxy phosphite diester to the H-phosphonate form. This side reaction was rectified by the use of aqueous iodine for the oxidation step in which the H-phosphonate is oxidised to the benzyl phosphorodiester which, on acidolytic treatment, gives the desired dihydrogen phosphate.     

Production of phosphatidylinositol 5‐phosphate via PIKfyve and MTMR3 regulates cell migration

Although phosphatidylinositol 5‐phosphate (PtdIns5P) is present in many cell types and its biogenesis is increased by diverse stimuli, its precise cellular function remains elusive. Here we show that PtdIns5P levels increase when cells are stimulated to move and we find PtdIns5P to promote cell migration in tissue culture and in a Drosophila in vivo model. First, class III phosphatidylinositol 3‐kinase, which produces PtdIns3P, was shown to be involved in migration of fibroblasts. In a cell migration screen for proteins containing PtdIns3P‐binding motifs, we identified the phosphoinositide 5‐kinase PIKfyve and the phosphoinositide 3‐phosphatase MTMR3, which together constitute a phosphoinositide loop that produces PtdIns5P via PtdIns(3,5)P₂. The ability of PtdIns5P to stimulate cell migration was demonstrated directly with exogenous PtdIns5P and a PtdIns5P‐producing bacterial enzyme. Thus, the identified phosphoinositide loop defines a new role for PtdIns5P in cell migration.     

Metabolism of 3- and 4-phosphorylated phosphatidylinositols in stomatal guard cells of Commelina communis L.

Within the plant kingdom the stomatal guard cell is presented as a model system of inositol 1,4,5-trisphosphate [Ins(1,4,5)P₃]-mediated signal transduction. Despite this it is only recently that the phosphoinositide components of animal signal transduction pathways have been identified in stomatal guard cells. Interestingly, stomatal guard cells contain both 3- and 4-phosphorylated phosphatidylinositols though their relative contributions to signalling remain undefined. An appraisal of the routes of synthesis and rates of turnover of these phosphatidylinositols would appear timely as the in vivo biosynthesis of these components is a much neglected facet of the phosphoinositide-mediated signalling paradigm as purported to apply to plants. A non-equilibrium [³²P]P_i labelling strategy and enzymic and chemical dissection of labelled phosphatidylinositols have been used to address not only the route of synthesis but also the rates of turnover of phosphatidylinositols in stomatal guard cells of Commelina communis L. The specific activity of the ATP pool of isolated guard cells was found to increase over a 4 h period when labelled from [³²P]P_i. In separate experiments, isolated guard cells were labelled over a 40–240 min period, their lipids extracted, deacylated and resolved by HPLC. Glycerophosphoinositol phosphate (GroPInsP) and glycerophosphoinositol bisphosphate (GroPInsP₂) peaks were desalted and enzymically cleaved with alkaline phosphatase and human erythrocyte ghosts, respectively. The monoester phosphate in phosphatidylinositol 4-monophosphate (PtdIns4P) accounted for 90–97% of the [³²P]P_i label while the 4- and 5-monoester phosphates of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P₂] accounted for typically 39% and 61% respectively. Therefore, the evidence is consistent with synthesis of PtdIns(4,5)P₂ by successive 4- and 5-phosphorylation of phosphatidylinositol (PtdIns). This study therefore represents the first report of the pathway of the synthesis of 4- and 5-phosphorylated phosphatidylinositols in a single defined hormone-responsive plant cell type. The monoester phosphate in phosphatidylinositol 3-monophosphate (PtdIns3P) accounted for 83–95% of the ³²P label. It was not possible, however, to determine the route of synthesis of phosphatidylinositol 3,4-bisphosphate [PtdIns(3,4)P₂] owing to the rapid attainment of equilibrium between the 3- and 4-monoester phosphates of PtdIns(3,4)P₂, each containing approximately 50% of the label at just 40 min of labelling. Turnover of PtdIns3P was quicker than that of PtdIns4P. Similarly, turnover of PtdIns(3,4)P₂ was quicker than that of PtdIns(4,5)P₂, and in mass terms PtdIns(3,4)P₂ appeared to predominate over PtdIns(4,5)P₂. By analogy with animal systems, in which signalling molecules such as PtdIns(4,5)P₂ show considerable basal turnover, the evidence presented is consistent with signalling roles for PtdIns3P and PtdIns(3,4)P₂ in addition to those previously indicated for PtdIns(4,5)P₂ in stomatal guard cells.