Phosphite Triester Research Articles

A Convenient Oligonucleotide Conjugation via Tandem Staudinger Reaction and Amide Bond Formation at the Internucleotidic Phosphate Position.

Staudinger reaction on the solid phase between an electronodeficit organic azide, such as sulfonyl azide, and the phosphite triester formed upon phosphoramidite coupling is a convenient method for the chemical modification of oligonucleotides at the internucleotidic phosphate position. In this work, 4-carboxybenzenesulfonyl azide, either with a free carboxy group or in the form of an activated ester such as pentafluorophenyl, 4-nitrophenyl, or pentafluorobenzyl, was used to introduce a carboxylic acid function to the terminal or internal internucleotidic phosphate of an oligonucleotide via the Staudinger reaction. A subsequent treatment with excess primary alkyl amine followed by the usual work-up, after prior activation with a suitable peptide coupling agent such as a uronium salt/1-hydroxybenzotriazole in the case of a free carboxyl, afforded amide-linked oligonucleotide conjugates in good yields including multiple conjugations of up to the exhaustive modification at each phosphate position for a weakly activated pentafluorobenzyl ester, whereas more strongly activated and, thus, more reactive aryl esters provided only single conjugations at the 5'-end. The conjugates synthesized include those with di- and polyamines that introduce a positively charged side chain to potentially assist the intracellular delivery of the oligonucleotide.

THF peroxide as a factor in generating desulphurised products from the solid-phase synthesis of phosphorothioate-modified oligonucleotides.

Antisense oligonucleotides (ASOs) are generally obtained via chemical synthesis on a solid support and phosphorothioate (PS) modification with a phosphate backbone to increase their in vivo stability and activity. However, desulphurised products, in which PS is partially replaced by phosphodiesters, are generally formed during the chemical synthesis of ASO and are difficult to separate from the desired PS-modified ASO by chromatography. Therefore, revealing the unknown factors that cause the formation of desulphurised products and proposing methods to inhibit their formation are highly desirable. In this study, it was found that peroxides in THF, which is used as a solvent for the acetyl capping agent, oxidise phosphite triesters to produce desulphurisation products. The use of THF with antioxidants effectively suppresses the oxidation caused by THF peroxides. Moreover, THF peroxide was found to oxidise phosphoramidites, which are the building blocks of oligonucleotide chemical syntheses, indicating that caution should be taken with the organic solvents used during the synthesis and purification of phosphoramidites.

New Zwitterionic Oligonucleotides: Preparation and Complementary Binding

New zwitter-ionic oligonucleotide derivatives containing 1,2,3,4-tetrahydroisoquinoline-7-sulfonyl phosphoramidate group are described. Automated synthesis of these compounds was carried out according to the β-cyanoethyl phosphoramidite scheme using the Staudinger reaction between 2-trifluoroacetyl-1,2,3,4-tetrahydroisoquinoline-7-sulfonyl azide and phosphite triester within an oligonucleotide grafted to a polymer support. 1,2,3,4-Tetrahydroisoquinoline-7-sulfonyl phosphoramidate group (THIQ) proved to be stable under the conditions of standard oligonucleotide synthesis, including the removal of protective groups and cleavage of the oligonucleotide from the polymer support by treatment with a mixture of concentrated aqueous solutions of ammonia and methylamine (1 : 1) at 55oC. Oligonucleotides modified by one to five THIQ groups in various positions were obtained. The zwitter-ionic character of the obtained derivatives was reflected in their different mobility under conditions of denaturing PAGE. The thermal stability of the duplexes of oligodeoxynucleotides containing THIQ groups with complementary DNA and RNA differed only slightly from that of natural DNA:DNA and DNA:RNA duplexes. The results obtained suggest the possible use of oligonucleotides modified with zwitterionic THIQ groups as antisense therapeutic agents.

New Zwitter-Ionic Oligonucleotides: Preparation and Complementary Binding

New zwitter-ionic oligonucleotide derivatives containing 1,2,3,4-tetrahydroisoquinoline-7-sulfonyl phosphoramidate group are described. Automated synthesis of these compounds was carried out according to the β-cyanoethyl phosphoramidite scheme via the Staudinger reaction between 2-trifluoroacetyl-1,2,3,4-tetrahydroisoquinoline-7-sulfonyl azide and phosphite triester within oligonucleotide grafted to polymer support. 1,2,3,4-Tetrahydroisoquinoline-7-sulfonyl phosphoramidate group (THIQ) was stable under the conditions of standard oligonucleotide synthesis, including the removal of protective groups and cleavage of the oligonucleotide from the polymer support by treatment with a mixture of concentrated aqueous solutions of ammonia and methylamine (1 : 1) at 55°C. Oligonucleotides modified by one to five THIQ groups in various positions were obtained. The zwitter-ionic character of the obtained derivatives was reflected in their varying mobility under conditions of denaturing PAGE. The thermal stability of the duplexes of oligodeoxynucleotides containing THIQ groups with complementary DNA and RNA only slightly differed from that of natural DNA:DNA and DNA:RNA duplexes. The results reported suggest that oligonucleotides modified with zwitter-ionic THIQ groups as antisense therapeutic agents.

Solution-Phase Chemical Synthesis of Modified RNA Dinucleotides.

This article describes a simple, reliable, efficient, and improved solution-phase method for the gram-scale chemical synthesis of RNA dinucleotides such as pAm pA, pAm pG, and pAm pU that utilizes phosphoramidite chemistry. The overall synthetic strategy involves three steps. The first step involves the coupling reaction between 5'-O-MMT protected nucleoside-3'-O-phosphoramidite and a protected nucleoside containing a free 5'-OH group in the presence of tetrazole, followed by the oxidation of phosphite triester using tert-butyl hydroperoxide to give the corresponding protected Nm pN. Next, the 5'-O-MMT is cleaved under 3% trichloroacetic acid in dichloromethane conditions. Finally, the 5'-hydroxyl group is phosphorylated by the use of an activated bis(2-cyanoethyl)-N,N-diisopropyl phosphoramidite using tetrazole, followed by the oxidation of trivalent to pentavalent phosphorus using tert-butyl hydroperoxide and subsequent deprotection using ammonium hydroxide to afford the corresponding RNA dinucleotide, pNm pN, in good yields with high purity (>99.5%). © 2022 Wiley Periodicals LLC.

Synthesis of Phosphorodiamidate Oligonucleotide Dimers.

Azido nucleosides couple with phosphoramidites via an initial iminophosphorane, which eliminates acrylonitrile to generate the coupled dimer P(V) product. The vulnerable phosphite triester intermediate is bypassed entirely, making the methodology very suitable to solution-phase synthesis. This new coupling protocol requires no protection of the 5'-OH function and provides a new method of installing internucleosidic phosphorodiamidate bonds with near quantitative yields.

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies.

Two phosphate modifications were introduced into the DNA backbone using the Staudinger reaction between the 3’,5’-dinucleoside β-cyanoethyl phosphite triester formed during DNA synthesis and sulfonyl azides, 4-(azidosulfonyl)-N,N,N-trimethylbutan-1-aminium iodide (N+ azide) or p-toluenesulfonyl (tosyl or Ts) azide, to provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts modification in the DNA sequence. The incorporation of these N+ and Ts modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts-modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs with modification in the middle of the sequence). Additionally, the incorporation of N+ modifications led to the formation of duplexes with a thermal stability that was less dependent on the ionic strength than native DNA duplexes. The thermodynamic analysis of the melting curves revealed that it is the reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is responsible for the stabilisation of duplexes with N+ modification. N+ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell uptake studies showed that Ts-ONs can enter the nucleus of mouse fibroblast NIH3T3 cells without any transfection reagent, whereas, N+ONs remain concentrated in vesicles within the cytoplasm. These results indicate that both N+ and Ts-modified ONs are promising for various in vivo applications.

Mechanochemical Synthesis of Short DNA Fragments.

We demonstrate the first mechanochemical synthesis of DNA fragments by ball milling, enabling the synthesis of oligomers of controllable sequence and length using multi-step, one-pot reactions, without bulk solvent or the need to isolate intermediates. Mechanochemistry allowed for coupling of phosphoramidite monomers to the 5'-hydroxyl group of nucleosides, iodine/water oxidation of the resulting phosphite triester linkage, and removal of the 5'-dimethoxytrityl (DMTr) protecting group in situ in good yields (up to 60 % over three steps) to produce DNA dimers in a one-pot manner. H-Phosphonate chemistry under milling conditions enabled coupling and protection of the H-phosphonate linkage, as well as removal of the 5'-DMTr protecting group in situ, enabling a one-pot process with good yields (up to 65 % over three steps, or ca. 87 % per step). Sulfurization of the internucleotide linkage was possible using elemental sulfur (S8) or sulfur transfer reagents, yielding the target DNA phosphorothioate dimers in good yield (up to 80 % over two steps). This work opens the door to creation of solvent-free synthesis methodologies for DNA and RNA therapeutics.

Cytotoxicity of phosphite and phosphate triesters

Cytotoxicity of phosphite and phosphate triesters

Desymmetrization of myo-inositol derivatives by lanthanide catalyzed phosphitylation with C2-symmetric phosphites

Desymmetrization by phosphorylation represents a promising method with potential impact in many different areas of research. C2-Symmetric phosphoramidites have been used to desymmetrize myo-inositol derivatives by functionalization at different positions. With this method, 1:1 mixtures of diastereomers are obtained that can be separated subsequently. In this work, activation of a C2-symmetric phosphoramidite is achieved by addition of pentafluorophenol (PFP) and leads to a reactive PFP phosphite, which can then be coupled to protected myo-inositol derivatives with reactive OH groups at the 1, 3, 4 and 6 positions. This strategy enhances the diastereoselectivity of the coupling reaction with a preference towards phosphitylation at position 6 (up to 3:1) or position 3 (up to 2:1). The concept of attenuative activation of phosphoramidites via in situ generated pentafluorophenol phosphite triesters is thus proven in these studies. It is further shown that Lewis–Acid catalysis enhances the rate of phosphite triester coupling without affecting the diastereoselectivity. This novel strategy improves access to different phosphorylated myo-inositol derivatives and will thus enable further studies into the function of these important intracellular second messengers.

Multiple phosphate-linked nucleotide couplings via 5′ silyl ether protection in the phosphite triester and phosphoramidite approaches

Phosphite triester and phosphoramidite coupling methodologies are described for performing fourfold solution phase installations of standard deoxynucleotides onto a single cavitand template molecule. The methodologies here are based on 5′ silyl ether protection of the appropriate nucleoside or nucleoside phosphoramidite. Synthesis of a novel water-soluble species incorporating four covalently-linked guanine nucleotides is shown.

ChemInform Abstract: Sulfurization of Dinucleoside Phosphite Triesters with Chiral Disulfides.

Sixteen chiral analogues of phenylacetyl disulfide (PADS) and 5-methyl-3H-1,2,4-dithiazol-3-one (MEDITH) were used to sulfurize five dithymidine phosphite triesters, each incorporating a β-cyanoethoxy or siloxy group. Each mixture of SP:RP phosphite triester diastereomers was combined with approximately one fourth of an equivalent of each of the sulfurizing reagents, and the RPS:SPS diastereomer ratios of the resulting phosphite sulfides or phosphorothioates were determined by reverse-phase HPLC. Diastereoselectivities and corresponding diastereomeric excess (de) values were calculated by correcting for the starting triester diastereomer ratios. The highest de values for RPS and SPS phosphorothioates were 14.7% and 7.9%, respectively, both using MEDITH analogues.

Sulfurization of Dinucleoside Phosphite Triesters with Chiral Disulfides

Sixteen chiral analogues of phenylacetyl disulfide (PADS) and 5-methyl-3H-1,2,4-dithiazol-3-one (MEDITH) were used to sulfurize five dithymidine phosphite triesters, each incorporating a β-cyanoethoxy or siloxy group. Each mixture of SP:RP phosphite triester diastereomers was combined with approximately one fourth of an equivalent of each of the sulfurizing reagents, and the RPS:SPS diastereomer ratios of the resulting phosphite sulfides or phosphorothioates were determined by reverse-phase HPLC. Diastereoselectivities and corresponding diastereomeric excess (de) values were calculated by correcting for the starting triester diastereomer ratios. The highest de values for RPS and SPS phosphorothioates were 14.7% and 7.9%, respectively, both using MEDITH analogues.

Synthesis And Biological Activity of Borane Phosphonate DNA

Borane phosphonate oligodeoxyribonucleotides are synthesized from 5′-O-[benzhydroxybis(trimethylsilyloxy)silyl]-2′-deoxyribonucleoside-3′-O-methylphosphoramidites. The exocyclic amine functions of adenine, guanine, and cytosine are protected with trimethoxytrityl, and thymine is unprotected. Using these synthons and under standard conditions via activation with S-ethylthiotetrazole, condensations on a highly crosslinked polystyrene support are in excess of 99%. Following the complete synthesis of the oligodeoxyribonucleotide phosphite triester, oxidation with THF·BH3 yields the oligodeoxyribonucleotide borane phosphonate. Further treatment with 80% aqueous acetic acid followed by disodium 2-carbamoyl-2-cyanoethylene-1,1-dithiolate removes trimethoxytrityl from the 2′-deoxyribonucleoside bases and the methyl protecting group from the internucleotide phosphate triester, respectively. Cleavage from the support with ammonium hydroxide and purification by reverse phase HPLC affords the pure oligodeoxyribonucleotide borane phosphonate. These oligomers are taken up by cells in the absence of cationic lipids and transport biologically active interfering RNA into cells.

Measurement of the barrier to inversion of configuration in acyclic phosphite triesters

Synthesis of three acyclic chiral phosphites is reported, in the form of dithymidine phosphite triesters. These diastereomerically pure P-stereogenic phosphites undergo epimerization at a measurable rate at 150 °C. When the alcohols on the deoxyribose moieties are protected as acyls, decomposition is minimized and by computer fitting, rate constants for epimerization can be extracted. These allow for the first time calculation of the barrier to inversion of configuration in phosphite triesters, giving Δ G †(150 °C) = 33.0 ± 0.2 kcal mol −1, comparable to the inversion barrier seen for phosphines.

Solid-phase synthesis of oligodeoxynucleotides containing 4-alkoxythymidine residues

Immobilized and fully protected oligodeoxynucleotides containing a 4-(1,2,4-triazolyl)-thymidine residue at a predetermined position were prepared according to a well-established phosphite triester methodology using 2-cyanoethyl phosphoramidites of a 4-(1,2,4-triazolyl)-substituted thymidine and standard protected nucleosides. Treatment of the immobilized oligomer with methanol, ethanol or n-propanol in the presence of DBU at 50°C gave the corresponding oligonucleotides containing 4-methoxy, 4-ethoxy- or 4-n-propoxythymidine residue.

5′-Bis-conjugation of Oligonucleotides by Amidative Oxidation and Click Chemistry

A pent-4-ynyl tert-butyl N,N-diisopropyl phosphoramidite was coupled at the 5'-end of oligonucleotides to give a phosphite triester linkage, which forms an H-phosphonate diester linkage during treatment with dichloroacetic acid. Then an amidative oxidation with CCl(4) in the presence of an amine and a 1,3-dipolar cycloaddition with an azide under copper(I) catalysis afforded the bis-conjugated oligonucleotides with high efficiency. The introduction of a bromoalkyl group as a precursor of azidoalkyl by amidative oxidation allowed the performance of two selective 1,3-dipolar cycloadditions.

ChemInform Abstract: Solid-Phase Synthesis of Oligodeoxynucleotides Containing 4- Alkoxythymidine Residues.

Immobilized and fully protected oligodeoxynucleotides containing a 4-(1,2,4-triazolyl)-thymidine residue at a predetermined position were prepared according to a well-established phosphite triester methodology using 2-cyanoethyl phosphoramidites of a 4-(1,2,4-triazolyl)-substituted thymidine and standard protected nucleosides. Treatment of the immobilized oligomer with methanol, ethanol or n-propanol in the presence of DBU at 50°C gave the corresponding oligonucleotides containing 4-methoxy, 4-ethoxy- or 4-n-propoxythymidine residue.

ChemInform Abstract: Diastereoselective Synthesis of Phosphite Triesters Through a New Bicyclic Intermediate.

Abstract The diastereoselective synthesis of phosphite triesters and their corresponding thiophosphate triesters is described. The new bicyclic imidazo-oxazaphosphorine, synthesized as a single diastereomer, is used as an intermediate that undergoes a diastereoselective displacement when reacted with an alcohol. This process eliminates the use of an acid catalyst.

Rapid glycosylations under extremely mild acidic conditions. Use of ammonium salts to activate glycosyl phosphites via P-protonation

Trifluoromethanesulfonic acid salts of tertiary amines were employed as extremely mild acidic activators for rapid glycosylations. Glycosyl phosphite triesters bearing an acid-labile 4,4′-dimethoxytrityl (DMTr) group for transient protection worked as glycosyl donors effectively in the presence of the activators to afford the corresponding disaccharides in good yields without loss of the DMTr group.