Synthesis of the 3′-Derivatives of Phosphorothioate Oligonucleotide Analogues

Abstract

3′-Derivatives of phosphorothioate (PS) oligonucleotide analogues have been synthesized by a selective activation of a 3′-terminal phosphate group of the deprotected PS oligonucleotides using a mixture of triphenylphosphine and 2,2′-dipyridyldisulfide.     

Synthesis of 3′,5′-Dithymidylyl-α-hydroxyphosphonate Dimer Building Blocks for Oligonucleotide Synthesis—A New Pro-oliguncleotide

Abstract

The synthesis of the dimer building blocks 1 and 2 and their introduction into (T)₁₅-oligonucleotides is described. The stability against 3′-exonuclease digestion (SVP) as well as the hybridization properties (T_m values) were examined.     

Synthesis of 5′-Substituted Analogues of Carbocyclic 3-Deazaadenosine as Potential Antivirals

Abstract

Various 5′-substituted analogues of carbocyclic 3-deazaadenosine (la), a potent antiviral agent, have been prepared and tested against nine viruses.     

Synthesis of Oligonucleotide Building Blocks of 2′-Deoxyguanosine Bearing a C8-Arylamine Modification

Abstract

C8-Arylamine-dG adducts were synthesized by palladium-catalyzed cross- coupling reactions. The corresponding 5′-O-DMTr-3′-O-phosphoramidite-C8-arylamine-dG adducts were synthesized as potential building blocks for the automated synthesis of site-specifically modified oligonucleotides.     

Synthesis and Properties of Oligonucleotide Chimeras Containing 5′-Amino-2′-deoxy-2′-fluoroarabinonucleosides

Abstract

Oligonucleotide analogues comprised of 2′-deoxy-2′-fluoro-β-D-arabinose units joined via P3′-N5′ phosphoramidate linkages (2′F-ANA^5′N) were prepared for the first time. Among the compounds prepared were a series of 2′OMe-RNA-[GAP]-2′OMe-RNA ‘chimeras’, whereby the “GAP” consisted of DNA, DNA^5′N, 2′F-ANA or 2′F-ANA^5′N segments. The chimeras with the 2′F-ANA and DNA gaps exhibited the highest affinity towards a complementary RNA target, followed by the 5′-amino derivatives, i.e., 2′F-ANA > DNA > 2′F-ANA^5′N > DNA^5′N. Importantly, hybrids between these chimeras and target RNA were all substrates of both human RNase HII and E.coli RNase HI. In terms of efficiency of the chimera in recruiting the bacterial enzyme, the following order was observed: gap DNA > 2′F-ANA > 2′F-ANA^5′N > DNA^5′N. The corresponding relative rates observed with the human enzyme were: gap DNA > 2′F-ANA^5′N > 2′F-ANA > DNA^5′N.     

A Novel Versatile Phosphoramidite Building Block for the Synthesis of 5′- and 3′-Hydrazide Modified Oligonucleotides

We introduce a novel versatile phosphoramidite building block for the modification of oligonucleotides (ONs) with acyl hydrazides on the 5′- or 3′-terminus, or both. The reaction of these hydrazide functionalized ONs with 4-methoxyphenylaldehyde is demonstrated for solution derivatization. Hydrazides are considered nowadays as promising reactants, which show enhanced reactivity at neutral and slightly acidic conditions and higher stability of yielding products as compared to the aliphatic amines, which are broadly used for ONs derivatization.

Our method to introduce hydrazides into ONs employs a phosphoramidite modifier designed to split, during ammonia or lithium hydroxide treatment, into two hydrazides via β-elimination of a central bis-2-carbonylethoxysulfone unit. It allows the creation of ONs derivatized with a hydrazide moiety at the 5′-, 3′- and both 5′- and 3′-termini, as well as two different hydrazide containing ONs at the same time, viz. in one sequence on the same solid support. In latter case one can, for example, synthesize two hydrazide containing ONs, where one is 5′-modified and second one is 3′-modified.     

Synthesis of Novel 2′-Spirocyclopropyl-5′- Deoxyphosphonic Acid Furanosyl Nucleoside Analogues as Potent Antiviral Agents

Novel 5′-deoxyfuranosyl purine phosphonic acid analogues with 2 ′-electropositive moiety, such as spirocyclopropanoid, were designed and synthesized from commercially available diethyl malonate. Condensation reaction successfully proceeded from a glycosyl donor 15 at low reaction temperature in Vorbruggen conditions to give desired phosphonate analogues 16b and 23b. The synthesized nucleotide analogues 19, 22, 26, and 29 were subjected to antiviral screening against HIV-1. Adenine phosphonic acid analogue 22 shows significant anti-HIV activity (EC₅₀ = 7.9 μM).     

The Synthesis of Carbocyclic 5′-Nor Thymidine and an Isomer as Oligonucleotide Monomers

Abstract

The chiral synthesis of (1S,3S,4S)-1-(3,4-dihydroxycyclopent-1-yl)-1H?thymine (carbocyclic 5′-nor thymidine, 4) has been achieved in 5 steps from (+)-(lR,4S)-4-hydroxy-2-cyclopenten-1-yl acetate (5) and N³?benzoylthymine. Compound 4 is viewed as a monomeric building block for poly-T-like oligomers.     

The Synthesis of the Sixteen Possible 2′-O-Methyl MMI Dimer Phosphoramidites: Building Blocks for the Synthesis of Novel Antisense Oligonucleotides

Abstract

The synthesis of Methylene(methylimino) or MMI linked nucleoside dimers in all sixteen possible configurations has been accomplished via a reductive coupling of a nucleosidic aldehyde with an hydroxylamine. This has allowed us to prepare all of the necessary 2′-O-methyl MMI dimer building blocks necessary for use in an antisense motif.     

Synthesis of Analogues of 3′-Deoxypsicothymidine

Abstract

Preparation of 3′-deoxypsicothymidines bearing a tether group at O1′ is described. Selective protection of the primary hydroxy functions of the starting nucleoside is briefly discussed.     

Synthesis of Isoxazolidino Analogues of 2′,3′-Dideoxynucleosides

Abstract

The complete set of the 4′-aza analogues of 2′,3′-dideoxynucleosides was synthesized by cycloaddition of N-tetrahydropiranyl or N-trityl methylene nitrones on suitably protected vinyl nucleobases. The convertible nucleoside approach was used in the preparation of cytosine and 5-methyl cytosine analogues.     

Synthesis of 1′,2′-Seco-nucleoside Analogues of AZT

Abstract

1′,2′-Seco-AZT (3) and its 3′R,4′S diastereomer (19) were prepared and evaluated as antiviral agents. The chiral, acyclic side chains of these thymine acyclonuleosides were derived from D-isoascorbic acid. The two AZT analogues, 3 and 19, were screened against HIV, other RNA viruses, and two DNA viruses and they were found to be inactive.     

Synthesis of 3′-Azido-3′-Deoxythymidine-Terminated Oligonucleotide

Abstract

A method of completely chemical synthesis of 3′-azido-3′-deoxythymidine-terminated oligonucleotides via 5′-H-phosphonate of AZT is described.     

Synthesis of 5-Substituted 2′-Deoxyuridine-5′- Phosphonate Analogues and Evaluation of their Antiviral Activity

A small series of 5-(hetero)aryl-modified nucleoside phosphonates was synthesized via an 8-step procedure including a Wittig reaction and Suzuki–Miyaura coupling. An unanticipated anomerization during phosphonate deprotection allowed us to isolate both anomers of the 5-substituted 2′-deoxy-uridine phosphonates and assess their antiviral activity against a broad panel of viruses.     

Synthesis of Novel 3′-Hydroxymethyl 5′-Deoxythreosyl Phosphonic Acid Nucleoside Analogues as Potent Antiviral Agents

A very efficient synthetic route to novel 3′-hydroxymethyl 5′-deoxythreosyl phosphonic acid nucleosides was described. The discovery of threosyl phosphonate nucleoside (PMDTA, EC₅₀ = 2.53 μM) as a potent antihuman immunodeficiency virus (anti-HIV) agent has led to the synthesis and biological evaluation of 3′-modified 5′-deoxy versions of the threosyl phosphonate nucleosides. 3′-Hydroxymethyl 5 ′-deoxythreosyl phosphonic acid nucleoside analogues 15, 19, 24, and 28 were synthesized from 1,3-dihydroxyacetone and tested for anti-HIV activity as well as cytotoxicity. The adenine analogue 19 exhibits moderate in vitro anti-HIV-1 activity (EC₅₀ = 10.2 μM).     

Synthesis and Properties of Halogenated 7-Deaza-2′-deoxyxanthosine and Protected Derivatives for Oligonucleotide Synthesis

Abstract

The 7-bromo- (4a) and 7-iodo- (4b) derivatives of 7-deaza-2′-deoxyxanthosine (5) are prepared. Furthermore, the building blocks 6–8 of 7-deaza-2′-deoxyxanthosine (5) are synthesized and tested for their usage in oligonucleotide synthesis.     

Synthesis of Monomers Bearing at the 2′‐Position Cyanomethoxycarbonyl Group for Phosphoramidite Oligonucleotide Synthesis

A novel series of phosphoroamidites for the synthesis of 2′‐modified oligonucleotides was designed and synthesized on the base of 2′‐amino uridine and 2′‐amino arabinoadenosine. The amino groups in these compounds were acidified by bis‐cyanomethyl esters of different dicarbonic acids. Generated reactive linker groups containing cyanomethoxycarbonyl groups are stable under conditions of oligonucleotide synthesis but could be easily functionalised in post‐synthetic stage by treatment with compounds bearing primary amino groups.     

Efficient Electrophilic Fluorination for the Synthesis of Novel 2′-Fluoro-3′-Methyl-5′-Deoxyphosphonic Acid Apiosyl Nucleoside Analogues

Novel 5′-deoxyapiosyl purine phosphonic acid analogues with a 2′-electropositive moiety, such as, a fluorine atom were designed and synthesized from commercially available hydroxylacetone. Condensation of a glycosyl donor 10 with purines under Vorbruggen conditions and cross-metathesis give the desired nucleoside phosphonic acid analogues 14, 17, 21, and 24. The synthesized nucleoside analogues were subjected to antiviral screening against HIV-1, and the adenine analogue 17 exhibited weak in vitro anti-HIV-1 activity (EC₅₀ = 26.6 μM)     

Synthesis of Protected 3′,5′-Di-2′-Deoxythymidine-(α-hydroxy-2-nitrobenzyl)-phosphonate Diesters as Dimer Building Blocks for Oligonucleotides

Abstract

The synthesis of 3′-succinyl-CPG bound 3′,5′-di-2′-deoxythymidyl-(α-hydroxy-2-nitrobenzyl)-phosphonate diester 1 and the 3′-phosphoamidite derivative 2 is descibed. The hydroxyl-groups of the backbone modification were protected with trialkylsilyl groups: TES and TBS. Compounds 1, 2 are suitable blocks for oligonucleotide synthesis.     

Synthesis of Novel 4′-Cyclopropyl-5′-norcarbocyclic Adenosine Phosphonic Acid Analogues

Novel 4′-cyclopropyl-5′-norcarbocyclic adenosine phosphonic acid analogues were designed and racemically synthesized from propionaldehyde 5 through a de novo acyclic stereoselective route using triple Grignard addition and ring-closing metathesis (RCM) as key reactions. To improve cellular permeability and enhance the anti-HIV activity of this phosphonic acid, SATE phosphonodiester nucleoside prodrug 23 was prepared. The synthesized adenosine phosphonic acids analogues 17, 18, 19, 21, and 23 were subjected to antiviral screening against HIV-1. Compound 23 exhibits enhanced anti-HIV activity than its parent nucleoside phosphonic acid 18.