Phosphoramidite building blocks for efficient incorporation of 2′-O-aminoethoxy(and propoxy)methyl nucleosides into oligonucleotides

A simple and efficient method for the preparation of eight phosphoramidite building blocks for incorporation of 2′-O-(2-aminoethoxymethyl)ribonucleosides and 2′-O-(3-aminopropoxymethyl)ribonucleosides into synthetic oligonucleotides has been developed. The synthetic routes are maximally convergent and provide sufficient amounts of phosphoramidites for several solid-phase synthesis coupling reactions. Using acyclic derivatives 17a,b the overall yields of phosphoramidites 2 and 3 were increased up to 50% for pyrimidine nucleosides and up to 30% for purine derivatives with substantial decrease of total reaction steps. The 2′-O-substituent was found to be stable during oligonucleotide synthesis. The resulting oligonucleotides are of particular interest for post-synthetic functionalization and conjugation.     

Generation of oligonucleotide conjugates via one-pot diselenide-selenoester ligation–deselenization/alkylation

A breadth of strategies are needed to efficiently modify oligonucleotides with peptides or lipids to capitalize on their therapeutic and diagnostic potential, including the modulation of in vivo chemical stability and for applications in cell-targeting and cell-permeability. The chemical linkages typically used in peptide oligonucleotide conjugates (POCs) have limitations in terms of stability and/or ease of synthesis. Herein, we report an efficient method for POC synthesis using a diselenide-selenoester ligation (DSL)-deselenization strategy that rapidly generates a stable amide linkage between the two biomolecules. This conjugation strategy is underpinned by a novel selenide phosphoramidite building block that can be incorporated into an oligonucleotide by solid-phase synthesis to generate diselenide dimer molecules. These can be rapidly ligated with peptide selenoesters and, following in situ deselenization, lead to the efficient generation of POCs. The diselenide within the oligonucleotide also serves as a flexible functionalisation handle that can be leveraged for fluorescent labelling, as well as for alkylation to generate micelles.

An efficient and versatile approach for the late-stage generation of oligonucleotide conjugates by diselenide-selenoester ligation (DSL)–deselenization/alkylation was developed.     

An enantioselective synthesis of (+)-azimic acid

Herein we report a concise enantioselective synthesis of (+)-azimic acid starting from (5S,6S)-6-methyl-5-benzyloxy-2-piperidinone 8a, which was prepared from protected (S)-3-hydroxyglutarimide 6 according to a method recently disclosed in our laboratory. The key step is a stepwise regioselective reductive alkylation of the imide 10, which established the 2,6-cis-stereochemistry in excellent diastereoselectivity.     

Enantiodivergent syntheses of cycloheptenone intermediates for guaiane sesquiterpenes

The syntheses of enantiomeric 6-isopropenyl-3-methyl-2-cycloheptenones 16 and 22 have been effected starting from (R)-(−)-carvone. In the synthesis of 16, (R)-(−)-carvone was reduced and the resulting dihydrocarvone transformed regioselectively into silyl enol ethers. Cyclopropanation with dibromocarbene and in situ rearrangement gave an α-bromo-cycloheptenone which was reduced to the (R)-(+)-cycloheptenone 16. In the synthesis of 22, (R)-(−)-carvone was cyclopropanated with a sulfur ylide, followed by reduction with LiAlH₄ and acid-catalyzed cyclopropylcarbinyl rearrangement to afford a cycloheptenol. Oxidation and double bond conjugation led to the (S)-(−)-cycloheptenone 22 in a partially racemized form. Four cycloheptenones have been obtained and are suitable intermediates for the enantiodivergent syntheses of guaiane sesquiterpenes.     

Synthesis of oligonucleotides with sequences identical with or analogous to the 3'-end of 16s ribosomal rna of escherichia coli: preparation op U-C-C-U-U-A and A-C-C-U-C-C-U-U-A via the modified phosphotriester method

The synthesis of oligoribonucleotides U-C-C-U-U-A and A-C-C-U-C-C-U-U-A, which are located at the 3'-terminus of 16S rRNA of E. coli, is described. The key-intermediates in the synthesis of these compounds are the fully-protected mononucleotides 5a-c, which can be rapidly (2–4 min) functionalized by either of the two following specific deblocking procedures: (i) at the 3'-tenninus with zinc in pyridine-2,4,6-triisopropylbenzenesul-phonic acid and (ii) at the 5'-terminus with 0.5M hydrazine in pyridine-acetic acid. The fully-protected hexamer 17a and nonamer 19, prepared by utilizing these deblocking conditions, were completely deprotected by the action of fluoride ion, followed by treatment with base and acid to give the required oligonucleotides in high yield.     

Selective sialylation of 2,3-di-O-(β-d-galactopyranosyl)-d-galactose catalyzed by Trypanosoma cruzi trans-sialidase

Trypanosoma cruzi, the agent of Chagas’ disease, expresses on its surface a trans-sialidase (TcTS) that transfers sialic acid from host glycoconjugates to terminal β-galactopyranosyl units of parasite mucins. This process is involved in infection and pathogenesis. The trisaccharide 2,3-di-O-(β-d-galactopyranosyl)-d-galactose 1 is an external unit in the larger oligosaccharides of the mucins and a site for sialylation. The trisaccharide was previously synthesized in our laboratory. The last step of the synthesis was the hydrogenolysis of the crystalline benzyl trisaccharide. Herein we prove that the trisaccharide 1, its alditol 3 and the benzyl glycoside 2 are good acceptors of sialic acid and effective inhibitors of the sialylation of N-acetyllactosamine catalyzed by TcTS. Furthermore, selective sialylation of the 1→3 linked galactopyranose in glycoside 2 was determined by one and two-dimensional NMR analysis. In contrast, the flexible 2,3-di-O-(β-d-galactopyranosyl)-d-galactitol 3 is sialylated in either one of the two possible sites.     

Synthesis and characterisation of novel 3′-O- and 5′-O- modified azobenzene-thymidine phosphoramidites and their oligonucleotide conjugates as colorimeter DNA probes and FRET quenchers

The synthesis of two new ‘first generation’ azobenzene based thymidine phosphoramidites 1 and 2 having the chromophore (DABCYL) covalently incorporated as an ester in the 3′-O- and 5′-O-positions of the deoxyribose, and the incorporation of these molecules into 16-mer Chronic Myeloid Leukaemia (CML) antisense oligonucleotides, giving 7 and 8, respectively, is described. These compounds were designed as highly coloured probes, and to participate in a Fluorescence Resonance Energy Transfer (FRET) mechanism in the design of novel molecular beacons.     

Synthesis and ‘double click’ density functionalization of 8-aza-7-deazaguanine DNA bearing branched side chains with terminal triple bonds

The 7-[di(prop-2-ynl)amino]prop-1-ynyl derivative of 8-aza-7-deaza-2′-deoxyguanosine (1) was synthesized from 7-iodo-8-aza-7-deaza-2′-deoxyguanosine (7) by Sonogashira cross-coupling and converted into the phosphoramidite building block 10. Oligonucleotides bearing branched side chains with terminal triple bonds were prepared by solid-phase synthesis containing single or multiple residues of 1 as 2′-deoxyguanosine surrogates. T_m measurements demonstrate that compound 1 has a positive effect on duplex stability, which is comparable to the stabilizing effect of the octa-1,7-diynylated non-branched nucleoside 2. Nucleoside 1 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition ‘double click’ reaction with diverse ligands (AZT 3, benzyl azide 4, 11-azidoundecanol 5 and m-dPEG™₄-azide 6). The conjugation reactions were carried out in solution and on solid support. Nucleoside 1 allowed ‘double’ functionalization of a single residue with two reporter groups. The ‘double click’ reaction proceeded smoothly even when two residues of nucleoside 1 were arranged in proximal positions. Hybridization with complementary strands led to a stable oligonucleotide duplex. Molecular modeling indicates that inspite of the crowded steric situation with four AZT ligands within closest proximal positions, all ligands are well accommodated in the major groove not disturbing the DNA helix.     

Simultaneous enzymatic synthesis of (S)-3-fluoroalanine and (R)-3-fluorolactic acid

A coupled enzymatic system for the simultaneous synthesis of (S)-3-fluoroalanine (1a) and (R)-3-fluorolactic acid (3) with l-alanine dehydrogenase (l-AlaDH) from Bacillus subtilis and rabbit muscle l-lactate dehydrogenase (l-LDH) using rac-1 and NAD⁺ is described. Analysis of isolated products of the laboratory preparative scale process revealed 1a in 60% yield and 88% ee and 3 in 80% yield and over 99% ee. The compounds 1a and 3 represent chiral building blocks for the synthesis of several products with pharmacological activity.     

Oligonucleotide conjugation to a cell-penetrating (TAT) peptide by Diels-Alder cycloaddition

Modifed oligonucleotides are routinely employed as analytical probes for use in diagnostics, e.g. in the examination of specific RNA sequences for infectious diseases, however, a major limiting factor in oligonucleotide-based diagnostics is poor cellular uptake of naked oligonucleotides. This problem can be overcome by covalent attachment of a so-called 'cell-penetrating peptide' to form an oligonucleotide peptide conjugate. Stepwise solid phase synthesis of such a conjugate is difficult and expensive due to the conflicting chemistries of oligonucleotides and peptides. A simple approach to overcome this is post-synthetic conjugation. Diels-Alder cycloaddition is an attractive methodology for oligonucleotide peptide conjugation; the reaction is fast, chemoselective and the reaction rate is greatly enhanced in aqueous media - ideal conditions for biological moieties. An oligodeoxyribonucleotide sequence has been derivatised with a series of dienes at the 5'-terminus, using a series of unique dienyl-modified phosphoramidites, and investigation into the effect of diene type on the efficiency of conjugation, using Diels-Alder cycloaddition with a maleimido-derivatised cell-penetrating (TAT) peptide, has been performed. This led to the observation that the optimal diene for conjugation was cyclohexadiene, allowing conjugation of oligodeoxyribonucleotides to a cell-penetrating peptide by Diels-Alder cycloaddition for the first time.     

The mechanism of the stereoisomerization of N-aryl ketenimines

Barriers to racemization of the o-mono and O'-disubstituted N-phenyl ketenimines la–j were measured by dynamic NMR spectroscopy. The structures of the ketenimines 1k, 1were established by X-ray diffraction analysis. According to the experimental results and ab initio calculations (STO-3G basis set) N-aryl ketenimines and N-aryl imines in general invert their configurations by a coupled mechanism: a rotation around the N-aryl bond is coupled to inversion at nitrogen. In the transition state of nitrogen inversion the arel π system is conjugated to the p lone electron pair of the nitrogen; in the ground state, however, conjugation between the aryl system and the C=N double bond is electronically preferred but may be sterically hindered.     

Design and synthesis of a novel protected mixed ligand siderophore

A novel siderophore analog (4) has been designed to facilitate iron transport-mediated drug delivery and drug release. This mixed ligand siderophore analog includes three bidentate ligands intended to octahedrally coordinate iron (III). The ligands include a 2,3-dihydroxy benzoic acid moiety, N⁵-acetyl-N⁵-hydroxy-l-ornithine, and a β-N-hydroxy-α,β-diaminopropionic acid derivative. The total synthesis of 15, a form of 4 that is suitably protected, yet contains a free carboxylic acid for subsequent drug conjugation, is described.     

A new dimeric imidazole alkaloid plasmid conjugation inhibitor from Lepidium sativum

Phytochemical investigation of the methanolic extract of Lepidium sativum seeds led to the isolation of a new compound, named 2-(3-(3-((1H-imidazol-2-yl)methyl)-5-methoxyphenoxy)benzyl)-1H-imidazole and given the trivial name Lepidine AK (1), along with three known compounds; Lepidine E (2), Lepidine B (3) and 2-(3-(2-((1H-imidazol-2-yl)methyl)-6-methoxyphenoxy)benzyl)-1H-imidazole (4). The structures were elucidated based on NMR spectroscopy, UV, IR and high-resolution electrospray ionization mass spectrometry. The isolated compounds were tested for bacterial conjugation inhibition. Lepidine AK (1, 100?μg/mL) reduced the conjugal transfer of the IncI₂ plasmid TP114 to 44.7?±?3.5% but interestingly promoted the conjugation of the IncN plasmid pKM101 to greater than 120%.     

A concise and divergent approach to radicamine B and hyacinthacine A3 based on a step-economic transformation

Based on our recently developed step-economic methodology of reductive alkylation of lactams/amides, we have developed a two-step synthesis of azasugar radicamine B (2a) and a four-step synthesis of azasugar hyacinthacine A₃ (5) from the common chiral building block 12. Hantzsch ester (HEH) was used as a milder hydride donor in the one-pot stereoselective reductive alkylation of lactam 12. The Wacker oxidation of fully substituted pyrrolidine derivative 2,5-trans-17 led to the synthesis of hyacinthacine A₃ (5). Compound 2,5-trans-17 could also serve as a plausible key intermediate for the synthesis of broussonetine sub-class of azasugars.     

Nucleoside and oligonucleotide pyrene conjugates with 1,2,3-triazolyl or ethynyl linkers: synthesis,duplex stability,and fluorescence changes generated by the DNA-dye connector

Fluorescent nucleosides and oligonucleotides functionalized with pyrene were synthesized using ‘click’ chemistry or the Sonogashira cross-coupling reaction. The dye was connected to position-7 of 7-deaza-2′-deoxyguanosine or to the 2′-deoxyribofuranose moiety. Four different DNA-dye connectors with 1,2,3-triazolyl residues or triple bonds were constructed. Phosphoramidites of the pyrene conjugates (9, 14, 25) were prepared and used in solid-phase synthesis. Short linkers (2, 4) destabilize DNA, while long linkers (1) increased duplex stability. Nucleosides and oligonucleotides with single dye incorporations show linker dependent fluorescence. Linker dependent excimer emission with pyrenes in proximal positions was also observed. A ‘superchromophore’ formed by the 7-deaza-2′-deoxyguanosine ethynylpyrene conjugate shows strong red shifted fluorescence emission at 495 nm.     

Novel methodology for the preparation and purification of oligonucleotides incorporating phosphorothiolate termini

A novel phosphoramidite; N,N-diisopropylamino-2-cyanoethyl-ortho-methylbenzylphosphoramidite 1, was prepared. The reaction of 1 with DMTrT and subsequent derivatisation of the phosphite triester product under solution-phase, Michaelis-Arbuzov conditions was investigated. Coupling of 1 with the terminal hydroxyl groups of support-bound oligodeoxyribonucleotides and subsequent reaction with an activated disulfide yielded oligonucleotides bearing a terminal, phosphorothiolate-linked, lipophilic moiety. The oligomers were readily purified using RP-HPLC. Silver(I)-mediated cleavage of the phosphorothiolate linkage and desalting of the oligonucleotides were performed readily in one step to yield cleanly the corresponding phosphate monester-terminated oligomers.     

Formal enantioselective synthesis of (+)-vincamine. The first enantioselective route to (+)-3,14-epivincamine and its enantiomer

A formal synthesis of (+)-vincamine (1) from (S)-(+)-2-ethyl-2-(2-methoxycarbonylethyl) cyclopentanone (6a) is described. This intermediate had previously been obtained by our research group in 90% ee through d'Angelo's deracemizing alkylation of the chiral imine 7, easily prepared from (R)-(+)-α-methylbenzylamine and 2-ethyl cyclopentanone with methyl acrylate. A potencial advanced intermediate for the synthesis of (+)-4, an epimer of (+)-1 at positions C-3 and C-14, has also been prepared from 6a.     

Total synthesis of diaportheone A

Diaportheone A (1), a chromone natural product was previously isolated from the endophytic fungi Diaporthe sp. P 133. Its structure was established by spectroscopic methods, however, its absolute configuration remained undefined. This study dealt on the total synthesis of diaportheone A (1) utilizing the cyclization and in situ thermal syn-elimination of a β-ketosulfoxide. The C-1R absolute configuration of the natural product was established by X-ray crystallography of the synthetic diaportheone A (1) (>99%?ee) and comparison with the optical rotation.     

Synthetic studies toward bicyclic endoperoxides presenting polar side chains

We developed a synthetic strategy for the preparation of tetrahydrofuro[2,3-c][1,2]dioxane and 2,3,8-trioxa[3,3,1]nonanes bearing polar functional groups at C3 and C4, respectively. The synthetic strategy has been applied to the synthesis of 2,3,8-trioxa[3,3,1]nonanes bearing various amides and amines at C3 useful for structure-activity relationships investigation as antiplasmodial compounds. The synthesis of 1 and the reaction conditions identified for its conversion to amides and amines could pose the basis for the use of this class of endoperoxides also in conjugation with other drugs for polypharmacology approaches.