Tandem oligonucleotide synthesis on solid-phase supports for the production of multiple oligonucleotides

More than one oligonucleotide can be synthesized at a time by linking multiple oligonucleotides end-to-end in a tandem manner on the surface of a solid-phase support. The 5'-terminal hydroxyl position of one oligonucleotide serves as the starting point for the next oligonucleotide synthesis. The two oligonucleotides are linked via a cleavable 3'-O-hydroquinone-O,O'-diacetic acid linker arm (Q-linker). The Q-linker is rapidly and efficiently coupled to the 5'-OH position of immobilized oligonucleotides using HATU, HBTU, or HCTU in the presence of 1 equiv of DMAP. This protocol avoids introduction of phosphate linkages on either the 3'- or 5'-end of oligonucleotides. A single NH(4)OH cleavage step can simultaneously release the products from the surface of the support and each other to produce free 5'- and 3'-hydroxyl termini. Selective cleavage of one oligonucleotide out of two sequences has also been accomplished via a combination of succinyl and Q-linker linker arms. Tandem synthesis of multiple oligonucleotides is useful for producing sets of primers for PCR, DNA sequencing, and other diagnostic applications as well as double-stranded oligonucleotides. Tandem synthesis of the same sequence multiple times increases the yield of material from any single synthesis column for maximum economy in large-scale synthesis. This method can also be combined with reusable solid-phase supports to further reduce the cost of oligonucleotide production.     

Total solid-phase synthesis of the azathiocoraline class of symmetric bicyclic peptides

Thiocoraline is a potent antitumor agent isolated from the marine organism Micromonospora sp. This symmetric bicyclic depsipeptide binds the minor groove of DNA. Here we report two solid-phase strategies for the syntheses of azathiocoraline and its analogues. The thioester linkage was replaced by an amide bond to improve the compound's pharmacokinetic properties. The first strategy is based on a convergent (4+4) approach, whilst the second is a stepwise synthesis, cyclizations in both approaches occurring on the solid support. These two strategies were designed to overcome problems caused by the presence of consecutive noncommercial N-methyl amino acids, to avoid epimerization during cyclization and/or fragment condensation, and to form the disulfide bridge under solid-phase conditions. The heterocyclic moiety was added in the last step of the synthesis to assist the preparation of libraries of new compounds with potential therapeutic applications.     

Ferrocene-modified pyrimidine nucleosides: synthesis, structure and electrochemistry

This paper reports syntheses, crystal structures and electrochemical results for two ferrocene(Fc)-modified pyrimidine nucleosides that could potentially be used for investigating electron transfer in DNA. Fc was directly attached to the 5-position of deoxyuridine and deoxycytidine via the Stille coupling reaction. Fc-modified uridine was incorporated into DNA trinucleotides with standard solid-phase synthesis. The structures of corresponding detritylated compounds were determined by single-crystal X-ray analysis. Electrochemical investigations of all compounds by cyclic voltammetry revealed reversible redox processes.     

Collective Total Synthesis of 4-Azafluorenone Alkaloids

4-Azafluorenones are typically obtained by acid-mediated cyclization of 2-arylnicotinates. However, this approach fails to give 5-oxygenated 4-azafluorenones due to lactonization of 2-(2-alkoxy)phenylnicotinate intermediates. Herein, we report two modifications of established approaches to 4-azafluorenone synthesis that, either in combination or by themselves, enable the flexible preparation of 4-azafluorenones with diverse oxygenation patterns in the benzenoid ring. Undesired lactonization was circumvented via tert-butyl hydroperoxide (TBHP)-mediated radical cyclization of 2-aryl-3-(hydroxymethyl)pyridines. In the absence of suitable protecting groups for phenolic intermediates, bromide substituents were regioselectively introduced as latent hydroxy groups and later converted under palladium catalysis. We present the first total syntheses of five 4-azafluorenone alkaloids muniranine, darienine, 5,8-dimethoxy-7-hydroxyonychine, 5,6,7,8-tetramethoxyonychine, and 6,8-dihydroxy-7-methoxyonychine in addition to new total syntheses of six 4-azafluorenone alkaloids and one related pyridocoumarin alkaloid.     

Synthesis and characterization of an isocyanate functionalized polyhedral oligosilsesquioxane and the subsequent formation of an organic-inorganic hybrid polyurethane

Organic-inorganic hybrids are an important class of new materials that offer improved thermal and mechanical properties over normal polymers. They may be produced by either the sol-gel route or through the use of inorganic compounds possessing reactive functional groups. Polyhedral oligosilsesquioxanes (POSS) are completely defined molecules of nanoscale dimensions that may be functionalized with reactive groups suitable for the synthesis of new organic-inorganic hybrids. Here we report the synthesis and characterization of a novel POSS possessing eight isocyanate groups via the hydrosilylation of octakis(hydridodimethylsiloxy)octasilsesquioxane (Q8M8H) and m-isopropenyl-alpha,alpha'-dimethylbenzyl isocyanate (m-TMI). The suitability of this new macromer to the synthesis of a organic-hybrids has been explored by forming a new type of highly cross-linked polyurethane elastomer via reaction of the macromer with poly(ethylene glycol) using dibutyltin dilaurate catalyst.     

The alpha-helical peptide nucleic acid concept: merger of peptide secondary structure and codified nucleic acid recognition

A novel platform for nucleic acid recognition that integrates the alpha-helix secondary structure of peptides with the codified base-pairing capability of nucleic acids is reported. The resulting alpha-helical peptide nucleic acids (alpha PNAs) are composed of a repeating tetrapeptidyl unit, aa(1)-aa(2)-aa(3)-Ser(B), where aa(1) through aa(3) represent generic ancillary amino acids and B = nucleobases linked to Ser via a methylene bridge. Effective syntheses of constituent Fmoc-protected nucleoamino acids (Fmoc-Ser(B)-OH, where B = thymine, cytosine, and uracil) are described along with a protocol for the solid-phase synthesis of 21mer alpha PNAs containing five such nucleobases. By varying the ancillary amino acids, two distinct classes of alpha PNAs were constructed, having a net charge of -1 or +6, respectively, at physiological pH. The modular nature of the alpha PNA platform was illustrated by the synthesis of symmetrical disulfide-bridged alpha PNA dimers containing 10 nucleobases. Hybridization of these alpha PNAs with ssDNA has been examined by thermal denaturation, gel electrophoresis, and circular dichroism (CD) and the data indicated that alpha PNA binds to ssDNA in a cooperative manner with high affinity and sequence specificity. In general, b2 alpha PNAs bind faster and more strongly with ssDNA than do the corresponding b1 alpha PNAs. Parallel alpha PNA-DNA complexes are more stable than their antiparallel counterparts. CD studies also revealed that the hybridization event involves the folding of both species into their helical conformations. Finally, NMR experiments provided conclusive evidence of Watson-Crick base pairing in alpha PNA-ssDNA hybrids.     

Recent progress on DNA block copolymer

Organic polymers are combined with DNA resulting DNA block copolymers (DBCs) that can simultaneously show the properties of the polymer and DNA. We will discuss some examples of recent developments in the syntheses, structure manipulations, and applications of DBCs.     

4-Alkoxy-2-hydroxybenzaldehyde (AHB): a versatile aldehyde linker for solid-phase synthesis of C-terminal modified peptides and peptidomimetics

[reaction: see text] A new and versatile 4-alkoxy-2-hydroxybenzaldehyde (AHB) linker for solid-phase syntheses is described. Acylation of the polymer-bound secondary amine obtained from reductive amination of the aldehyde in the AHB linker showed good reactivity. Following acylation of the phenolic hydroxyl group, the resulting carboxamide resin was stable to treatment with 95% TFA. The O-acyl functional group was removed with 20% piperidine and the desired compound was cleaved from the resin by TFA treatment.     

O-selectivity and utility of phosphorylation mediated by phosphite triester intermediates in the N-unprotected phosphoramidite method

Previously, O-selective phosphorylation on polymer supports in the N-unprotected phosphoramidite method could not be carried out because the amino groups of dA and dC have high reactivity toward tervalent phosphorus(III)-type phosphitylating reagents. In this paper, we developed a new coupling strategy named the "activated phosphite method" in which the phosphitylation is mediated by phosphite triester intermediates 1. Application of 1-hydroxybenzotriazole as the promoter to the solid-phase synthesis resulted in excellent O-selectivity of more than 99.7%. This O-selectivity was explained by the frontier molecular orbital interactions between the reactive intermediates and the nucleophiles such as the amino or hydroxyl groups of nucleosides. Furthermore, longer oligonucleotides were synthesized not only by a manual operation but also by a DNA synthesizer. The utility of our new method was demonstrated by the successful synthesis of a base-labile modified oligodeoxyribonucleotide having 4-N-acetyldeoxycytidine residues. Finally, DNA 20-mers containing dA or dC could be synthesized in good yields by use of a combined reagent of 6-trifluoromethyl-1-hydroxybenzotriazole and benzimidazolium triflate.     

NiFe2O4 as a magnetically recoverable nanocatalyst for odourless C–S bond formation via the cleavage of C–O bond in the presence of S8 under mild and green conditions

We present green methodologies for one‐pot and odourless syntheses of unsymmetric and symmetric diaryl sulfides via C─O bond activation using NiFe₂O₄ magnetic nanoparticles as a reusable heterogeneous nanocatalyst. The synthesis of unsymmetric sulfides is performed using the cross‐coupling reaction of phenolic esters such as acetates, triflates and tosylates with arylboronic acid/S₈ or triphenyltin chloride/S₈ as thiolating agents in the presence of base and NiFe₂O₄ magnetic nanoparticles as a catalyst in poly(ethylene glycol) as solvent at 60–85°C. Also, the synthesis of symmetric diaryl sulfides from phenolic compounds using S₈ as the sulfur source and NiFe₂O₄ as catalyst in dimethylformamide at 120°C is described. Using these protocols, the syntheses of various unsymmetric and symmetric sulfides become easier than using the available protocols due to the use of a magnetically reusable bimetallic nanocatalyst and avoiding the use of thiols and aryl halides.     

Combinatorial synthesis of MUC1 glycopeptides: polymer blotting facilitates chemical and enzymatic synthesis of highly complicated mucin glycopeptides

The chemoselective polymer blotting method allows for rapid and efficient synthesis of glycopeptides based on a "catch and release" strategy between solid-phase and water-soluble polymer supports. We have developed a heterobifunctional linker sensitive to glutamic acid specific protease (BLase). The general procedure consists of five steps, namely (i) the solid-phase synthesis of glycopeptide containing BLase sensitive linker, (ii) subsequent deprotections and the release of the glycopeptide from the resin, (iii) chemoselective blotting of the glycopeptide intermediates in the presence of water-soluble polymers with oxylamino functional groups, (iv) sugar elongations using glycosyltransferases, and (v) the release of target glycopeptides from the polymer platform by selective BLase promoted hydrolysis. The combined use of the solid-phase chemical syntheses of peptides and the enzymatic syntheses of carbohydrates on water-soluble polymers would greatly contribute to the production of complicated glycopeptide libraries, thereby enhancing applicative research. We report here a high-throughput synthetic system for the various types of MUC1 glycopeptides exhibiting a variety of sugar moieties. It is our belief that this concept will become part of the entrenched repertoire for the synthesis of biologically important glycopeptides on the basis of glycosyltransferase reactions in automated and combinatorial syntheses.     

Innovative macromolecular syntheses via isocyanide multicomponent reactions

Isocyanide multicomponent reactions assemble more than two reaction components by exploiting the reactivity of the isocyanide carbon atom toward addition of electrophiles and nucleophiles. Reactions such as the Passerini three‐component and Ugi four‐component coupling reactions have a long and successful history in organic synthesis, which has only recently been explored in polymer chemistry. In a short time, this class of multicomponent reactions has been established as a viable method for the synthesis of linear polymers as well as more complex architectures such as miktoarm star polymers and dendrimers. This highlight discusses the recent accomplishments made with regard to innovative syntheses of polymers and dendrimers via the Passerini and Ugi reactions. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 3985–3991     

Solid-phase synthesis of chiral N-acylethylenediamines and their use as ligands for the asymmetric addition of alkylzinc and alkenylzinc reagents to aldehydes

A solid-phase procedure has been developed for the synthesis of chiral N-acylethylenediamine ligands. The ligands are obtained in good yield and purity, without the need for chromatography or other purification methods. Several new and previously reported ligands were prepared using this procedure. These compounds were examined as catalysts for the enantioselective addition of alkylzinc reagents to aldehydes. In all cases, the crude ligands from the solid-phase syntheses catalyzed the reactions with similar yields and stereoselectivities when compared to reactions using ligands that had been purified by standard methods. Preliminary studies were also performed with ligands 3a and 3f as catalysts for the addition of alkenylzinc reagents to aldehydes to give chiral allylic alcohols. Ligand 3f was found to catalyze this addition reaction in up to 76% ee.     

Organic Chemistry on Solid Supports

Until recently, repetitive solid-phase synthesis procedures were used predominantly for the preparation of oligomers such as peptides, oligosaccharides, peptoids, oligocarbamates, peptide vinylogues, oligomers of pyrrolin-4-one, peptide phosphates, and peptide nucleic acids. However, the oligomers thus produced have a limited range of possible backbone structures due to the restricted number of building blocks and synthetic techniques available. Biologically active compounds of this type are generally not suitable as therapeutic agents but can serve as lead structures for optimization. “Combinatorial organic synthesis” has been developed with the aim of obtaining low molecular weight compounds by pathways other than those of oligomer synthesis. This concept was first described in 1971 by Ugi.^[56f,g,59c] Combinatorial synthesis offers new strategies for preparing diverse molecules, which can then be screened to provide lead structures. Combinatorial chemistry is compatible with both solution-phase and solid-phase synthesis. Moreover, this approach is conducive to automation, as proven by recent successes in the synthesis of peptide libraries. These developments have led to a renaissance in solid-phase organic synthesis (SPOS), which has been in use since the 1970s. Fully automated combinatorial chemistry relies not only on the testing and optimization of known chemical reactions on solid supports, but also on the development of highly efficient techniques for simultaneous multiple syntheses. Almost all of the standard reactions in organic chemistry can be carried out using suitable supports, anchors, and protecting groups with all the advantages of solid-phase synthesis, which until now have been exploited only sporadically by synthetic organic chemists. Among the reported organic reactions developed on solid supports are Diels–Alder reactions, 1,3-dipolar cycloadditions, Wittig and Wittig–Horner reactions, Michael additions, oxidations, reductions, and Pd-catalyzed C? C bond formation. In this article we present a comprehensive review of the previously published solid-phase syntheses of nonpeptidic organic compounds.     

NHC‐Catalyzed Asymmetric Synthesis of Functionalized Succinimides from Enals and α‐Ketoamides

The efficient asymmetric synthesis of highly substituted succinimides from α,β‐unsaturated aldehydes and α‐ketoamides via NHC‐catalyzed [3+2] cycloaddition has been developed. The new scalable protocol significantly expands the utility of NHC catalysis for the synthesis of heterocycles and provides easy access to assemble a wide range of succinimides from simple starting materials.     

Soluble peptidyl phosphoranes for metal-free, stereoselective ligations in organic and aqueous solution

Protocols for solid-phase syntheses of soluble peptidyl phosphoranes are presented. Various supported phosphoranylidene acetates were prepared on Rink amide or via alkylation of trialkyl- and triarylphosphines with bromoacetyl Wang ester. C-Acylation was conducted racemization-free with activated Fmoc-amino acids, followed by SPPS (solid-phase peptide synthesis). Acidic conditions released decarboxylated peptidyl phosphoranes into solution. The protocol allowed for the electronic variation of peptidyl phosphoranes which were investigated in ligation reactions with azides in organic and aqueous solvents.     

Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography

The derivatization of nucleic acids with selenium is a new and highly promising approach to facilitate their three-dimensional structure determination by X-ray crystallography. Here, we report a comprehensive study on the chemical and enzymatic syntheses of RNAs containing 2'-methylseleno (2'-Se-methyl) nucleoside labels. Our approach includes the first synthesis of an appropriate purine nucleoside phosphoramidite building block. Most importantly, a substantially changed RNA solid-phase synthesis cycle, comprising treatment with threo-1,4-dimercapto-2,3-butanediol (DTT) after the oxidation step, is required for a reliable strand elongation. This novel operation allows for the chemical syntheses of multiple Se-labeled RNAs in sizes that can typically be achieved only for nonmodified RNAs. In combination with enzymatic ligation, biologically important RNA targets become accessible for crystallography. Exemplarily, this has been demonstrated for the Diels-Alder ribozyme and the add adenine riboswitch sequences. We point out that the approach documented here has been the chemical basis for the very recent structure determination of the Diels-Alder ribozyme which represents the first novel RNA fold that has been solved via its Se-derivatives.     

Spongipyran synthetic studies. Evolution of a scalable total synthesis of (+)-spongistatin 1

Three syntheses of the architecturally complex, cytotoxic marine macrolide (+)-spongistatin 1 (1) are reported. Highlights of the first-generation synthesis include: use of a dithiane multicomponent linchpin coupling tactic for construction of the AB and CD spiroketals, and their union via a highly selective Evans boron-mediated aldol reaction en route to an ABCD aldehyde; introduction of the C(44)-C(51) side chain via a Lewis acid-mediated ring opening of a glucal epoxide with an allylstannane to assemble the EF subunit; and final fragment union via Wittig coupling of the ABCD and EF subunits to form the C(28)-C(29) olefin, followed by regioselective Yamaguchi macrolactonization and global deprotection. The second- and third-generation syntheses, designed with the goal of accessing 1 g of (+)-spongistatin 1 (1), maintain both the first-generation strategy for the ABCD aldehyde and final fragment union, while incorporating two more efficient approaches for construction of the EF Wittig salt. The latter combine the original chelation-controlled dithiane union of the E- and F-ring progenitors with application of a highly efficient cyanohydrin alkylation to append the F-ring side chain, in conjunction with two independent tactics to access the F-ring pyran. The first F-ring synthesis showcases a Petasis-Ferrier union/rearrangement protocol to access tetrahydropyrans, permitting the preparation of 750 mg of the EF Wittig salt, which in turn was converted to 80 mg of (+)-spongistatin 1, while the second F-ring strategy, incorporates an organocatalytic aldol reaction as the key construct, permitting completion of 1.009 g of totally synthetic (+)-spongistatin 1 (1). A brief analysis of the three syntheses alongside our earlier synthesis of (+)-spongistatin 2 is also presented.     

Side-chain-anchored N(alpha)-Fmoc-Tyr-OPfp for bidirectional solid-phase synthesis

[reaction: see text] A mild resin-immobilization strategy employing a readily prepared trityl bromide resin for anchoring building blocks via a phenol group has been developed. With N(alpha)-Fmoc-Tyr-OPfp as a starter building block, it was possible to prepare asymmetrically substituted hybrids of spider- and wasp-type polyamine toxins using solid-phase peptide synthesis conditions.     

N,O-Benzylidene Acetal Dipeptides (NBDs) Enable the Synthesis of Difficult Peptides via a Kinked Backbone Strategy

Proteins with highly hydrophobic regions or aggregation-prone sequences are typically difficult targets for chemical synthesis at the current stage, as obtaining such type of peptides via solid-phase peptide synthesis requires sophisticated operations. Herein, we report N,O-benzylidene acetal dipeptides (NBDs) as robust and effective building blocks to allow the direct synthesis of difficult peptides and proteins via a kinked backbone strategy. The effectiveness and easy accessibility of NBDs have been well demonstrated in our chemical syntheses of various challenging peptides and proteins, including chemokine, therapeutic hormones, histone, and glycosylated erythropoietin.