Cycloaddition Chemistry Research Articles

Cascade oxime formation, cyclization to a nitrone, and intermolecular dipolar cycloaddition.

Simple haloaldehydes, including enolisable aldehydes, were found to be suitable for the formation of cyclic products by cascade (domino) condensation, cyclisation, dipolar cycloaddition chemistry. This multi-component reaction approach to heterocyclic compounds was explored by using hydroxylamine, a selection of aldehydes, and a selection of activated dipolarophiles. Initial condensation gives intermediate oximes that undergo cyclisation with displacement of halide to give intermediate nitrones; these nitrones undergo in situ intermolecular dipolar cycloaddition reactions to give isoxazolidines. The cycloadducts from using dimethyl fumarate were treated with zinc/acetic acid to give lactam products and this provides an easy way to prepare pyrrolizinones, indolizinones, and pyrrolo[2,1-a]isoquinolinones. The chemistry is illustrated with a very short synthesis of the pyrrolizidine alkaloid macronecine and a formal synthesis of petasinecine.

Boron difluoride formazanate copolymers with 9,9-di-n-hexylfluorene prepared by copper-catalyzed alkyne–azide cycloaddition chemistry

The synthesis and characterization of copolymers with promising light-harvesting properties and closely related model compounds based on boron difluoride formazanate and 9,9-di-n-hexylfluorene units are described.

Cycloadditions for Studying Nucleic Acids.

Cycloaddition reactions for site-specific or global modification of nucleic acids have enabled the preparation of a plethora of previously inaccessible DNA and RNA constructs for structural and functional studies on naturally occurring nucleic acids, the assembly of nucleic acid nanostructures, therapeutic applications, and recently, the development of novel aptamers. In this chapter, recent progress in nucleic acid functionalization via a range of different cycloaddition (click) chemistries is presented. At first, cycloaddition/click chemistries already used for modifying nucleic acids are summarized, ranging from the well-established copper(I)-catalyzed alkyne-azide cycloaddition reaction to copper free methods, such as the strain-promoted azide-alkyne cycloaddition, tetrazole-based photoclick chemistry and the inverse electron demand Diels-Alder cycloaddition reaction between strained alkenes and tetrazine derivatives. The subsequent sections contain selected applications of nucleic acid functionalization via click chemistry; in particular, site-specific enzymatic labeling in vitro, either via DNA and RNA recognizing enzymes or by introducing unnatural base pairs modified for click reactions. Further sections report recent progress in metabolic labeling and fluorescent detection of DNA and RNA synthesis in vivo, click nucleic acid ligation, click chemistry in nanostructure assembly and click-SELEX as a novel method for the selection of aptamers.

Synthesis of a Liposomal MUC1 Glycopeptide-Based Immunotherapeutic and Evaluation of the Effect of l-Rhamnose Targeting on Cellular Immune Responses.

Generation of a CD8(+) response to extracellular antigen requires processing of the antigen by antigen presenting cells (APC) and cross-presentation to CD8(+) T cell receptors via MHC class I molecules. Cross-presentation is facilitated by efficient antigen uptake followed by immune-complex-mediated maturation of the APCs. We hypothesize that improved antigen uptake of a glycopeptide sequence containing a CD8(+) T cell epitope could be achieved by delivering it on a liposome surface decorated with an immune complex-targeting ligand, an l-Rhamnose (Rha) epitope. We synthesized a 20-amino-acid glycopeptide TSAPDT(GalNAc)RPAPGSTAPPAHGV from the variable number tandem repeat region of the tumor marker MUC1 containing an N-terminal azido moiety and a tumor-associated α-N-acetyl galactosamine (GalNAc) at the immunogenic DTR motif. The MUC1 antigen was attached to Pam3Cys, a Toll-like receptor-2 ligand via copper(I)-catalyzed azido-alkyne cycloaddition (CuAAc) chemistry. The Rha-decorated liposomal Pam3Cys-MUC1-Tn 4 vaccine was evaluated in groups of C57BL/6 mice. Some groups were previously immunized to generate anti-Rha antibodies. Anti-Rha antibody expressing mice that received the Rha liposomal vaccine showed higher cellular immunogenicity compared to the control group while maintaining a strong humoral response.

Menthols as Chiral Auxiliaries for Asymmetric Cycloadditive Oligomerization: Syntheses and Studies of β-Proline Hexamers

To produce a novel class of structurally ordered poly-β-prolines, an emergent method for synthesizing chiral β-peptide molecular frameworks was developed based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Functionalized short β-peptides with up to six monomeric residues were efficiently synthesized in homochiral forms using a cycloadditive oligomerization approach. X-ray, NMR, and CD structural analyses of the novel β-peptides revealed secondary structure features that were generated primarily by Z/E-β-peptide bond isomerism. Anticancer in cellulo activity of the new β-peptides toward hormone-refractory prostate cancer cells was observed and was dependent on the absolute configuration of the stereogenic centers and the chain length of the β-proline oligomers.

Genetically Encoded Azide Containing Amino Acid in Mammalian Cells Enables Site-Specific Antibody-Drug Conjugates Using Click Cycloaddition Chemistry.

Antibody-drug conjugates (ADC) have emerged as potent antitumor drugs that provide increased efficacy, specificity, and tolerability over chemotherapy for the treatment of cancer. ADCs generated by targeting cysteines and lysines on the antibody have shown efficacy, but these products are heterogeneous, and instability may limit their dosing. Here, a novel technology is described that enables site-specific conjugation of toxins to antibodies using chemistry to produce homogeneous, potent, and highly stable conjugates. We have developed a cell-based mammalian expression system capable of site-specific integration of a non-natural amino acid containing an azide moiety. The azide group enables click cycloaddition chemistry that generates a stable heterocyclic triazole linkage. Antibodies to Her2/neu were expressed to contain N6-((2-azidoethoxy)carbonyl)-l-lysine at four different positions. Each site allowed over 95% conjugation efficacy with the toxins auristatin F or a pyrrolobenzodiazepine (PBD) dimer to generate ADCs with a drug to antibody ratio of >1.9. The ADCs were potent and specific in in vitro cytotoxicity assays. An anti Her2/neu conjugate demonstrated stability in vivo and a PBD containing ADC showed potent efficacy in a mouse tumor xenograph model. This technology was extended to generate fully functional ADCs with four toxins per antibody. The high stability of the azide-alkyne linkage, combined with the site-specific nature of the expression system, provides a means for the generation of ADCs with optimized pharmacokinetic, biological, and biophysical properties.

Toward Anisotropic Hybrid Materials: Directional Crystallization of Amphiphilic Polyoxazoline-Based Triblock Terpolymers.

We present the design and synthesis of a linear ABC triblock terpolymer for the bottom-up synthesis of anisotropic organic/inorganic hybrid materials: polyethylene-block-poly(2-(4-(tert-butoxycarbonyl)amino)butyl-2-oxazoline)-block-poly(2-iso-propyl-2-oxazoline) (PE-b-PBocAmOx-b-PiPrOx). The synthesis was realized via the covalent linkage of azide-functionalized polyethylene and alkyne functionalized poly(2-alkyl-2-oxazoline) (POx)-based diblock copolymers exploiting copper-catalyzed azide-alkyne cycloaddition (CuAAC) chemistry. After purification of the resulting triblock terpolymer, the middle block was deprotected, resulting in a primary amine in the side chain. In the next step, solution self-assembly into core-shell-corona micelles in aqueous solution was investigated by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Subsequent directional crystallization of the corona-forming block, poly(2-iso-propyl-2-oxazoline), led to the formation of anisotropic superstructures as demonstrated by electron microscopy (SEM and TEM). We present hypotheses concerning the aggregation mechanism as well as first promising results regarding the selective loading of individual domains within such anisotropic nanostructures with metal nanoparticles (Au, Fe3O4).

Water Processable Polythiophene Nanowires by Photo-Cross-Linking and Click-Functionalization

Replacing or minimizing the use of halogenated organic solvents in the processing and manufacturing of conjugated polymer-based organic electronics has emerged as an important issue due to concerns regarding toxicity, environmental impact, and high cost. To date, however, the processing of well-ordered conjugated polymer nanostructures has been difficult to achieve using environmentally benign solvents. In this work, we report the development of water and alcohol processable nanowires (NWs) with well-defined crystalline nanostructure based on the solution assembly of azide functionalized poly(3-hexylthiophene) (P3HT-azide) and subsequent photo-cross-linking and functionalization of these NWs. The solution-assembled P3HT-azide NWs were successfully cross-linked by exposure to UV light, yielding good thermal and chemical stability. Residual azide units on the photo-cross-linked NWs were then functionalized with alkyne terminated polyethylene glycol (PEG-alkyne) using copper catalyzed azide-alkyne cycloaddition chemistry. PEG functionalization of the cross-linked P3HT-azide NWs allowed for stable dispersion in alcohols and water, while maintaining well-ordered NW structures with electronic properties suitable for the fabrication of organic field effect transistors (OFETs).

Magnetic and dendritic catalysts.

The recovery and reuse of catalysts is a major challenge in the development of sustainable chemical processes. Two methods at the frontier between homogeneous and heterogeneous catalysis have recently emerged for addressing this problem: loading the catalyst onto a dendrimer or onto a magnetic nanoparticle. In this Account, we describe representative examples of these two methods, primarily from our research group, and compare them. We then describe new chemistry that combines the benefits of these two methods of catalysis. Classic dendritic catalysis has involved either attaching the catalyst covalently at the branch termini or within the dendrimer core. We have used chelating pyridyltriazole ligands to insolubilize catalysts at the termini of dendrimers, providing an efficient, recyclable heterogeneous catalysts. With the addition of dendritic unimolecular micelles olefin metathesis reactions catalyzed by commercial Grubbs-type ruthenium-benzylidene complexes in water required unusually low amounts of catalyst. When such dendritic micelles include intradendritic ligands, both the micellar effect and ligand acceleration promote faster catalysis in water. With these types of catalysts, we could carry out azide alkyne cycloaddition ("click") chemistry with only ppm amounts of CuSO4·5H2O and sodium ascorbate under ambient conditions. Alternatively we can attach catalysts to the surface of superparamagnetic iron oxide nanoparticles (SPIONs), essentially magnetite (Fe3O4) or maghemite (γ-Fe2O3), offering the opportunity to recover the catalysts using magnets. Taking advantage of the merits of both of these strategies, we and others have developed a new generation of recyclable catalysts: dendritic magnetically recoverable catalysts. In particular, some of our catalysts with a γ-Fe2O3@SiO2 core and 1,2,3-triazole tethers and loaded with Pd nanoparticles generate strong positive dendritic effects with respect to ligand loading, catalyst loading, catalytic activity and recyclability. In other words, the dendritic catalysts were more efficient and more stable than their nondendritic γ-Fe2O3@SiO2 analogues. The bulk at the dendritic periphery helps to localize the metal nanoparticles at the SPION core surface, which confers these advantages. We could also use sonification as a remarkably simple and efficient method to impregnate the SPIONs with dendrimer-encapsulated PdNPs. Catalysis within the hydrophobic dendrimer pockets that include ligands leads to rapid turnover with or without a γ-Fe2O3@SiO2 core. In addition, catalytically active metal nanoparticles are more robust when they are loaded onto the surface of a γ-Fe2O3@SiO2 dendritic core. Herein, we illustrate this chemistry with examples including olefin metathesis, click chemistry, cross carbon-carbon bond forming reactions, and selective alcohol oxidation.

New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition.

The ubiD/ubiX or the homologous fdc/pad genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone biosynthesis1–3 or microbial biodegradation of aromatic compounds4–6 respectively. Despite biochemical studies on individual gene products, the composition and co-factor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear7–9. We show Fdc is solely responsible for (de)carboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesised by the associated UbiX/Pad10. Atomic resolution crystal structures reveal two distinct isomers of the oxidized cofactor can be observed: an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with drastically altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor-cofactor adduct suggests 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. While 1,3-dipolar cycloaddition is commonly used in organic chemistry11–12, we propose this presents the first example of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.

Biochemistry: Unexpected role for vitamin B2.

An enzyme has been found that alters the molecular structure of vitamin B2, adding a fourth ring to its existing three-ring system. The product catalyses new types of chemistry in concert with certain other enzymes. See Letters p.497 & p.502 A pair of manuscripts published this week [in this issue of Nature] describes detailed studies of the structure and mechanism of the enzymes UbiD and UbiX that together are responsible for non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone biosynthesis and microbial biodegradation of aromatic compounds. Mark White et al. show that UbiX is a flavin prenyltransferase, catalysing the covalent attachment of a fourth ring (the dimethylallyl group) to the N5 and C6 atoms of the three-ring riboflavin system. The unusual flavin-derived cofactor synthesized by UbiX is then used by UbiD, a decarboxylase, in the next step of the ubiquinone biosynthetic pathway. Karl Payne et al. show that the Fdc protein from Aspergillus niger (which is homologous to UbiD) uses 1,3-dipolar cycloaddition chemistry to catalyse the reversible decarboxylation of aromatic carboxylic acids. This is the first example of an enzyme-catalysed 1,3-dipolar cycloaddition reaction.

Encoded Library Synthesis Using Chemical Ligation and the Discovery of sEH Inhibitors from a 334-Million Member Library.

A chemical ligation method for construction of DNA-encoded small-molecule libraries has been developed. Taking advantage of the ability of the Klenow fragment of DNA polymerase to accept templates with triazole linkages in place of phosphodiesters, we have designed a strategy for chemically ligating oligonucleotide tags using cycloaddition chemistry. We have utilized this strategy in the construction and selection of a small molecule library, and successfully identified inhibitors of the enzyme soluble epoxide hydrolase.

Cycloadditions in modern polymer chemistry.

Synthetic polymer chemistry has undergone two major developments in the last two decades. About 20 years ago, reversible-deactivation radical polymerization processes started to give access to a wide range of polymeric architectures made from an almost infinite reservoir of functional building blocks. A few years later, the concept of click chemistry revolutionized the way polymer chemists approached synthetic routes. Among the few reactions that could qualify as click, the copper-catalyzed azide-alkyne cycloaddition (CuAAC) initially stood out. Soon, many old and new reactions, including cycloadditions, would further enrich the synthetic macromolecular chemistry toolbox. Whether click or not, cycloadditions are in any case powerful tools for designing polymeric materials in a modular fashion, with a high level of functionality and, sometimes, responsiveness. Here, we wish to describe cycloaddition methodologies that have been reported in the last 10 years in the context of macromolecular engineering, with a focus on those developed in our laboratories. The overarching structure of this Account is based on the three most commonly encountered cycloaddition subclasses in organic and macromolecular chemistry: 1,3-dipolar cycloadditions, (hetero-)Diels-Alder cycloadditions ((H)DAC), and [2+2] cycloadditions. Our goal is to briefly describe the relevant reaction conditions, the advantages and disadvantages, and the realized polymer applications. Furthermore, the orthogonality of most of these reactions is highlighted because it has proven highly beneficial for generating unique, multifunctional polymers in a one-pot reaction. The overview on 1,3-dipolar cycloadditions is mostly centered on the application of CuAAC as the most travelled route, by far. Besides illustrating the capacity of CuAAC to generate complex polymeric architectures, alternative 1,3-dipolar cycloadditions operating without the need for a catalyst are described. In the area of (H)DA cycloadditions, beyond the popular maleimide/furan couple, we present chemistries based on more reactive species, such as cyclopentadienyl or thiocarbonylthio moieties, particularly stressing the reversibility of these systems. In these two greater families, as well as in the last section on [2+2] cycloadditions, we highlight phototriggered chemistries as a powerful tool for spatially and temporally controlled materials synthesis. Clearly, cycloaddition chemistry already has and will continue to transform the field of polymer chemistry in the years to come. Applying this chemistry enables better control over polymer composition, the development of more complicated polymer architectures, the simplification of polymer library production, and the discovery of novel applications for all of these new polymers.

Reactivity of Boryl- and Silyl-Substituted Carbenoids toward Alkynes: Insertion and Cycloaddition Chemistry

Three modes of reactivity of phenyl-substituted alkynes toward acyclic tetrelenes are reported, with reaction pathways found to be dependent not only on the nature of the group 14 element but also on the supporting ligand set. Systems featuring Sn–B or Ge–B bonds undergo insertion chemistry, forming borane-appended (vinyl)SnII and GeII species. With a bis(amido)stannylene, phenylacetylene acts as a protic acid, generating a SnII acetylide with a unique bridged structure. Reactivity toward a more strongly reducing SiII system is dominated by the possibility of accessing SiIV via [2 + 1] cycloaddition chemistry.

Multiplex imaging and cellular target identification of kinase inhibitors via an affinity-based proteome profiling approach.

MLN8237 is a highly potent and presumably selective inhibitor of Aurora kinase A (AKA) and has shown promising antitumor activities. Like other kinase inhibitors which target the ATP-binding site of kinases, MLN8237 might be expected to have potential cellular off-targets. Herein, we report the first photoaffinity-based, small molecule AKA probe capable of both live-cell imaging of AKA activities and in situ proteome profiling of potential off-targets of MLN8237 (including AKA-associating proteins). By using two mutually compatible, bioorthogonal reactions (copper-catalyzed azide-alkyne cycloaddition chemistry and TCO-tetrazine ligation), we demostrate small molecule-based multiplex bioimaging for simultaneous in situ monitoring of two important cell-cycle regulating kinases (AKA and CDK1). A broad range of proteins, as potential off-targets of MLN8237 and AKA's-interacting partners, is subsequently identified by affinity-based proteome profiling coupled with large-scale LC-MS/MS analysis. From these studies, we discover novel AKA interactions which were further validated by cell-based immunoprecipitation (IP) experiments.

Synthesis of (Z)-fluoroallyl azides through aluminium-mediated defluorinative functionalization reactions

The reaction of difluorohomoallyl alcohols with Me2AlCl in CH2Cl2 selectively gave (Z)-fluoroallyl chlorides via SN2′ type defluorinative chlorination. These chlorides were easily converted to the corresponding (Z)-fluoroallyl azides by the sequential nucleophilic azidation reaction using NaN3. Direct defluorinative azidation of the difluorohomoallyl alcohols was also achieved by treating with Me3SiN3 in the presence of Al(Oi-Pr)3. Fluoroallyl azides thus obtained successfully applied to the Huisgen 1,3-dipolar cycloaddition chemistry.

Pyrrolidine-functionalized fluorine-containing graphene sheets

Pyrrolidine-functionalized fluorine-containing graphene sheets with high stability were prepared through the functionalization of graphite via 1,3-dipolar cycloaddition chemistry followed by exfoliation in various solvents.

Synthesis, self-assembly, and degradation of amphiphilic triblock copolymers with fully photodegradable hydrophobic blocks

The development of stimuli-responsive materials is of significant interest for many applications including drug delivery, medical imaging, sensors, and microfluidic devices. Among the available stimuli, light is particularly attractive as it can be applied with high spatial and temporal resolution. We describe here the synthesis of amphiphilic triblock copolymers composed of poly(ethylene glycol) and a hydrophobic block containing o-nitrobenzyl esters throughout the backbone using copper-catalyzed azide–alkyne cycloaddition chemistry. These materials were designed to have a high weight fraction of the hydrophobic block to favour nonmicellar aggregates. The self-assembly in water was studied using nanoprecipitation and the resulting assemblies were characterized by dynamic light scattering and transmission electron microscopy. Under optimized conditions, it was possible to prepare polymer vesicles, commonly referred to as polymersomes, with diameters of approximately 100 nm. The degradation of these materials in response to UV light was studied by spectroscopy, light scattering, and electron microscopy, demonstrating that the vesicles were broken down. These results suggest the potential of these materials for applications such as encapsulation and release.

Simple plate-based, parallel synthesis of disulfide fragments using the CuAAC click reaction.

Disulfide exchange screening is a site-directed approach to fragment-based lead discovery that requires a bespoke library of disulfide-containing fragments. Previously, we described a simple one-pot, two-step synthesis of disulfide fragments from amine- or acid-bearing starting materials. Here, we describe the synthesis of disulfide fragments that bear a 1,4-substituted-1,2,3-triazole linkage between disulfide and molecular diversity element. This work establishes the compatibility of copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) chemistry with a one-pot, two-step reaction sequence that can be readily parallelized. We performed 96 reactions in a single deep-well microtiter plate, employing 48 alkynes and two different azide linker reagents. From this effort, a total of 81 triazole-containing disulfide fragments were obtained in useful isolated yields. Thus, CuAAC chemistry offers an experimentally convenient method to rapidly prepare disulfide fragments that are structurally distinct from fragments accessed via amide, sulfonamide, or isocyanate chemistries.

Activated Cyclopropanes: A Remarkable Breadth of Recent Chemistry

The reactions of cyclopropanes activated by electron-withdrawing groups and electron-donating groups – donor–acceptor (DA) cyclopropanes – and with alkenyl or alkylidene substituents has been an area of recent intense research activity. This Cluster contains contributions from many of the leading research groups in this area, and provides a concise introduction to the rich ring-opening, ring-expansion, dimerization, and cycloaddition chemistry of these compounds.