Bioconjugatable Azo‐Based Dark‐Quencher Dyes: Synthesis and Application to Protease‐Activatable Far‐Red Fluorescent Probes

We describe the efficient synthesis and one‐step derivatization of novel, nonfluorescent azo dyes based on the Black Hole Quencher‐3 (BHQ‐3) scaffold. These dyes were equipped with various reactive and/or bioconjugatable groups (azido, α‐iodoacetyl, ketone, terminal alkyne, vicinal diol). The azido derivative was found to be highly reactive in the context of copper‐catalyzed azide–alkyne cycloaddition (CuAAC) reactions and allowed easy synthetic access to the first water‐soluble (sulfonated derivative) and aldehyde‐modified BHQ‐3 dyes, the direct preparation of which failed by means of conventional azo‐coupling reactions. The aldehyde‐ and α‐iodoacetyl‐containing fluorescence quenchers were readily conjugated to aminooxy‐ and cysteine‐containing peptides by the formation of a stable oxime or thioether linkage, respectively. Further fluorescent labeling of the resultant peptide conjugates with red‐ or far‐red‐emitting rhodamine or cyanine dyes through sequential and/or one‐pot bioconjugations, led to novel Förster resonance energy transfer (FRET) based probes suitable for the in vivo detection and imaging of urokinase plasminogen activator, a key protease in cancer invasion and metastasis.     

Direct Catalytic Asymmetric Aldol Reaction of an α‐Azido Amide

A direct aldol reaction of an α‐azido 7‐azaindolinylamide, promoted by a Cu‐based cooperative catalyst, is documented. Aromatic aldehydes bearing an ortho substituent exhibited diastereodivergency depending on the nature of the chiral ligands used. Smooth reactions with ynals highlighted the broad substrate scope. A vicinal azido alcohol unit in the product allowed direct access to the corresponding aziridine and facile hydrolysis of the 7‐azaindolinylamide moiety furnished enantioenriched β‐hydroxy‐α‐azido carboxylic acid derivatives.     

Theoretical Study on the Azido-cyclization of 3,6-Di(azido)-1,2,4,5-tetrazine

The reactions of azido‐cyclization in 3,6‐di(azido)‐1,2,4,5‐tetrazine were studied by B3LYP hybrid density functional method. The geometries of the reactants, transition states and products were optimized, and the conformation of the initial reactant was determined by IR spectra. In addition, the nucleus‐independent chemical shift (NICS) indices were used to discuss the aromaticity of the products. Moreover, solvent effects were investigated. Results show that the polar solvent DMSO can hardly influence the activation barriers of all the reaction paths; however, it can stabilize the products. Since the activation barriers of azido‐rotation are far less than that of the rate‐determining step (the cyclization of second azido), the products are most probably the mixtures of two isomers (DAT2c and DAT2c').     

Size‐matched alkyne‐conjugated cyanine fluorophores to identify differences in protein glycosylation

Currently, there are few methods to detect differences in posttranslational modifications (PTMs) in a specific manner from complex mixtures. Thus, we developed an approach that combines the sensitivity and specificity of click chemistry with the resolution capabilities of 2D‐DIGE. In “Click‐DIGE”, posttranslationally modified proteins are metabolically labeled with azido‐substrate analogs, then size‐ and charge‐matched alkyne‐Cy3 or alkyne‐Cy5 dyes are covalently attached to the azide of the PTM by click chemistry. The fluorescently‐tagged protein samples are then multiplexed for 2DE analysis. Whereas standard DIGE labels all proteins, Click‐DIGE focuses the analysis of protein differences to a targeted subset of posttranslationally modified proteins within a complex sample (i.e. specific labeling and analysis of azido glycoproteins within a cell lysate). Our data indicate that (i) Click‐DIGE specifically labels azido proteins, (ii) the resulting Cy‐protein conjugates are spectrally distinct, and (iii) the conjugates are size‐ and charge‐matched at the level of 2DE. We demonstrate the utility of this approach by detecting multiple differentially expressed glycoproteins between a mutant cell line defective in UDP‐galactose transport and the parental cell line. We anticipate that the diversity of azido substrates already available will enable Click‐DIGE to be compatible with analysis of a wide range of PTMs.     

Photochemical and Thermal Reactions of Azido‐oligopyridines: Diazepinones,a New Class of Metal‐Complex Ligands

Azido‐oligopyridines were prepared, and their photochemical reactions resulted in diazepinones linked to pyridine moieties. The thermal reactions of azido‐oligopyridines with triple bonds yielded 2H‐azirines directly attached to oligopyridines.     

Labeling Cell Surface GPIs and GPI‐Anchored Proteins through Metabolic Engineering with Artificial Inositol Derivatives

Glycosylphosphatidylinositol (GPI) anchoring of proteins to the cell surface is important for various biological processes, but GPI‐anchored proteins are difficult to study. An effective strategy was developed for the metabolic engineering of cell‐surface GPIs and GPI‐anchored proteins by using inositol derivatives carrying an azido group. The azide‐labeled GPIs and GPI‐anchored proteins were then tagged with biotin on live cells through a click reaction, which allows further elaboration with streptavidin‐conjugated dyes or other molecules. The strategy can be used to label GPI‐anchored proteins with various tags for biological studies.     

Chemoselective Staudinger‐Phosphite Reaction on the Azido Groups of 2,4,6‐Triazido‐3,5‐dibromopyridine

2,4,6‐Triazido‐3,5‐dibromopyridine reacts with an equimolar amount of triethyl phosphite in ether at room temperature chemoselectively on the γ‐azido group to form 2,6‐diazido‐3,5‐dibromo‐4‐triethoxyphosphoriminopyridine as a single product. The latter adds another molecule of triethyl phosphite to give a mixture of 6‐azido‐2,4‐bis(triethoxyphosphorimino)‐3,5‐dibromopyridine and its tetrazolo[1,5‐a]pyridine isomer, the acidic hydrolysis of which affords 6‐azido‐2,4‐bis(diethoxyphosphoramino)‐3,5‐dibromopyridine. The study shows that the Staudinger‐phosphite reactions with heterocyclic polyazides occur selectively on the most electron‐deficient azido groups, opening up new prospects for preparation of new polyfunctional heterocyclic compounds.     

Enantioselective Copper‐Catalyzed Intermolecular Amino‐ and Azidocyanation of Alkenes in a Radical Process

Asymmetric copper‐catalyzed intermolecular amino‐ and azidocyanation reactions of alkenes have been developed that proceed via a radical process in which a key benzylic radical intermediate is enantioselectively trapped by a chiral Box/Cu^II cyanide complex. A variety of enantiomerically enriched β‐amino/azido alkylnitriles were efficiently synthesized. The β‐azido alkylnitriles could be converted into a series of highly valuable optically active amine‐based building blocks and bioactive compounds.     

Clickable Periodic Mesoporous Organosilicas: Synthesis,Click Reactions,and Adsorption of Antibiotics

Pharmaceutical antibiotics are not easily removed from water by conventional water‐treatment technologies and have been recognized as new emerging pollutants. Herein, we report the synthesis of clickable azido periodic mesoporous organosilicas (PMOs) and their use as adsorbents for the adsorption of antibiotics. Ethane‐bridged PMOs, functionalized with azido groups at different densities, were synthesized by the co‐condensation of 1,2‐bis(trimethoxysilyl)ethane (BTME) and 3‐azidopropyltrimethoxysilane (AzPTMS), in the presence of nonionic‐surfactant triblock‐copolymer P123, in an acidic medium. Four different alkynes were conjugated to azide‐terminated PMOs by means of an efficient click reaction. The clicked PMOs showed improved adsorption capacity (241 μg g^?1) for antibiotics (ciprofloxacin hydrochloride) compared with azido‐functionalized PMOs because of the enhanced π–π stacking interactions. These results indicate that click reactions can introduce multifunctional groups onto PMOs, thus demonstrating the great potential of PMOs for environmental applications.     

Electrochemical Properties of Oxidized Carbon Nano‐Onions: DRIFTS‐FTIR and Raman Spectroscopic Analyses

The electrochemical reactions of carboxylic and lactone groups on carbon nano‐onions (CNOs) in aqueous solutions result in non‐Kolbe products: alcohols, ketones, ethers and epoxides. The anodic/cathodic conversion of ox‐CNOs was assessed by Boehm titrations and by Raman and DRIFTS‐FTIR (diffuse reflectance infrared Fourier transform spectroscopy). The electrochemical properties of oxidized carbon nano‐onions were investigated by cyclic voltammetry in aqueous solutions. The ox‐CNOs are electrochemically active as a result of the reduction of the oxygen‐containing groups.     

Synthesis and conformational analysis of fructose-derived scaffolds: molecular diversity from a single molecule

Bi- and tricyclic compounds were synthesized starting from fructose. The different hydroxyl groups present in fructose were exploited in the formation of a number of conformationally constrained sugar-based scaffolds, including azido acids. Introduction of an azido group and carboxy terminus into different bicyclic iodo ethers, allowed the synthesis of different conformationally constrained azido acids. Conformational analysis of compounds 10, 11, 17, and 20 by NMR experiments assisted by molecular mechanics, allowed the determination of the distances between the relevant functional groups, that is the azido and carboxy functionalities.     

Synthesis of 7‐Azido‐3‐Formylcoumarin – A Key Precursor in Bioorthogonally Applicable Fluorogenic Dye Synthesis

Coumarins represent an important group of natural products and a common part of various drugs and fluorescent dyestuffs. Herein, we present the synthesis of a coumarin that can serve as a key starting material in the design and synthesis of bioorthogonally applicable fluorogenic dyes. The synthesis of 7‐azido‐3‐formylcoumarin started from 7‐diallylaminocoumarin. This allyl protected aminocoumarin is otherwise hard to obtain by conventional methods but was conveniently accessed in good yields by a sequential, Wittig‐reaction–UV isomerization process. This sequential approach was studied in more details and applied for the synthesis of a series of substituted coumarins even in one‐pot.     

The Thermolysis of the Cycloadducts between Aryl Azides and Hexamethyl‐Dewar‐Benzene Revisited

The reactions of 1‐azido‐2,4,6‐trimethyl‐ and 1‐azido‐2,6‐dimethylbenzene with hexamethyl‐Dewar‐benzene (HMDB) give rise to the pentamethyl(iminoethyl)‐4H‐1,2‐diazepines 4 and 5 , respectively. The X‐ray crystal‐structure analysis of 5 unequivocally established these unexpected structures, which motivated us to re‐investigate the thermolysis of the adduct 1a of HMDB and azidobenzene. Previously, the triazonine 2 was reported to be the major product, but this interpretation could not be corroborated now, and, instead, the 1‐aminopyrrole 6 was identified as the true compound. The structure of the analogous compound 7 , obtained by thermolysis of the (1‐azido‐4‐nitrobenzene)‐HMDB adduct 1b , was confirmed by X‐ray diffraction. In the original literature investigation, a second product had been isolated, in addition to the alleged 2 , by chromatographic purificiation of the thermolysis mixture, and structure 3 had been ascribed to it. It turns out now that this compound is not a valence isomer of the major product, but a hydrolysis product, i.e., the ketone 8 . The formation of the rather different compounds 4 and 5 on the one hand, and 6 and 7 on the other hand, can be rationalized straightforwardly by a sequence of pericyclic reactions leading to 3H‐1,2‐diazepines 11 as common intermediates, which are converted to either 4 and 5 , or 6 and 7 , depending on the nature of the aromatic group.     

A fluorogenic ‘click’ reaction of azidoanthracene derivatives

Fluorogenic reactions have broad applications in biolabeling, combinatorial synthesis of fluorescent dyes, and materials development. It was recently reported that the highly selective and efficient Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction can be employed in designing new types of fluorogenic reactions. In this study, we report a fluorogenic reaction using anthracene azides as starting materials. The fluorescence of the anthryl core can be greatly inhibited upon introducing electron-donating azido groups in the proximity. Such weakly fluorescent anthracene azides demonstrate high reactivity with a variety of alkynes under the CuAAC conditions producing a strongly fluorescent triazole product with high quantum yields. This reaction can be used in the synthesis and screening of fluorescent dyes combinatorially. Compared with most existing methods, the fluorogenic CuAAC reaction is a much milder and simpler technique to prepare large libraries of fluorescent dyes without further purification. In order to demonstrate the efficiency of using anthracene azides for biolabeling applications, both small molecules and biomolecules including the multialkyne-derivatized cowpea mosaic virus and tobacco mosaic virus had been studied.     

A Visualizable Chain‐Terminating Inhibitor of Glycosaminoglycan Biosynthesis in Developing Zebrafish

Heparan sulfate (HS) and chondroitin sulfate (CS) glycosaminoglycans (GAG) are proteoglycan‐associated polysaccharides with essential functions in animals. They have been studied extensively by genetic manipulation of biosynthetic enzymes, but chemical tools for probing GAG function are limited. HS and CS possess a conserved xylose residue that links the polysaccharide chain to a protein backbone. Here we report that, in zebrafish embryos, the peptide‐proximal xylose residue can be metabolically replaced with a chain‐terminating 4‐azido‐4‐deoxyxylose (4‐XylAz) residue by administration of UDP‐4‐azido‐4‐deoxyxylose (UDP‐4‐XylAz). UDP‐4‐XylAz disrupted both HS and CS biosynthesis and caused developmental abnormalities reminiscent of GAG biosynthesis and laminin mutants. The azide substituent of protein‐bound 4‐XylAz allowed for rapid visualization of the organismal sites of chain termination in vivo through bioorthogonal reaction with fluorescent cyclooctyne probes. UDP‐4‐XylAz therefore complements genetic tools for studies of GAG function in zebrafish embryogenesis.     

Alkylation of 2‐pyridinones: Synthesis of novel acyclonucleosides

This paper presents the synthesis of some novel acyclonucleosides containing 2‐pyridinones and 2‐hydroxyethoxymethyl, 2,3‐dihydroxy‐propyl side chain. The tosylate of these nucleosides analogues could be modified to azido derivatives. Also, acyclonucleosides with 1‐ethoxymethyl, 1‐benzyloxymethyl, 1‐methylthiomethy 1 and 2‐hydroxyethyl side chains have been investigated. The O‐alkylated pyridine derivatives were obtained during most reactions.     

Three‐Dimensional Heterocycles by Iron‐Catalyzed Ring‐Closing Sulfoxide Imidation

A general and atom‐economical method for the synthesis of cyclic sulfoximines by intramolecular imidations of azido‐containing sulfoxides using a commercially available Fe^II phthalocyanine (Fe^IIPc) as catalyst has been developed. The method conveys a broad functional group tolerance and the resulting three‐dimensional heterocycles can be modified by cross‐coupling reactions.     

Synthesis and reactions of azides of heterocyclic compounds

Cyanine dyes containing azido groups in the 5 or 6 position of the benzazole ring were obtained from quaternary salts of azides of benzothiazole and benzimidazole. The introduction of an azido group into the dye molecule results in a considerable bathochromic effect.See [1] for communication II.Translated from Khimiya Geterotsiklicheskikh Soedinenii. No. 5, pp. 640–642, May, 1974.     

Solid‐State Hierarchical Cyclodextrin‐Based Supramolecular Polymer Constructed by Primary,Secondary, and Tertiary Azido Interactions

The crystallization of a di‐azido‐α‐cyclodextrin revealed a polymeric self‐assembly involving a variety of azido‐type interactions. The crystal arrangement relies on the cooperativity of a primary azido inclusion, a secondary azido–azido interaction involving an unprecedented distribution of canonical forms, and a tertiary azido–groove interaction. The second azido group brings in a major contribution to the supramolecular structure illustrating the benefit of a difunctionalization for the generation of hierarchy.     

Solid‐State Hierarchical Cyclodextrin‐Based Supramolecular Polymer Constructed by Primary,Secondary, and Tertiary Azido Interactions

The crystallization of a di‐azido‐α‐cyclodextrin revealed a polymeric self‐assembly involving a variety of azido‐type interactions. The crystal arrangement relies on the cooperativity of a primary azido inclusion, a secondary azido–azido interaction involving an unprecedented distribution of canonical forms, and a tertiary azido–groove interaction. The second azido group brings in a major contribution to the supramolecular structure illustrating the benefit of a difunctionalization for the generation of hierarchy.