Sydnone-based prosthetic groups for radioiodination

The potential of Strained-Promoted Sydnone-Alkyne Cycloaddition (SPSAC) for radioiodination was evaluated with model cyclooctyne-conjugated peptides. Starting with a series of sydnones with varying N3 and C4 substitution, a preliminary kinetic study with non-radioactive iodinated compounds highlighted the superiority of an arylsydnone substituted by a chlorine atom in C4 position. Interestingly, reaction rate up to 11 times higher than using an azide was achieved with the best system. Access to 125I-labelled sydnones was granted with high efficiency from arylboronic acid precursors by copper catalyzed nucleophilic substitution. Application of SPSAC on the model peptide in radiotracer conditions showed the same trend than in non-radioactive kinetic study and complete reactions could be achieved within less than an hour for the best systems. These results are favorable for use in the production of radiopharmaceuticals with heavy halogens and increase the diversity of available bioorthogonal reaction for nuclear imaging and therapy.

Ultrabright two-photon excitable red-emissive fluorogenic probes for fast and wash-free bioorthogonal labelling in live cells

Fluorogenic bioorthogonal reactions are promising tools for tracking small molecules or biomolecules in living organisms. Two-photon excitation, by shifting absorption towards the red, significantly increases the signal-to-noise ratio and decreases photodamage, while allowing imaging about 10 times deeper than with a confocal microscope. However, efficient two-photon excitable fluorogenic probes are currently lacking. We report here the design and synthesis of fluorogenic probes based on a two-photon excitable fluorophore and a tetrazine quenching moiety. These probes react with bicyclo[6.1.0]no-4-yn-9ylmethanol (BCN) with a good to impressive kinetic rate constant (up to 1.1 × 103 M-1 s-1) and emit in the red window with moderate to high turn-on ratios. TDDFT allowed the rationalization of both the kinetic and fluorogenic performance of the different probes. The best candidate displays a 13.8-fold turn-on measured by quantifying fluorescence intensities in live cells under one-photon excitation, whereas a value of 3 is sufficient for high contrast live-cell imaging. In addition, live-cell imaging under two-photon excitation confirmed that there was no need for washing to monitor the reaction between BCN and this probe since an 8.0-fold turn-on was measured under two-photon excitation. Finally, the high two-photon brightness of the clicked adduct (>300 GM) allows the use of a weak laser power compatible with in vivo imaging.

Metabolic glycoengineering - exploring glycosylation with bioorthogonal chemistry

Glycans are involved in numerous biological recognition events. Being secondary gene products, their labeling by genetic methods - comparable to GFP labeling of proteins - is not possible. To overcome this limitation, metabolic glycoengineering (MGE, also known as metabolic oligosaccharide engineering, MOE) has been developed. In this approach, cells or organisms are treated with synthetic carbohydrate derivatives that are modified with a chemical reporter group. In the cytosol, the compounds are metabolized and incorporated into newly synthesized glycoconjugates. Subsequently, the reporter groups can be further derivatized in a bioorthogonal ligation reaction. In this way, glycans can be visualized or isolated. Furthermore, diverse targeting strategies have been developed to direct drugs, nanoparticles, or whole cells to a desired location. This review summarizes research in the field of MGE carried out in recent years. After an introduction to the bioorthogonal ligation reactions that have been used in in connection with MGE, an overview on carbohydrate derivatives for MGE is given. The last part of the review focuses on the many applications of MGE starting from mammalian cells to experiments with animals and other organisms.

Sydnone: Synthesis, Reactivity and Biological Activities

Sydnones are among the most well-known mesoionic compounds. Since their synthesis in 1935 by Earl and Mecknay, numerous researches have shown that the chemical behavior, physical and biological properties of sydnones make them the most useful compounds in organic chemistry. Sydnones undergo thermal 1,3-dipolar cycloaddition reaction with dipolarophiles (alkynes or alkenes) to give exclusively derivatives containing a pyrazole moiety exhibiting numerous applications, such as pharmaceuticals and agrochemicals. However, the sydnone cycloaddition reaction with alkynes requires harsh conditions, like high temperatures and long reaction times, giving poor regioselectivity to the resulting products. To overcome these constraints, new reactions named CuSAC (Copper- Catalyzed Sydnone-Alkyne Cycloaddition) and SPSAC (Strain-Promoted Sydnone- Alkyne Cycloaddition) have been developed, leading to pyrazoles with interesting constant kinetics.

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

A Dansyl Amide N-Oxide Fluorogenic Probe Based on a Bioorthogonal Decaging Reaction

A smart fluorescence "turn-on" probe which contained a dansyl amide fluorophore and an N-oxide group was designed based on the bioorthogonal decaging reaction between N-oxide and the boron reagent. The reaction proceeds in a rapid kinetics (k2 =57.1±2.5 m-1  s-1 ), and the resulting reduction product showcases prominent fluorescence enhancement (up to 72-fold). Time dependent density functional theoretical (TD-DFT) calculation revealed that the process of photoinduced electron transfer (PET) from the N-oxide moiety to the dansyl amide fluorophore accounts for the quenching mechanism of N-oxide. This probe also showed high selectivity over various nucleophilic amino acids and good biocompatibility in physiological conditions. The successful application of the probe in HaloTag protein labeling and HepG2 live-cell imaging proves it a valuable tool for visualization of biomolecules.

Sydnone Methides-A Forgotten Class of Mesoionic Compounds for the Generation of Anionic N-Heterocyclic Carbenes

Sydnone methides are described from which only one single example has been mentioned in the literature so far. Their deprotonation gave anions which can be formulated as π-electron rich anionic N-heterocyclic carbenes. Sulfur and selenium adducts were stabilized as their methyl ethers, and mercury, gold as well as rhodium complexes of the sydnone methide carbenes were prepared. Sydnone methide anions also undergo C-C coupling reactions with 1-fluoro-4-iodobenzene under Pd(PPh3 )4 and CuBr catalysis. 77 Se NMR resonance frequencies and 1 JC4-Se as well as 1 JC4-H coupling constants have been determined to gain knowledge about the electronic properties of the anionic N-heterocyclic carbenes. The carbene carbon atom of the sydnone methide anion 3 j resonates at δ=155.2 ppm in 13 C NMR spectroscopy at -40 °C which is extremely shifted upfield in comparison to classical N-heterocyclic carbenes.

Click and Bio-Orthogonal Reactions with Mesoionic Compounds

Click and bio-orthogonal reactions are dominated by cycloaddition reactions in general and 1,3-dipolar cycloadditions in particular. Among the dipoles routinely used for click chemistry, azides, nitrones, isonitriles, and nitrile oxides are the most popular. This review is focused on the emerging click chemistry that uses mesoionic compounds as dipole partners. Mesoionics are a very old family of molecules, but their use as reactants for click and bio-orthogonal chemistry is quite recent. The facility to derivatize these dipoles and to tune their reactivity toward cycloaddition reactions makes mesoionics an attractive opportunity for future click chemistry development. In addition, some compounds from this family are able to undergo click-and-release reactions, finding interesting applications in cells, as well as in animals. This review covers the synthetic access to main mesoionics, their reaction with dipolarophiles, and recent applications in chemical biology and heterocycle synthesis.

Design of Nitroso-Modified Naphthylene-Based Fluorophores as Photoactivatable Bioorthogonal Turn-On Probes

We reported a series of nitroso-modified naphthylene-based fluorophores as novel bioorthogonal fluorescence turn-on probes. The cycloadducts from nitroso-diene Diels-Alder reaction could be either photochemically or spontaneously transformed into highly fluorescent rearrangement products with remarkable photophysical properties including significant fluorescence enhancement, large Stokes shift, high fluorescence quantum yield, superior photostability, and distinct solvatochromic effect. This strategy is suitable for selective labeling of diene-modified proteins and visualizing specific organelles in live mammalian cells under no-wash conditions.

A novel near-infrared-emitting aza-boron-dipyrromethene-based remarkable fluorescent probe for Hg2+ in living cells

A new near-infrared (NIR)-emitting aza-boron-dipyrromethene dye with two electron-donating amino groups at 1- and 7-positions has been prepared via several steps of reactions. This probe showed a NIR absorption at 748 nm with an obvious shoulder peak at 634 nm in CH₃CN/H₂O. Interestingly, a NIR fluorescence emission at 843 nm was observed with a large Stokes shift of 95 nm. This novel NIR-emitting aza-boron-dipyrromethene dye was further investigated as a Hg²⁺-sensing fluorescent probe, which selectively bound to Hg²⁺, showing a blue-shifted and sharp absorption band at 695 nm with the disappearance of the shoulder peak at 634 nm. Correspondingly, the color change could be easily seen from blue to green. Interestingly, the emission exhibited an absolutely "turn-on" peak at 725 nm with a significant blue shift by 118 nm (from 843 to 725 nm), due to the efficient inhibition of the intramolecular-charge-transfer process arising from two amino groups. This probe was finally introduced to Hela cells, showing a "OFF-ON" NIR emission upon exposure to Hg²⁺. The overall results confirmed that this novel NIR-emitting aza-boron-dipyrromethene fluorescent probe with a large Stokes shift could serve as a colorimetric and fluorescent "turn-on" sensor for Hg²⁺ in both solutions and living cells.

Sydnone Ribosides as a Platform for the Synthesis of Pyrazole C-Nucleosides: A Unified Synthesis of Formycin B and Pyrazofurin

The C-nucleoside natural products formycin B and pyrazofurin were synthesized in seven steps employing a sydnone riboside as common intermediate. Sydnone ribosides were synthesized via a direct Lewis acid catalyzed dehydrative glycosylation reaction. We demonstrated that these can be used for the diversity-oriented synthesis of pyrazole C-nucleoside analogues via thermal 1,3-dipolar cycloaddition reactions with various alkynes, giving access to the pyrazole C-nucleoside natural products, as well as opening new avenues for exploring nucleoside chemical space.

Conformation of G-quadruplex Controlled by Click Reaction

G-quadruplexes are non-canonical four stranded secondary structures possessing great biological importance. Controlling G-quadruplex conformation for further regulating biological processes is both exciting and challenging. In this study, we described a method for regulating G-quadruplex conformation by click chemistry for the first time. 8-ethynyl-2'-deoxyguanosine was synthesized and incorporated into a 12-nt telomere DNA sequence. Such a sequence, at first, formed mixed parallel/anti-parallel G-quadruplexes, while it changed to anti-parallel after reaction with azidobenzene. Meanwhile, the click reaction can give the sequence intense fluorescence.

Bioorthogonal Ligations and Cleavages in Chemical Biology

Bioorthogonal reactions including the bioorthogonal ligations and cleavages have become an active field of research in chemical biology, and they play important roles in chemical modification and functional regulation of biomolecules. This review summarizes the developments and applications of the representative bioorthogonal reactions including the Staudinger reactions, the metal-mediated bioorthogonal reactions, the strain-promoted cycloadditions, the inverse electron demand Diels-Alder reactions, the light-triggered bioorthogonal reactions, and the reactions of chloroquinoxalines and ortho-dithiophenols.

Fluorogenic iminosydnones: bioorthogonal tools for double turn-on click-and-release reactions

Iminosydnones are able to quench two fluorophores when connected to their core structure. Bioorthogonal click and release reaction with cyclooctynes provokes significant fluorescence enhancement of the two products, allowing their tracking in cells.

A bioorthogonally activatable photosensitiser for site-specific photodynamic therapy

Inverse-electron-demand Diels–Alder reaction of a 1,2,4,5-tetrazine-substituted boron dipyrromethene with a biotin-conjugated trans-cyclooctene results in site-specific activation of the photoactivity of the former photosensitiser.

Bioorthogonal Fluorescence Turn-On Labeling Based on Bicyclononyne-Tetrazine Cycloaddition Reactions that Form Pyridazine Products

Fluorogenic bioorthogonal reactions enable visualization of biomolecules with excellent signal-to-noise ratio. A bicyclononyne-tetrazine ligation that produces fluorescent pyridazine products has been developed. In stark contrast to previous approaches, the formation of the dye is an inherent result of the chemical reaction and no additional fluorophores are needed in the reagents. The crucial structural elements that determine dye formation are electron-donating groups present in the starting tetrazine unit. The newly formed pyridazine fluorophores show interesting photophysical properties the fluorescence intensity increase in the reaction can reach an excellent 900-fold. Model imaging experiments demonstrate the application potential of this new fluorogenic bioorthogonal reaction.

Development of 4-oxime-1,8-naphthalimide as a bioorthogonal turn-on probe for fluorogenic protein labeling

We report 4-oxime-1,8-naphthalimide as a novel bioorthogonal turn-on probe based on cascade 1,3-dipolar cycloaddition and photoisomerization for fluorogenic protein labeling.

Photo-accelerated “click” reaction between diarylsydnones and ring-strained alkynes for bioorthogonal ligation

A novel photo-click ligation reaction between diarylsydnones and ring-strained alkynes, exhibiting decent bioorthogonality, was established under 405 nm light irradiation.

Sydnone-based turn-on fluorogenic probes for no-wash protein labeling and in-cell imaging

Fluorogenic sydnone-based turn-on probes allow efficient labeling of proteins and cell imaging through a bioorthogonal strained promoted sydnone–alkyne cycloaddition reaction.

A strained alkyne-containing bipyridine reagent; synthesis, reactivity and fluorescence properties

We report the synthesis of a bipyridyl reagent containing a strained alkyne, which significantly restricts its flexibility. Upon strain-promoted alkyne-azide cycloaddition (SPAAC) with an azide, which does not require a Cu catalyst, the structure becomes significantly more flexible and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further. The reagent has the potential to act as a fluorescent labelling agent with azide-containing substrates, including biological molecules.

A bipyridyl reagent containing a strained alkyne 7, reacts with benzyl azide to give a significantly more flexible product 10 and an increase in fluorescence is observed. Upon addition of Zn(ii), the fluorescence is enhanced further.

A fluorogenic C4N4 probe for azide-based labelling

A new fluorogenic probe based on the recently identified 2,5-diaminopyrimidine (C4N4) fluorophore is introduced for azide-specific labelling.