Discovery of Chemoselective and Biocompatible Reactions Using a High-Throughput Immunoassay Screening

Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously

Bioorthogonal click chemistry has played a transformative role in many research fields, including chemistry, biology, and medicine. Click reactions are crucial to produce increasingly complex bioconjugates, to visualize and manipulate biomolecules in living systems and for various applications in bioengineering and drug delivery. As biological (model) systems grow more complex, researchers have an increasing need for using multiple orthogonal click reactions simultaneously. In this review, we will introduce the most common bioorthogonal reactions and discuss their orthogonal use on the basis of their mechanism and electronic or steric tuning. We provide an overview of strategies to create reaction orthogonality and show recent examples of mutual orthogonal chemistry used for simultaneous biomolecule labeling. We end by discussing some considerations for the type of chemistry needed for labeling biomolecules in a system of choice.

Exploration of the Copper-Catalyzed Sydnone and Sydnonimine-Alkyne Cycloaddition Reactions by High-Throughput Experimentation

The reactivity of sydnones and sydnonimines toward terminal alkynes under copper catalysis has been explored using High-Throughput-Experimentation. A large panel of ligands and reaction conditions have been tested to optimize the copper-catalyzed sydnone click reaction discovered by our group ten years ago. This screening approach led to the identification of new ligands, which boosted the catalytic properties of copper and allowed the discovery of a new copper-catalyzed click-and-release reaction involving sydnonimines. This reaction allowed chemoselective ligation of terminal alkynes with sydnonimines and, simultaneously, the release of an isocyanate fragment molecule that can be used for further transformations.

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.

Fluorescence turn-on by photoligation - bright opportunities for soft matter materials

Photochemical ligation has become an indispensable tool for applications that require spatially addressable functionalisation, both in biology and materials science. Interestingly, a number of photochemical ligations result in fluorescent products, enabling a self-reporting function that provides almost instantaneous visual feedback of the reaction's progress and efficiency. Perhaps no other chemical reaction system allows control in space and time to the same extent, while concomitantly providing inherent feedback with regard to reaction success and location. While photoactivable fluorescent properties have been widely used in biology for imaging purposes, the expansion of the array of photochemical reactions has further enabled its utility in soft matter materials. Herein, we concisely summarise the key developments of fluorogenic-forming photoligation systems and their emerging applications in both biology and materials science. We further summarise the current challenges and future opportunities of exploiting fluorescent self-reporting reactions in a wide array of chemical disciplines.

On Demand Flow Platform for the Generation of Anhydrous Dinitrogen Trioxide and Its Further Use in N-Nitrosative Reactions

Dinitrogen trioxide (N₂ O₃ ) is a powerful and efficient nitrosating agent that comes with an unprecedented atom economy. However, the synthetic application of N₂ O₃ is still underdeveloped mostly due to its inherent instability and the lack of reliable protocols for its preparation. This paper presents an open-source setup and procedure for the on-demand generation of anhydrous N₂ O₃ solution (up to 1 M), which can be further used for reactions under batch and flow conditions. The accuracy and stability of N₂ O₃ concentration are guaranteed with the absence of head-space in the setup and with the synchronization of the gas flows. The reliability of this protocol is demonstrated by >30 worked examples in the nitrosative synthesis of heterocycles-a library of structurally diverse benzotriazoles and sydnones. Kinetic and mechanistic aspects of the N-nitrosative steps are also explored.

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.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

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.

Light-Triggered Click Chemistry

The merging of click chemistry with discrete photochemical processes has led to the creation of a new class of click reactions, collectively known as photoclick chemistry. These light-triggered click reactions allow the synthesis of diverse organic structures in a rapid and precise manner under mild conditions. Because light offers unparalleled spatiotemporal control over the generation of the reactive intermediates, photoclick chemistry has become an indispensable tool for a wide range of spatially addressable applications including surface functionalization, polymer conjugation and cross-linking, and biomolecular labeling in the native cellular environment. Over the past decade, a growing number of photoclick reactions have been developed, especially those based on the 1,3-dipolar cycloadditions and Diels-Alder reactions owing to their excellent reaction kinetics, selectivity, and biocompatibility. This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science. A particular emphasis is placed on the historical contexts and mechanistic insights into each of the selected reactions. The in-depth discussion presented here should stimulate further development of the field, including the design of new photoactivation modalities, the continuous expansion of λ-orthogonal tandem photoclick chemistry, and the innovative use of these unique tools in bioconjugation and nanomaterial synthesis.

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.

Recent developments in bioorthogonal chemistry and the orthogonality within

The emergence of bioorthogonal reactions has greatly advanced research in the fields of biology and medicine. They are not only valuable for labeling, tracking, and understanding biomolecules within living organisms, but also important for constructing advanced bioengineering and drug delivery systems. As the systems studied are increasingly complex, the simultaneous use of multiple bioorthogonal reactions is equally desirable. In this review, we take a look at the different bioorthogonal reactions that have recently been developed, the methods of cellular incorporation and the strategies to create orthogonality within the bioorthogonal landscape.

Transition-Metal-Mediated Modification of Biomolecules

The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.

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.

Developing bioorthogonal probes to span a spectrum of reactivities

Bioorthogonal chemistries enable researchers to interrogate biomolecules in living systems. These reactions are highly selective and biocompatible and can be performed in many complex environments. However, like any organic transformation, there is no perfect bioorthogonal reaction. Choosing the "best fit" for a desired application is critical. Correspondingly, there must be a variety of chemistries-spanning a spectrum of rates and other features-to choose from. Over the past few years, significant strides have been made towards not only expanding the number of bioorthogonal chemistries, but also fine-tuning existing reactions for particular applications. In this Review, we highlight recent advances in bioorthogonal reaction development, focusing on how physical organic chemistry principles have guided probe design. The continued expansion of this toolset will provide more precisely tuned reagents for manipulating bonds in distinct environments.

Alkynes and Nitrogen Compounds: Useful Substrates for the Synthesis of Pyrazoles

The easy preparation and functionalization of pyrazoles associated with their innumerable biological properties have made this class of N-heterocycles very attractive for the development of new synthetic routes and applications. The cyclization reactions of alkynes and nitrogen compounds represent a powerful tool for the preparation of pyrazoles. This Review covers the recent advances in the preparation of pyrazoles by reacting alkynes and nitrogen compounds under transition-metal-catalyzed or metal-free conditions.

Molecular Design of Bioorthogonal Probes and Imaging Reagents Derived from Photofunctional Transition Metal Complexes

For more than 15 years, bioorthogonal chemistry has received increasing attention due to its successful applications in the detection and imaging of biomolecules in their native biological environments. The method typically proceeds with the incorporation of a biological substrate appended with a bioorthogonal functional group (chemical reporter), followed by the introduction of the substrate to biological systems. Biomolecules containing the substrate are then recognized by an exogenously delivered bioorthogonal probe. Despite the fact that many useful chemical reporters and bioorthogonal reactions have been developed, most of the bioorthogonal probes reported thus far are fluorescent dyes. A limitation is that stringent washing is required due to the interference caused by the background fluorescence of unreacted probes. Thus, fluorogenic probes with turn-on emission properties upon bioorthogonal labeling have been designed as an alternative strategy. These probes are highly appealing because excellent images can be obtained without the need for washing steps. Nearly all fluorogenic bioorthogonal probes designed are essentially organic dyes, their emission is limited to fluorescence, and the utilization of the probes is confined to bioimaging applications. Recently, there has been a growing interest in the bioimaging and therapeutic applications of luminescent inorganic and organometallic transition metal complexes due to their intriguing photophysical and photochemical properties, high membrane permeability, controllable cellular uptake, intracellular localization, and cytotoxicity. We anticipate that photofunctional transition metal complexes can be exploited as valuable bioorthogonal probes due to these appealing advantages. In this Account, we introduce the molecular design, photophysical and photochemical properties, and biological applications of various bioorthogonal probes and imaging reagents based on photofunctional transition metal complexes. The presence of a cationic metal center significantly enhances the bioorthogonal reactivity of the probes, yet their stability in aqueous solutions can be maintained. Interestingly, some of these metal complexes are strategically modified to display phosphorogenic properties, that is, phosphorescence turn-on upon bioorthogonal labeling reactions. Importantly, these probes not only exhibit favorable photophysical properties after bioorthogonal labeling, but also efficient photoinduced singlet oxygen (¹O₂) generation. This interesting bioorthogonal reaction-triggered photosensitization capability allows the modulation of ¹O₂ generation efficiency and contributes to the development of controllable photocytotoxic agents. The exploration of transition metal complex-based probes not only significantly widens the scope of bioorthogonal labeling but also further highlights the unique advantages of these complexes in the design of theranostic reagents. The development of these innovative reagents is expected to contribute to the basic understanding of biological processes in living systems and provide exciting opportunities for new diagnostic and therapeutic applications.

Photoisomerization-enhanced 1,3-dipolar cycloaddition of carbon-bridged octocyclic azobenzene with photo-released nitrile imine for peptide stapling and imaging in live cells

A novel photo-click ligation reaction between nitrile imines and photo-switchable octocyclic azobenzenes was established to both tune the conformation of the NoxaB peptide and conjugate probes with enhanced efficacy in cell apoptosis.

Accelerated Discovery in Photocatalysis by a Combined Screening Approach Involving MS Tags

Herein we report on the development of an MS tag screening strategy that accelerates the discovery of photocatalytic reactions. By efficiently combining mechanism- and reaction-based screening dimensions, the respective advantages of each strategy were retained, whereas the drawbacks inherent to each screening approach could be eliminated. Applying this approach led to the discovery of a mild photosensitized decarboxylative hydrazide synthesis from mesoionic sydnones and carboxylic acids as starting materials.

Copper-catalyzed chemoselective synthesis of 4-trifluoromethyl pyrazoles

A series of 4-trifluoromethyl pyrazoles have been prepared via the copper-catalyzed cycloaddition of 2-bromo-3,3,3-trifluoropropene with a variety of N-arylsydnone derivatives under mild conditions. This new protocol under optimized reaction conditions [Cu(OTf)₂/phen, DBU, CH₃CN, 35 °C] afforded 4-trifluoromethyl pyrazoles in moderate to excellent yields with excellent regioselectivity.

A copper-catalyzed chemoselective synthesis of 4-trifluoromethyl pyrazoles via cycloaddition of 2-bromo-3,3,3-trifluoropropene with N-arylsydnones has been developed.

New fluorine-18 pretargeting PET imaging by bioorthogonal chlorosydnone–cycloalkyne click reaction

A PET pretargeting approach using strain-promoted sydnone–alkyne cycloaddition.

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.

Synthesis and evaluation of photo-activatable β-diarylsydnone-l-alanines for fluorogenic photo-click cyclization of peptides

β-Diarylsydnone-l-alanines were designed and introduced into peptides allowing photo-cyclization only in phosphate containing buffer with concomitant fluorescence generation in live cells.

Bioorthogonal release of sulfonamides and mutually orthogonal liberation of two drugs

Sulfonamide derivatives have been used in pharmaceutics for decades. Here we report a new approach to release sulfonamides efficiently using a bioorthogonal reaction of sulfonyl sydnonimines and dibenzoazacyclooctyne (DIBAC). The second-order rate constant of the cycloaddition reaction can be up to 0.62 M-1 s-1, and the reactants are highly stable under physiological conditions. Most significantly, we also discovered the mutual orthogonality between the sydnonimine-DIBAC and benzonorbornadiene-tetrazine cycloaddition pairs, which can be used for selective and simultaneous liberation of sulfonamide and primary amine drugs.

One-Pot Tandem Amidation, Knoevenagel Condensation, and Palladium-Catalyzed Wacker Type Oxidation/C-O Coupling: Synthesis of Chromeno-Annulated Imidazopyridines

A direct one-pot synthesis of chromeno-annulated imidazo[1,2- a]pyridines is achieved by the reaction of 2-amino-1-(2-ethoxy-2-oxoethyl)pyridinium salts with 2-bromoarylaldehydes using Pd(TFA)₂ as a catalyst and Cu(OAc)₂ as an oxidant. The overall strategy involves tandem base-mediated amidation and Knoevenagel condensation, followed by palladium-catalyzed Wacker type oxidation and intramolecular C-O coupling reaction. The method is simple, tolerates different functional groups, and gives moderate to good yields of chromeno[2',3':4,5]imidazo[1,2- a]pyridin-12-one derivatives. The developed tandem reaction was also successfully applied for the synthesis of pyrano-fused imidazo[1,2- a]pyridines by using 3-bromo-3-arylacrylaldehydes.

[3 + 2]-Cycloaddition reaction of sydnones with alkynes

This review covers all known examples of [3 + 2]-cycloaddition between sydnones and both terminal as well as internal alkynes/cycloalkynes taken from literature since its discovery by Huisgen in 1962 up to the current date. Except enumeration of synthetic applications it also covers mechanistic studies, catalysis, effects of substituents and reaction conditions influencing reaction rate and regioselectivity.

Azide-Alkyne Click Conjugation on Quantum Dots by Selective Copper Coordination

Functionalization of nanocrystals is essential for their practical application, but synthesis on nanocrystal surfaces is limited by incompatibilities with certain key reagents. The copper-catalyzed azide-alkyne cycloaddition is among the most useful methods for ligating molecules to surfaces, but has been largely useless for semiconductor quantum dots (QDs) because Cu⁺ ions quickly and irreversibly quench QD fluorescence. To discover nonquenching synthetic conditions for Cu-catalyzed click reactions on QD surfaces, we developed a combinatorial fluorescence assay to screen >2000 reaction conditions to maximize cycloaddition efficiency while minimizing QD quenching. We identify conditions for complete coupling without significant quenching, which are compatible with common QD polymer surfaces and various azide/alkyne pairs. Based on insight from the combinatorial screen and mechanistic studies of Cu coordination and quenching, we find that superstoichiometric concentrations of Cu can promote full coupling if accompanied by ligands that selectively compete with the Cu from the QD surface but allow it to remain catalytically active. Applied to the conjugation of a K⁺ channel-specific peptidyl toxin to CdSe/ZnS QDs, we synthesize unquenched QD conjugates and image their specific and voltage-dependent affinity for K⁺ channels in live cells.