A Minimal,Unstrained S‐Allyl Handle for Pre‐Targeting Diels–Alder Bioorthogonal Labeling in Live Cells

The unstrained S‐allyl cysteine amino acid was site‐specifically installed on apoptosis protein biomarkers and was further used as a chemical handle and ligation partner for 1,2,4,5‐tetrazines by means of an inverse‐electron‐demand Diels–Alder reaction. We demonstrate the utility of this minimal handle for the efficient labeling of apoptotic cells using a fluorogenic tetrazine dye in a pre‐targeting approach. The small size, easy chemical installation, and selective reactivity of the S‐allyl handle towards tetrazines should be readily extendable to other proteins and biomolecules, which could facilitate their labeling within live cells.     

Photo‐induced and Rapid Labeling of Tetrazine‐Bearing Proteins via Cyclopropenone‐Caged Bicyclononynes

Inverse electron‐demand Diels–Alder cycloadditions (iEDDAC) between tetrazines and strained alkenes/alkynes have emerged as essential tools for studying and manipulating biomolecules. A light‐triggered version of iEDDAC (photo‐iEDDAC) is presented that confers spatio‐temporal control to bioorthogonal labeling in vitro and in cellulo. A cyclopropenone‐caged dibenzoannulated bicyclo[6.1.0]nonyne probe (photo‐DMBO) was designed that is unreactive towards tetrazines before light‐activation, but engages in iEDDAC after irradiation at 365 nm. Aminoacyl tRNA synthetase/tRNA pairs were discovered for efficient site‐specific incorporation of tetrazine‐containing amino acids into proteins in living cells. In situ light activation of photo‐DMBO conjugates allows labeling of tetrazine‐modified proteins in living E. coli. This allows proteins in living cells to be modified in a spatio‐temporally controlled manner and may be extended to photo‐induced and site‐specific protein labeling in animals.     

Metal‐Free Synthetic Approach to 3‐Monosubstituted Unsymmetrical 1,2,4,5‐Tetrazines Useful for Bioorthogonal Reactions

A facile, efficient and metal‐free synthetic approach to 3‐monosubstituted unsymmetrical 1,2,4,5‐tetrazines is presented. Dichloromethane (DCM) is for the first time recognized as a novel reagent in the synthetic chemistry of tetrazines. Using this novel approach 11 3‐aryl/alkyl 1,2,4,5‐tetrazines were prepared in excellent yields (up to 75 %). The mechanism of this new reaction, including the role of DCM in the tetrazine ring formation, has been investigated by ¹³C labeling of DCM, and is also presented and discussed as well as the photophysical and electrochemical properties.     

Divergent Synthesis of Monosubstituted and Unsymmetrical 3,6‐Disubstituted Tetrazines from Carboxylic Ester Precursors

Since tetrazines are important tools to the field of bioorthogonal chemistry, there is a need for new approaches to synthesize unsymmetrical and 3‐monosubstituted tetrazines. Described here is a general, one‐pot method for converting (3‐methyloxetan‐3‐yl)methyl carboxylic esters into 3‐thiomethyltetrazines. These versatile intermediates were applied to the synthesis of unsymmetrical tetrazines through Pd‐catalyzed cross‐coupling and in the first catalytic thioether reduction to access monosubstituted tetrazines. This method enables the development of new tetrazine compounds possessing a favorable combination of kinetics, small size, and hydrophilicity. It was applied to a broad range of aliphatic and aromatic ester precursors and to the synthesis of heterocycles including BODIPY fluorophores and biotin. In addition, a series of tetrazine probes for monoacylglycerol lipase (MAGL) were synthesized and the most reactive one was applied to the labeling of endogenous MAGL in live cells.     

Bridge‐Clamp Bis(tetrazine)s with [N]8 π‐Stacking Interactions and Azido‐s‐Aryl Tetrazines: Two Classes of Doubly Clickable Tetrazines

Click chemistry at a tetrazine core is useful for bioorthogonal labeling and crosslinking. Introduced here are two new classes of doubly clickable s‐aryl tetrazines synthesized by Cu‐catalyzed cross‐coupling. Homocoupling of o‐brominated s‐aryl tetrazines leads to bis(tetrazine)s structurally characterized by tetrazine cores arranged face‐to‐face. [N]₈ π‐stacking interactions are essential to the conformation. Upon inverse electron demand Diels–Alder (iEDDA) cycloaddition, the bis(tetrazine)s produce a unique staple structure. The o‐azidation of s‐aryl tetrazines introduces a second proximal intermolecular clickable function that leads to double click chemistry opportunities. The stepwise introduction of fluorophores and then iEDDA cycloaddition, including bioconjugation to antibodies, was achieved on this class of tetrazines. This method extends to (thio)etherification, phosphination, trifluoromethylation and the introduction of various bioactive nitrogen‐based heterocycles.     

Affinity‐Labeling‐Based Introduction of a Reactive Handle for Natural Protein Modification

A new chemical method to site‐specifically modify natural proteins without the need for genetic manipulation is described. Our strategy involves the affinity‐labeling‐based attachment of a unique reactive handle at the surface of the target protein, and the subsequent selective transformation of the reactive handle by a bioorthogonal reaction to introduce a variety of functional probes into the protein. To demonstrate this approach, we synthesized labeling reagents that contain: 1) a benzenesulfonamide ligand that directs specifically to bovine carbonic anhydrase II (bCA), 2) an electrophilic epoxide group for protein labeling, 3) an exchangeable hydrazone bond linking the ligand and the epoxide group, and 4) an iodophenyl or acetylene handle. By incubating the labeling reagent with bCA, the reactive handle was covalently attached at the surface of bCA through epoxide ring opening. Either after or before removing the ligand by a hydrazone/oxime‐exhange reaction, which restores the enzymatic activity, the reactive handle incorporated could be derivatized by Suzuki coupling or Huisgen cycloaddition reactions. This method is also applicable to the target‐specific multiple modification in a protein mixture. The availability of various (photo)affinity‐labeling reagents and bioorthogonal reactions should extend the flexibility of this strategy for the site‐selective incorporation of many functional molecules into proteins.     

Mechanism‐Based Fluorogenic trans‐Cyclooctene–Tetrazine Cycloaddition

The development of fluorogenic reactions which lead to the formation of fluorescent products from two nonfluorescent starting materials is highly desirable, but challenging. Reported herein is a new concept of fluorescent product formation upon the inverse electron‐demand Diels–Alder reaction of 1,2,4,5‐tetrazines with particular trans ‐cyclooctene (TCO) isomers. In sharp contrast to known fluorogenic reagents the presented chemistry leads to the rapid formation of unprecedented fluorescent 1,4‐dihydropyridazines so that the fluorophore is built directly upon the chemical reaction. Attachment of an extra fluorophore moiety is therefore not needed. The photochemical properties of the resulting dyes can be easily tuned by changing the substitution pattern of the starting 1,2,4,5‐tetrazine. We support the claim with NMR measurements and rationalize the data by computational study. Cell‐labeling experiments were performed to demonstrate the potential of the fluorogenic reaction for bioimaging.     

Highly Stable trans‐Cyclooctene Amino Acids for Live‐Cell Labeling

trans‐Cyclooctene groups incorporated into proteins via non‐canonical amino acids (ncAAs) are emerging as specific handles for bioorthogonal chemistry. Here, we present a highly improved synthetic access to the axially and the equatorially linked trans‐cyclooct‐2‐ene isomers ( 1 a , b ). We further show that the axially connected isomer has a half‐life about 10 times higher than the equatorial isomer and reacts with tetrazines much faster, as determined by stopped‐flow experiments. The improved properties resulted in different labeling performance of the insulin receptor on the surface of intact cells.     

Stereocontrolled Synthesis of Vinyl Boronates and Vinyl Silanes via Atom‐Economical Ruthenium‐Catalyzed Alkene–Alkyne Coupling

The synthesis of vinyl boronates and vinyl silanes was achieved by employing a Ru‐catalyzed alkene–alkyne coupling reaction of allyl boronates or allyl silanes with various alkynes. The double bond geometry in the generated vinyl boronates can be remotely controlled by the juxtaposing boron‐ and silicon groups on the alkyne substrate. The synthetic utility of the coupling products has been demonstrated in a variety of synthetic transformations, including iterative cross‐coupling reactions, and a Chan‐Lam‐type allyloxylation followed by a Claisen rearrangement. A sequential one‐pot alkene‐alkyne‐coupling/allylation‐sequence with an aldehyde to deliver a highly complex α‐silyl‐β‐hydroxy olefin with a handle for further functionalization was also realized.     

Synthesis and Electrochemical Behavior of Electron‐Rich s‐Tetrazine and Triazolo‐tetrazine Nitrate Esters

We have prepared energetic nitrate ester derivatives of 1,2,4,5‐tetrazine and 1,2,4‐triazolo[4,3‐b]‐[1,2,4,5]‐tetrazine ring systems as model compounds to study the electrochemical behavior of tetrazines in the presence of explosive groups. The model compounds showed lower thermal stabilities relative to PETN (pentaerythritol tetranitrate), but slightly improved mechanical sensitivities. The presence of electron‐rich amine donors leads to a cathodic shift of the tetrazine redox potentials relative to those of previously reported tetrazine explosives. At these potentials, electron‐rich tetrazines with either covalently bound or co‐dissolved nitrate ester groups are irreversibly reduced. Effectively, changes in the electronic structure of tetrazines affect their electrochemical response to the presence of nitrate ester groups. Thus, it may be possible to develop tetrazine‐based electrochemical sensors for the detection of specific explosives and electrocatalysts for their disposal.     

Genetic Encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels-Alder reactions

Rapid, site-specific labeling of proteins with diverse probes remains an outstanding challenge for chemical biologists. Enzyme-mediated labeling approaches may be rapid but use protein or peptide fusions that introduce perturbations into the protein under study and may limit the sites that can be labeled, while many "bioorthogonal" reactions for which a component can be genetically encoded are too slow to effect quantitative site-specific labeling of proteins on a time scale that is useful for studying many biological processes. We report a fluorogenic reaction between bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN) and tetrazines that is 3-7 orders of magnitude faster than many bioorthogonal reactions. Unlike the reactions of strained alkenes, including trans-cyclooctenes and norbornenes, with tetrazines, the BCN-tetrazine reaction gives a single product of defined stereochemistry. We have discovered aminoacyl-tRNA synthetase/tRNA pairs for the efficient site-specific incorporation of a BCN-containing amino acid, 1, and a trans-cyclooctene-containing amino acid 2 (which also reacts extremely rapidly with tetrazines) into proteins expressed in Escherichia coli and mammalian cells. We demonstrate the rapid fluorogenic labeling of proteins containing 1 and 2 in vitro, in E. coli , and in live mammalian cells. These approaches may be extended to site-specific protein labeling in animals, and we anticipate that they will have a broad impact on labeling and imaging studies.     

Terminal Alkenes as Versatile Chemical Reporter Groups for Metabolic Oligosaccharide Engineering

The Diels–Alder reaction with inverse electron demand (DAinv reaction) of 1,2,4,5‐tetrazines with electron rich or strained alkenes was proven to be a bioorthogonal ligation reaction that proceeds fast and with high yields. An important application of the DAinv reaction is metabolic oligosaccharide engineering (MOE) which allows the visualization of glycoconjugates in living cells. In this approach, a sugar derivative bearing a chemical reporter group is metabolically incorporated into cellular glycoconjugates and subsequently derivatized with a probe by means of a bioorthogonal ligation reaction. Here, we investigated a series of new mannosamine and glucosamine derivatives with carbamate‐linked side chains of varying length terminated by alkene groups and their suitability for labeling cell‐surface glycans. Kinetic investigations showed that the reactivity of the alkenes in DAinv reactions increases with growing chain length. When applied to MOE, one of the compounds, peracetylated N‐butenyloxycarbonylmannosamine, was especially well suited for labeling cell‐surface glycans. Obviously, the length of its side chain represents the optimal balance between incorporation efficiency and speed of the labeling reaction. Sialidase treatment of the cells before the bioorthogonal labeling reaction showed that this sugar derivative is attached to the glycans in form of the corresponding sialic acid derivative and not epimerized to another hexosamine derivative to a considerable extent.     

Regioselectivity of the reactions of 4,5‐diphenylimidazole‐2‐thione with 1‐chloro‐2,3‐epoxy‐propane and 1‐bromo‐propene,efficient precursors for imidazo[2,1‐b]thiazine and thiazole. Effect of microwave and solid support

A solid support under microwave (MW) irradiation without solvent allowed the synthesis of the 2,3‐epoxy‐propyl‐thioimidazole 4 , regioselectively, and prohibited its cyclization to give the imidazo[2,1‐b]thiazine 3 from the reaction of 4,5‐diphenylimidazole‐2‐thione ( 1 ) with 1‐chloro‐2,3‐epoxy‐propane ( 2 ). The formation of the latter required basic conditions whereby it became the sole product; the change of the basic catalyst changed the ratio of the two products under both conventional and microwave (MW) conditions. A regioselective allylation of 1 with allyl bromide in presence of triethylamine gave the S‐allyl 8 , while in presence of potassium carbonate led to the S,N‐bis(allylated) derivative 9 . The intramolecular ring closure of 8 in presence of sulfuric acid afforded the imidazothiazole 16 . Protection of the sulfur in 1 and subsequent reaction with allyl bromide gave the N‐allylated derivative and with 2 gave N‐3‐chloro‐prop‐1‐yl derivative that shed light on the preferred route for the formation of 3 and 4 . The reactivity encountered during the alkylation of 1 with 2 has been theoretically investigated by using the AM1 method.     

Ortho‐Functionalized Aryltetrazines by Direct Palladium‐Catalyzed C−H Halogenation: Application to Fast Electrophilic Fluorination Reactions

A general catalyzed direct C?H functionalization of s‐tetrazines is reported. Under mild reaction conditions, N‐directed ortho‐C?H activation of tetrazines allows the introduction of various functional groups, thus forming carbon–heteroatom bonds: C?X (X=I, Br, Cl) and C?O. Based on this methodology, we developed electrophilic mono‐ and poly‐ortho‐fluorination of tetrazines. Microwave irradiation was optimized to afford fluorinated s‐aryltetrazines, with satisfactory selectivity, within only ten minutes. This work provides an efficient and practical entry for further accessing highly substituted tetrazine derivatives (iodo, bromo, chloro, fluoro, and acetate precursors). It gives access to ortho‐functionalized aryltetrazines which are difficult to obtain by classical Pinner‐like syntheses.     

Fluorescent Triazole Urea Activity‐Based Probes for the Single‐Cell Phenotypic Characterization of Staphylococcus aureus

Phenotypically distinct cellular (sub)populations are clinically relevant for the virulence and antibiotic resistance of a bacterial pathogen, but functionally different cells are usually indistinguishable from each other. Herein, we introduce fluorescent activity‐based probes as chemical tools for the single‐cell phenotypic characterization of enzyme activity levels in Staphylococcus aureus. We screened a 1,2,3‐triazole urea library to identify selective inhibitors of fluorophosphonate‐binding serine hydrolases and lipases in S. aureus and synthesized target‐selective activity‐based probes. Molecular imaging and activity‐based protein profiling studies with these probes revealed a dynamic network within this enzyme family involving compensatory regulation of specific family members and exposed single‐cell phenotypic heterogeneity. We propose the labeling of enzymatic activities by chemical probes as a generalizable method for the phenotyping of bacterial cells at the population and single‐cell level.     

Synthesis and alkylation of 5‐(3‐chlorobenzo[b]thien‐2‐yl)‐4H‐1,2,4‐triazole‐3‐thiol under classical and microwave conditions. AM1 semiemperical calculations for investigating the regioselectivity of alkylation

Under microwave irradiation (MWI), 5‐(3‐chlorobenzo[b]thien‐2‐yl)‐4H‐1,2,4‐triazole‐3‐thiol ( 3 ) was synthesized in a good yield by intramolecular cyclization of the carbonyl thiosemicarbazide 2. A regioselective S‐alkylation of 3 with benzyl chloride or allyl bromide has been achieved by using triethylamine as a base, while other different basic conditions led to a mixture of bis(alkylated) derivatives N⁴, S‐ and S, N²‐, under both of classical and MWI conditions. The relative stabilities, charge densities, dipole moments and electronic energies of reactants, transition states and intermediates were calculated by the AM1 method and used for investigating the regioselectivity.     

Vinylboronic Acids as Fast Reacting,Synthetically Accessible,and Stable Bioorthogonal Reactants in the Carboni–Lindsey Reaction

Bioorthogonal reactions are widely used for the chemical modification of biomolecules. The application of vinylboronic acids (VBAs) as non‐strained, synthetically accessible and water‐soluble reaction partners in a bioorthogonal inverse electron‐demand Diels–Alder (iEDDA) reaction with 3,6‐dipyridyl‐s‐tetrazines is described. Depending on the substituents, VBA derivatives give second‐order rate constants up to 27 m ⁻¹ s⁻¹ in aqueous environments at room temperature, which is suitable for biological labeling applications. The VBAs are shown to be biocompatible, non‐toxic, and highly stable in aqueous media and cell lysate. Furthermore, VBAs can be used orthogonally to the strain‐promoted alkyne–azide cycloaddition for protein modification, making them attractive complements to the bioorthogonal molecular toolbox.     

N‐Oxide 1,2,4,5‐Tetrazine‐Based High‐Performance Energetic Materials

One route to high density and high performance energetic materials based on 1,2,4,5‐tetrazine is the introduction of 2,4‐di‐N‐oxide functionalities. Based on several examples and through theoretical analysis, the strategy of regioselective introduction of these moieties into 1,2,4,5‐tetrazines has been developed. Using this methodology, various new tetrazine structures containing the N‐oxide functionality were synthesized and fully characterized using IR, NMR, and mass spectroscopy, elemental analysis, and single‐crystal X‐ray analysis. Hydrogen peroxide (50 %) was used very effectively in lieu of the usual 90 % peroxide in this system to generate N‐oxide tetrazine compounds successfully. Comparison of the experimental densities of N‐oxide 1,2,4,5‐tetrazine compounds with their 1,2,4,5‐tetrazine precursors shows that introducing the N‐oxide functionality is a highly effective and feasible method to enhance the density of these materials. The heats of formation for all compounds were calculated with Gaussian 03 (revision D.01) and these values were combined with measured densities to calculate detonation pressures (P) and velocities (ν_D) of these energetic materials (Explo 5.0 v. 6.01). The new oxygen‐containing tetrazines exhibit high density, good thermal stability, acceptable oxygen balance, positive heat of formation, and excellent detonation properties, which, in some cases, are superior to those of 1,3,5‐tritnitrotoluene (TNT), 1,3,5‐trinitrotriazacyclohexane (RDX), and octahydro‐1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocine (HMX).     

Strain‐Promoted Reaction of 1,2,4‐Triazines with Bicyclononynes

Strain‐promoted inverse electron‐demand Diels–Alder cycloaddition (SPIEDAC) reactions between 1,2,4,5‐tetrazines and strained dienophiles, such as bicyclononynes, are among the fastest bioorthogonal reactions. However, the synthesis of 1,2,4,5‐tetrazines is complex and can involve volatile reagents. 1,2,4‐Triazines also undergo cycloaddition reactions with acyclic and unstrained dienophiles at elevated temperatures, but their reaction with strained alkynes has not been described. We postulated that 1,2,4‐triazines would react with strained alkynes at low temperatures and therefore provide an alternative to the tetrazine cycloaddition reaction for use in in vitro or in vivo labelling experiments. We describe the synthesis of a 1,2,4‐triazin‐3‐ylalanine derivative fully compatible with the fluorenylmethyloxycarbonyl (Fmoc) strategy for peptide synthesis and demonstrate its reaction with strained bicyclononynes at 37 °C with rates comparable to the reaction of azides with the same substrates. The synthetic route to triazinylalanine is readily adaptable to late‐stage functionalization of other probe molecules, and the 1,2,4‐triazine‐SPIEDAC therefore has potential as an alternative to tetrazine cycloaddition for applications in cellular and biochemical studies.     

Energetic Trinitro‐ and Fluorodinitroethyl Ethers of 1,2,4,5‐Tetrazines

Several new energetic ethyl ethers of 1,2,4,5‐tetrazine have been synthesized. These molecules display good thermal stability, good oxygen balance, and high densities. Included in these studies are a 2,2,2‐trinitroethoxy 1,2,4,5‐tetrazine and two fluorodinitroethoxy 1,2,4,5‐tetrazines. One of these compounds was converted into the di‐N‐oxide derivative. The sensitivity of these materials towards destructive stimuli was determined, and overall the materials show promising energetic performance properties.