Tetrazine-Triggered Release of Carboxylic-Acid-Containing Molecules for Activation of an Anti-inflammatory Drug

In addition to its use for the study of biomolecules in living systems, bioorthogonal chemistry has emerged as a promising strategy to enable protein or drug activation in a spatially and temporally controlled manner. This study demonstrates the application of a bioorthogonal inverse electron-demand Diels–Alder (iEDDA) reaction to cleave trans-cyclooctene (TCO) and vinyl protecting groups from carboxylic acid-containing molecules. The tetrazine-mediated decaging reaction proceeded under biocompatible conditions with fast reaction kinetics (<2 min). The anti-inflammatory activity of ketoprofen was successfully reinstated after decaging of the nontoxic TCOprodrug in live macrophages. Overall, this work expands the scope of functional groups and the application of decaging reactions to a new class of drugs.     

Comparison of Bioorthogonal β-Lactone Activity-Based Probes for Selective Labeling of Penicillin-Binding Proteins

Penicillin-binding proteins (PBPs) are a family of bacterial enzymes that are key components of cell-wall biosynthesis and the target of β-lactam antibiotics. Most microbial pathogens contain multiple structurally homologous PBP isoforms, making it difficult to target individual PBPs. To study the roles and regulation of specific PBP isoforms, a panel of bioorthogonal β-lactone probes was synthesized and compared. Fluorescent labeling confirmed selectivity, and PBPs were selectively enriched from Streptococcus pneumoniae lysates. Comparisons between fluorescent labeling of probes revealed that the accessibility of bioorthogonal reporter molecules to the bound probe in the native protein environment exerts a more significant effect on labeling intensity than the bioorthogonal reaction used, observations that are likely applicable beyond this class of probes or proteins. Selective, bioorthogonal activity-based probes for PBPs will facilitate the activity-based determination of the roles and regulation of specific PBP isoforms, a key gap in knowledge that has yet to be filled.     

Click‐Chemistry‐Mediated Rapid Microbubble Capture for Acute Thrombus Ultrasound Molecular Imaging

Bioorthogonal coupling chemistry has been studied as a potentially advantageous approach for molecular imaging because it offers rapid, efficient, and strong binding, which might also benefit stability, production, and chemical conjugation. The inverse‐electron‐demand Diels–Alder reaction between a 1,2,4,5‐tetrazine and trans‐cyclooctene (TCO) is an example of a highly selective and rapid bioorthogonal coupling reaction that has been used successfully to prepare targeted molecular imaging probes. Here we report a fast, reliable, and highly sensitive approach, based on a two‐step pretargeting bioorthogonal approach, to achieving activated‐platelet‐specific CD62p‐targeted thrombus ultrasound molecular imaging. Tetrazine‐modified microbubbles (tetra‐MBs) could be uniquely and rapidly captured by subsequent click chemistry of thrombus tagged with a trans‐cyclooctene‐pretreated CD62p antibody. Moreover, such tetra‐MBs showed great long‐term stability under physiological conditions, thus offering the ability to monitor thrombus changes in real time. We demonstrated for the first time that a bioorthogonal targeting molecular ultrasound imaging strategy based on tetra‐MBs could be a simple but powerful tool for rapid diagnosis of acute thrombosis.     

N3-Kethoxal-Based Bioorthogonal Intracellular RNA Labeling

There is growing interest in developing intracellular RNA tools. Herein, we describe a strategy for N₃-kethoxal (N₃K)-based bioorthogonal intracellular RNA functionalization. With N₃K labeling followed by an in vivo click reaction with DBCO derivatives, RNA can be modified with fluorescent or phenol groups. This strategy provides a new way of labeling RNA inside cells.     

New Biocompatible β-Phosphorylated Linear Nitrones Targeting Mitochondria: Protective Effect in Apoptotic Cells

The mitochondrion, an essential organelle involved in cellular respiration, energy production, and cell death, is the main cellular source of reactive oxygen species (ROS), including superoxide. Mitochondrial diseases resulting from uncontrolled/excess ROS generation are an emerging public health concern and there is current interest in specific mitochondriotropic probes to get information on in-situ ROS production. As such, nitrones vectorized by the triphenylphosphonium (TPP) cation have recently drawn attention despite reported cytotoxicity. Herein, we describe the synthesis of 13 low-toxic derivatives of N-benzylidene-1-diethoxyphosphoryl-1-methylethylamine N-oxide (PPN) alkyl chain-grafted to a pyridinium, triethylammonium or berberinium lipophilic cation. These nitrones showed in-vitro superoxide quenching activity and EPR/spin-trapping efficiency towards biologically relevant free radicals, including superoxide and hydroxyl radicals. Their mitochondrial penetration was confirmed by ³¹P NMR spectroscopy, and their anti-apoptotic properties were assessed in Schwann cells treated with hydrogen peroxide. Two pyridinium-substituted PPNs were identified as potentially better alternatives to TPP nitrones conjugates for studying mitochondrial oxidative damage.     

Micelle‐Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid‐Embedded Surface of a GPCR

Genetically encoded p‐azido‐phenylalanine (azF) residues in G protein‐coupled receptors (GPCRs) can be targeted with dibenzocyclooctyne‐modified (DIBO‐modified) fluorescent probes by means of strain‐promoted [3+2] azide–alkyne cycloaddition (SpAAC). Here we show that azF residues situated on the transmembrane surfaces of detergent‐solubilized receptors exhibit up to 1000‐fold rate enhancement relative to azF residues on water‐exposed surfaces. We show that the amphipathic moment of the labeling reagent, consisting of hydrophobic DIBO coupled to hydrophilic Alexa dye, results in strong partitioning of the DIBO group into the hydrocarbon core of the detergent micelle and consequently high local reactant concentrations. The observed rate constant for the micelleenhanced SpAAC is comparable with those of the fastest bioorthogonal labeling reactions known. Targeting hydrophobic regions of membrane proteins by use of micelle‐enhanced SpAAC should expand the utility of bioorthogonal labeling strategies.     

Optoelectronic multifunctionality of combustion-activated fluorine-doped tin oxide films with high optical transparency

As transparent conducting oxides (TCOs) have been widely used as a common component of many optoelectronic applications, ensuring high conductivity and transparency TCOs has become a pivotal concern. In the present study, we report developing the combustion-activated pyrolysis route of horizontal ultrasonic spray pyrolysis deposition (HUSPD) as a novel strategy to form highly transparent conducting fluorine-doped tin oxide (FTO) films. Compared to the basic route, the combustion-activated FTO films showed an attractive transparent conducting performance (figure of merit of 5.34?×?10^?2?Ω^?1) with a highly improved optical transparency (90.1%) due to the formation of a smooth and dense film structure to reduce light scattering on the surface, and a decrease of oxygen vacancies to broaden the optical bandgap, all of which yielded an excellent performance as compared to the previously reported studies on the FTO films. Moreover, when the combustion-activated FTO films were used as TCOs of electrochromic devices and dye-sensitized solar cells, they acquired multifunctional effects of (a) an efficient electron transfer by (200) preferred orientations of the FTO; (b) a relaxed light scattering on the interface due to smooth and dense surface morphology of the FTO films; and (c) a broad optical bandgap by decreased oxygen vacancies, resulting in an impressive improvement of both electrochromic and photovoltaic performances. Taken together, our results demonstrate that combustion-activated FTO films are an attractive technique for forming high-performance TCOs that can further be used in multifunctional optoelectronic devices.     

Ultrastructural Imaging of Salmonella–Host Interactions Using Super‐resolution Correlative Light‐Electron Microscopy of Bioorthogonal Pathogens

The imaging of intracellular pathogens inside host cells is complicated by the low resolution and sensitivity of fluorescence microscopy and by the lack of ultrastructural information to visualize the pathogens. Herein, we present a new method to visualize these pathogens during infection that circumvents these problems: by using a metabolic hijacking approach to bioorthogonally label the intracellular pathogen Salmonella Typhimurium and by using these bioorthogonal groups to introduce fluorophores compatible with stochastic optical reconstruction microscopy (STORM) and placing this in a correlative light electron microscopy (CLEM) workflow, the pathogen can be imaged within its host cell context Typhimurium with a resolution of 20 nm. This STORM‐CLEM approach thus presents a new approach to understand these pathogens during infection.     

Nitrones as Trapping Reagents of α,β‐Unsaturated Carbene Intermediates – [1,2]Oxazino[5,4‐b]indoles by a Platinum‐ Catalyzed Intermolecular [3+3] Cycloaddition

Some readily available Boc‐protected 2‐(3‐methoxy‐1‐propynyl)anilines and nitrones in platinum‐catalyzed reactions deliver [1,2]oxazino[5,4‐b]indoles. Twelve examples with yields of 41–95% are reported. Different substituents like nitro, trifluoromethyl, fluoro, bromo, and ester groups are tolerated. With regard to the mechanism, this reaction probably combines an initial intramolecular cyclization/elimination to vinylcarbenoid species and a subsequent stepwise intermolecular [3+3] cycloaddition with the nitrones.     

Nucleobase-Derived Nitrones: Synthesis and Antioxidant and Neuroprotective Activities in an In Vitro Model of Ischemia–Reperfusion

Herein, we report the synthesis, antioxidant, and neuroprotective properties of some nucleobase-derived nitrones named 9a–i. The neuroprotective properties of nitrones, 9a–i, were measured against an oxygen-glucose-deprivation in vitro ischemia model using human neuroblastoma SH-SY5Y cells. Our results indicate that nitrones, 9a–i, have better neuroprotective and antioxidant properties than α-phenyl-N-tert-butylnitrone (PBN) and are similar to N-acetyl-L-cysteine (NAC), a well-known antioxidant and neuroprotective agent. The nitrones with the highest neuroprotective capacity were those containing purine nucleobases (nitrones 9f, g, B = adenine, theophylline), followed by nitrones with pyrimidine nucleobases with H or F substituents at the C5 position (nitrones 9a, c). All of these possess EC₅₀ values in the range of 1–6 μM and maximal activities higher than 100%. However, the introduction of a methyl substituent (nitrone 9b, B = thymine) or hard halogen substituents such as Br and Cl (nitrones 9d, e, B = 5-Br and 5-Cl uracil, respectively) worsens the neuroprotective activity of the nitrone with uracil as the nucleobase (9a). The effects on overall metabolic cell capacity were confirmed by results on the high anti-necrotic (EC_50′s ≈ 2–4 μM) and antioxidant (EC_50′s ≈ 0.4–3.5 μM) activities of these compounds on superoxide radical production. In general, all tested nitrones were excellent inhibitors of superoxide radical production in cultured neuroblastoma cells, as well as potent hydroxyl radical scavengers that inhibit in vitro lipid peroxidation, particularly, 9c, f, g, presenting the highest lipoxygenase inhibitory activity among the tested nitrones. Finally, the introduction of two nitrone groups at 9a and 9d (bis-nitronas 9g, i) did not show better neuroprotective effects than their precursor mono-nitrones. These results led us to propose nitrones containing purine (9f, g) and pyrimidine (9a, c) nucleobases as potential therapeutic agents for the treatment of cerebral ischemia and/or neurodegenerative diseases, leading us to further investigate their effects using in vivo models of these pathologies.     

Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization

The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.     

Site-Specific and Multiple Fluorogenic Metabolic Glycan Labeling and Glycoproteomic Profiling in Live Cells

Multicolor labeling for monitoring the intracellular localization of the same target type in the native environment using chemical fluorescent dyes is a challenging task. This approach requires both bioorthogonal and biocompatible ligations with an excellent fluorescence signal-to-noise ratio. Here, we present a metabolic glycan labeling technique that uses homemade fluorogenic dyes to investigate glycosylation patterns in live cells. These dyes allowed us to demonstrate rapid and efficient simultaneous multilabeling of glycoconjugates with minimum fluorescence noise. Our results demonstrate that this approach is capable of not only probing sialylation and GlcNAcylation in cells but also specifically labeling the cell-surface and intracellular sialylated glycoconjugates in live cells. In particular, we performed site-specific dual-channel fluorescence imaging of extra and intracellular sialylated glycans in HeLa and PC9 cancer cells as well as identified fluorescently labeled sialylated glycoproteins and glycans by a direct enrichment approach combined with an MS-based proteomic analysis in the same experiment. In conclusion, this study provides multilabeling tools in cellular systems for simultaneous site-specific glycan imaging and glycoproteomic analysis to study potential cancer- and disease-associated glycoconjugates.     

Coordination‐Assisted Bioorthogonal Chemistry: Orthogonal Tetrazine Ligation with Vinylboronic Acid and a Strained Alkene

Bioorthogonal chemistry can be used for the selective modification of biomolecules without interfering with any other functionality that might be present. Recent developments in the field include orthogonal bioorthogonal reactions to modify multiple biomolecules simultaneously. During our research, we observed that the reaction rates for the bioorthogonal inverse‐electron‐demand Diels–Alder (iEDDA) reactions between nonstrained vinylboronic acids (VBAs) and dipyridyl‐s‐tetrazines were exceptionally higher than those between VBAs and tetrazines bearing a methyl or phenyl substituent. As VBAs are mild Lewis acids, we hypothesised that coordination of the pyridyl nitrogen atom to the boronic acid promoted tetrazine ligation. Herein, we explore the molecular basis and scope of VBA–tetrazine ligation in more detail and benefit from its unique reactivity in the simultaneous orthogonal tetrazine labelling of two proteins modified with VBA and norbornene, a widely used strained alkene. We further show that the two orthogonal iEDDA reactions can be performed in living cells by labelling the proteasome by using a nonselective probe equipped with a VBA and a subunit‐selective VBA bearing a norbornene moiety.     

Gold(I)‐Catalyzed Regio‐ and Stereoselective 1,3‐Dipolar Cycloaddition Reactions of 1‐(1‐Alkynyl)cyclopropyl Oximes with Nitrones: A Modular Entry to Highly Substituted Pyrrolo[3,4‐d][1,2]oxazepines

An efficient approach for the synthesis of highly substituted pyrrolo[3,4‐d][1,2]oxazepines has been achieved by gold(I)‐catalyzed 1,3‐dipolar cycloaddition reactions of 1‐(1‐alkynyl)cyclopropyl oximes with nitrones in good to excellent yields as a single diastereomer. A complete chirality transfer was observed in this transformation.     

Photocontrol of the refractive index of poly(methyl methacrylate) with a nitrone additive

Hydroxy‐substituted aromatic nitrone derivatives were used for the photochemical control of the refractive index of poly(methyl methacrylate) (PMMA) films. Upon irradiation with 366‐nm light in solution, these derivatives underwent rearrangement reactions, which eventually produced N,N‐diarylformamide derivatives in quantitative yields. Similar photoreactions of the aromatic nitrones in the PMMA films lowered the refractive index of the films by as much as 0.014. The magnitude of the observed refractive‐index change was enough for hydroxy‐substituted nitrones to be used as additives for the fabrication of graded‐index‐type polymer optical fibers. In addition, the refractive index of the PMMA films remained almost constant at any conversion of the starting nitrone derivatives for at least 70 days at room temperature. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 93: 2517–2520, 2004     

Small Ring Compounds and N-oxides: Cycloadditions and Related Processes

The review discusses the possibilities for reactions of small ring compounds (cyclopropanes, cyclobutanes, and their heteroanalogs) with various N-oxides (nitrones, nitronates, nitrile oxides, etc.). Two major paths include: formal cycloadditions of small cycles with N-oxide possessing dipoles, and [3+2] cycloadditions of small cyclic alkenes with N-oxides, followed by N−O bond cleavage-assisted rearrangement/ring opening.     

Hydrophilic trans‐Cyclooctenylated Noncanonical Amino Acids for Fast Intracellular Protein Labeling

Introduction of bioorthogonal functionalities (e.g., trans‐cyclooctene‐TCO) into a protein of interest by site‐specific genetic encoding of non‐canonical amino acids (ncAAs) creates uniquely targetable platforms for fluorescent labeling schemes in combination with tetrazine‐functionalized dyes. However, fluorescent labeling of an intracellular protein is usually compromised by high background, arising from the hydrophobicity of ncAAs; this is typically compensated for by hours‐long washout to remove excess ncAAs from the cellular interior. To overcome these problems, we designed, synthesized, and tested new, hydrophilic TCO‐ncAAs. One derivative, DOTCO‐lysine was genetically incorporated into proteins with good yield. The increased hydrophilicity shortened the excess ncAA washout time from hours to minutes, thus permitting rapid labeling and subsequent fluorescence microscopy.     

Catalytic Asymmetric 1, 3‐Dipolar Cycloaddition Reaction of Nitrones with α′‐Phosphoric Enones by a Chiral Ligand‐ Copper(II) Triflate Complex

Using the C₂‐symmetric bis‐oxazoline copper(II) catalyst 6f as a chiral Lewis acid, α′‐phosphoric enones 2 undergo 1,3‐dipolar cycloaddition with nitrones 3 to provide isoxazolidines 4 with very high enantioselectivity and endo/exo selectivity.     

Enantioselective Synthesis of 4‐Isoxazolines by 1,3‐Dipolar Cycloadditions of Nitrones to Alkynals Catalyzed by Fluorodiphenylmethylpyrrolidines

The first organocatalytic enantioselective 1,3‐dipolar reaction between nitrones and alkynals catalyzed by (S)‐2‐(fluorodiphenylmethyl)pyrrolidine to give 4‐isoxazolines (2,3‐dihydroisoxazoles) with high enantiomeric excess, excellent yields and low catalyst loading (1–5 mol%) is presented. The catalytic loading could be reduced to 1 mol% with only slight increases in reaction times.     

Bioorthogonal chemical reporters for analyzing protein lipidation and lipid trafficking

Protein lipidation and lipid trafficking control many key biological functions in all kingdoms of life. The discovery of diverse lipid species and their covalent attachment to many proteins has revealed a complex and regulated network of membranes and lipidated proteins that are central to fundamental aspects of physiology and human disease. Given the complexity of lipid trafficking and the protein targeting mechanisms involved with membrane lipids, precise and sensitive methods are needed to monitor and identify these hydrophobic molecules in bacteria, yeast, and higher eukaryotes. Although many analytical methods have been developed for characterizing membrane lipids and covalently modified proteins, traditional reagents and approaches have limited sensitivity, do not faithfully report on the lipids of interest, or are not readily accessible. The invention of bioorthogonal ligation reactions, such as the Staudinger ligation and azide-alkyne cycloadditions, has provided new tools to address these limitations, and their use has begun to yield fresh insight into the biology of protein lipidation and lipid trafficking. In this Account, we discuss how these new bioorthogonal ligation reactions and lipid chemical reporters afford new opportunities for exploring the biology of lipid-modified proteins and lipid trafficking. Lipid chemical reporters from our laboratory and several other research groups have enabled improved detection and large-scale proteomic analysis of fatty-acylated and prenylated proteins. For example, fatty acid and isoprenoid chemical reporters in conjunction with bioorthogonal ligation methods have circumvented the limited sensitivity and hazards of radioactive analogues, allowing rapid and robust fluorescent detection of lipidated proteins in all organisms tested. These chemical tools have revealed alterations in protein lipidation in different cellular states and are beginning to provide unique insights in mechanisms of regulation. Notably, the purification of proteins labeled with lipid chemical reporters has allowed both the large-scale analysis of lipidated proteins as well as the discovery of new lipidated proteins involved in metabolism, gene expression, and innate immunity. Specific lipid reporters have also been developed to monitor the trafficking of soluble lipids; these species are enabling bioorthogonal imaging of membranes in cells and tissues. Future advances in bioorthogonal chemistry, specific lipid reporters, and spectroscopy should provide important new insight into the functional roles of lipidated proteins and membranes in biology.