Spirohexene-Tetrazine Ligation Enables Bioorthogonal Labeling of Class B G Protein-Coupled Receptors in Live Cells

Cannabinoid Receptor Signaling is Dependent on Sub-Cellular Location

G protein-coupled receptors (GPCRs) are membrane bound signaling molecules that regulate many aspects of human physiology. Recent advances have demonstrated that GPCR signaling can occur both at the cell surface and internal cellular membranes. Our findings suggest that cannabinoid receptor 1 (CB1) signaling is highly dependent on its subcellular location. We find that intracellular CB1 receptors predominantly couple to Gαi while plasma membrane receptors couple to Gαs. Here we show subcellular location of CB1, and its signaling, is contingent on the choice of promoters and receptor tags. Heterologous expression with a strong promoter or N-terminal tag resulted in CB1 predominantly localizing to the plasma membrane and signaling through Gαs. Conversely, CB1 driven by low expressing promoters and lacking N-terminal genetic tags largely localized to internal membranes and signals via Gαi. Lastly, we demonstrate that genetically encodable non-canonical amino acids (ncAA) offer a solution to the problem of non-native N-terminal tags disrupting CB1 signaling. We identified sites in CB1R and CB2R which can be tagged with fluorophores without disrupting CB signaling or trafficking using (trans-cyclooctene attached to lysine (TCO*A)) and copper-free click chemistry to attach fluorophores in live cells. Together, our data demonstrate the origin of location bias in cannabinoid signaling which can be experimentally controlled and tracked in living cells through promoters and novel CBR tagging strategies.

Minimalist Tetrazine N-Acetyl Muramic Acid Probes for Rapid and Efficient Labeling of Commensal and Pathogenic Peptidoglycans in Living Bacterial Culture and During Macrophage Invasion

N-Acetyl muramic acid (NAM) probes containing alkyne or azide groups are commonly used to investigate aspects of cell wall synthesis because of their small size and ability to incorporate into bacterial peptidoglycan (PG). However, copper-catalyzed alkyne-azide cycloaddition (CuAAC) reactions are not compatible with live cells, and strain-promoted alkyne-azide cycloaddition (SPAAC) reaction rates are modest and, therefore, not as desirable for tracking the temporal alterations of bacterial cell growth, remodeling, and division. Alternatively, the tetrazine-trans-cyclooctene ligation (Tz-TCO), which is the fastest known bioorthogonal reaction and not cytotoxic, allows for rapid live-cell labeling of PG at biologically relevant time scales and concentrations. Previous work to increase reaction kinetics on the PG surface by using tetrazine probes was limited because of low incorporation of the probe. Described here are new approaches to construct a minimalist tetrazine (Tz)-NAM probe utilizing recent advancements in asymmetric tetrazine synthesis. This minimalist Tz-NAM probe was successfully incorporated into pathogenic and commensal bacterial PG where fixed and rapid live-cell, no-wash labeling was successful in both free bacterial cultures and in coculture with human macrophages. Overall, this probe allows for expeditious labeling of bacterial PG, thereby making it an exceptional tool for monitoring PG biosynthesis for the development of new antibiotic screens. The versatility and selectivity of this probe will allow for real-time interrogation of the interactions of bacterial pathogens in a human host and will serve a broader utility for studying glycans in multiple complex biological systems.

Two-Factor Fluorogenic Cyanine-Styryl Dyes with Yellow and Red Fluorescence for Bioorthogonal Labelling of DNA

An orange- and a red-emitting tetrazine-modified cyanine-styryl dyes were synthesized for bioorthogonal labelling of DNA by means of the Diels-Alder reaction with inverse electron demand. Both dyes use the concept of the "two-factor" fluorogenicity for nucleic acids: (i) The dyes are nucleic-acid sensitive by their non-covalent binding to DNA, and (ii) their covalently attached tetrazine moiety quench the fluorescence. As a result, the reaction with bicyclononyne- and spirohexene-modified DNA is significantly accelerated up to k2 =280,000 M-1  s-1 , and the fluorescence turn-on is enhanced up to 305. Both dyes are cell permeable even in low concentrations and undergo fluorogenic reactions with spirohexene-modified DNA in living HeLa cells. The fluorescence is enhanced in living cells to such an extent that washing procedures before cell imaging are not required. Their large Stokes shifts (up to 0.77 eV) also makes them well suited for imaging because the wavelength ranges for excitation and emission can be best possible separated. Furthermore, the spirohexene-modified nucleosides and DNA extend and improve the toolbox of already existing "clickable" dyes for live cell imaging.

Synthesis of Tetrazines from N-Allenylpyrrole-2-carbaldehydes and pH-Controlled Reversible Fragmentation

A one-pot highly selective approach to the synthesis of hitherto unknown tetrahydropyrrolo[2',1':3,4]pyrazino[1,2-b]pyrrolo[2',1':3,4]pyrazino[1,2-e][1,2,4,5]tetrazine ensembles from simple and available N-allenylpyrrole-2-carbaldehydes and hydrazines has been developed. The reaction proceeds in a very facile manner and tolerates different substituents in both pyrroles and hydrazines. The novel class of organic compounds, tetrahydrodipyrrolodipyrazinotetrazines, proves to be promising pH-sensitive switchers to deliver N-aminopyrrolopyrazinium salts in acidic media and then again tetrahydrodipyrrolodipyrazinotetrazines in basic media. Both transformations give the products in quantitative yields.

Detecting and measuring of GPCR signaling - comparison of human induced pluripotent stem cells and immortal cell lines

G protein-coupled receptors (GPCRs) are a large family of transmembrane proteins that play a major role in many physiological processes, and thus GPCR-targeted drug development has been widely promoted. Although research findings generated in immortal cell lines have contributed to the advancement of the GPCR field, the homogenous genetic backgrounds, and the overexpression of GPCRs in these cell lines make it difficult to correlate the results with clinical patients. Human induced pluripotent stem cells (hiPSCs) have the potential to overcome these limitations, because they contain patient specific genetic information and can differentiate into numerous cell types. To detect GPCRs in hiPSCs, highly selective labeling and sensitive imaging techniques are required. This review summarizes existing resonance energy transfer and protein complementation assay technologies, as well as existing and new labeling methods. The difficulties of extending existing detection methods to hiPSCs are discussed, as well as the potential of hiPSCs to expand GPCR research towards personalized medicine.

Quantitative Analysis and Optimization of Site-Specific Protein Bioconjugation in Mammalian Cells

Despite a range of covalent protein modifications, few techniques exist for quantification of protein bioconjugation in cells. Here, we describe a novel method for quantifying in cellulo protein bioconjugation through covalent bond formation with HaloTag. This approach utilizes unnatural amino acid (UAA) mutagenesis to selectively install a small and bioorthogonally reactive handle onto the surface of a protein. We utilized the fast kinetics and high selectivity of inverse electron-demand Diels-Alder cycloadditions to evaluate reactions of tetrazine phenylalanine (TetF) with strained trans-cyclooctene-chloroalkane (sTCO-CA) and trans-cyclooctene lysine (TCOK) with tetrazine-chloroalkane (Tet-CA). Following bioconjugation, the chloroalkane ligand is exposed for labeling by the HaloTag enzyme, allowing for straightforward quantification of bioconjugation via simple western blot analysis. We demonstrate the versatility of this tool for quickly and accurately determining the bioconjugation efficiency of different UAA/chloroalkane pairs and for different sites on different proteins of interest, including EGFP and the estrogen-related receptor ERRα.

Superfast Tetrazole-BCN Cycloaddition Reaction for Bioorthogonal Protein Labeling on Live Cells

Here we report the design of a superfast bioorthogonal ligation reactant pair comprising a sterically shielded, sulfonated tetrazole and bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN). The design involves placing a pair of water-soluble N-sulfonylpyrrole substituents at the C-phenyl ring of diphenyltetrazoles to favor the photoinduced cycloaddition reaction over the competing nucleophilic additions. First-principles computations provide vital insights into the origin of the tetrazole-BCN cycloaddition's superior kinetics compared to the tetrazole-spirohexene cycloaddition. The tetrazole-BCN cycloaddition also enabled rapid bioorthogonal labeling of glucagon receptors on live cells in as little as 15 s.

Dual fluorescent labeling of GLP-1R in live cells via enzymatic tagging and bioorthogonal chemistry

To study GPCR conformational dynamics in live cells, here we report an integrated approach combining enzymatic SNAP-tagging with bioorthogonal chemistry for dual fluorescent labeling of GLP-1R. The resulting GLP-1R conformational biosensors permit a FRET-based analysis of the receptor subdomain movement in response to ligand stimulation in live cells.

To study GPCR conformational dynamics in live cells, here we report an integrated approach combining enzymatic SNAP-tagging with bioorthogonal chemistry for dual fluorescent labeling of GLP-1R.

Bioorthogonal Chemistry and Its Applications

Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.

IEDDA: An Attractive Bioorthogonal Reaction for Biomedical Applications

The pretargeting strategy has recently emerged in order to overcome the limitations of direct targeting, mainly in the field of radioimmunotherapy (RIT). This strategy is directly dependent on chemical reactions, namely bioorthogonal reactions, which have been developed for their ability to occur under physiological conditions. The Staudinger ligation, the copper catalyzed azide-alkyne cycloaddition (CuAAC) and the strain-promoted [3 + 2] azide–alkyne cycloaddition (SPAAC) were the first bioorthogonal reactions introduced in the literature. However, due to their incomplete biocompatibility and slow kinetics, the inverse-electron demand Diels-Alder (IEDDA) reaction was advanced in 2008 by Blackman et al. as an optimal bioorthogonal reaction. The IEDDA is the fastest bioorthogonal reaction known so far. Its biocompatibility and ideal kinetics are very appealing for pretargeting applications. The use of a trans-cyclooctene (TCO) and a tetrazine (Tz) in the reaction encouraged researchers to study them deeply. It was found that both reagents are sensitive to acidic or basic conditions. Furthermore, TCO is photosensitive and can be isomerized to its cis-conformation via a radical catalyzed reaction. Unfortunately, the cis-conformer is significantly less reactive toward tetrazine than the trans-conformation. Therefore, extensive research has been carried out to optimize both click reagents and to employ the IEDDA bioorthogonal reaction in biomedical applications.

Arylethynyltrifluoroborate Dienophiles for on Demand Activation of IEDDA Reactions

Strained alkenes and alkynes are the predominant dienophiles used in inverse electron demand Diels–Alder (IEDDA) reactions. However, their instability, cross-reactivity, and accessibility are problematic. Unstrained dienophiles, although physiologically stable and synthetically accessible, react with tetrazines significantly slower relative to strained variants. Here we report the development of potassium arylethynyltrifluoroborates as unstrained dienophiles for fast, chemically triggered IEDDA reactions. By varying the substituents on the tetrazine (e.g., pyridyl- to benzyl-substituents), cycloaddition kinetics can vary from fast (k₂ = 21 M^–1 s^–1) to no reaction with an alkyne-BF₃ dienophile. The reported system was applied to protein labeling both in the test tube and fixed cells and even enabled mutually orthogonal labeling of two distinct proteins.

Photoclick Chemistry: A Bright Idea

At its basic conceptualization, photoclick chemistry embodies a collection of click reactions that are performed via the application of light. The emergence of this concept has had diverse impact over a broad range of chemical and biological research due to the spatiotemporal control, high selectivity, and excellent product yields afforded by the combination of light and click chemistry. While the reactions designated as "photoclick" have many important features in common, each has its own particular combination of advantages and shortcomings. A more extensive realization of the potential of this chemistry requires a broader understanding of the physical and chemical characteristics of the specific reactions. This review discusses the features of the most frequently employed photoclick reactions reported in the literature: photomediated azide-alkyne cycloadditions, other 1,3-dipolarcycloadditions, Diels-Alder and inverse electron demand Diels-Alder additions, radical alternating addition chain transfer additions, and nucleophilic additions. Applications of these reactions in a variety of chemical syntheses, materials chemistry, and biological contexts are surveyed, with particular attention paid to the respective strengths and limitations of each reaction and how that reaction benefits from its combination with light. Finally, challenges to broader employment of these reactions are discussed, along with strategies and opportunities to mitigate such obstacles.

Intracellular bioorthogonal labeling of glucagon receptor via tetrazine ligation

The third intracellular loop (ICL3) in the cytosolic face of glucagon receptor (GCGR) experiences significant conformational transition during receptor activation. It thus offers an attractive site for the introduction of organic fluorophores in our efforts to construct fluorescence-based GPCR biosensors. Herein, we report our confocal microscopic study of intracellular fluorescent labeling of ICL3 using a bioorthogonal chemistry strategy. Our approach involves the site-specific introduction of a strained alkene amino acid into the ICL3 through genetic code expansion, followed by a highly specific inverse electron-demand Diels-Alder reaction with the fluorescent tetrazine probes. Among the three strained alkene amino acids examined, both SphK and 2'-aTCOK offered successful fluorescent labeling of GCGR ICL3 with the appropriate tetrazine probes. At the same time, 4'-TCOK gave high background fluorescence due to its intracellular retention. The fluorescent tetrazine probes were designed following a computational model for background-free intracellular fluorescent labeling; however, their performance varied significantly in live-cell imaging as the strong non-specific signals interfered with the specific ones. Among all GCGR ICL3 mutants bearing a strained alkene, the H339SphK/2'-aTCOK mutants provided the best reaction partners for the BODIPY-Tz1/4 reagents in the bioorthogonal labeling reactions. The results from this study highlight the challenges in identifying bioorthogonal reactant pairs suitable for intracellular labeling of low-abundance receptors in live-cell imaging studies.

Bioorthogonal chemistry

Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.

Clicking of organelle-enriched probes for fluorogenic imaging of autophagic and endocytic fluxes

Autophagy and endocytosis are essential in regulating cellular homeostasis and cancer immunotherapeutic responses. Existing methods for autophagy and endocytosis imaging are susceptible to cellular micro-environmental changes, and direct fluorogenic visualization of their fluxes remains challenging. We develop a novel strategy via clicking of organelle-enriched probes (COP), which comprises a pair of trans-cyclooctenol (TCO) and tetrazine probes separately enriched in lysosomes and mitochondria (in autophagy) or plasma membrane (in endocytosis). These paired probes are merged and boost a fluorogenic click reaction in response to autophagic or endocytic flux that ultimately fuses mitochondria or plasma membrane into lysosomes. We demonstrate that this strategy enables direct visualization of autophagic and endocytic fluxes, and confer insight into correlation of autophagic or endocytic flux to cell surface expression of immunotherapeutic targets such as MHC-I and PD-L1. The COP strategy provides a new paradigm for imaging autophagic and endocytic fluxes, and affords potential for improved cancer immunotherapy using autophagy or endocytosis inhibitors.

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.

Fluorescent bioorthogonal labeling of class B GPCRs in live cells

In this method paper, we describe the protocols for selective labeling of GCGR, a member of the class B GPCR family regulating glucose homeostasis, in live cells. A two-step procedure is presented in which a strained alkene chemical reporter is inserted into any desired location within the GPCR in the first step, followed by a robust bioorthogonal ligation reaction with a fluorophore-conjugated tetrazine or tetrazole reagent in the second step. The amber codon suppression strategy was adopted for site-specific incorporation of the strained alkene reporter, either spirohexene or trans-cyclooctene, in HEK293T cells. Subsequently, the inverse electron-demand Diels-Alder reaction with an AF647-conjugated 3,6-di (2-pyridyl)-S-tetrazine (DpTz) was performed with the alkene-encoded GCGR on live-cell surface. Alternatively, a photo-induced cycloaddition with a Cy5-conjugated, sterically shielded tetrazole was carried out, giving rise to faster fluorescent labeling along with excellent selectivity. Owing to their robust reaction kinetics and excellent chemoselectivity, the bioorthogonal labeling protocols described here could be readily adapted to labeling any accessible protein targets, e.g., membrane proteins, in live cells.

Expanding the substrate selectivity of SNAP/CLIP-tagging of intracellular targets

SNAP-tag belongs to a class of genetic tools of protein labeling that complements fluorescent proteins. This single-turnover enzyme is a mutant of human DNA repair protein O⁶-alkylguanine-DNA alkyltransferase (hAGT). It accepts, in most cases, label-carrying O⁶-benzylguanines or benzyl-2-chloro-6-aminopyrimidines as suitable substrates. In this article, strategies and methods to expand the scope of the labels for intracellular proteins of live cells via the actions of SNAP-tag are presented. CLIP-tag is another mutant of the hAGT that was engineered to have mutually exclusive substrate specificity from SNAP-tag. The use of complementary bioorthogonal chemical reactions in conjunction with orthogonal enzymatic SNAP/CLIP-tags for the purpose of dual-color intracellular labeling is also described.

Optimized aqueous Kinugasa reactions for bioorthogonal chemistry applications

Kinugasa reactions hold potential for bioorthogonal chemistry in that the reagents can be biocompatible. Unlike other bioorthogonal reaction products, β-lactams are potentially reactive, which can be useful for synthesizing new biomaterials. A limiting factor for applications consists of slow reaction rates. Herein, we report an optimized aqueous copper(i)-catalyzed alkyne-nitrone cycloaddition involving rearrangement (CuANCR) with rate accelerations made possible by the use of surfactant micelles. We have investigated the factors that accelerate the aqueous CuANCR reaction and demonstrate enhanced modification of a model membrane-associated peptide. We discovered that lipids/surfactants and alkyne structure have a significant impact on the reaction rate, with biological lipids and electron-poor alkynes showing greater reactivity. These new findings have implications for the use of CuANCR for modifying integral membrane proteins as well as live cell labelling and other bioorthogonal applications.

Functionalizing nanoparticles with cancer-targeting antibodies: A comparison of strategies

Standard cancer therapies sometimes fail to deliver chemotherapeutic drugs to tumor cells in a safe and effective manner. Nanotechnology takes the lead in providing new therapeutic options for cancer due to major potential for selective targeting and controlled drug release. Antibodies and antibody fragments are attracting much attention as a source of targeting ligands to bind specific receptors that are overexpressed on cancer cells. Therefore, researchers are devoting time and effort to develop targeting strategies based on nanoparticles functionalized with antibodies, which hold great promise to enhance therapeutic efficacy and circumvent severe side effects. Several methods have been described to immobilize antibodies on the surface of nanoparticles. However, selecting the most appropriate for each application is challenging but also imperative to preserve antigen binding ability and yield stable antibody-conjugated nanoparticles. From this perspective, we aim to provide considerable knowledge on the most widely used methods of functionalization that can be helpful for decision-making and design of conjugation protocols as well. This review summarizes adsorption, covalent conjugation (carbodiimide, maleimide and "click" chemistries) and biotin-avidin interaction, while discussing the advantages, limitations and relevant therapeutic approaches currently under investigation.

Predicting reactivity for bioorthogonal cycloadditions involving nitrones

Nitrones are useful dipoles in both synthesis and in bioorthogonal transformations to report on biological phenomena. In bioorthogonal reactions, nitrones are both small and relatively easy to incorporate into biomolecules, while providing versatility in their ability to harbor different substituents that tune their reactivity. Herein, we examine the reactivities of some common and useful nitrone cycloadditions using density functional theory (DFT) and the distortion/interaction (D/I) model. The data show that relative reactivities can be predicted using these approaches, and useful insights gained further enchancing reactivities of both nitrones and their dipolarophile reaction partners. We find that D/I is a useful guide to understanding and predicting reactivities of cycloadditions involving nitrones.

Nitrones are useful dipoles in both synthesis and in bioorthogonal transformations to report on biological phenomena.

Addition of Isocyanide-Containing Amino Acids to the Genetic Code for Protein Labeling and Activation

Site-specific introduction of bioorthogonal handles into biomolecules provides powerful tools for studying and manipulating the structures and functions of proteins. Recent advances in bioorthogonal chemistry demonstrate that tetrazine-based bioorthogonal cycloaddition is a particularly useful methodology due to its high reactivity, biological selectivity, and turn-on property for fluorescence imaging. Despite its broad applications in protein labeling and imaging, utilization of tetrazine-based bioorthogonal cycloaddition has been limited to date by the requirement of a hydrophobic strained alkene reactive moiety. Circumventing this structural requirement, we report the site-specific incorporation of noncanonical amino acids (ncAAs) with a small isocyanide (or isonitrile) group into proteins in both bacterial and mammalian cells. We showed that under physiological conditions and in the absence of a catalyst these isocyanide-containing ncAAs could react selectively with tetrazine molecules via [4 + 1]-cycloaddition, thus providing a versatile bioorthogonal handle for site-specific protein labeling and protein decaging. Significantly, these bioorthogonal reactions between isocyanides and tetrazines also provide a unique mechanism for the activation of tetrazine-quenched fluorophores. The addition of these isocyanide-containing ncAAs to the list of 20 commonly used, naturally occurring amino acids expands our repertoire of reagents for bioorthogonal chemistry, therefore enabling new biological applications ranging from protein labeling and imaging studies to the chemical activation of proteins.

Fitness Factors for Bioorthogonal Chemical Probes

Bioorthogonal chemistry has offered an invaluable reactivity-based tool to chemical biology owing to its exquisite specificity in tagging a diverse set of biomolecules in their native environment. Despite tremendous progress in the field over the past decade, designing a suitable bioorthogonal chemical probe to investigate a given biological system remains a challenge. In this Perspective, we put forward a series of fitness factors that can be used to assess the performance of bioorthogonal chemical probes. The consideration of these criteria should encourage continuous innovation in bioorthogonal probe development as well as enhance the quality of biological data.

Protein Spin Labeling with a Photocaged Nitroxide Using Diels-Alder Chemistry

EPR spectroscopy of diamagnetic bio-macromolecules is based on site-directed spin labeling (SDSL). Herein, a novel labeling strategy for proteins is presented. A nitroxide-based spin label has been developed and synthesized that can be ligated to proteins by an inverse-electron-demand Diels-Alder (DAinv ) cycloaddition to genetically encoded noncanonical amino acids. The nitroxide moiety is shielded by a photoremovable protecting group with an attached tetra(ethylene glycol) unit to achieve water solubility. SDSL is demonstrated on two model proteins with the photoactivatable nitroxide for DAinv reaction (PaNDA) label. The strategy features high reaction rates, combined with high selectivity, and the possibility to deprotect the nitroxide in Escherichia coli lysate.

Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells

Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.

Quantitative Single-Residue Bioorthogonal Labeling of G Protein-Coupled Receptors in Live Cells

High-end microscopy studies of G protein-coupled receptors (GPCRs) require installing onto the receptors bright and photostable dyes. Labeling must occur in quantitative yields, to allow stoichiometric data analysis, and in a minimally invasive fashion, to avoid perturbing GPCR function. We demonstrate here that the genetic incorporation of trans-cyclooct-2-ene lysine (TCO*) allows achieving quantitative single-residue labeling of the extracellular loops of the β₂-adrenergic and the muscarinic M₂ class A GPCRs, as well as of the corticotropin releasing factor class B GPCR. Labeling occurs within a few minutes by reaction with dye-tetrazine conjugates on the surface of live cells and preserves the functionality of the receptors. To precisely quantify the labeling yields, we devise a method based on fluorescence fluctuation microscopy that extracts the number of labeling sites at the single-cell level. Further, we show that single-residue labeling is better suited for studies of GPCR diffusion than fluorescent-protein tags, since the latter can affect the mobility of the receptor. Finally, by performing dual-color competitive labeling on a single TCO* site, we devise a method to estimate the oligomerization state of a GPCR without the need for a biological monomeric reference, which facilitates the application of fluorescence methods to oligomerization studies. As TCO* and the dye-tetrazines used in this study are commercially available and the described microscopy techniques can be performed on a commercial microscope, we expect our approach to be widely applicable to fluorescence microscopy studies of membrane proteins in general.

Hydrophilic azaspiroalkenes as robust bioorthogonal reporters

Two hydrophilic spiroalkenes, azaspiro[2.3]hex-1-ene and azaspiro[2.4]hept-1-ene, were designed and synthesized. Compared to the previously reported spiro[2.3]hex-1-ene, the azaspiroalkenes exhibited greater water solubility and reactivity as dipolarophiles in the photoinduced tetrazole-alkene cycloaddition reaction. In addition, an azaspiro[2.3]hex-1-ene-containing amino acid, AsphK, was found to be charged by an engineered pyrrolysyl-tRNA synthetase into proteins via amber codon suppression in E. coli as well as in mammalian cells.

An Efficient Method for Labeling Single Domain Antibody Fragments with 18F Using Tetrazine- Trans-Cyclooctene Ligation and a Renal Brush Border Enzyme-Cleavable Linker

Single domain antibody fragments (sdAbs) labeled with ¹⁸F have shown promise for assessing the status of oncological targets such as the human epidermal growth factor receptor 2 (HER2) by positron emission tomography (PET). Earlier, we evaluated two residualizing prosthetic agents for ¹⁸F-labeling of anti-HER2 sdAbs; however, these methods resulted in poor labeling yields and high uptake of ¹⁸F activity in the kidneys. To potentially mitigate these limitations, we have now developed an ¹⁸F labeling method that utilizes the trans-cyclooctene (TCO)-tetrazine (Tz)-based inverse-electron demand Diels-Alder reaction (IEDDAR) in tandem with a renal brush border enzyme-cleavable glycine-lysine (GK) linker in the prosthetic moiety. The HER2-targeted sdAb 2Rs15d was derivatized with TCO-GK-PEG₄-NHS or TCO-PEG₄-NHS, which lacks the cleavable linker. As an additional control, the non HER2-specific sdAb R3B23 was derivatized with TCO-GK-PEG₄-NHS. The resultant sdAb conjugates were labeled with ¹⁸F by IEDDAR using [¹⁸F]AlF-NOTA-PEG₄-methyltetrazine. As a positive control, the 2Rs15d sdAb was radioiodinated using the well-characterized residualizing prosthetic agent, N-succinimidyl 4-guanidinomethyl-3-[¹²⁵I]iodobenzoate ([¹²⁵I]SGMIB). Synthesis of [¹⁸F]AlF-NOTA-Tz-TCO-GK-2Rs15d was achieved with an overall radiochemical yield (RCY) of 17.8 ± 1.5% ( n = 5) in 90 min, a significant improvement over prior methods (3-4% in 2-3 h). In vitro assays indicated that [¹⁸F]AlF-NOTA-Tz-TCO-GK-2Rs15d bound with high affinity and immunoreactivity to HER2. In normal mice, when normalized to coinjected [¹²⁵I]SGMIB-2Rs15d, the kidney uptake of [¹⁸F]AlF-NOTA-Tz-TCO-GK-2Rs15d was 15- and 28-fold lower ( P < 0.001) than that seen for the noncleavable control ([¹⁸F]AlF-NOTA-Tz-TCO-2Rs15d) at 1 and 3 h, respectively. Uptake of [¹⁸F]AlF-NOTA-Tz-TCO-GK-2Rs15d in HER2-expressing SKOV-3 ovarian carcinoma xenografts implanted in athymic mice was about 80% of that seen for coinjected [¹²⁵I]SGMIB-2Rs15d. On the other hand, kidney uptake was 5-6-fold lower, and as a result, tumor-to-kidney ratios were 4-fold higher for [¹⁸F]AlF-NOTA-Tz-TCO-GK-2Rs15d than those for [¹²⁵I]SGMIB-2Rs15d. SKOV-3 xenografts were clearly delineated even at 1 h after administration of [¹⁸F]AlF-NOTA-Tz-TCO-GK-2Rs15d by Micro-PET/CT imaging with even higher contrast observed thereafter. In conclusion, this strategy warrants further evaluation for labeling small proteins such as sdAbs because it offers the benefits of good radiochemical yields and enhanced tumor-to-normal tissue ratios, particularly in the kidney.

Achieving Controlled Biomolecule-Biomaterial Conjugation

The conjugation of biomolecules can impart materials with the bioactivity necessary to modulate specific cell behaviors. While the biological roles of particular polypeptide, oligonucleotide, and glycan structures have been extensively reviewed, along with the influence of attachment on material structure and function, the key role played by the conjugation strategy in determining activity is often overlooked. In this review, we focus on the chemistry of biomolecule conjugation and provide a comprehensive overview of the key strategies for achieving controlled biomaterial functionalization. No universal method exists to provide optimal attachment, and here we will discuss both the relative advantages and disadvantages of each technique. In doing so, we highlight the importance of carefully considering the impact and suitability of a particular technique during biomaterial design.

Nature-Inspired Bioorthogonal Reaction: Development of β-Caryophyllene as a Chemical Reporter in Tetrazine Ligation

A nature-inspired bioorthogonal reaction has been developed, hinging on an inverse-electron-demand Diels-Alder reaction of tetrazine with β-caryophyllene. Readily accessible from the cheap starting material through a scalable synthesis, the newly developed β-caryophyllene chemical reporter displays appealing reaction kinetics and excellent biocompatibility, which renders it applicable to both in vitro protein labeling and live cell imaging. Moreover, it can be used orthogonally to the strain-promoted alkyne-azide cycloaddition for dual protein labeling. This work not only provides an alternative to the existing bioorthogonal reaction toolbox, but also opens a new avenue to utilize naturally occurring scaffolds as bioorthogonal chemical reporters.

Constructing New Bioorthogonal Reagents and Reactions

Chemical tools are transforming our understanding of biomolecules and living systems. Included in this group are bioorthogonal reagents-functional groups that are inert to most biological species, but can be selectively ligated with complementary probes, even in live cells and whole organisms. Applications of these tools have revealed fundamental new insights into biomolecule structure and function-information often beyond the reach of genetic approaches. In many cases, the knowledge gained from bioorthogonal probes has enabled new questions to be asked and innovative research to be pursued. Thus, the continued development and application of these tools promises to both refine our view of biological systems and facilitate new discoveries. Despite decades of achievements in bioorthogonal chemistry, limitations remain. Several reagents are too large or insufficiently stable for use in cellular environments. Many bioorthogonal groups also cross-react with one another, restricting them to singular tasks. In this Account, we describe our work to address some of the voids in the bioorthogonal toolbox. Our efforts to date have focused on small reagents with a high degree of tunability: cyclopropenes, triazines, and cyclopropenones. These motifs react selectively with complementary reagents, and their unique features are enabling new pursuits in biology. The Account is organized by common themes that emerged in our development of novel bioorthogonal reagents and reactions. First, natural product structures can serve as valuable starting points for probe design. Cyclopropene, triazine, and cyclopropenone motifs are all found in natural products, suggesting that they would be metabolically stable and compatible with a variety of living systems. Second, fine-tuning bioorthogonal reagents is essential for their successful translation to biological systems. Different applications demand different types of probes; thus, generating a collection of tools that span a continuum of reactivities and stabilities remains an important goal. We have used both computational analyses and mechanistic studies to guide the optimization of various cyclopropene and triazine probes. Along the way, we identified reagents that are chemoselective but best suited for in vitro work. Others are selective and robust enough for use in living organisms. The last section of this Account highlights the need for the continued pursuit of new reagents and reactions. Challenges exist when bioorthogonal chemistries must be used in concert, given that many exploit similar mechanisms and cannot be used simultaneously. Such limitations have precluded certain multicomponent labeling studies and other biological applications. We have relied on mechanistic and computational insights to identify mutually orthogonal sets of reactions, in addition to exploring unique genres of reactivity. The continued development of mechanistically distinct, biocompatible reactions will further diversify the bioorthogonal reaction portfolio for examining biomolecules.

Advances in Tetrazine Bioorthogonal Chemistry Driven by the Synthesis of Novel Tetrazines and Dienophiles

Bioorthogonal chemistry has found increased application in living systems over the past decade. In particular, tetrazine bioorthogonal chemistry has become a powerful tool for imaging, detection, and diagnostic purposes, as reflected in the increased number of examples reported in the literature. The popularity of tetrazine ligations are likely due to rapid and tunable kinetics, the existence of high quality fluorogenic probes, and the selectivity of reaction. In this Account, we summarize our recent efforts to advance tetrazine bioorthogonal chemistry through improvements in synthetic methodology, with an emphasis on developing new routes to tetrazines and expanding the range of useful dienophiles. These efforts have removed specific barriers that previously limited tetrazine ligations and have broadened their potential applications. Among other advances, this Account describes how our group discovered new methodology for tetrazine synthesis by developing a Lewis acid-promoted, one-pot method for generating diverse symmetric and asymmetric alkyl tetrazines with functional substituents in satisfactory yields. We attached these tetrazines to microelectrodes and succeeded in controlling tetrazine ligation by changing the redox state of the reactants. Using this electrochemical control process, we were able to modify an electrode surface with redox probes and enzymes in a site-selective fashion. This Account also describes how our group improved the ability of tetrazines to act as fluorogenic probes by developing a novel elimination-Heck cascade reaction to synthesize alkenyl tetrazine derivatives. In this approach, tetrazine was conjugated to fluorophores to produce strongly quenched probes that, after bioorthogonal reaction, are "turned on" to enhance fluorescence, in many cases by >100-fold. These probes have allowed no-wash fluorescence imaging in living cells and intact animals. Finally, this Account reviews our efforts to expand the range of dienophile substrates to make tetrazine bioorthogonal chemistry compatible with specific biochemical and biomedical applications. We found that methylcyclopropene is sufficiently stable and reactive in the biological milieu to act as an efficient dienophile. The small size of the reactive tag minimizes steric hindrance, allowing cyclopropene to serve as a metabolic reporter group to reveal biological dynamics and function. We also used norbornadiene derivatives as strained dienophiles to undergo tetrazine-mediated transfer (TMT) reactions involving tetrazine ligation followed by a retro-Diels-Alder process. This TMT reaction generates a pair of nonligating products. Using nucleic acid-templated chemistry, we have combined the TMT reaction with our fluorogenic tetrazine probes to detect endogenous oncogenic microRNA at picomolar concentrations. In a further display of dienophile versatility, we used a novel vinyl ether to cage a near-infrared fluorophore in a nonfluorescent form. Then we opened the cage in a "click to release" tetrazine bioorthogonal reaction, restoring the fluorescent form of the fluorophore. Combining this label with a corresponding nucleic acid probe allowed fluorogenic detection of target mRNA. In summary, this Account describes improvements in tetrazine and dienophile synthesis and application to advance tetrazine bioorthogonal chemistry. These advances have further enabled application of tetrazine ligation chemistry, not only in fundamental research but also in diagnostic studies.

Sterically Shielded, Stabilized Nitrile Imine for Rapid Bioorthogonal Protein Labeling in Live Cells

In pursuit of fast bioorthogonal reactions, reactive moieties have been increasingly employed for selective labeling of biomolecules in living systems, posing a challenge in attaining reactivity without sacrificing selectivity. To address this challenge, here we report a bioinspired strategy in which molecular shape controls the selectivity of a transient, highly reactive nitrile imine dipole. By tuning the shape of structural pendants attached to the ortho position of the N-aryl ring of diaryltetrazoles-precursors of nitrile imines, we discovered a sterically shielded nitrile imine that favors the 1,3-dipolar cycloaddition over the competing nucleophilic addition. The photogenerated nitrile imine exhibits an extraordinarily long half-life of 102 s in aqueous medium, owing to its unique molecular shape that hinders the approach of a nucleophile as shown by DFT calculations. The utility of this sterically shielded nitrile imine in rapid (∼1 min) bioorthogonal labeling of glucagon receptor in live mammalian cells was demonstrated.

Fast, irreversible modification of cysteines through strain releasing conjugate additions of cyclopropenyl ketones

A method of cysteine alkylation using cyclopropenyl ketones is described. Due to the significant release of cyclopropene strain energy, reactions of thiols with cyclopropenyl ketones are both fast and irreversible and give rise to stable conjugate addition adducts. The resulting cyclopropenyl ketones have a low molecular weight and allow for simple attachment of amides via N-hydroxysuccinimide (NHS)-esters. While cyclopropenyl ketones do display slow background reactivity toward water, labeling by thiols is much more rapid. The reaction of a cyclopropenyl ketone with glutathione (GSH) proceeds with a rate of 595 M^-1 s^-1 in PBS at pH 7.4, which is considerably faster than α-halocarbonyl labeling reagents, and competitive with maleimide/thiol couplings. The method has been demonstrated in protein conjugation, and an arylthiolate conjugate was shown to be stable upon prolonged incubation in either GSH or human plasma. Finally, cyclopropenyl ketones were used to create PEG-based hydrogels that are stable to prolonged incubation in a reducing environment.

A novel iridium(iii) complex for sensitive HSA phosphorescence staining in proteome research

A novel iridium(iii) complex (Ir1) for sensitive HSA staining is reported. It is simpler and less time-consuming than Coomassie blue.