Cell-selective metabolic labeling of biomolecules with bioorthogonal functionalities

Tumor Acidity-Triggered Bioorthogonal Reactions for Biomedical Applications

Cancer is one of the most serious threats to human health. Over the past few years, researchers have incrementally uncovered the pivotal role of tumor acidity in tumor formation, development, and treatment. In addition, bioorthogonal reactions have been widely used in tumor diagnosis and therapy, owing to their advantageous characteristics, including small ligand size, biocompatibility, fast reaction kinetics, and high chemospecificity. Consequently, bioorthogonal reactions triggered by tumor acidity have become an emerging strategy in biomedical applications. On this basis, we first elucidate the concept and major strategies of tumor acidity-triggered bioorthogonal reactions. Additionally, we review the progress in biomedical applications, with a particular focus on their importance in disease diagnosis and treatment. Finally, clinical challenges and future trends are also outlooked.

Cell-selective bioorthogonal labeling

In classic bioorthogonal labeling experiments, the cell's biosynthetic machinery incorporates bioorthogonal tags, creating tagged biomolecules that are subsequently reacted with a corresponding bioorthogonal partner. This two-step approach labels biomolecules throughout the organism indiscriminate of cell type, which can produce background in applications focused on specific cell populations. In this review, we cover advances in bioorthogonal chemistry that enable targeting of bioorthogonal labeling to a desired cell type. Such cell-selective bioorthogonal labeling is achieved in one of three ways. The first approach restricts labeling to specific cells by cell-selective expression of engineered enzymes that enable the bioorthogonal tag's incorporation. The second approach preferentially localizes the bioorthogonal reagents to the desired cell types to restrict their uptake to the desired cells. Finally, the third approach cages the reactivity of the bioorthogonal reagents, allowing activation of the reaction in specific cells by uncaging the reagents selectively in those cell populations.

Engineered Cell Membrane-Camouflaged Nanomaterials for Biomedical Applications

Recent strides in nanomaterials science have paved the way for the creation of reliable, effective, highly accurate, and user-friendly biomedical systems. Pioneering the integration of natural cell membranes into sophisticated nanocarrier architectures, cell membrane camouflage has emerged as a transformative approach for regulated drug delivery, offering the benefits of minimal immunogenicity coupled with active targeting capabilities. Nevertheless, the utility of nanomaterials with such camouflage is curtailed by challenges like suboptimal targeting precision and lackluster therapeutic efficacy. Tailored cell membrane engineering stands at the forefront of biomedicine, equipping nanoplatforms with the capacity to conduct more complex operations. This review commences with an examination of prevailing methodologies in cell membrane engineering, spotlighting strategies such as direct chemical modification, lipid insertion, membrane hybridization, metabolic glycan labeling, and genetic engineering. Following this, an evaluation of the unique attributes of various nanomaterials is presented, delivering an in-depth scrutiny of the substantial advancements and applications driven by cutting-edge engineered cell membrane camouflage. The discourse culminates by recapitulating the salient influence of engineered cell membrane camouflage within nanomaterial applications and prognosticates its seminal role in transformative healthcare technologies. It is envisaged that the insights offered herein will catalyze novel avenues for the innovation and refinement of engineered cell membrane camouflaged nanotechnologies.

Coumarin-Conjugated Macromolecular Probe for Sequential Stimuli-Mediated Activation

Protein bioconjugation has emerged as one of the most valuable tools for the development of protein-based biochemical assays. Here, we report a fluorescent macromolecular material, RF16_Halo, in which the coumarin derivative RF16 is specifically conjugated onto HaloTag protein to achieve a dual-stimuli-mediated fluorescence response. RF16 is first obtained by installing a H2O2-sensitive boron cage onto the C7 hydroxy moiety of the coumarin fluorophore with a HaloTag ligand attaching to the pH-labile 1,3-dioxane moiety. Upon stimulation, RF16_Halo exhibits a sequential fluorescence response to H2O2/pH at both liquid and solid interfaces. The fluorescence of the RF16_Halo-based protein film increases linearly toward H2O2 with a higher sensitivity when compared with that of RF16. Subsequently, the H2O2-cleaved RF16_Halo presents a pH-dependent fluorescence decrease under acidic conditions. Such a stimulus-responsive fluorescence "off-on-off" multimode enables RF16_Halo to be applied as a sequential logic circuit. In addition, we evaluate the fluorescence labeling ability of RF16 to intracellular IRE1_Halo protein and demonstrate that RF16 containing the HaloTag ligand could be precisely retained in cells to track IRE1_Halo protein. Hence, we provide a unique structural design strategy to construct a fluorescence dual-responsive macromolecular probe for information encryption and protein tracking in cells.

Construction of Coumarin-Based Bioorthogonal Macromolecular Probes for Photoactivation

Photoactivatable fluorescence imaging is one of the most valuable methods for visualizing protein localization, trafficking, and interactions. Here, we designed four bioorthogonal fluorescent probes K1-K4 by installing photoactive cages and HaloTag ligands onto the different positions of the coumarin fluorophore. Although K1-K4 all exhibited rapid photostimulated responses in aqueous solution, only K3 was found to have an obvious aggregation-induced emission (AIE). Next, macromolecular fluorescent probes Kn=1/2/3/4_POIs were obtained by covalently attaching K1-K4 to HaloTag-fused proteins of interest (POIs). Kn=3/4_POIs exhibited a higher fluorescence increase than that of Kn=1/2_POIs upon photoactivation in both liquid and solid phases. Moreover, K3_GFP_Halo and K4_GFP_Halo presented the fluorescence resonance energy transfer (FRET) from photocleaved K3 and K4 to GFP in the protein complex. We further examined the fluorescence labeling ability of K1-K4 to intracellular IRE1_Halo protein and found that K3 and K4 containing the HaloTag ligand on the C4 position of coumarin could be retained in cells for long-term tracking of the IRE1_Halo protein. Hence, we established a platform of novel bioorthogonal fluorescent probes conjugating onto Halo-tagged POIs for rapid photoactivation in vitro and in cells.

Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry

Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.

Precise assembly of inside-out cell membrane camouflaged nanoparticles via bioorthogonal reactions for improving drug leads capturing

Cell membrane camouflaged nanoparticles have been widely used in the field of drug leads discovery attribute to their unique biointerface targeting function. However, random orientation of cell membrane coating does not guarantee effective and appropriate binding of drugs to specific sites, especially when applied to intracellular regions of transmembrane proteins. Bioorthogonal reactions have been rapidly developed as a specific and reliable method for cell membrane functionalization without disturbing living biosystem. Herein, inside-out cell membrane camouflaged magnetic nanoparticles (IOCMMNPs) were accurately constructed via bioorthogonal reactions to screen small molecule inhibitors targeting intracellular tyrosine kinase domain of vascular endothelial growth factor recptor-2. Azide functionalized cell membrane acted as a platform for specific covalently coupling with alkynyl functionalized magnetic Fe₃O₄ nanoparticles to prepare IOCMMNPs. The inside-out orientation of cell membrane was successfully verified by immunogold staining and sialic acid quantification assay. Ultimately, two compounds, senkyunolide A and ligustilidel, were successfully captured, and their potential antiproliferative activities were further testified by pharmacological experiments. It is anticipated that the proposed inside-out cell membrane coating strategy endows tremendous versatility for engineering cell membrane camouflaged nanoparticles and promotes the development of drug leads discovery platforms.

Cell-type-specific labeling and profiling of glycans in living mice

Metabolic labeling of glycans with clickable unnatural sugars has enabled glycan analysis in multicellular systems. However, cell-type-specific labeling of glycans in vivo remains challenging. Here we develop genetically encoded metabolic glycan labeling (GeMGL), a cell-type-specific strategy based on a bump-and-hole pair of an unnatural sugar and its matching engineered enzyme. N-pentynylacetylglucosamine (GlcNAl) serves as a bumped analog of N-acetylglucosamine (GlcNAc) that is specifically incorporated into glycans of cells expressing a UDP-GlcNAc pyrophosphorylase mutant, AGX2^F383G. GeMGL with the 1,3-di-O-propionylated GlcNAl (1,3-Pr₂GlcNAl) and AGX2^F383G pair was demonstrated in cell cocultures, and used for specific labeling of glycans in mouse xenograft tumors. By generating a transgenic mouse line with AGX2^F383G expressed under a cardiomyocyte-specific promoter, we performed specific imaging of cardiomyocyte glycans in the heart and identified 582 cardiomyocyte O-GlcNAcylated proteins with no interference from other cardiac cell types. GeMGL will facilitate cell-type-specific glycan imaging and glycoproteomics in various tissues and disease models.

O-GlcNAcylation mapping of single living cells by in situ quantitative SERS imaging

O-GlcNAcylation is involved in many biological processes including cancerization. Nevertheless, its in situ quantification in single living cells is still a bottleneck. Here we develop a quantitative SERS imaging strategy for mapping the O-GlcNAcylation distribution of single living cells. O-GlcNAcylated compounds (OGCs) can be quantified through their in situ azide labeling and then a click reaction competing with azide and Raman reporter labeled 15 nm-gold nanoparticles (AuNPs) for linking to dibenzocyclooctyne labeled 40 nm-AuNPs to produce OGC-negatively correlated SERS signals. The calibration curve obtained in vitro can be conveniently used for detecting OGCs in different areas of single living cells due to the negligible effect of cell medium on the click linkage and Raman signal. This method has been successfully applied in mapping O-GlcNAcylation distribution in different cell lines and monitoring O-GlcNAcylation variation during cell cycling, which demonstrate its great practicability and expansibility in glycosylation related analysis.

A quantitative SERS imaging strategy is developed for O-GlcNAcylation mapping of single living cells through a competitive click reaction.

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.

Design and Synthesis of Metabolic Chemical Reporters for the Visualization and Identification of Glycoproteins

Glycosylation events play an invaluable role in regulating cellular processes including enzymatic activity, immune recognition, protein stability, and cell-cell interactions. However, researchers have yet to realize the full range of glycan mediated biological functions due to a lack of appropriate chemical tools. Fortunately, the past 25 years has seen the emergence of modified sugar analogs, termed metabolic chemical reporters (MCRs), which are metabolized by endogenous enzymes to label complex glycan structures. Here, we review the major reporters for each class of glycosylation and highlight recent applications that have made a tremendous impact on the field of glycobiology.

Intramolecular trigger remodeling-induced HCR for amplified detection of protein-specific glycosylation

Dynamic changes of protein-glycosylation on cell surface act as an important indicator that reflects cellular physiological states and disease developments. The enhanced visualization of protein-specific glycosylation is of great value to interpret its functions and mechanisms. Hence, we present an intramolecular trigger remodeling-induced hybridization chain reaction (HCR) for imaging protein-specific glycosylation. This strategy relies on designing two DNA probes, protein and glycan probes, labeled respectively on protein by aptamer recognition and glycan through metabolic oligosaccharide engineering (MOE). Upon the same glycoprotein was labeled, the complementary domain of two probes induces hybridization and thus to remodel an intact trigger, followed by initiating HCR assembly. Applying this strategy, we successfully achieved imaging of specific protein-glycosylation on CEM cell surface and monitored dynamic changes of the glycosylation after treating with drugs. It provides a powerful tool with high flexibility, specificity and sensitivity in the research field of protein-specific glycosylation on living cells.

Cell-Membrane-Based Biomimetic Systems with Bioorthogonal Functionalities

During the past decade, there was a fast development of cell-based biomimetic systems, which are commonly derived from cell membranes, cell vesicles, or living cells. Such systems have unique and inherent bioinspired features originating from their parent biological systems. In particular, they are capable of (i) prolonging blood circulation time, (ii) avoiding immune response, (iii) targeting desired sites, (iv) providing antigens in cancer immunotherapy, and (v) loading and delivering therapeutic or imaging agents. Thus, these biomimetic systems are promising as prevention, detection, diagnosis, and therapeutic modalities. Though promising, these cell-based biomimetic systems are still far from wide application. One of the important reasons is the inevitable difficulty in their further efficient and precise functionalization. Bioorthogonal chemistry results in fast, specific, and high-yielding ligation under mild biological conditions without interactions with surrounding biomolecules or disturbance of the whole biosystem. Moreover, bioorthogonal chemical groups can be introduced into cells, especially into cell membranes, through cellular biosynthesis and metabolic incorporation. Hence, a specific and reliable approach for cell membrane functionalization based on bioorthogonal chemistry has been opportunely put forward and rapidly developed. In this Account, we summarize our recent research on the development of biomimetic systems by integrating bioorthogonal chemistry with biomimetic approaches. First, an exogenously supplied unnatural biosynthetic precursor (e.g., an amino acid or lipid) bearing a bioorthogonal group (e.g., azide or tetrazine) is fed to living cells and metabolically incorporated into targeted biomolecules via cellular biosynthesis regardless of the cell phenotype. After that, different functional molecules can be anchored to the cell membranes through bioorthogonal chemical reactions by using previously inserted "artificial chemical groups". Therefore, this safe, direct, and long-term engineering strategy endows the natural cell-based biomimetic systems with additional chemical or biological performances such as labeling, targeting, imaging, and therapeutic capabilities, providing a powerful tool for the construction of biomimetic systems. Interestingly, we have successfully fabricated various biomimetic systems and applied them in (1) living virus labeling, (2) targeting delivery and enrichment of drugs/imaging agents, and (3) disease theranostics. This Account may contribute to the further development of biomimetic systems and facilitate their biological and biomedical applications in the future. With this Account we also hope to attract more cooperative interests from different fields such as chemistry, materials science, biology, pharmacy, and medicine in promoting lab-to-clinic translation of cell-based biomimetic systems combined with these two cutting-edge techniques.

Bio-Orthogonal T Cell Targeting Strategy for Robustly Enhancing Cytotoxicity against Tumor Cells

T cells can kill tumor cells by cell surface immunological recognition, but low affinity for tumor-associated antigens could lead to T cell off-target effects. Herein, a universal T cell targeting strategy based on bio-orthogonal chemistry and glycol-metabolic engineering is introduced to enhance recognition and cytotoxicity of T cells in tumor immunotherapy. Three kinds of bicycle [6.1.0] nonyne (BCN)-modified sugars are designed and synthesized, in which Ac₄ ManN-BCN shows efficient incorporation into wide tumor cells with a BCN motif on surface glycans. Meanwhile, activated T cells are treated with Ac₄ GalNAz to introduce azide (N₃ ) on the cell surface, initiating specific tumor targeting through a bio-orthogonal click reaction between N₃ and BCN. This artificial targeting strategy remarkably enhances recognition and migration of T cells to tumor cells, and increases the cytotoxicity 2 to 4 times for T cells against different kinds of tumor cells. Surprisingly, based on this strategy, the T cells even exhibit similar cytotoxicity with the chimeric antigen receptor T-cell against Raji cells in vitro at the effector: target cell ratios (E:T) of 1:1. Such a universal bio-orthogonal T cell-targeting strategy might further broaden applications of T cell therapy against tumors and provide a new strategy for T cell modification.

Liposome-aided metabolic engineering of tumor surface immunogenicity

Approaches to increase tumor immunogenicity are of therapeutic potentials. We herein reported the use of liposomes for covalent incorporation of neoantigen on tumor surfaces with DNP-conjugated sialic acid (^DNPSia). Relative to free ^DNPSia, sugar-encapsulated biotinylated liposomes (^DNPSia@LP@biotin) enables effective cell surface expression of ^DNPSia on biotin receptor (BR)-expressing cells over BR-free cells in vitro, and on tumor cell surfaces with high tumor-to-normal tissue contrast in a mice model. These findings suggest the potentials of targetable liposomes for modulating tumor surface immunity via metabolic oligosaccharide engineering.

Mechanistic Investigation and Multiplexing of Liposome-Assisted Metabolic Glycan Labeling

Metabolic labeling of glycans with bioorthogonal reporters has been widely used for glycan imaging and glycoproteomic profiling. One of the intrinsic limitations of metabolic glycan labeling is the lack of cell-type selectivity. The recently developed liposome-assisted bioorthogonal reporter (LABOR) strategy provides a promising means to overcome this limitation, but the mechanism of LABOR has not been investigated in detail. In this work, we performed a mechanistic study on LABOR and explored its multiplexing capability. Our studies support an endocytosis-salvage mechanism. The ligand-targeted liposomes encapsulating azidosugars are internalized into the endosome via the receptor-mediated endocytosis. Unlike the conventional drug delivery, LABOR does not rely on the endosomal escape pathways. Rather, the liposomes are allowed to enter the lysosome, inside which the azidosugars are released from the liposomes. The released azidosugars then intercept the salvage pathways of monosaccharides and get transported into the cytosol by lysosomal sugar transporters. Based on this mechanism, we expanded the scope of LABOR by evaluating a series of ligand-receptor pairs for targeting sialoglycans in various cell types. Different ligand types including small molecules, antibodies, aptamers, and peptides could be easily implemented into LABOR. Finally, we demonstrated that the sialoglycans in two distinct cell populations in a co-cultured system could be selectively labeled with two distinct chemical reporters by performing a multiplexed LABOR labeling.

Quantitative Screening of Cell-Surface Gangliosides by Nondestructive Extraction and Hydrophobic Collection

A screening strategy involving designed extractors and collectors was used for the nondestructive quantitation of gangliosides on cell surfaces. The extractors were constructed by functionalizing maleimide silica bubbles with a DNA probe, which contains an endonuclease cleavage site and a boronic acid end to extract cell-surface sialic acid-containing compounds through simple centrifugation. After the extractors containing the extracted compounds were incubated with endonuclease, the released oligonucleotide-gangliosides were selectively collected by silanized collector bubbles through hydrophobic interactions. The in vitro fluorescent signals from the collectors were used for the quantitation of cell-surface gangliosides. By combining with sialidase cleavage, a protocol for the identification of ganglioside subtypes was developed. The successful monitoring of the regeneration of cell-surface gangliosides demonstrates the potential of this strategy in probing related biological processes.

Improved Tumor Targeting and Longer Retention Time of NIR Fluorescent Probes Using Bioorthogonal Chemistry

The traditional labeling method for targeted NIR fluorescence probes requires directly covalent-bonded conjugation of targeting domains and fluorophores in vitro. Although this strategy works well, it is not sufficient for detecting or treating cancers in vivo, due to steric hindrance effects that relatively large fluorophore molecules exert on the configurations and physiological functions of specific targeting domains. The copper-free, “click-chemistry”-assisted assembly of small molecules in living systems may enhance tumor accumulation of fluorescence probes by improving the binding affinities of the targeting factors. Here, we employed a vascular homing peptide, GEBP11, as a targeting factor for gastric tumors, and we demonstrate its effectiveness for in vivo imaging via click-chemistry-mediated conjugation with fluorescence molecules in tumor xenograft mouse models. This strategy showed higher binding affinities than those of the traditional conjugation method, and our results showed that the tumor accumulation of click-chemistry-mediated probes are 11-fold higher than that of directly labeled probes. The tracking life was prolonged by 12-fold, and uptake of the probes into the kidney was reduced by 6.5-fold. For lesion tumors of different sizes, click-chemistry-mediated probes can achieve sufficient signal-to-background ratios (3.5-5) for in vivo detection, and with diagnostic sensitivity approximately 3.5 times that of traditional labeling probes. The click-chemistry-assisted detection strategy utilizes the advantages of “small molecule” probes while not perturbing their physiological functions; this enables tumor detection with high sensitivity and specific selectivity.

Silver nanoparticle plasmonic enhanced förster resonance energy transfer (FRET) imaging of protein-specific sialylation on the cell surface

A large amount of proteins are post-translationally modified with a sialic acid terminal oligosaccharide, and sialylation directly affects the function of glycoproteins and adjusts relevant biological processes. Herein, we developed a method for imaging analysis of protein-specific sialylation on the cell surface via silver nanoparticle (AgNPs) plasmonic enhanced Förster resonance energy transfer (FRET). In this strategy, the target monosaccharide was labelled with the FRET acceptor of Cy5 via bioorthogonal chemistry. In addition, aptamer linked AgNPs were combined with the Cy3 fluorophore by DNA hybridization as the FRET donor probe, which could be conjugated to the target glycoprotein based on specific aptamer-protein recognition. The Cy5 fluorescence signal was obtained under the Cy3 excitation wavelength via FRET. Moreover, the FRET fluorescence signal was obviously enhanced owing to the plasmonic effect of AgNPs at an appropriate distance to Cy3 on the cell surface. Hence, the protein-specific sialic acids were detected with high contrast. The results showed that the AgNP plasmonic enhanced FRET method was not only superior to the bare FRET method but also can be used to evaluate the expression of sialoglycoproteins in different cell types under pharmacological treatments. The AgNP plasmonic enhanced FRET method provides a valuable tool in the research of glycan metabolism biological processes, the active site of glycoproteins and drug screening.

Nitrilase-Activatable Noncanonical Amino Acid Precursors for Cell-Selective Metabolic Labeling of Proteomes

Cell-selective protein metabolic labeling is of great interest for studying cell-cell communications and tissue homeostasis. We herein describe a nitrilase-activatable noncanonical amino acid tagging (NANCAT) strategy that exploits an exogenous nitrilase to enzymatically convert the nitrile-substituted precursors to their corresponding noncanonical amino acids (ncAAs), l-azidohomoalanine (Aha) or homopropargylglycine (Hpg), in living cells. Only cells expressing the nitrilase can generate Aha or Hpg in cellulo and metabolically incorporate them into the nascent proteins. Subsequent click-labeling of the azide- or alkyne-incorporated proteins with fluorescent probes or with affinity tags enables visualization and proteomic profiling of nascent proteomes, respectively. We have demonstrated that NANCAT can serve as a versatile strategy for cell-selective labeling of proteomes in both bacterial and mammalian cells.

Rapid probing of sialylated glycoproteins in vitro and in vivo via metabolic oligosaccharide engineering of a minimal cyclopropene reporter

ManNAc analogues are important chemical tools for probing sialylation dynamically via metabolic oligosaccharide engineering (MOE). The size of N-acyl and the nature of the chemical handle are two determinants of metabolic incorporation efficiency. We demonstrated a minimal, stable, bioorthogonal, and reactive N-Cp (N-(cycloprop-2-ene-1-ylcarbonyl)) group and the imaging of sialylated glycans using Ac4ManNCp in vitro and in vivo. The results revealed that the Cp group can efficiently be incorporated into the cellular sialic acid and detected rapidly by the reaction with FITC-Tz in different cells. The metabolic incorporation efficiency of non-cytotoxic Ac4ManNCp is not only superior to Ac4ManNMCp, but also superior to the widely-used Ac4ManNAz in some cell lines. Moreover, when Ac4ManNCp was administered to mice, a rapid and intense labelling of splenocytes as well as glycoproteins of sera and organs was observed. This is the first reported metabolic labelling of cyclopropene-modified sugars in vivo. Therefore, Ac4ManNCp is a powerful probe for efficient and rapid MOE and it may find wide applications in the labelling of glycans.

Metabolic Remodeling of Cell-Surface Sialic Acids: Principles, Applications, and Recent Advances

Cell-surface sialic acids are essential in mediating a variety of physiological and pathological processes. Sialic acid chemistry and biology remain challenging to investigate, demanding new tools for probing sialylation in living systems. The metabolic glycan labeling (MGL) strategy has emerged as an invaluable chemical biology tool that enables metabolic installation of useful functionalities into cell-surface sialoglycans by "hijacking" the sialic acid biosynthetic pathway. Here we review the principles of MGL and its applications in study and manipulation of sialic acid function, with an emphasis on recent advances.

Protein-specific Raman imaging of glycosylation on single cells with zone-controllable SERS effect

A zone-controllable SERS effect integrates the controlling of nano-substrate size to match the expression zone of protein-specific glycan for Raman imaging.

A zone-controllable SERS effect is presented for Raman imaging of protein-specific glycosylation on a cell surface using two types of newly designed nanoprobes. The signal probe, prepared using a Raman signal molecule and dibenzocyclooctyne-amine to functionalize a 10 nm Au nanoparticle, exhibits a negligible SERS effect and can recognize and link the azide-tagged glycan via a click reaction. The substrate probe, an aptamer modified 30 or 40 nm Au nanoparticles, can specifically recognize the target protein to create an efficient SERS zone on the target protein. By controlling the size of the substrate probe to match the expression zone of the protein-specific glycan, an efficient SERS signal can be generated. This method has been successfully used for in situ imaging of sialic acids on the target protein EpCAM on an MCF-7 cell surface and for the monitoring of the expression variation of protein-specific glycosylation during drug treatment. The concept of zone control can also be used to measure the distance between glycoproteins on a cell surface. This protocol shows promise in uncovering glycosylation-related biological processes.

A Bioorthogonal Chemical Reporter of Viral Infection

Pathogen‐selective labeling was achieved by using the novel gemcitabine metabolite analogue 2′‐deoxy‐2′,2′‐difluoro‐5‐ethynyluridine (dF‐EdU) and click chemistry. Cells infected with Herpes Simplex Virus‐1 (HSV‐1), but not uninfected cells, exhibit nuclear staining upon the addition of dF‐EdU and a fluorescent azide. The incorporation of the dF‐EdU into DNA depends on its phosphorylation by a herpes virus thymidine kinase (TK). Crystallographic analyses revealed how dF‐EdU is well accommodated in the active site of HSV‐1 TK, but steric clashes prevent dF‐EdU from binding human TK. These results provide the first example of pathogen‐enzyme‐dependent incorporation and labeling of bioorthogonal functional groups in human cells.

A Bioorthogonal Chemical Reporter of Viral Infection

Pathogen‐selective labeling was achieved by using the novel gemcitabine metabolite analogue 2′‐deoxy‐2′,2′‐difluoro‐5‐ethynyluridine (dF‐EdU) and click chemistry. Cells infected with Herpes Simplex Virus‐1 (HSV‐1), but not uninfected cells, exhibit nuclear staining upon the addition of dF‐EdU and a fluorescent azide. The incorporation of the dF‐EdU into DNA depends on its phosphorylation by a herpes virus thymidine kinase (TK). Crystallographic analyses revealed how dF‐EdU is well accommodated in the active site of HSV‐1 TK, but steric clashes prevent dF‐EdU from binding human TK. These results provide the first example of pathogen‐enzyme‐dependent incorporation and labeling of bioorthogonal functional groups in human cells.

Development of bioorthogonal reactions and their applications in bioconjugation

Biomolecule labeling using chemical probes with specific biological activities has played important roles for the elucidation of complicated biological processes. Selective bioconjugation strategies are highly-demanded in the construction of various small-molecule probes to explore complex biological systems. Bioorthogonal reactions that undergo fast and selective ligation under bio-compatible conditions have found diverse applications in the development of new bioconjugation strategies. The development of new bioorthogonal reactions in the past decade has been summarized with comments on their potentials as bioconjugation method in the construction of various biological probes for investigating their target biomolecules. For the applications of bioorthogonal reactions in the site-selective biomolecule conjugation, examples have been presented on the bioconjugation of protein, glycan, nucleic acids and lipids.

Development of a (18) F-labeled tetrazine with favorable pharmacokinetics for bioorthogonal PET imaging

A low-molecular-weight (18) F-labeled tetrazine derivative was developed as a highly versatile tool for bioorthogonal PET imaging. Prosthetic groups and undesired carrying of (18) F through additional steps were evaded by direct (18) F-fluorination of an appropriate tetrazine precursor. Reaction kinetics of the cycloaddition with trans-cyclooctenes were investigated by applying quantum chemical calculations and stopped-flow measurements in human plasma; the results indicated that the labeled tetrazine is suitable as a bioorthogonal probe for the imaging of dienophile-tagged (bio)molecules. In vitro and in vivo investigations revealed high stability and PET/MRI in mice showed fast homogeneous biodistribution of the (18) F-labeled tetrazine that also passes the blood-brain barrier. An in vivo click experiment confirmed the bioorthogonal behavior of this novel tetrazine probe. Due to favorable chemical and pharmacokinetic properties this bioorthogonal agent should find application in bioimaging and biomedical research.