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.     

An Azide‐Modified Nucleoside for Metabolic Labeling of DNA

Metabolic incorporation of azido nucleoside analogues into living cells can enable sensitive detection of DNA replication through copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) and strain‐promoted azide–alkyne cycloaddition (SPAAC) “click” reactions. One major limitation to this approach is the poor chemical stability of nucleoside derivatives containing an aryl azide group. For example, 5‐azido‐2′‐deoxyuridine (AdU) exhibits a 4 h half‐life in water, and it gives little or no detectable labeling of cellular DNA. In contrast, the benzylic azide 5‐(azidomethyl)‐2′‐deoxyuridine (AmdU) is stable in solution at 37 °C, and it gives robust labeling of cellular DNA upon addition of fluorescent alkyne derivatives. In addition to providing the first examples of metabolic incorporation into and imaging of azide groups in cellular DNA, these results highlight the general importance of assessing azide group stability in bioorthogonal chemical reporter strategies.     

Direct Intracellular Delivery of Cell‐Impermeable Probes of Protein Glycosylation by Using Nanostraws

Bioorthogonal chemistry is an effective tool for elucidating metabolic pathways and measuring cellular activity, yet its use is currently limited by the difficulty of getting probes past the cell membrane and into the cytoplasm, especially if more complex probes are desired. Here we present a simple and minimally perturbative technique to deliver functional probes of glycosylation into cells by using a nanostructured “nanostraw” delivery system. Nanostraws provide direct intracellular access to cells through fluid conduits that remain small enough to minimize cell perturbation. First, we demonstrate that our platform can deliver an unmodified azidosugar, N‐azidoacetylmannosamine, into cells with similar effectiveness to a chemical modification strategy (peracetylation). We then show that the nanostraw platform enables direct delivery of an azidosugar modified with a charged uridine diphosphate group (UDP) that prevents intracellular penetration, thereby bypassing multiple enzymatic processing steps. By effectively removing the requirement for cell permeability from the probe, the nanostraws expand the toolbox of bioorthogonal probes that can be used to study biological processes on a single, easy‐to‐use platform.     

Biosynthetic Labeling and Two‐Color Imaging of Phospholipids in Cells

Phospholipids with a choline head group are abundant components of all biological membranes, performing critical functions in cellular structure, metabolism, and signaling. In spite of their importance, our ability to visualize choline phospholipids in vivo remains very limited. We present a simple and robust chemical strategy to image choline phospholipids, based on the metabolic incorporation of azidocholine analogues, that accurately reflects the normal biosynthetic incorporation of choline into cellular phospholipids. Azidocholine‐labeled phospholipids can be imaged in cells with high sensitivity and resolution, following derivatization with fluorophores, by bio‐orthogonal chemical reactions compatible with live‐cell imaging. We used this method to visualize the subcellular localization of choline phospholipids. We also demonstrate that double metabolic labeling with azidocholine and propargylcholine allows sensitive two‐color imaging of choline phospholipids. Our method represents a powerful approach to directly image phospholipids, and to study their dynamics in cells and tissues.     

Quick Click: The DNA‐Templated Ligation of 3′‐O‐Propargyl‐ and 5′‐Azide‐Modified Strands Is as Rapid as and More Selective than Ligase

The copper(I)‐mediated azide–alkyne cycloaddition (CuAAC) of 3′‐propargyl ether and 5′‐azide oligonucleotides is a particularly promising ligation system because it results in triazole linkages that effectively mimic the phosphate–sugar backbone of DNA, leading to unprecedented tolerance of the ligated strands by polymerases. However, for a chemical ligation strategy to be a viable alternative to enzymatic systems, it must be equally as rapid, as discriminating, and as easy to use. We found that the DNA‐templated reaction with these modifications was rapid under aerobic conditions, with nearly quantitative conversion in 5 min, resulting in a k_obs value of 1.1 min^?1, comparable with that measured in an enzymatic ligation system by using the highest commercially available concentration of T4 DNA ligase. Moreover, the CuAAC reaction also exhibited greater selectivity in discriminating C:A or C:T mismatches from the C:G match than that of T4 DNA ligase at 29 °C; a temperature slightly below the perfect nicked duplex dissociation temperature, but above that of the mismatched duplexes. These results suggest that the CuAAC reaction of 3′‐propargyl ether and 5′‐azide‐terminated oligonucleotides represents a complementary alternative to T4 DNA ligase, with similar reaction rates, ease of setup and even enhanced selectivity for certain mismatches.     

In Vivo Incorporation of Azide Groups into DNA by Using Membrane‐Permeable Nucleotide Triesters

Metabolic incorporation of bioorthogonal functional groups into cellular nucleic acids can be impeded by insufficient phosphorylation of nucleosides. Previous studies found that 5azidomethyl‐2′‐deoxyuridine (AmdU) was incorporated into the DNA of HeLa cells expressing a low‐fidelity thymidine kinase, but not by wild‐type HeLa cells. Here we report that membrane‐permeable phosphotriester derivatives of AmdU can exhibit enhanced incorporation into the DNA of wild‐type cells and animals. AmdU monophosphate derivatives bearing either 5′‐bispivaloyloxymethyl (POM), 5′‐bis‐(4‐acetoxybenzyl) (AB), or “Protide” protective groups were used to mask the phosphate group of AmdU prior to its entry into cells. The POM derivative “POM‐AmdU” exhibited better chemical stability, greater metabolic incorporation efficiency, and lower toxicity than “AB‐AmdU”. Remarkably, the addition of POM‐AmdU to the water of zebrafish larvae enabled the biosynthesis of azide‐modified DNA throughout the body.     

Glyco‐Scan: Varying Glycosylation in the Sequence of the Peptide Hormone PYY3‐36 and Its Effect on Receptor Selectivity

The increasing prevalence of obesity worldwide calls for safe and highly efficacious satiety drugs. PYY3‐36 has been implicated in food intake regulation, and novel peptide analogues with high Y2 receptor‐subtype selectivity and potency have potential as drugs for the treatment of obesity. It has been hypothesized that PYY3‐36 associates with the plasma membrane prior to receptor activation such that the amphipathic α‐helix of PYY3‐36 possibly guides the C‐terminal pentapeptide into the correct conformation for receptor activation. Ala‐scans are used routinely to study the effect of individual amino acids in a given peptide sequence. Here we report the glyco‐scan of the peptide hormone PYY3‐36, in which hydroxyl side‐chain functionalities were glycosylated; in addition new glycosylation sites were introduced. An array of novel PYY3‐36 analogues with a glycan positioned in the water–membrane interface or in the N terminal were screened for Y‐receptor affinity and selectivity as well as metabolic stability. Interestingly, in contrast to the Y1 and Y4 receptors, the Y2 receptor readily accommodated glycosylations. Especially glycosylations in the α‐helical region of PYY3‐36 were favorable both in terms of Y‐receptor selectivity and endopeptidase resistance. We thus report several PYY3‐36 analogues with enhanced Y‐receptor selectivity. Our results can be used in the design of novel PYY analogues for the treatment of obesity. The glyco‐scan concept, as systematically demonstrated here, has the potential for a wider applicability.     

Characterisation of Photoaffinity‐Based Chemical Probes by Fluorescence Imaging and Native‐State Mass Spectrometry

Chemical probes are small‐molecule reagents used by researchers for labelling and detection of biomolecules. We present the design, synthesis, and characterisation of a panel of 11 structurally diverse photoaffinity labelling (PAL) probes as research tools for labelling the model enzyme carbonic anhydrase (CA) in challenging environments, including in protein mixtures and cell lysates. We targeted the ubiquitous CA II as well as the two cancer‐associated CAs (CA IX and CA XII) that are of high priority as potential biomarkers of aggressive and/or multidrug‐resistant cancer. We utilise an atypical biophysical approach, native state mass spectrometry, to monitor the initial protein–probe binding and subsequent UV crosslinking efficiency of the protein:probe complex. This mass spectrometry methodology represents a new approach for chemical probe optimisation and development that might have broader applications to chemical probe characterisation beyond this study. This also represents one of the first studies, to the best of our knowledge, in which a comprehensive set of PAL probes has been used to establish the relationship between probe structure, noncovalent protein–probe binding, and covalent protein–probe crosslinking efficiency. Our results demonstrate the benefits of a comprehensive analysis of chemical probe structure–activity relationships to support the development of optimum chemical probes.     

Copper‐Assisted Click Reactions for Activity‐Based Proteomics: Fine‐Tuned Ligands and Refined Conditions Extend the Scope of Application

Copper‐catalysed alkyne–azide 1,3‐dipolar cycloaddition (CuAAC) is the predominantly used bioconjugation method in the field of activity‐based protein profiling (ABPP). Several limitations, however, including conversion efficiency, protein denaturation and buffer compatibility, restrict the scope of established procedures. We introduce an ABPP customised click methodology based on refined CuAAC conditions together with new accelerating copper ligands. A screen of several triazole compounds revealed the cationic quaternary {3‐[4‐({bis[(1‐tert‐butyl‐1H‐1,2,3‐triazol‐4‐yl)methyl]amino}methyl)‐1H‐1,2,3‐triazol‐1‐yl]propyl}trimethylammonium trifluoroacetate (TABTA) to be a superior ligand. TABTA exhibited excellent in vitro conjugation kinetics and optimal ABPP labelling activity while almost exclusively preserving the native protein fold. The application of this CuAAC‐promoting system is amenable to existing protocols with minimal perturbations and is even compatible with previously unusable buffer systems such as Tris ? HCl.     

Click‐Chemistry‐Derived Tetracycline–Amino Acid Conjugates Exhibiting Exceptional Potency and Exclusive Recognition of the Reverse Tet Repressor

A click‐chemistry‐based synthesis of biologically active doxycycline–amino acid conjugates is described. Starting from 9‐aminodoxycycline derivatives and complementary functionalized amino acids, ligation was accomplished by copper(I)‐catalyzed azide–alkyne [3+2] cycloaddition (CuAAC). The final products were tested in a variety of TetR and revTetR systems, and the C‐terminally linked phenylalanine conjugate 12 c exhibited high selectivity for revTetR over TetR. Besides the unique property of the specific effector 12 c to effectively differentiate TetR and its reverse phenotype, the test compound proved to be almost devoid of any antibacterial activity; this will be highly beneficial for future applications to control gene expression in bacterial systems.     

Multimeric Lactoside “Click Clusters” as Tools to Investigate the Effect of Linker Length in Specific Interactions with Peanut Lectin,Galectin‐1, and ‐3

Multimeric lactosides based on carbohydrate scaffolds with valencies ranging from 1 to 4 and different linker lengths were synthesized by a copper‐catalyzed azide–alkyne cycloaddition (CuAAC). The binding affinities and crosslinking abilities of the new “click clusters” toward biologically relevant galectins (gal‐1, gal‐3) and peanut lectin were evaluated by fluorescent polarization assay (FPA) and enzyme‐linked lectin assay (ELLA), respectively. FPA indicated that the binding affinities of the synthetic multilactosides towards the galectins increased proportionally with their lactosyl content, without significant differences due to the spacer length. ELLA evidenced a modest cluster effect for the multivalent conjugates, with a relative potency per lactoside ranging from 2.1 to 3.2. Nearly identical binding affinities were recorded for derivatives differing in the length of the linkers, in agreement with the FPA data. These results demonstrate that this parameter does not significantly influence the recognition process when interactions occur at a single lectin site. Molecular dynamics revealed that glycoconjugates adopt a pseudoglobular structure with a random localization of the lactoside residues. These spatial distributions were observed irrespective of the linker length; this explains the virtually equal affinities recorded by ELLA. In contrast, two‐site “sandwich” ELLA clearly revealed that multivalent derivatives bearing the longest spacers were more efficient for crosslinking lectins. Intrinsic affinities, devoid of aggregation effects, and crosslinking capabilities are, therefore, not directly related phenomena that must be taking into consideration in neoglycoconjugate design for specific applications.     

Time‐Dependent Diaryl Ether Inhibitors of InhA: Structure–Activity Relationship Studies of Enzyme Inhibition,Antibacterial Activity,and in vivo Efficacy

The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl‐ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug‐sensitive and drug‐resistant strains of Mycobacterium tuberculosis. In the present work, we demonstrate that two time‐dependent B‐ring modified diaryl ether InhA inhibitors have antibacterial activity in a mouse model of TB infection when delivered by intraperitoneal injection. We propose that the efficacy of these compounds is related to their residence time on the enzyme, and to identify structural features that modulate drug–target residence time in this system, we have explored the inhibition of InhA by a series of B‐ring modified analogues. Seven ortho‐substituted compounds were found to be time‐dependent inhibitors of InhA, where the slow step leading to the final enzyme–inhibitor complex (EI*) is thought to correlate with closure and ordering of the InhA substrate binding loop. A detailed mechanistic understanding of the molecular basis for residence time in this system will facilitate the development of InhA inhibitors with improved in vivo activity.     

Integration of Bioorthogonal Probes and Q‐FRET for the Detection of Histone Acetyltransferase Activity

Histone acetyltransferases (HATs) are key players in the epigenetic regulation of gene function. The recent discovery of diverse HAT substrates implies a broad spectrum of cellular functions of HATs. Many pathological processes are also intimately associated with the dysregulation of HAT levels and activities. However, detecting the enzymatic activity of HATs has been challenging, and this has significantly impeded drug discovery. To advance the field, we developed a convenient one‐pot, mix‐and‐read strategy that is capable of directly detecting the acylated histone product through a fluorescent readout. The strategy integrates three technological platforms—bioorthogonal HAT substrate labeling, alkyne–azide click chemistry, and quenching FRET—into one system for effective probing of HAT enzyme activity.     

Phenol and Organic Bases Co‐Catalyzed Chemical Fixation of Carbon Dioxide with Terminal Epoxides to Form Cyclic Carbonates

Phenol can efficiently catalyze the reactions of terminal epoxides with carbon dioxide in the presence of catalytic amounts of various organic bases such as 4‐dimethylaminopyridine (DMAP), pyridine, 1,8‐diazabicyclo[5.4.0]undec‐7‐ene, and triethylamine to give the corresponding five‐membered cyclic carbonate in high yields (initial pressure 3.57 MPa; reaction temperature 120 °C). p‐Methoxyphenol with DMAP is the best combination to give the cyclic carbonate in the highest yield.     

Structure–Activity Relationships of Glucosamine‐Derived Glycerolipids: the Role of the Anomeric Linkage,the Cationic Charge and the Glycero Moiety on the Antitumor Activity

The potent antitumor activity of 1‐O‐hexadecyl‐2‐O‐methyl‐3‐O‐(2′‐amino‐2′‐deoxy‐β‐D ‐glucopyranosyl)‐sn‐glycerol ( 1 ) was previously shown to arise through an apoptosis‐independent pathway. Here, a systematic structure–activity study in which the effects of the anomeric linkage, the cationic charge and the glycero moiety on the antitumor activity is described. Eight analogues of 1 were synthesized, and their antitumor activity against breast (JIMT1 and BT549), pancreas (MiaPaCa2) and prostate (DU145, PC3) cancer was determined. 1‐O‐Hexadecyl‐2‐O‐methyl‐3‐O‐(2′‐amino‐2′‐deoxy‐α‐D ‐glucopyranosyl)‐sn‐glycerol ( 2 ) consistently displayed the most potent activity against all five cell lines with CC₅₀ values in the range of 6–10 μM . However, replacement of the O‐glycosidic linkage by a thioglycosidic linkage or replacement of the amino group by an azide or guanidino group leads to a threefold or greater decrease in potency. The glycero moiety also contributes to the overall activity of 1 and 2 but its effects are of lesser importance. Investigation into the mode of action of this class of compounds revealed that, in agreement with previous findings, the cytotoxic effects arise through induction of large acid vacuoles.     

Synthesis of alkyne‐terminated xanthate RAFT agents and their uses for the controlled radical polymerization of N‐vinylpyrrolidone and the synthesis of its block copolymer using click chemistry

Two new alkyne‐terminated xanthate reversible addition‐fragmentation chain‐transfer (RAFT) agents: (S)‐2‐(Propynyl propionate)‐(O‐ethyl xanthate) (X₃) and (S)‐2‐(Propynyl isobutyrate)‐(O‐ethyl xanthate) (X₄) were synthesized and characterized and used for the controlled radical polymerization of N‐vinylpyrrolidone (NVP). X₃ showed better chain transfer ability in the polymerization at 60°C. Molecular weight of the resulted polymer increased linearly with the increase in monomer loading. Kinetics study with X₃ showed the pseudo‐first order kinetics up to 67% monomer conversion. Molecular weight (M_n) of the resulting polymer increased linearly with the increase in the monomer conversion up to around 67%. With the increase in the monomer conversion, polydispersity of the corresponding poly(NVP)s initially decreased from 1.34 to 1.32 and then increased gradually to 1.58. Chain‐end analysis of the resulting polymer by ¹H‐NMR and FTIR showed clearly that polymerization started with radical forming out of xanthate RAFT agent. Living nature of the polymerization was also confirmed from the successful homo‐chain extension experiment and the hetero‐chain extension experiment involving synthesis of poly(NVP)‐b‐polystyrene amphiphilic diblock copolymer. Formed alkyne‐terminated poly(NVP) also allowed easy conjugation to azide‐terminated polystyrene by click chemistry to prepare well‐defined poly(NVP)‐b‐polystyrene block copolymers. Resulting polymers were characterized by GPC, ¹H‐NMR, FTIR, and thermal study. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013