Copper-free Click Reaction Research Articles

Chemical tags for site-specific fluorescent labeling of biomolecules.

This review focuses on the various approaches to covalently attach a chromophore to a biomolecule of interest in site-specific manner. Novel methods like inverse electron-demand Diels-Alder reaction, Pictet-Spengler ligation and enzyme tags like SNAP and Halo-tags are critically discussed and compared to established techniques like copper-free click reaction and native chemical ligation. Selected examples in which the tags have been exploited for in vitro or in vivo imaging are reviewed and evaluated.

One-pot modification of 5′-capped RNA based on methionine analogs

This paper outlines chemically and enzymatically synthesized S-adenosylmethionine (AdoMet) analogs and their use in the site-specific modification of RNA by methyltransferases, enabling the facile attachment of clickable moieties to the nucleic acid. We then focus on methodological aspects of setting up a methyltransferase-based enzymatic cascade reaction starting from methionine analogs. This strategy is applied to the one-pot modification of the mRNA cap which is subsequently derivatized in copper-free and copper-catalyzed click reactions. We show that high transfer efficiencies to the cap are obtained using Se-propargyl-, hexenynyl- and azido-bearing methionine analogs. By switching to other methyltransferases our one-pot modification approach should be directly applicable to the regiospecific modification of other target molecules including nucleic acids, proteins and small molecules.

High Fidelity, Efficiency and Functionalization of Ds-Px Unnatural Base Pairs in PCR Amplification for a Genetic Alphabet Expansion System.

Genetic alphabet expansion of DNA using an artificial extra base pair (unnatural base pair) could augment nucleic acid and protein functionalities by increasing their components. We previously developed an unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px), which exhibits high fidelity as a third base pair in PCR amplification. Here, the fidelity and efficiency of Ds-Px pairing using modified Px bases with functional groups, such as diol, azide, ethynyl and biotin, were evaluated by an improved method with optimized PCR conditions. The results revealed that all of the base pairs between Ds and either one of the modified Px bases functioned with high amplification efficiency (0.76-0.81), high selectivity (≥99.96% per doubling), and less sequence dependency, in PCR using 3'-exonuclease-proficient Deep Vent DNA polymerase. We also demonstrated that the azide-Px in PCR-amplified DNA was efficiently modified with any functional groups by copper-free click reaction. This genetic alphabet expansion system could endow nucleic acids with a wide variety of increased functionalities by the site-specific incorporation of modified Px bases at desired positions in DNA.

Cooperative capture synthesis: yet another playground for copper-free click chemistry.

Click chemistry describes a family of modular, efficient, versatile and reliable reactions which have acquired a pivotal role as one of the most useful synthetic tools with a potentially broad range of applications. While copper(i)-catalysed alkyne-azide cycloaddition is the most widely adopted click reaction in the family, the fact that it is cytotoxic restricts its practice in certain situations, e.g., bioconjugation. Consequently, researchers have been exploring the development of copper-free click reactions, the most popular example so far being strain-promoted alkyne-azide cycloadditions. An early example of copper-free click reactions that is rarely mentioned in the literature is the cucurbit[6]uril (CB6) catalysed alkyne-azide cycloaddition (CB-AAC). Despite the unique ability of CB-AAC to generate mechanically interlocked molecules (MIMs) - in particular, rotaxanes - its slow reaction rate and narrow substrate acceptance limit its scope. In this Tutorial Review, we describe our efforts of late in developing the fundamental principles and practical applications of a new copper-free click reaction - namely, cooperative capture synthesis, whereby introducing a cyclodextrin (CD) as an accelerator in CB-AAC, hydrogen bonding networks are formed between the rims of CD and CB6 in a manner that is positively cooperative, giving rise to a high level of pre-organisation during efficient and quick rotaxane formation. For example, [4]rotaxanes can be prepared nearly quantitatively within a minute in water. Furthermore, we have demonstrated that CB-AAC can accommodate a wider substrate tolerance by introducing pillararenes as promoters. To date, we have put cooperative capture synthesis into practice by (i) preparing polyrotaxanes containing up to 200 rings in nearly quantitative yields, (ii) trapping conformational isomers of polymacrocycles as rings in rotaxanes, (iii) demonstrating solid-state fluorescence and Förster resonance energy transfer (FRET) processes by fixing the fluorophores in a rotaxane and (iv) establishing the principle of supramolecular encryption in the preparation of dynamically and reversibly tunable fluorescent security inks.

ClickECM - a new approach to covalently immobilize human ECM on artificial surfaces

Event Abstract Back to Event clickECM - a new approach to covalently immobilize human ECM on artificial surfaces Sybil M. Ruff1, Silke Keller2, Daniel Wieland3, Valentin Wittmann3, Günter E. Tovar1, 2, Monika Bach1, 2 and Petra Kluger2, 4 1 University of Stuttgart, Institute of Interfacial Process Engineering and Plasma Technology, Germany 2 Fraunhofer Institute for Interfacial Engineering and Biotechnology, Cell and Tissue Engineering, Germany 3 University of Konstanz, Chemistry and Konstanz Research School Chemical Biology, Germany 4 Reutlingen University, School of Applied Chemistry, Germany The extracellular matrix (ECM) is a complex network of biomolecules that surround the cells in a human tissue. Primary cells are capable of producing an ECM in vitro which can be isolated after several days of culture[1]. Due to the high biological activity, different types of ECM are able to promote cell adhesion, proliferation, and differentiation in a tissue specific manner[2]. Because of its diverse functions, the isolated ECM is a promising coating material for the use in tissue engineering and regenerative medicine. However, a major limitation of physisorbed ECM coatings is the lack of mechanical stability (especially under physiological conditions) as no covalent linkages are formed[3]. To overcome this limitation our approach was to covalently immobilize the human ECM on artificial surfaces. Therefore, we performed metabolic oligosaccharide engineering (MOE) to introduce click groups into the glycan structures of the ECM. Here we demonstrate that this method is suitable to fabricate a “clickable” human ECM (clickECM) which can be covalently immobilized on alkyne-functionalized artificial surfaces via copper-free click reaction[4] (Fig. 1). We cultured primary human dermal fibroblasts over a period of six days to generate a human dermal ECM. By treating the cells with an azide-modified monosaccharide (Ac4GalNAz) we were able to introduce click functionalities into the glycans of the ECM. Histochemical and immunofluorescence analysis were performed to characterize the biological composition of clickECM in comparison with untreated ECM and human skin dermis. Then, silicon wafers were functionalized with activated alkynes for the covalent immobilization of clickECM. Coating of unmodified ECM via physisorption served as control. The stability of these coatings was compared by calculating the percentage area covered with ECM before and after an intensive washing step in detergent-supplemented buffer. The bioactive properties of these coatings were evaluated by quantifying the cell proliferation of HaCaT cells seeded on either clickECM-coated or uncoated glass substrates. We could for the first time show that MOE can be used to introduce click groups into the ECM of human dermal fibroblasts. This clickECM consists of glycans, collagens, and non-collagenous proteins whereby the ratio of these biomolecules is the same in clickECM and unmodified ECM. Furthermore, this composition is comparable to human skin dermis (Fig. 2). The clickECM can be covalently immobilized on alkyne-modified surfaces resulting in a significant increase in coating stability compared to a conventional ECM coating via physisorption (Fig. 3). Cell proliferation of HaCaT cells was significantly enhanced on the clickECM-coated surfaces compared to uncoated glass substrates. These results demonstrate that the covalent immobilization mediates a high stability while preserving the high biological activity of the human dermal ECM. We propose that clickECM is a promising coating technology to generate long-term stable coatings with high biological complexity. In future, this could be used to enhance the ingrowth of medical implants. By using autologous cells to generate a personalized clickECM coating, the risk of implant failure would be minimized.

Focal calcium monitoring with targeted nanosensors at the cytosolic side of endoplasmic reticulum

Ca2+ distribution is spatially and temporally non-uniform inside cells due to cellular compartmentalization. However, Ca2+ sensing with small organic dyes, such as fura-2 and fluo-4, has been practically applied at a single cell level where the averaged signal from freely diffusing dye molecules is acquired. In this study, we aimed to target azide-functionalized fura-2 (N3-fura-2) to a specific site of subcellular compartments to realize focal Ca2+ sensing. Using scAVD (single-chain avidin)–biotin interaction and a copper-free click reaction system, we linked N3-fura-2 to specifically-targeted scAVD protein fused with a red fluorescent protein mCherry, so that Ca2+ sensors conjugated with four N3-fura-2 dyes with dibenzocyclooctyne (DBCO)-PEG4-biotin as a linker were generated at subcellular compartments in living cells. In cytoplasm, N3-fura-2 showed a prolonged retention period after binding to scAVD. Furthermore, the reacted N3-fura-2 was retained inside cells even after free dyes were washed out by methanol fixation. When scAVD was overexpressed on endoplasmic reticulum (ER) membranes, N3-fura-2 was accumulated on ER membranes. Upon histamine stimulation, which increases cytosolic Ca2+ concentration, ER-localized N3-fura-2 successfully sensed the Ca2+ level changes at the cytosolic side of ER membrane. Our study demonstrated specific targeting of N3-fura-2 to subcellular compartments and the ability of sensing focal Ca2+ level changes with the specifically targeted Ca2+ sensors.

Synthesis and evaluation of an (125)I-labeled azide prosthetic group for efficient and bioorthogonal radiolabeling of cyclooctyne-group containing molecules using copper-free click reaction.

Herein we report the radiosynthesis of a pyridine derived azide prosthetic group for iodine radioisotope labeling of dibenzocyclooctyne (DBCO) conjugated molecules. The radiolabeling of the stannylated precursor 2 was conducted using [(125)I]NaI and chloramine-T to give (125)I-labeled azide ([(125)I]1) with high radiochemical yield (72±8%, n=4) and radiochemical purity (>99%). Using (125)I-labeled azide ([(125)I]1), cyclic RGD peptide and near infrared fluorescent molecule were efficiently labeled with modest to good radiochemical yields. The biodistribution study and SPECT/CT images showed that [(125)I]1 underwent rapid renal clearance. These results clearly demonstrated that [(125)I]1 could be used as an useful radiotracer for in vivo pre-targeted imaging as well as efficient in vitro radiolabeling of DBCO containing molecules.

Non-Catalyzed Click Reactions of ADIBO Derivatives with 5-Methyluridine Azides and Conformational Study of the Resulting Triazoles.

Copper-free click reactions between a dibenzoazocine derivative and azides derived from 5-methyluridine were investigated. The non-catalyzed reaction yielded both regioisomers in an approximately equivalent ratio. The NMR spectra of each regioisomer revealed conformational isomery. The ratio of isomers was dependent on the type of regioisomer and the type of solvent. The synthesis of various analogs, a detailed NMR study and computational modeling provided evidence that the isomery was dependent on the interaction of the azocine and pyrimidine parts.

SiRNA-Loaded Polyion Complex Micelle Decorated with Charge-Conversional Polymer Tuned to Undergo Stepwise Response to Intra-Tumoral and Intra-Endosomal pHs for Exerting Enhanced RNAi Efficacy.

Small interfering RNA (siRNA) needs an efficient delivery vehicle to reach the cytoplasm of target cells for successful RNA interference (RNAi) therapy. This study aimed to develop an siRNA-loaded polyion complex (PIC) micelle equipped with a smart polymeric shell featuring tumor targetability and endosome escapability for enhanced RNAi activity in cancer cells. To this end, an acidic pH-responsive polypeptide was designed to exert a stepwise change in its charged state from negative to modestly positive and highly positive in response to slightly acidic environment of tumor (pH ∼6.7) and further lowered-pH condition of late endosomal compartments (pH ∼5.0), respectively, for selective binding to cancer cell surface and subsequent endosome disruption. This polypeptide, termed PAsp(DET-CDM/DBCO), was synthesized by introducing acid-labile carboxydimethyl maleate (CDM) and dibenzylcyclooctyne (DBCO) moieties into a polyaspartamide derivative bearing two-repeated aminoethylene side chains (PAsp(DET)). Then, PAsp(DET-CDM/DBCO) was installed on the surface of disulfide cross-linked PIC micelles prepared from cholesterol-modified siRNA (Chol-siRNA) and azide-poly(ethylene glycol)-b-poly[(3-mercaptopropylamidine)-L-lysine] (N3-PEG-b-PLys(MPA)) through the copper-free click reaction. Successful PAsp(DET-CDM/DBCO) coverage of PIC micelles was confirmed by a significant decrease in ζ-potential as well as a narrowly distributed size of 40 nm. The PAsp(DET-CDM/DBCO)-installed micelles significantly improved the gene-silencing efficiency in cultured lung cancer cells, compared with nonmodified control micelles, especially after incubation at pH 6.7. This improved silencing activity was nicely correlated with the facilitated cellular uptake of siRNA payloads at the acidic pH and the efficient endosomal escape. These results demonstrate that the acidic pH-responsive polypeptide shell is a promising design strategy for tumor-targeted siRNA delivery.

In situ grafting MPEG on the surface of cell-loaded microcapsules for protein repellency

ABSTRACTThe protein repelled alginate-graft-BAT/chitosan/MPEG-norbornene (ABCPN) hydrogel microcapsules were achieved by copper-free click reaction between azides from BAT and alkylenes from norbornene. The MPEG modified polyelectrolyte microcapsules showed significant resistance to immune protein adsorption and good biocompatibility in vivo. Moreover, the mild reaction condition made it feasible that the microcapsules could be formed and modified in situ even when live cells were encapsulated, and precluded the damage cause by other violent modifications methods to transplanted cells or tissues.

Functionalized bismuth ferrite harmonic nanoparticles for cancer cells labeling and imaging

Bismuth ferrite (BFO) harmonic nanoparticles (NPs) display high nonlinear optical efficiency and excellent biocompatibility profile which make them attractive for the development of diagnostic applications as contrast agents. In this study, we present a general method for the functionalization of this material with chemical ligands targeting cancer molecular biomarkers. In particular, a conjugation protocol based on click reaction between alkynyl-containing targeting ligands and poly(ethylene glycol)-coated BFO NPs (67.7 nm) displaying surface reactive azido groups was developed. Copper-free click reaction allowed fast and efficient conjugation of a covalent inhibitor of prolyl-specific endopeptidases to coated BFO NPs. The ability of these functionalized nanomaterials (134.2 nm) to act as imaging probes for cancer cells was demonstrated by the selective labeling of human lung cancer cells.

Application of a Small Molecule Radiopharmaceutical Concept to Improve Kinetics.

Recently, large molecules or nanoparticles are actively studied as radiopharmaceuticals. However, their kinetics is problematic because of a slow penetration through the capillaries and slow distribution to the target. To improve the kinetics, a two-step targeting method can be applied by using small molecules and very rapid copper-free click reaction. Although this method might have limitations such as internalization of the first targeted conjugate, it will provide high target-to-non-target ratio imaging of radiopharmaceuticals.

The synthesis and fluorescence profile of novel thalidomide analogues

Herein we describe the synthesis of various simple N-alkyl thalidomide derivatives in order to determine their fluorescence excitation and emission profile. Following this, a series of more complex fragments were attached through a Huisgen 1,3-dipolar cycloaddition providing a more diverse fluorescence profile. A thalidomide azide derivative was also found to be particularly reactive in a copper-free click reaction with two known cyclooctynes.

Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry.

Site-specific labeling of long-chain RNAs with desired molecular probes is an imperative technique to facilitate studies of functional RNA molecules. By genetic alphabet expansion using an artificial third base pair, called an unnatural base pair, we present a post-transcriptional modification method for RNA transcripts containing an incorporated azide-linked unnatural base at specific positions, using a copper-free click reaction. The unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions in transcription. Thus, we chemically synthesized a triphosphate substrate of 4-(4-azidopentyl)-pyrrole-2-carbaldehyde (N3-PaTP), which can be site-specifically introduced into RNA, opposite Ds in templates by T7 transcription. The N3-Pa incorporated in the transcripts was modified with dibenzocyclooctyne (DIBO) derivatives. We demonstrated the transcription of 17-, 76- and 260-mer RNA molecules and their site-specific labeling with Alexa 488, Alexa 594 and biotin. This method will be useful for preparing RNA molecules labeled with any functional groups of interest, toward in vivo experiments.

Efficient method for iodine radioisotope labeling of cyclooctyne-containing molecules using strain-promoted copper-free click reaction

Herein we report an efficient method for iodine radioisotope labeling of cyclooctyne-containing molecules using copper-free click reaction. For this study, radioiodination using the tin precursor 2 was carried out at room temperature to give 125I-labeled azide ([125I]1) with high radiochemical yield (85%) and excellent radiochemical purity. Dibenzocyclooctyne (DBCO) containing cRGD peptide and gold nanoparticle were labeled with [125I]1 at 37°C for 30min to give triazoles with good radiochemical yields (67–95%). We next carried out tissue biodistribution study of [125I]1 in normal ICR mice to investigate the level of organ accumulation which needs to be considered for pre-targeted in vivo imaging. Large amount of [125I]1 distributed rapidly in liver and kidney from bloodstream and underwent rapid renal and hepatobiliary clearance. Moreover [125I]1 was found to be highly stable (>92%) in mouse serum for 24h. Therefore [125I]1 could be used as a potentially useful radiotracer for pre-targeted imaging. Those results clearly indicated that the present radiolabeling method using copper free click reaction would be quite useful for both in vitro and in vivo labeling of DBCO group containing molecules with iodine radioisotopes.

Efficient Cargo Delivery into Adult Brain Tissue Using Short Cell-Penetrating Peptides.

Zebrafish brains can regenerate lost neurons upon neurogenic activity of the radial glial progenitor cells (RGCs) that reside at the ventricular region. Understanding the molecular events underlying this ability is of great interest for translational studies of regenerative medicine. Therefore, functional analyses of gene function in RGCs and neurons are essential. Using cerebroventricular microinjection (CVMI), RGCs can be targeted efficiently but the penetration capacity of the injected molecules reduces dramatically in deeper parts of the brain tissue, such as the parenchymal regions that contain the neurons. In this report, we tested the penetration efficiency of five known cell-penetrating peptides (CPPs) and identified two– polyR and Trans – that efficiently penetrate the brain tissue without overt toxicity in a dose-dependent manner as determined by TUNEL staining and L-Plastin immunohistochemistry. We also found that polyR peptide can help carry plasmid DNA several cell diameters into the brain tissue after a series of coupling reactions using DBCO-PEG4-maleimide-based Michael’s addition and azide-mediated copper-free click reaction. Combined with the advantages of CVMI, such as rapidness, reproducibility, and ability to be used in adult animals, CPPs improve the applicability of the CVMI technique to deeper parts of the central nervous system tissues.

Controlling Localization and Excretion of Nanoparticles by Click Modification of the Surface Chemical Structures inside Living Cells.

Surface modification of silica nanoparticles (SiNPs) inside living cells was conducted by using the copper-free bioorthogonal click reaction to evaluate the effects of surface chemical structures on dynamic behavior and excretion of SiNPs. The results demonstrated the spatial translocation of intracellular SiNPs to the plasma membrane upon surface modification in situ with phospholipids. Moreover, the extent and kinetics of excretion of the SiNPs from inside the cell were enhanced by modification.

Development of next generation of therapeutic IFN-α2b via genetic code expansion

With the aim to overcome the heterogeneity associated with marketed IFN-α2b PEGylates and optimize the size of the PEG moiety and the site of PEGylation, we develop a viable and facile platform through genetic code expansion for PEGylation of IFN-α2b at any chosen site(s). This approach includes site-specific incorporation of an azide-bearing amino acid into IFN-α2b followed by orthogonal and stoichiometric conjugation of a variety of PEGs via a copper-free click reaction. By this approach, only the chosen site(s) within IFN-α2b is consistently PEGylated under mild conditions, leading to a single and homogenous conjugate. Furthermore, it makes the structure–activity relationship study of IFN-α2b possible by which the opposite effects of PEGylation on the biological and pharmacological properties are optimized. Upon re-examination of the PEGylated IFN-α2b isomers carrying different sizes of PEG at different sites, we find mono-PEGylates at H34, A74 and E107 with a 20-, 10- and 10-kDa PEG moiety, respectively, have both higher biological activities and better PK profiles than others. These might represent the direction for development of the next generation of PEGylated IFN-α2b.

GFP for EM: Site-Specific Labeling of Proteins for Electron Microscopy

Structural analysis of macromolecules by electron microscopy (EM) has been facilitated by a recent technological revolution in instrumentation and data processing, which has led to the achievement of their visualization at atomic resolution. However, moderate resolution electron density maps of protein complexes can be misleading, resulting in ambiguity when ascribing subunits to particular locations within the architecture of complexes. To this end, investigators have traditionally performed subunit mapping by N- or C-terminal fusions with tags, such as maltose binding protein (MBP), with mixed success. Toward the accurate determination of the location and orientation of protein subunits, as well as large scale movements of protein complexes, the establishment of a highly specific labeling technique would be a major breakthrough. Here we present a site-specific labeling strategy that exploits a unique chemical handle introduced by the incorporation of the unnatural amino acid (UAA). The UAA permits a site-specific copper-free click reaction for labeling with a modified label, such as MBP or Nanogold. We use this method to label a subunit within the recombinant yeast proteasome lid complex that was previously not amenable to labeling by MBP fusion. This technique is extremely versatile and precise; it can be readily expanded to other organisms and to other labels, and will be useful for a wide range of structural analyses.

Targeted imaging and proteomic analysis of tumor-associated glycans in living animals.

Although it has been well known that dynamic changes in glycosylation are associated with tumor progression, it remains challenging to selectively visualize the cancer glycome in vivo. Herein, a strategy for the targeted imaging of tumor-associated glycans by using ligand-targeted liposomes encapsulating azidosugars is described. The intravenously injected liposomal nanoparticles selectively bound to the cancer-cell-specific receptors and installed azides into the melanoma glycans in a xenograft mouse model in a tissue-specific manner. Subsequently, a copper-free click reaction was performed in vivo to chemoselectively conjugate the azides with a near-infrared fluorescent dye. The glycosylation dynamics during tumor growth were monitored by in vivo fluorescence imaging. Furthermore, the newly synthesized sialylated glycoproteins were enriched during tumor growth and identified by glycoproteomics. Compared with the labeling methods using free azidosugars, this method offers improved labeling efficiency and high specificity and should facilitate the elucidation of the functional role of glycans in cancer biology.