Strain-promoted Azide-alkyne Cycloaddition Research Articles

Post-polymerization functionalization of epoxide-containing copolymers in trifluoroethanol for synthesis of polymer-drug conjugates

Abstract Post-polymerization functionalization is a critical tool in preparing functional materials. The critical aspects of post-polymerization reactions are high yields, short reaction times, simple purification, near stoichiometric amounts of reactants, and facile reaction conditions. Polymeric epoxides (i.e. poly(glycidyl methacrylate)) represent an underutilized class of functionalized polymers due to long reaction times, high temperatures, and large excess of reactants to drive the reaction to high conversion in a reasonable time frame. In this manuscript we describe the use of a novel solvent trifluoroethanol (TFE) for the ring opening of amines with poly(glycidyl methacrylate). We demonstrate that TFE gives faster reaction times and higher yields than traditional solvents used for the ring opening reaction. We utilized TFE to prepare dual functionalized polymers that could be “clicked” using strain promoted azide alkyne cycloaddition and an amine-bearing drug ring opening of the polymeric backbone.

A high-throughput-compatible assay to measure the degradation of endogenous Huntingtin proteins.

Aim:The accumulation of disease-causing proteins is a common hallmark of many neurodegenerative disorders. Measuring the degradation of such proteins using high-throughput-compatible assays is highly desired for the identification of genetic and chemical modulators of degradation. For example, Huntington's disease (HD) is an incurable hereditary neurodegenerative disorder caused by the cytotoxicity of mutant huntingtin protein (mHTT). The high-throughput measurement of mHTT degradation is important in HD drug discovery and research. Existing methods for such purposes have limitations due to their dependence on protein tags or pan protein synthesis inhibitors. Here, we report a high-throughput-compatible pulse-chase method (CH-chase) for the measurement of endogenous tag-free huntingtin protein (HTT) degradation based on Click chemistry and Homogeneous Time Resolved Fluorescence (HTRF) technologies.Methods:The pulsed-labeled proteins were conjugated with biotin using the click reaction strain-promoted alkyne-azide cycloaddition (SPAAC), and the chase signals were calculated by measuring the reduction percentage of the HTT HTRF signals after pull-down with streptavidin beads.Results:We validated that the signals were within the linear detection range and were HTT-specific. We successfully measured the degradation of endogenous HTT in a high-throughput-compatible format using 96-well plates. The predicted changes of HTT degradation by known modifiers were observed, which confirmed that the assay is suitable for the identification of HTT degradation modifiers.Conclusion:We have established the first high-throughput-compatible assay capable of measuring endogenous, tag-free HTT degradation, providing a valuable tool for HD research and drug discovery. The method could be applied to other proteins and can facilitate research on other neurodegenerative disorders and proteinopathies.

Synthesis and evaluation of fluorescent Pam3Cys peptide conjugates

Chirally pure R- and S-epimers of TLR2 ligand Pam3CysSK4 were prepared and separately conjugated to an OVA model epitope, in which lysine was replaced by azidonorleucine. The azide function in the conjugate permitted labelling with different fluorophores by use of strain-promoted 3+2 cycloaddition. The R-epimer of the labelled conjugates induced TLR2-dependent DC maturation, while S-epimer proved to be inactive. Combining the lipophilicity of Pam3CysSK4 ligand with fluorophores influenced the solubility of the resulting conjugates in an unpredictable way and only the conjugates labelled with Cy-5 were suitable for confocal fluorescence microscopy experiments. It was shown that both epimers of the Cy-5 labelled lipopeptides were internalized equally well, indicating TLR2-independent cellular uptake. The presented results demonstrate the usefulness of strain-promoted azide-alkyne cycloaddition in the labelling of highly lipophilic lipopeptides without disturbing the in vitro activity of these conjugates with respect to activation of TLR-2.

Thermal Regulation of Colloidal Materials Architecture through Orthogonal Functionalizable Patchy Particles

This contribution presents a sol–gel based cluster encapsulation methodology to produce bifunctional patchy particles. The particles possess azide moieties on the surfaces of the patch and carboxylic acids on the shell. Two types of DNA with distinct terminal sequences are site-specifically conjugated to the particle patches or the shell employing two orthogonal coupling strategies: strain-promoted alkyne–azide cycloaddition and carbodiimide-mediated amidation. We can activate and deactivate assembly on the patches and/or the shell through thermal control, demonstrating reversible and stepwise self-assembly.

Multidentate Polysarcosine-Based Ligands for Water-Soluble Quantum Dots

We describe the synthesis of heterotelechelic polysarcosine polymers and their use as multidentate ligands in the preparation of stable water-soluble quantum dots (QDs). Orthogonally functionalized polysarcosine with amine and dibenzocyclooctyl (DBCO) end groups is obtained by ring-opening polymerization of N-methylglycine N-carboxyanhydride with DBCO amine as initiator. In a first postpolymerization modification step, the future biological activity of the polymeric ligands is adjusted by modification of the amine terminus. Then, in a second postpolymerization modification step, azide functionalized di- and tridentate anchor compounds are introduced to the DBCO terminus of the polysarcosine via strain-promoted azide–alkyne cycloaddition (SPAAC). Through the separate synthesis of the anchor compounds, it is possible to ensure reproducible introduction of a well-defined number of multiple anchor groups to all polymers studied. Finally, the obtained multidentate polymeric ligands are successfully used in the...

Surgical sealants with tunable swelling, burst pressures, and biodegradation rates.

We developed two types of polyethylene glycol (PEG)-based surgical sealants, which we have termed the PER and PRO series. In one, the PRO series, an 8-arm PEG containing activated carbonyl end-groups was reacted with a 4-armed amino-PEG. In the second, the PER series, a 4-arm PEG containing bi-functional end groups with four azides and four activated esters was reacted by strain-promoted alkyne-azide cycloaddition with a 4-arm cyclooctyne-PEG to give a near-ideal Tetra-PEG hydrogel. The sealants showed predictably tunable strength, swelling, adhesion, and gelation properties. The gels were compared to commercially available PEG-based sealants and exhibit physical properties equivalent to or better than the standards. Variants of each gel-format were prepared that contained a β-eliminative cleavable linker in the crosslinks to control degradation rate. Linkers of this type self-cleave with half-lives spanning from hours to years, and offer the unique ability to precisely tune the degradation to match the healing process. In addition, these linkers could serve as cleavable tethers for controlled drug release. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1602-1611, 2017.

Rapid cycloaddition of a diazo group with an unstrained dipolarophile

The cycloaddition of a diazoacetamide with ethyl 4,4,4-trifluorocrotonate proceeds with k=0.1M−1s−1. This second-order rate constant rivals those of optimized strain-promoted azide–alkyne cycloadditions, even though the reaction does not release strain. The regioselectivity and a computational distortion/interaction analysis of the reaction energetics are consistent with the formation of an NH⋯FC hydrogen bond in the transition state and the electronic character of the trifluorocrotonate. Analogous reactions with an azidoacetamide dipole or with an acrylate or crotonate dipolarophile are much slower. These findings suggest a new strategy for the design of diazo-selective reagents for chemical biology.

Conjugation of BSA onto PEG8 via Strain‐Promoted Azide‐Alkyne Cycloaddition (SPAAC) as a Drug Delivery System

The hydrophobicity of many drugs poses a major problem for delivery to target tissues. One current technique for hydrophobic drug delivery utilizes Human Serum Albumin (HSA). Hydrophobic binding pockets on HSA protect the molecule from degradation due to redox reactions, hydrolysis and immunogenic response. Bovine Serum Albumin (BSA) provides a cheaper, more readily available alternative to HSA. Structural similarities between binding pockets of both species suggest similar binding capabilities. Conjugation of multiple BSA molecules onto an 8‐arm polyethylene glycol backbone (PEG8‐BSAx) addresses concerns about the effect on osmotic pressure, competition for binding sites, and immunogenicity. Utilizing SPAAC, multiple dibenzocyclooctyl‐functionalized de‐fatted BSA were attached to an azido‐functionalized PEG8. CD demonstrated no loss of secondary structure after PEGylation. Four high molecular weight PEG8‐BSAx species were separated from the reaction mixture via SDS‐PAGE and reversed phase HPLC. Ligand‐binding capabilities and dissociation constants were determined using the fluorescent probe ANS. Multiple BSA molecules were successfully conjugated onto a PEG8 framework while maintaining ligand‐binding capabilities. These results suggest that PEG8‐BSAx is a viable delivery system for water‐insoluble pharmaceuticals.Support or Funding InformationLoyola University Chicago

Use of Ambient Ionization High-Resolution Mass Spectrometry for the Kinetic Analysis of Organic Surface Reactions.

In contrast to homogeneous systems, studying the kinetics of organic reactions on solid surfaces remains a difficult task due to the limited availability of appropriate analysis techniques that are general, high-throughput, and capable of offering quantitative, structural surface information. Here, we demonstrate how direct analysis in real time mass spectrometry (DART-MS) complies with above considerations and can be used for determining interfacial kinetic parameters. The presented approach is based on the use of a MS tag that--in principle--allows application to other reactions. To show the potential of DART-MS, we selected the widely applied strain-promoted alkyne-azide cycloaddition (SPAAC) as a model reaction to elucidate the effects of the nanoenvironment on the interfacial reaction rate.

A Double-Clicking Bis-Azide Fluorogenic Dye for Bioorthogonal Self-Labeling Peptide Tags.

Herein, we give the very first example for the development of a fluorogenic molecular probe that combines the two-point binding specificity of biarsenical-based dyes with the robustness of bioorthogonal click-chemistry. This proof-of-principle study reports on the synthesis and fluorogenic characterization of a new, double-quenched, bis-azide fluorogenic probe suitable for bioorthogonal two-point tagging of small peptide tags by double strain-promoted azide-alkyne cycloaddition. The presented probe exhibits remarkable increase in fluorescence intensity when reacted with bis-cyclooctynylated peptide sequences, which could also serve as possible self-labeling small peptide tag motifs.

Strain-Promoted 1,3-Dipolar Cycloaddition of Cycloalkynes and Organic Azides.

A nearly forgotten reaction discovered more than 60 years ago—the cycloaddition of a cyclic alkyne and an organic azide, leading to an aromatic triazole—enjoys a remarkable popularity. Originally discovered out of pure chemical curiosity, and dusted off early this century as an efficient and clean bioconjugation tool, the usefulness of cyclooctyne–azide cycloaddition is now adopted in a wide range of fields of chemical science and beyond. Its ease of operation, broad solvent compatibility, 100 % atom efficiency, and the high stability of the resulting triazole product, just to name a few aspects, have catapulted this so-called strain-promoted azide–alkyne cycloaddition (SPAAC) right into the top-shelf of the toolbox of chemical biologists, material scientists, biotechnologists, medicinal chemists, and more. In this chapter, a brief historic overview of cycloalkynes is provided first, along with the main synthetic strategies to prepare cycloalkynes and their chemical reactivities. Core aspects of the strain-promoted reaction of cycloalkynes with azides are covered, as well as tools to achieve further reaction acceleration by means of modulation of cycloalkyne structure, nature of azide, and choice of solvent.

Bio-Orthogonally Crosslinked, Engineered Protein Hydrogels with Tunable Mechanics and Biochemistry for Cell Encapsulation.

Covalently-crosslinked hydrogels are commonly used as 3D matrices for cell culture and transplantation. However, the crosslinking chemistries used to prepare these gels generally cross-react with functional groups present on the cell surface, potentially leading to cytotoxicity and other undesired effects. Bio-orthogonal chemistries have been developed that do not react with biologically relevant functional groups, thereby preventing these undesirable side reactions. However, previously developed biomaterials using these chemistries still possess less than ideal properties for cell encapsulation, such as slow gelation kinetics and limited tuning of matrix mechanics and biochemistry. Here, engineered elastin-like proteins (ELPs) are developed that cross-link via strain-promoted azide-alkyne cycloaddition (SPAAC) or Staudinger ligation. The SPAAC-crosslinked materials form gels within seconds and complete gelation within minutes. These hydrogels support the encapsulation and phenotypic maintenance of human mesenchymal stem cells, human umbilical vein endothelial cells, and murine neural progenitor cells. SPAAC-ELP gels exhibit independent tuning of stiffness and cell adhesion, with significantly improved cell viability and spreading observed in materials containing a fibronectin-derived arginine-glycine-aspartic acid (RGD) domain. The crosslinking chemistry used permits further material functionalization, even in the presence of cells and serum. These hydrogels are anticipated to be useful in a wide range of applications, including therapeutic cell delivery and bioprinting.

Biocompatible Azide-Alkyne "Click" Reactions for Surface Decoration of Glyco-Engineered Cells.

Bio-orthogonal copper (I)-catalyzed azide-alkyne cycloaddition (CuAAC) has been widely used to modify azide- or alkyne-bearing monosaccharides on metabolic glyco-engineered mammalian cells. Here, we present a systematic study to elucidate the design space for the cytotoxic effects of the copper catalyst on NIH 3T3 fibroblasts and on HEK 293-F cells. Monitoring membrane integrity by flow cytometry and RT-PCR analysis with apoptotic and anti-apoptotic markers elucidated the general feasibility of CuAAC, with exposure time of the CuAAC reaction mixture having the major influence on biocompatibility. A high labeling efficiency of HEK 293-F cells with a fluorescent alkyne dye was rapidly achieved by CuAAC in comparison to copper free strain-promoted azide-alkyne cycloaddition (SPAAC). The study details effective and biocompatible conditions for CuAAC-based modification of glyco-engineered cells in comparison to its copper free alternative.

A metal-free turn-on fluorescent probe for the fast and sensitive detection of inorganic azides

Sodium azide is toxic and widely used in agricultural, commercial products, and research laboratories. Thus it is of a significant environmental concern and there is a need for the development of a rapid detection method. A fluorogenic dibenzylcyclooctyne derivative (Fl-DIBO) is herein described as a fluorescent probe for the rapid detection of inorganic azide via Strain-Promoted Azide-Alkyne Cycloaddition (SPAAC). Fl-DIBO was found to be highly selective toward NaN3 in comparison to other common anions with good sensitivity and detection limit of 10μM.

Properties of Poly(ethylene glycol) Hydrogels Cross-Linked via Strain-Promoted Alkyne-Azide Cycloaddition (SPAAC).

A series of poly(ethylene glycol) (PEG) hydrogels was synthesized using strain-promoted alkyne-azide cycloaddition (SPAAC) between PEG chains terminated with either aza-dibenzocyclooctynes or azide functionalities. The gelation process was found to occur rapidly upon mixing the two components in aqueous solution without the need for external stimuli or catalysts, making the system a candidate for use as an injectable hydrogel. The mechanical and rheological properties of these hydrogels were found to be tunable by varying the polymer molecular weight and the number of cross-linking groups per chain. The gelation times of these hydrogels ranged from 10 to 60 s at room temperature. The mass-based swelling ratios varied from 45 to 76 at maximum swelling (relative to the dry state), while the weight percent of polymer in these hydrogels ranged from 1.31 to 2.05%, demonstrating the variations in amount of polymer required to maintain the structural integrity of the gel. Each hydrogel degraded at a different rate in PBS at pH = 7.4, with degradation times ranging from 1 to 35 days. By changing the composition of the two starting components, it was found that the Young's modulus of each hydrogel could be varied from 1 to 18 kPa. Hydrogel incubation with bovine serum albumin showed minimal protein adsorption. Finally, a cell cytotoxicity study of the precursor polymers with 3T3 fibroblasts demonstrated that the azide- and strained alkyne-functionalized PEGs are noncytotoxic.

Synthesis of linear and cyclic peptide-PEG-lipids for stabilization and targeting of cationic liposome-DNA complexes.

Because nucleic acids (NAs) have immense potential value as therapeutics, the development of safe and effective synthetic NA vectors continues to attract much attention. In vivo applications of NA vectors require stabilized, nanometer-scale particles, but the commonly used approaches of steric stabilization with a polymer coat (e.g., PEGylation; PEG=poly(ethylene glycol)) interfere with attachment to cells, uptake, and endosomal escape. Conjugation of peptides to PEG-lipids can improve cell attachment and uptake for cationic liposome-DNA (CL-DNA) complexes. We present several synthetic approaches to peptide-PEG-lipids and discuss their merits and drawbacks. A lipid-PEG-amine building block served as the common key intermediate in all synthetic routes. Assembling the entire peptide-PEG-lipid by manual solid phase peptide synthesis (employing a lipid-PEG-carboxylic acid) allowed gram-scale synthesis but is mostly applicable to linear peptides connected via their N-terminus. Conjugation via thiol-maleimide or strain-promoted (copper-free) azide-alkyne cycloaddition chemistry is highly amenable to on-demand preparation of peptide-PEG-lipids, and the appropriate PEG-lipid precursors are available in a single chemical step from the lipid-PEG-amine building block. Azide-alkyne cycloaddition is especially suitable for disulfide-bridged peptides such as iRGD (cyclic CRGDKGPDC). Added at 10 mol% of a cationic/neutral lipid mixture, the peptide-PEG-lipids stabilize the size of CL-DNA complexes. They also affect cell attachment and uptake of nanoparticles in a peptide-dependent manner, thereby providing a platform for preparing stabilized, affinity-targeted CL-DNA nanoparticles.

Abstract B18: A simple method to prepare oligonucleotide-conjugated antibodies for multiplex protein detection

Abstract With rapid advances in nucleic acid detection technologies, genomics studies are being conducted in highly multiplexed formats. However, multiplex analysis is still a daunting task in the proteomics field; it would be of great interest to use genomics tools for protein detection. One way to accomplish this is to use oligonucleotide-conjugated antibodies to bind to specific protein targets, and to monitor conjugated-oligonucleotide levels rather than to measure protein levels directly. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method’s application in oligo extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and linked covalently with an azide-modified oligonucleotide. The reaction condition and purification process were optimized to achieve maximum yield and best performance in the functional test. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain a six-base complementary region at their 3′ prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. The template is then detected by qPCR on the Biomark HD system. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM and CASP3, had an estimated limit of detection (LOD) of about 0.06 pg/mL and a dynamic range of ≥5 logs. These antibody binders were used in multiplex protein detection in single cells using the C1™ system. The results in individual cells showed the expression of similar protein levels for CSTB and CASP3, but highly varied protein levels for EpCAM, CCNB1 and MUC1. This simple method for the preparation of oligonucleotide-conjugated antibodies is essential for the development of affordable multiplex protein assays, which has the potential to accelerate proteomics research. Citation Format: Haibiao Gong, Ilona Holcomb, Aik Ooi, Xiaohui Wang, Daniel Majonis, Marc Unger, Ramesh Ramakrishnan. A simple method to prepare oligonucleotide-conjugated antibodies for multiplex protein detection. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B18.

Site-Specific Labeling of Proteins in Live Mammalian Cells using Click Chemistry

An ideal fluorescent tag to study protein structure and dynamics inside living cells using super-resolution microscopy (SRM) needs to be bright, photostable and should not interfere with the functionality of the protein. Since synthetic fluorophores have exceptional photophysical properties and small size, techniques have been developed in order to tag proteins with these fluorophores in a specific and straightforward manner. Among those, the most versatile way of tagging a fluorescent probe site-specifically to the protein of interest (POI) is to use genetic code expansion technology to incorporate noncanonical amino acids (ncAAs). These ncAAs contain reactive functional groups such as strained alkene/alkyne, which can be exploited to label the POI through rapid and biocompatible click chemistry reactions, namely, strain-promoted alkyne-azide cycloaddition (SPAAC) and strain-promoted inverse electron-demand Diels-Alder cycloaddition (SPIEDAC). In here, we utilize this technology in order to develop an improved labeling method to perform multicolor labeling of large protein complexes. Moreover, we fully explore the potential of the labeling method by testing newly available ncAAs and fluorophores to find the most efficient and specific pair, thus minimizing background labeling in live mammalian cells. Subsequent analysis with SRM provided us with profound insights into fundamental biological processes.

Efficient enzymatic synthesis and dual-colour fluorescent labelling of DNA probes using long chain azido-dUTP and BCN dyes.

A sterically undemanding azide analogue of dTTP (AHP dUTP) with an alkyl chain and ethynyl attachment to the nucleobase was designed and incorporated into DNA by primer extension, reverse transcription and polymerase chain reaction (PCR). An azide-modified 523 bp PCR amplicon with all 335 thymidines replaced by AHP dU was shown to be a perfect copy of the template from which it was amplified. Replacement of thymidine with AHP dU increases duplex stability, accounting in part for the high incorporation efficiency of the azide-modified triphosphate. Single-stranded azide-labelled DNA was conveniently prepared from PCR products by λ-exonuclease digestion and streptavidin magnetic bead isolation. Efficient fluorescent labelling of single and double-stranded DNA was carried out using dyes functionalized with bicyclo[6.1.0]non-4-yne (BCN) via the strain-promoted alkyne-azide cycloaddition (SPAAC) reaction. This revealed that the degree of labelling must be carefully controlled to achieve optimum fluorescence and avoid fluorescence quenching. Dual-coloured probes were obtained in a single tube fluorescent labelling reaction; and varying the ratios of the two dyes provides a simple method to prepare DNA probes with unique fluorescent signatures. AHP dUTP is a versatile clickable nucleotide with potentially wide applications in biology and nanotechnology including single molecule studies and synthesis of modified aptamer libraries via SELEX.

Mechanical Reversibility of Strain-Promoted Azide-Alkyne Cycloaddition Reactions.

Mechanophores, that is, molecules that show a defined response to force, are crucial building blocks of mechanoresponsive materials. The possibility of mechanically induced cycloreversion for a series of triazoles formed via strain-promoted azide-alkyne cycloaddition reactions was investigated by density functional theory calculations, and these triazoles were compared to the 1,4- and 1,5-regioisomers formed in the reaction of an azide with a terminal alkyne. We show that cycloreversion is in principal possible and that the pulling geometry is the most important parameter that determines the probability of cycloreversion. We further compared triazole stability to the mechanical stability of polymers that are frequently used as force transducers in mechanochemical experiments and identified DIBAC (azadibenzylcyclooctyne) as a promising mechanophore for future applications.