Bioconjugation Applications Research Articles

Water-soluble NHC-Cu catalysts: applications in click chemistry, bioconjugation and mechanistic analysis.

Copper(I)-catalyzed 1,3-dipolar cycloaddition of azides and terminal alkynes (CuAAC), better known as "click" reaction, has triggered the use of 1,2,3-triazoles in bioconjugation, drug discovery, materials science and combinatorial chemistry. Here we report a new series of water-soluble catalysts based on N-heterocyclic carbene (NHC)-Cu complexes which are additionally functionalized with a sulfonate group. The complexes show superior activity towards CuAAC reactions and display a high versatility, enabling the production of triazoles with different substitution patterns. Additionally, successful application of these complexes in bioconjugation using unprotected peptides acting as DNA binding domains was achieved for the first time. Mechanistic insight into the reaction mechanism is obtained by means of state-of-the-art first principles calculations.

Site-specific protein labelling and immobilization mediated by microbial transglutaminase.

Microbial transglutaminase (mTG) shows broad substrate specificity that is amenable to in vitro bio-conjugation applications. Herein, test proteins were genetically fused with peptide tags, followed by mTG-mediated propargylation of their reactive Gln residues. The propargylated proteins were subjected to copper-assisted azide-alkyne cycloaddition to demonstrate either fluorescent labelling or immobilization.

Pronounced Toxicity Differences between Homobifunctional Protein Cross-Linkers and Analogous Monofunctional Electrophiles

Bifunctional electrophiles have been used in various chemopreventive, chemotherapeutic, and bioconjugate applications. Many of their effects in biological systems are traceable to their reactive properties, whereby they can modify nucleophilic sites in DNA, proteins, and other cellular molecules. Previously, we found that two different bifunctional electrophiles--diethyl acetylenedicarboxylate and divinyl sulfone--exhibited a strong enhancement of toxicity when compared with analogous monofunctional electrophiles in both human colorectal carcinoma cells and baker's yeast. Here, we have compared the toxicities for a broader panel of homobifunctional electrophiles bearing diverse electrophilic centers (e.g., isothiocyanate, isocyanate, epoxide, nitrogen mustard, and aldehyde groups) to their monofunctional analogues. Each bifunctional electrophile showed at least a 3-fold enhancement of toxicity over its monofunctional counterpart, although in most cases, the differences were even more pronounced. To explain their enhanced toxicity, we tested the ability of each bifunctional electrophile to cross-link recombinant yeast thioredoxin 2 (Trx2), a known intracellular target of electrophiles. The bifunctional electrophiles were capable of cross-linking Trx2 to itself in vitro and to other proteins in cells exposed to toxic concentrations. Moreover, most cross-linkers were preferentially reactive with thiols in these experiments. Collectively, our results indicate that thiol-reactive protein cross-linkers in general are much more potent cytotoxins than analogous monofunctional electrophiles, irrespective of the electrophilic group studied.

Continuous enzyme-coupled assay for microbial transglutaminase activity

Transglutaminases (protein-glutamine:amine γ-glutamyltransferase, EC 2.3.2.13) are a family of calcium-dependent enzymes that catalyze an acyl transfer between glutamine residues and a wide variety of primary amines. When a lysine residue acts as the acyl-acceptor substrate, a γ-glutamyl-ε-lysine isopeptide bond is formed. This isopeptide bond formation represents protein cross-linking, which is critical to several biological processes. Microbial transglutaminase (mTG) is a bacterial variant of the transglutaminase family, distinct by virtue of its calcium-independent catalysis of the isopeptidic bond formation. Furthermore, mTG’s promiscuity in acyl-acceptor substrate preference highlights its biocatalytic potential. The acyl-donor substrate, however, is limited in its scope; the amino acid sequences flanking glutamine residues dramatically affect substrate specificity and activity. Here, we have developed and optimized a modified glutamate dehydrogenase assay with the intention of analyzing potential high-affinity peptides. This direct continuous assay presents significant advantages over the commonly used hydroxamate assay, including generality, sensitivity, and ease of manipulation. Furthermore, we identified 7M48 (WALQRPH), a high-affinity peptide that shows greater affinity with mTG (KM=3mM) than the commonly used Cbz-Gln-Gly (KM=58mM), attesting to its potential for application in biocatalysis and bioconjugation.

A Highly Efficient Catalyst for Oxime Ligation and Hydrazone–Oxime Exchange Suitable for Bioconjugation

Imine-based reactions are useful for a wide range of bioconjugation applications. Although aniline is known to catalyze the oxime ligation reaction under physiological conditions, it suffers from slow reaction kinetics, specifically when a ketone is being used or when hydrazone-oxime exchange is performed. Here, we report on the discovery of a new catalyst that is up to 15 times more efficient than aniline. That catalyst, m-phenylenediamine (mPDA), was initially used to analyze the kinetics of oxime ligation on aldehyde- and ketone-containing small molecules. While mPDA is only modestly more effective than aniline when used in equal concentrations (~2-fold), its much greater aqueous solubility relative to aniline allows it to be used at higher concentrations, resulting in significantly more efficient catalysis. In the context of protein labeling, it was first used to site-specifically label an aldehyde-functionalized protein through oxime ligation, and its kinetics were compared to reaction with aniline. Next, a protein was labeled with an aldehyde-containing substrate in crude cell lysate, captured with hydrazide-functionalized beads and then the kinetics of immobilized protein release via hydrazone-oxime exchange were analyzed. Our results show that mPDA can release and label 15 times more protein than aniline can in 3 h. Then, using the new catalyst, ciliary neurotrophic factor, a protein with therapeutic potential, was successfully labeled with a fluorophore in only 5 min. Finally, a protein containing the unnatural amino acid, p-acetyl phenylalanine, a ketone-containing residue, was prepared and PEGylated efficiently via oxime ligation using mPDA. This new catalyst should have a significant impact on the field of bioconjugation, where oxime ligation and hydrazone-oxime exchange are commonly employed.

Split Spy0128 as a Potent Scaffold for Protein Cross-Linking and Immobilization

Site-specific cross-linking techniques between proteins and additional functional groups have become increasingly important for expanding the utility of proteins in biochemistry and biotechnology. In order to explore powerful techniques for practical bioconjugation applications, we have validated a technique mediated by a unique property of Streptcoccus pyogenes pilin subunit Spy0128, an autocatalytic intramolecular isopeptide formation in Spy0128. Recently, it has been revealed that Spy0128 can be split into two fragments (split-Spy0128 (residues 18-299 of Spy0128) and isopeptag (residues 293-308 of Spy0128)) that were capable of forming an intermolecular covalent complex. We focused on this unique reconstitution property and first studied the bioconjugation of blue and green fluorescent proteins, enabling the direct monitoring of cross-linking reactions by Förster resonance energy transfer (FRET). A fluorescence lifetime study shows that spatial control of two proteins on the Spy0128 scaffold is possible when one protein is fused to the N-terminus of split-Spy0128 and another one is tethered at the N- or C-terminus of the isopeptag. Furthermore, we demonstrated site-specific protein immobilization mediated by the reconstitution of split-Spy0128 and isopeptag. In this case, a split-Spy0128 mutant with a free N-terminal Cys residue was first immobilized onto beads chemically modified with a maleimide group through a Michael addition process. Then, an isopeptagged protein was successfully immobilized onto the split-Spy0128-immobilized beads. These results suggest that Spy0128 is a potent proteinaceous scaffold available for bioconjugation both in solution and at a solid surface.

A comparison of the chiral counterion, solvent, and ligand used to induce a chiroptical response from Au25− nanoclusters

A 25-atom gold nanocluster capped with an achiral thiolate exhibits no chiroptical signals in circular dichroism (CD) measurements. Herein, we report a systematic study on the effects of the chiral environment on the CD response from the Au25 metal core. We found that Au25(SC2H4Ph)18(-)TOA(+) dissolved in a chiral solvent did not give rise to a CD response, nor did Au25(SC2H4Ph)18(-) when associated with a chiral counterion (e.g., (-)-N-dodecyl-N-methylephedrinium, DME(+)). Both scenarios imply that the interaction of the chiral counterion (or chiral solvent molecules) with the achiral Au25(SC2H4Ph)18(-) nanocluster is not strong enough to induce CD signals from the metal core. In contrast, when the metal core is capped with chiral ligands (i.e., Au25(SCH2C*H(NH2)CH2Ph)18), strong CD signals in the visible wavelength range were observed. Thus, the induction of CD signals by surface chiral ligands is much stronger than that by the external chiral environment (including the chiral solvent or counterion). This work reveals some further insight into the origin of the chiroptical response of the Au nanoclusters. These chiral nanoclusters hold potential for practical applications in bioconjugation, sensing, and chiral catalysis.

Vinyl sulfone-based ferrocenylation reagents: applications in conjugation and bioconjugation

The easy vinyl sulfone derivatization of ferrocene allows the preparation of some effective, versatile and valuable ferrocenylation reagents. The applicability of such compounds in conjugation and bioconjugation of amine and/or thiol containing molecules and biomolecules through Michael-type addition under mild conditions that preserve the biological function of the latter is described. The feasibility of the methodology is demonstrated by the preparation of a variety of conjugates and bioconjugates (ferrocenyl terminated dendrimers and ferrocene-sugar, ferrocene-cyclodextrin, ferrocene-peptide and ferrocene-protein conjugates).

Efficient synthesis of diverse heterobifunctionalized clickable oligo(ethylene glycol) linkers: potential applications in bioconjugation and targeted drug delivery

Herein we describe the sequential synthesis of a variety of azide-alkyne click chemistry-compatible heterobifunctional oligo(ethylene glycol) (OEG) linkers for bioconjugation chemistry applications. Synthesis of these bioorthogonal linkers was accomplished through desymmetrization of OEGs by conversion of one of the hydroxyl groups to either an alkyne or azido functionality. The remaining distal hydroxyl group on the OEGs was activated by either a 4-nitrophenyl carbonate or a mesylate (-OMs) group. The -OMs functional group served as a useful precursor to form a variety of heterobifunctionalized OEG linkers containing different highly reactive end groups, e.g., iodo, -NH(2), -SH and maleimido, that were orthogonal to the alkyne or azido functional group. Also, the alkyne- and azide-terminated OEGs are useful for generating larger discrete poly(ethylene glycol) (PEG) linkers (e.g., PEG(16) and PEG(24)) by employing a Cu(I)-catalyzed 1,3-dipolar cycloaddition click reaction. The utility of these clickable heterobifunctional OEGs in bioconjugation chemistry was demonstrated by attachment of the integrin (α(v)β(3)) receptor targeting peptide, cyclo-(Arg-Gly-Asp-D-Phe-Lys) (cRGfKD) and to the fluorescent probe sulfo-rhodamine B. The synthetic methodology presented herein is suitable for the large scale production of several novel heterobifunctionalized OEGs from readily available and inexpensive starting materials.

Conjugation of Proteins by Installing BIO-Orthogonally Reactive Groups at Their N-Termini

N-terminal site-specific modification of a protein has many advantages over methods targeting internal positions, but it is not easy to install reactive groups onto a protein in an N-terminal specific manner. We here report a strategy to incorporate amino acid analogues specifically in the N-terminus of a protein in vivo and demonstrate it by preparing green fluorescent protein (GFP) having bio-orthogonally reactive groups at its N-terminus. In the first step, GFP was engineered to be a foldable, internal methionine-free sequence via the semi-rational mutagenesis of five internal methionine residues and the introduction of mutations for GFP folding enhancement. In the second step, the N-terminus of the engineered protein was modified in vivo with bio-orthogonally functional groups by reassigning functional methionine surrogates such as L-homopropargylglycine and L-azidohomoalanine into the first methionine codon of the engineered internal methionine-free GFP. The N-terminal specific incorporation of unnatural amino acids was confirmed by ESI-MS analysis and the incorporation did not affect significantly the specific activity, refolding rate and folding robustness of the protein. The two proteins which have alkyne or azide groups at their N-termini were conjugated each other by bio-orthogonal Cu(I)-catalyzed click chemistry. The strategy used in this study is expected to facilitate bio-conjugation applications of proteins such as N-terminal specific glycosylation, labeling of fluorescent dyes, and immobilization on solid surfaces.

Synthesis, Characterization, and Biocompatibility of Biodegradable Hyperbranched Polyglycerols from Acid-Cleavable Ketal Group Functionalized Initiators

Herein we report the synthesis of biodegradable hyperbranched polyglycerols (BHPGs) having acid-cleavable core structure by anionic ring-opening multibranching polymerization (ROMBP) of glycidol using initiators bearing dimethyl and cyclohexyl ketal groups. Five different multifunctional initiators carrying one to four ketal groups and two to four hydroxyl groups per molecule were synthesized. The hydroxyl carrying initiators containing one ketal group per molecule were synthesized from ethylene glycol. An alkyne-azide click reaction was used for synthesizing initiators containing multiple cyclohexyl ketal linkages and hydroxyl groups. The synthesized BHPGs exhibited monomodal molecular weight distributions and polydispersity in the range of 1.2 to 1.6, indicating the controlled nature of the polymerizations. The polymers were relatively stable at physiological pH but degraded at acidic pH values. The polymer degradation was dependent on the type of ketal structure present in the BHPG; polymers with cyclohexyl ketal groups degraded at much slower rates than those with dimethyl ketal groups at a given pH. Good control of polymer degradation was achieved under mild acidic conditions by changing the structure of ketal linkages. A precise control of the molecular weight of the degraded HPG was achieved by controlling the number of ketal groups within the core, as revealed from the gel permeation chromatography (GPC) analyses. The decrease in the polymer molecular weights upon degradation was correlated well with the number of ketal groups in their core structure. Our data support the suggestion that glycidol was polymerized uniformly from all hydroxyl groups of the initiators. BHPGs and their degradation products were highly biocompatible, as measured by blood coagulation, complement activation, platelet activation, and cell viability assays. The controlled degradation profiles of these polymers together with their excellent biocompatibility make them suitable for drug delivery and bioconjugation applications.

Chemoselective Sequential “Click” Ligation Using Unsymmetrical Bisazides

Unsymmetrical bisazides containing chelating and nonchelating azido groups undergo chemoselective three-component copper(I)-catalyzed azide-alkyne conjugation reactions with two different alkyne molecules. In conjunction with the reactivity gap between aromatic and aliphatic alkynes, a bistriazole molecule can be generated with excellent regioselectivity by mixing two alkynes and a bisazide in a single reaction container. This method is applicable in aqueous solutions at neutral pH, which may lend utilities in bioconjugation applications.

Synthesis of heterobifunctional polyethylene glycols with azide functionality suitable for “click” chemistry

A heterobifunctional polyethylene glycol (PEG) derivative possessing both “click” and electrophilic functionalities was prepared for use in bioconjugation applications. We utilized a dibenzyl-protected amine functional initiator to prepare high purity amino-PEG-alcohol by the polymerization of ethylene oxide. Subsequent chain-end modification of the heterobifunctional PEG afforded the desired N-hydroxy succinimidyl-PEG-azide derivative in 33% overall yield. This PEG derivative allows for versatile bioconjugation chemistry where activated ester chemistry and “click” chemistry can be selectively performed, an area of orthogonal bioconjugation that has not previously been accessible.

Terminal functional glycopolymers via a combination of catalytic chain transfer polymerisation (CCTP) followed by three consecutive click reactions

The combination of catalytic chain transfer polymerisation (CCTP) with both thiol-ene and copper catalysed alkyne azide coupling (CuAAC) click chemistry has been employed to give a new route to functional glycopolymers for applications in bioconjugation and biological targeting. Ring opening of poly(glycidyl methacrylate) with sodium azide and subsequent reaction with alkyne functional carbohydrates, as prepared by Fischer glycosylation, has been exploited. This combination of a range of efficient chemistry gives a route to multi gram quantities of glycopolymers avoiding the need for living radical polymerisation chemistry.

Zinc complex mediated regioselective O-acylation of therapeutic agents

Several Zn β-diiminate reagents were developed and used to mediate regioselective O-acylation reactions of therapeutic agents with anhydrides. Various prodrugs were obtained in excellent yield and high regioselectivity, including derivatives of rapamycin and paclitaxel. Furthermore, the application of regioselective acylation was extended to one-pot reactions between therapeutics and carboxylic acids with various pendant functional groups. This rapid functionalization strategy will find application in either prodrug synthesis or bioconjugation for drug delivery.

Sulfated Ligands for the Copper(I)‐Catalyzed Azide–Alkyne Cycloaddition

The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), the prototypical reaction of click chemistry, is accelerated by tris(triazolylmethyl)amine-based ligands. Herein, we compare two new ligands in this family--3-[4-({bis[(1-tert-butyl-1H-1,2,3-triazol-4-yl)methyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propanol (BTTP) and the corresponding sulfated ligand 3-[4-({bis[(1-tert-butyl-1H-1,2,3-triazol-4-yl)methyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propyl hydrogen sulfate (BTTPS)--for three bioconjugation applications: 1) labeling of alkyne-tagged glycoproteins in crude cell lysates, 2) labeling of alkyne- or azide-tagged glycoproteins on the surface of live mammalian cells, and 3) labeling of azides in surface proteins of live Escherichia coli. Although BTTPS exhibits faster kinetics than BTTP in accelerating the CuAAC reaction in in vitro kinetic measurements, its labeling efficiency is slightly lower than BTTP in modifying biomolecules with a significant amount of negative charges due to electrostatic repulsion. Nevertheless, the negative charge conferred by the sulfate at physiological conditions significantly reduced the cellular internalization of the coordinated copper(I), thus making BTTPS-Cu(I) a better choice for live-cell labeling.

Crosslinking of viral nanoparticles with “clickable” fluorescent crosslinkers at the interface

Cu (I) catalyzed alkyne-azide cycloaddition (CuAAC) reaction, a typical “click“ reaction, is one of the modular synthetic approaches which has been broadly used in various organic syntheses, medicinal chemistry, materials development and bioconjugation applications. We have for the first time synthesized two dialkyne derivatized fluorescent crosslinkers which could be applied to crosslink two biomolecules using CuAAC reaction. Turnip yellow mosaic virus, a plant virus with unique structural and chemical properties, was used as a prototypical scaffold to form a 2D single layer at the interface of two immiscible liquids and crosslinked with these two linkers by the CuAAC reaction. Upon crosslinking, the fluorescence of both linkers diminished, likely due to the distortion of the polymethylene backbone, which therefore could be used to indicate the completion of the reaction.

Copper-catalyzed azide-alkyne cycloaddition (CuAAC) and beyond: new reactivity of copper(I) acetylides.

Copper-catalyzed azide-alkyne cycloaddition (CuAAC) is a widely utilized, reliable, and straightforward way for making covalent connections between building blocks containing various functional groups. It has been used in organic synthesis, medicinal chemistry, surface and polymer chemistry, and bioconjugation applications. Despite the apparent simplicity of the reaction, its mechanism involves multiple reversible steps involving coordination complexes of copper(I) acetylides of varying nuclearity. Understanding and controlling these equilibria is of paramount importance for channeling the reaction into the productive catalytic cycle. This tutorial review examines the history of the development of the CuAAC reaction, its key mechanistic aspects, and highlights the features that make it useful to practitioners in different fields of chemical science.

A universal and ready-to-use heterotrifunctional cross-linking reagent for facile synthetic access to sophisticated bioconjugates

We describe for the first time, the synthesis and some bioconjugation applications of an original heterotrifunctional cross-linking reagent (also named tripod) bearing three different bioorthogonal functional groups which are fully compatible amongst themselves. Contrary to the first generation tripod recently reported by us (Org. Biomol. Chem., 2008, 6, 3065), the use of an azido group instead of the nucleophile-sensitive active carbamate moiety enables us to reach the targeted chemical orthogonality without the use of temporary aminooxy- and thiol protecting groups. Thus, the preparation of sophisticated bioconjugates through the sequential derivatisation of the tripod by means of copper-mediated 1,3-dipolar cycloaddition, oxime ligation and aqueous compatible mild thiol-alkylation reactions, is significantly simpler and more convenient. The chemoselective bioconjugation protocols were optimised through the preparation of FRET cassettes based on cyanine and/or xanthene fluorescent dye pairs and subsequent anchoring to fragile biomolecules. The applicability of this universal cross-linking reagent was also illustrated by the preparation of biochips suitable for aflatoxin B1 detection through the SPIT-FRI method.

Azide reduction during peptide cleavage from solid support—the choice of thioscavenger?

Peptide azides acquired growing impact because of application in bioconjugation via 'click chemistry' or Staudinger ligation. Furthermore, there are many methods established in organic synthesis addressing the reduction of azides to amines, but no observation of a reductive transformation of peptide azides during SPPS cleavage was yet reported. In the present study, the reduction of peptide azides during SPPS cleavage was investigated depending on the choice of thioscavenger, reacting as reductive species. First observed for short PNA/peptide conjugates the occurring extensive side reaction was also validated for one of the applied azide amino acid building blocks and was further investigated by applying different cleavage cocktails to a series of peptides varying in hydrophobicity and position of the azide moiety in the oligomer sequence.