Bioconjugation Reactions Research Articles

Synthesis and Characterization of a Magnetically Active 19F Molecular Beacon.

Gene expression is used extensively to describe cellular characteristics and behaviors; however, most methods of assessing gene expression are unsuitable for living samples, requiring destructive processes such as fixation or lysis. Recently, molecular beacons have become a viable tool for live-cell imaging of mRNA molecules in situ. Historically, beacon-mediated imaging has been limited to fluorescence-based approaches. We propose the design and synthesis of a novel molecular beacon for magnetic resonance detection of any desired target nucleotide sequence. The biologically compatible synthesis incorporates commonly used bioconjugation reactions in aqueous conditions and is accessible for laboratories without extensive synthesis capabilities. The resulting beacon uses fluorine (19F) as a reporter, which is broadened, or turned "off", via paramagnetic relaxation enhancement from a stabilized nitroxide radical spin label when the beacon is not bound to its nucleic acid target. Therefore, the 19F NMR signal of the beacon is quenched in its hairpin conformation when the spin label and the 19F substituent are held in proximity, but the signal is recovered upon beacon hybridization to its specific complementary nucleotide sequence by physical separation of the radical from the 19F reporter. This study establishes a path for magnetic resonance-based assessment of specific mRNA expression, providing new possibilities for applying molecular beacon technology in living systems.

Aryl transition metal chemical warheads for protein bioconjugation.

The past seven years have witnessed the burgeoning of protein bioconjugation reactions highlighting aryl transition metal reagents as coupling partners. This new bioorthogonal organometallic chemistry, which sets the scene for stoichiometric processes in place of the catalytic procedures that developed in parallel, already enabled the forging of C-S and C-C bonds onto protein substrates, respectively in their native state or equipped with pre-installed non-natural terminal alkene or alkyne appendages. Although not yet applied to proteins, related transformations pointing to the creation of C-N bonds have, in addition, just been disclosed by targeting peptide lysine residues. Central to this research was the selection of ligands attached to the transition metal, in order to confer to metal complexes, not only their stability in aqueous medium, but also the desired chemoselectivity. We summarize here this body of work, which has already put in the limelight elaborated palladium and gold complexes equipped with biologically relevant appendages, such as fluorescent and affinity tags, as well as drug molecules. This research holds much promise, not only for the study of proteins themselves, but also for the design of new protein-based biotherapeutics, such as protein-drug conjugates or constrained analogs resulting from macrocyclisation reactions.

Molecular imaging of platelet-derived growth factor receptor-alpha (PDGFRα) in papillary thyroid cancer using immuno-PET

IntroductionReceptor tyrosine kinase (RTK) platelet-derived growth factor receptor-alpha (PDGFRα) was recently identified as a molecular switch for dedifferentiation in thyroid cancer that predicts resistance to therapy as well as recurrence of disease in papillary thyroid cancer. Here we describe the radiolabeling and functional characterization of an imaging probe based on a PDGFRα-specific monoclonal antibody (mAb) for immuno-PET imaging of PDGFRα in papillary thyroid cancer. MethodsAntibody D13C6 (Cell Signaling) was decorated with chelator NOTA using bioconjugation reaction with 2-(p-NCS-Bz)-NOTA. Radiolabeling was carried out using 40 μg of antibody-NOTA conjugate with 143–223 MBq of [64Cu]CuCl2 in 0.25 M NaOAc (pH 5.5) at 30 °C for 1 h. The reaction mixture was purified with size-exclusion chromatography (PD-10 column). PDGFRα and mock transfected B-CPAP thyroid cancer cells lines for validation of 64Cu-labeled immuno-conjugates were generated using LVX-Tet-On technology. PET imaging was performed in NSG mice bearing bilaterally-induced PDGFRα (+/−) B-CPAP tumors. ResultsBioconjugation of NOTA chelator to monoclonal antibody D13C6 resulted in 2.8 ± 1.3 chelator molecules per antibody as determined by radiometric titration with 64Cu. [64Cu]Cu-NOTA-D13C6 was isolated in high radiochemical purity (>98%) and good radiochemical yields (19–61%). The specific activity was 0.9–5.1 MBq/μg. Cellular uptake studies revealed a specific radiotracer uptake in PDGFRα expressing cells compared to control cells. PET imaging resulted in SUVmean values of ~5.5 for PDGFRα (+) and ~2 for PDGFRα (−) tumors, after 48 h p.i.. After 1 h, radiotracer uptake was also observed in the bone marrow (SUVmean ~5) and spleen (SUVmean ~8.5). ConclusionRadiolabeled antibody [64Cu]Cu-NOTA-D13C6 represents a novel and promising radiotracer for immuno-PET imaging of PDGFRα in metastatic papillary thyroid cancer. Advances in knowledge and implications for patient careThe presented work has the potential to allow physicians to identify papillary thyroid cancer patients at risk of metastases by using the novel immuno-PET imaging assay based on PDGFRα-targeting antibody [64Cu]Cu-NOTA-D13C6.

Surface engineered poly(dimethylsiloxane)/carbon nanotube nanocomposite pad as a flexible platform for chemical sensors

This study demonstrated the sensing performance of surface-patterned poly(dimethylsiloxane) (PDMS)/carbon nanotube (CNT: 3–5 wt%) nanocomposite pads. PDMS/CNT nanocomposite pads as a flexible sensing platform were prepared by employing a series of techniques: 3-roll milling for mixing, 2-roll for pad formation, and imprinting for pattern development. Then, tailored surface engineering strategy was introduced. First, the silane coupling agent was incorporated to improve the surface compatibility of the nanocomposite pads. The change in surface property was monitored by shift in contact angle from 132 to 141°. Subsequently, the beta-cyclodextrin (CD) molecules were introduced as a sensing medium through a simple bio-conjugation reaction. The nanocomposite pads showed a sensitive response to methylparaben (MePRB), a representative preservative for cosmetics through host-guest interactions between CD and MePRB in the range of 1–100 nmol. Owing to the surface hydrophobicity of the nanocomposite pads, the sensor was found most effective under nonpolar solvents. The feasibility of surface engineered PDMS/CNT pad as a flexible sensor was demonstrated by measurement after 50 times manual bending. This study can be a useful example for the application of nanocomposites that show unique surface structure and properties.

In Situ Quenching of Trialkylphosphine Reducing Agents Using Water-Soluble PEG-Azides Improves Maleimide Conjugation to Proteins.

Trialkylphosphines tris(2-carboxy-ethyl)-phosphine and tris(3-hydroxypropyl)-phosphine are popular reagents for the reduction of cysteine residues in bioconjugation reactions using maleimides. However, it has been demonstrated that these phosphines are reactive toward maleimide, necessitating their removal before the addition of the Michael acceptor. Here, a method using water-soluble PEG-azides is reported for the quenching of trialkylphosphines in situ, which is demonstrated to improve the level of maleimide conjugation to proteins.

Direct Electrochemical Bioconjugation on Metal Surfaces.

DNA has unique capabilities for molecular recognition and self-assembly, which have fostered its widespread incorporation into devices that are useful in science and medicine. Many of these platforms rely on thiol groups to tether DNA to gold surfaces, but this method is hindered by a lack of control over monolayer density and by secondary interactions between the nucleotide bases and the metal. In this work, we report an electrochemically activated bioconjugation reaction as a mild, reagent-free strategy to attach oligonucleotides to gold surfaces. Aniline-modified DNA was coupled to catechol-coated electrodes that were oxidized to o-quinones using an applied potential. High levels of coupling could be achieved in minutes. By changing the reaction time and the underlying catechol content, the final DNA surface coverage could be specified. The advantages of this method were demonstrated through the electrochemical detection of the endocrine disruptor bisphenol A, as well as the capture of living nonadherent cells on electrode surfaces by DNA hybridization. This method not only improves the attachment of DNA to metal surfaces but also represents a new direction for the site-specific attachment of biomolecules to device platforms.

Fluorescent Functionalization across Quaternary Structure in a Virus-like Particle.

Proteinaceous nanomaterials and, in particular, virus-like particles (VLPs) have emerged as robust and uniform platforms that are seeing wider use in biomedical research. However, there are a limited number of bioconjugation reactions for functionalizing the capsids, and very few of those involve functionalization across the supramolecular quaternary structure of protein assemblies. In this work, we exploit the recently described dibromomaleimide moiety as part of a bioconjugation strategy on VLP Qβ to break and rebridge the exposed and structurally important disulfides in good yields. Not only was the stability of the quaternary structure retained after the reaction, but the newly functionalized particles also became brightly fluorescent and could be tracked in vitro using a commercially available filter set. Consequently, we show that this highly efficient bioconjugation reaction not only introduces a new functional handle "between" the disulfides of VLPs without compromising their thermal stability but also can be used to create a fluorescent probe.

Targeting Prostate-Specific Membrane Antigen (PSMA) with F-18-Labeled Compounds: the Influence of Prosthetic Groups on Tumor Uptake and Clearance Profile.

Prostate-specific membrane antigen (PSMA) is an important biomarker expressed in the majority of prostate cancers. The favorable positron emission tomography (PET) imaging profile of the PSMA imaging agent 2-(3-(1-carboxy-5-[(6-[18F]fluoro-pyridine-3-carbonyl)-amino]-pentyl)-ureido)-pentane-dioic acid [18F]DCFPyL in preclinical prostate cancer models and in prostate cancer patients stimulated the development and validation of other fluorine-containing PSMA inhibitors to further enhance pharmacokinetics and simplify production methods. Here, we describe the synthesis and radiopharmacological evaluation of various F-18-labeled PSMA inhibitors which were prepared through different prosthetic group chemistry strategies. Prosthetic groups N-succinimidyl-4-[18F]fluorobenzoate ([18F]SFB), 4-[18F]fluorobenzaldehyde, and 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) were used for bioconjugation reactions to PSMA-binding lysine-urea-glutamate scaffold via acylation and oxime formation. All fluorine-containing PSMA inhibitors were tested for their PSMA inhibitory potency in an in vitro competitive binding assay in comparison to an established reference compound [125I]TAAG-PSMA. Tumor uptake and clearance profiles of three F-18-labeled PSMA inhibitors ([18F]4, [18F]7, and [18F]8) were studied with dynamic PET imaging using LNCaP tumor-bearing mice. F-18-labeled PSMA inhibitors were synthesized in 32-69% radiochemical yields using (1) acylation reaction at the primary amino group of the lysine residue with [18F]SFB and (2) oxime formation with 4-[18F]fluorobenzaldehyde and [18F]FDG using the respective aminooxy-functionalized lysine residue. Compound 7 displayed an IC50 value of 6nM reflecting very high affinity for PSMA. Compounds 4 and 8 showed IC50 values of 13 and 62nM, respectively. The IC50 value of reference compound DCFPyL was 13nM. Dynamic PET imaging revealed the following SUV60min for radiotracer uptake in PSMA(+) LNCaP tumors: 0.98 ([18F]DCFPyL), 2.11 ([18F]7), 0.40 ([18F]4), and 0.19 ([18F]8). The observed tumor uptake and clearance profiles demonstrate the importance of the selected prosthetic group on the pharmacokinetic profile of analyzed PSMA-targeting radiotracers. Radiotracer [18F]7 displayed the highest uptake and retention in LNCaP tumors, which exceeded uptake values of reference compound [18F]DCFPyL by more than 100%. Despite the higher kidney and liver uptake and retention of compound [18F]7, the simple radiosynthesis and the exceptionally high tumor uptake (SUV60min 2.11) and retention make radiotracer [18F]7 an interesting alternative to radiotracer [18F]DCFPyL for PET imaging of PSMA in prostate cancer.

In Situ Synthesis of Phospholipid Membranes.

Cells produce lipid membranes de novo through a complex sequence of enzymatic reactions that are difficult to reconstitute in a minimal system. We set out to take a different approach and mimic the synthesis of phospholipids using abiotic but highly selective bioconjugation reactions. Here, I outline several of our group's recent advances in exploring chemoselective reactions for stitching together lipid fragments to form membrane-forming lipids from non-membrane-forming precursors. Rapid chemical reactions can be harnessed to achieve facile de novo synthesis of lipid membranes, and spontaneous membrane formation can be applied for the reconstitution of membrane proteins, encapsulation and concentration of nanomaterials, and the study of lipid membrane remodeling. I conclude by briefly outlining future challenges and opportunities.

Dual display of proteins on the yeast cell surface simplifies quantification of binding interactions and enzymatic bioconjugation reactions.

Yeast surface display, a well-established technology for protein analysis and engineering, involves expressing a protein of interest as a genetic fusion to either the N- or C-terminus of the yeast Aga2p mating protein. Historically, yeast-displayed protein variants are flanked by peptide epitope tags that enable flow cytometric measurement of construct expression using fluorescent primary or secondary antibodies. Here, we built upon this technology to develop a new yeast display strategy that comprises fusion of two different proteins to Aga2p, one to the N-terminus and one to the C-terminus. This approach allows an antibody fragment, ligand, or receptor to be directly coupled to expression of a fluorescent protein readout, eliminating the need for antibody-staining of epitope tags to quantify yeast protein expression levels. We show that this system simplifies quantification of protein-protein binding interactions measured on the yeast cell surface. Moreover, we show that this system facilitates co-expression of a bioconjugation enzyme and its corresponding peptide substrate on the same Aga2p construct, enabling enzyme expression and catalytic activity to be measured on the surface of yeast.

Revisiting Boronate/Diol Complexation as a Double Stimulus-Responsive Bioconjugation.

This study presents a quantitative assessment of the complexation between boronic acids and diols as a reversible and double-stimulus (oxidation and acidification)-responsive bioconjugation reaction. First, by using a competition assay, we have evaluated the equilibrium constants (water, pH 7.4) of 34 boronate/diol pairs, using diols of both aliphatic and aromatic (catechols) nature; in general, catechols were characterized by constants 3 orders of magnitude higher than those of aliphatic diols. Second, we have demonstrated that successful complexation with diols generated in situ via enzymatic reactions, and the boronate complexation was also employed to calculate the Michaelis-Menten parameters for two catechol-producing reactions: the demethylation of 3-methoxytyramine and the 2-hydroxylation of estradiol, respectively, mediated by P4502D6 and P4501A2. Third, we have prepared phenylboronic acid-functionalized hyaluronic acid (HA) and demonstrated the pH and H2O2-responsive character of the adducts that it formed with Alizarin Red S (ARS) used as a model catechol. The versatility and selectivity of the complexation and the mild character of the chemical species involved therefore make the boronate/catechol reaction an interesting candidate for bioconjugation purposes.

Assessing the Suitability of Cellulose-Nanodiamond Composite As a Multifunctional Biointerface Material for Bone Tissue Regeneration.

Interfacial surface properties, both physical and chemical, are known to play a critical role in achieving long-term stability of cell-biomaterial interactions. Novel bone tissue engineering technologies, which provide a suitable interface between cells and biomaterials and mitigate aseptic osteolysis, are sought and can be developed via the incorporation of nanostructured materials. In this sense, engineered nanobased constructs provide an effective interface and suitable topography for direct interaction with cells, promoting faster osseointegration and anchoring. Therefore, herein we have investigated the surface functionalization, biocompatibility, and effect of cellulose-nanodiamond conjugates on osteoblast proliferation and differentiation. Cellulose nanocrystals (CNC) were aminated through a 3-aminopropyltriethyoxysilane (APTES) silylation, while nanodiamonds (ND) were treated with a strong acid oxidation reflux, as to produce carboxyl groups on the surface. Thereafter, the two products were covalently joined through an amide linkage, using a common bioconjugation reaction. Human fetal osteoblastic cells (hFOB) were seeded for 7 days to investigate the in vitro performance of the cellulose-nanodiamond conjugates. By employing immunocytochemistry, the bone matrix expression of osteocalcin (OC) and bone sialoprotein (BSP) was analyzed, demonstrating the viability and capacity of osteoblasts to proliferate and differentiate on the developed composite. These results suggest that cellulose-nanodiamond composites, which we call oxidized biocompatible interfacial nanocomposites (oBINC), have the potential to serve as a biointerface material for cell adhesion, proliferationand differentiation because of their osteoconductive properties and biocompatibility; furthermore, they show promising applications for bone tissue regeneration.

Selective Surface PEGylation of UiO-66 Nanoparticles for Enhanced Stability, Cell Uptake, and pH-Responsive Drug Delivery

SummaryThe high storage capacities and excellent biocompatibilities of metal-organic frameworks (MOFs) have made them emerging candidates as drug-delivery vectors. Incorporation of surface functionality is a route to enhanced properties, and here we report on a surface-modification procedure—click modulation—that controls their size and surface chemistry. The zirconium terephthalate MOF UiO-66 is (1) synthesized as ∼200 nm nanoparticles coated with functionalized modulators, (2) loaded with cargo, and (3) covalently surface modified with poly(ethylene glycol) (PEG) chains through mild bioconjugate reactions. At pH 7.4, the PEG chains endow the MOF with enhanced stability toward phosphates and overcome the “burst release” phenomenon by blocking interaction with the exterior of the nanoparticles, whereas at pH 5.5, stimuli-responsive drug release is achieved. The mode of cellular internalization is also tuned by nanoparticle surface chemistry, such that PEGylated UiO-66 potentially escapes lysosomal degradation through enhanced caveolae-mediated uptake. This makes it a highly promising vector, as demonstrated for dichloroacetic-acid-loaded materials, which exhibit enhanced cytotoxicity. The versatility of the click modulation protocol will allow a wide range of MOFs to be easily surface functionalized for a number of applications.

A Ligand-Dissociation-Involved Mechanism in Amide Formation of Monofluoroacylboronates with Hydroxylamines

Acylborons, as a growing class of boron reagents, were successfully applied to amide ligation and showed potential in chemoselective bioconjugation reactions in recent years. In this manuscript, a density functional theory (DFT) study was performed to investigate the mechanism of the amide formation between monofluoroacylboronates and hydroxylamines. An updated pathway was clarified herein, including water-assisted hemiaminal formation, pyridine ligand dissociation, elimination via a six-membered-ring transition state, and water-assisted tautomerization. The proposed mechanism was further examined by applying it to investigate the activation barriers of other monofluoroacylboronates, and the related calculations well reproduced the experimentally reported relative reactivities. On the basis of these results, we found that the ortho substitution of the pyridine ligand destabilizes the acylboron substrates and the hemiaminal intermediates by steric effects and thus lowers the energy demand of the ligand dissociation and elimination steps. By contrast, the para substitution of the pyridine ligand with an electron-donating group enhances the coordination of the ligand by electronic effects, which is a disadvantage to the ligand dissociation and elimination steps. The ligand bearing a rigid linkage blocks the rotation of the pyridine ligand and makes ligand dissociation difficult.

The discovery of pyridinium 1,2,4-triazines with enhanced performance in bioconjugation reactions.

1,2,4-Triazines have recently been identified as versatile dienes participating in the inverse electron-demand Diels-Alder reaction with strained dienophiles. However, their widespread utility in bioconjugation reactions is still limited. Herein, we report a systematic study on the reactivity of various 1,2,4-triazines with trans-cyclooctenes showing that the structure of both the triazine and the dienophile significantly affect the reaction rate. Our kinetic study led to the discovery of novel cationic 1,2,4-triazines with superior properties for bioconjugation reactions. We have developed an efficient method that enables their late-stage functionalization and allows for easy access to various useful heterobifunctional scaffolds. In addition, these charged dienes form unprecedented fluorescent products upon reaction with trans-cyclooctenes and can be used for fluorogenic labeling of subcellular compartments in live cells.

Characterizing the Overall Derivatization of Conjugated Oligomeric Proteins.

The analysis and accurate quantitation of bioconjugations proves challenging in the case of oligomeric proteins, especially when the size of the molecule or the nature of the conjugate do not allow the analysis of the intact protein under native conditions. In this case, analytical methods are frequently applied that result in a dissociation of non-covalently linked subunits. This limits the analysis to a description of individual subunits, thereby obscuring the accurate characterization of the overall functionalization. This situation is frequently encountered in the biopharmaceutically important case of protein PEGylation, as the biophysical properties of the PEG polymer generally make analysis and accurate quantitation for a protein with multiple conjugation sites challenging under native conditions. In this work we present a statistical measure for deriving the overall functionalization of an oligomeric protein from the data obtained from readily accessible assays that cause non-covalently associated subunits to dissociate. This approach is broadly applicable for the characterization and optimization of bioconjugation reactions for multimeric biomolecules. It should also be highly valuable for the accurate description of composition and manufacturing consistency of conjugated biotherapeutics in regulatory filings.LAY ABSTRACT: Conjugated proteins are an important class of biopharmaceuticals. For these molecules, successful drug development requires accurate methods for the quantitative characterization of protein conjugation. This task is particularly challenging in the case of proteins consisting of several, non-covalently linked subunits, especially when the size of the protein or nature of the conjugate do not allow for analysis of the intact oligomeric molecule. Many of the analytical methods used to characterize these conjugates, such as reverse phase high-performance liquid chromatography, cause the individual subunits to dissociate, making it difficult to fully understand quality attributes at the native oligomeric level. We present a method to accurately quantify the overall conjugation of an oligomeric protein in these cases when readily available assays describe only individual subunits. This should be highly valuable for process optimization and to correctly characterize the conjugated biopharmaceutical in interactions with regulatory agencies.

ChemInform Abstract: The Role of Boronic Acids in Accelerating Condensation Reactions of α‐Effect Amines with Carbonyls

AbstractReview: 36 refs.

Salt Effect Accelerates Site-Selective Cysteine Bioconjugation.

Highly efficient and selective chemical reactions are desired. For small molecule chemistry, the reaction rate can be varied by changing the concentration, temperature, and solvent used. In contrast for large biomolecules, the reaction rate is difficult to modify by adjusting these variables because stringent biocompatible reaction conditions are required. Here we show that adding salts can change the rate constant over 4 orders of magnitude for an arylation bioconjugation reaction between a cysteine residue within a four-residue sequence (π-clamp) and a perfluoroaryl electrophile. Biocompatible ammonium sulfate significantly enhances the reaction rate without influencing the site-specificity of π-clamp mediated arylation, enabling the fast synthesis of two site-specific antibody–drug conjugates that selectively kill HER2-positive breast cancer cells. Computational and structure–reactivity studies indicate that salts may tune the reaction rate through modulating the interactions between the π-clamp hydrophobic side chains and the electrophile. On the basis of this understanding, the salt effect is extended to other bioconjugation chemistry, and a new regioselective alkylation reaction at π-clamp cysteine is developed.

Template‐Directed Synthesis of Porous and Protective Core–Shell Bionanoparticles

AbstractMetal–organic frameworks (MOFs) are promising high surface area coordination polymers with tunable pore structures and functionality; however, a lack of good size and morphological control over the as‐prepared MOFs has persisted as an issue in their application. Herein, we show how a robust protein template, tobacco mosaic virus (TMV), can be used to regulate the size and shape of as‐fabricated MOF materials. We were able to obtain discrete rod‐shaped TMV@MOF core–shell hybrids with good uniformity, and their diameters could be tuned by adjusting the synthetic conditions, which can also significantly impact the stability of the core–shell composite. More interestingly, the virus particle underneath the MOF shell can be chemically modified using a standard bioconjugation reaction, showing mass transportation within the MOF shell.

Template-Directed Synthesis of Porous and Protective Core-Shell Bionanoparticles.

Metal-organic frameworks (MOFs) are promising high surface area coordination polymers with tunable pore structures and functionality; however, a lack of good size and morphological control over the as-prepared MOFs has persisted as an issue in their application. Herein, we show how a robust protein template, tobacco mosaic virus (TMV), can be used to regulate the size and shape of as-fabricated MOF materials. We were able to obtain discrete rod-shaped TMV@MOF core-shell hybrids with good uniformity, and their diameters could be tuned by adjusting the synthetic conditions, which can also significantly impact the stability of the core-shell composite. More interestingly, the virus particle underneath the MOF shell can be chemically modified using a standard bioconjugation reaction, showing mass transportation within the MOF shell.