Discovery of selective monosaccharide receptors via dynamic combinatorial chemistry.

The molecular recognition of saccharides by synthetic hosts has become an appealing but elusive task in the last decades. Herein, we combine Dynamic Combinatorial Chemistry (DCC) for the rapid self-assembly and screening of virtual libraries of receptors, with the use of ITC and NMR to validate the hits and molecular modelling to understand the binding mechanisms. We discovered a minimalistic receptor, 1F (N-benzyl-L-phenylalanine), with considerable affinity for fructose (Ka = 1762 M-1) and remarkable selectivity (>50-fold) over other common monosaccharides. The approach accelerates the discovery process of receptors for saccharides.

Highly Selective Aptamer-Molecularly Imprinted Polymer Hybrids for Recognition of SARS-CoV-2 Spike Protein Variants.

Virus recognition has been driven to the forefront of molecular recognition research due to the COVID-19 pandemic. Development of highly sensitive recognition elements, both natural and synthetic is critical to facing such a global issue. However, as viruses mutate, it is possible for their recognition to wane through changes in the target substrate, which can lead to detection avoidance and increased false negatives. Likewise, the ability to detect specific variants is of great interest for clinical analysis of all viruses. Here, a hybrid aptamer-molecularly imprinted polymer (aptaMIP), that maintains selective recognition for the spike protein template across various mutations, while improving performance over individual aptamer or MIP components (which themselves demonstrate excellent performance). The aptaMIP exhibits an equilibrium dissociation constant of 1.61 nM toward its template which matches or exceeds published examples of imprinting of the spike protein. The work here demonstrates that "fixing" the aptamer within a polymeric scaffold increases its capability to selectivity recognize its original target and points toward a methodology that will allow variant selective molecular recognition with exceptional affinity.

Recapitulating the Lateral Organization of Membrane Receptors at the Nanoscale.

Many cell membrane functions emerge from the lateral presentation of membrane receptors. The link between the nanoscale organization of the receptors and ligand binding remains, however, mostly unclear. In this work, we applied surface molecular imprinting and utilized the phase behavior of lipid bilayers to create platforms that recapitulate the lateral organization of membrane receptors at the nanoscale. We used liposomes decorated with amphiphilic boronic acids that commonly serve as synthetic saccharide receptors and generated three lateral modes of receptor presentation─random distribution, nanoclustering, and receptor crowding─and studied their interaction with saccharides. In comparison to liposomes with randomly dispersed receptors, surface-imprinted liposomes resulted in more than a 5-fold increase in avidity. Quantifying the binding affinity and cooperativity proved that the boost was mediated by the formation of the nanoclusters rather than a local increase in the receptor concentration. In contrast, receptor crowding, despite the presence of increased local receptor concentrations, prevented multivalent oligosaccharide binding due to steric effects. The findings demonstrate the significance of nanometric aspects of receptor presentation and generation of multivalent ligands including artificial lectins for the sensitive and specific detection of glycans.

Establishing a quantitative fluorescence assay for the rapid detection of kynurenine in urine.

The kynurenine metabolite is associated with many diseases and disorders, ranging from diabetes and sepsis to more recently COVID-19. Here we report a fluorescence-based assay for the detection of kynurenine in urine using a specific chemosensor, 3-formyl-4-(ethylthio)-7-(diethylamino)-coumarin. The assay produces a linear response at clinically relevant ranges (1-20 µM), with a limit of detection of 0.7 µM. The average standard addition recoveries of kynurenine in synthetic urine samples are near to 100%, and the relative standard deviation values are less than 8%. The established fluorescence assay for quantitative analysis of kynurenine in urine is facile, sensitive and accurate and holds great potential for low-cost and high-throughput analysis of kynurenine in clinical laboratory settings.

Platelet activation by charged ligands and nanoparticles: platelet glycoprotein receptors as pattern recognition receptors.

Charge interactions play a critical role in the activation of the innate immune system by damage- and pathogen-associated molecular pattern receptors. The ability of these receptors to recognize a wide spectrum of ligands through a common mechanism is critical in host defense. In this article, we argue that platelet glycoprotein receptors that signal through conserved tyrosine-based motifs function as pattern recognition receptors (PRRs) for charged endogenous and exogenous ligands, including sulfated polysaccharides, charged proteins and nanoparticles. This is exemplified by GPVI, CLEC-2 and PEAR1 which are activated by a wide spectrum of endogenous and exogenous ligands, including diesel exhaust particles, sulfated polysaccharides and charged surfaces. We propose that this mechanism has evolved to drive rapid activation of platelets at sites of injury, but that under some conditions it can drive occlusive thrombosis, for example, when blood comes into contact with infectious agents or toxins. In this Opinion Article, we discuss mechanisms behind charge-mediated platelet activation and opportunities for designing nanoparticles and related agents such as dendrimers as novel antithrombotics.

Förster Resonance Energy Transfer Nanoplatform Based on Recognition-Induced Fusion/Fission of DNA Mixed Micelles for Nucleic Acid Sensing.

The dynamic nature of micellar nanostructures is employed to form a self-assembled Förster resonance energy transfer (FRET) nanoplatform for enhanced sensing of DNA. The platform consists of lipid oligonucleotide FRET probes incorporated into micellar scaffolds, where single recognition events result in fusion and fission of DNA mixed micelles, triggering the fluorescence response of multiple rather than a single FRET pair. In comparison to conventional FRET substrates where a single donor interacts with a single acceptor, the micellar multiplex FRET system showed ∼20- and ∼3-fold enhancements in the limit of detection and FRET efficiency, respectively. This supramolecular signal amplification approach could potentially be used to improve FRET-based diagnostic assays of nucleic acid and non-DNA based targets.

Direct Immobilization of Engineered Nanobodies on Gold Sensors.

Single-domain antibodies, known as nanobodies, have great potential as biorecognition elements for sensors because of their small size, affinity, specificity, and robustness. However, facile and efficient methods of nanobody immobilization are sought that retain their maximum functionality. Herein, we describe the direct immobilization of nanobodies on gold sensors by exploiting a modified cysteine strategically positioned at the C-terminal end of the nanobody. The experimental data based on secondary ion mass spectrometry, circular dichroism, and surface plasmon resonance, taken together with a detailed computational work (molecular dynamics simulations), support the formation of stable and well-oriented nanobody monolayers. Furthermore, the nanobody structure and activity is preserved, wherein the nanobody is immobilized at a high density (approximately 1 nanobody per 13 nm2). The strategy for the spontaneous nanobody self-assembly is simple and effective and possesses exceptional potential to be used in numerous sensing platforms, ranging from clinical diagnosis to environmental monitoring.

Elucidating the Influence of Electrical Potentials on the Formation of Charged Oligopeptide Self-Assembled Monolayers on Gold.

Self-assembled monolayers (SAMs) based on oligopeptides have garnered immense interest for a wide variety of innovative biomedical and electronic applications. However, to exploit their full potential, it is necessary to understand and control the surface chemistry of oligopeptides. Herein, we report on how different electrical potentials affect the adsorption kinetics, stability and surface coverage of charged oligopeptide SAMs on gold surfaces. Kinetic analysis using electrochemical surface plasmon resonance (e-SPR) reveals a slower oligopeptide adsorption rate at more positive or negative electrical potentials. Additional analysis of the potential-assisted formed SAMs by X-ray photoelectron spectroscopy demonstrates that an applied electrical potential has minimal effect on the packing density. These findings not only reveal that charged oligopeptides exhibit a distinct potential-assisted assembly behaviour but that an electrical potential offers another degree of freedom in controlling their adsorption rate.

Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling.

Label-free protein characterization at surfaces is commonly achieved using digestion and/or matrix application prior to mass spectrometry. We report the assignment of undigested proteins at surfaces in situ using secondary ion mass spectrometry (SIMS). Ballistic fragmentation of proteins induced by a gas cluster ion beam (GCIB) leads to peptide cleavage producing fragments for subsequent OrbitrapTM analysis. In this work we annotate 16 example proteins (up to 272 kDa) by de novo peptide sequencing and illustrate the advantages of this approach by characterizing a protein monolayer biochip and the depth distribution of proteins in human skin.

Targeting Oligosaccharides and Glycoconjugates Using Superselective Binding Scaffolds.

Recognition of oligosaccharides is associated with very limited specificity due to their strong solvation in water and the high degree of subtle structural variations between them. Here, oligosaccharide recognition sites are created on material surfaces with unmatched, binary on-off binding behavior, sharply discriminating a target oligosaccharide over closely related carbohydrate structures. The basis for the superselective binding behavior relies on the highly efficient generation of a pure, high order complex of the oligosaccharide target with synthetic carbohydrate receptor sites, in which the spatial arrangement of the multiple receptors in the complex is preserved upon material surface incorporation. The synthetic binding scaffolds can easily be tailored to recognize different oligosaccharides and glycoconjugates, opening up a realm of possibilities for their use in a wide field of applications, ranging from life sciences to diagnostics.

Cooperative Multipoint Recognition of Sialic Acid by Benzoboroxole-Based Receptors Bearing Cationic Hydrogen-Bond Donors.

Sialic acid recognition remains an interesting and challenging target in molecular receptor design. Herein, we report a series of benzoboroxole-based receptors in which cationic hydrogen-bond donors have been introduced and shown to promote multipoint sialic acid recognition. One striking feature revealed by these receptors is that the carboxylate sialic acid residue is the primary binding determinant for recognition by benzoboroxole, in which the presence of charge-reinforced hydrogen bonds results in enhanced selectivity for sialic acid over other carbohydrates and a 4.5-fold increase in affinity. These findings open up wide possibilities for benzoboroxole-based receptors use in life science research, biotechnology, and diagnostics.

Correction: The challenges of glycan recognition with natural and artificial receptors.

Correction for 'The challenges of glycan recognition with natural and artificial receptors' by Stefano Tommasone et al., Chem. Soc. Rev., 2019, 48, 5488-5505.

The challenges of glycan recognition with natural and artificial receptors.

Glycans - simple or complex carbohydrates - play key roles as recognition determinants and modulators of numerous physiological and pathological processes. Thus, many biotechnological, diagnostic and therapeutic opportunities abound for molecular recognition entities that can bind glycans with high selectivity and affinity. This review begins with an overview of the current biologically and synthetically derived glycan-binding scaffolds that include antibodies, lectins, aptamers and boronic acid-based entities. It is followed by a more detailed discussion on various aspects of their generation, structure and recognition properties. It serves as the basis for highlighting recent key developments and technical challenges that must be overcome in order to fully deal with the specific recognition of a highly diverse and complex range of glycan structures.

Precise Generation of Selective Surface-Confined Glycoprotein Recognition Sites.

Since glycoproteins have become increasingly recognized as key players in a wide variety of disease processes, there is an increasing need for advanced affinity materials for highly selective glycoprotein binding. Herein, for the first time, a surface-initiated controlled radical polymerization is integrated with supramolecular templating and molecular imprinting to yield highly reproducible synthetic recognition sites on surfaces with dissociation constants (K D) in the low micromolar range for target glycoproteins and minimal binding to nontarget glycoproteins. Importantly, it is shown that the synthetic strategy has a remarkable ability to distinguish the glycosylated and nonglycosylated forms of the same glycoprotein, with a >5-fold difference in binding affinity. The precise control over the polymer film thickness and positioning of multiple carbohydrate receptors plays a crucial role in achieving an enhanced affinity and selectivity. The generated functional materials of unprecedented glycoprotein recognition performance open up a wealth of opportunities in the biotechnological and biomedical fields.

Reversible, High-Affinity Surface Capturing of Proteins Directed by Supramolecular Assembly.

The ability to design surfaces with reversible, high-affinity protein binding sites represents a significant step forward in the advancement of analytical methods for diverse biochemical and biomedical applications. Herein, we report a dynamic supramolecular strategy to directly assemble proteins on surfaces based on multivalent host-guest interactions. The host-guest interactions are achieved by one-step nanofabrication of a well-oriented ß-cyclodextrin host-derived self-assembled monolayer on gold (ß-CD-SAM) that forms specific inclusion complexes with hydrophobic amino acids located on the surface of the protein. Cytochrome c, insulin, α-chymotrypsin, and RNase A are used as model guest proteins. Surface plasmon resonance and static time-of-flight secondary ion mass spectrometry studies demonstrate that all four proteins interact with the ß-CD-SAM in a specific manner via the hydrophobic amino acids on the surface of the protein. The ß-CD-SAMs bind the proteins with high nanomolar to single-digit micromolar dissociation constants ( KD). Importantly, while the proteins can be captured with high affinity, their release from the surface can be achieved under very mild conditions. Our results expose the great advantages of using a supramolecular approach for controlling protein immobilization, in which the strategy described herein provides unprecedented opportunities to create advanced bioanalytic and biosensor technologies.

Acrylamide-dT: a polymerisable nucleoside for DNA incorporation.

The synthesis of a novel modified nucleoside phosphoramidite, Acrylamide-dT-CE phosphoramidite, obtained in three steps from commercially available starting materials, is reported. It was readily incorporated into thrombin binding aptamer (TBA) sequences using automated solid-phase synthesis under ultra-mild conditions, with the modification shown not to adversely affect duplex stability, G-quadruplex structure, or thrombin binding. The reaction and integration of the modified strands with acrylamide polymers was evidenced by gel electrophoresis. The Acrylamide-dT functional handle promises to be an ideal synthon for preparing DNA-polymer hybrids for use in various macromolecular materials applications.

On-Demand Electrical Switching of Antibody-Antigen Binding on Surfaces.

The development of stimuli-responsive interfaces between synthetic materials and biological systems is providing the unprecedented ability to modulate biomolecular interactions for a diverse range of biotechnological and biomedical applications. Antibody-antigen binding interactions are at the heart of many biosensing platforms, but no attempts have been made yet to control antibody-antigen binding in an on-demand fashion. Herein, a molecular surface was designed and developed that utilizes an electric potential to drive a conformational change in surface bound peptide moiety, to give on-demand control over antigen-antibody interactions on sensor chips. The molecularly engineered surfaces allow for propagation of conformational changes from the molecular switching unit to a distal progesterone antigen, resulting in promotion (ON state) or inhibition (OFF state) of progesterone antibody binding. The approach presented here can be generally applicable to other antigen-antibody systems and meets the technological needs for in situ long-term assessment of biological processes and disease monitoring on-demand.

Platelet aggregation induced by polystyrene and platinum nanoparticles is dependent on surface area.

Nanoparticles are key components underlying recent technological advances in various industrial and medical fields, and thus understanding their mode of interaction with biological systems is essential. However, while several nanoparticle systems have been shown to interact with blood platelets, many questions remain concerning the mechanisms of platelet activation and the role that the physicochemical properties of nanoparticles play in inducing platelet aggregation. Here, using negatively charged polystyrene nanoparticles with sizes of 25, 50, 119, 151, 201 nm and negatively charged platinum nanoparticles with sizes of 7 and 73 nm, we show that it is not the size of the nanoparticles but rather the nanoparticle surface area that is critical in mediating the effects on platelet activation. The nanoparticles stimulate platelet aggregation through passive (agglutination) and activation of integrin αIIbß3 through a pathway regulated by Src and Syk tyrosine kinase.

Tailoring the Electrochemical Properties of Carbon Nanotube Modified Indium Tin Oxide via in Situ Grafting of Aryl Diazonium.

Our ability to tailor the electronic properties of surfaces by nanomodification is paramount for various applications, including development of sensing, fuel cell, and solar technologies. Moreover, in order to improve the rational design of conducting surfaces, an improved understanding of structure/function relationships of nanomodifications and effect they have on the underlying electronic properties is required. Herein, we report on the tuning and optimization of the electrochemical properties of indium tin oxide (ITO) functionalized with single-walled carbon nanotubes (SWCNTs). This was achieved by controlling in situ grafting of aryl amine diazonium films on the nanoscale which were used to covalently tether SWCNTs. The structure/function relationship of these nanomodifications on the electronic properties of ITO was elucidated via time-of-flight secondary ion mass spectrometry and electrochemical and physical characterization techniques which has led to new mechanistic insights into the in situ grafting of diazonium. We discovered that the connecting bond is a nitro group which is covalently linked to a carbon on the aryl amine. The increased understanding of the surface chemistry gained through these studies enabled us to fabricate surfaces with optimized electron transfer kinetics. The knowledge gained from these studies allows for the rational design and tuning of the electronic properties of ITO-based conducting surfaces important for development of various electronic applications.