Multivalency as a chemical organization and action principle

Enrichment of histone tail methylated lysine residues via cavitand-decorated magnetic nanoparticles for ultra-sensitive proteomics

Nearly every protein in the human body is modified with post-translational modifications (PTMs). PTMs affect proteins on many levels, including their function, interaction, half-life, and localization. Specifically, for histone proteins, PTMs such as lysine methylation and acetylation play essential roles in chromatin dynamic regulations. For this reason, methods to accurately detect and quantify PTMs are of paramount importance in cell biology, biochemistry, and disease biology. Most protein modifications are sub-stoichiometric, so, to be analyzed, they need methods of enrichment, which are mostly based on antibodies. Antibodies are produced using animals, resulting in high costs, ecological concerns, significant batch variations, and ethical implications. We propose using ferromagnetic nanoparticles functionalized with synthetic receptors, namely tetraphosphonate cavitands, as a tool for selective enrichment of methylated lysines present on histone tails. Before the enrichment step, histone proteins from calf thymus were digested to facilitate the recognition process and to obtain small peptides suitable for mass analyses. Cavitands were anchored on ferromagnetic nanoparticles to easily separate the PTM-peptides of interest from the rest of the proteolytic peptides. Our approach detects more modified peptides with higher signal intensity, rivaling commercial antibodies. This chemical strategy offers a cost-effective and efficient alternative for PTM detection, potentially advancing proteomic research.

Scalable Synthesis and Electrocatalytic Performance of Highly Fluorinated Covalent Organic Frameworks for Oxygen Reduction

In this study, we present a novel approach for the synthesis of covalent organic frameworks (COFs) that overcomes the common limitations of non-scalable solvothermal procedures. Our method allows for the room-temperature and scalable synthesis of a highly fluorinated DFTAPB-TFTA-COF, which exhibits intrinsic hydrophobicity. We used DFT-based calculations to elucidate the role of the fluorine atoms in enhancing the crystallinity of the material through corrugation effects, resulting in maximized interlayer interactions, as disclosed both from PXRD structural resolution and theoretical simulations. We further investigated the electrocatalytic properties of this material towards the oxygen reduction reaction (ORR). Our results show that the fluorinated COF produces hydrogen peroxide selectively with low overpotential (0.062 V) and high turnover frequency (0.0757 s-1 ) without the addition of any conductive additives. These values are among the best reported for non-pyrolyzed and metal-free electrocatalysts. Finally, we employed DFT-based calculations to analyse the reaction mechanism, highlighting the crucial role of the fluorine atom in the active site assembly. Our findings shed light on the potential of fluorinated COFs as promising electrocatalysts for the ORR, as well as their potential applications in other fields.

Functionalized Calixarenes as Promising Antibacterial Drugs to Face Antimicrobial Resistance

Since the discovery of polyphenolic resins 150 years ago, the study of polymeric compounds named calix[n]arene has continued to progress, and those skilled in the art perfectly know now how to modulate this phenolic ring. Consequently, calix[n]arenes are now used in a large range of applications and notably in therapeutic fields. In particular, the calix[4]arene exhibits multiple possibilities for regioselective polyfunctionalization on both of its rims and offers researchers the possibility of precisely tuning the geometry of their structures. Thus, in the crucial research of new antibacterial active ingredients, the design of calixarenes finds its place perfectly. This review provides an overview of the work carried out in this aim towards the development of intrinsically active prodrogues or metallic calixarene complexes. Out of all the work of the community, there are some excellent activities emerging that could potentially place these original structures in a very good position for the development of new active ingredients.

Insights into Selective Removal by Dye Adsorption on Hydrophobic vs Multivalent Hydrophilic Functionalized MWCNTs

Hydrophilic functionalized carbon nanotubes (MWCNT-COOH) were developed via hydrothermal glucose-coated carbonization, mixing MWCNTs with glucose in different weight ratios. Methyl violet (MV), methylene blue (MB), alizarin yellow (AY), and methyl orange (MO) were used as dye models for adsorption studies. Comparative dye adsorption capacity onto the pristine (MWCNT-raw) and functionalized (MWCNT-COOH-11) CNTs was evaluated in aqueous solution. These results revealed that MWCNT-raw is capable of adsorbing either anionic or cationic dyes. In contrast, an induced selective cation dye adsorption capacity is significantly enhanced on multivalent hydrophilic MWCNT-COOH, in comparison to a pristine surface. This ability can be tuned to the selective adsorption of cations over anionic dyes or between anionic mixtures from binary systems. An insight into adsorbate-adsorbent interactions shows that hierarchical supramolecular interactions dominate the adsorption processes, which is ascribed to the chemical modification by switching from a hydrophobic to a hydrophilic surface, dye charge, temperature, and potential matching multivalent acceptor/donor capacity between chemical groups in the adsorbent interface. The dye adsorption isotherm and thermodynamics on both surfaces were also studied. Changes in the Gibbs free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) were evaluated. Thermodynamic parameters were endothermic on MWCNT-raw, whereas the adsorption process on MWCNT-COOH-11 revealed that adsorption processes were spontaneous and exothermic, accompanied by a significant reduction of entropy values as a consequence of a multivalent effect. This approach provides an eco-friendly, low-cost alternative for the preparation of supramolecular nanoadsorbents with unprecedented properties to achieve remarkable selective adsorption independent of the presence of intrinsic porosity.

One, two, many: Strategies to alter the number of carbohydrate binding sites of lectins

Carbohydrates are more than an energy-storage. They are ubiquitously found on cells and most proteins, where they encode biological information. Lectins bind these carbohydrates and are essential for translating the encoded information into biological functions and processes. Hundreds of lectins are known, and they are found in all domains of life. For half a century, researchers have been preparing variants of lectins in which the binding sites are varied. In this way, the traits of the lectins such as the affinity, avidity and specificity towards their ligands as well as their biological efficacy were changed. These efforts helped to unravel the biological importance of lectins and resulted in improved variants for biotechnological exploitation and potential medical applications. This review gives an overview on the methods for the preparation of artificial lectins and complexes thereof and how reducing or increasing the number of binding sites affects their function.

Bioconjugated chelates based on (methylpyridinyl)tacn: synthesis, 64Cu labeling and in vitro evaluation for prostate cancer targeting

Three new bifunctional copper chelators based on the 1,4,7-triazacyclononane (tacn) platform have been synthesized and conjugated to peptide. The first one is constituted of the tacn with two methylpyridinyl and one methylthiazolyl carboxylic acid pendant arms, while, in the second and third ones, the macrocycle is functionalized by three methylpyridinyl groups, with an additional hexynoic acid chain on a carbon of one or two pyridine rings. These three bifunctional chelators have been conjugated to the antagonist JMV594 peptide for targeting the gastrin releasing peptide receptor (GRP-r), which is overexpressed in prostate cancer. The resulting monomeric bioconjugates have shown their efficiency to be radiolabeled with β+ emitter 64Cu, and the hydrophilicity and PC-3 cell internalisation properties of these radiolabeled conjugates have been studied. PC-3 cell binding affinity of mono- and dimeric metal-free and natCu metallated conjugates have been evaluated by IC50 measurements. The results demonstrate the potential of these methylpyridinyl tacn derivatives for radiopharmaceutical applications.

Probing Multivalent Carbohydrate-Protein Interactions With On-Chip Synthesized Glycopeptides Using Different Functionalized Surfaces

Multivalent ligand-protein interactions are a commonly employed approach by nature in many biological processes. Single glycan-protein interactions are often weak, but their affinity and specificity can be drastically enhanced by engaging multiple binding sites. Microarray technology allows for quick, parallel screening of such interactions. Yet, current glycan microarray methodologies usually neglect defined multivalent presentation. Our laser-based array technology allows for a flexible, cost-efficient, and rapid in situ chemical synthesis of peptide scaffolds directly on functionalized glass slides. Using copper(I)-catalyzed azide-alkyne cycloaddition, different monomer sugar azides were attached to the scaffolds, resulting in spatially defined multivalent glycopeptides on the solid support. Studying their interaction with several different lectins showed that not only the spatially defined sugar presentation, but also the surface functionalization and wettability, as well as accessibility and flexibility, play an essential role in such interactions. Therefore, different commercially available functionalized glass slides were equipped with a polyethylene glycol (PEG) linker to demonstrate its effect on glycan-lectin interactions. Moreover, different monomer sugar azides with and without an additional PEG-spacer were attached to the peptide scaffold to increase flexibility and thereby improve binding affinity. A variety of fluorescently labeled lectins were probed, indicating that different lectin-glycan pairs require different surface functionalization and spacers for enhanced binding. This approach allows for rapid screening and evaluation of spacing-, density-, ligand and surface-dependent parameters, to find optimal lectin binders.

Synthesis of regioisomeric maltose-based Man/Glc glycoclusters to control glycoligand presentation in 3D space

The investigation of carbohydrate recognition in a natural environment suffers from the complexity of overlapping functional effects such as multivalency and heteromultivalency effects. Another key factor in carbohydrate recognition is the presentation mode of glycoligands in three-dimensional (3D) space. In order to trace out the effect of 3D ligand presentation, we utilized an oligosaccharide model to precisely control the spatial relation between a mannose ligand (Man) and a glucose moiety (Glc). A disaccharide (maltose) served as a scaffold to alternately conjugate Man and Glc at position 6 and 6' of a synthetic maltoside, resulting in a pair of regioisomeric heterobivalent glycoclusters. The biological effect of this specific structural tuning was tested in a native system employing mannose-specific adhesion of live E. coli cells. Indeed, the variable 3D presentation of the Man ligand resulted in a 2-fold difference between the regioisomeric heterobivalent glycoclusters as inhibitors of bacterial adhesion. This can be considered a remarkable effect, which could be interpreted by computer-aided modelling of the complexes between the bacterial lectin and the synthetic regioisomeric glycoligands.

Template-Controlled Synthesis of Polyimidazolium Salts by Multiple [2+2] Cycloaddition Reactions

The tetrakisimidazolium salt H4 -2(Br)4 , featuring a central benzene linker and 1,2,4,5-(nBu-imidazolium-Ph-CH=CH-) substituents reacts with Ag2 O in the presence of AgBF4 to yield the tetranuclear, oktakis-NHC assembly [3](BF4 )4 . Cation [3]4+ features four pairs of olefins from the two tetrakis-NHC ligands perfectly arranged for a subsequent [2+2] cycloaddition. Irradiation of [3](BF4 )4 with a high pressure Hg lamp connects the two tetra-NHC ligands through four cyclobutane linkers to give compound [4](BF4 )4 . Removal of the template metals yields the novel oktakisimidazolium salt H8 -5(BF4 )8 . The tetrakisimidazolium salt H4 -2(BF4 )4 and the oktakisimidazolium salt H8 -5(BF4 )8 have been used as multivalent anion receptors and their anion binding properties towards six different anions have been compared.

Click-Free Synthesis of a Multivalent Tricyclic Peptide as a Molecular Transporter

The cellular delivery of cell-impermeable and water-insoluble molecules remains an ongoing challenge to overcome. Previously, we reported amphipathic cyclic peptides c[WR]₄ and c[WR]₅ consisting of alternate arginine and tryptophan residues as nuclear-targeting molecular transporters. These peptides contain an optimal balance of positive charge and hydrophobicity, which is required for interactions with the phospholipid bilayer to facilitate their application as a drug delivery system. To further optimize them, we synthesized and evaluated a multivalent tricyclic peptide as an efficient molecular transporter. The monomeric cyclic peptide building blocks were synthesized using Fmoc/tBu solid-phase chemistry and cyclization in the solution and conjugated with each other through an amide bond to afford the tricyclic peptide, which demonstrated modest antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA), Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli (E. coli) with a minimum inhibitory concentration (MIC) of 64–128 µg/mL. The tricyclic peptide was found to be nontoxic up to 30 µM in the breast cancer cell lines (MDA-MB-231). The presence of tricyclic peptide enhanced cellular uptakes of fluorescently-labeled phosphopeptide (F’-GpYEEI, 18-fold), anti-HIV drugs (lamivudine (F’-3TC), emtricitabine (F’-FTC), and stavudine (F’-d4T), 1.7–12-fold), and siRNA (3.3-fold) in the MDA-MB-231 cell lines.

Boronic acid sensors with double recognition sites: a review

Boronic acids reversibly and covalently bind to Lewis bases and polyols, which facilitated the development of a large number of chemical sensors to recognize carbohydrates, catecholamines, ions, hydrogen peroxide, and so on. However, as the binding mechanism of boronic acids and analytes is not very clear, it is still a challenge to discover sensors with high affinity and selectivity. In this review, boronic acid sensors with two recognition sites, including diboronic acid sensors, and monoboronic acid sensors having another group or binding moiety, are summarized. Owing to double recognition sites working synergistically, the binding affinity and selectivity of sensors can be improved significantly. This review may help researchers to sort out the binding rules and develop ideal boronic acid-based sensors.

Pseudoenantiomeric glycoclusters: synthesis and testing of heterobivalency in carbohydrate–protein interactions

Multivalent carbohydrate–protein interactions are key events in cell recognition processes and have been extensively studied by means of synthetic glycomimetics.

Multivalent presentation of carbohydrates by 314-helical peptide templates: synthesis, conformational analysis using CD spectroscopy and saccharide recognition

A tetrameric glycoconjugate template, SSFT 1, was coupled with a variety of six aminooxy sugars to achieve multivalent glycoconjugates 2–7.