A Protein‐Based Pentavalent Inhibitor of the Cholera Toxin B‐Subunit

Protein toxins produced by bacteria are the cause of many life‐threatening diarrheal diseases. Many of these toxins, including cholera toxin (CT), enter the cell by first binding to glycolipids in the cell membrane. Inhibiting these multivalent protein/carbohydrate interactions would prevent the toxin from entering cells and causing diarrhea. Here we demonstrate that the site‐specific modification of a protein scaffold, which is perfectly matched in both size and valency to the target toxin, provides a convenient route to an effective multivalent inhibitor. The resulting pentavalent neoglycoprotein displays an inhibition potency (IC₅₀) of 104 pM for the CT B‐subunit (CTB), which is the most potent pentavalent inhibitor for this target reported thus far. Complexation of the inhibitor and CTB resulted in a protein heterodimer. This inhibition strategy can potentially be applied to many multivalent receptors and also opens up new possibilities for protein assembly strategies.     

Design of Monodisperse and Well‐Defined Polypeptide‐Based Polyvalent Inhibitors of Anthrax Toxin

The design of polyvalent molecules, presenting multiple copies of a specific ligand, represents a promising strategy to inhibit pathogens and toxins. The ability to control independently the valency and the spacing between ligands would be valuable for elucidating structure–activity relationships and for designing potent polyvalent molecules. To that end, we designed monodisperse polypeptide‐based polyvalent inhibitors of anthrax toxin in which multiple copies of an inhibitory toxin‐binding peptide were separated by flexible peptide linkers. By tuning the valency and linker length, we designed polyvalent inhibitors that were over four orders of magnitude more potent than the corresponding monovalent ligands. This strategy for the rational design of monodisperse polyvalent molecules may not only be broadly applicable for the inhibition of toxins and pathogens, but also for controlling the nanoscale organization of cellular receptors to regulate signaling and the fate of stem cells.     

Manipulation of Electrostatic and Saccharide Linker Interactions in the Design of Efficient Glycopolypeptide‐Based Cholera Toxin Inhibitors

Multivalent, glycopolymer inhibitors designed for the treatment of disease and pathogen infection have shown improvements in binding correlated with general changes in glycopolymer architecture and composition. We have previously demonstrated that control of glycopolypeptide backbone extension and ligand spacing significantly impacts the inhibition of the cholera toxin B subunit pentamer (CT B₅) by these polymers. In the studies reported here, we elucidate the role of backbone charge and linker length in modulating the inhibition event. Peptides of the sequence AXPXG (where X is a positive, neutral or negative amino acid), equipped with the alkyne functionality of propargyl glycine, were designed and synthesized via solid‐phase peptide synthetic methods and glycosylated via Cu(I)‐catalyzed alkyne‐azide cycloaddition reactions. The capacity of the glycopeptides to inhibit the binding of the B₅ subunit of cholera toxin was evaluated. These studies indicated that glycopeptides with a negatively charged backbone show improved inhibition of the binding event relative to the other glycopeptides. In addition, variations in the length of the linker between the peptide and the saccharide ligand also affected the inhibition of CT by the glycopeptides. Our findings suggest that, apart from appropriate saccharide spacing and polypeptide chain extension, saccharide linker conformation and the systematic placement of charges on the polypeptide backbone are also significant variables that can be tuned to improve the inhibitory potencies of glycopolypeptide‐based multivalent inhibitors.

     

catena‐Poly­[[[cis‐bis(1‐phenyl­tetra­zole‐κN4)copper(II)]‐di‐μ‐chloro] hemi(1‐phenyl­tetrazole)]

The title compound, {[CuCl₂(PhTz)₂]·0.5PhTz}_n (PhTz is 1‐­phenyl­tetrazole, C₇H₆N₄), has a polymeric structure, with uncoordinated disordered PhTz mol­ecules in the cavities. The coordination polyhedron of the Cu atom is a highly elongated octahedron. The equatorial positions are occupied by two Cl atoms [Cu—Cl = 2.2687 (9) and 2.2803 (7) Å] and two N atoms of the PhTz ligands [Cu—N = 2.0131 (19) and 2.0317 (18) Å]. The more distant axial positions are occupied by two Cl atoms [Cu—Cl = 3.0307 (12) and 2.8768 (11) Å] that lie in the equatorial planes of two neighbouring Cu octahedra. The [CuCl₂(PhTz)₂] units are linked by Cu—Cl bridges into infinite chains extending parallel to the a axis. The chains are linked into two‐dimensional networks by intermolecular C—H⋯N interactions between the phenyl and tetrazole fragments, and by face‐to‐face π–π interactions between symmetry‐related phenyl rings. These two‐dimensional networks, which lie parallel to the ac plane, are connected by intermolecular π–π stacking interactions between phenyl rings, thus forming a three‐dimensional network.     

Gold Manno‐Glyconanoparticles: Multivalent Systems to Block HIV‐1 gp120 Binding to the Lectin DC‐SIGN

The HIV envelope glycoprotein gp120 takes advantage of the high‐mannose clusters on its surface to target the C‐type lectin dendritic cell‐specific intracellular adhesion molecule‐3‐grabbing non‐integrin (DC‐SIGN) on dendritic cells. Mimicking the cluster presentation of oligomannosides on the virus surface is a strategy for designing carbohydrate‐based antiviral agents. Bio‐inspired by the cluster presentation of gp120, we have designed and prepared a small library of multivalent water‐soluble gold glyconanoparticles (manno‐GNPs) presenting truncated (oligo)mannosides of the high‐mannose undecasaccharide Man₉GlcNAc₂ and have tested them as inhibitors of DC‐SIGN binding to gp120. These glyconanoparticles are ligands for DC‐SIGN, which also interacts in the early steps of infection with a large number of pathogens through specific recognition of associated glycans. (Oligo)mannosides endowed with different spacers ending in thiol groups, which enable attachment of the glycoconjugates to the gold surface, have been prepared. manno‐GNPs with different spacers and variable density of mannose (oligo)saccharides have been obtained and characterized. Surface plasmon resonance (SPR) experiments with selected manno‐GNPs have been performed to study their inhibition potency towards DC‐SIGN binding to gp120. The tested manno‐GNPs completely inhibit the binding from the micro‐ to the nanomolar range, while the corresponding monovalent mannosides require millimolar concentrations. manno‐GNPs containing the disaccharide Manα1‐2Manα are the best inhibitors, showing more than 20 000‐fold increased activity (100 % inhibition at 115 nM ) compared to the corresponding monomeric disaccharide (100 % inhibition at 2.2 mM ). Furthermore, increasing the density of dimannoside on the gold platform from 50 to 100 % does not improve the level of inhibition.     

Mannose‐based graft polyesters with tunable binding affinity to concanavalin A

Glycopolymers have been widely used to understand the interactions between carbohydrates and lectins, which facilitate the diagnosis and detection of disease and pathogens as well as the development of vaccines. While studies have been focused on the correlation of glycopolymer structure and their binding to lectins, graft‐type glycopolyesters are uncommon. Herein, we report the design and synthesis of mannose‐based graft polyesters by “grafting‐from” method and investigate their interactions with Concanavalin A (Con A). As confirmed by ¹H NMR spectroscopy and sulfuric acid‐UV method, graft polyesters with different lengths of mannose graft were successfully synthesized. Our results from turbidimetry binding assay showed that graft polyesters with longer mannose graft exhibit higher initial binding rate (k_i). Isothermal titration calorimetry measurements of these graft polyesters with Con A showed that polymers exhibit higher binding affinity (k_a) with the number of side chain mannose. This study provides understanding of the interaction between Con A and mannose‐based graft polyesters, which can be employed for the development of glycopolymeric therapeutics. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 3908–3917     

Weak intermolecular interactions in isomorphous 5‐(2‐chloroethoxy)‐2,3‐dihydro‐1,4‐benzodioxine and 5‐(2‐bromoethoxy)‐2,3‐dihydro‐1,4‐benzodioxine: bonding or nonbonding interactions

The title compounds, C₁₀H₁₁ClO₃, (I), and C₁₀H₁₁BrO₃, (II), are isomorphous and effectively isostructural; all of the interatomic distances and angles are normal. The structures exhibit long intermolecular C—H...O and C—H...π contacts with attractive energies ranging from 1.17 to 2.30 kJ mol⁻¹. Weak C—H...O hydrogen bonds form C(3) and C(4) motifs, combining to form a two‐dimensional R₃⁴(12) net. No face‐to‐face stacking interactions are observed.     

Synthesis and crystal structure of a novel prochiral ketoimine: (E)‐acetophenone O‐diphenylphosphoryl oxime

A novel activated prochiral ketoimine, (E)‐acetophenone O‐diphenylphosphoryl oxime, C₂₀H₁₈NO₂P, with an electron‐withdrawing substituent on the imine N atom similar to other prochiral ketoimines, has been synthesized and the X‐ray crystal stucture determined. The molecules pack together in the solid state via weak intermolecular C—H...O interactions and both face‐to‐face and edge‐to‐face π‐stacking interactions.     

Multivalent Interactions of Polyamide Based Sequence‐Controlled Glycomacromolecules with Concanavalin A

Binding of mannose presenting macromolecules to the protein receptor concanavalin A (ConA) is investigated by means of single‐molecule atomic force spectroscopy (SMFS) in combination with dynamic light scattering and molecular modeling. Oligomeric (M_w ≈ 1.5–2.5 kDa) and polymeric (M_w ≈ 22–30 kDa) glycomacromolecules with controlled number and positioning of mannose units along the scaffolds accessible by combining solid phase synthesis and thiol–ene coupling are used as model systems to assess the molecular mechanisms that contribute to multivalent ConA–mannose complexes. SMFS measurements show increasing dissociation force from monovalent (≈57 pN) to pentavalent oligomers (≈75 pN) suggesting subsite binding to ConA. Polymeric glycomacromolecules with larger hydrodynamic diameters compared to the binding site spacing of ConA exhibit larger dissociation forces (≈80 pN), indicating simultaneous dissociation from multiple ConA binding sites. Nevertheless, although simultaneous dissociation of multiple ligands could be expected for such multivalent systems, predominantly single dissociation events are observed. This is rationalized by strong coiling of the macromolecules' polyamide backbone due to intramolecular hydrogen bonding hindering unfolding of the coil. Therefore, this study shows that the design of glycopolymers for multivalent receptor binding and clustering must consider 3D structure and intramolecular interactions of the scaffold.     

Distinctive MS/MS Fragmentation Pathways of Glycopeptide‐Generated Oxonium Ions Provide Evidence of the Glycan Structure

Post‐translational glycosylation of proteins play key roles in cellular processes and the site‐specific characterisation of glycan structures is critical to understanding these events. Given the challenges regarding identification of glycan isomers, glycoproteomic studies generally rely on the assumption of conserved biosynthetic pathways. However, in a recent study, we found characteristically different HexNAc oxonium ion fragmentation patterns that depend on glycan structure. Such patterns could be used to distinguish between glycopeptide structural isomers. To acquire a mechanistic insight, deuterium‐labelled glycopeptides were prepared and analysed. We found that the HexNAc‐derived m/z 126 and 144 oxonium ions, differing in mass by H₂O, had completely different structures and that high‐mannose N‐glycopeptides generated abundant Hex‐derived oxonium ions. We describe the oxonium ion decomposition mechanisms and the relative abundance of oxonium ions as a function of collision energy for a number of well‐defined glycan structures, which provide important information for future glycoproteomic studies.     

Two polymorphs of 2,5‐dichloro‐3,6‐bis(dibenzylamino)‐p‐hydroquinone with flexible dibenzylamino groups

We obtained two conformational polymorphs of 2,5‐dichloro‐3,6‐bis(dibenzylamino)‐p‐hydroquinone, C₃₄H₃₀Cl₂N₂O₂. Both polymorphs have an inversion centre at the centre of the hydroquinone ring (Z′ = ), and there are no significant differences between their bond lengths and angles. The most significant structural difference in the molecular conformations was found in the rotation of the phenyl rings of the two crystallographically independent benzyl groups. The crystal structures of the polymorphs were distinguishable with respect to the arrangement of the hydroquinone rings and the packing motif of the phenyl rings that form part of the benzyl groups. The phenyl groups of one polymorph are arranged in a face‐to‐edge motif between adjacent molecules, with intermolecular C—H…π interactions, whereas the phenyl rings in the other polymorph form a lamellar stacking pattern with no significant intermolecular interactions. We suggest that this partial conformational difference in the molecular structures leads to the significant structural differences observed in their molecular arrangements.     

C‐Glycosyl Amino Acids through Hydroboration–Cross‐Coupling of exo‐Glycals and Their Application in Automated Solid‐Phase Synthesis

O‐Glycosylation is one of the most important post‐translational modifications of proteins. The attachment of carbohydrates to the peptide backbone influences the conformation as well as the solubility of the conjugates and can even be essential for binding to specific ligands in cell–cell interactions or for active transport over membranes. This makes glycopeptides an interesting class of compounds for medical applications. To enhance the long‐term availability of these molecules in vivo, the stabilization of the glycosidic bond between the amino acid residue and the carbohydrate is of interest. The described modular approach affords β‐linked C‐glycosyl amino acids by a sequence of Petasis olefination of glyconolactones, stereoselective hydroboration and a mild B‐alkyl‐Suzuki coupling reaction. The coupling products were transformed to C‐glycosyl amino acid building‐blocks suitable for solid‐phase synthesis and successfully incorporated into a partial sequence of the tumor‐associated MUC1‐glycopeptide. The resulting C‐glycopeptides are candidates for the development of long‐term stable mimics of O‐glycopeptide vaccines.     

Structural and Kinetic Dissection of the endo‐α‐1,2‐Mannanase Activity of Bacterial GH99 Glycoside Hydrolases from Bacteroides spp.

Glycoside hydrolase family 99 (GH99) was created to categorize sequence‐related glycosidases possessing endo‐α‐mannosidase activity: the cleavage of mannosidic linkages within eukaryotic N‐glycan precursors (Glc_1–3Man₉GlcNAc₂), releasing mono‐, di‐ and triglucosylated‐mannose (Glc_1–3‐1,3‐Man). GH99 family members have recently been implicated in the ability of Bacteroides spp., present within the gut microbiota, to metabolize fungal cell wall α‐mannans, releasing α‐1,3‐mannobiose by hydrolysing αMan‐1,3‐αMan→1,2‐αMan‐1,2‐αMan sequences within branches off the main α‐1,6‐mannan backbone. We report the development of a series of substrates and inhibitors, which we use to kinetically and structurally characterise this novel endo‐α‐1,2‐mannanase activity of bacterial GH99 enzymes from Bacteroides thetaiotaomicron and xylanisolvens. These data reveal an approximate 5 kJ mol^?1 preference for mannose‐configured substrates in the ?2 subsite (relative to glucose), which inspired the development of a new inhibitor, α‐mannopyranosyl‐1,3‐isofagomine (ManIFG), the most potent (bacterial) GH99 inhibitor reported to date. X‐ray structures of ManIFG or a substrate in complex with wild‐type or inactive mutants, respectively, of B. xylanisolvens GH99 reveal the structural basis for binding to D ‐mannose‐ rather than D ‐glucose‐configured substrates.     

The Counterion Effect on the Assembly of Coordination Networks of Cationic (η3‐Allyl)palladium Complexes Containing 3,5‐Dimethyl‐4‐nitro‐1H‐pyrazole

Two new (η³‐allyl)palladium complexes containing the ligand 3,5‐dimethyl‐4‐nitro‐1H‐pyrazole (Hdmnpz) were synthesized and characterized as [Pd(η³‐C₃H₅)(Hdmnpz)₂]BF₄ ( 1 ) and [Pd(η³‐C₃H₅)(Hdmnpz)₂]NO₃ ( 2 ). The structures of these compounds were determined by single‐crystal X‐ray diffraction to evaluate the intermolecular assembly. Each complex exhibits similar coordination behavior consistent with cationic entities comprised of two pyrazole ligands coordinated with the [Pd(η³‐C₃H₅)]⁺ fragment in an almost square‐planar coordination geometry. In 1 , the cationic entities are propagated through strong intermolecular H‐bonds formed between the pyrazole NH groups and BF ions in one‐dimensional polymer chains along the a axis. These chains are extended into two‐dimensional sheet networks via bifurcated H‐bonds. New intermolecular interactions established between NO₂ and Me substituents at the pyrazole ligand of neighboring sheets give rise to a three‐dimensional network. By contrast, compound 2 presents molecular cyclic dimers formed through N? H???O H‐bonds between two NO counterions and the pyrazole NH groups of two cationic entities. The dimers are also connected to each other through C? H???O H‐bonds between the remaining O‐atom of each NO ion and the allyl CH₂ H‐atom. Those interactions expand in a layer which lies parallel to the face (101).     

Invariom‐model refinement and Hirshfeld surface analysis of well‐ordered solvent‐free dibenzo‐21‐crown‐7

Crown ethers and their supramolecular derivatives are well‐known chelators and scavengers for a variety of cations, most notably heavier alkali and alkaline‐earth ions. Although they are widely used in synthetic chemistry, available crystal structures of uncoordinated and solvent‐free crown ethers regularly suffer from disorder. In this study, we present the X‐ray crystal structure analysis of well‐ordered solvent‐free crystals of dibenzo‐21‐crown‐7 (systematic name: dibenzo[b ,k ]‐1,4,7,10,13,16,19‐heptaoxacycloheneicosa‐2,11‐diene, C₂₂H₂₈O₇). Because of the quality of the crystal and diffraction data, we have chosen invarioms, in addition to standard independent spherical atoms, for modelling and briefly discuss the different refinement results. The electrostatic potential, which is directly deducible from the invariom model, and the Hirshfeld surface are analysed and complemented with interaction‐energy computations to characterize intermolecular contacts. The boat‐like molecules stack along the a axis and are arranged as dimers of chains, which assemble as rows to form a three‐dimensional structure. Dispersive C—H…H—C and C—H…π interactions dominate, but nonclassical hydrogen bonds are present and reflect the overall rather weak electrostatic influence. A fingerprint plot of the Hirshfeld surface summarizes and visualizes the intermolecular interactions. The insight gained into the crystal structure of dibenzo‐21‐crown‐7 not only demonstrates the power of invariom refinement, Hirshfeld surface analysis and interaction‐energy computation, but also hints at favourable conditions for crystallizing solvent‐free crown ethers.     

Polymorphism of 3‐(5‐phenyl‐1,3,4‐oxadiazol‐2‐yl)‐ and 3‐[5‐(pyridin‐4‐yl)‐1,3,4‐oxadiazol‐2‐yl]‐2H‐chromen‐2‐ones

This study of 3‐(5‐phenyl‐1,3,4‐oxadiazol‐2‐yl)‐2H‐chromen‐2‐one, C₁₇H₁₀N₂O₃, 1 , and 3‐[5‐(pyridin‐4‐yl)‐1,3,4‐oxadiazol‐2‐yl]‐2H‐chromen‐2‐one, C₁₆H₉N₃O₃, 2 , was performed on the assumption of the potential anticancer activity of the compounds. Three polymorphic structures for 1 and two polymorphic structures for 2 have been studied thoroughly. The strongest intermolecular interaction is stacking of the `head‐to‐head' type in all the studied crystals. The polymorphic structures of 1 differ with respect to the intermolecular interactions between stacked columns. Two of the polymorphs have a columnar or double columnar type of crystal organization, while the third polymorphic structure can be classified as columnar‐layered. The difference between the two structures of 2 is less pronounced. Both crystals can be considered as having very similar arrangements of neighbouring columns. The formation of polymorphic modifications is caused by a subtle balance of very weak intermolecular interactions and packing differences can be identified only using an analysis based on a study of the pairwise interaction energies.     

Herring‐bone π–π interactions in trans‐2,6‐diphenyl‐2,3,5,6‐tetrahydrothiapyran‐4‐one

The structure of the title compound, C₁₇H₁₆OS, is primarily stabilized by T‐shaped and parallel‐displaced aromatic clusters. The distances between the centroids of the aromatic pairs are in the range 4.34–5.30 Å. In the crystal packing, the mol­ecules dimerize by means of π–π interactions of both face‐to‐face and edge‐to‐face types, and the aromatic rings associate in a cyclic edge‐to‐face tetrameric arrangement of the herring‐bone type. These herring‐bone interactions appear to insulate hydrogen‐bond interactions in the crystal structure.     

Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies

A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2 , and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1 , whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2 . In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2 . The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=K_D^intra/K_D^inter, where K_D^intra is the dissociation constant for intramolecular G‐quadruplex 2 and K_D^inter is the dissociation constant for intermolecular G‐quadruplex 1 . In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.     

Bridge‐Clamp Bis(tetrazine)s with [N]8 π‐Stacking Interactions and Azido‐s‐Aryl Tetrazines: Two Classes of Doubly Clickable Tetrazines

Click chemistry at a tetrazine core is useful for bioorthogonal labeling and crosslinking. Introduced here are two new classes of doubly clickable s‐aryl tetrazines synthesized by Cu‐catalyzed cross‐coupling. Homocoupling of o‐brominated s‐aryl tetrazines leads to bis(tetrazine)s structurally characterized by tetrazine cores arranged face‐to‐face. [N]₈ π‐stacking interactions are essential to the conformation. Upon inverse electron demand Diels–Alder (iEDDA) cycloaddition, the bis(tetrazine)s produce a unique staple structure. The o‐azidation of s‐aryl tetrazines introduces a second proximal intermolecular clickable function that leads to double click chemistry opportunities. The stepwise introduction of fluorophores and then iEDDA cycloaddition, including bioconjugation to antibodies, was achieved on this class of tetrazines. This method extends to (thio)etherification, phosphination, trifluoromethylation and the introduction of various bioactive nitrogen‐based heterocycles.     

(2E)‐N‐(2‐Iodo‐4,6‐dimethylphenyl)‐2‐methylbut‐2‐enamide

The title compound, C₁₄H₁₈INO, crystallizes as +sc/+sp/+sc 2‐iodoanilide molecules (and racemic opposites) and shows significant intermolecular I...O interactions in the solid state, forming dimeric pairs about centres of symmetry. Under asymmetric Heck conditions, the S enantiomer of the dihydroindol‐2‐one was obtained using (R)‐(+)‐2,2′‐bis(diphenylphosphino)‐1,1′‐binaphthyl [(R)‐BINAP], suggesting a mechanism that proceeds by oxidative addition to give the title (P) enantiomer of the compound and pro‐S coordination of the Re face of the alkene in a conformation similar to that defined crystallographically, except that rotation about the C—C bond of the butenyl group is required.